@article {pmid39604363, year = {2024}, author = {Ma, J and Yi, G and Ye, M and MacGregor-Chatwin, C and Sheng, Y and Lu, Y and Li, M and Li, Q and Wang, D and Gilbert, RJC and Zhang, P}, title = {Open architecture of archaea MCM and dsDNA complexes resolved using monodispersed streptavidin affinity CryoEM.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10304}, pmid = {39604363}, issn = {2041-1723}, support = {206422/Z/17/Z//Wellcome Trust (Wellcome)/ ; BB/S003339/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 101021133//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; U54 AI170791-7522//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R21 CA280467/CA/NCI NIH HHS/United States ; }, mesh = {*Cryoelectron Microscopy/methods ; *Streptavidin/chemistry/metabolism ; *Thermococcus/metabolism ; Archaeal Proteins/metabolism/chemistry/ultrastructure ; DNA/metabolism/chemistry ; Minichromosome Maintenance Proteins/metabolism/chemistry ; Biotinylation ; Models, Molecular ; DNA, Archaeal/metabolism/genetics/chemistry ; Saccharomyces cerevisiae/metabolism ; Adenosine Triphosphate/metabolism/chemistry ; }, abstract = {The cryo-electron microscopy (cryoEM) method has enabled high-resolution structure determination of numerous biomolecules and complexes. Nevertheless, cryoEM sample preparation of challenging proteins and complexes, especially those with low abundance or with preferential orientation, remains a major hurdle. We developed an affinity-grid method employing monodispersed single particle streptavidin on a lipid monolayer to enhance particle absorption on the grid surface and alleviate sample exposure to the air-water interface. Using this approach, we successfully enriched the Thermococcus kodakarensis mini-chromosome maintenance complex 3 (MCM3) on cryoEM grids through biotinylation and resolved its structure. We further utilized this affinity method to tether the biotin-tagged dsDNA to selectively enrich a stable MCM3-ATP-dsDNA complex for cryoEM structure determination. Intriguingly, both MCM3 apo and dsDNA bound structures exhibit left-handed open spiral conformations, distinct from other reported MCM structures. The large open gate is sufficient to accommodate a dsDNA which could potentially be melted. The value of mspSA affinity method was further demonstrated by mitigating the issue of preferential angular distribution of HIV-1 capsid protein hexamer and RNA polymerase II elongation complex from Saccharomyces cerevisiae.}, }
@article {pmid39577734, year = {2024}, author = {Di Giulio, M}, title = {The existence of the two domains of life, Bacteria and Archaea, would in itself imply that LUCA and the ancestors of these domains were progenotes.}, journal = {Bio Systems}, volume = {247}, number = {}, pages = {105375}, doi = {10.1016/j.biosystems.2024.105375}, pmid = {39577734}, issn = {1872-8324}, abstract = {The length of the deepest branches of the tree of life would tend to support the hypothesis that the distance of the branch that separates the sequences of archaea from those of bacteria, i.e. the interdomain one, is longer than the intradomain ones, i.e. those that separate the sequences of archaea and those of bacteria within them. Why should interdomain distance be larger than intradomain distances? The fact that the rate of amino acid substitutions was slowed as the domains of life appeared would seem to imply an evolutionary transition. The slowdown in the speed of evolution that occurred during the formation of the two domains of life would be the consequence of the progenote- > cell evolutionary transition. Indeed, the evolutionary stage of the progenote being characterized by an accelerated tempo and mode of evolution might explain the considerable interdomain distance because the accumulation of many amino acid substitutions on this branch would indicate the progenote stage that is also characterized by a high rate of amino acid substitutions. Furthermore, the fact that intradomain distances are smaller than interdomain distances would corroborate the hypothesis of the achievement of cellularity at the appearance of the main phyletic lineages. Indeed, the cell stage, unlike the progenotic one, definitively establishes the relationship between the genotype and phenotype, lowering the rate of evolution. Therefore, the arguments presented lead to the conclusion that LUCA was a progenote.}, }
@article {pmid39572458, year = {2024}, author = {Tamang, M and Sikorski, J and van Bommel, M and Piecha, M and Urich, T and Ruess, L and Huber, K and Neumann-Schaal, M and Pester, M}, title = {Succession of Bacteria and Archaea Within the Soil Micro-Food Web Shifts Soil Respiration Dynamics.}, journal = {Environmental microbiology}, volume = {26}, number = {11}, pages = {e70007}, pmid = {39572458}, issn = {1462-2920}, support = {HU3067/1-1//German Research Foundation (SPP 2322)/ ; NE2192/4-1//German Research Foundation (SPP 2322)/ ; PE2147/6-1//German Research Foundation (SPP 2322)/ ; RU 780/22-1//German Research Foundation (SPP 2322)/ ; UR198/7-1//German Research Foundation (SPP 2322)/ ; }, mesh = {*Soil Microbiology ; *Archaea/genetics/classification ; *Bacteria/classification/genetics ; *Soil/chemistry ; *Food Chain ; *Microbiota ; Animals ; *Zea mays/microbiology ; *RNA, Ribosomal, 16S/genetics ; Nematoda/microbiology ; }, abstract = {Bacterivorous nematodes are important grazers in the soil micro-food web. Their trophic regulation shapes the composition and ecosystem services of the soil microbiome, but the underlying population dynamics of bacteria and archaea are poorly understood. We followed soil respiration and 221 dominant bacterial and archaeal 16S rRNA gene amplicon sequencing variants (ASVs) in response to top-down control by a common bacterivorous soil nematode, Acrobeloides buetschlii, bottom-up control by maize litter amendment and their combination over 32 days. Maize litter amendment significantly increased soil respiration, while A. buetschlii addition caused an earlier peak in soil respiration. Underlying bacterial and archaeal population dynamics separated into five major response types, differentiating in their temporal abundance maxima and minima. In-depth analysis of these population dynamics identified a broad imprint of A. buetschlii grazing on dominant bacterial (Acidobacteriota, Bacteroidota, Gemmatimonadota, Pseudomonadota) and archaeal (Nitrososphaerota) ASVs. Combined bottom-up control by maize litter and top-down control by A. buetschlii grazing caused a succession of soil microbiota, driven by population changes first in the Bacteroidota, then in the Pseudomonadota and finally in the Acidobacteriota and Nitrososphaerota. Our results are an essential step forward in understanding trophic modulation of soil microbiota and its feedback on soil respiration.}, }
@article {pmid39568122, year = {2024}, author = {Matarredona, L and Zafrilla, B and Camacho, M and Bonete, MJ and Esclapez, J}, title = {Understanding the tolerance of halophilic archaea to stress landscapes.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70039}, doi = {10.1111/1758-2229.70039}, pmid = {39568122}, issn = {1758-2229}, support = {VIGROB-016//Universidad de Alicante/ ; CIAICO/2022/047//Generalitat Valenciana/ ; }, mesh = {*Stress, Physiological ; Salinity ; Salt Tolerance ; Sodium Chloride/metabolism ; Archaea/metabolism/drug effects ; }, abstract = {Haloarchaea, known for their resilience to environmental fluctuations, require a minimum salt concentration of 10% (w/v) for growth and can survive up to 35% (w/v) salinity. In biotechnology, these halophiles have diverse industrial applications. This study investigates the tolerance responses of nine haloarchaea: Haloferax mediterranei, Haloferax volcanii, Haloferax gibbonsii, Halorubrum californiense, Halorubrum litoreum, Natrinema pellirubrum, Natrinema altunense, Haloterrigena thermotolerans and Haloarcula sinaiiensis, under various stressful conditions. All these archaea demonstrated the ability to thrive in the presence of toxic metals such as chromium, nickel, cobalt and arsenic, and their tolerance to significantly elevated lithium concentrations in the medium was remarkable. Among the studied haloarchaea, Hfx. mediterranei exhibited superior resilience, particularly against lithium, with an impressive minimum inhibitory concentration (MIC) of up to 4 M LiCl, even replacing NaCl entirely. Haloferax species showed specificity for conditions with maximal growth rates, while Htg. thermotolerans and Nnm. altunense displayed high resilience without losing growth throughout the ranges, although these were generally low. ICP-MS results highlighted the impressive intracellular lithium accumulation in Nnm. pellirubrum, emphasizing its potential significance in bioremediation. This research highlights a new characteristic of haloarchaea, their tolerance to high lithium concentrations and the potential for new applications in extreme industrial processes and bioremediation.}, }
@article {pmid39567663, year = {2024}, author = {Nobu, MK}, title = {Engineering history with Asgard archaea of the kingdom Promethearchaeati.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {39567663}, issn = {2058-5276}, }
@article {pmid39562414, year = {2024}, author = {Kemp, JA and Schultz, J and Modolon, F and Ribeiro-Alves, M and Rosado, AS and Mafra, D}, title = {Is there a correlation between TMAO plasma levels and archaea in the gut of patients undergoing hemodialysis?.}, journal = {International urology and nephrology}, volume = {}, number = {}, pages = {}, pmid = {39562414}, issn = {1573-2584}, abstract = {PURPOSE: Patients with chronic kidney disease (CKD) present high plasma levels of trimethylamine N-oxide (TMAO), a uremic toxin produced by gut microbiota associated with atherogenesis. Experimental studies have shown that certain methanogenic archaea members use trimethylamine (TMA), the TMAO precursor in the human gut, to produce methane, suggesting a potential strategy to reduce TMAO levels in patients with CKD. Hence, this study aimed to evaluate the association of Archaea in the gut microbiota and TMAO plasma levels in patients with CKD undergoing hemodialysis.<br><br>METHODS: Twenty-five patients were enrolled in the study (15 women, 53 (18) years, BMI, 25.8 (6.75) kg/m[2]). TMAO plasma levels were evaluated using the HPLC-EM/EM method. Fecal DNA was extracted using a commercial kit. Subsequently, we sequenced the V4 region of the 16S rRNA gene to characterize the microbial composition. NCT04600258 was retrospectively registered in September 2022.<br><br>RESULTS: According to the reference values in the European Uremic Toxins Work Group (EUTox) database, the patients exhibited high TMAO plasma levels, as expected. The most abundant Archaea members were assigned to the Euryarchaeota phylum, the Methanobacteriaceae family, and the genus Methanobrevibacter. A significant negative correlation between TMAO and Methanobrevibacter was observed.<br><br>CONCLUSIONS: To our knowledge, this study represents the first investigation into the correlation between TMAO levels and the prevalence of Archaea in patients with CKD. Our findings support the archaebiotic hypothesis, suggesting that specific members of the archaea community could play a crucial role in reducing TMA production in the human gut, potentially decreasing TMAO synthesis in CKD patients.}, }
@article {pmid39560730, year = {2024}, author = {Liang, Y and Yan, Y and Shi, L and Wang, M and Yuan, X and Wang, S and Ye, L and Yan, Z}, title = {Molecular Basis of Thioredoxin-Dependent Arsenic Transformation in Methanogenic Archaea.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c06611}, pmid = {39560730}, issn = {1520-5851}, abstract = {Methanogenic archaea are known to play a crucial role in the biogeochemical cycling of arsenic (As); however, the molecular basis of As transformation mediated by methanogenic archaea remains poorly understood. Herein, the characterization of the redox transformation and methylation of As by Methanosarcina acetivorans, a model methanogenic archaeon, is reported. M. acetivorans was demonstrated to mediate As(V) reduction via a cytoplasmic As reductase (ArsC) in the exponential phase of methanogenic growth and to methylate As(III) via a cytoplasmic As(III) methyltransferase (ArsM) in the stationary phase. Characterization of the ArsC-catalyzed As(V) reduction and the ArsM-catalyzed As(III) methylation showed that a thioredoxin (Trx) encoded by MA4683 was preferentially utilized as a physiological electron donor for ArsC and ArsM, providing a redox link between methanogenesis and As transformation. The structures of ArsC and ArsM complexed with Trx were modeled using AlphaFold-Multimer. Site-directed mutagenesis of key cysteine residues at the interaction sites of the complexes indicated that the archaeal ArsC and ArsM employ evolutionarily distinct disulfide bonds for interacting with Trx compared to those used by bacterial ArsC or eukaryotic ArsM. The findings of this study present a major advance in our current understanding of the physiological roles and underlying mechanism of As transformation in methanogenic archaea.}, }
@article {pmid39545734, year = {2024}, author = {Xu, T and Ni, Y and Li, H and Wu, S and Yan, S and Chen, L and Yu, Y and Wang, Y}, title = {Discovery and characterization of complete genomes of 38 head-tailed proviruses in four predominant phyla of archaea.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0049224}, doi = {10.1128/spectrum.00492-24}, pmid = {39545734}, issn = {2165-0497}, abstract = {Archaea play a significant role in natural ecosystems and the human body. Archaeal viruses exert a considerable influence on the structure and composition of archaeal communities and their associated ecological environments. The present study revealed the complete genomes of 38 archaeal head-tailed proviruses through comprehensive data mining. The hosts of these proviruses were identified as belonging to the following four dominant phyla: Halobacteriota, Thermoplasmatota, Thermoproteota, and Nanoarchaeota. In addition to the 14 proviruses of halophilic archaea related to the Graaviviridae family, the remaining proviruses exhibited limited genetic similarities to known (pro)viruses, suggesting the existence of 14 potential novel families. Of the 38 archaeal proviruses, 30 have the potential to lyse host cells. Eleven proviruses contain genes linked to antiviral defense mechanisms, including those involved in restriction modification (RM), clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas) nucleases, defense island system associated with restriction-modification (DISARM), and DNA degradation (Dnd). Moreover, auxiliary metabolic genes were identified in the proviruses of Bathyarchaeia and Halobacteriota archaea, including those involved in carbohydrate and amino acid metabolism. Our findings indicate the diversity of archaeal viruses, their interactions with archaeal hosts, and their roles in the adaptation of the host.IMPORTANCEThe field of archaeal virology has seen a rapid expansion through the use of metagenomics, yet the diversity of these viruses remains largely uncharted. In this study, the complete genomes of 38 novel archaeal proviruses were identified for the following four dominant phyla: Halobacteriota, Thermoplasmatota, Thermoproteota, and Nanoarchaeota. Two families and six genera of Archaea were the first to be identified as hosts for viruses. The proviruses were found to contain diverse genes that were involved in distinct adaptation strategies of viruses to hosts. Our findings contribute to the expansion of the lineages of archaeal viruses and highlight their intricate interactions and essential roles in enabling host survival and adaptation to diverse environmental conditions.}, }
@article {pmid39544964, year = {2024}, author = {Abiola, C and Gwak, JH and Lee, UJ and Awala, SI and Jung, MY and Park, W and Rhee, SK}, title = {Growth of soil ammonia-oxidizing archaea on air-exposed solid surface.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae129}, pmid = {39544964}, issn = {2730-6151}, abstract = {Soil microorganisms often thrive as microcolonies or biofilms within pores of soil aggregates exposed to the soil atmosphere. However, previous studies on the physiology of soil ammonia-oxidizing microorganisms (AOMs), which play a critical role in the nitrogen cycle, were primarily conducted using freely suspended AOM cells (planktonic cells) in liquid media. In this study, we examined the growth of two representative soil ammonia-oxidizing archaea (AOA), Nitrososphaera viennensis EN76 and "Nitrosotenuis chungbukensis" MY2, and a soil ammonia-oxidizing bacterium, Nitrosomonas europaea ATCC 19718 on polycarbonate membrane filters floated on liquid media to observe their adaptation to air-exposed solid surfaces. Interestingly, ammonia oxidation activities of N. viennensis EN76 and "N. chungbukensis" MY2 were significantly repressed on floating filters compared to the freely suspended cells in liquid media. Conversely, the ammonia oxidation activity of N. europaea ATCC 19718 was comparable on floating filters and liquid media. N. viennensis EN76 and N. europaea ATCC 19718 developed microcolonies on floating filters. Transcriptome analysis of N. viennensis EN76 floating filter-grown cells revealed upregulation of unique sets of genes for cell wall and extracellular polymeric substance biosynthesis, ammonia oxidation (including ammonia monooxygenase subunit C (amoC3) and multicopper oxidases), and defense against H2O2-induced oxidative stress. These genes may play a pivotal role in adapting AOA to air-exposed solid surfaces. Furthermore, the floating filter technique resulted in the enrichment of distinct soil AOA communities dominated by the "Ca. Nitrosocosmicus" clade. Overall, this study sheds light on distinct adaptive mechanisms governing AOA growth on air-exposed solid surfaces.}, }
@article {pmid39541851, year = {2024}, author = {Wang, F and Huang, W and Chen, J and Luo, Y and Cao, J and Fang, F and Liu, X and Wu, Y and Luo, J}, title = {Non-antibiotic disinfectant synchronously interferes methane production and antibiotic resistance genes propagation during sludge anaerobic digestion: Activation of microbial adaptation and reconfiguration of bacteria-archaea synergies.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122773}, doi = {10.1016/j.watres.2024.122773}, pmid = {39541851}, issn = {1879-2448}, abstract = {Waste activated sludge (WAS) presents both resource recovery potential and pollution risks, making its efficient treatment challenging. Anaerobic digestion is broadly recognized as a green and sustainable approach to WAS treatment, whose efficiency is easily impacted by the exogeneous pollutants in WAS. However, the impact of polyhexamethylene guanidine (PHMG), as a widely-used non-antibiotic disinfectant, on WAS digestion under semi-continuous flow conditions remains unclear. In this study, CH4 production decreased from 16.1 mL/g volatile suspended solids (VSS) in the control to 13.2 mL/g VSS and 0.3 mL/g VSS under low and high PHMG exposure, respectively, while PHMG increased the number of antibiotic resistance gene (ARG) copies per bacterium by 4.6-12.7 %. Molecular docking analysis revealed that PHMG could spontaneously bind to and disintegrate WAS (binding energy:2.35 and -9.62 kcal/mol), increasing the likelihood of microbial exposure to PHMG. This led to an increase in bacterial abundance and a reduction in archaeal populations, resulting in bacterial dominance in ecological niches. The network topology index in PHMG-treated reactors was consistently lower than in the control, with a higher proportion of negatively correlated links, indicating a more antagonistic relationship between bacteria and archaea. Consequently, PHMG significantly interfered with key genes involved in CH4 biosynthesis (e.g., mch and mtd). Interestingly, methanogenic activity and archaeal chemotaxis (e.g., rfk and cheA) partially recovered under low PHMG exposure due to archaeal adaptation through quorum sensing and two-component systems. However, this adaptation process also contributed to the propagation of ARGs through horizontal gene transfer, facilitated by the enhancement of mobile genetic elements and ARGs hosts. These findings confirm the ecological risks of PHMG and highlight the need for effective WAS disposal strategies.}, }
@article {pmid39530672, year = {2024}, author = {Lee, U-J and Gwak, J-H and Choi, S and Jung, M-Y and Lee, TK and Ryu, H and Imisi Awala, S and Wanek, W and Wagner, M and Quan, Z-X and Rhee, S-K}, title = {"Ca. Nitrosocosmicus" members are the dominant archaea associated with plant rhizospheres.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0082124}, doi = {10.1128/msphere.00821-24}, pmid = {39530672}, issn = {2379-5042}, abstract = {UNLABELLED: Archaea catalyzing the first step of nitrification in the rhizosphere possibly have an influence on plant growth and development. In this study, we found a distinct archaeal community, dominated by ammonia-oxidizing archaea (AOA), associated with the root system of pepper (Capsicum anuum L.) and ginseng plants (Panax ginseng C.A. Mey.) compared to bulk soil not penetrated by roots. While the abundance of total AOA decreased in the rhizosphere soils, AOA related to "Candidatus Nitrosocosmicus," which harbor gene encoding manganese catalase (MnKat) in contrast to most other AOA, dominated the AOA community in the rhizosphere soils. For both plant species, the ratio of copy numbers of the AOA MnKat gene to the amoA gene (encoding the ammonia monooxygenase subunit A) was significantly higher in the rhizospheres than in bulk soils. In contrast to MnKat-negative strains from other AOA clades, the catalase activity of a representative isolate of "Ca. Nitrosocosmicus" was demonstrated. Members of this clade were enriched in H2O2-amended bulk soils, and constitutive expression of their MnKat gene was observed in both bulk and rhizosphere soils. Due to their abundance, "Ca. Nitrosocosmicus" members can be considered important players mediating the nitrification process in rhizospheres. The dominance of this MnKat-containing AOA in rhizospheres of agriculturally important plants hints at a previously overlooked AOA-plant interaction.<br><br>IMPORTANCE: Ammonia-oxidizing archaea (AOA) are widespread in terrestrial environments and outnumber other ammonia oxidizers in the rhizosphere, possibly exerting an influence on plant growth and development. However, little is known about the selection forces that shape their composition, functions, survival, and proliferation strategies in the rhizosphere. Here, we observed a distinct AOA community on root systems of two different plant species compared to bulk soil. Our results show that the "Ca. Nitrosocosmicus" clade, which possesses functional MnKat genes unlike most other AOA, dominated the rhizosphere soils. Moreover, members of this clade were enriched in H2O2-amended bulk soil, which mimics the ROS stress in root systems. While research on AOA-plant interactions in the rhizosphere is still in its infancy, these findings suggest that "Ca. Nitrosocosmicus" may be an important clade of AOA with potential AOA-plant interaction.}, }
@article {pmid39529672, year = {2024}, author = {Hernández-Magaña, E and Kraft, B}, title = {Corrigendum: Nitrous oxide production and consumption by marine ammonia-oxidizing archaea under oxygen depletion.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1506979}, doi = {10.3389/fmicb.2024.1506979}, pmid = {39529672}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2024.1410251.].}, }
@article {pmid39514410, year = {2024}, author = {Dodsworth, JA and Prakash, O}, title = {International Committee on Systematics of Prokaryotes: subcommittee on the taxonomy of methanogenic archaea. Minutes of the closed, online meeting held 06 September 2023.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {11}, pages = {}, doi = {10.1099/ijsem.0.006569}, pmid = {39514410}, issn = {1466-5034}, }
@article {pmid39511174, year = {2024}, author = {Chen, SC and Chen, S and Musat, N and Kümmel, S and Ji, J and Lund, MB and Gilbert, A and Lechtenfeld, OJ and Richnow, HH and Musat, F}, title = {Back flux during anaerobic oxidation of butane support archaea-mediated alkanogenesis.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9628}, pmid = {39511174}, issn = {2041-1723}, support = {NNF22OC0071609//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; ERC-RA-0020//Helmholtz Association/ ; 101059607//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; 12471341//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Oxidation-Reduction ; Anaerobiosis ; *Archaea/metabolism/genetics ; *Butanes/metabolism ; *Carbon Dioxide/metabolism ; Oxidoreductases/metabolism/genetics ; Kinetics ; Alkanes/metabolism ; Thermodynamics ; }, abstract = {Microbial formation and oxidation of volatile alkanes in anoxic environments significantly impacts biogeochemical cycles on Earth. The discovery of archaea oxidizing volatile alkanes via deeply branching methyl-coenzyme M reductase variants, dubbed alkyl-CoM reductases (ACR), prompted the hypothesis of archaea-catalysed alkane formation in nature (alkanogenesis). A combination of metabolic modelling, anaerobic physiology assays, and isotope labeling of Candidatus Syntrophoarchaeum archaea catalyzing the anaerobic oxidation of butane (AOB) show a back flux of CO2 to butane, demonstrating reversibility of the entire AOB pathway. Back fluxes correlate with thermodynamics and kinetics of the archaeal catabolic system. AOB reversibility supports a biological formation of butane, and generally of higher volatile alkanes, helping to explain the presence of isotopically light alkanes and deeply branching ACR genes in sedimentary basins isolated from gas reservoirs.}, }
@article {pmid39499858, year = {2024}, author = {Takamiya, H and Kouduka, M and Kato, S and Suga, H and Oura, M and Yokoyama, T and Suzuki, M and Mori, M and Kanai, A and Suzuki, Y}, title = {Genome-resolved metaproteogenomic and nanosolid characterization of an inactive vent chimney densely colonized by enigmatic DPANN archaea.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, doi = {10.1093/ismejo/wrae207}, pmid = {39499858}, issn = {1751-7370}, mesh = {*Hydrothermal Vents/microbiology ; *Archaea/genetics/metabolism/classification/isolation &amp; purification ; *Genome, Archaeal ; Phylogeny ; Metagenomics ; Proteomics ; Ecosystem ; }, abstract = {Recent successes in the cultivation of DPANN archaea with their hosts have demonstrated an episymbiotic lifestyle, whereas the lifestyle of DPANN archaea in natural habitats is largely unknown. A free-living lifestyle is speculated in oxygen-deprived fluids circulated through rock media, where apparent hosts of DPANN archaea are lacking. Alternatively, DPANN archaea may be detached from their hosts and/or rock surfaces. To understand the ecology of rock-hosted DPANN archaea, rocks rather than fluids should be directly characterized. Here, we investigated a deep-sea hydrothermal vent chimney without fluid venting where our previous study revealed the high proportion of Pacearchaeota, one of the widespread and enigmatic lineages of DPANN archaea. Using spectroscopic methods with submicron soft X-ray and infrared beams, the microbial habitat was specified to be silica-filled pores in the inner chimney wall comprising chalcopyrite. Metagenomic analysis of the inner wall revealed the lack of biosynthetic genes for nucleotides, amino acids, cofactors, and lipids in the Pacearchaeota genomes. Genome-resolved metaproteomic analysis clarified the co-occurrence of a novel thermophilic lineage actively fixing carbon and nitrogen and thermophilic archaea in the inner chimney wall. We infer that the shift in metabolically active microbial populations from the thermophiles to the mesophilic DPANN archaea occurs after the termination of fluid venting. The infilling of mineral pores by hydrothermal silica deposition might be a preferred environmental factor for the colonization of free-living Pacearchaeota with ultrasmall cells depending on metabolites synthesized by the co-occurring thermophiles during fluid venting.}, }
@article {pmid39499655, year = {2024}, author = {Medvedeva, S and Borrel, G and Gribaldo, S}, title = {Sheaths are diverse and abundant cell surface layers in archaea.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae225}, pmid = {39499655}, issn = {1751-7370}, abstract = {Prokaryotic cells employ multiple protective layers crucial for defense, structural integrity, and cellular interactions in the environment. Archaea often feature an S-layer, with some species possessing additional and remarkably resistant sheaths. The archaeal sheath has been studied in Methanothrix and Methanospirillum, revealing a complex structure consisting of amyloid proteins organized into rings. Here, we conducted a comprehensive survey of sheath-forming proteins (SH proteins) across archaeal genomes. Structural modeling reveals a rich diversity of SH proteins, indicating the presence of a sheath in members of the TACK superphylum (Thermoprotei), as well as in the methanotrophic ANME-1. SH proteins are present in up to 40 copies per genome and display diverse domain arrangements suggesting multifunctional roles within the sheath, and potential involvement in cell-cell interaction with syntrophic partners. We uncover a complex evolutionary dynamic, indicating active exchange of SH proteins in archaeal communities. We find that viruses infecting sheathed archaea encode a diversity of SH-like proteins and we use them as markers to identify 580 vOTUs potentially associated with sheathed archaea. Structural modeling suggests that viral SH proteins can form complexes with the host SH proteins. We propose a previously unreported egress strategy where the expression of viral SH-like proteins may disrupt the integrity of the host sheath and facilitate viral exit during lysis. Together, our results significantly expand knowledge of the diversity and evolution of the archaeal sheath, which has been largely understudied but might have an important role in shaping microbial communities.}, }
@article {pmid39495356, year = {2024}, author = {Ma, X and Hu, Y and Hou, J and Zhou, YG and Cui, HL}, title = {Genome-Based Classification of 'Haloarcula aidinensis' and Description of Three Novel Halophilic Archaea Isolated from an Inland Saline Lake, Coastal Saline Soil, and a Marine Solar Saltern.}, journal = {Current microbiology}, volume = {81}, number = {12}, pages = {442}, pmid = {39495356}, issn = {1432-0991}, support = {32070003//National Natural Science Foundation of China/ ; }, mesh = {*Phylogeny ; *Haloarcula/genetics/classification ; *Genome, Archaeal ; China ; *Lakes/microbiology ; *Soil Microbiology ; DNA, Archaeal/genetics/chemistry ; RNA, Ribosomal, 16S/genetics ; Phospholipids/analysis ; Sequence Analysis, DNA ; }, abstract = {'Haloarcula aidinensis' was described by a pioneer Chinese scientist focused on halophilic archaea thirty years ago, and the type strain of 'Haloarcula aidinensis' was recently classified based on phylogenetic, phylogenomic, and comparative genomic analyses. Other three novel halophilic archaeal strains, CK38[T], DT43[T], and SYNS111[T], isolated from diverse saline environments in China, were simultaneously subjected to polyphasic classification. 'Haloarcula aidinensis' A5 was found to be related to Haloarcula amylolytica, while strains CK38[T], DT43[T], and SYNS111[T] represented three novel species of Haloarcula based on phylogenetic, phylogenomic, and comparative genomic analyses. These strains can be distinguished from other species within the genus Haloarcula based on multiple phenotypic characteristics. The major phospholipids, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, and phosphatidylglycerol sulfate can be detected in these strains, while the glycolipid profiles of these strains are diverse. Strains A5 and DT43[T] contained glucosyl mannosyl glucosyl diether and a diglycosyl diether, while other strains CK38[T] and SYNS111[T] had sulfated mannosyl glucosyl diether and mannosyl glucosyl diether. Thus, strain A5 should be a reference strain of Har. amylolytica and three novel species of Haloarcula, Haloarcula sediminis sp. nov., Haloarcula brevis sp. nov., and Haloarcula regularis sp. nov. are proposed to accommodate strains CK38[T] (= CGMCC 1.62732[T] = JCM 36675[T]), DT43[T] (= CGMCC 1.18924[T] = JCM 36146[T]), and SYNS111[T] (= CGMCC 1.62601[T] = JCM 36149[T]).}, }
@article {pmid39490771, year = {2024}, author = {Li, T and Coker, OO and Sun, Y and Li, S and Liu, C and Lin, Y and Wong, SH and Miao, Y and Sung, JJ and Yu, J}, title = {Multi-cohort analysis reveals altered archaea in colorectal cancer fecal samples across populations.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2024.10.023}, pmid = {39490771}, issn = {1528-0012}, abstract = {BACKGROUND AND AIM: Archaea are important components of the host microbiome, but their roles in colorectal cancer (CRC) remain largely unclear. We aimed to elucidate the contribution of gut archaea to CRC across multiple populations.<br><br>METHODS: This study incorporated fecal metagenomic data from 10 independent cohorts from 7 countries and an additional in-house cohort, totaling 2101 metagenomes (748 CRC, 471 adenoma, and 882 healthy controls (HC)). Taxonomic profiling was performed using Kraken2 against the Genome Taxonomy Database. Alterations of archaeal communities and their interactions with bacteria and methanogenic functions were analyzed. Random Forest model was used to identify multicohort diagnostic microbial biomarkers in CRC.<br><br>RESULTS: The overall archaeal alpha diversity shifted from HC, adenoma patients to CRC patients with Methanobacteriota phylum enriched while order Methanomassiliicoccales depleted. At the species level, Methanobrevibacter_A smithii and Methanobrevibacter_A sp002496065 were enriched, while 8 species, including Methanosphaera stadtmanae and Methanomassiliicoccus_A intestinalis, were depleted in CRC patients across multiple cohorts. Among them, M. stadmanae, Methanobrevibacter_A sp900314695 and Methanocorpusculum sp001940805 exhibited a progressive decrease in the HC-adenoma-CRC sequence. CRC-depleted methanogenic archaea exhibited enhanced co-occurring interactions with butyrate-producing bacteria. Consistently, methanogenesis-related genes and pathways were enriched in CRC patients. A model incorporating archaeal and bacterial biomarkers outperformed single-kingdom models in discriminating CRC patients from healthy individuals with AUC ranging from 0.744 to 0.931 in leave-one-cohort-out analysis.<br><br>CONCLUSIONS: This multicohort analysis uncovered significant alterations in gut archaea and their interactions with bacteria in healthy individuals, adenoma patients and CRC patients. Archaeal biomarkers, combined with bacterial features, have potential as non-invasive diagnostic biomarkers for CRC.}, }
@article {pmid39486247, year = {2024}, author = {Ma, JY and Jiang, YQ and Liu, XY and Sun, XD and Jia, YN and Wang, Y and Tan, MM and Duan, JL and Yuan, XZ}, title = {Amplified selenite toxicity in methanogenic archaea mediated by cysteine.}, journal = {Ecotoxicology and environmental safety}, volume = {287}, number = {}, pages = {117263}, doi = {10.1016/j.ecoenv.2024.117263}, pmid = {39486247}, issn = {1090-2414}, abstract = {The challenge of understanding the interaction between trace elements and microbial life is critical for assessing environmental and ecological impacts. Nevertheless, cysteine (Cys), a low molecular weight thiol substance prevalent in the ecosystem, is able to influence the fate of certain trace elements, which increases the complexity of the interaction between trace elements and microorganisms. Therefore, we chose Cys, selenite and the model methanogenic archaeon Methanosarcina acetivorans C2A as research targets, and comprehensively explored the intricate role of Cys in modulating the biological effects of selenite on M. acetivorans C2A in terms of population growth, methane production and oxidative stress. Our results demonstrate that Cys significantly exacerbates the inhibitory effects of selenite on growth and methane production in M. acetivorans C2A. This increased toxicity is linked to heightened membrane permeability and oxidative stress, with a marked upregulation in reactive oxygen species and changes in NADPH levels. Transcriptomic analysis reveals alterations in genes associated with transmembrane transport and methanogenesis. Intriguingly, we also observed a potential interaction between selenite and phosphate transmembrane transporters, suggesting a novel pathway for selenite entry into cells. These findings highlight the complex interplay between trace elements and microbial processes, with significant implications for understanding environmental risks and developing remediation strategies.}, }
@article {pmid39466404, year = {2024}, author = {Ortjohann, M and Schönheit, P}, title = {Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica.}, journal = {Extremophiles : life under extreme conditions}, volume = {28}, number = {3}, pages = {48}, pmid = {39466404}, issn = {1433-4909}, mesh = {*Haloarcula/metabolism/genetics ; *Sorbitol/metabolism ; *Mannitol/metabolism ; Archaeal Proteins/metabolism/genetics ; Fructokinases/metabolism/genetics ; Fructose/metabolism ; ATP-Binding Cassette Transporters/metabolism/genetics ; }, abstract = {The halophilic archaeon Haloarcula hispanica utilizes the sugar alcohols mannitol and sorbitol as carbon and energy sources. Genes, enzymes, and transcriptional regulators involved in uptake and degradation of these sugar alcohols were identified by growth experiments with deletion mutants and enzyme characterization. It is shown that both mannitol and sorbitol are taken up via a single ABC transporter of the CUT1 transporter family. Then, mannitol and sorbitol are oxidized to fructose by two distinct dehydrogenases. Fructose is further phosphorylated to fructose-1-phosphate by a haloarchaeal ketohexokinase, providing the first evidence for a physiological function of ketohexokinase in prokaryotes. Finally, fructose-1-phosphate is phosphorylated via fructose-1-phosphate kinase to fructose-1,6-bisphosphate, which is cleaved to triosephosphates by a Class I fructose-1,6-bisphosphate aldolase. Two distinct transcriptional regulators, acting as activators, have been identified: an IclR-like regulator involved in activating genes for sugar alcohol uptake and oxidation to fructose, and a GfcR-like regulator that likely activates genes involved in the degradation of fructose to pyruvate. This is the first comprehensive analysis of a sugar alcohol degradation pathway in Archaea.}, }
@article {pmid39455151, year = {2024}, author = {Pan, YC and Zhao, JW and Niu, HJ and Huang, YL and Wang, Y and Zhang, XX}, title = {[Effects of Vegetable Planting Ages on Community Structure of Ammonia-oxidizing Archaea and Ammonia-oxidizing Bacteria in Greenhouse Vegetable Fields].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {45}, number = {10}, pages = {6077-6085}, doi = {10.13227/j.hjkx.202310135}, pmid = {39455151}, issn = {0250-3301}, mesh = {*Archaea/metabolism/growth &amp; development/classification ; *Ammonia/metabolism ; *Soil Microbiology ; *Bacteria/classification/growth &amp; development/metabolism ; *Oxidation-Reduction ; *Vegetables/growth &amp; development ; Soil/chemistry ; China ; Nitrous Oxide/metabolism/analysis ; Time Factors ; Agriculture/methods ; Nitrogen/metabolism ; }, abstract = {The ammonia oxidation process driven by microorganisms is a dominant source for nitrous oxide （N2O） emissions. Here, we examined the influence of greenhouse vegetable planting ages on soil ammonia-oxidizing archaea （AOA） and ammonia-oxidizing bacteria （AOB）, which is of great significance for assessing the soil quality status and greenhouse gas transformations. A field study was conducted at different times （1, 5, 10, and 20 a） in greenhouse vegetable soils of Gaoyi, Hebei Province. Chemical analysis and Illumina NovaSeq high-throughput sequencing were used to analyze the soil physicochemical properties and community structures and diversity of AOA and AOB. The variation in AOA and AOB communities and the driving factors in greenhouse soils at different ages were also investigated. The results showed that the contents of total nitrogen, organic matter, alkali-hydrolyzable nitrogen, available phosphorus, and available potassium first increased and then decreased with the prolongation of growth. The contents of nitrate nitrogen, ammonium nitrogen, and electrical conductivity first decreased and then increased with the prolongation of growth. The pH value of soils decreased with the prolongation of growth. The abundance and diversity index of AOA and AOB first decreased and then increased with the prolongation of growth. Nitrososphaeria, unclassified Thaumarchaeota, and Candidatus Nitrosocaldus were the dominant species of AOA, while Betaproteobacteria and Nitrosospira were the dominant species of AOB. The composition of the soil AOA community varied greatly compared to that of AOB with the prolongation of growth. Correlation analysis showed that the changes in soil nutrient factors had a significant correlation with AOA and AOB communities. Redundancy analysis indicated that ammonium nitrogen, alkali-hydrolyzable nitrogen, and nitrate nitrogen were key factors of AOA communities, while electrical conductivity, available potassium, and nitrate nitrogen were key factors for AOB. In summary, long-term planting of greenhouse vegetables significantly affected the abundance and composition of soil AOA and AOB communities. Our results provide a theoretical basis for further studies on the greenhouse gas transformation and microbial mechanisms of the nitrogen cycle in greenhouse soils.}, }
@article {pmid39437693, year = {2024}, author = {Zhang, L and Yang, J and Ge, AH and Xie, W and Yao, R and Wang, X}, title = {Salinity drives niche differentiation of soil bacteria and archaea in Hetao Plain, China.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122977}, doi = {10.1016/j.jenvman.2024.122977}, pmid = {39437693}, issn = {1095-8630}, abstract = {Soil salinization is a critical environmental issue that limits plant productivity and disrupts ecosystem functions. As important indicators of soil environment, soil microbes play essential roles in driving nutrient cycling and sustaining ecosystem services. Therefore, understanding how microbial communities and their functional potentials respond to varying levels of soil salinization across different land use types is crucial for the restoration and management of salt-affected ecosystems. In this study, we randomly selected 63 sites across the Hetao Plain, covering an area of ∼2500 km[2]. Our results showed that both salinity- and fertility-related soil parameters were significantly correlated with bacterial and archaeal diversities, with soil salinity emerging as the stronger predictor of prokaryotic diversity. Intriguingly, bacterial and archaeal communities were tightly interlinked but displayed opposite trends in response to environmental factors, indicating a clear microbial niche differentiation driven by soil salinity. Moreover, the generalist functions of bacteria and archaea (e.g., chemoheterotrophy) exhibited contrasting responses to environmental parameters, while their specialist functions (e.g., nitrification) responded consistently. These findings highlight the pivotal role of soil salinity in shaping the niche differentiation of bacterial and archaeal communities in saline soils, providing insights to guide salinity-centered restoration strategies for effective marginal land management.}, }
@article {pmid39436425, year = {2024}, author = {Dong, XY and Mao, YL and Zhang, QK and Zhu, LR and Hou, J and Cui, HL}, title = {Genome‑based classification of the family Natrialbaceae and description of four novel halophilic archaea from three saline lakes and a saline-alkaline land.}, journal = {Extremophiles : life under extreme conditions}, volume = {28}, number = {3}, pages = {47}, pmid = {39436425}, issn = {1433-4909}, support = {32070003//National Natural Science Foundation of China/ ; }, mesh = {*Phylogeny ; *Genome, Archaeal ; *Lakes/microbiology ; Halobacteriales/genetics/classification ; Salt Tolerance ; Salinity ; }, abstract = {The current representatives of the family Natrialbaceae within the class Halobacteria were subjected to phylogenetic, phylogenomic, and comparative genomic analyses. The current species of Halobiforma and Halomontanus were found to be related to those of Natronobacterium and Natronoglomus, respectively. According to the cutoff value of average amino acid identity (AAI) (≤ 76%) proposed to differentiate genera within the family Natrialbaceae, Halobiforma, and Natronoglomus should be merged with Natronobacterium and Halomontanus, respectively. Beyond these, four novel halophilic archaeal strains, CCL63[T], AD-5[T], CG52[T], and KLK7[T], isolated from three saline lakes and a saline-alkaline land in China, were simultaneously subjected to polyphasic classification. The phenotypic, phylogenetic, phylogenomic, and comparative genomic analyses indicated that strain CCL63[T] (= CGMCC 1.18663[T] = JCM 35096[T]) represents a novel genus of the family Natrialbaceae, strains AD-5[T] (= CGMCC 1.13783[T] = JCM 33734[T]) and CG52[T] (= CGMCC 1.17139[T] = JCM 34160[T]) represent two novel species of the genus Natronococcus, and strain KLK7[T] (= MCCC 4K00128[T] = KCTC 4307[T]) represents a novel species of Haloterrigena. Halovalidus salilacus gen. nov., sp. nov., Natronococcus wangiae sp. nov., Natronococcus zhouii sp. nov., and Haloterrigena salinisoli sp. nov. are further proposed based on these type strains accordingly.}, }
@article {pmid39433727, year = {2024}, author = {Lemaire, ON and Wegener, G and Wagner, T}, title = {Ethane-oxidising archaea couple CO2 generation to F420 reduction.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9065}, pmid = {39433727}, issn = {2041-1723}, support = {WA 4053/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; WE 5492/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; WA 4053/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Oxidation-Reduction ; *Carbon Dioxide/metabolism ; *Ethane/metabolism/chemistry ; Archaea/metabolism/genetics ; Aldehyde Oxidoreductases/metabolism/genetics/chemistry ; Multienzyme Complexes/metabolism/genetics/chemistry ; Crystallography, X-Ray ; Archaeal Proteins/metabolism/genetics/chemistry ; Anaerobiosis ; Ferredoxins/metabolism ; Riboflavin/analogs &amp; derivatives ; }, abstract = {The anaerobic oxidation of alkanes is a microbial process that mitigates the flux of hydrocarbon seeps into the oceans. In marine archaea, the process depends on sulphate-reducing bacterial partners to exhaust electrons, and it is generally assumed that the archaeal CO2-forming enzymes (CO dehydrogenase and formylmethanofuran dehydrogenase) are coupled to ferredoxin reduction. Here, we study the molecular basis of the CO2-generating steps of anaerobic ethane oxidation by characterising native enzymes of the thermophile Candidatus Ethanoperedens thermophilum obtained from microbial enrichment. We perform biochemical assays and solve crystal structures of the CO dehydrogenase and formylmethanofuran dehydrogenase complexes, showing that both enzymes deliver electrons to the F420 cofactor. Both multi-metalloenzyme harbour electronic bridges connecting CO and formylmethanofuran oxidation centres to a bound flavin-dependent F420 reductase. Accordingly, both systems exhibit robust coupled F420-reductase activities, which are not detected in the cell extract of related methanogens and anaerobic methane oxidisers. Based on the crystal structures, enzymatic activities, and metagenome mining, we propose a model in which the catabolic oxidising steps would wire electron delivery to F420 in this organism. Via this specific adaptation, the indirect electron transfer from reduced F420 to the sulphate-reducing partner would fuel energy conservation and represent the driving force of ethanotrophy.}, }
@article {pmid39413712, year = {2024}, author = {Wang, M and Peñuelas, J and Sardans, J and Zeng, Q and Song, Z and Zhou, J and Xu, X and Zhou, X and Fang, Y and Vancov, T and Wang, W}, title = {Conversion of coastal marsh to aquaculture ponds decreased the potential of methane production by altering soil chemical properties and methanogenic archaea community structure.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122608}, doi = {10.1016/j.watres.2024.122608}, pmid = {39413712}, issn = {1879-2448}, abstract = {Coastal wetlands are among the most productive and dynamic ecosystems globally, contributing significantly to atmospheric methane (CH4) emissions. The widespread conversion of these wetlands into aquaculture ponds degrades these ecosystems, yet its effects on CH4 production and associated microbial mechanisms are not well understood. This study aimed to assess the impact of land conversion on CH4 production potential, total and active soil organic C (SOC) content, and microbial communities. We conducted a comparative study on three brackish marshes and adjacent aquaculture ponds in southeastern China. Compared to costal marshes, aquaculture ponds exhibited significantly (P < 0.05) lower CH4 production potential (0.05 vs. 0.02 μg kg[-1] h[-1]), SOC (17.64 vs. 6.97 g kg[-1]), total nitrogen (TN) content (1.62 vs. 1.24 g kg[-1]) and carbon/nitrogen (C/N) ratio (10.85 vs. 5.66). CH4 production potential in aquaculture ponds was influenced by both microbial and abiotic factors. Specifically, the relative abundance of Methanosarcina slightly decreased in aquaculture ponds, while the potential for CH4 production declined with lower SOC contents and C/N ratio. Overall, our findings demonstrate that converting natural coastal marshes into aquaculture ponds reduces CH4 production by altering key soil properties and the structure and diversity of methanogenic archaea communities. These results provide empirical evidence to enhance global carbon models, improving predictions of carbon feedback from wetland land conversion in the context of climate change.}, }
@article {pmid39406503, year = {2024}, author = {Valentin-Alvarado, LE and Shi, LD and Appler, KE and Crits-Christoph, A and De Anda, V and Adler, BA and Cui, ML and Ly, L and Leão, P and Roberts, RJ and Sachdeva, R and Baker, BJ and Savage, DF and Banfield, JF}, title = {Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.279480.124}, pmid = {39406503}, issn = {1549-5469}, abstract = {Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth-resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into the Atabeyarchaeum deiterrae-1 chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.}, }
@article {pmid39404452, year = {2024}, author = {Villa, EA and Escalante-Semerena, JC}, title = {Corrinoid salvaging and cobamide remodeling in bacteria and archaea.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0028624}, doi = {10.1128/jb.00286-24}, pmid = {39404452}, issn = {1098-5530}, abstract = {Cobamides (Cbas) are cobalt-containing cyclic tetrapyrroles used by cells from all domains of life as co-catalyst of diverse reactions. There are several structural features that distinguish Cbas from one another. The most relevant of those features discussed in this review is the lower ligand, which is the nucleobase of a ribotide located in the lower face of the cyclic tetrapyrrole ring. The above-mentioned ribotide is known as the nucleotide loop, which is attached to the ring by a short linker. In Cbas, the nucleobase of the ribotide can be benzimidazole or derivatives of it, purine or derivatives of it, or phenolic compounds. Given the importance of Cbas in prokaryotic metabolism, it is not surprising that prokaryotes have evolved enzymes that cleave part or the entire nucleotide loop. This function is advantageous when Cbas contain nucleobases that somehow interfere with the function of Cba-dependent enzymes in the organism. After cleavage, Cbas are rebuilt via the nucleotide loop assembly (NLA) pathway, which includes enzymes that activate the nucleobase and the ring intermediate, followed by condensation of activated intermediates and a final dephosphorylation reaction. This exchange of nucleobases is known as Cba remodeling. The NLA pathway is used to salvage Cba precursors from the environment.}, }
@article {pmid39402493, year = {2024}, author = {Bobbo, T and Biscarini, F and Yaddehige, SK and Alberghini, L and Rigoni, D and Bianchi, N and Taccioli, C}, title = {Machine learning classification of archaea and bacteria identifies novel predictive genomic features.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {955}, pmid = {39402493}, issn = {1471-2164}, mesh = {*Archaea/genetics/classification ; *Machine Learning ; *Bacteria/genetics/classification ; *Genomics/methods ; *Genome, Archaeal ; Genome, Bacterial ; RNA, Transfer/genetics ; Phylogeny ; }, abstract = {BACKGROUND: Archaea and Bacteria are distinct domains of life that are adapted to a variety of ecological niches. Several genome-based methods have been developed for their accurate classification, yet many aspects of the specific genomic features that determine these differences are not fully understood. In this study, we used publicly available whole-genome sequences from bacteria (N = 2546) and archaea (N = 109). From these, a set of genomic features (nucleotide frequencies and proportions, coding sequences (CDS), non-coding, ribosomal and transfer RNA genes (ncRNA, rRNA, tRNA), Chargaff's, topological entropy and Shannon's entropy scores) was extracted and used as input data to develop machine learning models for the classification of archaea and bacteria.<br><br>RESULTS: The classification accuracy ranged from 0.993 (Random Forest) to 0.998 (Neural Networks). Over the four models, only 11 examples were misclassified, especially those belonging to the minority class (Archaea). From variable importance, tRNA topological and Shannon's entropy, nucleotide frequencies in tRNA, rRNA and ncRNA, CDS, tRNA and rRNA Chargaff's scores have emerged as the top discriminating factors. In particular, tRNA entropy (both topological and Shannon's) was the most important genomic feature for classification, pointing at the complex interactions between the genetic code, tRNAs and the translational machinery.<br><br>CONCLUSIONS: tRNA, rRNA and ncRNA genes emerged as the key genomic elements that underpin the classification of archaea and bacteria. In particular, higher nucleotide diversity was found in tRNA from bacteria compared to archaea. The analysis of the few classification errors reflects the complex phylogenetic relationships between bacteria, archaea and eukaryotes.}, }
@article {pmid39390113, year = {2024}, author = {Nagar, DN and Mani, K and Braganca, JM}, title = {Author Correction: Genomic insights on carotenoid synthesis by extremely halophilic archaea Haloarcularubripromontorii BS2, Haloferaxlucentense BBK2 and Halogeometricumborinquense E3 isolated from the solar salterns of India.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {23750}, doi = {10.1038/s41598-024-74079-z}, pmid = {39390113}, issn = {2045-2322}, }
@article {pmid39383165, year = {2024}, author = {, }, title = {Correction: A Versatile Medium for Cultivating Methanogenic Archaea.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0312093}, pmid = {39383165}, issn = {1932-6203}, abstract = {[This corrects the article DOI: 10.1371/journal.pone.0061563.].}, }
@article {pmid39363002, year = {2024}, author = {Mühling, L and Baur, T and Molitor, B}, title = {Methanothermobacter thermautotrophicus and Alternative Methanogens: Archaea-Based Production.}, journal = {Advances in biochemical engineering/biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39363002}, issn = {0724-6145}, abstract = {Methanogenic archaea convert bacterial fermentation intermediates from the decomposition of organic material into methane. This process has relevance in the global carbon cycle and finds application in anthropogenic processes, such as wastewater treatment and anaerobic digestion. Furthermore, methanogenic archaea that utilize hydrogen and carbon dioxide as substrates are being employed as biocatalysts for the biomethanation step of power-to-gas technology. This technology converts hydrogen from water electrolysis and carbon dioxide into renewable natural gas (i.e., methane). The application of methanogenic archaea in bioproduction beyond methane has been demonstrated in only a few instances and is limited to mesophilic species for which genetic engineering tools are available. In this chapter, we discuss recent developments for those existing genetically tractable systems and the inclusion of novel genetic tools for thermophilic methanogenic species. We then give an overview of recombinant bioproduction with mesophilic methanogenic archaea and thermophilic non-methanogenic microbes. This is the basis for discussing putative products with thermophilic methanogenic archaea, specifically the species Methanothermobacter thermautotrophicus. We give estimates of potential conversion efficiencies for those putative products based on a genome-scale metabolic model for M. thermautotrophicus.}, }
@article {pmid39360821, year = {2024}, author = {Han, S and Kim, S and Sedlacek, CJ and Farooq, A and Song, C and Lee, S and Liu, S and Brüggemann, N and Rohe, L and Kwon, M and Rhee, S-K and Jung, M-Y}, title = {Adaptive traits of Nitrosocosmicus clade ammonia-oxidizing archaea.}, journal = {mBio}, volume = {}, number = {}, pages = {e0216924}, doi = {10.1128/mbio.02169-24}, pmid = {39360821}, issn = {2150-7511}, abstract = {UNLABELLED: Nitrification is a core process in the global nitrogen (N) cycle mediated by ammonia-oxidizing microorganisms, including ammonia-oxidizing archaea (AOA) as a key player. Although much is known about AOA abundance and diversity across environments, the genetic drivers of the ecophysiological adaptations of the AOA are often less clearly defined. This is especially true for AOA within the genus Nitrosocosmicus, which have several unique physiological traits (e.g., high substrate tolerance, low substrate affinity, and large cell size). To better understand what separates the physiology of Nitrosocosmicus AOA, we performed comparative genomics with genomes from 39 cultured AOA, including five Nitrosocosmicus AOA. The absence of a canonical high-affinity type ammonium transporter and typical S-layer structural genes was found to be conserved across all Nitrosocosmicus AOA. In agreement, cryo-electron tomography confirmed the absence of a visible outermost S-layer structure, which has been observed in other AOA. In contrast to other AOA, the cryo-electron tomography highlighted the possibility that Nitrosocosmicus AOA may possess a glycoprotein or glycolipid-based glycocalyx cell covering outer layer. Together, the genomic, physiological, and metabolic properties revealed in this study provide insight into niche adaptation mechanisms and the overall ecophysiology of members of the Nitrosocosmicus clade in various terrestrial ecosystems.<br><br>IMPORTANCE: Nitrification is a vital process within the global biogeochemical nitrogen cycle but plays a significant role in the eutrophication of aquatic ecosystems and the production of the greenhouse gas nitrous oxide (N2O) from industrial agriculture ecosystems. While various types of ammonia-oxidizing microorganisms play a critical role in the N cycle, ammonia-oxidizing archaea (AOA) are often the most abundant nitrifiers in natural environments. Members of the genus Nitrosocosmicus are one of the prevalent AOA groups detected in undisturbed terrestrial ecosystems and have previously been reported to possess a range of physiological characteristics that set their physiology apart from other AOA species. This study provides significant progress in understanding these unique physiological traits and their genetic drivers. Our results highlight how physiological studies based on comparative genomics-driven hypotheses can contribute to understanding the unique niche of Nitrosocosmicus AOA.}, }
@article {pmid39359677, year = {2024}, author = {Pereira, O and Qin, W and Galand, PE and Debroas, D and Lami, R and Hochart, C and Zhou, Y and Zhou, J and Zhang, C}, title = {Metabolic activities of marine ammonia-oxidizing archaea orchestrated by quorum sensing.}, journal = {mLife}, volume = {3}, number = {3}, pages = {417-429}, pmid = {39359677}, issn = {2770-100X}, abstract = {Ammonia-oxidizing archaea (AOA) play crucial roles in marine carbon and nitrogen cycles by fixing inorganic carbon and performing the initial step of nitrification. Evaluation of carbon and nitrogen metabolism popularly relies on functional genes such as amoA and accA. Increasing studies suggest that quorum sensing (QS) mainly studied in biofilms for bacteria may serve as a universal communication and regulatory mechanism among prokaryotes; however, this has yet to be demonstrated in marine planktonic archaea. To bridge this knowledge gap, we employed a combination of metabolic activity markers (amoA, accA, and grs) to elucidate the regulation of AOA-mediated nitrogen, carbon processes, and their interactions with the surrounding heterotrophic population. Through co-transcription investigations linking metabolic markers to potential key QS genes, we discovered that QS molecules could regulate AOA's carbon, nitrogen, and lipid metabolisms under different conditions. Interestingly, specific AOA ecotypes showed a preference for employing distinct QS systems and a distinct QS circuit involving a typical population. Overall, our data demonstrate that QS orchestrates nitrogen and carbon metabolism, including the exchange of organic metabolites between AOA and surrounding heterotrophic bacteria, which has been previously overlooked in marine AOA research.}, }
@article {pmid39348174, year = {2024}, author = {Lehtovirta-Morley, LE and Ge, C and Ross, J and Yao, H and Hazard, C and Gubry-Rangin, C and Prosser, JI and Nicol, GW}, title = {Nitrosotalea devaniterrae gen. nov., sp. nov. and Nitrosotalea sinensis sp. nov., two acidophilic ammonia oxidising archaea isolated from acidic soil, and proposal of the new order Nitrosotaleales ord. nov. within the class Nitrososphaeria of the phylum Nitrososphaerota.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {9}, pages = {}, doi = {10.1099/ijsem.0.006387}, pmid = {39348174}, issn = {1466-5034}, mesh = {*Soil Microbiology ; *Phylogeny ; *Base Composition ; *RNA, Ribosomal, 16S/genetics ; *Sequence Analysis, DNA ; *Ammonia/metabolism ; *DNA, Archaeal/genetics ; *Oxidation-Reduction ; China ; Archaea/classification/genetics/isolation &amp; purification ; Hydrogen-Ion Concentration ; Nitrites/metabolism ; Chemoautotrophic Growth ; }, abstract = {Two obligately acidophilic, mesophilic and aerobic soil ammonia-oxidising archaea were isolated from a pH 4.5 arable sandy loam (UK) and pH 4.7 acidic sulphate paddy soil (PR China) and designated strains Nd1[T] and Nd2[T], respectively. The strains shared more than 99 % 16S rRNA gene sequence identity and their genomes were both less than 2 Mb in length, sharing 79 % average nucleotide identity, 81 % average amino acid identity and a DNA G+C content of approximately 37 mol%. Both strains were chemolithotrophs that fixed carbon dioxide and gained energy by oxidising ammonia to nitrite, with no evidence of mixotrophic growth. Neither strain was capable of using urea as a source of ammonia. Both strains were non-motile in culture, although Nd1[T] does possess genes encoding flagella components and therefore may be motile under certain conditions. Cells of Nd1[T] were small angular rods 0.5-1 µm in length and grew at pH 4.2-5.6 and at 20-30 °C. Cells of Nd1[T] were small angular rods 0.5-1 µm in length and grew at pH 4.0-6.1 and at 20-42 °C. Nd1[T] and Nd2[T] are distinct with respect to genomic and physiological features and are assigned as the type strains for the species Nitrosotalea devaniterrae sp. nov. (type strain, Nd1[T]=NCIMB 15248[T]=DSM 110862[T]) and Nitrosotalea sinensis sp. nov. (type strain, Nd2[T]=NCIMB 15249[T]=DSM 110863[T]), respectively, within the genus Nitrosotalea gen. nov. The family Nitrosotaleaceae fam. nov. and order Nitrosotaleales ord. nov. are also proposed officially.}, }
@article {pmid39304533, year = {2024}, author = {Zhang, QK and Zhu, LR and Dong, XY and Yang, XY and Hou, J and Cui, HL}, title = {Salinirarus marinus gen. nov., sp. nov., Haloplanus salilacus sp. nov., Haloplanus pelagicus sp. nov., Haloplanus halophilus sp. nov., Haloplanus halobius sp. nov., halophilic archaea isolated from commercial coarse salts with potential as starter cultures for salt-fermented foods.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnae075}, pmid = {39304533}, issn = {1574-6968}, abstract = {Five halophilic archaeal strains, XH8T, CK5-1T, GDY1T, HW8-1T, and XH21T, were isolated from commercial coarse salt produced in different regions of China. Their 16S rRNA and rpoB' gene sequences indicated that four of the strains (CK5-1T, GDY1T, HW8-1T, and XH21T) represent distinct species within the genus Haloplanus (family Haloferacaceae), while strain XH8T represents a novel genus within the same family. These assignments were supported by phylogenetic and phylogenomic analyses, which showed that strains CK5-1T, GDY1T, HW8-1T, and XH21T cluster with the current species of the genus Haloplanus, while strain XH8T forms a separate branch from the genus Haloplanus. The digital DNA-DNA hybridization and average amino acid identity (AAI) values among these four strains and the current members of the genus Haloplanus were 23.1-35.2% and 75.9-83.8%, respectively; and those values between strain XH8T and other genera in the family Haloferacaceae were 18.8-33.6% and 59.8-66.6%, respectively, much lower than the threshold values for species demarcation. Strain XH8T may represent a novel genus of the family Haloferacaceae according to the cut-off value of AAI (≤72.1%) proposed to differentiate genera within the family Haloferacaceae. These five strains could be distinguished from the related species according to differential phenotypic characteristics. Based on these results, it is proposed that strain XH8T represents a novel genus within the family Haloferacaceae, and strains CK5-1T, GDY1T, HW8-1T, and XH21T represent four novel species of the genus Haloplanus, respectively. Additionally, these five strains possess genes encoding enzymes critical for the fermentation process in salt-fermented foods, indicating their potential as starter cultures for these applications.}, }
@article {pmid39300577, year = {2024}, author = {Lezcano, M&#xc1; and Bornemann, TLV and Sánchez-García, L and Carrizo, D and Adam, PS and Esser, SP and Cabrol, NA and Probst, AJ and Parro, V}, title = {Hyperexpansion of genetic diversity and metabolic capacity of extremophilic bacteria and archaea in ancient Andean lake sediments.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {176}, pmid = {39300577}, issn = {2049-2618}, support = {FJC2018-037246-I//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RYC2018-023943-I//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RYC-2014-19446//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RTI2018-094368-B-I0//Spanish Ministry of Science and Innovation/State Agency of Research/ ; PEJD-2017- POST/TIC-4119//Spanish Ministry of Science and Innovation/State Agency of Research (EU Youth Employment Initiative)/ ; NAI-CAN7, 13NAI7_2-0018//NASA Astrobiology Institute/ ; DFG PR1603/2-1//German Research Foundation/ ; 161L0285E//German Federal Ministry of Education and Research/ ; }, mesh = {*Lakes/microbiology ; *Archaea/genetics/metabolism/classification ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Genetic Variation ; Chile ; Phylogeny ; Microbiota ; Extremophiles/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The Andean Altiplano hosts a repertoire of high-altitude lakes with harsh conditions for life. These lakes are undergoing a process of desiccation caused by the current climate, leaving terraces exposed to extreme atmospheric conditions and serving as analogs to Martian paleolake basins. Microbiomes in Altiplano lake terraces have been poorly studied, enclosing uncultured lineages and a great opportunity to understand environmental adaptation and the limits of life on Earth. Here we examine the microbial diversity and function in ancient sediments (10.3-11 kyr BP (before present)) from a terrace profile of Laguna Lejía, a sulfur- and metal/metalloid-rich saline lake in the Chilean Altiplano. We also evaluate the physical and chemical changes of the lake over time by studying the mineralogy and geochemistry of the terrace profile.<br><br>RESULTS: The mineralogy and geochemistry of the terrace profile revealed large water level fluctuations in the lake, scarcity of organic carbon, and high concentration of SO4[2-]-S, Na, Cl and Mg. Lipid biomarker analysis indicated the presence of aquatic/terrestrial plant remnants preserved in the ancient sediments, and genome-resolved metagenomics unveiled a diverse prokaryotic community with still active microorganisms based on in silico growth predictions. We reconstructed 591 bacterial and archaeal metagenome-assembled genomes (MAGs), of which 98.8% belonged to previously unreported species. The most abundant and widespread metabolisms among MAGs were the reduction and oxidation of S, N, As, and halogenated compounds, as well as aerobic CO oxidation, possibly as a key metabolic trait in the organic carbon-depleted sediments. The broad redox and CO2 fixation pathways among phylogenetically distant bacteria and archaea extended the knowledge of metabolic capacities to previously unknown taxa. For instance, we identified genomic potential for dissimilatory sulfate reduction in Bacteroidota and &#x3b1;- and &#x3b3;-Proteobacteria, predicted an enzyme for ammonia oxidation in a novel Actinobacteriota, and predicted enzymes of the Calvin-Benson-Bassham cycle in Planctomycetota, Gemmatimonadota, and Nanoarchaeota.<br><br>CONCLUSIONS: The high number of novel bacterial and archaeal MAGs in the Laguna Lej&#xed;a indicates the wide prokaryotic diversity discovered. In addition, the detection of genes in unexpected taxonomic groups has significant implications for the expansion of microorganisms involved in the biogeochemical cycles of carbon, nitrogen, and sulfur. Video Abstract.}, }
@article {pmid39299940, year = {2024}, author = {Obayori, OS and Salam, LB and Ashade, AO and Oseni, TD and Kalu, MD and Mustapha, FM}, title = {An animal charcoal contaminated cottage industry soil highlighted by halophilic archaea dominance and decimation of bacteria.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {40}, number = {10}, pages = {327}, pmid = {39299940}, issn = {1573-0972}, mesh = {*Metals, Heavy/analysis ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification/metabolism ; *Charcoal ; *Soil Pollutants/analysis ; *Soil/chemistry ; Nigeria ; High-Throughput Nucleotide Sequencing ; Animals ; Hydrocarbons/metabolism/analysis ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; }, abstract = {An animal charcoal contaminated cottage industry soil in Lagos, Nigeria (ACGT) was compared in an ex post facto study with a nearby unimpacted soil (ACGC). Hydrocarbon content was higher than regulatory limits in ACGT (180.2 mg/kg) but lower in ACGC (19.28 mg/kg). Heavy metals like nickel, cadmium, chromium and lead were below detection limit in ACGC. However, all these metals, except cadmium, were detected in ACGT, but at concentrations below regulatory limits. Furthermore, copper (253.205 mg/kg) and zinc (422.630 mg/kg) were above regulatory limits in ACGT. Next generation sequencing revealed that the procaryotic community was dominated by bacteria in ACGC (62%) while in ACGT archaea dominated (76%). Dominant phyla in ACGC were Euryarchaeota (37%), Pseudomonadota (16%) and Actinomycetota (12%). In ACGT it was Euryarchaeota (76%), Bacillota (9%), Pseudomonadota (7%) and Candidatus Nanohaloarchaeota (5%). Dominant Halobacteria genera in ACGT were Halobacterium (16%), Halorientalis (16%), unranked halophilic archaeon (13%) Salarchaeum (6%) and Candidatus Nanohalobium (5%), whereas ACGC showed greater diversity dominated by bacterial genera Salimicrobium (7%) and Halomonas (3%). Heavy metals homeostasis genes, especially for copper, were fairly represented in both soils but with bacterial taxonomic affiliations. Sites like ACGT, hitherto poorly studied and understood, could be sources of novel bioresources.}, }
@article {pmid39296579, year = {2024}, author = {Vershinin, Z and Zaretsky, M and Eichler, J}, title = {N-glycosylation in Archaea - Expanding the process, components and roles of a universal post-translational modification.}, journal = {BBA advances}, volume = {6}, number = {}, pages = {100120}, pmid = {39296579}, issn = {2667-1603}, abstract = {While performed by all three domains of life, N-glycosylation in Archaea is less well described than are the parallel eukaryal and bacterial processes. Still, what is known of the archaeal version of this universal post-translational modification reveals numerous seemingly domain-specific traits. Specifically, the biosynthesis of archaeal N-linked glycans relies on distinct pathway steps and components, rare sugars and sugar modifications, as well as unique lipid carriers upon which N-linked glycans are assembled. At the same time, Archaea possess the apparently unique ability to simultaneously modify their glycoproteins with very different N-linked glycans. In addition to these biochemical aspects of archaeal N-glycosylation, such post-translational modification has been found to serve a wide range of roles possibly unique to Archaea, including allowing these microorganisms to not only cope with the harsh physical conditions of the niches they can inhabit but also providing the ability to adapt to transient changes in such environments.}, }
@article {pmid39296305, year = {2024}, author = {Hernández-Magaña, E and Kraft, B}, title = {Nitrous oxide production and consumption by marine ammonia-oxidizing archaea under oxygen depletion.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1410251}, pmid = {39296305}, issn = {1664-302X}, abstract = {Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle and among the most abundant microorganisms in the ocean, thriving even in oxygen-depleted ecosystems. AOA produce the greenhouse gas nitrous oxide (N2O) as a byproduct of ammonia oxidation. Additionally, the recent discovery of a nitric oxide dismutation pathway in the AOA isolate Nitrosopumilus maritimus points toward other N2O production and consumption pathways in AOA. AOA that perform NO dismutation when exposed to oxygen depletion, produce oxygen and dinitrogen as final products. Based on the transient accumulation of N2O coupled with oxygen accumulation, N2O has been proposed as an intermediate in this novel archaeal pathway. In this study, we spiked N2O to oxygen-depleted incubations with pure cultures of two marine AOA isolates that were performing NO dismutation. By using combinations of N compounds with different isotopic signatures ([15]NO2 [-] pool +[44]N2O spike and [14]NO2 [-] pool +[46]N2O spike), we evaluated the N2O spike effects on the production of oxygen and the isotopic signature of N2 and N2O. The experiments confirmed that N2O is an intermediate in NO dismutation by AOA, distinguishing it from similar pathways in other microbial clades. Furthermore, we showed that AOA rapidly reduce high concentrations of spiked N2O to N2. These findings advance our understanding of microbial N2O production and consumption in oxygen-depleted settings and highlight AOA as potentially important key players in N2O turnover.}, }
@article {pmid39287442, year = {2024}, author = {Mattick, JSA and Bromley, RE and Watson, KJ and Adkins, RS and Holt, CI and Lebov, JF and Sparklin, BC and Tyson, TS and Rasko, DA and Dunning Hotopp, JC}, title = {Deciphering transcript architectural complexity in bacteria and archaea.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0235924}, pmid = {39287442}, issn = {2150-7511}, abstract = {RNA transcripts are potential therapeutic targets, yet bacterial transcripts have uncharacterized biodiversity. We developed an algorithm for transcript prediction called tp.py using it to predict transcripts (mRNA and other RNAs) in Escherichia coli K12 and E2348/69 strains (Bacteria:gamma-Proteobacteria), Listeria monocytogenes strains Scott A and RO15 (Bacteria:Firmicute), Pseudomonas aeruginosa strains SG17M and NN2 strains (Bacteria:gamma-Proteobacteria), and Haloferax volcanii (Archaea:Halobacteria). From >5 million E. coli K12 and >3 million E. coli E2348/69 newly generated Oxford Nanopore Technologies direct RNA sequencing reads, 2,487 K12 mRNAs and 1,844 E2348/69 mRNAs were predicted, with the K12 mRNAs containing more than half of the predicted E. coli K12 proteins. While the number of predicted transcripts varied by strain based on the amount of sequence data used, across all strains examined, the predicted average size of the mRNAs was 1.6-1.7 kbp, while the median size of the 5'- and 3'-untranslated regions (UTRs) were 30-90 bp. Given the lack of bacterial and archaeal transcript annotation, most predictions were of novel transcripts, but we also predicted many previously characterized mRNAs and ncRNAs, including post-transcriptionally generated transcripts and small RNAs associated with pathogenesis in the E. coli E2348/69 LEE pathogenicity islands. We predicted small transcripts in the 100-200 bp range as well as >10 kbp transcripts for all strains, with the longest transcript for two of the seven strains being the nuo operon transcript, and for another two strains it was a phage/prophage transcript. This quick, easy, and reproducible method will facilitate the presentation of transcripts, and UTR predictions alongside coding sequences and protein predictions in bacterial genome annotation as important resources for the research community.IMPORTANCEOur understanding of bacterial and archaeal genes and genomes is largely focused on proteins since there have only been limited efforts to describe bacterial/archaeal RNA diversity. This contrasts with studies on the human genome, where transcripts were sequenced prior to the release of the human genome over two decades ago. We developed software for the quick, easy, and reproducible prediction of bacterial and archaeal transcripts from Oxford Nanopore Technologies direct RNA sequencing data. These predictions are urgently needed for more accurate studies examining bacterial/archaeal gene regulation, including regulation of virulence factors, and for the development of novel RNA-based therapeutics and diagnostics to combat bacterial pathogens, like those with extreme antimicrobial resistance.}, }
@article {pmid39281633, year = {2024}, author = {Ben Hamad Bouhamed, S and Chaari, M and Baati, H and Zouari, S and Ammar, E}, title = {Extreme halophilic Archaea: Halobacterium salinarum carotenoids characterization and antioxidant properties.}, journal = {Heliyon}, volume = {10}, number = {17}, pages = {e36832}, pmid = {39281633}, issn = {2405-8440}, abstract = {Important marine microorganisms are resources of renewable energy that may face global population growth and needs. The application of biomass metabolites, such as carotenoids and their derivatives, may solve some agro-food health problems. Herein, a new halophilic Archaea Halobacterium salinarum producing carotenoid was screened from a Tunisian solar Saltworks (Sfax). The identification of the carotenoid pigments was carried out using HPLC-MS/MS. The predominant pigments produced by this Halobacterium were bacterioruberin and its derivatives and the carotenoids production was found to be of 21.51 mg/mL. Moreover, the data revealed that the carotenoids extract exhibited a high antioxidant activity across four oxidizing assays. The present results suggested that carotenoids extracted from halophilic Archaea are interesting sources of natural antioxidants for future innovative applications in agro-food, cosmetic and health fields.}, }
@article {pmid39215524, year = {2024}, author = {Chatziargyri, AG and Stasi, EA and Tsirigos, KI and Litou, ZI and Iconomidou, VA and Bagos, PG}, title = {CW-PRED: Prediction of C-terminal surface anchoring sorting signals in bacteria and Archaea.}, journal = {Journal of bioinformatics and computational biology}, volume = {22}, number = {4}, pages = {2450021}, doi = {10.1142/S0219720024500215}, pmid = {39215524}, issn = {1757-6334}, mesh = {*Protein Sorting Signals ; *Bacterial Proteins/metabolism/chemistry/genetics ; *Archaeal Proteins/metabolism/chemistry/genetics ; Archaea/metabolism/genetics ; Computational Biology/methods ; Cell Wall/metabolism/chemistry ; Markov Chains ; Amino Acid Motifs ; Software ; Bacteria/metabolism/genetics ; Algorithms ; }, abstract = {Sorting signals are crucial for the anchoring of proteins to the cell surface in archaea and bacteria. These proteins often feature distinct motifs at their C-terminus, cleaved by sortase or sortase-like enzymes. Gram-positive bacteria exhibit the LPXTGX consensus motif, cleaved by sortases, while Gram-negative bacteria employ exosortases recognizing motifs like PEP. Archaea utilize exosortase homologs known as archaeosortases for signal anchoring. Traditionally identification of such C-terminal sorting signals was performed with profile Hidden Markov Models (pHMMs). The Cell-Wall PREDiction (CW-PRED) method introduced for the first time a custom-made class HMM for proteins in Gram-positive bacteria that contain a cell wall sorting signal which begins with an LPXTG motif, followed by a hydrophobic domain and a tail of positively charged residues. Here we present a new and updated version of CW-PRED for predicting C-terminal sorting signals in Archaea, Gram-positive, and Gram-negative bacteria. We used a large training set and several model enhancements that improve motif identification in order to achieve better discrimination between C-terminal signals and other proteins. Cross-validation demonstrates CW-PRED's superiority in sensitivity and specificity compared to other methods. Application of the method in reference proteomes reveals a large number of potential surface proteins not previously identified. The method is available for academic use at http://195.251.108.230/apps.compgen.org/CW-PRED/ and as standalone software.}, }
@article {pmid39215388, year = {2024}, author = {Tejedor-Sanz, S and Song, YE and Sundstrom, ER}, title = {Utilization of formic acid by extremely thermoacidophilic archaea species.}, journal = {Microbial biotechnology}, volume = {17}, number = {9}, pages = {e70003}, pmid = {39215388}, issn = {1751-7915}, support = {CW367480//Energy Biosciences Institute/ ; }, mesh = {*Formates/metabolism ; Sulfolobales/metabolism/genetics ; }, abstract = {The exploration of novel hosts with the ability to assimilate formic acid, a C1 substrate that can be produced from renewable electrons and CO2, is of great relevance for developing novel and sustainable biomanufacturing platforms. Formatotrophs can use formic acid or formate as a carbon and/or reducing power source. Formatotrophy has typically been studied in neutrophilic microorganisms because formic acid toxicity increases in acidic environments below the pKa of 3.75 (25°C). Because of this toxicity challenge, utilization of formic acid as either a carbon or energy source has been largely unexplored in thermoacidophiles, species that possess the ability to produce a variety of metabolites and enzymes of high biotechnological relevance. Here we investigate the capacity of several thermoacidophilic archaea species from the Sulfolobales order to tolerate and metabolize formic acid. Metallosphaera prunae, Sulfolobus metallicus and Sulfolobus acidocaldarium were found to metabolize and grow with 1-2 mM of formic acid in batch cultivations. Formic acid was co-utilized by this species alongside physiological electron donors, including ferrous iron. To enhance formic acid utilization while maintaining aqueous concentrations below the toxicity threshold, we developed a bioreactor culturing method based on a sequential formic acid feeding strategy. By dosing small amounts of formic acid sequentially and feeding H2 as co-substrate, M. prunae could utilize a total of 16.3 mM of formic acid and grow to higher cell densities than when H2 was supplied as a sole electron donor. These results demonstrate the viability of culturing thermoacidophilic species with formic acid as an auxiliary substrate in bioreactors to obtain higher cell densities than those yielded by conventional autotrophic conditions. Our work underscores the significance of formic acid metabolism in extreme habitats and holds promise for biotechnological applications in the realm of sustainable energy production and environmental remediation.}, }
@article {pmid39215047, year = {2024}, author = {Nagar, DN and Mani, K and Braganca, JM}, title = {Genomic insights on carotenoid synthesis by extremely halophilic archaea Haloarcula rubripromontorii BS2, Haloferax lucentense BBK2 and Halogeometricum borinquense E3 isolated from the solar salterns of India.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {20214}, pmid = {39215047}, issn = {2045-2322}, support = {(Level III) BT/INF/22/SP2543/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; 2023-24//DSTE&amp;WM, Government of Goa/ ; }, mesh = {*Carotenoids/metabolism ; India ; *Phylogeny ; *Haloferax/genetics/metabolism ; *Haloarcula/genetics/metabolism ; Genome, Archaeal ; Whole Genome Sequencing ; RNA, Ribosomal, 16S/genetics ; Halobacteriaceae/genetics/metabolism/isolation &amp; purification/classification ; Genomics/methods ; Base Composition ; }, abstract = {Haloarchaeal cultures were isolated from solar salterns of Goa and Tamil Nadu and designated as BS2, BBK2 and E3. These isolates grew with a characteristic bright orange to pink pigmentation and were capable of growing in media containing upto 25% (w/vol) NaCl. Whole genome sequencing (WGS) of the three haloarchaeal strains BS2, BBK2 and E3 indicated an assembled genomic size of 4.1 Mb, 3.8 Mb and 4 Mb with G + C content of 61.8, 65.6 and 59.8% respectively. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the archaeal isolates belong to Haloarcula, Haloferax and Halogeometricum genera. Haloarcula rubripromontorii BS2 was predicted to have 4292 genes with 4242 CDS regions, 46 tRNAs, 6 rRNAs and 3 misc_RNAs. In case of Haloferax lucentense BBK2,, 3840 genes with 3780 CDS regions were detected along with 52 tRNAs, 5 rRNAs and 3 misc_RNAs. Halogeometricum borinquense E3 contained 4101 genes, 4043 CDS regions, 52 tRNAs, 4 rRNAs, and 2 misc_RNAs. The functional annotation and curation of the haloarchaeal genome, revealed C50 carotenoid biosynthetic genes like phytoene desaturase/carotenoid 3' -4' desaturase (crtI), lycopene elongase (ubiA/lyeJ) and carotenoid biosynthesis membrane protein (cruF) in the three isolates. Whereas crtD (C-3',4' desaturase), crtY (lycopene cyclase) and brp/blh (β-carotene dioxygenase) genes were identified only in BS2.}, }
@article {pmid39210225, year = {2024}, author = {da Costa Soares, S and Vezzani, FM and Favaretto, N and Auler, AC and da Silva Coelho, I and de Sousa Pires, A and Cruz, LM and de Souza, EM and Barth, G}, title = {Effect of long-term liquid dairy manure application on activity and structure of bacteria and archaea in no-till soils depends on plant in development.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {42}, pages = {54713-54728}, pmid = {39210225}, issn = {1614-7499}, mesh = {*Soil Microbiology ; *Manure/microbiology ; *Archaea ; *Bacteria ; *Soil/chemistry ; RNA, Ribosomal, 16S ; Brazil ; Agriculture/methods ; Dairying ; }, abstract = {This study aimed to evaluate the impact of long-term liquid dairy manure (LDM) application on the activity and structure of soil bacterial and archaea communities in two cropping seasons over 1 year of a no-till crop rotation system. The experiment was run in a sandy clay loam texture Oxisol, in Brazil, including LDM doses of 60, 120, and 180 m[3] ha[-1] year[-1], installed in 2005. Soil sampling was conducted during spring 2018 and autumn 2019 at 0-10-cm depth. Microbial biomass carbon and nitrogen, 16S rRNA gene sequencing, microbial respiration and quotient were performed. Over the 14-year period, LDM application increased soil microbial community activity. Analysis of 16S rRNA gene sequencing revealed dominance by Proteobacteria, Acidobacteria, and Actinobacteria phyla (67% in spring and 70% in autumn). Genera Pirulla and Nitrososphaera showed enrichment at LDM doses of 120 and 180 m[3] ha[-1] year[-1] doses, respectively. During spring, following black oat cropping, shifts in the relative abundance of Bacteroidetes, Proteobacteria, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Chloroflexi, Actinobacteria, and AD3 phyla were observed due to LDM application, correlating with soil chemical indicators such as pH, K, Ca, Mn, and Zn. Our findings indicate that plant development strongly influences microbial community composition, potentially outweighing the impact of LDM. Our findings indicate that the application of liquid dairy manure alters the soil bacterial activity and community; however, this effect depends on the developing plant.}, }
@article {pmid39207169, year = {2024}, author = {Baker, BJ and Sarno, N}, title = {Small archaea may form intimate partnerships to maximize their metabolic potential.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0034724}, pmid = {39207169}, issn = {2150-7511}, abstract = {DPANN archaea have characteristically small cells and unique genomes that were long overlooked in diversity surveys. Their reduced genomes often lack essential metabolic pathways, requiring symbiotic relationships with other archaeal and bacterial hosts for survival. Yet a long-standing question remains, what is the advantage of maintaining ultrasmall cells. A recent study by Zhang et al. examined genomes of DPANN archaea from marine oxygen deficient zones (ODZs) (I. H. Zhang, B. Borer, R. Zhao, S. Wilbert, et al., mBio 15:e02918-23, 2024, https://doi.org/10.1128/mbio.02918-23). Surprisingly, these genomes contain a broad array of metabolic pathways including genes predicted to be involved in nitrous oxide (N2O) reduction. However, N2O levels are likely too low in ODZs to make this metabolically feasible. Modeling co-localization of DPANN archaea (N2O consumers) with other larger cells (N2O producers) demonstrates that N2O uptake rates can be optimized by maximizing the producer-to-consumer size ratio and proximity of consumer cells to producers. This may explain why such a diversity of archaea maintain extremely small cell sizes.}, }
@article {pmid39203380, year = {2024}, author = {Bai, C and Wang, Q and Xu, J and Zhang, H and Huang, Y and Cai, L and Zheng, X and Yang, M}, title = {Impact of Nutrient Enrichment on Community Structure and Co-Occurrence Networks of Coral Symbiotic Microbiota in Duncanopsammia peltata: Zooxanthellae, Bacteria, and Archaea.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203380}, issn = {2076-2607}, support = {2022YFC3102003//the National Key Research and Development Program of China/ ; 2022ZD01//the Fund of Fujian Key Laboratory of Island Monitoring and Ecological Development (Island Research Center, MNR)/ ; 2019017//the Scientific Research Foundation of the Third Institute of Oceanography, Ministry of Natural Resources of China/ ; 41976127//the National Natural Science Foundation of China/ ; 2023J06043//the Fujian Provincial Natural Science Funds for Distinguished Young Scholar/ ; }, abstract = {Symbiotic microorganisms in reef-building corals, including algae, bacteria, archaea, fungi, and viruses, play critical roles in the adaptation of coral hosts to adverse environmental conditions. However, their adaptation and functional relationships in nutrient-rich environments have yet to be fully explored. This study investigated Duncanopsammia peltata and the surrounding seawater and sediments from protected and non-protected areas in the summer and winter in Dongshan Bay. High-throughput sequencing was used to characterize community changes, co-occurrence patterns, and factors influencing symbiotic coral microorganisms (zooxanthellae, bacteria, and archaea) in different environments. The results showed that nutrient enrichment in the protected and non-protected areas was the greatest in December, followed by the non-protected area in August. In contrast, the August protected area had the lowest nutrient enrichment. Significant differences were found in the composition of the bacterial and archaeal communities in seawater and sediments from different regions. Among the coral symbiotic microorganisms, the main dominant species of zooxanthellae is the C1 subspecies (42.22-56.35%). The dominant phyla of bacteria were Proteobacteria, Cyanobacteria, Firmicutes, and Bacteroidota. Only in the August protected area did a large number (41.98%) of SAR324_cladeMarine_group_B exist. The August protected and non-protected areas and December protected and non-protected areas contained beneficial bacteria as biomarkers. They were Nisaea, Spiroplasma, Endozoicomonas, and Bacillus. No pathogenic bacteria appeared in the protected area in August. The dominant phylum in Archaea was Crenarchaeota. These symbiotic coral microorganisms' relative abundances and compositions vary with environmental changes. The enrichment of dissolved inorganic nitrogen in environmental media is a key factor affecting the composition of coral microbial communities. Co-occurrence analysis showed that nutrient enrichment under anthropogenic disturbances enhanced the interactions between coral symbiotic microorganisms. These findings improve our understanding of the adaptations of coral holobionts to various nutritional environments.}, }
@article {pmid39194224, year = {2024}, author = {Nakagawa, S and Sakai, HD and Shimamura, S and Takamatsu, Y and Kato, S and Yagi, H and Yanaka, S and Yagi-Utsumi, M and Kurosawa, N and Ohkuma, M and Kato, K and Takai, K}, title = {N-linked protein glycosylation in Nanobdellati (formerly DPANN) archaea and their hosts.}, journal = {Journal of bacteriology}, volume = {206}, number = {9}, pages = {e0020524}, pmid = {39194224}, issn = {1098-5530}, support = {JP 20H03322//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP 23K20307//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; //MEXT | National Institutes of Natural Sciences (NINS)/ ; 22EXC601//MEXT | NINS | Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences (ExCELLS)/ ; }, mesh = {Glycosylation ; *Archaeal Proteins/metabolism/genetics/chemistry ; Nanoarchaeota/metabolism/genetics ; Glycoproteins/metabolism/genetics/chemistry ; Archaea/metabolism/genetics ; Polysaccharides/metabolism ; Membrane Glycoproteins ; }, abstract = {Members of the kingdom Nanobdellati, previously known as DPANN archaea, are characterized by ultrasmall cell sizes and reduced genomes. They primarily thrive through ectosymbiotic interactions with specific hosts in diverse environments. Recent successful cultivations have emphasized the importance of adhesion to host cells for understanding the ecophysiology of Nanobdellati. Cell adhesion is often mediated by cell surface carbohydrates, and in archaea, this may be facilitated by the glycosylated S-layer protein that typically coats their cell surface. In this study, we conducted glycoproteomic analyses on two co-cultures of Nanobdellati with their host archaea, as well as on pure cultures of both host and non-host archaea. Nanobdellati exhibited various glycoproteins, including archaellins and hypothetical proteins, with glycans that were structurally distinct from those of their hosts. This indicated that Nanobdellati autonomously synthesize their glycans for protein modifications probably using host-derived substrates, despite the high energy cost. Glycan modifications on Nanobdellati proteins consistently occurred on asparagine residues within the N-X-S/T sequon, consistent with patterns observed across archaea, bacteria, and eukaryotes. In both host and non-host archaea, S-layer proteins were commonly modified with hexose, N-acetylhexosamine, and sulfonated deoxyhexose. However, the N-glycan structures of host archaea, characterized by distinct sugars such as deoxyhexose, nonulosonate sugar, and pentose at the nonreducing ends, were implicated in enabling Nanobdellati to differentiate between host and non-host cells. Interestingly, the specific sugar, xylose, was eliminated from the N-glycan in a host archaeon when co-cultured with Nanobdella. These findings enhance our understanding of the role of protein glycosylation in archaeal interactions.IMPORTANCENanobdellati archaea, formerly known as DPANN, are phylogenetically diverse, widely distributed, and obligately ectosymbiotic. The molecular mechanisms by which Nanobdellati recognize and adhere to their specific hosts remain largely unexplored. Protein glycosylation, a fundamental biological mechanism observed across all domains of life, is often crucial for various cell-cell interactions. This study provides the first insights into the glycoproteome of Nanobdellati and their host and non-host archaea. We discovered that Nanobdellati autonomously synthesize glycans for protein modifications, probably utilizing substrates derived from their hosts. Additionally, we identified distinctive glycosylation patterns that suggest mechanisms through which Nanobdellati differentiate between host and non-host cells. This research significantly advances our understanding of the molecular basis of microbial interactions in extreme environments.}, }
@article {pmid39134651, year = {2024}, author = {Gutiérrez-Preciado, A and Dede, B and Baker, BA and Eme, L and Moreira, D and López-García, P}, title = {Extremely acidic proteomes and metabolic flexibility in bacteria and highly diversified archaea thriving in geothermal chaotropic brines.}, journal = {Nature ecology &amp; evolution}, volume = {8}, number = {10}, pages = {1856-1869}, pmid = {39134651}, issn = {2397-334X}, support = {doi.org/10.37807/GBMF9739//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 787904//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*Proteome ; *Archaea/genetics/metabolism ; *Bacteria/metabolism/genetics/classification ; Lakes/microbiology ; Metagenome ; Salinity ; Archaeal Proteins/genetics/metabolism ; Genome, Archaeal ; Hot Springs/microbiology ; }, abstract = {Few described archaeal, and fewer bacterial, lineages thrive under salt-saturating conditions, such as solar saltern crystallizers (salinity above 30% w/v). They accumulate molar K[+] cytoplasmic concentrations to maintain osmotic balance ('salt-in' strategy) and have proteins adaptively enriched in negatively charged acidic amino acids. Here we analysed metagenomes and metagenome-assembled genomes from geothermally influenced hypersaline ecosystems with increasing chaotropicity in the Danakil Depression. Normalized abundances of universal single-copy genes confirmed that haloarchaea and Nanohaloarchaeota encompass 99% of microbial communities in the near-life-limiting conditions of the Western-Canyon Lakes. Danakil metagenome- and metagenome-assembled-genome-inferred proteomes, compared with those of freshwater, seawater and solar saltern ponds up to saturation (6-14-32% salinity), showed that Western-Canyon Lake archaea encode the most acidic proteomes ever observed (median protein isoelectric points ≤4.4). We identified previously undescribed haloarchaeal families as well as an Aenigmatarchaeota family and a bacterial phylum independently adapted to extreme halophily. Despite phylum-level diversity decreasing with increasing salinity-chaotropicity, and unlike in solar salterns, adapted archaea exceedingly diversified in Danakil ecosystems, challenging the notion of decreasing diversity under extreme conditions. Metabolic flexibility to utilize multiple energy and carbon resources generated by local hydrothermalism along feast-and-famine strategies seemingly shapes microbial diversity in these ecosystems near life limits.}, }
@article {pmid39128722, year = {2024}, author = {Carilo, I and Senju, Y and Yokoyama, T and Robinson, RC}, title = {Intercompatibility of eukaryotic and Asgard archaea ribosome-translocon machineries.}, journal = {The Journal of biological chemistry}, volume = {300}, number = {9}, pages = {107673}, pmid = {39128722}, issn = {1083-351X}, mesh = {*Ribosomes/metabolism ; *Endoplasmic Reticulum/metabolism ; *Archaeal Proteins/metabolism/genetics ; Membrane Proteins/metabolism/genetics ; Archaea/metabolism/genetics ; Protein Transport ; Eukaryota/metabolism/genetics ; Phylogeny ; Protein Sorting Signals/physiology ; Eukaryotic Cells/metabolism ; }, abstract = {In all domains of life, the ribosome-translocon complex inserts nascent transmembrane proteins into, and processes and transports signal peptide-containing proteins across, membranes. Eukaryotic translocons are anchored in the endoplasmic reticulum, while the prokaryotic complexes reside in cell membranes. Phylogenetic analyses indicate the inheritance of eukaryotic Sec61/oligosaccharyltransferase/translocon-associated protein translocon subunits from an Asgard archaea ancestor. However, the mechanism for translocon migration from a peripheral membrane to an internal cellular compartment (the proto-endoplasmic reticulum) during eukaryogenesis is unknown. Here we show compatibility between the eukaryotic ribosome-translocon complex and Asgard signal peptides and transmembrane proteins. We find that Asgard translocon proteins from Candidatus Prometheoarchaeum syntrophicum strain Candidatus Prometheoarchaeum syntrophicum strain MK-D1, a Lokiarchaeon confirmed to contain no internal cellular membranes, are targeted to the eukaryotic endoplasmic reticulum on ectopic expression. Furthermore, we show that the cytoplasmic domain of Candidatus Prometheoarchaeum syntrophicum strain MK-D1 oligosaccharyltransferase 1 (ribophorin I) can interact with eukaryotic ribosomes. Our data indicate that the location of existing ribosome-translocon complexes, at the protein level, determines the future placement of yet-to-be-translated translocon subunits. This principle predicts that during eukaryogenesis, under positive selection pressure, the relocation of a few translocon complexes to the proto-endoplasmic reticulum will have contributed to propagating the new translocon location, leading to their loss from the cell membrane.}, }
@article {pmid39115222, year = {2024}, author = {Zhao, Z and Qin, W and Li, L and Zhao, H and Ju, F}, title = {Discovery of Candidatus Nitrosomaritimum as a New Genus of Ammonia-Oxidizing Archaea Widespread in Anoxic Saltmarsh Intertidal Aquifers.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {36}, pages = {16040-16054}, doi = {10.1021/acs.est.4c02321}, pmid = {39115222}, issn = {1520-5851}, mesh = {*Ammonia/metabolism ; *Archaea/metabolism/genetics ; Phylogeny ; Oxidation-Reduction ; }, abstract = {Ammonia-oxidizing archaea (AOA) are widely distributed in marine and terrestrial habitats, contributing significantly to global nitrogen and carbon cycles. However, their genomic diversity, ecological niches, and metabolic potentials in the anoxic intertidal aquifers remain poorly understood. Here, we discovered and named a novel AOA genus, Candidatus Nitrosomaritimum, from the intertidal aquifers of Yancheng Wetland, showing close metagenomic abundance to the previously acknowledged dominant Nitrosopumilus AOA. Further construction of ammonia monooxygenase-based phylogeny demonstrated the widespread distribution of Nitrosomaritimum AOA in global estuarine-coastal niches and marine sediment. Niche differentiation among sublineages of this new genus in anoxic intertidal aquifers is driven by salinity and dissolved oxygen gradients. Comparative genomics revealed that Candidatus Nitrosomaritimum has the genetic capacity to utilize urea and possesses high-affinity phosphate transporter systems (phnCDE) for surviving phosphorus-limited conditions. Additionally, it contains putative nosZ genes encoding nitrous-oxide (N2O) reductase for reducing N2O to nitrogen gas. Furthermore, we gained first genomic insights into the archaeal phylum Hydrothermarchaeota populations residing in intertidal aquifers and revealed their potential hydroxylamine-detoxification mutualism with AOA through utilizing the AOA-released extracellular hydroxylamine using hydroxylamine oxidoreductase. Together, this study unravels the overlooked role of priorly unknown but abundant AOA lineages of the newly discovered genus Candidatus Nitrosomaritimum in biological nitrogen transformation and their potential for nitrogen pollution mitigation in coastal environments.}, }
@article {pmid39097239, year = {2024}, author = {Manesh, MJH and Willard, DJ and John, KM and Kelly, RM}, title = {Chalcopyrite bioleaching efficacy by extremely thermoacidophilic archaea leverages balanced iron and sulfur biooxidation.}, journal = {Bioresource technology}, volume = {408}, number = {}, pages = {131198}, pmid = {39097239}, issn = {1873-2976}, support = {T32 GM008776/GM/NIGMS NIH HHS/United States ; T32 GM133366/GM/NIGMS NIH HHS/United States ; }, mesh = {*Sulfur/metabolism ; *Oxidation-Reduction ; *Copper/metabolism ; *Iron/metabolism ; Archaea/metabolism ; Hydrogen-Ion Concentration ; Temperature ; Sulfolobales/metabolism ; }, abstract = {Factors that contribute to optimal chalcopyrite bioleaching by extremely thermoacidophilic archaea were examined for ten species belonging to the order Sulfolobales from the genera Acidianus (A. brierleyi), Metallosphaera (M. hakonensis, M. sedula, M. prunae), Sulfuracidifex (S. metallicus, S. tepriarius), Sulfolobus (S. acidocaldarius), Saccharlobus (S. solfataricus) and Sulfurisphaera (S. ohwakuensis, S. tokodaii). Only A. brierleyi, M. sedula, S. metallicus, S. tepriarius, S. ohwakuensis, and S. tokodai exhibited significant amounts of bioleaching and were investigated further. At 70-75 °C, Chalcopyrite loadings of 10 g/l were leached for 21 days during which pH, redox potential, planktonic cell density, iron concentrations and sulfate levels were monitored, in addition to copper mobilization. S. ohwakuensis proved to be the most prolific bioleacher. This was attributed to balanced iron and sulfur oxidation, thereby reducing by-product (e.g., jarosites) formation and minimizing surface passivation. Comparative genomics suggest markers for bioleaching potential, but the results here point to the need for experimental verification.}, }
@article {pmid39096085, year = {2024}, author = {Blombach, F and Werner, F}, title = {Chromatin and gene regulation in archaea.}, journal = {Molecular microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mmi.15302}, pmid = {39096085}, issn = {1365-2958}, support = {207446/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, abstract = {The chromatinisation of DNA by nucleoid-associated proteins (NAPs) in archaea 'formats' the genome structure in profound ways, revealing both striking differences and analogies to eukaryotic chromatin. However, the extent to which archaeal NAPs actively regulate gene expression remains poorly understood. The dawn of quantitative chromatin mapping techniques and first NAP-specific occupancy profiles in different archaea promise a more accurate view. A picture emerges where in diverse archaea with very different NAP repertoires chromatin maintains access to regulatory motifs including the gene promoter independently of transcription activity. Our re-analysis of genome-wide occupancy data of the crenarchaeal NAP Cren7 shows that these chromatin-free regions are flanked by increased Cren7 binding across the transcription start site. While bacterial NAPs often form heterochromatin-like regions across islands with xenogeneic genes that are transcriptionally silenced, there is little evidence for similar structures in archaea and data from Haloferax show that the promoters of xenogeneic genes remain accessible. Local changes in chromatinisation causing wide-ranging effects on transcription restricted to one chromosomal interaction domain (CID) in Saccharolobus islandicus hint at a higher-order level of organisation between chromatin and transcription. The emerging challenge is to integrate results obtained at microscale and macroscale, reconciling molecular structure and function with dynamic genome-wide chromatin landscapes.}, }
@article {pmid39085212, year = {2024}, author = {Leão, P and Little, ME and Appler, KE and Sahaya, D and Aguilar-Pine, E and Currie, K and Finkelstein, IJ and De Anda, V and Baker, BJ}, title = {Asgard archaea defense systems and their roles in the origin of eukaryotic immunity.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6386}, pmid = {39085212}, issn = {2041-1723}, support = {73592LPI//Simons Foundation/ ; F-1808//Welch Foundation/ ; }, mesh = {*Phylogeny ; *Archaea/genetics/immunology/virology ; *Archaeal Proteins/metabolism/genetics ; Argonaute Proteins/metabolism/genetics ; Eukaryota/genetics/immunology ; Bacteriophages/genetics/physiology ; Evolution, Molecular ; }, abstract = {Dozens of new antiviral systems have been recently characterized in bacteria. Some of these systems are present in eukaryotes and appear to have originated in prokaryotes, but little is known about these defense mechanisms in archaea. Here, we explore the diversity and distribution of defense systems in archaea and identify 2610 complete systems in Asgardarchaeota, a group of archaea related to eukaryotes. The Asgard defense systems comprise 89 unique systems, including argonaute, NLR, Mokosh, viperin, Lassamu, and CBASS. Asgard viperin and argonaute proteins have structural homology to eukaryotic proteins, and phylogenetic analyses suggest that eukaryotic viperin proteins were derived from Asgard viperins. We show that Asgard viperins display anti-phage activity when heterologously expressed in bacteria. Eukaryotic and bacterial argonaute proteins appear to have originated in Asgardarchaeota, and Asgard argonaute proteins have argonaute-PIWI domains, key components of eukaryotic RNA interference systems. Our results support that Asgardarchaeota played important roles in the origin of antiviral defense systems in eukaryotes.}, }
@article {pmid39085194, year = {2024}, author = {Valentin-Alvarado, LE and Appler, KE and De Anda, V and Schoelmerich, MC and West-Roberts, J and Kivenson, V and Crits-Christoph, A and Ly, L and Sachdeva, R and Greening, C and Savage, DF and Baker, BJ and Banfield, JF}, title = {Asgard archaea modulate potential methanogenesis substrates in wetland soil.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6384}, pmid = {39085194}, issn = {2041-1723}, support = {INV-037174/GATES/Bill &amp; Melinda Gates Foundation/United States ; LI-SIAME-00002001//Simons Foundation/ ; }, mesh = {*Wetlands ; *Methane/metabolism ; *Soil Microbiology ; *Archaea/genetics/metabolism ; *Carbon Cycle ; *Soil/chemistry ; Phylogeny ; Genome, Archaeal ; Oxidation-Reduction ; }, abstract = {The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions in soil ecosystems remain unknown. Of particular interest are Asgard archaeal contributions to methane cycling in wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new Asgard lineage, and a complete genome of Freyarchaeia, and predicted their metabolism in situ. Metatranscriptomics reveals expression of genes for [NiFe]-hydrogenases, pyruvate oxidation and carbon fixation via the Wood-Ljungdahl pathway. Also expressed are genes encoding enzymes for amino acid metabolism, anaerobic aldehyde oxidation, hydrogen peroxide detoxification and carbohydrate breakdown to acetate and formate. Overall, soil-associated Asgard archaea are predicted to include non-methanogenic acetogens, highlighting their potential role in carbon cycling in terrestrial environments.}, }
@article {pmid39085041, year = {2024}, author = {Hayashi, M and Wada, Y and Yamamura, A and Inoue, H and Yamashita, N and Ichimura, S and Iida, Y}, title = {Evaluation of the enzymatic properties of DNA (cytosine-5)-methyltransferase M.ApeKI from archaea in the presence of metal ions.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {88}, number = {10}, pages = {1155-1163}, doi = {10.1093/bbb/zbae106}, pmid = {39085041}, issn = {1347-6947}, mesh = {*Metals/pharmacology/metabolism ; DNA-Cytosine Methylases/metabolism ; DNA/metabolism ; Archaea/enzymology/genetics ; Copper/metabolism/pharmacology ; Archaeal Proteins/metabolism/genetics ; }, abstract = {We previously identified M.ApeKI from Aeropyum pernix K1 as a highly thermostable DNA (cytosine-5)-methyltransferase. M.ApeKI uses the type II restriction-modification system (R-M system), among the best-studied R-M systems. Although endonucleases generally utilize Mg (II) as a cofactor, several reports have shown that MTases exhibit different reactions in the presence of metal ions. This study aim was to evaluate the enzymatic properties of DNA (cytosine-5)-methyltransferase M.ApeKI from archaea in the presence of metal ions. We evaluated the influence of metal ions on the catalytic activity and DNA binding of M.ApeKI. The catalytic activity was inhibited by Cu (II), Mg (II), Mn (II), and Zn (II), each at 5 m m. DNA binding was more strongly inhibited by 5 m m Cu (II) and 10 m m Zn (II). To our knowledge, this is the first report showing that DNA binding of type II MTase is inhibited by metal ions.}, }
@article {pmid39081362, year = {2024}, author = {Kaneko, M and Omori, T and Igai, K and Mabuchi, T and Sakai-Tazawa, M and Nishihara, A and Kihara, K and Yoshimura, T and Ohkuma, M and Hongoh, Y}, title = {Facultative endosymbiosis between cellulolytic protists and methanogenic archaea in the gut of the Formosan termite Coptotermes formosanus.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae097}, pmid = {39081362}, issn = {2730-6151}, abstract = {Anaerobic protists frequently harbour methanogenic archaea, which apparently contribute to the hosts' fermentative metabolism by consuming excess H2. However, the ecological properties of endosymbiotic methanogens remain elusive in many cases. Here we investigated the ecology and genome of the endosymbiotic methanogen of the Cononympha protists in the hindgut of the termite Coptotermes formosanus. Microscopic and 16S rRNA amplicon sequencing analyses revealed that a single species, designated here "Candidatus Methanobrevibacter cononymphae", is associated with both Cononympha leidyi and Cononympha koidzumii and that its infection rate in Cononympha cells varied from 0.0% to 99.8% among termite colonies. Fine-scale network analysis indicated that multiple 16S rRNA sequence variants coexisted within a single host cell and that identical variants were present in both Cononympha species and also on the gut wall. Thus, "Ca. Methanobrevibacter cononymphae" is a facultative endosymbiont, transmitted vertically with frequent exchanges with the gut environment. Indeed, transmission electron microscopy showed escape or uptake of methanogens from/by a Cononympha cell. The genome of "Ca. Methanobrevibacter cononymphae" showed features consistent with its facultative lifestyle: i.e., the genome size (2.7 Mbp) comparable to those of free-living relatives; the pseudogenization of the formate dehydrogenase gene fdhA, unnecessary within the non-formate-producing host cell; the dependence on abundant acetate in the host cell as an essential carbon source; and the presence of a catalase gene, required for colonization on the microoxic gut wall. Our study revealed a versatile endosymbiosis between the methanogen and protists, which may be a strategy responding to changing conditions in the termite gut.}, }
@article {pmid39077992, year = {2024}, author = {Rasmussen, AN and Francis, CA}, title = {Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39077992}, issn = {1751-7370}, support = {DE-AC02-05CH11231//Department of Energy/ ; //Stanford Data Science Scholars Program/ ; }, mesh = {*Ammonia/metabolism ; San Francisco ; *Archaea/genetics/classification/metabolism/isolation &amp; purification ; *Bays/microbiology ; *Oxidation-Reduction ; *Nitrification ; Metagenome ; Seasons ; Metagenomics ; }, abstract = {Transient or recurring blooms of ammonia-oxidizing archaea (AOA) have been reported in several estuarine and coastal environments, including recent observations of AOA blooms in South San Francisco Bay. Here, we measured nitrification rates, quantified AOA abundance, and analyzed both metagenomic and metatranscriptomic data to examine the dynamics and activity of nitrifying microorganisms over the course of an AOA bloom in South San Francisco Bay during the autumn of 2018 and seasonally throughout 2019. Nitrification rates were correlated with AOA abundance in quantitative polymerase chain reaction (PCR) data, and both increased several orders of magnitude between the autumn AOA bloom and spring and summer seasons. From bloom samples, we recovered an extremely abundant, high-quality Candidatus Nitrosomarinus catalina-like AOA metagenome-assembled genome that had high transcript abundance during the bloom and expressed >80% of genes in its genome. We also recovered a putative nitrite-oxidizing bacteria metagenome-assembled genome from within the Nitrospinaceae that was of much lower abundance and had lower transcript abundance than AOA. During the AOA bloom, we observed increased transcript abundance for nitrogen uptake and oxidative stress genes in non-nitrifier metagenome-assembled genomes. This study confirms AOA are not only abundant but also highly active during blooms oxidizing large amounts of ammonia to nitrite-a key intermediate in the microbial nitrogen cycle-and producing reactive compounds that may impact other members of the microbial community.}, }
@article {pmid39077943, year = {2024}, author = {Lin, MG and Yen, CY and Shen, YY and Huang, YS and Ng, IW and Barillà, D and Sun, YJ and Hsiao, CD}, title = {Unraveling the structure and function of a novel SegC protein interacting with the SegAB chromosome segregation complex in Archaea.}, journal = {Nucleic acids research}, volume = {52}, number = {16}, pages = {9966-9977}, pmid = {39077943}, issn = {1362-4962}, support = {NSTC 111-2311-B-001-001//National Science and Technology Council/ ; RPG-245//Leverhulme Trust/ ; BB/X00645X/1//BBSRC/ ; }, mesh = {*Chromosome Segregation ; *Archaeal Proteins/chemistry/metabolism/genetics ; *Models, Molecular ; Protein Binding ; Crystallography, X-Ray ; Adenosine Diphosphate/metabolism/chemistry ; Binding Sites ; DNA, Archaeal/metabolism/chemistry/genetics ; DNA-Binding Proteins/chemistry/metabolism/genetics/ultrastructure ; }, abstract = {Genome segregation is a fundamental process that preserves the genetic integrity of all organisms, but the mechanisms driving genome segregation in archaea remain enigmatic. This study delved into the unknown function of SegC (SSO0033), a novel protein thought to be involved in chromosome segregation in archaea. Using fluorescence polarization DNA binding assays, we discovered the ability of SegC to bind DNA without any sequence preference. Furthermore, we determined the crystal structure of SegC at 2.8 Å resolution, revealing the multimeric configuration and forming a large positively charged surface that can bind DNA. SegC has a tertiary structure folding similar to those of the ThDP-binding fold superfamily, but SegC shares only 5-15% sequence identity with those proteins. Unexpectedly, we found that SegC has nucleotide triphosphatase (NTPase) activity. We also determined the SegC-ADP complex structure, identifying the NTP binding pocket and relative SegC residues involved in the interaction. Interestingly, images from negative-stain electron microscopy revealed that SegC forms filamentous structures in the presence of DNA and NTPs. Further, more uniform and larger SegC-filaments are observed, when SegA-ATP was added. Notably, the introduction of SegB disrupts these oligomers, with ATP being essential for regulating filament formation. These findings provide insights into the functional and structural role of SegC in archaeal chromosome segregation.}, }
@article {pmid39071849, year = {2024}, author = {Sakoula, D and Schatteman, A and Blom, P and Jetten, MSM and van Kessel, MAHJ and Lehtovirta-Morley, L and Lücker, S}, title = {Activity-based labelling of ammonia- and alkane-oxidizing microorganisms including ammonia-oxidizing archaea.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae092}, pmid = {39071849}, issn = {2730-6151}, abstract = {Recently, an activity-based labelling protocol for the in vivo detection of ammonia- and alkane-oxidizing bacteria became available. This functional tagging technique enabled targeted studies of these environmentally widespread functional groups, but it failed to capture ammonia-oxidizing archaea (AOA). Since their first discovery, AOA have emerged as key players within the biogeochemical nitrogen cycle, but our knowledge regarding their distribution and abundance in natural and engineered ecosystems is mainly derived from PCR-based and metagenomic studies. Furthermore, the archaeal ammonia monooxygenase is distinctly different from its bacterial counterparts and remains poorly understood. Here, we report on the development of an activity-based labelling protocol for the fluorescent detection of all ammonia- and alkane-oxidizing prokaryotes, including AOA. In this protocol, 1,5-hexadiyne is used as inhibitor of ammonia and alkane oxidation and as bifunctional enzyme probe for the fluorescent labelling of cells via the Cu(I)-catalyzed alkyne-azide cycloaddition reaction. Besides efficient activity-based labelling of ammonia- and alkane-oxidizing microorganisms, this method can also be employed in combination with deconvolution microscopy for determining the subcellular localization of their ammonia- and alkane-oxidizing enzyme systems. Labelling of these enzymes in diverse ammonia- and alkane-oxidizing microorganisms allowed their visualization on the cytoplasmic membranes, the intracytoplasmic membrane stacks of ammonia- and methane-oxidizing bacteria, and, fascinatingly, on vesicle-like structures in one AOA species. The development of this novel activity-based labelling method for ammonia- and alkane-oxidizers will be a valuable addition to the expanding molecular toolbox available for research of nitrifying and alkane-oxidizing microorganisms.}, }
@article {pmid39060562, year = {2024}, author = {Harada, M and Endo, A and Wada, S and Watanabe, T and Epron, D and Asakawa, S}, title = {Ubiquity of methanogenic archaea in the trunk of coniferous and broadleaved tree species in a mountain forest.}, journal = {Antonie van Leeuwenhoek}, volume = {117}, number = {1}, pages = {107}, pmid = {39060562}, issn = {1572-9699}, support = {24K01797//Japan Society for the Promotion of Science/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Forests ; *Methane/metabolism ; *Phylogeny ; Trees/microbiology ; Archaea/classification/genetics/metabolism/isolation &amp; purification ; Wood/microbiology ; DNA, Archaeal/genetics ; }, abstract = {Wetwood of living trees is a habitat of methanogenic archaea, but the ubiquity of methanogenic archaea in the trunk of various trees has not been revealed. The present study analysed methanogenic archaeal communities inside coniferous and broadleaved trees in a cold temperate mountain forest by culture-dependent or independent techniques. Heartwood and sapwood segments were obtained from the trunk of seven tree species, Cryptomeria japonica, Quercus crispula, Fraxinus mandshurica, Acer pictum, Aesculus turbinata, Magnolia obovata, and Populus tremula. Amplicon sequencing analysis of 16S rRNA genes showed that Methanobacteriaceae predominated the archaeal communities and Methanomassiliicoccaceae also inhabited some trees. Real-time PCR analysis detected methanogenic archaeal mcrA genes from all the tree species, with a maximum of 10[7] copies g[-1] dry wood. Digital PCR analysis also detected mcrA genes derived from Methanobacterium spp. and Methanobrevibacter spp. from several samples, with a maximum of 10[5] and 10[4] copies g[-1] dry wood. The enumeration by the most probable number method demonstrated the inhabitation of viable methanogenic archaea inside the trees; 10[6] cells g[-1] dry wood was enumerated from a heartwood sample of C. japonica. Methanogenic archaea related to Methanobacterium beijingense were cultivated from a heartwood sample of Q. crispula and F. mandshurica. The present study demonstrated that the inside of various trees is a common habitat for methanogenic archaeal communities and a potential source of methane in forest ecosystems.}, }
@article {pmid39053544, year = {2024}, author = {Yan, A and Pan, Z and Liang, Y and Mo, X and Guo, T and Li, J}, title = {Archaea communities in aerobic granular sludge: A mini-review.}, journal = {The Science of the total environment}, volume = {949}, number = {}, pages = {174974}, doi = {10.1016/j.scitotenv.2024.174974}, pmid = {39053544}, issn = {1879-1026}, mesh = {*Sewage/microbiology ; *Archaea/physiology ; Aerobiosis ; Waste Disposal, Fluid/methods ; Bioreactors/microbiology ; }, abstract = {Recent research on the archaea community in aerobic granular sludge (AGS) has attracted considerable attention. This review summarizes the existing literature on composition, distribution, and related functions of archaea community in AGS. Furthermore, the effects of granulation, substrate, temperature, process types, and aeration models on the archaea community were discussed. Significantly, the layered structure of AGS facilitates the enrichment of archaea, including methanogenic archaea and ammonia-oxidizing archaea. Archaea engage in metabolic interactions with other microorganisms, enhancing the ecological functionalities of AGS and its tolerance to adverse conditions. Future investigations should focus on minimizing greenhouse gas emissions and exploring the roles and interactive mechanisms of archaea and other microorganisms within AGS.}, }
@article {pmid39052173, year = {2024}, author = {Tenorio-Salgado, S and Villalpando-Aguilar, JL and Hernandez-Guerrero, R and Poot-Hernández, AC and Perez-Rueda, E}, title = {Exploring the enzymatic repertoires of Bacteria and Archaea and their associations with metabolic maps.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {39052173}, issn = {1678-4405}, abstract = {The evolution, survival, and adaptation of microbes are consequences of gene duplication, acquisition, and divergence in response to environmental challenges. In this context, enzymes play a central role in the evolution of organisms, because they are fundamental in cell metabolism. Here, we analyzed the enzymatic repertoire in 6,467 microbial genomes, including their abundances, and their associations with metabolic maps. We found that the enzymes follow a power-law distribution, in relation to the genome sizes. Therefore, we evaluated the total proportion enzymatic classes in relation to the genomes, identifying a descending-order proportion: transferases (EC:2.-), hydrolases (EC:3.-), oxidoreductases (EC:1.-), ligases (EC:6.-), lyases (EC:4.-), isomerases (EC:5.-), and translocases (EC:7-.). In addition, we identified a preferential use of enzymatic classes in metabolism pathways for xenobiotics, cofactors and vitamins, carbohydrates, amino acids, glycans, and energy. Therefore, this analysis provides clues about the functional constraints associated with the enzymatic repertoire of functions in Bacteria and Archaea.}, }
@article {pmid39043438, year = {2024}, author = {Gemler, BT and Warner, BR and Bundschuh, R and Fredrick, K}, title = {Identification of leader-trailer helices of precursor ribosomal RNA in all phyla of bacteria and archaea.}, journal = {RNA (New York, N.Y.)}, volume = {30}, number = {10}, pages = {1264-1276}, pmid = {39043438}, issn = {1469-9001}, support = {R01 GM072528/GM/NIGMS NIH HHS/United States ; }, mesh = {*Nucleic Acid Conformation ; *RNA, Archaeal/genetics/chemistry/metabolism ; *Archaea/genetics ; *RNA, Bacterial/genetics/chemistry/metabolism ; RNA, Ribosomal/genetics/chemistry/metabolism ; Bacteria/genetics ; RNA Precursors/genetics/metabolism/chemistry ; RNA, Ribosomal, 23S/genetics/chemistry/metabolism ; Base Sequence ; RNA, Ribosomal, 16S/genetics/chemistry ; Base Pairing ; }, abstract = {Ribosomal RNAs are transcribed as part of larger precursor molecules. In Escherichia coli, complementary RNA segments flank each rRNA and form long leader-trailer (LT) helices, which are crucial for subunit biogenesis in the cell. A previous study of 15 representative species suggested that most but not all prokaryotes contain LT helices. Here, we use a combination of in silico folding and covariation methods to identify and characterize LT helices in 4464 bacterial and 260 archaeal organisms. Our results suggest that LT helices are present in all phyla, including Deinococcota, which had previously been suspected to lack LT helices. In very few organisms, our pipeline failed to detect LT helices for both 16S and 23S rRNA. However, a closer case-by-case look revealed that LT helices are indeed present but escaped initial detection. Over 3600 secondary structure models, many well supported by nucleotide covariation, were generated. These structures show a high degree of diversity. Yet, all exhibit extensive base-pairing between the leader and trailer strands, in line with a common and essential function.}, }
@article {pmid39043386, year = {2024}, author = {Duller, S and Moissl-Eichinger, C}, title = {Archaea in the Human Microbiome and Potential Effects on Human Infectious Disease.}, journal = {Emerging infectious diseases}, volume = {30}, number = {8}, pages = {1505-1513}, pmid = {39043386}, issn = {1080-6059}, mesh = {Humans ; *Archaea/genetics ; *Microbiota ; Communicable Diseases/microbiology ; }, abstract = {Archaea represent a separate domain of life, next to bacteria and eukarya. As components of the human microbiome, archaea have been associated with various diseases, including periodontitis, endodontic infections, small intestinal bacterial overgrowth, and urogenital tract infections. Archaea are generally considered nonpathogenic; the reasons are speculative because of limited knowledge and gene annotation challenges. Nevertheless, archaeal syntrophic principles that shape global microbial networks aid both archaea and potentially pathogenic bacteria. Evaluating archaea interactions remains challenging, requiring clinical studies on inflammatory potential and the effects of archaeal metabolism. Establishing a culture collection is crucial for investigating archaea functions within the human microbiome, which could improve health outcomes in infectious diseases. We summarize potential reasons for archaeal nonpathogenicity, assess the association with infectious diseases in humans, and discuss the necessary experimental steps to enable mechanistic studies involving archaea.}, }
@article {pmid39030685, year = {2024}, author = {Echeveste Medrano, MJ and Leu, AO and Pabst, M and Lin, Y and McIlroy, SJ and Tyson, GW and van Ede, J and Sánchez-Andrea, I and Jetten, MSM and Jansen, R and Welte, CU}, title = {Osmoregulation in freshwater anaerobic methane-oxidizing archaea under salt stress.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39030685}, issn = {1751-7370}, support = {VI.Vidi.223.012//NWO-VIDI/ ; FT190100211//Australian Research Council/ ; 854088//ERC/ ; 024.002.002//NWO/ ; }, mesh = {*Methane/metabolism ; *Fresh Water/microbiology ; Anaerobiosis ; *Archaea/metabolism/genetics/classification ; *Salt Stress ; *Phylogeny ; *Osmoregulation ; Oxidation-Reduction ; }, abstract = {Climate change-driven sea level rise threatens freshwater ecosystems and elicits salinity stress in microbiomes. Methane emissions in these systems are largely mitigated by methane-oxidizing microorganisms. Here, we characterized the physiological and metabolic response of freshwater methanotrophic archaea to salt stress. In our microcosm experiments, inhibition of methanotrophic archaea started at 1%. However, during gradual increase of salt up to 3% in a reactor over 12 weeks, the culture continued to oxidize methane. Using gene expression profiles and metabolomics, we identified a pathway for salt-stress response that produces the osmolyte of anaerobic methanotrophic archaea: N(ε)-acetyl-β-L-lysine. An extensive phylogenomic analysis on N(ε)-acetyl-β-L-lysine-producing enzymes revealed that they are widespread across both bacteria and archaea, indicating a potential horizontal gene transfer and a link to BORG extrachromosomal elements. Physicochemical analysis of bioreactor biomass further indicated the presence of sialic acids and the consumption of intracellular polyhydroxyalkanoates in anaerobic methanotrophs during salt stress.}, }
@article {pmid38967634, year = {2024}, author = {Imachi, H and Nobu, MK and Kato, S and Takaki, Y and Miyazaki, M and Miyata, M and Ogawara, M and Saito, Y and Sakai, S and Tahara, YO and Takano, Y and Tasumi, E and Uematsu, K and Yoshimura, T and Itoh, T and Ohkuma, M and Takai, K}, title = {Promethearchaeum syntrophicum gen. nov., sp. nov., an anaerobic, obligately syntrophic archaeon, the first isolate of the lineage 'Asgard' archaea, and proposal of the new archaeal phylum Promethearchaeota phyl. nov. and kingdom Promethearchaeati regn. nov.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {7}, pages = {}, pmid = {38967634}, issn = {1466-5034}, mesh = {*Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Base Composition ; *Sequence Analysis, DNA ; *DNA, Archaeal/genetics ; Geologic Sediments/microbiology ; Anaerobiosis ; Seawater/microbiology ; Vitamin K 2/analogs &amp; derivatives ; }, abstract = {An anaerobic, mesophilic, syntrophic, archaeon strain MK-D1[T], was isolated as a pure co-culture with Methanogenium sp. strain MK-MG from deep-sea methane seep sediment. This organism is, to our knowledge, the first cultured representative of 'Asgard' archaea, an archaeal group closely related to eukaryotes. Here, we describe the detailed physiology and phylogeny of MK-D1[T] and propose Promethearchaeum syntrophicum gen. nov., sp. nov. to accommodate this strain. Cells were non-motile, small cocci, approximately 300-750 nm in diameter and produced membrane vesicles, chains of blebs and membrane-based protrusions. MK-D1[T] grew at 4-30 °C with optimum growth at 20 °C. The strain grew chemoorganotrophically with amino acids, peptides and yeast extract with obligate dependence on syntrophy with H2-/formate-utilizing organisms. MK-D1[T] showed the fastest growth and highest maximum cell yield when grown with yeast extract as the substrate: approximately 3 months to full growth, reaching up to 6.7×10[6] 16S rRNA gene copies ml[-1]. MK-D1[T] had a circular 4.32 Mb chromosome with a DNA G+C content of 31.1 mol%. The results of phylogenetic analyses of the 16S rRNA gene and conserved marker proteins indicated that the strain is affiliated with 'Asgard' archaea and more specifically DHVC1/DSAG/MBG-B and 'Lokiarchaeota'/'Lokiarchaeia'. On the basis of the results of 16S rRNA gene sequence analysis, the most closely related isolated relatives were Infirmifilum lucidum 3507LT[T] (76.09 %) and Methanothermobacter tenebrarum RMAS[T] (77.45 %) and the closest relative in enrichment culture was Candidatus 'Lokiarchaeum ossiferum' (95.39 %). The type strain of the type species is MK-D1[T] (JCM 39240[T] and JAMSTEC no. 115508). We propose the associated family, order, class, phylum, and kingdom as Promethearchaeaceae fam. nov., Promethearchaeales ord. nov., Promethearchaeia class. nov., Promethearchaeota phyl. nov., and Promethearchaeati regn. nov., respectively. These are in accordance with ICNP Rules 8 and 22 for nomenclature, Rule 30(3)(b) for validation and maintenance of the type strain, and Rule 31a for description as a member of an unambiguous syntrophic association.}, }
@article {pmid38953360, year = {2024}, author = {Willard, DJ and H Manesh, MJ and Bing, RG and Alexander, BH and Kelly, RM}, title = {Phenotype-driven assessment of the ancestral trajectory of sulfur biooxidation in the thermoacidophilic archaea Sulfolobaceae.}, journal = {mBio}, volume = {15}, number = {8}, pages = {e0103324}, pmid = {38953360}, issn = {2150-7511}, support = {T32 GM008776/GM/NIGMS NIH HHS/United States ; CBET-1802939//National Science Foundation (NSF)/ ; T32 GM008776-16//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; FA9550-20-1-0216//US Air Force Office of Sponsored Projects/ ; }, mesh = {*Sulfur/metabolism ; *Oxidation-Reduction ; *Sulfolobaceae/metabolism/genetics ; Phenotype ; Phylogeny ; Gene Expression Profiling ; Genome, Archaeal ; }, abstract = {Certain members of the family Sulfolobaceae represent the only archaea known to oxidize elemental sulfur, and their evolutionary history provides a framework to understand the development of chemolithotrophic growth by sulfur oxidation. Here, we evaluate the sulfur oxidation phenotype of Sulfolobaceae species and leverage comparative genomic and transcriptomic analysis to identify the key genes linked to sulfur oxidation. Metabolic engineering of the obligate heterotroph Sulfolobus acidocaldarius revealed that the known cytoplasmic components of sulfur oxidation alone are not sufficient to drive prolific sulfur oxidation. Imaging analysis showed that Sulfolobaceae species maintain proximity to the sulfur surface but do not necessarily contact the substrate directly. This indicates that a soluble form of sulfur must be transported to initiate cytoplasmic sulfur oxidation. Conservation patterns and transcriptomic response implicate an extracellular tetrathionate hydrolase and putative thiosulfate transporter in a newly proposed mechanism of sulfur acquisition in the Sulfolobaceae.IMPORTANCESulfur is one of the most abundant elements on earth (2.9% by mass), so it makes sense that the earliest biology found a way to use sulfur to create and sustain life. However, beyond evolutionary significance, sulfur and the molecules it comprises have important technological significance, not only in chemicals such as sulfuric acid and in pyritic ores containing critical metals but also as a waste product from oil and gas production. The thermoacidophilic Sulfolobaceae are unique among the archaea as sulfur oxidizers. The trajectory for how sulfur biooxidation arose and evolved can be traced using experimental and bioinformatic analyses of the available genomic data set. Such analysis can also inform the process by which extracellular sulfur is acquired and transported by thermoacidophilic archaea, a phenomenon that is critical to these microorganisms but has yet to be elucidated.}, }
@article {pmid38951176, year = {2024}, author = {Martínez-Espinosa, RM}, title = {Halophilic archaea as tools for bioremediation technologies.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {401}, pmid = {38951176}, issn = {1432-0614}, support = {VIGROB-309//Universidad de Alicante/ ; PROMETEO/2021/055//Conselleria de Cultura, Educaci&#xf3;n y Ciencia, Generalitat Valenciana/ ; }, mesh = {*Biodegradation, Environmental ; Archaea/metabolism ; Halobacteriaceae/metabolism/genetics ; Metals, Heavy/metabolism ; Soil Pollutants/metabolism ; Soil Microbiology ; }, abstract = {Haloarchaea are extremophilic microorganisms belonging to the Archaea domain that require high salt concentrations to be alive, thus inhabiting ecosystems like salty ponds, salty marshes, or extremely salty lagoons. They are more abundantly and widely distributed worldwide than initially expected. Most of them are grouped into two families: Halobacteriaceae and Haloferacaceae. The extreme conditions under which haloarchaea survive contribute to their metabolic and molecular adaptations, thus making them good candidates for the design of bioremediation strategies to treat brines, salty water, and saline soils contaminated with toxic compounds such as nitrate, nitrite, oxychlorates such as perchlorate and chlorate, heavy metals, hydrocarbons, and aromatic compounds. New advances in understanding haloarchaea physiology, metabolism, biochemistry, and molecular biology suggest that biochemical pathways related to nitrogen and carbon, metals, hydrocarbons, or aromatic compounds can be used for bioremediation proposals. This review analyses the novelty of the most recent results showing the capability of some haloarchaeal species to assimilate, modify, or degrade toxic compounds for most living beings. Several examples of the role of these microorganisms in the treatment of polluted brine or salty soils are also discussed in connection with circular economy-based processes. KEY POINTS: • Haloarchaea are extremophilic microorganisms showing genuine metabolism • Haloarchaea can metabolise compounds that are highly toxic to most living beings • These metabolic capabilities are useful for designing soil and water bioremediation strategies.}, }
@article {pmid38926353, year = {2024}, author = {Schoelmerich, MC and Ly, L and West-Roberts, J and Shi, LD and Shen, C and Malvankar, NS and Taib, N and Gribaldo, S and Woodcroft, BJ and Schadt, CW and Al-Shayeb, B and Dai, X and Mozsary, C and Hickey, S and He, C and Beaulaurier, J and Juul, S and Sachdeva, R and Banfield, JF}, title = {Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5414}, pmid = {38926353}, issn = {2041-1723}, support = {INV-037174/GATES/Bill &amp; Melinda Gates Foundation/United States ; }, mesh = {*Genome, Archaeal ; *Methane/metabolism ; *Phylogeny ; Oxidation-Reduction ; Archaea/genetics/metabolism ; Nanopore Sequencing/methods ; DNA Methylation ; Soil Microbiology ; }, abstract = {Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming "Candidatus Methanoperedens" archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new genomes. 13 complete and four near-complete linear genomes share 40 genes that define a largely syntenous genome backbone. We use these conserved genes to identify new Borgs from peatland soil and to delineate Borg phylogeny, revealing two major clades. Remarkably, Borg genes encoding nanowire-like electron-transferring cytochromes and cell surface proteins are more highly expressed than those of host Methanoperedens, indicating that Borgs augment the Methanoperedens activity in situ. We reconstructed the first complete 4.00 Mbp genome for a Methanoperedens that is inferred to be a Borg host and predicted its methylation motifs, which differ from pervasive TC and CC methylation motifs of the Borgs. Thus, methylation may enable Methanoperedens to distinguish their genomes from those of Borgs. Very high Borg to Methanoperedens ratios and structural predictions suggest that Borgs may be capable of encapsulation. The findings clearly define Borgs as a distinct class of ECE with shared genomic signatures, establish their diversification from a common ancestor with genetic inheritance, and raise the possibility of periodic existence outside of host cells.}, }
@article {pmid38922750, year = {2024}, author = {Lawruk-Desjardins, C and Storck, V and Ponton, DE and Amyot, M and Walsh, DA}, title = {A genome catalogue of mercury-methylating bacteria and archaea from sediments of a boreal river facing human disturbances.}, journal = {Environmental microbiology}, volume = {26}, number = {6}, pages = {e16669}, doi = {10.1111/1462-2920.16669}, pmid = {38922750}, issn = {1462-2920}, support = {ALLRP 560330 - 20//Natural Sciences and Engineering Research Council of Canada/ ; RDCPJ493474-15//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Geologic Sediments/microbiology ; *Rivers/microbiology ; *Archaea/genetics/metabolism/classification ; *Bacteria/genetics/classification/metabolism ; *Mercury/metabolism ; *Methylmercury Compounds/metabolism ; Metagenomics ; Humans ; Genome, Bacterial ; Genome, Archaeal ; Ecosystem ; Microbiota ; }, abstract = {Methyl mercury, a toxic compound, is produced by anaerobic microbes and magnifies in aquatic food webs, affecting the health of animals and humans. The exploration of mercury methylators based on genomes is still limited, especially in the context of river ecosystems. To address this knowledge gap, we developed a genome catalogue of potential mercury-methylating microorganisms. This was based on the presence of hgcAB from the sediments of a river affected by two run-of-river hydroelectric dams, logging activities and a wildfire. Through the use of genome-resolved metagenomics, we discovered a unique and diverse group of mercury methylators. These were dominated by members of the metabolically versatile Bacteroidota and were particularly rich in microbes that ferment butyrate. By comparing the diversity and abundance of mercury methylators between sites subjected to different disturbances, we found that ongoing disturbances, such as the input of organic matter related to logging activities, were particularly conducive to the establishment of a mercury-methylating niche. Finally, to gain a deeper understanding of the environmental factors that shape the diversity of mercury methylators, we compared the mercury-methylating genome catalogue with the broader microbial community. The results suggest that mercury methylators respond to environmental conditions in a manner similar to the overall microbial community. Therefore, it is crucial to interpret the diversity and abundance of mercury methylators within their specific ecological context.}, }
@article {pmid38918468, year = {2024}, author = {Shi, LD and West-Roberts, J and Schoelmerich, MC and Penev, PI and Chen, L and Amano, Y and Lei, S and Sachdeva, R and Banfield, JF}, title = {Methanotrophic Methanoperedens archaea host diverse and interacting extrachromosomal elements.}, journal = {Nature microbiology}, volume = {9}, number = {9}, pages = {2422-2433}, pmid = {38918468}, issn = {2058-5276}, support = {INV-037174/GATES/Bill &amp; Melinda Gates Foundation/United States ; INV-037174/GATES/Bill &amp; Melinda Gates Foundation/United States ; }, mesh = {*Methane/metabolism ; *Phylogeny ; Genome, Archaeal ; DNA Transposable Elements/genetics ; Euryarchaeota/genetics/metabolism ; Genetic Variation ; }, abstract = {Methane emissions are mitigated by anaerobic methane-oxidizing archaea, including Methanoperedens. Some Methanoperedens host huge extrachromosomal genetic elements (ECEs) called Borgs that may modulate their activity, yet the broader diversity of Methanoperedens ECEs is understudied. Here we report small enigmatic linear ECEs, circular viruses and unclassified ECEs that are predicted to replicate within Methanoperedens. Linear ECEs have inverted terminal repeats, tandem repeats and coding patterns that are strongly reminiscent of Borgs, but they are only 52-145 kb in length. As they share proteins with Borgs and Methanoperedens, we refer to them as mini-Borgs. Mini-Borgs are genetically diverse and can be assigned to at least five family-level groups. We identify eight families of Methanoperedens viruses, some of which encode multi-haem cytochromes, and circular ECEs encoding transposon-associated TnpB genes with proximal population-heterogeneous CRISPR arrays. These ECEs exchange genetic information with each other and with Methanoperedens, probably impacting their archaeal host activity and evolution.}, }
@article {pmid38918384, year = {2024}, author = {Dueholm, MKD and Andersen, KS and Korntved, AC and Rudkjøbing, V and Alves, M and Bajón-Fernández, Y and Batstone, D and Butler, C and Cruz, MC and Davidsson, &#xc5; and Erijman, L and Holliger, C and Koch, K and Kreuzinger, N and Lee, C and Lyberatos, G and Mutnuri, S and O'Flaherty, V and Oleskowicz-Popiel, P and Pokorna, D and Rajal, V and Recktenwald, M and Rodríguez, J and Saikaly, PE and Tooker, N and Vierheilig, J and De Vrieze, J and Wurzbacher, C and Nielsen, PH}, title = {MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5361}, pmid = {38918384}, issn = {2041-1723}, support = {Dark Matter and grant 13351//Villum Fonden (Villum Foundation)/ ; 6111-00617 A//Det Frie Forskningsr&#xe5;d (Danish Council for Independent Research)/ ; }, mesh = {*Archaea/genetics/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; Anaerobiosis ; *Bacteria/genetics/classification/metabolism ; *Microbiota/genetics ; *Biodiversity ; *Phylogeny ; Wastewater/microbiology ; Bioreactors/microbiology ; Methane/metabolism ; Sequence Analysis, DNA ; }, abstract = {Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84-99% and 18-61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.}, }
@article {pmid38900790, year = {2024}, author = {Murali, R and Pace, LA and Sanford, RA and Ward, LM and Lynes, MM and Hatzenpichler, R and Lingappa, UF and Fischer, WW and Gennis, RB and Hemp, J}, title = {Diversity and evolution of nitric oxide reduction in bacteria and archaea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {26}, pages = {e2316422121}, pmid = {38900790}, issn = {1091-6490}, support = {U12AB123456//National Institute of Health (NIH)/ ; 503546//Joint Genome Institute (JGI)/ ; DE-AC02-05CH11231//Joint Genome Institute (JGI)/ ; DE-AC05-76RL01830//DOE | SC | PNNL | Environmental Molecular Sciences Laboratory (EMSL)/ ; }, mesh = {*Nitric Oxide/metabolism ; *Oxidoreductases/metabolism/genetics ; *Phylogeny ; *Oxidation-Reduction ; Archaea/metabolism/genetics ; Rhodothermus/metabolism/enzymology/genetics ; Evolution, Molecular ; Bacteria/metabolism/genetics ; Bacterial Proteins/metabolism/genetics/chemistry ; }, abstract = {Nitrous oxide is a potent greenhouse gas whose production is catalyzed by nitric oxide reductase (NOR) members of the heme-copper oxidoreductase (HCO) enzyme superfamily. We identified several previously uncharacterized HCO families, four of which (eNOR, sNOR, gNOR, and nNOR) appear to perform NO reduction. These families have novel active-site structures and several have conserved proton channels, suggesting that they might be able to couple NO reduction to energy conservation. We isolated and biochemically characterized a member of the eNOR family from the bacterium Rhodothermus marinus and found that it performs NO reduction. These recently identified NORs exhibited broad phylogenetic and environmental distributions, greatly expanding the diversity of microbes in nature capable of NO reduction. Phylogenetic analyses further demonstrated that NORs evolved multiple times independently from oxygen reductases, supporting the view that complete denitrification evolved after aerobic respiration.}, }
@article {pmid38898040, year = {2024}, author = {Li, Y and Yu, T and Feng, X and Zhao, B and Chen, H and Yang, H and Chen, X and Zhang, XH and Anderson, HR and Burns, NZ and Zeng, F and Tao, L and Zeng, Z}, title = {Biosynthesis of GMGT lipids by a radical SAM enzyme associated with anaerobic archaea and oxygen-deficient environments.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5256}, pmid = {38898040}, issn = {2041-1723}, support = {92351301//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; }, mesh = {*S-Adenosylmethionine/metabolism ; *Archaea/genetics/metabolism/enzymology ; *Oxygen/metabolism ; Anaerobiosis ; Archaeal Proteins/metabolism/genetics ; Glycerol/metabolism ; Metagenome ; Phylogeny ; }, abstract = {Archaea possess characteristic membrane-spanning lipids that are thought to contribute to the adaptation to extreme environments. However, the biosynthesis of these lipids is poorly understood. Here, we identify a radical S-adenosyl-L-methionine (SAM) enzyme that synthesizes glycerol monoalkyl glycerol tetraethers (GMGTs). The enzyme, which we name GMGT synthase (Gms), catalyzes the formation of a C(sp[3])-C(sp[3]) linkage between the two isoprenoid chains of glycerol dialkyl glycerol tetraethers (GDGTs). This conclusion is supported by heterologous expression of gene gms from a GMGT-producing species in a methanogen, as well as demonstration of in vitro activity using purified Gms enzyme. Additionally, we show that genes encoding putative Gms homologs are present in obligate anaerobic archaea and in metagenomes obtained from oxygen-deficient environments, and appear to be absent in metagenomes from oxic settings.}, }
@article {pmid38896033, year = {2024}, author = {Huang, B and Xiao, Y and Zhang, Y}, title = {Asgard archaeal selenoproteome reveals a roadmap for the archaea-to-eukaryote transition of selenocysteine incorporation machinery.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38896033}, issn = {1751-7370}, support = {32270680//National Natural Science Foundation of China/ ; 2023SHIBS0003//Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions/ ; }, mesh = {*Selenocysteine/metabolism/genetics ; *Archaea/genetics/metabolism/classification ; *Selenoproteins/genetics/metabolism ; *Eukaryota/genetics/classification/metabolism ; Genome, Archaeal ; Proteome ; Codon, Terminator/genetics ; Archaeal Proteins/genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Selenocysteine (Sec) is encoded by the UGA codon that normally functions as a stop signal and is specifically incorporated into selenoproteins via a unique recoding mechanism. The translational recoding of UGA as Sec is directed by an unusual RNA structure, the SECIS element. Although archaea and eukaryotes adopt similar Sec encoding machinery, the SECIS elements have no similarities to each other with regard to sequence and structure. We analyzed >400 Asgard archaeal genomes to examine the occurrence of both Sec encoding system and selenoproteins in this archaeal superphylum, the closest prokaryotic relatives of eukaryotes. A comprehensive map of Sec utilization trait has been generated, providing the most detailed understanding of the use of this nonstandard amino acid in Asgard archaea so far. By characterizing the selenoproteomes of all organisms, several selenoprotein-rich phyla and species were identified. Most Asgard archaeal selenoprotein genes possess eukaryotic SECIS-like structures with varying degrees of diversity. Moreover, euryarchaeal SECIS elements might originate from Asgard archaeal SECIS elements via lateral gene transfer, indicating a complex and dynamic scenario of the evolution of SECIS element within archaea. Finally, a roadmap for the transition of eukaryotic SECIS elements from archaea was proposed, and selenophosphate synthetase may serve as a potential intermediate for the generation of ancestral eukaryotic SECIS element. Our results offer new insights into a deeper understanding of the evolution of Sec insertion machinery.}, }
@article {pmid38890479, year = {2024}, author = {Du Toit, A}, title = {Gassy archaea.}, journal = {Nature reviews. Microbiology}, volume = {22}, number = {8}, pages = {456}, pmid = {38890479}, issn = {1740-1534}, mesh = {*Archaea/genetics ; Genome, Archaeal ; Phylogeny ; }, }
@article {pmid38890178, year = {2024}, author = {Cui, L and Hu, Y and Li, XX and Ma, X and Cheng, M and Tan, S and Hou, J and Cui, HL}, title = {Halobacterium yunchengense sp. nov., Natronomonas amylolytica sp. nov., Halorientalis halophila sp. nov., Halobellus salinisoli sp. nov., halophilic archaea isolated from a saline lake and inland saline soil.}, journal = {Extremophiles : life under extreme conditions}, volume = {28}, number = {2}, pages = {28}, pmid = {38890178}, issn = {1433-4909}, support = {32070003//National Natural Science Foundation of China/ ; }, mesh = {*Lakes/microbiology ; *Phylogeny ; Soil Microbiology ; Halobacterium/genetics/isolation &amp; purification ; Genome, Archaeal ; Halobacteriaceae/genetics/isolation &amp; purification/classification ; }, abstract = {Four halophilic archaeal strains YCN1[T], YCN58[T], LT38[T], and LT62[T] were isolated from Yuncheng Salt Lake (Shanxi, China) and Tarim Basin (Xinjiang, China), respectively. Phylogenetic and phylogenomic analyses showed that these four strains tightly cluster with related species of Halobacterium, Natronomonas, Halorientalis, and Halobellus, respectively. The AAI, ANI, and dDDH values between these four strains and their related species of respective genera were lower than the proposed threshold values for species delineation. Strains YCN1[T], YCN58[T], LT38[T], and LT62[T] could be differentiated from the current species of Halobacterium, Natronomonas, Halorientalis, and Halobellus, respectively, based on the comparison of diverse phenotypic characteristics. The polar lipid profiles of these four strains were closely similar to those of respective relatives within the genera Halobacterium, Natronomonas, Halorientalis, and Halobellus, respectively. The phenotypic, phylogenetic, and genome-based analyses indicated that strains YCN1[T], YCN58[T], LT38[T], and LT62[T] represent respective novel species within the genera Halobacterium, Natronomonas, Halorentalis, and Halobellus, for which the names Halobacterium yunchengense sp. nov., Natronomonas amylolytica sp. nov., Halorientalis halophila sp. nov., and Halobellus salinisoli sp. nov. are proposed, respectively.}, }
@article {pmid38887712, year = {2024}, author = {Rekadwad, BN and Gonzalez, JM and Li, WJ}, title = {Editorial: Last universal common ancestor and origin of life: what uncultivated Bacteria, Archaea, and extremophiles can tell us.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1412625}, pmid = {38887712}, issn = {1664-302X}, }
@article {pmid38885730, year = {2024}, author = {Lv, PL and Jia, C and Wei, CH and Zhao, HP and Chen, R}, title = {Biochar modulates intracellular electron transfer for nitrate reduction in denitrifying anaerobic methane oxidizing archaea.}, journal = {Bioresource technology}, volume = {406}, number = {}, pages = {130998}, doi = {10.1016/j.biortech.2024.130998}, pmid = {38885730}, issn = {1873-2976}, mesh = {*Methane/metabolism ; *Archaea/metabolism ; *Charcoal/metabolism ; *Nitrates/metabolism ; Electron Transport ; *Oxidation-Reduction ; Anaerobiosis ; *Denitrification/physiology ; Biofilms ; Extracellular Polymeric Substance Matrix/metabolism ; }, abstract = {Denitrifying anaerobic methane oxidizing (DAMO) archaea plays a significant role in simultaneously nitrogen removal and methane mitigation, yet its limited metabolic activity hinders engineering applications. This study employed biochar to explore its potential for enhancing the metabolic activity and nitrate reduction capacity of DAMO microorganisms. Sawdust biochar (7 g/L) was found to increase the nitrate reduction rate by 2.85 times, although it did not affect the nitrite reduction rate individually. Scanning electron microscopy (SEM) and fluorescence excitation-emission matrix (EEM) analyses revealed that biochar promoted microbial aggregation, and stimulated the secretion of extracellular polymeric substances (EPS). Moreover, biochar bolstered the redox capacity and conductivity of the biofilm, notably enhancing the activity of the electron transfer system by 1.65 times. Key genes involved in intracellular electron transport (Hdr, MHC, Rnf) and membrane transport proteins (BBP, ABC, NDH) of archaea were significantly up-regulated. These findings suggest that biochar regulates electrons generated by reverse methanogenesis to the membrane for nitrate reduction.}, }
@article {pmid38884810, year = {2024}, author = {Hu, Y and Ma, X and Tan, S and Li, XX and Cheng, M and Hou, J and Cui, HL}, title = {Correction: Genome-based classification of genera Halosegnis and Salella, and description of four novel halophilic archaea isolated from a tidal flat.}, journal = {Antonie van Leeuwenhoek}, volume = {117}, number = {1}, pages = {90}, doi = {10.1007/s10482-024-01983-9}, pmid = {38884810}, issn = {1572-9699}, }
@article {pmid38866018, year = {2024}, author = {Greening, C and Cabotaje, PR and Valentin Alvarado, LE and Leung, PM and Land, H and Rodrigues-Oliveira, T and Ponce-Toledo, RI and Senger, M and Klamke, MA and Milton, M and Lappan, R and Mullen, S and West-Roberts, J and Mao, J and Song, J and Schoelmerich, M and Stairs, CW and Schleper, C and Grinter, R and Spang, A and Banfield, JF and Berggren, G}, title = {Minimal and hybrid hydrogenases are active from archaea.}, journal = {Cell}, volume = {187}, number = {13}, pages = {3357-3372.e19}, pmid = {38866018}, issn = {1097-4172}, mesh = {*Archaea/genetics/enzymology ; Archaeal Proteins/metabolism/chemistry/genetics ; Genome, Archaeal ; *Hydrogen/metabolism ; *Hydrogenase/metabolism/genetics/chemistry ; Iron-Sulfur Proteins/metabolism/genetics/chemistry ; Models, Molecular ; *Phylogeny ; Protein Structure, Tertiary ; }, abstract = {Microbial hydrogen (H2) cycling underpins the diversity and functionality of diverse anoxic ecosystems. Among the three evolutionarily distinct hydrogenase superfamilies responsible, [FeFe] hydrogenases were thought to be restricted to bacteria and eukaryotes. Here, we show that anaerobic archaea encode diverse, active, and ancient lineages of [FeFe] hydrogenases through combining analysis of existing and new genomes with extensive biochemical experiments. [FeFe] hydrogenases are encoded by genomes of nine archaeal phyla and expressed by H2-producing Asgard archaeon cultures. We report an ultraminimal hydrogenase in DPANN archaea that binds the catalytic H-cluster and produces H2. Moreover, we identify and characterize remarkable hybrid complexes formed through the fusion of [FeFe] and [NiFe] hydrogenases in ten other archaeal orders. Phylogenetic analysis and structural modeling suggest a deep evolutionary history of hybrid hydrogenases. These findings reveal new metabolic adaptations of archaea, streamlined H2 catalysts for biotechnological development, and a surprisingly intertwined evolutionary history between the two major H2-metabolizing enzymes.}, }
@article {pmid38852635, year = {2024}, author = {Kong, L and Wang, Y and Cui, D and He, W and Zhang, C and Zheng, C}, title = {Application of single-cell Raman-deuterium isotope probing to reveal the resistance of marine ammonia-oxidizing archaea SCM1 against common antibiotics.}, journal = {Chemosphere}, volume = {362}, number = {}, pages = {142500}, doi = {10.1016/j.chemosphere.2024.142500}, pmid = {38852635}, issn = {1879-1298}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Archaea/genetics/drug effects/metabolism ; Ammonia/metabolism ; Microbial Sensitivity Tests ; Oxidation-Reduction ; Single-Cell Analysis ; Spectrum Analysis, Raman ; Drug Resistance, Microbial/genetics ; }, abstract = {Antimicrobial resistance (AMR) in oceans poses a significant threat to human health through the seafood supply chain. Ammonia-oxidizing archaea (AOA) are important marine microorganisms and play a key role in the biogeochemical nitrogen cycle around the world. However, the AMR of marine AOA to aquicultural antibiotics is poorly explored. Here, Raman-deuterium isotope probing (Raman-DIP), a single-cell tool, was developed to reveal the AMR of a typical marine species of AOA, Nitrosopumilus maritimus (designated SCM1), against six antibiotics, including erythromycin, tetracycline, novobiocin, neomycin, bacitracin, and vancomycin. The D2O concentration (30% v/v) and culture period (9 days) were optimized for the precise detection of metabolic activity in SCM1 cells through Raman-DIP. The relative metabolic activity of SCM1 upon exposure to antibiotics was semi-quantitatively calculated based on single-cell Raman spectra. SCM1 exhibited high resistance to erythromycin, tetracycline, novobiocin, neomycin, and vancomycin, with minimum inhibitory concentration (MIC) values between 100 and 400 mg/L, while SCM1 is very sensitive to bacitracin (MIC: 0.8 mg/L). Notably, SCM1 cells were completely inactive under the metabolic activity minimum inhibitory concentration conditions (MA-MIC: 1.6-800 mg/L) for the six antibiotics. Further genomic analysis revealed the antibiotic resistance genes (ARGs) of SCM1, including 14 types categorized into 33 subtypes. This work increases our knowledge of the AMR of marine AOA by linking the resistant phenome to the genome, contributing to the risk assessment of AMR in the underexplored ocean environment. As antibiotic resistance in marine microorganisms is significantly affected by the concentration of antibiotics in coastal environments, we encourage more studies concentrating on both the phenotypic and genotypic antibiotic resistance of marine archaea. This may facilitate a comprehensive evaluation of the capacity of marine microorganisms to spread AMR and the implementation of suitable control measures to protect environmental safety and human health.}, }
@article {pmid38829054, year = {2024}, author = {Ma, Y and Sun, Z and Yang, H and Xie, W and Song, M and Zhang, B and Sui, L}, title = {The biosynthesis mechanism of bacterioruberin in halophilic archaea revealed by genome and transcriptome analysis.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {7}, pages = {e0054024}, pmid = {38829054}, issn = {1098-5336}, support = {42306106//MOST | National Natural Science Foundation of China (NSFC)/ ; EMTUST-21-01//Key laboratory of Marine Resource Chemistry and Food Technology, Ministry of Education/ ; 2019KJ220//Tianjin Municipal Education Commission/ ; }, mesh = {*Genome, Archaeal ; *Carotenoids/metabolism ; *Gene Expression Profiling ; Halorubrum/genetics/metabolism/growth &amp; development ; Transcriptome ; Archaeal Proteins/genetics/metabolism ; }, abstract = {UNLABELLED: Halophilic archaea are promising microbial cell factories for bacterioruberin (BR) production. BR is a natural product with multi-bioactivities, allowing potential application in many fields. In the previous work, a haloarchaeon Halorubrum sp. HRM-150 with a high proportion of BR (about 85%) was isolated, but the low yield impeded its large-scale production. This work figured out BR synthesis characteristics and mechanisms, and proposed strategies for yield improvement. First, glucose (10 g/L) and tryptone (15 g/L) were tested to be better sources for BR production. Besides, the combination of glucose and starch achieved the diauxic growth, and the biomass and BR productivity increased by 85% and 54% than using glucose. Additionally, this work first proposed the BR synthesis pattern, which differs from that of other carotenoids. As a structural component of cell membranes, the BR synthesis is highly coupled with growth, which was most active in the logarithm phase. Meanwhile, the osmotic down shock at the logarithm phase could increase the BR productivity without sacrificing the biomass. Moreover, the de-novo pathway for BR synthesis with a key gene of lyeJ, and its competitive pathways (notably tetraether lipids and retinal) were revealed through genome, transcriptome, and osmotic down shock. Therefore, the BR yield is expected to be improved through mutant construction, such as the overexpression of key gene lyeJ and the knockout of competitive genes, which need to be further explored. The findings will contribute to a better understanding of the metabolism mechanism in haloarchaea and the development of haloarchaea as microbial cell factories.<br><br>IMPORTANCE: Recent studies have revealed that halophilic microorganism is a promising microbial factory for the next-generation industrialization. Among them, halophilic archaea are advantageous as microbial factories due to their low contamination risk and low freshwater consumption. The halophilic archaea usually accumulate long chain C50 carotenoids, which are barely found in other organisms. Bacterioruberin (BR), the major C50 carotenoid, has multi-bioactivities, allowing potential application in food, cosmetic, and biomedical industries. However, the low yield impedes its large-scale application. This work figured out the BR synthesis characteristics and mechanism, and proposed several strategies for BR yield improvement, encouraging halophilic archaea to function as microbial factories for BR production. Meanwhile, the archaea have special evolutionary status and unique characteristics in taxonomy, the revelation of BR biosynthesis mechanism is beneficial for a better understanding of archaea.}, }
@article {pmid38825783, year = {2024}, author = {Orgler, E and Baumgartner, M and Duller, S and Kumptisch, C and Hausmann, B and Moser, D and Khare, V and Lang, M and Köcher, T and Frick, A and Muttenthaler, M and Makristathis, A and Moissl-Eichinger, C and Gasche, C}, title = {Archaea influence composition of endoscopically visible ileocolonic biofilms.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2359500}, pmid = {38825783}, issn = {1949-0984}, mesh = {Humans ; *Biofilms/growth &amp; development ; *Gastrointestinal Microbiome ; *Archaea/classification/metabolism/genetics/isolation &amp; purification ; Adult ; Middle Aged ; Female ; Male ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Feces/microbiology ; Colon/microbiology ; Methanobrevibacter/metabolism/genetics/growth &amp; development/isolation &amp; purification ; Colitis, Ulcerative/microbiology/metabolism ; Irritable Bowel Syndrome/microbiology/metabolism ; Aged ; Intestinal Mucosa/microbiology/metabolism ; Ileum/microbiology ; Fatty Acids, Volatile/metabolism ; Young Adult ; Bile Acids and Salts/metabolism ; }, abstract = {The gut microbiota has been implicated as a driver of irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). Recently we described, mucosal biofilms, signifying alterations in microbiota composition and bile acid (BA) metabolism in IBS and ulcerative colitis (UC). Luminal oxygen concentration is a key factor in the gastrointestinal (GI) ecosystem and might be increased in IBS and UC. Here we analyzed the role of archaea as a marker for hypoxia in mucosal biofilms and GI homeostasis. The effects of archaea on microbiome composition and metabolites were analyzed via amplicon sequencing and untargeted metabolomics in 154 stool samples of IBS-, UC-patients and controls. Mucosal biofilms were collected in a subset of patients and examined for their bacterial, fungal and archaeal composition. Absence of archaea, specifically Methanobrevibacter, correlated with disrupted GI homeostasis including decreased microbial diversity, overgrowth of facultative anaerobes and conjugated secondary BA. IBS-D/-M was associated with absence of archaea. Presence of Methanobrevibacter correlated with Oscillospiraceae and epithelial short chain fatty acid metabolism and decreased levels of Ruminococcus gnavus. Absence of fecal Methanobrevibacter may indicate a less hypoxic GI environment, reduced fatty acid oxidation, overgrowth of facultative anaerobes and disrupted BA deconjugation. Archaea and Ruminococcus gnavus could distinguish distinct subtypes of mucosal biofilms. Further research on the connection between archaea, mucosal biofilms and small intestinal bacterial overgrowth should be performed.}, }
@article {pmid38814265, year = {2024}, author = {Rahn, HP and Sun, J and Li, Z and Waymouth, RM and Levy, R and Wender, PA}, title = {Isoprenoid CARTs: In Vitro and In Vivo mRNA Delivery by Charge-Altering Releasable Transporters Functionalized with Archaea-inspired Branched Lipids.}, journal = {Biomacromolecules}, volume = {25}, number = {7}, pages = {4305-4316}, doi = {10.1021/acs.biomac.4c00373}, pmid = {38814265}, issn = {1526-4602}, mesh = {Animals ; Mice ; *RNA, Messenger/genetics ; *Lipids/chemistry ; Humans ; Terpenes/chemistry ; Archaea/genetics/chemistry ; Nanoparticles/chemistry ; }, abstract = {The delivery of oligonucleotides across biological barriers is a challenge of unsurpassed significance at the interface of materials science and medicine, with emerging clinical utility in prophylactic and therapeutic vaccinations, immunotherapies, genome editing, and cell rejuvenation. Here, we address the role of readily available branched lipids in the design, synthesis, and evaluation of isoprenoid charge-altering releasable transporters (CARTs), a pH-responsive oligomeric nanoparticle delivery system for RNA. Systematic variation of the lipid block reveals an emergent relationship between the lipid block and the neutralization kinetics of the polycationic block. Unexpectedly, iA21A11, a CART with the smallest lipid side chain, isoamyl-, was identified as the lead isoprenoid CART for the in vitro transfection of immortalized lymphoblastic cell lines. When administered intramuscularly in a murine model, iA21A11-mRNA complexes induce higher protein expression levels than our previous lead CART, ONA. Isoprenoid CARTs represent a new delivery platform for RNA vaccines and other polyanion-based therapeutics.}, }
@article {pmid38811725, year = {2024}, author = {von Kügelgen, A and Cassidy, CK and van Dorst, S and Pagani, LL and Batters, C and Ford, Z and Löwe, J and Alva, V and Stansfeld, PJ and Bharat, TAM}, title = {Membraneless channels sieve cations in ammonia-oxidizing marine archaea.}, journal = {Nature}, volume = {630}, number = {8015}, pages = {230-236}, pmid = {38811725}, issn = {1476-4687}, mesh = {*Ammonia/chemistry/metabolism ; *Aquatic Organisms/chemistry/metabolism/ultrastructure ; *Archaea/chemistry/metabolism/ultrastructure ; Cations/chemistry/metabolism ; *Cell Membrane ; Cryoelectron Microscopy ; Models, Molecular ; Oxidation-Reduction ; Polysaccharides/metabolism/chemistry ; }, abstract = {Nitrosopumilus maritimus is an ammonia-oxidizing archaeon that is crucial to the global nitrogen cycle[1,2]. A critical step for nitrogen oxidation is the entrapment of ammonium ions from a dilute marine environment at the cell surface and their subsequent channelling to the cell membrane of N. maritimus. Here we elucidate the structure of the molecular machinery responsible for this process, comprising the surface layer (S-layer), using electron cryotomography and subtomogram averaging from cells. We supplemented our in situ structure of the ammonium-binding S-layer array with a single-particle electron cryomicroscopy structure, revealing detailed features of this immunoglobulin-rich and glycan-decorated S-layer. Biochemical analyses showed strong ammonium binding by the cell surface, which was lost after S-layer disassembly. Sensitive bioinformatic analyses identified similar S-layers in many ammonia-oxidizing archaea, with conserved sequence and structural characteristics. Moreover, molecular simulations and structure determination of ammonium-enriched specimens enabled us to examine the cation-binding properties of the S-layer, revealing how it concentrates ammonium ions on its cell-facing side, effectively acting as a multichannel sieve on the cell membrane. This in situ structural study illuminates the biogeochemically essential process of ammonium binding and channelling, common to many marine microorganisms that are fundamental to the nitrogen cycle.}, }
@article {pmid38806737, year = {2024}, author = {Cheng, M and Li, XX and Hou, J and Cui, HL}, title = {Halomarina litorea sp. nov., Halomarina pelagica sp. nov., Halomarina halobia sp. nov., and Halomarina ordinaria sp. nov., Halophilic Archaea Isolated from Coastal and Inland Saline Soil.}, journal = {Current microbiology}, volume = {81}, number = {7}, pages = {194}, pmid = {38806737}, issn = {1432-0991}, support = {32070003//National Natural Science Foundation of China/ ; }, mesh = {*Phylogeny ; *Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; *DNA, Archaeal/genetics/chemistry ; Halobacteriaceae/classification/genetics/isolation &amp; purification ; Base Composition ; Phospholipids/analysis ; Sequence Analysis, DNA ; }, abstract = {Four halophilic archaeal strains, BCD28[T], BND7[T], PSR21[T], and PSRA2[T], were isolated from coastal and inland saline soil, respectively. The 16S rRNA and rpoB' gene sequence similarities among these four strains and current species of Halomarina were 95.9-96.6% and 86.9-90.3%, respectively. Phylogenetic and phylogenomic analyses revealed that these four strains tightly cluster with the current species of the genus Halomarina. The AAI, ANI, and dDDH values among these four strains and current species of Halomarina were 65.3-68.4%, 75.8-77.7%, and 20.3-22.0%, respectively, clearly below the threshold values for species demarcation. Strains BCD28[T], BND7[T], PSR21[T], and PSRA2[T] could be differentiated from the current species of Halomarina based on the comparison of diverse phenotypic characteristics. The major polar lipids of these four strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), and four to five glycolipids. Phosphatidylglycerol sulfate (PGS) was only detected in strain BND7[T]. The phenotypic, phylogenetic, and genome-based analyses suggested that strains BCD28[T] (= CGMCC 1.18776[T] = JCM 34908[T]), BND7[T] (= CGMCC 1.18778[T] = JCM 34910[T]), PSR21[T] (= CGMCC 1.17027[T] = JCM 34147[T]), and PSRA2[T] (= CGMCC 1.17214[T] = JCM 34148[T]) represent four novel species of the genus Halomarina, for which the names Halomarina litorea sp. nov., Halomarina pelagica sp. nov., Halomarina halobia sp. nov., and Halomarina ordinaria sp. nov. are proposed.}, }
@article {pmid38799924, year = {2024}, author = {}, title = {Expression of Concern: Haloferax massiliensis sp. nov., the first human-associated halophilic archaea.}, journal = {New microbes and new infections}, volume = {59}, number = {}, pages = {101323}, pmid = {38799924}, issn = {2052-2975}, }
@article {pmid38765610, year = {2024}, author = {Basu, S and Kurgan, L}, title = {Taxonomy-specific assessment of intrinsic disorder predictions at residue and region levels in higher eukaryotes, protists, archaea, bacteria and viruses.}, journal = {Computational and structural biotechnology journal}, volume = {23}, number = {}, pages = {1968-1977}, pmid = {38765610}, issn = {2001-0370}, abstract = {Intrinsic disorder predictors were evaluated in several studies including the two large CAID experiments. However, these studies are biased towards eukaryotic proteins and focus primarily on the residue-level predictions. We provide first-of-its-kind assessment that comprehensively covers the taxonomy and evaluates predictions at the residue and disordered region levels. We curate a benchmark dataset that uniformly covers eukaryotic, archaeal, bacterial, and viral proteins. We find that predictive performance differs substantially across taxonomy, where viruses are predicted most accurately, followed by protists and higher eukaryotes, while bacterial and archaeal proteins suffer lower levels of accuracy. These trends are consistent across predictors. We also find that current tools, except for flDPnn, struggle with reproducing native distributions of the numbers and sizes of the disordered regions. Moreover, analysis of two variants of disorder predictions derived from the AlphaFold2 predicted structures reveals that they produce accurate residue-level propensities for archaea, bacteria and protists. However, they underperform for higher eukaryotes and generally struggle to accurately identify disordered regions. Our results motivate development of new predictors that target bacteria and archaea and which produce accurate results at both residue and region levels. We also stress the need to include the region-level assessments in future assessments.}, }
@article {pmid38753237, year = {2024}, author = {Zhang, Y and Xiang, Y and Yang, Z and Xu, R}, title = {Co-occurrence of dominant bacteria and methanogenic archaea and their metabolic traits in a thermophilic anaerobic digester.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {25}, pages = {36716-36727}, pmid = {38753237}, issn = {1614-7499}, support = {42007357//National Natural Science Foundation of China/ ; }, mesh = {*Archaea/genetics/metabolism ; *Bacteria/metabolism/genetics ; Anaerobiosis ; *Methane/metabolism ; Phylogeny ; Bioreactors/microbiology ; }, abstract = {Thermophilic anaerobic digestion (TAD) represents a promising biotechnology for both methane energy production and waste stream treatment. However, numerous critical microorganisms and their metabolic characteristics involved in this process remain unidentified due to the limitations of culturable isolates. This study investigated the phylogenetic composition and potential metabolic traits of bacteria and methanogenic archaea in a TAD system using culture-independent metagenomics. Predominant microorganisms identified in the stable phase of TAD included hydrogenotrophic methanogens (Methanothermobacter and Methanosarcina) and hydrogen-producing bacteria (Coprothermobacter, Acetomicrobium, and Defluviitoga). Nine major metagenome-assembled genomes (MAGs) associated with the dominant genera were selected to infer their metabolic potentials. Genes related to thermal resistance were widely found in all nine major MAGs, such as the molecular chaperone genes, Clp protease gene, and RNA polymerase genes, which may contribute to their predominance under thermophilic condition. Thermophilic temperatures may increase the hydrogen partial pressure of Coprothermobacter, Acetomicrobium, and Defluviitoga, subsequently altering the primary methanogenesis pathway from acetoclastic pathway to hydrogenotrophic pathway in the TAD. Consequently, genes encoding the hydrogenotrophic methanogenesis pathway were the most abundant in the recovered archaeal MAGs. The potential interaction between hydrogen-producing bacteria and hydrogenotrophic methanogens may play critical roles in TAD processes.}, }
@article {pmid38744628, year = {2024}, author = {Liu, X and Su, D and Huan, H and Zhang, J and Zhen, H and Jia, Q and Zhao, M}, title = {Corrigendum to "Rice-fish coculture without phosphorus addition improves paddy soil nitrogen availability by shaping ammonia-oxidizing archaea and bacteria in subtropical regions of South China" [Sci. Total Environ. 927 (2024): 171642].}, journal = {The Science of the total environment}, volume = {933}, number = {}, pages = {172946}, doi = {10.1016/j.scitotenv.2024.172946}, pmid = {38744628}, issn = {1879-1026}, }
@article {pmid38733792, year = {2024}, author = {Musat, F and Kjeldsen, KU and Rotaru, AE and Chen, SC and Musat, N}, title = {Archaea oxidizing alkanes through alkyl-coenzyme M reductases.}, journal = {Current opinion in microbiology}, volume = {79}, number = {}, pages = {102486}, doi = {10.1016/j.mib.2024.102486}, pmid = {38733792}, issn = {1879-0364}, mesh = {*Alkanes/metabolism ; *Archaea/enzymology/genetics/metabolism ; *Oxidation-Reduction ; *Oxidoreductases/metabolism/genetics ; *Phylogeny ; Electron Transport ; Archaeal Proteins/metabolism/genetics/chemistry ; Gene Transfer, Horizontal ; Bacteria/enzymology/genetics/metabolism/classification ; }, abstract = {This review synthesizes recent discoveries of novel archaea clades capable of oxidizing higher alkanes, from volatile ones like ethane to longer-chain alkanes like hexadecane. These archaea, termed anaerobic multicarbon alkane-oxidizing archaea (ANKA), initiate alkane oxidation using alkyl-coenzyme M reductases, enzymes similar to the methyl-coenzyme M reductases of methanogenic and anaerobic methanotrophic archaea (ANME). The polyphyletic alkane-oxidizing archaea group (ALOX), encompassing ANME and ANKA, harbors increasingly complex alkane degradation pathways, correlated with the alkane chain length. We discuss the evolutionary trajectory of these pathways emphasizing metabolic innovations and the acquisition of metabolic modules via lateral gene transfer. Additionally, we explore the mechanisms by which archaea couple alkane oxidation with the reduction of electron acceptors, including electron transfer to partner sulfate-reducing bacteria (SRB). The phylogenetic and functional constraints that shape ALOX-SRB associations are also discussed. We conclude by highlighting the research needs in this emerging research field and its potential applications in biotechnology.}, }
@article {pmid38700364, year = {2024}, author = {Padalko, A and Nair, G and Sousa, FL}, title = {Fusion/fission protein family identification in Archaea.}, journal = {mSystems}, volume = {9}, number = {6}, pages = {e0094823}, pmid = {38700364}, issn = {2379-5077}, support = {VRG15-007//Wien Wissenschafts- Forschungs- und TechnologieFonds/ ; }, mesh = {*Archaea/genetics ; *Archaeal Proteins/genetics/chemistry/metabolism ; *Genome, Archaeal/genetics ; *Phylogeny ; }, abstract = {The majority of newly discovered archaeal lineages remain without a cultivated representative, but scarce experimental data from the cultivated organisms show that they harbor distinct functional repertoires. To unveil the ecological as well as evolutionary impact of Archaea from metagenomics, new computational methods need to be developed, followed by in-depth analysis. Among them is the genome-wide protein fusion screening performed here. Natural fusions and fissions of genes not only contribute to microbial evolution but also complicate the correct identification and functional annotation of sequences. The products of these processes can be defined as fusion (or composite) proteins, the ones consisting of two or more domains originally encoded by different genes and split proteins, and the ones originating from the separation of a gene in two (fission). Fusion identifications are required for proper phylogenetic reconstructions and metabolic pathway completeness assessments, while mappings between fused and unfused proteins can fill some of the existing gaps in metabolic models. In the archaeal genome-wide screening, more than 1,900 fusion/fission protein clusters were identified, belonging to both newly sequenced and well-studied lineages. These protein families are mainly associated with different types of metabolism, genetic, and cellular processes. Moreover, 162 of the identified fusion/fission protein families are archaeal specific, having no identified fused homolog within the bacterial domain. Our approach was validated by the identification of experimentally characterized fusion/fission cases. However, around 25% of the identified fusion/fission families lack functional annotations for both composite and split states, showing the need for experimental characterization in Archaea.IMPORTANCEGenome-wide fusion screening has never been performed in Archaea on a broad taxonomic scale. The overlay of multiple computational techniques allows the detection of a fine-grained set of predicted fusion/fission families, instead of rough estimations based on conserved domain annotations only. The exhaustive mapping of fused proteins to bacterial organisms allows us to capture fusion/fission families that are specific to archaeal biology, as well as to identify links between bacterial and archaeal lineages based on cooccurrence of taxonomically restricted proteins and their sequence features. Furthermore, the identification of poorly characterized lineage-specific fusion proteins opens up possibilities for future experimental and computational investigations. This approach enhances our understanding of Archaea in general and provides potential candidates for in-depth studies in the future.}, }
@article {pmid38673759, year = {2024}, author = {Dobryakova, NV and Dumina, MV and Zhgun, AA and Pokrovskaya, MV and Aleksandrova, SS and Zhdanov, DD and Kudryashova, EV}, title = {L-Asparaginase Conjugates from the Hyperthermophilic Archaea Thermococcus sibiricus with Improved Biocatalytic Properties.}, journal = {International journal of molecular sciences}, volume = {25}, number = {8}, pages = {}, pmid = {38673759}, issn = {1422-0067}, support = {project No. 22-74-10100//Russian Science Foundation/ ; }, mesh = {*Asparaginase/chemistry/metabolism ; *Thermococcus/enzymology ; Hydrogen-Ion Concentration ; *Enzyme Stability ; *Biocatalysis ; Polyethylene Glycols/chemistry ; Temperature ; Archaeal Proteins/chemistry/metabolism ; }, abstract = {This study investigated the effect of polycationic and uncharged polymers (and oligomers) on the catalytic parameters and thermostability of L-asparaginase from Thermococcus sibiricus (TsA). This enzyme has potential applications in the food industry to decrease the formation of carcinogenic acrylamide during the processing of carbohydrate-containing products. Conjugation with the polyamines polyethylenimine and spermine (PEI and Spm) or polyethylene glycol (PEG) did not significantly affect the secondary structure of the enzyme. PEG contributes to the stabilization of the dimeric form of TsA, as shown by HPLC. Furthermore, neither polyamines nor PEG significantly affected the binding of the L-Asn substrate to TsA. The conjugates showed greater maximum activity at pH 7.5 and 85 °C, 10-50% more than for native TsA. The pH optima for both TsA-PEI and TsA-Spm conjugates were shifted to lower pH ranges from pH 10 (for the native enzyme) to pH 8.0. Additionally, the TsA-Spm conjugate exhibited the highest activity at pH 6.5-9.0 among all the samples. Furthermore, the temperature optimum for activity at pH 7.5 shifted from 90-95 °C to 80-85 °C for the conjugates. The thermal inactivation mechanism of TsA-PEG appeared to change, and no aggregation was observed in contrast to that of the native enzyme. This was visually confirmed and supported by the analysis of the CD spectra, which remained almost unchanged after heating the conjugate solution. These results suggest that TsA-PEG may be a more stable form of TsA, making it a potentially more suitable option for industrial use.}, }
@article {pmid38664262, year = {2024}, author = {Mukherjee, D and Selvi, VA and Ganguly, J and Masto, RE}, title = {New insights into the coal-associated methane architect: the ancient archaebacteria.}, journal = {Archives of microbiology}, volume = {206}, number = {5}, pages = {234}, pmid = {38664262}, issn = {1432-072X}, mesh = {*Methane/metabolism ; *Coal ; *Archaea/metabolism/genetics ; Ecosystem ; Phylogeny ; }, abstract = {Exploration and marketable exploitation of coalbed methane (CBM) as cleaner fuel has been started globally. In addition, incidence of methane in coal basins is an imperative fraction of global carbon cycle. Significantly, subsurface coal ecosystem contains methane forming archaea. There is a rising attention in optimizing microbial coal gasification to exploit the abundant or inexpensive coal reserves worldwide. Therefore, it is essential to understand the coalbeds in geo-microbial perspective. Current review provides an in-depth analysis of recent advances in our understanding of how methanoarchaea are distributed in coal deposits globally. Specially, we highlight the findings on coal-associated methanoarchaeal existence, abundance, diversity, metabolic activity, and biogeography in diverse coal basins worldwide. Growing evidences indicates that we have arrived an exciting era of archaeal research. Moreover, gasification of coal into methane by utilizing microbial methanogenesis is a considerable way to mitigate the energy crisis for the rising world population.}, }
@article {pmid38659982, year = {2024}, author = {Li, Q and Cheng, X and Liu, X and Gao, P and Wang, H and Su, C and Huang, Q}, title = {Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1377721}, pmid = {38659982}, issn = {1664-302X}, abstract = {Subsurface karst caves provide unique opportunities to study the deep biosphere, shedding light on microbial contribution to elemental cycling. Although ammonia oxidation driven by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is well explored in soil and marine environments, our understanding in the subsurface biosphere still remained limited to date. To address this gap, weathered rock and sediment samples were collected from the Xincuntun Cave in Guilin City, an alkaline karst cave, and subjected to high-throughput sequencing and quantification of bacterial and archaeal amoA, along with determination of the potential nitrification rates (PNR). Results revealed that AOA dominated in ammonia oxidation, contributing 48-100% to the PNR, and AOA amoA gene copies outnumbered AOB by 2 to 6 orders. Nitrososphaera dominated in AOA communities, while Nitrosopira dominated AOB communities. AOA demonstrated significantly larger niche breadth than AOB. The development of AOA communities was influenced by deterministic processes (50.71%), while AOB communities were predominantly influenced by stochastic processes. TOC, NH4[+], and Cl[-] played crucial roles in shaping the compositions of ammonia oxidizers at the OTU level. Cross-domain co-occurrence networks highlighted the dominance of AOA nodes in the networks and positive associations between AOA and AOB, especially in the inner zone, suggesting collaborative effort to thrive in extreme environments. Their high gene copies, dominance in the interaction with ammonia oxidizing bacteria, expansive niche breadth and substantial contribution to PNR collectively confirmed that AOA better adapted to alkaline, oligotrophic karst caves environments, and thus play a fundamental role in nitrogen cycling in subsurface biosphere.}, }
@article {pmid38655083, year = {2024}, author = {van Wolferen, M and Ithurbide, S and Santiago-Martínez, MG and Charles-Orszag, A}, title = {Editorial: Molecular Biology of Archaea - 2022.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1393932}, pmid = {38655083}, issn = {1664-302X}, }
@article {pmid38644887, year = {2024}, author = {Gulati, P and Singh, A and Patra, S and Bhat, S and Verma, A}, title = {Restriction modification systems in archaea: A panoramic outlook.}, journal = {Heliyon}, volume = {10}, number = {8}, pages = {e27382}, pmid = {38644887}, issn = {2405-8440}, abstract = {Restriction modification (RM) systems are one of the ubiquitous yet primitive defense responses employed by bacteria and archaea with the primary role of safeguarding themselves against invading bacteriophages. Protection of the host occurs by the cleavage of the invading foreign DNA via restriction endonucleases with concomitant methylation of host DNA with the aid of a methyltransferase counterpart. RM systems have been extensively studied in bacteria, however, in the case of archaea there are limited reports of RM enzymes that are investigated to date owing to their inhospitable growth demands. This review aims to broaden the knowledge about what is known about the diversity of RM systems in archaea and encapsulate the current knowledge on restriction and modification enzymes characterized in archaea so far and the role of RM systems in the milieu of archaeal biology.}, }
@article {pmid38640671, year = {2024}, author = {Wang, Q and Zheng, G and Ni, L and Wang, H and Li, W and Guo, P and Wang, Y and Zheng, D and Wu, J and Zhang, D}, title = {Colonization characteristics and dynamic transition of archaea communities on polyethylene and polypropylene microplastics in the sediments of mangrove ecosystems.}, journal = {Journal of hazardous materials}, volume = {471}, number = {}, pages = {134343}, doi = {10.1016/j.jhazmat.2024.134343}, pmid = {38640671}, issn = {1873-3336}, mesh = {*Polyethylene ; *Archaea/drug effects/metabolism ; *Geologic Sediments/microbiology/chemistry ; *Microplastics/toxicity ; *Polypropylenes ; *Wetlands ; *Biofilms/drug effects ; Water Pollutants, Chemical/toxicity/analysis ; Ecosystem ; }, abstract = {Microplastics are a growing concern in mangrove ecosystems; however, their effects on archaeal communities and related ecological processes remain unclear. We conducted in situ biofilm-enrichment experiments to investigate the ecological influence of polyethylene (PE) and polypropylene microplastics on archaeal communities in the sediments of mangrove ecosystems. The archaeal community present on microplastics was distinct from that of the surrounding sediments at an early stage but became increasingly similar over time. Bathyarchaeota, Thaumarchaeota, Euryarchaeota, and Asgardaeota were the most abundant phyla. Methanolobus, an archaeal biomarker, was enriched in PE biofilms, and significantly controlled by homogeneous selection in the plastisphere, indicating an increased potential risk of methane emission. The dominant archaeal assembly process in the sediments was deterministic (58.85%-70.47%), while that of the PE biofilm changed from stochastic to deterministic during the experiment. The network of PE plastispheres showed less complexity and competitive links, and higher modularity and stability than that of sediments. Functional prediction showed an increase in aerobic ammonia oxidation during the experiment, whereas methanogenesis and chemoheterotrophy were significantly higher in the plastisphere. This study provides novel insights into the impact of microplastic pollution on archaeal communities and their mediating ecological functions in mangrove ecosystems.}, }
@article {pmid38593165, year = {2024}, author = {Price, MN and Arkin, AP}, title = {A fast comparative genome browser for diverse bacteria and archaea.}, journal = {PloS one}, volume = {19}, number = {4}, pages = {e0301871}, pmid = {38593165}, issn = {1932-6203}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Genomics ; Proteins/genetics ; Chromosome Mapping ; }, abstract = {Genome sequencing has revealed an incredible diversity of bacteria and archaea, but there are no fast and convenient tools for browsing across these genomes. It is cumbersome to view the prevalence of homologs for a protein of interest, or the gene neighborhoods of those homologs, across the diversity of the prokaryotes. We developed a web-based tool, fast.genomics, that uses two strategies to support fast browsing across the diversity of prokaryotes. First, the database of genomes is split up. The main database contains one representative from each of the 6,377 genera that have a high-quality genome, and additional databases for each taxonomic order contain up to 10 representatives of each species. Second, homologs of proteins of interest are identified quickly by using accelerated searches, usually in a few seconds. Once homologs are identified, fast.genomics can quickly show their prevalence across taxa, view their neighboring genes, or compare the prevalence of two different proteins. Fast.genomics is available at https://fast.genomics.lbl.gov.}, }
@article {pmid38593075, year = {2024}, author = {Michimori, Y and Izaki, R and Su, Y and Fukuyama, Y and Shimamura, S and Nishimura, K and Miwa, Y and Hamakita, S and Shimosaka, T and Makino, Y and Takeno, R and Sato, T and Beppu, H and Cann, I and Kanai, T and Nunoura, T and Atomi, H}, title = {Removal of phosphoglycolate in hyperthermophilic archaea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {16}, pages = {e2311390121}, pmid = {38593075}, issn = {1091-6490}, support = {JP19H05679//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP19H05684//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JPNP22010//New Energy and Industrial Technology Development Organization (NEDO)/ ; }, mesh = {*Ribulose-Bisphosphate Carboxylase/genetics/metabolism ; *Archaea/metabolism ; Photosynthesis ; Glycolates/metabolism ; Phosphoric Monoester Hydrolases/metabolism ; Oxygenases/metabolism ; Pentoses ; }, abstract = {Many organisms that utilize the Calvin-Benson-Bassham (CBB) cycle for autotrophic growth harbor metabolic pathways to remove and/or salvage 2-phosphoglycolate, the product of the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). It has been presumed that the occurrence of 2-phosphoglycolate salvage is linked to the CBB cycle, and in particular, the C2 pathway to the CBB cycle and oxygenic photosynthesis. Here, we examined 2-phosphoglycolate salvage in the hyperthermophilic archaeon Thermococcus kodakarensis, an obligate anaerobe that harbors a Rubisco that functions in the pentose bisphosphate pathway. T. kodakarensis harbors enzymes that have the potential to convert 2-phosphoglycolate to glycine and serine, and their genes were identified by biochemical and/or genetic analyses. 2-phosphoglycolate phosphatase activity increased 1.6-fold when cells were grown under microaerobic conditions compared to anaerobic conditions. Among two candidates, TK1734 encoded a phosphatase specific for 2-phosphoglycolate, and the enzyme was responsible for 80% of the 2-phosphoglycolate phosphatase activity in T. kodakarensis cells. The TK1734 disruption strain displayed growth impairment under microaerobic conditions, which was relieved upon addition of sodium sulfide. In addition, glycolate was detected in the medium when T. kodakarensis was grown under microaerobic conditions. The results suggest that T. kodakarensis removes 2-phosphoglycolate via a phosphatase reaction followed by secretion of glycolate to the medium. As the Rubisco in T. kodakarensis functions in the pentose bisphosphate pathway and not in the CBB cycle, mechanisms to remove 2-phosphoglycolate in this archaeon emerged independent of the CBB cycle.}, }
@article {pmid38592380, year = {2024}, author = {Gao, X and Wang, S and Kong, W and Li, G and Zhang, L and Yin, X}, title = {Floristic changes and environmental drivers of soil fungi and archaea in different salt-tolerant plant communities in the intertidal habitat of coastal wetlands.}, journal = {Environmental geochemistry and health}, volume = {46}, number = {5}, pages = {167}, pmid = {38592380}, issn = {1573-2983}, support = {2022YSKY-41//Fundamental Research Funds for Central Public Welfare Scientific Research Institutes of China/ ; }, mesh = {*Ecosystem ; *Wetlands ; Salt-Tolerant Plants ; RNA, Ribosomal, 16S ; Archaea/genetics ; Poaceae ; Soil ; Fungi/genetics ; }, abstract = {Microorganisms are crucial elements of terrestrial ecosystems, which play significant roles in improving soil physicochemical properties, providing plant growth nutrients, degrading toxic and harmful chemicals, and biogeochemical cycling. Variations in the types and quantities of root exudates among different plants greatly alter soil physicochemical properties and result in variations in the diversity, structure, and function of soil microorganisms. Not much is understood about the differences of soil fungi and archaea communities for different plant communities in coastal wetlands, and their response mechanisms to environmental changes. In this study, fungal and archaea communities in soils of Suaeda salsa, Phragmites australis, and Spartina alterniflora in the intertidal habitat of coastal wetlands were selected for research. Soil fungi and archaea were analyzed for diversity, community structure, and function using high throughput ITS and 16S rRNA gene sequencing. The study revealed significant differences in fungi and archaea's diversity and community structure in the rhizosphere soil of three plant communities. At the same time, there is no significant difference in the functional groups. SOM, TP, AP, MC, EC and SOM, TN, TP, AP, MC, EC are the primary environmental determinants affecting changes in soil fungal and archaeal communities, respectively. Variations in the diversity, community structure, and ecological functions of fungi and archaea can be used as indicators characterizing the impact of external disturbances on the soil environment, providing a theoretical foundation for the effective utilization of soil microbial resources, thereby achieving the goal of environmental protection and health promotion.}, }
@article {pmid38570877, year = {2024}, author = {Yin, X and Zhou, G and Cai, M and Richter-Heitmann, T and Zhu, QZ and Maeke, M and Kulkarni, AC and Nimzyk, R and Elvert, M and Friedrich, MW}, title = {Physiological versatility of ANME-1 and Bathyarchaeotoa-8 archaea evidenced by inverse stable isotope labeling.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {68}, pmid = {38570877}, issn = {2049-2618}, support = {49926684//Cluster of Excellence EXC 309/ ; 49926684//Cluster of Excellence EXC 309/ ; 390741601//Cluster of Excellence EXC 2077/ ; 390741601//Cluster of Excellence EXC 2077/ ; }, mesh = {*Archaea/genetics ; Isotope Labeling ; Oxidation-Reduction ; *Methane/metabolism ; Carbon/metabolism ; DNA ; Anaerobiosis ; Geologic Sediments ; Phylogeny ; }, abstract = {BACKGROUND: The trophic strategy is one key principle to categorize microbial lifestyles, by broadly classifying microorganisms based on the combination of their preferred carbon sources, electron sources, and electron sinks. Recently, a novel trophic strategy, i.e., chemoorganoautotrophy-the utilization of organic carbon as energy source but inorganic carbon as sole carbon source-has been specifically proposed for anaerobic methane oxidizing archaea (ANME-1) and Bathyarchaeota subgroup 8 (Bathy-8).<br><br>RESULTS: To further explore chemoorganoautotrophy, we employed stable isotope probing (SIP) of nucleic acids (rRNA or DNA) using unlabeled organic carbon and [13]C-labeled dissolved inorganic carbon (DIC), i.e., inverse stable isotope labeling, in combination with metagenomics. We found that ANME-1 archaea actively incorporated [13]C-DIC into RNA in the presence of methane and lepidocrocite when sulfate was absent, but assimilated organic carbon when cellulose was added to incubations without methane additions. Bathy-8 archaea assimilated [13]C-DIC when lignin was amended; however, their DNA was derived from both inorganic and organic carbon sources rather than from inorganic carbon alone. Based on SIP results and supported by metagenomics, carbon transfer between catabolic and anabolic branches of metabolism is possible in these archaeal groups, indicating their anabolic versatility.<br><br>CONCLUSION: We provide evidence for the incorporation of the mixed organic and inorganic carbon by ANME-1 and&#xa0;Bathy-8 archaea in the environment. Video Abstract.}, }
@article {pmid38530473, year = {2024}, author = {Fry, M}, title = {The discovery of archaea: from observed anomaly to consequential restructuring of the phylogenetic tree.}, journal = {History and philosophy of the life sciences}, volume = {46}, number = {2}, pages = {16}, pmid = {38530473}, issn = {1742-6316}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Phylogeny ; *Archaea/genetics ; Biological Evolution ; *Biological Science Disciplines ; }, abstract = {Observational and experimental discoveries of new factual entities such as objects, systems, or processes, are major contributors to some advances in the life sciences. Yet, whereas discovery of theories was extensively deliberated by philosophers of science, very little philosophical attention was paid to the discovery of factual entities. This paper examines historical and philosophical aspects of the experimental discovery by Carl Woese of archaea, prokaryotes that comprise one of the three principal domains of the phylogenetic tree. Borrowing Kuhn's terminology, this discovery of a major biological entity was made during a 'normal science' project of building molecular taxonomy for prokaryotes. Unexpectedly, however, an observed anomaly instigated the discovery of archaea. Substantiation of the existence of the new archaeal entity and consequent reconstruction of the phylogenetic tree prompted replacement of a long-held model of a prokarya and eukarya bipartite tree of life by a new model of a tripartite tree comprising of bacteria, archaea, and eukarya. This paper explores the history and philosophical implications of the progression of Woese's project from normal science to anomaly-instigated model-changing discovery. It is also shown that the consequential discoveries of RNA splicing and of ribozymes were similarly prompted by unexpected irregularities during normal science activities. It is thus submitted that some discoveries of factual biological entities are triggered by unforeseen observational or experimental anomalies.}, }
@article {pmid38519541, year = {2024}, author = {Baker, BA and Gutiérrez-Preciado, A and Rodríguez Del Río, &#xc1; and McCarthy, CGP and López-García, P and Huerta-Cepas, J and Susko, E and Roger, AJ and Eme, L and Moreira, D}, title = {Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments.}, journal = {Nature microbiology}, volume = {9}, number = {4}, pages = {964-975}, pmid = {38519541}, issn = {2058-5276}, support = {787904//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 803151//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {Phylogeny ; *Salinity ; Archaea/genetics ; *Euryarchaeota/genetics ; Metagenome ; }, abstract = {Extremely halophilic archaea (Haloarchaea, Nanohaloarchaeota, Methanonatronarchaeia and Halarchaeoplasmatales) thrive in saturating salt concentrations where they must maintain osmotic equilibrium with their environment. The evolutionary history of adaptations enabling salt tolerance remains poorly understood, in particular because the phylogeny of several lineages is conflicting. Here we present a resolved phylogeny of extremely halophilic archaea obtained using improved taxon sampling and state-of-the-art phylogenetic approaches designed to cope with the strong compositional biases of their proteomes. We describe two uncultured lineages, Afararchaeaceae and Asbonarchaeaceae, which break the long branches at the base of Haloarchaea and Nanohaloarchaeota, respectively. We obtained 13 metagenome-assembled genomes (MAGs) of these archaea from metagenomes of hypersaline aquatic systems of the Danakil Depression (Ethiopia). Our phylogenomic analyses including these taxa show that at least four independent adaptations to extreme halophily occurred during archaeal evolution. Gene-tree/species-tree reconciliation suggests that gene duplication and horizontal gene transfer played an important role in this process, for example, by spreading key genes (such as those encoding potassium transporters) across extremely halophilic lineages.}, }
@article {pmid38500564, year = {2024}, author = {Batista, M and Langendijk-Genevaux, P and Kwapisz, M and Canal, I and Phung, DK and Plassart, L and Capeyrou, R and Moalic, Y and Jebbar, M and Flament, D and Fichant, G and Bouvier, M and Clouet-d'Orval, B}, title = {Evolutionary and functional insights into the Ski2-like helicase family in Archaea: a comparison of Thermococcales ASH-Ski2 and Hel308 activities.}, journal = {NAR genomics and bioinformatics}, volume = {6}, number = {1}, pages = {lqae026}, pmid = {38500564}, issn = {2631-9268}, abstract = {RNA helicases perform essential housekeeping and regulatory functions in all domains of life by binding and unwinding RNA molecules. The Ski2-like proteins are primordial helicases that play an active role in eukaryotic RNA homeostasis pathways, with multiple homologs having specialized functions. The significance of the expansion and diversity of Ski2-like proteins in Archaea, the third domain of life, has not yet been established. Here, by studying the phylogenetic diversity of Ski2-like helicases among archaeal genomes and the enzymatic activities of those in Thermococcales, we provide further evidence of the function of this protein family in archaeal metabolism of nucleic acids. We show that, in the course of evolution, ASH-Ski2 and Hel308-Ski2, the two main groups of Ski2-like proteins, have diverged in their biological functions. Whereas Hel308 has been shown to mainly act on DNA, we show that ASH-Ski2, previously described to be associated with the 5'-3' aRNase J exonuclease, acts on RNA by supporting an efficient annealing activity, but also an RNA unwinding with a 3'-5' polarity. To gain insights into the function of Ski2, we also analyse the transcriptome of Thermococcus barophilus ΔASH-Ski2 mutant strain and provide evidence of the importance of ASH-Ski2 in cellular metabolism pathways related to translation.}, }
@article {pmid38499200, year = {2024}, author = {Guo, K and Li, D and Hao, T and Teng, L and Li, S and Zeng, H and Zhang, J}, title = {Potential directions for future development of mainstream partial nitrification-anammox processes: Ammonia-oxidizing archaea as novel functional microorganisms providing nitrite.}, journal = {Bioresource technology}, volume = {399}, number = {}, pages = {130605}, doi = {10.1016/j.biortech.2024.130605}, pmid = {38499200}, issn = {1873-2976}, mesh = {*Archaea/genetics ; *Nitrification ; Ammonia ; Nitrites ; Anaerobic Ammonia Oxidation ; Wastewater ; Oxidation-Reduction ; Nitrogen/analysis ; Oxygen ; }, abstract = {The application of ammonia-oxidizing archaea (AOA)-based partial nitrification-anammox (PN-A) for mainstream wastewater treatment has attracted research interest because AOA can maintain higher activity in low-temperature environments and they have higher affinity for oxygen and ammonia-nitrogen compared with ammonia-oxidizing bacteria (AOB), thus facilitating stabilized nitrite production, deep removal of low-ammonia, and nitrite-oxidizing bacteria suppression. Moreover, the low affinity of AOA for ammonia makes them more tolerant to N-shock loading and more efficiently integrated with anaerobic ammonium oxidation (anammox). Based on the limitations of the AOB-based PN-A process, this review comprehensively summarizes the potential and significance of AOA for nitrite supply, then gives strategies and influencing factors for replacing AOB with AOA. Additionally, the methods and key influences on the coupling of AOA and anammox are explored. Finally, this review proposes four AOA-based oxygen- or ammonia-limited autotrophic nitritation/denitrification processes to address the low effluent quality and instability of mainstream PN-A processes.}, }
@article {pmid38486239, year = {2024}, author = {Alghamrawy, BT and Hegazy, GE and Sabry, SA and Ghozlan, H}, title = {Production, characterization and biomedical potential of biosurfactants produced by haloalkaliphilic archaea from Wadi El-Natrun, Egypt.}, journal = {Microbial cell factories}, volume = {23}, number = {1}, pages = {84}, pmid = {38486239}, issn = {1475-2859}, mesh = {*Sodium Chloride/pharmacology/metabolism ; Egypt ; Antioxidants/metabolism ; *Halobacteriaceae/metabolism ; Anti-Inflammatory Agents/metabolism ; }, abstract = {Extreme halophilic archaea that can live in high saline environments can offer potential applications in different biotechnological fields. This study delves into the fascinating field of halophilic archaea and their ability to produce biosurfactants. Some strains of haloarchaea were isolated from Wadi El-Natrun and were screened for biosurfactants production in a standard basal medium using emulsification index assay. Two strains were chosen as the potential strains for surface tension reduction. They were identified as Natrialba sp. BG1 and N3. The biosurfactants production was optimized and the produced emulsifiers were partially purified and identified using FTIR and NMR. Sequential statistical optimization, Plackett-Burman (PB) and Box-Behnken Designs (BBD) were carried out using 5 factors: oil, NaCl, casamino acids, pH, and inoculum size. The most significant factors were used for the next Response Surface Methodology experiment. The final optimal conditions for biosurfactants production were the inoculum size 2% pH 11 and NaCl 250 g/L, for Natrialba sp. BG1 and inoculum size 2.2%, pH 10 and NaCl 100 g/L for Natrialba sp. N3. The produced biosurfactants were tested for wound healing and the results indicated that Natrialba sp. BG1 biosurfactants is more efficient than Natrialba sp. N3 biosurfactants. Biosurfactants extracts were tested for their cytotoxic effects on normal cell line as well as on different cancer cells using MTT assay. The findings demonstrated that varying concentrations of the biosurfactants (31.25, 62.5, 125, 250, 500 and 1000 µg/mL) exhibited cytotoxic effects on the cell lines being tested. Additionally, the outcomes unveiled the presence of anti-inflammatory and antioxidant properties for both biosurfactants. Consequently, they could potentially serve as natural, safe, and efficient novel agents for combating cancer, promoting wound healing, and providing anti-inflammatory and antioxidant benefits.}, }
@article {pmid38479518, year = {2024}, author = {Liu, X and Sun, D and Huang, H and Zhang, J and Zheng, H and Jia, Q and Zhao, M}, title = {Rice-fish coculture without phosphorus addition improves paddy soil nitrogen availability by shaping ammonia-oxidizing archaea and bacteria in subtropical regions of South China.}, journal = {The Science of the total environment}, volume = {927}, number = {}, pages = {171642}, doi = {10.1016/j.scitotenv.2024.171642}, pmid = {38479518}, issn = {1879-1026}, mesh = {*Archaea/metabolism ; *Phosphorus ; China ; *Bacteria/metabolism ; *Soil Microbiology ; *Nitrogen ; *Ammonia/metabolism ; *Soil/chemistry ; *Oryza ; *Oxidation-Reduction ; Animals ; Fishes ; Fertilizers/analysis ; Agriculture/methods ; }, abstract = {Rice-fish coculture (RFC), as a traditional agricultural strategy in China, can optimally utilize the scarce resource, especially in subtropical regions where phosphorus (P) deficiency limits agricultural production. However, ammonia-oxidizing archaea (AOA) and bacteria (AOB) are involved in the ammonia oxidation, but it remains uncertain whether their community compositions are related to the RFC combined with and without P addition that improves soil nitrogen (N) use efficiency. Here, a microcosm experiment was conducted to assess the impacts of RFC combined with and without inorganic P (0 and 50 mg P kg[-1] as KH2PO4) addition on AOA and AOB community diversities, enzyme activities and N availability. The results showed that RFC significantly increased available N content without P addition compared with P addition. Moreover, RFC significantly increased urease activity and AOA shannon diversity, and reduced NAG activity and AOB shannon diversity without P addition, respectively. Higher diversity of AOA compared with that of AOB causes greater competition for resources and energy within their habitats, thereby resulting in lower network complexity. Our findings indicated that the abundances of AOA and AOB are influenced through the introduction of fish and/or P availability, of which AOB is linked to N availability. Overall, RFC could improve paddy soil N availability without P addition in subtropical region, which provides a scientific reference for promoting the practices that reduce N fertilizer application in RFC.}, }
@article {pmid38476944, year = {2024}, author = {von Hoyningen-Huene, AJE and Bang, C and Rausch, P and Rühlemann, M and Fokt, H and He, J and Jensen, N and Knop, M and Petersen, C and Schmittmann, L and Zimmer, T and Baines, JF and Bosch, TCG and Hentschel, U and Reusch, TBH and Roeder, T and Franke, A and Schulenburg, H and Stukenbrock, E and Schmitz, RA}, title = {The archaeome in metaorganism research, with a focus on marine models and their bacteria-archaea interactions.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1347422}, pmid = {38476944}, issn = {1664-302X}, abstract = {Metaorganism research contributes substantially to our understanding of the interaction between microbes and their hosts, as well as their co-evolution. Most research is currently focused on the bacterial community, while archaea often remain at the sidelines of metaorganism-related research. Here, we describe the archaeome of a total of eleven classical and emerging multicellular model organisms across the phylogenetic tree of life. To determine the microbial community composition of each host, we utilized a combination of archaea and bacteria-specific 16S rRNA gene amplicons. Members of the two prokaryotic domains were described regarding their community composition, diversity, and richness in each multicellular host. Moreover, association with specific hosts and possible interaction partners between the bacterial and archaeal communities were determined for the marine models. Our data show that the archaeome in marine hosts predominantly consists of Nitrosopumilaceae and Nanoarchaeota, which represent keystone taxa among the porifera. The presence of an archaeome in the terrestrial hosts varies substantially. With respect to abundant archaeal taxa, they harbor a higher proportion of methanoarchaea over the aquatic environment. We find that the archaeal community is much less diverse than its bacterial counterpart. Archaeal amplicon sequence variants are usually host-specific, suggesting adaptation through co-evolution with the host. While bacterial richness was higher in the aquatic than the terrestrial hosts, a significant difference in diversity and richness between these groups could not be observed in the archaeal dataset. Our data show a large proportion of unclassifiable archaeal taxa, highlighting the need for improved cultivation efforts and expanded databases.}, }
@article {pmid38472444, year = {2024}, author = {Hu, Y and Ma, X and Tan, S and Li, XX and Cheng, M and Hou, J and Cui, HL}, title = {Genome-based classification of genera Halosegnis and Salella, and description of four novel halophilic archaea isolated from a tidal flat.}, journal = {Antonie van Leeuwenhoek}, volume = {117}, number = {1}, pages = {51}, pmid = {38472444}, issn = {1572-9699}, support = {2021FY100900//National Science and Technology Fundamental Resources Investigation Program of China/ ; 32070003//National Natural Science Foundation of China/ ; }, mesh = {Sequence Analysis, DNA ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Halobacteriaceae/genetics ; China ; DNA ; DNA, Archaeal/genetics ; Fatty Acids/chemistry ; DNA, Bacterial/genetics ; }, abstract = {The current species of Halosegnis and Salella within the class Halobacteria are closely related based on phylogenetic, phylogenomic, and comparative genomic analyses. The Halosegnis species showed 99.8-100.0% 16S rRNA and 96.6-99.6% rpoB' gene similarities to the Salella species, respectively. Phylogenetic and phylogenomic analyses showed that Salella cibi CBA1133[T], the sole species of Salella, formed a single tight cluster with Halosegnis longus F12-1[T], then with Halosegnis rubeus F17-44[T]. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values between Salella cibi CBA1133[T] and Halosegnis longus F12-1[T] were 99.2, 94.2, and 98.6%, respectively, much higher than the thresholds for species demarcation. This genome-based classification revealed that the genus Salella should be merged with Halosegnis, and Salella cibi should be a later heterotypic synonym of Halosegnis longus. Halophilic archaeal strains DT72[T], DT80[T], DT85[T], and DT116[T], isolated from the saline soil of a tidal flat in China, were subjected to polyphasic taxonomic characterization. The phenotypic, chemotaxonomic, phylogenetic, and phylogenomic features indicated that strains DT72[T] (= CGMCC 1.18925[T] = JCM 35418[T]), DT80[T] (= CGMCC 1.18926[T] = JCM 35419[T]), DT85[T] (= CGMCC 1.19049[T] = JCM 35605[T]), and DT116[T] (= CGMCC 1.19045[T] = JCM 35606[T]) represent four novel species of the genera Halorussus, Halosegnis and Haloglomus, respectively, for which the names, Halorussus caseinilyticus sp. nov., Halorussus lipolyticus sp. nov., Halosegnis marinus sp. nov., and Haloglomus litoreum sp. nov., are proposed.}, }
@article {pmid38472392, year = {2024}, author = {Tran, LT and Akıl, C and Senju, Y and Robinson, RC}, title = {The eukaryotic-like characteristics of small GTPase, roadblock and TRAPPC3 proteins from Asgard archaea.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {273}, pmid = {38472392}, issn = {2399-3642}, support = {JPMJCR19S5//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; JP20H00476//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP19K23727//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23K05718//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23H04423//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; GBMF9743//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; GBMF9743//Simons Foundation/ ; }, mesh = {*Monomeric GTP-Binding Proteins/chemistry ; Archaea/metabolism ; Protein Transport ; }, abstract = {Membrane-enclosed organelles are defining features of eukaryotes in distinguishing these organisms from prokaryotes. Specification of distinct membranes is critical to assemble and maintain discrete compartments. Small GTPases and their regulators are the signaling molecules that drive membrane-modifying machineries to the desired location. These signaling molecules include Rab and Rag GTPases, roadblock and longin domain proteins, and TRAPPC3-like proteins. Here, we take a structural approach to assess the relatedness of these eukaryotic-like proteins in Asgard archaea, the closest known prokaryotic relatives to eukaryotes. We find that the Asgard archaea GTPase core domains closely resemble eukaryotic Rabs and Rags. Asgard archaea roadblock, longin and TRAPPC3 domain-containing proteins form dimers similar to those found in the eukaryotic TRAPP and Ragulator complexes. We conclude that the emergence of these protein architectures predated eukaryogenesis, however further adaptations occurred in proto-eukaryotes to allow these proteins to regulate distinct internal membranes.}, }
@article {pmid38471592, year = {2024}, author = {Chisholm, C and Di, H and Cameron, K and Podolyan, A and Shen, J and Zhang, L and Sirisena, K and Godsoe, W}, title = {Contrasting response of comammox Nitrospira, ammonia oxidising bacteria, and archaea to soil pH and nitrogen inputs.}, journal = {The Science of the total environment}, volume = {924}, number = {}, pages = {171627}, doi = {10.1016/j.scitotenv.2024.171627}, pmid = {38471592}, issn = {1879-1026}, mesh = {*Archaea ; Ammonia ; Soil/chemistry ; Nitrogen ; Phylogeny ; Oxidation-Reduction ; Soil Microbiology ; Bacteria ; Nitrification ; *Betaproteobacteria ; Hydrogen-Ion Concentration ; }, abstract = {This study aimed to investigate the effect of soil pH change, and nitrogen amendment on ammonia oxidiser abundance and comammox Nitrospira community composition. The experimental design used soil mesocosms placed in a temperature-controlled incubator for 90 days. A Templeton silt loam was used as its physiochemical properties are typical of the region's dairy farms. The results showed that comammox Nitrospira clade B preferred the natural (pH 6.1-6.2) soil pH with no applied nitrogen. Furthermore, synthetic urine (N700) decreased the abundance of comammox Nitrospira clade B. This may have been because the large amounts of available ammonia in the N700 treatments inhibited the growth of comammox Nitrospira. These results suggest that while comammox Nitrospira clade B are present in New Zealand dairy farm soils, but their role in nitrification in the very high nitrogen environment under a urine patch in grazed pastures may be limited. Further research is needed to confirm this. In contrast to comammox, the AOB community (dominated by Nitrosospira) responded positively to the application of synthetic urine. The response was greatest in the high pH soil (7.1), followed by the natural and then the low pH (4.9) soils. This may be due to the difference in ammonia availability. At high pH, the ammonia/ammonium equilibrium favours ammonia production. Calculated ammonia availability in the N700 treatments accurately predicted the AOB amoA gene abundance. Interestingly, the AOA community abundance (which was predominantly made up of Thaumarchaeota group I.1b clade E) seemed to prefer the natural and high pH soils over the low pH. This may be due to the specific lineage of AOA present. AOA did not respond to the application of nitrogen.}, }
@article {pmid38466496, year = {2024}, author = {Huda, N and Rana, MR and Huq, MA and Al-Mamun, A and Rahman, ST and Alam, MK and Rahman, MM}, title = {Understanding vermicompost and organic manure interactions: impact on toxic elements, nitrification activity, comammox Nitrospira inopinata, and archaea/bacteria.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {4}, pages = {355}, pmid = {38466496}, issn = {1573-2959}, mesh = {*Archaea ; *Nitrification ; Manure ; Ammonia ; Carbon ; Oxidation-Reduction ; Soil/chemistry ; Phylogeny ; Soil Microbiology ; Environmental Monitoring ; Bacteria ; Nitrites ; }, abstract = {Vermicompost is a substantial source of nutrients, promotes soil fertility, and maintains or increases soil organic matter levels. Potentially toxic elements (PTEs) in vermicompost impact on nitrification activity. However, it is yet unknown how vermicompost affects nitrifying bacteria and archaea, comammox Nitrospira inopinata (complete ammonia oxidizers), net nitrification rates (NNRs), and PTEs. The effects of vermicompost application on NNRs, potential nitrification rates (NPs), PTEs, and the abundances of comammox N. inopinata bacteria, nitrite-oxidizing bacteria (NOB), and ammonia-oxidizing bacteria (AOB)/archaea (AOA) were studied. NNRs and NPs were significantly higher (p < 0.05) in fresh cow-dung vermicompost (stored for 40 days) as compared with other organic manure. The level of PTEs (Cu[2+], Fe[2+], Pb[2+], Cd[2+], and Zn[2+]) was significantly lower (p < 0.05) in vermicompost as compared with compost of waste material with Trichoderma and cow dung. Comammox N. inopinata, NOB, AOB, and AOA were significantly higher (p < 0.05) in stored cow-dung vermicompost (more than 1 year) as compared with other organic manure. The results of the scatterplot matrix analysis suggested that Fe[2+], total nitrogen (TN), soil organic carbon (SOC), and total carbon (TC) were linearly correlated (p < 0.001) with NNRs and NPs in vermicompost and organic manure. Similarly, comammox N. inopinata bacteria, NOB, AOB, and AOA were linearly correlated (p < 0.001) with NNR and NP. These results indicated that vermicompost promoted nitrification activity by increasing microbial diversity and abundance, supplying nutrients and organic matter for microbial growth, and facilitating complex microbial interactions. It may be concluded that the influence of vermicompost, which played a great role in PTE concentration reduction, increased chemical, and biological properties, increased the growth rate of nitrifying bacteria/archaea and the nitrogen cycle.}, }
@article {pmid38458444, year = {2024}, author = {Peng, L and Jia, M and Li, S and Wang, X and Liang, C and Xu, Y}, title = {Developing antibiotics-based strategies to efficiently enrich ammonia-oxidizing archaea from wastewater treatment plants.}, journal = {The Science of the total environment}, volume = {923}, number = {}, pages = {171479}, doi = {10.1016/j.scitotenv.2024.171479}, pmid = {38458444}, issn = {1879-1026}, mesh = {*Archaea/genetics ; *Ammonia ; Anti-Bacterial Agents ; Nitrites ; Oxidation-Reduction ; Bacteria/genetics ; Phylogeny ; Soil Microbiology ; }, abstract = {The effects of five antibiotics (i.e., ampicillin, streptomycin, carbenicillin, kanamycin and tetracycline) on ammonia-oxidizing archaea (AOA) enrichment from anoxic activated sludge were investigated. The combined use of five antibiotics during 90-day cultivation could selectively inhibit nitrite-oxidizing bacteria (NOB) and ammonia-oxidizing bacteria (AOB) with AOA unaffected, as evidenced by the nitrite accumulation ratio of 100 % and the proportion of AOA in ammonia-oxidizing microbes over 91 %. The alternative use of five antibiotics was the optimal approach to screening for AOA during 348-day cultivation, which inhibited AOB growth at a level equivalent to the combined use of five antibiotics (the AOB-amoA gene decreased by over 99.90 %), further promoted AOA abundance (the much higher AOA-amoA to AOB-amoA gene copy number ratio (1453.30) than that in the groups with the combined use of five antibiotics (192.94)), eliminated bacterial adaptation to antibiotics and reduced antibiotic-resistant bacteria to form Nitrocosmicus-dominant community (42.35 % in abundance).}, }
@article {pmid38444950, year = {2024}, author = {Sun, D and Rozmoš, M and Kotianová, M and Hršelová, H and Jansa, J}, title = {Arbuscular mycorrhizal fungi suppress ammonia-oxidizing bacteria but not archaea across agricultural soils.}, journal = {Heliyon}, volume = {10}, number = {4}, pages = {e26485}, pmid = {38444950}, issn = {2405-8440}, abstract = {Arbuscular mycorrhizal (AM) fungi are supposedly competing with ammonia-oxidizing microorganisms (AO) for soil nitrogen in form of ammonium. Despite a few studies directly addressing AM fungal and AO interactions, mostly in artificial cultivation substrates, it is not yet clear whether AM fungi can effectively suppress AO in field soils containing complex indigenous microbiomes. To fill this knowledge gap, we conducted compartmentalized pot experiments using four pairs of cropland and grassland soils with varying physicochemical properties. To exclude the interference of roots, a fine nylon mesh was used to separate the rhizosphere and mesh bags, with the latter being filled with unsterile field soils. Inoculation of plants with AM fungus Rhizophagus irregularis LPA9 suppressed AO bacteria (AOB) but not archaea (AOA) in the soils, indicating how soil nitrification could be suppressed by AM fungal presence/activity. In addition, in rhizosphere filled with artificial substrate, AM inoculation did suppress both AOB and AOA, implying more complex interactions between roots, AO, and AM fungi. Besides, we also observed that indigenous AM fungi contained in the field soils eventually did colonize the roots of plants behind the root barrier, and that the extent of such colonization was higher if the soil has previously been taken from cropland than from grassland. Despite this, the effect of experimental AM fungal inoculation on suppression of indigenous AOB in the unsterile field soils did not vanish. It seems that studying processes at a finer temporal scale, using larger buffer zones between rhizosphere and mesh bags, and/or detailed characterization of indigenous AM fungal and AO communities would be needed to uncover further details of the biotic interactions between the AM fungi and indigenous soil AO.}, }
@article {pmid38436843, year = {2024}, author = {Wang, J and Wen, X and Fang, Z and Gao, P and Wu, P and Li, X and Zeng, G}, title = {Impact of salinity and organic matter on the ammonia-oxidizing archaea and bacteria in treating hypersaline industrial wastewater: amoA gene abundance and ammonia removal contributions.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {16}, pages = {24099-24112}, pmid = {38436843}, issn = {1614-7499}, support = {52000019//National Natural Science Foundation of China/ ; KJQN202101526//Chongqing Municipal Education Commission/ ; YS2021089//Chongqing Bayu Scholars Young Scholars Project/ ; }, mesh = {*Archaea/genetics ; *Wastewater ; Ammonia ; Salinity ; Sodium Chloride ; Oxidation-Reduction ; Bacteria/genetics ; Nitrification ; Phylogeny ; Soil Microbiology ; }, abstract = {Studies published recently proposed that ammonia-oxidizing archaea (AOA) may be beneficial for hypersaline (salinity > 50 g NaCl L[-1]) industrial wastewater treatment. However, knowledge of AOA activity in hypersaline bioreactors is limited. This study investigated the effects of salinity, organic matter, and practical pickled mustard tuber wastewater (PMTW) on AOA and ammonia-oxidizing bacteria (AOB) in two sequencing batch biofilm reactors (SBBRs). Results showed that despite observed salinity inhibition (p < 0.05), both AOA and AOB contributed to high ammonia removal efficiency at a salinity of 70 g NaCl L[-1] in the two SBBRs. The ammonia removal efficiency of SBBR2 did not significantly differ from that of SBBR1 in the absence of organic matter (p > 0.05). Batch tests and quantitative real-time PCR (qPCR) reveal that salinity and organic matter inhibition resulted in a sharp decline in specific ammonia oxidation rates and amoA gene copy numbers of AOA and AOB (p < 0.05). AOA demonstrated higher abundance and more active ammonia oxidation activity in hypersaline and high organic matter environments. Salinity was positively correlated with the potential ammonia oxidation contribution of AOA (p < 0.05), resulting in a potential transition from AOB dominance to AOA dominance in SBBR1 as salinity levels rose. Moreover, autochthonous AOA in PMTW promoted the abundance and ammonia oxidation activities of AOA in SBBR2, further elevating the nitrification removal efficiency after feeding the practical PMTW. AOA demonstrates greater tolerance to the challenging hypersaline environment, making it a valuable candidate for the treatment of practical industrial wastewater with high salinity and organic content.}, }
@article {pmid38435527, year = {2024}, author = {Liu, Y and Qian, Y and Fu, L and Zhu, C and Li, X and Wang, Q and Ling, H and Du, H and Zhou, S and Kong, XY and Jiang, L and Wen, L}, title = {Archaea-Inspired Switchable Nanochannels for On-Demand Lithium Detection by pH Activation.}, journal = {ACS central science}, volume = {10}, number = {2}, pages = {469-476}, pmid = {38435527}, issn = {2374-7943}, abstract = {With the rapid development of the lithium ion battery industry, emerging lithium (Li) enrichment in nature has attracted ever-growing attention due to the biotoxicity of high Li levels. To date, fast lithium ion (Li[+]) detection remains urgent but is limited by the selectivity, sensitivity, and stability of conventional technologies based on passive response processes. In nature, archaeal plasma membrane ion exchangers (NCLX_Mj) exhibit Li[+]-gated multi/monovalent ion transport behavior, activated by different stimuli. Inspired by NCLX_Mj, we design a pH-controlled biomimetic Li[+]-responsive solid-state nanochannel system for on-demand Li[+] detection using 2-(2-hydroxyphenyl)benzoxazole (HPBO) units as Li[+] recognition groups. Pristine HPBO is not reactive to Li[+], whereas negatively charged HPBO enables specific Li[+] coordination under alkaline conditions to decrease the ion exchange capacity of nanochannels. On-demand Li[+] detection is achieved by monitoring the decline in currents, thereby ensuring precise and stable Li[+] recognition (>0.1 mM) in the toxic range of Li[+] concentration (>1.5 mM) for human beings. This work provides a new approach to constructing Li[+] detection nanodevices and has potential for applications of Li-related industries and medical services.}, }
@article {pmid38428597, year = {2024}, author = {Lee, KC and Archer, SDJ and Kansour, MK and Al-Mailem, DM}, title = {Bioremediation of oily hypersaline soil via autochthonous bioaugmentation with halophilic bacteria and archaea.}, journal = {The Science of the total environment}, volume = {922}, number = {}, pages = {171279}, doi = {10.1016/j.scitotenv.2024.171279}, pmid = {38428597}, issn = {1879-1026}, mesh = {Archaea/metabolism ; Biodegradation, Environmental ; Soil ; Soil Microbiology ; Oils ; Bacteria/metabolism ; *Petroleum/analysis ; Hydrocarbons/metabolism ; *Soil Pollutants/analysis ; }, abstract = {Kuwaiti hypersaline soil samples were contaminated with 5 % (w/w) weathered Kuwaiti light crude oil and bioaugmented with autochthonous halophilic hydrocarbonoclastic archaeal and bacterial strains, two each, individually and as consortia. Residual oil contents were determined, and microbial communities were analyzed by culture-dependent and culture-independent approaches initially and seasonally for one year. After one year of the bioremediation process, the mean oil degradation rate was similar across all treated soils including the controlled unbioaugmented one. Oil hydrocarbons were drastically reduced in all soil samples with values ranging from 82.7 % to 93 %. During the bioremediation process, the number of culturable oil-degrading bacteria increased to a range of 142 to 344 CFUx10[4] g[-1] after 12 months of bioaugmentation. Although culture-independent analysis showed a high proportion of inoculants initially, none could be cultured throughout the bioremediation procedure. Within a year, microbial communities changed continually, and 33 species of halotolerant/halophilic hydrocarbonoclastic bacteria were isolated and identified belonged mainly to the three major bacterial phyla Actinobacteria, Proteobacteria, and Firmicutes. The archaeal phylum Halobacterota represented <1 % of the microbial community's relative abundance, which explains why none of its members were cultured. Improving the biodegradability of an already balanced environment by autochthonous bioaugmentation is more involved than just adding the proper oil degraders. This study emphasizes the possibility of a relatively large resistant population, a greater diversity of oil-degrading microorganisms, and the highly selective impacts of oil contamination on hypersaline soil bacterial communities.}, }
@article {pmid38422909, year = {2024}, author = {Cena, JA and Belmok, A and Kyaw, CM and Dame-Teixeira, N}, title = {The Archaea domain: Exploring historical and contemporary perspectives with in silico primer coverage analysis for future research in Dentistry.}, journal = {Archives of oral biology}, volume = {161}, number = {}, pages = {105936}, doi = {10.1016/j.archoralbio.2024.105936}, pmid = {38422909}, issn = {1879-1506}, mesh = {Humans ; *Archaea/genetics ; Bacteria ; *Microbiota ; Mouth ; Dentistry ; Phylogeny ; }, abstract = {OBJECTIVE: The complete picture of how the human microbiome interacts with its host is still largely unknown, particularly concerning microorganisms beyond bacteria. Although existing in very low abundance and not directly linked to causing diseases, archaea have been detected in various sites of the human body, including the gastrointestinal tract, oral cavity, skin, eyes, respiratory and urinary systems. But what exactly are these microorganisms? In the early 1990 s, archaea were classified as a distinct domain of life, sharing a more recent common ancestor with eukaryotes than with bacteria. While archaea's presence and potential significance in Dentistry remain under-recognized, there are concerns that they may contribute to oral dysbiosis. However, detecting archaea in oral samples presents challenges, including difficulties in culturing, the selection of DNA extraction methods, primer design, bioinformatic analysis, and databases.<br><br>DESIGN: This is a comprehensive review on the oral archaeome, presenting an in-depth in silico analysis of various primers commonly used for detecting archaea in human body sites.<br><br>RESULTS: Among several primer pairs used for detecting archaea in human samples across the literature, only one specifically designed for detecting methanogenic archaea in stool samples, exhibited exceptional coverage levels for the domain and various archaea phyla.<br><br>CONCLUSIONS: Our in silico analysis underscores the need for designing new primers targeting not only methanogenic archaea but also nanoarchaeal and thaumarchaeota groups to gain a comprehensive understanding of the archaeal oral community. By doing so, researchers can pave the way for further advancements in the field of oral archaeome research.}, }
@article {pmid38392629, year = {2024}, author = {Cisek, AA and Szymańska, E and Aleksandrzak-Piekarczyk, T and Cukrowska, B}, title = {The Role of Methanogenic Archaea in Inflammatory Bowel Disease-A Review.}, journal = {Journal of personalized medicine}, volume = {14}, number = {2}, pages = {}, pmid = {38392629}, issn = {2075-4426}, abstract = {Methanogenic archaea are a part of the commensal gut microbiota responsible for hydrogen sink and the efficient production of short-chain fatty acids. Dysbiosis of methanogens is suspected to play a role in pathogenesis of variety of diseases, including inflammatory bowel disease (IBD). Unlike bacteria, the diversity of archaea seems to be higher in IBD patients compared to healthy subjects, whereas the prevalence and abundance of gut methanogens declines in IBD, especially in ulcerative colitis. To date, studies focusing on methanogens in pediatric IBD are very limited; nevertheless, the preliminary results provide some evidence that methanogens may be influenced by the chronic inflammatory process in IBD. In this review, we demonstrated the development and diversity of the methanogenic community in IBD, both in adults and children.}, }
@article {pmid38380943, year = {2024}, author = {Zhang, IH and Borer, B and Zhao, R and Wilbert, S and Newman, DK and Babbin, AR}, title = {Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential.}, journal = {mBio}, volume = {15}, number = {3}, pages = {e0291823}, pmid = {38380943}, issn = {2150-7511}, support = {R01 HL152190/HL/NHLBI NIH HHS/United States ; }, mesh = {*Archaea/genetics ; Nitrous Oxide/metabolism ; Phylogeny ; Metagenome ; *Microbiota ; Methane/metabolism ; Oxygen/metabolism ; Carbon/metabolism ; Nitrogen/metabolism ; Sulfur/metabolism ; Water/metabolism ; }, abstract = {UNLABELLED: Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%-50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.<br><br>IMPORTANCE: Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.}, }
@article {pmid38368447, year = {2024}, author = {Ouboter, HT and Mesman, R and Sleutels, T and Postma, J and Wissink, M and Jetten, MSM and Ter Heijne, A and Berben, T and Welte, CU}, title = {Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1477}, pmid = {38368447}, issn = {2041-1723}, support = {024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; VI.Vidi.223.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 854088//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*Archaea/genetics/metabolism ; Electron Transport ; *Bacteria/metabolism ; Anaerobiosis ; Electrons ; Oxidation-Reduction ; Methane/metabolism ; }, abstract = {Anaerobic methanotrophic (ANME) archaea are environmentally important, uncultivated microorganisms that oxidize the potent greenhouse gas methane. During methane oxidation, ANME archaea engage in extracellular electron transfer (EET) with other microbes, metal oxides, and electrodes through unclear mechanisms. Here, we cultivate ANME-2d archaea ('Ca. Methanoperedens') in bioelectrochemical systems and observe strong methane-dependent current (91-93% of total current) associated with high enrichment of 'Ca. Methanoperedens' on the anode (up to 82% of the community), as determined by metagenomics and transmission electron microscopy. Electrochemical and metatranscriptomic analyses suggest that the EET mechanism is similar at various electrode potentials, with the possible involvement of an uncharacterized short-range electron transport protein complex and OmcZ nanowires.}, }
@article {pmid38366050, year = {2024}, author = {Baquero, DP and Bignon, EA and Krupovic, M}, title = {Pleomorphic viruses establish stable relationship with marine hyperthermophilic archaea.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38366050}, issn = {1751-7370}, support = {ANR-20-CE20-009//l'Agence Nationale de la Recherche/ ; }, mesh = {Archaea/genetics ; Phylogeny ; Ecosystem ; *Viruses/genetics ; Virion ; *Euryarchaeota ; *Archaeal Viruses/genetics ; }, abstract = {Non-lytic viruses with enveloped pleomorphic virions (family Pleolipoviridae) are ubiquitous in hypersaline environments across the globe and are associated with nearly all major lineages of halophilic archaea. However, their existence in other ecosystems remains largely unknown. Here, we show that evolutionarily-related viruses also infect hyperthermophilic archaea thriving in deep-sea hydrothermal vents. Archaeoglobus veneficus pleomorphic virus 1 (AvPV1), the first virus described for any member of the class Archaeoglobi, encodes a morphogenetic module typical of pleolipoviruses, including the characteristic VP4-like membrane fusion protein. We show that AvPV1 is a non-lytic virus chronically produced in liquid cultures without substantially affecting the growth dynamics of its host with a stable virus-to-host ratio of ~1. Mining of genomic and metagenomic databases revealed broad distribution of AvPV1-like viruses in geographically remote hydrothermal vents. Comparative genomics, coupled with phylogenetic analysis of VP4-like fusogens revealed deep divergence of pleomorphic viruses infecting halophilic, methanogenic, and hyperthermophilic archaea, signifying niche separation and coevolution of the corresponding virus-host pairs. Hence, we propose a new virus family, "Thalassapleoviridae," for classification of the marine hyperthermophilic virus AvPV1 and its relatives. Collectively, our results provide insights into the diversity and evolution of pleomorphic viruses beyond hypersaline environments.}, }
@article {pmid38365232, year = {2024}, author = {Zheng, Y and Wang, B and Gao, P and Yang, Y and Xu, B and Su, X and Ning, D and Tao, Q and Li, Q and Zhao, F and Wang, D and Zhang, Y and Li, M and Winkler, MH and Ingalls, AE and Zhou, J and Zhang, C and Stahl, DA and Jiang, J and Martens-Habbena, W and Qin, W}, title = {Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365232}, issn = {1751-7370}, support = {548565//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; //Florida Agricultural Experiment Station Hatch project/ ; //National Natural Science Foundation of China/ ; 2020Z01//Shanghai Sheshan National Geophysical Observatory/ ; 20200925173954005//Stable Support Plan Program of Shenzhen Natural Science Fund/ ; ZDSYS201802081843490//Southern University of Science and Technology/ ; //Shenzhen Key Laboratory of Marine Archaea Geo-Omics/ ; 2020KCXTD023//the Innovation Team Project of Universities/ ; //National Natural Science Foundation of China/ ; //Fundamental Research Funds for the Central Universities of China/ ; 92051114//National Natural Science Foundation of China/ ; }, mesh = {*Archaea ; *Ammonia/metabolism ; Ecosystem ; RNA, Ribosomal, 16S/genetics/metabolism ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; }, abstract = {Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.}, }
@article {pmid38358888, year = {2024}, author = {Lu, Z and Zhang, S and Liu, Y and Xia, R and Li, M}, title = {Origin of eukaryotic-like Vps23 shapes an ancient functional interplay between ESCRT and ubiquitin system in Asgard archaea.}, journal = {Cell reports}, volume = {43}, number = {2}, pages = {113781}, doi = {10.1016/j.celrep.2024.113781}, pmid = {38358888}, issn = {2211-1247}, mesh = {*Ubiquitin ; Ubiquitination ; *Archaea/genetics ; Cell Movement ; Endosomal Sorting Complexes Required for Transport ; }, abstract = {Functional interplay between the endosomal sorting complexes required for transport (ESCRT) and the ubiquitin system underlies the ubiquitin-dependent cargo-sorting pathway of the eukaryotic endomembrane system, yet its evolutionary origin remains unclear. Here, we show that a UEV-Vps23 protein family, which contains UEV and Vps23 domains, mediates an ancient ESCRT and ubiquitin system interplay in Asgard archaea. The UEV binds ubiquitin with high affinity, making the UEV-Vps23 a sensor for sorting ubiquitinated cargo. A steadiness box in the Vps23 domain undergoes ubiquitination through an Asgard E1, E2, and RING E3 cascade. The UEV-Vps23 switches between autoinhibited and active forms, regulating the ESCRT and ubiquitin system interplay. Furthermore, the shared sequence and structural homology among the UEV-Vps23, eukaryotic Vps23, and archaeal CdvA suggest a common evolutionary origin. Together, this work expands our understanding of the ancient ESCRT and ubiquitin system interplay that likely arose antedating divergent evolution between Asgard archaea and eukaryotes.}, }
@article {pmid38354884, year = {2024}, author = {Ju, H and Zhang, J and Zou, Y and Xie, F and Tang, X and Zhang, S and Li, J}, title = {Bacteria undergo significant shifts while archaea maintain stability in Pocillopora damicornis under sustained heat stress.}, journal = {Environmental research}, volume = {250}, number = {}, pages = {118469}, doi = {10.1016/j.envres.2024.118469}, pmid = {38354884}, issn = {1096-0953}, mesh = {*Anthozoa/microbiology/physiology ; Animals ; *Archaea/genetics/physiology ; *Bacteria/genetics/classification ; Heat-Shock Response ; Microbiota ; Hot Temperature ; Coral Reefs ; }, abstract = {Global warming reportedly poses a critical risk to coral reef ecosystems. Bacteria and archaea are crucial components of the coral holobiont. The response of archaea associated with warming is less well understood than that of the bacterial community in corals. Also, there have been few studies on the dynamics of the microbial community in the coral holobiont under long-term heat stress. In order to track the dynamic alternations in the microbial communities within the heat-stressed coral holobiont, three-week heat-stress monitoring was carried out on the coral Pocillopora damicornis. The findings demonstrate that the corals were stressed at 32 °C, and showed a gradual decrease in Symbiodiniaceae density with increasing duration of heat stress. The archaeal community in the coral holobiont remained relatively unaltered by the increasing temperature, whereas the bacterial community was considerably altered. Sustained heat stress exacerbated the dissimilarities among parallel samples of the bacterial community, confirming the Anna Karenina Principle in animal microbiomes. Heat stress leads to more complex and unstable microbial networks, characterized by an increased average degree and decreased modularity, respectively. With the extension of heat stress duration, the relative abundances of the gene (nifH) and genus (Tistlia) associated with nitrogen fixation increased in coral samples, as well as the potential pathogenic bacteria (Flavobacteriales) and opportunistic bacteria (Bacteroides). Hence, our findings suggest that coral hosts might recruit nitrogen-fixing bacteria during the initial stages of suffering heat stress. An environment that is conducive to the colonization and development of opportunistic and pathogenic bacteria when the coral host becomes more susceptible as heat stress duration increases.}, }
@article {pmid38349190, year = {2024}, author = {Ghimire-Kafle, S and Weaver, ME and Kimbrel, MP and Bollmann, A}, title = {Competition between ammonia-oxidizing archaea and complete ammonia oxidizers from freshwater environments.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {3}, pages = {e0169823}, pmid = {38349190}, issn = {1098-5336}, support = {IOS1755270//National Science Foundation (NSF)/ ; }, mesh = {*Archaea ; Ammonia ; Nitrites ; Nitrates ; Bacteria ; Nitrification ; Oxidation-Reduction ; Lakes ; *Ammonium Compounds ; Phylogeny ; }, abstract = {UNLABELLED: Aerobic ammonia oxidizers (AOs) are prokaryotic microorganisms that contribute to the global nitrogen cycle by performing the first step of nitrification, the oxidation of ammonium to nitrite and nitrate. While aerobic AOs are found ubiquitously, their distribution is controlled by key environmental conditions such as substrate (ammonium) availability. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are generally found in oligotrophic environments with low ammonium availability. However, whether AOA and comammox share these habitats or outcompete each other is not well understood. We assessed the competition for ammonium between an AOA and comammox enriched from the freshwater Lake Burr Oak. The AOA enrichment culture (AOA-BO1) contained Nitrosarchaeum sp. BO1 as the ammonia oxidizer and Nitrospira sp. BO1 as the nitrite oxidizer. The comammox enrichment BO4 (cmx-BO4) contained the comammox strain Nitrospira sp. BO4. The competition experiments were performed either in continuous cultivation with ammonium as a growth-limiting substrate or in batch cultivation with initial ammonium concentrations of 50 and 500 µM. Regardless of the ammonium concentration, Nitrospira sp. BO4 outcompeted Nitrosarchaeum sp. BO1 under all tested conditions. The dominance of Nitrospira sp. BO4 could be explained by the ability of comammox to generate more energy through the complete oxidation of ammonia to nitrate and their more efficient carbon fixation pathway-the reductive tricarboxylic acid cycle. Our results are supported by the higher abundance of comammox compared to AOA in the sediment of Lake Burr Oak.<br><br>IMPORTANCE: Nitrification is a key process in the global nitrogen cycle. Aerobic ammonia oxidizers play a central role in the nitrogen cycle by performing the first step of nitrification. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are the dominant nitrifiers in environments with low ammonium availability. While AOA have been studied for almost 20 years, comammox were only discovered 8 years ago. Until now, there has been a gap in our understanding of whether AOA and comammox can co-exist or if one strain would be dominant under ammonium-limiting conditions. Here, we present the first study characterizing the competition between freshwater AOA and comammox under varying substrate concentrations. Our results will help in elucidating the niches of two key nitrifiers in freshwater lakes.}, }
@article {pmid38323857, year = {2024}, author = {Kuroda, K and Nakajima, M and Nakai, R and Hirakata, Y and Kagemasa, S and Kubota, K and Noguchi, TQP and Yamamoto, K and Satoh, H and Nobu, MK and Narihiro, T}, title = {Microscopic and metatranscriptomic analyses revealed unique cross-domain parasitism between phylum Candidatus Patescibacteria/candidate phyla radiation and methanogenic archaea in anaerobic ecosystems.}, journal = {mBio}, volume = {15}, number = {3}, pages = {e0310223}, pmid = {38323857}, issn = {2150-7511}, support = {JP16H07403, JP21H01471//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; G-2019-1-052//Institute for Fermentation, Osaka (IFO)/ ; G-2022-1-014//Institute for Fermentation, Osaka (IFO)/ ; //A matching fund between National Institute of Advanced Industrial Science and Technology (AIST) and Tohoku University/ ; }, mesh = {Humans ; *Archaea/genetics ; Anaerobiosis ; Ecosystem ; In Situ Hybridization, Fluorescence ; Phylogeny ; Bacteria/genetics ; *Euryarchaeota/genetics ; }, abstract = {To verify whether members of the phylum Candidatus Patescibacteria parasitize archaea, we applied cultivation, microscopy, metatranscriptomic, and protein structure prediction analyses on the Patescibacteria-enriched cultures derived from a methanogenic bioreactor. Amendment of cultures with exogenous methanogenic archaea, acetate, amino acids, and nucleoside monophosphates increased the relative abundance of Ca. Patescibacteria. The predominant Ca. Patescibacteria were families Ca. Yanofskyibacteriaceae and Ca. Minisyncoccaceae, and the former showed positive linear relationships (r[2] ≥ 0.70) Methanothrix in their relative abundances, suggesting related growth patterns. Methanothrix and Methanospirillum cells with attached Ca. Yanofskyibacteriaceae and Ca. Minisyncoccaceae, respectively, had significantly lower cellular activity than those of the methanogens without Ca. Patescibacteria, as extrapolated from fluorescence in situ hybridization-based fluorescence. We also observed that parasitized methanogens often had cell surface deformations. Some Methanothrix-like filamentous cells were dented where the submicron cells were attached. Ca. Yanofskyibacteriaceae and Ca. Minisyncoccaceae highly expressed extracellular enzymes, and based on structural predictions, some contained peptidoglycan-binding domains with potential involvement in host cell attachment. Collectively, we propose that the interactions of Ca. Yanofskyibacteriaceae and Ca. Minisyncoccaceae with methanogenic archaea are parasitisms.IMPORTANCECulture-independent DNA sequencing approaches have explored diverse yet-to-be-cultured microorganisms and have significantly expanded the tree of life in recent years. One major lineage of the domain Bacteria, Ca. Patescibacteria (also known as candidate phyla radiation), is widely distributed in natural and engineered ecosystems and has been thought to be dependent on host bacteria due to the lack of several biosynthetic pathways and small cell/genome size. Although bacteria-parasitizing or bacteria-preying Ca. Patescibacteria have been described, our recent studies revealed that some lineages can specifically interact with archaea. In this study, we provide strong evidence that the relationship is parasitic, shedding light on overlooked roles of Ca. Patescibacteria in anaerobic habitats.}, }
@article {pmid38314098, year = {2023}, author = {Tirumalai, MR and Sivaraman, RV and Kutty, LA and Song, EL and Fox, GE}, title = {Ribosomal Protein Cluster Organization in Asgard Archaea.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2023}, number = {}, pages = {5512414}, pmid = {38314098}, issn = {1472-3654}, mesh = {*Archaea/genetics/metabolism ; *Ribosomal Proteins/genetics/metabolism ; Escherichia coli/genetics ; Bacteria/genetics ; Genome, Bacterial ; Phylogeny ; }, abstract = {It has been proposed that the superphylum of Asgard Archaea may represent a historical link between the Archaea and Eukarya. Following the discovery of the Archaea, it was soon appreciated that archaeal ribosomes were more similar to those of Eukarya rather than Bacteria. Coupled with other eukaryotic-like features, it has been suggested that the Asgard Archaea may be directly linked to eukaryotes. However, the genomes of Bacteria and non-Asgard Archaea generally organize ribosome-related genes into clusters that likely function as operons. In contrast, eukaryotes typically do not employ an operon strategy. To gain further insight into conservation of the r-protein genes, the genome order of conserved ribosomal protein (r-protein) coding genes was identified in 17 Asgard genomes (thirteen complete genomes and four genomes with less than 20 contigs) and compared with those found previously in non-Asgard archaeal and bacterial genomes. A universal core of two clusters of 14 and 4 cooccurring r-proteins, respectively, was identified in both the Asgard and non-Asgard Archaea. The equivalent genes in the E. coli version of the cluster are found in the S10 and spc operons. The large cluster of 14 r-protein genes (uS19-uL22-uS3-uL29-uS17 from the S10 operon and uL14-uL24-uL5-uS14-uS8-uL6-uL18-uS5-uL30-uL15 from the spc operon) occurs as a complete set in the genomes of thirteen Asgard genomes (five Lokiarchaeotes, three Heimdallarchaeotes, one Odinarchaeote, and four Thorarchaeotes). Four less conserved clusters with partial bacterial equivalents were found in the Asgard. These were the L30e (str operon in Bacteria) cluster, the L18e (alpha operon in Bacteria) cluster, the S24e-S27ae-rpoE1 cluster, and the L31e, L12..L1 cluster. Finally, a new cluster referred to as L7ae was identified. In many cases, r-protein gene clusters/operons are less conserved in their organization in the Asgard group than in other Archaea. If this is generally true for nonribosomal gene clusters, the results may have implications for the history of genome organization. In particular, there may have been an early transition to or from the operon approach to genome organization. Other nonribosomal cellular features may support different relationships. For this reason, it may be important to consider ribosome features separately.}, }
@article {pmid38302496, year = {2024}, author = {Tang, SK and Zhi, XY and Zhang, Y and Makarova, KS and Liu, BB and Zheng, GS and Zhang, ZP and Zheng, HJ and Wolf, YI and Zhao, YR and Jiang, SH and Chen, XM and Li, EY and Zhang, T and Chen, PR and Feng, YZ and Xiang, MX and Lin, ZQ and Shi, JH and Chang, C and Zhang, X and Li, R and Lou, K and Wang, Y and Chang, L and Yin, M and Yang, LL and Gao, HY and Zhang, ZK and Tao, TS and Guan, TW and He, FC and Lu, YH and Cui, HL and Koonin, EV and Zhao, GP and Xu, P}, title = {Addendum: Cellular differentiation into hyphae and spores in halophilic archaea.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {523}, pmid = {38302496}, issn = {2041-1723}, mesh = {*Hyphae ; Spores, Fungal ; *Archaea/genetics ; Phylogeny ; Cell Differentiation ; }, }
@article {pmid38299815, year = {2024}, author = {Scott, KM and Payne, RR and Gahramanova, A}, title = {Widespread dissolved inorganic carbon-modifying toolkits in genomes of autotrophic Bacteria and Archaea and how they are likely to bridge supply from the environment to demand by autotrophic pathways.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {2}, pages = {e0155723}, pmid = {38299815}, issn = {1098-5336}, support = {NSF-MCB-1952676//National Science Foundation (NSF)/ ; }, mesh = {*Archaea/genetics/metabolism ; *Bacteria/genetics/metabolism ; Autotrophic Processes/genetics ; Carbon/metabolism ; Hydroxybutyrates/metabolism ; Carbon Dioxide/metabolism ; Carbon Cycle/genetics ; }, abstract = {Using dissolved inorganic carbon (DIC) as a major carbon source, as autotrophs do, is complicated by the bedeviling nature of this substance. Autotrophs using the Calvin-Benson-Bassham cycle (CBB) are known to make use of a toolkit comprised of DIC transporters and carbonic anhydrase enzymes (CA) to facilitate DIC fixation. This minireview provides a brief overview of the current understanding of how toolkit function facilitates DIC fixation in Cyanobacteria and some Proteobacteria using the CBB and continues with a survey of the DIC toolkit gene presence in organisms using different versions of the CBB and other autotrophic pathways (reductive citric acid cycle, Wood-Ljungdahl pathway, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate cycle, and dicarboxylate-hydroxybutyrate cycle). The potential function of toolkit gene products in these organisms is discussed in terms of CO2 and HCO3[-] supply from the environment and demand by the autotrophic pathway. The presence of DIC toolkit genes in autotrophic organisms beyond those using the CBB suggests the relevance of DIC metabolism to these organisms and provides a basis for better engineering of these organisms for industrial and agricultural purposes.}, }
@article {pmid38297167, year = {2024}, author = {Qin, W and Wei, SP and Zheng, Y and Choi, E and Li, X and Johnston, J and Wan, X and Abrahamson, B and Flinkstrom, Z and Wang, B and Li, H and Hou, L and Tao, Q and Chlouber, WW and Sun, X and Wells, M and Ngo, L and Hunt, KA and Urakawa, H and Tao, X and Wang, D and Yan, X and Wang, D and Pan, C and Weber, PK and Jiang, J and Zhou, J and Zhang, Y and Stahl, DA and Ward, BB and Mayali, X and Martens-Habbena, W and Winkler, MH}, title = {Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences.}, journal = {Nature microbiology}, volume = {9}, number = {2}, pages = {524-536}, pmid = {38297167}, issn = {2058-5276}, support = {DE-SC0020356//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; 675459//Simons Foundation/ ; DEB-1664052//National Science Foundation (NSF)/ ; HR0011-17-2-0064//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; }, mesh = {*Archaea/metabolism ; *Bacteria/metabolism ; Ammonia/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Nitrification ; Phylogeny ; Soil Microbiology ; Urea/metabolism ; }, abstract = {Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia. How the coordination of ammonia and urea metabolism in AOM influences their ecology remains poorly understood. Here we use stable isotope tracing, kinetics and transcriptomics experiments to show that representatives of the AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct substrate competition. The tested AOA and comammox species preferentially used ammonia over urea, while β-AOB favoured urea utilization, repressed ammonia transport in the presence of urea and showed higher affinity for urea than for ammonia. Characterized γ-AOB co-utilized both substrates. These results reveal contrasting niche adaptation and coexistence patterns among the major AOM lineages.}, }
@article {pmid38297006, year = {2024}, author = {Maza-Márquez, P and Lee, MD and Bebout, BM}, title = {Community ecology and functional potential of bacteria, archaea, eukarya and viruses in Guerrero Negro microbial mat.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2561}, pmid = {38297006}, issn = {2045-2322}, mesh = {Archaea/genetics ; Bacteria/genetics ; Eukaryota/genetics ; Phylogeny ; Viruses/genetics ; *Microbiota ; }, abstract = {In this study, the microbial ecology, potential environmental adaptive mechanisms, and the potential evolutionary interlinking of genes between bacterial, archaeal and viral lineages in Guerrero Negro (GN) microbial mat were investigated using metagenomic sequencing across a vertical transect at millimeter scale. The community composition based on unique genes comprised bacteria (98.01%), archaea (1.81%), eukarya (0.07%) and viruses (0.11%). A gene-focused analysis of bacteria archaea, eukarya and viruses showed a vertical partition of the community. The greatest coverages of genes of bacteria and eukarya were detected in first layers, while the highest coverages of genes of archaea and viruses were found in deeper layers. Many genes potentially related to adaptation to the local environment were detected, such as UV radiation, multidrug resistance, oxidative stress, heavy metals, salinity and desiccation. Those genes were found in bacterial, archaeal and viral lineages with 6477, 44, and 1 genes, respectively. The evolutionary histories of those genes were studied using phylogenetic analysis, showing an interlinking between domains in GN mat.}, }
@article {pmid38292760, year = {2024}, author = {Candeliere, F and Sola, L and Raimondi, S and Rossi, M and Amaretti, A}, title = {Good and bad dispositions between archaea and bacteria in the human gut: New insights from metagenomic survey and co-occurrence analysis.}, journal = {Synthetic and systems biotechnology}, volume = {9}, number = {1}, pages = {88-98}, pmid = {38292760}, issn = {2405-805X}, abstract = {Archaea are an understudied component of the human microbiome. In this study, the gut archaeome and bacteriome of 60 healthy adults from different region were analyzed by whole-genome shotgun sequencing. Archaea were ubiquitously found in a wide range of abundances, reaching up to 7.2 %. The dominant archaeal phylum was Methanobacteriota, specifically the family Methanobacteriaceae, encompassing more than 50 % of Archaea in 50 samples. The previously underestimated Thermoplasmatota, mostly composed of Methanomassiliicoccaceae, dominated in 10 subjects (>50 %) and was present in all others except one. Halobacteriota, the sole other archaeal phylum, occurred in negligible concentration, except for two samples (4.6-4.8 %). This finding confirmed that the human gut archaeome is primarily composed of methanogenic organisms and among the known methanogenic pathway: i) hydrogenotrophic reduction of CO2 is the predominant, being the genus Methanobrevibacter and the species Methanobrevibacter smithii the most abundant in the majority of the samples; ii) the second pathway, that involved Methanomassiliicoccales, was the hydrogenotrophic reduction of methyl-compounds; iii) dismutation of acetate or methyl-compounds seemed to be absent. Co-occurrence analysis allowed to unravel correlations between Archaea and Bacteria that shapes the overall structure of the microbial community, allowing to depict a clearer picture of the human gut archaeome.}, }
@article {pmid38280122, year = {2024}, author = {Rao, A and Driessen, AJM}, title = {Unraveling the multiplicity of geranylgeranyl reductases in Archaea: potential roles in saturation of terpenoids.}, journal = {Extremophiles : life under extreme conditions}, volume = {28}, number = {1}, pages = {14}, pmid = {38280122}, issn = {1433-4909}, support = {024.003.019//BaSyC - Building a Synthetic Cell/ ; }, mesh = {*Terpenes/metabolism ; *Archaea/genetics/metabolism ; Phospholipids/metabolism ; Oxidoreductases/genetics/chemistry/metabolism ; }, abstract = {The enzymology of the key steps in the archaeal phospholipid biosynthetic pathway has been elucidated in recent years. In contrast, the complete biosynthetic pathways for proposed membrane regulators consisting of polyterpenes, such as carotenoids, respiratory quinones, and polyprenols remain unknown. Notably, the multiplicity of geranylgeranyl reductases (GGRs) in archaeal genomes has been correlated with the saturation of polyterpenes. Although GGRs, which are responsible for saturation of the isoprene chains of phospholipids, have been identified and studied in detail, there is little information regarding the structure and function of the paralogs. Here, we discuss the diversity of archaeal membrane-associated polyterpenes which is correlated with the genomic loci, structural and sequence-based analyses of GGR paralogs.}, }
@article {pmid38263861, year = {2024}, author = {Ni, Y and Xu, T and Yan, S and Chen, L and Wang, Y}, title = {Hiding in plain sight: The discovery of complete genomes of 11 hypothetical spindle-shaped viruses that putatively infect mesophilic ammonia-oxidizing archaea.}, journal = {Environmental microbiology reports}, volume = {16}, number = {1}, pages = {e13230}, pmid = {38263861}, issn = {1758-2229}, support = {32370151//National Natural Science Foundation of China/ ; 41376135//National Natural Science Foundation of China/ ; }, mesh = {*Archaea/genetics/metabolism ; Ammonia/metabolism ; Capsid Proteins/chemistry/genetics/metabolism ; *Archaeal Viruses/genetics/metabolism ; Oxidation-Reduction ; Phylogeny ; }, abstract = {The genome of a putative Nitrosopumilaceae virus with a hypothetical spindle-shaped particle morphology was identified in the Yangshan Harbour metavirome from the East China Sea through protein similarity comparison and structure analysis. This discovery was accompanied by a set of 10 geographically dispersed close relatives found in the environmental virus datasets from typical locations of ammonia-oxidizing archaeon distribution. Its host prediction was supported by iPHoP prediction and protein sequence similarity. The structure of the predicted major capsid protein, together with the overall N-glycosylation site, the transmembrane helices prediction, the hydrophilicity profile, and the docking simulation of the major capsid proteins, indicate that these viruses resemble spindle-shaped viruses. It suggests a similarly assembled structure and, consequently, a possibly spindle-shaped morphology of these newly discovered archaeal viruses.}, }
@article {pmid38261994, year = {2024}, author = {}, title = {Correction to 'Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome'.}, journal = {Nucleic acids research}, volume = {52}, number = {4}, pages = {2092}, doi = {10.1093/nar/gkae047}, pmid = {38261994}, issn = {1362-4962}, }
@article {pmid38259951, year = {2023}, author = {Beeckman, F and Drozdzecki, A and De Knijf, A and Audenaert, D and Beeckman, T and Motte, H}, title = {High-throughput assays to identify archaea-targeting nitrification inhibitors.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1283047}, pmid = {38259951}, issn = {1664-462X}, abstract = {Nitrification is a microbial process that converts ammonia (NH3) to nitrite (NO2 [-]) and then to nitrate (NO3 [-]). The first and rate-limiting step in nitrification is ammonia oxidation, which is conducted by both bacteria and archaea. In agriculture, it is important to control this process as high nitrification rates result in NO3 [-] leaching, reduced nitrogen (N) availability for the plants and environmental problems such as eutrophication and greenhouse gas emissions. Nitrification inhibitors can be used to block nitrification, and as such reduce N pollution and improve fertilizer use efficiency (FUE) in agriculture. Currently applied inhibitors target the bacteria, and do not block nitrification by ammonia-oxidizing archaea (AOA). While it was long believed that nitrification in agroecosystems was primarily driven by bacteria, recent research has unveiled potential significant contributions from ammonia-oxidizing archaea (AOA), especially when bacterial activity is inhibited. Hence, there is also a need for AOA-targeting nitrification inhibitors. However, to date, almost no AOA-targeting inhibitors are described. Furthermore, AOA are difficult to handle, hindering their use to test or identify possible AOA-targeting nitrification inhibitors. To address the need for AOA-targeting nitrification inhibitors, we developed two miniaturized nitrification inhibition assays using an AOA-enriched nitrifying community or the AOA Nitrosospaera viennensis. These assays enable high-throughput testing of candidate AOA inhibitors. We here present detailed guidelines on the protocols and illustrate their use with some examples. We believe that these assays can contribute to the discovery of future AOA-targeting nitrification inhibitors, which could complement the currently applied inhibitors to increase nitrification inhibition efficiency in the field and as such contribute to a more sustainable agriculture.}, }
@article {pmid38246077, year = {2024}, author = {Tang, M and Chen, Q and Zhong, H and Liu, S and Sun, W}, title = {CPR bacteria and DPANN archaea play pivotal roles in response of microbial community to antibiotic stress in groundwater.}, journal = {Water research}, volume = {251}, number = {}, pages = {121137}, doi = {10.1016/j.watres.2024.121137}, pmid = {38246077}, issn = {1879-2448}, mesh = {Archaea/genetics/metabolism ; Anti-Bacterial Agents/pharmacology/metabolism ; Bacteria/genetics/metabolism ; *Microbiota ; *Groundwater/microbiology ; Phylogeny ; }, abstract = {The accumulation of antibiotics in the natural environment can disrupt microbial population dynamics. However, our understanding of how microbial communities adapt to the antibiotic stress in groundwater ecosystems remains limited. By recovering 2675 metagenome-assembled genomes (MAGs) from 66 groundwater samples, we explored the effect of antibiotics on bacterial, archaeal, and fungal communities, and revealed the pivotal microbes and their mechanisms in coping with antibiotic stress. The results indicated that antibiotics had the most significant influence on bacterial and archaeal communities, while the impact on the fungal community was minimal. Analysis of co-occurrence networks between antibiotics and microbes revealed the critical roles of Candidate Phyla Radiation (CPR) bacteria and DPANN archaea, two representative microbial groups in groundwater ecosystem, in coping with antibiotic resistance and enhancing network connectivity and complexity. Further genomic analysis demonstrated that CPR bacteria carried approximately 6 % of the identified antibiotic resistance genes (ARGs), indicating their potential to withstand antibiotics on their own. Meanwhile, the genomes of CPR bacteria and DPANN archaea were found to encode diverse biosynthetic gene clusters (BGCs) responsible for producing antimicrobial metabolites, which could not only assist CPR and DPANN organisms but also benefit the surrounding microbes in combating antibiotic stress. These findings underscore the significant impact of antibiotics on prokaryotic microbial communities in groundwater, and highlight the importance of CPR bacteria and DPANN archaea in enhancing the overall resilience and functionality of the microbial community in the face of antibiotic stress.}, }
@article {pmid38243071, year = {2024}, author = {Müller, MC and Lemaire, ON and Kurth, JM and Welte, CU and Wagner, T}, title = {Differences in regulation mechanisms of glutamine synthetases from methanogenic archaea unveiled by structural investigations.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {111}, pmid = {38243071}, issn = {2399-3642}, support = {KU 3768/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Glutamine/metabolism ; *Archaea/genetics/metabolism ; Glutamate-Ammonia Ligase/metabolism ; Ketoglutaric Acids ; Bacteria/metabolism ; Nitrogen/metabolism ; }, abstract = {Glutamine synthetases (GS) catalyze the ATP-dependent ammonium assimilation, the initial step of nitrogen acquisition that must be under tight control to fit cellular needs. While their catalytic mechanisms and regulations are well-characterized in bacteria and eukaryotes, only limited knowledge exists in archaea. Here, we solved two archaeal GS structures and unveiled unexpected differences in their regulatory mechanisms. GS from Methanothermococcus thermolithotrophicus is inactive in its resting state and switched on by 2-oxoglutarate, a sensor of cellular nitrogen deficiency. The enzyme activation overlays remarkably well with the reported cellular concentration for 2-oxoglutarate. Its binding to an allosteric pocket reconfigures the active site through long-range conformational changes. The homolog from Methermicoccus shengliensis does not harbor the 2-oxoglutarate binding motif and, consequently, is 2-oxoglutarate insensitive. Instead, it is directly feedback-inhibited through glutamine recognition by the catalytic Asp50'-loop, a mechanism common to bacterial homologs, but absent in M. thermolithotrophicus due to residue substitution. Analyses of residue conservation in archaeal GS suggest that both regulations are widespread and not mutually exclusive. While the effectors and their binding sites are surprisingly different, the molecular mechanisms underlying their mode of action on GS activity operate on the same molecular determinants in the active site.}, }
@article {pmid38227606, year = {2024}, author = {Hackley, RK and Vreugdenhil-Hayslette, A and Darnell, CL and Schmid, AK}, title = {A conserved transcription factor controls gluconeogenesis via distinct targets in hypersaline-adapted archaea with diverse metabolic capabilities.}, journal = {PLoS genetics}, volume = {20}, number = {1}, pages = {e1011115}, pmid = {38227606}, issn = {1553-7404}, mesh = {*Transcription Factors/genetics/metabolism ; *Gluconeogenesis/genetics ; Archaea/genetics ; Gene Expression Regulation, Archaeal ; Carbohydrates ; Carbon/metabolism ; }, abstract = {Timely regulation of carbon metabolic pathways is essential for cellular processes and to prevent futile cycling of intracellular metabolites. In Halobacterium salinarum, a hypersaline adapted archaeon, a sugar-sensing TrmB family protein controls gluconeogenesis and other biosynthetic pathways. Notably, Hbt. salinarum does not utilize carbohydrates for energy, uncommon among Haloarchaea. We characterized a TrmB-family transcriptional regulator in a saccharolytic generalist, Haloarcula hispanica, to investigate whether the targets and function of TrmB, or its regulon, is conserved in related species with distinct metabolic capabilities. In Har. hispanica, TrmB binds to 15 sites in the genome and induces the expression of genes primarily involved in gluconeogenesis and tryptophan biosynthesis. An important regulatory control point in Hbt. salinarum, activation of ppsA and repression of pykA, is absent in Har. hispanica. Contrary to its role in Hbt. salinarum and saccharolytic hyperthermophiles, TrmB does not act as a global regulator: it does not directly repress the expression of glycolytic enzymes, peripheral pathways such as cofactor biosynthesis, or catabolism of other carbon sources in Har. hispanica. Cumulatively, these findings suggest rewiring of the TrmB regulon alongside metabolic network evolution in Haloarchaea.}, }
@article {pmid38225278, year = {2024}, author = {Lu, Z and Xia, R and Zhang, S and Pan, J and Liu, Y and Wolf, YI and Koonin, EV and Li, M}, title = {Evolution of optimal growth temperature in Asgard archaea inferred from the temperature dependence of GDP binding to EF-1A.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {515}, pmid = {38225278}, issn = {2041-1723}, mesh = {*Archaea/growth &amp; development ; Phylogeny ; Temperature ; *Guanosine Diphosphate/metabolism ; *Peptide Elongation Factor 1/metabolism ; }, abstract = {The archaeal ancestor of eukaryotes apparently belonged to the phylum Asgardarchaeota, but the ecology and evolution of Asgard archaea are poorly understood. The optimal GDP-binding temperature of a translation elongation factor (EF-1A or EF-Tu) has been previously shown to correlate with the optimal growth temperature of diverse prokaryotes. Here, we reconstruct ancestral EF-1A sequences and experimentally measure the optimal GDP-binding temperature of EF-1A from ancient and extant Asgard archaea, to infer the evolution of optimal growth temperatures in Asgardarchaeota. Our results suggest that the Asgard ancestor of eukaryotes was a moderate thermophile, with an optimal growth temperature around 53 °C. The origin of eukaryotes appears to coincide with a transition from thermophilic to mesophilic lifestyle during the evolution of Asgard archaea.}, }
@article {pmid38203843, year = {2024}, author = {Cisek, AA and Szymańska, E and Wierzbicka-Rucińska, A and Aleksandrzak-Piekarczyk, T and Cukrowska, B}, title = {Methanogenic Archaea in the Pediatric Inflammatory Bowel Disease in Relation to Disease Type and Activity.}, journal = {International journal of molecular sciences}, volume = {25}, number = {1}, pages = {}, pmid = {38203843}, issn = {1422-0067}, support = {M34/2019//Children's Memorial Health Institute/ ; 2017/25/N/NZ7/02905//National Science Center/ ; }, mesh = {Humans ; Child ; Archaea/genetics ; *Euryarchaeota ; *Inflammatory Bowel Diseases ; *Colitis, Ulcerative ; *Crohn Disease ; Leukocyte L1 Antigen Complex ; }, abstract = {The inflammatory bowel disease (IBD) is associated with gut microbiota dysbiosis; however, studies on methanogens-especially those focused on children-are extremely limited. The aim of this study was to determine the abundance of total methanogenic archaea and their three subgroups: Methanobrevibacter (Mb.) smithii, Methanosphaera (Ms.) stadtmanae, and Methanomassiliicoccales, in the feces of children with both active and inactive Crohn's disease (CD) and ulcerative colitis (UC). The results of a quantitative real-time PCR were cross-referenced with the disease type (CD vs. UC) and activity assessed with the use of Pediatric Crohn's Disease Activity Index (PCDAI) and Pediatric Ulcerative Colitis Activity Index (PUCAI) indices, and fecal calprotectin (FCP) concentration, and compared with controls. There was a significant decrease in the number of total methanogens in CD and UC compared to controls. The prevalence of total methanogens was also lower in UC compared to controls. Furthermore, patients from the inactive UC group were colonized by a lower number of Mb. smithii, and demonstrated the most pronounced positive correlation between the number of Ms. stadtmanae and the FCP concentration. Our results demonstrate that gut methanogens are related to the type and activity of pediatric IBD.}, }
@article {pmid38197785, year = {2024}, author = {Hu, Y and Ma, X and Li, XX and Tan, S and Cheng, M and Hou, J and Cui, HL}, title = {Halomicrococcus gelatinilyticus sp. nov. and Halosimplex aquaticum sp. nov., halophilic archaea isolated from saline soil and an inland solar saltern.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {1}, pages = {}, doi = {10.1099/ijsem.0.006231}, pmid = {38197785}, issn = {1466-5034}, mesh = {RNA, Ribosomal, 16S/genetics ; Phylogeny ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Base Composition ; Fatty Acids/chemistry ; *Halobacteriaceae/genetics ; *Halobacteriales ; Phosphatidylglycerols ; Soil ; Sulfates ; }, abstract = {Two extremely halophilic archaeal strains, GSLN9[T] and XZYJT29[T], were isolated from the saline soil in different regions of western China. Both strains GSLN9[T] and XZYJT29[T] have two 16S rRNA genes with similarities of 95.1 and 94.8 %, respectively. Strain GSLN9[T] was mostly related to the genus Halomicrococcus based on 16S rRNA (showing 91.0-96.0 % identities) and rpoB' genes (showing 92.0 % identity). Strain XZYJT29[T] showed 92.1-97.6 % (16S rRNA gene) and 91.4-93.1 % (rpoB' gene) sequence similarities to its relatives in the genus Halosimplex, respectively. The polar lipid profile of strain GSLN9[T] included phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulphate (PGS), sulphated mannosyl glucosyl diether (S-DGD-1) and sulphated galactosyl mannosyl glucosyl diether (S-TGD-1), mostly similar to that of Halomicrococcus hydrotolerans H22[T]. PA, PG, PGP-Me, S-DGD-1 (S-DGD-PA), S2-DGD, S-TGD-1 and an unidentified glycolipid were detected in strain XZYJT29[T]; this polar lipid composition is similar to those of members of the genus Halosimplex. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between these two strains and their relatives of the genera Halomicrococcus and Halosimplex were no more than 82, 27 and 80 %, respectively, much lower than the thresholds for species demarcation. Other phenotypic characterization results indicated that strains GSLN9[T] and XZYJT29[T] can be differentiated from the current species of the genera Halomicrococcus and Halosimplex, respectively. These results revealed that strains GSLN9[T] (=CGMCC 1.15215[T]=JCM 30842[T]) and XZYJT29[T] (=CGMCC 1.15828[T]=JCM 31853[T]) represent novel species of Halomicrococcus and Halosimplex, for which the names Halomicrococcus gelatinilyticus sp. nov. and Halosimplex aquaticum sp. nov. are proposed.}, }
@article {pmid38194256, year = {2024}, author = {Li, XX and Tan, S and Cheng, M and Hu, Y and Ma, X and Hou, J and Cui, HL}, title = {Halospeciosus flavus gen. nov., sp. nov. and Haladaptatus caseinilyticus sp. nov., halophilic archaea isolated from saline soil of an inland solar saltern and offshore sediment.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {1}, pages = {}, doi = {10.1099/ijsem.0.006220}, pmid = {38194256}, issn = {1466-5034}, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Base Composition ; Fatty Acids/chemistry ; *Halobacteriaceae/genetics ; *Halobacteriales ; Phosphatidylglycerols ; }, abstract = {Two novel halophilic archaeal strains (XZGYJ-43[T] and ZJ1[T]) were isolated from Mangkang ancient solar saltern (Tibet, PR China) and Zhujiang river inlet (Guangdong, PR China), respectively. The comparison of the 16S rRNA gene sequences revealed that strain XZGYJ-43[T] is related to the current species of the family Halobacteriaceae (89.2-91.7% similarity) and strain ZJ1[T] showed 94.7-98.3% similarity to the current species of the genus Haladaptatus. Phylogenetic analyses based on 16S rRNA genes, rpoB' genes and genomes indicated that strain XZGYJ-43[T] is separate from the related genera, Halocalculus, Salarchaeum and Halarchaeum of the family Halobacteriaceae, and strain ZJ1[T] tightly clusters with the current species of the genus Haladaptatus. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between strain XZGYJ-43[T] and the current species of the family Halobacteriaceae were 71-75, 20-25 and 59-68 %, and these values between strain ZJ1[T] and the current species of the genus Haladaptatus were 77-81, 27-32 and 76-82 %, respectively, clearly below the thresholds for prokaryotic species demarcation. These two strains could be distinguished from their relatives according to differential phenotypic characteristics. The major polar lipids of strain XZGYJ-43[T] were phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), mannosyl glucosyl diether (DGD-1; DGD-PA) and sulphated mannosyl glucosyl diether (S-DGD-1; S-DGD-PA), and those of strain ZJ1[T] were PA, PG, PGP-Me, DGD-PA, S-DGD-1 (S-DGD-PA) and sulphated galactosyl mannosyl glucosyl diether. Based on phenotypic, phylogenetic and genomic data, strain XZGYJ-43[T] (=CGMCC 1.13890[T]=JCM 33735[T]) represents a novel species of a new genus within the family Halobacteriaceae, and strain ZJ1[T] (=CGMCC 1.18785[T]=JCM 34917[T]) represents a novel species of the genus Haladaptatus, for which the names Halospeciosus flavus gen. nov., sp. nov. and Haladaptatus caseinilyticus sp. nov. are proposed, respectively.}, }
@article {pmid38189270, year = {2024}, author = {Makarova, KS and Zhang, C and Wolf, YI and Karamycheva, S and Whitaker, RJ and Koonin, EV}, title = {Computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaea.}, journal = {mBio}, volume = {15}, number = {2}, pages = {e0309223}, pmid = {38189270}, issn = {2150-7511}, support = {//HHS | National Institutes of Health (NIH)/ ; 1656869//National Science Foundation (NSF)/ ; GBMF9195//Gordon and Betty Moore Foundation (GBMF)/ ; 1656869//National Science Foundation (NSF)/ ; GBMF9195//Gordon and Betty Moore Foundation (GBMF)/ ; }, mesh = {*Archaea/genetics/metabolism ; Genes, Essential ; Genome, Archaeal ; Genomics ; Phenotype ; *Archaeal Proteins/genetics/metabolism ; }, abstract = {The identification of microbial genes essential for survival as those with lethal knockout phenotype (LKP) is a common strategy for functional interrogation of genomes. However, interpretation of the LKP is complicated because a substantial fraction of the genes with this phenotype remains poorly functionally characterized. Furthermore, many genes can exhibit LKP not because their products perform essential cellular functions but because their knockout activates the toxicity of other genes (conditionally essential genes). We analyzed the sets of LKP genes for two archaea, Methanococcus maripaludis and Sulfolobus islandicus, using a variety of computational approaches aiming to differentiate between essential and conditionally essential genes and to predict at least a general function for as many of the proteins encoded by these genes as possible. This analysis allowed us to predict the functions of several LKP genes including previously uncharacterized subunit of the GINS protein complex with an essential function in genome replication and of the KEOPS complex that is responsible for an essential tRNA modification as well as GRP protease implicated in protein quality control. Additionally, several novel antitoxins (conditionally essential genes) were predicted, and this prediction was experimentally validated by showing that the deletion of these genes together with the adjacent genes apparently encoding the cognate toxins caused no growth defect. We applied principal component analysis based on sequence and comparative genomic features showing that this approach can separate essential genes from conditionally essential ones and used it to predict essential genes in other archaeal genomes.IMPORTANCEOnly a relatively small fraction of the genes in any bacterium or archaeon is essential for survival as demonstrated by the lethal effect of their disruption. The identification of essential genes and their functions is crucial for understanding fundamental cell biology. However, many of the genes with a lethal knockout phenotype remain poorly functionally characterized, and furthermore, many genes can exhibit this phenotype not because their products perform essential cellular functions but because their knockout activates the toxicity of other genes. We applied state-of-the-art computational methods to predict the functions of a number of uncharacterized genes with the lethal knockout phenotype in two archaeal species and developed a computational approach to predict genes involved in essential functions. These findings advance the current understanding of key functionalities of archaeal cells.}, }
@article {pmid38188570, year = {2023}, author = {Hanišáková, N and Vítězová, M and Vítěz, T and Kushkevych, I and Kotrlová, E and Novák, D and Lochman, J and Zavada, R}, title = {Microbiological insight into various underground gas storages in Vienna Basin focusing on methanogenic Archaea.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1293506}, pmid = {38188570}, issn = {1664-302X}, abstract = {In recent years, there has been a growing interest in extending the potential of underground gas storage (UGS) facilities to hydrogen and carbon dioxide storage. However, this transition to hydrogen storage raises concerns regarding potential microbial reactions, which could convert hydrogen into methane. It is crucial to gain a comprehensive understanding of the microbial communities within any UGS facilities designated for hydrogen storage. In this study, underground water samples and water samples from surface technologies from 7 different UGS objects located in the Vienna Basin were studied using both molecular biology methods and cultivation methods. Results from 16S rRNA sequencing revealed that the proportion of archaea in the groundwater samples ranged from 20 to 58%, with methanogens being the predominant. Some water samples collected from surface technologies contained up to 87% of methanogens. Various species of methanogens were isolated from individual wells, including Methanobacterium sp., Methanocalculus sp., Methanolobus sp. or Methanosarcina sp. We also examined water samples for the presence of sulfate-reducing bacteria known to be involved in microbially induced corrosion and identified species of the genus Desulfovibrio in the samples. In the second part of our study, we contextualized our data by comparing it to available sequencing data from terrestrial subsurface environments worldwide. This allowed us to discern patterns and correlations between different types of underground samples based on environmental conditions. Our findings reveal presence of methanogens in all analyzed groups of underground samples, which suggests the possibility of unintended microbial hydrogen-to-methane conversion and the associated financial losses. Nevertheless, the prevalence of methanogens in our results also highlights the potential of the UGS environment, which can be effectively leveraged as a bioreactor for the conversion of hydrogen into methane, particularly in the context of Power-to-Methane technology.}, }
@article {pmid38185001, year = {2024}, author = {Mao, Y and Wu, J and Yang, R and Ma, Y and Ye, J and Zhong, J and Deng, N and He, X and Hong, Y}, title = {Novel database for accA gene revealed a vertical variability pattern of autotrophic carbon fixation potential of ammonia oxidizing archaea in a permeable subterranean estuary.}, journal = {Marine environmental research}, volume = {194}, number = {}, pages = {106342}, doi = {10.1016/j.marenvres.2024.106342}, pmid = {38185001}, issn = {1879-0291}, mesh = {*Archaea/genetics ; *Ammonia/metabolism ; Estuaries ; RNA, Ribosomal, 16S/genetics ; Oxidation-Reduction ; Carbon Cycle ; Phylogeny ; }, abstract = {The autotrophic carbon fixation pathway of ammonia-oxidizing archaea (AOA) was the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle, of which the acetyl-CoA carboxylase α-submit (accA) gene is widely recognized as the indicator. To date, there is no reference database or suitable cut-off value for operational taxonomic unit (OTU) clustering to analyze the diversity of AOA based on the accA gene. In this study, a reference database with 489 sequences was constructed, all the accA gene sequences was obtained from the AOA enrichment culture, pure culture and environmental samples. Additionally, the 79% was determined as the cut-off value for OTU clustering by comparing the similarity between the accA gene and the 16S rRNA gene. The developed method was verified by analyzing samples from the subterranean estuary and a vertical variation pattern of autotrophic carbon fixation potential of AOA was revealed. This study provided an effective method to analyze the diversity and autotrophic carbon fixation potential of AOA based on accA gene.}, }
@article {pmid38181064, year = {2024}, author = {Zhao, H and Wu, H and Guseman, A and Abeykoon, D and Camara, CM and Dalal, Y and Fushman, D and Papoian, GA}, title = {The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea.}, journal = {PLoS computational biology}, volume = {20}, number = {1}, pages = {e1011721}, pmid = {38181064}, issn = {1553-7358}, support = {R01 GM065334/GM/NIGMS NIH HHS/United States ; U54 CA272220/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Histones/chemistry ; *Archaea/genetics ; Molecular Dynamics Simulation ; DNA ; Eukaryota/genetics ; Protein Folding ; }, abstract = {Histones compact and store DNA in both Eukarya and Archaea, forming heterodimers in Eukarya and homodimers in Archaea. Despite this, the folding mechanism of histones across species remains unclear. Our study addresses this gap by investigating 11 types of histone and histone-like proteins across humans, Drosophila, and Archaea through multiscale molecular dynamics (MD) simulations, complemented by NMR and circular dichroism experiments. We confirm and elaborate on the widely applied "folding upon binding" mechanism of histone dimeric proteins and report a new alternative conformation, namely, the inverted non-native dimer, which may be a thermodynamically metastable configuration. Protein sequence analysis indicated that the inverted conformation arises from the hidden ancestral head-tail sequence symmetry underlying all histone proteins, which is congruent with the previously proposed histone evolution hypotheses. Finally, to explore the potential formations of homodimers in Eukarya, we utilized MD-based AWSEM and AI-based AlphaFold-Multimer models to predict their structures and conducted extensive all-atom MD simulations to examine their respective structural stabilities. Our results suggest that eukaryotic histones may also form stable homodimers, whereas their disordered tails bring significant structural asymmetry and tip the balance towards the formation of commonly observed heterotypic dimers.}, }
@article {pmid38179456, year = {2023}, author = {Medina-Chávez, NO and Torres-Cerda, A and Chacón, JM and Harcombe, WR and De la Torre-Zavala, S and Travisano, M}, title = {Disentangling a metabolic cross-feeding in a halophilic archaea-bacteria consortium.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1276438}, pmid = {38179456}, issn = {1664-302X}, abstract = {Microbial syntrophy, a cooperative metabolic interaction among prokaryotes, serves a critical role in shaping communities, due to the auxotrophic nature of many microorganisms. Syntrophy played a key role in the evolution of life, including the hypothesized origin of eukaryotes. In a recent exploration of the microbial mats within the exceptional and uniquely extreme Cuatro Cienegas Basin (CCB), a halophilic isolate, designated as AD140, emerged as a standout due to its distinct growth pattern. Subsequent genome sequencing revealed AD140 to be a co-culture of a halophilic archaeon from the Halorubrum genus and a marine halophilic bacterium, Marinococcus luteus, both occupying the same ecological niche. This intriguing coexistence hints at an early-stage symbiotic relationship that thrives on adaptability. By delving into their metabolic interdependence through genomic analysis, this study aims to uncover shared characteristics that enhance their symbiotic association, offering insights into the evolution of halophilic microorganisms and their remarkable adaptations to high-salinity environments.}, }
@article {pmid38172371, year = {2024}, author = {Guerra, A}, title = {Human associated Archaea: a neglected microbiome worth investigating.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {40}, number = {2}, pages = {60}, pmid = {38172371}, issn = {1573-0972}, mesh = {Animals ; Female ; Humans ; Pregnancy ; *Archaea ; Colostrum/microbiology ; Infectious Disease Transmission, Vertical ; *Microbiota ; Milk ; Infant ; Infant, Newborn ; }, abstract = {The majority of research in the field of human microbiota has predominantly focused on bacterial and fungal communities. Conversely, the human archaeome has received scant attention and remains poorly studied, despite its potential role in human diseases. Archaea have the capability to colonize various human body sites, including the gastrointestinal tract, skin, vagina, breast milk, colostrum, urinary tract, lungs, nasal and oral cavities. This colonization can occur through vertical transmission, facilitated by the transfer of breast milk or colostrum from mother to child, as well as through the consumption of dairy products, organic produce, salty foods, and fermented items. The involvement of these microorganisms in diseases, such as periodontitis, might be attributed to their production of toxic compounds and the detoxification of growth inhibitors for pathogens. However, the precise mechanisms through which these contributions occur remain incompletely understood, necessitating further studies to assess their impact on human health.}, }
@article {pmid38138100, year = {2023}, author = {Hinkle, JE and Mara, P and Beaudoin, DJ and Edgcomb, VP and Teske, AP}, title = {A PCR-Based Survey of Methane-Cycling Archaea in Methane-Soaked Subsurface Sediments of Guaymas Basin, Gulf of California.}, journal = {Microorganisms}, volume = {11}, number = {12}, pages = {}, pmid = {38138100}, issn = {2076-2607}, support = {512580/NASA/NASA/United States ; }, abstract = {The Guaymas Basin in the Gulf of California is characterized by active seafloor spreading, the rapid deposition of organic-rich sediments, steep geothermal gradients, and abundant methane of mixed thermogenic and microbial origin. Subsurface sediment samples from eight drilling sites with distinct geochemical and thermal profiles were selected for DNA extraction and PCR amplification to explore the diversity of methane-cycling archaea in the Guaymas Basin subsurface. We performed PCR amplifications with general (mcrIRD), and ANME-1 specific primers that target the alpha (α) subunit of methyl coenzyme M reductase (mcrA). Diverse ANME-1 lineages associated with anaerobic methane oxidation were detected in seven out of the eight drilling sites, preferentially around the methane-sulfate interface, and in several cases, showed preferences for specific sampling sites. Phylogenetically, most ANME-1 sequences from the Guaymas Basin subsurface were related to marine mud volcanoes, seep sites, and the shallow marine subsurface. The most frequently recovered methanogenic phylotypes were closely affiliated with the hyperthermophilic Methanocaldococcaceae, and found at the hydrothermally influenced Ringvent site. The coolest drilling site, in the northern axial trough of Guaymas Basin, yielded the greatest diversity in methanogen lineages. Our survey indicates the potential for extensive microbial methane cycling within subsurface sediments of Guaymas Basin.}, }
@article {pmid38138015, year = {2023}, author = {Wu, X and Zhang, W and Liu, G and Chen, T and Li, Z}, title = {Changes in Diversity and Abundance of Ammonia-Oxidizing Archaea and Bacteria along a Glacier Retreating Chronosequence in the Tianshan Mountains, China.}, journal = {Microorganisms}, volume = {11}, number = {12}, pages = {}, pmid = {38138015}, issn = {2076-2607}, abstract = {Glaciers retreating due to global warming create important new habitats, particularly suitable for studying ecosystem development where nitrogen is a limiting factor. Nitrogen availability mainly results from microbial decomposition and transformation processes, including nitrification. AOA and AOB perform the first and rate-limiting step of nitrification. Investigating the abundance and diversity of AOA and AOB is essential for understanding early ecosystem development. The dynamics of AOA and AOB community structure along a soil chronosequence in Tianshan No. 1 Glacier foreland were analyzed using qPCR and clone library methods. The results consistently showed low quantities of both AOA and AOB throughout the chronosequence. Initially, the copy numbers of AOB were higher than those of AOA, but they decreased in later stages. The AOB community was dominated by "Nitrosospira cluster ME", while the AOA community was dominated by "the soil and sediment 1". Both communities were potentially connected to supra- and subglacial microbial communities during early stages. Correlation analysis revealed a significant positive correlation between the ratios of AOA and AOB with soil ammonium and total nitrogen levels. These results suggest that variations in abundance and diversity of AOA and AOB along the chronosequences were influenced by ammonium availability during glacier retreat.}, }
@article {pmid38135695, year = {2023}, author = {Trouche, B and Schauberger, C and Bouderka, F and Auguet, JC and Belser, C and Poulain, J and Thamdrup, B and Wincker, P and Arnaud-Haond, S and Glud, RN and Maignien, L}, title = {Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {133}, pmid = {38135695}, issn = {2730-6151}, abstract = {Ammonia-oxidizing archaea of the phylum Thaumarchaeota play a central role in the biogeochemical cycling of nitrogen in benthic sediments, at the interface between pelagic and subsurface ecosystems. However, our understanding of their niche separation and of the processes controlling their population structure in hadal and abyssal surface sediments is still limited. Here, we reconstructed 47 AOA metagenome-assembled genomes (MAGs) from surface sediments of the Atacama and Kermadec trench systems. They formed deep-sea-specific groups within the family Nitrosopumilaceae and were assigned to six amoA gene-based clades. MAGs from different clades had distinct distribution patterns along oxygen-ammonium counter gradients in surface sediments. At the species level, MAGs thus seemed to form different ecotypes and follow deterministic niche-based distributions. In contrast, intraspecific population structure, defined by patterns of Single Nucleotide Variants (SNV), seemed to reflect more complex contributions of both deterministic and stochastic processes. Firstly, the bathymetric range had a strong effect on population structure, with distinct populations in abyssal plains and hadal trenches. Then, hadal populations were clearly separated by trench system, suggesting a strong isolation-by-topography effect, whereas abyssal populations were rather controlled by sediment depth or geographic distances, depending on the clade considered. Interestingly, genetic variability between samples was lowest in sediment layers where the mean MAG coverage was highest, highlighting the importance of selective pressure linked with each AOA clade's ecological niche. Overall, our results show that deep-sea AOA genome distributions seem to follow both deterministic and stochastic processes, depending on the genomic variability scale considered.}, }
@article {pmid38132325, year = {2023}, author = {Rafiq, M and Hassan, N and Rehman, M and Hayat, M and Nadeem, G and Hassan, F and Iqbal, N and Ali, H and Zada, S and Kang, Y and Sajjad, W and Jamal, M}, title = {Challenges and Approaches of Culturing the Unculturable Archaea.}, journal = {Biology}, volume = {12}, number = {12}, pages = {}, pmid = {38132325}, issn = {2079-7737}, abstract = {Since Carl Woese's discovery of archaea as a third domain of life, numerous archaeal species have been discovered, yet archaeal diversity is poorly characterized. Culturing archaea is complicated, but several queries about archaeal cell biology, evolution, physiology, and diversity need to be solved by culturing and culture-dependent techniques. Increasing interest in demand for innovative culturing methods has led to various technological and methodological advances. The current review explains frequent hurdles hindering uncultured archaea isolation and discusses features for more archaeal cultivation. This review also discusses successful strategies and available media for archaeal culturing, which might be helpful for future culturing practices.}, }
@article {pmid38098882, year = {2023}, author = {Xiang, Y and Zhou, T and Deng, S and Shao, Z and Liu, Y and He, Q and Chai, H}, title = {Nitrite improved nitrification efficiency and enriched ammonia-oxidizing archaea and bacteria in the simultaneous nitrification and denitrification process.}, journal = {Water research X}, volume = {21}, number = {}, pages = {100204}, pmid = {38098882}, issn = {2589-9147}, abstract = {Simultaneous nitrification and denitrification (SND) is effective and energy-saving for wastewater treatment. As an inevitable intermediate product in the SND process, nitrite affects the efficiency of ammonia oxidation and the composition of nitrifiers. To investigate the impact of nitrite on ammonia oxidation efficiency, two reactors performing SND were respectively operated without nitrite (R1 as control) and with 20 mg N/L nitrite addition (R2 as experimental). The total nitrogen removal efficiency was 74.5% in R1 while 99.0% in R2. With nitrite addition (i.e., 20 mg N/L), the ammonia removal rate in R2 increased to 4.5 times of that in R1. The ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) contributed to respective around 46.9% and 41.8% ammonia removal in R2 based on the results of experiments with specific inhibitors. The number of respective AOA and AOB ammonia monooxygenase gene (amoA) copies increased by 280 and 30 times due to nitrite addition, according to the qPCR results. The high-throughput sequencing results illustrated the increase of dominant AOB species from 0.40% in R1 to 1.59% in R2 and the phylogenetic tree analysis revealed a close link to Nitrosospira multiformis. These results indicated that the ammonia removal efficiency was improved and AOA/AOB were enriched by nitrite addition. The specific nitrite reductases in AOA and AOB boosted the adaptation of nitrite addition. This study demonstrated the positive impacts of nitrite addition on the ammonia removal efficiency and rate in the SND process.}, }
@article {pmid38075885, year = {2023}, author = {Boswinkle, K and Dinh, TA and Allen, KD}, title = {Biochemical and genetic studies define the functions of methylthiotransferases in methanogenic and methanotrophic archaea.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1304671}, pmid = {38075885}, issn = {1664-302X}, abstract = {Methylthiotransferases (MTTases) are radical S-adenosylmethionine (SAM) enzymes that catalyze the addition of a methylthio (-SCH3) group to an unreactive carbon center. These enzymes are responsible for the production of 2-methylthioadenosine (ms[2]A) derivatives found at position A37 of select tRNAs in all domains of life. Additionally, some bacteria contain the RimO MTTase that catalyzes the methylthiolation of the S12 ribosomal protein. Although the functions of MTTases in bacteria and eukaryotes have been established via detailed genetic and biochemical studies, MTTases from the archaeal domain of life are understudied and the substrate specificity determinants of MTTases remain unclear. Here, we report the in vitro enzymatic activities of an MTTase (C4B56_06395) from a thermophilic Ca. Methanophagales anaerobic methanotroph (ANME) as well as the MTTase from a hyperthermophilic methanogen - MJ0867 from Methanocaldococcus jannaschii. Both enzymes catalyze the methylthiolation of N[6]-threonylcarbamoyladenosine (t[6]A) and N[6]-hydroxynorvalylcarbamoyladenosine (hn[6]A) residues to produce 2-methylthio-N[6]-threonylcarbamoyladenosine (ms[2]t[6]A) and 2-methylthio-N[6]-hydroxynorvalylcarbamoyladenosine (ms[2]hn[6]A), respectively. To further assess the function of archaeal MTTases, we analyzed select tRNA modifications in a model methanogen - Methanosarcina acetivorans - and generated a deletion of the MTTase-encoding gene (MA1153). We found that M. acetivorans produces ms[2]hn[6]A in exponential phase of growth, but does not produce ms[2]t[6]A in detectable amounts. Upon deletion of MA1153, the ms[2]A modification was absent, thus confirming the function of MtaB-family MTTases in generating ms[2]hn[6]A modified nucleosides in select tRNAs.}, }
@article {pmid38062210, year = {2024}, author = {Zhang, J and Zhou, M and Shi, F and Lei, Z and Wang, Y and Hu, M and Zhao, J}, title = {The abundance of comammox bacteria was higher than that of ammonia-oxidizing archaea and bacteria in rhizosphere of emergent macrophytes in a typical shallow lake riparian.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {1}, pages = {67-79}, pmid = {38062210}, issn = {1618-1905}, support = {92047204//National Natural Science Foundation of China/ ; 42177383//National Natural Science Foundation of China/ ; U1802241//National Natural Science Foundation of China/ ; U2040211//National Natural Science Foundation of China/ ; 51679258//National Natural Science Foundation of China/ ; SKL2020TS07//the State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin/ ; }, mesh = {*Archaea/genetics ; *Ammonia ; Rhizosphere ; Ecosystem ; Lakes/microbiology ; Oxidation-Reduction ; Phylogeny ; Bacteria ; Soil Microbiology ; }, abstract = {Complete ammonia oxidation (comammox) bacteria can complete the whole nitrification process independently, which not only challenges the classical two-step nitrification theory but also updates long-held perspective of microbial ecological relationship in nitrification process. Although comammox bacteria have been found in many ecosystems in recent years, there is still a lack of research on the comammox process in rhizosphere of emergent macrophytes in lakeshore zone. Sediment samples were collected in this study from rhizosphere, far-rhizosphere, and non-rhizosphere of emergent macrophytes along the shore of Lake Liangzi, a shallow lake. The diversity of comammox bacteria and amoA gene abundance of comammox bacteria, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in these samples were measured. The results showed that comammox bacteria widely existed in the rhizosphere of emergent macrophytes and fell into clade A.1, clade A.2, and clade B, and clade A was the predominant community in all sampling sites. The abundance of comammox amoA gene (6.52 × 10[6]-2.45 × 10[8] copies g[-1] dry sediment) was higher than that of AOB amoA gene (6.58 × 10[4]-3.58 × 10[6] copies g[-1] dry sediment), and four orders of magnitude higher than that of AOA amoA gene (7.24 × 10[2]-6.89 × 10[3] copies g[-1] dry sediment), suggesting that the rhizosphere of emergent macrophytes is more favorable for the growth of comammox bacteria than that of AOB and AOA. Our study indicated that the comammox bacteria may play important roles in ammonia-oxidizing processes in all different rhizosphere regions.}, }
@article {pmid38047693, year = {2024}, author = {Qu, L and Li, M and Gong, F and He, L and Li, M and Zhang, C and Yin, K and Xie, W}, title = {Oxygen-driven divergence of marine group II archaea reflected by transitions of superoxide dismutases.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0203323}, pmid = {38047693}, issn = {2165-0497}, support = {92051117, 41776137//MOST | National Natural Science Foundation of China (NSFC)/ ; 91851210//MOST | National Natural Science Foundation of China (NSFC)/ ; 2021B1515120080//GDSTC | Basic and Applied Basic Research Foundation of Guangdong Province ()/ ; 2021B1515120080//GDSTC | Basic and Applied Basic Research Foundation of Guangdong Province ()/ ; ZDSYS201802081843490//Shenzhen Municipal Science and Technology Innovation Council | Shenzhen Key Laboratory Fund ()/ ; }, mesh = {*Archaea/genetics ; Reactive Oxygen Species ; *Oxygen ; Superoxide Dismutase/genetics ; Superoxides ; }, abstract = {Reactive oxygen species (ROS), including superoxide anion, is a series of substances that cause oxidative stress for all organisms. Marine group II (MGII) archaea are mainly live in the surface seawater and exposed to considerable ROS. Therefore, it is important to understand the antioxidant capacity of MGII. Our research found that Fe/Mn- superoxide dismutase (Fe/MnSOD) may be more suitable for MGII to resist oxidative damage, and the changes in oxygen concentrations and SOD metallic cofactors play an important role in the selection of SOD by the 17 clades of MGII, which in turn affects the species differentiation of MGII. Overall, this study provides insight into the co-evolutionary history of these uncultivated marine archaea with the earth system.}, }
@article {pmid38042190, year = {2024}, author = {Wu, Y and Zhou, S and Li, Y and Niu, L and Wang, L}, title = {Climate and local environment co-mediate the taxonomic and functional diversity of bacteria and archaea in the Qinghai-Tibet Plateau rivers.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {168968}, doi = {10.1016/j.scitotenv.2023.168968}, pmid = {38042190}, issn = {1879-1026}, mesh = {*Archaea ; Tibet ; Ecosystem ; Rivers/microbiology ; Bacteria ; Soil ; *Microbiota ; Water ; }, abstract = {Understanding the environmental response patterns of riverine microbiota is essential for predicting the potential impact of future environmental change on river ecosystems. Vulnerable plateau ecosystems are particularly sensitive to climate and local environmental changes, however, the environmental response patterns of the taxonomic and functional diversity of riverine microbiota remain unclear. Here, we conducted a systematic investigation of the taxonomic and functional diversity of bacteria and archaea from riparian soils, sediments, and water across the elevation of 1800- 4800 m in the Qinghai-Tibet Plateau rivers. We found that within the elevation range of 1800 to 3800 m, riparian soils and sediments exhibited similarities and stabilities in microbial taxonomic and functional diversity, and water microbiomes were more sensitive with great fluctuations in microbial diversity. Beyond the elevation of 3800 m, microbial diversity declined across all riverine matrixes. Local environmental conditions can influence the sensitivity of microbiomes to climate change. The combination of critical climate and local environmental factors, including total nitrogen, total organic carbon, as well as climate variables associated with temperature and precipitation, provided better explanations for microbial diversity than single-factor analyses. Under the extremely adverse scenario of high greenhouse gas emission concentrations (SSP585), we anticipate that by the end of this century, the bacterial, archaeal, and microbial functional diversity across the river network of the Yangtze and Yellow source basin would potentially change by -16.9- 5.2 %, -16.1- 5.7 %, and -9.3- 6.4 %, respectively. Overall, climate and local environments jointly shaped the microbial diversity in plateau river ecosystems, and water microbiomes would provide early signs of environmental changes. Our study provides effective theoretical foundations for the conservation of river biodiversity and functional stability under environmental changes.}, }
@article {pmid38041127, year = {2023}, author = {Diaz, GR and Gaire, TN and Ferm, P and Case, L and Caixeta, LS and Goldsmith, TJ and Armstrong, J and Noyes, NR}, title = {Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {61}, pmid = {38041127}, issn = {2524-4671}, support = {Grantee No. GNT-20212290//Fulbright Scholarship/ ; Contract No. 085-2020-FONDECYT//Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica from Peru/ ; MnDRIVE Graduate Student Professional Development award//MnDRIVE Global Food Ventures Program/ ; }, abstract = {BACKGROUND: Beef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key role of the rumen microbiome on productive traits of beef cattle, the effect of castration timing and weaning strategy on this microbial community has not been formally described. We assessed the effect of four castration time windows (at birth, turnout, pre-weaning and weaning) and two weaning strategies (fence-line and truck transportation) on the rumen microbiome in a randomized controlled study with 32 male calves across 3 collection days (i.e., time points). Ruminal fluid samples were submitted to shotgun metagenomic sequencing and changes in the taxonomic (microbiota) and functional profile (metagenome) of the rumen microbiome were described.<br><br>RESULTS: Using a comprehensive yet stringent taxonomic classification approach, we identified 10,238 unique taxa classified under 40 bacterial and 7 archaeal phyla across all samples. Castration timing had a limited long-term impact on the rumen microbiota and was not associated with changes in alpha and beta diversity. The interaction of collection day and weaning strategy was associated with changes in the rumen microbiota, which experienced a significant decrease in alpha diversity and shifts in beta diversity within 48&#xa0;h post-weaning, especially in calves abruptly weaned by truck transportation. Calves weaned using a fence-line weaning strategy had lower relative abundance of Bacteroides, Lachnospira, Fibrobacter and Ruminococcus genera compared to calves weaned by truck transportation. Some genes involved in the hydrogenotrophic methanogenesis pathway (fwdB and fwdF) had higher relative abundance in fence-line-weaned calves post-weaning. The antimicrobial resistance gene tetW consistently represented more than 50% of the resistome across time, weaning and castration groups, without significant changes in relative abundance.<br><br>CONCLUSIONS: Within the context of this study, castration timing had limited long-term effects on the rumen microbiota, while weaning strategy had short-term effects on the rumen microbiota and methane-associated metagenome, but not on the rumen resistome.}, }
@article {pmid38033561, year = {2023}, author = {Protasov, E and Nonoh, JO and Kästle Silva, JM and Mies, US and Hervé, V and Dietrich, C and Lang, K and Mikulski, L and Platt, K and Poehlein, A and Köhler-Ramm, T and Miambi, E and Boga, HI and Feldewert, C and Ngugi, DK and Plarre, R and Sillam-Dussès, D and Šobotník, J and Daniel, R and Brune, A}, title = {Diversity and taxonomic revision of methanogens and other archaea in the intestinal tract of terrestrial arthropods.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1281628}, pmid = {38033561}, issn = {1664-302X}, abstract = {Methane emission by terrestrial invertebrates is restricted to millipedes, termites, cockroaches, and scarab beetles. The arthropod-associated archaea known to date belong to the orders Methanobacteriales, Methanomassiliicoccales, Methanomicrobiales, and Methanosarcinales, and in a few cases also to non-methanogenic Nitrososphaerales and Bathyarchaeales. However, all major host groups are severely undersampled, and the taxonomy of existing lineages is not well developed. Full-length 16S rRNA gene sequences and genomes of arthropod-associated archaea are scarce, reference databases lack resolution, and the names of many taxa are either not validly published or under-classified and require revision. Here, we investigated the diversity of archaea in a wide range of methane-emitting arthropods, combining phylogenomic analysis of isolates and metagenome-assembled genomes (MAGs) with amplicon sequencing of full-length 16S rRNA genes. Our results allowed us to describe numerous new species in hitherto undescribed taxa among the orders Methanobacteriales (Methanacia, Methanarmilla, Methanobaculum, Methanobinarius, Methanocatella, Methanoflexus, Methanorudis, and Methanovirga, all gen. nova), Methanomicrobiales (Methanofilum and Methanorbis, both gen. nova), Methanosarcinales (Methanofrustulum and Methanolapillus, both gen. nova), Methanomassiliicoccales (Methanomethylophilaceae fam. nov., Methanarcanum, Methanogranum, Methanomethylophilus, Methanomicula, Methanoplasma, Methanoprimaticola, all gen. nova), and the new family Bathycorpusculaceae (Bathycorpusculum gen. nov.). Reclassification of amplicon libraries from this and previous studies using this new taxonomic framework revealed that arthropods harbor only CO2 and methyl-reducing hydrogenotrophic methanogens. Numerous genus-level lineages appear to be present exclusively in arthropods, suggesting long evolutionary trajectories with their termite, cockroach, and millipede hosts, and a radiation into various microhabitats and ecological niches provided by their digestive tracts (e.g., hindgut compartments, gut wall, or anaerobic protists). The distribution patterns among the different host groups are often complex, indicating a mixed mode of transmission and a parallel evolution of invertebrate and vertebrate-associated lineages.}, }
@article {pmid38029671, year = {2024}, author = {Sun, F and Wang, Y and Wang, Y and Sun, C and Cheng, H and Wu, M}, title = {Insights into the spatial distributions of bacteria, archaea, ammonia-oxidizing bacteria and archaea communities in sediments of Daya Bay, northern South China Sea.}, journal = {Marine pollution bulletin}, volume = {198}, number = {}, pages = {115850}, doi = {10.1016/j.marpolbul.2023.115850}, pmid = {38029671}, issn = {1879-3363}, mesh = {*Archaea/metabolism ; *Ammonia/metabolism ; Bays ; Oxidation-Reduction ; Geologic Sediments/chemistry ; Bacteria/metabolism ; China ; Nitrogen/metabolism ; Phylogeny ; Soil Microbiology ; }, abstract = {Microbe plays an important role in the biogeochemical cycles of the coastal waters. However, comprehensive information about the microbe in the gulf waters is lacking. This study employed high-throughput sequencing and quantitative PCR (qPCR) to investigate the distribution patterns of bacterial, archaeal, ammonia-oxidizing bacterial (AOB), and archaeal (AOA) communities in Daya Bay. Community compositions and principal coordinates analysis (PCoA) exhibited significant spatial characteristics in the diversity and distributions of bacteria, archaea, AOB, and AOA. Notably, various microbial taxa (bacterial, archaeal, AOB, and AOA) exhibited significant differences in different regions, playing crucial roles in nitrogen, sulfur metabolism, and organic carbon mineralization. Canonical correlation analysis (CCA) or redundancy analysis (RDA) indicated that environmental parameters such as temperature, salinity, nitrate, total nitrogen, silicate, and phosphate strongly influenced the distributions of bacterial, archaeal, AOB, and AOA. This study deepens the understanding of the composition and ecological function of prokaryotes in the bay.}, }
@article {pmid38029211, year = {2023}, author = {Huber, M and Vogel, N and Borst, A and Pfeiffer, F and Karamycheva, S and Wolf, YI and Koonin, EV and Soppa, J}, title = {Unidirectional gene pairs in archaea and bacteria require overlaps or very short intergenic distances for translational coupling via termination-reinitiation and often encode subunits of heteromeric complexes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1291523}, pmid = {38029211}, issn = {1664-302X}, abstract = {Genomes of bacteria and archaea contain a much larger fraction of unidirectional (serial) gene pairs than convergent or divergent gene pairs. Many of the unidirectional gene pairs have short overlaps of -4 nt and -1 nt. As shown previously, translation of the genes in overlapping unidirectional gene pairs is tightly coupled. Two alternative models for the fate of the post-termination ribosome predict either that overlaps or very short intergenic distances are essential for translational coupling or that the undissociated post-termination ribosome can scan through long intergenic regions, up to hundreds of nucleotides. We aimed to experimentally resolve the contradiction between the two models by analyzing three native gene pairs from the model archaeon Haloferax volcanii and three native pairs from Escherichia coli. A two reporter gene system was used to quantify the reinitiation frequency, and several stop codons in the upstream gene were introduced to increase the intergenic distances. For all six gene pairs from two species, an extremely strong dependence of the reinitiation efficiency on the intergenic distance was unequivocally demonstrated, such that even short intergenic distances of about 20 nt almost completely abolished translational coupling. Bioinformatic analysis of the intergenic distances in all unidirectional gene pairs in the genomes of H. volcanii and E. coli and in 1,695 prokaryotic species representative of 49 phyla showed that intergenic distances of -4 nt or -1 nt (= short gene overlaps of 4 nt or 1 nt) were by far most common in all these groups of archaea and bacteria. A small set of genes in E. coli, but not in H. volcanii, had intergenic distances of around +10 nt. Our experimental and bioinformatic analyses clearly show that translational coupling requires short gene overlaps, whereas scanning of intergenic regions by the post-termination ribosome occurs rarely, if at all. Short overlaps are enriched among genes that encode subunits of heteromeric complexes, and co-translational complex formation requiring precise subunit stoichiometry likely confers an evolutionary advantage that drove the formation and conservation of overlapping gene pairs during evolution.}, }
@article {pmid38012208, year = {2023}, author = {Mara, P and Geller-McGrath, D and Edgcomb, V and Beaudoin, D and Morono, Y and Teske, A}, title = {Metagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7768}, pmid = {38012208}, issn = {2041-1723}, support = {OCE-2046799//National Science Foundation (NSF)/ ; OCE-1829903//National Science Foundation (NSF)/ ; OCE-2046799//National Science Foundation (NSF)/ ; OCE-1829903//National Science Foundation (NSF)/ ; OCE-1829903//National Science Foundation (NSF)/ ; OCE-2046799//National Science Foundation (NSF)/ ; OCE-1829903//National Science Foundation (NSF)/ ; JP19H00730//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23H00154//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {*Archaea/genetics ; Metagenome/genetics ; Geologic Sediments/chemistry ; Phylogeny ; Bacteria/genetics ; *Crenarchaeota ; RNA, Ribosomal, 16S ; }, abstract = {Previous studies of microbial communities in subseafloor sediments reported that microbial abundance and diversity decrease with sediment depth and age, and microbes dominating at depth tend to be a subset of the local seafloor community. However, the existence of geographically widespread, subsurface-adapted specialists is also possible. Here, we use metagenomic and metatranscriptomic analyses of the hydrothermally heated, sediment layers of Guaymas Basin (Gulf of California, Mexico) to examine the distribution and activity patterns of bacteria and archaea along thermal, geochemical and cell count gradients. We find that the composition and distribution of metagenome-assembled genomes (MAGs), dominated by numerous lineages of Chloroflexota and Thermoproteota, correlate with biogeochemical parameters as long as temperatures remain moderate, but downcore increasing temperatures beyond ca. 45 ºC override other factors. Consistently, MAG size and diversity decrease with increasing temperature, indicating a downcore winnowing of the subsurface biosphere. By contrast, specific archaeal MAGs within the Thermoproteota and Hadarchaeota increase in relative abundance and in recruitment of transcriptome reads towards deeper, hotter sediments, marking the transition towards a specialized deep, hot biosphere.}, }
@article {pmid38007550, year = {2023}, author = {Yang, Y and Liu, H and Zhang, Y and Fang, X and Zhong, X and Lv, J}, title = {Contribution of ammonia-oxidizing archaea and bacteria to nitrogen transformation in a soil fertilized with urea and organic amendments.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {20722}, pmid = {38007550}, issn = {2045-2322}, support = {2452021124//Talent Special Fund Grant from Northwest A&amp;F university/ ; S202210712582//Innovation and entrepreneurship training program for College Students from Northwest A&amp;F university/ ; A314021402-202218//Foundation of the State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau/ ; 42077135//National natural science foundation of China/ ; }, mesh = {Animals ; Swine ; *Archaea ; Ammonia ; Soil ; Urea ; Nitrogen ; Dissolved Organic Matter ; Oxidation-Reduction ; Soil Microbiology ; Phylogeny ; Bacteria/genetics ; *Betaproteobacteria ; Nitrification ; }, abstract = {The contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) is crucial for nitrogen transformation. The effects of four organic amendments (OAs) plus urea on soil nitrogen transformation and the contribution of the ammonia-oxidizing microbial community were investigated using an incubation experiment. The OAs plus urea treatments included pig manure plus urea (PM + U), wheat straw plus urea (WS + U), compost plus urea (CP + U) and improved-compost plus urea (IC + U), while no OAs and urea amended control was noted as CK. The abundance and composition of AOA and AOB were determined using high through-put sequencing. Compared with CK, the OA plus urea treatments significantly enhanced the amount of total mineralized nitrogen released during the incubation process. After incubation, the highest mineralized nitrogen and net nitrogen mineralization was under the PM + U treatment and the lowest was in the WS + U treatment. In conclusion, among all OA plus urea treatments, the microbial biomass nitrogen content was the highest in WS + U treatment and dissolved organic nitrogen content was the highest with the PM + U treatment. Additionally, the abundance of AOB was inhibited in comparison to that of AOA; however, AOB contributed more to nitrification than AOA. Soil NO3[-]-N and dissolved organic nitrogen were the principal components influencing the distribution of AOA and AOB. The result illustrated that the OAs plus urea, especially PM plus urea promoted mineralization to produce more dissolved organic nitrogen and NH4[+]-N, thus accelerating the growth of AOB to strengthen nitrification in soil.}, }
@article {pmid38007076, year = {2024}, author = {Zhang, Z and Bo, L and Wang, S and Li, C and Zhang, X and Xue, B and Yang, X and He, X and Shen, Z and Qiu, Z and Zhao, C and Wang, J}, title = {Multidrug-resistant plasmid RP4 inhibits the nitrogen removal capacity of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and comammox in activated sludge.}, journal = {Environmental research}, volume = {242}, number = {}, pages = {117739}, doi = {10.1016/j.envres.2023.117739}, pmid = {38007076}, issn = {1096-0953}, mesh = {*Archaea/genetics/metabolism ; Sewage/microbiology ; Ammonia ; Nitrogen/metabolism ; Denitrification ; In Situ Hybridization, Fluorescence ; Oxidation-Reduction ; Bacteria/genetics/metabolism ; Plasmids/genetics ; *Betaproteobacteria/genetics/metabolism ; Anti-Bacterial Agents ; Phylogeny ; Soil Microbiology ; }, abstract = {In wastewater treatment plants (WWTPs), ammonia oxidation is primarily carried out by three types of ammonia oxidation microorganisms (AOMs): ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and comammox (CMX). Antibiotic resistance genes (ARGs), which pose an important public health concern, have been identified at every stage of wastewater treatment. However, few studies have focused on the impact of ARGs on ammonia removal performance. Therefore, our study sought to investigate the effect of the representative multidrug-resistant plasmid RP4 on the functional microorganisms involved in ammonia oxidation. Using an inhibitor-based method, we first evaluated the contributions of AOA, AOB, and CMX to ammonia oxidation in activated sludge, which were determined to be 13.7%, 41.1%, and 39.1%, respectively. The inhibitory effects of C2H2, C8H14, and 3,4-dimethylpyrazole phosphate (DMPP) were then validated by qPCR. After adding donor strains to the sludge, fluorescence in situ hybridization (FISH) imaging analysis demonstrated the co-localization of RP4 plasmids and all three AOMs, thus confirming the horizontal gene transfer (HGT) of the RP4 plasmid among these microorganisms. Significant inhibitory effects of the RP4 plasmid on the ammonia nitrogen consumption of AOA, AOB, and CMX were also observed, with inhibition rates of 39.7%, 36.2%, and 49.7%, respectively. Moreover, amoA expression in AOB and CMX was variably inhibited by the RP4 plasmid, whereas AOA amoA expression was not inhibited. These results demonstrate the adverse environmental effects of the RP4 plasmid and provide indirect evidence supporting plasmid-mediated conjugation transfer from bacteria to archaea.}, }
@article {pmid38004804, year = {2023}, author = {Borrel, G and Fadhlaoui, K and Ben Hania, W and Gaci, N and Pehau-Arnaudet, G and Chaudhary, PP and Vandekerckove, P and Ballet, N and Alric, M and O'Toole, PW and Fardeau, ML and Ollivier, B and Brugère, JF}, title = {Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004804}, issn = {2076-2607}, support = {NA/SFI_/Science Foundation Ireland/Ireland ; }, abstract = {The methanogenic strain Mx-05[T] was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order Methanomassiliicoccales. It shares 86.9% 16S rRNA gene sequence identity with Methanomassiliicoccus luminyensis, the only member of this order previously isolated. The cells of Mx-05[T] were non-motile cocci, with a diameter range of 0.4-0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H2 as an electron donor. H2/CO2, formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05[T] required an unknown medium factor(s) provided by Eggerthella lenta and present in rumen fluid. Mx-05[T] grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9-8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L[-1] NaCl (optimum 0.12 mol.L[-1] NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H4MPT Wood-Ljungdahl pathway, as described for other Methanomassiliicoccales members. Based on an average nucleotide identity analysis, we propose strain Mx-05[T] as being a novel representative of the order Methanomassiliicoccales, within the novel family Methanomethylophilaceae, for which the name Methanomethylophilus alvi gen. nov, sp. nov. is proposed. The type strain is Mx-05[T] (JCM 31474T).}, }
@article {pmid37996939, year = {2023}, author = {Tao, S and Veen, GFC and Zhang, N and Yu, T and Qu, L}, title = {Tree and shrub richness modifies subtropical tree productivity by regulating the diversity and community composition of soil bacteria and archaea.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {261}, pmid = {37996939}, issn = {2049-2618}, mesh = {*Trees ; *Ecosystem ; Archaea/genetics ; Soil ; Biodiversity ; Bacteria/genetics ; Plants ; }, abstract = {BACKGROUND: Declines in plant biodiversity often have negative consequences for plant community productivity, and it becomes increasingly acknowledged that this may be driven by shifts in soil microbial communities. So far, the role of fungal communities in driving tree diversity-productivity relationships has been well assessed in forests. However, the role of bacteria and archaea, which are also highly abundant in forest soils and perform pivotal ecosystem functions, has been less investigated in this context. Here, we investigated how tree and shrub richness affects stand-level tree productivity by regulating bacterial and archaeal community diversity and composition. We used a landscape-scale, subtropical tree biodiversity experiment (BEF-China) where tree (1, 2, or 4 species) and shrub richness (0, 2, 4, 8 species) were modified.<br><br>RESULTS: Our findings indicated a noteworthy decline in soil bacterial &#x3b1;-diversity as tree species richness increased from monoculture to 2- and 4- tree species mixtures, but a significant increase in archaeal &#x3b1;-diversity. Additionally, we observed that the impact of shrub species richness on microbial &#x3b1;-diversity was largely dependent on the level of tree species richness. The increase in tree species richness greatly reduced the variability in bacterial community composition and the complexity of co-occurrence network, but this effect was marginal for archaea. Both tree and shrub species richness increased the stand-level tree productivity by regulating the diversity and composition of bacterial community and archaeal diversity, with the effects being mediated via increases in soil C:N ratios.<br><br>CONCLUSIONS: Our findings provide insight into the importance of bacterial and archaeal communities in driving the relationship between plant diversity and productivity in subtropical forests and highlight the necessity for a better understanding of prokaryotic communities in forest soils. Video Abstract.}, }
@article {pmid37989750, year = {2023}, author = {Gomes-Filho, JV and Breuer, R and Morales-Filloy, HG and Pozhydaieva, N and Borst, A and Paczia, N and Soppa, J and Höfer, K and Jäschke, A and Randau, L}, title = {Identification of NAD-RNA species and ADPR-RNA decapping in Archaea.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7597}, pmid = {37989750}, issn = {2041-1723}, support = {882789//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*RNA ; *NAD/metabolism ; Adenosine Diphosphate Ribose/metabolism ; Archaea/metabolism ; Chromatography, Liquid ; Tandem Mass Spectrometry ; }, abstract = {NAD is a coenzyme central to metabolism that also serves as a 5'-terminal cap for bacterial and eukaryotic transcripts. Thermal degradation of NAD can generate nicotinamide and ADP-ribose (ADPR). Here, we use LC-MS/MS and NAD captureSeq to detect and identify NAD-RNAs in the thermophilic model archaeon Sulfolobus acidocaldarius and in the halophilic mesophile Haloferax volcanii. None of the four Nudix proteins of S. acidocaldarius catalyze NAD-RNA decapping in vitro, but one of the proteins (Saci_NudT5) promotes ADPR-RNA decapping. NAD-RNAs are converted into ADPR-RNAs, which we detect in S. acidocaldarius total RNA. Deletion of the gene encoding the 5'-3' exonuclease Saci-aCPSF2 leads to a 4.5-fold increase in NAD-RNA levels. We propose that the incorporation of NAD into RNA acts as a degradation marker for Saci-aCPSF2. In contrast, ADPR-RNA is processed by Saci_NudT5 into 5'-p-RNAs, providing another layer of regulation for RNA turnover in archaeal cells.}, }
@article {pmid37987001, year = {2023}, author = {Sarkar, S and Kazarina, A and Hansen, PM and Ward, K and Hargreaves, C and Reese, N and Ran, Q and Kessler, W and de Souza, LFT and Loecke, TD and Sarto, MVM and Rice, CW and Zeglin, LH and Sikes, BA and Lee, STM}, title = {Ammonia-oxidizing archaea and bacteria differentially contribute to ammonia oxidation in soil under precipitation gradients and land legacy.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37987001}, issn = {2692-8205}, support = {P30 GM122731/GM/NIGMS NIH HHS/United States ; S10 OD021743/OD/NIH HHS/United States ; U54 HD090216/HD/NICHD NIH HHS/United States ; UL1 TR002366/TR/NCATS NIH HHS/United States ; }, abstract = {BACKGROUND: Global change has accelerated the nitrogen cycle. Soil nitrogen stock degradation by microbes leads to the release of various gases, including nitrous oxide (N2O), a potent greenhouse gas. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) participate in the soil nitrogen cycle, producing N2O. There are outstanding questions regarding the impact of environmental processes such as precipitation and land use legacy on AOA and AOB structurally, compositionally, and functionally. To answer these questions, we analyzed field soil cores and soil monoliths under varying precipitation profiles and land legacies.<br><br>RESULTS: We resolved 28 AOA and AOB metagenome assembled genomes (MAGs) and found that they were significantly higher in drier environments and differentially abundant in different land use legacies. We further dissected AOA and AOB functional potentials to understand their contribution to nitrogen transformation capabilities. We identified the involvement of stress response genes, differential metabolic functional potentials, and subtle population dynamics under different environmental parameters for AOA and AOB. We observed that AOA MAGs lacked a canonical membrane-bound electron transport chain and F-type ATPase but possessed A/A-type ATPase, while AOB MAGs had a complete complex III module and F-type ATPase, suggesting differential survival strategies of AOA and AOB.<br><br>CONCLUSIONS: The outcomes from this study will enable us to comprehend how drought-like environments and land use legacies could impact AOA- and AOB-driven nitrogen transformations in soil.}, }
@article {pmid37973213, year = {2023}, author = {Wolff, P and Lechner, A and Droogmans, L and Grosjean, H and Westhof, E}, title = {Corrigendum: Identification of U[p]47 in three thermophilic archaea, one mesophilic archaeon, and one hyperthermophilic bacterium.}, journal = {RNA (New York, N.Y.)}, volume = {29}, number = {12}, pages = {1973}, doi = {10.1261/rna.079812.123}, pmid = {37973213}, issn = {1469-9001}, }
@article {pmid37961710, year = {2023}, author = {Zhang, IH and Borer, B and Zhao, R and Wilbert, S and Newman, DK and Babbin, AR}, title = {Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen deficient zones with diverse metabolic potential.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37961710}, issn = {2692-8205}, support = {R01 HL152190/HL/NHLBI NIH HHS/United States ; }, abstract = {Archaea belonging to the DPANN superphylum have been found within an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise 15-26% of the archaeal community within marine oxygen deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes belonging to DPANN phyla Nanoarchaeota, Pacearchaeota, Woesarchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and Arabian Sea. We find these archaea to be permanent, stable residents of all 3 major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25-50% of archaea. ODZ DPANN appear capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.}, }
@article {pmid37955638, year = {2023}, author = {Krawczyk, A and Gosiewski, T and Zapała, B and Kowalska-Duplaga, K and Salamon, D}, title = {Alterations in intestinal Archaea composition in pediatric patients with Crohn's disease based on next-generation sequencing - a pilot study.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2276806}, pmid = {37955638}, issn = {1949-0984}, mesh = {Humans ; Child ; Archaea/genetics ; Pilot Projects ; *Crohn Disease/genetics ; *Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {Intestinal dysbiosis can lead to the induction of systemic immune-mediated inflammatory diseases, such as Crohn's disease Although archaea are part of the commensal microbiota, they are still one of the least studied microorganisms. The aim of our study was the standardization of the optimal conditions and primers for sequencing of the gut archaeome using Next Generation Sequencing, and evaluation of the differences between the composition of archaea in patients and healthy volunteers, as well as analysis of the changes that occur in the archaeome of patients depending on disease activity. Newly diagnosed patients were characterized by similar archeal profiles at every taxonomic level as in healthy individuals (the dominance of Methanobacteria at the class level, and Methanobrevibacter at the genus level). In turn, in patients previously diagnosed with Crohn's disease (both in active and remission phase), an increased prevalence of Thermoplasmata, Thermoprotei, Halobacteria (at the class level), and Halococcus, Methanospaera or Picrophilus (at the genus level) were observed. Furthermore, we have found a significant correlation between the patient's parameters and the individual class or species of Archaea. Our study confirms changes in archaeal composition in pediatric patients with Crohn's disease, however, only in long-standing disease. At the beginning of the disease, the archeal profile is similar to that of healthy people. However, in the chronic form of the disease, significant differences in the composition of archaeome begin to appear. It seems that some archaea may be a good indicator of the chronicity and activity of Crohn's disease.}, }
@article {pmid37954235, year = {2023}, author = {Zhang, T and He, W and Liang, Q and Zheng, F and Xiao, X and Zeng, Z and Zhou, J and Yao, W and Chen, H and Zhu, Y and Zhao, J and Zheng, Y and Zhang, C}, title = {Lipidomic diversity and proxy implications of archaea from cold seep sediments of the South China Sea.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1241958}, pmid = {37954235}, issn = {1664-302X}, abstract = {Cold seeps on the continental margins are characterized by intense microbial activities that consume a large portion of methane by anaerobic methanotrophic archaea (ANME) through anaerobic oxidation of methane (AOM). Although ANMEs are known to contain unique ether lipids that may have an important function in marine carbon cycling, their full lipidomic profiles and functional distribution in particular cold-seep settings are still poorly characterized. Here, we combined the 16S rRNA gene sequencing and lipidomic approaches to analyze archaeal communities and their lipids in cold seep sediments with distinct methane supplies from the South China Sea. The archaeal community was dominated by ANME-1 in the moderate seepage area with strong methane emission. Low seepage area presented higher archaeal diversity covering Lokiarchaeia, Bathyarchaeia, and Thermoplasmata. A total of 55 core lipids (CLs) and intact polar lipids (IPLs) of archaea were identified, which included glycerol dialkyl glycerol tetraethers (GDGTs), hydroxy-GDGTs (OH-GDGTs), archaeol (AR), hydroxyarchaeol (OH-AR), and dihydroxyarchaeol (2OH-AR). Diverse polar headgroups constituted the archaeal IPLs. High concentrations of dissolved inorganic carbon (DIC) with depleted δ[13]CDIC and high methane index (MI) values based on both CLs (MICL) and IPLs (MIIPL) indicate that ANMEs were active in the moderate seepage area. The ANME-2 and ANME-3 clades were characterized by enhanced glycosidic and phosphoric diether lipids production, indicating their potential role in coupling carbon and phosphurus cycling in cold seep ecosystems. ANME-1, though representing a smaller proportion of total archaea than ANME-2 and ANME-3 in the low seepage area, showed a positive correlation with MIIPL, indicating a different mechanism contributing to the IPL-GDGT pool. This also suggests that MIIPL could be a sensitive index to trace AOM activities performed by ANME-1. Overall, our study expands the understanding of the archaeal lipid composition in the cold seep and improves the application of MI using intact polar lipids that potentially link to extent ANME activities.}, }
@article {pmid37949149, year = {2024}, author = {Manesh, MJH and Willard, DJ and Lewis, AM and Kelly, RM}, title = {Extremely thermoacidophilic archaea for metal bioleaching: What do their genomes tell Us?.}, journal = {Bioresource technology}, volume = {391}, number = {Pt B}, pages = {129988}, doi = {10.1016/j.biortech.2023.129988}, pmid = {37949149}, issn = {1873-2976}, mesh = {*Archaea/genetics/metabolism ; Oxidation-Reduction ; *Metals/metabolism ; Copper/metabolism ; Minerals ; }, abstract = {Elevated temperatures favor bioleaching processes through faster kinetics, more favorable mineral chemistry, lower cooling requirements, and less surface passivation. Extremely thermoacidophilic archaea from the order Sulfolobales exhibit novel mechanisms for bioleaching metals from ores and have great potential. Genome sequences of many extreme thermoacidophiles are now available and provide new insights into their biochemistry, metabolism, physiology and ecology as these relate to metal mobilization from ores. Although there are some molecular genetic tools available for extreme thermoacidophiles, further development of these is sorely needed to advance the study and application of these archaea for bioleaching applications. The evolving landscape for bioleaching technologies at high temperatures merits a closer look through a genomic lens at what is currently possible and what lies ahead in terms of new developments and emerging opportunities. The need for critical metals and the diminishing primary deposits for copper should provide incentives for high temperature bioleaching.}, }
@article {pmid37918493, year = {2024}, author = {Lv, PL and Jia, C and Guo, X and Zhao, HP and Chen, R}, title = {Microbial stratification protects denitrifying anaerobic methane oxidation archaea and bacteria from external oxygen shock in membrane biofilm reactor.}, journal = {Bioresource technology}, volume = {391}, number = {Pt A}, pages = {129966}, doi = {10.1016/j.biortech.2023.129966}, pmid = {37918493}, issn = {1873-2976}, mesh = {*Archaea/genetics/metabolism ; Anaerobiosis ; Methane/metabolism ; Bacteria/genetics/metabolism ; Oxidation-Reduction ; Biofilms ; Methanobacteriaceae/metabolism ; *Ammonium Compounds/metabolism ; Bioreactors/microbiology ; Denitrification ; }, abstract = {Different gradients of dissolved oxygen (DO) regulate the microbial community and nitrogen removal pathways of denitrifying anaerobic methane oxidation (DAMO) and anaerobic ammonium oxidation (Anammox) coupled process in a batch biofilm reactor. Under completely anaerobic condition, approximately 72 mg NO3[-]-N/L was removed at a daily rate of 6.55 mg N/L, whereas a peak accumulation of 95 mg NO3[-]-N/L was observed during DO reached 0.5 mg/L. There is a decrease in the abundance of Candidatus Methylomirabilis (24.1%), Candidatus Methanoperedens (23.3%), and Candidatus Kuenenia (22.6%) to below 5% when DO levels reached 0.2 mg/L. Moreover, key genes associated with the reverse methanogenesis (mcrA) and anaerobic ammonium oxidase (hzo) decreased. These findings indicate that during oxygen shock, methanotrophs and denitrifiers replace Anammox bacteria on the outer sphere of the biofilm, whereas DAMO bacteria and archaea are protected from external oxygen shock due to the microbial stratification of biofilm.}, }
@article {pmid37917544, year = {2023}, author = {Cheng, M and Li, XX and Tan, S and Ma, X and Hu, Y and Hou, J and Cui, HL}, title = {Salinigranum marinum sp. nov. and Halohasta salina sp. nov., halophilic archaea isolated from sediment of a marine saltern and inland saline soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {11}, pages = {}, doi = {10.1099/ijsem.0.006143}, pmid = {37917544}, issn = {1466-5034}, mesh = {Sodium Chloride/analysis ; Phylogeny ; Fatty Acids/chemistry ; DNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Base Composition ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; *Euryarchaeota ; *Halobacteriales ; China ; Glycolipids/chemistry ; Phosphatidylglycerols/analysis ; *Halobacteriaceae ; }, abstract = {Two halophilic archaeal strains, ZS-10[T] and GSL13[T], were isolated from the Zhoushan marine saltern in Zhejiang, and an inland saline soil from the Tarim Basin, Xinjiang, PR China, respectively. The cells of strain ZS-10[T] were pleomorphic while those of strain GSL13[T] were rod-shaped. Both of them stained Gram-negative and formed red-pigmented colonies on agar plates and their cells lysed in distilled water. The optimum growth of strain ZS-10[T] was observed at 40 °C, 3.4 M NaCl, 0.03 M MgCl2 and pH 7.5, while that of strain GSL13[T] was at 37 °C, 3.1 M NaCl, 0.5 M MgCl2 and pH 7.5. Phylogenetic and phylogenomic analyses indicated that these two strains were related to Salinigranum and Halohasta, respectively. Strains ZS-10[T] and GSL13[T] could be differentiated from the current members of Salinigranum and Halohasta based on the comparison of diverse phenotypic characteristics. The average amino acid identity, average nucleotide identity and digital DNA-DNA hybridization values among strain ZS-10[T] and current species of Salinigranum were 75.8-78.6 %, 80.6-81.9 % and 24.3-26.1 %, respectively. These values between strain GSL13[T] and current species of Halohasta were 78.4-80.8 %, 79.8-82.8% and 22.7-25.7 %, respectively, clearly below the threshold values for species demarcation. The polar lipids of strain ZS-10[T] were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me) and sulphated mannosyl glucosyl diether (S-DGD-1), while those of strain GSL13[T] were phosphatidic acid, PG, PGP-Me, phosphatidylglycerol sulphate and S-DGD-1. The polar lipid profile of strain GSL13[T] was identical to those of Halohasta, whereas strain ZS-10[T] did not contain the minor glycolipids detected in the current Salinigranum species. The phenotypic, phylogenetic and genome-based results suggested that strains ZS-10[T] (=CGMCC 1.12868[T]=JCM 30241[T]) and GSL13[T] (=CGMCC 1.15214[T]=JCM 30841[T]) represent two novel species, for which the names Salinigranum marinum sp. nov. and Halohasta salina sp. nov. are proposed.}, }
@article {pmid37917005, year = {2023}, author = {Prakash, O and Dodsworth, JA and Dong, X and Ferry, JG and L'Haridon, S and Imachi, H and Kamagata, Y and Rhee, SK and Sagar, I and Shcherbakova, V and Wagner, D and Whitman, WB}, title = {Corrigendum: Proposed minimal standards for description of methanogenic archaea.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {11}, pages = {}, doi = {10.1099/ijsem.0.006127}, pmid = {37917005}, issn = {1466-5034}, }
@article {pmid37907951, year = {2023}, author = {Romero, P and Belanche, A and Jiménez, E and Hueso, R and Ramos-Morales, E and Salwen, JK and Kebreab, E and Yáñez-Ruiz, DR}, title = {Rumen microbial degradation of bromoform from red seaweed (Asparagopsis taxiformis) and the impact on rumen fermentation and methanogenic archaea.}, journal = {Journal of animal science and biotechnology}, volume = {14}, number = {1}, pages = {133}, pmid = {37907951}, issn = {1674-9782}, support = {RYC2019-027764-I//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; }, abstract = {BACKGROUND: The red macroalgae Asparagopsis is an effective methanogenesis inhibitor due to the presence of halogenated methane (CH4) analogues, primarily bromoform (CHBr3). This study aimed to investigate the degradation process of CHBr3 from A. taxiformis in the rumen and whether this process is diet-dependent. An in vitro batch culture system was used according to a 2 × 2 factorial design, assessing two A. taxiformis inclusion rates [0 (CTL) and 2% DM diet (AT)] and two diets [high-concentrate (HC) and high-forage diet (HF)]. Incubations lasted for 72 h and samples of headspace and fermentation liquid were taken at 0, 0.5, 1, 3, 6, 8, 12, 16, 24, 48 and 72 h to assess the pattern of degradation of CHBr3 into dibromomethane (CH2Br2) and fermentation parameters. Additionally, an in vitro experiment with pure cultures of seven methanogens strains (Methanobrevibacter smithii, Methanobrevibacter ruminantium, Methanosphaera stadtmanae, Methanosarcina barkeri, Methanobrevibacter millerae, Methanothermobacter wolfei and Methanobacterium mobile) was conducted to test the effects of increasing concentrations of CHBr3 (0.4, 2, 10 and 50 µmol/L).<br><br>RESULTS: The addition of AT significantly decreased CH4 production (P&#x2009;=&#x2009;0.002) and the acetate:propionate ratio (P&#x2009;=&#x2009;0.003) during a 72-h incubation. The concentrations of CHBr3 showed a rapid decrease with nearly 90% degraded within the first 3&#xa0;h of incubation. On the contrary, CH2Br2 concentration quickly increased during the first 6&#xa0;h and then gradually decreased towards the end of the incubation. Neither CHBr3 degradation nor CH2Br2 synthesis were affected by the type of diet used as substrate, suggesting that the fermentation rate is not a driving factor involved in CHBr3 degradation. The in vitro culture of methanogens showed a dose-response effect of CHBr3 by inhibiting the growth of M. smithii, M. ruminantium, M. stadtmanae, M. barkeri, M. millerae, M. wolfei, and M. mobile.<br><br>CONCLUSIONS: The present work demonstrated that CHBr3 from A. taxiformis is quickly degraded to CH2Br2 in the rumen and that the fermentation rate promoted by different diets is not a driving factor involved in CHBr3 degradation.}, }
@article {pmid37895260, year = {2023}, author = {Ullah, N and Yang, N and Guan, Z and Xiang, K and Wang, Y and Diaby, M and Chen, C and Gao, B and Song, C}, title = {Comparative Analysis and Phylogenetic Insights of Cas14-Homology Proteins in Bacteria and Archaea.}, journal = {Genes}, volume = {14}, number = {10}, pages = {}, pmid = {37895260}, issn = {2073-4425}, mesh = {*Archaea/genetics ; Phylogeny ; Bacteria/genetics ; *CRISPR-Associated Proteins ; }, abstract = {Type-V-F Cas12f proteins, also known as Cas14, have drawn significant interest within the diverse CRISPR-Cas nucleases due to their compact size. This study involves analyzing and comparing Cas14-homology proteins in prokaryotic genomes through mining, sequence comparisons, a phylogenetic analysis, and an array/repeat analysis. In our analysis, we identified and mined a total of 93 Cas14-homology proteins that ranged in size from 344 aa to 843 aa. The majority of the Cas14-homology proteins discovered in this analysis were found within the Firmicutes group, which contained 37 species, representing 42% of all the Cas14-homology proteins identified. In archaea, the DPANN group had the highest number of species containing Cas14-homology proteins, a total of three species. The phylogenetic analysis results demonstrate the division of Cas14-homology proteins into three clades: Cas14-A, Cas14-B, and Cas14-U. Extensive similarity was observed at the C-terminal end (CTD) through a domain comparison of the three clades, suggesting a potentially shared mechanism of action due to the presence of cutting domains in that region. Additionally, a sequence similarity analysis of all the identified Cas14 sequences indicated a low level of similarity (18%) between the protein variants. The analysis of repeats/arrays in the extended nucleotide sequences of the identified Cas14-homology proteins highlighted that 44 out of the total mined proteins possessed CRISPR-associated repeats, with 20 of them being specific to Cas14. Our study contributes to the increased understanding of Cas14 proteins across prokaryotic genomes. These homologous proteins have the potential for future applications in the mining and engineering of Cas14 proteins.}, }
@article {pmid37890267, year = {2023}, author = {Notaro, A and Zaretsky, M and Molinaro, A and De Castro, C and Eichler, J}, title = {N-glycosylation in Archaea: Unusual sugars and unique modifications.}, journal = {Carbohydrate research}, volume = {534}, number = {}, pages = {108963}, doi = {10.1016/j.carres.2023.108963}, pmid = {37890267}, issn = {1873-426X}, mesh = {Glycosylation ; *Archaea/metabolism ; Sugars ; Polysaccharides ; *Archaeal Proteins/metabolism ; }, abstract = {Archaea are microorganisms that comprise a distinct branch of the universal tree of life and which are best known as extremophiles, residing in a variety of environments characterized by harsh physical conditions. One seemingly universal trait of Archaea is the ability to perform N-glycosylation. At the same time, archaeal N-linked glycans present variety in terms of both composition and architecture not seen in the parallel eukaryal or bacterial processes. In this mini-review, many of the unique and unusual sugars found in archaeal N-linked glycans as identified by nuclear magnetic resonance spectroscopy are described.}, }
@article {pmid37876779, year = {2023}, author = {Yang, J and Chen, R and Peng, Y and Chai, J and Li, Y and Deng, F}, title = {The role of gut archaea in the pig gut microbiome: a mini-review.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1284603}, pmid = {37876779}, issn = {1664-302X}, abstract = {The gastrointestinal microbiota of swine harbors an essential but often overlooked component: the gut archaea. These enigmatic microorganisms play pivotal roles in swine growth, health, and yield quality. Recent insights indicate that the diversity of gut archaea is influenced by various factors including breed, age, and diet. Such factors orchestrate the metabolic interactions within the porcine gastrointestinal environment. Through symbiotic relationships with bacteria, these archaea modulate the host's energy metabolism and digestive processes. Contemporary research elucidates a strong association between the abundance of these archaea and economically significant traits in swine. This review elucidates the multifaceted roles of gut archaea in swine and underscores the imperative for strategic interventions to modulate their population and functionality. By exploring the probiotic potential of gut archaea, we envisage novel avenues to enhance swine growth, health, and product excellence. By spotlighting this crucial, yet under-investigated, facet of the swine gut microbiome, we aim to galvanize further scientific exploration into harnessing their myriad benefits.}, }
@article {pmid37840747, year = {2023}, author = {Liu, H and Jing, H and Wang, F}, title = {Archaea predominate in the ammonia oxidation process in the sediments of the Yap and Mariana Trenches.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1268790}, pmid = {37840747}, issn = {1664-302X}, abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play an important role in oxidizing ammonia to nitrite in different marine environments; however, their relative contribution to ammonia oxidation in the deep-sea sediments is still largely unknown. Sediment samples from seamounts and the Challenger Deep along the arc of the Yap Trench and the Mariana Trench were used for the investigation of the geographical distribution of AOA and AOB at the cDNA level, with associated potential nitrification rates (PNRs) being measured. AOA was predominated by Candidatus Nitrosopumilus and Nitrosopumilaceae, while Methylophaga was the major group of AOB. Significantly higher transcript abundance of the AOA amoA gene than that of AOB appeared in all samples, corresponding to the much higher RNRs contributed to AOA. Both the total and AOA PNRs were significantly higher in the deeper layers due to the high sensitivity of AOA to ammonia and oxygen than in AOB. In the surface layers, TN and TOC had significant positive and negative effects on the distribution of the AOA amoA gene transcripts, respectively, while NH4+ concentration was positively correlated with the AOB amoA gene transcripts. Our study demonstrated that AOA played a more important role than AOB in the ammonia-oxidizing process that occurred in the sediments of the Yap and Mariana Trenches and would expand the understanding of their ecological contribution to the nitrification process and nitrogen flux of trenches.}, }
@article {pmid37819981, year = {2023}, author = {Cerna-Vargas, JP and Gumerov, VM and Krell, T and Zhulin, IB}, title = {Amine-recognizing domain in diverse receptors from bacteria and archaea evolved from the universal amino acid sensor.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {42}, pages = {e2305837120}, pmid = {37819981}, issn = {1091-6490}, support = {R35 GM131760/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Archaea/genetics/metabolism ; *Amino Acids/metabolism ; Bacterial Proteins/metabolism ; Bacteria/genetics/metabolism ; Biogenic Amines/metabolism ; }, abstract = {Bacteria possess various receptors that sense different signals and transmit information to enable an optimal adaptation to the environment. A major limitation in microbiology is the lack of information on the signal molecules that activate receptors. Signals recognized by sensor domains are poorly reflected in overall sequence identity, and therefore, the identification of signals from the amino acid sequence of the sensor alone presents a challenge. Biogenic amines are of great physiological importance for microorganisms and humans. They serve as substrates for aerobic and anaerobic growth and play a role of neurotransmitters and osmoprotectants. Here, we report the identification of a sequence motif that is specific for amine-sensing sensor domains that belong to the Cache superfamily of the most abundant extracellular sensors in prokaryotes. We identified approximately 13,000 sensor histidine kinases, chemoreceptors, receptors involved in second messenger homeostasis and Ser/Thr phosphatases from 8,000 bacterial and archaeal species that contain the amine-recognizing motif. The screening of compound libraries and microcalorimetric titrations of selected sensor domains confirmed their ability to specifically bind biogenic amines. Mutants in the amine-binding motif or domains that contain a single mismatch in the binding motif had either no or a largely reduced affinity for amines. We demonstrate that the amine-recognizing domain originated from the universal amino acid-sensing Cache domain, thus providing insight into receptor evolution. Our approach enables precise "wet"-lab experiments to define the function of regulatory systems and therefore holds a strong promise to enable the identification of signals stimulating numerous receptors.}, }
@article {pmid37815851, year = {2024}, author = {Laird, MG and Adlung, N and Koivisto, JJ and Scheller, S}, title = {Thiol-Disulfide Exchange Kinetics and Redox Potential of the Coenzyme M and Coenzyme B Heterodisulfide, an Electron Acceptor Coupled to Energy Conservation in Methanogenic Archaea.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {25}, number = {1}, pages = {e202300595}, doi = {10.1002/cbic.202300595}, pmid = {37815851}, issn = {1439-7633}, support = {NNF19OC0054329//Novo Nordisk Foundation/ ; NNF19OC0055464//Novo Nordisk Foundation/ ; 326020//Academy of Finland/ ; }, mesh = {*Mesna/metabolism ; *Archaea/metabolism ; Sulfhydryl Compounds ; Mercaptoethanol ; Disulfides/metabolism ; Carbon Dioxide/metabolism ; Electrons ; Electron Transport ; Methane/metabolism ; Oxidation-Reduction ; }, abstract = {Methanogenic and methanotrophic archaea play important roles in the global carbon cycle by interconverting CO2 and methane. To conserve energy from these metabolic pathways that happen close to the thermodynamic equilibrium, specific electron carriers have evolved to balance the redox potentials between key steps. Reduced ferredoxins required to activate CO2 are provided by energetical coupling to the reduction of the high-potential heterodisulfide (HDS) of coenzyme M (2-mercaptoethanesulfonate) and coenzyme B (7-mercaptoheptanoylthreonine phosphate). While the standard redox potential of this important HDS has been determined previously to be -143 mV (Tietze et al. 2003 DOI: 10.1002/cbic.200390053), we have measured thiol disulfide exchange kinetics and reassessed this value by equilibrating thiol-disulfide mixtures of coenzyme M, coenzyme B, and mercaptoethanol. We determined the redox potential of the HDS of coenzyme M and coenzyme B to be -16.4±1.7 mV relative to the reference thiol mercaptoethanol (E[0] '=-264 mV). The resulting E[0] ' values are -281 mV for the HDS, -271 mV for the homodisulfide of coenzyme M, and -270 mV for the homodisulfide of coenzyme B. We discuss the importance of these updated values for the physiology of methanogenic and methanotrophic archaea and their implications in terms of energy conservation.}, }
@article {pmid37805516, year = {2023}, author = {Hu, X and Huang, Y and Gu, G and Hu, H and Yan, H and Zhang, H and Zhang, R and Zhang, D and Wang, K}, title = {Distinct patterns of distribution, community assembly and cross-domain co-occurrence of planktonic archaea in four major estuaries of China.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {75}, pmid = {37805516}, issn = {2524-6372}, support = {41977192//National Natural Science Foundation of China/ ; 2021J060//Natural Science Foundation of Ningbo/ ; SJLY2022001//Fundamental Research Funds for the Provincial Universities of Zhejiang/ ; }, abstract = {BACKGROUND: Archaea are key mediators of estuarine biogeochemical cycles, but comprehensive studies comparing archaeal communities among multiple estuaries with unified experimental protocols during the same sampling periods are scarce. Here, we investigated the distribution, community assembly, and cross-domain microbial co-occurrence of archaea in surface waters across four major estuaries (Yellow River, Yangtze River, Qiantang River, and Pearl River) of China cross climatic zones (~ 1,800 km) during the winter and summer cruises.<br><br>RESULTS: The relative abundance of archaea in the prokaryotic community and archaeal community composition varied with estuaries, seasons, and stations (reflecting local environmental changes such as salinity). Archaeal communities in four estuaries were overall predominated by ammonia-oxidizing archaea (AOA) (aka. Marine Group (MG) I; primarily Nitrosopumilus), while the genus Poseidonia of Poseidoniales (aka. MGII) was occasionally predominant in Pearl River estuary. The cross-estuary dispersal of archaea was largely limited and the assembly mechanism of archaea varied with estuaries in the winter cruise, while selection governed archaeal assembly in all estuaries in the summer cruise. Although the majority of archaea taxa in microbial networks were peripherals and/or connectors, extensive and distinct cross-domain associations of archaea with bacteria were found across the estuaries, with AOA as the most crucial archaeal group. Furthermore, the expanded associations of MGII taxa with heterotrophic bacteria were observed, speculatively indicating the endogenous demand for co-processing high amount and diversity of organic matters in the estuarine ecosystem highly impacted by terrestrial/anthropogenic input, which is worthy of further study.<br><br>CONCLUSIONS: Our results highlight the lack of common patterns in the dynamics of estuarine archaeal communities along the geographic gradient, expanding the understanding of roles of archaea in microbial networks of this highly dynamic ecosystem.}, }
@article {pmid37793447, year = {2024}, author = {Salas, E and Gorfer, M and Bandian, D and Eichorst, SA and Schmidt, H and Horak, J and Rittmann, SKR and Schleper, C and Reischl, B and Pribasnig, T and Jansa, J and Kaiser, C and Wanek, W}, title = {Reevaluation and novel insights into amino sugar and neutral sugar necromass biomarkers in archaea, bacteria, fungi, and plants.}, journal = {The Science of the total environment}, volume = {906}, number = {}, pages = {167463}, doi = {10.1016/j.scitotenv.2023.167463}, pmid = {37793447}, issn = {1879-1026}, mesh = {*Archaea ; *Sugars ; Carbohydrates ; Amino Sugars/analysis ; Bacteria ; Carbon ; Fungi ; Soil/chemistry ; Biomarkers ; Soil Microbiology ; }, abstract = {Soil microbial necromass is an important contributor to soil organic matter (>50%) and it is largely composed of microbial residues. In soils, fragmented cell wall residues are mostly found in their polysaccharide forms of fungal chitin and bacterial peptidoglycan. Microbial necromass biomarkers, particularly amino sugars (AS) such as glucosamine (GlcN) and muramic acid (MurA) have been used to trace fungal and bacterial residues in soils, and to distinguish carbon (C) found in microbial residues from non-microbial organic C. Neutral sugars (NS), particularly the hexose/pentose ratio, have also been proposed as tracers of plant polysaccharides in soils. In our study, we extended the range of biomarkers to include AS and NS compounds in the biomass of 120 species belonging to archaea, bacteria, fungi, or plants. GlcN was the most common AS found in all taxa, contributing 42-91% to total AS content, while glucose was the most common NS found, contributing 56-79% to total NS. We identified talosaminuronic acid, found in archaeal pseudopeptidoglycan, as a new potential biomarker specific for Euryarchaeota. We compared the variability of these compounds between the different taxonomic groups using multivariate approaches, such as non-metric multidimensional scaling (NMDS) and partial least squares discriminant analysis (PLS-DA) and statistically evaluated their biomarker potential via indicator species analysis. Both NMDS and PLS-DA showcased the variability in the AS and NS contents between the different taxonomic groups, highlighting their potential as necromass residue biomarkers and allowing their extension from separating bacterial and fungal necromass to separating microbes from plants. Finally, we estimated new conversion factors where fungal GlcN is converted to fungal C by multiplying by 10 and MurA is converted to bacterial C by multiplying by 54. Conversion factors for talosaminuronic acid and galactosamine are also proposed to allow estimation of archaeal or all-microbial necromass residue C, respectively.}, }
@article {pmid37771611, year = {2023}, author = {}, title = {Correction to: Putative nucleotide-based second messengers in archaea.}, journal = {microLife}, volume = {4}, number = {}, pages = {uqad039}, doi = {10.1093/femsml/uqad039}, pmid = {37771611}, issn = {2633-6693}, abstract = {[This corrects the article DOI: 10.1093/femsml/uqad027.].}, }
@article {pmid37759261, year = {2023}, author = {Kowalewicz-Kulbat, M and Krawczyk, KT and Szulc-Kielbik, I and Rykowski, S and Denel-Bobrowska, M and Olejniczak, AB and Locht, C and Klink, M}, title = {Cytotoxic effects of halophilic archaea metabolites on ovarian cancer cell lines.}, journal = {Microbial cell factories}, volume = {22}, number = {1}, pages = {197}, pmid = {37759261}, issn = {1475-2859}, mesh = {Humans ; Female ; *Ovarian Neoplasms/drug therapy ; Cisplatin ; Cell Line, Tumor ; *Antineoplastic Agents/pharmacology ; HeLa Cells ; }, abstract = {BACKGROUND: Ovarian cancer is one of the most frequent and deadly gynaecological cancers, often resistant to platinum-based chemotherapy, the current standard of care. Halophilic microorganisms have been shown to produce a large variety of metabolites, some of which show toxicity to various cancer cell lines. However, none have yet been shown to be active against ovarian cancer cells. Here, we examined the effects of metabolites secreted by the halophilic archaea Halorhabdus rudnickae and Natrinema salaciae on various cancer cell lines, including ovarian cancer cell lines.<br><br>RESULTS: [1]H NMR analyses of Hrd. rudnickae and Nnm. salaciae culture supernatants contain a complex mixture of metabolites that differ between species, and even between two different strains of the same species, such as Hrd. rudnickae strains 64[T] and 66. By using the MTT and the xCELLigence RTCA assays, we found that the secreted metabolites of all three halophilic strains expressed cytotoxicity to the ovarian cancer cell lines, especially A2780, as well as its cisplatin-resistant derivative A2780cis, in a dose-dependent manner. The other tested cell lines A549, HepG2, SK-OV-3 and HeLa were only minimally, or not at all affected by the archaeal metabolites, and this was only seen with the MTT assay.<br><br>CONCLUSIONS: The halophilic archaea Hrd. rudnickae and Nnm. salaciae, isolated from a Polish salt mine and Lake Medee in the Mediterranean Sea, respectively, secrete metabolites that are active against ovarian cancer cells, including those that are resistant to cisplatin. This opens potential new possibilities for the treatment of these frequent and deadly gynaecological cancers.}, }
@article {pmid37754561, year = {2023}, author = {Liu, WW and Pan, P and Zhou, NY}, title = {The presence of benzene ring activating CoA ligases for aromatics degradation in the ANaerobic MEthanotrophic (ANME) archaea.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0176623}, pmid = {37754561}, issn = {2165-0497}, abstract = {Petroleum-source and black carbon-source aromatic compounds are present in the cold seep environments, where ANaerobic MEthanotrophic (ANME) archaea as the dominant microbial community mediates the anaerobic oxidation of methane to produce inorganic and organic carbon. Here, by predicting the aromatics catabolic pathways in ANME metagenome-assembled genomes, we provide genomic and biochemical evidences that ANME have the potential of metabolizing aromatics via the strategy of CoA activation of the benzene ring using phenylacetic acid and benzoate as the substrates. Two ring-activating enzymes phenylacetate-CoA ligase (PaaKANME) and benzoate-CoA ligase (BadAANME) are able to convert phenylacetate to phenylacetyl-CoA and benzoate to benzoyl-CoA in vitro, respectively. They are mesophilic, alkali resistance, and with broad substrate spectra showing different affinity with various substrates. An exploration of the relative gene abundance in ANME genomes and cold seep environments indicates that about 50% of ANME genomes contain PCL genes, and various bacteria and archaea contain PCL and BCL genes. The results provide evidences for the capability of heterotrophic metabolism of aromatic compounds by ANME. This has not only enhanced our understanding of the nutrient range of ANME but also helped to explore the additional ecological and biogeochemical significance of this ubiquitous sedimentary archaea in the carbon flow in the cold seep environments. IMPORTANCE ANaerobic MEthanotrophic (ANME) archaea is the dominant microbial community mediating the anaerobic oxidation of methane in the cold seep environments, where aromatic compounds are present. Then it is hypothesized that ANME may be involved in the metabolism of aromatics. Here, we provide genomic and biochemical evidences for the heterotrophic metabolism of aromatic compounds by ANME, enhancing our understanding of their nutrient range and also shedding light on the ecological and biogeochemical significance of these ubiquitous sedimentary archaea in carbon flow within cold seep environments. Overall, this study offers valuable insights into the metabolic capabilities of ANME and their potential contributions to the global carbon cycle.}, }
@article {pmid37749252, year = {2023}, author = {Medvedeva, S and Borrel, G and Krupovic, M and Gribaldo, S}, title = {A compendium of viruses from methanogenic archaea reveals their diversity and adaptations to the gut environment.}, journal = {Nature microbiology}, volume = {8}, number = {11}, pages = {2170-2182}, pmid = {37749252}, issn = {2058-5276}, support = {ANR-20-CE20-009-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE02-0005-01//Agence Nationale de la Recherche (French National Research Agency)/ ; }, mesh = {Humans ; Animals ; Archaea/genetics ; *Euryarchaeota/metabolism ; Bacteria/metabolism ; Methane/metabolism ; *Viruses/metabolism ; }, abstract = {Methanogenic archaea are major producers of methane, a potent greenhouse gas and biofuel, and are widespread in diverse environments, including the animal gut. The ecophysiology of methanogens is likely impacted by viruses, which remain, however, largely uncharacterized. Here we carried out a global investigation of viruses associated with all current diversity of methanogens by assembling an extensive CRISPR database consisting of 156,000 spacers. We report 282 high-quality (pro)viral and 205 virus-like/plasmid sequences assigned to hosts belonging to ten main orders of methanogenic archaea. Viruses of methanogens can be classified into 87 families, underscoring a still largely undiscovered genetic diversity. Viruses infecting gut-associated archaea provide evidence of convergence in adaptation with viruses infecting gut-associated bacteria. These viruses contain a large repertoire of lysin proteins that cleave archaeal pseudomurein and are enriched in glycan-binding domains (Ig-like/Flg_new) and diversity-generating retroelements. The characterization of this vast repertoire of viruses paves the way towards a better understanding of their role in regulating methanogen communities globally, as well as the development of much-needed genetic tools.}, }
@article {pmid37747940, year = {2023}, author = {Murali, R and Yu, H and Speth, DR and Wu, F and Metcalfe, KS and Crémière, A and Laso-Pèrez, R and Malmstrom, RR and Goudeau, D and Woyke, T and Hatzenpichler, R and Chadwick, GL and Connon, SA and Orphan, VJ}, title = {Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea.}, journal = {PLoS biology}, volume = {21}, number = {9}, pages = {e3002292}, pmid = {37747940}, issn = {1545-7885}, mesh = {*Archaea ; Anaerobiosis ; *Sulfates/metabolism ; Geologic Sediments/microbiology ; Bacteria/genetics ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.}, }
@article {pmid37728966, year = {2023}, author = {Tan, S and Cheng, M and Li, XX and Hu, Y and Ma, X and Hou, J and Cui, HL}, title = {Natronosalvus halobius gen. nov., sp. nov., Natronosalvus caseinilyticus sp. nov., Natronosalvus vescus sp. nov., Natronosalvus rutilus sp. nov. and Natronosalvus amylolyticus sp. nov., halophilic archaea isolated from salt lakes and soda lakes.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {9}, pages = {}, doi = {10.1099/ijsem.0.006036}, pmid = {37728966}, issn = {1466-5034}, mesh = {Animals ; Lakes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Base Composition ; Fatty Acids/chemistry ; *Halobacteriales ; *Euryarchaeota ; Amino Acids ; *Cyprinidae ; }, abstract = {Five halophilic archaeal strains (AGai3-5[T], KZCA101[T], CGA3[T], WLHS1[T] and WLHSJ1[T]) were isolated from salt lakes and soda lakes in PR China. These strains had low 16S rRNA gene similarities (91.3-96.0 %) to closely related species of the family Natrialbaceae and may represent a new genus of the family. Phylogenetic and phylogenomic analyses revealed that these strains formed a distinct clade, separate from the nearby genera Natronobiforma and Saliphagus. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity (AAI) values among these five strains and the current members of the family Natrialbaceae were 72-90, 20-42 and 62-91 %, respectively, clearly below the threshold values for species demarcation. According to the critical value of AAI (≤76 %) proposed to differentiate genera within the family Natrialbaceae, it was further indicated that these strains represented a novel genus within the family. These strains could be distinguished from the related genera according to differential phenotypic characteristics. The major lipids of these strains were phosphatidic acid (PA), phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, mannosyl glucosyl diether (DGD-PA), sulphated DGD-1 (S-DGD-PA) and sulphated galactosyl mannosyl glucosyl diether. The phenotypic, chemotaxonomic, phylogenetic and phylogenomic features indicated that strains AGai3-5[T] (=CGMCC 1.16078[T]=JCM 33549[T]), KZCA101[T] (=CGMCC 1.17431[T]=JCM 35074[T]), CGA3[T] (=CGMCC 1.17463[T]=JCM 34318[T]), WLHS1[T] (=CGMCC 1.13780[T]=JCM 33562[T]) and WLHSJ1[T] (=CGMCC 1.13784[T]=JCM 33563[T]) represent five novel species of a new genus within the family Natrialbaceae, named Natronosalvus halobius gen. nov., sp. nov., Natronosalvus caseinilyticus sp. nov., Natronosalvus vescus sp. nov., Natronosalvus rutilus sp. nov. and Natronosalvus amylolyticus sp. nov., respectively.}, }
@article {pmid37727289, year = {2023}, author = {Volmer, JG and McRae, H and Morrison, M}, title = {The evolving role of methanogenic archaea in mammalian microbiomes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1268451}, pmid = {37727289}, issn = {1664-302X}, abstract = {Methanogenic archaea (methanogens) represent a diverse group of microorganisms that inhabit various environmental and host-associated microbiomes. These organisms play an essential role in global carbon cycling given their ability to produce methane, a potent greenhouse gas, as a by-product of their energy production. Recent advances in culture-independent and -dependent studies have highlighted an increased prevalence of methanogens in the host-associated microbiome of diverse animal species. Moreover, there is increasing evidence that methanogens, and/or the methane they produce, may play a substantial role in human health and disease. This review addresses the expanding host-range and the emerging view of host-specific adaptations in methanogen biology and ecology, and the implications for host health and disease.}, }
@article {pmid37715368, year = {2023}, author = {Soza-Bolaños, AI and Domínguez-Pérez, RA and Ayala-Herrera, JL and Pérez-Serrano, RM and Soto-Barreras, U and Espinosa-Cristóbal, LF and Rivera-Albarrán, CA and Zaldívar-Lelo de Larrea, G}, title = {Presence of methanogenic archaea in necrotic root canals of patients with or without type 2 diabetes mellitus.}, journal = {Australian endodontic journal : the journal of the Australian Society of Endodontology Inc}, volume = {49}, number = {3}, pages = {641-647}, doi = {10.1111/aej.12797}, pmid = {37715368}, issn = {1747-4477}, mesh = {Humans ; *Diabetes Mellitus, Type 2/complications ; Dental Pulp Cavity ; Archaea ; Root Canal Therapy ; *Periapical Periodontitis/diagnostic imaging/therapy ; Necrosis ; *Euryarchaeota ; }, abstract = {Theoretically, a necrotic root canal fulfils all requirements as a niche for methanogens to inhabit. However, their presence in it and its implication in apical periodontitis (AP) is controversial. Therefore, to contribute to ending the controversy, this study aimed to detect and compare methanogens' presence in two distinct niches with supposedly different microenvironments; both were necrotic root canals associated with AP but one from patients with type 2 diabetes mellitus (T2DM) while the other from non-diabetic patients. A clinical examination was performed on 65 T2DM patients and 73 non-diabetic controls. Samples from necrotic root canals were obtained, and methanogens were identified. The presence of methanogens was three times higher (27.6%) in the T2DM group than in non-diabetic patients (8.2%). In addition, methanogens' presence was associated with a higher prevalence of periapical symptoms.}, }
@article {pmid37714340, year = {2023}, author = {Wang, W and Lei, J and Li, M and Zhang, X and Xiang, X and Wang, H and Lu, X and Ma, L and Liu, X and Tuovinen, OH}, title = {Archaea are better adapted to antimony stress than their bacterial counterparts in Xikuangshan groundwater.}, journal = {The Science of the total environment}, volume = {905}, number = {}, pages = {166999}, doi = {10.1016/j.scitotenv.2023.166999}, pmid = {37714340}, issn = {1879-1026}, mesh = {*Archaea/genetics ; Antimony/analysis ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Groundwater/chemistry ; }, abstract = {Archaea are important ecological components of microbial communities in various environments, but are currently poorly investigated in antimony (Sb) contaminated groundwater particularly on their ecological differences in comparison with bacteria. To address this issue, groundwater samples were collected from Xikuangshan aquifer along an Sb gradient and subjected to 16S rRNA gene amplicon sequencing and bioinformatic analysis. The results demonstrated that bacterial communities were more susceptibly affected by elevated Sb concentration than their archaeal counterparts, and the positive stimulation of Sb concentration on bacterial diversity coincided with the intermediate disturbance hypothesis. Overall, the balance of environmental variables (Sb, pH, and EC), competitive interactions, and stochastic events jointly regulated bacterial and archaeal communities. Linear fitting analysis revealed that Sb significantly drove the deterministic process (heterogeneous selection) of bacterial communities, whereas stochastic process (dispersal limitation) contributed more to archaeal community assembly. In contract, the assembly of Sb-resistant bacteria and archaea was dominated by the stochastic process (undominated), which implied the important role of diversification and drift instead of selection. Compared with Sb-resistant microorganisms, bacterial and archaeal communities showed lower niche width, which may result from the constraints of Sb concentration and competitive interaction. Moreover, Sb-resistant archaea had a higher niche than that of Sb-resistant bacteria via investing on flexible metabolic pathways such as organic metabolism, ammonia oxidation; and carbon fixation to enhance their competitiveness. Our results offered new insights into the ecological adaptation mechanisms of bacteria and archaea in Sb-contaminated groundwater.}, }
@article {pmid37707605, year = {2023}, author = {Deore, KS and Dhakephalkar, PK and Dagar, SS}, title = {Phylogenetically and physiologically diverse methanogenic archaea inhabit the Indian hot spring environments.}, journal = {Archives of microbiology}, volume = {205}, number = {10}, pages = {332}, pmid = {37707605}, issn = {1432-072X}, support = {Ref. No. 23/06/2013(i)EU-V//University Grants Commission/ ; YSS/2015/000718//Science and Engineering Research Board/ ; }, mesh = {Humans ; Archaea/genetics ; *Hot Springs ; *Euryarchaeota ; Culture Media ; India ; }, abstract = {Mesophilic and thermophilic methanogens belonging to the hydrogenotrophic, methylotrophic, and acetotrophic groups were isolated from Indian hot spring environments using BY and BCYT growth media. Following initial Hinf I-based PCR-RFLP screening, 70 methanogens were sequenced to ascertain their identity. These methanogens were phylogenetically and physiologically diverse and represented different taxa distributed across three physiological groups, i.e., hydrogenotrophs (53), methylotrophs (14) and acetotrophs (3). Overall, methanogens representing three families, five genera, and ten species, including two putative novel species, were recognized. The highest number and diversity of methanogens was observed at 40 ℃, dominated by Methanobacterium (10; 3 species), Methanosarcina (9; 3 species), Methanothermobacter (7; 2 species), Methanomethylovorans (5; 1 species) and Methanoculleus (3; 1 species). Both putative novel methanogen species were isolated at 40 ℃ and belonged to the genera Methanosarcina and Methanobacterium. At 55 ℃, limited diversity was observed, and resulted in the isolation of only two genera of methanogens, i.e., Methanothermobacter (28; 2 species) and Methanosarcina (4; 1 species). At 70 ℃, only members of the genus Methanothermobacter (5; 2 species) were isolated, whereas no methanogen could be cultured at 85 ℃. Ours is the first study that documents the extensive range of cultivable methanogenic archaea inhabiting hot springs across various geothermal provinces of India.}, }
@article {pmid37702790, year = {2023}, author = {Zou, D and Chen, J and Zhang, C and Kao, SJ and Liu, H and Li, M}, title = {Diversity and salinity adaptations of ammonia oxidizing archaea in three estuaries of China.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {22}, pages = {6897-6909}, pmid = {37702790}, issn = {1432-0614}, support = {32225003//National Natural Science Foundation of China/ ; 31970105//National Natural Science Foundation of China/ ; 2022M722175//Postdoctoral Research Foundation of China/ ; JCYJ20200109105010363//Shenzhen Science and Technology Innovation Program/ ; }, abstract = {Ammonia-oxidizing archaea (AOA) are ubiquitously found in diverse habitats and play pivotal roles in the nitrogen and carbon cycle, especially in estuarine and coastal environments. Despite the fact that the diversity and distribution of AOA are thought to be tightly linked to habitats, little is known about the relationship that underpins their genomic traits, adaptive potentials, and ecological niches. Here, we have characterized and compared the AOA community in three estuaries of China using metagenomics. AOA were the dominant ammonia oxidizers in the three estuaries. Through phylogenetic analyses, five major AOA groups were identified, including the Nitrosomarinus-like, Nitrosopumilus-like, Aestuariumsis-like, Nitrosarchaeum-like, and Nitrosopelagicus-like groups. Statistical analyses showed that the aquatic and sedimentary AOA communities were mainly influenced by spatial factors (latitude and water depth) and environmental factors (salinity, pH, and dissolved oxygen) in estuaries, respectively. Compared to AOA dwelling in terrestrial and marine habitats, estuarine AOA encoded more genes involved in glucose and amino acid metabolism, transport systems, osmotic control, and cell motility. The low proteome isoelectric points (pI), high content of acidic amino acids, and the presence of potassium ion and mechanosensitive channels suggest a "salt-in" strategy for estuarine AOA to counteract high osmolarity in their surroundings. Our findings have indicated potential adaptation strategies and highlighted their importance in the estuarine nitrogen and carbon cycles. KEY POINTS: • Spatial and environmental factors influence water and sediment AOA respectively. • Estuarine AOA share low proteome isoelectric value and high acid amino acids content. • AOA adaptation to estuaries is likely resulted from their unique genomic features.}, }
@article {pmid37700049, year = {2023}, author = {Spang, A}, title = {Uncovering the hidden world of nanosized archaea.}, journal = {Nature reviews. Microbiology}, volume = {21}, number = {10}, pages = {638}, pmid = {37700049}, issn = {1740-1534}, }
@article {pmid37698885, year = {2023}, author = {Oudova-Rivera, B and Crombie, AT and Murrell, JC and Lehtovirta-Morley, LE}, title = {Alcohols as inhibitors of ammonia oxidizing archaea and bacteria.}, journal = {FEMS microbiology letters}, volume = {370}, number = {}, pages = {}, pmid = {37698885}, issn = {1574-6968}, mesh = {Humans ; *Archaea/physiology ; *Ammonia ; Nitrates ; Bacteria ; Oxidation-Reduction ; Ethanol ; Nitrification ; }, abstract = {Ammonia oxidizers are key players in the global nitrogen cycle and are responsible for the oxidation of ammonia to nitrite, which is further oxidized to nitrate by other microorganisms. Their activity can lead to adverse effects on some human-impacted environments, including water pollution through leaching of nitrate and emissions of the greenhouse gas nitrous oxide (N2O). Ammonia monooxygenase (AMO) is the key enzyme in microbial ammonia oxidation and shared by all groups of aerobic ammonia oxidizers. The AMO has not been purified in an active form, and much of what is known about its potential structure and function comes from studies on its interactions with inhibitors. The archaeal AMO is less well studied as ammonia oxidizing archaea were discovered much more recently than their bacterial counterparts. The inhibition of ammonia oxidation by aliphatic alcohols (C1-C8) using the model terrestrial ammonia oxidizing archaeon 'Candidatus Nitrosocosmicus franklandus' C13 and the ammonia oxidizing bacterium Nitrosomonas europaea was examined in order to expand knowledge about the range of inhibitors of ammonia oxidizers. Methanol was the most potent specific inhibitor of the AMO in both ammonia oxidizers, with half-maximal inhibitory concentrations (IC50) of 0.19 and 0.31 mM, respectively. The inhibition was AMO-specific in 'Ca. N. franklandus' C13 in the presence of C1-C2 alcohols, and in N. europaea in the presence of C1-C3 alcohols. Higher chain-length alcohols caused non-specific inhibition and also inhibited hydroxylamine oxidation. Ethanol was tolerated by 'Ca. N. franklandus' C13 at a higher threshold concentration than other chain-length alcohols, with 80 mM ethanol being required for complete inhibition of ammonia oxidation.}, }
@article {pmid37668803, year = {2023}, author = {Vipindas, PV and Jabir, T and Venkatachalam, S and Yang, EJ and Jain, A and Krishnan, KP}, title = {Vertical segregation and phylogenetic characterization of archaea and archaeal ammonia monooxygenase gene in the water column of the western Arctic Ocean.}, journal = {Extremophiles : life under extreme conditions}, volume = {27}, number = {3}, pages = {24}, pmid = {37668803}, issn = {1433-4909}, mesh = {*Archaea/genetics ; Phylogeny ; *Euryarchaeota ; Water ; }, abstract = {Archaea constitute a substantial fraction of marine microbial biomass and play critical roles in the biogeochemistry of oceans. However, studies on their distribution and ecology in the Arctic Ocean are relatively scarce. Here, we studied the distributions of archaea and archaeal ammonia monooxygenase (amoA) gene in the western Arctic Ocean, using the amplicon sequencing approach from the sea surface to deep waters up to 3040 m depth. A total of five archaeal phyla, Nitrososphaerota, "Euryarchaeota", "Halobacteriota," "Nanoarchaeota", and Candidatus Thermoplasmatota, were detected. We observed a clear, depth-dependent vertical segregation among archaeal communities. Ca. Thermoplasmatota (66.8%) was the most dominant phylum in the surface waters. At the same time, Nitrososphaerota (55.9%) was dominant in the deep waters. Most of the amoA gene OTUs (99%) belonged to the Nitrosopumilales and were further clustered into five subclades ("NP-Alpha", "NP-Delta", "NP-Epsilon", "NP-Gamma", and "NP-Theta"). "NP-Epsilon" was the most dominant clade throughout the water column and "NP_Alpha" showed higher abundance only in the deeper water. Salinity and inorganic nutrient concentrations were the major factors that determined the vertical segregation of archaea. We anticipate that the observed differences in the vertical distribution of archaea might contribute to the compartmentalization of dark carbon fixation and nitrification in deeper water and organic matter degradation in surface waters of the Arctic Ocean.}, }
@article {pmid37652180, year = {2023}, author = {Di Giulio, M}, title = {The absence of the evolutionary state of the Prokaryote would imply a polyphyletic origin of proteins and that LUCA, the ancestor of bacteria and that of archaea were progenotes.}, journal = {Bio Systems}, volume = {233}, number = {}, pages = {105014}, doi = {10.1016/j.biosystems.2023.105014}, pmid = {37652180}, issn = {1872-8324}, abstract = {I analysed the similarity gradient observed in protein families - of phylogenetically deep fundamental traits - of bacteria and archaea, ranging from cases such as the core of the DNA replication apparatus where there is no sequence similarity between the proteins involved, to cases in which, as in the translation initiation factors, only some proteins involved would be homologs, to cases such as for aminoacyl-tRNA synthetases in which most of the proteins involved would be homologs. This pattern of similarity between bacteria and archaea would seem to be a very clear indication of a transitional evolutionary stage that preceded both the Last Bacterial Common Ancestor and the Last Archaeal Common Ancestor, i.e. progenotic stages. Indeed, this similarity pattern would seem to exemplify an ongoing transition as all the evolutionary phases would be represented in it. Instead, in the cellular stage it is expected that these evolutionary phases should have already been overcome, i.e. completed, and therefore no longer detectable. In fact, if we had really been in the presence of the prokaryotic stage then we should not have observed this similarity pattern in proteins involved in defining the ancestral characters of bacteria and archaea, as the completion of the different cellular structures should have required a very low number of proteins to be late evolved in lineages leading to bacteria and archaea. Indeed, the already reached state of the Prokaryote would have determined complete cellular structures therefore a total absence of proteins to evolve independently in the two main phyletic lineages and able to complete the evolution of a particular character already evidently in a definitive state, which, on the other hand, does not appear to have been the case. All this would have prevented the formation of this pattern of similarity which instead would appear to be real. In conclusion, the existence of this pattern of similarity observed in the families of homologous proteins of bacteria and archaea would imply the absence of the evolutionary stage of the Prokaryote and consequently a progenotic status to be assigned to the LUCA. Indeed, the LUCA stage would have been a stage of evolutionary transition because it is belatedly marked by the presence of all the different evolutionary phases, evidently more easily interpretable within the definition of progenote than that of genote precisely because they are inherent in an evolutionary transition and not to an evolution that has already been achieved. Finally, I discuss the importance of these arguments for the polyphyletic origin of proteins.}, }
@article {pmid37630563, year = {2023}, author = {Xie, L and Yu, S and Lu, X and Liu, S and Tang, Y and Lu, H}, title = {Different Responses of Bacteria and Archaea to Environmental Variables in Brines of the Mahai Potash Mine, Qinghai-Tibet Plateau.}, journal = {Microorganisms}, volume = {11}, number = {8}, pages = {}, pmid = {37630563}, issn = {2076-2607}, support = {DD20221703//China Geological Survey/ ; }, abstract = {Salt mines feature both autochthonous and allochthonous microbial communities introduced by industrialization. It is important to generate the information on the diversity of the microbial communities present in the salt mines and how they are shaped by the environment representing ecological diversification. Brine from Mahai potash mine (Qianghai, China), an extreme hypersaline environment, is used to produce potash salts for hundreds of millions of people. However, halophiles preserved in this niche during deposition are still unknown. In this study, using high-throughput 16S rRNA gene amplicon sequencing and estimation of physicochemical variables, we examined brine samples collected from locations with the gradient of industrial activity intensity and discrete hydrochemical compositions in the Mahai potash mine. Our findings revealed a highly diverse bacterial community, mainly composed of Pseudomonadota in the hypersaline brines from the industrial area, whereas in the natural brine collected from the upstream Mahai salt lake, most of the 16S rRNA gene reads were assigned to Bacteroidota. Halobacteria and halophilic methanogens dominated archaeal populations. Furthermore, we discovered that in the Mahai potash mining area, bacterial communities tended to respond to anthropogenic influences. In contrast, archaeal diversity and compositions were primarily shaped by the chemical properties of the hypersaline brines. Conspicuously, distinct methanogenic communities were discovered in sets of samples with varying ionic compositions, indicating their strong sensitivity to the brine hydrochemical alterations. Our findings provide the first taxonomic snapshot of microbial communities from the Mahai potash mine and reveal the different responses of bacteria and archaea to environmental variations in this high-altitude aquatic ecosystem.}, }
@article {pmid37629622, year = {2023}, author = {Garcia-Bonete, MJ and Rajan, A and Suriano, F and Layunta, E}, title = {The Underrated Gut Microbiota Helminths, Bacteriophages, Fungi, and Archaea.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {8}, pages = {}, pmid = {37629622}, issn = {2075-1729}, abstract = {The microbiota inhabits the gastrointestinal tract, providing essential capacities to the host. The microbiota is a crucial factor in intestinal health and regulates intestinal physiology. However, microbiota disturbances, named dysbiosis, can disrupt intestinal homeostasis, leading to the development of diseases. Classically, the microbiota has been referred to as bacteria, though other organisms form this complex group, including viruses, archaea, and eukaryotes such as fungi and protozoa. This review aims to clarify the role of helminths, bacteriophages, fungi, and archaea in intestinal homeostasis and diseases, their interaction with bacteria, and their use as therapeutic targets in intestinal maladies.}, }
@article {pmid37564293, year = {2023}, author = {Naitam, MG and Ramakrishnan, B and Grover, M and Kaushik, R}, title = {Rhizosphere-dwelling halophilic archaea: a potential candidate for alleviating salinity-associated stress in agriculture.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1212349}, pmid = {37564293}, issn = {1664-302X}, abstract = {Salinity is a serious environmental factor that impedes crop growth and drastically reduces yield. This study aimed to investigate the potential of halophilic archaea isolated from the Rann of Kutch to alleviate the negative impact of salinity on crop growth and yield. The halophilic archaea, which demonstrated high tolerance to salinity levels up to 4.5 M, were evaluated for their ability to promote plant growth in both salt-tolerant and salt-susceptible wheat cultivars. Our assessment focused on their capacity to solubilize essential nutrients, including phosphorus (14-61 mg L[-1]), potassium (37-78 mg L[-1]), and zinc (8-17 mg L[-1]), as well as their production of the phytohormone IAA (17.30 to 49.3 μg ml[-1]). To conduct the experiments, five wheat cultivars (two salt-tolerant and three salt-susceptible) were grown in triplicates using soft MS agar tubes (50 ml) and pots containing 10 kg of soil with an electrical conductivity (EC) of 8 dSm[-1]. Data were collected at specific time points: 21 days after sowing (DAS) for the MS agar experiment, 45 DAS for the pot experiment, and at the time of harvest. In the presence of haloarchaea, the inoculated treatments exhibited significant increases in total protein (46%), sugar (27%), and chlorophyll (31%) levels compared to the un-inoculated control. Furthermore, the inoculation led to an elevated accumulation of osmolyte proline (31.51%) and total carbohydrates (27.85%) while substantially reducing the activity of antioxidant enzymes such as SOD, catalase, and peroxidase by 57-76%, respectively. Notably, the inoculated treatments also showed improved plant vegetative growth parameters compared to the un-inoculated treatments. Interestingly, the positive effects of the halophilic archaea were more pronounced in the susceptible wheat cultivars than in the tolerant cultivars. These findings highlight the growth-promoting abilities of the halophilic archaeon Halolamina pelagica CDK2 and its potential to mitigate the detrimental effects of salinity. Consequently, further evaluation of this halophilic archaeon under field conditions is warranted to explore its potential use in the development of microbial inoculants.}, }
@article {pmid37549709, year = {2023}, author = {Ren, B and Wang, W and Shen, L and Yang, W and Yang, Y and Jin, J and Geng, C}, title = {Nitrogen fertilization rate affects communities of ammonia-oxidizing archaea and bacteria in paddy soils across different climatic zones of China.}, journal = {The Science of the total environment}, volume = {902}, number = {}, pages = {166089}, doi = {10.1016/j.scitotenv.2023.166089}, pmid = {37549709}, issn = {1879-1026}, mesh = {*Archaea/genetics ; Soil/chemistry ; Ammonia/chemistry ; Nitrogen/chemistry ; Oxidation-Reduction ; Soil Microbiology ; Phylogeny ; Bacteria/genetics ; *Betaproteobacteria/genetics ; Nitrification ; China ; Fertilization ; }, abstract = {Nitrogen fertilization has important effects on nitrification. However, how the rate of nitrogen fertilization affects nitrification potential, as well as the communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), remains unclear. We performed a large-scale investigation of nitrification potential and ammonia-oxidizer communities in Chinese paddy fields at different nitrogen fertilization rates across different climatic zones. It was found that the nitrification potential at the high nitrogen fertilization rate (≥150 kg[-1] N ha[-1]) was 23.35 % higher than that at the intermediate rate (100-150 kg[-1] N ha[-1]) and 20.77 % higher than that at the low rate (< 100 kg[-1] N ha[-1]). The nitrification potential showed no significant variation among different nitrogen fertilization rates across climatic zones. Furthermore, the AOA and AOB amoA gene abundance at the high nitrogen fertilization rate was 481.67 % and 292.74 % higher (p < 0.05) than that at the intermediate rate, respectively. Correlation analysis demonstrated a significant positive correlation between AOB abundance and nitrification potential. AOA and AOB community composition differed significantly among nitrogen fertilization rates. Moreover, soil NH4[+] content, pH, water content, bulk density, and annual average temperature were regarded as key environmental factors influencing the community structure of ammonia-oxidizers. Taken together, the nitrogen fertilization rate had a significant impact on the communities of AOA and AOB but did not significantly alter the nitrification potential. Our findings provide new insights into the impact of nitrogen fertilization management on nitrification in rice paddy fields.}, }
@article {pmid37516446, year = {2023}, author = {Manfredini, A and Malusà, E and Pinzari, F and Canfora, L}, title = {Quantification of nitrogen cycle functional genes from viable archaea and bacteria in paddy soil.}, journal = {Journal of applied microbiology}, volume = {134}, number = {8}, pages = {}, doi = {10.1093/jambio/lxad169}, pmid = {37516446}, issn = {1365-2672}, mesh = {*Archaea/genetics/metabolism ; *Soil/chemistry ; Bacteria/genetics/metabolism ; Nitrogen Cycle ; Soil Microbiology ; Ammonia/metabolism ; Oxidation-Reduction ; Nitrogen/metabolism ; }, abstract = {AIMS: One of the main challenges of culture-independent soil microbiology is distinguishing the microbial community's viable fraction from dead matter. Propidium monoazide (PMA) binds the DNA of dead cells, preventing its amplification. This dye could represent a robust means to overcome the drawbacks of other selective methods, such as ribonucleic acid-based analyses.<br><br>METHODS AND RESULTS: We quantified functional genes from viable archaea and bacteria in soil by combining the use of PMA and quantitative polymerase chain reaction. Four N-cycle-related functional genes (bacterial and archaeal ammonia monooxygenase, nitrate reductase, and nitrite reductase) were successfully quantified from the living fraction of bacteria and archaea of a paddy soil. The protocol was also tested with pure bacterial cultures and soils with different physical and chemical properties.<br><br>CONCLUSIONS: The experiment results revealed a contrasting impact of mineral and organic fertilizers on the abundance of microbial genes related to the N-cycle in paddy soil.}, }
@article {pmid37504286, year = {2023}, author = {Marín-Paredes, R and Bolívar-Torres, HH and Coronel-Gaytán, A and Martínez-Romero, E and Servín-Garcidueñas, LE}, title = {A Metagenome from a Steam Vent in Los Azufres Geothermal Field Shows an Abundance of Thermoplasmatales archaea and Bacteria from the Phyla Actinomycetota and Pseudomonadota.}, journal = {Current issues in molecular biology}, volume = {45}, number = {7}, pages = {5849-5864}, pmid = {37504286}, issn = {1467-3045}, support = {IA210617 IA208019//PAPIIT-UNAM/ ; }, abstract = {Los Azufres National Park is a geothermal field that has a wide number of thermal manifestations; nevertheless, the microbial communities in many of these environments remain unknown. In this study, a metagenome from a sediment sample from Los Azufres National Park was sequenced. In this metagenome, we found that the microbial diversity corresponds to bacteria (Actinomycetota, Pseudomonadota), archaea (Thermoplasmatales and Candidatus Micrarchaeota and Candidatus Parvarchaeota), eukarya (Cyanidiaceae), and viruses (Fussellovirus and Caudoviricetes). The functional annotation showed genes related to the carbon fixation pathway, sulfur metabolism, genes involved in heat and cold shock, and heavy-metal resistance. From the sediment, it was possible to recover two metagenome-assembled genomes from Ferrimicrobium and Cuniculiplasma. Our results showed that there are a large number of microorganisms in Los Azufres that deserve to be studied.}, }
@article {pmid37500801, year = {2023}, author = {Esser, SP and Rahlff, J and Zhao, W and Predl, M and Plewka, J and Sures, K and Wimmer, F and Lee, J and Adam, PS and McGonigle, J and Turzynski, V and Banas, I and Schwank, K and Krupovic, M and Bornemann, TLV and Figueroa-Gonzalez, PA and Jarett, J and Rattei, T and Amano, Y and Blaby, IK and Cheng, JF and Brazelton, WJ and Beisel, CL and Woyke, T and Zhang, Y and Probst, AJ}, title = {A predicted CRISPR-mediated symbiosis between uncultivated archaea.}, journal = {Nature microbiology}, volume = {8}, number = {9}, pages = {1619-1633}, pmid = {37500801}, issn = {2058-5276}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Archaea/genetics/metabolism ; *Symbiosis/genetics ; Genomics ; Plasmids ; DNA/metabolism ; }, abstract = {CRISPR-Cas systems defend prokaryotic cells from invasive DNA of viruses, plasmids and other mobile genetic elements. Here, we show using metagenomics, metatranscriptomics and single-cell genomics that CRISPR systems of widespread, uncultivated archaea can also target chromosomal DNA of archaeal episymbionts of the DPANN superphylum. Using meta-omics datasets from Crystal Geyser and Horonobe Underground Research Laboratory, we find that CRISPR spacers of the hosts Candidatus Altiarchaeum crystalense and Ca. A. horonobense, respectively, match putative essential genes in their episymbionts' genomes of the genus Ca. Huberiarchaeum and that some of these spacers are expressed in situ. Metabolic interaction modelling also reveals complementation between host-episymbiont systems, on the basis of which we propose that episymbionts are either parasitic or mutualistic depending on the genotype of the host. By expanding our analysis to 7,012 archaeal genomes, we suggest that CRISPR-Cas targeting of genomes associated with symbiotic archaea evolved independently in various archaeal lineages.}, }
@article {pmid37495052, year = {2023}, author = {Cai, Y and Li, H and Qu, G and Hu, Y and Zou, H and Zhao, S and Cheng, M and Chu, X and Ren, N}, title = {Responses of applied voltages on the archaea microbial distribution in sludge digestion.}, journal = {Chemosphere}, volume = {339}, number = {}, pages = {139639}, doi = {10.1016/j.chemosphere.2023.139639}, pmid = {37495052}, issn = {1879-1298}, mesh = {*Sewage ; *Archaea ; Carbon Dioxide ; Anaerobiosis ; Methane ; Biofuels ; Digestion ; Bioreactors ; }, abstract = {As the development of urban population led to the increase of domestic water consumption, consequently the generation of surplus sludge (SS) produced increasingly during sewage treatment processes. In order to enhance the SS resource utilization efficiency, an electricity-assisted anaerobic digestion (EAAD) system was employed to examine the alterations in the digestion broth and the characteristics of gas production. Additionally, the response of applied voltages on the distribution of archaeal community near various electrodes within the sludge was explored. The results revealed that the application of high voltages exceeding 3.0 V hindered the CH4 production but stimulated the CO2 generation. Subsequently, both CH4 and CO2 production were impeded by the applied voltages. Furthermore, the increased voltages significantly decreased the abundance of Methanomicrobia, Methanosaeta, and Methanosarcina, which were crucial determinants of CH4 content in biogas. Notably, the excessively high voltages intensities caused the AD process to halt and even inactivate the microbial flora. Interestingly, the distribution characteristics of archaeal community were influenced not only by the voltages intensity but also exhibited variations between the anode and cathode regions. Moreover, as the applied voltage intensified, the discrepancy of responses between the cathode and anode regions became more pronounced, offering novel theoretical and technical foundations for the advancement of electricity-assisted with AD technology.}, }
@article {pmid37491319, year = {2023}, author = {Williams, AM and Jolley, EA and Santiago-Martínez, MG and Chan, CX and Gutell, RR and Ferry, JG and Bevilacqua, PC}, title = {In vivo structure probing of RNA in Archaea: novel insights into the ribosome structure of Methanosarcina acetivorans.}, journal = {RNA (New York, N.Y.)}, volume = {29}, number = {10}, pages = {1610-1620}, pmid = {37491319}, issn = {1469-9001}, support = {R35 GM127064/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaea/genetics ; *RNA ; Methanosarcina/genetics ; Methanol ; Bacteria/genetics ; Ribosomes/genetics ; }, abstract = {Structure probing combined with next-generation sequencing (NGS) has provided novel insights into RNA structure-function relationships. To date, such studies have focused largely on bacteria and eukaryotes, with little attention given to the third domain of life, archaea. Furthermore, functional RNAs have not been extensively studied in archaea, leaving open questions about RNA structure and function within this domain of life. With archaeal species being diverse and having many similarities to both bacteria and eukaryotes, the archaea domain has the potential to be an evolutionary bridge. In this study, we introduce a method for probing RNA structure in vivo in the archaea domain of life. We investigated the structure of ribosomal RNA (rRNA) from Methanosarcina acetivorans, a well-studied anaerobic archaeal species, grown with either methanol or acetate. After probing the RNA in vivo with dimethyl sulfate (DMS), Structure-seq2 libraries were generated, sequenced, and analyzed. We mapped the reactivity of DMS onto the secondary structure of the ribosome, which we determined independently with comparative analysis, and confirmed the accuracy of DMS probing in M. acetivorans Accessibility of the rRNA to DMS in the two carbon sources was found to be quite similar, although some differences were found. Overall, this study establishes the Structure-seq2 pipeline in the archaea domain of life and informs about ribosomal structure within M. acetivorans.}, }
@article {pmid37474649, year = {2023}, author = {Kim, YB and Whon, TW and Kim, JY and Kim, J and Kim, Y and Lee, SH and Park, SE and Kim, EJ and Son, HS and Roh, SW}, title = {In-depth metataxonomic investigation reveals low richness, high intervariability, and diverse phylotype candidates of archaea in the human urogenital tract.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {11746}, pmid = {37474649}, issn = {2045-2322}, mesh = {Humans ; Archaea/genetics ; RNA, Ribosomal, 16S/genetics ; Urogenital System ; *Microbiota/genetics ; *Euryarchaeota/genetics ; *Crenarchaeota ; Phylogeny ; }, abstract = {The urogenital microbiota is the potential principal factor in the pathophysiology of urinary tract infection and the protection of urinary tract health. Little is known about the urogenital archaeome although several reports have indicated that the archaeomes of various regions of the human body are associated with health. Accordingly, we aimed to determine the presence and diversity of archaeomes in the human urogenital tract. To explore the urogenital archaeome, voided urine specimens from 373 asymptomatic Korean individuals were used. No difference was observed in body mass index, age, or gender, according to presence of archaea. Analysis of archaeal 16S rRNA gene amplicons of archaea positive samples consisted of simple community structures, including diverse archaea, such as the phyla Methanobacteriota, Thermoproteota, and Halobacteriota. Asymptomatic individuals showed high participant-dependent intervariability in their urogenital archaeomes. The mean relative archaeal abundance was estimated to be 0.89%, and fluorescence in situ hybridisation micrographs provided evidence of archaeal cells in the human urogenital tract. In addition, the urogenital archaeome shared partial taxonomic compositional characteristics with those of the other body sites. In this study, Methanobacteriota, Thermoproteota, and Halobacteriota were suggested as inhabitants of the human urogenital tract, and a distinct human urogenital archaeome was characterised. These findings expand our knowledge of archaea-host associations in the human urogenital tract and may lead to novel insights into the role of archaea in urinary tract health.}, }
@article {pmid37468677, year = {2023}, author = {Banas, I and Esser, SP and Turzynski, V and Soares, A and Novikova, P and May, P and Moraru, C and Hasenberg, M and Rahlff, J and Wilmes, P and Klingl, A and Probst, AJ}, title = {Spatio-functional organization in virocells of small uncultivated archaea from the deep biosphere.}, journal = {The ISME journal}, volume = {17}, number = {10}, pages = {1789-1792}, pmid = {37468677}, issn = {1751-7370}, support = {863664/ERC_/European Research Council/International ; }, mesh = {*Archaea/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Viruses/genetics ; DNA, Viral/genetics ; }, abstract = {Despite important ecological roles posited for virocells (i.e., cells infected with viruses), studying individual cells in situ is technically challenging. We introduce here a novel correlative microscopic approach to study the ecophysiology of virocells. By conducting concerted virusFISH, 16S rRNA FISH, and scanning electron microscopy interrogations of uncultivated archaea, we linked morphologies of various altiarchaeal cells to corresponding phylogenetic signals and indigenous virus infections. While uninfected cells exhibited moderate separation between fluorescence signals of ribosomes and DNA, virocells displayed complete cellular segregation of chromosomal DNA from viral DNA, the latter co-localizing with host ribosome signals. A similar spatial separation was observed in dividing cells, with viral signals congregating near ribosomes at the septum. These observations suggest that replication of these uncultivated viruses occurs alongside host ribosomes, which are used to generate the required proteins for virion assembly. Heavily infected cells sometimes displayed virus-like particles attached to their surface, which agree with virus structures in cells observed via transmission electron microscopy. Consequently, this approach is the first to link genomes of uncultivated viruses to their respective structures and host cells. Our findings shed new light on the complex ecophysiology of archaeal virocells in deep subsurface biofilms and provide a solid framework for future in situ studies of virocells.}, }
@article {pmid37464403, year = {2023}, author = {Bargiela, R and Korzhenkov, AA and McIntosh, OA and Toshchakov, SV and Yakimov, MM and Golyshin, PN and Golyshina, OV}, title = {Evolutionary patterns of archaea predominant in acidic environment.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {61}, pmid = {37464403}, issn = {2524-6372}, support = {N 810280//European Regional Development Fund/ ; N 810280//European Regional Development Fund/ ; N 810280//European Regional Development Fund/ ; RPG-2020-190//Leverhulme Trust/ ; RPG-2020-190//Leverhulme Trust/ ; RPG-2020-190//Leverhulme Trust/ ; }, abstract = {BACKGROUND: Archaea of the order Thermoplasmatales are widely distributed in natural acidic areas and are amongst the most acidophilic prokaryotic organisms known so far. These organisms are difficult to culture, with currently only six genera validly published since the discovery of Thermoplasma acidophilum in 1970. Moreover, known great diversity of uncultured Thermoplasmatales represents microbial dark matter and underlines the necessity of efforts in cultivation and study of these archaea. Organisms from the order Thermoplasmatales affiliated with the so-called "alphabet-plasmas", and collectively dubbed "E-plasma", were the focus of this study. These archaea were found predominantly in the hyperacidic site PM4 of Parys Mountain, Wales, UK, making up to 58% of total metagenomic reads. However, these archaea escaped all cultivation attempts.<br><br>RESULTS: Their genome-based metabolism revealed its peptidolytic potential, in line with the physiology of the previously studied Thermoplasmatales isolates. Analyses of the genome and evolutionary history reconstruction have shown both the gain and loss of genes, that may have contributed to the success of the "E-plasma" in hyperacidic environment compared to their community neighbours. Notable genes among them are involved in the following molecular processes: signal transduction, stress response and glyoxylate shunt, as well as multiple copies of genes associated with various cellular functions; from energy production and conversion, replication, recombination, and repair, to cell wall/membrane/envelope biogenesis and archaella production. History events reconstruction shows that these genes, acquired by putative common ancestors, may determine the evolutionary and functional divergences of "E-plasma", which is much more developed than other representatives of the order Thermoplasmatales. In addition, the ancestral hereditary reconstruction strongly indicates the placement of Thermogymnomonas acidicola close to the root of the Thermoplasmatales.<br><br>CONCLUSIONS: This study has analysed the metagenome-assembled genome of "E-plasma", which denotes the basis of their predominance in Parys Mountain environmental microbiome, their global ubiquity, and points into the right direction of further cultivation attempts. The results suggest distinct evolutionary trajectories of organisms comprising the order Thermoplasmatales, which is important for the understanding of their evolution and lifestyle.}, }
@article {pmid37461084, year = {2023}, author = {Feehan, B and Ran, Q and Dorman, V and Rumback, K and Pogranichniy, S and Ward, K and Goodband, R and Niederwerder, MC and Lee, STM}, title = {Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {35}, pmid = {37461084}, issn = {2524-4671}, support = {P30 GM122731/GM/NIGMS NIH HHS/United States ; U54 HD090216/HD/NICHD NIH HHS/United States ; S10 OD021743/OD/NIH HHS/United States ; UL1 TR002366/TR/NCATS NIH HHS/United States ; }, abstract = {BACKGROUND: Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focusing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea dynamics, including detection and methanogenic functions, while assessing global, temporal and host distribution of our novel archaeal metagenome-assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, MAG taxonomic assignment and functional annotation. MAGs were utilized in downstream phylogenetic analysis for global, temporal and host distribution in addition to methanogenic functional potential determination.<br><br>RESULTS: We generated 1130 non-redundant MAGs, representing 588 unique taxa at the species level, with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in archaea of monogastric hosts which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further improve our understanding of microbiome development and functions.}, }
@article {pmid37452095, year = {2023}, author = {Wright, CL and Lehtovirta-Morley, LE}, title = {Nitrification and beyond: metabolic versatility of ammonia oxidising archaea.}, journal = {The ISME journal}, volume = {17}, number = {9}, pages = {1358-1368}, pmid = {37452095}, issn = {1751-7370}, mesh = {*Archaea/metabolism ; *Nitrification ; Ammonia/metabolism ; Nitrogen Cycle/physiology ; Oxidation-Reduction ; Soil Microbiology ; }, abstract = {Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.}, }
@article {pmid37446705, year = {2023}, author = {Padilla-Vaca, F and de la Mora, J and García-Contreras, R and Ramírez-Prado, JH and Alva-Murillo, N and Fonseca-Yepez, S and Serna-Gutiérrez, I and Moreno-Galván, CL and Montufar-Rodríguez, JM and Vicente-Gómez, M and Rangel-Serrano, &#xc1; and Vargas-Maya, NI and Franco, B}, title = {Two-Component System Sensor Kinases from Asgardian Archaea May Be Witnesses to Eukaryotic Cell Evolution.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {13}, pages = {}, pmid = {37446705}, issn = {1420-3049}, mesh = {*Archaea/genetics/metabolism ; *Eukaryotic Cells ; Bacteria/genetics ; Eukaryota/genetics ; Prokaryotic Cells ; Evolution, Molecular ; Phylogeny ; }, abstract = {The signal transduction paradigm in bacteria involves two-component systems (TCSs). Asgardarchaeota are archaea that may have originated the current eukaryotic lifeforms. Most research on these archaea has focused on eukaryotic-like features, such as genes involved in phagocytosis, cytoskeleton structure, and vesicle trafficking. However, little attention has been given to specific prokaryotic features. Here, the sequence and predicted structural features of TCS sensor kinases analyzed from two metagenome assemblies and a genomic assembly from cultured Asgardian archaea are presented. The homology of the sensor kinases suggests the grouping of Lokiarchaeum closer to bacterial homologs. In contrast, one group from a Lokiarchaeum and a meta-genome assembly from Candidatus Heimdallarchaeum suggest the presence of a set of kinases separated from the typical bacterial TCS sensor kinases. AtoS and ArcB homologs were found in meta-genome assemblies along with defined domains for other well-characterized sensor kinases, suggesting the close link between these organisms and bacteria that may have resulted in the metabolic link to the establishment of symbiosis. Several kinases are predicted to be cytoplasmic; some contain several PAS domains. The data shown here suggest that TCS kinases in Asgardian bacteria are witnesses to the transition from bacteria to eukaryotic organisms.}, }
@article {pmid37429213, year = {2023}, author = {Sun, J and Zhang, A and Zhang, Z and Liu, Y and Zhou, H and Cheng, H and Chen, Z and Li, H and Zhang, R and Wang, Y}, title = {Distinct assembly processes and environmental adaptation of abundant and rare archaea in Arctic marine sediments.}, journal = {Marine environmental research}, volume = {190}, number = {}, pages = {106082}, doi = {10.1016/j.marenvres.2023.106082}, pmid = {37429213}, issn = {1879-0291}, mesh = {*Archaea/genetics ; Arctic Regions ; *Geologic Sediments ; }, abstract = {Revealing the ecological processes and environmental adaptation of abundant and rare archaea is a central, but poorly understood, topic in ecology. Here, abundant and rare archaeal diversity, community assembly processes and co-occurrence patterns were comparatively analyzed in Arctic marine sediments. Our findings revealed that the rare taxa exhibited significantly higher diversity compared to the abundant taxa. Additionally, the abundant taxa displayed stronger environmental adaptation than the rare taxa. The co-occurrence network analysis demonstrated that the rare taxa developed more interspecies interactions and modules in response to environmental disturbance. Furthermore, the community assembly of abundant and rare taxa in sediments was primarily controlled by stochastic and deterministic processes, respectively. These findings provide valuable insights into the archaeal community assembly processes and significantly contribute to a deeper understanding of the environmental adaptability of abundant and rare taxa in Arctic marine sediments.}, }
@article {pmid37404173, year = {2023}, author = {Kiledal, EA and Shaw, M and Polson, SW and Maresca, JA}, title = {Metagenomic Analysis of a Concrete Bridge Reveals a Microbial Community Dominated by Halophilic Bacteria and Archaea.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0511222}, pmid = {37404173}, issn = {2165-0497}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaea/genetics ; *Microbiota/genetics ; Metagenome ; Sewage ; Sequence Analysis, DNA ; Metagenomics/methods ; Bacteria/genetics ; }, abstract = {Concrete hosts a small but diverse microbiome that changes over time. Shotgun metagenomic sequencing would enable assessment of both the diversity and function of the microbial community in concrete, but a number of unique challenges make this difficult for concrete samples. The high concentration of divalent cations in concrete interferes with nucleic acid extraction, and the extremely low biomass in concrete means that DNA from laboratory contamination may be a large fraction of the sequence data. Here, we develop an improved method for DNA extraction from concrete, with higher yield and lower laboratory contamination. To show that this method provides DNA of sufficient quality and quantity to do shotgun metagenomic sequencing, DNA was extracted from a sample of concrete obtained from a road bridge and sequenced with an Illumina MiSeq system. This microbial community was dominated by halophilic Bacteria and Archaea, with enriched functional pathways related to osmotic stress responses. Although this was a pilot-scale effort, we demonstrate that metagenomic sequencing can be used to characterize microbial communities in concrete and that older concrete structures may host different microbes than recently poured concrete. IMPORTANCE Prior work on the microbial communities of concrete focused on the surfaces of concrete structures such as sewage pipes or bridge pilings, where thick biofilms were easy to observe and sample. Because the biomass inside concrete is so low, more recent analyses of the microbial communities inside concrete used amplicon sequencing methods to describe those communities. However, to understand the activity and physiology of microbes in concrete, or to develop living infrastructure, we must develop more direct methods of community analysis. The method developed here for DNA extraction and metagenomic sequencing can be used for analysis of microbial communities inside concrete and can likely be adapted for other cementitious materials.}, }
@article {pmid37400737, year = {2023}, author = {Li, XX and Tan, S and Cheng, M and Hu, Y and Ma, X and Hou, J and Cui, HL}, title = {Salinilacihabitans rarus gen. nov., sp. nov., Natrononativus amylolyticus gen. nov., sp. nov., Natronobeatus ordinarius gen. nov., sp. nov., and Halovivax gelatinilyticus sp. nov., halophilic archaea, isolated from a salt lake and soda lakes.}, journal = {Extremophiles : life under extreme conditions}, volume = {27}, number = {2}, pages = {15}, pmid = {37400737}, issn = {1433-4909}, support = {32070003//National Natural Science Foundation of China/ ; }, mesh = {Phylogeny ; Lakes ; RNA, Ribosomal, 16S/genetics ; DNA, Archaeal/genetics ; Sequence Analysis, DNA ; Nucleic Acid Hybridization ; *Halobacteriaceae ; China ; Glycolipids ; *Euryarchaeota/genetics ; }, abstract = {Four halophilic archaea strains, AD-4[T], CGA30[T], CGA73[T], and WLHSJ27[T], were isolated from a salt lake and two soda lakes located in different regions of China. The 16S rRNA and rpoB' gene sequence similarities among strains AD-4[T], CGA30[T], CGA73[T], WLHSJ27[T], and the current species of the family Natrialbaceae were 90.9-97.5% and 83.1-91.8%, respectively. The phylogenetic and phylogenomic analyses revealed that these four strains separated from existing genera in the family Natrialbaceae and formed distant branches. The ANI, isDDH, and AAI values among these four strains and the current members of the family Natrialbaceae were 72-79%, 20-25%, and 63-73%, respectively, much lower than the threshold values for species demarcation. Strains AD-4[T], CGA73[T], and WLHSJ27[T] may represent three novel genera of the family Natrialbaceae according to the cutoff value of AAI (≤ 76%) proposed to differentiate genera within the family Natrialbaceae. These four strains could be distinguished from the related genera according to differential phenotypic characteristics. The major phospholipids of these four strains were identical while their glycolipid profiles were diverse. DGD-1 is a major glycolipid found in strain AD-4[T], trace glycolipids, DGD-1, and S-DGD-1, and (or) S-TGD-1 was found in the other three strains. The major respiratory quinones detected in the four strains were menaquinone MK-8 and MK-8(H2). This polyphasic classification indicated that strains AD-4[T], CGA73[T], and WLHSJ27[T] represent three novel species of three new genera with the family Natrialbaceae, and strain CGA30[T] represents a novel species of Halovivax.}, }
@article {pmid37399976, year = {2023}, author = {Li, B and Liang, J and Phillips, MA and Michael, AJ}, title = {Neofunctionalization of S-adenosylmethionine decarboxylase into pyruvoyl-dependent L-ornithine and L-arginine decarboxylases is widespread in bacteria and archaea.}, journal = {The Journal of biological chemistry}, volume = {299}, number = {8}, pages = {105005}, pmid = {37399976}, issn = {1083-351X}, support = {R01 AI034432/AI/NIAID NIH HHS/United States ; R37 AI034432/AI/NIAID NIH HHS/United States ; }, mesh = {*Adenosylmethionine Decarboxylase/genetics/metabolism ; Archaea/genetics/metabolism ; Ornithine ; Phylogeny ; *Carboxy-Lyases/genetics/metabolism ; Polyamines/metabolism ; Bacteria/metabolism ; Ornithine Decarboxylase/metabolism ; Arginine/genetics ; }, abstract = {S-adenosylmethionine decarboxylase (AdoMetDC/SpeD) is a key polyamine biosynthetic enzyme required for conversion of putrescine to spermidine. Autocatalytic self-processing of the AdoMetDC/SpeD proenzyme generates a pyruvoyl cofactor from an internal serine. Recently, we discovered that diverse bacteriophages encode AdoMetDC/SpeD homologs that lack AdoMetDC activity and instead decarboxylate L-ornithine or L-arginine. We reasoned that neofunctionalized AdoMetDC/SpeD homologs were unlikely to have emerged in bacteriophages and were probably acquired from ancestral bacterial hosts. To test this hypothesis, we sought to identify candidate AdoMetDC/SpeD homologs encoding L-ornithine and L-arginine decarboxylases in bacteria and archaea. We searched for the anomalous presence of AdoMetDC/SpeD homologs in the absence of its obligatory partner enzyme spermidine synthase, or the presence of two AdoMetDC/SpeD homologs encoded in the same genome. Biochemical characterization of candidate neofunctionalized genes confirmed lack of AdoMetDC activity, and functional presence of L-ornithine or L-arginine decarboxylase activity in proteins from phyla Actinomycetota, Armatimonadota, Planctomycetota, Melainabacteria, Perigrinibacteria, Atribacteria, Chloroflexota, Sumerlaeota, Omnitrophota, Lentisphaerota, and Euryarchaeota, the bacterial candidate phyla radiation and DPANN archaea, and the δ-Proteobacteria class. Phylogenetic analysis indicated that L-arginine decarboxylases emerged at least three times from AdoMetDC/SpeD, whereas L-ornithine decarboxylases arose only once, potentially from the AdoMetDC/SpeD-derived L-arginine decarboxylases, revealing unsuspected polyamine metabolic plasticity. Horizontal transfer of the neofunctionalized genes appears to be the more prevalent mode of dissemination. We identified fusion proteins of bona fide AdoMetDC/SpeD with homologous L-ornithine decarboxylases that possess two, unprecedented internal protein-derived pyruvoyl cofactors. These fusion proteins suggest a plausible model for the evolution of the eukaryotic AdoMetDC.}, }
@article {pmid37387308, year = {2023}, author = {Johnsen, U and Ortjohann, M and Reinhardt, A and Turner, JM and Stratton, C and Weber, KR and Sanchez, KM and Maupin-Furlow, J and Davies, C and Schönheit, P}, title = {Discovery of a novel transcriptional regulator of sugar catabolism in archaea.}, journal = {Molecular microbiology}, volume = {120}, number = {2}, pages = {224-240}, pmid = {37387308}, issn = {1365-2958}, support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaea/metabolism ; *Pyruvate Kinase ; Glycerol ; Glucose/metabolism ; Fructose/metabolism ; Glyceraldehyde-3-Phosphate Dehydrogenases/metabolism ; }, abstract = {The haloarchaeon Haloferax volcanii degrades D-glucose via the semiphosphorylative Entner-Doudoroff pathway and D-fructose via a modified Embden-Meyerhof pathway. Here, we report the identification of GfcR, a novel type of transcriptional regulator that functions as an activator of both D-glucose and D-fructose catabolism. We find that in the presence of D-glucose, GfcR activates gluconate dehydratase, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase and also acts as activator of the phosphotransferase system and of fructose-1,6-bisphosphate aldolase, which are involved in uptake and degradation of D-fructose. In addition, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase are activated by GfcR in the presence of D-fructose and also during growth on D-galactose and glycerol. Electrophoretic mobility shift assays indicate that GfcR binds directly to promoters of regulated genes. Specific intermediates of the degradation pathways of the three hexoses and of glycerol were identified as inducer molecules of GfcR. GfcR is composed of a phosphoribosyltransferase (PRT) domain with an N-terminal helix-turn-helix motif and thus shows homology to PurR of Gram-positive bacteria that is involved in the transcriptional regulation of nucleotide biosynthesis. We propose that GfcR of H. volcanii evolved from a PRT-like enzyme to attain a function as a transcriptional regulator of central sugar catabolic pathways in archaea.}, }
@article {pmid37379385, year = {2023}, author = {Wang, J and Qu, YN and Evans, PN and Guo, Q and Zhou, F and Nie, M and Jin, Q and Zhang, Y and Zhai, X and Zhou, M and Yu, Z and Fu, QL and Xie, YG and Hedlund, BP and Li, WJ and Hua, ZS and Wang, Z and Wang, Y}, title = {Evidence for nontraditional mcr-containing archaea contributing to biological methanogenesis in geothermal springs.}, journal = {Science advances}, volume = {9}, number = {26}, pages = {eadg6004}, pmid = {37379385}, issn = {2375-2548}, mesh = {*Archaea/genetics/metabolism ; Ecosystem ; *Hot Springs ; Methane/metabolism ; Temperature ; Phylogeny ; }, abstract = {Recent discoveries of methyl-coenzyme M reductase-encoding genes (mcr) in uncultured archaea beyond traditional euryarchaeotal methanogens have reshaped our view of methanogenesis. However, whether any of these nontraditional archaea perform methanogenesis remains elusive. Here, we report field and microcosm experiments based on [13]C-tracer labeling and genome-resolved metagenomics and metatranscriptomics, revealing that nontraditional archaea are predominant active methane producers in two geothermal springs. Archaeoglobales performed methanogenesis from methanol and may exhibit adaptability in using methylotrophic and hydrogenotrophic pathways based on temperature/substrate availability. A five-year field survey found Candidatus Nezhaarchaeota to be the predominant mcr-containing archaea inhabiting the springs; genomic inference and mcr expression under methanogenic conditions strongly suggested that this lineage mediated hydrogenotrophic methanogenesis in situ. Methanogenesis was temperature-sensitive , with a preference for methylotrophic over hydrogenotrophic pathways when incubation temperatures increased from 65° to 75°C. This study demonstrates an anoxic ecosystem wherein methanogenesis is primarily driven by archaea beyond known methanogens, highlighting diverse nontraditional mcr-containing archaea as previously unrecognized methane sources.}, }
@article {pmid37367666, year = {2023}, author = {Mapelli-Brahm, P and Gómez-Villegas, P and Gonda, ML and León-Vaz, A and León, R and Mildenberger, J and Rebours, C and Saravia, V and Vero, S and Vila, E and Meléndez-Martínez, AJ}, title = {Microalgae, Seaweeds and Aquatic Bacteria, Archaea, and Yeasts: Sources of Carotenoids with Potential Antioxidant and Anti-Inflammatory Health-Promoting Actions in the Sustainability Era.}, journal = {Marine drugs}, volume = {21}, number = {6}, pages = {}, pmid = {37367666}, issn = {1660-3397}, mesh = {Carotenoids/pharmacology/metabolism ; Antioxidants/pharmacology/metabolism ; *Microalgae/metabolism ; Archaea ; *Seaweed ; Aquatic Organisms ; Anti-Inflammatory Agents/pharmacology/metabolism ; Bacteria ; Yeasts ; }, abstract = {Carotenoids are a large group of health-promoting compounds used in many industrial sectors, such as foods, feeds, pharmaceuticals, cosmetics, nutraceuticals, and colorants. Considering the global population growth and environmental challenges, it is essential to find new sustainable sources of carotenoids beyond those obtained from agriculture. This review focuses on the potential use of marine archaea, bacteria, algae, and yeast as biological factories of carotenoids. A wide variety of carotenoids, including novel ones, were identified in these organisms. The role of carotenoids in marine organisms and their potential health-promoting actions have also been discussed. Marine organisms have a great capacity to synthesize a wide variety of carotenoids, which can be obtained in a renewable manner without depleting natural resources. Thus, it is concluded that they represent a key sustainable source of carotenoids that could help Europe achieve its Green Deal and Recovery Plan. Additionally, the lack of standards, clinical studies, and toxicity analysis reduces the use of marine organisms as sources of traditional and novel carotenoids. Therefore, further research on the processing of marine organisms, the biosynthetic pathways, extraction procedures, and examination of their content is needed to increase carotenoid productivity, document their safety, and decrease costs for their industrial implementation.}, }
@article {pmid37349893, year = {2023}, author = {Carré, L and Gonzalez, D and Girard, &#xc9; and Franzetti, B}, title = {Effects of chaotropic salts on global proteome stability in halophilic archaea: Implications for life signatures on Mars.}, journal = {Environmental microbiology}, volume = {25}, number = {11}, pages = {2216-2230}, doi = {10.1111/1462-2920.16451}, pmid = {37349893}, issn = {1462-2920}, mesh = {Proteome ; Salts ; Extraterrestrial Environment ; *Mars ; *Haloferax volcanii/genetics ; Biomarkers ; }, abstract = {Halophilic archaea thriving in hypersaline environments, such as salt lakes, offer models for putative life in extraterrestrial brines such as those found on Mars. However, little is known about the effect of the chaotropic salts that could be found in such brines, such as MgCl2 , CaCl2 and (per)chlorate salts, on complex biological samples like cell lysates which could be expected to be more representative of biomarkers left behind putative extraterrestrial life forms. We used intrinsic fluorescence to study the salt dependence of proteomes extracted from five halophilic strains: Haloarcula marismortui, Halobacterium salinarum, Haloferax mediterranei, Halorubrum sodomense and Haloferax volcanii. These strains were isolated from Earth environments with different salt compositions. Among the five strains that were analysed, H. mediterranei stood out as a results of its high dependency on NaCl for its proteome stabilization. Interestingly, the results showed contrasting denaturation responses of the proteomes to chaotropic salts. In particular, the proteomes of strains that are most dependent or tolerant on MgCl2 for growth exhibited higher tolerance towards chaotropic salts that are abundant in terrestrial and Martian brines. These experiments bridge together global protein properties and environmental adaptation and help guide the search for protein-like biomarkers in extraterrestrial briny environments.}, }
@article {pmid37341134, year = {2023}, author = {Iacono, R and De Lise, F and Moracci, M and Cobucci-Ponzano, B and Strazzulli, A}, title = {Glycoside hydrolases from (hyper)thermophilic archaea: structure, function, and applications.}, journal = {Essays in biochemistry}, volume = {67}, number = {4}, pages = {731-751}, doi = {10.1042/EBC20220196}, pmid = {37341134}, issn = {1744-1358}, mesh = {*Glycoside Hydrolases/chemistry ; *Archaea/chemistry ; Hot Temperature ; Hydrolysis ; }, abstract = {(Hyper)thermophilic archaeal glycosidases are enzymes that catalyze the hydrolysis of glycosidic bonds to break down complex sugars and polysaccharides at high temperatures. These enzymes have an unique structure that allows them to remain stable and functional in extreme environments such as hot springs and hydrothermal vents. This review provides an overview of the current knowledge and milestones on the structures and functions of (hyper)thermophilic archaeal glycosidases and their potential applications in various fields. In particular, this review focuses on the structural characteristics of these enzymes and how these features relate to their catalytic activity by discussing different types of (hyper)thermophilic archaeal glycosidases, including β-glucosidases, chitinase, cellulases and α-amylases, describing their molecular structures, active sites, and mechanisms of action, including their role in the hydrolysis of carbohydrates. By providing a comprehensive overview of (hyper)thermophilic archaeal glycosidases, this review aims to stimulate further research into these fascinating enzymes.}, }
@article {pmid37332501, year = {2022}, author = {Pessi, IS and Rutanen, A and Hultman, J}, title = {Candidatus Nitrosopolaris, a genus of putative ammonia-oxidizing archaea with a polar/alpine distribution.}, journal = {FEMS microbes}, volume = {3}, number = {}, pages = {xtac019}, pmid = {37332501}, issn = {2633-6685}, abstract = {Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle of polar soils. Here, we analyzed metagenomic data from tundra soils in Rásttigáisá, Norway, and recovered four metagenome-assembled genomes (MAGs) assigned to the genus 'UBA10452', an uncultured lineage of putative AOA in the order Nitrososphaerales ('terrestrial group I.1b'), phylum Thaumarchaeota. Analysis of other eight previously reported MAGs and publicly available amplicon sequencing data revealed that the UBA10452 lineage is predominantly found in acidic polar and alpine soils. In particular, UBA10452 MAGs were more abundant in highly oligotrophic environments such as mineral permafrost than in more nutrient-rich, vegetated tundra soils. UBA10452 MAGs harbour multiple copies of genes related to cold tolerance, particularly genes involved in DNA replication and repair. Based on the phylogenetic, biogeographic, and ecological characteristics of 12 UBA10452 MAGs, which include a high-quality MAG (90.8% complete, 3.9% redundant) with a nearly complete 16S rRNA gene, we propose a novel Candidatus genus, Ca. Nitrosopolaris, with four species representing clear biogeographic/habitat clusters.}, }
@article {pmid37323904, year = {2023}, author = {Elcheninov, AG and Ugolkov, YA and Elizarov, IM and Klyukina, AA and Kublanov, IV and Sorokin, DY}, title = {Cellulose metabolism in halo(natrono)archaea: a comparative genomics study.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1112247}, pmid = {37323904}, issn = {1664-302X}, abstract = {Extremely halophilic archaea are one of the principal microbial community components in hypersaline environments. The majority of cultivated haloarchaea are aerobic heterotrophs using peptides or simple sugars as carbon and energy sources. At the same time, a number of novel metabolic capacities of these extremophiles were discovered recently among which is a capability of growing on insoluble polysaccharides such as cellulose and chitin. Still, polysaccharidolytic strains are in minority among cultivated haloarchaea and their capacities of hydrolyzing recalcitrant polysaccharides are hardly investigated. This includes the mechanisms and enzymes involved in cellulose degradation, which are well studied for bacterial species, while almost unexplored in archaea and haloarchaea in particular. To fill this gap, a comparative genomic analysis of 155 cultivated representatives of halo(natrono)archaea, including seven cellulotrophic strains belonging to the genera Natronobiforma, Natronolimnobius, Natrarchaeobius, Halosimplex, Halomicrobium and Halococcoides was performed. The analysis revealed a number of cellulases, encoded in the genomes of cellulotrophic strains but also in several haloarchaea, for which the capacity to grow on cellulose was not shown. Surprisingly, the cellulases genes, especially of GH5, GH9 and GH12 families, were significantly overrepresented in the cellulotrophic haloarchaea genomes in comparison with other cellulotrophic archaea and even cellulotrophic bacteria. Besides cellulases, the genes for GH10 and GH51 families were also abundant in the genomes of cellulotrophic haloarchaea. These results allowed to propose the genomic patterns, determining the capability of haloarchaea to grow on cellulose. The patterns helped to predict cellulotrophic capacity for several halo(natrono)archaea, and for three of them it was experimentally confirmed. Further genomic search revealed that glucose and cellooligosaccharides import occurred by means of porters and ABC (ATP-binding cassette) transporters. Intracellular glucose oxidation occurred through glycolysis or the semi-phosphorylative Entner-Dudoroff pathway which occurrence was strain-specific. Comparative analysis of CAZymes toolbox and available cultivation-based information allowed proposing two possible strategies used by haloarchaea capable of growing on cellulose: so-called specialists are more effective in degradation of cellulose while generalists are more flexible in nutrient spectra. Besides CAZymes profiles the groups differed in genome sizes, as well as in variability of mechanisms of import and central metabolism of sugars.}, }
@article {pmid37322123, year = {2023}, author = {Taglialegna, A}, title = {A plasmid to modify Archaea.}, journal = {Nature reviews. Microbiology}, volume = {21}, number = {8}, pages = {483}, pmid = {37322123}, issn = {1740-1534}, mesh = {*Archaea/genetics ; Plasmids/genetics ; }, }
@article {pmid37317245, year = {2023}, author = {Thompson, TP and Busetti, A and Gilmore, BF}, title = {Quorum Sensing in Halorubrum saccharovorum Facilitates Cross-Domain Signaling between Archaea and Bacteria.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317245}, issn = {2076-2607}, abstract = {Quorum Sensing (QS) is a well-studied intercellular communication mechanism in bacteria, regulating collective behaviors such as biofilm formation, virulence, and antibiotic resistance. However, cell-cell signaling in haloarchaea remains largely unexplored. The coexistence of bacteria and archaea in various environments, coupled with the known cell-cell signaling mechanisms in both prokaryotic and eukaryotic microorganisms and the presence of cell-cell signaling mechanisms in both prokaryotic and eukaryotic microorganisms, suggests a possibility for haloarchaea to possess analogous cell-cell signaling or QS systems. Recently, N-acylhomoserine lactone (AHL)-like compounds were identified in haloarchaea; yet, their precise role-for example, persister cell formation-remains ambiguous. This study investigated the capacity of crude supernatant extract from the haloarchaeon Halorubrum saccharovorum CSM52 to stimulate bacterial AHL-dependent QS phenotypes using bioreporter strains. Our findings reveal that these crude extracts induced several AHL-dependent bioreporters and modulated pyocyanin and pyoverdine production in Pseudomonas aeruginosa. Importantly, our study suggests cross-domain communication between archaea and bacterial pathogens, providing evidence for archaea potentially influencing bacterial virulence. Using Thin Layer Chromatography overlay assays, lactonolysis, and colorimetric quantification, the bioactive compound was inferred to be a chemically modified AHL-like compound or a diketopiperazine-like molecule, potentially involved in biofilm formation in H. saccharovorum CSM52. This study offers new insights into putative QS mechanisms in haloarchaea and their potential role in interspecies communication and coordination, thereby enriching our understanding of microbial interactions in diverse environments.}, }
@article {pmid37317170, year = {2023}, author = {Payá, G and Bautista, V and Camacho, M and Esclapez, J and Bonete, MJ}, title = {Comprehensive Bioinformatics Analysis of the Biodiversity of Lsm Proteins in the Archaea Domain.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317170}, issn = {2076-2607}, support = {ACIF/2018/200//Generalitat Valenciana/ ; VIGROB_016//University of Alicante/ ; }, abstract = {The Sm protein superfamily includes Sm, like-Sm (Lsm), and Hfq proteins. Sm and Lsm proteins are found in the Eukarya and Archaea domains, respectively, while Hfq proteins exist in the Bacteria domain. Even though Sm and Hfq proteins have been extensively studied, archaeal Lsm proteins still require further exploration. In this work, different bioinformatics tools are used to understand the diversity and distribution of 168 Lsm proteins in 109 archaeal species to increase the global understanding of these proteins. All 109 archaeal species analyzed encode one to three Lsm proteins in their genome. Lsm proteins can be classified into two groups based on molecular weight. Regarding the gene environment of lsm genes, many of these genes are located adjacent to transcriptional regulators of the Lrp/AsnC and MarR families, RNA-binding proteins, and ribosomal protein L37e. Notably, only proteins from species of the class Halobacteria conserved the internal and external residues of the RNA-binding site identified in Pyrococcus abyssi, despite belonging to different taxonomic orders. In most species, the Lsm genes show associations with 11 genes: rpl7ae, rpl37e, fusA, flpA, purF, rrp4, rrp41, hel308, rpoD, rpoH, and rpoN. We propose that most archaeal Lsm proteins are related to the RNA metabolism, and the larger Lsm proteins could perform different functions and/or act through other mechanisms of action.}, }
@article {pmid37308591, year = {2023}, author = {Tong, Y and Wu, X and Liu, Y and Chen, H and Zhou, Y and Jiang, L and Li, M and Zhao, S and Zhang, Y}, title = {Alternative Z-genome biosynthesis pathway shows evolutionary progression from Archaea to phage.}, journal = {Nature microbiology}, volume = {8}, number = {7}, pages = {1330-1338}, pmid = {37308591}, issn = {2058-5276}, mesh = {*Bacteriophages/genetics ; Archaea/genetics ; Biosynthetic Pathways ; Phylogeny ; Guanosine Triphosphate ; Adenosine Triphosphate ; }, abstract = {Many bacteriophages evade bacterial immune recognition by substituting adenine with 2,6-diaminopurine (Z) in their genomes. The Z-genome biosynthetic pathway involves PurZ that belongs to the PurA (adenylosuccinate synthetase) family and bears particular similarity to archaeal PurA. However, how the transition of PurA to PurZ occurred during evolution is not clear; recapturing this process may shed light on the origin of Z-containing phages. Here we describe the computer-guided identification and biochemical characterization of a naturally existing PurZ variant, PurZ0, which uses guanosine triphosphate as the phosphate donor rather than the ATP used by PurZ. The atomic resolution structure of PurZ0 reveals a guanine nucleotide binding pocket highly analogous to that of archaeal PurA. Phylogenetic analyses suggest PurZ0 as an intermediate during the evolution of archaeal PurA to phage PurZ. Maintaining the balance of different purines necessitates further evolvement of guanosine triphosphate-using PurZ0 to ATP-using PurZ in adaptation to Z-genome life.}, }
@article {pmid37305433, year = {2023}, author = {van der Does, C and Braun, F and Ren, H and Albers, SV}, title = {Putative nucleotide-based second messengers in archaea.}, journal = {microLife}, volume = {4}, number = {}, pages = {uqad027}, pmid = {37305433}, issn = {2633-6693}, abstract = {Second messengers transfer signals from changing intra- and extracellular conditions to a cellular response. Over the last few decades, several nucleotide-based second messengers have been identified and characterized in especially bacteria and eukaryotes. Also in archaea, several nucleotide-based second messengers have been identified. This review will summarize our understanding of nucleotide-based second messengers in archaea. For some of the nucleotide-based second messengers, like cyclic di-AMP and cyclic oligoadenylates, their roles in archaea have become clear. Cyclic di-AMP plays a similar role in osmoregulation in euryarchaea as in bacteria, and cyclic oligoadenylates are important in the Type III CRISPR-Cas response to activate CRISPR ancillary proteins involved in antiviral defense. Other putative nucleotide-based second messengers, like 3',5'- and 2',3'-cyclic mononucleotides and adenine dinucleotides, have been identified in archaea, but their synthesis and degradation pathways, as well as their functions as secondary messengers, still remain to be demonstrated. In contrast, 3'-3'-cGAMP has not yet been identified in archaea, but the enzymes required to synthesize 3'-3'-cGAMP have been found in several euryarchaeotes. Finally, the widely distributed bacterial second messengers, cyclic diguanosine monophosphate and guanosine (penta-)/tetraphosphate, do not appear to be present in archaea.}, }
@article {pmid37293225, year = {2023}, author = {Jia, Z and Lipus, D and Burckhardt, O and Bussert, R and Sondermann, M and Bartholomäus, A and Wagner, D and Kallmeyer, J}, title = {Enrichment of rare methanogenic Archaea shows their important ecological role in natural high-CO2 terrestrial subsurface environments.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1105259}, pmid = {37293225}, issn = {1664-302X}, abstract = {INTRODUCTION: Long-term stability of underground CO2 storage is partially affected by microbial activity but our knowledge of these effects is limited, mainly due to a lack of sites. A consistently high flux of mantle-derived CO2 makes the Eger Rift in the Czech Republic a natural analogue to underground CO2 storage. The Eger Rift is a seismically active region and H2 is produced abiotically during earthquakes, providing energy to indigenous microbial communities.<br><br>METHODS: To investigate the response of a microbial ecosystem to high levels of CO2 and H2, we enriched microorganisms from samples from a 239.5 m long drill core from the Eger Rift. Microbial abundance, diversity and community structure were assessed using qPCR and 16S rRNA gene sequencing. Enrichment cultures were set up with minimal mineral media and H2/CO2 headspace to simulate a seismically active period with elevated H2.<br><br>RESULTS AND DISCUSSION: Methane headspace concentrations in the enrichments indicated that active methanogens were almost exclusively restricted to enrichment cultures from Miocene lacustrine deposits (50-60 m), for which we observed the most significant growth. Taxonomic assessment showed microbial communities in these enrichments to be less diverse than those with little or no growth. Active enrichments were especially abundant in methanogens of the taxa Methanobacterium and Methanosphaerula. Concurrent to the emergence of methanogenic archaea, we also observed sulfate reducers with the metabolic ability to utilize H2 and CO2, specifically the genus Desulfosporosinus, which were able to outcompete methanogens in several enrichments. Low microbial abundance and a diverse non-CO2 driven microbial community, similar to that in drill core samples, also reflect the inactivity in these cultures. Significant growth of sulfate reducing and methanogenic microbial taxa, which make up only a small fraction of the total microbial community, emphasize the need to account for rare biosphere taxa when assessing the metabolic potential of microbial subsurface populations. The observation that CO2 and H2-utilizing microorganisms could only be enriched from a narrow depth interval suggests that factors such as sediment heterogeneity may also be important. This study provides new insight on subsurface microbes under the influence of high CO2 concentrations, similar to those found in CCS sites.}, }
@article {pmid37277532, year = {2023}, author = {Catchpole, RJ and Barbe, V and Magdelenat, G and Marguet, E and Terns, M and Oberto, J and Forterre, P and Da Cunha, V}, title = {A self-transmissible plasmid from a hyperthermophile that facilitates genetic modification of diverse Archaea.}, journal = {Nature microbiology}, volume = {8}, number = {7}, pages = {1339-1347}, pmid = {37277532}, issn = {2058-5276}, support = {R35 GM118160/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaea/genetics ; Plasmids/genetics ; *DNA/genetics ; Bacteria/genetics ; Genome, Archaeal ; }, abstract = {Conjugative plasmids are self-transmissible mobile genetic elements that transfer DNA between host cells via type IV secretion systems (T4SS). While T4SS-mediated conjugation has been well-studied in bacteria, information is sparse in Archaea and known representatives exist only in the Sulfolobales order of Crenarchaeota. Here we present the first self-transmissible plasmid identified in a Euryarchaeon, Thermococcus sp. 33-3. The 103 kbp plasmid, pT33-3, is seen in CRISPR spacers throughout the Thermococcales order. We demonstrate that pT33-3 is a bona fide conjugative plasmid that requires cell-to-cell contact and is dependent on canonical, plasmid-encoded T4SS-like genes. Under laboratory conditions, pT33-3 transfers to various Thermococcales and transconjugants propagate at 100 °C. Using pT33-3, we developed a genetic toolkit that allows modification of phylogenetically diverse Archaeal genomes. We demonstrate pT33-3-mediated plasmid mobilization and subsequent targeted genome modification in previously untransformable Thermococcales species, and extend this process to interphylum transfer to a Crenarchaeon.}, }
@article {pmid37264141, year = {2023}, author = {Zehnle, H and Laso-Pérez, R and Lipp, J and Riedel, D and Benito Merino, D and Teske, A and Wegener, G}, title = {Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes.}, journal = {Nature microbiology}, volume = {8}, number = {7}, pages = {1199-1212}, pmid = {37264141}, issn = {2058-5276}, mesh = {Archaea ; *Petroleum/metabolism ; *Hydrothermal Vents ; Anaerobiosis ; Alkanes/metabolism ; Sulfates/metabolism ; }, abstract = {Methanogenic and methanotrophic archaea produce and consume the greenhouse gas methane, respectively, using the reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multicarbon alkanes have been recovered from archaeal enrichment cultures. These enzymes, called alkyl-coenzyme M reductase (Acrs), are widespread in the environment but remain poorly understood. Here we produced anoxic cultures degrading mid-chain petroleum n-alkanes between pentane (C5) and tetradecane (C14) at 70 °C using oil-rich Guaymas Basin sediments. In these cultures, archaea of the genus Candidatus Alkanophaga activate the alkanes with Acrs and completely oxidize the alkyl groups to CO2. Ca. Alkanophaga form a deep-branching sister clade to the methanotrophs ANME-1 and are closely related to the short-chain alkane oxidizers Ca. Syntrophoarchaeum. Incapable of sulfate reduction, Ca. Alkanophaga shuttle electrons released from alkane oxidation to the sulfate-reducing Ca. Thermodesulfobacterium syntrophicum. These syntrophic consortia are potential key players in petroleum degradation in heated oil reservoirs.}, }
@article {pmid37256053, year = {2023}, author = {Hou, G and Wazir, ZG and Liu, J and Wang, G and Rong, F and Xu, Y and Li, M and Liu, K and Liu, A and Liu, H and Wang, F}, title = {Effects of sulfadiazine and Cu on soil potential nitrification and ammonia-oxidizing archaea and bacteria communities across different soils.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1153199}, pmid = {37256053}, issn = {1664-302X}, abstract = {INTRODUCTION: Sulfadiazine (SDZ) and copper (Cu) are frequently detected in agricultural soils, but little is known on their single or combined impact on ammonia oxidizing microbial community and function across different soils.<br><br>METHODS: In this study, a microcosm was conducted to distinguish the microbial ecotoxicity of SDZ and Cu across different soils by analyzing soil potential nitrification rate (PNR) and the amoA gene sequences.<br><br>RESULTS: The results showed that the single spiking of SDZ caused a consistent decrease of soil PNR among three tested soils, but no consistent synergistic inhibition of SDZ and Cu was observed across these soils. Moreover, across three tested soils, the distinct responses to the single or joint exposure of SDZ and Cu were found in amoA gene abundance, and diversity as well as the identified genus taxa of ammonia-oxidizing archaea (AOA) and bacteria (AOB). Meanwhile, only the specific genus taxa of AOA or AOB consistently corresponded to the variation of soil PNR across different treated soils. The further principal component analysis (PCA) exhibited that the variable influence of SDZ and Cu on ammonia oxidizing microbial community and function was greatly dependent on soil type.<br><br>DISCUSSION: Therefore, in addition to ecological functionality and the specific prokaryotic taxa, soil microbial ecotoxicity of SDZ and Cu also was dependent on edaphic factors derived from soil types. This study proposes an integrative assessment of soil properties and multiple microbial targets to soil contamination management.}, }
@article {pmid37252776, year = {2023}, author = {Wang, BB and Bao, CX and Sun, YP and Hou, J and Cui, HL}, title = {Halobacterium wangiae sp. nov. and Halobacterium zhouii sp. nov., two extremely halophilic archaea isolated from sediment of a salt lake and saline soil of an inland saltern.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {5}, pages = {}, doi = {10.1099/ijsem.0.005922}, pmid = {37252776}, issn = {1466-5034}, mesh = {*Halobacterium ; RNA, Ribosomal, 16S/genetics ; Lakes/microbiology ; Fatty Acids/chemistry ; Phylogeny ; Base Composition ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Glycolipids/chemistry ; China ; DNA, Archaeal/genetics ; *Halobacteriaceae ; }, abstract = {Two novel halophilic archaeal strains, Gai3-17[T] and XZYJT26[T], were isolated from the sediment of Gaize salt lake and the saline soil of Mangkang ancient solar saltern in Tibet, PR China, respectively. Strains Gai3-17[T] and XZYJT26[T] were related to each other (96.5 and 89.7% similarity, respectively) and showed 97.5-95.4 and 91.5-87.7% similarities to the current members of Halobacterium based on 16S rRNA and rpoB' genes. The phylogenomic analysis indicated that strains Gai3-17[T] and XZYJT26[T] formed two distinct clades and clustered with the Halobacterium species. The two strains can be differentiated from the type strains of the six species with validly published names based on several phenotypic characteristics. The phospholipids of the two strains were phosphatidic acid, phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. One major glycolipid, sulphated galactosyl mannosyl glucosyl diether, was detected in strain Gai3-17[T], while four glycolipids, mannosyl glucosyl diether, sulphated mannosyl glucosyl diether, disulphated mannosyl glucosyl diether and sulphated galactosyl mannosyl glucosyl diether were observed in strain XZYJT26[T]. The average nucleotide identity, digital DNA-DNA hybridization and amino acid identity values among the two strains and the members of Halobacterium were no more than 81, 25 and 77 %, respectively. These overall genome-related indices were below the threshold values for species boundary, indicating that strains Gai3-17[T] and XZYJT26[T] represent two novel species of Halobacterium. Thus, two novel species, Halobacterium wangiae sp. nov. and Halobacterium zhouii sp. nov., are proposed to accommodate strains Gai3-17[T] (=CGMCC 1.16101[T]=JCM 33551[T]) and XZYJT26[T] (=CGMCC 1.16682[T]=JCM 33556[T]), respectively.}, }
@article {pmid37237946, year = {2023}, author = {Ávila-Román, J and Gómez-Villegas, P and de Carvalho, CCCR and Vigara, J and Motilva, V and León, R and Talero, E}, title = {Up-Regulation of the Nrf2/HO-1 Antioxidant Pathway in Macrophages by an Extract from a New Halophilic Archaea Isolated in Odiel Saltworks.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, pmid = {37237946}, issn = {2076-3921}, support = {US-1380844//Operative FEDER Program-Andaluc&#xed;a 2014-2020/ ; UHU-1257518//Operative FEDER Program-Andaluc&#xed;a 2014-2020/ ; PID2019-110438RB-C22 -AEI/FEDER//Spanish Agencia Estatal de Investigaci&#xf3;n/ ; 2020-PY20//the Andalusian government (I+D+i-JA-PAIDI-Retos projects/ ; }, abstract = {The production of reactive oxygen species (ROS) plays an important role in the progression of many inflammatory diseases. The search for antioxidants with the ability for scavenging free radicals from the body cells that reduce oxidative damage is essential to prevent and treat these pathologies. Haloarchaea are extremely halophilic microorganisms that inhabit hypersaline environments, such as saltworks or salt lakes, where they have to tolerate high salinity, and elevated ultraviolet (UV) and infrared radiations. To cope with these extreme conditions, haloarchaea have developed singular mechanisms to maintain an osmotic balance with the medium, and are endowed with unique compounds, not found in other species, with bioactive properties that have not been fully explored. This study aims to assess the potential of haloarchaea as a new source of natural antioxidant and anti-inflammatory agents. A carotenoid-producing haloarchaea was isolated from Odiel Saltworks (OS) and identified on the basis of its 16S rRNA coding gene sequence as a new strain belonging to the genus Haloarcula. The Haloarcula sp. OS acetone extract (HAE) obtained from the biomass contained bacterioruberin and mainly C18 fatty acids, and showed potent antioxidant capacity using ABTS assay. This study further demonstrates, for the first time, that pretreatment with HAE of lipopolysaccharide (LPS)-stimulated macrophages results in a reduction in ROS production, a decrease in the pro-inflammatory cytokines TNF-α and IL-6 levels, and up-regulation of the factor Nrf2 and its target gene heme oxygenase-1 (HO-1), supporting the potential of the HAE as a therapeutic agent in the treatment of oxidative stress-related inflammatory diseases.}, }
@article {pmid37204206, year = {2023}, author = {Ma, X and Hu, Y and Li, XX and Tan, S and Cheng, M and Hou, J and Cui, HL}, title = {Halomicroarcula laminariae sp. nov. and Halomicroarcula marina sp. nov., extremely halophilic archaea isolated from salted brown alga Laminaria and coastal saline-alkali lands.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {5}, pages = {}, doi = {10.1099/ijsem.0.005889}, pmid = {37204206}, issn = {1466-5034}, mesh = {*Laminaria ; *Halobacteriaceae ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Glycolipids/chemistry ; Fatty Acids/chemistry ; Base Composition ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Sodium Chloride ; *Halobacteriales ; *Haloarcula ; Comparative Genomic Hybridization ; China ; DNA, Archaeal/genetics ; }, abstract = {Four extremely halophilic archaeal strains, LYG-108[T], LYG-24, DT1[T] and YSSS71, were isolated from salted Laminaria produced in Lianyungang and saline soil from the coastal beach at Jiangsu, PR China. The four strains were found to be related to the current species of Halomicroarcula (showing 88.1-98.5% and 89.3-93.6% similarities, respectively) as revealed by phylogenetic analysis based on 16S rRNA and rpoB' genes. These phylogenies were fully supported by the phylogenomic analysis, and the overall genome-related indexes (average nucleotide identity, DNA-DNA hybridization and average amino acid identity) among these four strains and the Halomicroarcula species were 77-84 %, 23-30 % and 71-83 %, respectively, clearly below the threshold values for species demarcation. Additionally, the phylogenomic and comparative genomic analyses revealed that Halomicroarcula salina YGH18[T] is related to the current species of Haloarcula rather than those of Halomicroarcula, Haloarcula salaria Namwong et al. 2011 is a later heterotypic synonym of Haloarcula argentinensis Ihara et al. 1997, and Haloarcula quadrata Oren et al. 1999 is a later heterotypic synonym of Haloarcula marismortui Oren et al. 1990. The major polar lipids of strains LYG-108[T], LYG-24, DT1[T] and YSSS71 were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulphate, sulphated mannosyl glucosyl diether and additional glycosyl-cardiolipins. All these results showed that strains LYG-108[T] (=CGMCC 1.13607[T]=JCM 32950[T]) and LYG-24 (=CGMCC 1.13605=JCM 32949) represent a new species of the genus Halomicroarcula, for which the name Halomicroarcula laminariae sp. nov. is proposed; strains DT1[T] (=CGMCC 1.18928[T]=JCM 35414[T]) and YSSS71 (=CGMCC 1.18783=JCM 34915) also represent a new species of the genus Halomicroarcula, for which the name Halomicroarcula marina sp. nov. is proposed.}, }
@article {pmid37202434, year = {2023}, author = {Wang, Z and Li, Y and Zheng, W and Ji, Y and Duan, M and Ma, L}, title = {Ammonia oxidizing archaea and bacteria respond to different manure application rates during organic vegetable cultivation in Northwest China.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8064}, pmid = {37202434}, issn = {2045-2322}, mesh = {*Archaea/genetics ; *Ammonia ; Vegetables ; Manure/microbiology ; Oxidation-Reduction ; Bacteria/genetics ; China ; Nitrification ; Carbon ; Nitrogen ; Soil Microbiology ; Phylogeny ; }, abstract = {Ammonia oxidization is a critical process in nitrogen cycling that involves ammonia oxidizing archaea (AOA) and bacteria (AOB). However, the effects of different manure amounts on ammonia-oxidizing microorganisms (AOMs) over the course of organic vegetables production remains unclear. We used the amoA gene to evaluated AOMs abundance and community structure in organic vegetable fields. Quantitative PCR revealed that AOB were more abundant than AOA. Among them, the amoA copy number of AOB treated with 900 kgN ha[-1] was 21.3 times that of AOA. The potential nitrification rate was significantly correlated with AOB abundance (P < 0.0001) but not with AOA, suggesting that AOB might contribute more to nitrification than AOA. AOB sequences were classified into Nitrosomonas and Nitrosospira, and AOA into Nitrosopumilus and Nitrososphaera. Nitrosomonas and Nitrosopumilus were predominant in treatments that received manure nitrogen at ≥ 900 kg ha[-1] (52.7-56.5%) and when manure was added (72.7-99.8%), respectively, whereas Nitrosospira and Nitrososphaera occupied more than a half percentage in those that received ≤ 600 kg ha[-1] (58.4-84.9%) and no manure (59.6%). A similar manure rate resulted in more identical AOMs' community structures than greater difference manure rate. The bacterial amoA gene abundances and ratios of AOB and AOA showed significantly positive correlations with soil electrical conductivity, total carbon and nitrogen, nitrate, phosphorus, potassium, and organic carbon, indicating that these were potential key factors influencing AOMs. This study explored the AOMs' variation in organic vegetable fields in Northwest China and provided a theoretical basis and reference for the subsequent formulation of proper manure management.}, }
@article {pmid37198640, year = {2023}, author = {Dondjou, DT and Diedhiou, AG and Mbodj, D and Mofini, MT and Pignoly, S and Ndiaye, C and Diedhiou, I and Assigbetse, K and Manneh, B and Laplaze, L and Kane, A}, title = {Rice developmental stages modulate rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization in a West African Sahelian agro-ecosystem.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {42}, pmid = {37198640}, issn = {2524-6372}, abstract = {BACKGROUND: Rhizosphere microbial communities are important components of the soil-plant continuum in paddy field ecosystems. These rhizosphere communities contribute to nutrient cycling and rice productivity. The use of fertilizers is a common agricultural practice in rice paddy fields. However, the long-term impact of the fertilizers usage on the rhizosphere microbial communities at different rice developmental stages remains poorly investigated. Here, we examined the effects of long-term (27 years) N and NPK-fertilization on bacterial and archaeal community inhabiting the rice rhizosphere at three developmental stages (tillering, panicle initiation and booting) in the Senegal River Delta.<br><br>RESULTS: We found that the effect of long-term inorganic fertilization on rhizosphere microbial communities varied with the rice developmental stage, and between microbial communities in their response to N and NPK-fertilization. The microbial communities inhabiting the rice rhizosphere at panicle initiation appear to be more sensitive to long-term inorganic fertilization than those at tillering and booting stages. However, the effect of developmental stage on microbial sensitivity to long-term inorganic fertilization was more pronounced for bacterial than archaeal community. Furthermore, our data reveal dynamics of bacteria and archaea co-occurrence patterns in the rice rhizosphere, with differentiated bacterial and archaeal pivotal roles in the microbial inter-kingdom networks across developmental stages.<br><br>CONCLUSIONS: Our study brings new insights on rhizosphere bacteria and archaea co-occurrence and the long-term inorganic fertilization impact on these communities across developmental stages in field-grown rice. It would help in developing strategies for the successful manipulation of microbial communities to improve rice yields.}, }
@article {pmid37196775, year = {2023}, author = {Aparici-Carratalá, D and Esclapez, J and Bautista, V and Bonete, MJ and Camacho, M}, title = {Archaea: current and potential biotechnological applications.}, journal = {Research in microbiology}, volume = {174}, number = {7}, pages = {104080}, doi = {10.1016/j.resmic.2023.104080}, pmid = {37196775}, issn = {1769-7123}, mesh = {*Archaea/genetics/metabolism ; *Biotechnology ; }, abstract = {Archaea are microorganisms with great ability to colonize some of the most inhospitable environments in nature, managing to survive in places with extreme characteristics for most microorganisms. Its proteins and enzymes are stable and can act under extreme conditions in which other proteins and enzymes would degrade. These attributes make them ideal candidates for use in a wide range of biotechnological applications. This review describes the most important applications, both current and potential, that archaea present in Biotechnology, classifying them according to the sector to which the application is directed. It also analyzes the advantages and disadvantages of its use.}, }
@article {pmid37194083, year = {2023}, author = {Romero, R and Gervasi, MT and DiGiulio, DB and Jung, E and Suksai, M and Miranda, J and Theis, KR and Gotsch, F and Relman, DA}, title = {Are bacteria, fungi, and archaea present in the midtrimester amniotic fluid?.}, journal = {Journal of perinatal medicine}, volume = {51}, number = {7}, pages = {886-890}, pmid = {37194083}, issn = {1619-3997}, support = {HHSN275201300006C/HD/NICHD NIH HHS/United States ; Z01 HD002400/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Pregnancy ; Female ; Humans ; *Amniotic Fluid/microbiology ; Pregnancy Trimester, Second ; *Chorioamnionitis/microbiology ; Archaea ; Retrospective Studies ; Bacteria ; Inflammation ; Fungi ; }, abstract = {OBJECTIVES: This study was conducted to determine whether bacteria, fungi, or archaea are detected in the amniotic fluid of patients who underwent midtrimester amniocentesis for clinical indications.<br><br>METHODS: Amniotic fluid samples from 692 pregnancies were tested by using a combination of culture and end-point polymerase chain reaction (PCR) techniques. Intra-amniotic inflammation was defined as an interleukin-6 concentration >2,935 pg/mL.<br><br>RESULTS: Microorganisms were detected in 0.3% (2/692) of cases based on cultivation, 1.73% (12/692) based on broad-range end-point PCR, and 2% (14/692) based on the combination of both methods. However, most (13/14) of these cases did not have evidence of intra-amniotic inflammation and delivered at term. Therefore, a positive culture or end-point PCR in most patients appears to have no apparent clinical significance.<br><br>CONCLUSIONS: Amniotic fluid in the midtrimester of pregnancy generally does not contain bacteria, fungi, or archaea. Interpretation of amniotic fluid culture and molecular microbiologic results is aided by the assessment of the inflammatory state of the amniotic cavity. The presence of microorganisms, as determined by culture or a microbial signal in the absence of intra-amniotic inflammation, appears to be a benign condition.}, }
@article {pmid37192814, year = {2023}, author = {Grünberger, F and Jüttner, M and Knüppel, R and Ferreira-Cerca, S and Grohmann, D}, title = {Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea.}, journal = {RNA (New York, N.Y.)}, volume = {29}, number = {8}, pages = {1255-1273}, pmid = {37192814}, issn = {1469-9001}, mesh = {RNA, Ribosomal/genetics ; RNA ; Archaea/genetics ; *Nanopore Sequencing ; DNA, Complementary ; *Nanopores ; Sequence Analysis, RNA ; }, abstract = {Ribosomal RNA (rRNA) maturation in archaea is a complex multistep process that requires well-defined endo- and exoribonuclease activities to generate fully mature linear rRNAs. However, technical challenges prevented detailed mapping of rRNA processing steps and a systematic analysis of rRNA maturation pathways across the tree of life. In this study, we used long-read (PCR)-cDNA and direct RNA nanopore-based sequencing to study rRNA maturation in three archaeal model organisms, namely the Euryarchaea Haloferax volcanii and Pyrococcus furiosus and the Crenarchaeon Sulfolobus acidocaldarius Compared to standard short-read protocols, nanopore sequencing facilitates simultaneous readout of 5'- and 3'-positions, which is required for the classification of rRNA processing intermediates. More specifically, we (i) accurately detect and describe rRNA maturation stages by analysis of terminal read positions of cDNA reads and thereupon (ii) explore the stage-dependent installation of the KsgA-mediated dimethylations in H. volcanii using base-calling and signal characteristics of direct RNA reads. Due to the single-molecule sequencing capacity of nanopore sequencing, we could detect hitherto unknown intermediates with high confidence, revealing details about the maturation of archaea-specific circular rRNA intermediates. Taken together, our study delineates common principles and unique features of rRNA processing in euryarchaeal and crenarchaeal representatives, thereby significantly expanding our understanding of rRNA maturation pathways in archaea.}, }
@article {pmid37171866, year = {2023}, author = {Pallen, MJ and Rodriguez-R, LM and Alikhan, NF}, title = {Corrigendum: Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {5}, pages = {}, doi = {10.1099/ijsem.0.005885}, pmid = {37171866}, issn = {1466-5034}, }
@article {pmid37154724, year = {2023}, author = {Demey, LM and Gumerov, VM and Xing, J and Zhulin, IB and DiRita, VJ}, title = {Transmembrane Transcription Regulators Are Widespread in Bacteria and Archaea.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0026623}, pmid = {37154724}, issn = {2165-0497}, support = {R35 GM131760/GM/NIGMS NIH HHS/United States ; T32 GM092715/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Archaea/genetics/metabolism ; *Bacteria/genetics/metabolism ; Cell Membrane/metabolism ; Signal Transduction ; Protein Domains ; Bacterial Proteins/genetics/metabolism ; }, abstract = {To adapt and proliferate, bacteria must sense and respond to the ever-changing environment. Transmembrane transcription regulators (TTRs) are a family of one-component transcription regulators that respond to extracellular information and influence gene expression from the cytoplasmic membrane. How TTRs function to modulate expression of their target genes while localized to the cytoplasmic membrane remains poorly understood. In part, this is due to a lack of knowledge regarding the prevalence of TTRs among prokaryotes. Here, we show that TTRs are highly diverse and prevalent throughout bacteria and archaea. Our work demonstrates that TTRs are more common than previously appreciated and are enriched within specific bacterial and archaeal phyla and that many TTRs have unique transmembrane region properties that can facilitate association with detergent-resistant membranes. IMPORTANCE One-component signal transduction systems are the major class of signal transduction systems among bacteria and are commonly cytoplasmic. TTRs are a group of unique one-component signal transduction systems that influence transcription from the cytoplasmic membrane. TTRs have been implicated in a wide array of biological pathways critical for both pathogens and human commensal organisms but were considered to be rare. Here, we demonstrate that TTRs are in fact highly diverse and broadly distributed in bacteria and archaea. Our findings suggest that transcription factors can access the chromosome and influence transcription from the membrane in both archaea and bacteria. This study challenges thus the commonly held notion that signal transduction systems require a cytoplasmic transcription factor and highlights the importance of the cytoplasmic membrane in directly influencing signal transduction.}, }
@article {pmid37117330, year = {2023}, author = {Hodgskiss, LH and Melcher, M and Kerou, M and Chen, W and Ponce-Toledo, RI and Savvides, SN and Wienkoop, S and Hartl, M and Schleper, C}, title = {Correction to: Unexpected complexity of the ammonia monooxygenase in archaea.}, journal = {The ISME journal}, volume = {17}, number = {6}, pages = {947}, doi = {10.1038/s41396-023-01403-2}, pmid = {37117330}, issn = {1751-7370}, }
@article {pmid37100405, year = {2023}, author = {Jaffe, AL and Castelle, CJ and Banfield, JF}, title = {Habitat Transition in the Evolution of Bacteria and Archaea.}, journal = {Annual review of microbiology}, volume = {77}, number = {}, pages = {193-212}, doi = {10.1146/annurev-micro-041320-032304}, pmid = {37100405}, issn = {1545-3251}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; *Bacteriophages ; Genomics ; *Microbiota ; }, abstract = {Related groups of microbes are widely distributed across Earth's habitats, implying numerous dispersal and adaptation events over evolutionary time. However, relatively little is known about the characteristics and mechanisms of these habitat transitions, particularly for populations that reside in animal microbiomes. Here, we review the literature concerning habitat transitions among a variety of bacterial and archaeal lineages, considering the frequency of migration events, potential environmental barriers, and mechanisms of adaptation to new physicochemical conditions, including the modification of protein inventories and other genomic characteristics. Cells dependent on microbial hosts, particularly bacteria from the Candidate Phyla Radiation, have undergone repeated habitat transitions from environmental sources into animal microbiomes. We compare their trajectories to those of both free-living cells-including the Melainabacteria, Elusimicrobia, and methanogenic archaea-and cellular endosymbionts and bacteriophages, which have made similar transitions. We conclude by highlighting major related topics that may be worthy of future study.}, }
@article {pmid37098974, year = {2023}, author = {Chen, X and Molenda, O and Brown, CT and Toth, CRA and Guo, S and Luo, F and Howe, J and Nesbø, CL and He, C and Montabana, EA and Cate, JHD and Banfield, JF and Edwards, EA}, title = {"Candidatus Nealsonbacteria" Are Likely Biomass Recycling Ectosymbionts of Methanogenic Archaea in a Stable Benzene-Degrading Enrichment Culture.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {5}, pages = {e0002523}, pmid = {37098974}, issn = {1098-5336}, support = {P01 GM051487/GM/NIGMS NIH HHS/United States ; R01 GM065050/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaea/metabolism ; Benzene/metabolism ; Phylogeny ; Biomass ; RNA, Ribosomal, 16S/genetics/metabolism ; In Situ Hybridization, Fluorescence ; Bacteria/genetics ; *Euryarchaeota/metabolism ; }, abstract = {The Candidate Phyla Radiation (CPR), also referred to as superphylum Patescibacteria, is a very large group of bacteria with no pure culture representatives discovered by 16S rRNA sequencing or genome-resolved metagenomic analyses of environmental samples. Within the CPR, candidate phylum Parcubacteria, previously referred to as OD1, is prevalent in anoxic sediments and groundwater. Previously, we had identified a specific member of the Parcubacteria (referred to as DGGOD1a) as an important member of a methanogenic benzene-degrading consortium. Phylogenetic analyses herein place DGGOD1a within the clade "Candidatus Nealsonbacteria." Because of its persistence over many years, we hypothesized that "Ca. Nealsonbacteria" DGGOD1a must play an important role in sustaining anaerobic benzene metabolism in the consortium. To try to identify its growth substrate, we amended the culture with a variety of defined compounds (pyruvate, acetate, hydrogen, DNA, and phospholipid), as well as crude culture lysate and three subfractions thereof. We observed the greatest (10-fold) increase in the absolute abundance of "Ca. Nealsonbacteria" DGGOD1a only when the consortium was amended with crude cell lysate. These results implicate "Ca. Nealsonbacteria" in biomass recycling. Fluorescence in situ hybridization and cryogenic transmission electron microscope images revealed that "Ca. Nealsonbacteria" DGGOD1a cells were attached to larger archaeal Methanothrix cells. This apparent epibiont lifestyle was supported by metabolic predictions from a manually curated complete genome. This is one of the first examples of bacterial-archaeal episymbiosis and may be a feature of other "Ca. Nealsonbacteria" found in anoxic environments. IMPORTANCE An anaerobic microbial enrichment culture was used to study members of candidate phyla that are difficult to grow in the lab. We were able to visualize tiny "Candidatus Nealsonbacteria" cells attached to a large Methanothrix cell, revealing a novel episymbiosis.}, }
@article {pmid37097839, year = {2023}, author = {Prakash, O and Dodsworth, JA and Dong, X and Ferry, JG and L'Haridon, S and Imachi, H and Kamagata, Y and Rhee, SK and Sagar, I and Shcherbakova, V and Wagner, D and Whitman, WB}, title = {Proposed minimal standards for description of methanogenic archaea.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {4}, pages = {}, doi = {10.1099/ijsem.0.005500}, pmid = {37097839}, issn = {1466-5034}, mesh = {*Archaea/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; Base Composition ; Bacterial Typing Techniques/methods ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Euryarchaeota/genetics ; Methane/metabolism ; }, abstract = {Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA-DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.}, }
@article {pmid37093039, year = {2023}, author = {Dithugoe, CD and Bezuidt, OKI and Cavan, EL and Froneman, WP and Thomalla, SJ and Makhalanyane, TP}, title = {Bacteria and Archaea Regulate Particulate Organic Matter Export in Suspended and Sinking Marine Particle Fractions.}, journal = {mSphere}, volume = {8}, number = {3}, pages = {e0042022}, pmid = {37093039}, issn = {2379-5042}, support = {0182/2017//Department of Science and Technology, Republic of South Africa (DST)/ ; 110729//National Research Foundation (NRF)/ ; 148867//National Research Foundation (NRF)/ ; }, mesh = {*Archaea/genetics/metabolism ; *Seawater/microbiology ; Particulate Matter/metabolism ; Bacteria/genetics/metabolism ; Dissolved Organic Matter ; Carbon/metabolism ; }, abstract = {The biological carbon pump (BCP) in the Southern Ocean is driven by phytoplankton productivity and is a significant organic matter sink. However, the role of particle-attached (PA) and free-living (FL) prokaryotes (bacteria and archaea) and their diversity in influencing the efficiency of the BCP is still unclear. To investigate this, we analyzed the metagenomes linked to suspended and sinking marine particles from the Sub-Antarctic Southern Ocean Time Series (SOTS) by deploying a Marine Snow Catcher (MSC), obtaining suspended and sinking particulate material, determining organic carbon and nitrogen flux, and constructing metagenome-assembled genomes (MAGs). The suspended and sinking particle-pools were dominated by bacteria with the potential to degrade organic carbon. Bacterial communities associated with the sinking fraction had more genes related to the degradation of complex organic carbon than those in the suspended fraction. Archaea had the potential to drive nitrogen metabolism via nitrite and ammonia oxidation, altering organic nitrogen concentration. The data revealed several pathways for chemoautotrophy and the secretion of recalcitrant dissolved organic carbon (RDOC) from CO2, with bacteria and archaea potentially sequestering particulate organic matter (POM) via the production of RDOC. These findings provide insights into the diversity and function of prokaryotes in suspended and sinking particles and their role in organic carbon/nitrogen export in the Southern Ocean. IMPORTANCE The biological carbon pump is crucial for the export of particulate organic matter in the ocean. Recent studies on marine microbes have shown the profound influence of bacteria and archaea as regulators of particulate organic matter export. Yet, despite the importance of the Southern Ocean as a carbon sink, we lack comparable insights regarding microbial contributions. This study provides the first insights regarding prokaryotic contributions to particulate organic matter export in the Southern Ocean. We reveal evidence that prokaryotic communities in suspended and sinking particle fractions harbor widespread genomic potential for mediating particulate organic matter export. The results substantially enhance our understanding of the role played by microorganisms in regulating particulate organic matter export in suspended and sinking marine fractions in the Southern Ocean.}, }
@article {pmid37083735, year = {2023}, author = {Roux, S and Camargo, AP and Coutinho, FH and Dabdoub, SM and Dutilh, BE and Nayfach, S and Tritt, A}, title = {iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria.}, journal = {PLoS biology}, volume = {21}, number = {4}, pages = {e3002083}, pmid = {37083735}, issn = {1545-7885}, mesh = {*Archaea/genetics ; Metagenome/genetics ; *Viruses/genetics ; Bacteria/genetics ; Metagenomics/methods ; Machine Learning ; Genome, Viral/genetics ; }, abstract = {The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied through metagenomics. While metagenomes enable high-throughput exploration of the viral sequence space, metagenome-derived sequences lack key information compared to isolated viruses, in particular host association. Different computational approaches are available to predict the host(s) of uncultivated viruses based on their genome sequences, but thus far individual approaches are limited either in precision or in recall, i.e., for a number of viruses they yield erroneous predictions or no prediction at all. Here, we describe iPHoP, a two-step framework that integrates multiple methods to reliably predict host taxonomy at the genus rank for a broad range of viruses infecting bacteria and archaea, while retaining a low false discovery rate. Based on a large dataset of metagenome-derived virus genomes from the IMG/VR database, we illustrate how iPHoP can provide extensive host prediction and guide further characterization of uncultivated viruses.}, }
@article {pmid37082172, year = {2023}, author = {Zhang, Z and Fusco, S}, title = {Editorial: New insights into the genetic mechanisms of thermophilic archaea.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1185784}, pmid = {37082172}, issn = {1664-302X}, }
@article {pmid37072332, year = {2023}, author = {Nikonov, OS and Nikonova, EY and Tarabarova, AG and Mikhaylina, AO and Kravchenko, OV and Nevskaya, NA and Nikonov, SV}, title = {Recognition of γ-Subunit by β-Subunit in Translation Initiation Factor 2. Stabilization of the GTP-Bound State of I/F 2 in Archaea and Eukaryotes.}, journal = {Biochemistry. Biokhimiia}, volume = {88}, number = {2}, pages = {221-230}, doi = {10.1134/S0006297923020062}, pmid = {37072332}, issn = {1608-3040}, mesh = {Binding Sites ; *Prokaryotic Initiation Factor-2/chemistry ; *Eukaryota/genetics/metabolism ; Archaea/genetics/metabolism ; Guanosine Triphosphate ; }, abstract = {Eukaryotic and archaeal translation initiation factor 2 (e/aIF2) functions as a heterotrimeric complex. It consists of three subunits (α, β, γ). α- and β-subunits are bound to γ-subunit by hydrogen bonds and van der Waals interactions, but do not contact each other. Although main functions of the factor are performed by the γ-subunit, reliable formation of αγ and βγ complexes is necessary for its proper functioning. In this work, we introduced mutations in the recognition part of the βγ interface and showed that hydrophobic effect plays a crucial role in the recognition of subunits both in eukaryotes and archaea. Shape and properties of the groove on the surface of γ-subunit facilitates transition of the disordered recognition part of the β-subunit into an α-helix containing approximately the same number of residues in archaea and eukaryotes. In addition, based on the newly obtained data, it was concluded that in archaea and eukaryotes, transition of the γ-subunit to the active state leads to additional contact between the region of switch 1 and C-terminal part of the β-subunit, which stabilizes helical conformation of the switch.}, }
@article {pmid37066253, year = {2023}, author = {Cerna-Vargas, JP and Gumerov, VM and Krell, T and Zhulin, IB}, title = {Amine recognizing domain in diverse receptors from bacteria and archaea evolved from the universal amino acid sensor.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37066253}, issn = {2692-8205}, support = {R35 GM131760/GM/NIGMS NIH HHS/United States ; }, abstract = {Bacteria contain many different receptor families that sense different signals permitting an optimal adaptation to the environment. A major limitation in microbiology is the lack of information on the signal molecules that activate receptors. Due to a significant sequence divergence, the signal recognized by sensor domains is only poorly reflected in overall sequence identity. Biogenic amines are of central physiological relevance for microorganisms and serve for example as substrates for aerobic and anaerobic growth, neurotransmitters or osmoprotectants. Based on protein structural information and sequence analysis, we report here the identification of a sequence motif that is specific for amine-sensing dCache sensor domains (dCache_1AM). These domains were identified in more than 13,000 proteins from 8,000 bacterial and archaeal species. dCache_1AM containing receptors were identified in all major receptor families including sensor kinases, chemoreceptors, receptors involved in second messenger homeostasis and Ser/Thr phosphatases. The screening of compound libraries and microcalorimetric titrations of selected dCache_1AM domains confirmed their capacity to specifically bind amines. Mutants in the amine binding motif or domains that contain a single mismatch in the binding motif, had either no or a largely reduced affinity for amines, illustrating the specificity of this motif. We demonstrate that the dCache_1AM domain has evolved from the universal amino acid sensing domain, providing novel insight into receptor evolution. Our approach enables precise "wet"-lab experiments to define the function of regulatory systems and thus holds a strong promise to address an important bottleneck in microbiology: the identification of signals that stimulate numerous receptors.}, }
@article {pmid37066119, year = {2023}, author = {Lach, J and Strapagiel, D and Matera-Witkiewicz, A and Stączek, P}, title = {Draft genomes of halophilic Archaea strains isolated from brines of the Carpathian Foreland, Poland.}, journal = {Journal of genomics}, volume = {11}, number = {}, pages = {20-25}, pmid = {37066119}, issn = {1839-9940}, abstract = {Halophilic Archaea are a unique group of microorganisms living in saline environments. They constitute a complex group whose biodiversity has not been thoroughly studied. Here, we report three draft genomes of halophilic Archaea isolated from brines, representing the genera of Halorubrum, Halopenitus, and Haloarcula. Two of these strains, Boch-26 and POP-27, were identified as members of the genera Halorubrum and Halopenitus, respectively. However, they could not be assigned to any known species because of the excessive difference in genome sequences between these strains and any other described genomes. In contrast, the third strain, Boch-26, was identified as Haloarcula hispanica. Genome lengths of these isolates ranged from 2.7 Mbp to 3.0 Mbp, and GC content was in the 63.77%-68.77% range. Moreover, functional analysis revealed biosynthetic gene clusters (BGCs) related to terpenes production in all analysed genomes and one BGC for RRE (RiPP recognition element)-dependent RiPP (post-translationally modified peptides) biosynthesis. Moreover, the obtained results enhanced the knowledge about the salt mines microbiota biodiversity as a poorly explored environment so far.}, }
@article {pmid37060102, year = {2023}, author = {Liang, H and Song, ZM and Zhong, Z and Zhang, D and Yang, W and Zhou, L and Older, EA and Li, J and Wang, H and Zeng, Z and Li, YX}, title = {Genomic and metabolic analyses reveal antagonistic lanthipeptides in archaea.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {74}, pmid = {37060102}, issn = {2049-2618}, mesh = {*Archaea/genetics/metabolism ; *Archaeal Proteins/genetics/metabolism ; Bacteria/genetics ; Genomics ; Microbial Interactions ; }, abstract = {BACKGROUND: Microbes produce diverse secondary metabolites (SMs) such as signaling molecules and antimicrobials that mediate microbe-microbe interaction. Archaea, the third domain of life, are a large and diverse group of microbes that not only exist in extreme environments but are abundantly distributed throughout nature. However, our understanding of archaeal SMs lags far behind our knowledge of those in bacteria and eukarya.<br><br>RESULTS: Guided by genomic and metabolic analysis of archaeal SMs, we discovered two new lanthipeptides with distinct ring topologies from a halophilic archaeon of class Haloarchaea. Of these two lanthipeptides, archalan &#x3b1; exhibited anti-archaeal activities against halophilic archaea, potentially mediating the archaeal antagonistic interactions in the halophilic niche. To our best knowledge, archalan &#x3b1; represents the first lantibiotic and the first anti-archaeal SM from the archaea domain.<br><br>CONCLUSIONS: Our study investigates the biosynthetic potential of lanthipeptides in archaea, linking lanthipeptides to antagonistic interaction via genomic and metabolic analyses and bioassay. The discovery of these archaeal lanthipeptides is expected to stimulate the experimental study of poorly characterized archaeal chemical biology and highlight the potential of archaea as a new source of bioactive SMs. Video Abstract.}, }
@article {pmid37014908, year = {2023}, author = {Cumsille, A and Durán, RE and Rodríguez-Delherbe, A and Saona-Urmeneta, V and Cámara, B and Seeger, M and Araya, M and Jara, N and Buil-Aranda, C}, title = {GenoVi, an open-source automated circular genome visualizer for bacteria and archaea.}, journal = {PLoS computational biology}, volume = {19}, number = {4}, pages = {e1010998}, pmid = {37014908}, issn = {1553-7358}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Genomics/methods ; Software ; Genome, Microbial ; }, abstract = {The increase in microbial sequenced genomes from pure cultures and metagenomic samples reflects the current attainability of whole-genome and shotgun sequencing methods. However, software for genome visualization still lacks automation, integration of different analyses, and customizable options for non-experienced users. In this study, we introduce GenoVi, a Python command-line tool able to create custom circular genome representations for the analysis and visualization of microbial genomes and sequence elements. It is designed to work with complete or draft genomes, featuring customizable options including 25 different built-in color palettes (including 5 color-blind safe palettes), text formatting options, and automatic scaling for complete genomes or sequence elements with more than one replicon/sequence. Using a Genbank format file as the input file or multiple files within a directory, GenoVi (i) visualizes genomic features from the GenBank annotation file, (ii) integrates a Cluster of Orthologs Group (COG) categories analysis using DeepNOG, (iii) automatically scales the visualization of each replicon of complete genomes or multiple sequence elements, (iv) and generates COG histograms, COG frequency heatmaps and output tables including general stats of each replicon or contig processed. GenoVi's potential was assessed by analyzing single and multiple genomes of Bacteria and Archaea. Paraburkholderia genomes were analyzed to obtain a fast classification of replicons in large multipartite genomes. GenoVi works as an easy-to-use command-line tool and provides customizable options to automatically generate genomic maps for scientific publications, educational resources, and outreach activities. GenoVi is freely available and can be downloaded from https://github.com/robotoD/GenoVi.}, }
@article {pmid37005419, year = {2023}, author = {Tang, SK and Zhi, XY and Zhang, Y and Makarova, KS and Liu, BB and Zheng, GS and Zhang, ZP and Zheng, HJ and Wolf, YI and Zhao, YR and Jiang, SH and Chen, XM and Li, EY and Zhang, T and Chen, PR and Feng, YZ and Xiang, MX and Lin, ZQ and Shi, JH and Chang, C and Zhang, X and Li, R and Lou, K and Wang, Y and Chang, L and Yin, M and Yang, LL and Gao, HY and Zhang, ZK and Tao, TS and Guan, TW and He, FC and Lu, YH and Cui, HL and Koonin, EV and Zhao, GP and Xu, P}, title = {Cellular differentiation into hyphae and spores in halophilic archaea.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1827}, pmid = {37005419}, issn = {2041-1723}, mesh = {Hyphae/genetics ; Proteomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Streptomyces/genetics ; *Halobacteriaceae/genetics ; Spores ; Cell Differentiation ; Sequence Analysis, DNA ; China ; }, abstract = {Several groups of bacteria have complex life cycles involving cellular differentiation and multicellular structures. For example, actinobacteria of the genus Streptomyces form multicellular vegetative hyphae, aerial hyphae, and spores. However, similar life cycles have not yet been described for archaea. Here, we show that several haloarchaea of the family Halobacteriaceae display a life cycle resembling that of Streptomyces bacteria. Strain YIM 93972 (isolated from a salt marsh) undergoes cellular differentiation into mycelia and spores. Other closely related strains are also able to form mycelia, and comparative genomic analyses point to gene signatures (apparent gain or loss of certain genes) that are shared by members of this clade within the Halobacteriaceae. Genomic, transcriptomic and proteomic analyses of non-differentiating mutants suggest that a Cdc48-family ATPase might be involved in cellular differentiation in strain YIM 93972. Additionally, a gene encoding a putative oligopeptide transporter from YIM 93972 can restore the ability to form hyphae in a Streptomyces coelicolor mutant that carries a deletion in a homologous gene cluster (bldKA-bldKE), suggesting functional equivalence. We propose strain YIM 93972 as representative of a new species in a new genus within the family Halobacteriaceae, for which the name Actinoarchaeum halophilum gen. nov., sp. nov. is herewith proposed. Our demonstration of a complex life cycle in a group of haloarchaea adds a new dimension to our understanding of the biological diversity and environmental adaptation of archaea.}, }
@article {pmid37000350, year = {2023}, author = {Hu, Y and Ma, X and Li, XX and Tan, S and Cheng, M and Hou, J and Cui, HL}, title = {Natrinema caseinilyticum sp. nov., Natrinema gelatinilyticum sp. nov., Natrinema marinum sp. nov., Natrinema zhouii sp. nov., extremely halophilic archaea isolated from marine environments and a salt mine.}, journal = {Extremophiles : life under extreme conditions}, volume = {27}, number = {1}, pages = {9}, pmid = {37000350}, issn = {1433-4909}, support = {32070003//National Natural Science Foundation of China/ ; }, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Glycolipids ; Sodium Chloride ; *Halobacteriaceae/genetics ; China ; DNA, Archaeal/genetics ; Sequence Analysis, DNA ; }, abstract = {Four extremely halophilic archaeal strains (ZJ2[T], BND6[T], DT87[T], and YPL30[T]) were isolated from marine environments and a salt mine in China. The 16S rRNA and rpoB' gene sequence similarities among strains ZJ2[T], BND6[T], DT87[T], YPL30[T] and the current species of Natrinema were 93.2-99.3% and 89.2-95.8%, respectively. Both phylogenetic and phylogenomic analyses revealed that strains ZJ2[T], BND6[T], DT87[T], and YPL30[T] cluster with the Natrinema members. The overall genome-related indexes (ANI, isDDH, and AAI) among these four strains and the current species of genus Natrinema were 70-88%, 22-43% and 75-89%, respectively, clearly below the threshold values for species boundary. Strains ZJ2[T], BND6[T], DT87[T], and YPL30[T] could be distinguished from the related species according to differential phenotypic characteristics. The major polar lipids of the four strains were phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), and disulfated mannosyl glucosyl diether (S2-DGD). The phenotypic, chemotaxonomic, phylogenetic and phylogenomic features indicated that strains ZJ2[T] (= CGMCC 1.18786[ T] = JCM 34918[ T]), BND6[T] (= CGMCC 1.18777[ T] = JCM 34909[ T]), DT87[T] (= CGMCC 1.18921[ T] = JCM 35420[ T]), and YPL30[T] (= CGMCC 1.15337[ T] = JCM 31113[ T]) represent four novel species of the genus Natrinema, for which the names, Natrinema caseinilyticum sp. nov., Natrinema gelatinilyticum sp. nov., Natrinema marinum sp. nov., and Natrinema zhouii sp. nov., are proposed.}, }
@article {pmid37000227, year = {2023}, author = {Iguchi, A and Takemura, Y and Danshita, T and Kurihara, T and Aoki, M and Hori, S and Shigematsu, T and Syutsubo, K}, title = {Isolation and physiological properties of methanogenic archaea that degrade tetramethylammonium hydroxide.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {9}, pages = {3047-3056}, pmid = {37000227}, issn = {1432-0614}, mesh = {*Archaea/genetics/metabolism ; Wastewater ; Sewage/chemistry ; In Situ Hybridization, Fluorescence ; RNA, Ribosomal, 16S/genetics/metabolism ; Bioreactors ; *Euryarchaeota/metabolism ; Methanosarcinaceae/genetics ; Anaerobiosis ; Waste Disposal, Fluid/methods ; }, abstract = {Tetramethylammonium hydroxide (TMAH) is a known toxic chemical used in the photolithography process of semiconductor photoelectronic processes. Significant amounts of wastewater containing TMAH are discharged from electronic industries. It is therefore attractive to apply anaerobic treatment to industrial wastewater containing TMAH. In this study, a novel TMAH-degrading methanogenic archaeon was isolated from the granular sludge of a psychrophilic upflow anaerobic sludge blanket (UASB) reactor treating synthetic wastewater containing TMAH. Although the isolate (strain NY-STAYD) was phylogenetically related to Methanomethylovorans uponensis, it was the only isolated Methanomethylovorans strain capable of TMAH degradation. Strain NY-STAYD was capable of degrading methylamine compounds, similar to the previously isolated Methanomethylovorans spp. While the strain was able to grow at temperatures ranging from 15 to 37°C, the cell yield was higher at lower temperatures. The distribution of archaeal cells affiliated with the genus Methanomethylovorans in the original granular sludge was investigated by fluorescence in situ hybridization (FISH) using specific oligonucleotide probe targeting 16S rRNA. The results demonstrated that the TMAH-degrading cells associated with the genus Methanomethylovorans were not intermingled with other microorganisms but rather isolated on the granule's surface as a lone dominant archaeon. KEY POINTS: • A TMAH-degrading methanogenic Methanomethylovorans strain was isolated • This strain was the only known Methanomethylovorans isolate that can degrade TMAH • The highest cell yield of the isolate was obtained at psychrophilic conditions.}, }
@article {pmid36999249, year = {2023}, author = {D'Alò, F and Zucconi, L and Onofri, S and Canini, F and Cannone, N and Malfasi, F and Morais, DK and Starke, R}, title = {Effects of 5-year experimental warming in the Alpine belt on soil Archaea: Multi-omics approaches and prospects.}, journal = {Environmental microbiology reports}, volume = {15}, number = {4}, pages = {291-297}, pmid = {36999249}, issn = {1758-2229}, mesh = {*Archaea/genetics ; *Soil/chemistry ; Multiomics ; Climate Change ; Italy ; Soil Microbiology ; }, abstract = {We currently lack a predictive understanding of how soil archaeal communities may respond to climate change, particularly in Alpine areas where warming is far exceeding the global average. Here, we characterized the abundance, structure, and function of total (by metagenomics) and active soil archaea (by metatranscriptomics) after 5-year experimental field warming (+1°C) in Italian Alpine grasslands and snowbeds. Our multi-omics approach unveiled an increasing abundance of Archaea during warming in snowbeds, which was negatively correlated with the abundance of fungi (by qPCR) and micronutrients (Ca and Mg), but positively correlated with soil water content. In the snowbeds transcripts, warming resulted in the enrichment of abundances of transcription and nucleotide biosynthesis. Our study provides novel insights into possible changes in soil Archaea composition and function in the climate change scenario.}, }
@article {pmid36985233, year = {2023}, author = {Cisek, AA and Bąk, I and Cukrowska, B}, title = {Improved Quantitative Real-Time PCR Protocol for Detection and Quantification of Methanogenic Archaea in Stool Samples.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985233}, issn = {2076-2607}, support = {2017/25/N/NZ7/02905//National Science Center/ ; }, abstract = {Methanogenic archaea are an important component of the human and animal intestinal microbiota, and yet their presence is rarely reported in publications describing the subject. One of the methods of quantifying the prevalence of methanogens is quantitative real-time PCR (qPCR) of the methanogen-specific mcrA gene, and one of the possible reasons for detection failure is usually a methodology bias. Here, we refined the existing protocol by changing one of the primers and improving the conditions of the qPCR reaction. As a result, at the expense of a slightly lower yet acceptable PCR efficiency, the new assay was characterized by increased specificity and sensitivity and a wider linear detection range of 7 orders of magnitude. The lowest copy number of mcrA quantified at a frequency of 100% was 21 copies per reaction. The other validation parameters tested, such as reproducibility and linearity, also gave satisfactory results. Overall, we were able to minimize the negative impacts of primer dimerization and other cross-reactions on qPCR and increase the number of not only detectable but also quantifiable stool samples-or in this case, chicken droppings.}, }
@article {pmid36985129, year = {2023}, author = {Slobodkin, AI and Ratnikova, NM and Slobodkina, GB and Klyukina, AA and Chernyh, NA and Merkel, AY}, title = {Composition and Metabolic Potential of Fe(III)-Reducing Enrichment Cultures of Methanotrophic ANME-2a Archaea and Associated Bacteria.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985129}, issn = {2076-2607}, support = {22-14-00011//Russian Science Foundation/ ; No number//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {The key microbial group involved in anaerobic methane oxidation is anaerobic methanotrophic archaea (ANME). From a terrestrial mud volcano, we enriched a microbial community containing ANME-2a, using methane as an electron donor, Fe(III) oxide (ferrihydrite) as an electron acceptor, and anthraquinone-2,6-disulfonate as an electron shuttle. Ferrihydrite reduction led to the formation of a black, highly magnetic precipitate. A significant relative abundance of ANME-2a in batch cultures was observed over five subsequent transfers. Phylogenetic analysis revealed that, in addition to ANME-2a, two bacterial taxa belonging to uncultured Desulfobulbaceae and Anaerolineaceae were constantly present in all enrichments. Metagenome-assembled genomes (MAGs) of ANME-2a contained a complete set of genes for methanogenesis and numerous genes of multiheme c-type cytochromes (MHC), indicating the capability of methanotrophs to transfer electrons to metal oxides or to a bacterial partner. One of the ANME MAGs encoded respiratory arsenate reductase (Arr), suggesting the potential for a direct coupling of methane oxidation with As(V) reduction in the single microorganism. The same MAG also encoded uptake [NiFe] hydrogenase, which is uncommon for ANME-2. The MAG of uncultured Desulfobulbaceae contained genes of dissimilatory sulfate reduction, a Wood-Ljungdahl pathway for autotrophic CO2 fixation, hydrogenases, and 43 MHC. We hypothesize that uncultured Desulfobulbaceae is a bacterial partner of ANME-2a, which mediates extracellular electron transfer to Fe(III) oxide.}, }
@article {pmid36949474, year = {2023}, author = {Regueira-Iglesias, A and Vázquez-González, L and Balsa-Castro, C and Vila-Blanco, N and Blanco-Pintos, T and Tamames, J and Carreira, MJ and Tomás, I}, title = {In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {58}, pmid = {36949474}, issn = {2049-2618}, mesh = {Humans ; *Archaea/genetics ; RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; DNA Primers/genetics ; Bacteria/genetics ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; }, abstract = {BACKGROUND: Sequencing has been widely used to study the composition of the oral microbiome present in various health conditions. The extent of the coverage of the 16S rRNA gene primers employed for this purpose has not, however, been evaluated in silico using oral-specific databases. This paper analyses these primers using two databases containing 16S rRNA sequences from bacteria and archaea found in the human mouth and describes some of the best primers for each domain.<br><br>RESULTS: A total of 369 distinct individual primers were identified from sequencing studies of the oral microbiome and other ecosystems. These were evaluated against a database reported in the literature of 16S rRNA sequences obtained from oral bacteria, which was modified by our group, and a self-created oral archaea database. Both databases contained the genomic variants detected for each included species. Primers were evaluated at the variant and species levels, and those with a species coverage (SC) &#x2265;75.00% were selected for the pair analyses. All possible combinations of the forward and reverse primers were identified, with the resulting 4638 primer pairs also evaluated using the two databases. The best bacteria-specific pairs targeted the 3-4, 4-7, and 3-7 16S rRNA gene regions, with SC levels of 98.83-97.14%; meanwhile, the optimum archaea-specific primer pairs amplified regions 5-6, 3-6, and 3-6, with SC estimates of 95.88%. Finally, the best pairs for detecting both domains targeted regions 4-5, 3-5, and 5-9, and produced SC values of 95.71-94.54% and 99.48-96.91% for bacteria and archaea, respectively.<br><br>CONCLUSIONS: Given the three amplicon length categories (100-300, 301-600, and >600 base&#xa0;pairs), the primer pairs with the best coverage values for detecting oral bacteria were as follows: KP_F048-OP_R043 (region 3-4; primer pair position for Escherichia coli J01859.1: 342-529), KP_F051-OP_R030 (4-7; 514-1079), and KP_F048-OP_R030 (3-7; 342-1079). For detecting oral archaea, these were as follows: OP_F066-KP_R013 (5-6; 784-undefined), KP_F020-KP_R013 (3-6; 518-undefined), and OP_F114-KP_R013 (3-6; 340-undefined). Lastly, for detecting both domains jointly they were KP_F020-KP_R032 (4-5; 518-801), OP_F114-KP_R031 (3-5; 340-801), and OP_F066-OP_R121 (5-9; 784-1405). The primer pairs with the best coverage identified herein are not among those described most widely in the oral microbiome literature. Video Abstract.}, }
@article {pmid36949220, year = {2023}, author = {Lynes, MM and Krukenberg, V and Jay, ZJ and Kohtz, AJ and Gobrogge, CA and Spietz, RL and Hatzenpichler, R}, title = {Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {22}, pmid = {36949220}, issn = {2730-6151}, support = {DBI-1736255//National Science Foundation (NSF)/ ; DBI-1736255//National Science Foundation (NSF)/ ; DBI-1736255//National Science Foundation (NSF)/ ; DBI-1736255//National Science Foundation (NSF)/ ; DBI-1736255//National Science Foundation (NSF)/ ; DBI-1736255//National Science Foundation (NSF)/ ; DBI-1736255//National Science Foundation (NSF)/ ; }, abstract = {Metagenomic studies on geothermal environments have been central in recent discoveries on the diversity of archaeal methane and alkane metabolism. Here, we investigated methanogenic populations inhabiting terrestrial geothermal features in Yellowstone National Park (YNP) by combining amplicon sequencing with metagenomics and mesocosm experiments. Detection of methyl-coenzyme M reductase subunit A (mcrA) gene amplicons demonstrated a wide diversity of Mcr-encoding archaea inhabit geothermal features with differing physicochemical regimes across YNP. From three selected hot springs we recovered twelve Mcr-encoding metagenome assembled genomes (MAGs) affiliated with lineages of cultured methanogens as well as Candidatus (Ca.) Methanomethylicia, Ca. Hadesarchaeia, and Archaeoglobi. These MAGs encoded the potential for hydrogenotrophic, aceticlastic, hydrogen-dependent methylotrophic methanogenesis, or anaerobic short-chain alkane oxidation. While Mcr-encoding archaea represent minor fractions of the microbial community of hot springs, mesocosm experiments with methanogenic precursors resulted in the stimulation of methanogenic activity and the enrichment of lineages affiliated with Methanosaeta and Methanothermobacter as well as with uncultured Mcr-encoding archaea including Ca. Korarchaeia, Ca. Nezhaarchaeia, and Archaeoglobi. We revealed that diverse Mcr-encoding archaea with the metabolic potential to produce methane from different precursors persist in the geothermal environments of YNP and can be enriched under methanogenic conditions. This study highlights the importance of combining environmental metagenomics with laboratory-based experiments to expand our understanding of uncultured Mcr-encoding archaea and their potential impact on microbial carbon transformations in geothermal environments and beyond.}, }
@article {pmid36927099, year = {2023}, author = {Chen, J and Li, Y and Zhong, C and Xu, Z and Lu, G and Jing, H and Liu, H}, title = {Genomic Insights into Niche Partitioning across Sediment Depth among Anaerobic Methane-Oxidizing Archaea in Global Methane Seeps.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0117922}, pmid = {36927099}, issn = {2379-5077}, mesh = {*Archaea/genetics ; Anaerobiosis ; *Methane/metabolism ; Oxidation-Reduction ; Metagenomics ; }, abstract = {Marine sediments are important methane reservoirs. Methane efflux from the seabed is significantly restricted by anaerobic methanotrophic (ANME) archaea through a process known as anaerobic oxidation of methane (AOM). Different clades of ANME archaea occupy distinct niches in methane seeps, but their underlying molecular mechanisms still need to be fully understood. To provide genetic explanations for the niche partitioning of ANME archaea, we applied comparative genomic analysis to ANME archaeal genomes retrieved from global methane seeps. Our results showed that ANME-2 archaea are more prevalent than ANME-1 archaea in shallow sediments because they carry genes that encode a significantly higher number of outer membrane multiheme c-type cytochromes and flagellar proteins. These features make ANME-2 archaea perform direct interspecies electron transfer better and benefit more from electron acceptors in AOM. Besides, ANME-2 archaea carry genes that encode extra peroxidase compared to ANME-1 archaea, which may lead to ANME-2 archaea better tolerating oxygen toxicity. In contrast, ANME-1 archaea are more competitive in deep layers than ANME-2 archaea because they carry extra genes (mtb and mtt) for methylotrophic methanogenesis and a significantly higher number of frh and mvh genes for hydrogenotrophic methanogenesis. Additionally, ANME-1 archaea carry exclusive genes (sqr, TST, and mddA) involved in sulfide detoxification compared to ANME-2 archaea, leading to stronger sulfide tolerance. Overall, this study reveals the genomic mechanisms shaping the niche partitioning among ANME archaea in global methane seeps. IMPORTANCE Anaerobic methanotrophic (ANME) archaea are important methanotrophs in marine sediment, controlling the flux of biologically generated methane, which plays an essential role in the marine carbon cycle and climate change. So far, no strain of this lineage has been isolated in pure culture, which makes metagenomics one of the fundamental approaches to reveal their metabolic potential. Although the niche partitioning of ANME archaea was frequently reported in different studies, whether this pattern was consistent in global methane seeps had yet to be verified, and little was known about the genetic mechanisms underlying it. Here, we reviewed and analyzed the community structure of ANME archaea in global methane seeps and indicated that the niche partitioning of ANME archaea was statistically supported. Our comparative genomic analysis indicated that the capabilities of interspecies electron transfer, methanogenesis, and the resistance of oxygen and hydrogen sulfide could be critical in defining the distribution of ANME archaea in methane seep sediment.}, }
@article {pmid36920214, year = {2023}, author = {Adlung, N and Scheller, S}, title = {Application of the Fluorescence-Activating and Absorption-Shifting Tag (FAST) for Flow Cytometry in Methanogenic Archaea.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {4}, pages = {e0178622}, pmid = {36920214}, issn = {1098-5336}, mesh = {*Archaea/metabolism ; Flow Cytometry ; *Methane/metabolism ; Methanosarcina/metabolism ; }, abstract = {Methane-producing archaea play a crucial role in the global carbon cycle and are used for biotechnological fuel production. Methanogenic model organisms such as Methanococcus maripaludis and Methanosarcina acetivorans have been biochemically characterized and can be genetically engineered by using a variety of existing molecular tools. The anaerobic lifestyle and autofluorescence of methanogens, however, restrict the use of common fluorescent reporter proteins (e.g., GFP and derivatives), which require oxygen for chromophore maturation. Recently, the use of a novel oxygen-independent fluorescent activation and absorption-shifting tag (FAST) was demonstrated with M. maripaludis. Similarly, we now describe the use of the tandem activation and absorption-shifting tag protein 2 (tdFAST2), which fluoresces when the cell-permeable fluorescent ligand (fluorogen) 4-hydroxy-3,5-dimethoxybenzylidene rhodanine (HBR-3,5DOM) is present. Expression of tdFAST2 in M. acetivorans and M. maripaludis is noncytotoxic and tdFAST2:HBR-3,5DOM fluorescence is clearly distinguishable from the autofluorescence. In flow cytometry experiments, mixed methanogen cultures can be distinguished, thereby allowing for the possibility of high-throughput investigations of the characteristic dynamics within single and mixed cultures. IMPORTANCE Methane-producing archaea play an essential role in the global carbon cycle and demonstrate great potential for various biotechnological applications, e.g., biofuel production, carbon dioxide capture, and electrochemical systems. Oxygen sensitivity and high autofluorescence hinder the use of common fluorescent proteins for studying methanogens. By using tdFAST2:HBR-3,5DOM fluorescence, which functions under anaerobic conditions and is distinguishable from the autofluorescence, real-time reporter studies and high-throughput investigation of the mixed culture dynamics of methanogens via flow cytometry were made possible. This will further help accelerate the sustainable exploitation of methanogens.}, }
@article {pmid36912626, year = {2023}, author = {Li, D and Ren, Z and Zhou, Y and Jiang, L and Zheng, M and Liu, G}, title = {Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {3}, pages = {e0004723}, pmid = {36912626}, issn = {1098-5336}, mesh = {Humans ; Archaea/metabolism ; Ammonia/metabolism ; *Ammonium Compounds/metabolism ; Lakes ; RNA, Ribosomal, 16S/genetics/metabolism ; Oxidation-Reduction ; Bacteria ; Nitrification ; Phylogeny ; *Leukemia, Myeloid, Acute ; }, abstract = {Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate in the nitrifying guild in sediments of an acid mine lake (AML). The lake water was characterized by acidic pH below 5 with a high ammonium concentration of 175 mg-N/liter, which is rare on the earth. Nitrification was active in sediments with a maximum nitrate production potential of 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined that in AML sediments, comammox Nitrospira and AOA amoA genes had relative abundances of 52% and 41%, respectively, among the total amoA genes. Further assays with 16S rRNA and amoA gene amplicon sequencing and metagenomics confirmed their dominance and revealed that the comammox Nitrospira found in sediments belonged to comammox Nitrospira clade A.2. Metagenomic binning retrieved a metagenome-assembled genome (MAG) of the comammox Nitrospira from sediments (completeness = 96.76%), and phylogenomic analysis suggested that it was a novel comammox Nitrospira. Comparative genomic investigation revealed that this comammox Nitrospira contained diverse metal resistance genes and an acidophile-affiliated F-type ATPase. Moreover, it had a more diverse genomic characteristic on nitrogen metabolism than the AOA in sediments and canonical AOB did. The results suggest that comammox Nitrospira is a versatile nitrifier that can adapt to acidic environments even with high ammonium concentrations. IMPORTANCE Ammonia-oxidizing archaea (AOA) was previously considered the sole dominant ammonia oxidizer in acidic environments. This study, however, found that complete ammonia oxidation (comammox) Nitrospira was also a dominant ammonia oxidizer in the sediments of an acidic mine lake, which had an acidic pH < 5 and a high ammonium concentration of 175 mg-N/liter. In combination with average nucleotide identity analysis, phylogenomic analysis suggested it is a novel strain of comammox Nitrospira. Moreover, the adaption of comammox Nitrospira to the acidic lake had been comprehensively investigated based on genome-centric metagenomic approaches. The outcomes of this study significantly expand our understanding of the diversity and adaptability of ammonia oxidizers in the acidic environments.}, }
@article {pmid36893867, year = {2023}, author = {Cheng, H and Yang, Y and He, Y and Zhan, X and Liu, Y and Hu, Z and Huang, H and Yao, X and Yang, W and Jin, J and Ren, B and Liu, J and Hu, Q and Jin, Y and Shen, L}, title = {Spatio-temporal variations of activity of nitrate-driven anaerobic oxidation of methane and community structure of Candidatus Methanoperedens-like archaea in sediment of Wuxijiang river.}, journal = {Chemosphere}, volume = {324}, number = {}, pages = {138295}, doi = {10.1016/j.chemosphere.2023.138295}, pmid = {36893867}, issn = {1879-1298}, mesh = {*Archaea/genetics/metabolism ; *Nitrates/metabolism ; Ecosystem ; Rivers ; Methane/metabolism ; Anaerobiosis ; Oxidation-Reduction ; }, abstract = {Nitrate-driven anaerobic oxidation of methane (AOM), catalyzing by Candidatus Methanoperedens-like archaea, is a new addition in the global CH4 cycle. This AOM process acts as a novel pathway for CH4 emission reduction in freshwater aquatic ecosystems; however, its quantitative importance and regulatory factors in riverine ecosystems are nearly unknown. Here, we examined the spatio-temporal changes of the communities of Methanoperedens-like archaea and nitrate-driven AOM activity in sediment of Wuxijiang River, a mountainous river in China. These archaeal community composition varied significantly among reaches (upper, middle, and lower reaches) and between seasons (winter and summer), but their mcrA gene diversity showed no significant spatial or temporal variations. The copy numbers of Methanoperedens-like archaeal mcrA genes were 1.32 × 10[5]-2.47 × 10[7] copies g[-1] (dry weight), and the activity of nitrate-driven AOM was 0.25-1.73 nmol CH4 g[-1] (dry weight) d[-1], which could potentially reduce 10.3% of CH4 emissions from rivers. Significant spatio-temporal variations of mcrA gene abundance and nitrate-driven AOM activity were found. Both the gene abundance and activity increased significantly from upper to lower reaches in both seasons, and were significantly higher in sediment collected in summer than in winter. In addition, the variations of Methanoperedens-like archaeal communities and nitrate-driven AOM activity were largely impacted by the sediment temperature, NH4[+] and organic carbon contents. Taken together, both time and space scales need to be considered for better evaluating the quantitative importance of nitrate-driven AOM in reducing CH4 emissions from riverine ecosystems.}, }
@article {pmid36888658, year = {2023}, author = {Wan, XS and Hou, L and Kao, SJ and Zhang, Y and Sheng, HX and Shen, H and Tong, S and Qin, W and Ward, BB}, title = {Pathways of N2O production by marine ammonia-oxidizing archaea determined from dual-isotope labeling.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {11}, pages = {e2220697120}, pmid = {36888658}, issn = {1091-6490}, mesh = {*Archaea/metabolism ; *Ammonia/metabolism ; Nitrification ; Nitrites/metabolism ; Isotope Labeling ; Oxygen/metabolism ; Oxidation-Reduction ; Nitrous Oxide/metabolism ; }, abstract = {The ocean is a net source of the greenhouse gas and ozone-depleting substance, nitrous oxide (N2O), to the atmosphere. Most of that N2O is produced as a trace side product during ammonia oxidation, primarily by ammonia-oxidizing archaea (AOA), which numerically dominate the ammonia-oxidizing community in most marine environments. The pathways to N2O production and their kinetics, however, are not completely understood. Here, we use [15]N and [18]O isotopes to determine the kinetics of N2O production and trace the source of nitrogen (N) and oxygen (O) atoms in N2O produced by a model marine AOA species, Nitrosopumilus maritimus. We find that during ammonia oxidation, the apparent half saturation constants of nitrite and N2O production are comparable, suggesting that both processes are enzymatically controlled and tightly coupled at low ammonia concentrations. The constituent atoms in N2O are derived from ammonia, nitrite, O2, and H2O via multiple pathways. Ammonia is the primary source of N atoms in N2O, but its contribution varies with ammonia to nitrite ratio. The ratio of [45]N2O to [46]N2O (i.e., single or double labeled N) varies with substrate ratio, leading to widely varying isotopic signatures in the N2O pool. O2 is the primary source for O atoms. In addition to the previously demonstrated hybrid formation pathway, we found a substantial contribution by hydroxylamine oxidation, while nitrite reduction is an insignificant source of N2O. Our study highlights the power of dual [15]N-[18]O isotope labeling to disentangle N2O production pathways in microbes, with implications for interpretation of pathways and regulation of marine N2O sources.}, }
@article {pmid36880756, year = {2023}, author = {Taubner, RS and Baumann, LMF and Steiner, M and Pfeifer, K and Reischl, B and Korynt, K and Bauersachs, T and Mähnert, B and Clifford, EL and Peckmann, J and Schuster, B and Birgel, D and Rittmann, SKR}, title = {Lipidomics and Comparative Metabolite Excretion Analysis of Methanogenic Archaea Reveal Organism-Specific Adaptations to Varying Temperatures and Substrate Concentrations.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0115922}, pmid = {36880756}, issn = {2379-5077}, mesh = {*Archaea/metabolism ; Temperature ; Lipidomics ; *Euryarchaeota/metabolism ; Methane ; Water/metabolism ; }, abstract = {Methanogenic archaea possess diverse metabolic characteristics and are an ecologically and biotechnologically important group of anaerobic microorganisms. Although the scientific and biotechnological value of methanogens is evident with regard to their methane-producing physiology, little is known about their amino acid excretion, and virtually nothing is known about the lipidome at different substrate concentrations and temperatures on a quantitative comparative basis. Here, we present the lipidome and a comprehensive quantitative analysis of proteinogenic amino acid excretion as well as methane, water, and biomass production of the three autotrophic, hydrogenotrophic methanogens Methanothermobacter marburgensis, Methanothermococcus okinawensis, and Methanocaldococcus villosus under varying temperatures and nutrient supplies. The patterns and rates of production of excreted amino acids and the lipidome are unique for each tested methanogen and can be modulated by varying the incubation temperature and substrate concentration, respectively. Furthermore, the temperature had a significant influence on the lipidomes of the different archaea. The water production rate was much higher, as anticipated from the rate of methane production for all studied methanogens. Our results demonstrate the need for quantitative comparative physiological studies connecting intracellular and extracellular constraints of organisms to holistically investigate microbial responses to environmental conditions. IMPORTANCE Biological methane production by methanogenic archaea has been well studied for biotechnological purposes. This study reveals that methanogenic archaea actively modulate their lipid inventory and proteinogenic amino acid excretion pattern in response to environmental changes and the possible utilization of methanogenic archaea as microbial cell factories for the targeted production of lipids and amino acids.}, }
@article {pmid36874274, year = {2023}, author = {Mei, R and Kaneko, M and Imachi, H and Nobu, MK}, title = {The origin and evolution of methanogenesis and Archaea are intertwined.}, journal = {PNAS nexus}, volume = {2}, number = {2}, pages = {pgad023}, pmid = {36874274}, issn = {2752-6542}, abstract = {Methanogenesis has been widely accepted as an ancient metabolism, but the precise evolutionary trajectory remains hotly debated. Disparate theories exist regarding its emergence time, ancestral form, and relationship with homologous metabolisms. Here, we report the phylogenies of anabolism-involved proteins responsible for cofactor biosynthesis, providing new evidence for the antiquity of methanogenesis. Revisiting the phylogenies of key catabolism-involved proteins further suggests that the last Archaea common ancestor (LACA) was capable of versatile H2-, CO2-, and methanol-utilizing methanogenesis. Based on phylogenetic analyses of the methyl/alkyl-S-CoM reductase family, we propose that, in contrast to current paradigms, substrate-specific functions emerged through parallel evolution traced back to a nonspecific ancestor, which likely originated from protein-free reactions as predicted from autocatalytic experiments using cofactor F430. After LACA, inheritance/loss/innovation centered around methanogenic lithoautotrophy coincided with ancient lifestyle divergence, which is clearly reflected by genomically predicted physiologies of extant archaea. Thus, methanogenesis is not only a hallmark metabolism of Archaea, but the key to resolve the enigmatic lifestyle that ancestral archaea took and the transition that led to physiologies prominent today.}, }
@article {pmid36842598, year = {2023}, author = {Zheng, P and Zhang, Q and Zou, J and Han, Q and Han, J and Wang, Q and Yao, L and Yu, G and Liang, Y}, title = {A new strategy for the enrichment of ammonia-oxidizing archaea in wastewater treatment systems: The positive role of quorum-sensing signaling molecules.}, journal = {The Science of the total environment}, volume = {873}, number = {}, pages = {162385}, doi = {10.1016/j.scitotenv.2023.162385}, pmid = {36842598}, issn = {1879-1026}, mesh = {*Archaea ; *Ammonia ; Bacteria ; Oxidation-Reduction ; Quorum Sensing ; Nitrification ; }, abstract = {Ammonia-oxidizing archaea (AOA) play an important role in natural nitrogen cycle, but are difficult to be enriched in wastewater treatment systems. In this experiment, under ambient temperature and high dissolved oxygen, different types of acyl-homoserine lactones (C6-HSL, C8-HSL, C10-HSL, C14-HSL and 3-oxo-C14-HSL) were added to five wastewater nitrification systems to achieve AOA enrichment. Results showed that AOA couldn't be detected in the blank group without the addition of signaling molecules, while the AOA could be detected in all the reactors with the addition. The enrichment effect of AOA was not obvious with added 100 or 200 nmol/L signaling molecules, while the enrichment effect was both obvious with added C8-HSL of 400 nmol/L and C10-HSL of 800 nmol/L. And relative abundance of AOA increased from undetected in the control group to 1.10 % and 0.96 %, respectively. The exogenous signaling molecules may provide new view for AOA enrichment in wastewater treatment systems.}, }
@article {pmid36835573, year = {2023}, author = {Ngcobo, PE and Nkosi, BVZ and Chen, W and Nelson, DR and Syed, K}, title = {Evolution of Cytochrome P450 Enzymes and Their Redox Partners in Archaea.}, journal = {International journal of molecular sciences}, volume = {24}, number = {4}, pages = {}, pmid = {36835573}, issn = {1422-0067}, support = {C686//Universit of Zululand/ ; MND200527525406//National Research Foundation (NRF), South Africa/ ; }, mesh = {Humans ; *Ferredoxins/metabolism ; *Archaea/metabolism ; Phylogeny ; Oxidation-Reduction ; Cytochrome P-450 Enzyme System/metabolism ; Bacteria/metabolism ; }, abstract = {Cytochrome P450 monooxygenases (CYPs/P450s) and their redox partners, ferredoxins, are ubiquitous in organisms. P450s have been studied in biology for over six decades owing to their distinct catalytic activities, including their role in drug metabolism. Ferredoxins are ancient proteins involved in oxidation-reduction reactions, such as transferring electrons to P450s. The evolution and diversification of P450s in various organisms have received little attention and no information is available for archaea. This study is aimed at addressing this research gap. Genome-wide analysis revealed 1204 P450s belonging to 34 P450 families and 112 P450 subfamilies, where some families and subfamilies are expanded in archaea. We also identified 353 ferredoxins belonging to the four types 2Fe-2S, 3Fe-4S, 7Fe-4S and 2[4Fe-4S] in 40 archaeal species. We found that bacteria and archaea shared the CYP109, CYP147 and CYP197 families, as well as several ferredoxin subtypes, and that these genes are co-present on archaeal plasmids and chromosomes, implying the plasmid-mediated lateral transfer of these genes from bacteria to archaea. The absence of ferredoxins and ferredoxin reductases in the P450 operons suggests that the lateral transfer of these genes is independent. We present different scenarios for the evolution and diversification of P450s and ferredoxins in archaea. Based on the phylogenetic analysis and high affinity to diverged P450s, we propose that archaeal P450s could have diverged from CYP109, CYP147 and CYP197. Based on this study's results, we propose that all archaeal P450s are bacterial in origin and that the original archaea had no P450s.}, }
@article {pmid36817958, year = {2023}, author = {Kisly, I and Tamm, T}, title = {Archaea/eukaryote-specific ribosomal proteins - guardians of a complex structure.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {1249-1261}, pmid = {36817958}, issn = {2001-0370}, abstract = {In three domains of life, proteins are synthesized by large ribonucleoprotein particles called ribosomes. All ribosomes are composed of ribosomal RNAs (rRNA) and numerous ribosomal proteins (r-protein). The three-dimensional shape of ribosomes is mainly defined by a tertiary structure of rRNAs. In addition, rRNAs have a major role in decoding the information carried by messenger RNAs and catalyzing the peptide bond formation. R-proteins are essential for shaping the network of interactions that contribute to a various aspects of the protein synthesis machinery, including assembly of ribosomes and interaction of ribosomal subunits. Structural studies have revealed that many key components of ribosomes are conserved in all life domains. Besides the core structure, ribosomes contain domain-specific structural features that include additional r-proteins and extensions of rRNA and r-proteins. This review focuses specifically on those r-proteins that are found only in archaeal and eukaryotic ribosomes. The role of these archaea/eukaryote specific r-proteins in stabilizing the ribosome structure is discussed. Several examples illustrate their functions in the formation of the internal network of ribosomal subunits and interactions between the ribosomal subunits. In addition, the significance of these r-proteins in ribosome biogenesis and protein synthesis is highlighted.}, }
@article {pmid36814573, year = {2023}, author = {Cheng, X and Xiang, X and Yun, Y and Wang, W and Wang, H and Bodelier, PLE}, title = {Archaea and their interactions with bacteria in a karst ecosystem.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1068595}, pmid = {36814573}, issn = {1664-302X}, abstract = {Karst ecosystems are widely distributed around the world, accounting for 15-20% of the global land area. However, knowledge on microbial ecology of these systems does not match with their global importance. To close this knowledge gap, we sampled three niches including weathered rock, sediment, and drip water inside the Heshang Cave and three types of soils overlying the cave (forest soil, farmland soil, and pristine karst soil). All these samples were subjected to high-throughput sequencing of V4-V5 region of 16S rRNA gene and analyzed with multivariate statistical analysis. Overall, archaeal communities were dominated by Thaumarchaeota, whereas Actinobacteria dominated bacterial communities. Thermoplasmata, Nitrosopumilaceae, Aenigmarchaeales, Crossiella, Acidothermus, and Solirubrobacter were the important predictor groups inside the Heshang Cave, which were correlated to NH4 [+] availability. In contrast, Candidatus Nitrososphaera, Candidatus Nitrocosmicus, Thaumarchaeota Group 1.1c, and Pseudonocardiaceae were the predictors outside the cave, whose distribution was correlated with pH, Ca[2+], and NO2 [-]. Tighter network structures were found in archaeal communities than those of bacteria, whereas the topological properties of bacterial networks were more similar to those of total prokaryotic networks. Both chemolithoautotrophic archaea (Candidatus Methanoperedens and Nitrosopumilaceae) and bacteria (subgroup 7 of Acidobacteria and Rokubacteriales) were the dominant keystone taxa within the co-occurrence networks, potentially playing fundamental roles in obtaining energy under oligotrophic conditions and thus maintaining the stability of the cave ecosystem. To be noted, all the keystone taxa of karst ecosystems were related to nitrogen cycling, which needs further investigation, particularly the role of archaea. The predicted ecological functions in karst soils mainly related to carbohydrate metabolism, biotin metabolism, and synthesis of fatty acid. Our results offer new insights into archaeal ecology, their potential functions, and archaeal interactions with bacteria, which enhance our understanding about the microbial dark matter in the subsurface karst ecosystems.}, }
@article {pmid36808147, year = {2023}, author = {Gios, E and Mosley, OE and Weaver, L and Close, M and Daughney, C and Handley, KM}, title = {Ultra-small bacteria and archaea exhibit genetic flexibility towards groundwater oxygen content, and adaptations for attached or planktonic lifestyles.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {13}, pmid = {36808147}, issn = {2730-6151}, support = {UOAX1720//Ministry of Business, Innovation and Employment (MBIE)/ ; UOAX1720//Ministry of Business, Innovation and Employment (MBIE)/ ; UOAX1720//Ministry of Business, Innovation and Employment (MBIE)/ ; UOAX1720//Ministry of Business, Innovation and Employment (MBIE)/ ; UOAX1720//Ministry of Business, Innovation and Employment (MBIE)/ ; UOAX1720//Ministry of Business, Innovation and Employment (MBIE)/ ; }, abstract = {Aquifers are populated by highly diverse microbial communities, including unusually small bacteria and archaea. The recently described Patescibacteria (or Candidate Phyla Radiation) and DPANN radiation are characterized by ultra-small cell and genomes sizes, resulting in limited metabolic capacities and probable dependency on other organisms to survive. We applied a multi-omics approach to characterize the ultra-small microbial communities over a wide range of aquifer groundwater chemistries. Results expand the known global range of these unusual organisms, demonstrate the wide geographical range of over 11,000 subsurface-adapted Patescibacteria, Dependentiae and DPANN archaea, and indicate that prokaryotes with ultra-small genomes and minimalistic metabolism are a characteristic feature of the terrestrial subsurface. Community composition and metabolic activities were largely shaped by water oxygen content, while highly site-specific relative abundance profiles were driven by a combination of groundwater physicochemistries (pH, nitrate-N, dissolved organic carbon). We provide insights into the activity of ultra-small prokaryotes with evidence that they are major contributors to groundwater community transcriptional activity. Ultra-small prokaryotes exhibited genetic flexibility with respect to groundwater oxygen content, and transcriptionally distinct responses, including proportionally greater transcription invested into amino acid and lipid metabolism and signal transduction in oxic groundwater, along with differences in taxa transcriptionally active. Those associated with sediments differed from planktonic counterparts in species composition and transcriptional activity, and exhibited metabolic adaptations reflecting a surface-associated lifestyle. Finally, results showed that groups of phylogenetically diverse ultra-small organisms co-occurred strongly across sites, indicating shared preferences for groundwater conditions.}, }
@article {pmid36804975, year = {2023}, author = {Zhang, Q and Chen, M and Leng, Y and Wang, X and Fu, Y and Wang, D and Zhao, X and Gao, W and Li, N and Chen, X and Fan, C and Li, Q}, title = {Organic substitution stimulates ammonia oxidation-driven N2O emissions by distinctively enriching keystone species of ammonia-oxidizing archaea and bacteria in tropical arable soils.}, journal = {The Science of the total environment}, volume = {872}, number = {}, pages = {162183}, doi = {10.1016/j.scitotenv.2023.162183}, pmid = {36804975}, issn = {1879-1026}, mesh = {*Archaea ; Soil/chemistry ; Ammonia ; Oxidation-Reduction ; Soil Microbiology ; Bacteria ; *Betaproteobacteria ; Nitrification ; }, abstract = {Partial organic substitution (POS) is pivotal in enhancing soil productivity and changing nitrous oxide (N2O) emissions by profoundly altering soil nitrogen (N) cycling, where ammonia oxidation is a fundamental core process. However, the regulatory mechanisms of N2O production by ammonia oxidizers at the microbial community level under POS regimes remain unclear. This study explored soil ammonia oxidation and related N2O production, further building an understanding of the correlations between ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) activity and community structure in tropical arable soils under four-year field management regimes (CK, without fertilizer N; N, with only inorganic N; M1N1, with 1/2 organic N + 1/2 inorganic N; M1N2, with 1/3 organic N + 2/3 inorganic N). AOA contributed more to potential ammonia oxidation (PAO) than AOB across all treatments. In comparison with CK, N treatment had no obvious effects on PAO and lowered related N2O emissions by decreasing soil pH and downregulating the abundance of AOA- and AOB-amoA. POS regimes significantly enhanced PAO and N2O emissions relative to N treatment by promoting the abundances and contributions of AOA and AOB. The stimulated AOA-dominated N2O production under M1N1 was correlated with promoted development of Nitrososphaera. By contrast, the increased AOB-dominated N2O production under M1N2 was linked to the enhanced development of Nitrosospira multiformis. Our study suggests organic substitutions with different proportions of inorganic and organic N distinctively regulate the development of specific species of ammonia oxidizers to increase associated N2O emissions. Accordingly, appropriate options should be adopted to reduce environmental risks under POS regimes in tropical croplands.}, }
@article {pmid36796795, year = {2023}, author = {Diao, M and Balkema, C and Suárez-Muñoz, M and Huisman, J and Muyzer, G}, title = {Succession of bacteria and archaea involved in the nitrogen cycle of a seasonally stratified lake.}, journal = {FEMS microbiology letters}, volume = {370}, number = {}, pages = {}, pmid = {36796795}, issn = {1574-6968}, mesh = {Humans ; *Archaea/genetics ; Lakes/microbiology ; RNA, Ribosomal, 16S/genetics ; Nitrates ; Oxidation-Reduction ; Bacteria/genetics ; Nitrogen Cycle ; Ammonia ; *Ammonium Compounds ; Nitrogen ; Phylogeny ; Geologic Sediments/microbiology ; }, abstract = {Human-driven changes affect nutrient inputs, oxygen solubility, and the hydrodynamics of lakes, which affect biogeochemical cycles mediated by microbial communities. However, information on the succession of microbes involved in nitrogen cycling in seasonally stratified lakes is still incomplete. Here, we investigated the succession of nitrogen-transforming microorganisms in Lake Vechten over a period of 19 months, combining 16S rRNA gene amplicon sequencing and quantification of functional genes. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) and anammox bacteria were abundant in the sediment during winter, accompanied by nitrate in the water column. Nitrogen-fixing bacteria and denitrifying bacteria emerged in the water column in spring when nitrate was gradually depleted. Denitrifying bacteria containing nirS genes were exclusively present in the anoxic hypolimnion. During summer stratification, abundances of AOA, AOB, and anammox bacteria decreased sharply in the sediment, and ammonium accumulated in hypolimnion. After lake mixing during fall turnover, abundances of AOA, AOB, and anammox bacteria increased and ammonium was oxidized to nitrate. Hence, nitrogen-transforming microorganisms in Lake Vechten displayed a pronounced seasonal succession, which was strongly determined by the seasonal stratification pattern. These results imply that changes in stratification and vertical mixing induced by global warming are likely to alter the nitrogen cycle of seasonally stratified lakes.}, }
@article {pmid36794928, year = {2023}, author = {Akpudo, YM and Bezuidt, OK and Makhalanyane, TP}, title = {Metagenome-Assembled Genomes of Four Southern Ocean Archaea Harbor Multiple Genes Linked to Polyethylene Terephthalate and Polyhydroxybutyrate Plastic Degradation.}, journal = {Microbiology resource announcements}, volume = {12}, number = {3}, pages = {e0109822}, pmid = {36794928}, issn = {2576-098X}, support = {//National Research Foundation (NRF)/ ; //Technology Innovation Agency/ ; }, abstract = {Here, we present four archaeal metagenome-assembled genomes (MAGs) (three Thaumarchaeota MAGs and one Thermoplasmatota MAG) from a polar upwelling zone in the Southern Ocean. These archaea harbor putative genes encoding enzymes such as polyethylene terephthalate (PET) hydrolases (PETases) and polyhydroxybutyrate (PHB) depolymerases, which are associated with microbial degradation of PET and PHB plastics.}, }
@article {pmid36792581, year = {2023}, author = {Filée, J and Becker, HF and Mellottee, L and Eddine, RZ and Li, Z and Yin, W and Lambry, JC and Liebl, U and Myllykallio, H}, title = {Bacterial origins of thymidylate metabolism in Asgard archaea and Eukarya.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {838}, pmid = {36792581}, issn = {2041-1723}, mesh = {*Archaea/metabolism ; *Eukaryota/genetics/metabolism ; Phylogeny ; Thymidylate Synthase/genetics/metabolism ; Bacteria/genetics/metabolism ; Amino Acids/metabolism ; Folic Acid/metabolism ; DNA/metabolism ; }, abstract = {Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, we investigate the evolution and function of Asgard thymidylate synthases and other folate-dependent enzymes required for the biosynthesis of DNA, RNA, amino acids and vitamins, as well as syntrophic amino acid utilization. Phylogenies of Asgard folate-dependent enzymes are consistent with their horizontal transmission from various bacterial groups. We experimentally validate the functionality of thymidylate synthase ThyX of the cultured 'Candidatus Prometheoarchaeum syntrophicum'. The enzyme efficiently uses bacterial-like folates and is inhibited by mycobacterial ThyX inhibitors, even though the majority of experimentally tested archaea are known to use carbon carriers distinct from bacterial folates. Our phylogenetic analyses suggest that the eukaryotic thymidylate synthase, required for de novo DNA synthesis, is not closely related to archaeal enzymes and might have been transferred from bacteria to protoeukaryotes during eukaryogenesis. Altogether, our study suggests that the capacity of eukaryotic cells to duplicate their genetic material is a sum of archaeal (replisome) and bacterial (thymidylate synthase) characteristics. We also propose that recent prevalent lateral gene transfer from bacteria has markedly shaped the metabolism of Asgard archaea.}, }
@article {pmid36759127, year = {2023}, author = {Wolff, P and Lechner, A and Droogmans, L and Grosjean, H and Westhof, E}, title = {Identification of U[p]47 in three thermophilic archaea, one mesophilic archaeon, and one hyperthermophilic bacterium.}, journal = {RNA (New York, N.Y.)}, volume = {29}, number = {5}, pages = {551-556}, pmid = {36759127}, issn = {1469-9001}, mesh = {*Archaea/genetics ; Bacteria/genetics ; *Sulfolobus/genetics ; }, abstract = {Analysis of the profile of the tRNA modifications in several Archaea allowed us to observe a novel modified uridine in the V-loop of several tRNAs from two species: Pyrococcus furiosus and Sulfolobus acidocaldarius Recently, Ohira and colleagues characterized 2'-phosphouridine (U[p]) at position 47 in tRNAs of thermophilic Sulfurisphaera tokodaii, as well as in several other archaea and thermophilic bacteria. From the presence of the gene arkI corresponding to the RNA kinase responsible for U[p]47 formation, they also concluded that U[p]47 should be present in tRNAs of other thermophilic Archaea Reanalysis of our earlier data confirms that the unidentified residue in tRNAs of both P. furiosus and S. acidocaldarius is indeed 2'-phosphouridine followed by m[5]C48. Moreover, we find this modification in several tRNAs of other Archaea and of the hyperthermophilic bacterium Aquifex aeolicus.}, }
@article {pmid36752722, year = {2023}, author = {Cooper, CR and Lewis, AM and Notey, JS and Mukherjee, A and Willard, DJ and Blum, PH and Kelly, RM}, title = {Interplay between transcriptional regulators and VapBC toxin-antitoxin loci during thermal stress response in extremely thermoacidophilic archaea.}, journal = {Environmental microbiology}, volume = {25}, number = {6}, pages = {1200-1215}, pmid = {36752722}, issn = {1462-2920}, support = {R01 GM090209/GM/NIGMS NIH HHS/United States ; T32 GM008776/GM/NIGMS NIH HHS/United States ; T32 GM133366/GM/NIGMS NIH HHS/United States ; }, mesh = {*Antitoxins/genetics ; *Toxins, Biological/genetics/metabolism ; Heat-Shock Response/genetics ; *Sulfolobus solfataricus/genetics/metabolism ; Escherichia coli/genetics ; }, abstract = {Thermoacidophilic archaea lack sigma factors and the large inventory of heat shock proteins (HSPs) widespread in bacterial genomes, suggesting other strategies for handling thermal stress are involved. Heat shock transcriptomes for the thermoacidophilic archaeon Saccharolobus (f. Sulfolobus) solfataricus 98/2 revealed genes that were highly responsive to thermal stress, including transcriptional regulators YtrASs (Ssol_2420) and FadRSs (Ssol_0314), as well as type II toxin-antitoxin (TA) loci VapBC6 (Ssol_2337, Ssol_2338) and VapBC22 (Ssol_0819, Ssol_0818). The role, if any, of type II TA loci during stress response in microorganisms, such as Escherichia coli, is controversial. But, when genes encoding YtrASs , FadRSs , VapC22, VapB6, and VapC6 were systematically mutated in Sa. solfataricus 98/2, significant up-regulation of the other genes within this set was observed, implicating an interconnected regulatory network during thermal stress response. VapBC6 and VapBC22 have close homologues in other Sulfolobales, as well as in other archaea (e.g. Pyrococcus furiosus and Archaeoglobus fulgidus), and their corresponding genes were also heat shock responsive. The interplay between VapBC TA loci and heat shock regulators in Sa solfataricus 98/2 not only indicates a cellular mechanism for heat shock response that differs from bacteria but one that could have common features within the thermophilic archaea.}, }
@article {pmid36752534, year = {2023}, author = {Dahl, MB and Kreyling, J and Petters, S and Wang, H and Mortensen, MS and Maccario, L and Sørensen, SJ and Urich, T and Weigel, R}, title = {Warmer winters result in reshaping of the European beech forest soil microbiome (bacteria, archaea and fungi)-With potential implications for ecosystem functioning.}, journal = {Environmental microbiology}, volume = {25}, number = {6}, pages = {1118-1135}, doi = {10.1111/1462-2920.16347}, pmid = {36752534}, issn = {1462-2920}, mesh = {Ecosystem ; *Fagus ; Archaea/genetics ; Soil/chemistry ; Forests ; Bacteria/genetics ; Climate Change ; *Mycorrhizae ; Seasons ; Snow ; Nitrogen ; }, abstract = {In temperate regions, climate warming alters temperature and precipitation regimes. During winter, a decline in insulating snow cover changes the soil environment, where especially frost exposure can have severe implications for soil microorganisms and subsequently for soil nutrient dynamics. Here, we investigated winter climate change responses in European beech forests soil microbiome. Nine study sites with each three treatments (snow exclusion, insolation, and ambient) were investigated. Long-term adaptation to average climate was explored by comparing across sites. Triplicated treatment plots were used to evaluate short-term (one single winter) responses. Community profiles of bacteria, archaea and fungi were created using amplicon sequencing. Correlations between the microbiome, vegetation and soil physicochemical properties were found. We identify core members of the forest-microbiome and link them to key processes, for example, mycorrhizal symbiont and specialized beech wood degraders (fungi) and nitrogen cycling (bacteria, archaea). For bacteria, the shift of the microbiome composition due to short-term soil temperature manipulations in winter was similar to the community differences observed between long-term relatively cold to warm conditions. The results suggest a strong link between the changes in the microbiomes and changes in environmental processes, for example, nitrogen dynamics, driven by variations in winter climate.}, }
@article {pmid36729913, year = {2023}, author = {Denise, R and Babor, J and Gerlt, JA and de Crécy-Lagard, V}, title = {Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes.}, journal = {Microbial genomics}, volume = {9}, number = {2}, pages = {}, pmid = {36729913}, issn = {2057-5858}, support = {R01 GM129793/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaea/genetics/metabolism ; *Pyridoxal/metabolism ; Bacteria/genetics/metabolism ; Phosphates ; }, abstract = {Pyridoxal 5’-phosphate or PLP is a cofactor derived from B6 vitamers and essential for growth in all known organisms. PLP synthesis and salvage pathways are well characterized in a few model species even though key components, such as the vitamin B6 transporters, are still to be identified in many organisms including the model bacteria Escherichia coli or Bacillus subtilis . Using a comparative genomic approach, PLP synthesis and salvage pathways were predicted in 5840 bacterial and archaeal species with complete genomes. The distribution of the two known de novo biosynthesis pathways and previously identified cases of non-orthologous displacements were surveyed in the process. This analysis revealed that several PLP de novo pathway genes remain to be identified in many organisms, either because sequence similarity alone cannot be used to discriminate among several homologous candidates or due to non-orthologous displacements. Candidates for some of these pathway holes were identified using published TnSeq data, but many remain. We find that ~10 % of the analysed organisms rely on salvage but further analyses will be required to identify potential transporters. This work is a starting point to model the exchanges of B6 vitamers in communities, predict the sensitivity of a given organism to drugs targeting PLP synthesis enzymes, and identify numerous gaps in knowledge that will need to be tackled in the years to come.}, }
@article {pmid36724220, year = {2023}, author = {Ngugi, DK and Salcher, MM and Andrei, AS and Ghai, R and Klotz, F and Chiriac, MC and Ionescu, D and Büsing, P and Grossart, HP and Xing, P and Priscu, JC and Alymkulov, S and Pester, M}, title = {Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes.}, journal = {Science advances}, volume = {9}, number = {5}, pages = {eadc9392}, pmid = {36724220}, issn = {2375-2548}, mesh = {*Archaea/genetics ; *Lakes ; Ammonia ; Ecosystem ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, "Candidatus Nitrosopumilus limneticus," is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia.}, }
@article {pmid36721520, year = {2022}, author = {Beddal, A and Boutaiba, S and Laassami, A and Hamaidi, F and Enache, M}, title = {Characterization by polyphasic approach of some indigenous halophilic archaea of Djelfa's rock salt "Hadjr el Meelh", Algeria.}, journal = {Iranian journal of microbiology}, volume = {14}, number = {4}, pages = {535-544}, pmid = {36721520}, issn = {2008-3289}, abstract = {BACKGROUND AND OBJECTIVES: Hadjr El Melh of Djelfa is an example of hypersaline ecosystems, which can harbor a wide variety of microorganisms under hostile physicochemical conditions. Given the importance of the study of halophilic microorganisms present there in terms of fundamental and applied microbiology, the purpose of this study was to characterize some halophilic archaea isolated from the brines of this environment.<br><br>MATERIALS AND METHODS: Eight water samples were chosen randomly and collected for physicochemical and microbiological analyses. Isolation of halophilic archaea was carried out by membrane filter technique. Ten strains were identified by polyphasic approach and tested for enzymes production.<br><br>RESULTS: Water samples of Djelfa's rock salt were slightly acidic to neutral in pH (6.55-7.36) with salinity ranging from 258.68 g/l to 493.91 g/l. Phenotypic, biochemical, taxonomic and phylogenetic characteristics indicated that all strains were classified within the family of Halobacteiaceae. Based on the comparison of DNA sequences encoded 16S rRNA, it was determined that seven strains were affiliated to the genus Haloarcula, two strains were related to the genus Halobacterium and one strain within the genus Haloferax. Production of different enzymes such as protease, amylase, esterase, lipase, lecithinase, gelatinase and cellulase on solid medium indicated that one strain (S2-2) produced amylase, esterase, lecithinase and protease. However, no strains showed cellulolytic or lipolytic activity. Gelatinase was found in all tested strains.<br><br>CONCLUSION: This report constitutes the first preliminary study of culturable halophilic archaea recovered from the brines of Djelfa's rock salt with a promising enzymatic potential in various fields of biotechnology.}, }
@article {pmid36721060, year = {2023}, author = {Hodgskiss, LH and Melcher, M and Kerou, M and Chen, W and Ponce-Toledo, RI and Savvides, SN and Wienkoop, S and Hartl, M and Schleper, C}, title = {Unexpected complexity of the ammonia monooxygenase in archaea.}, journal = {The ISME journal}, volume = {17}, number = {4}, pages = {588-599}, pmid = {36721060}, issn = {1751-7370}, mesh = {*Archaea/classification/enzymology ; *Oxidoreductases/chemistry/genetics/metabolism ; Nitrification ; Native Polyacrylamide Gel Electrophoresis ; Phylogeny ; Gene Expression ; }, abstract = {Ammonia oxidation, as the first step of nitrification, constitutes a critical process in the global nitrogen cycle. However, fundamental knowledge of its key enzyme, the copper-dependent ammonia monooxygenase, is lacking, in particular for the environmentally abundant ammonia-oxidizing archaea (AOA). Here the structure of the enzyme is investigated by blue-native gel electrophoresis and proteomics from native membrane complexes of two AOA. Besides the known AmoABC subunits and the earlier predicted AmoX, two new protein subunits, AmoY and AmoZ, were identified. They are unique to AOA, highly conserved and co-regulated, and their genes are linked to other AMO subunit genes in streamlined AOA genomes. Modeling and in-gel cross-link approaches support an overall protomer structure similar to the distantly related bacterial particulate methane monooxygenase but also reveals clear differences in extracellular domains of the enzyme. These data open avenues for further structure-function studies of this ecologically important nitrification complex.}, }
@article {pmid36720870, year = {2023}, author = {Daugeron, MC and Missoury, S and Da Cunha, V and Lazar, N and Collinet, B and van Tilbeurgh, H and Basta, T}, title = {A paralog of Pcc1 is the fifth core subunit of the KEOPS tRNA-modifying complex in Archaea.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {526}, pmid = {36720870}, issn = {2041-1723}, mesh = {*Adenosine ; *Archaea/genetics ; Biological Evolution ; Eukaryota ; RNA, Transfer/genetics ; }, abstract = {In Archaea and Eukaryotes, the synthesis of a universal tRNA modification, N[6]-threonyl-carbamoyl adenosine (t[6]A), is catalyzed by the KEOPS complex composed of Kae1, Bud32, Cgi121, and Pcc1. A fifth subunit, Gon7, is found only in Fungi and Metazoa. Here, we identify and characterize a fifth KEOPS subunit in Archaea. This protein, dubbed Pcc2, is a paralog of Pcc1 and is widely conserved in Archaea. Pcc1 and Pcc2 form a heterodimer in solution, and show modest sequence conservation but very high structural similarity. The five-subunit archaeal KEOPS does not form dimers but retains robust tRNA binding and t[6]A synthetic activity. Pcc2 can substitute for Pcc1 but the resulting KEOPS complex is inactive, suggesting a distinct function for the two paralogs. Comparative sequence and structure analyses point to a possible evolutionary link between archaeal Pcc2 and eukaryotic Gon7. Our work indicates that Pcc2 regulates the oligomeric state of the KEOPS complex, a feature that seems to be conserved from Archaea to Eukaryotes.}, }
@article {pmid36715325, year = {2023}, author = {Yang, Y and Liu, J and Fu, X and Zhou, F and Zhang, S and Zhang, X and Huang, Q and Krupovic, M and She, Q and Ni, J and Shen, Y}, title = {A novel RHH family transcription factor aCcr1 and its viral homologs dictate cell cycle progression in archaea.}, journal = {Nucleic acids research}, volume = {51}, number = {4}, pages = {1707-1723}, pmid = {36715325}, issn = {1362-4962}, mesh = {*Transcription Factors/genetics ; Archaea ; Cell Division ; *Sulfolobus/genetics ; Gene Expression Regulation ; }, abstract = {Cell cycle regulation is of paramount importance for all forms of life. Here, we report that a conserved and essential cell cycle-specific transcription factor (designated as aCcr1) and its viral homologs control cell division in Sulfolobales. We show that the transcription level of accr1 reaches peak during active cell division (D-phase) subsequent to the expression of CdvA, an archaea-specific cell division protein. Cells over-expressing the 58-aa-long RHH (ribbon-helix-helix) family cellular transcription factor as well as the homologs encoded by large spindle-shaped viruses Acidianus two-tailed virus (ATV) and Sulfolobus monocaudavirus 3 (SMV3) display significant growth retardation and cell division failure, manifesting as enlarged cells with multiple chromosomes. aCcr1 over-expression results in downregulation of 17 genes (>4-fold), including cdvA. A conserved motif, aCcr1-box, located between the TATA-binding box and the translation initiation site of 13 out of the 17 highly repressed genes, is critical for aCcr1 binding. The aCcr1-box is present in the promoters and 5' UTRs of cdvA genes across Sulfolobales, suggesting that aCcr1-mediated cdvA repression is an evolutionarily conserved mechanism by which archaeal cells dictate cytokinesis progression, whereas their viruses take advantage of this mechanism to manipulate the host cell cycle.}, }
@article {pmid36709544, year = {2023}, author = {Umegawa, Y and Kawatake, S and Murata, M and Matsuoka, S}, title = {Combined effect of the head groups and alkyl chains of archaea lipids when interacting with bacteriorhodopsin.}, journal = {Biophysical chemistry}, volume = {294}, number = {}, pages = {106959}, doi = {10.1016/j.bpc.2023.106959}, pmid = {36709544}, issn = {1873-4200}, mesh = {*Bacteriorhodopsins/chemistry/metabolism ; Phospholipids/chemistry ; Membrane Lipids/chemistry ; Halobacterium salinarum/chemistry/metabolism ; Phosphates/metabolism ; }, abstract = {Bacteriorhodopsin (bR), a transmembrane protein with seven α-helices, is highly expressed in the purple membrane (PM) of archaea such as Halobacterium salinarum. It is well known that bR forms two-dimensional crystals with acidic lipids such as phosphatidylglycerol phosphate methyl ester (PGP-Me)-a major component of PM lipids bearing unique chemical structures-methyl-branched alkyl chains, ether linkages, and divalent anionic head groups with two phosphodiester groups. Therefore, we aimed to determine which functional groups of PGP-Me are essential for the boundary lipids of bR and how these functionalities interact with bR. To this end, we compared various well-known phospholipids (PLs) that carry one of the structural features of PGP-Me, and evaluated the affinity of PLs to bR using the centerband-only analysis of rotor-unsynchronized spin echo (COARSE) method in solid-state NMR measurements and thermal shift assays. The results clearly showed that the branched methyl groups of alkyl chains and double negative charges in the head groups are important for PL interactions with bR. We then examined the effect of phospholipids on the monomer-trimer exchange of bR using circular dichroism (CD) spectra. The results indicated that the divalent negative charge in a head group stabilizes the trimer structure, while the branched methyl chains significantly enhance the PLs' affinity for bR, thus dispersing bR trimers in the PM even at high concentrations. Finally, we investigated the effects of PL on the proton-pumping activity of bR based on the decay rate constant of the M intermediate of a bR photocycle. The findings showed that bR activities decreased to 20% in 1,2-dimyristoyl-sn-glycero-3-phosphate (DMPA), and in 1,2-diphytanoyl-sn-glycero-3-phosphocholine (DPhPC) bilayers as compared to that in PM. Meanwhile, 1,2-Diphytanoyl-sn-glycero-3-phosphate (DPhPA) bilayers bearing both negative charges and branched methyl groups preserved over 80% of the activity. These results strongly suggest that the head groups and alkyl chains of phospholipids are essential for boundary lipids and greatly influence the biological function of bR.}, }
@article {pmid36694212, year = {2023}, author = {Jaffe, AL and Bardot, C and Le Jeune, AH and Liu, J and Colombet, J and Perrière, F and Billard, H and Castelle, CJ and Lehours, AC and Banfield, JF}, title = {Variable impact of geochemical gradients on the functional potential of bacteria, archaea, and phages from the permanently stratified Lac Pavin.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {14}, pmid = {36694212}, issn = {2049-2618}, support = {S10 OD018174/OD/NIH HHS/United States ; }, mesh = {*Archaea/genetics/metabolism ; *Bacteriophages/metabolism ; Bacteria/genetics/metabolism ; Lakes/microbiology ; Oxygen/metabolism ; Water ; Methane/metabolism ; Phylogeny ; Geologic Sediments/microbiology ; }, abstract = {BACKGROUND: Permanently stratified lakes contain diverse microbial communities that vary with depth and so serve as useful models for studying the relationships between microbial community structure and geochemistry. Recent work has shown that these lakes can also harbor numerous bacteria and archaea from novel lineages, including those from the Candidate Phyla Radiation (CPR). However, the extent to which geochemical stratification differentially impacts carbon metabolism and overall genetic potential in CPR bacteria compared to other organisms is not well defined.<br><br>RESULTS: Here, we determine the distribution of microbial lineages along an oxygen gradient in Lac Pavin, a deep, stratified lake in central France, and examine the influence of this gradient on their metabolism. Genome-based analyses revealed an enrichment of distinct C1 and CO2 fixation pathways in the oxic lake interface and anoxic zone/sediments, suggesting that oxygen likely plays a role in structuring metabolic strategies in non-CPR bacteria and archaea. Notably, we find that the oxidation of methane and its byproducts is largely spatially separated from methane production, which is mediated by diverse communities of sediment methanogens that vary on the centimeter scale. In contrast, we detected evidence for RuBisCO throughout the water column and sediments, including form II/III and form III-related enzymes encoded by CPR bacteria in the water column and DPANN archaea in the sediments. On the whole, though, CPR bacteria and phages did not show strong signals of gene content differentiation by depth, despite the fact that distinct species groups populate different lake and sediment compartments.<br><br>CONCLUSIONS: Overall, our analyses suggest that environmental gradients in Lac Pavin select for capacities of CPR bacteria and phages to a lesser extent than for other bacteria and archaea. This may be due to the fact that selection in the former groups is indirect and depends primarily on host characteristics. Video Abstract.}, }
@article {pmid36690779, year = {2023}, author = {Yu, Y and Wang, P and Cao, HY and Teng, ZJ and Zhu, Y and Wang, M and McMinn, A and Chen, Y and Xiang, H and Zhang, YZ and Chen, XL and Zhang, YQ}, title = {Novel D-glutamate catabolic pathway in marine Proteobacteria and halophilic archaea.}, journal = {The ISME journal}, volume = {17}, number = {4}, pages = {537-548}, pmid = {36690779}, issn = {1751-7370}, mesh = {*Glutamic Acid/metabolism ; *Proteobacteria ; Ecosystem ; Bacteria ; Archaea/genetics/metabolism ; }, abstract = {D-glutamate (D-Glu) is an essential component of bacterial peptidoglycans, representing an important, yet overlooked, pool of organic matter in global oceans. However, little is known on D-Glu catabolism by marine microorganisms. Here, a novel catabolic pathway for D-Glu was identified using the marine bacterium Pseudoalteromonas sp. CF6-2 as the model. Two novel enzymes (DgcN, DgcA), together with a transcriptional regulator DgcR, are crucial for D-Glu catabolism in strain CF6-2. Genetic and biochemical data confirm that DgcN is a N-acetyltransferase which catalyzes the formation of N-acetyl-D-Glu from D-Glu. DgcA is a racemase that converts N-acetyl-D-Glu to N-acetyl-L-Glu, which is further hydrolyzed to L-Glu. DgcR positively regulates the transcription of dgcN and dgcA. Structural and biochemical analyses suggested that DgcN and its homologs, which use D-Glu as the acyl receptor, represent a new group of the general control non-repressible 5 (GCN5)-related N-acetyltransferases (GNAT) superfamily. DgcA and DgcN occur widely in marine bacteria (particularly Rhodobacterales) and halophilic archaea (Halobacteria) and are abundant in marine and hypersaline metagenome datasets. Thus, this study reveals a novel D-Glu catabolic pathway in ecologically important marine bacteria and halophilic archaea and helps better understand the catabolism and recycling of D-Glu in these ecosystems.}, }
@article {pmid36687602, year = {2022}, author = {Corona Ramírez, A and Cailleau, G and Fatton, M and Dorador, C and Junier, P}, title = {Diversity of Lysis-Resistant Bacteria and Archaea in the Polyextreme Environment of Salar de Huasco.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {826117}, pmid = {36687602}, issn = {1664-302X}, abstract = {The production of specialized resting cells is a remarkable strategy developed by several organisms to survive unfavorable environmental conditions. Spores are specialized resting cells that are characterized by low to absent metabolic activity and higher resistance. Spore-like cells are known from multiple groups of bacteria, which can form spores under suboptimal growth conditions (e.g., starvation). In contrast, little is known about the production of specialized resting cells in archaea. In this study, we applied a culture-independent method that uses physical and chemical lysis, to assess the diversity of lysis-resistant bacteria and archaea and compare it to the overall prokaryotic diversity (direct DNA extraction). The diversity of lysis-resistant cells was studied in the polyextreme environment of the Salar de Huasco. The Salar de Huasco is a high-altitude athalassohaline wetland in the Chilean Altiplano. Previous studies have shown a high diversity of bacteria and archaea in the Salar de Huasco, but the diversity of lysis-resistant microorganisms has never been investigated. The underlying hypothesis was that the combination of extreme abiotic conditions might favor the production of specialized resting cells. Samples were collected from sediment cores along a saline gradient and microbial mats were collected in small surrounding ponds. A significantly different diversity and composition were found in the sediment cores or microbial mats. Furthermore, our results show a high diversity of lysis-resistant cells not only in bacteria but also in archaea. The bacterial lysis-resistant fraction was distinct in comparison to the overall community. Also, the ability to survive the lysis-resistant treatment was restricted to a few groups, including known spore-forming phyla such as Firmicutes and Actinobacteria. In contrast to bacteria, lysis resistance was widely spread in archaea, hinting at a generalized resistance to lysis, which is at least comparable to the resistance of dormant cells in bacteria. The enrichment of Natrinema and Halarchaeum in the lysis-resistant fraction could hint at the production of cyst-like cells or other resistant cells. These results can guide future studies aiming to isolate and broaden the characterization of lysis-resistant archaea.}, }
@article {pmid36683362, year = {2022}, author = {Tandon, K and Ricci, F and Costa, J and Medina, M and Kühl, M and Blackall, LL and Verbruggen, H}, title = {Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {36683362}, issn = {2047-217X}, support = {DP200101613//Australian Research Council/ ; //University of Melbourne/ ; GBMF9206//Gordon and Betty Moore Foundation/ ; }, mesh = {Animals ; *Anthozoa/genetics ; Archaea/genetics ; Coral Reefs ; Bacteria/genetics ; Metagenome ; Genomics ; }, abstract = {At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward the millimeter-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals Porites lutea and Isopora palifera, through a compendium of ∼400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 classes. Skeletal microbiomes harbored a diverse array of stress response genes, including dimethylsulfoniopropionate synthesis (dsyB) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22 ± 15 genes in P. lutea and 28 ± 23 in I. palifera with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulfate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.}, }
@article {pmid36674956, year = {2023}, author = {Baehren, C and Pembaur, A and Weil, PP and Wewers, N and Schult, F and Wirth, S and Postberg, J and Aydin, M}, title = {The Overlooked Microbiome-Considering Archaea and Eukaryotes Using Multiplex Nanopore-16S-/18S-rDNA-Sequencing: A Technical Report Focusing on Nasopharyngeal Microbiomes.}, journal = {International journal of molecular sciences}, volume = {24}, number = {2}, pages = {}, pmid = {36674956}, issn = {1422-0067}, support = {IFF 2021-02//Witten/Herdecke University/ ; 2021-0246//Helios Kliniken/ ; }, mesh = {Humans ; Archaea/genetics ; Eukaryota/genetics ; Phylogeny ; DNA, Ribosomal ; *Nanopores ; Pilot Projects ; *Microbiota/genetics ; Bacteria ; Nasopharynx ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In contrast to bacteria, microbiome analyses often neglect archaea, but also eukaryotes. This is partly because they are difficult to culture due to their demanding growth requirements, or some even have to be classified as uncultured microorganisms. Consequently, little is known about the relevance of archaea in human health and diseases. Contemporary broad availability and spread of next generation sequencing techniques now enable a stronger focus on such microorganisms, whose cultivation is difficult. However, due to the enormous evolutionary distances between bacteria, archaea and eukaryotes, the implementation of sequencing strategies for smaller laboratory scales needs to be refined to achieve as a holistic view on the microbiome as possible. Here, we present a technical approach that enables simultaneous analyses of archaeal, bacterial and eukaryotic microbial communities to study their roles in development and courses of respiratory disorders. We thus applied combinatorial 16S-/18S-rDNA sequencing strategies for sequencing-library preparation. Considering the lower total microbiota density of airway surfaces, when compared with gut microbiota, we optimized the DNA purification workflow from nasopharyngeal swab specimens. As a result, we provide a protocol that allows the efficient combination of bacterial, archaeal, and eukaryotic libraries for nanopore-sequencing using Oxford Nanopore Technologies MinION devices and subsequent phylogenetic analyses. In a pilot study, this workflow allowed the identification of some environmental archaea, which were not correlated with airway microbial communities before. Moreover, we assessed the protocol's broader applicability using a set of human stool samples. We conclude that the proposed protocol provides a versatile and adaptable tool for combinatorial studies on bacterial, archaeal, and eukaryotic microbiomes on a small laboratory scale.}, }
@article {pmid36671499, year = {2023}, author = {De Lise, F and Iacono, R and Moracci, M and Strazzulli, A and Cobucci-Ponzano, B}, title = {Archaea as a Model System for Molecular Biology and Biotechnology.}, journal = {Biomolecules}, volume = {13}, number = {1}, pages = {}, pmid = {36671499}, issn = {2218-273X}, support = {2019-3-U.O.//Agenzia Spaziale Italiana/ ; }, mesh = {*Archaea/metabolism ; Bacteria/genetics ; *Euryarchaeota/genetics/metabolism ; Biotechnology ; Molecular Biology ; }, abstract = {Archaea represents the third domain of life, displaying a closer relationship with eukaryotes than bacteria. These microorganisms are valuable model systems for molecular biology and biotechnology. In fact, nowadays, methanogens, halophiles, thermophilic euryarchaeota, and crenarchaeota are the four groups of archaea for which genetic systems have been well established, making them suitable as model systems and allowing for the increasing study of archaeal genes' functions. Furthermore, thermophiles are used to explore several aspects of archaeal biology, such as stress responses, DNA replication and repair, transcription, translation and its regulation mechanisms, CRISPR systems, and carbon and energy metabolism. Extremophilic archaea also represent a valuable source of new biomolecules for biological and biotechnological applications, and there is growing interest in the development of engineered strains. In this review, we report on some of the most important aspects of the use of archaea as a model system for genetic evolution, the development of genetic tools, and their application for the elucidation of the basal molecular mechanisms in this domain of life. Furthermore, an overview on the discovery of new enzymes of biotechnological interest from archaea thriving in extreme environments is reported.}, }
@article {pmid36660825, year = {2023}, author = {Nissley, AJ and Penev, PI and Watson, ZL and Banfield, JF and Cate, JHD}, title = {Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome.}, journal = {Nucleic acids research}, volume = {51}, number = {4}, pages = {1880-1894}, pmid = {36660825}, issn = {1362-4962}, support = {T32 GM066698/GM/NIGMS NIH HHS/United States ; }, mesh = {*RNA, Ribosomal/metabolism ; *Peptidyl Transferases/metabolism ; Escherichia coli/genetics ; Archaea/genetics ; Base Sequence ; Ribosomes/metabolism ; Bacteria/genetics ; Binding Sites ; Uridine/metabolism ; Cytidine/metabolism ; RNA, Ribosomal, 23S/metabolism ; RNA, Bacterial/metabolism ; }, abstract = {The ribosome serves as the universally conserved translator of the genetic code into proteins and supports life across diverse temperatures ranging from below freezing to above 120°C. Ribosomes are capable of functioning across this wide range of temperatures even though the catalytic site for peptide bond formation, the peptidyl transferase center, is nearly universally conserved. Here we find that Thermoproteota, a phylum of thermophilic Archaea, substitute cytidine for uridine at large subunit rRNA positions 2554 and 2555 (Escherichia coli numbering) in the A loop, immediately adjacent to the binding site for the 3'-end of A-site tRNA. We show by cryo-EM that E. coli ribosomes with uridine to cytidine mutations at these positions retain the proper fold and post-transcriptional modification of the A loop. Additionally, these mutations do not affect cellular growth, protect the large ribosomal subunit from thermal denaturation, and increase the mutational robustness of nucleotides in the peptidyl transferase center. This work identifies sequence variation across archaeal ribosomes in the peptidyl transferase center that likely confers stabilization of the ribosome at high temperatures and develops a stable mutant bacterial ribosome that can act as a scaffold for future ribosome engineering efforts.}, }
@article {pmid36658397, year = {2023}, author = {Laso-Pérez, R and Wu, F and Crémière, A and Speth, DR and Magyar, JS and Zhao, K and Krupovic, M and Orphan, VJ}, title = {Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome.}, journal = {Nature microbiology}, volume = {8}, number = {2}, pages = {231-245}, pmid = {36658397}, issn = {2058-5276}, mesh = {*Archaea ; *Ecosystem ; Phylogeny ; Virome ; Geologic Sediments ; Anaerobiosis ; Methane/metabolism ; Alkanes/metabolism ; }, abstract = {'Candidatus Methanophagales' (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus-host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, 'Candidatus Methanospirareceae', closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems.}, }
@article {pmid36639538, year = {2023}, author = {Zhang, CJ and Liu, YR and Cha, G and Liu, Y and Zhou, XQ and Lu, Z and Pan, J and Cai, M and Li, M}, title = {Potential for mercury methylation by Asgard archaea in mangrove sediments.}, journal = {The ISME journal}, volume = {17}, number = {3}, pages = {478-485}, pmid = {36639538}, issn = {1751-7370}, mesh = {*Mercury/metabolism ; Archaea/genetics/metabolism ; Ecosystem ; Methylation ; Phylogeny ; *Methylmercury Compounds/metabolism ; Geologic Sediments/microbiology ; }, abstract = {Methylmercury (MeHg) is a potent neurotoxin that bioaccumulates along food chains. The conversion of MeHg from mercury (Hg) is mediated by a variety of anaerobic microorganisms carrying hgcAB genes. Mangrove sediments are potential hotspots of microbial Hg methylation; however, the microorganisms responsible for Hg methylation are poorly understood. Here, we conducted metagenomic and metatranscriptomic analyses to investigate the diversity and distribution of putative microbial Hg-methylators in mangrove ecosystems. The highest hgcA abundance and expression occurred in surface sediments in Shenzhen, where the highest MeHg concentration was also observed. We reconstructed 157 metagenome-assembled genomes (MAGs) carrying hgcA and identified several putative novel Hg-methylators, including one Asgard archaea (Lokiarchaeota). Further analysis of MAGs revealed that Deltaproteobacteria, Euryarchaeota, Bacteroidetes, Chloroflexi, and Lokiarchaeota were the most abundant and active Hg-methylating groups, implying their crucial role in MeHg production. By screening publicly available MAGs, 104 additional Asgard MAGs carrying hgcA genes were identified from a wide range of coast, marine, permafrost, and lake sediments. Protein homology modelling predicts that Lokiarchaeota HgcAB proteins contained the highly conserved amino acid sequences and folding structures required for Hg methylation. Phylogenetic tree revealed that hgcA genes from Asgard clustered with fused hgcAB genes, indicating a transitional stage of Asgard hgcA genes. Our findings thus suggest that Asgard archaea are potential novel Hg-methylating microorganisms and play an important role in hgcA evolution.}, }
@article {pmid36622233, year = {2023}, author = {Jia, Y and Lahm, M and Chen, Q and Powers, L and Gonsior, M and Chen, F}, title = {The Predominance of Ammonia-Oxidizing Archaea in an Oceanic Microbial Community Amended with Cyanobacterial Lysate.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0240522}, pmid = {36622233}, issn = {2165-0497}, mesh = {Archaea ; Ammonia ; Dissolved Organic Matter ; Oceans and Seas ; *Ammonium Compounds ; Oxidation-Reduction ; *Microbiota ; *Synechococcus ; Carbon ; Phylogeny ; }, abstract = {When the oligotrophic microbial community was amended with Synechococcus-derived dissolved organic matter (SDOM) and incubated under the dark condition, archaea relative abundance was initially very low but made up more than 60% of the prokaryotic community on day 60, and remained dominant for at least 9 months. The archaeal sequences were dominated by Candidatus Nitrosopumilus, the Group I.1a Thaumarchaeota. The increase of Thaumarchaeota in the dark incubation corresponded to the period of delayed ammonium oxidation upon an initially steady increase in ammonia, supporting the remarkable competency of Thaumarchaeota in energy utilization and fixation of inorganic carbon in the ocean. IMPORTANCE Thaumarchaeota, which are ammonia-oxidizing archaea (AOA), are mainly chemolithoautotrophs that can fix inorganic carbon to produce organic matter in the dark. Their distinctive physiological traits and high abundance in the water column indicate the significant ecological roles they play in the open ocean. In our study, we found predominant Thaumarchaeota in the microbial community amended with cyanobacteria-derived lysate under the dark condition. Furthermore, Thaumarchaeota remained dominant in the microbial community even after 1 year of incubation. Through the ammonification process, dissolved organic matter (DOM) from cyanobacterial lysate was converted to ammonium which was used as an energy source for Thaumarchaeota to fix inorganic carbon into biomass. Our study further advocates the important roles of Thaumarchaeota in the ocean's biogeochemical cycle.}, }
@article {pmid36584837, year = {2023}, author = {Yang, WT and Shen, LD and Bai, YN}, title = {Role and regulation of anaerobic methane oxidation catalyzed by NC10 bacteria and ANME-2d archaea in various ecosystems.}, journal = {Environmental research}, volume = {219}, number = {}, pages = {115174}, doi = {10.1016/j.envres.2022.115174}, pmid = {36584837}, issn = {1096-0953}, mesh = {*Archaea ; *Ecosystem ; Nitrites ; Methane ; Anaerobiosis ; Bacteria ; Oxidation-Reduction ; Catalysis ; Geologic Sediments ; Phylogeny ; }, abstract = {Freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands are recognized as important sources of atmospheric methane (CH4). Currently, increasing evidence shows the potential importance of the anaerobic oxidation of methane (AOM) mediated by NC10 bacteria and a novel cluster of anaerobic methanotrophic archaea (ANME)-ANME-2d in mitigating CH4 emissions from different ecosystems. To better understand the role of NC10 bacteria and ANME-2d archaea in CH4 emission reduction, the current review systematically summarizes different AOM processes and the functional microorganisms involved in freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands. NC10 bacteria are widely present in these ecosystems, and the nitrite-dependent AOM is identified as an important CH4 sink and induces nitrogen loss. Nitrite- and nitrate-dependent AOM co-occur in the environment, and they are mainly affected by soil/sediment inorganic nitrogen and organic carbon contents. Furthermore, salinity is another key factor regulating the two AOM processes in coastal wetlands. In addition, ANME-2d archaea have the great potential to couple AOM to the reduction of iron (III), manganese (IV), sulfate, and even humics in different ecosystems. However, the study on the environmental distribution of ANME-2d archaea and their role in CH4 mitigation in environments is insufficient. In this study, we propose several directions for future research on the different AOM processes and respective functional microorganisms.}, }
@article {pmid36573238, year = {2022}, author = {Moll, J and Hoppe, B}, title = {Evaluation of primers for the detection of deadwood-inhabiting archaea via amplicon sequencing.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e14567}, pmid = {36573238}, issn = {2167-8359}, mesh = {*Archaea/genetics ; Ecosystem ; Bacteria/genetics ; *Euryarchaeota ; Wood/microbiology ; Trees/microbiology ; }, abstract = {Archaea have been reported from deadwood of a few different tree species in temperate and boreal forest ecosystems in the past. However, while one of their functions is well linked to methane production any additional contribution to wood decomposition is not understood and underexplored which may be also attributed to lacking investigations on their diversity in this substrate. With this current work, we aim at encouraging further investigations by providing aid in primer choice for DNA metabarcoding using Illumina amplicon sequencing. We tested 16S primer pairs on genomic DNA extracted from woody tissue of four temperate deciduous tree species. Three primer pairs were specific to archaea and one prokaryotic primer pair theoretically amplifies both, bacterial and archaeal DNA. Methanobacteriales and Methanomassiliicoccales have been consistently identified as dominant orders across all datasets but significant variability in ASV richness was observed using different primer combinations. Nitrososphaerales have only been identified when using archaea-specific primer sets. In addition, the most commonly applied primer combination targeting prokaryotes in general yielded the lowest relative proportion of archaeal sequences per sample, which underlines the fact, that using target specific primers unraveled a yet unknown diversity of archaea in deadwood. Hence, archaea seem to be an important group of the deadwood-inhabiting community and further research is needed to explore their role during the decomposition process.}, }
@article {pmid36567186, year = {2023}, author = {Zhang, X and Zhang, C and Liu, Y and Zhang, R and Li, M}, title = {Non-negligible roles of archaea in coastal carbon biogeochemical cycling.}, journal = {Trends in microbiology}, volume = {31}, number = {6}, pages = {586-600}, doi = {10.1016/j.tim.2022.11.008}, pmid = {36567186}, issn = {1878-4380}, mesh = {*Archaea/genetics/metabolism ; Ecosystem ; *Microbiota ; Methane/metabolism ; Carbon/metabolism ; }, abstract = {Coastal zones are among the world's most productive ecosystems. They store vast amounts of organic carbon, as 'blue carbon' reservoirs, and impact global climate change. Archaeal communities are integral components of coastal microbiomes but their ecological roles are often overlooked. However, archaeal diversity, metabolism, evolution, and interactions, revealed by recent studies using rapidly developing cutting-edge technologies, place archaea as important players in coastal carbon biogeochemical cycling. We here summarize the latest advances in the understanding of archaeal carbon cycling processes in coastal ecosystems, specifically, archaeal involvement in CO2 fixation, organic biopolymer transformation, and methane metabolism. We also showcase the potential to use of archaeal communities to increase carbon sequestration and reduce methane production, with implications for mitigating climate change.}, }
@article {pmid36552364, year = {2022}, author = {Li, Q and Wang, N and Han, W and Zhang, B and Zang, J and Qin, Y and Wang, L and Liu, J and Zhang, T}, title = {Soil Geochemical Properties Influencing the Diversity of Bacteria and Archaea in Soils of the Kitezh Lake Area, Antarctica.}, journal = {Biology}, volume = {11}, number = {12}, pages = {}, pmid = {36552364}, issn = {2079-7737}, support = {No.ZR2020KC036//Natural Science Foundation of Shandong Province/ ; No.GY0219Q10//Basic Scientific Fund for National Public Research Institutes of China/ ; No.41776198//National Natural Science Foundation of China/ ; }, abstract = {It is believed that polar regions are influenced by global warming more significantly, and because polar regions are less affected by human activities, they have certain reference values for future predictions. This study aimed to investigate the effects of climate warming on soil microbial communities in lake areas, taking Kitezh Lake, Antarctica as the research area. Below-peak soil, intertidal soil, and sediment were taken at the sampling sites, and we hypothesized that the diversity and composition of the bacterial and archaeal communities were different among the three sampling sites. Through 16S rDNA sequencing and analysis, bacteria and archaea with high abundance were obtained. Based on canonical correspondence analysis and redundancy analysis, pH and phosphate had a great influence on the bacterial community whereas pH and nitrite had a great influence on the archaeal community. Weighted gene coexpression network analysis was used to find the hub bacteria and archaea related to geochemical factors. The results showed that in addition to pH, phosphate, and nitrite, moisture content, ammonium, nitrate, and total carbon content also play important roles in microbial diversity and structure at different sites by changing the abundance of some key microbiota.}, }
@article {pmid36544005, year = {2023}, author = {Löwe, J}, title = {Mysterious Asgard archaea microbes reveal their inner secrets.}, journal = {Nature}, volume = {613}, number = {7943}, pages = {246-248}, pmid = {36544005}, issn = {1476-4687}, mesh = {*Archaea/genetics ; Phylogeny ; *Eukaryotic Cells ; Eukaryota/genetics ; Genome, Archaeal ; }, }
@article {pmid36543797, year = {2022}, author = {Zhao, W and Zhong, B and Zheng, L and Tan, P and Wang, Y and Leng, H and de Souza, N and Liu, Z and Hong, L and Xiao, X}, title = {Proteome-wide 3D structure prediction provides insights into the ancestral metabolism of ancient archaea and bacteria.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7861}, pmid = {36543797}, issn = {2041-1723}, mesh = {*Archaea/genetics/metabolism ; *Proteome/metabolism ; Phylogeny ; Evolution, Molecular ; Bacteria/genetics/metabolism ; }, abstract = {Ancestral metabolism has remained controversial due to a lack of evidence beyond sequence-based reconstructions. Although prebiotic chemists have provided hints that metabolism might originate from non-enzymatic protometabolic pathways, gaps between ancestral reconstruction and prebiotic processes mean there is much that is still unknown. Here, we apply proteome-wide 3D structure predictions and comparisons to investigate ancestorial metabolism of ancient bacteria and archaea, to provide information beyond sequence as a bridge to the prebiotic processes. We compare representative bacterial and archaeal strains, which reveal surprisingly similar physiological and metabolic characteristics via microbiological and biophysical experiments. Pairwise comparison of protein structures identify the conserved metabolic modules in bacteria and archaea, despite interference from overly variable sequences. The conserved modules (for example, middle of glycolysis, partial TCA, proton/sulfur respiration, building block biosynthesis) constitute the basic functions that possibly existed in the archaeal-bacterial common ancestor, which are remarkably consistent with the experimentally confirmed protometabolic pathways. These structure-based findings provide a new perspective to reconstructing the ancestral metabolism and understanding its origin, which suggests high-throughput protein 3D structure prediction is a promising approach, deserving broader application in future ancestral exploration.}, }
@article {pmid36541769, year = {2023}, author = {Bai, T and Pu, X and Guo, X and Liu, J and Zhao, L and Zhang, X and Zhang, S and Cheng, L}, title = {Effects of Dietary Nonfibrous Carbohydrate/Neutral Detergent Fiber Ratio on Methanogenic Archaea and Cellulose-Degrading Bacteria in the Rumen of Karakul Sheep: a 16S rRNA Gene Sequencing Study.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {1}, pages = {e0129122}, pmid = {36541769}, issn = {1098-5336}, mesh = {Animals ; *Archaea/metabolism ; *Bacteria/metabolism ; Cellulose/metabolism ; Diet/veterinary ; *Dietary Carbohydrates/metabolism ; *Dietary Fiber/metabolism ; Methane/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; *Rumen/metabolism/microbiology ; Sheep, Domestic ; }, abstract = {The study was conducted to investigate the effects of dietary nonfibrous carbohydrate (NFC)/neutral detergent fiber (NDF) ratio on methanogenic archaea and cellulose-degrading bacteria in Karakul sheep by 16S rRNA gene sequencing. Twelve Karakul sheep were randomly divided into four groups, each group with three replicates, and they were fed with four dietary NFC/NDF ratios at 0.54, 0.96, 1.37, and 1.90 as groups 1, 2, 3, and 4, respectively. The experiment lasted for four periods: I (1 to 18 days), II (19 to 36 days), III (37 to 54 days), and IV (55 to 72 days); during each period, rumen contents were collected before morning feeding to investigate on methanogenic archaea and cellulose-degrading bacteria. The results showed that with an increase in dietary NFC/NDF ratio, the number of rumen archaea operational taxonomic units and the diversity of archaea decrease. The most dominant methanogens did not change with dietary NFC/NDF ratio and prolongation of experimental periods. Methanobrevibacter was the most dominant genus. At the species level, the relative abundance of Methanobrevibacter ruminantium first increased and then decreased when the NFC/NDF ratio increased. When the dietary NFC/NDF ratio was 0.96, the structure of archaea was largely changed, and the relative abundance of Fibrobacter sp. strain UWCM, Ruminococcus flavefaciens, and Ruminococcus albus were the highest. When the dietary NFC/NDF ratio was 1.37, the relative abundance of Butyrivibrio fibrisolvens was higher than for other groups. Based on all the data, we concluded that a dietary NFC/NDF ratio of ca. 0.96 to 1.37 was a suitable ratio to support optimal sheep production. IMPORTANCE CH4 produced by ruminants aggravates the greenhouse effect and cause wastage of feed energy, and CH4 emissions are related to methanogens. According to the current literature, there is a symbiotic relationship between methanogens and cellulolytic bacteria, so reducing methane will inevitably affect the degradation of fiber materials. This experiment used 16S rRNA gene high-throughput sequencing technology to explore the balance relationship between methanogens and cellulolytic bacteria for the first time through a long-term feeding period. The findings provide fundamental data, supporting for the diet structures with potential to reduce CH4 emission.}, }
@article {pmid36529166, year = {2023}, author = {Jiang, Z and Tang, S and Liao, Y and Li, S and Wang, S and Zhu, X and Ji, G}, title = {Effect of low temperature on contributions of ammonia oxidizing archaea and bacteria to nitrous oxide in constructed wetlands.}, journal = {Chemosphere}, volume = {313}, number = {}, pages = {137585}, doi = {10.1016/j.chemosphere.2022.137585}, pmid = {36529166}, issn = {1879-1298}, mesh = {*Archaea/genetics ; *Nitrous Oxide ; Ammonia ; Wetlands ; Temperature ; Nitrification ; Oxidation-Reduction ; Soil Microbiology ; Bacteria/genetics ; Phylogeny ; }, abstract = {Constructed wetlands (CWs) have been widely used for ecological remediation of micro-polluted source water. Nitrous oxide (N2O) from CWs has caused great concern as a greenhouse gas. However, the contribution of ammonia oxidation driven by ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) to N2O emission, especially at low temperature, was unknown. This study aimed to quantify the contributions of AOA and AOB to N2O through lab-scale subsurface CWs. The N2O emission flux of CW at 8 °C was 1.23 mg m[-2]·h[-1], significantly lower than that at 25 °C (1.92 mg m[-2]·h[-1]). The contribution of ammonia oxidation to N2O at 8 °C (33.04%) was significantly higher than that at 25 °C (24.17%). The N2O production from AOA increased from 1.91 ng N·g[-1] at 25 °C to 4.11 ng N·g[-1] soil at 8 °C and its contribution increased from 23.38% to 30.18% (P < 0.05). Low temperature impaired functional gene groups and inhibited the activity of AOB, resulting in its declined contribution. Based on the transcriptional analysis, AOA was less affected by low temperature, thus stably contributing to N2O. Moreover, community diversity and relationships of AOA were enhanced at 8 °C, while AOB declined. The results confirmed the significant contribution of AOA and demonstrated molecular mechanisms (higher activity and community stability) of the increased contribution of AOA to N2O at low temperature.}, }
@article {pmid38818484, year = {2022}, author = {Zhou, Z and Liu, Y and Anantharaman, K and Li, M}, title = {The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis.}, journal = {mLife}, volume = {1}, number = {4}, pages = {374-381}, pmid = {38818484}, issn = {2770-100X}, abstract = {The division of organisms on the Tree of Life into either a three-domain (3D) tree or a two-domain (2D) tree has been disputed for a long time. Ever since the discovery of Archaea by Carl Woese in 1977 using 16S ribosomal RNA sequence as the evolutionary marker, there has been a great advance in our knowledge of not only the growing diversity of Archaea but also the evolutionary relationships between different lineages of living organisms. Here, we present this perspective to summarize the progress of archaeal diversity and changing notion of the Tree of Life. Meanwhile, we provide the latest progress in genomics/physiology-based discovery of Asgard archaeal lineages as the closest relative of Eukaryotes. Furthermore, we propose three major directions for future research on exploring the "next one" closest Eukaryote relative, deciphering the function of archaeal eukaryotic signature proteins and eukaryogenesis from both genomic and physiological aspects, and understanding the roles of horizontal gene transfer, viruses, and mobile elements in eukaryogenesis.}, }
@article {pmid36519377, year = {2023}, author = {Kucukyildirim, S and Ozdemirel, HO and Lynch, M}, title = {Similar mutation rates but different mutation spectra in moderate and extremely halophilic archaea.}, journal = {G3 (Bethesda, Md.)}, volume = {13}, number = {3}, pages = {}, pmid = {36519377}, issn = {2160-1836}, support = {R35 GM122566/GM/NIGMS NIH HHS/United States ; }, mesh = {Mutation Rate ; *Haloferax volcanii/genetics/metabolism ; Mutation ; DNA Repair ; *Archaeal Proteins/genetics/metabolism ; Archaea/genetics ; }, abstract = {Archaea are a major part of Earth's microbiota and extremely diverse. Yet, we know very little about the process of mutation that drives such diversification. To expand beyond previous work with the moderate halophilic archaeal species Haloferax volcanii, we performed a mutation-accumulation experiment followed by whole-genome sequencing in the extremely halophilic archaeon Halobacterium salinarum. Although Hfx. volcanii and Hbt. salinarum have different salt requirements, both species have highly polyploid genomes and similar GC content. We accumulated mutations for an average of 1250 generations in 67 mutation accumulation lines of Hbt. salinarum, and revealed 84 single-base substitutions and 10 insertion-deletion mutations. The estimated base-substitution mutation rate of 3.99 × 10-10 per site per generation or 1.0 × 10-3 per genome per generation in Hbt. salinarum is similar to that reported for Hfx. volcanii (1.2 × 10-3 per genome per generation), but the genome-wide insertion-deletion rate and spectrum of mutations are somewhat dissimilar in these archaeal species. The spectra of spontaneous mutations were AT biased in both archaea, but they differed in significant ways that may be related to differences in the fidelity of DNA replication/repair mechanisms or a simple result of the different salt concentrations.}, }
@article {pmid36512566, year = {2022}, author = {, }, title = {Expression of Concern: A Versatile Medium for Cultivating Methanogenic Archaea.}, journal = {PloS one}, volume = {17}, number = {12}, pages = {e0278740}, pmid = {36512566}, issn = {1932-6203}, }
@article {pmid36499474, year = {2022}, author = {Ginsbach, LF and Gonzalez, JM}, title = {Understanding Life at High Temperatures: Relationships of Molecular Channels in Enzymes of Methanogenic Archaea and Their Growth Temperatures.}, journal = {International journal of molecular sciences}, volume = {23}, number = {23}, pages = {}, pmid = {36499474}, issn = {1422-0067}, support = {EQC2019-005634-P//Ministerio de Ciencia e Innovaci&#xf3;n/ ; EQC2019-005634-P//Feder/ ; PID2020-119373GB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; Laura Ginsbach//German Academic Exchange Service/ ; }, mesh = {*Archaea/metabolism ; Phylogeny ; *Methane/metabolism ; Temperature ; Hot Temperature ; }, abstract = {Analyses of protein structures have shown the existence of molecular channels in enzymes from Prokaryotes. Those molecular channels suggest a critical role of spatial voids in proteins, above all, in those enzymes functioning under high temperature. It is expected that these spaces within the protein structure are required to access the active site and to maximize availability and thermal stability of their substrates and cofactors. Interestingly, numerous substrates and cofactors have been reported to be highly temperature-sensitive biomolecules. Methanogens represent a singular phylogenetic group of Archaea that performs anaerobic respiration producing methane during growth. Methanogens inhabit a variety of environments including the full range of temperatures for the known living forms. Herein, we carry out a dimensional analysis of molecular tunnels in key enzymes of the methanogenic pathway from methanogenic Archaea growing optimally over a broad temperature range. We aim to determine whether the dimensions of the molecular tunnels are critical for those enzymes from thermophiles. Results showed that at increasing growth temperature the dimensions of molecular tunnels in the enzymes methyl-coenzyme M reductase and heterodisulfide reductase become increasingly restrictive and present strict limits at the highest growth temperatures, i.e., for hyperthermophilic methanogens. However, growth at lower temperature allows a wide dimensional range for the molecular spaces in these enzymes. This is in agreement with previous suggestions on a potential major role of molecular tunnels to maintain biomolecule stability and activity of some enzymes in microorganisms growing at high temperatures. These results contribute to better understand archaeal growth at high temperatures. Furthermore, an optimization of the dimensions of molecular tunnels would represent an important adaptation required to maintain the activity of key enzymes of the methanogenic pathway for those methanogens growing optimally at high temperatures.}, }
@article {pmid36461738, year = {2023}, author = {Ponlachantra, K and Suginta, W and Robinson, RC and Kitaoku, Y}, title = {AlphaFold2: A versatile tool to predict the appearance of functional adaptations in evolution: Profilin interactions in uncultured Asgard archaea: Profilin interactions in uncultured Asgard archaea.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {2}, pages = {e2200119}, doi = {10.1002/bies.202200119}, pmid = {36461738}, issn = {1521-1878}, support = {JPMJCR19S5//JST CREST/ ; //Moore-Simons Project/ ; GBMF9743//Origin of the Eukaryotic Cell/ ; //Vidyasirimedhi Institute of Science and Technology (VISTEC)/ ; }, mesh = {*Archaea/metabolism ; *Profilins/genetics/metabolism ; Actins ; Phylogeny ; Furylfuramide/metabolism ; Eukaryota/metabolism ; }, abstract = {The release of AlphaFold2 (AF2), a deep-learning-aided, open-source protein structure prediction program, from DeepMind, opened a new era of molecular biology. The astonishing improvement in the accuracy of the structure predictions provides the opportunity to characterize protein systems from uncultured Asgard archaea, key organisms in evolutionary biology. Despite the accumulation in metagenomics-derived Asgard archaea eukaryotic-like protein sequences, limited structural and biochemical information have restricted the insight in their potential functions. In this review, we focus on profilin, an actin-dynamics regulating protein, which in eukaryotes, modulates actin polymerization through (1) direct actin interaction, (2) polyproline binding, and (3) phospholipid binding. We assess AF2-predicted profilin structures in their potential abilities to participate in these activities. We demonstrate that AF2 is a powerful new tool for understanding the emergence of biological functional traits in evolution.}, }
@article {pmid36445127, year = {2022}, author = {Woo, Y and Cruz, MC and Wuertz, S}, title = {Selective Enrichment of Nitrososphaera viennensis-Like Ammonia-Oxidizing Archaea over Ammonia-Oxidizing Bacteria from Drinking Water Biofilms.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0184522}, pmid = {36445127}, issn = {2165-0497}, mesh = {*Archaea ; *Drinking Water ; Ammonia ; Nitrites ; Oxidation-Reduction ; Soil Microbiology ; Bacteria/genetics ; Biofilms ; Pyruvates ; Phylogeny ; }, abstract = {Ammonia-oxidizing archaea (AOA) can oxidize ammonia to nitrite for energy gain. They have been detected in chloraminated drinking water distribution systems (DWDS) along with the more common ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). To date, no members of the AOA have been isolated or enriched from drinking water environments. To begin the investigation of the role of AOA in chloraminated DWDS, we developed a selective approach using biofilm samples from a full-scale operational network as inoculum. A Nitrososphaera viennensis-like AOA taxon was enriched from a mixed community that also included Nitrosomonas-like AOB while gradually scaling up the culture volume. Dimethylthiourea (DMTU) and pyruvate at 100 μM were added to promote the growth of AOA while inhibiting AOB. This resulted in the eventual washout of AOB, while NOB were absent after 2 or 3 rounds of amendment with 24 μM sodium azide. The relative abundance of AOA in the enrichment increased from 0.2% to 39.5% after adding DMTU and pyruvate, and further to 51.6% after filtration through a 0.45-μm pore size membrane, within a period of approximately 6 months. IMPORTANCE Chloramination has been known to increase the risk of nitrification episodes in DWDS due to the presence of ammonia-oxidizing microorganisms. Among them, AOB are more frequently detected than AOA. All publicly available cultures of AOA have been isolated from soil, marine or surface water environments, meaning they are allochthonous to DWDS. Hence, monochloramine exposure studies involving these strains may not accurately reflect their role in DWDS. The described method allows for the rapid enrichment of autochthonous AOA from drinking water nitrifying communities. The high relative abundance of AOA in the resulting enrichment culture reduces any confounding effects of co-existing heterotrophic bacteria when investigating the response of AOA to varied levels of monochloramine in drinking water.}, }
@article {pmid36444822, year = {2023}, author = {Hagagy, N and Abdel-Mawgoud, M and Akhtar, N and Selim, S and AbdElgawad, H}, title = {The new isolated Archaea strain improved grain yield, metabolism and quality of wheat plants under Co stress conditions.}, journal = {Journal of plant physiology}, volume = {280}, number = {}, pages = {153876}, doi = {10.1016/j.jplph.2022.153876}, pmid = {36444822}, issn = {1618-1328}, mesh = {*Triticum/metabolism ; *Edible Grain ; Soil/chemistry ; Cobalt/metabolism ; Sugars/metabolism ; }, abstract = {Heavy metal (e.g. cobalt) pollution causes a serious of environmental and agricultural problems. On the other hand, plant growth-promoting microorganisms enhance plant growth and mitigate heavy metal stress. Herein, we isolated and identified the unclassified species strain NARS9, belong to Haloferax,. Cobalt (Co, 200 mg/kg soil) stress mitigating impact of the identified on wheat grains yield, primary and secondary metabolism and grain quality was investigated. Co alone significantly induced Co accumulation in wheat grain (260%), and consequently reduced wheat yield (130%) and quality. Haloferax NARS9 alone significantly enhanced grain chemicals composition (i.e., total sugars (89%) and organic acids (e.g., oxalic and isobutyric acids), essential amino acids (e.g., threonine, lysine, and histidine) and unsaturated fatty acids (e.g. eicosenoic, erucic and tetracosenoic acids). Interestingly, Co stress induced wheat grain yield, reduction were significantly mitigated by Haloferax NARS9 treatment by 26% compared to Co stress alone. Under Co stress, Haloferax NARS9 significantly increased sugar metabolism including sucrose and starch levels and their metabolic enzymes (i.e. invertases, sucrose synthase, starch synthase). This in turn increased organic acid (e.g. oxalic (70%) and malic acids (60%)) and amino acids. levels and biosynthetic enzymes, e.g. glutamine synthetase and threonine synthase. Increased sugars levels by Haloferax NARS9 under Co treatment also provided a route for the biosynthesis of saturated fatty acids, particularly palmitic and stearic acids. Furthermore, Haloferax NARS9 treatment supported the wheat nutritive value through increasing minerals (Ca, Fe, Mn, Zn) and antioxidants i.e., polyphenol, flavonoids, ASC and GSH and total polyamines by 50%, 110%, 400%, 30%, and 90% respectively). These in parallel with the increase in the activity of (phenylalanine ammonia-lyase (110%) in phenolic metabolism). Overall, this study demonstrates the potentiality of Haloferax NARS9 in harnessing carbon and nitrogen metabolism differentially in wheat plants to cope with Co toxicity. Our results also suggested that the use of Haloferax NARS9 in agricultural fields can improve growth and nutritional value of wheat grains.}, }
@article {pmid36434094, year = {2022}, author = {Sato, T and Utashima, SH and Yoshii, Y and Hirata, K and Kanda, S and Onoda, Y and Jin, JQ and Xiao, S and Minami, R and Fukushima, H and Noguchi, A and Manabe, Y and Fukase, K and Atomi, H}, title = {A non-carboxylating pentose bisphosphate pathway in halophilic archaea.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1290}, pmid = {36434094}, issn = {2399-3642}, mesh = {*Ribulose-Bisphosphate Carboxylase/genetics/metabolism ; *Ribose/metabolism ; Pentoses/metabolism ; Archaea/genetics/metabolism ; Guanosine/metabolism ; Phosphates ; }, abstract = {Bacteria and Eucarya utilize the non-oxidative pentose phosphate pathway to direct the ribose moieties of nucleosides to central carbon metabolism. Many archaea do not possess this pathway, and instead, Thermococcales utilize a pentose bisphosphate pathway involving ribose-1,5-bisphosphate (R15P) isomerase and ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco). Intriguingly, multiple genomes from halophilic archaea seem only to harbor R15P isomerase, and do not harbor Rubisco. In this study, we identify a previously unrecognized nucleoside degradation pathway in halophilic archaea, composed of guanosine phosphorylase, ATP-dependent ribose-1-phosphate kinase, R15P isomerase, RuBP phosphatase, ribulose-1-phosphate aldolase, and glycolaldehyde reductase. The pathway converts the ribose moiety of guanosine to dihydroxyacetone phosphate and ethylene glycol. Although the metabolic route from guanosine to RuBP via R15P is similar to that of the pentose bisphosphate pathway in Thermococcales, the downstream route does not utilize Rubisco and is unique to halophilic archaea.}, }
@article {pmid36414709, year = {2023}, author = {Lee, S and Sieradzki, ET and Nicol, GW and Hazard, C}, title = {Propagation of viral genomes by replicating ammonia-oxidising archaea during soil nitrification.}, journal = {The ISME journal}, volume = {17}, number = {2}, pages = {309-314}, pmid = {36414709}, issn = {1751-7370}, mesh = {*Archaea/metabolism ; *Soil/chemistry ; Nitrification ; Bacteria/genetics ; Ammonia/metabolism ; Soil Microbiology ; Oxidation-Reduction ; Genome, Viral ; Phylogeny ; }, abstract = {Ammonia-oxidising archaea (AOA) are a ubiquitous component of microbial communities and dominate the first stage of nitrification in some soils. While we are beginning to understand soil virus dynamics, we have no knowledge of the composition or activity of those infecting nitrifiers or their potential to influence processes. This study aimed to characterise viruses having infected autotrophic AOA in two nitrifying soils of contrasting pH by following transfer of assimilated CO2-derived [13]C from host to virus via DNA stable-isotope probing and metagenomic analysis. Incorporation of [13]C into low GC mol% AOA and virus genomes increased DNA buoyant density in CsCl gradients but resulted in co-migration with dominant non-enriched high GC mol% genomes, reducing sequencing depth and contig assembly. We therefore developed a hybrid approach where AOA and virus genomes were assembled from low buoyant density DNA with subsequent mapping of [13]C isotopically enriched high buoyant density DNA reads to identify activity of AOA. Metagenome-assembled genomes were different between the two soils and represented a broad diversity of active populations. Sixty-four AOA-infecting viral operational taxonomic units (vOTUs) were identified with no clear relatedness to previously characterised prokaryote viruses. These vOTUs were also distinct between soils, with 42% enriched in [13]C derived from hosts. The majority were predicted as capable of lysogeny and auxiliary metabolic genes included an AOA-specific multicopper oxidase suggesting infection may augment copper uptake essential for central metabolic functioning. These findings indicate virus infection of AOA may be a frequent process during nitrification with potential to influence host physiology and activity.}, }
@article {pmid36413802, year = {2023}, author = {Matse, DT and Jeyakumar, P and Bishop, P and Anderson, CWN}, title = {Copper induces nitrification by ammonia-oxidizing bacteria and archaea in pastoral soils.}, journal = {Journal of environmental quality}, volume = {52}, number = {1}, pages = {49-63}, doi = {10.1002/jeq2.20440}, pmid = {36413802}, issn = {1537-2537}, mesh = {*Archaea/genetics ; *Soil ; Bacteria/genetics ; Nitrification ; Ammonia ; Copper ; Oxidation-Reduction ; Soil Microbiology ; Phylogeny ; }, abstract = {Copper (Cu) is the main co-factor in the functioning of the ammonia monooxygenase (AMO) enzyme, which is responsible for the first step of ammonia oxidation. We report a greenhouse-based pot experiment that examines the response of ammonia-oxidizing bacteria and archaea (AOB and AOA) to different bioavailable Cu concentrations in three pastoral soils (Recent, Pallic, and Pumice soils) planted with ryegrass (Lolium perenne L.). Five treatments were used: control (no urine and Cu), urine only at 300 mg N kg[-1] soil (Cu0), urine + 1 mg Cu kg[-1] soil (Cu1), urine + 10 mg Cu kg[-1] soil (Cu10), and urine + 100 mg Cu kg[-1] soil (Cu100). Pots were destructively sampled at Day 0, 1, 7, 15, and 25 after urine application. The AOB/AOA amoA gene abundance was analyzed by real-time quantitative polymerase chain reaction at Days 1 and 15. The AOB amoA gene abundance increased 10.0- and 22.6-fold in the Recent soil and 2.1- and 2.5-fold in the Pallic soil for the Cu10 compared with Cu0 on Days 1 and 15, respectively. In contrast, the Cu100 was associated with a reduction in AOB amoA gene abundance in the Recent and Pallic soils but not in the Pumice soil. This may be due to the influence of soil cation exchange capacity differences on the bioavailable Cu. Bioavailable Cu in the Recent and Pallic soils influenced nitrification and AOB amoA gene abundance, as evidenced by the strong positive correlation between bioavailable Cu, nitrification, and AOB amoA. However, bioavailable Cu did not influence the nitrification and AOA amoA gene abundance increase.}, }
@article {pmid36406397, year = {2022}, author = {Yuan, H and Zhang, W and Yin, H and Zhang, R and Wang, J}, title = {Taxonomic dependency of beta diversity for bacteria, archaea, and fungi in a semi-arid lake.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {998496}, pmid = {36406397}, issn = {1664-302X}, abstract = {Microbial beta diversity has been recently studied along the water depth in aquatic ecosystems, however its turnover and nestedness components remain elusive especially for multiple taxonomic groups. Based on the beta diversity partitioning developed by Baselga and Local Contributions to Beta Diversity (LCBD) partitioning by Legendre, we examined the water-depth variations in beta diversity components of bacteria, archaea and fungi in surface sediments of Hulun Lake, a semi-arid lake in northern China, and further explored the relative importance of environmental drivers underlying their patterns. We found that the relative abundances of Proteobacteria, Chloroflexi, Euryarchaeota, and Rozellomycota increased toward deep water, while Acidobacteria, Parvarchaeota, and Chytridiomycota decreased. For bacteria and archaea, there were significant (p < 0.05) decreasing water-depth patterns for LCBD and LCBDRepl (i.e., species replacement), while increasing patterns for total beta diversity and turnover, implying that total beta diversity and LCBD were dominated by species turnover or LCBDRepl. Further, bacteria showed a strong correlation with archaea regarding LCBD, total beta diversity and turnover. Such parallel patterns among bacteria and archaea were underpinned by similar ecological processes like environmental selection. Total beta diversity and turnover were largely affected by sediment total nitrogen, while LCBD and LCBDRepl were mainly constrained by water NO2 [-]-N and NO3 [-]-N. For fungal community variation, no significant patterns were observed, which may be due to different drivers like water nitrogen or phosphorus. Taken together, our findings provide compelling evidences for disentangling the underlying mechanisms of community variation in multiple aquatic microbial taxonomic groups.}, }
@article {pmid36402873, year = {2022}, author = {Hu, L and Dong, Z and Wang, Z and Xiao, L and Zhu, B}, title = {The contributions of ammonia oxidizing bacteria and archaea to nitrification-dependent N2O emission in alkaline and neutral purple soils.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {19928}, pmid = {36402873}, issn = {2045-2322}, support = {U20A20107//the Key Project of National Science Foundation of China/ ; 41301266//National Natural Science Foundation of China/ ; }, mesh = {*Archaea/genetics ; Nitrification ; Soil/chemistry ; Ammonia ; Soil Microbiology ; Bacteria/genetics ; Oxidation-Reduction ; *Betaproteobacteria/genetics ; }, abstract = {Nitrification is believed to be one of the primary processes of N2O emission in the agroecological system, which is controlled by soil microbes and mainly regulated by soil pH, oxygen content and NH4[+] availability. Previous studies have proved that the relative contributions of ammonia oxidizing bacteria (AOB) and archaea (AOA) to N2O production were varied with soil pH, however, there is still no consensus on the regulating mechanism of nitrification-derived N2O production by soil pH. In this study, 1-octyne (a selective inhibitor of AOB) and acetylene (an inhibitor of AOB and AOA) were used in a microcosm incubation experiment to differentiate the relative contribution of AOA and AOB to N2O emissions in a neutral (pH = 6.75) and an alkaline (pH = 8.35) soils. We found that the amendment of ammonium (NH4[+]) observably stimulated the production of both AOA and AOB-related N2O and increased the ammonia monooxygenase (AMO) gene abundances of AOA and AOB in the two test soils. Among which, AOB dominated the process of ammonia oxidation in the alkaline soil, contributing 70.8% of N2O production derived from nitrification. By contrast, the contribution of AOA and AOB accounted for about one-third of nitrification-related N2O in acidic soil, respectively. The results indicated that pH was a key factor to change abundance and activity of AOA and AOB, which led to the differentiation of derivation of N2O production in purple soils. We speculate that both NH4[+] content and soil pH mediated specialization of ammonia-oxidizing microorganisms together; and both specialization results and N2O yield led to the different N2O emission characteristics in purple soils. These results may help inform the development of N2O reduction strategies in the future.}, }
@article {pmid36400771, year = {2022}, author = {Schoelmerich, MC and Ouboter, HT and Sachdeva, R and Penev, PI and Amano, Y and West-Roberts, J and Welte, CU and Banfield, JF}, title = {A widespread group of large plasmids in methanotrophic Methanoperedens archaea.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7085}, pmid = {36400771}, issn = {2041-1723}, mesh = {*Archaea/metabolism ; Anaerobiosis ; *Methane/metabolism ; Oxidation-Reduction ; Plasmids/genetics ; }, abstract = {Anaerobic methanotrophic (ANME) archaea obtain energy from the breakdown of methane, yet their extrachromosomal genetic elements are little understood. Here we describe large plasmids associated with ANME archaea of the Methanoperedens genus in enrichment cultures and other natural anoxic environments. By manual curation we show that two of the plasmids are large (155,605 bp and 191,912 bp), circular, and may replicate bidirectionally. The plasmids occur in the same copy number as the main chromosome, and plasmid genes are actively transcribed. One of the plasmids encodes three tRNAs, ribosomal protein uL16 and elongation factor eEF2; these genes appear to be missing in the host Methanoperedens genome, suggesting an obligate interdependence between plasmid and host. Our work opens the way for the development of genetic vectors to shed light on the physiology and biochemistry of Methanoperedens, and potentially genetically edit them to enhance growth and accelerate methane oxidation rates.}, }
@article {pmid36385454, year = {2023}, author = {Zhou, Y and Zhou, L and Yan, S and Chen, L and Krupovic, M and Wang, Y}, title = {Diverse viruses of marine archaea discovered using metagenomics.}, journal = {Environmental microbiology}, volume = {25}, number = {2}, pages = {367-382}, doi = {10.1111/1462-2920.16287}, pmid = {36385454}, issn = {1462-2920}, mesh = {*Archaea/genetics/virology ; *Archaeal Viruses/genetics ; Genome, Viral ; Metagenomics/methods ; Phylogeny ; Viral Proteins/genetics ; }, abstract = {During the past decade, metagenomics became a method of choice for the discovery of novel viruses. However, host assignment for uncultured viruses remains challenging, especially for archaeal viruses, which are grossly undersampled compared to viruses of bacteria and eukaryotes. Here, we assessed the utility of CRISPR spacer targeting, tRNA gene matching and homology searches for viral signature proteins, such as major capsid proteins, for the assignment of archaeal hosts and validated these approaches on metaviromes from Yangshan Harbor (YSH). We report 35 new genomes of viruses which could be confidently assigned to hosts representing diverse lineages of marine archaea. We show that the archaeal YSH virome is highly diverse, with some viruses enriching the previously described virus groups, such as magroviruses of Marine Group II Archaea (Poseidoniales), and others representing novel groups of marine archaeal viruses. Metagenomic recruitment of Tara Oceans datasets on the YSH viral genomes demonstrated the presence of YSH Poseidoniales and Nitrososphaeria viruses in the global oceans, but also revealed the endemic YSH-specific viral lineages. Furthermore, our results highlight the relationship between the soil and marine thaumarchaeal viruses. We propose three new families within the class Caudoviricetes for the classification of the five complete viral genomes predicted to replicate in marine Poseidoniales and Nitrososphaeria, two ecologically important and widespread archaeal groups. This study illustrates the utility of viral metagenomics in exploring the archaeal virome and provides new insights into the diversity, distribution and evolution of marine archaeal viruses.}, }
@article {pmid36383678, year = {2022}, author = {Ghaly, TM and Tetu, SG and Penesyan, A and Qi, Q and Rajabal, V and Gillings, MR}, title = {Discovery of integrons in Archaea: Platforms for cross-domain gene transfer.}, journal = {Science advances}, volume = {8}, number = {46}, pages = {eabq6376}, pmid = {36383678}, issn = {2375-2548}, abstract = {Horizontal gene transfer between different domains of life is increasingly being recognized as an important evolutionary driver, with the potential to increase the pace of biochemical innovation and environmental adaptation. However, the mechanisms underlying the recruitment of exogenous genes from foreign domains are mostly unknown. Integrons are a family of genetic elements that facilitate this process within Bacteria. However, they have not been reported outside Bacteria, and thus their potential role in cross-domain gene transfer has not been investigated. Here, we discover that integrons are also present in 75 archaeal metagenome-assembled genomes from nine phyla, and are particularly enriched among Asgard archaea. Furthermore, we provide experimental evidence that integrons can facilitate the recruitment of archaeal genes by bacteria. Our findings establish a previously unknown mechanism of cross-domain gene transfer whereby bacteria can incorporate archaeal genes from their surrounding environment via integron activity. These findings have important implications for prokaryotic ecology and evolution.}, }
@article {pmid36372432, year = {2022}, author = {Kuroda, K and Kubota, K and Kagemasa, S and Nakai, R and Hirakata, Y and Yamamoto, K and Nobu, MK and Narihiro, T}, title = {Novel Cross-domain Symbiosis between Candidatus Patescibacteria and Hydrogenotrophic Methanogenic Archaea Methanospirillum Discovered in a Methanogenic Ecosystem.}, journal = {Microbes and environments}, volume = {37}, number = {4}, pages = {}, pmid = {36372432}, issn = {1347-4405}, mesh = {*Archaea/genetics ; Methanospirillum/genetics ; Symbiosis ; Ecosystem ; In Situ Hybridization, Fluorescence ; Phylogeny ; *Euryarchaeota ; Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {To identify novel cross-domain symbiosis between Candidatus Patescibacteria and Archaea, we performed fluorescence in situ hybridization (FISH) on enrichment cultures derived from methanogenic bioreactor sludge with the newly designed 32-520-1066 probe targeting the family-level uncultured clade 32-520/UBA5633 lineage in the class Ca. Paceibacteria. All FISH-detectable 32-520/UBA5633 cells were attached to Methanospirillum, indicating high host specificity. Transmission electron microscopy observations revealed 32-520/UBA5633-like cells that were specifically adherent to the plug structure of Methanospirillum-like rod-shaped cells. The metagenome-assembled genomes of 32-520/UBA5633 encoded unique gene clusters comprising pilin signal peptides and type IV pilins. These results provide novel insights into unseen symbiosis between Ca. Patescibacteria and Archaea.}, }
@article {pmid36367391, year = {2023}, author = {Boyd, ES and Spietz, RL and Kour, M and Colman, DR}, title = {A naturalist perspective of microbiology: Examples from methanogenic archaea.}, journal = {Environmental microbiology}, volume = {25}, number = {1}, pages = {184-198}, doi = {10.1111/1462-2920.16285}, pmid = {36367391}, issn = {1462-2920}, mesh = {Humans ; *Archaea/genetics ; *Euryarchaeota ; }, abstract = {Storytelling has been the primary means of knowledge transfer over human history. The effectiveness and reach of stories are improved when the message is appropriate for the target audience. Oftentimes, the stories that are most well received and recounted are those that have a clear purpose and that are told from a variety of perspectives that touch on the varied interests of the target audience. Whether scientists realize or not, they are accustomed to telling stories of their own scientific discoveries through the preparation of manuscripts, presentations, and lectures. Perhaps less frequently, scientists prepare review articles or book chapters that summarize a body of knowledge on a given subject matter, meant to be more holistic recounts of a body of literature. Yet, by necessity, such summaries are often still narrow in their scope and are told from the perspective of a particular discipline. In other words, interdisciplinary reviews or book chapters tend to be the rarity rather than the norm. Here, we advocate for and highlight the benefits of interdisciplinary perspectives on microbiological subjects.}, }
@article {pmid36358054, year = {2022}, author = {Gu, S and Wang, R and Xing, H and Yu, M and Shen, S and Zhao, L and Sun, J and Li, Y}, title = {Effects of different low temperature conditions on anaerobic digestion efficiency of pig manure and composition of archaea community.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {86}, number = {5}, pages = {1181-1192}, doi = {10.2166/wst.2022.267}, pmid = {36358054}, issn = {0273-1223}, mesh = {Swine ; Animals ; *Manure ; *Archaea/metabolism ; Anaerobiosis ; Temperature ; Fatty Acids, Volatile/metabolism ; Bioreactors ; Methane/metabolism ; }, abstract = {To explore the effect of low temperature on the anaerobic digestion of pig manure, the anaerobic digestion experiment was carried out under the conditions of inoculum concentration of 30% and TS of 8%. Five low-temperature gradients of 4, 8, 12, 16 and 20 °C were set to study the activities of gas production, pH, solluted chemical oxygen demand (SCOD), volatile fatty acids (VFAs), coenzymes F420 and archaea community composition in the digestion process. The results were demonstrated: as the temperature decreased, the more unstable the gas production became, the less gas production produced, and the later the gas peak occurred. There were no significant peaks at either 4 °C or 8 °C, and the SCOD was unstable over time. From 12 °C, the SCOD increased over time, and the higher the temperature, the faster the growth trend. The pH was always greater than 7.6. 8, 12, 16, 20 °C had different degrees of VFAs accumulation at the late digestion stage. The higher the temperature, the greater the amount of volatile acid accumulation. When the VFAs of each reactor reached the maximum, the proportion of acetic acid also reached the highest. The digestion system of the five treatment groups was dominated by hydrogen-nutrient methanogenic pathway. The results could provide a further reference for the mechanism of anaerobic digestion of pig manure at low temperatures.}, }
@article {pmid36350548, year = {2023}, author = {Hepowit, NL and Maupin-Furlow, JA}, title = {Application of Archaea in Deubiquitinase-Like Enzyme Discovery and Activity Assay.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2591}, number = {}, pages = {151-169}, pmid = {36350548}, issn = {1940-6029}, support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; }, mesh = {*Ubiquitins/metabolism ; *Archaea/metabolism ; Ubiquitin/metabolism ; Eukaryotic Cells/metabolism ; Deubiquitinating Enzymes ; }, abstract = {Archaea can be used as microbial platforms to discover new types of deubiquitinase-like (DUB-like) enzymes and to produce ubiquitin/ubiquitin-like (Ub/Ubl) protein conjugates as substrates for DUB/DUB-like activity assays. Here we outline how to use archaea to synthesize, purify, and assay the activity of DUB-like enzymes with unusual properties, including catalytic activity in hypersaline conditions, organic solvents, and high temperatures. We also outline the application of archaea in forming Ub/Ubl isopeptide linkages that include the covalent attachments of diverse archaeal and eukaryotic Ub/Ubls to target proteins. Archaea form these Ub/Ubl-linked protein conjugates in vivo, and the resulting products are found to serve as useful DUB substrates for in vitro assays.}, }
@article {pmid36332026, year = {2022}, author = {Adam, PS and Kolyfetis, GE and Bornemann, TLV and Vorgias, CE and Probst, AJ}, title = {Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling.}, journal = {Science advances}, volume = {8}, number = {44}, pages = {eabm9651}, pmid = {36332026}, issn = {2375-2548}, abstract = {Anaerobic methane metabolism is among the hallmarks of Archaea, originating very early in their evolution. Here, we show that the ancestor of methane metabolizers was an autotrophic CO2-reducing hydrogenotrophic methanogen that possessed the two main complexes, methyl-CoM reductase (Mcr) and tetrahydromethanopterin-CoM methyltransferase (Mtr), the anaplerotic hydrogenases Eha and Ehb, and a set of other genes collectively called "methanogenesis markers" but could not oxidize alkanes. Overturning recent inferences, we demonstrate that methyl-dependent hydrogenotrophic methanogenesis has emerged multiple times independently, either due to a loss of Mtr while Mcr is inherited vertically or from an ancient lateral acquisition of Mcr. Even if Mcr is lost, Mtr, Eha, Ehb, and the markers can persist, resulting in mixotrophic metabolisms centered around the Wood-Ljungdahl pathway. Through their methanogenesis remnants, Thorarchaeia and two newly reconstructed order-level lineages in Archaeoglobi and Bathyarchaeia act as metabolically versatile players in carbon cycling of anoxic environments across the globe.}, }
@article {pmid36332013, year = {2022}, author = {Verma, A and Åberg-Zingmark, E and Sparrman, T and Mushtaq, AU and Rogne, P and Grundström, C and Berntsson, R and Sauer, UH and Backman, L and Nam, K and Sauer-Eriksson, E and Wolf-Watz, M}, title = {Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases.}, journal = {Science advances}, volume = {8}, number = {44}, pages = {eabm4089}, pmid = {36332013}, issn = {2375-2548}, mesh = {Humans ; *Archaea/genetics ; *Adenylate Kinase/chemistry ; Catalysis ; Catalytic Domain ; }, abstract = {Enzymatic catalysis is critically dependent on selectivity, active site architecture, and dynamics. To contribute insights into the interplay of these properties, we established an approach with NMR, crystallography, and MD simulations focused on the ubiquitous phosphotransferase adenylate kinase (AK) isolated from Odinarchaeota (OdinAK). Odinarchaeota belongs to the Asgard archaeal phylum that is believed to be the closest known ancestor to eukaryotes. We show that OdinAK is a hyperthermophilic trimer that, contrary to other AK family members, can use all NTPs for its phosphorylation reaction. Crystallographic structures of OdinAK-NTP complexes revealed a universal NTP-binding motif, while [19]F NMR experiments uncovered a conserved and rate-limiting dynamic signature. As a consequence of trimerization, the active site of OdinAK was found to be lacking a critical catalytic residue and is therefore considered to be "atypical." On the basis of discovered relationships with human monomeric homologs, our findings are discussed in terms of evolution of enzymatic substrate specificity and cold adaptation.}, }
@article {pmid36316034, year = {2023}, author = {Peiter, N and Rother, M}, title = {In vivo probing of SECIS-dependent selenocysteine translation in Archaea.}, journal = {Life science alliance}, volume = {6}, number = {1}, pages = {}, pmid = {36316034}, issn = {2575-1077}, mesh = {*Selenocysteine/genetics ; Archaea/genetics ; *Selenium ; 3' Untranslated Regions ; Base Sequence ; Selenoproteins/genetics ; }, abstract = {Cotranslational insertion of selenocysteine (Sec) proceeds by recoding UGA to a sense codon. This recoding is governed by the Sec insertion sequence (SECIS) element, an RNA structure on the mRNA, but size, location, structure determinants, and mechanism differ for Bacteria, Eukarya, and Archaea. For Archaea, the structure-function relation of the SECIS is poorly understood, as only rather laborious experimental approaches are established. Furthermore, these methods do not allow for quantitative probing of Sec insertion. In order to overcome these limitations, we engineered bacterial β-lactamase into an archaeal selenoprotein, thereby establishing a reporter system, which correlates enzyme activity to Sec insertion. Using this system, in vivo Sec insertion depending on the availability of selenium and the presence of a SECIS element was assessed in Methanococcus maripaludis Furthermore, a minimal SECIS element required for Sec insertion in M. maripaludis was defined and a conserved structural motif shown to be essential for function. Besides developing a convenient tool for selenium research, converting a bacterial enzyme into an archaeal selenoprotein provides proof of concept that novel selenoproteins can be engineered in Archaea.}, }
@article {pmid36314867, year = {2022}, author = {Cha, G and Liu, Y and Yang, Q and Bai, L and Cheng, L and Fan, W}, title = {Comparative Genomic Insights into Chemoreceptor Diversity and Habitat Adaptation of Archaea.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {22}, pages = {e0157422}, pmid = {36314867}, issn = {1098-5336}, mesh = {*Archaea ; Phylogeny ; Ligands ; *Genomics ; Ecosystem ; }, abstract = {Diverse archaea, including many unknown species and phylogenetically deeply rooted taxa, survive in extreme environments. They play crucial roles in the global carbon cycle and element fluxes in many terrestrial, marine, saline, host-associated, hot-spring, and oilfield environments. There is little knowledge of the diversity of chemoreceptors that are presumably involved in their habitat adaptation. Thus, we have explored this diversity through phylogenetic and comparative genomic analyses of complete archaeal genomes. The results show that chemoreceptors are significantly richer in archaea of mild environments than in those of extreme environments, that specific ligand-binding domains of the chemoreceptors are strongly associated with specific habitats, and that the number of chemoreceptors correlates with genome size. The results indicate that the successful adaptation of archaea to specific habitats has been associated with the acquisition and maintenance of chemoreceptors, which may be crucial for their survival in these environments. IMPORTANCE Archaea are capable of sensing and responding to environmental changes by several signal transduction systems with different mechanisms. Much attention is paid to model organisms with complex signaling networks to understand their composition and function, but general principles regarding how an archaeal species organizes its chemoreceptor diversity and habitat adaptation are poorly understood. Here, we have explored this diversity through phylogenetic and comparative genomic analyses of complete archaeal genomes. Signaling sensing and adaptation processes are tightly related to the ligand-binding domain, and it is clear that evolution and natural selection in specialized niches under constant conditions have selected for smaller genome sizes. Taken together, our results extend the understanding of archaeal adaptations to different environments and emphasize the importance of ecological constraints in shaping their evolution.}, }
@article {pmid36301308, year = {2023}, author = {Khan, F and Kaza, S}, title = {Crystal structure of an L-type lectin domain from archaea.}, journal = {Proteins}, volume = {91}, number = {4}, pages = {456-465}, doi = {10.1002/prot.26440}, pmid = {36301308}, issn = {1097-0134}, mesh = {Animals ; *Lectins/chemistry ; *Archaea/genetics/metabolism ; Phylogeny ; Plant Lectins ; Binding Sites ; Crystallography, X-Ray ; }, abstract = {The crystal structures of an L-type lectin domain from Methanocaldococcus jannaschii in apo and mannose-bound forms have been determined. A thorough investigation of L-type lectin domains from several organisms provides insight into the differences in these domains from different kingdoms of life. While the overall fold of the L-type lectin domain is conserved, differences in the lengths of the carbohydrate-binding loops and significant variations in the Mn[2+] -binding site compared to the Ca[2+] -binding site are observed. Furthermore, the sequence and phylogenetic analyses suggest that the archaeal L-type lectin domain is evolutionarily closer to the plant legume lectins than to its bacterial or animal counterparts. This is the first report of the biochemical, structural, sequence, and phylogenetic analyses of an L-type lectin domain from archaea and serves to enhance our understanding of the species-specific differences and evolution of L-type lectin domains.}, }
@article {pmid36280648, year = {2022}, author = {Baati, H and Siala, M and Azri, C and Ammar, E and Trigui, M}, title = {Hydrolytic enzyme screening and carotenoid production evaluation of halophilic archaea isolated from highly heavy metal-enriched solar saltern sediments.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {53}, number = {4}, pages = {1893-1906}, pmid = {36280648}, issn = {1678-4405}, mesh = {RNA, Ribosomal, 16S/genetics ; *Carotenoids ; Antioxidants ; Archaea/genetics ; *Metals, Heavy ; }, abstract = {This paper aimed to screen the enzymatic activities and evaluate the carotenoid production level of twenty-two halophilic archaea isolated from Sfax solar saltern sediments. The molecular identification performed by sequencing the 16S rRNA genes showed that all strains have a high similarity degree (99.7-100%) with Halobacterium salinarum NRC-1. The strains were screened for the presence of eight hydrolase activities using agar plate-based assays. The most detected enzyme was gelatinase (77.27% of total strains), followed by protease (63.63%) and amylase activities (50%). The carotenoid production yields of the strains ranged between 2.027 and 14.880 mg/l. The UV-Visible spectroscopy of pigments revealed that it was a bacterioruberin type. When evaluated and compared to the standard β-carotene, the antioxidant capacities of these pigments showed a scavenging activity of more than 75% at a concentration of 5 μg/ml for three strains (AS16, AS17, and AS18). Then a sequence of one-step optimization processes was performed, using the one-factor-at-a-time approach, to define the optimum conditions for growth and carotenoid production of the highest carotenoid producing strain (AS17). Different environmental factors and nutritional conditions were tested. Variations in these factors were found to deeply influence growth and carotenoid production. A maximum carotenoid production (16.490 mg/l), higher than that of the control (14.880 mg/l), was observed at 37 °C, pH 7, 250 g/l of salinity, with 80% air phase in the flask at 110 rpm, in presence of light and in culture media containing (g/l) 10, yeast extract; 7.5, casamino acid; 20, MgSO4; 4, KCl; and 3, trisodium citrate.}, }
@article {pmid36270146, year = {2022}, author = {Yan, G and Sun, X and Dong, Y and Gao, W and Gao, P and Li, B and Yan, W and Zhang, H and Soleimani, M and Yan, B and Häggblom, MM and Sun, W}, title = {Vanadate reducing bacteria and archaea may use different mechanisms to reduce vanadate in vanadium contaminated riverine ecosystems as revealed by the combination of DNA-SIP and metagenomic-binning.}, journal = {Water research}, volume = {226}, number = {}, pages = {119247}, doi = {10.1016/j.watres.2022.119247}, pmid = {36270146}, issn = {1879-2448}, mesh = {Humans ; *Archaea/genetics/metabolism ; *Metagenome ; Vanadates/metabolism ; Vanadium/metabolism ; Ecosystem ; Anaerobiosis ; Bacteria/genetics/metabolism ; Methane/metabolism ; Methanosarcina/genetics ; Oxidation-Reduction ; Isotopes ; DNA/metabolism ; }, abstract = {Vanadium (V) is a transitional metal that poses health risks to exposed humans. Microorganisms play an important role in remediating V contamination by reducing more toxic and mobile vanadate (V(V)) to less toxic and mobile V(IV). In this study, DNA-stable isotope probing (SIP) coupled with metagenomic-binning was used to identify microorganisms responsible for V(V) reduction and determine potential metabolic mechanisms in cultures inoculated with a V-contaminated river sediment. Anaeromyxobacter and Geobacter spp. were identified as putative V(V)-reducing bacteria, while Methanosarcina spp. were identified as putative V(V)-reducing archaea. The bacteria may use the two nitrate reductases NarG and NapA for respiratory V(V) reduction, as has been demonstrated previously for other species. It is proposed that Methanosarcina spp. may reduce V(V) via anaerobic methane oxidation pathways (AOM-V) rather than via respiratory V(V) reduction performed by their bacterial counterparts, as indicated by the presence of genes associated with anaerobic methane oxidation coupled with metal reduction in the metagenome assembled genome (MAG) of Methanosarcina. Briefly, methane may be oxidized through the "reverse methanogenesis" pathway to produce electrons, which may be further captured by V(V) to promote V(V) reduction. More specially, V(V) reduction by members of Methanosarcina may be driven by electron transport (CoMS-SCoB heterodisulfide reductase (HdrDE), F420H2 dehydrogenases (Fpo), and multi-heme c-type cytochrome (MHC)). The identification of putative V(V)-reducing bacteria and archaea and the prediction of their different pathways for V(V) reduction expand current knowledge regarding the potential fate of V(V) in contaminated sites.}, }
@article {pmid36266535, year = {2022}, author = {Shao, N and Fan, Y and Chou, CW and Yavari, S and Williams, RV and Amster, IJ and Brown, SM and Drake, IJ and Duin, EC and Whitman, WB and Liu, Y}, title = {Expression of divergent methyl/alkyl coenzyme M reductases from uncultured archaea.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1113}, pmid = {36266535}, issn = {2399-3642}, support = {S10 OD025118/OD/NIH HHS/United States ; S10 RR028859/RR/NCRR NIH HHS/United States ; }, mesh = {*Archaea/genetics/metabolism ; *Mesna/metabolism ; Oxidoreductases/metabolism ; Methane/metabolism ; }, abstract = {Methanogens and anaerobic methane-oxidizing archaea (ANME) are important players in the global carbon cycle. Methyl-coenzyme M reductase (MCR) is a key enzyme in methane metabolism, catalyzing the last step in methanogenesis and the first step in anaerobic methane oxidation. Divergent mcr and mcr-like genes have recently been identified in uncultured archaeal lineages. However, the assembly and biochemistry of MCRs from uncultured archaea remain largely unknown. Here we present an approach to study MCRs from uncultured archaea by heterologous expression in a methanogen, Methanococcus maripaludis. Promoter, operon structure, and temperature were important determinants for MCR production. Both recombinant methanococcal and ANME-2 MCR assembled with the host MCR forming hybrid complexes, whereas tested ANME-1 MCR and ethyl-coenzyme M reductase only formed homogenous complexes. Together with structural modeling, this suggests that ANME-2 and methanogen MCRs are structurally similar and their reaction directions are likely regulated by thermodynamics rather than intrinsic structural differences.}, }
@article {pmid36266339, year = {2022}, author = {Hocher, A and Borrel, G and Fadhlaoui, K and Brugère, JF and Gribaldo, S and Warnecke, T}, title = {Growth temperature and chromatinization in archaea.}, journal = {Nature microbiology}, volume = {7}, number = {11}, pages = {1932-1942}, pmid = {36266339}, issn = {2058-5276}, support = {MC_UP_1102/7/MRC_/Medical Research Council/United Kingdom ; MC-A658-5TY40/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Archaea/genetics ; Chromatin/genetics ; *Proteomics ; Temperature ; }, abstract = {DNA in cells is associated with proteins that constrain its structure and affect DNA-templated processes including transcription and replication. HU and histones are the main constituents of chromatin in bacteria and eukaryotes, respectively, with few exceptions. Archaea, in contrast, have diverse repertoires of nucleoid-associated proteins (NAPs). To analyse the evolutionary and ecological drivers of this diversity, we combined a phylogenomic survey of known and predicted NAPs with quantitative proteomic data. We identify the Diaforarchaea as a hotbed of NAP gain and loss, and experimentally validate candidate NAPs in two members of this clade, Thermoplasma volcanium and Methanomassiliicoccus luminyensis. Proteomic analysis across a diverse sample of 19 archaea revealed that NAP investment varies from <0.03% to >5% of total protein. This variation is predicted by growth temperature. We propose that high levels of chromatinization have evolved as a mechanism to prevent uncontrolled helix denaturation at higher temperatures, with implications for the origin of chromatin in both archaea and eukaryotes.}, }
@article {pmid36256551, year = {2022}, author = {Xin, YJ and Bao, CX and Tan, S and Hou, J and Cui, HL}, title = {Haladaptatus halobius sp. nov. and Haladaptatus salinisoli sp. nov., two extremely halophilic archaea isolated from Gobi saline soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {10}, pages = {}, doi = {10.1099/ijsem.0.005543}, pmid = {36256551}, issn = {1466-5034}, mesh = {RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Soil ; DNA, Archaeal/genetics ; Base Composition ; Sequence Analysis, DNA ; Fatty Acids/chemistry ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; *Halobacteriaceae ; Glycolipids/chemistry ; Sulfates ; Phosphatidylglycerols/analysis ; Nucleotides ; Amino Acids ; Phosphatidic Acids/analysis ; Esters ; }, abstract = {Two extremely halophilic archaeal strains, PSR5[T] and PSR8[T], were isolated from a saline soil sample collected from the Tarim Basin, Xinjiang, PR China. Both strains had two copies of the 16S rRNA genes rrn1 and rrn2, showing 2.6 and 3.9% divergence, respectively. The rrn1 gene of PSR5[T] showed 98.4 and 95.3% similarity to the rrn1 and rrn2 genes of strain PSR8[T]; the rrn2 gene of PSR5[T] displayed 97.4 and 96.7% similarity to those of strain PSR8[T], respectively. Phylogenetic analyses based on the 16S rRNA and rpoB' genes revealed that strains PSR5[T] and PSR8[T] formed a single cluster, and then tightly clustered with the current four Haladaptatus species (93.5-97.1% similarities for the 16S rRNA gene and 89.3-90.9% similarities for the rpoB' gene, respectively). Several phenotypic characteristics differentiate strains PSR5[T] and PSR8[T] from current Haladaptatus members. The polar lipids of the two strains are phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester phosphatidylglycerol sulphate and three glycolipids. One of the glycolipids is sulphated mannosyl glucosyl diether, and the remaining two glycolipids are unidentified. The average nucleotide identity, in silico DNA-DNA hybridization, amino acid identity and percentage of conserved proteins values between the two strains were 88.5, 39.1, 89.3 and 72.8 %, respectively, much lower than the threshold values proposed as a species boundary. These values among the two strains and Haladaptatus members were 77.9-79.2, 22.0-23.5, 75.1-78.2 and 56.8-69.9 %, respectively, much lower than the recommended threshold values for species delimitation. These results suggested that strains PSR5[T] and PSR8[T] represent two novel species of Haladaptatus. Based on phenotypic, chemotaxonomic, genomic and phylogenetic properties, strains PSR5[T] (=CGMCC 1.16851[T]=JCM 34141[T]) and PSR8[T] (=CGMCC 1.17025[T]=JCM 34142[T]) represent two novel species of the genus Haladaptatus, for which the names Haladaptatus halobius sp. nov. and Haladaptatus salinisoli sp. nov. are proposed.}, }
@article {pmid36253512, year = {2022}, author = {van Wolferen, M and Pulschen, AA and Baum, B and Gribaldo, S and Albers, SV}, title = {The cell biology of archaea.}, journal = {Nature microbiology}, volume = {7}, number = {11}, pages = {1744-1755}, pmid = {36253512}, issn = {2058-5276}, support = {203276/WT_/Wellcome Trust/United Kingdom ; BB/P001440/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MC_UP_1201/27/MRC_/Medical Research Council/United Kingdom ; 203276/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Archaea ; Phylogeny ; *Biological Evolution ; Eukaryota ; Ecology ; }, abstract = {The past decade has revealed the diversity and ubiquity of archaea in nature, with a growing number of studies highlighting their importance in ecology, biotechnology and even human health. Myriad lineages have been discovered, which expanded the phylogenetic breadth of archaea and revealed their central role in the evolutionary origins of eukaryotes. These discoveries, coupled with advances that enable the culturing and live imaging of archaeal cells under extreme environments, have underpinned a better understanding of their biology. In this Review we focus on the shape, internal organization and surface structures that are characteristic of archaeal cells as well as membrane remodelling, cell growth and division. We also highlight some of the technical challenges faced and discuss how new and improved technologies will help address many of the key unanswered questions.}, }
@article {pmid36251741, year = {2022}, author = {Hofmann, M and Norris, PR and Malik, L and Schippers, A and Schmidt, G and Wolf, J and Neumann-Schaal, M and Hedrich, S}, title = {Metallosphaera javensis sp. nov., a novel species of thermoacidophilic archaea, isolated from a volcanic area.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {10}, pages = {}, doi = {10.1099/ijsem.0.005536}, pmid = {36251741}, issn = {1466-5034}, mesh = {*Archaea/genetics ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Iron ; Nucleotides ; Phylogeny ; Quinones ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sugars ; Sulfides ; *Sulfolobaceae ; Sulfur ; Sulfur Compounds ; }, abstract = {A novel thermoacidophilic archeaon, strain J1[T] (=DSM 112778[T],=JCM 34702[T]), was isolated from a hot pool in a volcanic area of Java, Indonesia. Cells of the strain were irregular, motile cocci of 1.0-1.2 µm diameter. Aerobic, organoheterotrophic growth with casamino acids was observed at an optimum temperature of 70 °C in a range of 55-78 °C and at an optimum pH of 3 in a range of 1.5 to 5. Various organic compounds were utilized, including a greater variety of sugars than has been reported for growth of other species of the genus. Chemolithoautotrophic growth was observed with reduced sulphur compounds, including mineral sulphides. Ferric iron was reduced during anaerobic growth with elemental sulphur. Cellular lipids were calditoglycerocaldarchaeol and caldarchaeol with some derivates. The organism contained the respiratory quinone caldariellaquinone. On the basis of phylogenetic and chemotaxonomic comparison with its closest relatives, it was concluded that strain J1[T] represents a novel species, for which the name Metallosphaera javensis is proposed. Low DNA-DNA relatedness values (16S rRNA gene <98.4%, average nucleotide identity (ANI) <80.1%) distinguished J1[T] from other species of the genus Metallosphaera and the DNA G+C content of 47.3% is the highest among the known species of the genus.}, }
@article {pmid36239851, year = {2022}, author = {Zheng, XW and Wu, ZP and Sun, YP and Wang, BB and Hou, J and Cui, HL}, title = {Halorussus vallis sp. nov., Halorussus aquaticus sp. nov., Halorussus gelatinilyticus sp. nov., Halorussus limi sp. nov., Halorussus salilacus sp. nov., Halorussus salinisoli sp. nov.: six extremely halophilic archaea isolated from solar saltern, salt lake and saline soil.}, journal = {Extremophiles : life under extreme conditions}, volume = {26}, number = {3}, pages = {32}, pmid = {36239851}, issn = {1433-4909}, support = {32070003//National Natural Science Foundation of China/ ; }, mesh = {Base Composition ; China ; DNA, Archaeal/genetics ; Esters ; Glycolipids ; *Halobacteriaceae ; *Lakes ; Nucleotides ; Phosphatidylglycerols ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; Sulfates ; }, abstract = {Six novel halophilic archaeal strains of XZYJT10[T], XZYJ18[T], XZYJT40[T], XZYJT49[T], YCN54[T] and LT46[T] were isolated from a solar saltern in Tibet, a salt lake in Shanxi, and a saline soil in Xinjiang, China. Sequence similarities of 16S rRNA and rpoB' genes among strains XZYJT10[T], XZYJ18[T], XZYJT40[T], XZYJT49[T], YCN54[T], LT46[T] and current members of Halorussus were 90.6-97.8% and 87.8-96.4%, respectively. The average nucleotide identity and in silico DNA-DNA hybridization values among these six strains and current Halorussus members were in the range of 76.5-87.5% and 21.0-33.8%, respectively. These values were all below the species boundary threshold values. The phylogenomic tree based on 122 conserved archaeal protein marker genes revealed that the six novel strains formed individual distinct branches and clustered tightly with Halorussus members. Several phenotypic characteristics distinguished the six strains from current Halorussus members. Polar lipid analysis showed that the six novel strains contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and two to three glycolipids. Phenotypic, chemotaxonomic and phylogenetic properties showed that the six strains represented six novel species within the genus Halorussus, for which the names Halorussus vallis sp. nov., Halorussus aquaticus sp. nov., Halorussus gelatinilyticus sp. nov., Halorussus limi sp. nov., Halorussus salilacus sp. nov., and Halorussus salinisoli sp. nov. are proposed.}, }
@article {pmid36232866, year = {2022}, author = {Uzelac, M and Li, Y and Chakladar, J and Li, WT and Ongkeko, WM}, title = {Archaea Microbiome Dysregulated Genes and Pathways as Molecular Targets for Lung Adenocarcinoma and Squamous Cell Carcinoma.}, journal = {International journal of molecular sciences}, volume = {23}, number = {19}, pages = {}, pmid = {36232866}, issn = {1422-0067}, mesh = {*Adenocarcinoma of Lung/pathology ; Archaea/genetics ; *Carcinoma, Non-Small-Cell Lung/genetics ; *Carcinoma, Squamous Cell/pathology ; Female ; Humans ; *Lung Neoplasms/pathology ; Male ; *Microbiota/genetics ; }, abstract = {The human microbiome is a vast collection of microbial species that exist throughout the human body and regulate various bodily functions and phenomena. Of the microbial species that exist in the human microbiome, those within the archaea domain have not been characterized to the extent of those in more common domains, despite their potential for unique metabolic interaction with host cells. Research has correlated tumoral presence of bacterial microbial species to the development and progression of lung cancer; however, the impacts and influences of archaea in the microbiome remain heavily unexplored. Within the United States lung cancer remains highly fatal, responsible for over 100,000 deaths every year with a 5-year survival rate of roughly 22.9%. This project attempts to investigate specific archaeal species' correlation to lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) incidence, patient staging, death rates across individuals of varying ages, races, genders, and smoking-statuses, and potential molecular targets associated with archaea microbiome. Archaeal species abundance was assessed across lung tissue samples of 527 LUAD patients, 479 LUSC patients, and 99 healthy individuals. Nine archaeal species were found to be of significantly altered abundance in cancerous samples as compared to normal counterparts, 6 of which are common to both LUAD and LUSC subgroups. Several of these species are of the taxonomic class Thermoprotei or the phylum Euryarchaeota, both known to contain metabolic processes distinct from most bacterial species. Host-microbe metabolic interactions may be responsible for the observed correlation of these species' abundance with cancer incidence. Significant microbes were correlated to patient gene expression to reveal genes of altered abundance with respect to high and low archaeal presence. With these genes, cellular oncogenic signaling pathways were analyzed for enrichment across cancer and normal samples. In comparing gene expression between LUAD and adjacent normal samples, 2 gene sets were found to be significantly enriched in cancers. In LUSC comparison, 6 sets were significantly enriched in cancer, and 34 were enriched in normals. Microbial counts across healthy and cancerous patients were then used to develop a machine-learning based predictive algorithm, capable of distinguishing lung cancer patients from healthy normal with 99% accuracy.}, }
@article {pmid36229494, year = {2022}, author = {Jeter, VL and Schwarzwalder, AH and Rayment, I and Escalante-Semerena, JC}, title = {Structural studies of the phosphoribosyltransferase involved in cobamide biosynthesis in methanogenic archaea and cyanobacteria.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {17175}, pmid = {36229494}, issn = {2045-2322}, support = {R35 GM130399/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Monophosphate ; Archaea/metabolism ; Aspartic Acid ; Cobamides/metabolism ; Crystallography, X-Ray ; *Cyanobacteria/metabolism ; *Euryarchaeota/metabolism ; Glutamates ; Ligands ; Pentosyltransferases/genetics/metabolism ; Phosphates/metabolism ; }, abstract = {Cobamides (Cbas) are coenzymes used by cells across all domains of life, but de novo synthesis is only found in some bacteria and archaea. Five enzymes assemble the nucleotide loop in the alpha phase of the corrin ring. Condensation of the activated ring and nucleobase yields adenosyl-Cba 5'-phosphate, which upon dephosphorylation yields the biologically active coenzyme (AdoCba). Base activation is catalyzed by a phosphoribosyltransferase (PRTase). The structure of the Salmonella enterica PRTase enzyme (i.e., SeCobT) is well-characterized, but archaeal PRTases are not. To gain insights into the mechanism of base activation by the PRTase from Methanocaldococcus jannaschii (MjCobT), we solved crystal structures of the enzyme in complex with substrate and products. We determined several structures: (i) a 2.2 Å structure of MjCobT in the absence of ligand (apo), (ii) structures of MjCobT bound to nicotinate mononucleotide (NaMN) and α-ribazole 5'-phosphate (α-RP) or α-adenylyl-5'-phosphate (α-AMP) at 2.3 and 1.4 Å, respectively. In MjCobT the general base that triggers the reaction is an aspartate residue (Asp 52) rather than a glutamate residue (E317) as in SeCobT. Notably, the dimer interface in MjCobT is completely different from that observed in SeCobT. Finally, entry PDB 3L0Z does not reflect the correct structure of MjCobT.}, }
@article {pmid36212815, year = {2022}, author = {Benito Merino, D and Zehnle, H and Teske, A and Wegener, G}, title = {Deep-branching ANME-1c archaea grow at the upper temperature limit of anaerobic oxidation of methane.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {988871}, pmid = {36212815}, issn = {1664-302X}, abstract = {In seafloor sediments, the anaerobic oxidation of methane (AOM) consumes most of the methane formed in anoxic layers, preventing this greenhouse gas from reaching the water column and finally the atmosphere. AOM is performed by syntrophic consortia of specific anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Cultures with diverse AOM partners exist at temperatures between 12°C and 60°C. Here, from hydrothermally heated sediments of the Guaymas Basin, we cultured deep-branching ANME-1c that grow in syntrophic consortia with Thermodesulfobacteria at 70°C. Like all ANME, ANME-1c oxidize methane using the methanogenesis pathway in reverse. As an uncommon feature, ANME-1c encode a nickel-iron hydrogenase. This hydrogenase has low expression during AOM and the partner Thermodesulfobacteria lack hydrogen-consuming hydrogenases. Therefore, it is unlikely that the partners exchange hydrogen during AOM. ANME-1c also does not consume hydrogen for methane formation, disputing a recent hypothesis on facultative methanogenesis. We hypothesize that the ANME-1c hydrogenase might have been present in the common ancestor of ANME-1 but lost its central metabolic function in ANME-1c archaea. For potential direct interspecies electron transfer (DIET), both partners encode and express genes coding for extracellular appendages and multiheme cytochromes. Thermodesulfobacteria encode and express an extracellular pentaheme cytochrome with high similarity to cytochromes of other syntrophic sulfate-reducing partner bacteria. ANME-1c might associate specifically to Thermodesulfobacteria, but their co-occurrence is so far only documented for heated sediments of the Gulf of California. However, in the deep seafloor, sulfate-methane interphases appear at temperatures up to 80°C, suggesting these as potential habitats for the partnership of ANME-1c and Thermodesulfobacteria.}, }
@article {pmid36203131, year = {2022}, author = {Somee, MR and Amoozegar, MA and Dastgheib, SMM and Shavandi, M and Maman, LG and Bertilsson, S and Mehrshad, M}, title = {Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {690}, pmid = {36203131}, issn = {1471-2164}, mesh = {*Archaea ; Bacteria ; Biodegradation, Environmental ; Carbon/metabolism ; Hydrocarbons/metabolism ; Hydrogen/metabolism ; *Petroleum/metabolism ; Phylogeny ; }, abstract = {BACKGROUND: Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. RESULTS: Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria.<br><br>CONCLUSION: Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.}, }
@article {pmid36181435, year = {2022}, author = {Zhang, X and Huang, Y and Liu, Y and Xu, W and Pan, J and Zheng, X and Du, H and Zhang, C and Lu, Z and Zou, D and Liu, Z and Cai, M and Xiong, J and Zhu, Y and Dong, Z and Jiang, H and Dong, H and Jiang, J and Luo, Z and Huang, L and Li, M}, title = {An Ancient Respiratory System in the Widespread Sedimentary Archaea Thermoprofundales.}, journal = {Molecular biology and evolution}, volume = {39}, number = {10}, pages = {}, pmid = {36181435}, issn = {1537-1719}, mesh = {*Archaea/genetics/metabolism ; *Hydrogenase/chemistry/genetics/metabolism ; Sodium Chloride/metabolism ; Phylogeny ; Respiratory System/metabolism ; Amino Acids/genetics ; Antiporters/genetics/metabolism ; }, abstract = {Thermoprofundales, formerly Marine Benthic Group D (MBG-D), is a ubiquitous archaeal lineage found in sedimentary environments worldwide. However, its taxonomic classification, metabolic pathways, and evolutionary history are largely unexplored because of its uncultivability and limited number of sequenced genomes. In this study, phylogenomic analysis and average amino acid identity values of a collection of 146 Thermoprofundales genomes revealed five Thermoprofundales subgroups (A-E) with distinct habitat preferences. Most of the microorganisms from Subgroups B and D were thermophiles inhabiting hydrothermal vents and hot spring sediments, whereas those from Subgroup E were adapted to surface environments where sunlight is available. H2 production may be featured in Thermoprofundales as evidenced by a gene cluster encoding the ancient membrane-bound hydrogenase (MBH) complex. Interestingly, a unique structure separating the MBH gene cluster into two modular units was observed exclusively in the genomes of Subgroup E, which included a peripheral arm encoding the [NiFe] hydrogenase domain and a membrane arm encoding the Na+/H+ antiporter domain. These two modular structures were confirmed to function independently by detecting the H2-evolving activity in vitro and salt tolerance to 0.2 M NaCl in vivo, respectively. The peripheral arm of Subgroup E resembles the proposed common ancestral respiratory complex of modern respiratory systems, which plays a key role in the early evolution of life. In addition, molecular dating analysis revealed that Thermoprofundales is an early emerging archaeal lineage among the extant MBH-containing microorganisms, indicating new insights into the evolution of this ubiquitous archaea lineage.}, }
@article {pmid36160229, year = {2022}, author = {Meng, K and Chung, CZ and Söll, D and Krahn, N}, title = {Unconventional genetic code systems in archaea.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1007832}, pmid = {36160229}, issn = {1664-302X}, support = {R35 GM122560/GM/NIGMS NIH HHS/United States ; }, abstract = {Archaea constitute the third domain of life, distinct from bacteria and eukaryotes given their ability to tolerate extreme environments. To survive these harsh conditions, certain archaeal lineages possess unique genetic code systems to encode either selenocysteine or pyrrolysine, rare amino acids not found in all organisms. Furthermore, archaea utilize alternate tRNA-dependent pathways to biosynthesize and incorporate members of the 20 canonical amino acids. Recent discoveries of new archaeal species have revealed the co-occurrence of these genetic code systems within a single lineage. This review discusses the diverse genetic code systems of archaea, while detailing the associated biochemical elements and molecular mechanisms.}, }
@article {pmid36152750, year = {2022}, author = {Guo, LT and Amikura, K and Jiang, HK and Mukai, T and Fu, X and Wang, YS and O'Donoghue, P and Söll, D and Tharp, JM}, title = {Ancestral archaea expanded the genetic code with pyrrolysine.}, journal = {The Journal of biological chemistry}, volume = {298}, number = {11}, pages = {102521}, pmid = {36152750}, issn = {1083-351X}, support = {K99 GM141320/GM/NIGMS NIH HHS/United States ; R35 GM122560/GM/NIGMS NIH HHS/United States ; 165985//CIHR/Canada ; }, mesh = {*Amino Acyl-tRNA Synthetases/metabolism ; *Archaea/enzymology/genetics ; *Genetic Code ; *Lysine/analogs &amp; derivatives/genetics ; Methanosarcina ; RNA, Transfer/genetics ; }, abstract = {The pyrrolysyl-tRNA synthetase (PylRS) facilitates the cotranslational installation of the 22nd amino acid pyrrolysine. Owing to its tolerance for diverse amino acid substrates, and its orthogonality in multiple organisms, PylRS has emerged as a major route to install noncanonical amino acids into proteins in living cells. Recently, a novel class of PylRS enzymes was identified in a subset of methanogenic archaea. Enzymes within this class (ΔPylSn) lack the N-terminal tRNA-binding domain that is widely conserved amongst PylRS enzymes, yet remain active and orthogonal in bacteria and eukaryotes. In this study, we use biochemical and in vivo UAG-readthrough assays to characterize the aminoacylation efficiency and substrate spectrum of a ΔPylSn class PylRS from the archaeon Candidatus Methanomethylophilus alvus. We show that, compared with the full-length enzyme from Methanosarcina mazei, the Ca. M. alvus PylRS displays reduced aminoacylation efficiency but an expanded amino acid substrate spectrum. To gain insight into the evolution of ΔPylSn enzymes, we performed molecular phylogeny using 156 PylRS and 105 pyrrolysine tRNA (tRNA[Pyl]) sequences from diverse archaea and bacteria. This analysis suggests that the PylRS•tRNA[Pyl] pair diverged before the evolution of the three domains of life, placing an early limit on the evolution of the Pyl-decoding trait. Furthermore, our results document the coevolutionary history of PylRS and tRNA[Pyl] and reveal the emergence of tRNA[Pyl] sequences with unique A73 and U73 discriminator bases. The orthogonality of these tRNA[Pyl] species with the more common G73-containing tRNA[Pyl] will enable future efforts to engineer PylRS systems for further genetic code expansion.}, }
@article {pmid36150484, year = {2022}, author = {Guo, Z and Jalalah, M and Alsareii, SA and Harraz, FA and Thakur, N and Salama, ES}, title = {Biochar addition augmented the microbial community and aided the digestion of high-loading slaughterhouse waste: Active enzymes of bacteria and archaea.}, journal = {Chemosphere}, volume = {309}, number = {Pt 1}, pages = {136535}, doi = {10.1016/j.chemosphere.2022.136535}, pmid = {36150484}, issn = {1879-1298}, mesh = {Archaea/metabolism ; Biofuels ; Anaerobiosis ; Bioreactors ; Abattoirs ; Methane/metabolism ; *Hydrogenase/metabolism ; Bacteria/metabolism ; *Microbiota ; Fatty Acids, Volatile/metabolism ; *Lyases/metabolism ; Transaminases ; Digestion ; }, abstract = {The biogas production (BP), volatile fatty acids (VFAs), microbial communities, and microbes' active enzymes were studied upon the addition of biochar (0-1.5%) at 6% and 8% slaughterhouse waste (SHW) loadings. The 0.5% biochar enhanced BP by 1.5- and 1.6-folds in 6% and 8% SHW-loaded reactors, respectively. Increasing the biochar up to 1.5% caused a reduction in BP at 6% SHW. However, the BP from 8% of SHW was enhanced by 1.4-folds at 1.5% biochar. The VFAs production in all 0.5% biochar amended reactors was highly significant compared to control (p-value < 0.05). The biochar addition increased the bacterial and archaeal diversity at both 6% and 8% SHW loadings. The highest number of OTUs at 0.5% biochar were 567 and 525 in 6% and 8% SHW, respectively. Biochar prompted the Clostridium abundance and increased the lyases and transaminases involved in the degradation of lipids and protein, respectively. Biochar addition improved the Methanosaeta and Methanosphaera abundance in which the major enzymes were reductase and hydrogenase. The archaeal enzymes showed mixed acetoclastic and hydrogenotrophic methanogenesis.}, }
@article {pmid36144426, year = {2022}, author = {Pilotto, S and Werner, F}, title = {How to Shut Down Transcription in Archaea during Virus Infection.}, journal = {Microorganisms}, volume = {10}, number = {9}, pages = {}, pmid = {36144426}, issn = {2076-2607}, support = {206166/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; WT 207446/Z/17/Z//Wellcome Investigator Award in Science/ ; /WT_/Wellcome Trust/United Kingdom ; 207446/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; 202679/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Multisubunit RNA polymerases (RNAPs) carry out transcription in all domains of life; during virus infection, RNAPs are targeted by transcription factors encoded by either the cell or the virus, resulting in the global repression of transcription with distinct outcomes for different host-virus combinations. These repressors serve as versatile molecular probes to study RNAP mechanisms, as well as aid the exploration of druggable sites for the development of new antibiotics. Here, we review the mechanisms and structural basis of RNAP inhibition by the viral repressor RIP and the crenarchaeal negative regulator TFS4, which follow distinct strategies. RIP operates by occluding the DNA-binding channel and mimicking the initiation factor TFB/TFIIB. RIP binds tightly to the clamp and locks it into one fixed position, thereby preventing conformational oscillations that are critical for RNAP function as it progresses through the transcription cycle. TFS4 engages with RNAP in a similar manner to transcript cleavage factors such as TFS/TFIIS through the NTP-entry channel; TFS4 interferes with the trigger loop and bridge helix within the active site by occlusion and allosteric mechanisms, respectively. The conformational changes in RNAP described above are universally conserved and are also seen in inactive dimers of eukaryotic RNAPI and several inhibited RNAP complexes of both bacterial and eukaryotic RNA polymerases, including inactive states that precede transcription termination. A comparison of target sites and inhibitory mechanisms reveals that proteinaceous repressors and RNAP-specific antibiotics use surprisingly common ways to inhibit RNAP function.}, }
@article {pmid36135934, year = {2022}, author = {Groult, B and Bredin, P and Lazar, CS}, title = {Ecological processes differ in community assembly of Archaea, Bacteria and Eukaryotes in a biogeographical survey of groundwater habitats in the Quebec region (Canada).}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {5898-5910}, doi = {10.1111/1462-2920.16219}, pmid = {36135934}, issn = {1462-2920}, mesh = {Archaea/genetics ; Eukaryota ; Quebec ; RNA, Ribosomal, 16S ; Bacteria/genetics ; *Groundwater/microbiology ; *Microbiota ; }, abstract = {Aquifers are inhabited by microorganisms from the three major domains of life: Archaea, Eukaryotes and Bacteria. Although interest in the processes that govern the assembly of these microbial communities is growing, their study is almost systematically limited to one of the three domains of life. Archaea, Bacteria and Eukaryotes are however interconnected and essential to understand the functioning of their living ecosystems. We, therefore, conducted a spatial study of the distribution of microorganisms by sampling 35 wells spread over an area of 10,000 km[2] in the Quebec region (Canada). The obtained data allowed us to define the impact of geographic distance and geochemical water composition on the microbial communities. A null model approach was used to infer the relative influence of stochastic and determinist ecological processes on the assembly of the microbial community from all three domains. We found that the organisms from these three groups are mainly governed by stochastic mechanisms. However, this apparent similarity does not reflect the differences in the processes that govern the phyla assembly. The results obtained highlight the importance of considering all the microorganisms without neglecting their individual specificities.}, }
@article {pmid36125864, year = {2022}, author = {Pallen, MJ and Rodriguez-R, LM and Alikhan, NF}, title = {Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {9}, pages = {}, doi = {10.1099/ijsem.0.005482}, pmid = {36125864}, issn = {1466-5034}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Archaea/genetics ; Bacteria/genetics ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; *Fatty Acids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.}, }
@article {pmid36125771, year = {2022}, author = {Adam, PS and Bornemann, TLV and Probst, AJ}, title = {Progress and Challenges in Studying the Ecophysiology of Archaea.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2522}, number = {}, pages = {469-486}, pmid = {36125771}, issn = {1940-6029}, mesh = {Alkanes ; *Archaea/genetics ; *Genome, Archaeal ; Methane ; Phylogeny ; }, abstract = {It has been less than two decades since the study of archaeal ecophysiology has become unshackled from the limitations of cultivation and amplicon sequencing through the advent of metagenomics. As a primer to the guide on producing archaeal genomes from metagenomes, we briefly summarize here how different meta'omics, imaging, and wet lab methods have contributed to progress in understanding the ecophysiology of Archaea. We then peer into the history of how our knowledge on two particularly important lineages was assembled: the anaerobic methane and alkane oxidizers, encountered primarily among Euryarchaeota, and the nanosized, mainly parasitic, members of the DPANN superphylum.}, }
@article {pmid36125745, year = {2022}, author = {Thomsen, J and Weidenbach, K and Metcalf, WW and Schmitz, RA}, title = {Genetic Methods and Construction of Chromosomal Mutations in Methanogenic Archaea.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2522}, number = {}, pages = {105-117}, pmid = {36125745}, issn = {1940-6029}, mesh = {*Archaea ; *Hypoxanthine Phosphoribosyltransferase/genetics ; Mutation ; Purines ; }, abstract = {Genetic manipulation through markerless exchange enables the modification of several genomic regions without leaving a selection marker in the genome. Here, a method using hpt coding for hypoxanthine phosphoribosyltransferase as a counter selectable marker is described. For Methanosarcina species a chromosomal deletion of the hpt gene is firstly generated, which confers resistance to the purine analogue 8-aza-2,6-diaminopurine (8-ADP). In a second step, the reintroduction of the hpt gene on a plasmid leads to a selectable loss of 8-ADP resistance after a homologous recombination event (pop-in). A subsequent pop-out event restores the 8-ADP resistance and can generate chromosomal mutants with frequencies of about 50%.}, }
@article {pmid36125740, year = {2022}, author = {Forterre, P}, title = {Archaea: A Goldmine for Molecular Biologists and Evolutionists.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2522}, number = {}, pages = {1-21}, pmid = {36125740}, issn = {1940-6029}, mesh = {*Archaea/genetics ; Bacteria/genetics ; *Biological Evolution ; Eukaryota/genetics ; Genome, Archaeal ; RNA, Ribosomal, 16S ; }, abstract = {The rebuttal of the prokaryote-eukaryote dichotomy and the elaboration of the three domains concept by Carl Woese and colleagues has been a breakthrough in biology. With the methodologies available at this time, they have shown that a single molecule, the 16S ribosomal RNA, could reveal the global organization of the living world. Later on, mining archaeal genomes led to major discoveries in archaeal molecular biology, providing a third model for comparative molecular biology. These analyses revealed the strong eukaryal flavor of the basic molecular fabric of Archaea and support rooting the universal tree between Bacteria and Arcarya (the clade grouping Archaea and Eukarya). However, in contradiction with this conclusion, it remains to understand why the archaeal and bacterial mobilomes are so similar and so different from the eukaryal one. These last years, the number of recognized archaea lineages (phyla?) has exploded. The archaeal nomenclature is now in turmoil and debates about the nature of the last universal common ancestor, the last archaeal common ancestor, and the topology of the tree of life are still going on. Interestingly, the expansion of the archaeal eukaryome, especially in the Asgard archaea, has provided new opportunities to study eukaryogenesis. In recent years, the application to Archaea of the new methodologies described in the various chapters of this book have opened exciting avenues to study the molecular biology and the physiology of these fascinating microorganisms.}, }
@article {pmid36125558, year = {2022}, author = {Chow, C and Padda, KP and Puri, A and Chanway, CP}, title = {An Archaic Approach to a Modern Issue: Endophytic Archaea for Sustainable Agriculture.}, journal = {Current microbiology}, volume = {79}, number = {11}, pages = {322}, pmid = {36125558}, issn = {1432-0991}, support = {GR006717//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Agriculture/methods ; Amino Acids/metabolism ; *Archaea/genetics ; *Coffee/metabolism ; Endophytes/genetics/metabolism ; Plant Growth Regulators/metabolism ; Plants ; }, abstract = {Archaea have existed for over 3.5 billion years, yet they were detected in the plant endosphere only in the recent past and still, not much is known about them. Archaeal endophytes may be important microorganisms for sustainable agriculture, particularly in the face of climate change and increasing food demand due to population growth. Recent advances in culture-independent methods of research have revealed a diverse abundance of archaea from the phyla Euryarchaeota, Crenarchaeaota, and Thaumarchaeota globally that are associated with significant crops such as maize, rice, coffee, and olive. Novel insights into the plant microbiome have revealed specific genes in archaea that may be involved in numerous plant metabolic functions including amino acid production and phytohormone modulation. This is the first review article to address what is known about archaea as endophytes, including their patterns of colonization and abundance in various parts of different crop plants grown under diverse environmental conditions. This review aims to facilitate mainstream discussions and encourage future research regarding the occurrence and role of endophytic archaea in plants, particularly in relation to agricultural applications.}, }
@article {pmid36111740, year = {2022}, author = {Yue, Y and Wang, F and Pan, J and Chen, XP and Tang, Y and Yang, Z and Ma, J and Li, M and Yang, M}, title = {Spatiotemporal dynamics, community assembly and functional potential of sedimentary archaea in reservoirs: coaction of stochasticity and nutrient load.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {11}, pages = {}, doi = {10.1093/femsec/fiac109}, pmid = {36111740}, issn = {1574-6941}, mesh = {*Archaea/genetics ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Geologic Sediments/chemistry ; Nutrients ; China ; Phylogeny ; DNA, Archaeal/genetics ; }, abstract = {Archaea participate in biogeochemical cycles in aquatic ecosystems, and deciphering their community dynamics and assembly mechanisms is key to understanding their ecological functions. Here, sediments from 12 selected reservoirs from the Wujiang and Pearl River basins in southwest China were investigated using 16S rRNA Illumina sequencing and quantitative PCR for archaeal abundance and richness in all seasons. Generally, archaeal abundance and α-diversity were significantly correlated with temperature; however, β-diversity analysis showed that community structures varied greatly among locations rather than seasons, indicating a distance-decay pattern with geographical variation. The null model revealed the major contribution of stochasticity to archaeal community assembly, which was further confirmed by the neutral community model that could explain 71.7% and 90.2% of the variance in archaeal assembly in the Wujiang and Pearl River basins, respectively. Moreover, sediment total nitrogen and organic carbon levels were significantly correlated with archaeal abundance and α-diversity. Interestingly, these nutrient levels were positively and negatively correlated, respectively, with the abundance of methanogenic and ammonia-oxidized archaea: the dominant sedimentary archaea in these reservoirs. Taken together, this work systematically characterized archaeal community profiles in reservoir sediments and demonstrated the combined action of stochastic processes and nutrient load in shaping archaeal communities in reservoir ecosystems.}, }
@article {pmid36083447, year = {2022}, author = {Zhu, Q and Mirarab, S}, title = {Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2569}, number = {}, pages = {137-165}, pmid = {36083447}, issn = {1940-6029}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; Software ; }, abstract = {Phylogenomics is the inference of phylogenetic trees based on multiple marker genes sampled in the genomes of interest. An important challenge in phylogenomics is the potential incongruence among the evolutionary histories of individual genes, which can be widespread in microorganisms due to the prevalence of horizontal gene transfer. This protocol introduces the procedures for building a phylogenetic tree of a large number of microbial genomes using a broad sampling of marker genes that are representative of whole-genome evolution. The protocol highlights the use of a gene tree summary method, which can effectively reconstruct the species tree while accounting for the topological conflicts among individual gene trees. The pipeline described in this protocol is scalable to tens of thousands of genomes while retaining high accuracy. We discussed multiple software tools, libraries, and scripts to enable convenient adoption of the protocol. The protocol is suitable for microbiology and microbiome studies based on public genomes and metagenomic data.}, }
@article {pmid36050385, year = {2022}, author = {Hoegenauer, C and Hammer, HF and Mahnert, A and Moissl-Eichinger, C}, title = {Methanogenic archaea in the human gastrointestinal tract.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {19}, number = {12}, pages = {805-813}, pmid = {36050385}, issn = {1759-5053}, support = {P 32697/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Humans ; *Archaea/physiology ; *Euryarchaeota ; Gastrointestinal Tract/microbiology ; Methane ; Bacteria ; }, abstract = {The human microbiome is strongly interwoven with human health and disease. Besides bacteria, viruses and eukaryotes, numerous archaea are located in the human gastrointestinal tract and are responsible for methane production, which can be measured in clinical methane breath analyses. Methane is an important readout for various diseases, including intestinal methanogen overgrowth. Notably, the archaea responsible for methane production are largely overlooked in human microbiome studies due to their non-bacterial biology and resulting detection issues. As such, their importance for health and disease remains largely unclear to date, in particular as not a single archaeal representative has been deemed to be pathogenic. In this Perspective, we discuss the current knowledge on the clinical relevance of methanogenic archaea. We explain the archaeal unique response to antibiotics and their negative and positive effects on human physiology, and present the current understanding of the use of methane as a diagnostic marker.}, }
@article {pmid36043790, year = {2022}, author = {Kuroda, K and Yamamoto, K and Nakai, R and Hirakata, Y and Kubota, K and Nobu, MK and Narihiro, T}, title = {Symbiosis between Candidatus Patescibacteria and Archaea Discovered in Wastewater-Treating Bioreactors.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0171122}, pmid = {36043790}, issn = {2150-7511}, mesh = {*Archaea/metabolism ; Symbiosis/genetics ; Wastewater ; Phylogeny ; In Situ Hybridization, Fluorescence ; Sewage ; Bacteria/genetics ; *Euryarchaeota ; Bioreactors ; Protein Sorting Signals/genetics ; }, abstract = {Each prokaryotic domain, Bacteria and Archaea, contains a large and diverse group of organisms characterized by their ultrasmall cell size and symbiotic lifestyles (potentially commensal, mutualistic, and parasitic relationships), namely, Candidatus Patescibacteria (also known as the Candidate Phyla Radiation/CPR superphylum) and DPANN archaea, respectively. Cultivation-based approaches have revealed that Ca. Patescibacteria and DPANN symbiotically interact with bacterial and archaeal partners and hosts, respectively, but that cross-domain symbiosis and parasitism have never been observed. By amending wastewater treatment sludge samples with methanogenic archaea, we observed increased abundances of Ca. Patescibacteria (Ca. Yanofskybacteria/UBA5738) and, using fluorescence in situ hybridization (FISH), discovered that nearly all of the Ca. Yanofskybacteria/UBA5738 cells were attached to Methanothrix (95.7 ± 2.1%) and that none of the cells were attached to other lineages, implying high host dependency and specificity. Methanothrix filaments (multicellular) with Ca. Yanofskybacteria/UBA5738 attached had significantly more cells with no or low detectable ribosomal activity (based on FISH fluorescence) and often showed deformations at the sites of attachment (based on transmission electron microscopy), suggesting that the interaction is parasitic. Metagenome-assisted metabolic reconstruction showed that Ca. Yanofskybacteria/UBA5738 lacks most of the biosynthetic pathways necessary for cell growth and universally conserves three unique gene arrays that contain multiple genes with signal peptides in the metagenome-assembled genomes of the Ca. Yanofskybacteria/UBA5738 lineage. The results shed light on a novel cross-domain symbiosis and inspire potential strategies for culturing CPR and DPANN. IMPORTANCE One highly diverse phylogenetic group of Bacteria, Ca. Patescibacteria, remains poorly understood, but, from the few cultured representatives and metagenomic investigations, they are thought to live symbiotically or parasitically with other bacteria or even with eukarya. We explored the possibility of symbiotic interactions with Archaea by amending wastewater treatment sludge samples that were rich in Ca. Patescibacteria and Archaea with an isolate archaeon that is closely related to a methanogen population abundant in situ (Methanothrix). This strategic cultivation successfully established enrichment cultures that were mainly comprised of Ca. Patescibacteria (family level lineage Ca. Yanofskybacteria/UBA5738) and Methanothrix, in which we found highly specific physical interactions between the two organisms. Microscopic observations based on transmission electron microscopy, target-specific fluorescence in situ hybridization, and metagenomic analyses showed evidence that the interaction is likely parasitic. The results show a novel cross-domain parasitism between Bacteria and Archaea and suggest that the amendment of host Archaea may be an effective approach in culturing novel Ca. Patescibacteria.}, }
@article {pmid36030953, year = {2022}, author = {Gou, Y and Song, Y and Yang, S and Yang, Y and Cheng, Y and Li, J and Zhang, T and Cheng, Y and Wang, H}, title = {Polycyclic aromatic hydrocarbon removal from subsurface soil mediated by bacteria and archaea under methanogenic conditions: Performance and mechanisms.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {313}, number = {}, pages = {120023}, doi = {10.1016/j.envpol.2022.120023}, pmid = {36030953}, issn = {1873-6424}, mesh = {Archaea/metabolism ; Bacteria/metabolism ; Biodegradation, Environmental ; Carbon Dioxide/metabolism ; *Polycyclic Aromatic Hydrocarbons/analysis ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {In situ anoxic bioremediation is an easy-to-use technology to remediate polycyclic aromatic hydrocarbon (PAH)-contaminated soil. Degradation of PAHs mediated by soil bacteria and archaea using CO2 as the electron acceptor is an important process for eliminating PAHs under methanogenic conditions; however, knowledge of the performance and mechanisms involved is poorly unveiled. In this study, the effectiveness and efficiency of NaHCO3 (CO2) as an electron acceptor to stimulate the degradation of PAHs by bacteria and archaea in highly contaminated soil were investigated. The results showed that CO2 addition (EC2000) promoted PAH degradation compared to soil without added CO2 (EC0), with 4.18%, 9.01%-8.05%, and 6.19%-12.45% increases for 2-, 3- and 4-ring PAHs after 250 days of incubation, respectively. Soil bacterial abundances increased with increasing incubation time, especially for EC2000 (2.90 × 10[8] g[-1] soil higher than EC0, p < 0.05). Different succession patterns of the soil bacterial and archaeal communities during PAH degradation were observed. According to the PCoA and ANOSIM results, the soil bacterial communities were greatly (ANOSIM: R = 0.7232, P = 0.001) impacted by electron acceptors, whereas significant differences in the archaeal communities were not observed (ANOSIM: R = 0.553, P = 0.001). Soil bacterial and archaeal co-occurrence network analyses showed that positive correlations outnumbered the negative correlations throughout the incubation period for both treatments (e.g., EC0 and EC2000), suggesting the prevalence of coexistence/cooperation within and between these two domains rather than competition. The higher complexity, connectance, edge, and node numbers in EC2000 revealed stronger linkage and a more stable co-occurrence network compared to EC0. The results of this study could improve the knowledge on the removal of PAHs and the responses of soil bacteria and archaea to CO2 application, as well as a scientific basis for the in situ anoxic bioremediation of PAH-contaminated industrial sites.}, }
@article {pmid36029340, year = {2022}, author = {Amores, GR and Zepeda-Ramos, G and García-Fajardo, LV and Hernández, E and Guillén-Navarro, K}, title = {The gut microbiome analysis of Anastrepha obliqua reveals inter-kingdom diversity: bacteria, fungi, and archaea.}, journal = {Archives of microbiology}, volume = {204}, number = {9}, pages = {579}, pmid = {36029340}, issn = {1432-072X}, support = {CB-2008-01-101389//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Fellowship 17171//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; }, mesh = {Animals ; Archaea ; Bacteria ; Fungi ; *Gastrointestinal Microbiome ; Male ; *Tephritidae ; }, abstract = {The fruit fly Anastrepha obliqua is an economically important pest. The sterile insect technique to control it involves mass production and release of sterile flies to reduce the reproduction of the wild population. As noted in different Tephritidae, the performance of sterile males may be affected by the assimilation of nutrients under mass-rearing conditions. In the wild, the fly's life cycle suggests the acquisition of different organisms that could modulate its fitness and physiology. For A. obliqua, there is no information regarding microorganisms other than bacteria. This study analyzed bacteria, fungal, and archaea communities in the A. obliqua gut through denaturing gradient gel electrophoresis (DGGE) profiles of 16S (using a different set of primers for bacteria and archaea) and 18S ribosomal DNA markers. We found that wild flies presented higher microbial diversity related to fructose assimilation than laboratory species, suggesting that microorganisms have led to a specialized metabolism to process nutrients associated with an artificial diet. We identified species that have not been previously described in this fruit fly, especially actinobacteria and archaea, by employing different primer sets aimed at the same molecular marker but targeting diverse hypervariable regions of 16S rDNA. The possibility that Archaea affect fly fitness should not be ignored. This report on the intestinal microbial (bacteria, archaea, and fungi) composition of A. obliqua contributes to our understanding of the role of microorganisms in the development and physiology of the flies.}, }
@article {pmid36009875, year = {2022}, author = {Alharbi, F and Knura, T and Siebers, B and Ma, K}, title = {Thermostable and O2-Insensitive Pyruvate Decarboxylases from Thermoacidophilic Archaea Catalyzing the Production of Acetaldehyde.}, journal = {Biology}, volume = {11}, number = {8}, pages = {}, pmid = {36009875}, issn = {2079-7737}, support = {NA//Natural Sciences and Engineering Research Council (Canada)/ ; 031L0078A//HotSysAPP project within the e:bio initiative by the Federal Ministry of Education and Research (BMBF)/ ; }, abstract = {Pyruvate decarboxylase (PDC) is a key enzyme involved in ethanol fermentation, and it catalyzes the decarboxylation of pyruvate to acetaldehyde and CO2. Bifunctional PORs/PDCs that also have additional pyruvate:ferredoxin oxidoreductase (POR) activity are found in hyperthermophiles, and they are mostly oxygen-sensitive and CoA-dependent. Thermostable and oxygen-stable PDC activity is highly desirable for biotechnological applications. The enzymes from the thermoacidophiles Saccharolobus (formerly Sulfolobus) solfataricus (Ss, Topt = 80 °C) and Sulfolobus acidocaldarius (Sa, Topt = 80 °C) were purified and characterized, and their biophysical and biochemical properties were determined comparatively. Both enzymes were shown to be heterodimeric, and their two subunits were determined by SDS-PAGE to be 37 ± 3 kDa and 65 ± 2 kDa, respectively. The purified enzymes from S. solfataricus and S. acidocaldarius showed both PDC and POR activities which were CoA-dependent, and they were thermostable with half-life times of 2.9 ± 1 and 1.1 ± 1 h at 80 °C, respectively. There was no loss of activity in the presence of oxygen. Optimal pH values for their PDC and POR activity were determined to be 7.9 and 8.6, respectively. In conclusion, both thermostable SsPOR/PDC and SaPOR/PDC catalyze the CoA-dependent production of acetaldehyde from pyruvate in the presence of oxygen.}, }
@article {pmid36005527, year = {2022}, author = {Grivard, A and Goubet, I and Duarte Filho, LMS and Thiéry, V and Chevalier, S and de Oliveira-Junior, RG and El Aouad, N and Guedes da Silva Almeida, JR and Sitarek, P and Quintans-Junior, LJ and Grougnet, R and Agogué, H and Picot, L}, title = {Archaea Carotenoids: Natural Pigments with Unexplored Innovative Potential.}, journal = {Marine drugs}, volume = {20}, number = {8}, pages = {}, pmid = {36005527}, issn = {1660-3397}, support = {2022 Pr Val&#xe9;rie THIERY//Ligue Nationale contre le Cancer/ ; }, mesh = {*Archaea/metabolism ; Biotechnology ; *Carotenoids/metabolism ; Pigmentation ; }, abstract = {For more than 40 years, marine microorganisms have raised great interest because of their major ecological function and their numerous applications for biotechnology and pharmacology. Particularly, Archaea represent a resource of great potential for the identification of new metabolites because of their adaptation to extreme environmental conditions and their original metabolic pathways, allowing the synthesis of unique biomolecules. Studies on archaeal carotenoids are still relatively scarce and only a few works have focused on their industrial scale production and their biotechnological and pharmacological properties, while the societal demand for these bioactive pigments is growing. This article aims to provide a comprehensive review of the current knowledge on carotenoid metabolism in Archaea and the potential applications of these pigments in biotechnology and medicine. After reviewing the ecology and classification of these microorganisms, as well as their unique cellular and biochemical characteristics, this paper highlights the most recent data concerning carotenoid metabolism in Archaea, the biological properties of these pigments, and biotechnological considerations for their production at industrial scale.}, }
@article {pmid35992648, year = {2022}, author = {Yoshinaga, M and Nakayama, T and Inagaki, Y}, title = {A novel structural maintenance of chromosomes (SMC)-related protein family specific to Archaea.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {913088}, pmid = {35992648}, issn = {1664-302X}, abstract = {The ATPases belonging to the structural maintenance of chromosomes (SMC) superfamily are involved in the maintenance of chromosome organization and dynamics, as well as DNA repair. The major proteins in this superfamily recognized to date are either conserved among the three domains of Life (i.e., SMC and Rad50) or specific to Bacteria (i.e., RecF, RecN, and MukB). In Archaea, no protein related to SMC (SMC-related protein) with a broad taxonomic distribution has been reported. Nevertheless, two SMC-related proteins, namely coalescin and Sph, have been identified in crenarchaea Sulfolobus spp. and the euryarchaeon Halobacterium salinarum, respectively, hinting that the diversity of SMC-related proteins has been overlooked in Archaea. In this study, we report a novel SMC-related protein that is distributed among broad archaeal lineages and termed "Archaea-specific SMC-related proteins" or "ASRPs." We further demonstrate that the ASRP family encloses both coalescin and Sph but the two proteins represent only a tip of the diversity of this family.}, }
@article {pmid35985606, year = {2022}, author = {Mafra, D and Ribeiro, M and Fonseca, L and Regis, B and Cardozo, LFMF and Fragoso Dos Santos, H and Emiliano de Jesus, H and Schultz, J and Shiels, PG and Stenvinkel, P and Rosado, A}, title = {Archaea from the gut microbiota of humans: Could be linked to chronic diseases?.}, journal = {Anaerobe}, volume = {77}, number = {}, pages = {102629}, doi = {10.1016/j.anaerobe.2022.102629}, pmid = {35985606}, issn = {1095-8274}, mesh = {Humans ; Archaea/genetics ; *Gastrointestinal Microbiome ; Methanobrevibacter/genetics ; *Euryarchaeota ; Methane ; Chronic Disease ; }, abstract = {Archaea comprise a unique domain of organisms with distinct biochemical and genetic differences from bacteria. Methane-forming archaea, methanogens, constitute the predominant group of archaea in the human gut microbiota, with Methanobrevibacter smithii being the most prevalent. However, the effect of methanogenic archaea and their methane production on chronic disease remains controversial. As perturbation of the microbiota is a feature of chronic conditions, such as cardiovascular disease, neurodegenerative diseases and chronic kidney disease, assessing the influence of archaea could provide a new clue to mitigating adverse effects associated with dysbiosis. In this review, we will discuss the putative role of archaea in the gut microbiota in humans and the possible link to chronic diseases.}, }
@article {pmid35968005, year = {2022}, author = {Peng, Y and Xie, T and Wu, Z and Zheng, W and Zhang, T and Howe, S and Chai, J and Deng, F and Li, Y and Zhao, J}, title = {Archaea: An under-estimated kingdom in livestock animals.}, journal = {Frontiers in veterinary science}, volume = {9}, number = {}, pages = {973508}, pmid = {35968005}, issn = {2297-1769}, abstract = {Archaea are considered an essential group of gut microorganisms in both humans and animals. However, they have been neglected in previous studies, especially those involving non-ruminants. In this study, we re-analyzed published metagenomic and metatranscriptomic data sequenced from matched samples to explore the composition and the expression activity of gut archaea in ruminants (cattle and sheep) and monogastric animals (pig and chicken). Our results showed that the alpha and beta diversity of each host species, especially cattle and chickens, calculated from metagenomic and metatranscriptomic data were significantly different, suggesting that metatranscriptomic data better represent the functional status of archaea. We detected that the relative abundance of 17 (cattle), 7 (sheep), 20 (pig), and 2 (chicken) archaeal species were identified in the top 100 archaeal taxa when analyzing the metagenomic datasets, and these species were classified as the "active archaeal species" for each host species by comparison with corresponding metatranscriptomic data. For example, The expressive abundance in metatranscriptomic dataset of Methanosphaera cuniculi and Methanosphaera stadtmanae were 30- and 27-fold higher than that in metagenomic abundance, indicating their potentially important function in the pig gut. Here we aim to show the potential importance of archaea in the livestock digestive tract and encourage future research in this area, especially on the gut archaea of monogastric animals.}, }
@article {pmid35965098, year = {2022}, author = {Zhao, H and Zhang, L}, title = {Metagenome-assembled Genomes of Six Novel Ammonia-oxidizing Archaea (AOA) from Agricultural Upland Soil.}, journal = {Microbes and environments}, volume = {37}, number = {3}, pages = {}, pmid = {35965098}, issn = {1347-4405}, mesh = {*Ammonia/metabolism ; *Archaea ; Bacteria ; Metagenome ; Nitrites/metabolism ; Oxidation-Reduction ; Soil ; Soil Microbiology ; }, abstract = {Ammonia-oxidizing archaea (AOA), key players in agricultural upland soil nitrification, convert soil ammonium to nitrite. The microbial oxidation of ammonia to nitrite is an important part of the global biogeochemical nitrogen cycle. In the present study, we recovered six novel AOA metagenome-assembled genomes (MAGs) containing genes for carbon (C) fixation and nitrogen (N) metabolism by using a deep shotgun metagenomic sequencing strategy. We also found that these AOA MAGs possessed cobalamin synthesis genes, suggesting that AOA are vitamin suppliers in agricultural upland soil. Collectively, the present results deepen our understanding of the metabolic potential and phylogeny of AOA in agroecosystems.}, }
@article {pmid35922624, year = {2022}, author = {Ledesma, L and Hernandez-Guerrero, R and Perez-Rueda, E}, title = {Prediction of DNA-Binding Transcription Factors in Bacteria and Archaea Genomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2516}, number = {}, pages = {103-112}, pmid = {35922624}, issn = {1940-6029}, mesh = {Archaea/metabolism ; Bacteria/metabolism ; DNA/metabolism ; *Genome, Archaeal/genetics ; Genome, Bacterial ; Humans ; *Transcription Factors/metabolism ; }, abstract = {DNA-binding transcription factors (TFs) play a central role in the gene expression of all organisms, from viruses to humans, including bacteria and archaea. The role of these proteins is the fate of gene expression in the context of environmental challenges. Because thousands of genomes have been sequenced to date, predictions of the encoded proteins are validated through the use of bioinformatics tools to obtain the necessary experimental, posterior knowledge. In this chapter, we describe three approaches to identify TFs in protein sequences. The first approach integrates the results of sequence comparisons and PFAM assignments, using as reference a manually curated collection of TFs. The second approach considers the prediction of DNA-binding structures, such as the classical helix-turn-helix (HTH); and the third approach considers a deep learning model. We suggest that all approaches must be considered together to increase the possibility of identifying new TFs in bacterial and archaeal genomes.}, }
@article {pmid35922623, year = {2022}, author = {Sybers, D and Charlier, D and Peeters, E}, title = {In Vitro Transcription Assay for Archaea Belonging to Sulfolobales.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2516}, number = {}, pages = {81-102}, pmid = {35922623}, issn = {1940-6029}, mesh = {*Archaea/genetics/metabolism ; *Archaeal Proteins/chemistry ; DNA-Binding Proteins/metabolism ; DNA-Directed RNA Polymerases/genetics/metabolism ; Sulfolobales/genetics/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic ; }, abstract = {Archaeal transcription and its regulation are characterized by a mosaic of eukaryotic and bacterial features. Molecular analysis of the functioning of the archaeal RNA polymerase, basal transcription factors, and specific promoter-containing DNA templates allows to unravel the mechanisms of transcription regulation in archaea. In vitro transcription is a technique that allows the study of this process in a simplified and controlled environment less complex than the archaeal cell. In this chapter, we present an in vitro transcription methodology for the study of transcription in Sulfolobales. It is described how to purify the RNA polymerase and the basal transcription factors TATA-binding protein and transcription factor B of Saccharolobus solfataricus and how to perform in vitro transcription reactions and transcript detection. Application of this protocol for other archaeal species could require minor modifications to protein overexpression and purification conditions.}, }
@article {pmid35922619, year = {2022}, author = {Maruyama, H}, title = {Micrococcal Nuclease Digestion Assays for the Analysis of Chromosome Structure in Archaea.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2516}, number = {}, pages = {29-38}, pmid = {35922619}, issn = {1940-6029}, mesh = {*Archaea/genetics/metabolism ; Chromatin/genetics ; DNA/genetics ; Digestion ; *Micrococcal Nuclease/metabolism ; Nucleosomes ; }, abstract = {The digestion of chromosomes using micrococcal nuclease (MNase) enables the analysis of their fundamental structural units. For example, the digestion of eukaryotic chromatin using MNase results in laddered DNA fragments (~150 bp increment), which reflects the length of the DNA wrapped around regularly spaced nucleosomes. Here, we describe the application of MNase to examine the chromosome structure in Archaea. We used Thermococcus kodakarensis, a hyperthermophilic euryarchaeon that encodes proteins homologous to eukaryotic histones. Methods for chromosome extraction and agarose gel electrophoresis of MNase-digested DNA including small fragments (~30 bp) are also described.}, }
@article {pmid35922618, year = {2022}, author = {Rashid, FM and Detmar, L and Dame, RT}, title = {Chromosome Conformation Capture in Bacteria and Archaea.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2516}, number = {}, pages = {1-28}, pmid = {35922618}, issn = {1940-6029}, mesh = {*Archaea/genetics ; Bacteria/genetics ; Chromatin/genetics ; *Chromosomes/genetics ; High-Throughput Nucleotide Sequencing/methods ; Nucleic Acid Conformation ; }, abstract = {The three-dimensional structure of the chromosome is encoded within its sequence and regulates activities such as replication and transcription. This necessitates the study of the spatial organization of the chromosome in relation to the underlying sequence. Chromosome conformation capture (3C) techniques are proximity ligation-based approaches that simplify the three-dimensional architecture of the chromosome into a one-dimensional library of hybrid ligation junctions. Deciphering the information contained in these libraries resolves chromosome architecture in a sequence-specific manner. This chapter describes the preparation of 3C libraries for bacteria and archaea. It details how the three-dimensional architecture of local chromatin can be extracted from the 3C library using qPCR (3C-qPCR), and it summarizes the processing of 3C libraries for next-generation sequencing (3C-Seq) for a study of global chromosome organization.}, }
@article {pmid35922580, year = {2022}, author = {Wang, BB and Sun, YP and Wu, ZP and Zheng, XW and Hou, J and Cui, HL}, title = {Halorientalis salina sp. nov., Halorientalis marina sp. nov., Halorientalis litorea sp. nov.: three extremely halophilic archaea isolated from a salt lake and coarse sea salt.}, journal = {Extremophiles : life under extreme conditions}, volume = {26}, number = {3}, pages = {26}, pmid = {35922580}, issn = {1433-4909}, support = {32070003//National Natural Science Foundation of China/ ; }, mesh = {Base Composition ; China ; DNA, Archaeal/genetics ; Glycolipids/metabolism ; *Halobacteriaceae ; *Lakes ; Phosphatidic Acids/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Three halophilic archaeal strains, NEN8[T], GDY88[T] and ZY14[T], were isolated from a salt lake in Tibet and coarse sea salt samples from Guangdong and Hebei, China, respectively. These strains formed three separate clades (showing 94.4-95.8% and 87.1-89.4% similarities, respectively) and then clustered with the current Halorientalis members (showing 90.7-97.6% and 87.0-91.2% similarities, respectively), as revealed by phylogenetic analyses based on 16S rRNA and rpoB' genes. The overall genome-related index, average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), average amino acid identity (AAI) and the percentage of conserved proteins (POCP) values, among the three strains and members of the genus Halorientalis were 76.0-88.0%, 21.3-37.2%, 69.0-88.3% and 57.7-78.1%, clearly below the threshold values for species demarcation. Strains NEN8[T], GDY88[T] and ZY14[T] could be distinguished from current Halorientalis species according to differential phenotypic characteristics. The major polar lipids of the three strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1) and disulfated mannosyl glucosyl diether (S2-DGD). In addition, mannosyl glucosyl diether (DGD-1) was detected in strain NEN8[T] and phosphatidic acid (PA), posssulfated galactosyl mannosyl glucosyl diether (S-TGD-1) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA) were observed in strain ZY14[T]. These results revealed that strains NEN8[T] (= CGMCC 1.17213[T] = JCM 34155[T]), GDY88[T] (= CGMCC 1.18548[T] = JCM 34481[T]) and ZY14[T] (= CGMCC 1.17178[T] = JCM 34154[T]) represent three novel species of the genus Halorientalis, for which the names Halorientalis salina sp. nov., Halorientalis marina sp. nov. and Halorientalis litorea sp. nov. are proposed.}, }
@article {pmid35917471, year = {2022}, author = {Wegener, G and Laso-Pérez, R and Orphan, VJ and Boetius, A}, title = {Anaerobic Degradation of Alkanes by Marine Archaea.}, journal = {Annual review of microbiology}, volume = {76}, number = {}, pages = {553-577}, doi = {10.1146/annurev-micro-111021-045911}, pmid = {35917471}, issn = {1545-3251}, mesh = {*Alkanes/metabolism ; Anaerobiosis ; *Archaea ; Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Alkanes are saturated apolar hydrocarbons that range from their simplest form, methane, to high-molecular-weight compounds. Although alkanes were once considered biologically recalcitrant under anaerobic conditions, microbiological investigations have now identified several microbial taxa that can anaerobically degrade alkanes. Here we review recent discoveries in the anaerobic oxidation of alkanes with a specific focus on archaea that use specific methyl coenzyme M reductases to activate their substrates. Our understanding of the diversity of uncultured alkane-oxidizing archaea has expanded through the use of environmental metagenomics and enrichment cultures of syntrophic methane-, ethane-, propane-, and butane-oxidizing marine archaea with sulfate-reducing bacteria. A recently cultured group of archaea directly couples long-chain alkane degradation with methane formation, expanding the range of substrates used for methanogenesis. This article summarizes the rapidly growing knowledge of the diversity, physiology, and habitat distribution of alkane-degrading archaea.}, }
@article {pmid35905325, year = {2022}, author = {Rattanasriampaipong, R and Zhang, YG and Pearson, A and Hedlund, BP and Zhang, S}, title = {Archaeal lipids trace ecology and evolution of marine ammonia-oxidizing archaea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {31}, pages = {e2123193119}, pmid = {35905325}, issn = {1091-6490}, mesh = {*Ammonia/metabolism ; *Archaea/genetics ; *Diglycerides ; *Evolution, Molecular ; *Membrane Lipids ; Oxidation-Reduction ; Phylogeny ; Water ; }, abstract = {Archaeal membrane lipids are widely used for paleotemperature reconstructions, yet these molecular fossils also bear rich information about ecology and evolution of marine ammonia-oxidizing archaea (AOA). Here we identified thermal and nonthermal behaviors of archaeal glycerol dialkyl glycerol tetraethers (GDGTs) by comparing the GDGT-based temperature index (TEX86) to the ratio of GDGTs with two and three cyclopentane rings (GDGT-2/GDGT-3). Thermal-dependent biosynthesis should increase TEX86 and decrease GDGT-2/GDGT-3 when the ambient temperature increases. This presumed temperature-dependent (PTD) trend is observed in GDGTs derived from cultures of thermophilic and mesophilic AOA. The distribution of GDGTs in suspended particulate matter (SPM) and sediments collected from above the pycnocline-shallow water samples-also follows the PTD trend. These similar GDGT distributions between AOA cultures and shallow water environmental samples reflect shallow ecotypes of marine AOA. While there are currently no cultures of deep AOA clades, GDGTs derived from deep water SPM and marine sediment samples exhibit nonthermal behavior deviating from the PTD trend. The presence of deep AOA increases the GDGT-2/GDGT-3 ratio and distorts the temperature-controlled correlation between GDGT-2/GDGT-3 and TEX86. We then used Gaussian mixture models to statistically characterize these diagnostic patterns of modern AOA ecology from paleo-GDGT records to infer the evolution of marine AOA from the Mid-Mesozoic to the present. Long-term GDGT-2/GDGT-3 trends suggest a suppression of today's deep water marine AOA during the Mesozoic-early Cenozoic greenhouse climates. Our analysis provides invaluable insights into the evolutionary timeline and the expansion of AOA niches associated with major oceanographic and climate changes.}, }
@article {pmid35886964, year = {2022}, author = {Chong, PL and Chang, A and Yu, A and Mammedova, A}, title = {Vesicular and Planar Membranes of Archaea Lipids: Unusual Physical Properties and Biomedical Applications.}, journal = {International journal of molecular sciences}, volume = {23}, number = {14}, pages = {}, pmid = {35886964}, issn = {1422-0067}, mesh = {*Archaea ; Lipids ; *Liposomes ; Membranes ; Protons ; }, abstract = {Liposomes and planar membranes made of archaea or archaea-like lipids exhibit many unusual physical properties compared to model membranes composed of conventional diester lipids. Here, we review several recent findings in this research area, which include (1) thermosensitive archaeosomes with the capability to drastically change the membrane surface charge, (2) MthK channel's capability to insert into tightly packed tetraether black lipid membranes and exhibit channel activity with surprisingly high calcium sensitivity, and (3) the intercalation of apolar squalane into the midplane space of diether bilayers to impede proton permeation. We also review the usage of tetraether archaeosomes as nanocarriers of therapeutics and vaccine adjuvants, as well as the biomedical applications of planar archaea lipid membranes. The discussion on archaeosomal therapeutics is focused on partially purified tetraether lipid fractions such as the polar lipid fraction E (PLFE) and glyceryl caldityl tetraether (GCTE), which are the main components of PLFE with the sugar and phosphate removed.}, }
@article {pmid35880875, year = {2022}, author = {Boswinkle, K and McKinney, J and Allen, KD}, title = {Highlighting the Unique Roles of Radical S-Adenosylmethionine Enzymes in Methanogenic Archaea.}, journal = {Journal of bacteriology}, volume = {204}, number = {8}, pages = {e0019722}, pmid = {35880875}, issn = {1098-5530}, support = {CHE-2105598//National Science Foundation (NSF)/ ; }, mesh = {Archaea/genetics/metabolism ; Catalysis ; *Greenhouse Gases/metabolism ; *Iron-Sulfur Proteins/metabolism ; S-Adenosylmethionine/chemistry/metabolism ; }, abstract = {Radical S-adenosylmethionine (SAM) enzymes catalyze an impressive variety of difficult biochemical reactions in various pathways across all domains of life. These metalloenzymes employ a reduced [4Fe-4S] cluster and SAM to generate a highly reactive 5'-deoxyadenosyl radical that is capable of initiating catalysis on otherwise unreactive substrates. Interestingly, the genomes of methanogenic archaea encode many unique radical SAM enzymes with underexplored or completely unknown functions. These organisms are responsible for the yearly production of nearly 1 billion tons of methane, a potent greenhouse gas as well as a valuable energy source. Thus, understanding the details of methanogenic metabolism and elucidating the functions of essential enzymes in these organisms can provide insights into strategies to decrease greenhouse gas emissions as well as inform advances in bioenergy production processes. This minireview provides an overview of the current state of the field regarding the functions of radical SAM enzymes in methanogens and discusses gaps in knowledge that should be addressed.}, }
@article {pmid35852729, year = {2023}, author = {Flusche, T and Rajan, R}, title = {Molecular Details of DNA Integration by CRISPR-Associated Proteins During Adaptation in Bacteria and Archaea.}, journal = {Advances in experimental medicine and biology}, volume = {1414}, number = {}, pages = {27-43}, pmid = {35852729}, issn = {0065-2598}, support = {P20 GM103640/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaea/genetics ; Bacteria/genetics ; Acclimatization ; Biotechnology ; RNA ; *CRISPR-Associated Proteins/genetics ; }, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute an adaptive immune system in bacteria and archaea, where immunological memory is retained in the CRISPR locus as short pieces of the intruding nucleic acid, termed spacers. The adaptation to new infections occurs through the integration of a new spacer into the CRISPR array. For immune protection, spacers are transcribed into CRISPR RNAs (crRNA) that are used to guide the effector nuclease of the system in sequence-dependent target cleavage. Spacers originate as a prespacer from either DNA or RNA depending on the CRISPR-Cas system being observed, and the nearly universal Cas proteins, Cas1 and Cas2, insert the prespacer into the CRISPR locus during adaptation in all systems that contain them. The mechanism of site-specific prespacer integration varies across CRISPR classes and types, and distinct differences can even be found within the same subtype. In this review, the current knowledge on the mechanisms of prespacer integration in type II-A CRISPR-Cas systems will be described. Comparisons of the currently characterized type II-A systems show that distinct mechanisms exist within different members of this subtype and are correlated to sequence-specific interactions of Cas proteins and the DNA elements present in the CRISPR array. These observations indicate that nature has fine-tuned the mechanistic details while performing the basic step of DNA integration by Cas proteins, which offers unique advantages to develop Cas1-Cas2-based biotechnology.}, }
@article {pmid35811376, year = {2022}, author = {Villain, P and Catchpole, R and Forterre, P and Oberto, J and da Cunha, V and Basta, T}, title = {Expanded Dataset Reveals the Emergence and Evolution of DNA Gyrase in Archaea.}, journal = {Molecular biology and evolution}, volume = {39}, number = {8}, pages = {}, pmid = {35811376}, issn = {1537-1719}, mesh = {*Archaea/genetics/metabolism ; Bacteria/genetics ; *DNA Gyrase/genetics ; DNA Topoisomerases, Type I/genetics ; Gene Transfer, Horizontal ; }, abstract = {DNA gyrase is a type II topoisomerase with the unique capacity to introduce negative supercoiling in DNA. In bacteria, DNA gyrase has an essential role in the homeostatic regulation of supercoiling. While ubiquitous in bacteria, DNA gyrase was previously reported to have a patchy distribution in Archaea but its emergent function and evolutionary history in this domain of life remains elusive. In this study, we used phylogenomic approaches and an up-to date sequence dataset to establish global and archaea-specific phylogenies of DNA gyrases. The most parsimonious evolutionary scenario infers that DNA gyrase was introduced into the lineage leading to Euryarchaeal group II via a single horizontal gene transfer from a bacterial donor which we identified as an ancestor of Gracilicutes and/or Terrabacteria. The archaea-focused trees indicate that DNA gyrase spread from Euryarchaeal group II to some DPANN and Asgard lineages via rare horizontal gene transfers. The analysis of successful recent transfers suggests a requirement for syntropic or symbiotic/parasitic relationship between donor and recipient organisms. We further show that the ubiquitous archaeal Topoisomerase VI may have co-evolved with DNA gyrase to allow the division of labor in the management of topological constraints. Collectively, our study reveals the evolutionary history of DNA gyrase in Archaea and provides testable hypotheses to understand the prerequisites for successful establishment of DNA gyrase in a naive archaeon and the associated adaptations in the management of topological constraints.}, }
@article {pmid35810262, year = {2022}, author = {Ou, YF and Dong, HP and McIlroy, SJ and Crowe, SA and Hallam, SJ and Han, P and Kallmeyer, J and Simister, RL and Vuillemin, A and Leu, AO and Liu, Z and Zheng, YL and Sun, QL and Liu, M and Tyson, GW and Hou, LJ}, title = {Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis.}, journal = {The ISME journal}, volume = {16}, number = {10}, pages = {2373-2387}, pmid = {35810262}, issn = {1751-7370}, support = {41725002//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030411//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Archaea/genetics/metabolism ; Cytochromes/genetics ; Cytochromes b/genetics/metabolism ; *Euryarchaeota/metabolism ; *Hydrogenase/metabolism ; Methane/metabolism ; Phylogeny ; }, abstract = {Methane produced by methanogenic archaea has an important influence on Earth's changing climate. Methanogenic archaea are phylogenetically diverse and widespread in anoxic environments. These microorganisms can be divided into two subgroups based on whether or not they use b-type cytochromes for energy conservation. Methanogens with b-type cytochromes have a wider substrate range and higher growth yields than those without them. To date, methanogens with b-type cytochromes were found exclusively in the phylum "Ca. Halobacteriota" (formerly part of the phylum Euryarchaeota). Here, we present the discovery of metagenome-assembled genomes harboring methyl-coenzyme M reductase genes reconstructed from mesophilic anoxic sediments, together with the previously reported thermophilic "Ca. Methylarchaeum tengchongensis", representing a novel archaeal order, designated the "Ca. Methylarchaeales", of the phylum Thermoproteota (formerly the TACK superphylum). These microorganisms contain genes required for methyl-reducing methanogenesis and the Wood-Ljundahl pathway. Importantly, the genus "Ca. Methanotowutia" of the "Ca. Methylarchaeales" encode a cytochrome b-containing heterodisulfide reductase (HdrDE) and methanophenazine-reducing hydrogenase complex that have similar gene arrangements to those found in methanogenic Methanosarcinales. Our results indicate that members of the "Ca. Methylarchaeales" are methanogens with cytochromes and can conserve energy via membrane-bound electron transport chains. Phylogenetic and amalgamated likelihood estimation analyses indicate that methanogens with cytochrome b-containing electron transfer complexes likely evolved before diversification of Thermoproteota or "Ca. Halobacteriota" in the early Archean Eon. Surveys of public sequence databases suggest that members of the lineage are globally distributed in anoxic sediments and may be important players in the methane cycle.}, }
@article {pmid35796992, year = {2022}, author = {Kern, M and Ferreira-Cerca, S}, title = {Differential Translation Activity Analysis Using Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) in Archaea.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2533}, number = {}, pages = {229-246}, pmid = {35796992}, issn = {1940-6029}, mesh = {Alkynes/chemistry ; *Amino Acids/metabolism ; Archaea/metabolism ; *Azides/chemistry ; Click Chemistry/methods ; Proteins/chemistry ; Proteomics/methods ; }, abstract = {The study of protein production and degradation in a quantitative and time-dependent manner is a major challenge to better understand cellular physiological response. Among available technologies bioorthogonal noncanonical amino acid tagging (BONCAT) is an efficient approach allowing for time-dependent labeling of proteins through the incorporation of chemically reactive noncanonical amino acids like L-azidohomoalanine (L-AHA). The azide-containing amino-acid derivative enables a highly efficient and specific reaction termed click chemistry, whereby the azide group of the L-AHA reacts with a reactive alkyne derivate, like dibenzocyclooctyne (DBCO) derivatives, using strain-promoted alkyne-azide cycloaddition (SPAAC). Moreover, available DBCO containing reagents are versatile and can be coupled to fluorophore (e.g., Cy7) or affinity tag (e.g., biotin) derivatives, for easy visualization and affinity purification, respectively.Here, we describe a step-by-step BONCAT protocol optimized for the model archaeon Haloferax volcanii , but which is also suitable to harness other biological systems. Finally, we also describe examples of downstream visualization, affinity purification of L-AHA-labeled proteins and differential expression analysis.In conclusion, the following BONCAT protocol expands the available toolkit to explore proteostasis using time-resolved semiquantitative proteomic analysis in archaea .}, }
@article {pmid35773279, year = {2022}, author = {Buessecker, S and Palmer, M and Lai, D and Dimapilis, J and Mayali, X and Mosier, D and Jiao, JY and Colman, DR and Keller, LM and St John, E and Miranda, M and Gonzalez, C and Gonzalez, L and Sam, C and Villa, C and Zhuo, M and Bodman, N and Robles, F and Boyd, ES and Cox, AD and St Clair, B and Hua, ZS and Li, WJ and Reysenbach, AL and Stott, MB and Weber, PK and Pett-Ridge, J and Dekas, AE and Hedlund, BP and Dodsworth, JA}, title = {An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3773}, pmid = {35773279}, issn = {2041-1723}, mesh = {Anaerobiosis ; *Archaea/metabolism ; Metagenome ; Phylogeny ; *Tungsten ; }, abstract = {Trace metals have been an important ingredient for life throughout Earth's history. Here, we describe the genome-guided cultivation of a member of the elusive archaeal lineage Caldarchaeales (syn. Aigarchaeota), Wolframiiraptor gerlachensis, and its growth dependence on tungsten. A metagenome-assembled genome (MAG) of W. gerlachensis encodes putative tungsten membrane transport systems, as well as pathways for anaerobic oxidation of sugars probably mediated by tungsten-dependent ferredoxin oxidoreductases that are expressed during growth. Catalyzed reporter deposition-fluorescence in-situ hybridization (CARD-FISH) and nanoscale secondary ion mass spectrometry (nanoSIMS) show that W. gerlachensis preferentially assimilates xylose. Phylogenetic analyses of 78 high-quality Wolframiiraptoraceae MAGs from terrestrial and marine hydrothermal systems suggest that tungsten-associated enzymes were present in the last common ancestor of extant Wolframiiraptoraceae. Our observations imply a crucial role for tungsten-dependent metabolism in the origin and evolution of this lineage, and hint at a relic metabolic dependence on this trace metal in early anaerobic thermophiles.}, }
@article {pmid35770746, year = {2022}, author = {Cai, M and Tang, X}, title = {Human Archaea and Associated Metabolites in Health and Disease.}, journal = {Biochemistry}, volume = {61}, number = {24}, pages = {2835-2840}, doi = {10.1021/acs.biochem.2c00232}, pmid = {35770746}, issn = {1520-4995}, mesh = {Humans ; *Archaea/metabolism ; Bacteria/metabolism ; Fungi ; *Euryarchaeota ; }, abstract = {Trillions of microorganisms, including bacteria, archaea, fungi, and viruses, live in or on the human body. Microbe-microbe and microbe-host interactions are often influenced by diffusible and microbe-associated small molecules. Over the past few years, it has become evident that these interactions have a substantial impact on human health and disease. In this Perspective, we summarize the research involving the discovery of methanogenic and non-methanogenic archaea associated with the human body. In particular, we emphasize the importance of some archaeal metabolites in mediating intra- and interspecies interactions in the ecological environment of the human body. A deep understanding of the archaeal metabolites as well as their biological functions may reveal in more detail whether and how archaea are involved in maintaining human health and/or causing certain diseases.}, }
@article {pmid35765181, year = {2022}, author = {Kropp, C and Lipp, J and Schmidt, AL and Seisenberger, C and Linde, M and Hinrichs, KU and Babinger, P}, title = {Identification of acetylated diether lipids in halophilic Archaea.}, journal = {MicrobiologyOpen}, volume = {11}, number = {3}, pages = {e1299}, pmid = {35765181}, issn = {2045-8827}, mesh = {*Archaea/metabolism ; *Bacillales ; Ethers/chemistry/metabolism ; Mass Spectrometry ; Terpenes/metabolism ; }, abstract = {As a hallmark of Archaea, their cell membranes are comprised of ether lipids. However, Archaea-type ether lipids have recently been identified in Bacteria as well, with a somewhat different composition: In Bacillales, sn-glycerol 1-phosphate is etherified with one C35 isoprenoid chain, which is longer than the typical C20 chain in Archaea, and instead of a second isoprenoid chain, the product heptaprenylglyceryl phosphate becomes dephosphorylated and afterward diacetylated by the O-acetyltransferase YvoF. Interestingly, database searches have revealed YvoF homologs in Halobacteria (Archaea), too. Here, we demonstrate that YvoF from Haloferax volcanii can acetylate geranylgeranylglycerol in vitro. Additionally, we present the first-time identification of acetylated diether lipids in H. volcanii and Halobacterium salinarum by mass spectrometry. A variety of different acetylated lipids, namely acetylated archaeol, and acetylated archaetidylglycerol, were found, suggesting that halobacterial YvoF has a broad substrate range. We suppose that the acetyl group might serve to modify the polarity of the lipid headgroup, with still unknown biological effects.}, }
@article {pmid37938729, year = {2022}, author = {Wang, L and Wang, Y and Huang, X and Ma, R and Li, J and Wang, F and Jiao, N and Zhang, R}, title = {Potential metabolic and genetic interaction among viruses, methanogen and methanotrophic archaea, and their syntrophic partners.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {50}, pmid = {37938729}, issn = {2730-6151}, support = {91951209//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42006097//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2020M671942//China Postdoctoral Science Foundation/ ; }, abstract = {The metabolism of methane in anoxic ecosystems is mainly mediated by methanogens and methane-oxidizing archaea (MMA), key players in global carbon cycling. Viruses are vital in regulating their host fate and ecological function. However, our knowledge about the distribution and diversity of MMA viruses and their interactions with hosts is rather limited. Here, by searching metagenomes containing mcrA (the gene coding for the α-subunit of methyl-coenzyme M reductase) from a wide variety of environments, 140 viral operational taxonomic units (vOTUs) that potentially infect methanogens or methane-oxidizing archaea were retrieved. Four MMA vOTUs (three infecting the order Methanobacteriales and one infecting the order Methanococcales) were predicted to cross-domain infect sulfate-reducing bacteria. By facilitating assimilatory sulfur reduction, MMA viruses may increase the fitness of their hosts in sulfate-depleted anoxic ecosystems and benefit from synthesis of the sulfur-containing amino acid cysteine. Moreover, cell-cell aggregation promoted by MMA viruses may be beneficial for both the viruses and their hosts by improving infectivity and environmental stress resistance, respectively. Our results suggest a potential role of viruses in the ecological and environmental adaptation of methanogens and methane-oxidizing archaea.}, }
@article {pmid35761090, year = {2022}, author = {Banciu, HL and Gridan, IM and Zety, AV and Baricz, A}, title = {Asgard archaea in saline environments.}, journal = {Extremophiles : life under extreme conditions}, volume = {26}, number = {2}, pages = {21}, pmid = {35761090}, issn = {1433-4909}, support = {PN-III-P4-ID-PCE-2020-1559//Ministry of Research, Innovation and Digitization, CNCS/CCCDI - UEFISCDI/ ; }, mesh = {*Archaea ; Eukaryotic Cells/metabolism ; *Genome, Archaeal ; Metagenome ; Phylogeny ; }, abstract = {Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.}, }
@article {pmid35760837, year = {2022}, author = {Rambo, IM and Langwig, MV and Leão, P and De Anda, V and Baker, BJ}, title = {Genomes of six viruses that infect Asgard archaea from deep-sea sediments.}, journal = {Nature microbiology}, volume = {7}, number = {7}, pages = {953-961}, pmid = {35760837}, issn = {2058-5276}, mesh = {*Archaea/genetics/metabolism ; Eukaryota/genetics ; Genome, Archaeal ; Metagenome ; Phylogeny ; *Viruses/genetics ; }, abstract = {Asgard archaea are globally distributed prokaryotic microorganisms related to eukaryotes; however, viruses that infect these organisms have not been described. Here, using metagenome sequences recovered from deep-sea hydrothermal sediments, we characterize six relatively large (up to 117 kb) double-stranded DNA (dsDNA) viral genomes that infected two Asgard archaeal phyla, Lokiarchaeota and Helarchaeota. These viruses encode Caudovirales-like structural proteins, as well as proteins distinct from those described in known archaeal viruses. Their genomes contain around 1-5% of genes associated with eukaryotic nucleocytoplasmic large DNA viruses (NCLDVs) and appear to be capable of semi-autonomous genome replication, repair, epigenetic modifications and transcriptional regulation. Moreover, Helarchaeota viruses may hijack host ubiquitin systems similar to eukaryotic viruses. Genomic analysis of these Asgard viruses reveals that they contain features of both prokaryotic and eukaryotic viruses, and provides insights into their potential infection and host interaction mechanisms.}, }
@article {pmid35759872, year = {2022}, author = {Garcia, PS and Gribaldo, S and Borrel, G}, title = {Diversity and Evolution of Methane-Related Pathways in Archaea.}, journal = {Annual review of microbiology}, volume = {76}, number = {}, pages = {727-755}, doi = {10.1146/annurev-micro-041020-024935}, pmid = {35759872}, issn = {1545-3251}, mesh = {*Archaea ; *Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Methane is one of the most important greenhouse gases on Earth and holds an important place in the global carbon cycle. Archaea are the only organisms that use methanogenesis to produce energy and rely on the methyl-coenzyme M reductase complex (Mcr). Over the last decade, new results have significantly reshaped our view of the diversity of methane-related pathways in the Archaea. Many new lineages that synthesize or use methane have been identified across the whole archaeal tree, leading to a greatly expanded diversity of substrates and mechanisms. In this review, we present the state of the art of these advances and how they challenge established scenarios of the origin and evolution of methanogenesis, and we discuss the potential trajectories that may have led to this strikingly wide range of metabolisms.}, }
@article {pmid35751084, year = {2022}, author = {Xiong, X and Rao, Y and Tu, X and Wang, Z and Gong, J and Yang, Y and Wu, H and Liu, X}, title = {Gut archaea associated with bacteria colonization and succession during piglet weaning transitions.}, journal = {BMC veterinary research}, volume = {18}, number = {1}, pages = {243}, pmid = {35751084}, issn = {1746-6148}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; *Mucorales ; *Physical Conditioning, Animal ; Swine ; Weaning ; }, abstract = {BACKGROUND: Host-associated gut microbial communities are key players in shaping the fitness and health of animals. However, most current studies have focused on the gut bacteria, neglecting important gut fungal and archaeal components of these communities. Here, we investigated the gut fungi and archaea community composition in Large White piglets using shotgun metagenomic sequencing, and systematically evaluated how community composition association with gut microbiome, functional capacity, and serum metabolites varied across three weaning periods.<br><br>RESULTS: We found that Mucoromycota, Ascomycota and Basidiomycota were the most common fungi phyla and Euryarchaeota was the most common archaea phyla across individuals. We identified that Methanosarcina siciliae was the most significantly different archaea species among three weaning periods, while Parasitella parasitica, the only differential fungi species, was significantly and positively correlated with Methanosarcina siciliae enriched in day 28 group. The random forest analysis also identified Methanosarcina siciliae and Parasitella parasitica as weaning-biased archaea and fungi at the species level. Additionally, Methanosarcina siciliae was significantly correlated with P. copri and the shifts of functional capacities of the gut microbiome and several CAZymes in day 28 group. Furthermore, characteristic successional alterations in gut archaea, fungi, bacteria, and serum metabolites with each weaning step revealed a weaning transition coexpression network, e.g., Methanosarcina siciliae and P. copri were positively and significantly correlated with 15-HEPE, 8-O-Methyloblongine, and Troxilin B3.<br><br>CONCLUSION: Our findings provide a deep insight into the interactions among gut archaea, fungi, bacteria, and serum metabolites and will present a theoretical framework for understanding gut bacterial colonization and succession association with archaea during piglet weaning transitions.}, }
@article {pmid35743947, year = {2022}, author = {Doytchinov, VV and Dimov, SG}, title = {Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {6}, pages = {}, pmid = {35743947}, issn = {2075-1729}, support = {70-25-72 from 03.08.2021//NATIONAL CENTER FOR POLAR STUDIES - SOFIA UNIVERSITY "ST. KLIMENT OHRIDSKI"/ ; }, abstract = {Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.}, }
@article {pmid35741701, year = {2022}, author = {Ding, R and Yang, N and Liu, J}, title = {The Osmoprotectant Switch of Potassium to Compatible Solutes in an Extremely Halophilic Archaea Halorubrum kocurii 2020YC7.}, journal = {Genes}, volume = {13}, number = {6}, pages = {}, pmid = {35741701}, issn = {2073-4425}, mesh = {Betaine/metabolism ; *Halobacteriales ; *Halorubrum ; Potassium/metabolism ; Sodium Chloride/metabolism ; Trehalose ; }, abstract = {The main osmoadaptive mechanisms of extremely halophilic archaea include the "salt-in" strategy and the "compatible solutes" strategy. Here we report the osmoadaptive mechanism of an extremely halophilic archaea H. kocurii 2020YC7, isolated from a high salt environment sample. Genomic data revealed that strain 2020YC7 harbors genes trkA, trkH, kch for K[+] uptake, kefB for K[+] output, treS for trehalose production from polysaccharide, and betaine/carnitine/choline transporter family gene for glycine betaine uptake. Strain 2020YC7 could accumulate 8.17 to 28.67 μmol/mg protein K[+] in a defined medium, with its content increasing along with the increasing salinity from 100 to 200 g/L. When exogenous glycine betaine was added, glycine betaine functioned as the primary osmotic solute between 200 and 250 g/L NaCl, which was accumulated up to 15.27 mg/mg protein in 2020YC7 cells. RT-qPCR results completely confirmed these results. Notably, the concentrations of intracellular trehalose decreased from 5.26 to 2.61 mg/mg protein as the NaCl increased from 50 to 250 g/L. In combination with this result, the transcript level of gene treS, which catalyzes the production of trehalose from polysaccharide, was significantly up-regulated at 50-100 g/L NaCl. Therefore, trehalose does not act as an osmotic solute at high NaCl concentrations (more than 100 g/L) but at relatively low NaCl concentrations (50-100 g/L). And we propose that the degradation of cell wall polysaccharide, as a source of trehalose in a low-salt environment, may be one of the reasons for the obligate halophilic characteristics of strain 2020YC7.}, }
@article {pmid35720372, year = {2022}, author = {Krawczyk, KT and Locht, C and Kowalewicz-Kulbat, M}, title = {Halophilic Archaea Halorhabdus Rudnickae and Natrinema Salaciae Activate Human Dendritic Cells and Orient T Helper Cell Responses.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {833635}, pmid = {35720372}, issn = {1664-3224}, mesh = {Cytokines ; Dendritic Cells ; *Halobacteriaceae ; Humans ; *Interleukin-13/pharmacology ; T-Lymphocytes, Helper-Inducer ; }, abstract = {Halophilic archaea are procaryotic organisms distinct from bacteria, known to thrive in hypersaline environments, including salt lakes, salterns, brines and salty food. They have also been identified in the human microbiome. The biological significance of halophiles for human health has rarely been examined. The interactions between halophilic archaea and human dendritic cells (DCs) and T cells have not been identified so far. Here, we show for the first time that the halophilic archaea Halorhabdus rudnickae and Natrinema salaciae activate human monocyte-derived DCs, induce DC maturation, cytokine production and autologous T cell activation. In vitro both strains induced DC up-regulation of the cell-surface receptors CD86, CD80 and CD83, and cytokine production, including IL-12p40, IL-10 and TNF-α, but not IL-23 and IL-12p70. Furthermore, autologous CD4[+] T cells produced significantly higher amounts of IFN-γ and IL-13, but not IL-17A when co-cultured with halophile-stimulated DCs in comparison to T cells co-cultured with unstimulated DCs. IFN-γ was almost exclusively produced by naïve T cells, while IL-13 was produced by both naïve and memory CD4[+] T cells. Our findings thus show that halophilic archaea are recognized by human DCs and are able to induce a balanced cytokine response. The immunomodulatory functions of halophilic archaea and their potential ability to re-establish the immune balance may perhaps participate in the beneficial effects of halotherapies.}, }
@article {pmid35706137, year = {2022}, author = {Hu, W and Hou, Q and Delgado-Baquerizo, M and Stegen, JC and Du, Q and Dong, L and Ji, M and Sun, Y and Yao, S and Gong, H and Xiong, J and Xia, R and Liu, J and Aqeel, M and Akram, MA and Ran, J and Deng, J}, title = {Continental-scale niche differentiation of dominant topsoil archaea in drylands.}, journal = {Environmental microbiology}, volume = {24}, number = {11}, pages = {5483-5497}, doi = {10.1111/1462-2920.16099}, pmid = {35706137}, issn = {1462-2920}, mesh = {*Archaea/genetics ; *Ecosystem ; Soil Microbiology ; Ammonia ; Soil ; Oxidation-Reduction ; Nitrification ; Phylogeny ; }, abstract = {Archaea represent a diverse group of microorganisms often associated with extreme environments. However, an integrated understanding of biogeographical patterns of the specialist Haloarchaea and the potential generalist ammonia-oxidizing archaea (AOA) across large-scale environmental gradients remains limited. We hypothesize that niche differentiation determines their distinct distributions along environmental gradients. To test the hypothesis, we use a continental-scale research network including 173 dryland sites across northern China. Our results demonstrate that Haloarchaea and AOA dominate topsoil archaeal communities. As hypothesized, Haloarchaea and AOA show strong niche differentiation associated with two ecosystem types mainly found in China's drylands (i.e. deserts vs. grasslands), and they differ in the degree of habitat specialization. The relative abundance and richness of Haloarchaea are higher in deserts due to specialization to relatively high soil salinity and extreme climates, while those of AOA are greater in grassland soils. Our results further indicate a divergence in ecological processes underlying the segregated distributions of Haloarchaea and AOA. Haloarchaea are governed primarily by environmental-based processes while the more generalist AOA are assembled mostly via spatial-based processes. Our findings add to existing knowledge of large-scale biogeography of topsoil archaea, advancing our predictive understanding on changes in topsoil archaeal communities in a drier world.}, }
@article {pmid35697693, year = {2022}, author = {Hatano, T and Palani, S and Papatziamou, D and Salzer, R and Souza, DP and Tamarit, D and Makwana, M and Potter, A and Haig, A and Xu, W and Townsend, D and Rochester, D and Bellini, D and Hussain, HMA and Ettema, TJG and Löwe, J and Baum, B and Robinson, NP and Balasubramanian, M}, title = {Asgard archaea shed light on the evolutionary origins of the eukaryotic ubiquitin-ESCRT machinery.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3398}, pmid = {35697693}, issn = {2041-1723}, support = {MC_U105184326/MRC_/Medical Research Council/United Kingdom ; MC_UP_1201/27/MRC_/Medical Research Council/United Kingdom ; 203276/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; WT101885MA/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Archaea/genetics/metabolism ; *Endosomal Sorting Complexes Required for Transport/metabolism ; *Eukaryota/genetics/metabolism ; Eukaryotic Cells/metabolism ; Ubiquitin/genetics ; }, abstract = {The ESCRT machinery, comprising of multiple proteins and subcomplexes, is crucial for membrane remodelling in eukaryotic cells, in processes that include ubiquitin-mediated multivesicular body formation, membrane repair, cytokinetic abscission, and virus exit from host cells. This ESCRT system appears to have simpler, ancient origins, since many archaeal species possess homologues of ESCRT-III and Vps4, the components that execute the final membrane scission reaction, where they have been shown to play roles in cytokinesis, extracellular vesicle formation and viral egress. Remarkably, metagenome assemblies of Asgard archaea, the closest known living relatives of eukaryotes, were recently shown to encode homologues of the entire cascade involved in ubiquitin-mediated membrane remodelling, including ubiquitin itself, components of the ESCRT-I and ESCRT-II subcomplexes, and ESCRT-III and Vps4. Here, we explore the phylogeny, structure, and biochemistry of Asgard homologues of the ESCRT machinery and the associated ubiquitylation system. We provide evidence for the ESCRT-I and ESCRT-II subcomplexes being involved in ubiquitin-directed recruitment of ESCRT-III, as it is in eukaryotes. Taken together, our analyses suggest a pre-eukaryotic origin for the ubiquitin-coupled ESCRT system and a likely path of ESCRT evolution via a series of gene duplication and diversification events.}, }
@article {pmid35695998, year = {2022}, author = {Verma, D and Kumar, V and Satyanarayana, T}, title = {Genomic attributes of thermophilic and hyperthermophilic bacteria and archaea.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {38}, number = {8}, pages = {135}, pmid = {35695998}, issn = {1573-0972}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Genes, Archaeal ; Genomics ; Metagenome ; Phylogeny ; }, abstract = {Thermophiles and hyperthermophiles are immensely useful in understanding the evolution of life, besides their utility in environmental and industrial biotechnology. Advancements in sequencing technologies have revolutionized the field of microbial genomics. The massive generation of data enhances the sequencing coverage multi-fold and allows to analyse the entire genomic features of microbes efficiently and accurately. The mandate of a pure isolate can also be bypassed where whole metagenome-assembled genomes and single cell-based sequencing have fulfilled the majority of the criteria to decode various attributes of microbial genomes. A boom has, therefore, been seen in analysing the extremophilic bacteria and archaea using sequence-based approaches. Due to extensive sequence analysis, it becomes easier to understand the gene flow and their evolution among the members of bacteria and archaea. For instance, sequencing unveiled that Thermotoga maritima shares around 24% of genes of archaeal origin. Comparative and functional genomics provide an analytical view to understanding the microbial diversity of thermophilic bacteria and archaea, their interactions with other microbes, their adaptations, gene flow, and evolution over time. In this review, the genomic features of thermophilic bacteria and archaea are dealt with comprehensively.}, }
@article {pmid35667126, year = {2022}, author = {Gophna, U and Altman-Price, N}, title = {Horizontal Gene Transfer in Archaea-From Mechanisms to Genome Evolution.}, journal = {Annual review of microbiology}, volume = {76}, number = {}, pages = {481-502}, doi = {10.1146/annurev-micro-040820-124627}, pmid = {35667126}, issn = {1545-3251}, mesh = {*Archaea/genetics ; Bacteria/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Archaea remains the least-studied and least-characterized domain of life despite its significance not just to the ecology of our planet but also to the evolution of eukaryotes. It is therefore unsurprising that research into horizontal gene transfer (HGT) in archaea has lagged behind that of bacteria. Indeed, several archaeal lineages may owe their very existence to large-scale HGT events, and thus understanding both the molecular mechanisms and the evolutionary impact of HGT in archaea is highly important. Furthermore, some mechanisms of gene exchange, such as plasmids that transmit themselves via membrane vesicles and the formation of cytoplasmic bridges that allows transfer of both chromosomal and plasmid DNA, may be archaea-specific. This review summarizes what we know about HGT in archaea, and the barriers that restrict it, highlighting exciting recent discoveries and pointing out opportunities for future research.}, }
@article {pmid35665142, year = {2022}, author = {Selim, S and Akhtar, N and Hagagy, N and Alanazi, A and Warrad, M and El Azab, E and Elamir, MYM and Al-Sanea, MM and Jaouni, SKA and Abdel-Mawgoud, M and Shah, AA and Abdelgawad, H}, title = {Selection of Newly Identified Growth-Promoting Archaea Haloferax Species With a Potential Action on Cobalt Resistance in Maize Plants.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {872654}, pmid = {35665142}, issn = {1664-462X}, abstract = {Soil contamination with cobalt (Co) negatively impacts plant growth and production. To combat Co toxicity, plant growth-promoting microorganisms for improving plant growth are effectively applied. To this end, unclassified haloarchaeal species strain NRS_31 (OL912833), belonging to Haloferax genus, was isolated, identified for the first time, and applied to mitigate the Co phytotoxic effects on maize plants. This study found that high Co levels in soil lead to Co accumulation in maize leaves. Co accumulation in the leaves inhibited maize growth and photosynthetic efficiency, inducing oxidative damage in the tissue. Interestingly, pre-inoculation with haloarchaeal species significantly reduced Co uptake and mitigated the Co toxicity. Induced photosynthesis improved sugar metabolism, allocating more carbon to defend against Co stress. Concomitantly, the biosynthetic key enzymes involved in sucrose (sucrose-P-synthase and invertases) and proline (pyrroline-5- carboxylate synthetase (P5CS), pyrroline-5-carboxylate reductase (P5CR)) biosynthesis significantly increased to maintain plant osmotic potential. In addition to their osmoregulation potential, soluble sugars and proline can contribute to maintaining ROS hemostasis. Maize leaves managed their oxidative homeostasis by increasing the production of antioxidant metabolites (such as phenolics and tocopherols) and increasing the activity of ROS-scavenging enzymes (such as POX, CAT, SOD, and enzymes involved in the AsA/GSH cycle). Inside the plant tissue, to overcome heavy Co toxicity, maize plants increased the synthesis of heavy metal-binding ligands (metallothionein, phytochelatins) and the metal detoxifying enzymes (glutathione S transferase). Overall, the improved ROS homeostasis, osmoregulation, and Co detoxification systems were the basis underlying Co oxidative stress, mitigating haloarchaeal treatment's impact.}, }
@article {pmid35660788, year = {2022}, author = {Lim, JK and Yang, JI and Kim, YJ and Park, YJ and Kim, YH}, title = {Bioconversion of CO to formate by artificially designed carbon monoxide:formate oxidoreductase in hyperthermophilic archaea.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {539}, pmid = {35660788}, issn = {2399-3642}, mesh = {*Carbon Monoxide/metabolism ; Formate Dehydrogenases/genetics/metabolism ; Formates/metabolism ; Hydrogen/metabolism ; *Thermococcus/genetics/metabolism ; }, abstract = {Ferredoxin-dependent metabolic engineering of electron transfer circuits has been developed to enhance redox efficiency in the field of synthetic biology, e.g., for hydrogen production and for reduction of flavoproteins or NAD(P)[+]. Here, we present the bioconversion of carbon monoxide (CO) gas to formate via a synthetic CO:formate oxidoreductase (CFOR), designed as an enzyme complex for direct electron transfer between non-interacting CO dehydrogenase and formate dehydrogenase using an electron-transferring Fe-S fusion protein. The CFOR-introduced Thermococcus onnurineus mutant strains showed CO-dependent formate production in vivo and in vitro. The maximum formate production rate from purified CFOR complex and specific formate productivity from the bioreactor were 2.2 ± 0.2 μmol/mg/min and 73.1 ± 29.0 mmol/g-cells/h, respectively. The CO-dependent CO2 reduction/formate production activity of synthetic CFOR was confirmed, indicating that direct electron transfer between two unrelated dehydrogenases was feasible via mediation of the FeS-FeS fusion protein.}, }
@article {pmid35651488, year = {2022}, author = {Zhong, L and Qing, J and Liu, M and Cai, X and Li, G and Li, FY and Chen, G and Xu, X and Xue, K and Wang, Y}, title = {Fungi and Archaea Control Soil N2O Production Potential in Chinese Grasslands Rather Than Bacteria.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {844663}, pmid = {35651488}, issn = {1664-302X}, abstract = {Nitrous oxide (N2O) is a powerful greenhouse gas and the predominant stratospheric ozone-depleting substance. Soil is a major source of N2O but remains largely uncertain due to the complicated processes of nitrification and denitrification performed by various groups of microbes such as bacteria, fungi, and archaea. We used incubation experiments to measure the total fungal, archaeal, and bacterial N2O production potential and the microbial functional genes in soils along 3,000 km Chinese grassland transect, including meadow steppe, typical steppe, desert steppe, alpine meadow, and alpine steppe. The results indicated that fungi, archaea, and bacteria contributed 25, 34, and 19% to nitrification and 46, 29, and 15% to denitrification, respectively. The AOA and AOB genes were notably correlated with the total nitrification enzyme activity (TNEA), whereas both narG and nirK genes were significantly correlated with total denitrification enzyme activity (TDEA) at p < 0.01. The correlations between AOA and ANEA (archaeal nitrification enzyme activity), AOB and BNEA (bacterial nitrification enzyme activity), and narG, nirK, and BDEA (bacterial denitrification enzyme activity) showed higher coefficients than those between the functional genes and TNEA/TDEA. The structural equation modeling (SEM) results showed that fungi are dominant in N2O production processes, followed by archaea in the northern Chinese grasslands. Our findings indicate that the microbial functional genes are powerful predictors of the N2O production potential, after distinguishing bacterial, fungal, and archaeal processes. The key variables of N2O production and the nitrogen (N) cycle depend on the dominant microbial functional groups in the N-cycle in soils.}, }
@article {pmid38817676, year = {2022}, author = {Liu, Y and Li, M}, title = {The unstable evolutionary position of Korarchaeota and its relationship with other TACK and Asgard archaea.}, journal = {mLife}, volume = {1}, number = {2}, pages = {218-222}, pmid = {38817676}, issn = {2770-100X}, abstract = {The applications of marker gene concatenation have been advanced to resolve the key questions in the Tree of Life. However, the interphylum evolutionary relationship between Korarchaeota of TACK (Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota) and Asgard archaea remains uncertain. We applied a marker gene ranking procedure to examine their evolutionary history. Our updated trees showed confident placements of (1) Korarchaeota as the basal branch to other TACK archaea and as a sister group to Asgard archaea; (2) Njordarchaeota at basal branch to Korarchaeota instead of within Asgard archaea. They highlight the importance of evaluating marker genes for phylogeny inference of the Archaea domain.}, }
@article {pmid35639688, year = {2022}, author = {Thevasundaram, K and Gallagher, JJ and Cherng, F and Chang, MCY}, title = {Engineering nonphotosynthetic carbon fixation for production of bioplastics by methanogenic archaea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {23}, pages = {e2118638119}, pmid = {35639688}, issn = {1091-6490}, support = {T32 GM066698/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaea/metabolism ; Carbon Cycle ; Carbon Dioxide/metabolism ; Chemoautotrophic Growth ; *Euryarchaeota/metabolism ; }, abstract = {The conversion of CO2 to value-added products allows both capture and recycling of greenhouse gas emissions. While plants and other photosynthetic organisms play a key role in closing the global carbon cycle, their dependence on light to drive carbon fixation can be limiting for industrial chemical synthesis. Methanogenic archaea provide an alternative platform as an autotrophic microbial species capable of non-photosynthetic CO2 fixation, providing a potential route to engineered microbial fermentation to synthesize chemicals from CO2 without the need for light irradiation. One major challenge in this goal is to connect upstream carbon-fixation pathways with downstream biosynthetic pathways, given the distinct differences in metabolism between archaea and typical heterotrophs. We engineered the model methanogen, Methanococcus maripaludis, to divert acetyl-coenzyme A toward biosynthesis of value-added chemicals, including the bioplastic polyhydroxybutyrate (PHB). A number of studies implicated limitations in the redox pool, with NAD(P)(H) pools in M. maripaludis measured to be <15% of that of Escherichia coli, likely since methanogenic archaea utilize F420 and ferredoxins instead. Multiple engineering strategies were used to precisely target and increase the cofactor pool, including heterologous expression of a synthetic nicotinamide salvage pathway as well as an NAD+-dependent formate dehydrogenase from Candida boidinii. Engineered strains of M. maripaludis with improved NADH pools produced up to 171 ± 4 mg/L PHB and 24.0 ± 1.9% of dry cell weight. The metabolic engineering strategies presented in this study broaden the utility of M. maripaludis for sustainable chemical synthesis using CO2 and may be transferable to related archaeal species.}, }
@article {pmid35633707, year = {2022}, author = {Zheng, J and Tao, L and Dini-Andreote, F and Luan, L and Kong, P and Xue, J and Zhu, G and Xu, Q and Jiang, Y}, title = {Dynamic Responses of Ammonia-Oxidizing Archaea and Bacteria Populations to Organic Material Amendments Affect Soil Nitrification and Nitrogen Use Efficiency.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {911799}, pmid = {35633707}, issn = {1664-302X}, abstract = {Organic material amendments have been proposed as an effective strategy to promote soil health by enhancing soil fertility and promoting nitrogen (N) cycling and N use efficiency (NUE). Thus, it is important to investigate the extent to which the structure and function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) differentially respond to the organic material amendments in field settings. Here, we conducted a 9-year field experiment to track the responses of AOA and AOB populations to the organic material amendments and measured the potential nitrification activity (PNA), plant productivity, and NUE in the plant rhizosphere interface. Our results revealed that the organic material amendments significantly enhanced the abundance and diversity of AOA and AOB populations. Further, significant differences were observed in the composition and co-occurrence network of AOA and AOB. A higher occurrence of potential competitive interactions between taxa and enumerated potential keystone taxa was observed in the AOA-AOB network. Moreover, we found that AOA was more important than AOB for PNA under the organic material amendments. Structural equation modeling suggested that the diversity of AOA and AOB populations induced by the potential competitive interactions with keystone taxa dynamically accelerated the rate of PNA, and positively affected plant productivity and NUE under the organic material amendments. Collectively, our study offers new insights into the ecology and functioning of ammonia oxidizers and highlights the positive effects of organic material amendments on nitrogen cycling dynamics.}, }
@article {pmid35630397, year = {2022}, author = {Liu, H and Zhou, P and Cheung, S and Lu, Y and Liu, H and Jing, H}, title = {Distribution and Oxidation Rates of Ammonia-Oxidizing Archaea Influenced by the Coastal Upwelling off Eastern Hainan Island.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, pmid = {35630397}, issn = {2076-2607}, support = {41776147//the National Natural Science Foundation of China/ ; 91751116//the Training Program of the Major Research Plan of the National Natural Science Foundation of China/ ; 2016YFC0304905//the National Key Research and Development Program of China/ ; 420RC677//the Hainan Provincial Natural Science Foundation of China for High-level Talents/ ; }, abstract = {Coastal upwelling causes variations in temperature, salinity and inorganic nutrients in the water column, consequently leading to the shift of microbial populations and their metabolic activities. Impacts of the eastern Hainan upwelling (EHU) on the ammonia-oxidizing archaea (AOA) were investigated based on the amoA gene using pyrosequencing and quantitative PCR at both DNA and cDNA levels, together with the determination of the ammonia oxidation (AO) rate measured with [15]N-labelled ammonium. By comparing stations with and without upwelling influence, we found that coastal upwelling correlated with an increase in amoA gene abundance, the dominance of distinct clades for AOA communities at the respective gene and transcript levels, and a large increase in the proportion of the SCM1-like (Nitrosopumilus maritimus-like) cluster as well. The AO rates were generally higher in the deeper water (~25 m), which was in significant positive correlation with the proportion of cluster Water Column A (WCA) at the transcript level, indicating the potential contribution of this cluster to in situ ammonia oxidization. Our study demonstrated that coastal upwelling had a significant impact on the AOA community and ammonia oxidization rate; therefore, this physical forcing should be considered in the future assessment of the global nitrogen budgets and biogeochemical nitrogen cycles.}, }
@article {pmid35625610, year = {2022}, author = {Pastor, MM and Sakrikar, S and Rodriguez, DN and Schmid, AK}, title = {Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea.}, journal = {Biomolecules}, volume = {12}, number = {5}, pages = {}, pmid = {35625610}, issn = {2218-273X}, support = {T32 GM136627/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaea/genetics/metabolism ; RNA, Messenger/genetics ; *RNA, Ribosomal/genetics/metabolism ; RNA-Seq ; Sequence Analysis, RNA/methods ; }, abstract = {Despite intense recent research interest in archaea, the scientific community has experienced a bottleneck in the study of genome-scale gene expression experiments by RNA-seq due to the lack of commercial and specifically designed rRNA depletion kits. The high rRNA:mRNA ratio (80-90%: ~10%) in prokaryotes hampers global transcriptomic analysis. Insufficient ribodepletion results in low sequence coverage of mRNA, and therefore, requires a substantially higher number of replicate samples and/or sequencing reads to achieve statistically reliable conclusions regarding the significance of differential gene expression between case and control samples. Here, we show that after the discontinuation of the previous version of RiboZero (Illumina, San Diego, CA, USA) that was useful in partially or completely depleting rRNA from archaea, archaeal transcriptomics studies have experienced a slowdown. To overcome this limitation, here, we analyze the efficiency for four different hybridization-based kits from three different commercial suppliers, each with two sets of sequence-specific probes to remove rRNA from four different species of halophilic archaea. We conclude that the key for transcriptomic success with the currently available tools is the probe-specificity for the rRNA sequence hybridization. With this paper, we provide insights into the archaeal community for selecting certain reagents and strategies over others depending on the archaeal species of interest. These methods yield improved RNA-seq sensitivity and enhanced detection of low abundance transcripts.}, }
@article {pmid35623507, year = {2022}, author = {Fonseca de Souza, L and Alvarez, DO and Domeignoz-Horta, LA and Gomes, FV and de Souza Almeida, C and Merloti, LF and Mendes, LW and Andreote, FD and Bohannan, BJM and Mazza Rodrigues, JL and Nüsslein, K and Tsai, SM}, title = {Maintaining grass coverage increases methane uptake in Amazonian pastures, with a reduction of methanogenic archaea in the rhizosphere.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 2}, pages = {156225}, doi = {10.1016/j.scitotenv.2022.156225}, pmid = {35623507}, issn = {1879-1026}, mesh = {Animals ; *Archaea ; Cattle ; *Methane ; Poaceae/genetics ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Cattle ranching is the largest driver of deforestation in the Brazilian Amazon. The rainforest-to-pasture conversion affects the methane cycle in upland soils, changing it from sink to source of atmospheric methane. However, it remains unknown if management practices could reduce the impact of land-use on methane cycling. In this work, we evaluated how pasture management can regulate the soil methane cycle either by maintaining continuous grass coverage on pasture soils, or by liming the soil to amend acidity. Methane fluxes from forest and pasture soils were evaluated in moisture-controlled greenhouse experiments with and without grass cover (Urochloa brizantha cv. Marandu) or liming. We also assessed changes in the soil microbial community structure of both bare (bulk) and rhizospheric pasture soils through high throughput sequencing of the 16S rRNA gene, and quantified the methane cycling microbiota by their respective marker genes related to methane generation (mcrA) or oxidation (pmoA). The experiments used soils from eastern and western Amazonia, and concurrent field studies allowed us to confirm greenhouse data. The presence of a grass cover not only increased methane uptake by up to 35% in pasture soils, but also reduced the abundance of the methane-producing community. In the grass rhizosphere this reduction was up to 10-fold. Methane-producing archaea belonged to the genera Methanosarcina sp., Methanocella sp., Methanobacterium sp., and Rice Cluster I. Further, we showed that soil liming to increasing pH compromised the capacity of forest and pasture soils to be a sink for methane, and instead converted formerly methane-consuming forest soils to become methane sources in only 40-80 days. Liming reduced the relative abundance of Beijerinckiacea family in forest soils, which account for many known methanotrophs. Our results demonstrate that pasture management that maintains grass coverage can mitigate soil methane emissions, compared to bare (bulk) pasture soil.}, }
@article {pmid35618771, year = {2022}, author = {Badel, C and Samson, RY and Bell, SD}, title = {Chromosome organization affects genome evolution in Sulfolobus archaea.}, journal = {Nature microbiology}, volume = {7}, number = {6}, pages = {820-830}, pmid = {35618771}, issn = {2058-5276}, support = {R01 GM135178/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea/genetics ; Chromosomes ; Evolution, Molecular ; Replication Origin ; *Sulfolobus/genetics ; }, abstract = {In all organisms, the DNA sequence and the structural organization of chromosomes affect gene expression. The extremely thermophilic crenarchaeon Sulfolobus has one circular chromosome with three origins of replication. We previously revealed that this chromosome has defined A and B compartments that have high and low gene expression, respectively. As well as higher levels of gene expression, the A compartment contains the origins of replication. To evaluate the impact of three-dimensional organization on genome evolution, we characterized the effect of replication origins and compartmentalization on primary sequence evolution in eleven Sulfolobus species. Using single-nucleotide polymorphism analyses, we found that distance from an origin of replication was associated with increased mutation rates in the B but not in the A compartment. The enhanced polymorphisms distal to replication origins suggest that replication termination may have a causal role in their generation. Further mutational analyses revealed that the sequences in the A compartment are less likely to be mutated, and that there is stronger purifying selection than in the B compartment. Finally, we applied the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to show that the B compartment is less accessible than the A compartment. Taken together, our data suggest that compartmentalization of chromosomal DNA can influence chromosome evolution in Sulfolobus. We propose that the A compartment serves as a haven for stable maintenance of gene sequences, while sequences in the B compartment can be diversified.}, }
@article {pmid35616996, year = {2022}, author = {Bao, CX and Li, SY and Xin, YJ and Hou, J and Cui, HL}, title = {Natrinema halophilum sp. nov., Natrinema salinisoli sp. nov., Natrinema amylolyticum sp. nov. and Haloterrigena alkaliphila sp. nov., four extremely halophilic archaea isolated from salt mine, saline soil and salt lake.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {5}, pages = {}, doi = {10.1099/ijsem.0.005385}, pmid = {35616996}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Glycolipids/chemistry ; *Halobacteriaceae ; *Lakes ; Phosphatidic Acids ; Phosphatidylglycerols ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; }, abstract = {Four halophilic archaeal strains, YPL8[T], SLN56[T], LT61[T] and KZCA68[T], were isolated from a salt mine, saline soil and a salt lake located in different regions of China. Sequence similarities of 16S rRNA and rpoB' genes among strains YPL8[T], SLN56[T], LT61[T] and the current members of Natrinema were 94.1-98.2 % and 89.3-95.1 %, respectively, while these values among strain KZCA68[T] and the current members of Haloterrigena were 97.2-97.4 % and 91.7-91.9 %, respectively. The average nucleotide identity, in silico DNA-DNA hybridization and average amino acid identity values among these four strains and their closely related species were all lower than the threshold values for species boundary. All four strains were unable to hydrolyse casein, gelatin, or Tween 80. Strain YPL8[T] contained phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), disulfated mannosyl glucosyl diether (S2-DGD) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA). Strain SLN56[T] contained PA, PG, phosphatidylglycerol sulphate (PGS), PGP-Me, S-DGD-1, S2-DGD and S-DGD-PA. Strain LT61[T] contained PA, PG, PGS, PGP-Me, S-DGD-1 and S2-DGD. The phospholipids of strain KZCA68[T] were PA, PG and PGP-Me. These results showed that strains YPL8[T] (=CGMCC 1.13883[T]=JCM 31181[T]), SLN56[T] (=CGMCC 1.14945[T]=JCM 30832[T]) and LT61[T] (=CGMCC 1.14942[T]=JCM 30668[T]) represent novel species of the genus Natrinema, for which the names, Natrinema halophilum sp. nov., Natrinema salinisoli sp. nov. and Natrinema amylolyticum sp. nov. are proposed. Strain KZCA68[T] (=CGMCC 1.17211[T]=JCM 34158[T]) represents a novel species of Haloterrigena, for which the name Haloterrigena alkaliphila sp. nov. is proposed.}, }
@article {pmid35615789, year = {2022}, author = {Dyksma, S and Gallert, C}, title = {Effect of magnetite addition on transcriptional profiles of syntrophic Bacteria and Archaea during anaerobic digestion of propionate in wastewater sludge.}, journal = {Environmental microbiology reports}, volume = {14}, number = {4}, pages = {664-678}, doi = {10.1111/1758-2229.13080}, pmid = {35615789}, issn = {1758-2229}, mesh = {Anaerobiosis ; *Archaea/genetics ; Bacteria/genetics ; *Euryarchaeota/genetics ; Ferrosoferric Oxide/pharmacology ; Formates/pharmacology ; Methane ; Propionates ; Sewage ; Wastewater ; }, abstract = {Anaerobic digestion (AD) is an important technology for the effective conversion of waste and wastewater to methane. Here, syntrophic bacteria transfer molecular hydrogen (H2), formate, or directly supply electrons (direct interspecies electron transfer, DIET) to the methanogens. Evidence is accumulating that the methanation of short-chain fatty acids can be enhanced by the addition of conductive material to the anaerobic digester, which has often been attributed to the stimulation of DIET. Since little is known about the transcriptional response of a complex AD microbial community to the addition of conductive material, we added magnetite to propionate-fed laboratory-scale reactors that were inoculated with wastewater sludge. Compared to the control reactors, the magnetite-amended reactors showed improved methanation of propionate. A genome-centric metatranscriptomics approach identified the active SCFA-oxidizing bacteria that affiliated with Firmicutes, Desulfobacterota and Cloacimonadota. The transcriptional profiles revealed that the syntrophic bacteria transferred acetate, H2 and formate to acetoclastic and hydrogenotrophic methanogens, whereas transcription of potential determinants for DIET such as conductive pili and outer-membrane cytochromes did not significantly change with magnetite addition. Overall, changes in the transcriptional profiles of syntrophic Bacteria and Archaea in propionate-fed lab-scale reactors amended with magnetite refute a major role of DIET in the studied system.}, }
@article {pmid35610383, year = {2023}, author = {Pierangeli, GMF and Domingues, MR and Choueri, RB and Hanisch, WS and Gregoracci, GB and Benassi, RF}, title = {Spatial Variation and Environmental Parameters Affecting the Abundant and Rare Communities of Bacteria and Archaea in the Sediments of Tropical Urban Reservoirs.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {297-310}, pmid = {35610383}, issn = {1432-184X}, mesh = {*Archaea/genetics ; *Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Water Quality ; }, abstract = {Microbial communities in freshwater sediments play an important role in organic matter remineralization, contributing to biogeochemical cycles, nutrient release, and greenhouse gases emissions. Bacterial and archaeal communities might show spatial or seasonal patterns and were shown to be influenced by distinct environmental parameters and anthropogenic activities, including pollution and damming. Here, we determined the spatial variation and the environmental variables influencing the abundant and rare bacterial and archaeal communities in the sediments of eutrophic-hypereutrophic reservoirs from a tropical urban area in Brazil. The most abundant microbes included mainly Anaerolineae and Deltaproteobacteria genera from the Bacteria domain, and Methanomicrobia genera from the Archaea domain. Microbial communities differed spatially in each reservoir, reflecting the establishment of specific environmental conditions. Locations with better or worst water quality, or close to a dam, showed more distinct microbial communities. Besides the water column depth, microbial communities were affected by some pollution indicators, including total phosphorus, orthophosphate, electrical conductivity, and biochemical oxygen demand. Distinct proportions of variation were explained by spatial and environmental parameters for each microbial community. Furthermore, spatial variations in environmental parameters affecting these communities, especially the most distinct ones, contributed to microbial variations mediated by spatial and environmental properties together. Finally, our study showed that different pressures in each reservoir affected the sediment microbiota, promoting different responses and possible adaptations of abundant and rare bacterial and archaeal communities.}, }
@article {pmid35607968, year = {2022}, author = {Semler, AC and Fortney, JL and Fulweiler, RW and Dekas, AE}, title = {Cold Seeps on the Passive Northern U.S. Atlantic Margin Host Globally Representative Members of the Seep Microbiome with Locally Dominant Strains of Archaea.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {11}, pages = {e0046822}, pmid = {35607968}, issn = {1098-5336}, mesh = {*Archaea/metabolism ; Geologic Sediments/microbiology ; Methane/metabolism ; Methanosarcinales/genetics ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Seawater/microbiology ; }, abstract = {Marine cold seeps are natural sites of methane emission and harbor distinct microbial communities capable of oxidizing methane. The majority of known cold seeps are on tectonically active continental margins, but recent discoveries have revealed abundant seeps on passive margins as well, including on the U.S. Atlantic Margin (USAM). We sampled in and around four USAM seeps and combined pore water geochemistry measurements with amplicon sequencing of 16S rRNA and mcrA (DNA and RNA) to investigate the microbial communities present, their assembly processes, and how they compare to communities at previously studied sites. We found that the USAM seeps contained communities consistent with the canonical seep microbiome at the class and order levels but differed markedly at the sequence variant level, especially within the anaerobic methanotrophic (ANME) archaea. The ANME populations were highly uneven, with just a few dominant mcrA sequence variants at each seep. Interestingly, the USAM seeps did not form a distinct phylogenetic cluster when compared with other previously described seeps around the world. Consistent with this, we found only a very weak (though statistically significant) distance-decay trend in seep community similarity across a global data set. Ecological assembly indices suggest that the USAM seep communities were assembled primarily deterministically, in contrast to the surrounding nonseep sediments, where stochastic processes dominated. Together, our results suggest that the primary driver of seep microbial community composition is local geochemistry-specifically methane, sulfide, nitrate, acetate, and ammonium concentrations-rather than the geologic context, the composition of nearby seeps, or random events of dispersal. IMPORTANCE Cold seeps are now known to be widespread features of passive continental margins, including the northern U.S. Atlantic Margin (USAM). Methane seepage is expected to intensify at these relatively shallow seeps as bottom waters warm and underlying methane hydrates dissociate. While methanotrophic microbial communities might reduce or prevent methane release, microbial communities on passive margins have rarely been characterized. In this study, we investigated the Bacteria and Archaea at four cold seeps on the northern USAM and found that despite being colocated on the same continental slope, the communities significantly differ by site at the sequence variant level, particularly methane-cycling community members. Differentiation by site was not observed in similarly spaced background sediments, raising interesting questions about the dispersal pathways of cold seep microorganisms. Understanding the genetic makeup of these discrete seafloor ecosystems and how their microbial communities develop will be increasingly important as the climate changes.}, }
@article {pmid35605022, year = {2022}, author = {Martinez-Gutierrez, CA and Aylward, FO}, title = {Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales.}, journal = {PLoS genetics}, volume = {18}, number = {5}, pages = {e1010220}, pmid = {35605022}, issn = {1553-7404}, mesh = {*Archaea/genetics ; Bacteria/genetics ; *Evolution, Molecular ; Genome Size ; Phylogeny ; }, abstract = {The evolutionary forces that determine genome size in bacteria and archaea have been the subject of intense debate over the last few decades. Although the preferential loss of genes observed in prokaryotes is explained through the deletional bias, factors promoting and preventing the fixation of such gene losses often remain unclear. Importantly, statistical analyses on this topic typically do not consider the potential bias introduced by the shared ancestry of many lineages, which is critical when using species as data points because of the potential dependence on residuals. In this study, we investigated the genome size distributions across a broad diversity of bacteria and archaea to evaluate if this trait is phylogenetically conserved at broad phylogenetic scales. After model fit, Pagel's lambda indicated a strong phylogenetic signal in genome size data, suggesting that the diversification of this trait is influenced by shared evolutionary histories. We used a phylogenetic generalized least-squares analysis (PGLS) to test whether phylogeny influences the predictability of genome size from dN/dS ratios and 16S copy number, two variables that have been previously linked to genome size. These results confirm that failure to account for evolutionary history can lead to biased interpretations of genome size predictors. Overall, our results indicate that although bacteria and archaea can rapidly gain and lose genetic material through gene transfers and deletions, respectively, phylogenetic signal for genome size distributions can still be recovered at broad phylogenetic scales that should be taken into account when inferring the drivers of genome size evolution.}, }
@article {pmid35604119, year = {2022}, author = {Popp, PF and Gumerov, VM and Andrianova, EP and Bewersdorf, L and Mascher, T and Zhulin, IB and Wolf, D}, title = {Phyletic Distribution and Diversification of the Phage Shock Protein Stress Response System in Bacteria and Archaea.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0134821}, pmid = {35604119}, issn = {2379-5077}, support = {R35 GM131760/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacterial Proteins/genetics ; Archaea/genetics ; Heat-Shock Proteins/genetics ; Escherichia coli/genetics ; *Bacteriophages/metabolism ; }, abstract = {Maintaining cell envelope integrity is of vital importance for all microorganisms. Not surprisingly, evolution has shaped conserved protein protection networks that connect stress perception, transmembrane signal transduction, and mediation of cellular responses upon cell envelope stress. The phage shock protein (Psp) stress response is one such conserved protection network. Most knowledge about the Psp response derives from studies in the Gram-negative model bacterium Escherichia coli, where the Psp system consists of several well-defined protein components. Homologous systems were identified in representatives of the Proteobacteria, Actinobacteria, and Firmicutes. However, the Psp system distribution in the microbial world remains largely unknown. By carrying out a large-scale, unbiased comparative genomics analysis, we found components of the Psp system in many bacterial and archaeal phyla and describe that the predicted Psp systems deviate dramatically from the known prototypes. The core proteins PspA and PspC have been integrated into various (often phylum-specifically) conserved protein networks during evolution. Based on protein domain-based and gene neighborhood analyses of pspA and pspC homologs, we built a natural classification system for Psp networks in bacteria and archaea. We validate our approach by performing a comprehensive in vivo protein interaction study of Psp domains identified in the Gram-positive model organism Bacillus subtilis and found a strong interconnected protein network. Our study highlights the diversity of Psp domain organizations and potentially diverse functions across the plethora of the microbial landscape, thus laying the ground for studies beyond known Psp functions in underrepresented organisms. IMPORTANCE The PspA protein domain is found in all domains of life, highlighting its central role in Psp networks. To date, all insights into the core functions of Psp responses derive mainly from protein network blueprints representing only three bacterial phyla. Despite large overlaps in function and regulation, the evolutionary diversity of Psp networks remains largely elusive. Here, we present an unbiased protein domain- and genomic context-centered approach that describes and classifies Psp systems. Our results suggest so-far-unknown Psp-associated roles with other protein networks giving rise to new functions. We demonstrate the applicability of our approach by dissecting the Psp protein network present in Bacillus subtilis and demonstrate Psp domains working in concert with other cell envelope stress response systems. We find that the Psp-like protein universe reflects a surprising diversity within the bacterial and archaeal microbial world.}, }
@article {pmid35602962, year = {2022}, author = {Wu, J and Hong, Y and He, X and Liu, X and Ye, J and Jiao, L and Li, Y and Wang, Y and Ye, F and Yang, Y and Du, J}, title = {Niche differentiation of ammonia-oxidizing archaea and related autotrophic carbon fixation potential in the water column of the South China Sea.}, journal = {iScience}, volume = {25}, number = {5}, pages = {104333}, pmid = {35602962}, issn = {2589-0042}, abstract = {The significant primary production by ammonia-oxidizing archaea (AOA) in the ocean was reported, but the carbon fixation process of AOA and its community composition along the water depth remain unclear. Here, we investigated the abundance, community composition, and potential carbon fixation of AOA in water columns of the South China Sea. Higher abundances of the amoA and accA genes of AOA were found below the euphotic zone. Similarly, higher carbon fixation potential of AOA, evaluated by the ratios of amoA to accA gene, was also observed below euphotic zone and the ratios increased with increasing water depth. The vertical niche differentiation of AOA was further evidenced, with the dominant genus shifting from Nitrosopelagicus in the epipelagic zone to uncultured genus in the meso- and bathypelagic zones. Our findings highlight the higher carbon fixation potential of AOA in deep water and the significance of AOA to the ocean carbon budget.}, }
@article {pmid35544775, year = {2022}, author = {Tunçkanat, T and Gendron, A and Sadler, Z and Neitz, A and Byquist, S and Lie, TJ and Allen, KD}, title = {Lysine 2,3-Aminomutase and a Newly Discovered Glutamate 2,3-Aminomutase Produce β-Amino Acids Involved in Salt Tolerance in Methanogenic Archaea.}, journal = {Biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.biochem.2c00014}, pmid = {35544775}, issn = {1520-4995}, abstract = {Many methanogenic archaea synthesize β-amino acids as osmolytes that allow survival in high salinity environments. Here, we investigated the radical S-adenosylmethionine (SAM) aminomutases involved in the biosynthesis of N[ε]-acetyl-β-lysine and β-glutamate in Methanococcus maripaludis C7. Lysine 2,3-aminomutase (KAM), encoded by MmarC7_0106, was overexpressed and purified from Escherichia coli, followed by biochemical characterization. In the presence of l-lysine, SAM, and dithionite, this archaeal KAM had a kcat = 14.3 s[-1] and a Km = 19.2 mM. The product was shown to be 3(S)-β-lysine, which is like the well-characterized Clostridium KAM as opposed to the E. coli KAM that produces 3(R)-β-lysine. We further describe the function of MmarC7_1783, a putative radical SAM aminomutase with a ∼160 amino acid extension at its N-terminus. Bioinformatic analysis of the possible substrate-binding residues suggested a function as glutamate 2,3-aminomutase, which was confirmed here through heterologous expression in a methanogen followed by detection of β-glutamate in cell extracts. β-Glutamate has been known to serve as an osmolyte in select methanogens for a long time, but its biosynthetic origin remained unknown until now. Thus, this study defines the biosynthetic routes for β-lysine and β-glutamate in M. maripaludis and expands the importance and diversity of radical SAM enzymes in all domains of life.}, }
@article {pmid35508560, year = {2022}, author = {Fisk, LM and Barton, L and Maccarone, LD and Jenkins, SN and Murphy, DV}, title = {Seasonal dynamics of ammonia-oxidizing bacteria but not archaea influence soil nitrogen cycling in a semi-arid agricultural soil.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {7299}, pmid = {35508560}, issn = {2045-2322}, mesh = {Ammonia/metabolism ; *Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; *Betaproteobacteria/metabolism ; Nitrification ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; Seasons ; Soil/chemistry ; Soil Microbiology ; Water/metabolism ; }, abstract = {Nitrification, a key pathway of nitrogen (N) loss from agricultural soils, is performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). We examined the seasonal dynamics (2 years) of ammonia oxidizer gene abundances across a gradient of soil carbon (C) and N in a semi-arid soil after 8 years of tillage and crop residue treatments. AOB was more dominant than AOA in the surface soil, as AOA were undetected in 96% of samples. Seasonal variation in AOB abundance was related to substrate availability; AOB gene copy numbers increased at the end of the growing season (during summer fallow) following higher concentrations in dissolved organic matter soil water. This suggests increased co-location between AOB and substrate resources in pores still filled with water as the soils dried. AOB was however not statistically related to soil ammonium concentrations, soil water content, rainfall or temperature. Organic matter inputs enhanced AOB abundance independent of seasonal variation. AOB abundance was greatest in autumn and immediately preceding the start of the growing season, and coincided with elevated soil nitrate concentrations. The growth of the AOB population is likely to contribute to increased risk of N loss through leaching and/or denitrification at the start of the crop growing season following summer fallow.}, }
@article {pmid35500274, year = {2022}, author = {Lemaire, ON and Wagner, T}, title = {A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea.}, journal = {Biochemistry}, volume = {61}, number = {10}, pages = {805-821}, pmid = {35500274}, issn = {1520-4995}, mesh = {*Alkanes/metabolism ; Anaerobiosis ; *Archaea/chemistry ; Catalysis ; Mesna/metabolism ; Methane/metabolism ; Oxidation-Reduction ; Oxidoreductases/metabolism ; Phylogeny ; }, abstract = {Microbial anaerobic oxidation of alkanes intrigues the scientific community by way of its impact on the global carbon cycle, and its biotechnological applications. Archaea are proposed to degrade short- and long-chain alkanes to CO2 by reversing methanogenesis, a theoretically reversible process. The pathway would start with alkane activation, an endergonic step catalyzed by methyl-coenzyme M reductase (MCR) homologues that would generate alkyl-thiols carried by coenzyme M. While the methane-generating MCR found in methanogens has been well characterized, the enzymatic activity of the putative alkane-fixing counterparts has not been validated so far. Such an absence of biochemical investigations contrasts with the current explosion of metagenomics data, which draws new potential alkane-oxidizing pathways in various archaeal phyla. Therefore, validating the physiological function of these putative alkane-fixing machines and investigating how their structures, catalytic mechanisms, and cofactors vary depending on the targeted alkane have become urgent needs. The first structural insights into the methane- and ethane-capturing MCRs highlighted unsuspected differences and proposed some explanations for their substrate specificity. This Perspective reviews the current physiological, biochemical, and structural knowledge of alkyl-CoM reductases and offers fresh ideas about the expected mechanistic and chemical differences among members of this broad family. We conclude with the challenges of the investigation of these particular enzymes, which might one day generate biofuels for our modern society.}, }
@article {pmid35489791, year = {2022}, author = {Glodowska, M and Welte, CU and Kurth, JM}, title = {Metabolic potential of anaerobic methane oxidizing archaea for a broad spectrum of electron acceptors.}, journal = {Advances in microbial physiology}, volume = {80}, number = {}, pages = {157-201}, doi = {10.1016/bs.ampbs.2022.01.003}, pmid = {35489791}, issn = {2162-5468}, mesh = {Anaerobiosis ; *Archaea/metabolism ; Electrons ; Ferric Compounds/metabolism ; Methane/metabolism ; *Microbiota ; Oxidation-Reduction ; }, abstract = {Methane (CH4) is a potent greenhouse gas significantly contributing to the climate warming we are currently facing. Microorganisms play an important role in the global CH4 cycle that is controlled by the balance between anaerobic production via methanogenesis and CH4 removal via methanotrophic oxidation. Research in recent decades advanced our understanding of CH4 oxidation, which until 1976 was believed to be a strictly aerobic process. Anaerobic oxidation of methane (AOM) coupled to sulfate reduction is now known to be an important sink of CH4 in marine ecosystems. Furthermore, in 2006 it was discovered that anaerobic CH4 oxidation can also be coupled to nitrate reduction (N-DAMO), demonstrating that AOM may be much more versatile than previously thought and linked to other electron acceptors. In consequence, an increasing number of studies in recent years showed or suggested that alternative electron acceptors can be used in the AOM process including Fe[III], Mn[IV], As[V], Cr[VI], Se[VI], Sb[V], V[V], and Br[V]. In addition, humic substances as well as biochar and perchlorate (ClO4[-]) were suggested to mediate AOM. Anaerobic methanotrophic archaea, the so-called ANME archaea, are key players in the AOM process, yet we are still lacking deeper understanding of their metabolism, electron acceptor preferences and their interaction with other microbial community members. It is still not clear whether ANME archaea can oxidize CH4 and reduce metallic electron acceptors independently or via electron transfer to syntrophic partners, interspecies electron transfer, nanowires or conductive pili. Therefore, the aim of this review is to summarize and discuss the current state of knowledge about ANME archaea, focusing on their physiology, metabolic flexibility and potential to use various electron acceptors.}, }
@article {pmid35437913, year = {2022}, author = {Campbell, BC and Greenfield, P and Gong, S and Barnhart, EP and Midgley, DJ and Paulsen, IT and George, SC}, title = {Methanogenic archaea in subsurface coal seams are biogeographically distinct: an analysis of metagenomically-derived mcrA sequences.}, journal = {Environmental microbiology}, volume = {24}, number = {9}, pages = {4065-4078}, pmid = {35437913}, issn = {1462-2920}, mesh = {Animals ; Archaea/metabolism ; Coal/microbiology ; *Euryarchaeota/genetics ; *Greenhouse Gases/metabolism ; Methane/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Soil ; }, abstract = {The production of methane as an end-product of organic matter degradation in the absence of other terminal electron acceptors is common, and has often been studied in environments such as animal guts, soils and wetlands due to its potency as a greenhouse gas. To date, however, the study of the biogeographic distribution of methanogens across coal seam environments has been minimal. Here, we show that coal seams are host to a diverse range of methanogens, which are distinctive to each geological basin. Based on comparisons to close relatives from other methanogenic environments, the dominant methanogenic pathway in these basins is hydrogenotrophic, with acetoclastic being a second major pathway in the Surat Basin. Finally, mcrA and 16S rRNA gene primer biases were predominantly seen to affect the detection of Methanocellales, Methanomicrobiales and Methanosarcinales taxa in this study. Subsurface coal methanogenic community distributions and pathways presented here provide insights into important metabolites and bacterial partners for in situ coal biodegradation.}, }
@article {pmid35422794, year = {2022}, author = {Kamruzzaman, M and Yan, A and Castro-Escarpulli, G}, title = {Editorial: CRISPR-Cas Systems in Bacteria and Archaea.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {887778}, pmid = {35422794}, issn = {1664-302X}, }
@article {pmid35420474, year = {2022}, author = {He, W and Gao, H and Wu, D and Jiang, S and Huang, W and Chen, C and Deng, Z and Xiong, L and Wu, G and Wang, L}, title = {Structural and Functional Analysis of DndE Involved in DNA Phosphorothioation in the Haloalkaliphilic Archaea Natronorubrum bangense JCM10635.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0071622}, pmid = {35420474}, issn = {2150-7511}, mesh = {DNA/metabolism ; DNA, Bacterial/metabolism ; *DNA, Superhelical/metabolism ; Escherichia coli/genetics/metabolism ; *Halobacteriaceae/genetics/metabolism ; Oxygen/metabolism ; Sulfur/metabolism ; }, abstract = {Phosphorothioate (PT) modification, a sequence-specific modification that replaces the nonbridging oxygen atom with sulfur in a DNA phosphodiester through the gene products of dndABCDE or sspABCD, is widely distributed in prokaryotes. DNA PT modification functions together with gene products encoded by dndFGH, pbeABCD, or sspE to form defense systems that can protect against invasion by exogenous DNA particles. While the functions of the multiple enzymes in the PT system have been elucidated, the exact role of DndE in the PT process is still obscure. Here, we solved the crystal structure of DndE from the haloalkaliphilic archaeal strain Natronorubrum bangense JCM10635 at a resolution of 2.31 Å. Unlike the tetrameric conformation of DndE in Escherichia coli B7A, DndE from N. bangense JCM10635 exists in a monomeric conformation and can catalyze the conversion of supercoiled DNA to nicked or linearized products. Moreover, DndE exhibits preferential binding affinity to nicked DNA by virtue of the R19- and K23-containing positively charged surface. This work provides insight into how DndE functions in PT modification and the potential sulfur incorporation mechanism of DNA PT modification. IMPORTANCE DndABCDE proteins have been demonstrated to catalyze DNA PT modification with the nonbridging oxygen in the DNA sugar-phosphate backbone replaced by sulfur. In the PT modification pathway, DndA exerts cysteine desulfurase activity capable of catalyzing the mobilization of sulfur from l-cysteine, which involves the ion-sulfur cluster assembly of DndC. This is regarded as the initial step of the DNA PT modification. Moreover, DndD has ATPase activity in vitro, which is believed to provide energy for the oxygen-sulfur swap, while the function of DndE is unknown. However, the exact function of the key enzyme DndE remains to be elucidated. By determining the structure of DndE from the haloalkaliphilic strain Natronorubrum bangense JCM10635, we showed that the archaeal DndE adopts a monomer conformation. Notably, DndE can introduce nicks to supercoiled DNA and exhibits a binding preference for nicked DNA; the nicking is believed to be the initial step for DNA to facilitate the sulfur incorporation.}, }
@article {pmid35408816, year = {2022}, author = {Huang, C and Liu, X and Chen, Y and Zhou, J and Li, W and Ding, N and Huang, L and Chen, J and Zhang, Z}, title = {A Novel Family of Winged-Helix Single-Stranded DNA-Binding Proteins from Archaea.}, journal = {International journal of molecular sciences}, volume = {23}, number = {7}, pages = {}, pmid = {35408816}, issn = {1422-0067}, support = {2020YFA0906800//National Key R&amp;D Program of China/ ; 32170050//National Natural Science Foundation of China/ ; 92051109//National Natural Science Foundation of China/ ; }, mesh = {Archaea/metabolism ; DNA/chemistry ; DNA, Single-Stranded ; *DNA-Binding Proteins/metabolism ; *Sulfolobus/genetics ; }, abstract = {The winged helix superfamily comprises a large number of structurally related nucleic acid-binding proteins. While these proteins are often shown to bind dsDNA, few are known to bind ssDNA. Here, we report the identification and characterization of Sul7s, a novel winged-helix single-stranded DNA binding protein family highly conserved in Sulfolobaceae. Sul7s from Sulfolobus islandicus binds ssDNA with an affinity approximately 15-fold higher than that for dsDNA in vitro. It prefers binding oligo(dT)30 over oligo(dC)30 or a dG-rich 30-nt oligonucleotide, and barely binds oligo(dA)30. Further, binding by Sul7s inhibits DNA strand annealing, but shows little effect on the melting temperature of DNA duplexes. The solution structure of Sul7s determined by NMR shows a winged helix-turn-helix fold, consisting of three α-helices, three β-strands, and two short wings. It interacts with ssDNA via a large positively charged binding surface, presumably resulting in ssDNA deformation. Our results shed significant light on not only non-OB fold single-stranded DNA binding proteins in Archaea, but also the divergence of the winged-helix proteins in both function and structure during evolution.}, }
@article {pmid35405221, year = {2022}, author = {Yang, P and Tang, KW and Tong, C and Lai, DYF and Wu, L and Yang, H and Zhang, L and Tang, C and Hong, Y and Zhao, G}, title = {Changes in sediment methanogenic archaea community structure and methane production potential following conversion of coastal marsh to aquaculture ponds.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {305}, number = {}, pages = {119276}, doi = {10.1016/j.envpol.2022.119276}, pmid = {35405221}, issn = {1873-6424}, mesh = {Aquaculture ; Archaea ; Ecosystem ; Methane ; *Ponds ; *Wetlands ; }, abstract = {Widespread conversion of coastal wetlands into aquaculture ponds in coastal region often results in degradation of the wetland ecosystems, but its effects on sediment's potential to produce greenhouse gases remain unclear. Using field sampling, incubation experiments and molecular analysis, we studied the sediment CH4 production potential and the relevant microbial communities in a brackish marsh and the nearby aquaculture ponds in the Min River Estuary in southeastern China. Sediment CH4 production potential was higher in the summer and autumn months than in spring and winter months, and it was significantly correlated with sediment carbon content among all environmental variables. The mean sediment CH4 production potential in the aquaculture ponds (20.1 ng g[-1] d[-1]) was significantly lower than that in the marsh (45.2 ng g[-1] d[-1]). While Methanobacterium dominated in both habitats (41-59%), the overall composition of sediment methanogenic archaea communities differed significantly between the two habitats (p < 0.05) and methanogenic archaea alpha diversity was lower in the aquaculture ponds (p < 0.01). Network analysis revealed that interactions between sediment methanogenic archaea were much weaker in the ponds than in the marsh. Overall, these findings suggest that conversion of marsh land to aquaculture ponds significantly altered the sediment methanogenic archaea community structure and diversity and lowered the sediment's capacity to produce CH4.}, }
@article {pmid35402889, year = {2022}, author = {Al-Ajeel, S and Spasov, E and Sauder, LA and McKnight, MM and Neufeld, JD}, title = {Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems.}, journal = {Water research X}, volume = {15}, number = {}, pages = {100131}, pmid = {35402889}, issn = {2589-9147}, abstract = {Nitrification, the oxidation of ammonia to nitrate via nitrite, is important for many engineered water treatment systems. The sequential steps of this respiratory process are carried out by distinct microbial guilds, including ammonia-oxidizing bacteria (AOB) and archaea (AOA), nitrite-oxidizing bacteria (NOB), and newly discovered members of the genus Nitrospira that conduct complete ammonia oxidation (comammox). Even though all of these nitrifiers have been identified within water treatment systems, their relative contributions to nitrogen cycling are poorly understood. Although AOA contribute to nitrification in many wastewater treatment plants, they are generally outnumbered by AOB. In contrast, AOA and comammox Nitrospira typically dominate relatively low ammonia environments such as drinking water treatment, tertiary wastewater treatment systems, and aquaculture/aquarium filtration. Studies that focus on the abundance of ammonia oxidizers may misconstrue the actual role that distinct nitrifying guilds play in a system. Understanding which ammonia oxidizers are active is useful for further optimization of engineered systems that rely on nitrifiers for ammonia removal. This review highlights known distributions of AOA and comammox Nitrospira in engineered water treatment systems and suggests future research directions that will help assess their contributions to nitrification and identify factors that influence their distributions and activity.}, }
@article {pmid35384236, year = {2022}, author = {Vuong, P and Moreira-Grez, B and Wise, MJ and Whiteley, AS and Kumaresan, D and Kaur, P}, title = {From rags to enriched: metagenomic insights into ammonia-oxidizing archaea following ammonia enrichment of a denuded oligotrophic soil ecosystem.}, journal = {Environmental microbiology}, volume = {24}, number = {7}, pages = {3097-3110}, pmid = {35384236}, issn = {1462-2920}, mesh = {*Ammonia/metabolism ; *Archaea/metabolism ; Bacteria ; Ecosystem ; Metagenome ; Nitrification ; Nitrogen/metabolism ; Oxidation-Reduction ; Soil ; Soil Microbiology ; }, abstract = {Stored topsoil acts as a microbial inoculant for ecological restoration of land after disturbance, but the altered circumstances frequently create unfavourable conditions for microbial survival. Nitrogen cycling is a critical indicator for ecological success and this study aimed to investigate the cornerstone taxa driving the process. Previous in silico studies investigating stored topsoil discovered persistent archaeal taxa with the potential for re-establishing ecological activity. Ammonia oxidization is the limiting step in nitrification and as such, ammonia-oxidizing archaea (AOA) can be considered one of the gatekeepers for the re-establishment of the nitrogen cycle in disturbed soils. Semi-arid soil samples were enriched with ammonium sulfate to promote the selective enrichment of ammonia oxidizers for targeted genomic recovery, and to investigate the microbial response of the microcosm to nitrogen input. Ammonia addition produced an increase in AOA population, particularly within the genus Candidatus Nitrosotalea, from which metagenome-assembled genomes (MAGs) were successfully recovered. The Ca. Nitrosotalea archaeon candidates' ability to survive in extreme conditions and rapidly respond to ammonia input makes it a potential bioprospecting target for application in ecological restoration of semi-arid soils and the recovered MAGs provide a metabolic blueprint for developing potential strategies towards isolation of these acclimated candidates.}, }
@article {pmid35380107, year = {2022}, author = {Gupta, D and Shalvarjian, KE and Nayak, DD}, title = {An Archaea-specific c-type cytochrome maturation machinery is crucial for methanogenesis in Methanosarcina acetivorans.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35380107}, issn = {2050-084X}, mesh = {*Archaea/metabolism ; Cytochromes/metabolism ; Electron Transport/genetics ; Methane/metabolism ; *Methanosarcina/genetics ; }, abstract = {c-Type cytochromes (cyt c) are proteins that undergo post-translational modification to covalently bind heme, which allows them to facilitate redox reactions in electron transport chains across all domains of life. Genomic evidence suggests that cyt c are involved in electron transfer processes among the Archaea, especially in members that produce or consume the potent greenhouse gas methane. However, neither the maturation machinery for cyt c in Archaea nor their role in methane metabolism has ever been functionally characterized. Here, we have used CRISPR-Cas9 genome editing tools to map a distinct pathway for cyt c biogenesis in the model methanogenic archaeon Methanosarcina acetivorans, and have also identified substrate-specific functional roles for cyt c during methanogenesis. Although the cyt c maturation machinery from M. acetivorans is universally conserved in the Archaea, our evolutionary analyses indicate that different clades of Archaea acquired this machinery through multiple independent horizontal gene transfer events from different groups of Bacteria. Overall, we demonstrate the convergent evolution of a novel Archaea-specific cyt c maturation machinery and its physiological role during methanogenesis, a process which contributes substantially to global methane emissions.}, }
@article {pmid35369442, year = {2022}, author = {Thirumalaisamy, G and Malik, PK and Trivedi, S and Kolte, AP and Bhatta, R}, title = {Effect of Long-Term Supplementation With Silkworm Pupae Oil on the Methane Yield, Ruminal Protozoa, and Archaea Community in Sheep.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {780073}, pmid = {35369442}, issn = {1664-302X}, abstract = {Supplementation with lipids and oils is one of the most efficient strategies for reducing enteric methane emission. However, high costs and adverse impacts on fiber degradation restrict the use of conventional oils. Silkworm pupae, a non-conventional oil source rarely used for human consumption in India, could be one of the cheaper alternatives for methane mitigation. The objective of this study was to investigate the effect on sheep of long-term supplementation (180 days) of silkworm pupae oil (SWPO) with two distinct supplementation regimes (daily and biweekly) on daily enteric methane emission, methane yield, nutrient digestibility, rumen fermentation, ruminal archaea community composition, and protozoal population. The effect of the discontinuation of oil supplementation on enteric methane emission was also investigated. Eighteen adult male sheep, randomly divided into three groups (n = 6), were provisioned with a mixed diet consisting of 10.1% crude protein (CP) and 11.7 MJ/kg metabolizable energy formulated using finger millet straw and concentrate in a 55:45 ratio. SWPO was supplemented at 2% of dry matter intake (DMI) in test groups either daily (CON) or biweekly (INT), while no oil was supplemented in the control group (CTR). DMI (p = 0.15) and CP (p = 0.16) in the CON and INT groups were similar to that of the CTR group; however, the energy intake (MJ/kg) in the supplemented groups (CON and INT) was higher (p < 0.001) than in CTR. In the CON group, body weight gain (kg, p = 0.02) and average daily gain (g, p = 0.02) were both higher than in the CTR. The daily methane emission in the CON (17.5 g/day) and INT (18.0 g/day) groups was lower (p = 0.01) than the CTR group (23.6 g/day), indicating a reduction of 23-25% due to SWPO supplementation. Similarly, compared with the CTR group, methane yields (g/kg DMI) in test groups were also significantly lower (p < 0.01). The transient nature of the anti-methanogenic effect of SWPO was demonstrated in the oil discontinuation study, where daily methane emission reverted to pre-supplementation levels after a short period. The recorded methanogens were affiliated to the families Methanobacteriaceae, Methanomassilliicoccaceae, and Methanosarcinaceae. The long-term supplementation of oil did not induce any significant change in the rumen archaeal community, whereas minor species such as Group3b exhibited differing abundance among the groups. Methanobrevibacter, irrespective of treatment, was the largest genus, while Methanobrevibacter gottschalkii was the dominant species. Oil supplementation in CON and INT compared with CTR decreased (p < 0.01) the numbers of total protozoa (× 10[7] cells/ml), Entodiniomorphs (× 10[7] cells/ml), and Holotrichs (× 10[6] cells/ml). SWPO continuous supplementation (CON group) resulted in the largest reduction in enteric methane emission and relatively higher body weight gain (p = 0.02) in sheep.}, }
@article {pmid38818328, year = {2022}, author = {Wang, Y and Xie, R and Hou, J and Lv, Z and Li, L and Hu, Y and Huang, H and Wang, F}, title = {The late Archaean to early Proterozoic origin and evolution of anaerobic methane-oxidizing archaea.}, journal = {mLife}, volume = {1}, number = {1}, pages = {96-100}, pmid = {38818328}, issn = {2770-100X}, abstract = {Microorganisms, called anaerobic methane-oxidizing archaea (ANME), can reduce a large amount of greenhouse gas methane and therefore have the potential to cool the Earth. We collected nearly all ANMEs genomes in public databases and performed a comprehensive comparative genomic analysis and molecular dating. Our results show that ANMEs originated in the late Archaean to early Proterozoic eon. During this period of time, our planet Earth was experiencing the Great Oxygenation Event and Huronian Glaciation, a dramatic drop in the Earth's surface temperature. This suggests that the emergence of ANMEs may contribute to the reduction of methane at that time, which is an unappreciated potential cause that led to the Huronian Glaciation.}, }
@article {pmid35347497, year = {2022}, author = {Yuan, B and Wu, W and Yue, S and Zou, P and Yang, R and Zhou, X}, title = {Community structure, distribution pattern, and influencing factors of soil Archaea in the construction area of a large-scale photovoltaic power station.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {25}, number = {3}, pages = {571-586}, pmid = {35347497}, issn = {1618-1905}, support = {51979222//National Natural Science Foundation of China/ ; }, mesh = {*Archaea/genetics ; Humans ; *Microbiota ; RNA, Ribosomal, 16S ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The photovoltaic power station in Qinghai has been built for 8 years; however, its impact on the regional soil ecological environment has not been studied in depth. To reveal the structure and distribution pattern of archaeal communities in desert soil under the influence of a large photovoltaic power station, a comparative study was carried out between the soil affected by photovoltaic panels and the bare land samples outside the photovoltaic station in Gonghe, Qinghai Province. The abundance, community structure, diversity, and distribution characteristics of archaea were analyzed by quantitative PCR and Illumina-MiSeq high-throughput sequencing, and the main environmental factors affecting the variation in soil archaeal community were identified by RDA. The contribution rate of environmental factors and human factors to microbial community diversity was quantitatively evaluated by VPA. The results showed that there was no significant difference in soil nutrients and other physicochemical factors between the photovoltaic power station and bare land. Thaumarchaeota was the dominant archaeal phylum in the area, accounting for more than 99% of archaeal phylum, while at the level of genus, Nitrososphaera was the dominant archaeal genera. There was no significant difference in archaeal community structure between and under different types of PV panels. The analysis has shown that the construction of a photovoltaic station has little effect on the community structure of soil archaea in a desert area, and it was speculated that the selection of niche played a leading role in the distribution pattern of soil archaeal community. This study provides the basis for a scientific understanding of the characteristics and distribution patterns of soil archaeal communities affected by the construction of a photovoltaic power station.}, }
@article {pmid35340443, year = {2022}, author = {Schiller, H and Young, C and Schulze, S and Tripepi, M and Pohlschroder, M}, title = {A Twist to the Kirby-Bauer Disk Diffusion Susceptibility Test: an Accessible Laboratory Experiment Comparing Haloferax volcanii and Escherichia coli Antibiotic Susceptibility to Highlight the Unique Cell Biology of Archaea.}, journal = {Journal of microbiology &amp; biology education}, volume = {23}, number = {1}, pages = {}, pmid = {35340443}, issn = {1935-7877}, abstract = {Archaea, once thought to only live in extreme environments, are present in many ecosystems, including the human microbiome, and they play important roles ranging from nutrient cycling to bioremediation. Yet this domain is often overlooked in microbiology classes and rarely included in laboratory exercises. Excluding archaea from high school and undergraduate curricula prevents students from learning the uniqueness and importance of this domain. Here, we have modified a familiar and popular microbiology experiment-the Kirby-Bauer disk diffusion antibiotic susceptibility test-to include, together with the model bacterium Escherichia coli, the model archaeon Haloferax volcanii. Students will learn the differences and similarities between archaea and bacteria by using antibiotics that target, for example, the bacterial peptidoglycan cell wall or the ribosome. Furthermore, the experiment provides a platform to reiterate basic cellular biology concepts that students may have previously discussed. We have developed two versions of this experiment, one designed for an undergraduate laboratory curriculum and the second, limited to H. volcanii, that high school students can perform in their classrooms. This nonpathogenic halophile can be cultured aerobically at ambient temperature in high-salt media, preventing contamination, making the experiment low-cost and safe for use in the high school setting.}, }
@article {pmid35336099, year = {2022}, author = {Cisek, AA and Bąk, I and Stefańska, I and Binek, M}, title = {Selection and Optimization of High-Yielding DNA Isolation Protocol for Quantitative Analyses of Methanogenic Archaea.}, journal = {Microorganisms}, volume = {10}, number = {3}, pages = {}, pmid = {35336099}, issn = {2076-2607}, support = {2017/25/N/NZ7/02905//National Science Center/ ; }, abstract = {Methanogenic archaea are a functionally important component of the intestinal microbiota of humans and animals, participating in the utilization of detrimental hydrogen produced during gut fermentation. Despite this, archaeal DNA has rarely been found in intestinal microbiome analyses, which prompts the need to optimize detecting procedures of these microorganisms, including the DNA isolation step. Three commercially available kits for DNA isolation and one extra purification kit that removes PCR inhibitors were evaluated on chicken droppings. In addition, different variants of mechanical lysis and a double elution were tested to ensure the maximum efficiency of DNA isolation from archaea as well as bacteria. A quantitative real-time PCR was used to monitor the optimization progress. As a result, the combination of the selected Genomic Mini AX Bacteria+ kit with a 2-min-long sonication by ultrasonic probe and enzymatic pretreatment gave excellent extraction efficiency rates for DNA of methanogenic archaea (an approximate 50-fold increase compared to the standard enzymatic lysis described by the producer) and, at the same time, provided optimal protection of DNA extracted from bacteria susceptible to enzymatic lysis. The presented results indicate that the optimized protocol allows for highly efficient extraction of total DNA, which is well-suited for quantitative microbial analyses by real-time PCR.}, }
@article {pmid35323924, year = {2022}, author = {Klein, T and Poghosyan, L and Barclay, JE and Murrell, JC and Hutchings, MI and Lehtovirta-Morley, LE}, title = {Cultivation of ammonia-oxidising archaea on solid medium.}, journal = {FEMS microbiology letters}, volume = {369}, number = {1}, pages = {}, pmid = {35323924}, issn = {1574-6968}, support = {BBS/E/J/000PR9790/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Agar ; *Ammonia ; *Archaea/genetics ; Culture Media ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; }, abstract = {Ammonia-oxidising archaea (AOA) are environmentally important microorganisms involved in the biogeochemical cycling of nitrogen. Routine cultivation of AOA is exclusively performed in liquid cultures and reports on their growth on solid medium are scarce. The ability to grow AOA on solid medium would be beneficial for not only the purification of enrichment cultures but also for developing genetic tools. The aim of this study was to develop a reliable method for growing individual colonies from AOA cultures on solid medium. Three phylogenetically distinct AOA strains were tested: 'Candidatus Nitrosocosmicus franklandus C13', Nitrososphaera viennensis EN76 and 'Candidatus Nitrosotalea sinensis Nd2'. Of the gelling agents tested, agar and Bacto-agar severely inhibited growth of all three strains. In contrast, both 'Ca. N. franklandus C13' and N. viennensis EN76 tolerated Phytagel™ while the acidophilic 'Ca. N. sinensis Nd2' was completely inhibited. Based on these observations, we developed a Liquid-Solid (LS) method that involves immobilising cells in Phytagel™ and overlaying with liquid medium. This approach resulted in the development of visible distinct colonies from 'Ca. N. franklandus C13' and N. viennensis EN76 cultures and lays the groundwork for the genetic manipulation of this group of microorganisms.}, }
@article {pmid38818326, year = {2022}, author = {Da Cunha, V and Gaïa, M and Forterre, P}, title = {The expanding Asgard archaea and their elusive relationships with Eukarya.}, journal = {mLife}, volume = {1}, number = {1}, pages = {3-12}, pmid = {38818326}, issn = {2770-100X}, abstract = {The discovery of Asgard archaea and the exploration of their diversity over the last 6 years have deeply impacted the scientific community working on eukaryogenesis, rejuvenating an intense debate on the topology of the universal tree of life (uTol). Here, we discuss how this debate is impacted by two recent publications that expand the number of Asgard lineages and eukaryotic signature proteins (ESPs). We discuss some of the main difficulties that can impair the phylogenetic reconstructions of the uTol and suggest that the debate about its topology is not settled. We notably hypothesize the existence of horizontal gene transfers between ancestral Asgards and proto-eukaryotes that could result in the observed abnormal behaviors of some Asgard ESPs and universal marker proteins. This hypothesis is relevant regardless of the scenario considered regarding eukaryogenesis. It implies that the Asgards were already diversified before the last eukaryotic common ancestor and shared the same biotopes with proto-eukaryotes. We suggest that some Asgards might be still living in symbiosis today with modern Eukarya.}, }
@article {pmid35276174, year = {2022}, author = {Wang, JT and Zhang, YB and Xiao, Q and Zhang, LM}, title = {Archaea is more important than bacteria in driving soil stoichiometry in phosphorus deficient habitats.}, journal = {The Science of the total environment}, volume = {827}, number = {}, pages = {154417}, doi = {10.1016/j.scitotenv.2022.154417}, pmid = {35276174}, issn = {1879-1026}, mesh = {*Archaea ; Bacteria ; Forests ; *Microbiota ; Nitrogen/analysis ; Phosphorus/analysis ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Phosphorus deficiency is a critical limit on the cycling of carbon (C), nitrogen (N) and phosphorus (P) in forest ecosystems. Despite the pivotal roles of microbes in driving the biogeochemical cycling of C/N/P, our knowledge on the relationships of soil bacteria and archaea to P deficiency in forest ecosystems remains scarce. Here, we studied 110 acidic soils (average pH 4.5) collected across 700-km subtropical forests with a gradient of available phosphorus (AP) ranging from 0.21 to 17.6 mg/kg. We analyzed the soil C/N/P stoichiometry and studied soil bacterial and archaeal diversity/abundance via high throughput sequencing and qPCR approaches. Our results show that soil P decoupled with N or C when below 3 mg/kg but coupled with C and N when above 3 mg/kg. Archaeal diversity and abundance were significantly higher in low AP (< 3 mg/kg) soils than in high AP (>3 mg/kg) soils, while bacterial were less changed. Compared with bacteria, archaea are more strongly related with soil stoichiometry (C:N, C:P, N:P), especially when AP was less than 3 mg/kg. Taxonomic and functional composition analysis further confirmed that archaeal rather than bacterial taxonomic composition was significantly related with functional composition of microbial communities. Taken together, our results show that archaea are more important than bacteria in driving soil stoichiometry in phosphorus deficient habitats and suggest a niche differentiation of soil bacteria and archaea in regulating the soil C/N/P cycling in subtropical forests.}, }
@article {pmid35270425, year = {2022}, author = {Xu, A and Li, L and Xie, J and Gopalakrishnan, S and Zhang, R and Luo, Z and Cai, L and Liu, C and Wang, L and Anwar, S and Jiang, Y}, title = {Changes in Ammonia-Oxidizing Archaea and Bacterial Communities and Soil Nitrogen Dynamics in Response to Long-Term Nitrogen Fertilization.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {5}, pages = {}, pmid = {35270425}, issn = {1660-4601}, mesh = {*Ammonia/metabolism ; *Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Fertilization ; Fertilizers ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Ammonia oxidizing archaea (AOA) and bacteria (AOB) mediate a crucial step in nitrogen (N) metabolism. The effect of N fertilizer rates on AOA and AOB communities is less studied in the wheat-fallow system from semi-arid areas. Based on a 17-year wheat field experiment, we explored the effect of five N fertilizer rates (0, 52.5, 105, 157.5, and 210 kg ha[-1] yr[-1]) on the AOA and AOB community composition. This study showed that the grain yield of wheat reached the maximum at 105 kg N ha[-1] (49% higher than control), and no further significant increase was observed at higher N rates. With the increase of N, AOA abundance decreased in a regular trend from 4.88 × 10[7] to 1.05 × 10[7] copies g[-1] dry soil, while AOB abundance increased from 3.63 × 10[7] up to a maximum of 8.24 × 10[7] copies g[-1] dry soil with the N105 treatment (105 kg N ha[-1] yr[-1]). Application rates of N fertilizer had a more significant impact on the AOB diversity than on AOA diversity, and the highest AOB diversity was found under the N105 treatment in this weak alkaline soil. The predominant phyla of AOA and AOB were Thaumarchaeota and Proteobacteria, respectively, and higher N treatment (N210) resulted in a significant decrease in the relative abundance of genus Nitrosospira. In addition, AOA and AOB communities were significantly associated with grain yield of wheat, soil potential nitrification activity (PNA), and some soil physicochemical parameters such as pH, NH4-N, and NO3-N. Among them, soil moisture was the most influential edaphic factor for structuring the AOA community and NH4-N for the AOB community. Overall, 105 kg N ha[-1] yr[-1] was optimum for the AOB community and wheat yield in the semi-arid area.}, }
@article {pmid35260828, year = {2022}, author = {Klotz, F and Kitzinger, K and Ngugi, DK and Büsing, P and Littmann, S and Kuypers, MMM and Schink, B and Pester, M}, title = {Quantification of archaea-driven freshwater nitrification from single cell to ecosystem levels.}, journal = {The ISME journal}, volume = {16}, number = {6}, pages = {1647-1656}, pmid = {35260828}, issn = {1751-7370}, support = {GRK 2272/1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Ammonia/metabolism ; *Archaea/genetics/metabolism ; Ecosystem ; Lakes ; *Nitrification ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Deep oligotrophic lakes sustain large populations of the class Nitrososphaeria (Thaumarchaeota) in their hypolimnion. They are thought to be the key ammonia oxidizers in this habitat, but their impact on N-cycling in lakes has rarely been quantified. We followed this archaeal population in one of Europe's largest lakes, Lake Constance, for two consecutive years using metagenomics and metatranscriptomics combined with stable isotope-based activity measurements. An abundant (8-39% of picoplankton) and transcriptionally active archaeal ecotype dominated the nitrifying community. It represented a freshwater-specific species present in major inland water bodies, for which we propose the name "Candidatus Nitrosopumilus limneticus". Its biomass corresponded to 12% of carbon stored in phytoplankton over the year´s cycle. Ca. N. limneticus populations incorporated significantly more ammonium than most other microorganisms in the hypolimnion and were driving potential ammonia oxidation rates of 6.0 ± 0.9 nmol l[‒1] d[‒1], corresponding to potential cell-specific rates of 0.21 ± 0.11 fmol cell[-1] d[-1]. At the ecosystem level, this translates to a maximum capacity of archaea-driven nitrification of 1.76 × 10[9] g N-ammonia per year or 11% of N-biomass produced annually by phytoplankton. We show that ammonia-oxidizing archaea play an equally important role in the nitrogen cycle of deep oligotrophic lakes as their counterparts in marine ecosystems.}, }
@article {pmid35246355, year = {2022}, author = {Ithurbide, S and Gribaldo, S and Albers, SV and Pende, N}, title = {Spotlight on FtsZ-based cell division in Archaea.}, journal = {Trends in microbiology}, volume = {30}, number = {7}, pages = {665-678}, doi = {10.1016/j.tim.2022.01.005}, pmid = {35246355}, issn = {1878-4380}, mesh = {*Archaea/metabolism ; *Bacteria/metabolism ; Bacterial Proteins/genetics/metabolism ; Cell Division ; Eukaryota/metabolism ; }, abstract = {Compared with the extensive knowledge on cell division in model eukaryotes and bacteria, little is known about how archaea divide. Interestingly, both endosomal sorting complex required for transport (ESCRT)-based and FtsZ-based cell division systems are found in members of the Archaea. In the past couple of years, several studies have started to shed light on FtsZ-based cell division processes in members of the Euryarchaeota. In this review we highlight recent findings in this emerging field of research. We present current knowledge of the cell division machinery of halophiles which relies on two FtsZ proteins, and we compare it with that of methanobacteria, which relies on only one FtsZ. Finally, we discuss how these differences relate to the distinct cell envelopes of these two archaeal model systems.}, }
@article {pmid35221208, year = {2023}, author = {Stevens, KM and Warnecke, T}, title = {Histone variants in archaea - An undiscovered country.}, journal = {Seminars in cell &amp; developmental biology}, volume = {135}, number = {}, pages = {50-58}, doi = {10.1016/j.semcdb.2022.02.016}, pmid = {35221208}, issn = {1096-3634}, support = {MC_UP_1102/7/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Histones/genetics ; *Archaea/genetics/chemistry ; Nucleosomes/genetics ; Chromatin ; Eukaryotic Cells ; }, abstract = {Exchanging core histones in the nucleosome for paralogous variants can have important functional ramifications. Many of these variants, and their physiological roles, have been characterized in exquisite detail in model eukaryotes, including humans. In comparison, our knowledge of histone biology in archaea remains rudimentary. This is true in particular for our knowledge of histone variants. Many archaea encode several histone genes that differ in sequence, but do these paralogs make distinct, adaptive contributions to genome organization and regulation in a manner comparable to eukaryotes? Below, we review what we know about histone variants in archaea at the level of structure, regulation, and evolution. In all areas, our knowledge pales when compared to the wealth of insight that has been gathered for eukaryotes. Recent findings, however, provide tantalizing glimpses into a rich and largely undiscovered country that is at times familiar and eukaryote-like and at times strange and uniquely archaeal. We sketch a preliminary roadmap for further exploration of this country; an undertaking that may ultimately shed light not only on chromatin biology in archaea but also on the origin of histone-based chromatin in eukaryotes.}, }
@article {pmid35220398, year = {2022}, author = {Yin, X and Zhou, G and Cai, M and Zhu, QZ and Richter-Heitmann, T and Aromokeye, DA and Liu, Y and Nimzyk, R and Zheng, Q and Tang, X and Elvert, M and Li, M and Friedrich, MW}, title = {Catabolic protein degradation in marine sediments confined to distinct archaea.}, journal = {The ISME journal}, volume = {16}, number = {6}, pages = {1617-1626}, pmid = {35220398}, issn = {1751-7370}, support = {project-ID 49926684//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; project-ID 390741601//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; No. 2018M633111//China Postdoctoral Science Foundation/ ; No. 91851105, 31622002, 31600093, and 31700430//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Archaea/genetics/metabolism ; Carbon/metabolism ; *Geologic Sediments ; Peptide Hydrolases/metabolism ; Phylogeny ; Proteolysis ; RNA, Ribosomal, 16S/metabolism ; }, abstract = {Metagenomic analysis has facilitated prediction of a variety of carbon utilization potentials by uncultivated archaea including degradation of protein, which is a wide-spread carbon polymer in marine sediments. However, the activity of detrital catabolic protein degradation is mostly unknown for the vast majority of archaea. Here, we show actively executed protein catabolism in three archaeal phyla (uncultivated Thermoplasmata, SG8-5; Bathyarchaeota subgroup 15; Lokiarchaeota subgroup 2c) by RNA- and lipid-stable isotope probing in incubations with different marine sediments. However, highly abundant potential protein degraders Thermoprofundales (MBG-D) and Lokiarchaeota subgroup 3 were not incorporating [13]C-label from protein during incubations. Nonetheless, we found that the pathway for protein utilization was present in metagenome associated genomes (MAGs) of active and inactive archaea. This finding was supported by screening extracellular peptidases in 180 archaeal MAGs, which appeared to be widespread but not correlated to organisms actively executing this process in our incubations. Thus, our results have important implications: (i) multiple low-abundant archaeal groups are actually catabolic protein degraders; (ii) the functional role of widespread extracellular peptidases is not an optimal tool to identify protein catabolism, and (iii) catabolic degradation of sedimentary protein is not a common feature of the abundant archaeal community in temperate and permanently cold marine sediments.}, }
@article {pmid35189237, year = {2022}, author = {Li, M and He, H and Mi, T and Zhen, Y}, title = {Spatiotemporal dynamics of ammonia-oxidizing archaea and bacteria contributing to nitrification in sediments from Bohai Sea and South Yellow Sea, China.}, journal = {The Science of the total environment}, volume = {825}, number = {}, pages = {153972}, doi = {10.1016/j.scitotenv.2022.153972}, pmid = {35189237}, issn = {1879-1026}, mesh = {*Ammonia ; *Archaea/genetics ; Bacteria/genetics ; China ; Geologic Sediments/microbiology ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; }, abstract = {Nitrification is a central process in nitrogen cycle in the ocean. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play significant roles in ammonia oxidation which is the first and rate-limiting step in nitrification, and their differential contribution to nitrification is an important issue, attracting extensive attention. In this study, based on the quantification of archaeal and bacterial amoA gene and the measurement of potential nitrification rate (PNR), we investigated the spatiotemporal dynamics of PNRs and the amoA gene abundance and transcript abundance of aerobic ammonia oxidizers in surface sediments collected in summer and spring across ~900 km of the Bohai Sea and Yellow Sea in China. The results revealed that the contribution of AOA to nitrification was greater than that of AOB in coastal sediments, probably due to salinity and ammonia concentration. Besides, seasons had significant effect on amoA gene abundance and transcript abundance, especially for AOA, while both seasons and sea areas had significant influence on PNR of AOA and AOB. Further analysis showed complex relationships among amoA gene abundances, transcript abundances and PNRs. More importantly, both spatial (geographic distance) and environmental factors were vital in explaining the variations of ammonia-oxidizing microorganism abundances and the PNRs.}, }
@article {pmid35181078, year = {2022}, author = {Wei, W and Hu, X and Yang, S and Wang, K and Zeng, C and Hou, Z and Cui, H and Liu, S and Zhu, L}, title = {Denitrifying halophilic archaea derived from salt dominate the degradation of nitrite in salted radish during pickling.}, journal = {Food research international (Ottawa, Ont.)}, volume = {152}, number = {}, pages = {110906}, doi = {10.1016/j.foodres.2021.110906}, pmid = {35181078}, issn = {1873-7145}, mesh = {China ; Nitrates ; *Nitrites/metabolism ; Nitrogen/metabolism ; *Raphanus/chemistry ; }, abstract = {Salted radish is a popular high-salinity table food in China, and nitrite is always generated during the associated pickling process. However, this nitrite can be naturally degraded, and the underlying mechanism is unknown. Here, we identified the microbial groups that dominate the natural degradation of nitrite in salted radish and clarified the related metabolic mechanism. Based on dynamic monitoring of pH and the concentrations of nitrogen compounds as well as high-throughput sequencing analysis of the structural succession of microbial communities in the tested salted radish, we determined that the halophilic archaea derived from pickling salt dominate the natural degradation of nitrite via denitrification. Based on isolation, identification, nitrite reduction assays, and genome annotation, we further determined that Haloarcula, Halolamina, and Halobacterium were the key genera. These halophilic archaea might cope with high salt stress through the "salt-in" mechanism with the assistance of the accumulation of potassium ions, obtain electrons necessary for "truncated denitrification" from the metabolism of extracellular glucose absorbed from salted radish, and efficiently reduce nitrite to nitrogen, bypassing nitrite generation from nitrate reduction. The present study provides important information for the prevention and control of nitrite hazards in salted vegetables with high salinity, such as salted radish.}, }
@article {pmid35165305, year = {2022}, author = {Xu, B and Li, F and Cai, L and Zhang, R and Fan, L and Zhang, C}, title = {A holistic genome dataset of bacteria, archaea and viruses of the Pearl River estuary.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {49}, pmid = {35165305}, issn = {2052-4463}, support = {91951120//National Natural Science Foundation of China (National Science Foundation of China)/ ; 91851210//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Estuaries ; Genome ; *Microbiota/genetics ; Rivers ; *Viruses/genetics ; }, abstract = {Estuaries are one of the most important coastal ecosystems. While microbiomes and viromes have been separately investigated in some estuaries, few studies holistically deciphered the genomes and connections of viruses and their microbial hosts along an estuarine salinity gradient. Here we applied deep metagenomic sequencing on microbial and viral communities in surface waters of the Pearl River estuary, one of China's largest estuaries with strong anthropogenic impacts. Overall, 1,205 non-redundant prokaryotic genomes with ≥50% completeness and ≤10% contamination, and 78,502 non-redundant viral-like genomes were generated from samples of three size fractions and five salinity levels. Phylogenomic analysis and taxonomy classification show that majority of these estuarine prokaryotic and viral genomes are novel at species level according to public databases. Potential connections between the microbial and viral populations were further investigated by host-virus matching. These combined microbial and viral genomes provide an important complement of global marine genome datasets and should greatly facilitate our understanding of microbe-virus interactions, evolution and their implications in estuarine ecosystems.}, }
@article {pmid35165204, year = {2022}, author = {Schorn, S and Ahmerkamp, S and Bullock, E and Weber, M and Lott, C and Liebeke, M and Lavik, G and Kuypers, MMM and Graf, JS and Milucka, J}, title = {Diverse methylotrophic methanogenic archaea cause high methane emissions from seagrass meadows.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {9}, pages = {}, pmid = {35165204}, issn = {1091-6490}, mesh = {Aerobiosis ; Alismatales/*metabolism ; Anaerobiosis ; Euryarchaeota/classification/*metabolism ; Geologic Sediments ; Mediterranean Sea ; Methane/*metabolism ; Microbiota ; Oxidation-Reduction ; Phylogeny ; Species Specificity ; }, abstract = {Marine coastlines colonized by seagrasses are a net source of methane to the atmosphere. However, methane emissions from these environments are still poorly constrained, and the underlying processes and responsible microorganisms remain largely unknown. Here, we investigated methane turnover in seagrass meadows of Posidonia oceanica in the Mediterranean Sea. The underlying sediments exhibited median net fluxes of methane into the water column of ca. 106 µmol CH4 ⋅ m[-2] ⋅ d[-1] Our data show that this methane production was sustained by methylated compounds produced by the plant, rather than by fermentation of buried organic carbon. Interestingly, methane production was maintained long after the living plant died off, likely due to the persistence of methylated compounds, such as choline, betaines, and dimethylsulfoniopropionate, in detached plant leaves and rhizomes. We recovered multiple mcrA gene sequences, encoding for methyl-coenzyme M reductase (Mcr), the key methanogenic enzyme, from the seagrass sediments. Most retrieved mcrA gene sequences were affiliated with a clade of divergent Mcr and belonged to the uncultured Candidatus Helarchaeota of the Asgard superphylum, suggesting a possible involvement of these divergent Mcr in methane metabolism. Taken together, our findings identify the mechanisms controlling methane emissions from these important blue carbon ecosystems.}, }
@article {pmid35145493, year = {2021}, author = {Chen, S and Tao, J and Chen, Y and Wang, W and Fan, L and Zhang, C}, title = {Interactions Between Marine Group II Archaea and Phytoplankton Revealed by Population Correlations in the Northern Coast of South China Sea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {785532}, pmid = {35145493}, issn = {1664-302X}, abstract = {Marine Group II (MGII) archaea (Poseidoniales) are the most abundant surface marine planktonic archaea and are widely distributed in both coastal and pelagic waters. The factors affecting their distribution and activity are poorly understood. MGII archaea have the metabolic potential to utilize algae-derived organic matter and are frequently observed in high abundance during or following phytoplankton blooms, suggesting that they are key players of the marine food web. In this study, we studied interactions between MGII archaea and the diverse taxa of phytoplankton in the northern coast of South China Sea. Non-metric multidimensional scaling and cluster analyses demonstrated distinct MGII community patterns in the Pearl River plume (PRP) and the open regions of the northern South China Sea (ONSCS), with MGIIb dominating the former and MGIIa and MGIIb showing remarkable variations in the latter for the same sampling season. Nevertheless, positive correlations (Pearson correlation: R > 0.8 and P < 0.01) in absolute abundances of ribosomal RNA (rRNA)-derived complementary DNA and rRNA genes from network analyses were found between MGII archaea and phytoplankton (cyanobacteria, haptophytes, and stramenopiles in both PRP and ONSCS) among different particle size fractions, indicating their intrinsic relationships under changing environmental conditions. The results of this study may shed light on the multiple interactions between co-existing species in the micro-niches of different oceanic regions.}, }
@article {pmid35142133, year = {2022}, author = {Cui, L and Fan, X and Zheng, Y}, title = {[Enhanced heterologous expression of the cytochrome c from uncultured anaerobic methanotrophic archaea].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {38}, number = {1}, pages = {226-237}, doi = {10.13345/j.cjb.210193}, pmid = {35142133}, issn = {1872-2075}, mesh = {Anaerobiosis ; Archaea/metabolism ; *Cytochromes c/genetics/metabolism ; *Escherichia coli/genetics/metabolism ; Heme/metabolism ; }, abstract = {Cytochrome c is a type of heme proteins that are widely distributed in living organisms. It consists of heme and apocytochrome c, and has potential applications in bioelectronics, biomedicine and pollutant degradation. However, heterologous overexpression of cytochrome c is still challenging. To date, expression of the cytochrome c from uncultured anaerobic methanotrophic archaea has not been reported, and nothing is known about the function of this cytochrome c. A his tagged cytochrome c was successfully expressed in E. coli by introducing a thrombin at the N-terminus of CytC4 and co-expressing CcmABCDEFGH, which is responsible for the maturation of cytochrome c. Shewanella oneidensis, which naturally has enzymes for cytochrome c maturation, was then used as a host to further increase the expression of CytC4. Indeed, a significantly higher expression of CytC4 was achieved in S. oneidensis when compared with in E. coli. The successful heterologous overexpression of CytC4 will facilitate the exploitation of its physiological functions and biotechnological applications.}, }
@article {pmid35126338, year = {2021}, author = {Hedlund, BP and Zhang, C and Wang, F and Rinke, C and Martin, WF}, title = {Editorial: Ecology, Metabolism and Evolution of Archaea-Perspectives From Proceedings of the International Workshop on Geo-Omics of Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {827229}, pmid = {35126338}, issn = {1664-302X}, }
@article {pmid35101434, year = {2022}, author = {Liu, BB and Govindan, R and Muthuchamy, M and Cheng, S and Li, X and Ye, L and Wang, LY and Guo, SX and Li, WJ and Alharbi, NS and M Khaled, J and Kadaikunnan, S}, title = {Halophilic archaea and their extracellular polymeric compounds in the treatment of high salt wastewater containing phenol.}, journal = {Chemosphere}, volume = {294}, number = {}, pages = {133732}, doi = {10.1016/j.chemosphere.2022.133732}, pmid = {35101434}, issn = {1879-1298}, mesh = {Archaea/metabolism ; Extracellular Polymeric Substance Matrix/metabolism ; *Phenol/metabolism ; Phenols ; *Wastewater ; }, abstract = {Phenol is one of the major organic pollutants in high salt industrial wastewaters. The biological treatment of such waste using microorganisms is considered to be a cost-effective and eco-friendly method. However, in this process, salt tolerance of microorganisms is one of the main limiting factors. Halophilic microorganisms, especially halophilic archaea are thought to be appropriate for such treatment. To develop a novel effective biological method for high salt phenol wastewater treatment, the influence of phenol in high salt phenol wastewater on halophilic archaea and their extracellular polymeric substances (EPS) should be investigated. In the present study, using phenol enrichment method, 75 halophilic archaeal strains were isolated from Wuyongbulake salt lake sediment sample. The majority of the identified strains were phenol-tolerant. Six strains with high phenol tolerance were chosen, and the phenol scavenging effect was observed in the microbial suspension, supernatant, and EPS. It was noticed that the phenol degradation rate of suspensions of both strains 869-1, and 121-1 in salt water exhibited the highest rates of 83.7%, while the supernatant of strain 869-1 reached the highest rate of 78.2%. When combined with the comprehensive analysis of the artificial wastewater simulation experiment, it was discovered that in the artificial wastewater containing phenol, the phenol degradation rate of suspension of strain A387 exhibited the highest rates of 55.74% both, and supernatant of strain 630-3 reached the highest rate of 62.3%. The EPS produced by strains A00135, 558-1, 869-1, 121-1 and A387 removed 100% phenol within 96 h, and the phenol removal efficiency of EPS produced by 869-1 reached 56.1% under an artificial wastewater simulation experiment with high salt (15%NaCl) condition. The present study suggests that halophilic archaea and their EPS play an important role in phenol degradation. This approach could be potentially used for industrial high-salt wastewater treatment.}, }
@article {pmid35098330, year = {2023}, author = {Shen, LD and Geng, CY and Ren, BJ and Jin, JH and Huang, HC and Liu, X and Yang, WT and Yang, YL and Liu, JQ and Tian, MH}, title = {Detection and Quantification of Candidatus Methanoperedens-Like Archaea in Freshwater Wetland Soils.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {441-453}, pmid = {35098330}, issn = {1432-184X}, support = {41977037//National Natural Science Foundation of China/ ; BK20190092//Natural Science Foundation of Jiangsu Province/ ; }, mesh = {*Archaea/genetics ; *Wetlands ; Nitrates ; Soil ; Phylogeny ; Oxidation-Reduction ; Fresh Water ; Methane ; Water ; Iron ; Anaerobiosis ; }, abstract = {Candidatus Methanoperedens-like archaea, which can use multiple electron acceptors (nitrate, iron, manganese, and sulfate) for anaerobic methane oxidation, could play an important role in reducing methane emissions from freshwater wetlands. Currently, very little is known about the distribution and community composition of Methanoperedens-like archaea in freshwater wetlands, particularly based on their alpha subunit of methyl-coenzyme M reductase (mcrA) genes. Here, the community composition, diversity, and abundance of Methanoperedens-like archaea were investigated in a freshwater wetland through high-throughput sequencing and quantitative PCR on their mcrA genes. A large number of Methanoperedens-like mcrA gene sequences (119,250) were recovered, and a total of 31 operational taxonomic units (OTUs) were generated based on 95% sequence similarity cut-off. The majority of Methanoperedens-like sequences can be grouped into three distinct clusters that were closely associated with the known Methanoperedens species which can couple anaerobic methane oxidation to nitrate or iron reduction. The community composition of Methanoperedens-like archaea differed significantly among different sampling sites, and their mcrA gene abundance was 1.49 × 10[6] ~ 4.62 × 10[6] copies g[-1] dry soil in the examined wetland. In addition, the community composition of Methanoperedens-like archaea was significantly affected by the soil water content, and the archaeal abundance was significantly positively correlated with the water content. Our results suggest that the mcrA gene is a good biomarker for detection and quantification of Methanoperedens-like archaea, and provide new insights into the distribution and environmental regulation of these archaea in freshwater wetlands.}, }
@article {pmid35076275, year = {2022}, author = {Rasmussen, AN and Francis, CA}, title = {Genome-Resolved Metagenomic Insights into Massive Seasonal Ammonia-Oxidizing Archaea Blooms in San Francisco Bay.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0127021}, pmid = {35076275}, issn = {2379-5077}, mesh = {*Archaea ; *Ammonia ; Metagenomics ; Bays ; Metagenome ; San Francisco ; RNA, Ribosomal, 16S ; Seasons ; Nitrites ; Urease/genetics ; Oxidation-Reduction ; Geologic Sediments/microbiology ; Water ; Nitrogen ; }, abstract = {Ammonia-oxidizing archaea (AOA) are key for the transformation of ammonia to oxidized forms of nitrogen in aquatic environments around the globe, including nutrient-rich coastal and estuarine waters such as San Francisco Bay (SFB). Using metagenomics and 16S rRNA gene amplicon libraries, we found that AOA are more abundant than ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), except in the freshwater stations in SFB. In South SFB, we observed recurrent AOA blooms of "Candidatus Nitrosomarinus catalina" SPOT01-like organisms, which account for over 20% of 16S rRNA gene amplicons in both surface and bottom waters and co-occur with weeks of high nitrite concentrations (>10 μM) in the oxic water column. We observed pronounced nitrite peaks occurring in the autumn for 7 of the last 9 years (2012 to 2020), suggesting that seasonal AOA blooms are common in South SFB. We recovered two high-quality AOA metagenome-assembled genomes (MAGs), including a Nitrosomarinus-like genome from the South SFB bloom and another Nitrosopumilus genome originating from Suisun Bay in North SFB. Both MAGs cluster with genomes from other estuarine/coastal sites. Analysis of Nitrosomarinus-like genomes show that they are streamlined, with low GC content and high coding density, and harbor urease genes. Our findings support the unique niche of Nitrosomarinus-like organisms which dominate coastal/estuarine waters and provide insights into recurring AOA blooms in SFB. IMPORTANCE Ammonia-oxidizing archaea (AOA) carry out key transformations of ammonia in estuarine systems such as San Francisco Bay (SFB)-the largest estuary on the west coast of North America-and play a significant role in both local and global nitrogen cycling. Using metagenomics and 16S rRNA gene amplicon libraries, we document a massive, recurrent AOA bloom in South SFB that co-occurs with months of high nitrite concentrations in the oxic water column. Our study is the first to generate metagenome-assembled genomes (MAGs) from SFB, and through this process we recovered two high-quality AOA MAGs, one of which originated from bloom samples. These AOA MAGs yield new insight into the Nitrosopumilus and Nitrosomarinus-like lineages and their potential niches in coastal and estuarine systems. Nitrosomarinus-like AOA are abundant in coastal regions around the globe, and we highlight the common occurrence of urease genes, low GC content, and range of salinity tolerances within this lineage.}, }
@article {pmid35069467, year = {2021}, author = {Rodríguez-Gijón, A and Nuy, JK and Mehrshad, M and Buck, M and Schulz, F and Woyke, T and Garcia, SL}, title = {A Genomic Perspective Across Earth's Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {761869}, pmid = {35069467}, issn = {1664-302X}, abstract = {Our view of genome size in Archaea and Bacteria has remained skewed as the data has been dominated by genomes of microorganisms that have been cultivated under laboratory settings. However, the continuous effort to catalog Earth's microbiomes, specifically propelled by recent extensive work on uncultivated microorganisms, provides an opportunity to revise our perspective on genome size distribution. We present a meta-analysis that includes 26,101 representative genomes from 3 published genomic databases; metagenomic assembled genomes (MAGs) from GEMs and stratfreshDB, and isolates from GTDB. Aquatic and host-associated microbial genomes present on average the smallest estimated genome sizes (3.1 and 3.0 Mbp, respectively). These are followed by terrestrial microbial genomes (average 3.7 Mbp), and genomes from isolated microorganisms (average 4.3 Mbp). On the one hand, aquatic and host-associated ecosystems present smaller genomes sizes in genera of phyla with genome sizes above 3 Mbp. On the other hand, estimated genome size in phyla with genomes under 3 Mbp showed no difference between ecosystems. Moreover, we observed that when using 95% average nucleotide identity (ANI) as an estimator for genetic units, only 3% of MAGs cluster together with genomes from isolated microorganisms. Although there are potential methodological limitations when assembling and binning MAGs, we found that in genome clusters containing both environmental MAGs and isolate genomes, MAGs were estimated only an average 3.7% smaller than isolate genomes. Even when assembly and binning methods introduce biases, estimated genome size of MAGs and isolates are very similar. Finally, to better understand the ecological drivers of genome size, we discuss on the known and the overlooked factors that influence genome size in different ecosystems, phylogenetic groups, and trophic strategies.}, }
@article {pmid35052563, year = {2021}, author = {Neira, G and Vergara, E and Cortez, D and Holmes, DS}, title = {A Large-Scale Multiple Genome Comparison of Acidophilic Archaea (pH ≤ 5.0) Extends Our Understanding of Oxidative Stress Responses in Polyextreme Environments.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {11}, number = {1}, pages = {}, pmid = {35052563}, issn = {2076-3921}, support = {1181717//Fondecyt/ ; FB210008//Centro Ciencia &amp; Vida, Financiamiento Basal para Centros Cient&#xed;ficos y Tecnol&#xf3;gicos de Excelencia de ANID/ ; }, abstract = {Acidophilic archaea thrive in anaerobic and aerobic low pH environments (pH < 5) rich in dissolved heavy metals that exacerbate stress caused by the production of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), hydroxyl radical (·OH) and superoxide (O2[-]). ROS react with lipids, proteins and nucleic acids causing oxidative stress and damage that can lead to cell death. Herein, genes and mechanisms potentially involved in ROS mitigation are predicted in over 200 genomes of acidophilic archaea with sequenced genomes. These organisms are often be subjected to simultaneous multiple stresses such as high temperature, high salinity, low pH and high heavy metal loads. Some of the topics addressed include: (1) the phylogenomic distribution of these genes and what this can tell us about the evolution of these mechanisms in acidophilic archaea; (2) key differences in genes and mechanisms used by acidophilic versus non-acidophilic archaea and between acidophilic archaea and acidophilic bacteria and (3) how comparative genomic analysis predicts novel genes or pathways involved in oxidative stress responses in archaea and likely horizontal gene transfer (HGT) events.}, }
@article {pmid35049347, year = {2022}, author = {McMahon, FT and Lonergan, CM and Gilmore, BF and Megaw, J}, title = {Draft Genome Sequences of Halobacterium sp. Strains KA-4 and KA-6, Two Extremely Halophilic Archaea Isolated from a Triassic Salt Deposit in Northern Ireland.}, journal = {Microbiology resource announcements}, volume = {11}, number = {1}, pages = {e0116521}, pmid = {35049347}, issn = {2576-098X}, abstract = {Here, we report the draft genome sequences of Halobacterium sp. strains KA-4 and KA-6. These extremely halophilic archaea were isolated from a Triassic halite deposit in Northern Ireland. Based on 16S sequence identity, they were deemed to be closely related strains of Halobacterium noricense but with some notable phenotypic differences.}, }
@article {pmid37938653, year = {2022}, author = {Vigneron, A and Cruaud, P and Lovejoy, C and Vincent, WF}, title = {Genomic evidence of functional diversity in DPANN archaea, from oxic species to anoxic vampiristic consortia.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {4}, pmid = {37938653}, issn = {2730-6151}, abstract = {DPANN archaea account for half of the archaeal diversity of the biosphere, but with few cultivated representatives, their metabolic potential and environmental functions are poorly understood. The extreme geochemical and environmental conditions in meromictic ice-capped Lake A, in the Canadian High Arctic, provided an isolated, stratified model ecosystem to resolve the distribution and metabolism of uncultured aquatic DPANN archaea living across extreme redox and salinity gradients, from freshwater oxygenated conditions, to saline, anoxic, sulfidic waters. We recovered 28 metagenome-assembled genomes (MAGs) of DPANN archaea that provided genetic insights into their ecological function. Thiosulfate oxidation potential was detected in aerobic Woesearchaeota, whereas diverse metabolic functions were identified in anaerobic DPANN archaea, including degradation and fermentation of cellular compounds, and sulfide and polysulfide reduction. We also found evidence for "vampiristic" metabolism in several MAGs, with genes coding for pore-forming toxins, peptidoglycan degradation, and RNA scavenging. The vampiristic MAGs co-occurred with other DPANNs having complementary metabolic capacities, leading to the possibility that DPANN form interspecific consortia that recycle microbial carbon, nutrients and complex molecules through a DPANN archaeal shunt, adding hidden novel complexity to anaerobic microbial food webs.}, }
@article {pmid35040218, year = {2022}, author = {Papenfort, K and Woodson, SA and Schmitz, RA and Winkler, WC}, title = {Special Issue: Regulating with RNA in Microbes: In conjunction with the 6th Meeting on Regulating with RNA in Bacteria and Archaea.}, journal = {Molecular microbiology}, volume = {117}, number = {1}, pages = {1-3}, doi = {10.1111/mmi.14867}, pmid = {35040218}, issn = {1365-2958}, support = {R13 AI147570/AI/NIAID NIH HHS/United States ; R13 AI154714/AI/NIAID NIH HHS/United States ; }, mesh = {Archaea/*genetics/physiology ; Bacteria/*genetics ; Bacterial Physiological Phenomena ; Evolution, Molecular ; *RNA Processing, Post-Transcriptional ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Untranslated/*genetics ; RNA-Binding Proteins/genetics/*metabolism ; }, }
@article {pmid35027677, year = {2022}, author = {Wu, F and Speth, DR and Philosof, A and Crémière, A and Narayanan, A and Barco, RA and Connon, SA and Amend, JP and Antoshechkin, IA and Orphan, VJ}, title = {Unique mobile elements and scalable gene flow at the prokaryote-eukaryote boundary revealed by circularized Asgard archaea genomes.}, journal = {Nature microbiology}, volume = {7}, number = {2}, pages = {200-212}, pmid = {35027677}, issn = {2058-5276}, mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Bacteria/genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; *Gene Flow ; *Genome, Archaeal ; Metagenomics ; Phylogeny ; Prokaryotic Cells/*metabolism ; }, abstract = {Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. Bacterial gene import has thus likely been a continuous process unaltered by eukaryogenesis and scaled up through genome expansion. Our data further highlight the importance of viewing eukaryogenesis in a pan-Asgard context, which led to the proposal of a conceptual framework, that is, the Heimdall nucleation-decentralized innovation-hierarchical import model that accounts for the emergence of eukaryotic complexity.}, }
@article {pmid35022241, year = {2022}, author = {Sakai, HD and Nur, N and Kato, S and Yuki, M and Shimizu, M and Itoh, T and Ohkuma, M and Suwanto, A and Kurosawa, N}, title = {Insight into the symbiotic lifestyle of DPANN archaea revealed by cultivation and genome analyses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {3}, pages = {}, pmid = {35022241}, issn = {1091-6490}, mesh = {Archaea/classification/cytology/*genetics/*physiology ; Coculture Techniques ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Archaeal ; Genomics ; Nanoarchaeota ; Phylogeny ; Symbiosis/*genetics/*physiology ; }, abstract = {Decades of culture-independent analyses have resulted in proposals of many tentative archaeal phyla with no cultivable representative. Members of DPANN (an acronym of the names of the first included phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota, and Nanoarchaeota), an archaeal superphylum composed of at least 10 of these tentative phyla, are generally considered obligate symbionts dependent on other microorganisms. While many draft/complete genome sequences of DPANN archaea are available and their biological functions have been considerably predicted, only a few examples of their successful laboratory cultivation have been reported, limiting our knowledge of their symbiotic lifestyles. Here, we investigated physiology, morphology, and host specificity of an archaeon of the phylum "Candidatus Micrarchaeota" (ARM-1) belonging to the DPANN superphylum by cultivation. We constructed a stable coculture system composed of ARM-1 and its original host Metallosphaera sp. AS-7 belonging to the order Sulfolobales Further host-switching experiments confirmed that ARM-1 grew on five different archaeal species from three genera-Metallosphaera, Acidianus, and Saccharolobus-originating from geologically distinct hot, acidic environments. The results suggested the existence of DPANN archaea that can grow by relying on a range of hosts. Genomic analyses showed inferred metabolic capabilities, common/unique genetic contents of ARM-1 among cultivated micrarchaeal representatives, and the possibility of horizontal gene transfer between ARM-1 and members of the order Sulfolobales Our report sheds light on the symbiotic lifestyles of DPANN archaea and will contribute to the elucidation of their biological/ecological functions.}, }
@article {pmid35021862, year = {2022}, author = {Salter, TL and Magee, BA and Waite, JH and Sephton, MA}, title = {Mass Spectrometric Fingerprints of Bacteria and Archaea for Life Detection on Icy Moons.}, journal = {Astrobiology}, volume = {22}, number = {2}, pages = {143-157}, doi = {10.1089/ast.2020.2394}, pmid = {35021862}, issn = {1557-8070}, mesh = {Archaea ; Bacteria ; *Exobiology/methods ; Extraterrestrial Environment/chemistry ; Mass Spectrometry ; *Moon ; }, abstract = {The icy moons of the outer Solar System display evidence of subsurface liquid water and, therefore, potential habitability for life. Flybys of Saturn's moon Enceladus by the Cassini spacecraft have provided measurements of material from plumes that suggest hydrothermal activity and the presence of organic matter. Jupiter's moon Europa may have similar plumes and is the target for the forthcoming Europa Clipper mission that carries a high mass resolution and high sensitivity mass spectrometer, called the MAss Spectrometer for Planetary EXploration (MASPEX), with the capability for providing detailed characterization of any organic materials encountered. We have performed a series of experiments using pyrolysis-gas chromatography-mass spectrometry to characterize the mass spectrometric fingerprints of microbial life. A range of extremophile Archaea and Bacteria have been analyzed and the laboratory data converted to MASPEX-type signals. Molecular characteristics of protein, carbohydrate, and lipid structures were detected, and the characteristic fragmentation patterns corresponding to these different biological structures were identified. Protein pyrolysis fragments included phenols, nitrogen heterocycles, and cyclic dipeptides. Oxygen heterocycles, such as furans, were detected from carbohydrates. Our data reveal how mass spectrometry on Europa Clipper can aid in the identification of the presence of life, by looking for characteristic bacterial fingerprints that are similar to those from simple Earthly organisms.}, }
@article {pmid38716123, year = {2022}, author = {Kanno, N and Kato, S and Itoh, T and Ohkuma, M and Shigeto, S}, title = {Resonance Raman analysis of intracellular vitamin B12 analogs in methanogenic archaea.}, journal = {Analytical science advances}, volume = {3}, number = {5-6}, pages = {165-173}, pmid = {38716123}, issn = {2628-5452}, abstract = {Methanogenic archaea (methanogens) are microorganisms that can synthesize methane. They are found in diverse environments ranging from paddy fields to animal digestive tracts to deep-sea hydrothermal vents. Investigating their distribution and physiological activity is crucial for the detailed analysis of the dynamics of greenhouse gas generation and the search for the environmental limits of life. In methanogens, cobamide cofactors (vitamin B12 analogs) play a key role in methane synthesis and carbon fixation, thus serving as a marker compound that metabolically characterizes them. Here, we report on resonance Raman detection of cobamides in methanogenic cells without destroying cells and provide structural insights into those cobamides. We succeeded in detecting cobamides in four representative methanogens Methanosarcina mazei, Methanosarcina barkeri, Methanopyrus kandleri, and Methanocaldococcus jannaschii. The former two are mesophilic, cytochrome-containing methanogens, whereas the latter two are hyperthermophilic, non-cytochrome-containing methanogens. The 532 nm-excited Raman spectra of single or multiple cells of the four species all showed resonance Raman bands of cobamides arising mainly from the corrin ring, with the most intense one at ∼1500 cm[-1]. We envision that resonance Raman microspectroscopy could be useful for in situ, nondestructive identification of methanogenic cells that produce high levels of cobamides.}, }
@article {pmid34987183, year = {2022}, author = {Diamond, S and Lavy, A and Crits-Christoph, A and Matheus Carnevali, PB and Sharrar, A and Williams, KH and Banfield, JF}, title = {Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs).}, journal = {The ISME journal}, volume = {16}, number = {5}, pages = {1348-1362}, pmid = {34987183}, issn = {1751-7370}, mesh = {Ammonia/metabolism ; *Archaea/metabolism ; Carbon/metabolism ; Copper/metabolism ; *Euryarchaeota/metabolism ; Mixed Function Oxygenases/genetics ; Phylogeny ; Soil ; }, abstract = {Copper membrane monooxygenases (CuMMOs) play critical roles in the global carbon and nitrogen cycles. Organisms harboring these enzymes perform the first, and rate limiting, step in aerobic oxidation of ammonia, methane, or other simple hydrocarbons. Within archaea, only organisms in the order Nitrososphaerales (Thaumarchaeota) encode CuMMOs, which function exclusively as ammonia monooxygenases. From grassland and hillslope soils and aquifer sediments, we identified 20 genomes from distinct archaeal species encoding divergent CuMMO sequences. These archaea are phylogenetically clustered in a previously unnamed Thermoplasmatota order, herein named the Ca. Angelarchaeales. The CuMMO proteins in Ca. Angelarchaeales are more similar in structure to those in Nitrososphaerales than those of bacteria, and contain all functional residues required for general monooxygenase activity. Ca. Angelarchaeales genomes are significantly enriched in blue copper proteins (BCPs) relative to sibling lineages, including plastocyanin-like electron carriers and divergent nitrite reductase-like (nirK) 2-domain cupredoxin proteins co-located with electron transport machinery. Ca. Angelarchaeales also encode significant capacity for peptide/amino acid uptake and degradation and share numerous electron transport mechanisms with the Nitrososphaerales. Ca. Angelarchaeales are detected at high relative abundance in some of the environments where their genomes originated from. While the exact substrate specificities of the novel CuMMOs identified here have yet to be determined, activity on ammonia is possible given their metabolic and ecological context. The identification of an archaeal CuMMO outside of the Nitrososphaerales significantly expands the known diversity of CuMMO enzymes in archaea and suggests previously unaccounted organisms contribute to critical global nitrogen and/or carbon cycling functions.}, }
@article {pmid34986784, year = {2022}, author = {Aouad, M and Flandrois, JP and Jauffrit, F and Gouy, M and Gribaldo, S and Brochier-Armanet, C}, title = {A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {1}, pmid = {34986784}, issn = {2730-7182}, mesh = {*Archaea/genetics ; *Eukaryota ; Phylogeny ; }, abstract = {BACKGROUND: The recent rise in cultivation-independent genome sequencing has provided key material to explore uncharted branches of the Tree of Life. This has been particularly spectacular concerning the Archaea, projecting them at the center stage as prominently relevant to understand early stages in evolution and the emergence of fundamental metabolisms as well as the origin of eukaryotes. Yet, resolving deep divergences remains a challenging task due to well-known tree-reconstruction artefacts and biases in extracting robust ancient phylogenetic signal, notably when analyzing data sets including the three Domains of Life. Among the various strategies aimed at mitigating these problems, divide-and-conquer approaches remain poorly explored, and have been primarily based on reconciliation among single gene trees which however notoriously lack ancient phylogenetic signal.<br><br>RESULTS: We analyzed sub-sets of full supermatrices&#xa0;covering the whole Tree of Life with specific taxonomic sampling to robustly resolve different parts of the archaeal phylogeny in light of their current diversity. Our results strongly support the existence and early emergence of two main clades, Cluster I and Cluster II, which we name Ouranosarchaea and Gaiarchaea, and we clarify the placement of important novel archaeal lineages within these two clades. However, the monophyly and branching of the fast evolving nanosized DPANN members remains unclear and worth of further study.<br><br>CONCLUSIONS: We inferred a well resolved rooted phylogeny of the Archaea that includes all recently described phyla of high taxonomic rank. This phylogeny represents a valuable reference to study the evolutionary events associated to the early steps of the diversification of the archaeal domain. Beyond the specifics of archaeal phylogeny, our results demonstrate the power of divide-and-conquer approaches to resolve deep phylogenetic relationships, which should be applied to progressively resolve the entire Tree of Life.}, }
@article {pmid34986141, year = {2022}, author = {Chadwick, GL and Skennerton, CT and Laso-Pérez, R and Leu, AO and Speth, DR and Yu, H and Morgan-Lang, C and Hatzenpichler, R and Goudeau, D and Malmstrom, R and Brazelton, WJ and Woyke, T and Hallam, SJ and Tyson, GW and Wegener, G and Boetius, A and Orphan, VJ}, title = {Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea.}, journal = {PLoS biology}, volume = {20}, number = {1}, pages = {e3001508}, pmid = {34986141}, issn = {1545-7885}, mesh = {Anaerobiosis ; *Archaea/genetics/metabolism ; *Electrons ; Genomics ; Geologic Sediments/microbiology ; Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; Sulfates/metabolism ; }, abstract = {The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.}, }
@article {pmid34984789, year = {2022}, author = {Chazan, A and Rozenberg, A and Mannen, K and Nagata, T and Tahan, R and Yaish, S and Larom, S and Inoue, K and Béjà, O and Pushkarev, A}, title = {Diverse heliorhodopsins detected via functional metagenomics in freshwater Actinobacteria, Chloroflexi and Archaea.}, journal = {Environmental microbiology}, volume = {24}, number = {1}, pages = {110-121}, doi = {10.1111/1462-2920.15890}, pmid = {34984789}, issn = {1462-2920}, mesh = {*Actinobacteria/genetics ; Archaea/genetics ; *Chloroflexi ; Fresh Water ; Metagenomics ; Rhodopsins, Microbial ; }, abstract = {The recently discovered rhodopsin family of heliorhodopsins (HeRs) is abundant in diverse microbial environments. So far, the functional and biological roles of HeRs remain unknown. To tackle this issue, we combined experimental and computational screens to gain some novel insights. Here, 10 readily expressed HeR genes were found using functional metagenomics on samples from two freshwater environments. These HeRs originated from diverse prokaryotic groups: Actinobacteria, Chloroflexi and Archaea. Heterologously expressed HeRs absorbed light in the green and yellow wavelengths (543-562 nm) and their photocycles exhibited diverse kinetic characteristics. To approach the physiological function of the HeRs, we used our environmental clones along with thousands of microbial genomes to analyze genes neighbouring HeRs. The strongest association was found with the DegV family involved in activation of fatty acids, which allowed us to hypothesize that HeRs might be involved in light-induced membrane lipid modifications.}, }
@article {pmid34962596, year = {2021}, author = {Li, SY and Xin, YJ and Bao, CX and Hou, J and Cui, HL}, title = {Haloprofundus salilacus sp. nov., Haloprofundus halobius sp. nov. and Haloprofundus salinisoli sp. nov.: three extremely halophilic archaea isolated from salt lake and saline soil.}, journal = {Extremophiles : life under extreme conditions}, volume = {26}, number = {1}, pages = {6}, pmid = {34962596}, issn = {1433-4909}, support = {31770005//National Natural Science Foundation of China/ ; }, mesh = {Base Composition ; China ; DNA, Archaeal ; Glycolipids ; *Halobacteriaceae/genetics ; *Lakes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; }, abstract = {Three halophilic archaeal strains, Gai1-5[T], SEDH52[T] and SQT7-1[T] were isolated from Gaize salt lake and Xiadi salt lake in Tibet, and saline soil from Xinjiang, respectively. Phylogenetic analysis based on 16S rRNA gene and rpoB' gene sequences showed that these three strains formed different branches separating them from Haloprofundus halophilus NK23[T] (97.7-98.3% similarities for 16S rRNA gene and 94.7-94.8% similarities for rpoB' gene, respectively) and Haloprofundus marisrubri SB9[T] (94.7-96.4% similarities for 16S rRNA gene and 92.3-93.2% similarities for rpoB' gene, respectively). Several phenotypic characteristics distinguish the strains Gai1-5[ T], SEDH52[T] and SQT7-1[T] from Haloprofundus halophilus NK23[T] and Haloprofundus marisrubri SB9[T]. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values among the three strains and current Haloprofundus members were in the range of 83.3-88.3% and 27.2-35.7%, respectively, far below the species boundary threshold values. The major polar lipids of three strains were phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol sulphate (PGS), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), mannosyl glucosyl diether-phosphatidic acid (DGD-PA) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA). These results showed that strains Gai1-5[T] (= CGMCC 1.16079[T] = JCM 33561[T]), SQT7-1[T] (= CGMCC 1.16063[T] = JCM 33553[ T]) and SEDH52[T] (= CGMCC 1.17434[T]) represented three novel species in the genus Haloprofundus, for which the names Haloprofundus salilacus sp. nov., Haloprofundus salinisoli sp. nov., and Haloprofundus halobius sp. nov. are proposed.}, }
@article {pmid34948099, year = {2021}, author = {De Falco, M and De Felice, M}, title = {Take a Break to Repair: A Dip in the World of Double-Strand Break Repair Mechanisms Pointing the Gaze on Archaea.}, journal = {International journal of molecular sciences}, volume = {22}, number = {24}, pages = {}, pmid = {34948099}, issn = {1422-0067}, support = {FOE-2019, DSB.AD004.271//CNR project NUTR-AGE/ ; F/200050/01-03/X45//NUTRABEST/ ; }, mesh = {*Archaea/genetics/metabolism ; *DNA Breaks, Double-Stranded ; *DNA Repair ; *DNA, Archaeal/genetics/metabolism ; *Genomic Instability ; Humans ; }, abstract = {All organisms have evolved many DNA repair pathways to counteract the different types of DNA damages. The detection of DNA damage leads to distinct cellular responses that bring about cell cycle arrest and the induction of DNA repair mechanisms. In particular, DNA double-strand breaks (DSBs) are extremely toxic for cell survival, that is why cells use specific mechanisms of DNA repair in order to maintain genome stability. The choice among the repair pathways is mainly linked to the cell cycle phases. Indeed, if it occurs in an inappropriate cellular context, it may cause genome rearrangements, giving rise to many types of human diseases, from developmental disorders to cancer. Here, we analyze the most recent remarks about the main pathways of DSB repair with the focus on homologous recombination. A thorough knowledge in DNA repair mechanisms is pivotal for identifying the most accurate treatments in human diseases.}, }
@article {pmid34927901, year = {2021}, author = {Otzen, DE and Dueholm, MS and Najarzadeh, Z and Knowles, TPJ and Ruggeri, FS}, title = {In situ Sub-Cellular Identification of Functional Amyloids in Bacteria and Archaea by Infrared Nanospectroscopy.}, journal = {Small methods}, volume = {5}, number = {6}, pages = {e2001002}, doi = {10.1002/smtd.202001002}, pmid = {34927901}, issn = {2366-9608}, support = {8021-00208B//Independent Research Foundation Denmark | Natural Sciences/ ; 6111-00241B//Independent Research Foundation Denmark | Technology and Production/ ; 13351//Villum Foundation/ ; }, mesh = {Amyloid/chemistry/*isolation &amp; purification/*metabolism ; Amyloidogenic Proteins/chemistry/isolation &amp; purification/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; Bacterial Outer Membrane ; Biofilms ; Escherichia coli/metabolism ; Escherichia coli Proteins ; Humans ; Protein Structure, Secondary ; Pseudomonas/metabolism ; }, abstract = {Formation of amyloid structures is originally linked to human disease. However, amyloid materials are found extensively in the animal and bacterial world where they stabilize intra- and extra-cellular environments like biofilms or cell envelopes. To date, functional amyloids have largely been studied using optical microscopy techniques in vivo, or after removal from their biological context for higher-resolution studies in vitro. Furthermore, conventional microscopies only indirectly identify amyloids based on morphology or unspecific amyloid dyes. Here, the high chemical and spatial (≈20 nm) resolution of Infrared Nanospectroscopy (AFM-IR) to investigate functional amyloid from Escherichia coli (curli), Pseudomonas (Fap), and the Archaea Methanosaeta (MspA) in situ is exploited. It is demonstrated that AFM-IR identifies amyloid protein within single intact cells through their cross β-sheet secondary structure, which has a unique spectroscopic signature in the amide I band of protein. Using this approach, nanoscale-resolved chemical images and spectra of purified curli and Methanosaeta cell wall sheaths are provided. The results highlight significant differences in secondary structure between E. coli cells with and without curli. Taken together, these results suggest that AFM-IR is a new and powerful label-free tool for in situ investigations of the biophysical state of functional amyloid and biomolecules in general.}, }
@article {pmid34917055, year = {2021}, author = {Lu, S and Liu, X and Liu, C and Cheng, G and Zhou, R and Li, Y}, title = {A Review of Ammonia-Oxidizing Archaea and Anaerobic Ammonia-Oxidizing Bacteria in the Aquaculture Pond Environment in China.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {775794}, pmid = {34917055}, issn = {1664-302X}, abstract = {The excessive ammonia produced in pond aquaculture processes cannot be ignored. In this review, we present the distribution and diversity of ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing bacteria (AnAOB) in the pond environment. Combined with environmental conditions, we analyze the advantages of AOA and AnAOB in aquaculture water treatment and discuss the current situation of pond water treatment engineering involving these microbes. AOA and AnAOB play an important role in the nitrogen removal process of aquaculture pond water, especially in seasonal low temperatures and anoxic sediment layers. Finally, we prospect the application of bioreactors to purify pond aquaculture water using AOA and AnAOB, in autotrophic nitrogen removal, which can reduce the production of greenhouse gases (such as nitrous oxide) and is conducive to the development of environmentally sustainable pond aquaculture.}, }
@article {pmid34910467, year = {2021}, author = {Wang, Y and Xu, J and Cui, D and Kong, L and Chen, S and Xie, W and Zhang, C}, title = {Classification and Identification of Archaea Using Single-Cell Raman Ejection and Artificial Intelligence: Implications for Investigating Uncultivated Microorganisms.}, journal = {Analytical chemistry}, volume = {93}, number = {51}, pages = {17012-17019}, doi = {10.1021/acs.analchem.1c03495}, pmid = {34910467}, issn = {1520-6882}, mesh = {*Artificial Intelligence ; In Situ Hybridization, Fluorescence ; *Lipids ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Archaea can produce special cellular components such as polyhydroxyalkanoates, carotenoids, rhodopsin, and ether lipids, which have valuable applications in medicine and green energy production. Most of the archaeal species are uncultivated, posing challenges to investigating their biomarker components and biochemical properties. In this study, we applied Raman spectroscopy to examine the biological characteristics of nine archaeal isolates, including halophilic archaea (Haloferax larsenii, Haloarcula argentinensis, Haloferax mediterranei, Halomicrobium mukohataei, Halomicrobium salinus, Halorussus sp., Natrinema gari), thermophilic archaea (Sulfolobus acidocaldarius), and marine group I (MGI) archaea (Nitrosopumilus maritimus). Linear discriminant analysis of the Raman spectra allowed visualization of significant separations among the nine archaeal isolates. Machine-learning classification models based on support vector machine achieved accuracies of 88-100% when classifying the nine archaeal species. The predicted results were validated by DNA sequencing analysis of cells isolated from the mixture by Raman-activated cell sorting. Raman spectra of uncultured archaea (MGII) were also obtained based on Raman spectroscopy and fluorescence in situ hybridization. The results combining multiple Raman-based techniques indicated that MGII may have the ability to produce lipids distinct from other archaeal species. Our study provides a valuable approach for investigating and classifying archaea, especially uncultured species, at the single-cell level.}, }
@article {pmid34894218, year = {2022}, author = {Stevens, KM and Hocher, A and Warnecke, T}, title = {Deep Conservation of Histone Variants in Thermococcales Archaea.}, journal = {Genome biology and evolution}, volume = {14}, number = {1}, pages = {}, pmid = {34894218}, issn = {1759-6653}, support = {MC_UP_1102/7/MRC_/Medical Research Council/United Kingdom ; MC-A658-5TY40/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Archaea/genetics/metabolism ; Chromatin ; *Histones/genetics ; Nucleosomes/genetics ; Phylogeny ; *Thermococcales/genetics/metabolism ; }, abstract = {Histones are ubiquitous in eukaryotes where they assemble into nucleosomes, binding and wrapping DNA to form chromatin. One process to modify chromatin and regulate DNA accessibility is the replacement of histones in the nucleosome with paralogous variants. Histones are also present in archaea but whether and how histone variants contribute to the generation of different physiologically relevant chromatin states in these organisms remains largely unknown. Conservation of paralogs with distinct properties can provide prima facie evidence for defined functional roles. We recently revealed deep conservation of histone paralogs with different properties in the Methanobacteriales, but little is known experimentally about these histones. In contrast, the two histones of the model archaeon Thermococcus kodakarensis, HTkA and HTkB, have been examined in some depth, both in vitro and in vivo. HTkA and HTkB exhibit distinct DNA-binding behaviors and elicit unique transcriptional responses when deleted. Here, we consider the evolution of HTkA/B and their orthologs across the order Thermococcales. We find histones with signature HTkA- and HTkB-like properties to be present in almost all Thermococcales genomes. Phylogenetic analysis indicates the presence of one HTkA- and one HTkB-like histone in the ancestor of Thermococcales and long-term maintenance of these two paralogs throughout Thermococcales diversification. Our results support the notion that archaea and eukaryotes have convergently evolved histone variants that carry out distinct adaptive functions. Intriguingly, we also detect more highly diverged histone-fold proteins, related to those found in some bacteria, in several Thermococcales genomes. The functions of these bacteria-type histones remain unknown, but structural modeling suggests that they can form heterodimers with HTkA/B-like histones.}, }
@article {pmid34871608, year = {2022}, author = {Liu, Y and Wang, Q and Pan, Q and Zhou, X and Peng, Z and Jahng, D and Yang, B and Pan, X}, title = {Ventilation induced evolution pattern of archaea, fungi, bacteria and their potential roles during co-bioevaporation treatment of concentrated landfill leachate and food waste.}, journal = {Chemosphere}, volume = {289}, number = {}, pages = {133122}, doi = {10.1016/j.chemosphere.2021.133122}, pmid = {34871608}, issn = {1879-1298}, mesh = {Archaea/genetics ; Bacteria/genetics ; Bioreactors ; Food ; Fungi/genetics ; *Refuse Disposal ; Waste Disposal Facilities ; *Water Pollutants, Chemical/analysis ; }, abstract = {To obtain a favorable aeration type in co-bioevaporation treatment of concentrated landfill leachate and food waste, and to deeply understand the co-bioevaporation mechanisms, the temporal evolution differences of archaea, fungi and bacteria as well as the related microbial metabolism genes and functional enzymes under intermittent ventilation (IV) and continuous ventilation (CV) were investigated. Results through metagenomics analysis showed that the less sufficient oxygen and longer thermophilic phase in IV stimulated the vigorous growth of archaea, while CV was beneficial for fungal growth. Even genes of carbohydrates and lipids metabolism and ATP-associated enzymes (enzyme 2.7.13.3 and 3.6.4.12), as well as peptidoglycan biosynthesis enzyme (enzyme 3.4.16.4), were more abundant in CV, IV hold better DNA repair ability, higher microbial viability, and less dehydrogenase sensitivity to temperatures due to the critical contribution of Pseudomonas (3.1-45.9%). Furthermore, IV consumed a similar amount of heat for water evaporation with nearly half of the ventilation of CV and was a favorable aeration type in the practical application of co-bioevaporation.}, }
@article {pmid34850144, year = {2021}, author = {Yen, CY and Lin, MG and Chen, BW and Ng, IW and Read, N and Kabli, AF and Wu, CT and Shen, YY and Chen, CH and Barillà, D and Sun, YJ and Hsiao, CD}, title = {Chromosome segregation in Archaea: SegA- and SegB-DNA complex structures provide insights into segrosome assembly.}, journal = {Nucleic acids research}, volume = {49}, number = {22}, pages = {13150-13164}, pmid = {34850144}, issn = {1362-4962}, support = {BB/M007839/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R006369/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphatases/chemistry/genetics/metabolism ; Adenosine Triphosphate/metabolism ; Archaeal Proteins/chemistry/*genetics/metabolism ; Chromatin/genetics/metabolism/ultrastructure ; *Chromosome Segregation ; Chromosomes, Archaeal/*genetics ; Crystallography, X-Ray ; DNA, Archaeal/chemistry/*genetics/metabolism ; DNA-Binding Proteins/chemistry/genetics/metabolism ; Microscopy, Electron ; Models, Molecular ; Multiprotein Complexes/chemistry/metabolism/ultrastructure ; Mutation ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Sulfolobus solfataricus/*genetics/metabolism ; }, abstract = {Genome segregation is a vital process in all organisms. Chromosome partitioning remains obscure in Archaea, the third domain of life. Here, we investigated the SegAB system from Sulfolobus solfataricus. SegA is a ParA Walker-type ATPase and SegB is a site-specific DNA-binding protein. We determined the structures of both proteins and those of SegA-DNA and SegB-DNA complexes. The SegA structure revealed an atypical, novel non-sandwich dimer that binds DNA either in the presence or in the absence of ATP. The SegB structure disclosed a ribbon-helix-helix motif through which the protein binds DNA site specifically. The association of multiple interacting SegB dimers with the DNA results in a higher order chromatin-like structure. The unstructured SegB N-terminus plays an essential catalytic role in stimulating SegA ATPase activity and an architectural regulatory role in segrosome (SegA-SegB-DNA) formation. Electron microscopy results also provide a compact ring-like segrosome structure related to chromosome organization. These findings contribute a novel mechanistic perspective on archaeal chromosome segregation.}, }
@article {pmid34846953, year = {2022}, author = {Vavilin, VA and Lokshina, LY and Rytov, SV}, title = {Anaerobic oxidation of methane coupled with sulphate reduction: high concentration of methanotrophic archaea might be responsible for low stable isotope fractionation factors in methane.}, journal = {Isotopes in environmental and health studies}, volume = {58}, number = {1}, pages = {44-59}, doi = {10.1080/10256016.2021.2000405}, pmid = {34846953}, issn = {1477-2639}, mesh = {Anaerobiosis ; *Archaea ; Factor VII ; Geologic Sediments ; Isotopes ; *Methane ; Oxidation-Reduction ; Sulfates ; }, abstract = {The changes in δ[13]CH4 and δ[12]C[1]H3[2]H during sulphate-dependent anaerobic oxidation of methane (AOM) were described using dynamic modelling. The batch sulphate-dependent AOM at the nearly linear dynamics of methane oxidation with different enriched cultures originating from three marine sediments was simulated. The traditional Rayleigh equation for carbon and hydrogen stable isotopes in methane was derived from the basic dynamic isotope equation. The general and reduced models, taking into account the reaction stoichiometry and based on balances of chemical elements and their isotopes, describes a redistribution of stable isotope values in the sulphate-dependent AOM process. It was shown that AOM is the first and rate-limiting step in the whole AOM + SR (sulphate reduction) process. The different fractionation factors of carbon and hydrogen isotopes in methane were obtained for three marine sediments. It was concluded that during incubation the highest concentration of methanotrophic archaea might be responsible for the lowest fractionation factors of stable isotopes of carbon and hydrogen in methane. The interpretation of this phenomenon was suggested. Different concentrations of methanotrophic archaea can lead to variations of isotope fractionation factors.}, }
@article {pmid34841354, year = {2021}, author = {Tan, RSG and Zhou, M and Li, F and Guan, LL}, title = {Identifying active rumen epithelial associated bacteria and archaea in beef cattle divergent in feed efficiency using total RNA-seq.}, journal = {Current research in microbial sciences}, volume = {2}, number = {}, pages = {100064}, pmid = {34841354}, issn = {2666-5174}, abstract = {To date, the role of ruminal epithelial attached microbiota in cattle feed efficiency is undefined. In this study, we aimed to characterize transcriptionally active bacteria and archaea attached to the rumen epithelial wall and to determine whether they differ in cattle with varied feed efficiency. RNA-sequencing was performed to obtain the rumen epithelial transcriptomes from 9 of the most efficient (low RFI) and 9 of the most inefficient (high RFI) animals. The bacteria and archaea 16S rRNA transcripts were identified using an in-house developed pipeline, enriched from filtered reads that did not map to the bovine genome. Archaea from unclassified genera belonging to the Euryarchaeota phylum showed the most activity on the rumen epithelium of low RFI (81.3 ± 1.9%) and high RFI (76.4 ± 3.0%) steers. Bacteria from the Succinivibrionaceae family showed the greatest activity of bacteria on the low RFI (28.7 ± 9.0%) and high RFI (33.9± 8.8%) epithelium. Of the bacterial families, Campylobacteraceae and Neisseriaceae had significantly greater activity on the low RFI epithelium (p < 0.05) and are known to play a role in oxygen scavenging. Greater activity of rumen epithelial attached oxygen scavenging bacteria may provide more optimal feed fermentation conditions, which contributes to high fermentation efficiency in the rumen.}, }
@article {pmid34827555, year = {2021}, author = {Amin, K and Tranchimand, S and Benvegnu, T and Abdel-Razzak, Z and Chamieh, H}, title = {Glycoside Hydrolases and Glycosyltransferases from Hyperthermophilic Archaea: Insights on Their Characteristics and Applications in Biotechnology.}, journal = {Biomolecules}, volume = {11}, number = {11}, pages = {}, pmid = {34827555}, issn = {2218-273X}, mesh = {*Archaea/enzymology/genetics ; *Glycoside Hydrolases/genetics/metabolism/chemistry ; *Biotechnology ; *Glycosyltransferases/metabolism/genetics/chemistry ; Archaeal Proteins/metabolism/genetics/chemistry ; }, abstract = {Hyperthermophilic Archaea colonizing unnatural habitats of extremes conditions such as volcanoes and deep-sea hydrothermal vents represent an unmeasurable bioresource for enzymes used in various industrial applications. Their enzymes show distinct structural and functional properties and are resistant to extreme conditions of temperature and pressure where their mesophilic homologs fail. In this review, we will outline carbohydrate-active enzymes (CAZymes) from hyperthermophilic Archaea with specific focus on the two largest families, glycoside hydrolases (GHs) and glycosyltransferases (GTs). We will present the latest advances on these enzymes particularly in the light of novel accumulating data from genomics and metagenomics sequencing technologies. We will discuss the contribution of these enzymes from hyperthermophilic Archaea to industrial applications and put the emphasis on newly identifed enzymes. We will highlight their common biochemical and distinct features. Finally, we will overview the areas that remain to be explored to identify novel promising hyperthermozymes.}, }
@article {pmid34825404, year = {2022}, author = {Coker, OO}, title = {Non-bacteria microbiome (virus, fungi, and archaea) in gastrointestinal cancer.}, journal = {Journal of gastroenterology and hepatology}, volume = {37}, number = {2}, pages = {256-262}, doi = {10.1111/jgh.15738}, pmid = {34825404}, issn = {1440-1746}, mesh = {Archaea ; Fungi ; *Gastrointestinal Microbiome ; *Gastrointestinal Neoplasms/microbiology/prevention &amp; control ; Humans ; Viruses ; }, abstract = {The gastrointestinal tract houses millions of microbes collectively referred to as the gut microbiome. The gut microbes comprise of bacteria, viruses, fungi, archaea, and microscopic eukaryotes, which co-evolved or colonize the gut forming complex symbiotic and mutualistic relationships. A state of homeostasis is required between host and gut microbiome relationship to maintain several host beneficial processes. Alterations in the taxonomic and functional composition of the gut microbes are associated with several human diseases including gastrointestinal cancers. Owed to their overwhelming abundance and ease of characterization, several studies focus on the role of bacteria in gastrointestinal cancers. There is however growing evidence that non-bacteria gut microbes are associated with the pathogenesis of gastrointestinal cancers. This review details the association of non-bacteria gut microbes including fungi, viruses, and archaea and their potential manipulation in the prevention and treatment of human gastrointestinal cancers.}, }
@article {pmid34808316, year = {2022}, author = {Fan, Q and Fan, X and Fu, P and Li, Y and Zhao, Y and Hua, D}, title = {Anaerobic digestion of wood vinegar wastewater using domesticated sludge: Focusing on the relationship between organic degradation and microbial communities (archaea, bacteria, and fungi).}, journal = {Bioresource technology}, volume = {347}, number = {}, pages = {126384}, doi = {10.1016/j.biortech.2021.126384}, pmid = {34808316}, issn = {1873-2976}, mesh = {Acetic Acid ; Anaerobiosis ; Archaea ; Bacteria ; Bioreactors ; Fungi ; Methane ; Methanol ; *Microbiota ; *Sewage ; Wastewater ; }, abstract = {Thermochemical process of biomass is one of the promising renewable energy technologies; however, the by-product (wood vinegar wastewater) is rich in refractory organics, which is harmful to the environment and inhibits the conversion efficiency of microorganisms. Consequently, the dominant functional microbial communities corresponding to the various substrate were obtained through the continuous domestication, and the relationship between the dominant functional communities and the degradation of organic compounds was comprehensively analyzed. The bacterial community was absolutely dominant (approximately 85%), while archaea and fungi had similar relative abundance. The diversity showed that glucose was not conducive to the development of microbial diversity, while the substrate containing wood vinegar wastewater showed the opposite trend. The functional analysis revealed that the enrichment of bacteria associated with the hydrolysis and acidification of organics increased in the domestication process. Glucose facilitated hydrogen-trophic methanogenesis as the main methanogenic pathway in the methanogenic stage.}, }
@article {pmid34803972, year = {2021}, author = {Durán-Viseras, A and Sánchez-Porro, C and Ventosa, A}, title = {Genomic Insights Into New Species of the Genus Halomicroarcula Reveals Potential for New Osmoadaptative Strategies in Halophilic Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {751746}, pmid = {34803972}, issn = {1664-302X}, abstract = {Metagenomic studies on prokaryotic diversity of hypersaline soils from the Odiel saltmarshes, South-west Spain, revealed a high proportion of genomic sequences not related to previously cultivated taxa, that might be related to haloarchaea with a high environmental and nutritional flexibility. In this study, we used a culturomics approach in order to isolate new haloarchaeal microorganisms from these hypersaline soils. Four haloarchaeal strains, designated strains F24A[T], F28, F27[T], and F13[T], phylogenetically related to the genus Halomicroarcula, were isolated and characterized in detail. The phylogenomic tree based on the 100 orthologous single-copy genes present in the genomes of these four strains as well as those of the type strains of the species Halomicroarcula pellucida CECT 7537[T], Halomicroarcula salina JCM 18369[T] and Halomicroarcula limicola JCM 18640[T], that were determined in this study, revealed that these four new isolates clustered on three groups, with strains F24A[T] and F28 within a single cluster, and altogether with the species of Halomicroarcula. Additionally, Orthologous Average Nucleotide Identity (OrthoANI), digital DNA-DNA hybridization (dDDH) and Average Amino-acid Identity (AAI) values, likewise phenotypic characteristics, including their polar lipids profiles, permitted to determine that they represent three new species, for which we propose the names Halomicroarcula rubra sp. nov. (type strain F13[T]), Halomicroarcula nitratireducens sp. nov. (type strain F27[T]) and Halomicroarcula salinisoli sp. nov. (type strain F24A[T]). An in deep comparative genomic analysis of species of the genus Halomicroarcula, including their metabolism, their capability to biosynthesize secondary metabolites and their osmoregulatory adaptation mechanisms was carried out. Although they use a salt-in strategy, the identification of the complete pathways for the biosynthesis of the compatible solutes trehalose and glycine betaine, not identified before in any other haloarchaea, might suggest alternative osmoadaptation strategies for this group. This alternative osmoregulatory mechanism would allow this group of haloarchaea to be versatile and eco-physiologically successful in hypersaline environments and would justify the capability of the species of this genus to grow not only on environments with high salt concentrations [up to 30% (w/v) salts], but also under intermediate to low salinities.}, }
@article {pmid34796612, year = {2022}, author = {Saghaï, A and Banjeree, S and Degrune, F and Edlinger, A and García-Palacios, P and Garland, G and van der Heijden, MGA and Herzog, C and Maestre, FT and Pescador, DS and Philippot, L and Rillig, MC and Romdhane, S and Hallin, S}, title = {Diversity of archaea and niche preferences among putative ammonia-oxidizing Nitrososphaeria dominating across European arable soils.}, journal = {Environmental microbiology}, volume = {24}, number = {1}, pages = {341-356}, doi = {10.1111/1462-2920.15830}, pmid = {34796612}, issn = {1462-2920}, mesh = {*Ammonia ; *Archaea ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; }, abstract = {Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of environmental filters on AOA and the delineation of niche preferences of nitrososphaerial lineages remain poorly understood. We used phylogenetic information at fine scale and machine learning approaches to identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea along a 3000 km European gradient. Only limited insights into the ecology of the low-abundant archaeal classes could be inferred, but our analyses underlined the multifactorial nature of niche differentiation within Nitrososphaeria. Mean annual temperature, C:N ratio and pH were the best predictors of their diversity, evenness and distribution. Thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Furthermore, multiple, independent and recent specializations to soil pH were detected in the Nitrososphaeria phylogeny. The coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria highlights that their ecology is best studied at fine phylogenetic scale.}, }
@article {pmid34790173, year = {2021}, author = {Trouche, B and Brandt, MI and Belser, C and Orejas, C and Pesant, S and Poulain, J and Wincker, P and Auguet, JC and Arnaud-Haond, S and Maignien, L}, title = {Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria and Archaea Along a Mediterranean-Atlantic Gradient.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {702016}, pmid = {34790173}, issn = {1664-302X}, abstract = {Seafloor sediments cover the majority of planet Earth and microorganisms inhabiting these environments play a central role in marine biogeochemical cycles. Yet, description of the biogeography and distribution of sedimentary microbial life is still too sparse to evaluate the relative contribution of processes driving this distribution, such as the levels of drift, connectivity, and specialization. To address this question, we analyzed 210 archaeal and bacterial metabarcoding libraries from a standardized and horizon-resolved collection of sediment samples from 18 stations along a longitudinal gradient from the eastern Mediterranean to the western Atlantic. Overall, we found that biogeographic patterns depended on the scale considered: while at local scale the selective influence of contemporary environmental conditions appeared strongest, the heritage of historic processes through dispersal limitation and drift became more apparent at regional scale, and ended up superseding contemporary influences at inter-regional scale. When looking at environmental factors, the structure of microbial communities was correlated primarily with water depth, with a clear transition between 800 and 1,200 meters below sea level. Oceanic basin, water temperature, and sediment depth were other important explanatory parameters of community structure. Finally, we propose increasing dispersal limitation and ecological drift with sediment depth as a probable factor for the enhanced divergence of deeper horizons communities.}, }
@article {pmid34777272, year = {2021}, author = {Satari, L and Guillén, A and Latorre-Pérez, A and Porcar, M}, title = {Beyond Archaea: The Table Salt Bacteriome.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {714110}, pmid = {34777272}, issn = {1664-302X}, abstract = {Commercial table salt is a condiment with food preservative properties by decreasing water activity and increasing osmotic pressure. Salt is also a source of halophilic bacteria and archaea. In the present research, the diversity of halotolerant and halophilic microorganisms was studied in six commercial table salts by culture-dependent and culture-independent techniques. Three table salts were obtained from marine origins: Atlantic Ocean, Mediterranean (Ibiza Island), and Odiel marshes (supermarket marine salt). Other salts supplemented with mineral and nutritional ingredients were also used: Himalayan pink, Hawaiian black, and one with dried vegetables known as Viking salt. The results of 16S rRNA gene sequencing reveal that the salts from marine origins display a similar archaeal taxonomy, but with significant variations among genera. Archaeal taxa Halorubrum, Halobacterium, Hallobellus, Natronomonas, Haloplanus, Halonotius, Halomarina, and Haloarcula were prevalent in those three marine salts. Furthermore, the most abundant archaeal genera present in all salts were Natronomonas, Halolamina, Halonotius, Halapricum, Halobacterium, Haloarcula, and uncultured Halobacterales. Sulfitobacter sp. was the most frequent bacteria, represented almost in all salts. Other genera such as Bacillus, Enterococcus, and Flavobacterium were the most frequent taxa in the Viking, Himalayan pink, and black salts, respectively. Interestingly, the genus Salinibacter was detected only in marine-originated salts. A collection of 76 halotolerant and halophilic bacterial and haloarchaeal species was set by culturing on different media with a broad range of salinity and nutrient composition. Comparing the results of 16S rRNA gene metataxonomic and culturomics revealed that culturable bacteria Acinetobacter, Aquibacillus, Bacillus, Brevundimonas, Fictibacillus, Gracilibacillus, Halobacillus, Micrococcus, Oceanobacillus, Salibacterium, Salinibacter, Terribacillus, Thalassobacillus, and also Archaea Haloarcula, Halobacterium, and Halorubrum were identified at least in one sample by both methods. Our results show that salts from marine origins are dominated by Archaea, whereas salts from other sources or salt supplemented with ingredients are dominated by bacteria.}, }
@article {pmid34740642, year = {2022}, author = {Zou, W and Lang, M and Zhang, L and Liu, B and Chen, X}, title = {Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea dominate nitrification in a nitrogen-fertilized calcareous soil.}, journal = {The Science of the total environment}, volume = {811}, number = {}, pages = {151402}, doi = {10.1016/j.scitotenv.2021.151402}, pmid = {34740642}, issn = {1879-1026}, mesh = {Ammonia ; *Archaea/genetics ; *Betaproteobacteria ; Ecosystem ; Fertilization ; Nitrification ; Nitrogen ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; }, abstract = {Microbe-driven nitrification is a key process that affects nitrogen (N) utilization by plants and N loss to the environment in agro-ecosystems. Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are important microorganisms that dominate the ammonia oxidation process (the first and rate-limiting step of nitrification). Calcareous soils are widely distributed, accounting for more than 30% of the Earth's land. However, the effects of long-term N fertilization on the potential nitrification rate (PNR) and on AOA and AOB in calcareous soils are poorly understood. In this study, we comprehensively assessed the effects of N application (applied at five rates as urea with 0, 73.5, 105, 136.5 and 250 kg N ha[-1] for 12 years) on soil chemical characteristics, PNR, N use efficiency (NUE) and the community characteristics of AOB and AOA in a calcareous soil. N application rate affected AOB beta diversity more than that of AOA. Compared to no N control, N application significantly decreased the relative abundance of Group I.1b clade A of AOA and Nitrosospira cluster 3a.2 of AOB, but increased Nitrosomonas cluster 7 of AOB. The relative abundance of Nitrosospira cluster 3a.2 of AOB was negatively correlated with PNR. A structural equation model showed a direct effect of N application rate on the content of soil organic matter and nitrate, the alpha and beta diversity of AOA and AOB. Nitrate and AOB beta diversity were the key factors affecting PNR. Overall, the alpha, beta diversity and community composition of AOB contribute more to PNR than AOA in calcareous soils with high organic matter content. Understanding the relationship between the characteristics of AOA and AOB in calcareous soils and PNR will help to improve NUE.}, }
@article {pmid34737728, year = {2021}, author = {Vázquez-Campos, X and Kinsela, AS and Bligh, MW and Payne, TE and Wilkins, MR and Waite, TD}, title = {Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {732575}, pmid = {34737728}, issn = {1664-302X}, abstract = {During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (LFLS, Sydney, Australia). The microbial function and population dynamics in a waste trench during a rainfall event have been previously investigated revealing a broad abundance of candidate and potentially undescribed taxa in this iron-rich, radionuclide-contaminated environment. Applying genome-based metagenomic methods, we recovered 37 refined archaeal MAGs, mainly from undescribed DPANN Archaea lineages without standing in nomenclature and 'Candidatus Methanoperedenaceae' (ANME-2D). Within the undescribed DPANN, the newly proposed orders 'Ca. Gugararchaeales', 'Ca. Burarchaeales' and 'Ca. Anstonellales', constitute distinct lineages with a more comprehensive central metabolism and anabolic capabilities within the 'Ca. Micrarchaeota' phylum compared to most other DPANN. The analysis of new and extant 'Ca. Methanoperedens spp.' MAGs suggests metal ions as the ancestral electron acceptors during the anaerobic oxidation of methane while the respiration of nitrate/nitrite via molybdopterin oxidoreductases would have been a secondary acquisition. The presence of genes for the biosynthesis of polyhydroxyalkanoates in most 'Ca. Methanoperedens' also appears to be a widespread characteristic of the genus for carbon accumulation. This work expands our knowledge about the roles of the Archaea at the LFLS, especially, DPANN Archaea and 'Ca. Methanoperedens', while exploring their diversity, uniqueness, potential role in elemental cycling, and evolutionary history.}, }
@article {pmid34725736, year = {2021}, author = {Sutter, JM and Johnsen, U and Reinhardt, A and Schönheit, P}, title = {Correction to: Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways.}, journal = {Extremophiles : life under extreme conditions}, volume = {25}, number = {5-6}, pages = {527}, doi = {10.1007/s00792-021-01248-7}, pmid = {34725736}, issn = {1433-4909}, }
@article {pmid34721370, year = {2021}, author = {Liu, LJ and Jiang, Z and Wang, P and Qin, YL and Xu, W and Wang, Y and Liu, SJ and Jiang, CY}, title = {Physiology, Taxonomy, and Sulfur Metabolism of the Sulfolobales, an Order of Thermoacidophilic Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {768283}, pmid = {34721370}, issn = {1664-302X}, abstract = {The order Sulfolobales (phylum Crenarchaeota) is a group of thermoacidophilic archaea. The first member of the Sulfolobales was discovered in 1972, and current 23 species are validly named under the International Code of Nomenclature of Prokaryotes. The majority of members of the Sulfolobales is obligately or facultatively chemolithoautotrophic. When they grow autotrophically, elemental sulfur or reduced inorganic sulfur compounds are their energy sources. Therefore, sulfur metabolism is the most important physiological characteristic of the Sulfolobales. The functions of some enzymes and proteins involved in sulfur reduction, sulfur oxidation, sulfide oxidation, thiosulfate oxidation, sulfite oxidation, tetrathionate hydrolysis, and sulfur trafficking have been determined. In this review, we describe current knowledge about the physiology, taxonomy, and sulfur metabolism of the Sulfolobales, and note future challenges in this field.}, }
@article {pmid34691003, year = {2021}, author = {Anchal,  and Kaushik, V and Goel, M}, title = {Distribution of Peptidyl-Prolyl Isomerase (PPIase) in the Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {751049}, pmid = {34691003}, issn = {1664-302X}, abstract = {Cis-trans isomerization of the peptide bond prior to proline is an intrinsically slow process but plays an essential role in protein folding. In vivo cis-trans isomerization reaction is catalyzed by Peptidyl-prolyl isomerase (PPIases), a category of proteins widely distributed among all the three domains of life. The present study is majorly focused on the distribution of different types of PPIases in the archaeal domain. All the three hitherto known families of PPIases (namely FKBP, Cyclophilin and parvulin) were studied to identify the evolutionary conservation across the phylum archaea. The basic function of cyclophilin, FKBP and parvulin has been conserved whereas the sequence alignment suggested variations in each clade. The conserved residues within the predicted motif of each family are unique. The available protein structures of different PPIase across various domains were aligned to ascertain the structural variation in the catalytic site. The structural alignment of native PPIase proteins among various groups suggested that the apo-protein may have variable conformations but when bound to their specific inhibitors, they attain similar active site configuration. This is the first study of its kind which explores the distribution of archaeal PPIases, along with detailed structural and functional analysis of each type of PPIase found in archaea.}, }
@article {pmid34688753, year = {2022}, author = {Wunderer, M and Markt, R and Lackner, N and Wagner, AO}, title = {The glutamyl tail length of the cofactor F420 in the methanogenic Archaea Methanosarcina thermophila and Methanoculleus thermophilus.}, journal = {The Science of the total environment}, volume = {809}, number = {}, pages = {151112}, doi = {10.1016/j.scitotenv.2021.151112}, pmid = {34688753}, issn = {1879-1026}, mesh = {Methane ; *Methanomicrobiaceae/enzymology ; Methanosarcina/*enzymology ; Riboflavin/analogs &amp; derivatives ; }, abstract = {The cofactor F420 is synthesized by many different organisms and as a redox cofactor, it plays a crucial role in the redox reactions of catabolic and biosynthetic metabolic pathways. It consists of a deazaflavin structure, which is linked via lactate to an oligoglutamate chain, that can vary in length. In the present study, the methanogenic Archaea Methanosarcina thermophila and Methanoculleus thermophilus were cultivated on different carbon sources and their coenzyme F420 composition has been assayed by reversed-phase ion-pair high-performance liquid chromatography with fluorometric detection regarding both, overall cofactor F420 production and distribution of F420 glutamyl tail length. In Methanosarcina thermophila cultivated on methanol, acetate, and a mixture of acetate and methanol, the most abundant cofactors were F420-5 and F420-4, whereby the last digit refers to the number of expressed glutamyl rests. By contrast, in the obligate CO2 reducing Methanoculleus thermophilus the most abundant cofactors were F420-3 and F420-4. In Methanosarcina thermophila, the relative proportions of the expressed F420 tail length changed during batch growth on all three carbon sources. Over time F420-3 and F420-4 decreased while F420-5 and F420-6 increased in their relative proportion in comparison to total F420 content. In contrast, in Methanoculleus thermophilus the relative abundance of the different F420 cofactors remained stable. It was also possible to differentiate the two methanogenic Archaea based on the glutamyl tail length of the cofactor F420. The cofactor F420-5 in concentrations >2% could only be assigned to Methanosarcina thermophila. In all four variants a trend for a positive correlation between the DNA concentration and the total concentration of the cofactor could be shown. Except for the variant Methanosarcinathermophila with acetate as sole carbon source the same could be shown between the concentration of the mcrA gene copy number and the total concentration of the cofactor.}, }
@article {pmid36697601, year = {2021}, author = {Sumi, T and Harada, K}, title = {Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea.}, journal = {Communications chemistry}, volume = {4}, number = {1}, pages = {149}, pmid = {36697601}, issn = {2399-3669}, support = {JP20K05431//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, abstract = {The origin of life is believed to be chemoautotrophic, deriving all biomass components from carbon dioxide, and all energy from inorganic redox couples in the environment. The reductive tricarboxylic acid cycle (rTCA) and the Wood-Ljungdahl pathway (WL) have been recognized as the most ancient carbon fixation pathways. The rTCA of the chemolithotrophic Thermosulfidibacter takaii, which was recently demonstrated to take place via an unexpected reverse reaction of citrate synthase, was reproduced using a kinetic network model, and a competition between reductive and oxidative fluxes on rTCA due to an acetyl coenzyme A (ACOA) influx upon acetate uptake was revealed. Avoiding ACOA direct influx into rTCA from WL is, therefore, raised as a kinetically necessary condition to maintain a complete rTCA. This hypothesis was confirmed for deep-branching bacteria and archaea, and explains the kinetic factors governing elementary processes in carbon metabolism evolution from the last universal common ancestor.}, }
@article {pmid34666825, year = {2021}, author = {Wang, B and Liu, N and Yang, M and Wang, L and Liang, X and Liu, CQ}, title = {Co-occurrence of planktonic bacteria and archaea affects their biogeographic patterns in China's coastal wetlands.}, journal = {Environmental microbiome}, volume = {16}, number = {1}, pages = {19}, pmid = {34666825}, issn = {2524-6372}, support = {U1612441//national natural science foundation of china/ ; 2016YFA0601001//key technologies research and development program/ ; }, abstract = {Planktonic bacteria and archaea play a key role in maintaining ecological functions in aquatic ecosystems; however, their biogeographic patterns and underlying mechanisms have not been well known in coastal wetlands including multiple types and at a large space scale. Therefore, planktonic bacteria and archaea and related environmental factors were investigated in twenty-one wetlands along China's coast to understand the above concerns. The results indicated that planktonic bacteria had different biogeographic pattern from planktonic archaea, and both patterns were not dependent on the wetland's types. Deterministic selection shapes the former's community structure, whereas stochastic processes regulate the latter's, being consistent with the fact that planktonic archaea have a larger niche breadth than planktonic bacteria. Planktonic bacteria and archaea co-occur, and their co-occurrence rather than salinity is more important in shaping their community structure although salinity is found to be a main environmental deterministic factor in the coastal wetland waters. This study highlights the role of planktonic bacteria-archaea co-occurrence on their biogeographic patterns, and thus provides a new insight into studying underlying mechanisms of microbial biogeography in coastal wetlands.}, }
@article {pmid34665251, year = {2021}, author = {Westoby, M and Nielsen, DA and Gillings, MR and Gumerov, VM and Madin, JS and Paulsen, IT and Tetu, SG}, title = {Strategic traits of bacteria and archaea vary widely within substrate-use groups.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {11}, pages = {}, doi = {10.1093/femsec/fiab142}, pmid = {34665251}, issn = {1574-6941}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Genome Size ; Phenotype ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Quantitative traits such as maximum growth rate and cell radial diameter are one facet of ecological strategy variation across bacteria and archaea. Another facet is substrate-use pathways, such as iron reduction or methylotrophy. Here, we ask how these two facets intersect, using a large compilation of data for culturable species and examining seven quantitative traits (genome size, signal transduction protein count, histidine kinase count, growth temperature, temperature-adjusted maximum growth rate, cell radial diameter and 16S rRNA operon copy number). Overall, quantitative trait variation within groups of organisms possessing a particular substrate-use pathway was very broad, outweighing differences between substrate-use groups. Although some substrate-use groups had significantly different means for some quantitative traits, standard deviation of quantitative trait values within each substrate-use pathway mostly averaged between 1.6 and 1.8 times larger than standard deviation across group means. Most likely, this wide variation reflects ecological strategy: for example, fast maximum growth rate is likely to express an early successional or copiotrophic strategy, and maximum growth varies widely within most substrate-use pathways. In general, it appears that these quantitative traits express different and complementary information about ecological strategy, compared with substrate use.}, }
@article {pmid34661841, year = {2022}, author = {Ye, H and Tang, C and Cao, Y and Li, X and Huang, P}, title = {Contribution of ammonia-oxidizing archaea and bacteria to nitrification under different biogeochemical factors in acidic soils.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {12}, pages = {17209-17222}, pmid = {34661841}, issn = {1614-7499}, support = {No. 2017B020236001//Applied Science and Technology Research and Development Project of Guangdong Province, China/ ; No.41877470//General Program of the National Natural Science Foundation of China/ ; No.42077154//General Program of the National Natural Science Foundation of China/ ; }, mesh = {Ammonia/chemistry ; *Archaea/genetics ; Bacteria/genetics ; Ecosystem ; *Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Nitrification in soils is an essential process that involves archaeal and bacterial ammonia-oxidizers. Despite its importance, the relative contributions of soil factors to the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and their nitrification performances are seldom discussed. The aim of this study was to determine the effects of AOA and AOB abundance and different environmental conditions (pH, TC, TN, moisture, and temperature) on nitrification performance. The soils of the long-term fertilized tea orchards and forests were sampled in the field, and nitrification experiments were conducted in the laboratory. The acid soils were collected from the field and used in laboratory incubation experiments to calculate the nitrification rate, including the net nitrification rate (NN rate), nitrification potential (NP), and nitrification kinetics. The basic parameters, different forms of nitrogen content, and AOA and AOB amoA gene copies were also analyzed. Compared with the forest soil, the tea orchard soil had a lower pH and higher nitrogen content (p < 0.05). The AOA and AOB abundance in the soils of the forests and tea orchards were pH-dependent. The NN rate and NP had good relationships with AOA or AOB in the forest soil; however, poor relationships were observed in the tea orchard soil. When pH < 4, the performances of AOA and AOB were restricted by pH and the environment, especially in long-term fertilized farmlands. Long-term fertilization can cause soil acidification, which regulates the abundance of AOA and AOB and their nitrifying ability. The soil environment rather than AOA or AOB could control nitrification in long-term fertilized farmlands with a pH below 4. These findings could improve fertilization efficiency and control nutrient runoff in hilly agricultural ecosystems.}, }
@article {pmid34655277, year = {2022}, author = {Chouhan, BPS and Gade, M and Martinez, D and Toledo-Patino, S and Laurino, P}, title = {Implications of divergence of methionine adenosyltransferase in archaea.}, journal = {FEBS open bio}, volume = {12}, number = {1}, pages = {130-145}, pmid = {34655277}, issn = {2211-5463}, mesh = {*Archaea/genetics/metabolism ; Catalytic Domain ; Methionine ; *Methionine Adenosyltransferase/chemistry/genetics/metabolism ; S-Adenosylmethionine/chemistry ; }, abstract = {Methionine adenosyltransferase (MAT) catalyzes the biosynthesis of S-adenosyl methionine from l-methionine and ATP. MAT enzymes are ancient, believed to share a common ancestor, and are highly conserved in all three domains of life. However, the sequences of archaeal MATs show considerable divergence compared with their bacterial and eukaryotic counterparts. Furthermore, the structural significance and functional significance of this sequence divergence are not well understood. In the present study, we employed structural analysis and ancestral sequence reconstruction to investigate archaeal MAT divergence. We observed that the dimer interface containing the active site (which is usually well conserved) diverged considerably between the bacterial/eukaryotic MATs and archaeal MAT. A detailed investigation of the available structures supports the sequence analysis outcome: The protein domains and subdomains of bacterial and eukaryotic MAT are more similar than those of archaea. Finally, we resurrected archaeal MAT ancestors. Interestingly, archaeal MAT ancestors show substrate specificity, which is lost during evolution. This observation supports the hypothesis of a common MAT ancestor for the three domains of life. In conclusion, we have demonstrated that archaeal MAT is an ideal system for studying an enzyme family that evolved differently in one domain compared with others while maintaining the same catalytic activity.}, }
@article {pmid34650523, year = {2021}, author = {Bhattarai, B and Bhattacharjee, AS and Coutinho, FH and Goel, RK}, title = {Viruses and Their Interactions With Bacteria and Archaea of Hypersaline Great Salt Lake.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {701414}, pmid = {34650523}, issn = {1664-302X}, abstract = {Viruses play vital biogeochemical and ecological roles by (a) expressing auxiliary metabolic genes during infection, (b) enhancing the lateral transfer of host genes, and (c) inducing host mortality. Even in harsh and extreme environments, viruses are major players in carbon and nutrient recycling from organic matter. However, there is much that we do not yet understand about viruses and the processes mediated by them in the extreme environments such as hypersaline habitats. The Great Salt Lake (GSL) in Utah, United States is a hypersaline ecosystem where the biogeochemical role of viruses is poorly understood. This study elucidates the diversity of viruses and describes virus-host interactions in GSL sediments along a salinity gradient. The GSL sediment virosphere consisted of Haloviruses (32.07 ± 19.33%) and members of families Siphoviridae (39.12 ± 19.8%), Myoviridae (13.7 ± 6.6%), and Podoviridae (5.43 ± 0.64%). Our results demonstrate that salinity alongside the concentration of organic carbon and inorganic nutrients (nitrogen and phosphorus) governs the viral, bacteria, and archaeal diversity in this habitat. Computational host predictions for the GSL viruses revealed a wide host range with a dominance of viruses that infect Proteobacteria, Actinobacteria, and Firmicutes. Identification of auxiliary metabolic genes for photosynthesis (psbA), carbon fixation (rbcL, cbbL), formaldehyde assimilation (SHMT), and nitric oxide reduction (NorQ) shed light on the roles played by GSL viruses in biogeochemical cycles of global relevance.}, }
@article {pmid34628131, year = {2021}, author = {Castro, I and Costa, H and Turgeman-Grott, I and Allers, T and Mendo, S and Caetano, T}, title = {The lanthipeptide biosynthetic clusters of the domain Archaea.}, journal = {Microbiological research}, volume = {253}, number = {}, pages = {126884}, doi = {10.1016/j.micres.2021.126884}, pmid = {34628131}, issn = {1618-0623}, mesh = {*Archaea/genetics ; Eukaryota ; Euryarchaeota ; *Peptides/genetics ; }, abstract = {Research on Archaea's secondary metabolites is still lagging behind that of Bacteria and Eukarya. Our goal was to contribute to this knowledge gap by analyzing the lanthipeptide's clusters in Archaea. As previously proposed, Archaea encodes only class II synthetases (LanMs), which we found to be confined to the class Halobacteria (also known as haloarchaea). In total, we analyzed the phylogeny and the domains of 42 LanMs. Four types were identified, and the majority of them belong to the CCG group due to their cyclization domain, which includes LanMs of Cyanobacteria. Putative cognate peptides were predicted for most of LanMs and are a very diverse group of molecules that share a Kx(Y/F)(D/E)xx(F/Y) motif in their leader peptides. According to their homology, some of them were categorized into subfamilies, including Halolancins, Haladacins, Haloferaxcins and Halobiforcins. Many LanM genes were associated with mobile genetic elements, and their vicinities mainly encode ABC and MFS transporters, tailoring enzymes and uncharacterized proteins. Our results suggest that the biosynthesis of lanthipeptides in haloarchaea can entail distinct enzymology that must lead to the production of peptides with novel structures and unpredicted biological and ecological roles. Finally, an Haloferax mediterranei knockout, lacking its three lanM genes, was generated, and it was concluded that its antimicrobial activity is not primarily related to the production of lanthipeptides.}, }
@article {pmid34606606, year = {2021}, author = {Payne, LJ and Todeschini, TC and Wu, Y and Perry, BJ and Ronson, CW and Fineran, PC and Nobrega, FL and Jackson, SA}, title = {Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types.}, journal = {Nucleic acids research}, volume = {49}, number = {19}, pages = {10868-10878}, pmid = {34606606}, issn = {1362-4962}, mesh = {Adenosine Triphosphatases/genetics/metabolism ; Antibiosis/*genetics ; Archaea/classification/*genetics/metabolism/virology ; Archaeal Proteins/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism/virology ; Bacterial Proteins/*genetics/metabolism ; Bacteriophages/*genetics/growth &amp; development ; CRISPR-Cas Systems ; DNA Helicases/genetics/metabolism ; DNA Modification Methylases/genetics/metabolism ; Markov Chains ; Phylogeny ; *Software ; Terminology as Topic ; }, abstract = {To provide protection against viral infection and limit the uptake of mobile genetic elements, bacteria and archaea have evolved many diverse defence systems. The discovery and application of CRISPR-Cas adaptive immune systems has spurred recent interest in the identification and classification of new types of defence systems. Many new defence systems have recently been reported but there is a lack of accessible tools available to identify homologs of these systems in different genomes. Here, we report the Prokaryotic Antiviral Defence LOCator (PADLOC), a flexible and scalable open-source tool for defence system identification. With PADLOC, defence system genes are identified using HMM-based homologue searches, followed by validation of system completeness using gene presence/absence and synteny criteria specified by customisable system classifications. We show that PADLOC identifies defence systems with high accuracy and sensitivity. Our modular approach to organising the HMMs and system classifications allows additional defence systems to be easily integrated into the PADLOC database. To demonstrate application of PADLOC to biological questions, we used PADLOC to identify six new subtypes of known defence systems and a putative novel defence system comprised of a helicase, methylase and ATPase. PADLOC is available as a standalone package (https://github.com/padlocbio/padloc) and as a webserver (https://padloc.otago.ac.nz).}, }
@article {pmid34578152, year = {2021}, author = {Krawczyk, A and Salamon, D and Kowalska-Duplaga, K and Bogiel, T and Gosiewski, T}, title = {Association of Fungi and Archaea of the Gut Microbiota with Crohn's Disease in Pediatric Patients-Pilot Study.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {9}, pages = {}, pmid = {34578152}, issn = {2076-0817}, support = {2019/33/N/NZ5/00698//National Science Center in Poland/ ; }, abstract = {The composition of bacteria is often altered in Crohn's disease (CD), but its connection to the disease is not fully understood. Gut archaea and fungi have recently been suggested to play a role as well. In our study, the presence and number of selected species of fungi and archaea in pediatric patients with CD and healthy controls were evaluated. Stool samples were collected from children with active CD (n = 54), non-active CD (n = 37) and control subjects (n = 33). The prevalence and the number of selected microorganisms were assessed by real-time PCR. The prevalence of Candida tropicalis was significantly increased in active CD compared to non-active CD and the control group (p = 0.011 and p = 0.036, respectively). The number of Malassezia spp. cells was significantly lower in patients with active CD compared to the control group, but in non-active CD, a significant increase was observed (p = 0.005 and p = 0.020, respectively). There were no statistically significant differences in the colonization by archaea. The obtained results indicate possible correlations with the course of the CD; however, further studies of the entire archeobiome and the mycobiome are necessary in order to receive a complete picture.}, }
@article {pmid34575103, year = {2021}, author = {Merkel, AY and Chernyh, NA and Pimenov, NV and Bonch-Osmolovskaya, EA and Slobodkin, AI}, title = {Diversity and Metabolic Potential of the Terrestrial Mud Volcano Microbial Community with a High Abundance of Archaea Mediating the Anaerobic Oxidation of Methane.}, journal = {Life (Basel, Switzerland)}, volume = {11}, number = {9}, pages = {}, pmid = {34575103}, issn = {2075-1729}, support = {. 17-74-30025//Russian Science Foundation/ ; n/a//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Terrestrial mud volcanoes (TMVs) are important natural sources of methane emission. The microorganisms inhabiting these environments remain largely unknown. We studied the phylogenetic composition and metabolic potential of the prokaryotic communities of TMVs located in the Taman Peninsula, Russia, using a metagenomic approach. One of the examined sites harbored a unique community with a high abundance of anaerobic methane-oxidizing archaea belonging to ANME-3 group (39% of all 16S rRNA gene reads). The high number of ANME-3 archaea was confirmed by qPCR, while the process of anaerobic methane oxidation was demonstrated by radioisotopic experiments. We recovered metagenome-assembled genomes (MAGs) of archaeal and bacterial community members and analyzed their metabolic capabilities. The ANME-3 MAG contained a complete set of genes for methanogenesis as well as of ribosomal RNA and did not encode proteins involved in dissimilatory nitrate or sulfate reduction. The presence of multiheme c-type cytochromes suggests that ANME-3 can couple methane oxidation with the reduction of metal oxides or with the interspecies electron transfer to a bacterial partner. The bacterial members of the community were mainly represented by autotrophic, nitrate-reducing, sulfur-oxidizing bacteria, as well as by fermentative microorganisms. This study extends the current knowledge of the phylogenetic and metabolic diversity of prokaryotes in TMVs and provides a first insight into the genomic features of ANME-3 archaea.}, }
@article {pmid34543104, year = {2022}, author = {Weidenbach, K and Gutt, M and Cassidy, L and Chibani, C and Schmitz, RA}, title = {Small Proteins in Archaea, a Mainly Unexplored World.}, journal = {Journal of bacteriology}, volume = {204}, number = {1}, pages = {e0031321}, pmid = {34543104}, issn = {1098-5530}, mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/genetics/*metabolism ; Gene Expression Regulation, Archaeal/*physiology ; Genome, Archaeal ; }, abstract = {In recent years, increasing numbers of small proteins have moved into the focus of science. Small proteins have been identified and characterized in all three domains of life, but the majority remains functionally uncharacterized, lack secondary structure, and exhibit limited evolutionary conservation. While quite a few have already been described for bacteria and eukaryotic organisms, the amount of known and functionally analyzed archaeal small proteins is still very limited. In this review, we compile the current state of research, show strategies for systematic approaches for global identification of small archaeal proteins, and address selected functionally characterized examples. Besides, we document exemplarily for one archaeon the tool development and optimization to identify small proteins using genome-wide approaches.}, }
@article {pmid34535658, year = {2021}, author = {Blombach, F and Fouqueau, T and Matelska, D and Smollett, K and Werner, F}, title = {Promoter-proximal elongation regulates transcription in archaea.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5524}, pmid = {34535658}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; WT 207446/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {CRISPR-Cas Systems/genetics ; DNA/metabolism ; DNA-Directed RNA Polymerases/metabolism ; Oxidative Stress/genetics ; *Promoter Regions, Genetic ; Regression Analysis ; Sulfolobus solfataricus/*genetics/growth &amp; development ; *Transcription Elongation, Genetic ; }, abstract = {Recruitment of RNA polymerase and initiation factors to the promoter is the only known target for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation are involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Saccharolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome. Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.}, }
@article {pmid34531846, year = {2021}, author = {Lin, T and Zhang, L and Wu, M and Jiang, D and Li, Z and Yang, Z}, title = {Repair of Hypoxanthine in DNA Revealed by DNA Glycosylases and Endonucleases From Hyperthermophilic Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {736915}, pmid = {34531846}, issn = {1664-302X}, abstract = {Since hyperthermophilic Archaea (HA) thrive in high-temperature environments, which accelerate the rates of deamination of base in DNA, their genomic stability is facing a severe challenge. Hypoxanthine (Hx) is one of the common deaminated bases in DNA. Generally, replication of Hx in DNA before repaired causes AT → GC mutation. Biochemical data have demonstrated that 3-methyladenine DNA glycosylase II (AlkA) and Family V uracil DNA glycosylase (UDG) from HA could excise Hx from DNA, thus triggering a base excision repair (BER) process for Hx repair. Besides, three endonucleases have been reported from HA: Endonuclease V (EndoV), Endonuclease Q (EndoQ), and Endonuclease NucS (EndoNucS), capable of cleaving Hx-containing DNA, thereby providing alternative pathways for Hx repair. Both EndoV and EndoQ could cleave one DNA strand with Hx, thus forming a nick and further initiating an alternative excision repair (AER) process for the follow-up repair. By comparison, EndoNucS cleaves both strands of Hx-containing DNA in a restriction endonuclease manner, thus producing a double-stranded break (DSB). This created DSB might be repaired by homologous recombination (HR) or by a combination activity of DNA polymerase (DNA pol), flap endonuclease 1 (FEN1), and DNA ligase (DNA lig). Herein, we reviewed the most recent advances in repair of Hx in DNA triggered by DNA glycosylases and endonucleases from HA, and proposed future research directions.}, }
@article {pmid34526983, year = {2021}, author = {Franke, JD and Fuerst, JA and Poole, AM}, title = {Editorial: Structure, Function and Evolution of Complex Cellular Organization in Bacteria and Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {751416}, pmid = {34526983}, issn = {1664-302X}, }
@article {pmid34516368, year = {2021}, author = {Pallen, MJ}, title = {The status Candidatus for uncultured taxa of Bacteria and Archaea: SWOT analysis.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {71}, number = {9}, pages = {}, pmid = {34516368}, issn = {1466-5034}, mesh = {*Archaea/classification ; *Bacteria/classification ; Phylogeny ; Terminology as Topic ; }, abstract = {The status Candidatus was introduced to bacterial taxonomy in the 1990s to accommodate uncultured taxa defined by analyses of DNA sequences. Here I review the strengths, weaknesses, opportunities and threats (SWOT) associated with the status Candidatus in the light of a quarter century of use, twinned with recent developments in bacterial taxonomy and sequence-based taxonomic discovery. Despite ambiguities as to its scope, philosophical objections to its use and practical problems in implementation, the status Candidatus has now been applied to over 1000 taxa and has been widely adopted by journals and databases. Although lacking priority under the International Code for Nomenclature of Prokaryotes, many Candidatus names have already achieved de facto standing in the academic literature and in databases via description of a taxon in a peer-reviewed publication, alongside deposition of a genome sequence and there is a clear path to valid publication of such names on culture. Continued and increased use of Candidatus names provides an alternative to the potential upheaval that might accompany creation of a new additional code of nomenclature and provides a ready solution to the urgent challenge of naming many thousands of newly discovered but uncultured species.}, }
@article {pmid34509601, year = {2021}, author = {Kumar, V and Singh, B and van Belkum, MJ and Diep, DB and Chikindas, ML and Ermakov, AM and Tiwari, SK}, title = {Halocins, natural antimicrobials of Archaea: Exotic or special or both?.}, journal = {Biotechnology advances}, volume = {53}, number = {}, pages = {107834}, doi = {10.1016/j.biotechadv.2021.107834}, pmid = {34509601}, issn = {1873-1899}, mesh = {Anti-Bacterial Agents ; *Anti-Infective Agents/pharmacology ; *Archaea ; Sodium Chloride ; }, abstract = {Haloarchaea are adapted to survive under extreme saline conditions by accumulating osmolytes and salts to counteract the high osmotic pressure in their habitats. As a consequence, their proteins have evolved to remain active, or even most active, at very high ionic strength. Halocins are proteinaceous antimicrobial substances that are ribosomally-synthesized by haloarchaea and they provide the producers an advantage in the competition for nutrients and ecological niches. These antimicrobials are stable at high temperature, elevated salt concentrations, and alkaline pH conditions. These properties have endowed them with great potential in diverse biotechnological applications, which involve extreme processing conditions (such as high salt concentrations, high pressure, or high temperatures). They kill target cells by inhibition of Na[+]/H[+] antiporter in the membrane or modification/disruption of the cell membrane leading to cell lysis. In general, the taxonomy of haloarchaea and their typical phenotypic and genotypic characteristics are well studied; however, information regarding their halocins, especially aspects related to genetics, biosynthetic pathways, mechanism of action, and structure-function relationship is very limited. A few studies have demonstrated the potential applications of halocins in the preservation of salted food products and brine-cured hides in leather industries, protecting the myocardium from ischemia and reperfusion injury, as well as from life-threatening diseases such as cardiac arrest and cancers. In recent years, genome mining has been an essential tool to decipher the genetic basis of halocin biosynthesis. Nevertheless, this is likely the tip of the iceberg as genome analyses have revealed many putative halocins in databases waiting for further investigation. Identification and characterization of this source of halocins may lead to antimicrobials for future therapeutics and/or food preservation. Hence, the present review analyzes different aspects of halocins such as biosynthesis, mechanism of action against target cells, and potential biotechnological applications.}, }
@article {pmid37938279, year = {2021}, author = {Thomas, CM and Taib, N and Gribaldo, S and Borrel, G}, title = {Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {47}, pmid = {37938279}, issn = {2730-6151}, support = {ANR-19-CE02-0005-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-16-CE02-0005-01//Agence Nationale de la Recherche (French National Research Agency)/ ; }, abstract = {Other than the Methanobacteriales and Methanomassiliicoccales, the characteristics of archaea that inhabit the animal microbiome are largely unknown. Methanimicrococcus blatticola, a member of the Methanosarcinales, currently reunites two unique features within this order: it is a colonizer of the animal digestive tract and can only reduce methyl compounds with H2 for methanogenesis, a increasingly recognized metabolism in the archaea and whose origin remains debated. To understand the origin of these characteristics, we have carried out a large-scale comparative genomic analysis. We infer the loss of more than a thousand genes in M. blatticola, by far the largest genome reduction across all Methanosarcinales. These include numerous elements for sensing the environment and adapting to more stable gut conditions, as well as a significant remodeling of the cell surface components likely involved in host and gut microbiota interactions. Several of these modifications parallel those previously observed in phylogenetically distant archaea and bacteria from the animal microbiome, suggesting large-scale convergent mechanisms of adaptation to the gut. Strikingly, M. blatticola has lost almost all genes coding for the H4MPT methyl branch of the Wood-Ljungdahl pathway (to the exception of mer), a phenomenon never reported before in any member of Class I or Class II methanogens. The loss of this pathway illustrates one of the evolutionary processes that may have led to the emergence of methyl-reducing hydrogenotrophic methanogens, possibly linked to the colonization of organic-rich environments (including the animal gut) where both methyl compounds and hydrogen are abundant.}, }
@article {pmid34491083, year = {2021}, author = {Li, L and Zhang, W and Zhang, S and Song, L and Sun, Q and Zhang, H and Xiang, H and Dong, X}, title = {Bacteria and Archaea Synergistically Convert Glycine Betaine to Biogenic Methane in the Formosa Cold Seep of the South China Sea.}, journal = {mSystems}, volume = {6}, number = {5}, pages = {e0070321}, pmid = {34491083}, issn = {2379-5077}, support = {2018YFC0310801//Ministry of Science and Technology of the People's Republic of China (MOST)/ ; }, abstract = {Cold seeps are globally widespread seafloor ecosystems that feature abundant methane production and flourishing chemotrophic benthic communities. Chemical evidence indicates that cold seep methane is largely biogenic; however, the primary methane-producing organisms and associated pathways involved in methanogenesis remain elusive. This work detected methane production when glycine betaine (GBT) or trimethylamine (TMA) was added to the sediment microcosms of the Formosa cold seep, South China Sea. The methane production was suppressed by antibiotic inhibition of bacteria, while GBT was accumulated. This suggests that the widely used osmoprotectant GBT could be converted to cold seep biogenic methane via the synergistic activity of bacteria and methanogenic archaea because archaea are not sensitive to antibiotics and no bacteria are known to produce ample methane (mM). 16S rRNA gene diversity analyses revealed that the predominant bacterial and archaeal genera in the GBT-amended methanogenic microcosms included Oceanirhabdus and Methanococcoides. Moreover, metagenomic analyses detected the presence of grdH and mtgB genes that are involved in GBT reduction and demethylation, respectively. Two novel species were obtained, including bacterium Oceanirhabdus seepicola, which reduces GBT to TMA, and a methanogenic archaeon, Methanococcoides seepicolus, which produces methane from TMA and GBT. The two strains reconstituted coculture efficiently converted GBT to methane at 18°C; however, at 4°C addition of dimethylglycine (DMG), the GBT demethylation product, was necessary. Therefore, this work demonstrated that GBT is the precursor not only of the biogenic methane but also of the cryoprotectant DMG to the microorganisms at the Formosa cold seep. IMPORTANCE Numerous cold seeps have been found in global continental margins where methane is enriched in pore waters that are forced upward from sediments. Therefore, high concerns have been focused on the methane-producing organisms and the metabolic pathways in these environments because methane is a potent greenhouse gas. In this study, GBT was identified as the main precursor for methane in the Formosa cold seep of the South China Sea. Further, synergism of bacteria and methanogenic archaea was identified in GBT conversion to methane via the GBT reduction pathway, while methanogen-mediated GBT demethylation to methane was also observed. In addition, GBT-demethylated product dimethyl glycine acted as a cryoprotectant that promoted the cold seep microorganisms at cold temperatures. GBT is an osmoprotectant that is widely used by marine organisms, and therefore, the GBT-derived methanogenic pathway reported here could be widely distributed among global cold seep environments.}, }
@article {pmid34490397, year = {2021}, author = {Hu, D and Yang, J and Qi, Y and Li, B and Li, K and Mok, KM}, title = {Metagenomic Analysis of Fecal Archaea, Bacteria, Eukaryota, and Virus in Przewalski's Horses Following Anthelmintic Treatment.}, journal = {Frontiers in veterinary science}, volume = {8}, number = {}, pages = {708512}, pmid = {34490397}, issn = {2297-1769}, abstract = {Intestinal microbiota is involved in immune response and metabolism of the host. The frequent use of anthelmintic compounds for parasite expulsion causes disturbance to the equine intestinal microbiota. However, most studies were on the effects of such treatment on the intestinal bacterial microbes; none is on the entire microbial community including archaea and eukaryotic and viral community in equine animals. This study is the first to explore the differences of the microbial community composition and structure in Przewalski's horses prior to and following anthelmintic treatment, and to determine the corresponding changes of their functional attributes based on metagenomic sequencing. Results showed that in archaea, the methanogen of Euryarchaeota was the dominant phylum. Under this phylum, anthelmintic treatment increased the Methanobrevibacter genus and decreased the Methanocorpusculum genus and two other dominant archaea species, Methanocorpusculum labreanum and Methanocorpusculum bavaricum. In bacteria, Firmicutes and Bacteroidetes were the dominant phyla. Anthelmintic treatment increased the genera of Clostridium and Eubacterium and decreased those of Bacteroides and Prevotella and dominant bacteria species. These altered genera were associated with immunity and digestion. In eukaryota, anthelmintic treatment also changed the genera related to digestion and substantially decreased the relative abundances of identified species. In virus, anthelmintic treatment increased the genus of unclassified_d__Viruses and decreased those of unclassified_f__Siphoviridae and unclassified_f__Myoviridae. Most of the identified viral species were classified into phage, which were more sensitive to anthelmintic treatment than other viruses. Furthermore, anthelmintic treatment was found to increase the number of pathogens related to some clinical diseases in horses. The COG and KEGG function analysis showed that the intestinal microbiota of Przewalski's horse mainly participated in the carbohydrate and amino acid metabolism. The anthelmintic treatment did not change their overall function; however, it displaced the population of the functional microbes involved in each function or pathway. These results provide a complete view on the changes caused by anthelmintic treatment in the intestinal microbiota of the Przewalski's horses.}, }
@article {pmid34489912, year = {2021}, author = {Makarova, KS and Wolf, YI and Karamycheva, S and Koonin, EV}, title = {A Unique Gene Module in Thermococcales Archaea Centered on a Hypervariable Protein Containing Immunoglobulin Domains.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {721392}, pmid = {34489912}, issn = {1664-302X}, abstract = {Molecular mechanisms involved in biological conflicts and self vs nonself recognition in archaea remain poorly characterized. We apply phylogenomic analysis to identify a hypervariable gene module that is widespread among Thermococcales. These loci consist of an upstream gene coding for a large protein containing several immunoglobulin (Ig) domains and unique combinations of downstream genes, some of which also contain Ig domains. In the large Ig domain containing protein, the C-terminal Ig domain sequence is hypervariable, apparently, as a result of recombination between genes from different Thermococcales. To reflect the hypervariability, we denote this gene module VARTIG (VARiable Thermococcales IG). The overall organization of the VARTIG modules is similar to the organization of Polymorphic Toxin Systems (PTS). Archaeal genomes outside Thermococcales encode a variety of Ig domain proteins, but no counterparts to VARTIG and no Ig domains with comparable levels of variability. The specific functions of VARTIG remain unknown but the identified features of this system imply three testable hypotheses: (i) involvement in inter-microbial conflicts analogous to PTS, (ii) role in innate immunity analogous to the vertebrate complement system, and (iii) function in self vs nonself discrimination analogous to the vertebrate Major Histocompatibility Complex. The latter two hypotheses seem to be of particular interest given the apparent analogy to the vertebrate immunity.}, }
@article {pmid34487604, year = {2022}, author = {Haiming, T and Chao, L and Kaikai, C and Lihong, S and Li, W and Weiyan, L and Xiaoping, X and Ke, W}, title = {Effects of short-term soil tillage practice on activity and community structure of ammonia-oxidizing bacteria and archaea under the double-cropping rice field.}, journal = {Journal of applied microbiology}, volume = {132}, number = {2}, pages = {1307-1318}, doi = {10.1111/jam.15289}, pmid = {34487604}, issn = {1365-2672}, support = {//National Natural Science Foundation of China/ ; 2019JJ10003//Innovative Research Groups of the Natural Science Foundation of Hunan Province/ ; }, mesh = {Ammonia ; Archaea/genetics ; *Betaproteobacteria ; Nitrification ; *Oryza ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; }, abstract = {AIMS: The potential nitrification activity (PNA), population size and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in paddy soil from a short-term (5 years) tillage field experiment conducted at tillering stage of late rice were investigated using the shaken slurry method and quantitative real-time polymerase chain reaction.<br><br>METHODS AND RESULTS: The experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue returning (NT) and rotary tillage with all crop residues removed as a control (RTO). The results showed that PNA in paddy soil of CT, RT and NT treatments was higher than that of RTO treatment, and the abundance of AOA and AOB was much higher in paddy soil of CT, RT and NT treatments than RTO treatment. Meanwhile, PNA and the abundance of AOB and AOA in paddy soil were greatly enhanced by combined application of tillage and crop residue, whereas PNA and the abundance of AOB and AOA in paddy soil were decreased by combined application of no-tillage and crop residue. Moreover, PNA was closely correlated with the abundance and community structure of AOB rather than AOA. The results also showed that PNA and the population sizes of AOB and AOA in crop incorporation treatments were higher than that of crop residue removed treatment. Cluster and redundancy analyses indicated that crop residue effect played a more important role in shaping AOA community structure compared to short-term tillage management.<br><br>CONCLUSIONS: The results indicated that AOB rather than AOA functionally dominated ammonia oxidation in the double-cropping rice paddy soil, the activities of AOB and AOA were increased and the community structure was also changed under the combination of conventional tillage, rotary tillage and crop residue condition.<br><br>The activity and community structure of AOB and AOA, which were affected by the combination of tillage and crop residue managements, play an important role in cycling of nitrogen.}, }
@article {pmid34464803, year = {2022}, author = {Cai, M and Yin, X and Tang, X and Zhang, C and Zheng, Q and Li, M}, title = {Metatranscriptomics reveals different features of methanogenic archaea among global vegetated coastal ecosystems.}, journal = {The Science of the total environment}, volume = {802}, number = {}, pages = {149848}, doi = {10.1016/j.scitotenv.2021.149848}, pmid = {34464803}, issn = {1879-1026}, mesh = {*Archaea/genetics ; *Ecosystem ; Methane ; Methanosarcinaceae ; Methanosarcinales ; Phylogeny ; }, abstract = {Vegetated coastal ecosystems (VCEs; i.e., mangroves, saltmarshes, and seagrasses) represent important sources of natural methane emission. Despite recent advances in the understanding of novel taxa and pathways associated with methanogenesis in these ecosystems, the key methanogenic players and the contribution of different substrates to methane formation remain elusive. Here, we systematically investigate the community and activity of methanogens using publicly available metatranscriptomes at a global scale together with our in-house metatranscriptomic dataset. Taxonomic profiling reveals that 13 groups of methanogenic archaea were transcribed in the investigated VCEs, and they were predominated by Methanosarcinales. Among these VCEs, methanogens exhibited all the three known methanogenic pathways in some mangrove sediments, where methylotrophic methanogens Methanosarcinales/Methanomassiliicoccales grew on diverse methyl compounds and coexisted with hydrogenotrophic (mainly Methanomicrobiales) and acetoclastic (mainly Methanothrix) methanogens. Contrastingly, the predominant methanogenic pathway in saltmarshes and seagrasses was constrained to methylotrophic methanogenesis. These findings reveal different archaeal methanogens in VCEs and suggest the potentially distinct methanogenesis contributions in these VCEs to the global warming.}, }
@article {pmid34442741, year = {2021}, author = {Koirala, A and Brözel, VS}, title = {Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea.}, journal = {Microorganisms}, volume = {9}, number = {8}, pages = {}, pmid = {34442741}, issn = {2076-2607}, abstract = {The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico prediction of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocumented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes are currently supported by biochemical evidence of diazotrophy. In addition, this work provides reference for any inter-phyla comparison of Nif sequences and a quality database of Nif proteins that can be used for identifying new Nif sequences.}, }
@article {pmid34436605, year = {2021}, author = {Martinez-Gutierrez, CA and Aylward, FO}, title = {Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea.}, journal = {Molecular biology and evolution}, volume = {38}, number = {12}, pages = {5514-5527}, pmid = {34436605}, issn = {1537-1719}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Biological Evolution ; Phylogeny ; Uncertainty ; }, abstract = {Reconstruction of the Tree of Life is a central goal in biology. Although numerous novel phyla of bacteria and archaea have recently been discovered, inconsistent phylogenetic relationships are routinely reported, and many inter-phylum and inter-domain evolutionary relationships remain unclear. Here, we benchmark different marker genes often used in constructing multidomain phylogenetic trees of bacteria and archaea and present a set of marker genes that perform best for multidomain trees constructed from concatenated alignments. We use recen