@article {pmid35962889, year = {2022}, author = {Oliveira, MET and Paulino, GVB and Dos Santos Júnior, ED and da Silva Oliveira, FA and Melo, VMM and Ursulino, JS and de Aquino, TM and Shetty, AK and Landell, MF and Gitaí, DLG}, title = {Multi-omic Analysis of the Gut Microbiome in Rats with Lithium-Pilocarpine-Induced Temporal Lobe Epilepsy.}, journal = {Molecular neurobiology}, volume = {}, number = {}, pages = {}, pmid = {35962889}, issn = {1559-1182}, support = {311553/2018-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 313769/2018-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 312889/2021-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 315895/2021-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Evidence supports that the gut microbiota and bacteria-dependent metabolites influence the maintenance of epileptic brain activity. However, the alterations in the gut microbiota between epileptic versus healthy individuals are poorly understood. We used a multi-omic approach to evaluate the changes in the composition of gut metagenome as well in the fecal metabolomic profile in rats before and after being submitted to status epilepticus (SE)-induced temporal lobe epilepsy (TLE). The 16S ribosomal RNA (rRNA) sequencing of fecal samples coupled to bioinformatic analysis revealed taxonomic, compositional, and functional shifts in epileptic rats. The species richness (Chao1 index) was significantly lower in the post-TLE group, and the β-diversity analysis revealed clustering separated from the pre-TLE group. The taxonomic abundance analysis showed a significant increase of phylum Desulfobacterota and a decrease of Patescibacteria in the post-TLE group. The DESEq2 and LEfSe analysis resulted in 18 genera significantly enriched between post-TLE and pre-TLE groups at the genus level. We observed that epileptic rats present a peculiar metabolic phenotype, including a lower concentration of D-glucose and L-lactic acid and a higher concentration of L-glutamic acid and glycine. The microbiota-host metabolic correlation analysis showed that the genera differentially abundant in post-TLE rats are associated with the altered metabolites, especially the proinflammatory Desulfovibrio and Marvinbryantia, which were enriched in epileptic animals and positively correlated with these excitatory neurotransmitters and carbohydrate metabolites. Therefore, our data revealed a correlation between dysbacteriosis in epileptic animals and fecal metabolites that are known to be relevant for maintaining epileptic brain activity by enhancing chronic inflammation, an excitatory-inhibitory imbalance, and/or a metabolic disturbance. These data are promising and suggest that targeting the gut microbiota could provide a novel avenue for preventing and treating acquired epilepsy. However, the causal relationship between these microbial/metabolite components and the SRS occurrence still needs further exploration.}, }
@article {pmid35962839, year = {2022}, author = {Gadoin, E and Desnues, C and d'Orbcastel, ER and Bouvier, T and Auguet, JC and Dagorn, L and Moroh, JL and Adingra, A and Bettarel, Y}, title = {Fishing for the Microbiome of Tropical Tuna.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35962839}, issn = {1432-184X}, abstract = {Although tunas represent a significant part of the global fish economy and a major nutritional resource worldwide, their microbiome still remains poorly documented. Here, we conducted an analysis of the taxonomic composition of the bacterial communities inhabiting the gut, skin, and liver of two most consumed tropical tuna species (skipjack and yellowfin), from individuals caught in the Atlantic and Indian oceans. We hypothesized that each organ harbors a specific microbial assemblage whose composition might vary according to different biotic (sex, species) and/or abiotic (environmental) factors. Our results revealed that the composition of the tuna microbiome was totally independent of fish sex, regardless of the species and ocean considered. Instead, the main determinants of observed diversity were (i) tuna species for the gut and (ii) sampling site for the skin mucus layer and (iii) a combination of both parameters for the liver. Interestingly, 4.5% of all amplicon sequence variants (ASV) were shared by the three organs, highlighting the presence of a core-microbiota whose most abundant representatives belonged to the genera Mycoplasma, Cutibacterium, and Photobacterium. Our study also revealed the presence of a unique and diversified bacterial assemblage within the tuna liver, comprising a substantial proportion of potential histamine-producing bacteria, well known for their pathogenicity and their contribution to fish poisoning cases. These results indicate that this organ is an unexplored microbial niche whose role in the health of both the host and consumers remains to be elucidated.}, }
@article {pmid35962280, year = {2022}, author = {Bizarria, R and de Castro Pietrobon, T and Rodrigues, A}, title = {Uncovering the Yeast Communities in Fungus-Growing Ant Colonies.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35962280}, issn = {1432-184X}, support = {2019/03746-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2019/24412-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 305269/2018-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 142396/2019-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Yeast-insect interactions are compelling models to study the evolution, ecology, and diversification of yeasts. Fungus-growing (attine) ants are prominent insects in the Neotropics that evolved an ancient fungiculture of basidiomycete fungi over 55-65 million years, supplying an environment for a hidden yeast diversity. Here we assessed the yeast diversity in the attine ant environment by thoroughly sampling fungus gardens across four out of five ant fungiculture systems: Acromyrmex coronatus and Mycetomoellerius tucumanus standing for leaf-cutting and higher-attine fungicultures, respectively; Apterostigma sp., Mycetophylax sp., and Mycocepurus goeldii as ants from the lower-attine fungiculture. Among the fungus gardens of all fungus-growing ants examined, we found taxonomically unique and diverse microbial yeast communities across the different fungicultures. Ascomycete yeasts were the core taxa in fungus garden samples, with Saccharomycetales as the most frequent order. The genera Aureobasidium, Candida, Papiliotrema, Starmerella, and Sugiyamaella had the highest incidence in fungus gardens. Despite the expected similarity within the same fungiculture system, colonies of the same ant species differed in community structure. Among Saccharomycotina yeasts, few were distinguishable as killer yeasts, with a classical inhibition pattern for the killer phenotype, differing from earlier observations in this environment, which should be further investigated. Yeast mycobiome in fungus gardens is distinct between colonies of the same fungiculture and each ant colony harbors a distinguished and unique yeast community. Fungus gardens of attine ants are emergent environments to study the diversity and ecology of yeasts associated with insects.}, }
@article {pmid35960845, year = {2022}, author = {Amend, AS and Swift, SOI and Darcy, JL and Belcaid, M and Nelson, CE and Buchanan, J and Cetraro, N and Fraiola, KMS and Frank, K and Kajihara, K and McDermot, TG and McFall-Ngai, M and Medeiros, M and Mora, C and Nakayama, KK and Nguyen, NH and Rollins, RL and Sadowski, P and Sparagon, W and Téfit, MA and Yew, JY and Yogi, D and Hynson, NA}, title = {A ridge-to-reef ecosystem microbial census reveals environmental reservoirs for animal and plant microbiomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {33}, pages = {e2204146119}, doi = {10.1073/pnas.2204146119}, pmid = {35960845}, issn = {1091-6490}, support = {NA//W.M. Keck Foundation/ ; NA//The Office of the OVCR of the University of Hawaiʻi at Mānoa/ ; P20GM125508//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, abstract = {Microbes are found in nearly every habitat and organism on the planet, where they are critical to host health, fitness, and metabolism. In most organisms, few microbes are inherited at birth; instead, acquiring microbiomes generally involves complicated interactions between the environment, hosts, and symbionts. Despite the criticality of microbiome acquisition, we know little about where hosts' microbes reside when not in or on hosts of interest. Because microbes span a continuum ranging from generalists associating with multiple hosts and habitats to specialists with narrower host ranges, identifying potential sources of microbial diversity that can contribute to the microbiomes of unrelated hosts is a gap in our understanding of microbiome assembly. Microbial dispersal attenuates with distance, so identifying sources and sinks requires data from microbiomes that are contemporary and near enough for potential microbial transmission. Here, we characterize microbiomes across adjacent terrestrial and aquatic hosts and habitats throughout an entire watershed, showing that the most species-poor microbiomes are partial subsets of the most species-rich and that microbiomes of plants and animals are nested within those of their environments. Furthermore, we show that the host and habitat range of a microbe within a single ecosystem predicts its global distribution, a relationship with implications for global microbial assembly processes. Thus, the tendency for microbes to occupy multiple habitats and unrelated hosts enables persistent microbiomes, even when host populations are disjunct. Our whole-watershed census demonstrates how a nested distribution of microbes, following the trophic hierarchies of hosts, can shape microbial acquisition.}, }
@article {pmid35960594, year = {2022}, author = {Koistinen, VM and Hedberg, M and Shi, L and Johansson, A and Savolainen, O and Lehtonen, M and Aura, AM and Hanhineva, K and Landberg, R}, title = {Metabolite Pattern Derived from Lactiplantibacillus plantarum-fermented rye Foods and in vitro Gut Fermentation Synergistically Inhibits Bacterial Growth.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e2101096}, doi = {10.1002/mnfr.202101096}, pmid = {35960594}, issn = {1613-4133}, abstract = {SCOPE: Fermentation improves many food characteristics using microbes, such as lactic acid bacteria (LAB). Recent studies suggest fermentation may also enhance the health properties, but mechanistic evidence is lacking. We aimed to identify a metabolite pattern reproducibly produced during sourdough and in vitro colonic fermentation of various whole-grain rye products and how it affects the growth of bacterial species of potential importance to health and disease.<br><br>METHODS AND RESULTS: We used Lactiplantibacillus plantarum DSMZ 13890 strain, previously shown to favour rye as its substrate. Using LC-MS metabolomics, we found seven microbial metabolites commonly produced during the fermentations, including dihydroferulic acid, dihydrocaffeic acid, and five amino acid metabolites, and stronger inhibition was achieved when exposing the bacteria to a mixture of the metabolites in vitro compared to individual compound exposures.<br><br>CONCLUSION: Our study suggests that metabolites produced by LAB may synergistically modulate the local microbial ecology, such as in the gut. This could provide new hypotheses on how fermented foods influence human health via diet-microbiota interactions. This article is protected by copyright. All rights reserved.}, }
@article {pmid35959366, year = {2022}, author = {Lopez, LR and Ahn, JH and Alves, T and Arthur, JC}, title = {Microenvironmental Factors that Shape Bacterial Metabolites in Inflammatory Bowel Disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {934619}, doi = {10.3389/fcimb.2022.934619}, pmid = {35959366}, issn = {2235-2988}, abstract = {Inflammatory bowel disease (IBD) is a significant global health problem that involves chronic intestinal inflammation and can involve severe comorbidities, including intestinal fibrosis and inflammation-associated colorectal cancer (CRC). Disease-associated alterations to the intestinal microbiota often include fecal enrichment of Enterobacteriaceae, which are strongly implicated in IBD development. This dysbiosis of intestinal flora accompanies changes in microbial metabolites, shaping host:microbe interactions and disease risk. While there have been numerous studies linking specific bacterial taxa with IBD development, our understanding of microbial function in the context of IBD is limited. Several classes of microbial metabolites have been directly implicated in IBD disease progression, including bacterial siderophores and genotoxins. Yet, our microbiota still harbors thousands of uncharacterized microbial products. In-depth discovery and characterization of disease-associated microbial metabolites is necessary to target these products in IBD treatment strategies. Towards improving our understanding of microbiota metabolites in IBD, it is important to recognize how host relevant factors influence microbiota function. For example, changes in host inflammation status, metal availability, interbacterial community structure, and xenobiotics all play an important role in shaping gut microbial ecology. In this minireview, we outline how each of these factors influences gut microbial function, with a specific focus on IBD-associated Enterobacteriaceae metabolites. Importantly, we discuss how altering the intestinal microenvironment could improve the treatment of intestinal inflammation and associated disorders, like intestinal fibrosis and CRC.}, }
@article {pmid35954765, year = {2022}, author = {Kuczewski, E and Henaff, L and Regard, A and Argaud, L and Lukaszewicz, AC and Rimmelé, T and Cassier, P and Fredenucci, I and Loeffert-Frémiot, S and Khanafer, N and Vanhems, P}, title = {Bacterial Cross-Transmission between Inanimate Surfaces and Patients in Intensive Care Units under Real-World Conditions: A Repeated Cross-Sectional Study.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {15}, pages = {}, doi = {10.3390/ijerph19159401}, pmid = {35954765}, issn = {1660-4601}, support = {n. 69HCL19_0496//ANIOS-ECOLAB Laboratories/ ; }, abstract = {Background/Objectives: Contaminated surfaces play an important role in the nosocomial infection of patients in intensive care units (ICUs). This study, conducted in two ICUs at Edouard Herriot Hospital (Lyon, France), aimed to describe rooms' microbial ecology and explore the potential link between environmental contamination and patients' colonization and/or infection. Methods: Environmental samples were realized once monthly from January 2020 to December 2021 on surfaces close to the patient (bedrails, bedside table, and dedicated stethoscope) and healthcare workers' high-touch surfaces, which were distant from the patient (computer, worktop/nurse cart, washbasin, and hydro-alcoholic solution/soap dispenser). Environmental bacteria were compared to the cultures of the patients hospitalized in the sampled room over a period of ± 10 days from the environmental sampling. Results: Overall, 137 samples were collected: 90.7% of the samples close to patients, and 87.9% of the distant ones were positives. Overall, 223 bacteria were isolated, mainly: Enterococcus faecalis (15.7%), Pantoea agglomerans (8.1%), Enterobacter cloacae/asburiae (6.3%), Bacillus cereus and other Bacillus spp (6.3%), Enterococcusfaecium (5.8%), Stenotrophomonas maltophilia (5.4%), and Acinetobacter baumannii (4.9%). Throughout the study, 142 patients were included, of which, n = 67 (47.2%) were infected or colonized by at least one bacterium. In fourteen cases, the same bacterial species were found both in environment and patient samples, with the suspicion of a cross-contamination between the patient-environment (n = 10) and environment-patient (n = 4). Conclusions: In this work, we found a high level of bacterial contamination on ICU rooms' surfaces and described several cases of potential cross-contamination between environment and patients in real-world conditions.}, }
@article {pmid35953677, year = {2022}, author = {Grisnik, M and Grinath, JB and Munafo, JP and Walker, DM}, title = {Functional Redundancy in Bat Microbial Assemblage in the Presence of the White Nose Pathogen.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35953677}, issn = {1432-184X}, support = {1016031//National Institute of Food and Agriculture/ ; 32801-00803//Tennessee Wildlife Resources Agency/ ; }, abstract = {Understanding how host-associated microbial assemblages respond to pathogen invasion has implications for host health. Until recently, most investigations have focused on understanding the taxonomic composition of these assemblages. However, recent studies have suggested that microbial assemblage taxonomic composition is decoupled from its function, with assemblages being taxonomically varied but functionally constrained. The objective of this investigation was to understand how the Tri-colored bat, Perimyotis subflavus cutaneous microbial assemblage responds to fungal pathogen invasion within a functional context. We hypothesized that at a broad scale (e.g., KEGG pathways), there will be no difference in the functional assemblages between the white nose pathogen, Pseudogymnoascus destructans, positive and negative bats; and this pattern will be driven by the functional redundancy of bacterial taxa. At finer scales (e.g., gene models), we postulate differences in function attributed to interactions between bacteria and P. destructans, resulting in the production of antifungal metabolites. To test this, we used a combination of shotgun metagenomic and amplicon sequencing to characterize the bat cutaneous microbial assemblage in the presence/absence of P. destructans. Results showed that while there was a shift in taxonomic assemblage composition between P. destructans positive and negative bats, there was little overall difference in microbial function. Functional redundancy across bacterial taxa was clear at a broad-scale; however, both redundancy and variation in bacterial capability related to defense against pathogens was evident at finer scales. While functionality of the microbial assemblage was largely conserved in relation to P. destructans, the roles of particular functional pathways in resistance to fungal pathogens require further attention.}, }
@article {pmid35948833, year = {2022}, author = {Díaz-Pérez, SP and Solis, CS and López-Bucio, JS and Valdez Alarcón, JJ and Villegas, J and Reyes-De la Cruz, H and Campos-Garcia, J}, title = {Pathogenesis in Pseudomonas aeruginosa PAO1 Biofilm-Associated Is Dependent on the Pyoverdine and Pyocyanin Siderophores by Quorum Sensing Modulation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35948833}, issn = {1432-184X}, support = {256119//Consejo Nacional de Ciencia y Tecnología/ ; 2.14//Universidad Michoacana de San Nicolás de Hidalgo/ ; }, abstract = {Pseudomonas aeruginosa is an opportunistic pathogenic bacterium for humans, animals, and plants, through producing different molecular factors such as biofilm, siderophores, and other virulence factors which favor bacterial establishment and infection in the host. In P. aeruginosa PAO1, the production of these factors is regulated by the bacterial quorum sensing (QS) mechanisms. From them, siderophores are involved in iron acquisition, transport, and homeostasis. They are also considered some of the main virulence factors in P. aeruginosa; however, detailed mechanisms to induce bacterial pathogenesis are poorly understood. In this work, through reverse genetics, we evaluated the function of bacterial pathogenesis in the pvd cluster genes, which are required for synthesizing the siderophore pyoverdine (PVD). Single pvdI, pvdJ, pvdL, and double mutant strains were analyzed, and contrary to expected, the pvdL and pvdI mutations increased the concentration of PVD and other phenazines, such as pyocyanin (PYO) and phenazine-1-carboxylic acid (PCA) and also an increased biofilm production and morphology depending on the autoinducer 2-alkyl-4-quinolone (PQS) and the QS molecules acyl-homoserine lactones. Consequently, in the in vivo pathogenicity model of Caenorhabditis elegans, the mutations in pvdI, pvdJ, and pvdL increased the survival of the worms exposed to supernatants or biofilms of the bacterial cultures. However, the double mutant pvdI/pvdJ increased its toxicity in agreeing with the biofilm production, PVD, PYO, and PCA. The findings indicate that the mutations in pvd genes encode non-ribosomal peptide synthetases impacted the biofilm's structure, but suppressively also of the phenazines, confirming that the siderophores contribute to the bacterial establishment and pathogenicity of P. aeruginosa PAO1.}, }
@article {pmid35948832, year = {2022}, author = {Ali, A and Elrys, AS and Liu, L and Xia, Q and Wang, B and Li, Y and Dan, X and Iqbal, M and Zhao, J and Huang, X and Cai, Z}, title = {Deciphering the Synergies of Reductive Soil Disinfestation Combined with Biochar and Antagonistic Microbial Inoculation in Cucumber Fusarium Wilt Suppression Through Rhizosphere Microbiota Structure.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35948832}, issn = {1432-184X}, support = {42090060//National Natural Science Foundation of China/ ; U21A20226//National Natural Science Foundation of China/ ; 2021 M691622//Postdoctoral Research Foundation of China/ ; }, abstract = {Application of reductive soil disinfestation (RSD), biochar, and antagonistic microbes have become increasingly popular strategies in a microbiome-based approach to control soil-borne diseases. The combined effect of these remediation methods on the suppression of cucumber Fusarium wilt associated with microbiota reconstruction, however, is still unknown. In this study, we applied RSD treatment together with biochar and microbial application of Trichoderma and Bacillus spp. in Fusarium-diseased cucumbers to investigate their effects on wilt suppression, soil chemical changes, microbial abundances, and the rhizosphere communities. The results showed that initial RSD treatment followed by biochar amendment (RSD-BC) and combined applications of microbial inoculation and biochar (RSD-SQR-T37-BC) decreased nitrate concentration and raised soil pH, soil organic carbon (SOC), and ammonium in the treated soils. Under RSD, the applications of Bacillus (RSD-SQR), Trichoderma (RSD-T37), and biochar (RSD-BC) suppressed wilt incidence by 26.8%, 37.5%, and 32.5%, respectively, compared to non-RSD treatments. Moreover, RSD-SQR-T37-BC and RSD-T37 caused greater suppressiveness of Fusarium wilt and F. oxysporum by 57.0 and 33.5%, respectively. Rhizosphere beta diversity and alpha diversity revealed a difference between RSD-treated and non-RSD microbial groups. The significant increase in the abundance, richness, and diversity of bacteria, and the decrease in the abundance and diversity of fungi under RSD-induced treatments attributed to the general suppression. Identified bacterial (Bacillus, Pseudoxanthomonas, Flavobacterium, Flavisolibacter, and Arthrobacter) and fungal (Trichoderma, Chaetomium, Cladosporium, Psathyrella, and Westerdykella) genera were likely the potential antagonists of specific disease suppression for their significant increase of abundances under RSD-treated soils and high relative importance in linear models. This study infers that the RSD treatment induces potential synergies with biochar amendment and microbial applications, resulting in enhanced general-to-specific suppression mechanisms by changing the microbial community composition in the cucumber rhizosphere.}, }
@article {pmid35948105, year = {2022}, author = {Han, T and Wang, K and Rushimisha, IE and Ye, H and Sun, Y and Zhao, L and Weng, L and Li, Y and Li, X}, title = {Influence of biocurrent self-generated by indigenous microorganisms on soil quality.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {135864}, doi = {10.1016/j.chemosphere.2022.135864}, pmid = {35948105}, issn = {1879-1298}, abstract = {The redox process driven by anaerobic respiration is a link between matter conversion and energy exchange in soil biogeochemistry. Microbial extracellular electron transfer forming biocurrents is a force in element cycling and community living in soil. However, the effect of indigenous microorganisms generating biocurrents on soil quality is unclear. We found that soil biocurrent showed little adverse influence on soil pH, cation exchange capacity, and available nitrogen, phosphorus and potassium and deblocked sequestered organic matter (29%). In addition, the bioelectric field derived from biocurrent obviously forced the migration of mineral elements, which was a supplement to the theory of water-salt transport, providing a new perspective on element transport. Moreover, the soil biocurrent directly regulated the availability of Ca and Fe (increase of 7-fold), indicating that electron transfer plays an important role in weathering and mineralization and thus pedogenesis. From a microbial ecology point of view, the soil bacterial richness and diversity were perfectly restored to their original state when the biocurrent stopped; including bacterial functions; although a temporary enrichment of certain species was observed. The above results provide new insights into the interactions between electron transfer and soil quality and confirm the safety of soil bioelectrochemical technology.}, }
@article {pmid35799308, year = {2022}, author = {Holderman, NR and Ferrer-González, FX and Glushka, J and Moran, MA and Edison, AS}, title = {Dissolved organic metabolite extraction from high-salt media.}, journal = {NMR in biomedicine}, volume = {}, number = {}, pages = {e4797}, doi = {10.1002/nbm.4797}, pmid = {35799308}, issn = {1099-1492}, support = {//Georgia Research Alliance/ ; 5503//Gordon and Betty Moore Foundation/ ; OCE-2019589//National Science Foundation/ ; 1948104//National Science Foundation/ ; 1656311//National Science Foundation/ ; 1S10OD021623-01/NH/NIH HHS/United States ; 1S10OD021623-01/NH/NIH HHS/United States ; }, abstract = {We describe considerations and strategies for developing a nuclear magnetic resonance (NMR) sample preparation method to extract low molecular weight metabolites from high-salt spent media in a model coculture system of phytoplankton and marine bacteria. Phytoplankton perform half the carbon fixation and oxygen generation on Earth. A substantial fraction of fixed carbon becomes part of a metabolite pool of small molecules known as dissolved organic matter (DOM), which are taken up by marine bacteria proximate to phytoplankton. There is an urgent need to elucidate these metabolic exchanges due to widespread anthropogenic transformations on the chemical, phenotypic, and species composition of seawater. These changes are increasing water temperature and the amount of CO2 absorbed by the ocean at energetic costs to marine microorganisms. Little is known about the metabolite-mediated, structured interactions occurring between phytoplankton and associated marine bacteria, in part because of challenges in studying high-salt solutions on various analytical platforms. NMR analysis is problematic due to the high-salt content of both natural seawater and culture media for marine microbes. High-salt concentration degrades the performance of the radio frequency coil, reduces the efficiency of some pulse sequences, limits signal-to-noise, and prolongs experimental time. The method described herein can reproducibly extract low molecular weight DOM from small-volume, high-salt cultures. It is a promising tool for elucidating metabolic flux between marine microorganisms and facilitates genetic screens of mutant microorganisms.}, }
@article {pmid35499337, year = {2022}, author = {Stapelfeldt, HRD and Barnes, SJ and Henson, MW and Thrash, JC}, title = {Draft Genome Sequence of the Marine Flavobacteriaceae sp. Strain LSUCC0859.}, journal = {Microbiology resource announcements}, volume = {11}, number = {5}, pages = {e0018622}, pmid = {35499337}, issn = {2576-098X}, support = {LEQSF[2014-2017]-RDA-06//Louisiana Board of Regents (Board of Regents)/ ; Gulf Research Program Early Career Research Fellowship//National Academies of Sciences, Engineering, and Medicine (NASEM)/ ; Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation (SF)/ ; }, abstract = {A new marine Flavobacteriaceae sp. strain, LSUCC0859, was isolated off the coast of Louisiana with artificial seawater via high-throughput dilution-to-extinction (DTE) cultivation. The 2,168,862-bp genome sequence provides opportunities to investigate the biology of a poorly understood lineage within the Bacteroidetes.}, }
@article {pmid35944516, year = {2022}, author = {Goldman, AD and Kaçar, B}, title = {Very early evolution from the perspective of microbial ecology.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16144}, pmid = {35944516}, issn = {1462-2920}, support = {/NASA/NASA/United States ; //National Science Foundation/ ; }, abstract = {The universal ancestor at the root of the species tree of life depicts a population of organisms with a surprising degree of complexity, posessing genomes and translation systems much like that of microbial life today. As the first life forms were most likely to have been simple replicators, considerable evolutionary change must have taken place prior to the last universal common ancestor. It is often assumed that the lack of earlier branches on the tree of life is due to a prevalence of random horizontal gene transfer that obscured the delineations between lineages and hindered their divergence. Therefore, principles of microbial evolution and ecology may give us some insight into these early stages in the history of life. Here, we synthesize the current understanding of organismal and genome evolution from the perspective of microbial ecology and apply these evolutionary principles to the earliest stages of life on Earth. We focus especially on broad evolutionary modes pertaining to horizontal gene transfer, pangenome structure, and microbial mat communities.}, }
@article {pmid35943262, year = {2022}, author = {Laanbroek, HJ and Cassman, NA and Keijzer, RM and Kuramae, EE}, title = {The Stochastic Assembly of Nitrobacter winogradskyi-Selected Microbiomes with Heterotrophs from Sewage Sludge or Grassland Soil.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0078322}, doi = {10.1128/aem.00783-22}, pmid = {35943262}, issn = {1098-5336}, abstract = {Chemolitho-autotrophic microorganisms like the nitrite-oxidizing Nitrobacter winogradskyi create an environment for heterotrophic microorganisms that profit from the production of organic compounds. It was hypothesized that the assembly of a community of heterotrophic microorganisms around N. winogradskyi depends on the ecosystem from which the heterotrophs are picked. To test this hypothesis, pure cultures of N. winogradskyi were grown in continuously nitrite-fed bioreactors in a mineral medium free of added organic carbon that had been inoculated with diluted sewage sludge or with a suspension from a grassland soil. Samples for chemical and 16S rRNA gene amplicon analyses were taken after each volume change in the bioreactor. At the end of the enrichment runs, samples for shotgun metagenomics were also collected. Already after two volume changes, the transformations in community structure became less dynamic. The enrichment of heterotrophs from both sewage and soil was highly stochastic and yielded different dominant genera in most of the enrichment runs that were independent of the origin of the inoculum. Hence, the hypothesis had to be refuted. Notwithstanding the large variation in taxonomic community structure among the enrichments, the functional compositions of the communities were statistically not different between soil- and sludge-based enrichments. IMPORTANCE In the process of aerobic nitrification, nitrite-oxidizing bacteria together with ammonia-oxidizing microorganisms convert mineral nitrogen from its most reduced appearance, i.e., ammonium, into its most oxidized form, i.e., nitrate. Because the form of mineral nitrogen has large environmental implications, nitrite-oxidizing bacteria such as Nitrobacter winogradskyi play a central role in the global biogeochemical nitrogen cycle. In addition to this central role, the autotrophic nitrite-oxidizing bacteria also play a fundamental role in the global carbon cycle. They form the basis of heterotrophic food webs, in which the assimilated carbon is recycled. Little is known about the heterotrophic microorganisms that participate in these food webs, let alone their assembly in different ecosystems. This study showed that the assembly of microbial food webs by N. winogradskyi was a highly stochastic process and independent of the origin of the heterotrophic microorganisms, but the functional characteristics of the different food webs were similar.}, }
@article {pmid35942165, year = {2022}, author = {Abid, L and Smiri, M and Federici, E and Lievens, B and Manai, M and Yan, Y and Sadfi-Zouaoui, N}, title = {Diversity of rhizospheric and endophytic bacteria isolated from dried fruit of Ficus carica.}, journal = {Saudi journal of biological sciences}, volume = {29}, number = {9}, pages = {103398}, doi = {10.1016/j.sjbs.2022.103398}, pmid = {35942165}, issn = {1319-562X}, abstract = {There is currently an increasing demand for the characterization of endophytic bacteria isolated from different parts of plants (rhizosphere, roots, fruit, leaf) in order to improve the organic agriculture practices. The current research was performed to identify both rhizospheric bacteria isolated from the rhizosphere of Ficus carica in three different sites in the north of Tunisia and endophytic bacteria isolated from dried figs. We then characterized them for a diversity of plant growth-promoting (PGP) activities. A collection of 120 isolates from rhizospheric soil and 9 isolates from dried figs was obtained and purified. 16SrDNA gene amplification of rhizospheric bacteria revealed significant diversity and allowed for the assigning of the isolates to 6 phyla: Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Representative strains of the collection (90 strains) were tested for numerous PGP activities and resistance to abiotic stresses. The most common PGP trait for all bacteria from the three regions was siderophore production (62%), followed by cellulase (38%), then protease activity (37%), then by lipases activity (17%) and lastly by solubilization of phosphates (9%). Twenty -three strains that showed most PGP traits were selected, 8 strains presented 12 or more, and 15 strains displayed between 7 and 11 of 17 PGP activities. The majority of the isolates manifested a possible adaptation to abiotic stress and unfavorable environments. PCR-DGGE analysis of soil rhizosphere of the three sites allowed also for the acquisition of a Cluster analysis of rhizospheric bacterial communities. Our current study identified and characterized for the first time in Tunisia rhizospheric and endophytic bacteria from dried fruit of Ficus carica.}, }
@article {pmid35941249, year = {2022}, author = {de La Harpe, M and Gütlin, A and Chiang, C and Dietemann, V and Dainat, B}, title = {Influence of Honey bee Nutritive Jelly Type and Dilution on its Bactericidal Effect on Melissococcus plutonius, the Etiological Agent of European Foulbrood.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35941249}, issn = {1432-184X}, abstract = {To defend themselves against pathogenic microorganisms, honey bees resort to social immunity mechanisms, such as the secretion of antibiotic compounds in the jelly they feed to their larvae. Whereas the bactericidal activity of jelly fed to queen larvae is well studied, little is known about the bioactivity of compositionally different jelly fed to worker larvae. However, the numerous worker larvae are likely to drive the spread of the microorganism and influence its virulence and pathogenesis. Diluted jelly or extracts are mostly used for jelly bioactivity tests, which may bias the evaluation of the pathogen's resistance and virulence. Here, we compared the bactericidal effect of pure and diluted jellies destined for queen and worker larvae on Melissococcus plutonius, the etiological agent of the European foulbrood (EFB) disease of honey bees, and on a secondary invader bacteria, Enterococcus faecalis. We tested three strains of M. plutonius with varying virulence to investigate the association between resistance to antibacterial compounds and virulence. The resistance of the bacteria varied but was not strictly correlated with their virulence and was lower in pure than in diluted jelly. Resistance differed according to whether the jelly was destined for queen or worker larvae, with some strains being more resistant to queen jelly and others to worker jelly. Our results provide a biologically realistic assessment of host defenses via nutritive jelly and contribute to a better understanding of the ecology of M. plutonius and of secondary invaders bacteria in the honey bee colony environment, thus shedding light on the selective forces affecting their virulence and on their role in EFB pathogenesis.}, }
@article {pmid35940746, year = {2022}, author = {Xian, S and Zhong, H and Yi, B and Liu, X and Shen, G and Li, M and Zhang, Z and Luo, Q and Li, S and Zhou, M and Xu, F and Chen, A}, title = {Identification of pellicle formation related microorganisms in traditional Sichuan paocai through metagenomic sequence and the effects of Baijiu/Salt on pellicle and volatile components.}, journal = {Food research international (Ottawa, Ont.)}, volume = {159}, number = {}, pages = {111130}, doi = {10.1016/j.foodres.2022.111130}, pmid = {35940746}, issn = {1873-7145}, abstract = {The occurrence of pellicle on the surface of paocai brine is a common undesirable phenomenon during the multi-rounds of paocai fermentation, which is mainly caused by the growth of microorganisms related to pellicle formation. But the detailed information on these microorganisms and volatile components produced by them, as well as the changes of the microorganisms during the process of paocai recovery, are still rare in the literature. Therefore, the purpose of this study was (1) to analyze the pellicle formation related microorganisms by comparing the differential microorganisms in initial brine and the brine when pellicle occurred through metagenomic sequencing technology, (2) to explore the changes of microorganisms in the fermentation system after addition Baijiu and/or salt, and (3) to further detect the VOCs in paocai samples by gas chromatography-mass spectrometry (GC-MS). The relationship between VOCs and the selected marker microorganisms was also determined. The results showed that the diversity of fungi was increased when pellicle formed, the pellicle formation related microorganisms mainly belonged to six genus, including Kazachstania, Lactobacillus, Pichia, Candida, Lachancea, and Saccharomyces. Apart from the unknown function and basic life activities of microorganisms, the metabolic activities of these pellicle formation related microorganisms were mainly carbohydrate transport and metabolism, and amino acid transport and metabolism. The growth of pellicle formation related microorganisms could be inhibited by adding Baijiu (1.5% v/v), but the addition of salt (7% salt (w/v) did not promote this inhibitory effect. Through PCA analysis, it was found that the VOCs of paocai were significantly affected by adding Baijiu and Baijiu and salt. The undesirable smell at the beginning of pellicle formation may be related to Propanoic acid, hexyl ester, 1,3-Dimethyl-1-cyclohexene, Oxime-, methoxy-phenyl- and Phenylethyl Alcohol.}, }
@article {pmid35940271, year = {2022}, author = {Selak, L and Marković, T and Pjevac, P and Orlić, S}, title = {Microbial marker for seawater intrusion in a coastal Mediterranean shallow Lake, Lake Vrana, Croatia.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {157859}, doi = {10.1016/j.scitotenv.2022.157859}, pmid = {35940271}, issn = {1879-1026}, abstract = {Climate change-induced rising sea levels and prolonged dry periods impose a global threat to the freshwater scarcity on the coastline: salinization. Lake Vrana is the largest surface freshwater resource in mid-Dalmatia, while the local springs are heavily used in agriculture. The karstified carbonate ridge that separates this shallow lake from the Adriatic Sea enables seawater intrusion if the lakes' precipitation-evaporation balance is disturbed. In this study, the impact of anthropogenic activities and drought exuberated salinization on microbial communities was tracked in Lake Vrana and its inlets, using 16S rRNA gene sequencing. The lack of precipitation and high water temperatures in summer months introduced an imbalance in the water regime of the lake, allowing for seawater intrusion, mainly via the karst conduit Jugovir. The determined microbial community spatial differences in the lake itself and the main drainage canals were driven by salinity, drought, and nutrient loading. Particle-associated and free-living microorganisms both strongly responded to the ecosystem perturbations, and their co-occurrence was driven by the salinization event. Notably, a bloom of halotolerant taxa, predominant the sulfur-oxidizing genus Sulfurovum, emerged with increased salinity and sulfate concentrations, having the potential to be used as an indicator for salinization of shallow coastal lakes. Following summer salinization, lake water column homogenization took from a couple of weeks up to a few months, while the entire system displayed increased salinity despite increased precipitation. This study represents a valuable contribution to understanding the impact of the Freshwater Salinization Syndrome on Mediterranean lakes' microbial communities and the ecosystem resilience.}, }
@article {pmid35940233, year = {2022}, author = {Fox, A and Widmer, F and Lüscher, A}, title = {Soil microbial community structures are shaped by agricultural systems revealing little temporal variation.}, journal = {Environmental research}, volume = {}, number = {}, pages = {113915}, doi = {10.1016/j.envres.2022.113915}, pmid = {35940233}, issn = {1096-0953}, abstract = {Many studies in soil microbial ecology are undertaken with a single sampling event, with the influence of temporal progression rarely being considered. Under field conditions, soil samples were taken from different agricultural systems; a sown grassland to maize rotation (MC), an intensively managed permanent grassland (INT), as well as extensively managed permanent grasslands with high (EXT_HP), low to sufficient (EXT_LP) and deficient available P (EXT_DP), six times throughout the 2017 growing season. Thus, this study aimed to determine if any differences in soil microbiome structures between both sharply contrasting (MC - INT - EXT), slightly differing (EXT_HP - EXT_DP) and quite similar (EXT_HP - EXT_LP and EXT_LP - EXT_DP) agricultural systems persist through changing growth conditions within the growing season. For both fungal and bacterial community structure, the influence of agricultural system (√CV = 0.256 and 0.145, respectively, both at least P < 0.01) was much greater than that of temporal progression (√CV = 0.065 and 0.042, respectively, both P < 0.001). Importantly, nearly all agricultural systems persistently harbored significantly distinct fungal community structures across each of the six sampling events (all at least P < 0.05). There were not as many pairwise differences in bacterial community structure between the agricultural systems, but some did persist (MC and EXT_HP ∼ EXT_DP, all P < 0.001). Additionally, persistent indicator fungal OTUs (IndVal >0.7, P ≤ 0.05) associated to each agricultural system (except EXT_LP) were found in each of the six sampling events. These results highlight the temporal stability of pairwise differences in soil microbiome structures between established agricultural systems through changing plant growth conditions, even between those with a comparable management regime. This is a highly relevant finding in informing the sampling strategy of studies in soil microbial ecology as well as for designing efficient soil biodiversity monitoring systems.}, }
@article {pmid35938717, year = {2022}, author = {Okazaki, Y and Nakano, SI and Toyoda, A and Tamaki, H}, title = {Long-Read-Resolved, Ecosystem-Wide Exploration of Nucleotide and Structural Microdiversity of Lake Bacterioplankton Genomes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0043322}, doi = {10.1128/msystems.00433-22}, pmid = {35938717}, issn = {2379-5077}, abstract = {Reconstruction of metagenome-assembled genomes (MAGs) has become a fundamental approach in microbial ecology. However, a MAG is hardly complete and overlooks genomic microdiversity because metagenomic assembly fails to resolve microvariants among closely related genotypes. Aiming at understanding the universal factors that drive or constrain prokaryotic genome diversification, we performed an ecosystem-wide high-resolution metagenomic exploration of microdiversity by combining spatiotemporal (2 depths × 12 months) sampling from a pelagic freshwater system, high-quality MAG reconstruction using long- and short-read metagenomic sequences, and profiling of single nucleotide variants (SNVs) and structural variants (SVs) through mapping of short and long reads to the MAGs, respectively. We reconstructed 575 MAGs, including 29 circular assemblies, providing high-quality reference genomes of freshwater bacterioplankton. Read mapping against these MAGs identified 100 to 101,781 SNVs/Mb and 0 to 305 insertions, 0 to 467 deletions, 0 to 41 duplications, and 0 to 6 inversions for each MAG. Nonsynonymous SNVs were accumulated in genes potentially involved in cell surface structural modification to evade phage recognition. Most (80.2%) deletions overlapped with a gene coding region, and genes of prokaryotic defense systems were most frequently (>8% of the genes) overlapped with a deletion. Some such deletions exhibited a monthly shift in their allele frequency, suggesting a rapid turnover of genotypes in response to phage predation. MAGs with extremely low microdiversity were either rare or opportunistic bloomers, suggesting that population persistency is key to their genomic diversification. The results concluded that prokaryotic genomic diversification is driven primarily by viral load and constrained by a population bottleneck. IMPORTANCE Identifying intraspecies genomic diversity (microdiversity) is crucial to understanding microbial ecology and evolution. However, microdiversity among environmental assemblages is not well investigated, because most microbes are difficult to culture. In this study, we performed cultivation-independent exploration of bacterial genomic microdiversity in a lake ecosystem using a combination of short- and long-read metagenomic analyses. The results revealed the broad spectrum of genomic microdiversity among the diverse bacterial species in the ecosystem, which has been overlooked by conventional approaches. Our ecosystem-wide exploration further allowed comparative analysis among the genomes and genes and revealed factors behind microbial genomic diversification, namely, that diversification is driven primarily by resistance against viral infection and constrained by the population size.}, }
@article {pmid35937361, year = {2022}, author = {Cardini, U and Marín-Guirao, L and Montilla, LM and Marzocchi, U and Chiavarini, S and Rimauro, J and Quero, GM and Petersen, JM and Procaccini, G}, title = {Nested interactions between chemosynthetic lucinid bivalves and seagrass promote ecosystem functioning in contaminated sediments.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {918675}, doi = {10.3389/fpls.2022.918675}, pmid = {35937361}, issn = {1664-462X}, abstract = {In seagrass sediments, lucinid bivalves and their chemoautotrophic bacterial symbionts consume H2S, relying indirectly on the plant productivity for the presence of the reduced chemical. Additionally, the role of lucinid bivalves in N provisioning to the plant (through N2 fixation by the symbionts) was hypothesized. Thus, lucinids may contribute to sediment detoxification and plant fitness. Seagrasses are subject to ever-increasing human pressure in coastal environments. Here, disentangling nested interactions between chemosynthetic lucinid bivalves and seagrass exposed to pollution may help to understand seagrass ecosystem dynamics and to develop successful seagrass restoration programs that consider the roles of animal-microbe symbioses. We evaluated the capacity of lucinid bivalves (Loripes orbiculatus) to promote nutrient cycling and seagrass (Cymodocea nodosa) growth during a 6-week mesocosm experiment. A fully crossed design was used to test for the effect of sediment contamination (metals, nutrients, and hydrocarbons) on plant and bivalve (alone or interacting) fitness, assessed by mortality, growth, and photosynthetic efficiency, and for the effect of their nested interaction on sediment biogeochemistry. Plants performed better in the contaminated sediment, where a larger pool of dissolved nitrogen combined with the presence of other trace elements allowed for an improved photosynthetic efficiency. In fact, pore water nitrogen accumulated during the experiment in the controls, while it was consumed in the contaminated sediment. This trend was accentuated when lucinids were present. Concurrently, the interaction between clams and plants benefitted both organisms and promoted plant growth irrespective of the sediment type. In particular, the interaction with lucinid clams resulted in higher aboveground biomass of C. nodosa in terms of leaf growth, leaf surface, and leaf biomass. Our results consolidate the notion that nested interactions involving animal-microbe associations promote ecosystem functioning, and potentially help designing unconventional seagrass restoration strategies that exploit chemosynthetic symbioses.}, }
@article {pmid35937348, year = {2022}, author = {Zhu, M and Liu, Y and Cai, P and Duan, X and Sang, S and Qiu, Z}, title = {Jasmonic acid pretreatment improves salt tolerance of wheat by regulating hormones biosynthesis and antioxidant capacity.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {968477}, doi = {10.3389/fpls.2022.968477}, pmid = {35937348}, issn = {1664-462X}, abstract = {Salt stress is a severe environmental factor that detrimentally affects wheat growth and production worldwide. Previous studies illustrate that exogenous jasmonic acid (JA) significantly improved salt tolerance in plants. However, little is known about the underlying molecular mechanisms of JA induced physiochemical changes in wheat seedlings under salt stress conditions. In this study, biophysiochemical and transcriptome analysis was conducted to explore the mechanisms of exogenous JA induced salt tolerance in wheat. Exogenous JA increased salt tolerance of wheat seedlings by alleviating membrane lipid oxidation, improving root morphology, enhancing the contents of ABA, JA and SA and increasing relative water content. In the RNA-seq profiles, we identified a total of 54,263 unigenes and 1,407 unigenes showed differentially expressed patterns in JA pretreated wheat seedlings exposed to salt stress comparing to those with salt stress alone. Subsequently, gene ontology (GO) and KEGG pathway enrichment analysis characterized that DEGs involved in linoleic acid metabolism and plant hormone signal transduction pathways were up-regulated predominantly in JA pretreated wheat seedlings exposed to salt stress. We noticed that genes that involved in antioxidative defense system and that encoding transcription factors were mainly up- or down-regulated. Moreover, SOD, POD, CAT and APX activities were increased in JA pretreated wheat seedlings exposed to salt stress, which is in accordance with the transcript profiles of the relevant genes. Taken together, our results demonstrate that the genes and enzymes involved in physiological and biochemical processes of antioxidant system, plant hormones and transcriptional regulation contributed to JA-mediated enhancement of salt tolerance in wheat. These findings will facilitate the elucidation of the potential molecular mechanisms associated with JA-dependent amelioration of salt stress in wheat and lay theoretical foundations for future studies concerning the improvement of plant tolerance to abiotic environmental stresses.}, }
@article {pmid35935893, year = {2021}, author = {Crous, PW and Cowan, DA and Maggs-Kölling, G and Yilmaz, N and Thangavel, R and Wingfield, MJ and Noordeloos, ME and Dima, B and Brandrud, TE and Jansen, GM and Morozova, OV and Vila, J and Shivas, RG and Tan, YP and Bishop-Hurley, S and Lacey, E and Marney, TS and Larsson, E and Le Floch, G and Lombard, L and Nodet, P and Hubka, V and Alvarado, P and Berraf-Tebbal, A and Reyes, JD and Delgado, G and Eichmeier, A and Jordal, JB and Kachalkin, AV and Kubátová, A and Maciá-Vicente, JG and Malysheva, EF and Papp, V and Rajeshkumar, KC and Sharma, A and Spetik, M and Szabóová, D and Tomashevskaya, MA and Abad, JA and Abad, ZG and Alexandrova, AV and Anand, G and Arenas, F and Ashtekar, N and Balashov, S and Bañares, Á and Baroncelli, R and Bera, I and Biketova, AY and Blomquist, CL and Boekhout, T and Boertmann, D and Bulyonkova, TM and Burgess, TI and Carnegie, AJ and Cobo-Diaz, JF and Corriol, G and Cunnington, JH and da Cruz, MO and Damm, U and Davoodian, N and de A Santiago, ALCM and Dearnaley, J and de Freitas, LWS and Dhileepan, K and Dimitrov, R and Di Piazza, S and Fatima, S and Fuljer, F and Galera, H and Ghosh, A and Giraldo, A and Glushakova, AM and Gorczak, M and Gouliamova, DE and Gramaje, D and Groenewald, M and Gunsch, CK and Gutiérrez, A and Holdom, D and Houbraken, J and Ismailov, AB and Istel, Ł and Iturriaga, T and Jeppson, M and Jurjević, Ž and Kalinina, LB and Kapitonov, VI and Kautmanová, I and Khalid, AN and Kiran, M and Kiss, L and Kovács, Á and Kurose, D and Kušan, I and Lad, S and Læssøe, T and Lee, HB and Luangsa-Ard, JJ and Lynch, M and Mahamedi, AE and Malysheva, VF and Mateos, A and Matočec, N and Mešić, A and Miller, AN and Mongkolsamrit, S and Moreno, G and Morte, A and Mostowfizadeh-Ghalamfarsa, R and Naseer, A and Navarro-Ródenas, A and Nguyen, TTT and Noisripoom, W and Ntandu, JE and Nuytinck, J and Ostrý, V and Pankratov, TA and Pawłowska, J and Pecenka, J and Pham, THG and Polhorský, A and Pošta, A and Raudabaugh, DB and Reschke, K and Rodríguez, A and Romero, M and Rooney-Latham, S and Roux, J and Sandoval-Denis, M and Smith, MT and Steinrucken, TV and Svetasheva, TY and Tkalčec, Z and van der Linde, EJ and V D Vegte, M and Vauras, J and Verbeken, A and Visagie, CM and Vitelli, JS and Volobuev, SV and Weill, A and Wrzosek, M and Zmitrovich, IV and Zvyagina, EA and Groenewald, JZ}, title = {Fungal Planet description sheets: 1182-1283.}, journal = {Persoonia}, volume = {46}, number = {}, pages = {313-528}, doi = {10.3767/persoonia.2021.46.11}, pmid = {35935893}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Algeria, Phaeoacremonium adelophialidum from Vitis vinifera. Antarctica, Comoclathris antarctica from soil. Australia, Coniochaeta salicifolia as endophyte from healthy leaves of Geijera salicifolia, Eremothecium peggii in fruit of Citrus australis, Microdochium ratticaudae from stem of Sporobolus natalensis, Neocelosporium corymbiae on stems of Corymbia variegata, Phytophthora kelmanii from rhizosphere soil of Ptilotus pyramidatus, Pseudosydowia backhousiae on living leaves of Backhousia citriodora, Pseudosydowia indooroopillyensis, Pseudosydowia louisecottisiae and Pseudosydowia queenslandica on living leaves of Eucalyptus sp. Brazil, Absidia montepascoalis from soil. Chile, Ilyonectria zarorii from soil under Maytenus boaria. Costa Rica, Colletotrichum filicis from an unidentified fern. Croatia, Mollisia endogranulata on deteriorated hardwood. Czech Republic, Arcopilus navicularis from tea bag with fruit tea, Neosetophoma buxi as endophyte from Buxus sempervirens, Xerochrysium bohemicum on surface of biscuits with chocolate glaze and filled with jam. France, Entoloma cyaneobasale on basic to calcareous soil, Fusarium aconidiale from Triticum aestivum, Fusarium juglandicola from buds of Juglans regia. Germany, Tetraploa endophytica as endophyte from Microthlaspi perfoliatum roots. India, Castanediella ambae on leaves of Mangifera indica, Lactifluus kanadii on soil under Castanopsis sp., Penicillium uttarakhandense from soil. Italy, Penicillium ferraniaense from compost. Namibia, Bezerromyces gobabebensis on leaves of unidentified succulent, Cladosporium stipagrostidicola on leaves of Stipagrostis sp., Cymostachys euphorbiae on leaves of Euphorbia sp., Deniquelata hypolithi from hypolith under a rock, Hysterobrevium walvisbayicola on leaves of unidentified tree, Knufia hypolithi and Knufia walvisbayicola from hypolith under a rock, Lapidomyces stipagrostidicola on leaves of Stipagrostis sp., Nothophaeotheca mirabibensis (incl. Nothophaeotheca gen. nov.) on persistent inflorescence remains of Blepharis obmitrata, Paramyrothecium salvadorae on twigs of Salvadora persica, Preussia procaviicola on dung of Procavia sp., Sordaria equicola on zebra dung, Volutella salvadorae on stems of Salvadora persica. Netherlands, Entoloma ammophilum on sandy soil, Entoloma pseudocruentatum on nutrient poor (acid) soil, Entoloma pudens on plant debris, amongst grasses. New Zealand, Amorocoelophoma neoregeliae from leaf spots of Neoregelia sp., Aquilomyces metrosideri and Septoriella callistemonis from stem discolouration and leaf spots of Metrosideros sp., Cadophora neoregeliae from leaf spots of Neoregelia sp., Flexuomyces asteliae (incl. Flexuomyces gen. nov.) and Mollisia asteliae from leaf spots of Astelia chathamica, Ophioceras freycinetiae from leaf spots of Freycinetia banksii, Phaeosphaeria caricis-sectae from leaf spots of Carex secta. Norway, Cuphophyllus flavipesoides on soil in semi-natural grassland, Entoloma coracis on soil in calcareous Pinus and Tilia forests, Entoloma cyaneolilacinum on soil semi-natural grasslands, Inocybe norvegica on gravelly soil. Pakistan, Butyriboletus parachinarensis on soil in association with Quercus baloot. Poland, Hyalodendriella bialowiezensis on debris beneath fallen bark of Norway spruce Picea abies. Russia, Bolbitius sibiricus on à moss covered rotting trunk of Populus tremula, Crepidotus wasseri on debris of Populus tremula, Entoloma isborscanum on soil on calcareous grasslands, Entoloma subcoracis on soil in subalpine grasslands, Hydropus lecythiocystis on rotted wood of Betula pendula, Meruliopsis faginea on fallen dead branches of Fagus orientalis, Metschnikowia taurica from fruits of Ziziphus jujube, Suillus praetermissus on soil, Teunia lichenophila as endophyte from Cladonia rangiferina. Slovakia, Hygrocybe fulgens on mowed grassland, Pleuroflammula pannonica from corticated branches of Quercus sp. South Africa, Acrodontium burrowsianum on leaves of unidentified Poaceae, Castanediella senegaliae on dead pods of Senegalia ataxacantha, Cladophialophora behniae on leaves of Behnia sp., Colletotrichum cliviigenum on leaves of Clivia sp., Diatrype dalbergiae on bark of Dalbergia armata, Falcocladium heteropyxidicola on leaves of Heteropyxis canescens, Lapidomyces aloidendricola as epiphyte on brown stem of Aloidendron dichotomum, Lasionectria sansevieriae and Phaeosphaeriopsis sansevieriae on leaves of Sansevieria hyacinthoides, Lylea dalbergiae on Diatrype dalbergiae on bark of Dalbergia armata, Neochaetothyrina syzygii (incl. Neochaetothyrina gen. nov.) on leaves of Syzygium chordatum, Nothophaeomoniella ekebergiae (incl. Nothophaeomoniella gen. nov.) on leaves of Ekebergia pterophylla, Paracymostachys euphorbiae (incl. Paracymostachys gen. nov.) on leaf litter of Euphorbia ingens, Paramycosphaerella pterocarpi on leaves of Pterocarpus angolensis, Paramycosphaerella syzygii on leaf litter of Syzygium chordatum, Parateichospora phoenicicola (incl. Parateichospora gen. nov.) on leaves of Phoenix reclinata, Seiridium syzygii on twigs of Syzygium chordatum, Setophoma syzygii on leaves of Syzygium sp., Starmerella xylocopis from larval feed of an Afrotropical bee Xylocopa caffra, Teratosphaeria combreti on leaf litter of Combretum kraussii, Teratosphaericola leucadendri on leaves of Leucadendron sp., Toxicocladosporium pterocarpi on pods of Pterocarpus angolensis. Spain, Cortinarius bonachei with Quercus ilex in calcareus soils, Cortinarius brunneovolvatus under Quercus ilex subsp. ballota in calcareous soil, Extremopsis radicicola (incl. Extremopsis gen. nov.) from root-associated soil in a wet heathland, Russula quintanensis on acidic soils, Tubaria vulcanica on volcanic lapilii material, Tuber zambonelliae in calcareus soil. Sweden, Elaphomyces borealis on soil under Pinus sylvestris and Betula pubescens. Tanzania, Curvularia tanzanica on inflorescence of Cyperus aromaticus. Thailand, Simplicillium niveum on Ophiocordyceps camponoti-leonardi on underside of unidentified dicotyledonous leaf. USA, Calonectria californiensis on leaves of Umbellularia californica, Exophiala spartinae from surface sterilised roots of Spartina alterniflora, Neophaeococcomyces oklahomaensis from outside wall of alcohol distillery. Vietnam, Fistulinella aurantioflava on soil. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Cowan DA, Maggs-Kölling, et al. 2021. Fungal Planet description sheets: 1182-1283. Persoonia 46: 313-528. https://doi.org/10.3767/persoonia.2021.46.11.}, }
@article {pmid35935241, year = {2022}, author = {Bergmann, GE and Leveau, JHJ}, title = {A metacommunity ecology approach to understanding microbial community assembly in developing plant seeds.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {877519}, doi = {10.3389/fmicb.2022.877519}, pmid = {35935241}, issn = {1664-302X}, abstract = {Microorganisms have the potential to affect plant seed germination and seedling fitness, ultimately impacting plant health and community dynamics. Because seed-associated microbiota are highly variable across individual plants, plant species, and environments, it is challenging to identify the dominant processes that underlie the assembly, composition, and influence of these communities. We propose here that metacommunity ecology provides a conceptually useful framework for studying the microbiota of developing seeds, by the application of metacommunity principles of filtering, species interactions, and dispersal at multiple scales. Many studies in seed microbial ecology already describe individual assembly processes in a pattern-based manner, such as correlating seed microbiome composition with genotype or tracking diversity metrics across treatments in dispersal limitation experiments. But we see a lot of opportunities to examine understudied aspects of seed microbiology, including trait-based research on mechanisms of filtering and dispersal at the micro-scale, the use of pollination exclusion experiments in macro-scale seed studies, and an in-depth evaluation of how these processes interact via priority effect experiments and joint species distribution modeling.}, }
@article {pmid35933499, year = {2022}, author = {Ray, AE and Zaugg, J and Benaud, N and Chelliah, DS and Bay, S and Wong, HL and Leung, PM and Ji, M and Terauds, A and Montgomery, K and Greening, C and Cowan, DA and Kong, W and Williams, TJ and Hugenholtz, P and Ferrari, BC}, title = {Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {35933499}, issn = {1751-7370}, support = {FT170100341//Department of Education and Training | Australian Research Council (ARC)/ ; APP5191146//Department of Health | National Health and Medical Research Council (NHMRC)/ ; }, abstract = {Cold desert soil microbiomes thrive despite severe moisture and nutrient limitations. In Eastern Antarctic soils, bacterial primary production is supported by trace gas oxidation and the light-independent RuBisCO form IE. This study aims to determine if atmospheric chemosynthesis is widespread within Antarctic, Arctic and Tibetan cold deserts, to identify the breadth of trace gas chemosynthetic taxa and to further characterize the genetic determinants of this process. H2 oxidation was ubiquitous, far exceeding rates reported to fulfill the maintenance needs of similarly structured edaphic microbiomes. Atmospheric chemosynthesis occurred globally, contributing significantly (p < 0.05) to carbon fixation in Antarctica and the high Arctic. Taxonomic and functional analyses were performed upon 18 cold desert metagenomes, 230 dereplicated medium-to-high-quality derived metagenome-assembled genomes (MAGs) and an additional 24,080 publicly available genomes. Hydrogenotrophic and carboxydotrophic growth markers were widespread. RuBisCO IE was discovered to co-occur alongside trace gas oxidation enzymes in representative Chloroflexota, Firmicutes, Deinococcota and Verrucomicrobiota genomes. We identify a novel group of high-affinity [NiFe]-hydrogenases, group 1m, through phylogenetics, gene structure analysis and homology modeling, and reveal substantial genetic diversity within RuBisCO form IE (rbcL1E), and high-affinity 1h and 1l [NiFe]-hydrogenase groups. We conclude that atmospheric chemosynthesis is a globally-distributed phenomenon, extending throughout cold deserts, with significant implications for the global carbon cycle and bacterial survival within environmental reservoirs.}, }
@article {pmid35933411, year = {2022}, author = {Zhang, H and Wang, M and Wang, H and Chen, H and Cao, L and Zhong, Z and Lian, C and Zhou, L and Li, C}, title = {Metagenome sequencing and 768 microbial genomes from cold seep in South China Sea.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {480}, pmid = {35933411}, issn = {2052-4463}, support = {42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076091//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076091//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Cold seep microbial communities are fascinating ecosystems on Earth which provide unique models for understanding the living strategies in deep-sea distinct environments. In this study, 23 metagenomes were generated from samples collected in the Site-F cold seep field in South China Sea, including the sea water closely above the invertebrate communities, the cold seep fluids, the fluids under the invertebrate communities and the sediment column around the seep vent. By binning tools, we retrieved a total of 768 metagenome assembled genome (MAGs) that were estimated to be >60% complete. Of the MAGs, 61 were estimated to be >90% complete, while an additional 105 were >80% complete. Phylogenomic analysis revealed 597 bacterial and 171 archaeal MAGs, of which nearly all were distantly related to known cultivated isolates. In the 768 MAGs, the abundant Bacteria in phylum level included Proteobacteria, Desulfobacterota, Bacteroidota, Patescibacteria and Chloroflexota, while the abundant Archaea included Asgardarchaeota, Thermoplasmatota, and Thermoproteota. These results provide a dataset available for further interrogation of deep-sea microbial ecology.}, }
@article {pmid35933162, year = {2022}, author = {Kumar, S and Kumar, V and Ambika, AAA and Nag, D and Kumar, V and Darnal, S and Thakur, V and Patial, V and Singh, D}, title = {Microbial pigments: Learning from Himalayan perspective to industrial applications.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jimb/kuac017}, pmid = {35933162}, issn = {1476-5535}, abstract = {Pigments are an essential part of life on earth, ranging from microbes to plants and humans. The physiological and environmental cues induce microbes to produce a broad spectrum of pigments, giving them adaptation and survival advantages. Microbial pigments are of great interest due to their natural origin, diverse biological activities, and wide applications in the food, pharmaceutical, cosmetics, and textile industries. Despite noticeable research on pigment-producing microbes, commercial successes are scarce, primarily from higher, remote, and inaccessible Himalayan niches. Therefore, substantial bioprospection integrated with advanced biotechnological strategies is required to commercialize microbial pigments successfully. The current review elaborates on pigment-producing microbes from a Himalayan perspective, offering tremendous opportunities for industrial applications. Additionally, it illustrates the ecological significance of microbial pigments and emphasizes the current status and prospects of microbial pigments production above the test tube scale.}, }
@article {pmid35932316, year = {2022}, author = {Pedrolo, AM and Matteoli, FP and Soares, CRFS and Arisi, ACM}, title = {Comparative Genomics Reveal the High Conservation and Scarce Distribution of Nitrogen Fixation nif Genes in the Plant-Associated Genus Herbaspirillum.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35932316}, issn = {1432-184X}, abstract = {The genus Herbaspirillum gained the spotlight due to the several reports of diazotrophic strains and promising results in plant-growth field assays. However, as diversity exploration of Herbaspirillum species gained momentum, it became clearer that the plant beneficial lifestyle was not the only form of ecological interaction in this genus, due to reports of phytopathogenesis and nosocomial infections. Here we performed a deep search across all publicly available Herbaspirillum genomes. Using a robust core genome phylogeny, we have found that all described species are well delineated, being the only exception H. aquaticum and H. huttiense clade. We also uncovered that the nif genes are only highly prevalent in H. rubrisubalbicans; however, irrespective to the species, all nif genes share the same gene arrangement with high protein identity, and are present in only two main types, in inverted strands. By means of a NifHDKENB phylogenetic tree, we have further revealed that the Herbaspirillum nif sequences may have been acquired from the same last common ancestor belonging to the Nitrosomonadales order.}, }
@article {pmid35931774, year = {2022}, author = {Gómez-Molina, E and Sánchez, S and Puig-Pey, M and García-Barreda, S}, title = {Intraspecific Competition Results in Reduced Evenness of Tuber melanosporum Mating-Type Abundance from the Nursery Stage.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35931774}, issn = {1432-184X}, support = {Collaboration agreement for the operation of CIET//Diputación de Huesca/ ; }, abstract = {The highly prized black truffle is a fungus mostly harvested in orchards planted with mycorrhizal seedlings. It is an obligatory outcrossing fungus with a single MAT locus containing two alternative mating-type idiomorphs. In the orchards, at the mycorrhizal level, these mating types are frequently spatially segregated. Some studies found that this segregation was pronounced from the nursery stage, whereas others did not find such a marked segregation. Besides, information on the host tree species and nursery conditions used in Spain, one of the main truffle-producing countries, are very scarce. In this study, we investigated the temporal dynamics of mating types in nursery seedlings of Quercus ilex and Quercus faginea, as well as the influence of cultural conditions in the nursery. Our results indicated that at the plant level, there was a trend for one of the mating types to dominate over the other from the first to the second year in the nursery, in both host species and both nursery conditions tested. However, this segregation process was not so sharp as previously reported. Our results support the hypothesis that intraspecific competition results in reduced evenness of mating-type abundance from the nursery stage, although almost all seedlings maintained both mating types and, at the seedling batch scale, the occurrence of both mating types was roughly balanced.}, }
@article {pmid35930073, year = {2022}, author = {Morales-Poole, JR and de Vega, C and Tsuji, K and Jacquemyn, H and Junker, RR and Herrera, CM and Michiels, C and Lievens, B and Álvarez-Pérez, S}, title = {Sugar Concentration, Nitrogen Availability, and Phylogenetic Factors Determine the Ability of Acinetobacter spp. and Rosenbergiella spp. to Grow in Floral Nectar.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35930073}, issn = {1432-184X}, support = {742964//H2020 Marie Skłodowska-Curie Actions/ ; RYC2018-023847-I//Ministerio de Ciencia, Innovación y Universidades/ ; DFG//Deutsche Forschungsgemeinschaft/ ; JU2856/2-2//Deutsche Forschungsgemeinschaft/ ; }, abstract = {The floral nectar of angiosperms harbors a variety of microorganisms that depend predominantly on animal visitors for their dispersal. Although some members of the genus Acinetobacter and all currently known species of Rosenbergiella are thought to be adapted to thrive in nectar, there is limited information about the response of these bacteria to variation in the chemical characteristics of floral nectar. We investigated the growth performance of a diverse collection of Acinetobacter (n = 43) and Rosenbergiella (n = 45) isolates obtained from floral nectar and the digestive tract of flower-visiting bees in a set of 12 artificial nectars differing in sugar content (15% w/v or 50% w/v), nitrogen content (3.48/1.67 ppm or 348/167 ppm of total nitrogen/amino nitrogen), and sugar composition (only sucrose, 1/3 sucrose + 1/3 glucose + 1/3 fructose, or 1/2 glucose + 1/2 fructose). Growth was only observed in four of the 12 artificial nectars. Those containing elevated sugar concentration (50% w/v) and low nitrogen content (3.48/1.67 ppm) were limiting for bacterial growth. Furthermore, phylogenetic analyses revealed that the ability of the bacteria to grow in different types of nectar is highly conserved between closely related isolates and genotypes, but this conservatism rapidly vanishes deeper in phylogeny. Overall, these results demonstrate that the ability of Acinetobacter spp. and Rosenbergiella spp. to grow in floral nectar largely depends on nectar chemistry and bacterial phylogeny.}, }
@article {pmid35929359, year = {2022}, author = {Mandal, S and Kundu, S and Uddin, MR and Das, P and Paul, P and Roy, P and Tribedi, P and Sahoo, P}, title = {Identification of a novel quinoline-based UV-protective pigment from a psychrotrophic Arctic bacterium.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.15760}, pmid = {35929359}, issn = {1365-2672}, abstract = {AIMS: Psychrotrophs are extremophilic microorganisms that grow optimally in low temperature having many unique bioactive molecules of biotechnological applications. In this study we characterized a pigment from an arctic bacterium with protective activity towards UV exposure.<br><br>METHODS AND RESULTS: The present research reports isolation and characterization of a psychrotrophic bacteria, RSAP2, from the soil sample of NyAlesund (78°56"N, 11°54"E), Svalbard, Norway. The strain showed closest 16S rRNA gene sequence similarity (99.9%) with Kocuria indica NIO-1021. RSAP2 is a Gram-positive, coccoid aerobe which produces a yellow pigment. The optimal parameters for pigment production while grown in LB medium were 3% (w/v) NaCl and 4 days of incubation of the culture at 20°C and pH 9 with shaking (180 rpm). The pigment was extracted in methanol and acetone (2:1) and further purified through column chromatography. It was characterized by mass spectrometry, UV-Visible, fluorescence, IR, 1 H NMR, 13 C NMR spectroscopy and CHNS/O -analysis. The pigment has a molecular weight of about 258 daltons and the molecular formula was determined as C15 H18 N2 O2 and is a quinoline derivative. We show that the pigment can protect E. coli against UV-mediated mutagenesis. We further demonstrate that the pigment displays a significant antimicrobial effect and in sublethal concentrations it impairs biofilm formation ability of the model organism Staphylococcus aureus.<br><br>CONCLUSIONS: The pigment of a psychrotrophic Arctic bacterium, most likely a strain of K. indica, was purified and its chemical structure was determined. The quinoline-based pigment has the ability to protect live cells from UV induced damage.<br><br>Analysis and characterization of this newly isolated quinoline-based pigment is a potential candidate for future application in skin care products.}, }
@article {pmid35927589, year = {2022}, author = {Zhu, W and Zhu, M and Liu, X and Xia, J and Yin, H and Li, X}, title = {Different Responses of Bacteria and Microeukaryote to Assembly Processes and Co-occurrence Pattern in the Coastal Upwelling.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35927589}, issn = {1432-184X}, support = {42076108//the National Natural Science Foundation of China/ ; 42161144006 or 3511/21//the National Natural Science Foundation of China/ ; 2021RC169//the Natural Science Foundation of Hainan Province/ ; ZDYF2020177//the Hainan Provincial Key Research and Development Program/ ; KYQD(ZR)1805//the Foundation of Hainan University/ ; }, abstract = {Upwelling may generate unique hydrological and environmental heterogeneity, leading to enhanced diffusion to reshape microbial communities. However, it remains largely unknown how different microbial taxa respond to highly complex and dynamic upwelling systems. In the present study, geographic patterns and co-occurrence network of different microbial communities in response to upwelling were examined. Our results showed that coastal upwelling shaped prokaryotic and eukaryotic microbial community and decreased their diversity. In addition, bacteria and microeukaryote had similar biogeographical patterns with distinct assembly mechanisms. The impact of stochastic processes on bacteria was significantly stronger compared with microeukaryote in upwelling. Lower network complexity but more frequent interaction was found in upwelling microbial co-occurrence. However, the upwelling environment increased the robustness and modularity of bacterial network, while eukaryotic network was just the opposite. Co-occurrence networks of bacteria and microeukaryote showed significant distance-decay patterns, while the bacterial network had a stronger spatial variation. Temperature and salinity were the strongest environmental factors affecting microbial coexistence, whereas the topological characteristics of bacterial and eukaryotic networks had different responses to the upwelling environment. These findings expanded our understanding of biogeographic patterns of microbial community and ecological network and the underlying mechanisms of different microbial taxa in upwelling.}, }
@article {pmid35927588, year = {2022}, author = {He, D and Guo, Z and Shen, W and Ren, L and Sun, D and Yao, Q and Zhu, H}, title = {Fungal Communities Are More Sensitive to the Simulated Environmental Changes than Bacterial Communities in a Subtropical Forest: the Single and Interactive Effects of Nitrogen Addition and Precipitation Seasonality Change.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35927588}, issn = {1432-184X}, abstract = {Increased nitrogen deposition (N factor) and changes in precipitation patterns (W factor) can greatly impact soil microbial communities in tropical/subtropical forests. Although knowledge about the effects of a single factor on soil microbial communities is growing rapidly, little is understood about the interactive effects of these two environmental change factors. In this study, we investigated the responses of soil bacterial and fungal communities to the short-term simulated environmental changes (nitrogen addition, precipitation seasonality change, and their combination) in a subtropical forest in South China. The interaction between N and W factors was detected significant for affecting some soil physicochemical properties (such as pH, soil water, and NO3- contents). Fungi were more susceptible to treatment than bacteria in a variety of community traits (alpha, beta diversity, and network topological features). The N and W factors act antagonistically to affect fungal alpha diversity, and the interaction effect was detected significant for the dry season. The topological features of the meta-community (containing both bacteria and fungi) network overrode the alpha and beta diversity of bacterial or fungal communities in explaining the variation of soil enzyme activities. The associations between Ascomycota fungi and Gammaproteobacteria or Alphaproteobacteria might be important in mediating the inter-kingdom interactions. In summary, our results suggested that fungal communities were more sensitive to N and W factors (and their interaction) than bacterial communities, and the treatments' effects were more prominent in the dry season, which may have great consequences in soil processes and ecosystem functions in subtropical forests.}, }
@article {pmid35925231, year = {2022}, author = {Chinta, YD and Araki, H}, title = {Cover Crop Amendments and Lettuce Plant Growth Stages Alter Rhizobacterial Properties and Roles in Plant Performance.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35925231}, issn = {1432-184X}, support = {18H02310//japan society for the promotion of science/ ; }, abstract = {Lettuce plants respond differently to cover crop amendments by altering their biomass and nitrogen uptake (Nup) at different plant growth stages. Nonetheless, plant-microbe interactions involved in the alterations are scarcely studied. This study elucidated how the properties of the soil microbial community inhabiting the rhizosphere associated with lettuce (Lactuca sativa L. var. crispa "Red fire") change during plant growth stages. Lettuce plants were cultivated in control soil and soil with rye, hairy vetch (HV), and rye plus HV (rye + HV) cover crop amendments. Rhizosphere soil samples were collected at the mid-growth and mature stages of plant development. DNA was extracted from the soil, and the 16S rRNA region was amplified using polymerase chain reaction to analyze bacterial genes and community structures and functions. Cover crop amendments and plant growth stages increased or decreased the relative abundances of bacterial taxa at the genus level. Plant maturity decreased 16S rRNA gene expression and the number of bacterial operational taxonomic units in all treatments. The unique, core, and shared taxa with low relative abundances may be associated with improved lettuce Nup and lettuce shoot and root biomass at each plant growth stage under different cover crop amendments based on multivariate analysis between plant indicators and bacterial genera groups. This study revealed the importance of bacterial groups with low relative abundance in plant-microbe interactions; such bacteria may promote the cover crop application for high lettuce productivity.}, }
@article {pmid35925016, year = {2022}, author = {Cheng, X and Wang, H and Zeng, Z and Li, L and Zhao, R and Bodelier, PLE and Wang, Y and Liu, X and Su, C and Liu, S}, title = {Niche differentiation of atmospheric methane-oxidizing bacteria and their community assembly in subsurface karst caves.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.13112}, pmid = {35925016}, issn = {1758-2229}, support = {91951208//National Natural Science Foundation of China/ ; 2020GXNSFAA297025//Natural Science Foundation of Guangxi Province/ ; }, abstract = {Karst caves are recently proposed as atmospheric methane sinks in terrestrial ecosystems. Despite of the detection of atmospheric methane-oxidizing bacteria (atmMOB) in caves, we still know little about their ecology and potential ability of methane oxidation in this ecosystem. To understand atmMOB ecology and their potential in methane consumption, we collected weathered rocks and sediments from three different caves in southwestern China. We determined the potential methane oxidization rates in the range of 1.25 ± 0.08 to 1.87 ± 0.41 ng CH4 g-1 DW h-1 , which are comparable to those reported in forest and grassland soils. Results showed that alkaline oligotrophic caves harbour high numbers of atmMOB, particularly upland soil cluster (USC), which significantly correlated with temperature, CH4 and CO2 concentrations. The absolute abundance of USCγ was higher than that of USCα. USCγ-OPS (open patch soil) and USCγ-SS (subsurface soil) dominated in most samples, whereas USCα-BFS (boreal forest soil) only predominated in the sediments near cave entrances, indicating niche differentiation of atmMOB in caves. Overwhelming dominance of homogenous selection in community assembly resulted in convergence of atmMOB communities. Collectively, our results demonstrated the niche differentiation of USC in subsurface alkaline caves and their non-negligible methane-oxidizing potential, providing brand-new knowledge about atmMOB ecology in subsurface biosphere.}, }
@article {pmid35924847, year = {2022}, author = {Gude, S and Pherribo, GJ and Taga, ME}, title = {A Salvaging Strategy Enables Stable Metabolite Provisioning among Free-Living Bacteria.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0028822}, doi = {10.1128/msystems.00288-22}, pmid = {35924847}, issn = {2379-5077}, abstract = {All organisms rely on complex metabolites such as amino acids, nucleotides, and cofactors for essential metabolic processes. Some microbes synthesize these fundamental ingredients of life de novo, while others rely on uptake to fulfill their metabolic needs. Although certain metabolic processes are inherently "leaky," the mechanisms enabling stable metabolite provisioning among microbes in the absence of a host remain largely unclear. In particular, how can metabolite provisioning among free-living bacteria be maintained under the evolutionary pressure to economize resources? Salvaging, the process of "recycling and reusing," can be a metabolically efficient route to obtain access to required resources. Here, we show experimentally how precursor salvaging in engineered Escherichia coli populations can lead to stable, long-term metabolite provisioning. We find that salvaged cobamides (vitamin B12 and related enzyme cofactors) are readily made available to nonproducing population members, yet salvagers are strongly protected from overexploitation. We also describe a previously unnoted benefit of precursor salvaging, namely, the removal of the nonfunctional, proliferation-inhibiting precursor. As long as compatible precursors are present, any microbe possessing the terminal steps of a biosynthetic process can, in principle, forgo de novo biosynthesis in favor of salvaging. Consequently, precursor salvaging likely represents a potent, yet overlooked, alternative to de novo biosynthesis for the acquisition and provisioning of metabolites in free-living bacterial populations. IMPORTANCE Recycling gives new life to old things. Bacteria have the ability to recycle and reuse complex molecules they encounter in their environment to fulfill their basic metabolic needs in a resource-efficient way. By studying the salvaging (recycling and reusing) of vitamin B12 precursors, we found that metabolite salvaging can benefit others and provide stability to a bacterial community at the same time. Salvagers of vitamin B12 precursors freely share the result of their labor yet cannot be outcompeted by freeloaders, likely because salvagers retain preferential access to the salvaging products. Thus, salvaging may represent an effective, yet overlooked, mechanism of acquiring and provisioning nutrients in microbial populations.}, }
@article {pmid35920032, year = {2022}, author = {Heinz, J and Doellinger, J and Maus, D and Schneider, A and Lasch, P and Grossart, HP and Schulze-Makuch, D}, title = {Perchlorate-Specific Proteomic Stress Responses of Debaryomyces hansenii Could Enable Microbial Survival in Martian Brines.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16152}, pmid = {35920032}, issn = {1462-2920}, abstract = {If life exists on Mars, it would face several challenges including the presence of perchlorates, which destabilize biomacromolecules by inducing chaotropic stress. However, little is known about perchlorate toxicity for microorganism on the cellular level. Here we present the first proteomic investigation on the perchlorate-specific stress responses of the halotolerant yeast Debaryomyces hansenii and compare these to generally known salt stress adaptations. We found that the responses to NaCl and NaClO4 -induced stresses share many common metabolic features, e.g., signaling pathways, elevated energy metabolism, or osmolyte biosynthesis. Nevertheless, several new perchlorate-specific stress responses could be identified, such as protein glycosylation and cell wall remodulations, presumably in order to stabilize protein structures and the cell envelope. These stress responses would also be relevant for life on Mars, which - given the environmental conditions - likely developed chaotropic defense strategies such as stabilized confirmations of biomacromolecules and the formation of cell clusters. This article is protected by copyright. All rights reserved.}, }
@article {pmid35919909, year = {2014}, author = {Legin, AA and Schintlmeister, A and Jakupec, MA and Galanski, MS and Lichtscheidl, I and Wagner, M and Keppler, BK}, title = {NanoSIMS combined with fluorescence microscopy as a tool for subcellular imaging of isotopically labeled platinum-based anticancer drugs.}, journal = {Chemical science}, volume = {5}, number = {8}, pages = {3135-3143}, doi = {10.1039/c3sc53426j}, pmid = {35919909}, issn = {2041-6520}, abstract = {Multi-elemental, isotope selective nano-scale secondary ion mass spectrometry (NanoSIMS) combined with confocal laser-scanning microscopy was used to characterize the subcellular distribution of 15N-labeled cisplatin in human colon cancer cells. These analyses indicated predominant cisplatin colocalisation with sulfur-rich structures in both the nucleus and cytoplasm. Furthermore, colocalisation of platinum with phosphorus-rich chromatin regions was observed, which is consistent with its binding affinity to DNA as the generally accepted crucial target of the drug. Application of 15N-labeled cisplatin and subsequent measurement of the nitrogen isotopic composition and determination of the relative intensities of platinum and nitrogen associated secondary ion signals in different cellular compartments with NanoSIMS suggested partial dissociation of Pt-N bonds during the accumulation process, in particular within nucleoli at elevated cisplatin concentrations. This finding raises the question as to whether the observed intracellular dissociation of the drug has implications for the mechanism of action of cisplatin. Within the cytoplasm, platinum mainly accumulated in acidic organelles, as demonstrated by a direct combination of specific fluorescent staining, confocal laser scanning microscopy and NanoSIMS. Different processing of platinum drugs in acidic organelles might be relevant for their detoxification, as well as for their mode of action.}, }
@article {pmid35918440, year = {2022}, author = {Wu, Q and Ji, M and Yu, S and Li, J and Wu, X and Ju, X and Liu, B and Zhang, X}, title = {Distinct Denitrifying Phenotypes of Predominant Bacteria Modulate Nitrous Oxide Metabolism in Two Typical Cropland Soils.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35918440}, issn = {1432-184X}, support = {31971526//National Natural Science Foundation of China/ ; 31861133018//National Natural Science Foundation of China/ ; XDB40020204//Chinese Academy of Sciences/ ; 2017YFD0200102//Key Technologies Research and Development Program/ ; }, abstract = {Denitrifying nitrous oxide (N2O) emissions in agroecosystems result from variations in microbial composition and soil properties. However, the microbial mechanisms of differential N2O emissions in agricultural soils are less understood. In this study, microcosm experiments using two main types of Chinese cropland soil were conducted with different supplements of nitrate and glucose to simulate the varying nitrogen and carbon conditions. The results show that N2O accumulation in black soil (BF) was significantly higher than that in fluvo-aquic soil (FF) independent of nitrogen and carbon. The abundance of most denitrifying genes was significantly higher in FF, but the ratios of genes responsible for N2O production (nirS and nirK) to the gene responsible for N2O reduction (nosZ) did not significantly differ between the two soils. However, the soils showed obvious discrepancies in denitrifying bacterial communities, with a higher abundance of N2O-generating bacteria in BF and a higher abundance of N2O-reducing bacteria in FF. High accumulation of N2O was verified by the bacterial isolates of Rhodanobacter predominated in BF due to a lack of N2O reduction capacity. The dominance of Castellaniella and others in FF led to a rapid reduction in N2O and thus less N2O accumulation, as demonstrated when the corresponding isolate was inoculated into the studied soils. Therefore, the different phenotypes of N2O metabolism of the distinct denitrifiers predominantly colonized the two soils, causing differing N2O accumulation. This knowledge would help to develop a strategy for mitigating N2O emissions in agricultural soils by regulating the phenotypes of N2O metabolism.}, }
@article {pmid35918056, year = {2022}, author = {Santos Correa, S and Schultz, J and Lauersen, KJ and Soares Rosado, A}, title = {Natural carbon fixation and advances in synthetic engineering for redesigning and creating new fixation pathways.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2022.07.011}, pmid = {35918056}, issn = {2090-1224}, abstract = {BACKGROUND: Autotrophic carbon fixation is the primary route through which organic carbon enters the biosphere, and it is a key step in the biogeochemical carbon cycle. The Calvin-Benson-Bassham pathway, which is predominantly found in plants, algae, and some bacteria (mainly cyanobacteria), was previously considered to be the sole carbon-fixation pathway. However, the discovery of a new carbon-fixation pathway in sulfurous green bacteria almost two decades ago encouraged further research on previously overlooked ancient carbon-fixation pathways in taxonomically and phylogenetically distinct microorganisms.<br><br>AIM OF REVIEW: In this review, we summarize the six known natural carbon-fixation pathways and outline the newly proposed additions to this list. We also discuss the recent achievements in synthetic carbon fixation and the importance of the metabolism of thermophilic microorganisms in this field.<br><br>Currently, at least six carbon-fixation routes have been confirmed in Bacteria and Archaea. Other possible candidate routes have also been suggested on the basis of emerging "omics" data analyses, expanding our knowledge and stimulating discussions on the importance of these pathways in the way organisms acquire carbon. Notably, the currently known natural fixation routes cannot balance the excessive anthropogenic carbon emissions in a highly unbalanced global carbon cycle. Therefore, significant efforts have also been made to improve the existing carbon-fixation pathways and/or design new efficient in vitro and in vivo synthetic pathways.}, }
@article {pmid35916938, year = {2022}, author = {Tang, Y and Wang, S and Jin, X and Zhou, D and Lin, Q and Liu, Z and Zhang, X and Dumont, HJ}, title = {Extensive Carbon Contribution of Inundated Terrestrial Plants to Zooplankton Biomass in a Eutrophic Lake.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35916938}, issn = {1432-184X}, support = {32071566//National Natural Science Foundation of China/ ; 2022A1515011074//Natural Science Foundation of Guangdong Province/ ; }, abstract = {Organic carbon derived from terrestrial plants contributes to aquatic consumers, e.g., zooplankton in lakes. The degree of the contribution depends on the availability of terrestrial organic carbon in lake organic pool and the transfer efficiency of the carbon. Terrestrial organic carbon is poor-quality food for zooplankton with a mismatch of nutrition content and was incorporated to zooplankton with much lower efficiency than phytoplankton. Contributions of terrestrial carbon to zooplankton generally decrease with an increase in phytoplankton production, indicating a preferential incorporation of phytoplankton in previous investigations. However, in eutrophic lakes, the dominating cyanobacteria were of poor quality and incorporated to consumers inefficiently too. In that case, zooplankton in eutrophic wetlands, where cyanobacteria dominate the phytoplankton production and massive terrestrial plants are inundated, may not preferentially incorporate poor food-quality phytoplankton resource to their biomass. Therefore, we hypothesize that carbon contributions of terrestrial vegetation to zooplankton and to lake particulate organic pool should be similar in such aquatic ecosystems. We tested this hypothesis by sampling zooplankton and carbon sources in Ming Lake (Jinan University Campus, southern China) which was overgrown by terrestrial plants after drying and re-flooded. After 60 days of observations at weekly (or biweekly) intervals, applying stable carbon (13C), nitrogen (15 N), and hydrogen (2H) isotopic analysis and a stable isotope mixing model, we estimated the occurrence of extensive carbon contribution (≥ 50%) of flooded terrestrial plants to cladocerans and copepods. Contribution of inundated terrestrial plants to cladocerans was similar to that to lake particulate organic pool. Thus, our study quantified the role of terrestrial carbon in eutrophic wetlands, enhancing our understanding of cross-ecosystem interactions in food webs with an emphasis on the resource quality.}, }
@article {pmid35916937, year = {2022}, author = {Pellegrinetti, TA and Cotta, SR and Sarmento, H and Costa, JS and Delbaje, E and Montes, CR and Camargo, PB and Barbiero, L and Rezende-Filho, AT and Fiore, MF}, title = {Bacterial Communities Along Environmental Gradients in Tropical Soda Lakes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35916937}, issn = {1432-184X}, support = {2016/14227-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, abstract = {Soda lake environments are known to be variable and can have distinct differences according to geographical location. In this study, we investigated the effects of different environmental conditions of six adjacent soda lakes in the Pantanal biome (Mato Grosso do Sul state, Brazil) on bacterial communities and their functioning using a metagenomic approach combined with flow cytometry and chemical analyses. Ordination analysis using flow cytometry and water chemistry data from two sampling periods (wet and dry) clustered soda lakes into three different profiles: eutrophic turbid (ET), oligotrophic turbid (OT), and clear vegetated oligotrophic (CVO). Analysis of bacterial community composition and functioning corroborated this ordination; the exception was one ET lake, which was similar to one OT lake during the wet season, indicating drastic shifts between seasons. Microbial abundance and diversity increased during the dry period, along with a considerable number of limnological variables, all indicative of a strong effect of the precipitation-evaporation balance in these systems. Cyanobacteria were associated with high electric conductivity, pH, and nutrient availability, whereas Actinobacteria, Alphaproteobacteria, and Betaproteobacteria were correlated with landscape morphology variability (surface water, surface perimeter, and lake volume) and with lower salinity and pH levels. Stress response metabolism was enhanced in OT and ET lakes and underrepresented in CVO lakes. The microbiome dataset of this study can serve as a baseline for restoring impacted soda lakes. Altogether, the results of this study demonstrate the sensitivity of tropical soda lakes to climate change, as slight changes in hydrological regimes might produce drastic shifts in community diversity.}, }
@article {pmid35915645, year = {2022}, author = {Mitiku, G and Rybka, D and Klein-Gunnewiek, P and Tessema, T and Raaijmakers, JM and Etalo, DW}, title = {Molecular detection and quantification of the Striga seedbank in agricultural soils.}, journal = {Weed research}, volume = {62}, number = {3}, pages = {181-191}, doi = {10.1111/wre.12535}, pmid = {35915645}, issn = {0043-1737}, abstract = {Striga hermonthica (Del.) Benth is a devastating parasitic weed in Sub-Saharan Africa (SSA) and its soil seedbank is the major factor contributing to its prevalence and persistence. To date, there is a little information on the Striga seedbank density in agricultural fields in SSA due to the lack of reliable detection and quantification methods. We developed a high-throughput method that combines density- and size-based separation techniques with quantitative polymerase chain reaction (qPCR)-based detection of Striga seeds in soil. The method was optimised and validated by introducing increasing numbers of Striga seeds in two physicochemically different Striga-free agricultural soils. The results showed that as little as one seed of S. hermonthica per 150 g of soil could be detected. This technique was subsequently tested on soil samples of 48 sorghum fields from different agro-ecological zones in Ethiopia to map the geospatial distribution of the Striga seedbank along a trajectory of more than 1500 km. Considerable variation in Striga seed densities was observed. Striga seeds were detectable in 75% of the field soils with densities up to 86 seeds per 150 g of soil. The Striga seed density in soil and the number of emerged Striga plants in the field showed a non-linear relationship. In conclusion, the method developed allows for accurate mapping of the Striga seedbank in physicochemically diverse SSA field soils and can be used to assess the impact of management strategies on Striga seedbank dynamics.}, }
@article {pmid35914169, year = {2022}, author = {Gwak, JH and Awala, SI and Nguyen, NL and Yu, WJ and Yang, HY and von Bergen, M and Jehmlich, N and Kits, KD and Loy, A and Dunfield, PF and Dahl, C and Hyun, JH and Rhee, SK}, title = {Sulfur and methane oxidation by a single microorganism.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {32}, pages = {e2114799119}, doi = {10.1073/pnas.2114799119}, pmid = {35914169}, issn = {1091-6490}, support = {2020R1A6A1A06046235//National Research Foundation of Korea (NRF)/ ; 2021R1A2C3004015//National Research Foundation of Korea (NRF)/ ; PJ01700703//Rural Development Administration (RDA)/ ; P 31996-B//Austrian Science Fund (FWF)/ ; NSERC-RGPIN-2019-06265//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; 796687 - H2Gut//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, abstract = {Natural and anthropogenic wetlands are major sources of the atmospheric greenhouse gas methane. Methane emissions from wetlands are mitigated by methanotrophic bacteria at the oxic-anoxic interface, a zone of intense redox cycling of carbon, sulfur, and nitrogen compounds. Here, we report on the isolation of an aerobic methanotrophic bacterium, 'Methylovirgula thiovorans' strain HY1, which possesses metabolic capabilities never before found in any methanotroph. Most notably, strain HY1 is the first bacterium shown to aerobically oxidize both methane and reduced sulfur compounds for growth. Genomic and proteomic analyses showed that soluble methane monooxygenase and XoxF-type alcohol dehydrogenases are responsible for methane and methanol oxidation, respectively. Various pathways for respiratory sulfur oxidation were present, including the Sox-rDsr pathway and the S4I system. Strain HY1 employed the Calvin-Benson-Bassham cycle for CO2 fixation during chemolithoautotrophic growth on reduced sulfur compounds. Proteomic and microrespirometry analyses showed that the metabolic pathways for methane and thiosulfate oxidation were induced in the presence of the respective substrates. Methane and thiosulfate could therefore be independently or simultaneously oxidized. The discovery of this versatile bacterium demonstrates that methanotrophy and thiotrophy are compatible in a single microorganism and underpins the intimate interactions of methane and sulfur cycles in oxic-anoxic interface environments.}, }
@article {pmid35913610, year = {2022}, author = {Cusumano, A and Bella, P and Peri, E and Rostás, M and Guarino, S and Lievens, B and Colazza, S}, title = {Nectar-Inhabiting Bacteria Affect Olfactory Responses of an Insect Parasitoid by Altering Nectar Odors.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35913610}, issn = {1432-184X}, support = {FFR_D13-2018/2021//Università degli Studi di Palermo/ ; }, abstract = {Floral nectar is ubiquitously colonized by a variety of microorganisms among which yeasts and bacteria are the most common. Microorganisms inhabiting floral nectar can alter several nectar traits, including nectar odor by producing microbial volatile organic compounds (mVOCs). Evidence showing that mVOCs can affect the foraging behavior of insect pollinators is increasing in the literature, whereas the role of mVOCs in altering the foraging behavior of third-trophic level organisms such as insect parasitoids is largely overlooked. Parasitoids are frequent visitors of flowers and are well known to feed on nectar. In this study, we isolated bacteria inhabiting floral nectar of buckwheat, Fagopyrum esculentum (Polygonales: Polygonaceae), to test the hypothesis that nectar bacteria affect the foraging behavior of the egg parasitoid Trissolcus basalis (Hymenoptera: Scelionidae) via changes in odors of nectar. In behavioral assays, we found that T. basalis wasps are attracted toward nectar fermented by 4 out of the 14 bacterial strains isolated, which belong to Staphylococcus epidermidis, Terrabacillus saccharophilus (both Firmicutes), Pantoea sp. (Proteobacteria), and Curtobacterium sp. (Actinobacteria). Results of chemical investigations revealed significant differences in the volatile blend composition of nectars fermented by the bacterial isolates. Our results indicate that nectar-inhabiting bacteria play an important role in the interactions between flowering plants and foraging parasitoids. These results are also relevant from an applied perspective as flowering resources, such as buckwheat, are largely used in agriculture to promote conservation biological control of insect pests.}, }
@article {pmid35913161, year = {2022}, author = {Lesniak, NA and Tomkovich, S and Henry, A and Taylor, A and Colovas, J and Bishop, L and McBride, K and Schloss, PD}, title = {Diluted Fecal Community Transplant Restores Clostridioides difficile Colonization Resistance to Antibiotic-Perturbed Murine Communities.}, journal = {mBio}, volume = {}, number = {}, pages = {e0136422}, doi = {10.1128/mbio.01364-22}, pmid = {35913161}, issn = {2150-7511}, abstract = {Fecal communities transplanted into individuals can eliminate recurrent Clostridioides difficile infection (CDI) with high efficacy. However, this treatment is only used once CDI becomes resistant to antibiotics or has recurred multiple times. We sought to investigate whether a fecal community transplant (FCT) pretreatment could be used to prevent CDI altogether. We treated male C57BL/6 mice with either clindamycin, cefoperazone, or streptomycin and then inoculated them with the microbial community from untreated mice before challenge with C. difficile. We measured colonization and sequenced the V4 region of the 16S rRNA gene to understand the dynamics of the murine fecal community in response to the FCT and C. difficile challenge. Clindamycin-treated mice became colonized with C. difficile but cleared it naturally and did not benefit from the FCT. Cefoperazone-treated mice became colonized by C. difficile, but the FCT enabled clearance of C. difficile. In streptomycin-treated mice, the FCT was able to prevent C. difficile from colonizing. We then diluted the FCT and repeated the experiments. Cefoperazone-treated mice no longer cleared C. difficile. However, streptomycin-treated mice colonized with 1:102 dilutions resisted C. difficile colonization. Streptomycin-treated mice that received an FCT diluted 1:103 became colonized with C. difficile but later cleared the infection. In streptomycin-treated mice, inhibition of C. difficile was associated with increased relative abundance of a group of bacteria related to Porphyromonadaceae and Lachnospiraceae. These data demonstrate that C. difficile colonization resistance can be restored to a susceptible community with an FCT as long as it complements the missing populations. IMPORTANCE Antibiotic use, ubiquitous with the health care environment, is a major risk factor for Clostridioides difficile infection (CDI), the most common nosocomial infection. When C. difficile becomes resistant to antibiotics, a fecal microbiota transplant from a healthy individual can effectively restore the gut bacterial community and eliminate the infection. While this relationship between the gut bacteria and CDI is well established, there are no therapies to treat a perturbed gut community to prevent CDI. This study explored the potential of restoring colonization resistance to antibiotic-induced susceptible gut communities. We described the effect that gut bacterial community variation has on the effectiveness of a fecal community transplant for inhibiting CDI. These data demonstrated that communities susceptible to CDI can be supplemented with fecal communities but that the effectiveness depended on the structure of the community following the perturbation. Thus, a reduced bacterial community may be able to recover colonization resistance in patients treated with antibiotics.}, }
@article {pmid35909604, year = {2022}, author = {Jepsen, T and Jensen, B and Jørgensen, NOG}, title = {Volatiles produced by Streptomyces spp. delay rot in apples caused by Colletotrichum acutatum.}, journal = {Current research in microbial sciences}, volume = {3}, number = {}, pages = {100121}, doi = {10.1016/j.crmicr.2022.100121}, pmid = {35909604}, issn = {2666-5174}, abstract = {Volatile organic compounds (VOCs) produced by microorganisms may prevent postharvest rot in fruits. Here, it was examined if VOCs from different species of Streptomyces can control infection in apples caused by the fungal pathogen Colletotrichum acutatum. Incubation of C. acutatum-infected apples in semi-closed boxes with actively growing strains of three Streptomyces (S. coelicolor, S. diastatochromogenes and Streptomyces strain 2R) showed that VOCs reduced rot areas of the apples by 45-66% after 8 days and 39-57% after 10 days, relative to infected apples incubated without Streptomyces. No differences in inhibition among the three strains were seen. In contrast, a mutant strain of Streptomyces that lacks major genes involved in biosynthesis of secondary metabolites, did not reduce development of rot in the apples. Furthermore, Streptomyces VOCs reduced radial hyphal growth of C. acutatum on agar. Several of the VOCs produced by three Streptomyces strains have previously shown fungicidal properties. Although the specific VOCs being active in inhibition of C. acutatum remain to be determined, VOCs may have a great potential as biofumigants to minimize postharvest diseases in fruits.}, }
@article {pmid35903477, year = {2022}, author = {Olmo, R and Wetzels, SU and Armanhi, JSL and Arruda, P and Berg, G and Cernava, T and Cotter, PD and Araujo, SC and de Souza, RSC and Ferrocino, I and Frisvad, JC and Georgalaki, M and Hansen, HH and Kazou, M and Kiran, GS and Kostic, T and Krauss-Etschmann, S and Kriaa, A and Lange, L and Maguin, E and Mitter, B and Nielsen, MO and Olivares, M and Quijada, NM and Romaní-Pérez, M and Sanz, Y and Schloter, M and Schmitt-Kopplin, P and Seaton, SC and Selvin, J and Sessitsch, A and Wang, M and Zwirzitz, B and Selberherr, E and Wagner, M}, title = {Microbiome Research as an Effective Driver of Success Stories in Agrifood Systems - A Selection of Case Studies.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {834622}, doi = {10.3389/fmicb.2022.834622}, pmid = {35903477}, issn = {1664-302X}, abstract = {Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describe products, methodologies, applications, tools, and processes that created an economic and societal impact. Additionally, they cover a broad range of fields within the agrifood chain: the management of diseases and putative pathogens; the use of microorganism as soil fertilizers and plant strengtheners; the investigation of the microbial dynamics occurring during food fermentation; the presence of microorganisms and/or genes associated with hazards for animal and human health (e.g., mycotoxins, spoilage agents, or pathogens) in feeds, foods, and their processing environments; applications to improve HACCP systems; and the identification of novel probiotics and prebiotics to improve the animal gut microbiome or to prevent chronic non-communicable diseases in humans (e.g., obesity complications). The microbiomes of soil, plants, and animals are pivotal for ensuring human and environmental health and this review highlights the impact that microbiome applications have with this regard.}, }
@article {pmid35902889, year = {2022}, author = {Ma, X and Wang, T and Shi, Z and Chiariello, NR and Docherty, K and Field, CB and Gutknecht, J and Gao, Q and Gu, Y and Guo, X and Hungate, BA and Lei, J and Niboyet, A and Le Roux, X and Yuan, M and Yuan, T and Zhou, J and Yang, Y}, title = {Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {112}, pmid = {35902889}, issn = {2049-2618}, support = {DEB-0092642//the US National Science Foundation/ ; 41825016//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Anthropogenic activities have increased the inputs of atmospheric reactive nitrogen (N) into terrestrial ecosystems, affecting soil carbon stability and microbial communities. Previous studies have primarily examined the effects of nitrogen deposition on microbial taxonomy, enzymatic activities, and functional processes. Here, we examined various functional traits of soil microbial communities and how these traits are interrelated in a Mediterranean-type grassland administrated with 14 years of 7 g m-2 year-1 of N amendment, based on estimated atmospheric N deposition in areas within California, USA, by the end of the twenty-first century.<br><br>RESULTS: Soil microbial communities were significantly altered by N deposition. Consistent with higher aboveground plant biomass and litter, fast-growing bacteria, assessed by abundance-weighted average rRNA operon copy number, were favored in N deposited soils. The relative abundances of genes associated with labile carbon (C) degradation (e.g., amyA and cda) were also increased. In contrast, the relative abundances of functional genes associated with the degradation of more recalcitrant C (e.g., mannanase and chitinase) were either unchanged or decreased. Compared with the ambient control, N deposition significantly reduced network complexity, such as average degree and connectedness. The network for N deposited samples contained only genes associated with C degradation, suggesting that C degradation genes became more intensely connected under N deposition.<br><br>CONCLUSIONS: We propose a conceptual model to summarize the mechanisms of how changes in above- and belowground ecosystems by long-term N deposition collectively lead to more soil C accumulation. Video Abstract.}, }
@article {pmid35896536, year = {2022}, author = {Lin, C and Peñaranda, JSD and Dendooven, J and Detavernier, C and Schaubroeck, D and Boon, N and Baets, R and Le Thomas, N}, title = {UV photonic integrated circuits for far-field structured illumination autofluorescence microscopy.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {4360}, pmid = {35896536}, issn = {2041-1723}, support = {01IO1320//Bijzonder Onderzoeksfonds (Special Research Fund)/ ; }, mesh = {Light ; *Lighting ; *Microscopy/methods ; Photons ; }, abstract = {Ultra-violet (UV) light has still a limited scope in optical microscopy despite its potential advantages over visible light in terms of optical resolution and of interaction with a wide variety of biological molecules. The main challenge is to control in a robust, compact and cost-effective way UV light beams at the level of a single optical spatial mode and concomitantly to minimize the light propagation loss. To tackle this challenge, we present here photonic integrated circuits made of aluminum oxide thin layers that are compatible with both UV light and high-volume manufacturing. These photonic circuits designed at a wavelength of 360 nm enable super-resolved structured illumination microscopy with conventional wide-field microscopes and without modifying the usual protocol for handling the object to be imaged. As a biological application, we show that our UV photonic chips enable to image the autofluorescence of yeast cells and reveal features unresolved with standard wide-field microscopy.}, }
@article {pmid35893569, year = {2022}, author = {Mugani, R and Khalloufi, FE and Redouane, EM and Haida, M and Zerrifi, SEA and Campos, A and Kasada, M and Woodhouse, J and Grossart, HP and Vasconcelos, V and Oudra, B}, title = {Bacterioplankton Associated with Toxic Cyanobacteria Promote Pisum sativum (Pea) Growth and Nutritional Value through Positive Interactions.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, doi = {10.3390/microorganisms10081511}, pmid = {35893569}, issn = {2076-2607}, support = {823860//European Commission/ ; }, abstract = {Research on Plant Growth-Promoting Bacteria (PGPB) has focused much more on rhizospheric bacteria. However, PGPB associated with toxic cyanobacterial bloom (TCB) could enter the rhizosphere through irrigation water, helping plants such as Pisum sativum L. (pea) overcome oxidative stress induced by microcystin (MC) and improve plant growth and nutritional value. This study aimed to isolate bacteria associated with toxic cyanobacteria, test PGPB properties, and inoculate them as a consortium to pea seedlings irrigated with MC to investigate their role in plant protection as well as in improving growth and nutritional value. Two bacterioplankton isolates and one rhizosphere isolate were isolated and purified on a mineral salt medium supplemented with 1000 μg/L MC and identified via their 16S rRNA gene. The mixed strains were inoculated to pea seedlings in pots irrigated with 0, 50, and 100 μg/L MC. We measured the morphological and physiological parameters of pea plants at maturity and evaluated the efficiency of the plant's enzymatic and non-enzymatic antioxidant responses to assess the role and contribution of PGPB. Both bacterioplankton isolates were identified as Starkeya sp., and the rhizobacterium was identified as Brevundimonas&amp;nbsp;aurantiaca. MC addition significantly (p < 0.05) reduced all the growth parameters of the pea, i.e., total chlorophyll content, leaf quantum yield, stomatal conductance, carotenoids, and polyphenol contents, in an MC concentration-dependent manner, while bacterial presence positively affected all the measured parameters. In the MC treatment, the levels of the pea's antioxidant traits, including SOD, CAT, POD, PPO, GST, and ascorbic acid, were increased in the sterile pots. In contrast, these levels were reduced with double and triple PGPB addition. Additionally, nutritional values such as sugars, proteins, and minerals (Ca and K) in pea fruits were reduced under MC exposure but increased with PGPB addition. Overall, in the presence of MC, PGPB seem to positively interact with pea plants and thus may constitute a natural alternative for soil fertilization when irrigated with cyanotoxin-contaminated water, increasing the yield and nutritional value of crops.}, }
@article {pmid35892285, year = {2022}, author = {von Gastrow, L and Michel, E and Legrand, J and Amelot, R and Segond, D and Guezenec, S and Rué, O and Chable, V and Goldringer, I and Dousset, X and Serpolay-Bessoni, E and Taupier-Letage, B and Vindras-Fouillet, C and Onno, B and Valence, F and Sicard, D}, title = {Microbial community dispersal from wheat grains to sourdoughs : a contribution of participatory research.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16630}, pmid = {35892285}, issn = {1365-294X}, abstract = {Understanding microbial dispersal is critical to understand the dynamics and evolution of microbial communities. However, microbial dispersal is difficult to study because of uncertainty about their vectors of migration. This applies to both microbial communities in natural and human-associated environments. Here, we studied microbial dispersal along the sourdoughs bread making chain using a participatory research approach. Sourdough is a naturally fermented mixture of flour and water. It hosts a community of bacteria and yeasts whose origins are only partially known. We analysed the potential of wheat grains and flour to serve as an inoculum for sourdough microbial communities using 16S rDNA and ITS1 metabarcoding. First, in an experiment involving farmers, a miller and bakers, we followed the microbiota from grains to newly initiated and propagated sourdoughs. Second, we compared the microbiota of 46 sourdough samples collected everywhere in France, and of the flour used for their backslopping. The core microbiota detected on the seeds, in the flour and in the sourdough was composed mainly of microbes known to be associated with plants and not living in sourdoughs. No sourdough yeast species were detected on grains and flours. Sourdough lactic acid bacteria were rarely found in flour. When they were, they did not have the same amplicon sequence variant (ASV) as found in the corresponding sourdough. However, the low sequencing depth for bacteria in flour did not allow us to draw definitive conclusion. Thus, our results showed that sourdough yeasts did not come from flour, and suggest that neither do sourdough LAB.}, }
@article {pmid35890046, year = {2022}, author = {Orsini, M and Petrin, S and Corrò, M and Baggio, G and Spagnolo, E and Losasso, C}, title = {Anthroponotic-Based Transfer of Staphylococcus to Dog: A Case Study.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, doi = {10.3390/pathogens11070802}, pmid = {35890046}, issn = {2076-0817}, support = {RC IZSVE 16/18//Ministero della Salute/ ; }, abstract = {Although usually harmless, Staphylococcus spp. can cause nosocomial and community-onset skin and soft tissue infections in both humans and animals; thus, it is considered a significant burden for healthcare systems worldwide. Companion animals have been identified as potential reservoirs of pathogenic Staphylococcus with specific reference to Methicillin Resistant Staphylococcus aureus (MRSA). In this study, we investigated the circulation and the genetic relationships of a collection of Staphylococcus spp. isolates in a family composed of four adults (a mother, father, grandmother, and grandfather), one child, and a dog, which were sampled over three years. The routes of transmission among humans and between humans and the dog werelyzed. The results displayed the circulation of many Staphylococcus lineages, belonging to different species and sequence types (ST) and being related to both human and pet origins. However, among the observed host-switch events, one of them clearly underpinnthroponotic route from a human to a dog. This suggests that companion animals can potentially have a role as a carrier of Staphylococcus, thus posing a serious concern about MRSA spreading within human and animal microbial communities.}, }
@article {pmid35889095, year = {2022}, author = {Melo-Bolívar, JF and Ruiz Pardo, RY and Junca, H and Sidjabat, HE and Cano-Lozano, JA and Villamil Díaz, LM}, title = {Competitive Exclusion Bacterial Culture Derived from the Gut Microbiome of Nile Tilapia (Oreochromis niloticus) as a Resource to Efficiently Recover Probiotic Strains: Taxonomic, Genomic, and Functional Proof of Concept.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, doi = {10.3390/microorganisms10071376}, pmid = {35889095}, issn = {2076-2607}, support = {ING181-2016//Universidad de La Sabana/ ; INGPHD-6-2017//Universidad de La Sabana/ ; INGPHD-9-2019//Universidad de La Sabana/ ; 808-2018-contract CT 329-2019//MINCIENCIAS- Patrimonio Autónomo Fondo Nacional de Financiamiento para la Ciencia, la Tecnología y la Innovación Francisco José de Caldas/ ; 727-2015, contract CT 122-2017//MINCIENCIAS/ ; }, abstract = {This study aims to mine a previously developed continuous-flow competitive exclusion culture (CFCEC) originating from the Tilapia gut microbiome as a rational and efficient autochthonous probiotic strain recovery source. Three isolated strains were tested on their adaptability to host gastrointestinal conditions, their antibacterial activities against aquaculture bacterial pathogens, and their antibiotic susceptibility patterns. Their genomes were fully sequenced, assembled, annotated, and relevant functions inferred, such as those related to pinpointed probiotic activities and phylogenomic comparative analyses to the closer reported strains/species relatives. The strains are possible candidates of novel genus/species taxa inside Lactococcus spp. and Priestia spp. (previously known as Bacillus spp.) These results were consistent with reports on strains inside these phyla exhibiting probiotic features, and the strains we found are expanding their known diversity. Furthermore, their pangenomes showed that these bacteria have indeed a set of so far uncharacterized genes that may play a role in the antagonism to competing strains or specific symbiotic adaptations to the fish host. In conclusion, CFCEC proved to effectively allow the enrichment and further pure culture isolation of strains with probiotic potential.}, }
@article {pmid35886559, year = {2022}, author = {Shen, W and Long, Y and Qiu, Z and Gao, N and Masuda, Y and Itoh, H and Ohba, H and Shiratori, Y and Rajasekar, A and Senoo, K}, title = {Investigation of Rice Yields and Critical N Losses from Paddy Soil under Different N Fertilization Rates with Iron Application.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {14}, pages = {}, doi = {10.3390/ijerph19148707}, pmid = {35886559}, issn = {1660-4601}, support = {CX(21)3183//Jiangsu Agricultural Science and Technology Innovation Fund/ ; 41771291//National Natural Science Foundation of China/ ; JP20H05679//JSPS KAKENHI/ ; JPMJMI20E5//JST-Mirai Program/ ; }, mesh = {Agriculture ; Fertilization ; Fertilizers/analysis ; Iron ; Nitrogen/analysis ; Nitrous Oxide/analysis ; *Oryza/chemistry ; Powders ; *Soil/chemistry ; Urea ; }, abstract = {The application of iron powder stimulated the growth of iron-reducing bacteria as a respiratory substrate and enhanced their nitrogen (N)-fixing activity in flooded paddy soils. High N fertilization (urea) in the flooded paddy soils has caused adverse environmental impacts such as ammonia (NH3) volatilization, nitrous oxide (N2O) emissions, and nitrate (NO3-) leaching. This study aims to investigate the effects of N fertilization rates in combination with an iron amendment on rice yields and N losses from flooded paddy fields. We performed a 2-year field plot experiment with traditional rice-wheat rotation in China's Yangtze River Delta. The investigation consisted of seven treatments, including 100%, 80%, 60%, and 0% of the conventional N (urea and commercial organic manure) fertilization rate, and 80%, 60%, and 0% of the conventional N with the iron powder (≥99% purity) amendment. The rice yields decreased with a reduction in the conventional N fertilization rate, whereas they were comparable after the iron application under the 80% and 60% conventional N rate. The critical N losses, including NH3 volatilization, N2O emissions, and NO3- and NH4+ leaching, generally decreased with a reduction in the conventional N fertilization rate. These N losses were significantly greater after the iron amendment compared with the non-amended treatments under the 80% and 60% conventional N fertilization rate in the first rice-growing season. However, it was comparable between the iron-amended and the non-amended treatments in the second season. Furthermore, NO3- leaching was the most significant N loss throughout the two rice seasons, followed by NH3 volatilization. The iron amendment significantly increased soil Fe2+ content compared with the non-amended treatments irrespective of N fertilization, suggesting the reduction of amended iron by iron-reducing bacteria and their simultaneous N fixation. A combination of the iron application with 60-80% of the conventional N fertilization rate could maintain rice yields similar to the conventional N fertilization rate while reducing the critical N losses in the flooded paddy field tested in this study. Our study leads to the establishment of novel and practical rice cultivation, which is a step towards the development of green agriculture.}, }
@article {pmid35884216, year = {2022}, author = {Duysburgh, C and Van den Abbeele, P and Franckenstein, D and Westphal, M and Kuchinka-Koch, A and Marzorati, M}, title = {Co-Administration of Lactulose Crystals with Amoxicillin Followed by Prolonged Lactulose Treatment Promotes Recovery of the Human Gut Microbiome In Vitro.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, doi = {10.3390/antibiotics11070962}, pmid = {35884216}, issn = {2079-6382}, abstract = {The validated SHIME model was used to assess the effect of repeated administration of two different lactulose dosages (5 g/d and 10 g/d) on the human gut microbiome during and following amoxicillin-clavulanic acid treatment. First, antibiotic treatment strongly decreased Bifidobacteriaceae levels from 54.4% to 0.6% and from 23.8% to 2.3% in the simulated proximal and distal colon, respectively, coinciding with a marked reduction in butyrate concentrations. Treatment with lactulose enhanced acetate and lactate levels during antibiotic treatment, likely through lactulose fermentation by Lachnospiraceae and Lactobacillaceae. One week after cessation of antibiotic treatment, Bifidobacteriaceae levels re-increased to 20.4% and 7.6% in the proximal and distal colon of the 5 g lactulose/d co-administered unit, as compared with 1.0% and 2.2% in the antibiotic-treated unit, and were even further stimulated upon extension of lactulose administration. Marked butyrogenic effects were observed upon prolonged lactulose supplementation, suggesting the establishment of cross-feeding interactions between Bifidobacteriaceae and butyrate producers. Furthermore, a limited Enterobacteriaceae outgrowth following antibiotic treatment was observed upon dosing with 10 g lactulose/d, indicating inhibition of pathogenic colonization by lactulose following antibiotic therapy. Overall, lactulose seems to be an interesting candidate for limiting the detrimental effects of amoxicillin-clavulanic acid on the human gut microbiome, though further studies are warranted to confirm these findings.}, }
@article {pmid35883112, year = {2022}, author = {Romo Bechara, N and Wasserberg, G and Raymann, K}, title = {Microbial ecology of sand fly breeding sites: aging and larval conditioning alter the bacterial community composition of rearing substrates.}, journal = {Parasites &amp; vectors}, volume = {15}, number = {1}, pages = {265}, pmid = {35883112}, issn = {1756-3305}, support = {R01AI123327//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Aged ; Aging ; Animals ; Bacteria/genetics ; Breeding ; Female ; Humans ; Larva ; Mosquito Vectors ; *Phlebotomus/genetics ; *Psychodidae/genetics ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Sand flies vector several human pathogens, including Leishmania species, which cause leishmaniases. A leishmaniasis vaccine does not yet exist, so the most common prevention strategies involve personal protection and insecticide spraying. However, insecticides can impact non-target organisms and are becoming less effective because of the evolution of resistance. An alternative control strategy is the attract-and-kill approach, where the vector is lured to a lethal trap, ideally located in oviposition sites that will attract gravid females. Oviposition traps containing attractive microbes have proven successful for the control of some mosquito populations but have not been developed for sand flies. Gravid female sand flies lay their eggs in decomposing organic matter on which the larvae feed and develop. Studies have demonstrated that gravid females are particularly attracted to larval conditioned (containing eggs and larvae) and aged rearing substrates. An isolate-based study has provided some evidence that bacteria play a role in the attraction of sand flies to conditioned substrates. However, the overall bacterial community structure of conditioned and aged substrates and how they change over time has not been investigated.<br><br>METHODS: The goal of this study was to characterize the bacterial communities of rearing and oviposition substrates that have been shown to vary in attractiveness to gravid sand flies in previous behavioral studies. Using 16S rRNA amplicon sequencing we determined the bacterial composition in fresh, aged, and larval-conditioned substrates at four time points representing the main life-cycle stages of developing sand flies. We compared the diversity, presence, and abundance of taxa across substrate types and time points in order to identify how aging and larval-conditioning impact bacterial community structure.<br><br>RESULTS: We found that the bacterial communities significantly change within and between substrates over time. We also identified bacteria that might be responsible for attraction to conditioned and aged substrates, which could be potential candidates for the development of attract-and-kill strategies for sand flies.<br><br>CONCLUSION: This study demonstrated that both aging and larval conditioning induce shifts in the bacterial communities of sand fly oviposition and rearing substrates, which may explain the previously observed preference of gravid female sand flies to substrates containing second/third-instar larvae (conditioned) and substrates aged the same amount of time without larvae (aged).}, }
@article {pmid35882347, year = {2022}, author = {Aziz, A and Rameez, H and Sengar, A and Sharma, D and Farooqi, IH and Basheer, F}, title = {Biogas production and nutrients removal from slaughterhouse wastewater using integrated anaerobic and aerobic granular intermittent SBRs - Bioreactors stability and microbial dynamics.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {157575}, doi = {10.1016/j.scitotenv.2022.157575}, pmid = {35882347}, issn = {1879-1026}, abstract = {Slaughterhouse wastewater (SWW) was effectively treated in sequential anaerobic and aerobic granular intermittent sequencing batch reactors (ASBR+ISBR) for 665 days at different HRTs (48 h, 32 h, 24 h, and 12 h). The ASBR was stable at each HRT but performed relatively well at 12 h (OLR - 7.8-9.8 kg COD/m3-d) in terms of pollutants removal and biogas production than previously conducted research. The average biogas production was about 17.3 L/day having 70-76 % of CH4 which could subsidize around 52 % of electricity demand while saving 103 US dollars/day if installed at full scale. In the case of post aerobic granular ISBR, carbon and nutrients removal (N&amp;P) was achieved by enriching granules (1.7-2.2 mm) at low DO (0.5-0.8 mg/L) via the nitrite pathway. The ISBR was also well stable at 12 h HRT (average OLR of 2.1 kg COD/m3-d) and met the effluent discharge guidelines recommended by the Central Pollution Control Board of India. During steady-state conditions (12 h HRT), the average removal efficiencies for COD, TSS, O&amp;G, TN, and PO4-P were 98.8 %, 96.4 %, 98.7 %, 93.4 %, and 86.6 % respectively from combined ASBR and ISBR. The microbial analysis confirmed Euryarchaeota, Proteobacteria, Firmicutes, Chloroflexi, Bacteroidetes, Planctomycetes, and Synergistetes as the dominant phyla in ASBR. Methanosaeta (21.56 %) and Methanosarcina (6.48 %) were the prevailing methanogens for CH4 production. The leading phyla observed in ISBR were Bacteroidetes, Proteobacteria, Firmicutes, Armatimonadetes, Verrucomicrobia, Chloroflexi, and Planctomycetes. Heterotrophic AOB (Thauera, Xanthomonadaceae, Pseudomonas, Sphingomonadaceae, and Rhodococcus) were mainly detected in the system for ammonia oxidation besides common autotrophic AOB. Similarly, a known PAO (Accumulibacter) was not identified but other PAO (Rhodocyclaceae, Dechloromonas, Pseudomonas, Flavobacteriaceae, and Sphingobacteriaceae) were prevalent inside aerobic granular ISBR that contributed to both carbon and nutrients removal. The results obtained would help implement the investigated reactor configurations at the pilot and full scale for SWW treatment.}, }
@article {pmid35882195, year = {2022}, author = {Lyng, M and Kovács, ÁT}, title = {Microbial ecology: Metabolic heterogeneity and the division of labor in multicellular structures.}, journal = {Current biology : CB}, volume = {32}, number = {14}, pages = {R771-R774}, doi = {10.1016/j.cub.2022.06.008}, pmid = {35882195}, issn = {1879-0445}, abstract = {Many bacterial species are capable of differentiating to create phenotypic heterogeneity. Using the aggregate-forming marine bacterium Vibrio splendidus, a new study reveals how this organism differentiates to form spherical structures with a motile, carbon-storing core and a non-motile shell.}, }
@article {pmid35881247, year = {2022}, author = {King, NG and Smale, DA and Thorpe, JM and McKeown, NJ and Andrews, AJ and Browne, R and Malham, SK}, title = {Core Community Persistence Despite Dynamic Spatiotemporal Responses in the Associated Bacterial Communities of Farmed Pacific Oysters.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35881247}, issn = {1432-184X}, abstract = {A breakdown in host-bacteria relationships has been associated with the progression of a number of marine diseases and subsequent mortality events. For the Pacific oyster, Crassostrea gigas, summer mortality syndrome (SMS) is one of the biggest constraints to the growth of the sector and is set to expand into temperate systems as ocean temperatures rise. Currently, a lack of understanding of natural spatiotemporal dynamics of the host-bacteria relationship limits our ability to develop microbially based monitoring approaches. Here, we characterised the associated bacterial community of C. gigas, at two Irish oyster farms, unaffected by SMS, over the course of a year. We found C. gigas harboured spatiotemporally variable bacterial communities that were distinct from bacterioplankton in surrounding seawater. Whilst the majority of bacteria-oyster associations were transient and highly variable, we observed clear patterns of stability in the form of a small core consisting of six persistent amplicon sequence variants (ASVs). This core made up a disproportionately large contribution to sample abundance (34 ± 0.14%), despite representing only 0.034% of species richness across the study, and has been associated with healthy oysters in other systems. Overall, our study demonstrates the consistent features of oyster bacterial communities across spatial and temporal scales and provides an ecologically meaningful baseline to track environmental change.}, }
@article {pmid35880896, year = {2022}, author = {Sun, Y and Shi, J and Wang, X and Ding, C and Wang, J}, title = {Deciphering the Mechanisms Shaping the Plastisphere Microbiota in Soil.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0035222}, doi = {10.1128/msystems.00352-22}, pmid = {35880896}, issn = {2379-5077}, abstract = {The gradual accumulation of microplastics has aroused increasing concern for the unique niche, termed "plastisphere." As research so far has focused on their characteristics in aquatic ecosystems, our understanding of the colonization and assembly of the attached bacterial communities on microplastics in soil ecosystems remains poor. Here, we aimed to characterize the plastisphere microbiomes of two types of microplastics (polylactic acid [PLA] and polyethylene [PE]) differing in their biodegradability in two different soils. After incubation for 60 days, considerably lower alpha diversity of bacterial community was observed on the microplastic surfaces, and prominent divergences occurred in the microbial community compositions between the plastisphere and the bulk soil. The temperature, rather than polymer type, significantly induced the differences between the plastisphere communities. The rRNA gene operon (rrn) copy numbers were significantly higher in the PLA plastisphere, suggesting potential degradation. The co-occurrence network analysis showed that the PE plastisphere exhibited greater network complexity and stronger stability than those in the PLA plastisphere. The stochasticity ratio indicated the remarkable importance of stochastic process on community assembly in PE and PLA plastispheres, while the null model analysis showed the nonnegligible roles of deterministic processes in shaping the plastisphere communities. Higher contributions of homogenous selection in the PLA plastisphere were observed in comparison with the PE plastisphere, which could probably be attributed to the selective pressure induced by microplastic degradation. Our findings enhance our mechanistic understanding of the diversity patterns and assembly processes of plastisphere in soil environments and have important implications for microbial ecology and microplastic risk assessment. IMPORTANCE The increasing pervasive microplastic pollution is creating a new environmental compartment, termed plastisphere. Even though there was conclusive information characterizing the plastisphere, the underlying mechanisms shaping the bacterial communities in the plastisphere in the soil remain unclear. Therefore, we incubated two types of microplastics (PE and PLA) in two different soils and explored the differences between plastisphere and bulk soil communities. Additionally, the co-occurrence network and the assembly processes of plastisphere were subjected to further analysis. Our results highlight the importance of selective recruitment of microplastics and contribute to the understanding of the diversity patterns and assembly processes of plastisphere in soil environments.}, }
@article {pmid35880097, year = {2022}, author = {Strik, DPBTB and Ganigué, R and Angenent, LT}, title = {Editorial: Microbial Chain Elongation- Close the Carbon Loop by Connecting-Communities.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {894490}, pmid = {35880097}, issn = {2296-4185}, }
@article {pmid35878855, year = {2022}, author = {Camacho-Sanchez, M and Camacho, M and Redondo-Gómez, S and Mateos-Naranjo, E}, title = {Bacterial assemblage in Mediterranean salt marshes: Disentangling the relative importance of seasonality, zonation and halophytes.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {157514}, doi = {10.1016/j.scitotenv.2022.157514}, pmid = {35878855}, issn = {1879-1026}, abstract = {Salt marshes gather a high diversity of prokaryotes across their environmental gradients. Most of this diversity and the factors determining their community assemblage are unknown. We massively sequenced a portion of the 16S gene to characterize the diversity of prokaryotes in soils from a salt marsh in Río Piedras, Southern Spain. We sampled in the four seasons, and in five plots dominated by a different halophyte (Spartina maritima, S. densiflora, Salicornia ramosissima, Arthrocaulon macrostachyum and Atriplex portulacoides) growing under different environmental conditions and representing different stages in the marsh ecological succession. Soil was sampled in their rhizosphere and adjacent bulk soil. We report the effects of different factors explaining prokaryotic beta diversity in the marsh: zonation (50 %), seasonality (14 %), and halophyte rhizosphere (7 %). Proteobacteria and Bacteroidota were the most abundant phyla. Firmicutes had a peak in winter and Desulfobacterota with other bacteria involved in sulfur cycling were abundant in the low marsh plots from S. maritima. Alpha diversity was highest in spring and decreased in winter. We detected a marked phylogenetic turnover between seasons and in rhizospheric soil respect to adjacent bulk soil for most pairwise comparisons. The effect of halophyte on its rhizosphere was species-specific, being S. maritima the species with more differentiated taxa between rhizosphere versus surrounding bulk soil. Our work highlights how the complex interaction between marsh zonation, seasonality and rhizosphere, onsets processes structuring bacterial community assemblage in salt marsh soils.}, }
@article {pmid35876854, year = {2022}, author = {Perliński, P and Mudryk, ZJ and Zdanowicz, M and Kubera, Ł}, title = {Abundance of Live and Dead Bacteriopsammon Inhabiting Sandy Ecosystems of Recreational Marine Beaches of the Southern Baltic Sea.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35876854}, issn = {1432-184X}, abstract = {The study was carried out on four non-tidal sandy marine beaches located on the Polish part of the southern Baltic Sea coast. We applied a LIVE/DEAD™ BacLight™ Bacterial Viability Kit (Invitrogen™) method to determine the abundance of live and dead bacteriopsammon. Live psammon bacteria cells constituted 31-53% of the total number of bacteria inhabiting sand of the studied beaches. Abundance of live and dead psammon bacteria generally differed along the horizontal profile in all beaches. The maximum density of bacteria was noted in the dune and the middle part of the beach (dry zones) and the minimum in wet zones, i.e., under seawater surface and at the swash zone. Generally along the vertical profile, the highest numbers of two studied bacterial groups were noted in the surface sand layer, while with increasing sediment depth their numbers significantly decreased. The abundance of live and dead bacteria showed a distinct seasonal variation.}, }
@article {pmid35873980, year = {2022}, author = {Gouka, L and Vogels, C and Hansen, LH and Raaijmakers, JM and Cordovez, V}, title = {Genetic, Phenotypic and Metabolic Diversity of Yeasts From Wheat Flag Leaves.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {908628}, pmid = {35873980}, issn = {1664-462X}, abstract = {The phyllosphere, the aboveground part of a plant, is a harsh environment with diverse abiotic and biotic stresses, including oscillating nutrient availability and temperature as well as exposure to UV radiation. Microbial colonization of this dynamic environment requires specific adaptive traits, including tolerance to fluctuating temperatures, the production of secondary metabolites and pigments to successfully compete with other microorganisms and to withstand abiotic stresses. Here, we isolated 175 yeasts, comprising 15 different genera, from the wheat flag leaf and characterized a selection of these for various adaptive traits such as substrate utilization, tolerance to different temperatures, biofilm formation, and antagonism toward the fungal leaf pathogen Fusarium graminearum. Collectively our results revealed that the wheat flag leaf is a rich resource of taxonomically and phenotypically diverse yeast genera that exhibit various traits that can contribute to survival in the harsh phyllosphere environment.}, }
@article {pmid35872283, year = {2022}, author = {Macêdo, WV and Poulsen, JS and Zaiat, M and Nielsen, JL}, title = {Proteogenomics identification of TBBPA degraders in anaerobic bioreactor.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {119786}, doi = {10.1016/j.envpol.2022.119786}, pmid = {35872283}, issn = {1873-6424}, abstract = {Tetrabromobisphenol A (TBBPA) is the most used flame retardant worldwide and has become a threat to aquatic ecosystems. Previous research into the degradation of this micropollutant in anaerobic bioreactors has suggested several identities of putative TBBPA degraders. However, the organisms actively degrading TBBPA under in situ conditions have so far not been identified. Protein-stable isotope probing (protein-SIP) has become a cutting-edge technique in microbial ecology for enabling the link between identity and function under in situ conditions. Therefore, it was hypothesized that combining protein-based stable isotope probing with metagenomics could be used to identify and provide genomic insight into the TBBPA-degrading organisms. The identified 13C-labelled peptides were found to belong to organisms affiliated to Phytobacter, Clostridium, Sporolactobacillus, and Klebsilla genera. The functional classification of identified labelled peptides revealed that TBBPA is not only transformed by cometabolic reactions, but also assimilated into the biomass. By application of the proteogenomics with labelled micropollutants (protein-SIP) and metagenome-assembled genomes, it was possible to extend the current perspective of the diversity of TBBPA degraders in wastewater and predict putative TBBPA degradation pathways. The study provides a link to the active TBBPA degraders and which organisms to favor for optimized biodegradation.}, }
@article {pmid35869541, year = {2022}, author = {Palomo, A and Azevedo, D and Touceda-Suárez, M and Domingo-Félez, C and Mutlu, AG and Dechesne, A and Wang, Y and Zhang, T and Smets, BF}, title = {Efficient management of the nitritation-anammox microbiome through intermittent aeration: absence of the NOB guild and expansion and diversity of the NOx reducing guild suggests a highly reticulated nitrogen cycle.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {39}, pmid = {35869541}, issn = {2524-6372}, support = {REA 607492//FP7 People: Marie-Curie Actions/ ; REA 607492//FP7 People: Marie-Curie Actions/ ; Expa-N 13391//Villlum Fonden/ ; Expa-N 13391//Villlum Fonden/ ; }, abstract = {Obtaining efficient autotrophic ammonia removal (aka partial nitritation-anammox, or PNA) requires a balanced microbiome with abundant aerobic and anaerobic ammonia oxidizing bacteria and scarce nitrite oxidizing bacteria. Here, we analyzed the microbiome of an efficient PNA process that was obtained by sequential feeding and periodic aeration. The genomes of the dominant community members were inferred from metagenomes obtained over a 6 month period. Three Brocadia spp. genomes and three Nitrosomonas spp. genomes dominated the autotrophic community; no NOB genomes were retrieved. Two of the Brocadia spp. genomes lacked the genomic potential for nitrite reduction. A diverse set of heterotrophic genomes was retrieved, each with genomic potential for only a fraction of the denitrification pathway. A mutual dependency in amino acid and vitamin synthesis was noted between autotrophic and heterotrophic community members. Our analysis suggests a highly-reticulated nitrogen cycle in the examined PNA microbiome with nitric oxide exchange between the heterotrophs and the anammox guild.}, }
@article {pmid35870225, year = {2022}, author = {Collinge, DB and Jensen, B and Jørgensen, HJ}, title = {Fungal endophytes in plants and their relationship to plant disease.}, journal = {Current opinion in microbiology}, volume = {69}, number = {}, pages = {102177}, doi = {10.1016/j.mib.2022.102177}, pmid = {35870225}, issn = {1879-0364}, abstract = {The enigmatic endophytic fungi are beginning to reveal their secrets. Like pathogens, they can manipulate the host for their own benefit to create their own optimal habitat. Some endophytic manipulations induce resistance or otherwise outcompete pathogens and can thus be exploited for biological control. Like pathogens and other symbionts, endophytes produce effector proteins and other molecules, ranging from specialised metabolites, phytohormones and microRNAs, to manipulate their hosts and other microorganisms they meet. There is a continuum from endophyte to pathogen: some organisms can infest or cause disease in some hosts, but not in others. Molecular genetics approaches coupled with functional characterisation have demonstrated their worth for understanding the biological phenomena underlying endophytic fungal interactions.}, }
@article {pmid35869999, year = {2022}, author = {Pant, A and Maiti, TK and Mahajan, D and Das, B}, title = {Human Gut Microbiota and Drug Metabolism.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35869999}, issn = {1432-184X}, support = {DST/INSPIRE/04/2020/001246//Department of Science and Technology, Government of India/ ; THSTI Intramural//Department of Biotechnology, Government of India/ ; 2021//Department of Biotechnology, Government of India/ ; }, abstract = {The efficacy of drugs widely varies in individuals, and the gut microbiota plays an important role in this variability. The commensal microbiota living in the human gut encodes several enzymes that chemically modify systemic and orally administered drugs, and such modifications can lead to activation, inactivation, toxification, altered stability, poor bioavailability, and rapid excretion. Our knowledge of the role of the human gut microbiome in therapeutic outcomes continues to evolve. Recent studies suggest the existence of complex interactions between microbial functions and therapeutic drugs across the human body. Therapeutic drugs or xenobiotics can influence the composition of the gut microbiome and the microbial encoded functions. Both these deviations can alter the chemical transformations of the drugs and hence treatment outcomes. In this review, we provide an overview of (i) the genetic ecology of microbially encoded functions linked with xenobiotic degradation; (ii) the effect of drugs on the composition and function of the gut microbiome; and (iii) the importance of the gut microbiota in drug metabolism.}, }
@article {pmid35867140, year = {2022}, author = {López-Hernández, J and García-Cárdenas, E and López-Bucio, JS and Jiménez-Vázquez, KR and de la Cruz, HR and Ferrera-Rodríguez, O and Santos-Rodríguez, DL and Ortiz-Castro, R and López-Bucio, J}, title = {Screening of Phosphate Solubilization Identifies Six Pseudomonas Species with Contrasting Phytostimulation Properties in Arabidopsis Seedlings.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35867140}, issn = {1432-184X}, support = {A1-S-34768//Consejo Nacional de Ciencia y Tecnología/ ; }, abstract = {The interaction of plants with bacteria and the long-term success of their adaptation to challenging environments depend upon critical traits that include nutrient solubilization, remodeling of root architecture, and modulation of host hormonal status. To examine whether bacterial promotion of phosphate solubilization, root branching and the host auxin response may account for plant growth, we isolated and characterized ten bacterial strains based on their high capability to solubilize calcium phosphate. All strains could be grouped into six Pseudomonas species, namely P. brassicae, P. baetica, P. laurylsulfatiphila, P. chlororaphis, P. lurida, and P. extremorientalis via 16S rRNA molecular analyses. A Solibacillus isronensis strain was also identified, which remained neutral when interacting with Arabidopsis roots, and thus could be used as inoculation control. The interaction of Arabidopsis seedlings with bacterial streaks from pure cultures in vitro indicated that their phytostimulation properties largely differ, since P. brassicae and P. laurylsulfatiphila strongly increased shoot and root biomass, whereas the other species did not. Most bacterial isolates, except P. chlororaphis promoted lateral root formation, and P. lurida and P. chlororaphis strongly enhanced expression of the auxin-inducible gene construct DR5:GUS in roots, but the most bioactive probiotic bacterium P. brassicae could not enhance the auxin response. Inoculation with P. brassicae and P. lurida improved shoot and root growth in medium supplemented with calcium phosphate as the sole Pi source. Collectively, our data indicate the differential responses of Arabidopsis seedlings to inoculation with several Pseudomonas species and highlight the potential of P. brassicae to manage phosphate nutrition and plant growth in a more eco-friendly manner.}, }
@article {pmid35867139, year = {2022}, author = {Birnbaum, C and Wood, J and Lilleskov, E and Lamit, LJ and Shannon, J and Brewer, M and Grover, S}, title = {Degradation Reduces Microbial Richness and Alters Microbial Functions in an Australian Peatland.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35867139}, issn = {1432-184X}, support = {DEB-1 146 149//National Science Foundation/ ; ID 1445//U.S. Department of Energy/ ; SLaM/2020/118//Australian Centre for International Agricultural Research/ ; }, abstract = {Peatland ecosystems cover only 3% of the world's land area; however, they store one-third of the global soil carbon (C). Microbial communities are the main drivers of C decomposition in peatlands, yet we have limited knowledge of their structure and function. While the microbial communities in the Northern Hemisphere peatlands are well documented, we have limited understanding of microbial community composition and function in the Southern Hemisphere peatlands, especially in Australia. We investigated the vertical stratification of prokaryote and fungal communities from Wellington Plains peatland in the Australian Alps. Within the peatland complex, bog peat was sampled from the intact peatland and dried peat from the degraded peatland along a vertical soil depth gradient (i.e., acrotelm, mesotelm, and catotelm). We analyzed the prokaryote and fungal community structure, predicted functional profiles of prokaryotes using PICRUSt, and assigned soil fungal guilds using FUNGuild. We found that the structure and function of prokaryotes were vertically stratified in the intact bog. Soil carbon, manganese, nitrogen, lead, and sodium content best explained the prokaryote composition. Prokaryote richness was significantly higher in the intact bog acrotelm compared to degraded bog acrotelm. Fungal composition remained similar across the soil depth gradient; however, there was a considerable increase in saprotroph abundance and decrease in endophyte abundance along the vertical soil depth gradient. The abundance of saprotrophs and plant pathogens was two-fold higher in the degraded bog acrotelm. Soil manganese and nitrogen content, electrical conductivity, and water table level (cm) best explained the fungal composition. Our results demonstrate that both fungal and prokaryote communities are shaped by soil abiotic factors and that peatland degradation reduces microbial richness and alters microbial functions. Thus, current and future changes to the environmental conditions in these peatlands may lead to altered microbial community structures and associated functions which may have implications for broader ecosystem function changes in peatlands.}, }
@article {pmid35867138, year = {2022}, author = {Mathur, V and Ulanova, D}, title = {Microbial Metabolites Beneficial to Plant Hosts Across Ecosystems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35867138}, issn = {1432-184X}, support = {ECR/2017/001466//SERB (Ministry of S&amp;T, Govt. of India)/ ; Four dimensions Kuroshio Marine Science (4D-KMS) Project//Ministry of Education, Culture, Sports, Science and Technology, Japan/ ; }, abstract = {Plants are intimately connected with their associated microorganisms. Chemical interactions via natural products between plants and their microbial symbionts form an important aspect in host health and development, both in aquatic and terrestrial ecosystems. These interactions range from negative to beneficial for microbial symbionts as well as their hosts. Symbiotic microbes synchronize their metabolism with their hosts, thus suggesting a possible coevolution among them. Metabolites, synthesized from plants and microbes due to their association and coaction, supplement the already present metabolites, thus promoting plant growth, maintaining physiological status, and countering various biotic and abiotic stress factors. However, environmental changes, such as pollution and temperature variations, as well as anthropogenic-induced monoculture settings, have a significant influence on plant-associated microbial community and its interaction with the host. In this review, we put the prominent microbial metabolites participating in plant-microbe interactions in the natural terrestrial and aquatic ecosystems in a single perspective and have discussed commonalities and differences in these interactions for adaptation to surrounding environment and how environmental changes can alter the same. We also present the status and further possibilities of employing chemical interactions for environment remediation. Our review thus underlines the importance of ecosystem-driven functional adaptations of plant-microbe interactions in natural and anthropogenically influenced ecosystems and their possible applications.}, }
@article {pmid35866234, year = {2022}, author = {Mahmud, MR and Akter, S and Tamanna, SK and Mazumder, L and Esti, IZ and Banerjee, S and Akter, S and Hasan, MR and Acharjee, M and Hossain, MS and Pirttilä, AM}, title = {Impact of gut microbiome on skin health: gut-skin axis observed through the lenses of therapeutics and skin diseases.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2096995}, doi = {10.1080/19490976.2022.2096995}, pmid = {35866234}, issn = {1949-0984}, abstract = {The human intestine hosts diverse microbial communities that play a significant role in maintaining gut-skin homeostasis. When the relationship between gut microbiome and the immune system is impaired, subsequent effects can be triggered on the skin, potentially promoting the development of skin diseases. The mechanisms through which the gut microbiome affects skin health are still unclear. Enhancing our understanding on the connection between skin and gut microbiome is needed to find novel ways to treat human skin disorders. In this review, we systematically evaluate current data regarding microbial ecology of healthy skin and gut, diet, pre- and probiotics, and antibiotics, on gut microbiome and their effects on skin health. We discuss potential mechanisms of the gut-skin axis and the link between the gut and skin-associated diseases, such as psoriasis, atopic dermatitis, acne vulgaris, rosacea, alopecia areata, and hidradenitis suppurativa. This review will increase our understanding of the impacts of gut microbiome on skin conditions to aid in finding new medications for skin-associated diseases.}, }
@article {pmid35864173, year = {2022}, author = {Tian, C and Pang, J and Bu, C and Wu, S and Bai, H and Li, Y and Guo, Q and Siddique, KHM}, title = {The Microbiomes in Lichen and Moss Biocrust Contribute Differently to Carbon and Nitrogen Cycles in Arid Ecosystems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35864173}, issn = {1432-184X}, support = {2016YFE0203400//National Key Research and Development Program of China/ ; 2017YFC0504703//National Key Research and Development Program of China/ ; 41971131//National Natural Scientific Foundation of China/ ; }, abstract = {Biological soil crusts (biocrusts) are distributed in arid and semiarid regions across the globe. Microorganisms are an essential component in biocrusts. They add and accelerate critical biochemical processes. However, little is known about the functional genes and metabolic processes of microbiomes in lichen and moss biocrust. This study used shotgun metagenomic sequencing to compare the microbiomes of lichen-dominated and moss-dominated biocrust and reveal the microbial genes and metabolic pathways involved in carbon and nitrogen cycling. The results showed that Actinobacteria, Bacteroidetes, and Acidobacteria were more abundant in moss biocrust than lichen biocrust, while Proteobacteria and Cyanobacteria were more abundant in lichen biocrust than moss biocrust. The relative abundance of carbohydrate-active enzymes and enzymes associated with carbon and nitrogen metabolism differed significantly between microbiomes of the two biocrust types. However, in the microbial communities of both biocrust types, respiration pathways dominated over carbon fixation pathways. The genes encoding carbon monoxide dehydrogenase were more abundant than those encoding ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo) involved in carbon fixation. Similarly, metabolic N-pathway diversity was dominated by nitrogen reduction, followed by denitrification, with nitrogen fixation the lowest proportion. Gene diversity involved in N cycling differed between the microbiomes of the two biocrust types. Assimilatory nitrate reduction genes had higher relative abundance in lichen biocrust, whereas dissimilatory nitrate reduction genes had higher relative abundance in moss biocrust. As dissolved organic carbon and soil organic carbon are considered the main drivers of the community structure in the microbiome of biocrust, these results indicate that biocrust type has a pivotal role in microbial diversity and related biogeochemical cycling.}, }
@article {pmid35863929, year = {2022}, author = {Ouamba, AJK and Gagnon, M and LaPointe, G and Chouinard, PY and Roy, D}, title = {Graduate Student Literature Review: Farm management practices: Potential microbial sources that determine the microbiota of raw bovine milk.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2021-21758}, pmid = {35863929}, issn = {1525-3198}, abstract = {Environmental and herd-associated factors such as geographical location, climatic conditions, forage types, bedding, soil, animal genetics, herd size, housing, lactation stage, and udder health are exploited by farmers to dictate specific management strategies that ensure dairy operation profitability and enhance the sustainability of milk production. Along with milking routines, milking systems, and storage conditions, these farming practices greatly influence the microbiota of raw milk, as evidenced by several recent studies. During the past few years, the increased interest in high-throughput sequencing technologies combined with culture-dependent methods to investigate dairy microbial ecology has improved our understanding of raw milk community dynamics throughout storage and processing. However, knowledge is still lacking on the niche-specific communities in the farm environment, and on the factors that determine bacteria transfer to the raw milk. This review summarizes findings from the past 2 decades regarding the effects of farm management practices on the diversity of bacterial species that determine the microbiological quality of raw cow milk.}, }
@article {pmid35862964, year = {2022}, author = {Zhang, Q and Zou, X and Wu, S and Wu, N and Chen, X and Zhou, W}, title = {Effects of Pyroligneous Acid on Diversity and Dynamics of Antibiotic Resistance Genes in Alfalfa Silage.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0155422}, doi = {10.1128/spectrum.01554-22}, pmid = {35862964}, issn = {2165-0497}, abstract = {Antibiotic resistance genes (ARGs) are recognized as contaminants due to their potential risk for human and environment. The aim of the present study is to investigate the effects of pyroligneous acid (PA), a waste of biochar production, on fermentation characteristics, diversity, and dynamics of ARGs during ensiling of alfalfa using metagenomic analysis. The results indicated that PA decreased (P < 0.05) dry matter loss, pH value, gas production, coliform bacteria count, protease activity, and nonprotein-N, ammonia-N, and butyric acid contents and increased (P < 0.05) lactic acid content during ensiling. During fermentation, Bacteria, Firmicutes, and Lactobacillus were the most abundant at kingdom, phylum, and genus levels, respectively. Pyroligneous acid reduced the relative abundance of Bacteria and Firmicutes and increased that of Lactobacillus. The detected ARGs belonged to 36 drug classes, including mainly macrolides, tetracycline, lincosamides, and phenicol. These types of ARGs decreased during fermentation and were further reduced by PA. These types of ARGs were positively correlated (P < 0.05) with fermentation parameters like pH value and ammonia-N content and with bacterial communities. At the genus level, the top several drug classes, including macrolide, tetracycline, lincosamide, phenicol, oxazolidinone, streptogramin, pleuromutilin, and glycopeptide, were positively correlated with Staphylococcus, Streptococcus, Listeria, Bacillus, Klebsiella, Clostridium, and Enterobacter, the potential hosts of ARGs. Overall, ARGs in alfalfa silage were abundant and were influenced by the fermentation parameters and microbial community composition. Ensiling could be a feasible way to mitigate ARGs in forages. The addition of PA could not only improve fermentation quality but also reduce ARG pollution of alfalfa silage. IMPORTANCE Antibiotic resistance genes (ARGs) are considered environmental pollutants posing a potential human health risk. Silage is an important and traditional feed, mainly for ruminants. ARGs in silages might influence the diversity and distribution of ARGs in animal intestinal and feces and then the manure and the manured soil. However, the diversity and dynamics of ARGs in silage during fermentation are still unknown. We ensiled alfalfa, one of the most widely used forages, with or without pyroligneous acid (PA), which was proved to have the ability to reduce ARGs in soils. The results showed that ARGs in alfalfa silage were abundant and were influenced by the fermentation parameters and microbial community. The majority of ARGs in alfalfa silage reduced during fermentation. The addition of PA could improve silage quality and reduce ARG pollution in alfalfa silage. This study can provide useful information for understanding and controlling ARG pollution in animal production.}, }
@article {pmid35862940, year = {2022}, author = {Molina-Santiago, C and Pearson, JR and Berlanga-Clavero, MV and Pérez-Lorente, AI and de Vicente, A and Romero, D}, title = {A Noninvasive Method for Time-Lapse Imaging of Microbial Interactions and Colony Dynamics.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0093922}, doi = {10.1128/spectrum.00939-22}, pmid = {35862940}, issn = {2165-0497}, abstract = {Complex interactions between microbial populations can greatly affect the overall properties of a microbial community, sometimes leading to cooperation and mutually beneficial coexistence, or competition and the death or displacement of organisms or subpopulations. Interactions between different biofilm populations are highly relevant in diverse scientific areas, from antimicrobial resistance to microbial ecology. The utilization of modern microscopic techniques has provided a new and interesting insight into how bacteria interact at the cellular level to form and maintain microbial biofilms. However, our ability to follow complex intraspecies and interspecies interactions in vivo at the microscopic level has remained somewhat limited. Here, we detailed BacLive, a novel noninvasive method for tracking bacterial growth and biofilm dynamics using high-resolution fluorescence microscopy and an associated ImageJ processing macro (https://github.com/BacLive) for easier data handling and image analysis. Finally, we provided examples of how BacLive can be used in the analysis of complex bacterial communities. IMPORTANCE Communication and interactions between single cells are continuously defining the structure and composition of microbial communities temporally and spatially. Methods routinely used to study these communities at the cellular level rely on sample manipulation which makes microscopic time-lapse experiments impossible. BacLive was conceived as a method for the noninvasive study of the formation and development of bacterial communities, such as biofilms, and the formation dynamics of specialized subpopulations in time-lapse experiments at a colony level. In addition, we developed a tool to simplify the processing and analysis of the data generated by this method.}, }
@article {pmid35862824, year = {2022}, author = {Schultz, J and Modolon, F and Rosado, AS and Voolstra, CR and Sweet, M and Peixoto, RS}, title = {Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0036722}, doi = {10.1128/msystems.00367-22}, pmid = {35862824}, issn = {2379-5077}, abstract = {The vast majority of environmental microbes have not yet been cultured, and most of the knowledge on coral-associated microbes (CAMs) has been generated from amplicon sequencing and metagenomes. However, exploring cultured CAMs is key for a detailed and comprehensive characterization of the roles of these microbes in shaping coral health and, ultimately, for their biotechnological use as, for example, coral probiotics and other natural products. Here, the strategies and technologies that have been used to access cultured CAMs are presented, while advantages and disadvantages associated with each of these strategies are discussed. We highlight the existing gaps and potential improvements in culture-dependent methodologies, indicating several possible alternatives (including culturomics and in situ diffusion devices) that could be applied to retrieve the CAM "dark matter" (i.e., the currently undescribed CAMs). This study provides the most comprehensive synthesis of the methodologies used to recover the cultured coral microbiome to date and draws suggestions for the development of the next generation of CAM culturomics.}, }
@article {pmid35862808, year = {2022}, author = {Dove, NC and Carrell, AA and Engle, NL and Klingeman, DM and Rodriguez, M and Wahl, T and Tschaplinski, TJ and Muchero, W and Schadt, CW and Cregger, MA}, title = {Relationships between Sphaerulina musiva Infection and the Populus Microbiome and Metabolome.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0012022}, doi = {10.1128/msystems.00120-22}, pmid = {35862808}, issn = {2379-5077}, abstract = {Pathogenic fungal infections in plants may, in some cases, lead to downstream systematic impacts on the plant metabolome and microbiome that may either alleviate or exacerbate the effects of the fungal pathogen. While Sphaerulina musiva is a well-characterized fungal pathogen which infects Populus tree species, an important wood fiber and biofuel feedstock, little is known about its systematic effects on the metabolome and microbiome of Populus. Here, we investigated the metabolome of Populus trichocarpa and Populus deltoides leaves and roots and the microbiome of the leaf and root endospheres, phylloplane, and rhizosphere to understand the systematic impacts of S. musiva abundance and infection on Populus species in a common garden field setting. We found that S. musiva is indeed present in both P. deltoides and P. trichocarpa, but S. musiva abundance was not statistically related to stem canker onset. We also found that the leaf and root metabolomes significantly differ between the two Populus species and that certain leaf metabolites, particularly the phenolic glycosides salirepin and salireposide, are diminished in canker-infected P. trichocarpa trees compared to their uninfected counterparts. Furthermore, we found significant associations between the metabolome, S. musiva abundance, and microbiome composition and α-diversity, particularly in P. trichocarpa leaves. Our results show that S. musiva colonizes both resistant and susceptible hosts and that the effects of S. musiva on susceptible trees are not confined to the site of canker infection. IMPORTANCE Poplar (Populus spp.) trees are ecologically and economically important trees throughout North America. However, many western North American poplar plantations are at risk due to the introduction of the nonnative fungal pathogen Sphaerulina musiva, which causes leaf spot and cankers, limiting their production. To better understand the interactions among the pathogen S. musiva, the poplar metabolome, and the poplar microbiome, we collected leaf, root, and rhizosphere samples from poplar trees consisting of 10 genotypes and two species with differential resistance to S. musiva in a common garden experiment. Here, we outline the nuanced relationships between the poplar metabolome, microbiome, and S. musiva, showing that S. musiva may affect poplar trees in tissues distal to the site of infection (i.e., stem). Our research contributes to improving the fundamental understanding of S. musiva and Populus sp. ecology and the utility of a holobiont approach in understanding plant disease.}, }
@article {pmid35862804, year = {2022}, author = {Green, EA and Klassen, JL}, title = {Trachymyrmex septentrionalis Ant Microbiome Assembly Is Unique to Individual Colonies and Castes.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0098921}, doi = {10.1128/msphere.00989-21}, pmid = {35862804}, issn = {2379-5042}, abstract = {Within social insect colonies, microbiomes often differ between castes due to their different functional roles and between colony locations. Trachymyrmex septentrionalis fungus-growing ants form colonies throughout the eastern United States and northern Mexico that include workers, female and male alates (unmated reproductive castes), larvae, and pupae. How T. septentrionalis microbiomes vary across this geographic range and between castes is unknown. Our sampling of individual ants from colonies across the eastern United States revealed a conserved T. septentrionalis worker ant microbiome and revealed that worker ant microbiomes are more conserved within colonies than between them. A deeper sampling of individual ants from two colonies that included all available castes (pupae, larvae, workers, and female and male alates), from both before and after adaptation to controlled laboratory conditions, revealed that ant microbiomes from each colony, caste, and rearing condition were typically conserved within but not between each sampling category. Tenericute bacterial symbionts were especially abundant in these ant microbiomes and varied widely in abundance between sampling categories. This study demonstrates how individual insect colonies primarily drive the composition of their microbiomes and shows that these microbiomes are further modified by developmental differences between insect castes and the different environmental conditions experienced by each colony. IMPORTANCE This study investigates microbiome assembly in the fungus-growing ant Trachymyrmex septentrionalis, showing how colony, caste, and lab adaptation influence the microbiome and revealing unique patterns of mollicute symbiont abundance. We find that ant microbiomes differ strongly between colonies but less so within colonies. Microbiomes of different castes and following lab adaptation also differ in a colony-specific manner. This study advances our understanding of the nature of individuality in social insect microbiomes and cautions against the common practice of only sampling a limited number of populations to understand microbiome diversity and function.}, }
@article {pmid35862792, year = {2022}, author = {Wale, N}, title = {mSphere of Influence: There's More to (a Pathogen's) Life than Growing Fast.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0027722}, doi = {10.1128/msphere.00277-22}, pmid = {35862792}, issn = {2379-5042}, abstract = {Nina Wale works in the field of infectious disease evolution and ecology. In this mSphere of Influence article, she reflects on how the paper by Roller and Schmidt, "The physiology and ecological implications of efficient growth" (B. R. Roller and T. M. Schmidt, ISME J 9:1481-1487, 2015, https://doi.org/10.1038/ismej.2014.235) broadened her thinking about how microbes acquire and allocate resources and, in so doing, set her research on pathogen virulence evolution in a new direction.}, }
@article {pmid35862730, year = {2022}, author = {Smith, DJ and Kharbush, JJ and Kersten, RD and Dick, GJ}, title = {Uptake of Phytoplankton-Derived Carbon and Cobalamins by Novel Acidobacteria Genera in Microcystis Blooms Inferred from Metagenomic and Metatranscriptomic Evidence.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0180321}, doi = {10.1128/aem.01803-21}, pmid = {35862730}, issn = {1098-5336}, abstract = {Interactions between bacteria and phytoplankton can influence primary production, community composition, and algal bloom development. However, these interactions are poorly described for many consortia, particularly for freshwater bloom-forming cyanobacteria. Here, we assessed the gene content and expression of two uncultivated Acidobacteria from Lake Erie Microcystis blooms. These organisms were targeted because they were previously identified as important catalase producers in Microcystis blooms, suggesting that they protect Microcystis from H2O2. Metatranscriptomics revealed that both Acidobacteria transcribed genes for uptake of organic compounds that are known cyanobacterial products and exudates, including lactate, glycolate, amino acids, peptides, and cobalamins. Expressed genes for amino acid metabolism and peptide transport and degradation suggest that use of amino acids and peptides by Acidobacteria may regenerate nitrogen for cyanobacteria and other organisms. The Acidobacteria genomes lacked genes for biosynthesis of cobalamins but expressed genes for its transport and remodeling. This indicates that the Acidobacteria obtained cobalamins externally, potentially from Microcystis, which has a complete gene repertoire for pseudocobalamin biosynthesis; expressed them in field samples; and produced pseudocobalamin in axenic culture. Both Acidobacteria were detected in Microcystis blooms worldwide. Together, the data support the hypotheses that uncultured and previously unidentified Acidobacteria taxa exchange metabolites with phytoplankton during harmful cyanobacterial blooms and influence nitrogen available to phytoplankton. Thus, novel Acidobacteria may play a role in cyanobacterial physiology and bloom development. IMPORTANCE Interactions between heterotrophic bacteria and phytoplankton influence competition and successions between phytoplankton taxa, thereby influencing ecosystem-wide processes such as carbon cycling and algal bloom development. The cyanobacterium Microcystis forms harmful blooms in freshwaters worldwide and grows in buoyant colonies that harbor other bacteria in their phycospheres. Bacteria in the phycosphere and in the surrounding community likely influence Microcystis physiology and ecology and thus the development of freshwater harmful cyanobacterial blooms. However, the impacts and mechanisms of interaction between bacteria and Microcystis are not fully understood. This study explores the mechanisms of interaction between Microcystis and uncultured members of its phycosphere in situ with population genome resolution to investigate the cooccurrence of Microcystis and freshwater Acidobacteria in blooms worldwide.}, }
@article {pmid35852610, year = {2022}, author = {Kankonkar, HT and Khandeparker, RS}, title = {Microplastics a Novel Substratum for Polyhydroxyalkanoate (PHA)-Producing Bacteria in Aquatic Environments.}, journal = {Current microbiology}, volume = {79}, number = {9}, pages = {258}, pmid = {35852610}, issn = {1432-0991}, mesh = {*Bacillus/genetics/metabolism ; Bacteria/genetics/metabolism ; Carbon/metabolism ; Microplastics ; Plastics/metabolism ; *Polyhydroxyalkanoates ; }, abstract = {Polyhydroxyalkanoates (PHA) being biological polymers have attracted great attention. PHA have similar properties to that of synthetic plastic and are biodegradable. To discourage plastic pollution in the environment alternative solutions to the plastic pollution has to be readily available. High cost in production of PHA limits the production of these polymers at industrial scale. Bacteria are screened for PHA from diverse niches to meet the current requirements of cheap PHA production at industrial level. The microbial biofilm formed on the surface of microplastic could be a potential source in providing bacteria of economic importance. This paper is an attempt to search microplastic niche for potential PHA producers. PHA production variation was observed with different parameters such as type of carbon source, nitrogen source concentration and also time of incubation. Bacillus sp. CM27 showed maximum PHA yield up to 32.1% among other isolates at 48 h with 2% glucose as carbon source. Optimization of media leads to increase in PHA yield (37.69%) of CDW in Bacillus sp. CM27. Amino acid sequence of Bacillus sp.CM27 showed the presence of PhaC box with sequence, G-Y-C-M-G-G having cysteine in the middle of the box. The extracted polymer was confirmed by FTIR spectroscopy.}, }
@article {pmid35859070, year = {2022}, author = {Ienes-Lima, J and Prichula, J and Abadie, M and Borges-Martins, M and Frazzon, APG}, title = {First Report of Culturable Skin Bacteria in Melanophryniscus admirabilis (Admirable Redbelly Toad).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35859070}, issn = {1432-184X}, support = {#305495/2018-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico do Brasil/ ; #309769/2020-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; PROAP//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {Melanophryniscus admirabilis is a small toad, critically endangered with a microendemic distribution in the Atlantic Forest in southern Brazil. The amphibian skin microbiome is considered one of the first lines of defense against pathogenic infections, such as Batrachochytrium dendrobatidis (Bd). The knowledge of skin amphibian microbiomes is important to numerous fields, including species conservation, detection, and quantification of environmental changes and stressors. In the present study, we investigated, for the first time, cultivable bacteria in the skin of wild M. admirabilis, and detected Bd fungus by nested polymerase chain reaction (PCR) technique. Skin swab samples were collected from 15 wild M. admirabilis, and the isolation of bacteria was performed by means of different culture strategies. A total of 62 bacterial isolates being Bacillus (n = 22; 34.48%), Citrobacter (n = 10; 16.13%), and Serratia (n = 12; 19.35%) were more frequently isolated genera. Interestingly, all skin samples tested were Bd negative. Some bacterial genera identified in our study might be acting in a synergic relationship and protecting them against the Bd fungus. In addition, these bacteria may play an essential role in maintaining this species in an environment modulated by anthropic actions. This first report of skin cultivable bacteria from M. admirabilis natural population improves our knowledge of skin amphibian microbiomes, contributing to a better understanding of their ecology and how this species has survived in an environment modulated by anthropic action.}, }
@article {pmid35859069, year = {2022}, author = {Alvarenga, DO and Elmdam, IV and Timm, AB and Rousk, K}, title = {Chemical Stimulation of Heterocyte Differentiation by the Feather Moss Hylocomium splendens: a Potential New Step in Plant-Cyanobacteria Symbioses.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35859069}, issn = {1432-184X}, support = {7027-00011B//Danmarks Frie Forskningsfond/ ; }, abstract = {Cyanobacteria associated with mosses play a key role in the nitrogen (N) cycle in unpolluted ecosystems. Mosses have been found to release molecules that induce morphophysiological changes in epiphytic cyanobionts. Nevertheless, the extent of moss influence on these microorganisms remains unknown. To evaluate how mosses or their metabolites influence N2 fixation rates by cyanobacteria, we assessed the nitrogenase activity, heterocyte frequency and biomass of a cyanobacterial strain isolated from the feather moss Hylocomium splendens and a non-symbiotic strain when they were either growing by themselves, together with H. splendens or exposed to H. splendens water, acetone, ethanol, or isopropanol extracts. The same cyanobacterial strains were added to another moss (Taxiphyllum barbieri) and a liverwort (Monosolenium tenerum) to assess if these bryophytes affect N2 fixation differently. Although no significant increases in nitrogenase activity by the cyanobacteria were observed when in contact with H. splendens shoots, both the symbiotic and non-symbiotic cyanobacteria increased nitrogenase activity as well as heterocyte frequency significantly upon exposure to H. splendens ethanol extracts. Contact with T. barbieri shoots, on the other hand, did lead to increases in nitrogenase activity, indicating low host-specificity to cyanobacterial activity. These findings suggest that H. splendens produces heterocyte-differentiating factors (HDFs) that are capable of stimulating cyanobacterial N2 fixation regardless of symbiotic competency. Based on previous knowledge about the chemical ecology and dynamics of moss-cyanobacteria interactions, we speculate that HDF expression by the host takes place in a hypothetical new step occurring after plant colonization and the repression of hormogonia.}, }
@article {pmid35858363, year = {2022}, author = {Miller, SD}, title = {Boat encounter with the 2019 Java bioluminescent milky sea: Views from on-deck confirm satellite detection.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {29}, pages = {e2207612119}, doi = {10.1073/pnas.2207612119}, pmid = {35858363}, issn = {1091-6490}, support = {JPSS Program Office//DOC | National Oceanic and Atmospheric Administration (NOAA)/ ; }, mesh = {*Bacteria ; Indonesia ; Oceans and Seas ; *Ships ; }, abstract = {"Milky seas" are massive swaths of uniformly and steadily glowing ocean seen at night. The phenomenon is thought to be caused by luminous bacteria, but details of milky sea composition, structure, cause, and implications in nature remain largely uncertain. Between late July and early September 2019, specialized low-light satellite sensors detected a possible bioluminescent milky sea south of Java, Indonesia, spanning >100,000 km2. Upon learning of these findings, crew members of the yacht Ganesha reached out to confirm and share details of their personal encounter with this same event. Here, we document Ganesha's experience as recalled by the crew, compare their course to satellite data, and assess their photography of this milky sea.}, }
@article {pmid35857039, year = {2022}, author = {Matsumura, E and Morinaga, K and Fukuda, K}, title = {Host Specificity and Seasonal Variation in the Colonization of Tubakia sensu lato Associated with Evergreen Oak Species in Eastern Japan.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35857039}, issn = {1432-184X}, support = {JP16H06737//Japan Society for the Promotion of Science/ ; }, abstract = {Foliar fungal endophytes are ubiquitous and hyperdiverse, and tend to be host-specific among dominant forest tree species. The fungal genus Tubakia sensu lato is comprised of foliar pathogens and endophytes that exhibit host preference for Quercus and other Fagaceae species. To clarify interspecific differences in ecological characteristics among Tubakia species, we examined the endophyte communities of seven evergreen Quercus spp. at three sites in eastern Japan during summer and winter. Host tree species was the most significant factor affecting endophyte community composition. Tubakia species found at the study sites were divided into five specialists and three generalists according to their relative abundance in each host species and their host ranges. Specialists were dominant on their own host in summer, and their abundance declined in winter. To test the hypothesis that generalists are more widely adapted to their environment than specialists, we compared their spore germination rates at different temperatures. Spores of generalist Tubakia species were more tolerant of colder temperatures than were spores of specialist Tubakia species, supporting our hypothesis. Seasonal and site variations among Tubakia species were also consistent with our hypothesis. Host identity and ecology were significantly associated with endophyte community structure.}, }
@article {pmid35856685, year = {2022}, author = {Forchielli, E and Sher, D and Segrè, D}, title = {Metabolic Phenotyping of Marine Heterotrophs on Refactored Media Reveals Diverse Metabolic Adaptations and Lifestyle Strategies.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0007022}, doi = {10.1128/msystems.00070-22}, pmid = {35856685}, issn = {2379-5077}, abstract = {Microbial communities, through their metabolism, drive carbon cycling in marine environments. These complex communities are composed of many different microorganisms including heterotrophic bacteria, each with its own nutritional needs and metabolic capabilities. Yet, models of ecosystem processes typically treat heterotrophic bacteria as a "black box," which does not resolve metabolic heterogeneity nor address ecologically important processes such as the successive modification of different types of organic matter. Here we directly address the heterogeneity of metabolism by characterizing the carbon source utilization preferences of 63 heterotrophic bacteria representative of several major marine clades. By systematically growing these bacteria on 10 media containing specific subsets of carbon sources found in marine biomass, we obtained a phenotypic fingerprint that we used to explore the relationship between metabolic preferences and phylogenetic or genomic features. At the class level, these bacteria display broadly conserved patterns of preference for different carbon sources. Despite these broad taxonomic trends, growth profiles correlate poorly with phylogenetic distance or genome-wide gene content. However, metabolic preferences are strongly predicted by a handful of key enzymes that preferentially belong to a few enriched metabolic pathways, such as those involved in glyoxylate metabolism and biofilm formation. We find that enriched pathways point to enzymes directly involved in the metabolism of the corresponding carbon source and suggest potential associations between metabolic preferences and other ecologically relevant traits. The availability of systematic phenotypes across multiple synthetic media constitutes a valuable resource for future quantitative modeling efforts and systematic studies of interspecies interactions. IMPORTANCE Half of the Earth's annual primary production is carried out by phytoplankton in the surface ocean. However, this metabolic activity is heavily impacted by heterotrophic bacteria, which dominate the transformation of organic matter released from phytoplankton. Here, we characterize the diversity of metabolic preferences across many representative heterotrophs by systematically growing them on different fractions of dissolved organic carbon. Our analysis suggests that different clades of bacteria have substantially distinct preferences for specific carbon sources, in a way that cannot be simply mapped onto phylogeny. These preferences are associated with the presence of specific genes and pathways, reflecting an association between metabolic capabilities and ecological lifestyles. In addition to helping understand the importance of heterotrophs under different conditions, the phenotypic fingerprint we obtained can help build higher resolution quantitative models of global microbial activity and biogeochemical cycles in the oceans.}, }
@article {pmid35856563, year = {2022}, author = {Lesniak, NA and Schubert, AM and Flynn, KJ and Leslie, JL and Sinani, H and Bergin, IL and Young, VB and Schloss, PD}, title = {The Gut Bacterial Community Potentiates Clostridioides difficile Infection Severity.}, journal = {mBio}, volume = {}, number = {}, pages = {e0118322}, doi = {10.1128/mbio.01183-22}, pmid = {35856563}, issn = {2150-7511}, abstract = {The severity of Clostridioides difficile infections (CDI) has increased over the last few decades. Patient age, white blood cell count, and creatinine levels as well as C. difficile ribotype and toxin genes have been associated with disease severity. However, it is unclear whether specific members of the gut microbiota are associated with variations in disease severity. The gut microbiota is known to interact with C. difficile during infection. Perturbations to the gut microbiota are necessary for C. difficile to colonize the gut. The gut microbiota can inhibit C. difficile colonization through bile acid metabolism, nutrient consumption, and bacteriocin production. Here, we sought to demonstrate that members of the gut bacterial communities can also contribute to disease severity. We derived diverse gut communities by colonizing germfree mice with different human fecal communities. The mice were then infected with a single C. difficile ribotype 027 clinical isolate, which resulted in moribundity and histopathologic differences. The variation in severity was associated with the human fecal community that the mice received. Generally, bacterial populations with pathogenic potential, such as Enterococcus, Helicobacter, and Klebsiella, were associated with more-severe outcomes. Bacterial groups associated with fiber degradation and bile acid metabolism, such as Anaerotignum, Blautia, Lactonifactor, and Monoglobus, were associated with less-severe outcomes. These data indicate that, in addition to the host and C. difficile subtype, populations of gut bacteria can influence CDI disease severity. IMPORTANCE Clostridioides difficile colonization can be asymptomatic or develop into an infection ranging in severity from mild diarrhea to toxic megacolon, sepsis, and death. Models that predict severity and guide treatment decisions are based on clinical factors and C. difficile characteristics. Although the gut microbiome plays a role in protecting against CDI, its effect on CDI disease severity is unclear and has not been incorporated into disease severity models. We demonstrated that variation in the microbiome of mice colonized with human feces yielded a range of disease outcomes. These results revealed groups of bacteria associated with both severe and mild C. difficile infection outcomes. Gut bacterial community data from patients with CDI could improve our ability to identify patients at risk of developing more severe disease and improve interventions that target C. difficile and the gut bacteria to reduce host damage.}, }
@article {pmid35849862, year = {2022}, author = {Vaezzadeh, V and Thomes, MW and Kunisue, T and Tue, NM and Zhang, G and Zakaria, MP and Affendi, YA and Yap, FC and Chew, LL and Teoh, HW and Lee, CW and Bong, CW}, title = {Corrigendum to "Examination of barnacles' potential to be used as bioindicators of persistent organic pollutants in coastal ecosystem: A Malaysia case study" [Chemosphere 263 (2021) 128272].}, journal = {Chemosphere}, volume = {307}, number = {Pt 1}, pages = {135742}, doi = {10.1016/j.chemosphere.2022.135742}, pmid = {35849862}, issn = {1879-1298}, }
@article {pmid35846090, year = {2021}, author = {Ludwig, H and Hausmann, B and Schreder, M and Pönisch, W and Zojer, N and Knop, S and Gunsilius, E and Egle, A and Petzer, A and Einsele, H and Hajek, R and Weisel, K and Krenosz, KJ and Lang, A and Lechner, D and Greil, R and Berry, D}, title = {Reduced alpha diversity of the oral microbiome correlates with short progression-free survival in patients with relapsed/refractory multiple myeloma treated with ixazomib-based therapy (AGMT MM 1, phase II trial).}, journal = {EJHaem}, volume = {2}, number = {1}, pages = {99-103}, pmid = {35846090}, issn = {2688-6146}, abstract = {Alterations in the human microbiome have been linked to several malignant diseases. Here, we investigated the oral microbiome of 79 patients with relapsed/refractory multiple myeloma (MM) treated with ixazomib-thalidomide-dexamethasone. Increased alpha diversity (Shannon index) at the phylum level was associated with longer progression-free survival (PFS) (10.2 vs 8.5 months, P = .04), particularly in patients with very long (>75% quartile) PFS . Additionally, alpha diversity was lower in patients with progressive disease (P < .05). These findings suggest an interrelationship between the oral microbiome and outcome in patients with MM and encourage a novel direction for diagnostic and/or therapeutic strategies.}, }
@article {pmid35845424, year = {2022}, author = {Hessler, T and Harrison, STL and Huddy, RJ}, title = {Integrated Kinetic Modelling and Microbial Profiling Provide Insights Into Biological Sulfate-Reducing Reactor Design and Operation.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {897094}, pmid = {35845424}, issn = {2296-4185}, abstract = {Biological sulfate reduction (BSR) is an attractive approach for the bioremediation of sulfate-rich wastewater streams. Many sulfate-reducing microorganisms (SRM), which facilitate this process, have been well-studied in pure culture. However, the role of individual members of microbial communities within BSR bioreactors remains understudied. In this study we investigated the performance of two up-flow anaerobic packed bed reactors (UAPBRs) supplemented primarily with acetate and with lactate, respectively, during a hydraulic retention time (HRT) study set up to remediate sulfate-rich synthetic wastewater over the course of 1,000 + days. Plug-flow hydrodynamics led to a continuum of changing volumetric sulfate reduction rates (VSRRs), available electron donors, degrees of biomass retention and compositions of microbial communities throughout these reactors. Microbial communities throughout the successive zones of the reactors were resolved using 16S rRNA gene amplicon sequencing which allowed the association of features of performance with discrete microorganisms. The acetate UAPBR achieved a maximum VSRR of 23.2 mg.L-1. h-1 at a one-day HRT and a maximum sulfate conversion of the 1 g/L sulfate of 96% at a four-day HRT. The sulfate reduction reactions in this reactor could be described with a reaction order of 2.9, an important observation for optimisation and future scale-up. The lactate UAPBR achieved a 96% sulfate conversion at one-day HRT, corresponding with a VSRR of 40.1 mg.L-1. h-1. Lactate was supplied in this reactor at relatively low concentrations necessitating the subsequent use of propionate and acetate, by-products of lactate fermentation with acetate also a by-product of incomplete lactate oxidation, to achieve competitive performance. The consumption of these electron donors could be associated with specific SRM localised within biofilms of discrete zones. The sulfate reduction rates in the lactate UAPBR could be modelled as first-order reactions, indicating effective rates were conferred by these propionate- and acetate-oxidising SRM. Our results demonstrate how acetate, a low-cost substrate, can be used effectively despite low associated SRM growth rates, and that lactate, a more expensive substrate, can be used sparingly to achieve high VSRR and sulfate conversions. We further identified the preferred environment of additional microorganisms to inform how these microorganisms could be enriched or diminished in BSR reactors.}, }
@article {pmid35844603, year = {2022}, author = {Zhang, Q and Chen, Q and Yan, C and Niu, C and Zhou, J and Liu, J and Song, Y and Zhou, F and Fan, Y and Ren, J and Xu, H and Zhang, B}, title = {The Absence of STING Ameliorates Non-Alcoholic Fatty Liver Disease and Reforms Gut Bacterial Community.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {931176}, pmid = {35844603}, issn = {1664-3224}, mesh = {Animals ; Bacteria ; CD8-Positive T-Lymphocytes/metabolism ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Inflammation ; Mice ; Mice, Inbred C57BL ; *Non-alcoholic Fatty Liver Disease/etiology/metabolism ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD) is one of the primary causes of cirrhosis and a major risk factor for hepatocellular carcinoma and liver-related death. It has been correlated with changes in the gut microbiota, which promote its development by regulating insulin resistance, bile acid and choline metabolism, and inflammation. Recent studies suggested a controversial role of the stimulator of interferon genes (STING) in the development of NAFLD. Here, we showed that as an immune regulator, STING aggravates the progression of NAFLD in diet-induced mice and correlated it with the changes in hepatic lipid metabolism and gut microbiota diversity. After feeding wild-type (WT) and STING deletion mice with a normal control diet (NCD) or a high-fat diet (HFD), the STING deletion mice showed decreased lipid accumulation and liver inflammation compared with WT mice fed the same diet. In addition, STING specifically produced this hepatoprotective effect by inhibiting the activation of CD8+ T cells. The gut microbiota analysis revealed significant differences in intestinal bacteria between STING deletion mice and WT mice under the same diet and environmental conditions; moreover, differential bacterial genera were associated with altered metabolic phenotypes and involved in related metabolic pathways. Overall, our findings reveal the important regulatory role that STING plays in the progression of NAFLD. In addition, the change in intestinal microbiota diversity may be the contributing factor.}, }
@article {pmid35842525, year = {2022}, author = {Kou, Y and Li, C and Tu, B and Li, J and Li, X}, title = {The Responses of Ammonia-Oxidizing Microorganisms to Different Environmental Factors Determine Their Elevational Distribution and Assembly Patterns.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35842525}, issn = {1432-184X}, support = {32171550//the National Natural Science Foundation of China/ ; 31870473//the National Natural Science Foundation of China/ ; XDA20020401//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2021371//the Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; 2019QZKK0600//the Second Tibetan Plateau Scientic Expedition and Research Program/ ; Sino BON//China Biodiversity Observation Networks/ ; }, abstract = {The assembly mechanisms shaping the elevational patterns of diversity and community structure in ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are not well understood. We investigated the diversities, co-occurrence network patterns, key drivers, and potential activities of AOA and AOB communities along a large altitudinal gradient. The α-diversity of the AOA communities exhibited a monotonically decreasing pattern with increasing elevation, whereas a sinusoidal pattern was observed for the AOB communities. The mean annual temperature was the single factor that most strongly influenced the α-diversity of the AOA communities; however, the interactions of plant richness, soil conductivity, and total nitrogen made comparable contributions to the α-diversity of the AOB communities. Moreover, the β-diversities of the AOA and AOB communities were divided into two distinct clusters by elevation, i.e., low- (1800-2600 m) and high-altitude (2800-4100 m) sections. These patterns were attributed mainly to the soil pH, followed by variations in plant richness along the altitudinal gradient. In addition, the AOB communities were more important to the soil nitrification potential in the low-altitude section, whereas the AOA communities contributed more to the soil nitrification potential in the high-altitude section. Overall, this study revealed the key factors shaping the elevational patterns of ammonia-oxidizing communities and might predict the consequences of changes in ammonia-oxidizing communities.}, }
@article {pmid35842340, year = {2022}, author = {Gouka, L and Raaijmakers, JM and Cordovez, V}, title = {Ecology and functional potential of phyllosphere yeasts.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2022.06.007}, pmid = {35842340}, issn = {1878-4372}, abstract = {The phyllosphere (i.e., the aerial parts of plants) harbors a rich microbial life, including bacteria, fungi, viruses, and yeasts. Current knowledge of yeasts stems primarily from industrial and medical research on Saccharomyces cerevisiae and Candida albicans, both of which can be found on plant tissues. For most other yeasts found in the phyllosphere, little is known about their ecology and functions. Here, we explore the diversity, dynamics, interactions, and genomics of yeasts associated with plant leaves and how tools and approaches developed for model yeasts can be adopted to disentangle the ecology and natural functions of phyllosphere yeasts. A first genomic survey exemplifies that we have only scratched the surface of the largely unexplored functional potential of phyllosphere yeasts.}, }
@article {pmid35840683, year = {2022}, author = {Hubert, J and Nesvorna, M and Bostlova, M and Sopko, B and Green, SJ and Phillips, TW}, title = {The Effect of Residual Pesticide Application on Microbiomes of the Storage Mite Tyrophagus putrescentiae.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35840683}, issn = {1432-184X}, support = {21-337-J//Kansas State Research and Extension/ ; LTAUSA19012//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; }, abstract = {Arthropods can host well-developed microbial communities, and such microbes can degrade pesticides and confer tolerance to most types of pests. Two cultures of the stored-product mite Tyrophagus putrescentiae, one with a symbiotic microbiome containing Wolbachia and the other without Wolbachia, were compared on pesticide residue (organophosphate: pirimiphos-methyl and pyrethroid: deltamethrin, deltamethrin + piperonyl butoxide)-containing diets. The microbiomes from mite bodies, mite feces and debris from the spent mite diet were analyzed using barcode sequencing. Pesticide tolerance was different among mite cultures and organophosphate and pyrethroid pesticides. The pesticide residues influenced the microbiome composition in both cultures but without any remarkable trend for mite cultures with and without Wolbachia. The most influenced bacterial taxa were Bartonella-like and Bacillus for both cultures and Wolbachia for the culture containing this symbiont. However, there was no direct evidence of any effect of Wolbachia on pesticide tolerance. The high pesticide concentration residues in diets reduced Wolbachia, Bartonella-like and Bacillus in mites of the symbiotic culture. This effect was low for Bartonella-like and Bacillus in the asymbiotic microbiome culture. The results showed that the microbiomes of mites are affected by pesticide residues in the diets, but the effect is not systemic. No actual detoxification effect by the microbiome was observed for the tested pesticides.}, }
@article {pmid35840682, year = {2022}, author = {Williams, A and Birt, HWG and Raghavendra, A and Dennis, PG}, title = {Cropping System Diversification Influences Soil Microbial Diversity in Subtropical Dryland Farming Systems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35840682}, issn = {1432-184X}, abstract = {Conventional dryland cropping systems are characterised by low crop diversity and frequent fallows. This has significant impacts on soil microbes that underpin soil function. Diversifying crop rotations can potentially counter these effects; however, limited data exists on the impacts of diversified crop rotations on soil microbes in drylands. Using phylogenetic marker gene sequencing, we characterised soil microbial diversity in conventional and diversified dryland crop rotations in subtropical Australia. This included winter and summer dominant rotations. Conventional systems were cereal-dominant with a crop-fallow rotation. Diversified systems included greater crop diversity, double crops, cover crops, and a multi-year ley pasture. In summer rotations with increased crop diversity and cover crops, bacterial and fungal richness increased, and distinct communities were formed compared to fallow land. Often, these community shifts were associated with greater soil organic carbon (SOC) and nitrogen. All winter rotations had distinct fungal communities and ley pasture resulted in greater fungal diversity compared to other rotations. No effects of the winter rotations were evident on bacterial communities. Our results show that diversification of dryland crop rotations leads to significant shifts in soil microbial communities in both winter and summer cropping systems. Both summer and winter rotations incorporating cover crops and ley pasture had greater soil respiration and nitrogen, indicating increases in soil fertility. These rotations may offer an alternative to conventional crop-fallow rotations to counter ongoing declines in soil health.}, }
@article {pmid35839698, year = {2022}, author = {Babaahmadifooladia, M and da Silva Junior, EC and Van de Wiele, T and Du Laing, G and Jacxsens, L}, title = {Probabilistic chronic dietary exposure assessment adjusted for bioaccessible fraction to metals by consumption of seaweed and derived foods.}, journal = {Food chemistry}, volume = {395}, number = {}, pages = {133588}, doi = {10.1016/j.foodchem.2022.133588}, pmid = {35839698}, issn = {1873-7072}, abstract = {The chronic exposure to heavy elements, i.e. Ni, As, Cd, Hg and Pb the evaluation of toxicological risk through intake of raw or seaweed based foods for Belgian consumers is presented in this study. The bioaccessible fraction, obtained for different metals, were used to refine the exposure values to avoid overestimation in the reported exposures. The decrease in the exposure values was higher for As with average bioaccessible fraction of 56.8% followed by Pb, Cd, Ni and Hg. The pure seaweeds show more approximation or exceeding of toxicological limits compared to the composite foodstuffs. For all elements (except Hg), toxicological limits are approached at the maximum exposure situation due to consumption of certain seaweed-based foods. Further, the study demonstrates that the introduction of innovative foods on an emerging market may result in potential health issues due to the shift in consumption patterns as the increased consumption of seaweed and their derivatives in Europe.}, }
@article {pmid35838347, year = {2022}, author = {Rijkers, R and Rousk, J and Aerts, R and Sigurdsson, BD and Weedon, JT}, title = {Optimal growth temperature of Arctic soil bacterial communities increases under experimental warming.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.16342}, pmid = {35838347}, issn = {1365-2486}, abstract = {Future climate warming in the Arctic will likely increase the vulnerability of soil carbon stocks to microbial decomposition. However, it remains uncertain to what extent decomposition rates will change in a warmer Arctic, because extended soil warming could induce temperature adaptation of bacterial communities. Here we show that experimental warming induces shifts in the temperature-growth relationships of bacterial communities, which is driven by community turnover and is common across a diverse set of 8 (sub) arctic soils. The optimal growth temperature (Topt) of the soil bacterial communities increased 0.27 ± 0.039 (s.e.) and 0.07 ± 0.028 °C per °C of warming over a 0-30 °C gradient, depending on the sampling moment. We identify a potential role for substrate depletion and time-lag effects as drivers of temperature adaption in soil bacterial communities, which possibly explain discrepancies between earlier incubation and field studies. The changes in Topt were accompanied by species-level shifts in bacterial community composition, which were mostly soil-specific. Despite the clear physiological responses to warming, there was no evidence for a common set of temperature-responsive bacterial amplicon sequence variants (ASVs). This implies that community composition data without accompanying physiological measurements may have limited utility for the identification of (potential) temperature adaption of soil bacterial communities in the Arctic. Since bacterial communities in arctic soils are likely to adapt to increasing soil temperature under future climate change, this adaptation to higher temperature should be implemented in soil organic carbon modeling for accurate predictions of the dynamics of arctic soil carbon stocks.}, }
@article {pmid35836424, year = {2022}, author = {Muster, C and Leiva, D and Morales, C and Grafe, M and Schloter, M and Carú, M and Orlando, J}, title = {Peltigera frigida Lichens and Their Substrates Reduce the Influence of Forest Cover Change on Phosphate Solubilizing Bacteria.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {843490}, pmid = {35836424}, issn = {1664-302X}, abstract = {Phosphorus (P) is one of the most critical macronutrients in forest ecosystems. More than 70 years ago, some Chilean Patagonian temperate forests suffered wildfires and the subsequent afforestation with foreign tree species such as pines. Since soil P turnover is interlinked with the tree cover, this could influence soil P content and bioavailability. Next to soil microorganisms, which are key players in P transformation processes, a vital component of Patagonian temperate forest are lichens, which represent microbial hotspots for bacterial diversity. In the present study, we explored the impact of forest cover on the abundance of phosphate solubilizing bacteria (PSB) from three microenvironments of the forest floor: Peltigera frigida lichen thallus, their underlying substrates, and the forest soil without lichen cover. We expected that the abundance of PSB in the forest soil would be strongly affected by the tree cover composition since the aboveground vegetation influences the edaphic properties; but, as P. frigida has a specific bacterial community, lichens would mitigate this impact. Our study includes five sites representing a gradient in tree cover types, from a mature forest dominated by the native species Nothofagus pumilio, to native second-growth forests with a gradual increase in the presence of Pinus contorta in the last sites. In each site, we measured edaphic parameters, P fractions, and the bacterial potential to solubilize phosphate by quantifying five specific marker genes by qPCR. The results show higher soluble P, labile mineral P, and organic matter in the soils of the sites with a higher abundance of P. contorta, while most of the molecular markers were less abundant in the soils of these sites. Contrarily, the abundance of the molecular markers in lichens and substrates was less affected by the tree cover type. Therefore, the bacterial potential to solubilize phosphate is more affected by the edaphic factors and tree cover type in soils than in substrates and thalli of P. frigida lichens. Altogether, these results indicate that the microenvironments of lichens and their substrates could act as an environmental buffer reducing the influence of forest cover composition on bacteria involved in P turnover.}, }
@article {pmid35835965, year = {2022}, author = {Larsen, S and Albanese, D and Stegen, J and Franceschi, P and Coller, E and Zanzotti, R and Ioriatti, C and Stefani, E and Pindo, M and Cestaro, A and Donati, C}, title = {Distinct and Temporally Stable Assembly Mechanisms Shape Bacterial and Fungal Communities in Vineyard Soils.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35835965}, issn = {1432-184X}, abstract = {Microbial communities in agricultural soils are fundamental for plant growth and in vineyard ecosystems contribute to defining regional wine quality. Managing soil microbes towards beneficial outcomes requires knowledge of how community assembly processes vary across taxonomic groups, spatial scales, and through time. However, our understanding of microbial assembly remains limited. To quantify the contributions of stochastic and deterministic processes to bacterial and fungal assembly across spatial scales and through time, we used 16 s rRNA gene and ITS sequencing in the soil of an emblematic wine-growing region of Italy.Combining null- and neutral-modelling, we found that assembly processes were consistent through time, but bacteria and fungi were governed by different processes. At the within-vineyard scale, deterministic selection and homogenising dispersal dominated bacterial assembly, while neither selection nor dispersal had clear influence over fungal assembly. At the among-vineyard scale, the influence of dispersal limitation increased for both taxonomic groups, but its contribution was much larger for fungal communities. These null-model-based inferences were supported by neutral modelling, which estimated a dispersal rate almost two orders-of-magnitude lower for fungi than bacteria.This indicates that while stochastic processes are important for fungal assembly, bacteria were more influenced by deterministic selection imposed by the biotic and/or abiotic environment. Managing microbes in vineyard soils could thus benefit from strategies that account for dispersal limitation of fungi and the importance of environmental conditions for bacteria. Our results are consistent with theoretical expectations whereby larger individual size and smaller populations can lead to higher levels of stochasticity.}, }
@article {pmid35834007, year = {2022}, author = {Mańkowska, K and Marchelek-Myśliwiec, M and Kochan, P and Kosik-Bogacka, D and Konopka, T and Grygorcewicz, B and Roszkowska, P and Cecerska-Heryć, E and Siennicka, A and Konopka, J and Dołęgowska, B}, title = {Microbiota in sports.}, journal = {Archives of microbiology}, volume = {204}, number = {8}, pages = {485}, pmid = {35834007}, issn = {1432-072X}, abstract = {The influence of microbiota on the human body is currently the subject of many studies. The composition of bacteria colonizing the gastrointestinal tract varies depending on genetic make-up, lifestyle, use of antibiotics or the presence of diseases. The diet is also important in the species diversity of the microbiota. This study is an analysis of the relationships between physical activity, diet, and the microbiota of the gastrointestinal tract in athletes. This review shows the differences in the microbial composition in various sports disciplines, the influence of probiotics on the microbiome, the consequence of which may be achieved even better sports results. Physical activity increases the number of bacteria, mainly of the Clostridiales order and the genus: Lactobacillus, Prevotella, Bacteroides, and Veillonella, and their number varies depending on the sports discipline. These bacteria are present in athletes in sports that require a high VO2 max. The players' diet also influences the composition of the microbiota. A diet rich in dietary fiber increases the amount of Lactobacillus or Bifidobacterium bacteria, probiotic microorganisms, which indicates the need to supplement the diet with probiotic preparations. It is impossible to suggest an unambiguous answer to how the microbiota of the gastrointestinal tract changes in athletes and requires further analyzes.}, }
@article {pmid35831642, year = {2022}, author = {Kluting, K and Strid, Y and Six, D and Rosling, A}, title = {Forest Fire Influence on Tomicus piniperda-Associated Fungal Communities and Phloem Nutrient Availability of Colonized Pinus sylvestris.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35831642}, issn = {1432-184X}, support = {2014-458//Svenska Forskningsrådet Formas/ ; SSWF 17-1-Chdre//Stiftelsen Stina Werners Fond/ ; }, abstract = {Forest fire is known to positively affect bark beetle populations by providing fire-damaged trees with impaired defenses for infestation. Tomicus piniperda, the common pine shoot beetle, breeds and lays eggs under the bark of stressed pine trees and is considered a serious forest pest within its native range. Wood-colonizing fungi have been hypothesized to improve substrate quality and detoxify tree defensive chemistry to indirectly facilitate tree colonization by beetles. While some bark beetle species form symbiotic associations with fungi and actively vector their partners when colonizing new trees, T. piniperda does not have mycangia or body hairs for specific vectoring of fungi. To explore the T. piniperda-associated fungal community for signs of specific association, we used ITS metabarcoding to separately characterize fungal communities associated with surface and gut of male and female beetles. We also characterized the temporal changes in fungal community and nutrient status of pine phloem with and without beetle galleries. Sampling was performed 2 years after a natural forest fire and included both burnt and unburnt sites. In our study system, we find that forest fire significantly impacts the fungal community composition associated with T. piniperda and that fire may also indirectly change nutrient availability in phloem to beetle galleries. We conclude that T. piniperda can vector fungi to newly colonized trees but the absence of positive effects on substrate quality and minimal effects of sex indicate that vectoring of associated fungal communities is not a strategy associated with the T. piniperda life cycle.}, }
@article {pmid35822810, year = {2022}, author = {Senn, S and Pangell, K and Bowerman, AL}, title = {Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia.}, journal = {Biotech (Basel (Switzerland))}, volume = {11}, number = {1}, pages = {}, doi = {10.3390/biotech11010001}, pmid = {35822810}, issn = {2673-6284}, abstract = {The purpose of this paper is to elucidate the roles that microbes may be playing in the rootzone of the medicinal plant Daturainoxia. We hypothesized that the microbes associated with the Datura rootzone would be significantly different than the similar surrounding fields in composition and function. We also hypothesized that rhizospheric and endophytic microbes would be associated with similar metabolic functions to the plant rootzone they inhabited. The methods employed were microbial barcoding, tests of essential oils against antibiotic resistant bacteria and other soil bacterial isolates, 16S Next Generation Sequencing (NGS) metabarcoding, and Whole Genome Shotgun (WGS) taxonomic and functional analyses. A few of the main bacterial genera of interest that were differentially abundant in the Datura root microbiome were Flavobacterium (p = 0.007), Chitinophaga (p = 0.0007), Pedobacter (p = 6 × 10-5), Bradyhizobium (p = 1 × 10-8), and Paenibacillus (p = 1.46 × 10-6). There was significant evidence that the microbes associated with the Datura rootzone had elevated function related to bacterial chalcone synthase (p = 1.49 × 10-3) and permease genes (p < 0.003). There was some evidence that microbial functions in the Datura rootzone provided precursors to important plant bioactive molecules or were beneficial to plant growth. This is important because these compounds are phyto-protective antioxidants and are precursors to many aromatic bioactive compounds that are relevant to human health. In the context of known interactions, and current results, plants and microbes influence the flavonoid biosynthetic pathways of one other, in terms of the regulation of the phenylpropanoid pathway. This is the first study to focus on the microbial ecology of the Datura rootzone. There are possible biopharmaceutical and agricultural applications of the natural interplay that was discovered during this study of the Datura inoxia rhizosphere.}, }
@article {pmid35822787, year = {2022}, author = {Khoo, C and Duysburgh, C and Marzorati, M and Van den Abbeele, P and Zhang, D}, title = {A Freeze-Dried Cranberry Powder Consistently Enhances SCFA Production and Lowers Abundance of Opportunistic Pathogens In Vitro.}, journal = {Biotech (Basel (Switzerland))}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/biotech11020014}, pmid = {35822787}, issn = {2673-6284}, abstract = {The American cranberry, Vaccinium macrocarpon, contains fibers and (poly)phenols that could exert health-promoting effects through modulation of gut microbiota. This study aimed to investigate how a freeze-dried whole cranberry powder (FCP) modulated metabolite production and microbial composition using both a 48-h incubation strategy and a long-term human gut simulator study with the M-SHIME (Mucosal Simulator of the Human Intestinal Microbial Ecosystem). FCP was repeatedly administered over three weeks. The studies included five and three study subjects, respectively. In both models, FCP significantly increased levels of health-related short-chain fatty acids (SCFA: acetate, propionate and butyrate), while decreased levels of branched-chain fatty acids (markers of proteolytic fermentation). Interestingly, FCP consistently increased luminal Bacteroidetes abundances in the proximal colon of the M-SHIME (+17.5 ± 9.3%) at the expense of Proteobacteria (-10.2 ± 1.5%). At family level, this was due to the stimulation of Bacteroidaceae and Prevotellaceae and a decrease of Pseudomonodaceae and Enterobacteriaceae. Despite of interpersonal differences, FCP also increased the abundance of families of known butyrate producers. Overall, FCP displayed an interesting prebiotic potential in vitro given its selective utilization by host microorganisms and potential health-related effects on inhibition of pathogens and selective stimulation of beneficial metabolites.}, }
@article {pmid35818006, year = {2022}, author = {Mesa, V}, title = {Rhizosphere and Endosphere Bacterial Communities Survey by Metagenomics Approach.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2512}, number = {}, pages = {181-197}, doi = {10.1007/978-1-0716-2429-6_11}, pmid = {35818006}, issn = {1940-6029}, mesh = {Bacteria/genetics ; *Metagenomics ; Plant Roots/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil Microbiology ; }, abstract = {The diversity of microbes associated with plant roots is in the order of tens of thousands of species. It is estimated that only 0.1-1.0% of the living bacteria present in soils can be cultured under standard conditions. The microbial marker-gene sequence data and the next-generation sequencing technologies have enabled systemic studies of root-associated microbiomes. Molecular techniques can be used to generate comprehensive taxonomic profiles of the microorganisms present in roots. The aim of this chapter is to provide a standard method for the obtention of rhizosphere and endosphere fractions, and a generic workflow of the Quantitative Insights Into Microbial Ecology version 2 (QIIME2) software to analysis of 16S rRNA marker-gene.}, }
@article {pmid35821127, year = {2022}, author = {Roy, J and Reichel, R and Brüggemann, N and Rillig, MC}, title = {Functional, not Taxonomic, Composition of Soil Fungi Reestablishes to Pre-mining Initial State After 52 Years of Recultivation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35821127}, issn = {1432-184X}, abstract = {Open-cast mining leads to the loss of naturally developed soils and their ecosystem functions and services. Soil restoration after mining aims to restore the agricultural productivity in which the functions of the fungal community play a crucial role. Whether fungi reach a comparable functional state as in the soil before mining within half a century of recultivation is still unanswered. Here, we characterised the soil fungal community using ITS amplicon Illumina sequencing across a 52-year chronosequence of agricultural recultivation after open-cast mining in northern Europe. Both taxonomic and functional community composition showed profound shifts over time, which could be attributed to the changes in nutrient status, especially phosphorus availability. However, taxonomic composition did not reach the pre-mining state, whereas functional composition did. Importantly, we identified a positive development of arbuscular mycorrhizal root fungal symbionts after the initial three years of alfalfa cultivation, followed by a decline after conversion to conventional farming, with arbuscular mycorrhizal fungi being replaced by soil saprobes. We conclude that appropriate agricultural management can steer the fungal community to its functional pre-mining state despite stochasticity in the reestablishment of soil fungal communities. Nonetheless, conventional agricultural management results in the loss of plant symbionts, favouring non-symbiotic fungi.}, }
@article {pmid35819480, year = {2022}, author = {Alberoni, D and Gioia, DD and Baffoni, L}, title = {Alterations in the Microbiota of Caged Honeybees in the Presence of Nosema ceranae Infection and Related Changes in Functionality.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35819480}, issn = {1432-184X}, abstract = {Several studies have outlined that changes in the honeybee gut microbial composition may impair important metabolic functions supporting the honeybees' life. Gut dysbiosis may be caused by diseases like Nosema ceranae or by other anthropic, environmental or experimental stressors. The present work contributes to increasing knowledge on the dynamics of the gut microbiome acquisition in caged honeybees, an experimental condition frequently adopted by researchers, with or without infection with N. ceranae, and fed with a bacterial mixture to control N. ceranae development. Changes of the gut microbiota were elucidated comparing microbial profile of caged and open-field reared honeybees. The absolute abundance of the major gut microbial taxa was studied with both NGS and qPCR approaches, whereas changes in the functionality were based on RAST annotations and manually curated. In general, all caged honeybees showed important changes in the gut microbiota, with [Formula: see text]-proteobacteria (Frischella, Gilliamella and Snodgrassella) lacking in all caged experimental groups. Caged honeybees infected with N. ceranae showed also a strong colonization of environmental taxa like Citrobacter, Cosenzaea and Morganella, as well as possibly pathogenic bacteria such as Serratia. The colonization of Serratia did not occur in presence of the bacterial mixture. The functionality prediction revealed that environmental bacteria or the supplemented bacterial mixture increased the metabolic potential of the honeybee gut microbiome compared to field and caged controls.}, }
@article {pmid35818766, year = {2022}, author = {Sánchez-Suárez, J and Díaz, L and Junca, H and Garcia-Bonilla, E and Villamil, L}, title = {Microbiome composition of the marine sponge Cliona varians at the Neotropical Southern Caribbean Sea displays a predominant core of Rhizobiales and Nitrosopumilaceae.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.15714}, pmid = {35818766}, issn = {1365-2672}, abstract = {AIMS: This work aims to characterize the microbial diversity of the encrusting sponge Cliona varians, a pore-forming and coral reef bioeroding marine sponge of emerging spread related to ocean acidification.<br><br>METHODS AND RESULTS: We analyzed the microbiome composition by 16S V4 amplicon next-generation sequencing in a community of the bioeroding coral-reef encrusting/excavating marine sponge Cliona varians thriving at the Southern Caribbean Sea. 87.21% and 6.76% of the sequences retrieved were assigned to the domain Bacteria and Archaea. The most predominant operational taxonomic units were classified as members of the order Rhizobiales and family Nitrosopumilaceae, representing members of not yet characterized genera. Features found strictly conserved in the strain/genomic representatives reported in those microbial taxa are nitrogen fixation and transformation.<br><br>CONCLUSION: Our results suggest, in accordance with recent results, that these microbiome members and associated functions could be contributing to the biological fitness of the sponge to be able to colonize and bioerode in environments with low access and scarce availability of nitrogen source.<br><br>Coral reefs bioresources such as sponge holobionts are intriguing and complex ecosystems units. This study contributes to the knowledge of how C. varians microbiota is composed or shaped, which is crucial to understand its ecological functions.}, }
@article {pmid35817179, year = {2022}, author = {Liu, Y and Xi, Y and Xie, T and Liu, H and Su, Z and Huang, Y and Xu, W and Wang, D and Zhang, C and Li, X}, title = {Enhanced removal of diclofenac via coupling Pd catalytic and microbial processes in a H2-based membrane biofilm reactor: Performance, mechanism and biofilm microbial ecology.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {135597}, doi = {10.1016/j.chemosphere.2022.135597}, pmid = {35817179}, issn = {1879-1298}, abstract = {Diclofenac (DCF) is a most widely used anti-inflammatory drug, which has attracted worldwide attention given its low biodegradability and ecological damage, especially toxic effects on mammals including humans. In this study, a H2-based membrane biofilm reactor (H2-MBfR) was constructed with well-dispersed Pd nanoparticles generated in situ. The Pd-MBfR was applied for catalytic reductive dechlorination of DCF. In batch tests, DCF concentration had significantly effect on the rate and extent DCF removal, and NO3- had negative impact on DCF reductive dechlorination. Over 67% removal of 0.5 mg/L DCF and 99% removal of 10 mg/L NO3--N were achieved in 90 min, and the highest removal of 97% was obtained at 0.5 mg/L DCF in the absence of NO3-. Over 78 days of continuous operation, the highest steady-state removal flux of DCF was 0.0097 g/m2/d. LC-MS analysis indicated that the major product was 2-anilinephenylacetic acid (APA). Dechlorination was the main removal process of DCF mainly owing to the catalytic reduction by PdNPs, microbial reduction, and the synergistic reduction of microbial and PdNPs catalysis using direct delivery of H2. Moreover, DCF reductive Dechlorination shifted the microbial community in the biofilms and Sporomusa was responsible for DCF degradation. In summary, this work expands a remarkable feasibility of sustainable catalytic removal of DCF.}, }
@article {pmid35817167, year = {2022}, author = {Khan, MA and Singh, D and Arif, A and Sodhi, KK and Singh, DK and Islam, SN and Ahmad, A and Akhtar, K and Siddique, HR}, title = {Protective effect of green synthesized Selenium Nanoparticles against Doxorubicin induced multiple adverse effects in Swiss albino mice.}, journal = {Life sciences}, volume = {}, number = {}, pages = {120792}, doi = {10.1016/j.lfs.2022.120792}, pmid = {35817167}, issn = {1879-0631}, abstract = {AIMS: Doxorubicin (DOX) is a widely used drug against multiple cancers. However, its clinical Use is often restricted due to multiple adverse effects. Recently, Selenium Nanoparticles (SeNPs) are gaining attention due to their low toxicity and higher biocompatibility, making them attractive nanoparticles (NPs) in medical and pharmaceutical sciences. Therefore, the current study aimed to assess if our biosynthesized SeNP from the endophytic fungus Fusarium oxysporum conjugated with DOX could alleviate the DOX-induced adverse effects.<br><br>MAIN METHODS: For this purpose, we investigated various genotoxic, biochemical, histopathological, and immunohistochemical parameters and finally analyzed the metabolite profile by LC-MS/MS.<br><br>KEY FINDINGS: We observed that DOX causes an increase in reactive oxygen and nitrogen species (ROS, RNS), 8-OHdG, and malondialdehyde (MDA), decreases antioxidant defense systems and reduces BCL-2 expression in cardiac tissue. In addition, a significant increase in DNA damage and alteration in the cytoarchitecture of the liver, kidney, and heart tissues was observed by Comet Tail Length and histopathological studies, respectively. Interestingly, the DOX-SeNP conjugate reduced ROS/RNS, 8-OHdG, and MDA levels in the liver, kidney, and heart tissues. It also restored the antioxidant enzymes and cytoarchitectures of the examined tissues, reduced genotoxicity, and increased the BCL-2 levels. Finally, metabolic profiling showed that DOX reduced the number of cardioprotective metabolites, which DOX-SeNP restored.<br><br>SIGNIFICANCE: Collectively, the present results describe the protective effect of DOX-conjugated SeNP against DOX-induced toxicities. In conclusion, DOX-SeNP conjugate might be better for treating patients receiving DOX alone. However, it warrants further thorough investigation.}, }
@article {pmid35811862, year = {2022}, author = {Li, Y and Liu, B and Chen, J and Yue, X}, title = {Carbon-Nitrogen-Sulfur-Related Microbial Taxa and Genes Maintained the Stability of Microbial Communities in Coals.}, journal = {ACS omega}, volume = {7}, number = {26}, pages = {22671-22681}, doi = {10.1021/acsomega.2c02126}, pmid = {35811862}, issn = {2470-1343}, abstract = {Coal microbes are the predominant form of life in the subsurface ecosystem, which play a vital role in biogeochemical cycles. However, the systematic information about carbon-nitrogen-sulfur (C-N-S)-related microbial communities in coal seams is limited. In this study, 16S rRNA gene data from a total of 93 microbial communities in coals were collected for meta-analysis. The results showed that 718 functional genera were related to the C-N-S cycle, wherein N2 fixation, denitrification, and C degradation groups dominated in relative abundance, Chao1 richness, Shannon diversity, and niche width. Genus Pseudomonas having the most C-N-S-related functions showed the highest relative abundance, and genus Herbaspirillum with a higher abundance participated in C degradation, CH4 oxidation, N2 fixation, ammoxidation, and denitrification. Such Herbaspirillum was a core genus in the co-occurrence network of microbial prokaryotes and showed higher levels in weight degree, betweenness centrality, and eigenvector centrality. In addition, most of the methanogens could fix N2 and dominated in the N2 fixation groups. Among them, genera Methanoculleus and Methanosaeta showed higher levels in the betweenness centrality index. In addition, the genus Clostridium was linked to the methanogenesis co-occurrence network module. In parallel, the S reduction gene was present in the highest total relative abundance of genes, followed by the C degradation and the denitrification genes, and S genes (especially cys genes) were the main genes linked to the co-occurrence network of the C-N-S-related genes. In summary, this study strengthened our knowledge regarding the C-N-S-related coal microbial communities, which is of great significance in understanding the microbial ecology and geochemical cycle of coals.}, }
@article {pmid35809121, year = {2022}, author = {Carvalho, MJ and S Oliveira, AL and Santos Pedrosa, S and Pintado, M and Pinto-Ribeiro, I and Madureira, AR}, title = {Skin Microbiota and the Cosmetic Industry.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35809121}, issn = {1432-184X}, support = {027578//Fundo Europeu de Desenvolvimento Regional (FEDER)/ ; 01-0247//Programa Operacional Competitividade e Internacionalização (POCI)/ ; UID/Multi/50016/2019//Fundo Regional para a Ciência e Tecnologia/ ; }, abstract = {Skin harbors an important microbial ecosystem - the skin microbiota that is in homeostasis with its host and is beneficial for human health. Cosmetic products have the potential to interfere with this microbial community; therefore their impact should be assessed. The aim of this review is to highlight the importance of skin microbiota in the cosmetic industry. Several studies determined that cosmetic ingredients have the potential to disrupt the skin microbiota equilibrium leading to the development of skin diseases and dysregulation of immune response. These studies led their investigation by using different methodologies and models, concluding that methods must be chosen according to the aim of the study, the skin site to be evaluated, and the target population of the cosmetics. Overall, it is crucial to test the impact of cosmetics in the skin microbiota and to stablish standard procedures, as well as specific criteria that allow to classify a cosmetic product as skin microbiota friendly.}, }
@article {pmid35804731, year = {2022}, author = {Clodoveo, ML and Muraglia, M and Crupi, P and Hbaieb, RH and De Santis, S and Desantis, A and Corbo, F}, title = {The Tower of Babel of Pharma-Food Study on Extra Virgin Olive Oil Polyphenols.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {13}, pages = {}, doi = {10.3390/foods11131915}, pmid = {35804731}, issn = {2304-8158}, abstract = {Much research has been conducted to reveal the functional properties of extra virgin olive oil polyphenols on human health once EVOO is consumed regularly as part of a balanced diet, as in the Mediterranean lifestyle. Despite the huge variety of research conducted, only one effect of EVOO polyphenols has been formally approved by EFSA as a health claim. This is probably because EFSA's scientific opinion is entrusted to scientific expertise about food and medical sciences, which adopt very different investigative methods and experimental languages, generating a gap in the scientific communication that is essential for the enhancement of the potentially useful effects of EVOO polyphenols on health. Through the model of the Tower of Babel, we propose a challenge for science communication, capable of disrupting the barriers between different scientific areas and building bridges through transparent data analysis from the different investigative methodologies at each stage of health benefits assessment. The goal of this work is the strategic, distinctive, and cost-effective integration of interdisciplinary experiences and technologies into a highly harmonious workflow, organized to build a factual understanding that translates, because of trade, into health benefits for buyers, promoting EVOOs as having certified health benefits, not just as condiments.}, }
@article {pmid35802409, year = {2022}, author = {Edwards, A and Soares, A and Debbonaire, A and Edwards Rassner, SM}, title = {Before you go: a packing list for portable DNA sequencing of microbiomes and metagenomes.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {7}, pages = {}, doi = {10.1099/mic.0.001220}, pmid = {35802409}, issn = {1465-2080}, }
@article {pmid35802173, year = {2022}, author = {Rocha, FP and Ronque, MUV and Lyra, ML and Bacci, M and Oliveira, PS}, title = {Habitat and Host Species Drive the Structure of Bacterial Communities of Two Neotropical Trap-Jaw Odontomachus Ants : Habitat and Host Species Drive the Structure of Bacterial Communities of Two Neotropical Trap-Jaw Odontomachus Ants.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35802173}, issn = {1432-184X}, support = {Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 2017/26162-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/04824-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2014/23141-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/16645-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 163546/2020-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 441036/2016-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 307541/2018-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 306115/2013-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 302219/2017-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 303730/2021-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Ants have long been known for their associations with other taxa, including macroscopic fungi and symbiotic bacteria. Recently, many ant species have had the composition and function of their bacterial communities investigated. Due to its behavioral and ecological diversity, the subfamily Ponerinae deserves more attention regarding its associated microbiota. Here, we used the V4 region of the 16S rRNA gene to characterize the bacterial communities of Odontomachus chelifer (ground-nesting) and Odontomachus hastatus (arboreal), two ponerine trap-jaw species commonly found in the Brazilian savanna ("Cerrado") and Atlantic rainforest. We investigated habitat effects (O. chelifer in the Cerrado and the Atlantic rainforest) and species-specific effects (both species in the Atlantic rainforest) on the bacterial communities' structure (composition and abundance) in two different body parts: cuticle and gaster. Bacterial communities differed in all populations studied. Cuticular communities were more diverse, while gaster communities presented variants common to other ants, including Wolbachia and Candidatus Tokpelaia hoelldoblerii. Odontomachus chelifer populations presented different communities in both body parts, highlighting the influence of habitat type. In the Atlantic rainforest, the outcome depended on the body part targeted. Cuticular communities were similar between species, reinforcing the habitat effect on bacterial communities, which are mainly composed of environmentally acquired taxa. Gaster communities, however, differed between the two Odontomachus species, suggesting species-specific effects and selective filters. Unclassified Firmicutes and uncultured Rhizobiales variants are the main components accounting for the observed differences. Our study indicates that both host species and habitat act synergistically, but to different degrees, to shape the bacterial communities in these Odontomachus species.}, }
@article {pmid35802172, year = {2022}, author = {Mejia, MP and Rojas, CA and Curd, E and Renshaw, MA and Edalati, K and Shih, B and Vincent, N and Lin, M and Nguyen, PH and Wayne, R and Jessup, K and Parker, SS}, title = {Soil Microbial Community Composition and Tolerance to Contaminants in an Urban Brownfield Site.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35802172}, issn = {1432-184X}, support = {CA-16-376437//Office of the President, University of California/ ; 443952-SR-69085//La Kretz and Stunt Ranch Reserve Grant/ ; }, abstract = {Brownfields are unused sites that contain hazardous substances due to previous commercial or industrial use. The sites are inhospitable for many organisms, but some fungi and microbes can tolerate and thrive in the nutrient-depleted and contaminated soils. However, few studies have characterized the impacts of long-term contamination on soil microbiome composition and diversity at brownfields. This study focuses on an urban brownfield-a former rail yard in Los Angeles that is contaminated with heavy metals, volatile organic compounds, and petroleum-derived pollutants. We anticipate that heavy metals and organic pollutants will shape soil microbiome diversity and that several candidate fungi and bacteria will be tolerant to the contaminants. We sequence three gene markers (16S ribosomal RNA, 18S ribosomal RNA, and the fungal internal transcribed spacer (FITS)) in 55 soil samples collected at five depths to (1) profile the composition of the soil microbiome across depths; (2) determine the extent to which hazardous chemicals predict microbiome variation; and (3) identify microbial taxonomic groups that may metabolize these contaminants. Detected contaminants in the samples included heavy metals, petroleum hydrocarbons, polycyclic aromatic hydrocarbons, and volatile organic compounds. Bacterial, eukaryotic, and fungal communities all varied with depth and with concentrations of arsenic, chromium, cobalt, and lead. 18S rRNA microbiome richness and fungal richness were positively correlated with lead and cobalt levels, respectively. Furthermore, bacterial Paenibacillus and Iamia, eukaryotic Actinochloris, and fungal Alternaria were enriched in contaminated soils compared to uncontaminated soils and represent taxa of interest for future bioremediation research. Based on our results, we recommend incorporating DNA-based multi-marker microbial community profiling at multiple sites and depths in brownfield site assessment standard methods and restoration.}, }
@article {pmid35802014, year = {2022}, author = {Zhu, M and Duan, X and Cai, P and Chai, J and Ji, J and Li, Y}, title = {First report of Podosphaera fusca Causing Powdery Mildew on Coreopsis lanceolata in China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-12-20-2630-PDN}, pmid = {35802014}, issn = {0191-2917}, abstract = {Coreopsis lanceolata, known as lance-leaf coreopsis, is a perennial plant with high ornamental value. It is widely grown in many public parks and home gardens in China due to its showy flowers. From May to June 2020, typical powdery mildew-signs and symptoms were seen on leaves of C. lanceolata cultivated in the east campus of Henan Normal University, Henan Province, China. Abundant white powder-like masses in spot- or coalesced-lesions were on ad- and abaxial surfaces of plant leaves and covered up to 50 % of the leaf area. The infected leaves were deformed and eventually prematurely senescent. Approximately 80 % of observed C. lanceolata plants showed these signs and symptoms. Unbranched conidiophores (n = 25) were 90 to 200 × 12 to 20 μm and showed a foot cell, followed by 1 to 3 short cells and conidia. Ellipsoid-ovoid shaped conidia (n = 30) were 22 to 36 × 15 to 23 μm, with a length/width ratio of 1.4 to 2.4. No chasmothecia were detected. The powdery mildew fungus was initially identified as Podosphaera fusca based on the morphological characteristics. Total genomic DNA of the pathogen was extracted and the rDNA internal transcribed spacer (ITS) region was amplified and sequenced using the primers ITS1/ITS4 (White et al. 1990; Zhu et al. 2019). The obtained sequence was deposited into GenBank under Accession No. MT899186 and was 100 % identical to P. fusca (JX546297) from Herba eupatorii (Ding et al. 2013). To perform pathogenicity assays, leaf surface of three healthy plants was inoculated with fungal conidia according to a previously described method (Zhu et al. 2021). As a control, three non-inoculated plants were used. The control and inoculated plants were placed separately in two growth chambers (light/dark, 16 h/8 h; humidity, 65 %; temperature, 20 ℃). Fourteen- to sixteen-days post inoculation, powdery mildew signs were noticed on inoculated plants, whereas control remained asymptomatic. Similar results were found by performing two repeated pathogenicity assays. Therefore, based on the morphological and molecular analysis, the pathogen was identified and confirmed as P. fusca. This fungus has been reported on C. lanceolata in Korea (Park et al. 2010) and Italy (Garibaldi et al. 2007). This is, to the best of our knowledge, the first report of P. fusca on C. lanceolata in China. The sudden occurrence of this powdery mildew disease on C. lanceolata may adversely affect the health of valuable ornamentals in China. The precise identification of the causal agent of this powdery mildew of C. lanceolata is a preliminary step in developing effective disease management strategies.}, }
@article {pmid35795698, year = {2022}, author = {Salerno, B and Cornaggia, M and Sabatino, R and Di Cesare, A and Furlan, M and Barco, L and Orsini, M and Cordioli, B and Mantovani, C and Bano, L and Losasso, C}, title = {Calves as Main Reservoir of Antibiotic Resistance Genes in Dairy Farms.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {918658}, doi = {10.3389/fpubh.2022.918658}, pmid = {35795698}, issn = {2296-2565}, abstract = {A side effect of antibiotic usage is the emergence and dissemination of antibiotic resistance genes (ARGs) within microbial communities. The spread of ARGs among pathogens has emerged as a public health concern. While the distribution of ARGs is documented on a global level, their routes of transmission have not been clarified yet; for example, it is not clear whether and to what extent the emergence of ARGs originates in farms, following the selective pressure exerted by antibiotic usage in animal husbandry, and if they can spread into the environment. Here we address this cutting edge issue by combining data regarding antimicrobial usage and quantitative data from selected ARGs (bla TEM, bla CTXM , ermB, vanA, qnrS, tetA, sul2, and mcr-1) encoding for resistance to penicillins, macrolides-lincosamides-streptogramins, glycopeptides, quinolones, tetracyclines, sulfonamides, and colistin at the farm level. Results suggest that dairy farms could be considered a hotspot of ARGs, comprising those classified as the highest risk for human health and that a correlation existed between the usage of penicillins and bla TEM abundances, meaning that, although the antibiotic administration is not exclusive, it remains a certain cause of the ARGs' selection and spread in farms. Furthermore, this study identified the role of calves as the main source of ARGs spread in dairy farms, claiming the need for targeted actions in this productive category to decrease the load of ARGs along the production chain.}, }
@article {pmid35788867, year = {2022}, author = {Kim, SB and Lyou, ES and Kim, MS and Lee, TK}, title = {Bacterial Resuscitation from Starvation-Induced Dormancy Results in Phenotypic Diversity Coupled with Translational Activity Depending on Carbon Substrate Availability.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35788867}, issn = {1432-184X}, support = {2020R1C1C1006249//National Research Foundation of Korea/ ; 2020R1C1C1006249//National Research Foundation of Korea/ ; 2020R1C1C1006249//National Research Foundation of Korea/ ; }, abstract = {Dormancy is a survival strategy of stressed bacteria inhabiting a various environment. Frequent dormant-active transitions owing to environmental changes play an important role in functional redundancy. However, a proper understanding of the phenotypic changes in bacteria during these transitions remains to be clarified. In this study, orthogonal approaches, such as electron microscopy, flow cytometry, and Raman spectroscopy, which can evaluate phenotypic heterogeneity at the single-cell level, were used to observe morphological and molecular phenotypic changes in resuscitated cells, and RNA sequencing (RNASeq) was used to determine the genetic characteristics associated with phenotypes. Within 12 h of the resuscitation process, morphological (cell size and shape) and physiological (growth and viability) characteristics as well as molecular phenotypes (cellular components) were found to be recovered to the extent that they were similar to those in active cells. The recovery rate and detailed phenotypic properties of the resuscitated cells differed significantly depending on the type or concentration of carbon sources. RNASeq analysis revealed that genes related to translation were significantly upregulated under all resuscitation conditions. The simpler the carbon source (e.g., glucose), the higher the expression of genes involved in cellular repair, and the more complex the carbon source (e.g., beef extract), the higher the expression of genes associated with increased energy production associated with cellular aerobic respiration. This study of phenotypic plasticity of resuscitated cells provides fundamental insight into understanding the adaptive fine-tuning of the microbiome in response to environmental changes and the functional redundancy resulting from phenotype heterogeneity.}, }
@article {pmid35788422, year = {2022}, author = {Baubin, C and Ran, N and Siebner, H and Gillor, O}, title = {Divergence of Biocrust Active Bacterial Communities in the Negev Desert During a Hydration-Desiccation Cycle.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35788422}, issn = {1432-184X}, support = {993/11//Israeli Science Academy/ ; }, abstract = {Rain events in arid environments are highly unpredictable and intersperse extended periods of drought. Therefore, tracking changes in desert soil bacterial communities during rain events, in the field, was seldom attempted. Here, we assessed rain-mediated dynamics of active bacterial communities in the Negev Desert biological soil crust (biocrust). Biocrust samples were collected during, and after a medium rainfall and dry soil was used as a control; we evaluated the changes in active bacterial composition, potential function, potential photosynthetic activity, and extracellular polysaccharide (EPS) production. We hypothesized that rain would activate the biocrust phototrophs (mainly Cyanobacteria), while desiccation would inhibit their activity. In contrast, the biocrust Actinobacteria would decline during rewetting and revive with desiccation. Our results showed that hydration increased chlorophyll content and EPS production. As expected, biocrust rewetting activated Cyanobacteria, which replaced the former dominant Actinobacteria, boosting potential autotrophic functions. However, desiccation of the biocrust did not immediately change the bacterial composition or potential function and was followed by a delayed decrease in chlorophyll and EPS levels. This dramatic shift in the community upon rewetting led to modifications in ecosystem services. We propose that following a rain event, the response of the active bacterial community lagged behind the biocrust water content due to the production of EPS which delayed desiccation and temporarily sustained the biocrust community activity.}, }
@article {pmid35785246, year = {2022}, author = {Jiang, X and Wang, L}, title = {Grassland-based ruminant farming systems in China: Potential, challenges and a way forward.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {10}, number = {}, pages = {243-248}, doi = {10.1016/j.aninu.2022.04.007}, pmid = {35785246}, issn = {2405-6383}, abstract = {With an increasing demand for high-quality, eco-friendly food products and growing concerns over ecological conservation, the development of ecology-based alternatives for ruminant production in China is urgently needed. This review discusses the capabilities for integrating grassland grazing into existing livestock farming systems to meet the contemporary human needs for high-quality foods and ecologically stable environments. Additionally, this review provides a critical analysis of the challenges and future directions associated with grassland-based ruminant farming systems. Integrating nutritional manipulation with grazing manipulation is critical for improving the productivity of grassland-based ecosystems and natural ecological functions. Biodiversity is the primary determinant of grassland ecosystem functions, while the composition and function of rumen microbiomes determine ruminant production performance. Future studies should focus on the following aspects: 1) how livestock grazing regulates grassland biodiversity and the mechanisms of grassland biodiversity maintenance, offering an important scientific basis for guiding grazing manipulation practices, including grazing intensity, livestock types, and grazing management practices; to 2) characterize the microbial ecology within the rumen of grazing ruminants to offer clarified instruction for the nutritional manipulation of grazing ruminants. Our recommendation includes creating a transdisciplinary system that integrates ecology, animal nutrition, and animal behavior to develop grassland-based ruminant farming systems sustainably, thereby achieving high-quality animal production and environmentally sustainable goals.}, }
@article {pmid35783424, year = {2022}, author = {O'Brien, J and McParland, EL and Bramucci, AR and Ostrowski, M and Siboni, N and Ingleton, T and Brown, MV and Levine, NM and Laverock, B and Petrou, K and Seymour, J}, title = {The Microbiological Drivers of Temporally Dynamic Dimethylsulfoniopropionate Cycling Processes in Australian Coastal Shelf Waters.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {894026}, doi = {10.3389/fmicb.2022.894026}, pmid = {35783424}, issn = {1664-302X}, abstract = {The organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) play major roles in the marine microbial food web and have substantial climatic importance as sources and sinks of dimethyl sulfide (DMS). Seasonal shifts in the abundance and diversity of the phytoplankton and bacteria that cycle DMSP are likely to impact marine DMS (O) (P) concentrations, but the dynamic nature of these microbial interactions is still poorly resolved. Here, we examined the relationships between microbial community dynamics with DMS (O) (P) concentrations during a 2-year oceanographic time series conducted on the east Australian coast. Heterogenous temporal patterns were apparent in chlorophyll a (chl a) and DMSP concentrations, but the relationship between these parameters varied over time, suggesting the phytoplankton and bacterial community composition were affecting the net DMSP concentrations through differential DMSP production and degradation. Significant increases in DMSP were regularly measured in spring blooms dominated by predicted high DMSP-producing lineages of phytoplankton (Heterocapsa, Prorocentrum, Alexandrium, and Micromonas), while spring blooms that were dominated by predicted low DMSP-producing phytoplankton (Thalassiosira) demonstrated negligible increases in DMSP concentrations. During elevated DMSP concentrations, a significant increase in the relative abundance of the key copiotrophic bacterial lineage Rhodobacterales was accompanied by a three-fold increase in the gene, encoding the first step of DMSP demethylation (dmdA). Significant temporal shifts in DMS concentrations were measured and were significantly correlated with both fractions (0.2-2 μm and >2 μm) of microbial DMSP lyase activity. Seasonal increases of the bacterial DMSP biosynthesis gene (dsyB) and the bacterial DMS oxidation gene (tmm) occurred during the spring-summer and coincided with peaks in DMSP and DMSO concentration, respectively. These findings, along with significant positive relationships between dsyB gene abundance and DMSP, and tmm gene abundance with DMSO, reinforce the significant role planktonic bacteria play in producing DMSP and DMSO in ocean surface waters. Our results highlight the highly dynamic nature and myriad of microbial interactions that govern sulfur cycling in coastal shelf waters and further underpin the importance of microbial ecology in mediating important marine biogeochemical processes.}, }
@article {pmid35783390, year = {2022}, author = {Sanchez-Cid, C and Keuschnig, C and Torzewski, K and Stachnik, Ł and Kępski, D and Luks, B and Nawrot, A and Niedzielski, P and Vogel, TM and Larose, C}, title = {Environmental and Anthropogenic Factors Shape the Snow Microbiome and Antibiotic Resistome.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {918622}, doi = {10.3389/fmicb.2022.918622}, pmid = {35783390}, issn = {1664-302X}, abstract = {Winter tourism can generate environmental pollution and affect microbial ecology in mountain ecosystems. This could stimulate the development of antibiotic resistance in snow and its dissemination through the atmosphere and through snow melting. Despite these potential impacts, the effect of winter tourism on the snow antibiotic resistome remains to be elucidated. In this study, snow samples subjected to different levels of anthropogenic activities and surrounding forest were obtained from the Sudety Mountains in Poland to evaluate the impact of winter tourism on snow bacteria using a metagenomic approach. Bacterial community composition was determined by the sequencing of the V3-V4 hypervariable region of the 16S rRNA gene and the composition of the antibiotic resistome was explored by metagenomic sequencing. Whereas environmental factors were the main drivers of bacterial community and antibiotic resistome composition in snow, winter tourism affected resistome composition in sites with similar environmental conditions. Several antibiotic resistance genes (ARGs) showed a higher abundance in sites subjected to human activities. This is the first study to show that anthropogenic activities may influence the antibiotic resistome in alpine snow. Our results highlight the need to survey antibiotic resistance development in anthropogenically polluted sites.}, }
@article {pmid35780192, year = {2022}, author = {Borsanelli, AC and Athayde, FRF and Saraiva, JR and Riggio, MP and Dutra, IS}, title = {Dysbiosis and Predicted Functions of the Dental Biofilm of Dairy Goats with Periodontitis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35780192}, issn = {1432-184X}, support = {4-299//United States Agency for International Development/ ; }, abstract = {Periodontitis is a polymicrobial biofilm-induced inflammatory disease associated with a dysbiotic microbial community and severely affects the health and welfare of animals. However, little is known regarding the dental microbiota associated with this disease in goats. In this study, we used high-throughput sequencing, network analysis, and predicted functions to investigate the microbiota of clinically healthy goats and those with periodontitis and identify possible pathogens and proteins associated with the disease. Dental microbiomes of goats with periodontitis were richer, and network analyses showed that the number of negative interactions was higher in the networks of animals with periodontitis. Based on the interrelationships, Porphyromonas, Fusobacterium, and Prevotella were suggested to play an important role in the dental microbiota associated with goat periodontitis. Protein families linked to translation, cytoplasmatic translation, and rRNA processing were more abundant in the dental microbiota of goats with periodontitis. In conclusion, the dental biofilm microbiota associated with goat periodontitis seems to be dysbiotic and has significant antagonistic interactions, which discriminate healthy animals from diseased animals and highlight the importance of key bacteria. Thus, these novel findings contribute to the evolution of knowledge regarding the etiopathogenesis of goat periodontitis and possibly to the development of periodontitis control measures.}, }
@article {pmid35778570, year = {2022}, author = {Lee, HJ and Whang, KS}, title = {Roseomonas rosulenta sp. nov., isolated from rice paddy soil.}, journal = {Archives of microbiology}, volume = {204}, number = {7}, pages = {445}, pmid = {35778570}, issn = {1432-072X}, abstract = {Three bacterial isolates, Gram-stain-negative, non-motile, coccobacilli-shaped bacteria, strains OP-27T, OP-5 and OP-30, were isolated from rice paddy soil. Phylogenetic analyses based on 16S rRNA gene sequences revealed that three isolates belonged to the genus Roseomonas, showing the highest sequence similarities to Roseomonas sediminicola FW-3T (98.1%) and Roseomonas lacus TH-G33T (98.0%). The genome size of strain OP-27T was 5.2 Mb in a single contig with DNA G+C content of 71.2%. The genome included 5164 predicted protein-coding genes, as well as 48 tRNA, 4 rRNA and 4 mRNA genes. The average nucleotide identity value between strain OP-27T and type strains of related species of the genus Roseomonas were 81.1-83.1%, and the digital DNA-DNA hybridization values of strain OP-27T and the related strains were 24.6-26.8%, respectively. The DNA-DNA hybridization values between strains OP-27T, OP-5 and OP-30 were 84-100% and its closest relative, Roseomonas sediminicola KACC 16616T was 21.1%. The major fatty acids were C18:1 ω7c, C18:1 2-OH and C16:0 and predominant quinone was Q-10. Based on its distinctive phenotypic, phylogenetic, and chemotaxonomic characteristics, the three strains are considered to represent novel species of the genus Roseomonas, for which the name Roseomonas rosulenta sp. nov. is proposed. The type strain is OP-27T (=KACC 21501T= NBRC 114497T).}, }
@article {pmid35777363, year = {2022}, author = {Schwartzman, JA and Ebrahimi, A and Chadwick, G and Sato, Y and Roller, BRK and Orphan, VJ and Cordero, OX}, title = {Bacterial growth in multicellular aggregates leads to the emergence of complex life cycles.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2022.06.011}, pmid = {35777363}, issn = {1879-0445}, abstract = {Facultative multicellular behaviors expand the metabolic capacity and physiological resilience of bacteria. Despite their ubiquity in nature, we lack an understanding of how these behaviors emerge from cellular-scale phenomena. Here, we show how the coupling between growth and resource gradient formation leads to the emergence of multicellular lifecycles in a marine bacterium. Under otherwise carbon-limited growth conditions, Vibrio splendidus 12B01 forms clonal multicellular groups to collectively harvest carbon from soluble polymers of the brown-algal polysaccharide alginate. As they grow, groups phenotypically differentiate into two spatially distinct sub-populations: a static "shell" surrounding a motile, carbon-storing "core." Differentiation of these two sub-populations coincides with the formation of a gradient in nitrogen-source availability within clusters. Additionally, we find that populations of cells containing a high proportion of carbon-storing individuals propagate and form new clusters more readily on alginate than do populations with few carbon-storing cells. Together, these results suggest that local metabolic activity and differential partitioning of resources leads to the emergence of reproductive cycles in a facultatively multicellular bacterium.}, }
@article {pmid35776963, year = {2022}, author = {Viitamäki, S and Pessi, IS and Virkkala, AM and Niittynen, P and Kemppinen, J and Eronen-Rasimus, E and Luoto, M and Hultman, J}, title = {The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiac079}, pmid = {35776963}, issn = {1574-6941}, abstract = {Due to climate change, increased microbial activity in high-latitude soils may lead to higher greenhouse gas (GHG) emissions. However, microbial GHG production and consumption mechanisms in tundra soils are not thoroughly understood. To investigate how the diversity and functional potential of bacterial and archaeal communities vary across vegetation types and soil layers, we analyzed 116 soil metatranscriptomes from 73 sites in the Finnish sub-Arctic. Meadow soils were characterized by higher pH and lower soil organic matter (SOM) and carbon/nitrogen ratio. In contrast, dwarf shrub-dominated ecosystems had higher SOM and lower pH. Although Actinobacteria, Acidobacteria, Alphaproteobacteria, and Planctomycetes were dominant in all communities, there were significant differences at the genus level between vegetation types; plant polymer degrading groups were more active in shrub-dominated soils than in meadows. Given that climate-change scenarios predict the expansion of shrubs at high latitudes, our results indicate that tundra soil microbial communities harbor potential decomposers of increased plant litter, which may affect the rate of carbon turnover in tundra soils. Additionally, transcripts of methanotrophs were detected in the mineral layer of all soils, which may moderate methane fluxes. This study provides new insights into possible shifts in tundra microbial diversity and activity due to climate change.}, }
@article {pmid35775832, year = {2022}, author = {Muurinen, J and Muziasari, WI and Hultman, J and Pärnänen, K and Narita, V and Lyra, C and Fadlillah, LN and Rizki, LP and Nurmi, W and Tiedje, JM and Dwiprahasto, I and Hadi, P and Virta, MPJ}, title = {Antibiotic Resistomes and Microbiomes in the Surface Water along the Code River in Indonesia Reflect Drainage Basin Anthropogenic Activities.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.2c01570}, pmid = {35775832}, issn = {1520-5851}, abstract = {Water and sanitation are important factors in the emergence of antimicrobial resistance in low- and middle-income countries. Drug residues, metals, and various wastes foster the spread of antibiotic resistance genes (ARGs) with the help of mobile genetic elements (MGEs), and therefore, rivers receiving contaminants and effluents from multiple sources are of special interest. We followed both the microbiome and resistome of the Code River in Indonesia from its pristine origin at the Merapi volcano through rural and then city areas to the coast of the Indian Ocean. We used a SmartChip quantitative PCR with 382 primer pairs for profiling the resistome and MGEs and 16S rRNA gene amplicon sequencing to analyze the bacterial communities. The community structure explained the resistome composition in rural areas, while the city sampling sites had lower bacterial diversity and more ARGs, which correlated with MGEs, suggesting increased mobility potential in response to pressures from human activities. Importantly, the vast majority of ARGs and MGEs were no longer detectable in marine waters at the ocean entrance. Our work provides information on the impact of different influents on river health as well as sheds light on how land use contributes to the river resistome and microbiome.}, }
@article {pmid35771243, year = {2022}, author = {Bai, X and Dinkla, IJT and Muyzer, G}, title = {Microbial ecology of biofiltration used for producing safe drinking water.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {35771243}, issn = {1432-0614}, support = {17840//NWO-TTW/ ; }, abstract = {Biofiltration is a water purification technology playing a pivotal role in producing safe drinking water. This technology attracts many interests worldwide due to its advantages, such as no addition of chemicals, a low energy input, and a high removal efficiency of organic compounds, undesirable taste and odours, and pathogens. The current review describes the microbial ecology of three biofiltration processes that are routinely used in drinking water treatment plants, i.e. (i) rapid sand filtration (RSF), (ii) granular activated carbon filtration (GACF), and (iii) slow sand filtration (SSF). We summarised and compared the characteristics, removal performance, and corresponding (newly revealed) mechanisms of the three biofiltration processes. Specifically, the microbial ecology of the different biofilter processes and the role of microbial communities in removing nutrients, organic compounds, and pathogens were reviewed. Finally, we highlight the limitations and challenges in the study of biofiltration in drinking water production, and propose future perspectives for obtaining a comprehensive understanding of the microbial ecology of biofiltration, which is needed to promote and optimise its further application. KEY POINTS: • Biofilters are composed of complex microbiomes, primarily shaped by water quality. • Conventional biofilters contribute to address safety challenges in drinking water. • Studies may underestimate the active/functional role of microbiomes in biofilters.}, }
@article {pmid35770362, year = {2022}, author = {Sridhar, B and Wilhelm, RC and Debenport, SJ and Fahey, TJ and Buckley, DH and Goodale, CL}, title = {Microbial community shifts correspond with suppression of decomposition 25 years after liming of acidic forest soils.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.16321}, pmid = {35770362}, issn = {1365-2486}, abstract = {Microbial community structure and function regularly covary with soil pH, yet effects of these interactions on soil carbon are rarely tested experimentally within natural ecosystems. We investigated the enduring (25 year) impacts of liming on microbial community structure and decomposition at an acidic northern hardwood forest, where experimental liming increased pH one unit and surprisingly doubled the organic carbon stocks of the forest floor. We show that this increase in carbon storage corresponded with restructuring of the bacterial and fungal communities that drive decomposition. In the Oe horizon, liming reduced the activities of five extracellular enzymes that mediate decomposition, while the Oa horizon showed an especially large (64%) reduction in the activity of a sixth, peroxidase, which is an oxidative enzyme central to lignocellulose degradation. Decreased enzyme activities corresponded with loss of microbial taxa important for lignocellulose decay, including large reductions in the dominant ectomycorrhizal genera Russula and Cenococcum, saprotrophic and wood decaying fungi, and Actinobacteria (Thermomonosporaceae). These results demonstrate the importance of pH as a dominant regulator of microbial community structure and illustrate how changes to this structure can produce large, otherwise unexpected increases in carbon storage in forest soils.}, }
@article {pmid35770167, year = {2022}, author = {Girolamini, L and Pascale, MR and Mazzotta, M and Spiteri, S and Marino, F and Salaris, S and Grottola, A and Orsini, M and Cristino, S}, title = {Combining Traditional and Molecular Techniques Supports the Discovery of a Novel Legionella Species During Environmental Surveillance in a Healthcare Facility.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {900936}, doi = {10.3389/fmicb.2022.900936}, pmid = {35770167}, issn = {1664-302X}, abstract = {Legionella surveillance plays a significant role not only to prevent the risk of infection but also to study the ecology of isolates, their characteristics, and how their prevalence changes in the environment. The difficulty in Legionella isolation, identification, and typing results in a low notification rate; therefore, human infection is still underestimated. In addition, during Legionella surveillance, the special attention given to Legionella pneumophila leads to an underestimation of the prevalence and risk of infection for other species. This study describes the workflow performed during environmental Legionella surveillance that resulted in the isolation of two strains, named 8cVS16 and 9fVS26, associated with the genus Legionella. Traditional and novel approaches such as standard culture technique, MALDI-TOF MS, gene sequencing, and whole-genome sequencing (WGS) analysis were combined to demonstrate that isolates belong to a novel species. The strain characteristics, the differences between macrophage infectivity potential (mip), RNA polymerase β subunit (rpoB), and reference gene sequences, the average nucleotide identity (ANI) of 90.4%, and the DNA-DNA digital hybridization (dDDH) analysis of 43% demonstrate that these isolates belong to a new Legionella species. The finding suggests that, during the culture technique, special attention should be paid to the characteristics of the isolates that are less associated with the Legionella genus in order to investigate the differences found using more sensitive methods. The characterization of the two newly discovered isolates based on morphological, biochemical, and microscopic characteristics is currently underway and will be described in another future study.}, }
@article {pmid35770161, year = {2022}, author = {Pan, Y and Li, G and Su, L and Zheng, P and Wang, Y and Shen, Z and Chen, Z and Han, Q and Gong, J}, title = {Seagrass Colonization Alters Diversity, Abundance, Taxonomic, and Functional Community Structure of Benthic Microbial Eukaryotes.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {901741}, doi = {10.3389/fmicb.2022.901741}, pmid = {35770161}, issn = {1664-302X}, abstract = {Seagrass form high productive ecosystems in coastal environments. However, the effects of these coastal plants on the structure and function of the belowground eukaryotic microbiome remain elusive. In this study, we characterized the community of microbial eukaryotes (microeukaryotes) in both vegetated and unvegetated sediments using 18S rRNA gene amplicon sequencing and quantitative PCR. Analysis of sequencing data showed that the eelgrass (Zostera marina) colonization decreased the alpha diversity indices of benthic microeukaryotes. Apicomplexa represented an average of 83% of reads across all samples, with a higher proportion at the vegetated sites. The taxonomic community structure was significantly different between these two types of sediments, for which the concentration of NH 4 + in sediment porewater and salinity could account. Phylogenetic analyses of long 18S rRNA genes (around 1,030 bp) indicated these apicomplexan parasites are closely related to gregarine Lecudina polymorpha. Determination of 18S rRNA gene abundances provided evidence that the eelgrass markedly promoted the biomass of the gregarine and all microeukaryotes in the seagrass-colonized sediments and confirmed that the gregarine was hosted by a polychaete species. Significantly higher gene abundances of heterotrophs and mixotrophs were found at the vegetated sites, which could be explained by the finer sediments and short supply of dissolved inorganic nitrogen, respectively. The pigmented protists were more abundant in 18S rRNA gene copies at the lower and higher pH levels than at the intermediate. Nevertheless, the fractions of heterotrophs and phototrophs in the community were significantly related to porewater N:P ratio. These results indicate that seagrass colonization significantly induces an increase in overall biomass and a decrease in diversity of benthic microeukaryotes, making them more heterotrophic. This study also highlights that the hotspot of eukaryotic parasites could be linked with the high productivity of a natural ecosystem.}, }
@article {pmid35769467, year = {2022}, author = {Qing, J and Li, C and Hu, X and Song, W and Tirichen, H and Yaigoub, H and Li, Y}, title = {Differentiation of T Helper 17 Cells May Mediate the Abnormal Humoral Immunity in IgA Nephropathy and Inflammatory Bowel Disease Based on Shared Genetic Effects.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {916934}, doi = {10.3389/fimmu.2022.916934}, pmid = {35769467}, issn = {1664-3224}, abstract = {Background: IgA nephropathy (IgAN) is the most frequent glomerulonephritis in inflammatory bowel disease (IBD). However, the inter-relational mechanisms between them are still unclear. This study aimed to explore the shared gene effects and potential immune mechanisms in IgAN and IBD.<br><br>Methods: The microarray data of IgAN and IBD in the Gene Expression Omnibus (GEO) database were downloaded. The differential expression analysis was used to identify the shared differentially expressed genes (SDEGs). Besides, the shared transcription factors (TFs) and microRNAs (miRNAs) in IgAN and IBD were screened using humanTFDB, HMDD, ENCODE, JASPAR, and ChEA databases. Moreover, weighted gene co-expression network analysis (WGCNA) was used to identify the shared immune-related genes (SIRGs) related to IgAN and IBD, and R software package org.hs.eg.db (Version3.1.0) were used to identify common immune pathways in IgAN and IBD.<br><br>Results: In this study, 64 SDEGs and 28 SIRGs were identified, and the area under the receiver operating characteristic curve (ROC) of 64 SDEGs was calculated and two genes (MVP, PDXK) with high area under the curve (AUC) in both IgAN and IBD were screened out as potential diagnostic biomarkers. We then screened 3 shared TFs (SRY, MEF2D and SREBF1) and 3 miRNAs (hsa-miR-146, hsa-miR-21 and hsa-miR-320), and further found that the immune pathways of 64SDEGs, 28SIRGs and 3miRNAs were mainly including B cell receptor signaling pathway, FcγR-mediated phagocytosis, IL-17 signaling pathway, toll-like receptor signaling pathway, TNF signaling pathway, TRP channels, T cell receptor signaling pathway, Th17 cell differentiation, and cytokine-cytokine receptor interaction.<br><br>Conclusion: Our work revealed the differentiation of Th17 cells may mediate the abnormal humoral immunity in IgAN and IBD patients and identified novel gene candidates that could be used as biomarkers or potential therapeutic targets.}, }
@article {pmid35768458, year = {2022}, author = {Catania, T and Li, Y and Winzer, T and Harvey, D and Meade, F and Caridi, A and Leech, A and Larson, TR and Ning, Z and Chang, J and Van de Peer, Y and Graham, IA}, title = {Author Correction: A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3755}, doi = {10.1038/s41467-022-31568-x}, pmid = {35768458}, issn = {2041-1723}, }
@article {pmid35768269, year = {2022}, author = {Yin, H and Huang, J and Hu, M}, title = {Moderate-Intensity Exercise Improves Endothelial Function by Altering Gut Microbiome Composition in Rats Fed a High-Fat Diet.}, journal = {Journal of Nippon Medical School = Nippon Ika Daigaku zasshi}, volume = {89}, number = {3}, pages = {316-327}, doi = {10.1272/jnms.JNMS.2022_89-307}, pmid = {35768269}, issn = {1347-3409}, abstract = {BACKGROUND: Obesity changes gut microbial ecology and is related to endothelial dysfunction. Although the correlation between gut microbial ecology and endothelial dysfunction has been studied in obese persons, the underlying mechanisms by which exercise enhances endothelial function in this group remain unclear. This study investigated whether exercise improves endothelial function and alters gut microbiome composition in rats fed a high-fat diet (HFD).<br><br>METHODS: Obesity was induced by an HFD for 11 weeks. Whole-body composition and endothelium-dependent relaxation of mesenteric arteries were measured. Blood biochemical tests were performed, and gut microbiomes were characterized by 16S rRNA gene sequencing on an Illumina HiSeq platform.<br><br>RESULTS: Exercise training for 8 weeks improved body composition in HFD-fed rats. Furthermore, compared with the untrained/HFD group, aerobic exercise significantly increased acetylcholine-induced, endothelium-dependent relaxation in mesenteric arteries (P < 0.05) and circulating vascular endothelial growth factor levels (P < 0.01) and decreased circulating C-reactive protein levels (P < 0.05). In addition, exercise and HFD resulted in alterations in the composition of the gut microbiome; exercise reduced the relative abundance of Clostridiales and Romboutsia. Moreover, 12 species of bacteria, including Romboutsia, were significantly associated with parameters of endothelial function in the overall sample.<br><br>CONCLUSIONS: These results suggest that aerobic exercise enhances endothelial function in HFD-fed rats by altering the composition of the gut microbiota. These findings provide new insights on the application of physical exercise for improving endothelial function in obese persons.}, }
@article {pmid35764676, year = {2022}, author = {Van den Wyngaert, S and Ganzert, L and Seto, K and Rojas-Jimenez, K and Agha, R and Berger, SA and Woodhouse, J and Padisak, J and Wurzbacher, C and Kagami, M and Grossart, HP}, title = {Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {35764676}, issn = {1751-7370}, support = {WY175/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; AG 284/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; WU 890/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GR1540/30-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Zoosporic fungi of the phylum Chytridiomycota (chytrids) regularly dominate pelagic fungal communities in freshwater and marine environments. Their lifestyles range from obligate parasites to saprophytes. Yet, linking the scarce available sequence data to specific ecological traits or their host ranges constitutes currently a major challenge. We combined 28 S rRNA gene amplicon sequencing with targeted isolation and sequencing approaches, along with cross-infection assays and analysis of chytrid infection prevalence to obtain new insights into chytrid diversity, ecology, and seasonal dynamics in a temperate lake. Parasitic phytoplankton-chytrid and saprotrophic pollen-chytrid interactions made up the majority of zoosporic fungal reads. We explicitly demonstrate the recurrent dominance of parasitic chytrids during frequent diatom blooms and saprotrophic chytrids during pollen rains. Distinct temporal dynamics of diatom-specific parasitic clades suggest mechanisms of coexistence based on niche differentiation and competitive strategies. The molecular and ecological information on chytrids generated in this study will aid further exploration of their spatial and temporal distribution patterns worldwide. To fully exploit the power of environmental sequencing for studies on chytrid ecology and evolution, we emphasize the need to intensify current isolation efforts of chytrids and integrate taxonomic and autecological data into long-term studies and experiments.}, }
@article {pmid35762794, year = {2022}, author = {Roguet, A and Newton, RJ and Eren, AM and McLellan, SL}, title = {Guts of the Urban Ecosystem: Microbial Ecology of Sewer Infrastructure.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0011822}, doi = {10.1128/msystems.00118-22}, pmid = {35762794}, issn = {2379-5077}, abstract = {Microbes have inhabited the oceans and soils for millions of years and are uniquely adapted to their habitat. In contrast, sewer infrastructure in modern cities dates back only ~150 years. Sewer pipes transport human waste and provide a view into public health, but the resident organisms that likely modulate these features are relatively unexplored. Here, we show that the bacterial assemblages sequenced from untreated wastewater in 71 U.S. cities were highly coherent at a fine sequence level, suggesting that urban infrastructure separated by great spatial distances can give rise to strikingly similar communities. Within the overall microbial community structure, temperature had a discernible impact on the distribution patterns of closely related amplicon sequence variants, resulting in warm and cold ecotypes. Two bacterial genera were dominant in most cities regardless of their size or geographic location; on average, Arcobacter accounted for 11% and Acinetobacter 10% of the entire community. Metagenomic analysis of six cities revealed these highly abundant resident organisms carry clinically important antibiotic resistant genes blaCTX-M, blaOXA, and blaTEM. In contrast, human fecal bacteria account for only ~13% of the community; therefore, antibiotic resistance gene inputs from human sources to the sewer system could be comparatively small, which will impact measurement capabilities when monitoring human populations using wastewater. With growing awareness of the metabolic potential of microbes within these vast networks of pipes and the ability to examine the health of human populations, it is timely to increase our understanding of the ecology of these systems. IMPORTANCE Sewer infrastructure is a relatively new habitat comprised of thousands of kilometers of pipes beneath cities. These wastewater conveyance systems contain large reservoirs of microbial biomass with a wide range of metabolic potential and are significant reservoirs of antibiotic resistant organisms; however, we lack an adequate understanding of the ecology or activity of these communities beyond wastewater treatment plants. The striking coherence of the sewer microbiome across the United States demonstrates that the sewer environment is highly selective for a particular microbial community composition. Therefore, results from more in-depth studies or proven engineering controls in one system could be extrapolated more broadly. Understanding the complex ecology of sewer infrastructure is critical for not only improving our ability to treat human waste and increasing the sustainability of our cities but also to create scalable and effective sewage microbial observatories, which are inevitable investments of the future to monitor health in human populations.}, }
@article {pmid35761925, year = {2022}, author = {Modin, O and Fuad, N and Abadikhah, M and I'Ons, D and Ossiansson, E and Gustavsson, DJI and Edefell, E and Suarez, C and Persson, F and Wilén, BM}, title = {A relationship between phages and organic carbon in wastewater treatment plant effluents.}, journal = {Water research X}, volume = {16}, number = {}, pages = {100146}, doi = {10.1016/j.wroa.2022.100146}, pmid = {35761925}, issn = {2589-9147}, abstract = {With stringent effluent requirements and the implementation of new processes for micropollutant removal, it is increasingly important for wastewater treatment plants (WWTPs) to understand the factors affecting effluent quality. Phages (viruses infecting prokaryotes) are abundant in the biological treatment processes. They can contribute to organic carbon in the treated effluent both because they are organic in nature and occur in the effluent and because they cause lysis of microorganisms. Today very little is known about the effects of phages on effluent quality. The goal of this study was, therefore, to determine the relationship between phages and organic carbon in WWTP effluents. We also examined the diversity, taxonomy, and host-association of DNA phages using metagenomics. Effluent samples were collected from four WWTPs treating municipal wastewater. Significant differences in both organic carbon and virus-like particle concentrations were observed between the plants and there was a linear relationship between the two parameters. The phage communities were diverse with many members being taxonomically unclassified. Putative hosts were dominated by bacteria known to be abundant in activated sludge systems such as Comamonadaceae. The composition of phages differed between the WWTPs, suggesting that local conditions shape the communities. Overall, our findings suggest that the abundance and composition of phages are related to effluent quality. Thus, there is a need for further research clarifying the association between phage dynamics and WWTP function.}, }
@article {pmid35761577, year = {2022}, author = {Kothe, CI and Mohellibi, N and Renault, P}, title = {Revealing the microbial heritage of traditional Brazilian cheeses through metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {157}, number = {}, pages = {111265}, doi = {10.1016/j.foodres.2022.111265}, pmid = {35761577}, issn = {1873-7145}, abstract = {Brazilian artisanal cheeses date from the first Portuguese settlers and evolved via local factors, resulting in unique products that are now part of the patrimony and identity of different Brazilian regions. In this study, we combined several culture-independent approaches, including 16S/ITS metagenetics, assembly- and deep profiling-metagenomics to characterize the originality of the microbiota of five varieties of Brazilian artisanal cheeses from the South and Southeast regions of Brazil. Their core microbiota contained mainly lactic acid bacteria (LAB), of which Lactococcus lactis subsp. lactis was the most frequent, followed by Streptococcus thermophilus in the South region. Moreover, several samples from the Southeast region contained, as dominant LAB, two other food Streptococci belonging to a new species of the salivarius group and S. infantarius. Rinds of samples from the Southeast region were dominated by the halotolerant bacterium Corynebacterium variabile, and the yeasts Diutina catenulata, followed by Debaryomyces hansenii and Kodamaea ohmeri. Rinds from the South region contained mainly LAB due to their short ripening time, and the predominant yeast was D. hansenii. Phylogenomic analysis based on L. lactis metagenome-assembled genomes (MAGs) showed that most Brazilian strains are closely related and form a different clade from those whose genomes are available at this time, indicating that they belong to a specific group. Lastly, functional analysis showed that S. infantarius acquired a ∼ 26 kb DNA fragment from S. thermophilus starter strains that carry the LacSZ system, allowing fast lactose assimilation, an adaptation advantage for growth in milk. Finally, our study identified several areas of concern, such as the presence of somatic cell DNA and high levels of antibiotic resistance genes in several cheese microbiota, suggesting that milk from diseased animals may still be used occasionally. Overall, the data from this study highlight the potential value of the traditional and artisanal cheese production network in Brazil, and provide a metagenomic-based scheme to help manage this resource safely.}, }
@article {pmid35761554, year = {2022}, author = {Sequino, G and Valentino, V and Villani, F and De Filippis, F}, title = {Omics-based monitoring of microbial dynamics across the food chain for the improvement of food safety and quality.}, journal = {Food research international (Ottawa, Ont.)}, volume = {157}, number = {}, pages = {111242}, doi = {10.1016/j.foodres.2022.111242}, pmid = {35761554}, issn = {1873-7145}, abstract = {The diffusion of high-throughput sequencing has dramatically changed the study of food microbial ecology. Amplicon-based description of the microbial community may be routinary implemented in the food industry to understand how the processing parameters and the raw material quality may affect the microbial community of the final product, as well as how the community changes during the shelf-life. In addition, application of shotgun metagenomics may represent an invaluable resource to understand the functional potential of the microbial community, identifying the presence of spoilage-associated activities or genes related to pathogenesis. Finally, retrieving Metagenome-Assembled Genomes (MAGs) of relevant species may be useful for strain-tracking along the food chain and in case of food poisoning outbreaks. This review gives an overview of the possible applications of sequencing-based approaches in the study of food microbial ecology, highlighting limitations that still prevent the spreading of these techniques to the food industry.}, }
@article {pmid35761415, year = {2022}, author = {Liu, Y and Yang, M and Tang, L and Wang, F and Huang, S and Liu, S and Lei, Y and Wang, S and Xie, Z and Wang, W and Zhao, X and Tang, B and Yang, S}, title = {TLR4 regulates RORγt+ regulatory T-cell responses and susceptibility to colon inflammation through interaction with Akkermansia muciniphila.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {98}, pmid = {35761415}, issn = {2049-2618}, abstract = {BACKGROUND: Well-balanced interactions between gut microbiota and the immune system are essential to prevent chronic intestinal inflammation, as observed in inflammatory bowel diseases (IBD). Toll-like receptor 4 (TLR4) functions as a sensor mediating the crosstalk between the intestinal commensal microbiome and host immunity, but the influence of TLR4 on the shaping of intestinal microbiota and immune responses during colon inflammation remains poorly characterized. We investigated whether the different susceptibilities to colitis between wild-type (WT) and TLR4-/- mice were gut microbiota-dependent and aimed to identify the potential immunity modulation mechanism.<br><br>METHODS: We performed antibiotic depletion of the microbiota, cohousing experiments, and faecal microbiota transplantation (FMT) in WT and TLR4-/- mice to assess the influence of TLR4 on intestinal microbial ecology. 16S rRNA sequencing was performed to dissect microbial discrepancies, and dysbiosis-associated immune perturbation was investigated by flow cytometry. Akkermansia muciniphila (A. muciniphila)-mediated immune modulation was confirmed through the T-cell transfer colitis model and bone marrow chimaera construction.<br><br>RESULTS: TLR4-/- mice experienced enhanced susceptibility to DSS-induced colitis. 16S rRNA sequencing showed notable discrepancy in the gut microbiota between WT and TLR4-/- mice. In particular, A. muciniphila contributed most to distinguishing the two groups. The T-cell transfer colitis model and bone marrow transplantation (BMT) consistently demonstrated that A. muciniphila ameliorated colitis by upregulating RORγt+ Treg cell-mediated immune responses. Mucosal biopsies from human manifested parallel outcomes with colon tissue from WT mice, as evidenced by the positive correlation between TLR4 expression and intestinal A. muciniphila colonization during homeostasis.<br><br>CONCLUSIONS: Our results demonstrate a novel protective role of TLR4 against intestinal inflammation, wherein it can modulate A. muciniphila-associated immune responses. These findings provide a new perspective on host-commensal symbiosis, which may be beneficial for developing potential therapeutic strategies. Video abstract.}, }
@article {pmid35760840, year = {2022}, author = {Piel, D and Bruto, M and Labreuche, Y and Blanquart, F and Goudenège, D and Barcia-Cruz, R and Chenivesse, S and Le Panse, S and James, A and Dubert, J and Petton, B and Lieberman, E and Wegner, KM and Hussain, FA and Kauffman, KM and Polz, MF and Bikard, D and Gandon, S and Rocha, EPC and Le Roux, F}, title = {Phage-host coevolution in natural populations.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {35760840}, issn = {2058-5276}, support = {LIFE ID 572792//Donald R. and Esther Simon Foundation/ ; 884988//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; AANR-16-CE32-0008-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-20-CE35-0014//Agence Nationale de la Recherche (French National Research Agency)/ ; }, abstract = {Coevolution between bacteriophages (phages) and their bacterial hosts occurs through changes in resistance and counter-resistance mechanisms. To assess phage-host evolution in wild populations, we isolated 195 Vibrio crassostreae strains and 243 vibriophages during a 5-month time series from an oyster farm and combined these isolates with existing V. crassostreae and phage isolates. Cross-infection studies of 81,926 host-phage pairs delineated a modular network where phages are best at infecting co-occurring hosts, indicating local adaptation. Successful propagation of phage is restricted by the ability to adsorb to closely related bacteria and further constrained by strain-specific defence systems. These defences are highly diverse and predominantly located on mobile genetic elements, and multiple defences are active within a single genome. We further show that epigenetic and genomic modifications enable phage to adapt to bacterial defences and alter host range. Our findings reveal that the evolution of bacterial defences and phage counter-defences is underpinned by frequent genetic exchanges with, and between, mobile genetic elements.}, }
@article {pmid35754723, year = {2022}, author = {Waring, B and Gee, A and Liang, G and Adkins, S}, title = {A quantitative analysis of microbial community structure-function relationships in plant litter decay.}, journal = {iScience}, volume = {25}, number = {7}, pages = {104523}, doi = {10.1016/j.isci.2022.104523}, pmid = {35754723}, issn = {2589-0042}, abstract = {Soil microbes play a central role in ecosystem element cycling. Yet a central question in microbial ecology remains unanswered: to what extent does the taxonomic composition of soil microbial communities mediate biogeochemical process rates? In this quantitative review, we explore the mechanisms that lead to variation in the strength of microbial community structure-function relationships over space and time. To evaluate these mechanisms, we conduct a meta-analysis of studies that have monitored the decomposition of sterilized plant litter inoculated with different microbial assemblages. We find that the influence of microbial community composition on litter decay is pervasive and strong, rivalling in magnitude the influence of litter chemistry on decomposition. However, no single environmental or experimental attribute was correlated with variation in the inoculum effect. These results emphasize the need to better understand ecological dynamics within microbial communities, particularly emergent features such as cross-feeding networks, to improve predictions of soil biogeochemical function.}, }
@article {pmid35753302, year = {2022}, author = {Zhang, K and Hu, J and Yang, S and Xu, W and Wang, Z and Zhuang, P and Grossart, HP and Luo, Z}, title = {Biodegradation of polyester polyurethane by the marine fungus Cladosporium halotolerans 6UPA1.}, journal = {Journal of hazardous materials}, volume = {437}, number = {}, pages = {129406}, doi = {10.1016/j.jhazmat.2022.129406}, pmid = {35753302}, issn = {1873-3336}, abstract = {Lack of degradability and the accumulation of polymeric wastes increase the risk for the health of the environment. Recently, recycling of polymeric waste materials becomes increasingly important as raw materials for polymer synthesis are in short supply due to the rise in price and supply chain disruptions. As an important polymer, polyurethane (PU) is widely used in modern life, therefore, PU biodegradation is desirable to avoid its accumulation in the environment. In this study, we isolated a fungal strain Cladosporium halotolerans from the deep sea which can grow in mineral medium with a polyester PU (Impranil DLN) as a sole carbon source. Further, we demonstrate that it can degrade up to 80% of Impranil PU after 3 days of incubation at 28 ℃ by breaking the carbonyl groups (1732 cm-1) and C-N-H bonds (1532 cm-1 and 1247 cm-1) as confirmed by Fourier-transform infrared (FTIR) spectroscopy analysis. Gas chromatography-mass spectrometry (GC-MS) analysis revealed polyols and alkanes as PU degradation intermediates, indicating the hydrolysis of ester and urethane bonds. Esterase and urease activities were detected in 7 days-old cultures with PU as a carbon source. Transcriptome analysis showed a number of extracellular protein genes coding for enzymes such as cutinase, lipase, peroxidase and hydrophobic surface binding proteins A (HsbA) were expressed when cultivated on Impranil PU. The yeast two-hybrid assay revealed that the hydrophobic surface binding protein ChHsbA1 directly interacts with inducible esterases, ChLip1 (lipase) and ChCut1 (cutinase). Further, the KEGG pathway for "fatty acid degradation" was significantly enriched in Impranil PU inducible genes, indicating that the fungus may use the degradation intermediates to generate energy via this pathway. Taken together, our data indicates secretion of both esterase and hydrophobic surface binding proteins by C. halotolerans plays an important role in Impranil PU absorption and subsequent degradation. Our study provides a mechanistic insight into Impranil PU biodegradation by deep sea fungi and provides the basis for future development of biotechnological PU recycling.}, }
@article {pmid35752808, year = {2022}, author = {Wang, Q and Chen, Y and Yang, Q and Zhao, J and Feng, L and Wang, M}, title = {SR5AL serves as a key regulatory gene in lycopene biosynthesis by Blakeslea trispora.}, journal = {Microbial cell factories}, volume = {21}, number = {1}, pages = {126}, pmid = {35752808}, issn = {1475-2859}, support = {21A180014//Key Scientific Research Project of Colleges and Universities in Henan Province/ ; 212102110322//Science and Technology Department of Henan Province/ ; }, abstract = {BACKGROUND: Trisporic acids are considered to be key regulators of carotenoid biosynthesis and sexual reproduction in zygomycetes, but the mechanisms underlying this regulation have not been fully elucidated.<br><br>RESULTS: In this study, the relationships between trisporic acids and lycopene synthesis were investigated in Blakeslea trispora. The lycopene concentration in single fermentation by the (-) strain with the addition of 24 μg/L trisporic acids was slightly higher than that observed in mated fermentation. After transcriptomic analysis, a steroid 5α-reductase-like gene, known as SR5AL in B. trispora, was first reported. 5α-Reductase inhibitors reduced lycopene biosynthesis and downregulated the expression of sex determination and carotenoid biosynthesis genes. Overexpression of the SR5AL gene upregulated these genes, regardless of whether trisporic acids were added.<br><br>CONCLUSION: These findings indicated that the SR5AL gene is a key gene associated with the response to trisporic acids.}, }
@article {pmid35752802, year = {2022}, author = {Darcy, JL and Amend, AS and Swift, SOI and Sommers, PS and Lozupone, CA}, title = {specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {34}, pmid = {35752802}, issn = {2524-6372}, support = {5 T15 LM009451-12/NH/NIH HHS/United States ; 1255972//National Science Foundation/ ; }, abstract = {BACKGROUND: Understanding the factors that influence microbes' environmental distributions is important for determining drivers of microbial community composition. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogeny. In microbial ecology, "specificity" is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Rao's (Theor Popul Biol, 1982. https://doi.org/10.1016/0040-5809(82)90004-1, Sankhya A, 2010. https://doi.org/10.1007/s13171-010-0016-3) Quadratic Entropy can be conveniently applied to calculate specificity of a feature, such as a species, to many different environmental variables.<br><br>RESULTS: We present our R package specificity for performing the above analyses, and apply it to four real-life microbial data sets to demonstrate its application. We found that many fungi within the leaves of native Hawaiian plants had strong specificity to rainfall and elevation, even though these variables showed minimal importance in a previous analysis of fungal beta-diversity. In Antarctic cryoconite holes, our tool revealed that many bacteria have specificity to co-occurring algal community composition. Similarly, in the human gut microbiome, many bacteria showed specificity to the composition of bile acids. Finally, our analysis of the Earth Microbiome Project data set showed that most bacteria show strong ontological specificity to sample type. Our software performed as expected on synthetic data as well.<br><br>CONCLUSIONS: specificity is well-suited to analysis of microbiome data, both in synthetic test cases, and across multiple environment types and experimental designs. The analysis and software we present here can reveal patterns in microbial taxa that may not be evident from a community-level perspective. These insights can also be visualized and interactively shared among researchers using specificity's companion package, specificity.shiny.}, }
@article {pmid35752717, year = {2022}, author = {Leung, PM and Daebeler, A and Chiri, E and Hanchapola, I and Gillett, DL and Schittenhelm, RB and Daims, H and Greening, C}, title = {A nitrite-oxidising bacterium constitutively consumes atmospheric hydrogen.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {35752717}, issn = {1751-7370}, support = {P30570-B29//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; T938//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P2EZP3_178421//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; }, abstract = {Chemolithoautotrophic nitrite-oxidising bacteria (NOB) of the genus Nitrospira contribute to nitrification in diverse natural environments and engineered systems. Nitrospira are thought to be well-adapted to substrate limitation owing to their high affinity for nitrite and capacity to use alternative energy sources. Here, we demonstrate that the canonical nitrite oxidiser Nitrospira moscoviensis oxidises hydrogen (H2) below atmospheric levels using a high-affinity group 2a nickel-iron hydrogenase [Km(app) = 32 nM]. Atmospheric H2 oxidation occurred under both nitrite-replete and nitrite-deplete conditions, suggesting low-potential electrons derived from H2 oxidation promote nitrite-dependent growth and enable survival during nitrite limitation. Proteomic analyses confirmed the hydrogenase was abundant under both conditions and indicated extensive metabolic changes occur to reduce energy expenditure and growth under nitrite-deplete conditions. Thermodynamic modelling revealed that H2 oxidation theoretically generates higher power yield than nitrite oxidation at low substrate concentrations and significantly contributes to growth at elevated nitrite concentrations. Collectively, this study suggests atmospheric H2 oxidation enhances the growth and survival of NOB amid variability of nitrite supply, extends the phenomenon of atmospheric H2 oxidation to an eighth phylum (Nitrospirota), and reveals unexpected new links between the global hydrogen and nitrogen cycles. Long classified as obligate nitrite oxidisers, our findings suggest H2 may primarily support growth and survival of certain NOB in natural environments.}, }
@article {pmid35751580, year = {2022}, author = {Akritidou, T and Smet, C and Akkermans, S and Tonti, M and Williams, J and Van de Wiele, T and Van Impe, JFM}, title = {A protocol for the cultivation and monitoring of ileal gut microbiota surrogates.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.15684}, pmid = {35751580}, issn = {1365-2672}, abstract = {AIMS: This research aimed to develop and validate a cultivation and monitoring protocol that is suitable for a surrogate microbial community that accounts for the gut microbiota of the ileum of the small intestine.<br><br>METHODS AND RESULTS: Five bacterial species have been selected as representatives of the ileal gut microbiota and a general anaerobic medium (MS-BHI, as minimally supplemented BHI) has been constructed and validated against BCCM/LGM recommended and commercial media. Moreover, appropriate selective/differential media have been investigated for monitoring each ileal gut microbiota surrogate. Results showed that MS-BHI was highly efficient in displaying individual and collective behavior of the ileal gut microbiota species, when compared with other types of media. Likewise, the selective/differential media managed to identify and describe the behavior of their targeted species.<br><br>CONCLUSIONS: MS-BHI renders a highly efficient, inexpensive and easy-to-prepare cultivation and enumeration alternative for the surrogate ileal microbiota species. Additionally, the selective/differential media can identify and quantify the bacteria of the surrogate ileal microbial community.<br><br>The selected gut microbiota species can represent an in vitro ileal community, forming the basis for future studies on small intestinal microbiota. MS-BHI and the proposed monitoring protocol can be used as a standard for gut microbiota studies that utilize conventional microbiological techniques.}, }
@article {pmid35751418, year = {2022}, author = {Jeon, JS and Rybka, D and Carreno-Quintero, N and De Vos, R and Raaijmakers, JM and Etalo, DW}, title = {Metabolic signatures of rhizobacteria-induced plant growth promotion.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.14385}, pmid = {35751418}, issn = {1365-3040}, abstract = {Various root-colonizing bacterial species can promote plant growth and trigger systemic resistance against aboveground leaf pathogens and herbivore insects. To date, the underlying metabolic signatures of these rhizobacteria-induced plant phenotypes are poorly understood. To identify core metabolic pathways that are targeted by growth-promoting rhizobacteria, we used combinations of three plant species and three rhizobacterial species and interrogated plant shoot chemistry by untargeted metabolomics. A substantial part (50-64%) of the metabolites detected in plant shoot tissue was differentially affected by the rhizobacteria. Among others, the phenylpropanoid pathway was targeted by the rhizobacteria in each of the three plant species. Differential regulation of the various branches of the phenylpropanoid pathways showed an association with either plant growth promotion or growth reduction. Overall, suppression of flavonoid biosynthesis was associated with growth promotion, while growth reduction showed elevated levels of flavonoids. Subsequent assays with twelve Arabidopsis flavonoid biosynthetic mutants revealed that the proanthocyanidin branch plays an essential role in rhizobacteria-mediated growth promotion. Our study also showed that a number of pharmaceutically and nutritionally relevant metabolites in the plant shoot were significantly increased by rhizobacterial treatment, providing new avenues to use rhizobacteria to tilt plant metabolism towards the biosynthesis of valuable natural plant products. This article is protected by copyright. All rights reserved.}, }
@article {pmid35750182, year = {2022}, author = {Mishra, S and Wang, W and Xia, S and Lin, L and Yang, X}, title = {Spatial pattern of functional genes abundance reveals the importance of PhoD gene harboring bacterial community for maintaining plant growth in the tropical forest of Southwestern China.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {156863}, doi = {10.1016/j.scitotenv.2022.156863}, pmid = {35750182}, issn = {1879-1026}, abstract = {The concept of microbial functional genes has added a new dimension in microbial ecology research by improving the model of microbial community-ecosystem functions relationship. However, our knowledge vis-à-vis fine-scale spatial distribution pattern of functional genes and their probable impact on plant community in the hyper-diverse tropical forest ecosystem is very limited. Here, we investigated the spatial pattern of functional genes abundance (NirK, AOA, AOB, and PhoD), identified key influencing factors, and distinguished the key functional group supporting the plant community in a tropical rainforest located in Xishuangbanna. Total 200 soil samples and vegetation data of ~4800 individuals of plants across a 1 ha study area were collected. Our results detected higher spatial variability with a maximum magnitude of abundance for PhoD gene (4.53 × 107 copies) followed by NirK (2.71 × 106 copies), AOA (1.97 × 106 copies), and AOB (7.38 × 104 copies). A strong spatial dependence was observed for PhoD and NirK over the distance of 17 and 18 m, respectively. Interestingly, the N:P stoichiometry played a critical role in structuring the spatial pattern of the most abundant PhoD gene. The significant positive and negative relationship of PhoD with N:P ratio and available phosphorus, respectively, indicated that the P-limiting environment was a driving factor for recruitment of PhoD gene community. The structural equation modeling ascertained the direct positive impact of PhoD on plant biomass and high demand of available P by plants suggesting that the organic phosphorus mineralization process is essential to maintain plant productivity by re-establishing the availability of the most limiting P nutrient. Our preliminary study improves our understanding of how microbial functional genes-environment associations could be used for monitoring soil health and its overall impact on ecosystem multifunctionality. Finally, we intend to conduct the study at a large spatial scale for achieving a holistic view.}, }
@article {pmid35749983, year = {2022}, author = {Chavez-Rico, VS and Bodelier, PLE and van Eekert, M and Sechi, V and Veeken, A and Buisman, C}, title = {Producing organic amendments: Physicochemical changes in biowaste used in anaerobic digestion, composting, and fermentation.}, journal = {Waste management (New York, N.Y.)}, volume = {149}, number = {}, pages = {177-185}, doi = {10.1016/j.wasman.2022.06.005}, pmid = {35749983}, issn = {1879-2456}, abstract = {Organic amendments (OAs) produced via composting, anaerobic digestion, or lactic acid fermentation, can be used to replenish soil carbon. Not all OAs production technologies preserve C and nutrients in the same way. In this study, we compared the influence of these technologies (i.e., treatments) on C and nutrient preservation and OAs chemical composition after production. We produced compost, digestate, and lactic-acid fermentation product using the same biowaste-resembling model substrate using three reactors under laboratory conditions. We compared the chemical conversions and end-products using mass balances over C, N, and P. Overall results show that losses are minimal under reducing production conditions. Fermentation and digestion conserved 99% and 64% of C; and 93% and 100% of N, respectively. While compost conservation of nutrients was limited to 25% of C and 38% of N. Digestate had the highest concentrations of C, N, and P in the water-soluble phase, enabling their accessibility for soil microbes. Concentrations in the fermentation product were one order of magnitude lower but still higher than in compost. The treatments also influence the final availability of C, N, and P, which could potentially improve the fertilising and soil-improving properties of produced OAs. Our results show that under reducing conditions, losses of C, N, and P can be decreased while increasing OAs applications in terms of sources for soil-microbial development.}, }
@article {pmid35749381, year = {2022}, author = {Favila, N and Madrigal-Trejo, D and Legorreta, D and Sánchez-Pérez, J and Espinosa-Asuar, L and Eguiarte, LE and Souza, V}, title = {MicNet toolbox: Visualizing and unraveling a microbial network.}, journal = {PloS one}, volume = {17}, number = {6}, pages = {e0259756}, doi = {10.1371/journal.pone.0259756}, pmid = {35749381}, issn = {1932-6203}, abstract = {Applications of network theory to microbial ecology are an emerging and promising approach to understanding both global and local patterns in the structure and interplay of these microbial communities. In this paper, we present an open-source python toolbox which consists of two modules: on one hand, we introduce a visualization module that incorporates the use of UMAP, a dimensionality reduction technique that focuses on local patterns, and HDBSCAN, a clustering technique based on density; on the other hand, we have included a module that runs an enhanced version of the SparCC code, sustaining larger datasets than before, and we couple the resulting networks with network theory analyses to describe the resulting co-occurrence networks, including several novel analyses, such as structural balance metrics and a proposal to discover the underlying topology of a co-occurrence network. We validated the proposed toolbox on 1) a simple and well described biological network of kombucha, consisting of 48 ASVs, and 2) we validate the improvements of our new version of SparCC. Finally, we showcase the use of the MicNet toolbox on a large dataset from Archean Domes, consisting of more than 2,000 ASVs. Our toolbox is freely available as a github repository (https://github.com/Labevo/MicNetToolbox), and it is accompanied by a web dashboard (http://micnetapplb-1212130533.us-east-1.elb.amazonaws.com) that can be used in a simple and straightforward manner with relative abundance data. This easy-to-use implementation is aimed to microbial ecologists with little to no experience in programming, while the most experienced bioinformatics will also be able to manipulate the source code's functions with ease.}, }
@article {pmid35746816, year = {2022}, author = {Aguirre Sourrouille, Z and Schwarzer, S and Lequime, S and Oksanen, HM and Quax, TEF}, title = {The Viral Susceptibility of the Haloferax Species.}, journal = {Viruses}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/v14061344}, pmid = {35746816}, issn = {1999-4915}, support = {411069969//Deutsche Forschungsgemeinschaft/ ; Hector Fellow Academy//Hector-Stiftung/ ; FINStruct and Instruct-FI, part of Biocenter Finland and Instruct-ERIC, respectively.//Academy of Finland/ ; }, abstract = {Viruses can infect members of all three domains of life. However, little is known about viruses infecting archaea and the mechanisms that determine their host interactions are poorly understood. Investigations of molecular mechanisms of viral infection rely on genetically accessible virus-host model systems. Euryarchaea belonging to the genus Haloferax are interesting models, as a reliable genetic system and versatile microscopy methods are available. However, only one virus infecting the Haloferax species is currently available. In this study, we tested ~100 haloarchaeal virus isolates for their infectivity on 14 Haloferax strains. From this, we identified 10 virus isolates in total capable of infecting Haloferax strains, which represented myovirus or siphovirus morphotypes. Surprisingly, the only susceptible strain of all 14 tested was Haloferax gibbonsii LR2-5, which serves as an auspicious host for all of these 10 viruses. By applying comparative genomics, we shed light on factors determining the host range of haloarchaeal viruses on Haloferax. We anticipate our study to be a starting point in the study of haloarchaeal virus-host interactions.}, }
@article {pmid35745275, year = {2022}, author = {Natividad, JM and Marsaux, B and Rodenas, CLG and Rytz, A and Vandevijver, G and Marzorati, M and Van den Abbeele, P and Calatayud, M and Rochat, F}, title = {Human Milk Oligosaccharides and Lactose Differentially Affect Infant Gut Microbiota and Intestinal Barrier In Vitro.}, journal = {Nutrients}, volume = {14}, number = {12}, pages = {}, doi = {10.3390/nu14122546}, pmid = {35745275}, issn = {2072-6643}, support = {NA//Nestlé Research, Société des Produits Nestlé/ ; 812969//European Union's Horizon 2020 research and innovation program/ ; }, abstract = {BACKGROUND: The infant gut microbiota establishes during a critical window of opportunity when metabolic and immune functions are highly susceptible to environmental changes, such as diet. Human milk oligosaccharides (HMOs) for instance are suggested to be beneficial for infant health and gut microbiota. Infant formulas supplemented with the HMOs 2'-fucosyllactose (2'-FL) and lacto-N-neotetraose (LNnT) reduce infant morbidity and medication use and promote beneficial bacteria in the infant gut ecosystem. To further improve infant formula and achieve closer proximity to human milk composition, more complex HMO mixtures could be added. However, we currently lack knowledge about their effects on infants' gut ecosystems.<br><br>METHOD: We assessed the effect of lactose, 2'-FL, 2'-FL + LNnT, and a mixture of six HMOs (HMO6: consisting of 2'-FL, LNnT, difucosyllactose, lacto-N-tetraose, 3'- and 6'-sialyllactose) on infant gut microbiota and intestinal barrier integrity using a combination of in vitro models to mimic the microbial ecosystem (baby M-SHIME®) and the intestinal epithelium (Caco-2/HT29-MTX co-culture).<br><br>RESULTS: All the tested products had bifidogenic potential and increased SCFA levels; however, only the HMOs' fermented media protected against inflammatory intestinal barrier disruption. 2'-FL/LNnT and HMO6 promoted the highest diversification of OTUs within the Bifidobactericeae family, whereas beneficial butyrate-producers were specifically enriched by HMO6.<br><br>CONCLUSION: These results suggest that increased complexity in HMO mixture composition may benefit the infant gut ecosystem, promoting different bifidobacterial communities and protecting the gut barrier against pro-inflammatory imbalances.}, }
@article {pmid35744740, year = {2022}, author = {Kozień, Ł and Gallienne, E and Martin, O and Front, S and Strus, M and Heczko, P}, title = {PDIA, an Iminosugar Compound with a Wide Biofilm Inhibitory Spectrum Covering Both Gram-Positive and Gram-Negative Human Bacterial Pathogens.}, journal = {Microorganisms}, volume = {10}, number = {6}, pages = {}, doi = {10.3390/microorganisms10061222}, pmid = {35744740}, issn = {2076-2607}, support = {2018/31/B/NZ6/02443//National Science Center/ ; N N401 547040//National Science Center/ ; }, abstract = {Many difficult-to-treat human infections related to catheters and other indwelling devices are caused by bacteria residing in biofilms. One of the key properties of microorganisms residing in a biofilm is decreased susceptibility towards antimicrobial agents. Therefore, many different approaches have been researched to destroy or inhibit biofilm production by bacteria. Different iminosugars (IS) were reported to inhibit biofilm formation in S. mutans, S. aureus, and P. aeruginosa. The aim of this study was to look for a spectrum of the activity in one of these IS. The iminosugar PDIA beta-1-C-propyl-1,4-dideoxy-1,4-imino-L-arabinitol was tested in vitro at the same concentration against 30 different strains of the most important Gram-negative and Gram-positive human pathogens looking for their biofilm production and viability at different time intervals. It appeared that PDIA inhibited biofilm production of Enterobacter spp., P. aeruginosa, Enterococcus spp. and S. aureus in 8 h, and Klebsiella spp., Acinetobacter spp. and S.epidermidis in 24 h. PDIA caused no growth inhibition of the tested bacteria at a concentration of 0.9 mM. Our results indicate a broad-spectrum biofilm inhibitory activity of PDIA. which may be the basis for future application studies that will help in control of the associated device and biofilm-related infections caused by a wide spectrum of the causative agents.}, }
@article {pmid35744736, year = {2022}, author = {Shi, Z and Kong, Q and Li, X and Xu, W and Mao, C and Wang, Y and Song, W and Huang, J}, title = {The Effects of DNA Extraction Kits and Primers on Prokaryotic and Eukaryotic Microbial Community in Freshwater Sediments.}, journal = {Microorganisms}, volume = {10}, number = {6}, pages = {}, doi = {10.3390/microorganisms10061213}, pmid = {35744736}, issn = {2076-2607}, support = {2018YFD0900701//the National Key Research and Development Program of China/ ; 31801984, 32030015//National Natural Science Foundation of China/ ; 2019333//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; }, abstract = {DNA based sequencing technology has revolutionized the field of microbial ecology and environmental studies. However, biases can be introduced at all experimental steps and, thus, affect the interpretation of microbial community. So far, previous studies on the biases introduced from the key steps of DNA extraction and primer sets mainly focused on the bacterial communities in soil or sediment samples, while little is known about the effect on the eukaryotic microbial communities. Here, we studied the effects of three different DNA extraction kits on both prokaryotic and micro-eukaryotic communities by 16S and 18S rRNA gene amplicon sequencing, and further disentangled the influence of primer choice on the micro-eukaryotic communities. Our results showed that the FastDNA SPIN Kit for Soil and DNeasy PowerSoil Kit produced much higher DNA yield with good reproducibility, and observed more eukaryotic OTUs compared to the MinkaGene DNA extraction kit, but all three kits exhibited comparable ability in recovering bacterial alpha diversity. Of the two primer sets, both targeting the V4 region of the 18S rRNA gene, the TAR primer set detected higher number of unique OTUs than the EK primer set, while the EK primer set resulted in longer amplicons and better reproducibility between replicates. Based on our findings, we recommend using the DNeasy PowerSoil Kit with the EK primer set to capture the abundant micro-eukaryotic taxa from freshwater sediment samples. If a more complete picture of the eukaryotic microbial community is desired, the TAR primer set in combination with the FastDNA SPIN Kit is more efficient in this study.}, }
@article {pmid35744686, year = {2022}, author = {Hossain, KS and Amarasena, S and Mayengbam, S}, title = {B Vitamins and Their Roles in Gut Health.}, journal = {Microorganisms}, volume = {10}, number = {6}, pages = {}, doi = {10.3390/microorganisms10061168}, pmid = {35744686}, issn = {2076-2607}, support = {Funding no. 20210719//Memorial University of Newfoundland/ ; }, abstract = {B vitamins act as coenzymes in a myriad of cellular reactions. These include energy production, methyl donor generation, neurotransmitter synthesis, and immune functions. Due to the ubiquitous roles of these vitamins, their deficiencies significantly affect the host's metabolism. Recently, novel roles of B vitamins in the homeostasis of gut microbial ecology and intestinal health continue to be unravelled. This review focuses on the functional roles and biosynthesis of B vitamins and how these vitamins influence the growth and proliferation of the gut microbiota. We have identified the gut bacteria that can produce vitamins, and their biosynthetic mechanisms are presented. The effects of B vitamin deficiencies on intestinal morphology, inflammation, and its effects on intestinal disorders are also discussed.}, }
@article {pmid35744611, year = {2022}, author = {Costa, OYA and de Hollander, M and Kuramae, EE and Bodelier, PLE}, title = {PhyloFunDB: A Pipeline to Create and Update Functional Gene Taxonomic Databases.}, journal = {Microorganisms}, volume = {10}, number = {6}, pages = {}, doi = {10.3390/microorganisms10061093}, pmid = {35744611}, issn = {2076-2607}, abstract = {The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a process that demands the processing of large amounts of data and use of several different software. Here, we present PhyloFunDB, a pipeline for extracting, processing, and inferring phylogenetic trees from specific functional genes. The goal of our work is to decrease processing time and facilitate the grouping of sequences that can be used for improved taxonomic classification of functional gene datasets.}, }
@article {pmid35741397, year = {2022}, author = {Micci, A and Zhang, Q and Chang, X and Kingsley, K and Park, L and Chiaranunt, P and Strickland, R and Velazquez, F and Lindert, S and Elmore, M and Vines, PL and Crane, S and Irizarry, I and Kowalski, KP and Johnston-Monje, D and White, JF}, title = {Histochemical Evidence for Nitrogen-Transfer Endosymbiosis in Non-Photosynthetic Cells of Leaves and Inflorescence Bracts of Angiosperms.}, journal = {Biology}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/biology11060876}, pmid = {35741397}, issn = {2079-7737}, abstract = {We used light and confocal microscopy to visualize bacteria in leaf and bract cells of more than 30 species in 18 families of seed plants. Through histochemical analysis, we detected hormones (including ethylene and nitric oxide), superoxide, and nitrogenous chemicals (including nitric oxide and nitrate) around bacteria within plant cells. Bacteria were observed in epidermal cells, various filamentous and glandular trichomes, and other non-photosynthetic cells. Most notably, bacteria showing nitrate formation based on histochemical staining were present in glandular trichomes of some dicots (e.g., Humulus lupulus and Cannabis sativa). Glandular trichome chemistry is hypothesized to function to scavenge oxygen around bacteria and reduce oxidative damage to intracellular bacterial cells. Experiments to assess the differential absorption of isotopic nitrogen into plants suggest the assimilation of nitrogen into actively growing tissues of plants, where bacteria are most active and carbohydrates are more available. The leaf and bract cell endosymbiosis types outlined in this paper have not been previously reported and may be important in facilitating plant growth, development, oxidative stress resistance, and nutrient absorption into plants. It is unknown whether leaf and bract cell endosymbioses are significant in increasing the nitrogen content of plants. From the experiments that we conducted, it is impossible to know whether plant trichomes evolved specifically as organs for nitrogen fixation or if, instead, trichomes are structures in which bacteria easily colonize and where some casual nitrogen transfer may occur between bacteria and plant cells. It is likely that the endosymbioses seen in leaves and bracts are less efficient than those of root nodules of legumes in similar plants. However, the presence of endosymbioses that yield nitrate in plants could confer a reduced need for soil nitrogen and constitute increased nitrogen-use efficiency, even if the actual amount of nitrogen transferred to plant cells is small. More research is needed to evaluate the importance of nitrogen transfer within leaf and bract cells of plants.}, }
@article {pmid35739682, year = {2022}, author = {Wang, C and Wang, L and Ok, YS and Tsang, DCW and Hou, D}, title = {Soil plastisphere: Exploration methods, influencing factors, and ecological insights.}, journal = {Journal of hazardous materials}, volume = {430}, number = {}, pages = {128503}, doi = {10.1016/j.jhazmat.2022.128503}, pmid = {35739682}, issn = {1873-3336}, abstract = {Microplastic (MP), an emerging contaminant, is globally prevalent and poses potential environmental threats and ecological risks to both aquatic and terrestrial ecosystems. When MPs enter into natural environments, they may serve as artificial substrates for microbial colonization and plastisphere formation, providing new ecological niches for microorganisms. Recent studies of the plastisphere have focused on aquatic ecosystems. However, our understanding of the soil plastisphere e.g. its formation process, microbial ecology, co-transport of organic pollutants and heavy metals, and effects on biogeochemical processes is still very limited. This review summarizes latest methods used to explore the soil plastisphere, assesses the factors influencing the microbial ecology of the soil plastisphere, and sheds light on potential ecological risks caused by the soil plastisphere. The formation and succession of soil plastisphere communities can be driven by MP characteristics and soil environmental factors. The soil plastisphere may affect a series of ecological processes, especially the co-transport of environmental contaminants, biodegradation of MPs, and soil carbon cycling. We aim to narrow the knowledge gap between the soil and aquatic plastisphere, and provide valuable guidance for future research on the soil plastisphere in MP-contaminated soils.}, }
@article {pmid35739580, year = {2022}, author = {Dey, S and Rout, AK and Behera, BK and Ghosh, K}, title = {Plastisphere community assemblage of aquatic environment: plastic-microbe interaction, role in degradation and characterization technologies.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {32}, pmid = {35739580}, issn = {2524-6372}, abstract = {It is undeniable that plastics are ubiquitous and a threat to global ecosystems. Plastic waste is transformed into microplastics (MPs) through physical and chemical disruption processes within the aquatic environment. MPs are detected in almost every environment due to their worldwide transportability through ocean currents or wind, which allows them to reach even the most remote regions of our planet. MPs colonized by biofilm-forming microbial communities are known as the ''plastisphere". The revelation that this unique substrate can aid microbial dispersal has piqued interest in the ground of microbial ecology. MPs have synergetic effects on the development, transportation, persistence, and ecology of microorganisms. This review summarizes the studies of plastisphere in recent years and the microbial community assemblage (viz. autotrophs, heterotrophs, predators, and pathogens). We also discussed plastic-microbe interactions and the potential sources of plastic degrading microorganisms. Finally, it also focuses on current technologies used to characterize those microbial inhabitants and recommendations for further research.}, }
@article {pmid35739325, year = {2022}, author = {Legeay, J and Hijri, M}, title = {A Comprehensive Insight of Current and Future Challenges in Large-Scale Soil Microbiome Analyses.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35739325}, issn = {1432-184X}, abstract = {In the last decade, various large-scale projects describing soil microbial diversity across large geographical gradients have been undertaken. However, many questions remain unanswered about the best ways to conduct these studies. In this review, we present an overview of the experience gathered during these projects, and of the challenges that future projects will face, such as standardization of protocols and results, considering the temporal variation of microbiomes, and the legal constraints limiting such studies. We also present the arguments for and against the exhaustive description of soil microbiomes. Finally, we look at future developments of soil microbiome studies, notably emphasizing the important role of cultivation techniques.}, }
@article {pmid35738377, year = {2022}, author = {Merino, N and Jackson, TR and Campbell, JH and Kersting, AB and Sackett, J and Fisher, JC and Bruckner, JC and Zavarin, M and Hamilton-Brehm, SD and Moser, DP}, title = {Subsurface microbial communities as a tool for characterizing regional-scale groundwater flow.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {156768}, doi = {10.1016/j.scitotenv.2022.156768}, pmid = {35738377}, issn = {1879-1026}, abstract = {Subsurface microbial community distribution patterns are influenced by biogeochemical and groundwater fluxes and may inform hydraulic connections along groundwater-flow paths. This study examined the regional-scale microbial community of the Death Valley Regional Flow System and evaluated whether subsurface communities can be used to identify groundwater-flow paths between recharge and discharge areas. Samples were collected from 36 sites in three groundwater basins: Pahute Mesa-Oasis Valley (PMOV), Ash Meadows (AM), and Alkali Flat-Furnace Creek Ranch (AFFCR). Microbial diversity within and between communities varied by location, and communities were separated into two overall groups that affiliated with the AM and PMOV/AFFCR basins. Network analysis revealed patterns between clusters of common microbes that represented groundwaters with similar geochemical conditions and largely corroborated hydraulic connections between recharge and discharge areas. Null model analyses identified deterministic and stochastic ecological processes contributing to microbial community assemblages. Most communities were more different than expected and governed by dispersal limitation, geochemical differences, or undominating processes. However, certain communities from sites located within or near the Nevada National Security Site were more similar than expected and dominated by homogeneous dispersal or selection. Overall, the (dis)similarities between the microbial communities of DVRFS recharge and discharge areas supported previously documented hydraulic connections between: (1) Spring Mountains and Ash Meadows; (2) Frenchman and Yucca Flat and Amargosa Desert; and (3) Amargosa Desert and Death Valley. However, only a portion of the flow path between Pahute Mesa and Oasis Valley could be supported by microbial community analyses, likely due to well-associated artifacts in samples from the two Oasis Valley sites. This study demonstrates the utility of combining microbial data with hydrologic, geologic, and water-chemistry information to comprehensively characterize groundwater systems, highlighting both strengths and limitations of this approach.}, }
@article {pmid35730934, year = {2022}, author = {Morris, MM and Kimbrel, JA and Geng, H and Tran-Gyamfi, MB and Yu, ET and Sale, KL and Lane, TW and Mayali, X}, title = {Bacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salina.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0023122}, doi = {10.1128/msphere.00231-22}, pmid = {35730934}, issn = {2379-5042}, abstract = {Outdoor cultivation of microalgae has promising potential for renewable bioenergy, but there is a knowledge gap on the structure and function of the algal microbiome that coinhabits these ecosystems. Here, we describe the assembly mechanisms, taxonomic structure, and metabolic potential of bacteria associated with Microchloropsis salina cultivated outdoors. Open mesocosms were inoculated with algal cultures that were either free of bacteria or coincubated with one of two different strains of alga-associated bacteria and were sampled across five time points taken over multiple harvesting rounds of a 40-day experiment. Using quantitative analyses of metagenome-assembled genomes (MAGs), we tracked bacterial community compositional abundance and taxon-specific functional capacity involved in algal-bacterial interactions. One of the inoculated bacteria (Alteromonas sp.) persisted and dispersed across mesocosms, whereas the other inoculated strain (Phaeobacter gallaeciensis) disappeared by day 17 while a taxonomically similar but functionally distinct Phaeobacter strain became established. The inoculated strains were less abundant than 6 numerically dominant newly recruited taxa with functional capacities for mutualistic or saprophytic lifestyles, suggesting a generalist approach to persistence. This includes a highly abundant unclassified Rhodobacteraceae species that fluctuated between 25% and 77% of the total community. Overall, we did not find evidence for priority effects exerted by the distinct inoculum conditions; all mesocosms converged with similar microbial community compositions by the end of the experiment. Instead, we infer that the 15 total populations were retained due to host selection, as they showed high metabolic potential for algal-bacterial interactions such as recycling alga-produced carbon and nitrogen and production of vitamins and secondary metabolites associated with algal growth and senescence, including B vitamins, tropodithietic acid, and roseobacticides. IMPORTANCE Bacteria proliferate in nutrient-rich aquatic environments, including engineered algal biofuel systems, where they remineralize photosynthates, exchange secondary metabolites with algae, and can influence system output of biomass or oil. Despite this, knowledge on the microbial ecology of algal cultivation systems is lacking, and the subject is worthy of investigation. Here, we used metagenomics to characterize the metabolic capacities of the predominant bacteria associated with the biofuel-relevant microalga Microchloropsis salina and to predict testable metabolic interactions between algae and manipulated communities of bacteria. We identified a previously undescribed and uncultivated organism that dominated the community. Collectively, the microbial community may interact with the alga in cultivation via exchange of secondary metabolites which could affect algal success, which we demonstrate as a possible outcome from controlled experiments with metabolically analogous isolates. These findings address the scalability of lab-based algal-bacterial interactions through to cultivation systems and more broadly provide a framework for empirical testing of genome-based metabolic predictions.}, }
@article {pmid35729185, year = {2022}, author = {Beterams, A and Calatayud Arroyo, M and De Paepe, K and De Craemer, AS and Elewaut, D and Venken, K and Van de Wiele, T}, title = {In vitro triple coculture with gut microbiota from spondyloarthritis patients is characterized by inter-individual differences in inflammatory responses.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {10475}, pmid = {35729185}, issn = {2045-2322}, support = {G062519N//Fonds Wetenschappelijk Onderzoek/ ; G062519N//Fonds Wetenschappelijk Onderzoek/ ; G062519N//Fonds Wetenschappelijk Onderzoek/ ; G062519N//Fonds Wetenschappelijk Onderzoek/ ; BOF17/GOA/032//Bijzonder Onderzoeksfonds UGent/ ; BOF17/GOA/032//Bijzonder Onderzoeksfonds UGent/ ; BOF17/GOA/032//Bijzonder Onderzoeksfonds UGent/ ; BOF17/GOA/032//Bijzonder Onderzoeksfonds UGent/ ; BOF17/GOA/032//Bijzonder Onderzoeksfonds UGent/ ; BOF17/GOA/032//Bijzonder Onderzoeksfonds UGent/ ; BOF17/GOA/032//Bijzonder Onderzoeksfonds UGent/ ; }, abstract = {Spondyloarthritis is a group of chronic inflammatory diseases that primarily affects axial or peripheral joints and is frequently associated with inflammation at non-articular sites. The disease is multifactorial, involving genetics, immunity and environmental factors, including the gut microbiota. In vivo, microbiome contributions are difficult to assess due to the multifactorial disease complexity. In a proof-of-concept approach, we therefore used a triple coculture model of immune-like, goblet and epithelial cells to investigate whether we could detect a differential impact from spondyloarthritis- vs. healthy-derived gut microbiota on host cell response. Despite their phylogenetic resemblance, flow cytometry-based phenotypic clustering revealed human-derived gut microbiota from healthy origin to cluster together and apart from spondyloarthritis donors. At host level, mucus production was higher upon exposure to healthy microbiota. Pro-inflammatory cytokine responses displayed more inter-individual variability in spondyloarthritis than in healthy donors. Interestingly, the high dominance in the initial sample of one patient of Prevotella, a genus previously linked to spondyloarthritis, resulted in the most differential host response upon 16 h host-microbe coincubation. While future research should further focus on inter-individual variability by using gut microbiota from a large cohort of patients, this study underscores the importance of the gut microbiota during the SpA disease course.}, }
@article {pmid35726107, year = {2022}, author = {Khuntia, HK and Paliwal, A and Kumar, DR and Chanakya, HN}, title = {Review on solid-state anaerobic digestion of lignocellulosic biomass and organic solid waste.}, journal = {Environmental monitoring and assessment}, volume = {194}, number = {7}, pages = {514}, pmid = {35726107}, issn = {1573-2959}, mesh = {Anaerobiosis ; Biofuels/analysis ; Biomass ; Bioreactors ; Environmental Monitoring ; Lignin ; Methane ; *Refuse Disposal/methods ; *Solid Waste/analysis ; }, abstract = {Sustainable management of organic solid wastes especially the municipal solid waste (MSW) is essential for the realization of various sustainable development goals (SDGs). Resource recovery centric waste processing technologies generate valorizable products to meet the operations and maintenance (O&amp;M) costs while reducing the GHG emissions. Solid-state anaerobic digestion (SSAD) of organic solid wastes is a biomethanation process performed at a relatively higher total solids (TS) loading in the range of 10-45%. SSAD overcomes various limitations posed by conventional anaerobic slurry digesters such as higher degradable matter per unit volume of the bioreactor resulting in a smaller footprint, low freshwater consumption, low wastewater generation, simple upstream and downstream processes, relatively lower operation, and maintenance costs. This review elucidates the recent developments and critical assessment of different aspects of SSAD, such as bioreactor design, operational strategy, process performances, mass balance, microbial ecology, applications, and mathematical models. A critical assessment revealed that the operating scale of SSAD varies between 1000 and 100,000 ts/year at organic loading rate (OLR) of 2-15 g volatile solids (VS)/L·day. The SSAD experiences process failures due to the formation of volatile fatty acids (VFAs), biogas pockets and clogging of the digestate outlet. Acclimatization of microbes accelerates the startup phase, steady-state performances, and the enrichment of syntrophic microbes with 10-50 times greater population of cellulolytic and xylanolytic microbes in thermophilic SSAD over mesophilic SSAD. Experimental limitations in the accurate determination of rate constants and the oversimplification of biochemical reactions result in an inaccurate prediction by the models.}, }
@article {pmid35724776, year = {2022}, author = {Chang, J and van Veen, JA and Tian, C and Kuramae, EE}, title = {A review on the impact of domestication of the rhizosphere of grain crops and a perspective on the potential role of the rhizosphere microbial community for sustainable rice crop production.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {156706}, doi = {10.1016/j.scitotenv.2022.156706}, pmid = {35724776}, issn = {1879-1026}, abstract = {The rhizosphere-associated microbiome impacts plant performance and tolerance to abiotic and biotic stresses. Despite increasing recognition of the enormous functional role of the rhizomicrobiome on the survival of wild plant species growing under harsh environmental conditions, such as nutrient, water, temperature, and pathogen stresses, the utilization of the rhizosphere microbial community in domesticated rice production systems has been limited. Better insight into how this role of the rhizomicrobiome for the performance and survival of wild plants has been changed during domestication and development of present domesticated crops, may help to assess the potential of the rhizomicrobial community to improve the sustainable production of these crops. Here, we review the current knowledge of the effect of domestication on the microbial rhizosphere community of rice and other crops by comparing its diversity, structure, and function in wild versus domesticated species. We also examine the existing information on the impact of the plant on their physico-chemical environment. We propose that a holobiont approach should be explored in future studies by combining detailed analysis of the dynamics of the physicochemical microenvironment surrounding roots to systematically investigate the microenvironment-plant-rhizomicrobe interactions during rice domestication, and suggest focusing on the use of beneficial microbes (arbuscular mycorrhizal fungi and Nitrogen fixers), denitrifiers and methane consumers to improve the sustainable production of rice.}, }
@article {pmid35722352, year = {2022}, author = {Paddock, KJ and Finke, DL and Kim, KS and Sappington, TW and Hibbard, BE}, title = {Patterns of Microbiome Composition Vary Across Spatial Scales in a Specialist Insect.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {898744}, doi = {10.3389/fmicb.2022.898744}, pmid = {35722352}, issn = {1664-302X}, abstract = {Microbial communities associated with animals vary based on both intrinsic and extrinsic factors. Of many possible determinants affecting microbiome composition, host phylogeny, host diet, and local environment are the most important. How these factors interact across spatial scales is not well understood. Here, we seek to identify the main influences on microbiome composition in a specialist insect, the western corn rootworm (WCR; Diabrotica virgifera virgifera), by analyzing the bacterial communities of adults collected from their obligate host plant, corn (Zea mays), across several geographic locations and comparing the patterns in communities to its congeneric species, the northern corn rootworm (NCR; Diabrotica barberi). We found that bacterial communities of WCR and NCR shared a portion of their bacterial communities even when collected from disparate locations. However, within each species, the location of collection significantly influenced the composition of their microbiome. Correlations of geographic distance between sites with WCR bacterial community composition revealed different patterns at different spatial scales. Community similarity decreased with increased geographic distance at smaller spatial scales (~25 km between the nearest sites). At broad spatial scales (>200 km), community composition was not correlated with distances between sites, but instead reflected the historical invasion path of WCR across the United States. These results suggest bacterial communities are structured directly by dispersal dynamics at small, regional spatial scales, while landscape-level genetic or environmental differences may drive community composition across broad spatial scales in this specialist insect.}, }
@article {pmid35722289, year = {2022}, author = {Rocha, ADL and Ferrari, RG and Pereira, WE and de Lima, LA and Givisiez, PEN and Moreno-Switt, AI and Toro, M and Delgado-Suárez, EJ and Meng, J and de Oliveira, CJB}, title = {Revisiting the Biological Behavior of Salmonella enterica in Hydric Resources: A Meta-Analysis Study Addressing the Critical Role of Environmental Water on Food Safety and Public Health.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {802625}, doi = {10.3389/fmicb.2022.802625}, pmid = {35722289}, issn = {1664-302X}, abstract = {The increasing number of studies reporting the presence of Salmonella in environmental water sources suggests that it is beyond incidental findings originated from sparse fecal contamination events. However, there is no consensus on the occurrence of Salmonella as its relative serovar representation across non-recycled water sources. We conducted a meta-analysis of proportions by fitting a random-effects model using the restricted maximum-likelihood estimator to obtain the weighted average proportion and between-study variance associated with the occurrence of Salmonella in water sources. Moreover, meta-regression and non-parametric supervised machine learning method were performed to predict the effect of moderators on the frequency of Salmonella in non-recycled water sources. Three sequential steps (identification of information sources, screening and eligibility) were performed to obtain a preliminary selection from identified abstracts and article titles. Questions related to the frequency of Salmonella in aquatic environments, as well as putative differences in the relative frequencies of the reported Salmonella serovars and the role of potential variable moderators (sample source, country, and sample volume) were formulated according to the population, intervention, comparison, and outcome method (PICO). The results were reported according to the Preferred Reporting Items for Systematic Review and Meta-Analyzes statement (PRISMA). A total of 26 eligible papers reporting 148 different Salmonella serovars were retrieved. According to our model, the Salmonella frequency in non-recycled water sources was 0.19 [CI: 0.14; 0.25]. The source of water was identified as the most import variable affecting the frequency of Salmonella, estimated as 0.31 and 0.17% for surface and groundwater, respectively. There was a higher frequency of Salmonella in countries with lower human development index (HDI). Small volume samples of surface water resulted in lower detectable Salmonella frequencies both in high and low HDI regions. Relative frequencies of the 148 serovars were significantly affected only by HDI and volume. Considering that serovars representation can also be affected by water sample volume, efforts toward the standardization of water samplings for monitoring purposes should be considered. Further approaches such as metagenomics could provide more comprehensive insights about the microbial ecology of fresh water and its importance for the quality and safety of agricultural products.}, }
@article {pmid35722279, year = {2022}, author = {Egenriether, S and Sanford, R and Yang, WH and Kent, AD}, title = {Nitrogen Cycling Microbial Diversity and Operational Taxonomic Unit Clustering: When to Prioritize Accuracy Over Speed.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {730340}, doi = {10.3389/fmicb.2022.730340}, pmid = {35722279}, issn = {1664-302X}, abstract = {Background: Assessments of the soil microbiome provide valuable insight to ecosystem function due to the integral role microorganisms play in biogeochemical cycling of carbon and nutrients. For example, treatment effects on nitrogen cycling functional groups are often presented alongside one another to demonstrate how agricultural management practices affect various nitrogen cycling processes. However, the functional groups commonly evaluated in nitrogen cycling microbiome studies range from phylogenetically narrow (e.g., N-fixation, nitrification) to broad [e.g., denitrification, dissimilatory nitrate reduction to ammonium (DNRA)]. The bioinformatics methods used in such studies were developed for 16S rRNA gene sequence data, and how these tools perform across functional genes of different phylogenetic diversity has not been established. For example, an OTU clustering method that can accurately characterize sequences harboring comparatively little diversity may not accurately resolve the diversity within a gene comprised of a large number of clades. This study uses two nitrogen cycling genes, nifH, a gene which segregates into only three distinct clades, and nrfA, a gene which is comprised of at least eighteen clades, to investigate differences which may arise when using heuristic OTU clustering (abundance-based greedy clustering, AGC) vs. true hierarchical OTU clustering (Matthews Correlation Coefficient optimizing algorithm, Opti-MCC). Detection of treatment differences for each gene were evaluated to demonstrate how conclusions drawn from a given dataset may differ depending on clustering method used.<br><br>Results: The heuristic and hierarchical methods performed comparably for the more conserved gene, nifH. The hierarchical method outperformed the heuristic method for the more diverse gene, nrfA; this included both the ability to detect treatment differences using PERMANOVA, as well as higher resolution in taxonomic classification. The difference in performance between the two methods may be traced to the AGC method's preferential assignment of sequences to the most abundant OTUs: when analysis was limited to only the largest 100 OTUs, results from the AGC-assembled OTU table more closely resembled those of the Opti-MCC OTU table. Additionally, both AGC and Opti-MCC OTU tables detected comparable treatment differences using the rank-based ANOSIM test. This demonstrates that treatment differences were preserved using both clustering methods but were structured differently within the OTU tables produced using each method.<br><br>Conclusion: For questions which can be answered using tests agnostic to clustering method (e.g., ANOSIM), or for genes of relatively low phylogenetic diversity (e.g., nifH), most upstream processing methods should lead to similar conclusions from downstream analyses. For studies involving more diverse genes, however, care should be exercised to choose methods that ensure accurate clustering for all genes. This will mitigate the risk of introducing Type II errors by allowing for detection of comparable treatment differences for all genes assessed, rather than disproportionately detecting treatment differences in only low-diversity genes.}, }
@article {pmid35720594, year = {2022}, author = {Kong, Z and Liu, H}, title = {Modification of Rhizosphere Microbial Communities: A Possible Mechanism of Plant Growth Promoting Rhizobacteria Enhancing Plant Growth and Fitness.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {920813}, doi = {10.3389/fpls.2022.920813}, pmid = {35720594}, issn = {1664-462X}, abstract = {Plant beneficial bacteria, defined as plant growth-promoting rhizobacteria (PGPR), play a crucial role in plants' growth, stress tolerance and disease prevention. In association with the rhizosphere of plants, PGPR facilitate plant growth and development either directly or indirectly through multiple mechanisms, including increasing available mineral nutrients, moderating phytohormone levels and acting as biocontrol agents of phytopathogens. It is generally accepted that the effectiveness of PGPR inoculants is associated with their ability to colonize, survive and persist, as well as the complex network of interactions in the rhizosphere. Despite the promising plant growth promotion results commonly reported and mostly attributed to phytohormones or other organic compounds produced by PGPR inoculants, little information is available on the potential mechanisms underlying such positive effects via modifying rhizosphere microbial community and soil functionality. In this review, we overviewed the effects of PGPR inoculants on rhizosphere microbial ecology and soil function, hypothesizing that PGPR may indirectly promote plant growth and health via modifying the composition and functioning of rhizosphere microbial community, and highlighting the further directions for investigating the role of PGPR in rhizosphere from an ecological perspective.}, }
@article {pmid35717339, year = {2022}, author = {Grote, M}, title = {Microbes before microbiology: Christian Gottfried Ehrenberg and Berlin's infusoria.}, journal = {Endeavour}, volume = {}, number = {}, pages = {100815}, doi = {10.1016/j.endeavour.2022.100815}, pmid = {35717339}, issn = {1873-1929}, abstract = {Naturalist Christian Gottfried Ehrenberg pioneered research on living and fossil infusoria (including protists and bacteria) since the 1830s by collecting samples from all over the world, thus describing numerous microbes and discussing their effects for the planet and for humankind. This article introduces Ehrenberg as a natural historian of microbes and situates his work in the nineteenth century life sciences with respect to debates about cell theory, evolution, and concepts of disease. I argue that in spite of occurring before these major conceptual innovations of the life sciences, Ehrenberg's work on the diversity of microbes found in earth or air is more exciting than historiography has made it appear so far, especially in light of today's ecological microbiology.}, }
@article {pmid35714745, year = {2022}, author = {DeVilbiss, SE and Steele, MK and Brown, BL and Badgley, BD}, title = {Stream bacterial diversity peaks at intermediate freshwater salinity and varies by salt type.}, journal = {The Science of the total environment}, volume = {840}, number = {}, pages = {156690}, doi = {10.1016/j.scitotenv.2022.156690}, pmid = {35714745}, issn = {1879-1026}, abstract = {Anthropogenic freshwater salinization is an emerging and widespread water quality stressor that increases salt concentrations of freshwater, where specific upland land-uses produce distinct ionic profiles. In-situ studies find salinization in disturbed landscapes is correlated with declines in stream bacterial diversity, but cannot isolate the effects of salinization from multiple co-occurring stressors. By manipulating salt concentration and type in controlled microcosm studies, we identified direct and complex effects of freshwater salinization on bacterial diversity in the absence of other stressors common in field studies using chloride salts. Changes in both salt concentration and cation produced distinct bacterial communities. Bacterial richness, or the total number of amplicon sequence variants (ASVs) detected, increased at conductivities as low as 350 μS cm-1, which is opposite the observations from field studies. Richness remained elevated at conductivities as high as 1500 μS cm-1 in communities exposed to a mixture of Ca, Mg, and K chloride salts, but decreased in communities exposed to NaCl, revealing a classic subsidy-stress response. Exposure to different chloride salts at the same conductivity resulted in distinct bacterial community structure, further supporting that salt type modulates responses of bacterial communities to freshwater salinization. Community variability peaked at 125-350 μS cm-1 and was more similar at lower and upper conductivities suggesting possible shifts in deterministic vs. stochastic assembly mechanisms across freshwater salinity gradients. Based on these results, we hypothesize that modest freshwater salinization (125-350 μS cm-1) lessens hypo-osmotic stress, reducing the importance of salinity as an environmental filter at intermediate freshwater ranges but effects of higher salinities at the upper freshwater range differ based on salt type. Our results also support previous findings that ~300 μS cm-1 is a biological effect concentration and effective salt management strategies may need to consider variable effects of different salt types associated with land-use.}, }
@article {pmid35714546, year = {2022}, author = {Kazmi, SSUH and Uroosa,  and Warren, A and Zhong, X and Xu, H}, title = {Corrigendum to "Insights into the ecotoxicity of nitrofurazone in marine ecosystems based on body-size spectra of periphytic ciliates" [Mar. Pollut. Bull. 174 (2022) 113217 1-8].}, journal = {Marine pollution bulletin}, volume = {181}, number = {}, pages = {113841}, doi = {10.1016/j.marpolbul.2022.113841}, pmid = {35714546}, issn = {1879-3363}, }
@article {pmid35713683, year = {2022}, author = {Lau, NS and Ting, SY and Sam, KK and M, J and Wong, SC and Wu, X and Waiho, K and Fazhan, H and Shu-Chien, AC}, title = {Correction to: Comparative Analyses of Scylla olivacea Gut Microbiota Composition and Function Suggest the Capacity for Polyunsaturated Fatty Acid Biosynthesis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-022-02059-9}, pmid = {35713683}, issn = {1432-184X}, }
@article {pmid35713682, year = {2022}, author = {Sandy, M and Bui, TI and Abá, KS and Ruiz, N and Paszalek, J and Connor, EW and Hawkes, CV}, title = {Plant Host Traits Mediated by Foliar Fungal Symbionts and Secondary Metabolites.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35713682}, issn = {1432-184X}, support = {2017-67013-29207//National Institute of Food and Agriculture/ ; HATCH accesssion no 1018688//National Institute of Food and Agriculture/ ; }, abstract = {Fungal symbionts living inside plant leaves ("endophytes") can vary from beneficial to parasitic, but the mechanisms by which the fungi affect the plant host phenotype remain poorly understood. Chemical interactions are likely the proximal mechanism of interaction between foliar endophytes and the plant, as individual fungal strains are often exploited for their diverse secondary metabolite production. Here, we go beyond single strains to examine commonalities in how 16 fungal endophytes shift plant phenotypic traits such as growth and physiology, and how those relate to plant metabolomics profiles. We inoculated individual fungi on switchgrass, Panicum virgatum L. This created a limited range of plant growth and physiology (2-370% of fungus-free controls on average), but effects of most fungi overlapped, indicating functional similarities in unstressed conditions. Overall plant metabolomics profiles included almost 2000 metabolites, which were broadly correlated with plant traits across all the fungal treatments. Terpenoid-rich samples were associated with larger, more physiologically active plants and phenolic-rich samples were associated with smaller, less active plants. Only 47 metabolites were enriched in plants inoculated with fungi relative to fungus-free controls, and of these, Lasso regression identified 12 metabolites that explained from 14 to 43% of plant trait variation. Fungal long-chain fatty acids and sterol precursors were positively associated with plant photosynthesis, conductance, and shoot biomass, but negatively associated with survival. The phytohormone gibberellin, in contrast, was negatively associated with plant physiology and biomass. These results can inform ongoing efforts to develop metabolites as crop management tools, either by direct application or via breeding, by identifying how associations with more beneficial components of the microbiome may be affected.}, }
@article {pmid35712047, year = {2022}, author = {Guseva, K and Darcy, S and Simon, E and Alteio, LV and Montesinos-Navarro, A and Kaiser, C}, title = {From diversity to complexity: Microbial networks in soils.}, journal = {Soil biology &amp; biochemistry}, volume = {169}, number = {}, pages = {108604}, doi = {10.1016/j.soilbio.2022.108604}, pmid = {35712047}, issn = {0038-0717}, abstract = {Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research. Analysing microbial networks in soils opens a window to a better understanding of the complexity of microbial communities. However, this approach is unfortunately often used to draw conclusions which are far beyond the scientific evidence it can provide, which has damaged its reputation for soil microbial analysis. In this Perspectives Paper, we would like to sharpen the view for the real potential of microbial co-occurrence analysis in soils, and at the same time raise awareness regarding its limitations and the many ways how it can be misused or misinterpreted.}, }
@article {pmid35711777, year = {2022}, author = {Jiang, Y and Luo, J and Huang, D and Liu, Y and Li, DD}, title = {Machine Learning Advances in Microbiology: A Review of Methods and Applications.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {925454}, doi = {10.3389/fmicb.2022.925454}, pmid = {35711777}, issn = {1664-302X}, abstract = {Microorganisms play an important role in natural material and elemental cycles. Many common and general biology research techniques rely on microorganisms. Machine learning has been gradually integrated with multiple fields of study. Machine learning, including deep learning, aims to use mathematical insights to optimize variational functions to aid microbiology using various types of available data to help humans organize and apply collective knowledge of various research objects in a systematic and scaled manner. Classification and prediction have become the main achievements in the development of microbial community research in the direction of computational biology. This review summarizes the application and development of machine learning and deep learning in the field of microbiology and shows and compares the advantages and disadvantages of different algorithm tools in four fields: microbiome and taxonomy, microbial ecology, pathogen and epidemiology, and drug discovery.}, }
@article {pmid35711776, year = {2022}, author = {You, J and Zhang, H and Zhu, H and Xue, Y and Cai, Y and Zhang, G}, title = {Microbial Community, Fermentation Quality, and in vitro Degradability of Ensiling Caragana With Lactic Acid Bacteria and Rice Bran.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {804429}, doi = {10.3389/fmicb.2022.804429}, pmid = {35711776}, issn = {1664-302X}, abstract = {This study aimed to assess the effects of microbial inoculants and growth stage on fermentation quality, microbial community, and in vitro degradability of Caragana silage from different varieties. Caragana intermedia (CI) and Caragana korshinskii (CK) harvested at the budding (BU) and blooming (BL) stages were used as raw materials to prepare silage, respectively. The silages at each growth stage were treated for ensiling alone (control), with 5% rice bran (RB), a combination of RB with commercial Lactobacillus plantarum (RB + LP), and a combination of RB with a selected strain Lactobacillus plantarum L694 (RB + L694). The results showed that the crude protein (CP) content of CI was higher than that of CK, and delay in harvest resulted in greater CP content in Caragana at BL stage. After 60 days of fermentation, the concentrations of lactic acid (LA) in the RB + L694 treatments were higher than those in control treatments (p < 0.05), while the pH, concentrations of NH3-N, neutral detergent fiber with the addition of α-amylase (aNDF) were lower than those in control treatments (p < 0.05). RB + L694 treatments could decrease acid detergent fiber (ADF) content except in CIBL. In CK silages, adding RB + L694 could reduce bacterial diversity and richness (p < 0.05). Compared with the control, RB + L694 treatment contained higher Lactobacillus and Enterobacter (p < 0.05). In vitro NDF and DM degradability (IVNDFD and IVDMD) was mostly affected by growth period, and additive RB + l694 treatment had higher IVDMD and lower IVNDFD than other treatments (p < 0.05). Consequently, the varieties, growth stages, and additives could influence the fermentation process, while the blooming stage should be selected in both Caragana. Furthermore, the results showed that RB and L. plantarum could exert a positive effect on fermentation quality of Caragana silage by shifting bacterial community composition, and RB + L694 treatments outperformed other additives.}, }
@article {pmid35711751, year = {2022}, author = {Bannon, C and Rapp, I and Bertrand, EM}, title = {Community Interaction Co-limitation: Nutrient Limitation in a Marine Microbial Community Context.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {846890}, doi = {10.3389/fmicb.2022.846890}, pmid = {35711751}, issn = {1664-302X}, abstract = {The simultaneous limitation of productivity by two or more nutrients, commonly referred to as nutrient co-limitation, affects microbial communities throughout the marine environment and is of profound importance because of its impacts on various biogeochemical cycles. Multiple types of co-limitation have been described, enabling distinctions based on the hypothesized mechanisms of co-limitation at a biochemical level. These definitions usually pertain to individuals and do not explicitly, or even implicitly, consider complex ecological dynamics found within a microbial community. However, limiting and co-limiting nutrients can be produced in situ by a subset of microbial community members, suggesting that interactions within communities can underpin co-limitation. To address this, we propose a new category of nutrient co-limitation, community interaction co-limitation (CIC). During CIC, one part of the community is limited by one nutrient, which results in the insufficient production or transformation of a biologically produced nutrient that is required by another part of the community, often primary producers. Using cobalamin (vitamin B12) and nitrogen fixation as our models, we outline three different ways CIC can arise based on current literature and discuss CIC's role in biogeochemical cycles. Accounting for the inherent and complex roles microbial community interactions play in generating this type of co-limitation requires an expanded toolset - beyond the traditional approaches used to identify and study other types of co-limitation. We propose incorporating processes and theories well-known in microbial ecology and evolution to provide meaningful insight into the controls of community-based feedback loops and mechanisms that give rise to CIC in the environment. Finally, we highlight the data gaps that limit our understanding of CIC mechanisms and suggest methods to overcome these and further identify causes and consequences of CIC. By providing this framework for understanding and identifying CIC, we enable systematic examination of the impacts this co-limitation can have on current and future marine biogeochemical processes.}, }
@article {pmid35710629, year = {2022}, author = {Oyserman, BO and Flores, SS and Griffioen, T and Pan, X and van der Wijk, E and Pronk, L and Lokhorst, W and Nurfikari, A and Paulson, JN and Movassagh, M and Stopnisek, N and Kupczok, A and Cordovez, V and Carrión, VJ and Ligterink, W and Snoek, BL and Medema, MH and Raaijmakers, JM}, title = {Disentangling the genetic basis of rhizosphere microbiome assembly in tomato.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3228}, pmid = {35710629}, issn = {2041-1723}, mesh = {Iron/metabolism ; *Lycopersicon esculentum/metabolism ; *Microbiota/genetics ; Plant Breeding ; Plants/metabolism ; Rhizosphere ; }, abstract = {Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, we map the molecular features of the rhizosphere microbiome as quantitative traits of a diverse hybrid population of wild and domesticated tomato. Gene content analysis of prioritized tomato quantitative trait loci suggests a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31 Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the water channel aquaporin SlTIP2.3. Within metagenome-assembled genomes of root-associated Streptomyces and Cellvibrio, we identify bacterial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associates with specific tomato QTLs. By integrating 'microbiomics' and quantitative plant genetics, we pinpoint putative plant and reciprocal rhizobacterial traits underlying microbiome assembly, thereby providing a first step towards plant-microbiome breeding programs.}, }
@article {pmid35707452, year = {2021}, author = {Werbin, ZR and Hackos, B and Lopez-Nava, J and Dietze, MC and Bhatnagar, JM}, title = {The National Ecological Observatory Network's soil metagenomes: assembly and basic analysis.}, journal = {F1000Research}, volume = {10}, number = {}, pages = {299}, doi = {10.12688/f1000research.51494.2}, pmid = {35707452}, issn = {2046-1402}, mesh = {Computational Biology/methods ; *Metagenome ; Metagenomics/methods ; Neon ; *Soil ; }, abstract = {The largest dataset of soil metagenomes has recently been released by the National Ecological Observatory Network (NEON), which performs annual shotgun sequencing of soils at 47 sites across the United States. NEON serves as a valuable educational resource, thanks to its open data and programming tutorials, but there is currently no introductory tutorial for accessing and analyzing the soil shotgun metagenomic dataset. Here, we describe methods for processing raw soil metagenome sequencing reads using a bioinformatics pipeline tailored to the high complexity and diversity of the soil microbiome. We describe the rationale, necessary resources, and implementation of steps such as cleaning raw reads, taxonomic classification, assembly into contigs or genomes, annotation of predicted genes using custom protein databases, and exporting data for downstream analysis. The workflow presented here aims to increase the accessibility of NEON's shotgun metagenome data, which can provide important clues about soil microbial communities and their ecological roles.}, }
@article {pmid35705745, year = {2022}, author = {Song, L and Wang, Y and Zhang, R and Yang, S}, title = {Microbial Mediation of Carbon, Nitrogen, and Sulfur Cycles During Solid Waste Decomposition.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35705745}, issn = {1432-184X}, support = {52000016//National Natural Science Foundation of China/ ; 51578642//National Natural Science Foundation of China/ ; }, abstract = {Landfills are a unique "terrestrial ecosystem" and serve as a significant carbon sink. Microorganisms convert biodegradable substances in municipal solid waste (MSW) to CH4, CO2, and microbial biomass, consisting of the carbon cycling in landfills. Microbial-mediated N and S cycles are also the important biogeochemical process during MSW decomposition, resulting in N2O and H2S emission, respectively. Meanwhile, microbial-mediated N and S cycles affect carbon cycling. How microbial community structure and function respond to C, N, and S cycling during solid waste decomposition, however, are not well-characterized. Here, we show the response of bacterial and archaeal community structure and functions to C, N, and S cycling during solid waste decomposition in a long-term (265 days) operation laboratory-scale bioreactor through 16S rRNA-based pyrosequencing and metagenomics analysis. Bacterial and archaeal community composition varied during solid waste decomposition. Aerobic respiration was the main pathway for CO2 emission, while anaerobic C fixation was the main pathway in carbon fixation. Methanogenesis and denitrification increased during solid waste decomposition, suggesting increasing CH4 and N2O emission. In contract, fermentation decreased along solid waste decomposition. Interestingly, Clostridiales were abundant and showed potential for several pathways in C, N, and S cycling. Archaea were involved in many pathways of C and N cycles. There is a shift between bacteria and archaea involvement in N2 fixation along solid waste decomposition that bacteria Clostridiales and Bacteroidales were initially dominant and then Methanosarcinales increased and became dominant in methanogenic phase. These results provide extensive microbial mediation of C, N, and S cycling profiles during solid waste decomposition.}, }
@article {pmid35705744, year = {2022}, author = {García-Sánchez, JC and Arredondo-Centeno, J and Segovia-Ramírez, MG and Tenorio Olvera, AM and Parra-Olea, G and Vredenburg, VT and Rovito, SM}, title = {Factors Influencing Bacterial and Fungal Skin Communities of Montane Salamanders of Central Mexico.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35705744}, issn = {1432-184X}, support = {221614//Conacyt/ ; 2015-01-721//Conacyt/ ; 1633948//National Science Foundation/ ; }, abstract = {Host microbial communities are increasingly seen as an important component of host health. In amphibians, the first land vertebrates that are threatened by a fungal skin disease globally, our understanding of the factors influencing the microbiome of amphibian skin remains incomplete because recent studies have focused almost exclusively on bacteria, and little information exists on fungal communities associated with wild amphibian species. In this study, we describe the effects of host phylogeny, climate, geographic distance, and infection with a fungal pathogen on the composition and structure of bacterial and fungal communities in seven tropical salamander species that occur in the Trans-Mexican Volcanic Belt of Central Mexico. We find that host phylogenetic relatedness is correlated with bacterial community composition while a composite climatic variable of temperature seasonality and precipitation is significantly associated with fungal community composition. We also estimated co-occurrence networks for bacterial and fungal taxa and found differences in the degree of connectivity and the distribution of negative associations between the two networks. Our results suggest that different factors may be responsible for structuring the bacterial and fungal communities of amphibian skin and that the inclusion of fungi in future studies could shed light on important functional interactions within the microbiome.}, }
@article {pmid35710200, year = {2022}, author = {Antosiak, A and Šulčius, S and Malec, P and Tokodi, N and Łobodzińska, A and Dziga, D}, title = {Cyanophage infections reduce photosynthetic activity and expression of CO2 fixation genes in the freshwater bloom-forming cyanobacterium Aphanizomenon flos-aquae.}, journal = {Harmful algae}, volume = {116}, number = {}, pages = {102215}, doi = {10.1016/j.hal.2022.102215}, pmid = {35710200}, issn = {1878-1470}, mesh = {Aphanizomenon ; Carbon ; *Carbon Dioxide ; *Cyanobacteria ; DNA Replication ; DNA, Viral ; Ecosystem ; Fresh Water ; Photosynthesis ; Virus Replication ; }, abstract = {Cyanobacteria play a significant role in ecosystem functioning as photosynthetic and CO2 fixing microorganisms. Whether and to what extent cyanophages alter these carbon and energy cycles in their cyanobacterial hosts is still poorly understood. In this study, we investigated changes in photosynthetic activity (PSII), expression of genes associated with the light phase of photosynthesis (psbA, petA, ndhK) and carbon metabolism (rbcL, zwf) as well as intracellular ATP and NADHP concentrations in freshwater bloom-forming filamentous cyanobacterium Aphanizomenon flos-aquae infected by cyanophage vB_AphaS-CL131. We found that PSII activity and expression level of rbcL genes, indicating potential for CO2 fixation, had decreased in response to cyanophage adsorption and DNA injection. During the period of viral DNA replication and assembly, PSII performance and gene expression remained at this decreased level and did not change significantly, indicating lack of transcriptional shutdown by the cyanophage. Combined, these observations suggest that although there is little to no interference between cyanophage DNA replication, host transcription and cellular metabolism, A. flos-aquae underwent a physiological state-shift toward lower efficiency of carbon and energy cycling. This further suggest potential cascading effect for co-occurring non-infected members of the microbial community.}, }
@article {pmid35706139, year = {2022}, author = {Purkamo, L and Dochartaigh, BÓ and MacDonald, A and Cousins, C}, title = {Following the flow - microbial ecology in surface- and groundwaters in the glacial forefield of a rapidly retreating glacier in Iceland.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16104}, pmid = {35706139}, issn = {1462-2920}, abstract = {The retreat of glaciers in response to climate change has major impacts on the hydrology and ecosystems of glacier forefield catchments. Microbes are key players in ecosystem functionality, supporting the supply of ecosystem services that glacier systems provide. The interaction between surface and groundwaters in glacier forefields has only recently gained much attention, and how these interactions influence the microbiology is still unclear. Here, we identify the microbial communities in groundwater from shallow (<15m deep) boreholes in a glacial forefield floodplain ('sandur') aquifer at different distances from the rapidly retreating Virkisjökull glacier, Iceland, and with varying hydraulic connectivity with the glacial meltwater river that flows over the sandur. Groundwater communities are shown to differ from those in nearby glacial and non-glacial surface water communities. Groundwater-meltwater interactions and groundwater flow dynamics affect the microbial community structure, leading to different microbial communities at different sampling points in the glacier forefield. Groundwater communities differ from those in nearby glacial and non-glacial surface waters. Functional potential for microbial nitrogen and methane cycling was detected, although the functional gene copy numbers of specific groups were low. This article is protected by copyright. All rights reserved.}, }
@article {pmid35537512, year = {2022}, author = {Cui, G and Liu, Z and Xu, W and Gao, Y and Yang, S and Grossart, HP and Li, M and Luo, Z}, title = {Metagenomic exploration of antibiotic resistance genes and their hosts in aquaculture waters of the semi-closed Dongshan Bay (China).}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 1}, pages = {155784}, doi = {10.1016/j.scitotenv.2022.155784}, pmid = {35537512}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Aquaculture ; Bays ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; *Metagenome ; beta-Lactamases/genetics ; }, abstract = {In marine environments, increasing occurrence and numbers of microbial Antibiotic Resistance Gene (ARG) subtypes, especially of new beta-lactamases, have received lots of attention in recent years. Updated databases with novel developed tools provide new opportunities to obtain more comprehensive ARG profiles as well as ARG-carrying hosts. Yet, ARGs in human-associated marine aquaculture environments, e.g. in China, remains largely unknown. Using metagenomic data, we revealed high numbers of Multi-drug Resistance, beta-lactamase and aminoglycoside genes throughout the year. Thereby, Alpha- and Gamma-proteobacteria were assigned to the majority of beta-lactamase-carrying hosts. From Metagenome-assembled genomes, three blaF-like beta-lactamases (91.7-94.7% identity with beta-lactamase from Mycobacterium fortuitum (blaF)) were exclusively observed in an unclassified Mycobacterium genus. Notably, other new beta-lactamases, VMB-1-like (n = 3) (58.5-67.4% identity to Vibrio metallo-beta-lactamase 1 (VMB-1)), were found in Gammaproteobacteria. Additionally, 175 Multi-drug Resistant Organisms possessed at least 3 ARG subtypes, and seven of the potentially pathogenic genera (n = 17) were assigned to Gammaproteobacteria. These results, together with high-risk ARGs (e.g. tetM, dfrA14 and dfrA17), provide hosts and new beta-lactamases of ARGs in Chinese coastal aquaculture.}, }
@article {pmid35703548, year = {2022}, author = {Honeyman, AS and Fegel, TS and Peel, HF and Masters, NA and Vuono, DC and Kleiber, W and Rhoades, CC and Spear, JR}, title = {Statistical Learning and Uncommon Soil Microbiota Explain Biogeochemical Responses after Wildfire.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0034322}, doi = {10.1128/aem.00343-22}, pmid = {35703548}, issn = {1098-5336}, abstract = {Wildfires are a perennial event globally, and the biogeochemical underpinnings of soil responses at relevant spatial and temporal scales are unclear. Soil biogeochemical processes regulate plant growth and nutrient losses that affect water quality, yet the response of soil after variable intensity fire is difficult to explain and predict. To address this issue, we examined two wildfires in Colorado, United States, across the first and second postfire years and leveraged statistical learning (SL) to predict and explain biogeochemical responses. We found that SL predicts biogeochemical responses in soil after wildfire with surprising accuracy. Of the 13 biogeochemical analytes analyzed in this study, 9 are best explained with a hybrid microbiome + biogeochemical SL model. Biogeochemical-only models best explain 3 features, and 1 feature is explained equally well with the hybrid and biogeochemical-only models. In some cases, microbiome-only SL models are also effective (such as predicting NH4+). Whenever a microbiome component is employed, selected features always involve uncommon soil microbiota (i.e., the "rare biosphere" [existing at <1% mean relative abundance]). Here, we demonstrate that SL paired with DNA sequence and biogeochemical data predicts environmental features in postfire soils, although this approach could likely be applied to any biogeochemical system. IMPORTANCE Soil biogeochemical processes are critical to plant growth and water quality and are substantially disturbed by wildfire. However, soil responses to fire are difficult to predict. To address this issue, we developed a large environmental data set that tracks postfire changes in soil and used statistical learning (SL) to build models that exploit complex data to make predictions about biogeochemical responses. Here, we show that SL depends upon uncommon microbiota in soil (the "rare biosphere") to make surprisingly accurate predictions about soil biogeochemical responses to wildfire. Using SL to explain variation in a natively chaotic environmental system is mechanism independent. Likely, the approach that we describe for combining SL with microbiome and biogeochemical parameters has practical applications across a range of issues in the environmental sciences where predicting responses would be useful.}, }
@article {pmid35701635, year = {2022}, author = {Vignale, FA and Bernal Rey, D and Pardo, AM and Almasqué, FJ and Ibarra, JG and Fernández Do Porto, D and Turjanski, AG and López, NI and Helman, RJM and Raiger Iustman, LJ}, title = {Spatial and Seasonal Variations in the Bacterial Community of an Anthropogenic Impacted Urban Stream.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35701635}, issn = {1432-184X}, support = {PUE2016 22920160100064CO//conicet/ ; 20020170200338BA//Secretaría de Ciencia y Técnica, Universidad de Buenos Aires/ ; 20020170100310BA//Secretaría de Ciencia y Técnica, Universidad de Buenos Aires/ ; }, abstract = {Environmental changes and human activities can alter the structure and diversity of aquatic microbial communities. In this work, we analyzed the bacterial community dynamics of an urban stream to understand how these factors affect the composition of river microbial communities. Samples were taken from a stream situated in Buenos Aires, Argentina, which flows through residential, peri-urban horticultural, and industrial areas. For sampling, two stations were selected: one influenced by a series of industrial waste treatment plants and horticultural farms (PL), and the other influenced by residential areas (R). Microbial communities were analyzed by sequence analysis of 16S rRNA gene amplicons along an annual cycle. PL samples showed high nutrient content compared with R samples. The diversity and richness of the R site were more affected by seasonality than those of the PL site. At the amplicon sequence variants level, beta diversity analysis showed a differentiation between cool-season (fall and winter) and warm-season (spring and summer) samples, as well as between PL and R sites. This demonstrated that there is spatial and temporal heterogeneity in the composition of the bacterial community, which should be considered if a bioremediation strategy is applied. The taxonomic composition analysis also revealed a differential seasonal cycle of phototrophs and chemoheterotrophs between the sampling sites, as well as different taxa associated with each sampling site. This analysis, combined with a comparative analysis of global rivers, allowed us to determine the genera Arcobacter, Simplicispira, Vogesella, and Sphingomonas as potential bioindicators of anthropogenic disturbance.}, }
@article {pmid35700773, year = {2022}, author = {Chen, H and Pan, Y and Zhou, Q and Liang, C and Wong, CC and Zhou, Y and Huang, D and Liu, W and Zhai, J and Gou, H and Su, H and Zhang, X and Xu, H and Wang, Y and Kang, W and Kei Wu, WK and Yu, J}, title = {METTL3 inhibits anti-tumor immunity by targeting m6A-BHLHE41-CXCL1/CXCR2 axis to promote colorectal cancer.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2022.06.024}, pmid = {35700773}, issn = {1528-0012}, abstract = {BACKGROUND &amp; AIMS: N6-Methyladenosine (m6A) is the most prevalent RNA modification and recognized as an important epitranscriptomic mechanism in colorectal cancer (CRC). We aim to exploit whether and how tumor-intrinsic m6A modification drove by methyltransferase like 3 (METTL3) can dictate the immune landscape of CRC.<br><br>METHODS: Mettl3 knockout mice, CD34+ humanized mice and different syngeneic mice models were employed. Immune cells composition and cytokines level were analyzed by flow cytometry and Cytokine 23-Plex immunoassay, respectively. M6A-seq and RNA-seq were performed to identify downstream targets and pathways of METTL3. Human CRC specimens (n=176) were used to evaluate correlation between METTL3 expression and myeloid-derived suppressor cells (MDSCs) infiltration.<br><br>RESULTS: We demonstrated that silencing of METTL3 in CRC cells reduced MDSCs accumulation to sustain activation and proliferation of CD4+ and CD8+ T cell, and eventually suppressed CRC in ApcMin/+Mettl3+/- mice, CD34+ humanized mice and syngeneic mice models. Mechanistically, METTL3 activated m6A-BHLHE41-CXCL1 axis by analysis of m6A-seq, RNA-seq and cytokines arrays. METTL3 promoted BHLHE41 expression in m6A-dependent manner, which subsequently induced CXCL1 transcription to enhance MDSC migration in vitro. However, the effect was negligible upon BHLHE41 depletion, CXCL1 protein or CXCR2 inhibitor SB265610 administration, inferring that METTL3 promotes MDSC migration via BHLHE41-CXCL1/CXCR2. Consistently, depletion of MDSCs by anti-Gr1 antibody or SB265610 blocked tumor-promoting effect of METTL3 in vivo. Importantly, targeting METTL3 by METTL3-sgRNA or specific inhibitor potentiated the effect of anti-PD1 treatment.<br><br>CONCLUSIONS: Our study identifies METTL3 as a potential therapeutic target for CRC immunotherapy whose inhibition reverses immune suppression through m6A-BHLHE41-CXCL1 axis. METTL3 inhibition plus anti-PD-1 treatment show promising antitumor efficacy against CRC.}, }
@article {pmid35700135, year = {2022}, author = {Deng, Z and Hou, K and Valencak, TG and Luo, XM and Liu, J and Wang, H}, title = {AI-2/LuxS Quorum Sensing System Promotes Biofilm Formation of Lactobacillus rhamnosus GG and Enhances the Resistance to Enterotoxigenic Escherichia coli in Germ-Free Zebrafish.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0061022}, doi = {10.1128/spectrum.00610-22}, pmid = {35700135}, issn = {2165-0497}, abstract = {The LuxS enzyme plays a key role in both quorum sensing (QS) and the regulation of bacterial growth. It catalyzes the production of autoinducer-2 (AI-2) signaling molecule, which is a component of the methyl cycle and methionine metabolism. This study aimed at investigating the differences between the Lactobacillus rhamnosus GG (LGG) wild-type strain (WT) and its luxS mutant (ΔluxS) during biofilm formation and when resisting to inflammation caused by Enterotoxigenic Escherichia coli (ETEC) in germ-free zebrafish. Our results suggest that in the absence of luxS when LGG was knocked out, biofilm formation, extracellular polysaccharide secretion and adhesion were all compromised. Addition of synthetic AI-2 indeed rescued, at least partially, the deficiencies observed in the mutant strain. The colonizing and immunomodulatory function in WT versus ΔluxS mutants were further studied in a germ-free zebrafish model. The concentration of AI-2 signaling molecules decreased sharply in zebrafish infected with the ΔluxS. At the same time, compared with the ΔluxS, the wild-type strain could colonize the germ-free zebrafish more effectively. Our transcriptome results suggest that genes involved in immunity, signal transduction, and cell adhesion were downregulated in zebrafish infected with ΔluxS and WT. In the WT, the immune system of germ-free zebrafish was activated more effectively through the MAPK and NF-κB pathway, and its ability to fight the infection against ETEC was increased. Together, our results demonstrate that the AI-2/LuxS system plays an important role in biofilm formation to improve LGG and alleviate inflammation caused by ETEC in germ-free zebrafish. IMPORTANCE Lactobacillus rhamnosus GG is a widely used probiotic to improve host intestinal health, promote growth, reduce diarrhea, and modulate immunity. In recent years, the bacterial quorum sensing system has attracted much attention; however, there has not been much research on the effect of the LuxS/AI-2 quorum sensing system of Lactobacillus on bacteriostasis, microbial ecology balance, and immune regulation in intestine. In this study, we used germ-free zebrafish as an animal model to compare the differences between wild-type and luxS mutant strains. We showed how AI-2/LuxS QS affects the release of AI-2 and how QS regulates the colonization, EPS synthesis and biofilm formation of LGG. This study provides an idea for the targeted regulation of animal intestinal health with probiotics by controlling bacteria quorum sensing system.}, }
@article {pmid35697795, year = {2022}, author = {Wu, L and Zhang, Y and Guo, X and Ning, D and Zhou, X and Feng, J and Yuan, MM and Liu, S and Guo, J and Gao, Z and Ma, J and Kuang, J and Jian, S and Han, S and Yang, Z and Ouyang, Y and Fu, Y and Xiao, N and Liu, X and Wu, L and Zhou, A and Yang, Y and Tiedje, JM and Zhou, J}, title = {Reduction of microbial diversity in grassland soil is driven by long-term climate warming.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {35697795}, issn = {2058-5276}, abstract = {Anthropogenic climate change threatens ecosystem functioning. Soil biodiversity is essential for maintaining the health of terrestrial systems, but how climate change affects the richness and abundance of soil microbial communities remains unresolved. We examined the effects of warming, altered precipitation and annual biomass removal on grassland soil bacterial, fungal and protistan communities over 7 years to determine how these representative climate changes impact microbial biodiversity and ecosystem functioning. We show that experimental warming and the concomitant reductions in soil moisture play a predominant role in shaping microbial biodiversity by decreasing the richness of bacteria (9.6%), fungi (14.5%) and protists (7.5%). Our results also show positive associations between microbial biodiversity and ecosystem functional processes, such as gross primary productivity and microbial biomass. We conclude that the detrimental effects of biodiversity loss might be more severe in a warmer world.}, }
@article {pmid35697683, year = {2022}, author = {Paredes, GF and Viehboeck, T and Markert, S and Mausz, MA and Sato, Y and Liebeke, M and König, L and Bulgheresi, S}, title = {Differential regulation of degradation and immune pathways underlies adaptation of the ectosymbiotic nematode Laxus oneistus to oxic-anoxic interfaces.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9725}, pmid = {35697683}, issn = {2045-2322}, support = {P28743-B22//Austrian Science Fund/ ; P28743-B22//Austrian Science Fund/ ; P28743-B22//Austrian Science Fund/ ; P28743-B22//Austrian Science Fund/ ; }, abstract = {Eukaryotes may experience oxygen deprivation under both physiological and pathological conditions. Because oxygen shortage leads to a reduction in cellular energy production, all eukaryotes studied so far conserve energy by suppressing their metabolism. However, the molecular physiology of animals that naturally and repeatedly experience anoxia is underexplored. One such animal is the marine nematode Laxus oneistus. It thrives, invariably coated by its sulfur-oxidizing symbiont Candidatus Thiosymbion oneisti, in anoxic sulfidic or hypoxic sand. Here, transcriptomics and proteomics showed that, whether in anoxia or not, L. oneistus mostly expressed genes involved in ubiquitination, energy generation, oxidative stress response, immune response, development, and translation. Importantly, ubiquitination genes were also highly expressed when the nematode was subjected to anoxic sulfidic conditions, together with genes involved in autophagy, detoxification and ribosome biogenesis. We hypothesize that these degradation pathways were induced to recycle damaged cellular components (mitochondria) and misfolded proteins into nutrients. Remarkably, when L. oneistus was subjected to anoxic sulfidic conditions, lectin and mucin genes were also upregulated, potentially to promote the attachment of its thiotrophic symbiont. Furthermore, the nematode appeared to survive oxygen deprivation by using an alternative electron carrier (rhodoquinone) and acceptor (fumarate), to rewire the electron transfer chain. On the other hand, under hypoxia, genes involved in costly processes (e.g., amino acid biosynthesis, development, feeding, mating) were upregulated, together with the worm's Toll-like innate immunity pathway and several immune effectors (e.g., bactericidal/permeability-increasing proteins, fungicides). In conclusion, we hypothesize that, in anoxic sulfidic sand, L. oneistus upregulates degradation processes, rewires the oxidative phosphorylation and reinforces its coat of bacterial sulfur-oxidizers. In upper sand layers, instead, it appears to produce broad-range antimicrobials and to exploit oxygen for biosynthesis and development.}, }
@article {pmid35697586, year = {2022}, author = {Ayeni, KI and Berry, D and Wisgrill, L and Warth, B and Ezekiel, CN}, title = {Early-life chemical exposome and gut microbiome development: African research perspectives within a global environmental health context.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2022.05.008}, pmid = {35697586}, issn = {1878-4380}, abstract = {The gut microbiome of neonates, infants, and toddlers (NITs) is very dynamic, and only begins to stabilize towards the third year of life. Within this period, exposure to xenobiotics may perturb the gut environment, thereby driving or contributing to microbial dysbiosis, which may negatively impact health into adulthood. Despite exposure of NITs globally, but especially in Africa, to copious amounts and types of xenobiotics - such as mycotoxins, pesticide residues, and heavy metals - little is known about their influence on the early-life microbiome or their effects on acute or long-term health. Within the African context, the influence of fermented foods, herbal mixtures, and the delivery environment on the early-life microbiome are often neglected, despite being potentially important factors that influence the microbiome. Consequently, data on in-depth understanding of the microbiome-exposome interactions is lacking in African cohorts. Collecting and evaluating such data is important because exposome-induced gut dysbiosis could potentially favor disease progression.}, }
@article {pmid35696896, year = {2022}, author = {Kazmi, SSUH and Uroosa,  and Xu, H and Xuexi, T}, title = {Corrigendum to "An approach to determining the nitrofurazone-induced toxic dynamics for ecotoxicity assessment using protozoan periphytons in marine ecosystems" [Mar. Pollut. Bull. 175 (2022) 113329 1-7].}, journal = {Marine pollution bulletin}, volume = {180}, number = {}, pages = {113836}, doi = {10.1016/j.marpolbul.2022.113836}, pmid = {35696896}, issn = {1879-3363}, }
@article {pmid35695510, year = {2022}, author = {Maciá-Vicente, JG and Bai, B and Qi, R and Ploch, S and Breider, F and Thines, M}, title = {Nutrient Availability Does Not Affect Community Assembly in Root-Associated Fungi but Determines Fungal Effects on Plant Growth.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0030422}, doi = {10.1128/msystems.00304-22}, pmid = {35695510}, issn = {2379-5077}, abstract = {Nonmycorrhizal root-colonizing fungi are key determinants of plant growth, driving processes ranging from pathogenesis to stress alleviation. Evidence suggests that they might also facilitate host access to soil nutrients in a mycorrhiza-like manner, but the extent of their direct contribution to plant nutrition is unknown. To study how widespread such capacity is across root-colonizing fungi, we surveyed soils in nutrient-limiting habitats using plant baits to look for fungal community changes in response to nutrient conditions. We established a fungal culture collection and used Arabidopsis thaliana inoculation bioassays to assess the ability of fungi to facilitate host's growth in the presence of organic nutrients unavailable to plants. Plant baits captured a representation of fungal communities extant in natural habitats and showed that nutrient limitation has little influence on community assembly. Arabidopsis thaliana inoculated with 31 phylogenetically diverse fungi exhibited a consistent fungus-driven growth promotion when supplied with organic nutrients compared to untreated plants. However, direct phosphorus measurement and RNA-seq data did not support enhanced nutrient uptake but rather that growth effects may result from changes in the plant's immune response to colonization. The widespread and consistent host responses to fungal colonization suggest that distinct, locally adapted nonmycorrhizal fungi affect plant performance across habitats. IMPORTANCE Recent studies have shown that root-associated fungi that do not engage in classical mycorrhizal associations can facilitate the hosts' access to nutrients in a mycorrhiza-like manner. However, the generality of this capacity remains to be tested. Root-associated fungi are frequently deemed major determinants of plant diversity and performance, but in the vast majority of cases their ecological roles in nature remain unknown. Assessing how these plant symbionts affect plant productivity, diversity, and fitness is important to understanding how plant communities function. Recent years have seen important advances in the understanding of the main drivers of the diversity and structure of plant microbiomes, but a major challenge is still linking community properties with function. This study contributes to the understanding of the cryptic function of root-associated fungi by testing their ability to participate in a specific process: nutrient acquisition by plants.}, }
@article {pmid35694162, year = {2022}, author = {Karl, CM and Vidakovic, A and Pjevac, P and Hausmann, B and Schleining, G and Ley, JP and Berry, D and Hans, J and Wendelin, M and König, J and Somoza, V and Lieder, B}, title = {Individual Sweet Taste Perception Influences Salivary Characteristics After Orosensory Stimulation With Sucrose and Noncaloric Sweeteners.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {831726}, doi = {10.3389/fnut.2022.831726}, pmid = {35694162}, issn = {2296-861X}, abstract = {Emerging evidence points to a major role of salivary flow and viscoelastic properties in taste perception and mouthfeel. It has been proposed that sweet-tasting compounds influence salivary characteristics. However, whether perceived differences in the sensory properties of structurally diverse sweet-tasting compounds contribute to salivary flow and saliva viscoelasticity as part of mouthfeel and overall sweet taste perception remains to be clarified. In this study, we hypothesized that the sensory diversity of sweeteners would differentially change salivary characteristics in response to oral sweet taste stimulation. Therefore, we investigated salivary flow and saliva viscoelasticity from 21 healthy test subjects after orosensory stimulation with sucrose, rebaudioside M (RebM), sucralose, and neohesperidin dihydrochalcone (NHDC) in a crossover design and considered the basal level of selected influencing factors, including the basal oral microbiome. All test compounds enhanced the salivary flow rate by up to 1.51 ± 0.12 g/min for RebM compared to 1.10 ± 0.09 g/min for water within the 1st min after stimulation. The increase in flow rate was moderately correlated with the individually perceived sweet taste (r = 0.3, p < 0.01) but did not differ between the test compounds. The complex viscosity of saliva was not affected by the test compounds, but the analysis of covariance showed that it was associated (p < 0.05) with mucin 5B (Muc5B) concentration. The oral microbiome was of typical composition and diversity but was strongly individual-dependent (permutational analysis of variance (PERMANOVA): R 2 = 0.76, p < 0.001) and was not associated with changes in salivary characteristics. In conclusion, this study indicates an impact of individual sweet taste impressions on the flow rate without measurable changes in the complex viscosity of saliva, which may contribute to the overall taste perception and mouthfeel of sweet-tasting compounds.}, }
@article {pmid35691180, year = {2022}, author = {Kazmi, SSUH and Uroosa,  and Xu, H and Warren, A}, title = {Corrigendum to "A community-based approach to analyzing the ecotoxicity of nitrofurazone using periphytic protozoa" [Mar. Pollut. Bull. 175 (2022) 113165 1-6].}, journal = {Marine pollution bulletin}, volume = {180}, number = {}, pages = {113837}, doi = {10.1016/j.marpolbul.2022.113837}, pmid = {35691180}, issn = {1879-3363}, }
@article {pmid35689685, year = {2022}, author = {Mills, JG and Selway, CA and Thomas, T and Weyrich, LS and Lowe, AJ}, title = {Schoolyard Biodiversity Determines Short-Term Recovery of Disturbed Skin Microbiota in Children.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35689685}, issn = {1432-184X}, abstract = {Creating biodiverse urban habitat has been proposed, with growing empirical support, as an intervention for increasing human microbial diversity and reducing associated diseases. However, ecological understanding of urban biodiversity interventions on human skin microbiota remains limited. Here, we experimentally test the hypotheses that disturbed skin microbiota recover better in outdoor schoolyard environments and that greater biodiversity provides a greater response. Repeating the experiment three times, we disturbed skin microbiota of fifty-seven healthy 10-to-11-year-old students with a skin swab (i.e., cleaning), then exposed them to one school environment-either a 'classroom' (n = 20), 'sports field' (n = 14), or biodiverse 'forest' (n = 23)-for 45 min. Another skin swab followed the exposure to compare 'before' and 'after' microbial communities. After 45 min, the disturbance immediately followed by outdoor exposure, especially the 'forest', had an enriching and diversifying effect on skin microbiota, while 'classroom' exposure homogenised inter-personal variability. Each effect compounded over consecutive days indicating longer-term exposure outcomes. The experimental disturbance also reduced the core skin microbiota, and only outdoor environments were able to replenish lost species richness to core membership (n species > 50% prevalent). Overall, we find that environmental setting, especially including biodiversity, is important in human microbiota recovery periods and that the outdoors provide resilience to skin communities. This work also has implications for the inclusion of short periods of outside or forest exposure in school scheduling. Future investigations of the health impacts of permanent urban biodiversity interventions are needed.}, }
@article {pmid35687346, year = {2022}, author = {Morata, A and Arroyo, T and Bañuelos, MA and Blanco, P and Briones, A and Cantoral, JM and Castrillo, D and Cordero-Bueso, G and Del Fresno, JM and Escott, C and Escribano-Viana, R and Fernández-González, M and Ferrer, S and García, M and González, C and Gutiérrez, AR and Loira, I and Malfeito-Ferreira, M and Martínez, A and Pardo, I and Ramírez, M and Ruiz-Muñoz, M and Santamaría, P and Suárez-Lepe, JA and Vilela, A and Capozzi, V}, title = {Wine yeast selection in the Iberian Peninsula: Saccharomyces and non-Saccharomyces as drivers of innovation in Spanish and Portuguese wine industries.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-29}, doi = {10.1080/10408398.2022.2083574}, pmid = {35687346}, issn = {1549-7852}, abstract = {Yeast selection for the wine industry in Spain started in 1950 for the understanding of the microbial ecology, and for the selection of optimal strains to improve the performance of alcoholic fermentation and the overall wine quality. This process has been strongly developed over the last 30 years, firstly on Saccharomyces cerevisiae, and, lately, with intense activity on non-Saccharomyces. Several thousand yeast strains have been isolated, identified and tested to select those with better performance and/or specific technological properties. The present review proposes a global survey of this massive ex-situ preservation of eukaryotic microorganisms, a reservoir of biotechnological solutions for the wine sector, overviewing relevant screenings that led to the selection of strains from 12 genera and 22 species of oenological significance. In the first part, the attention goes to the selection programmes related to relevant wine-producing areas (i.e. Douro, Extremadura, Galicia, La Mancha and Uclés, Ribera del Duero, Rioja, Sherry area, and Valencia). In the second part, the focus shifted on specific non-Saccharomyces genera/species selected from different Spanish and Portuguese regions, exploited to enhance particular attributes of the wines. A fil rouge of the dissertation is the design of tailored biotechnological solutions for wines typical of given geographic areas.}, }
@article {pmid35687002, year = {2022}, author = {Sterling, JJ and Sakihara, TS and Brannock, PM and Pearson, ZG and Maclaine, KD and Santos, SR and Havird, JC}, title = {Primary microbial succession in the anchialine ecosystem.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icac087}, pmid = {35687002}, issn = {1557-7023}, abstract = {When new land is created, initial microbial colonization lays the foundation for further ecological succession of plant and animal communities. Primary microbial succession of new aquatic habitats formed during volcanic activity has received little attention. The anchialine ecosystem, which includes coastal ponds in young lava flows, offers an opportunity to examine this process. Here, we characterized microbial communities of anchialine habitats in Hawaii that were created during volcanic eruptions in 2018. Benthic samples from three habitats were collected ∼2 years after their formation and at later time points spanning ∼1 year. Sequence profiling (16S and 18S) of prokaryotic and eukaryotic communities was used to test whether communities were similar to those from older, established anchialine habitats, and if community structure changed over time. Results show that microbial communities from the new habitats were unlike any from established anchialine microbial communities, having higher proportions of Planctomycetota and Chloroflexi but lower proportions of green algae. Each new habitat also harbored its own unique community relative to other habitats. While community composition in each habitat underwent statistically significant changes over time, they remained distinctive from established anchialine habitats. New habitats also had highly elevated temperatures compared to other habitats. These results suggest idiosyncratic microbial consortia form during early succession of Hawaiian anchialine habitats. Future monitoring will reveal whether the early communities described here remain stable after temperatures decline and macro-organisms become more abundant, or if microbial communities will continue to change and eventually resemble those of established habitats. This work is a key first step in examining primary volcanic succession in aquatic habitats and suggests young anchialine habitats may warrant special conservation status.}, }
@article {pmid35685924, year = {2022}, author = {Barcoto, MO and Rodrigues, A}, title = {Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {812143}, doi = {10.3389/fmicb.2022.812143}, pmid = {35685924}, issn = {1664-302X}, abstract = {Anthropogenic activities have extensively transformed the biosphere by extracting and disposing of resources, crossing boundaries of planetary threat while causing a global crisis of waste overload. Despite fundamental differences regarding structure and recalcitrance, lignocellulose and plastic polymers share physical-chemical properties to some extent, that include carbon skeletons with similar chemical bonds, hydrophobic properties, amorphous and crystalline regions. Microbial strategies for metabolizing recalcitrant polymers have been selected and optimized through evolution, thus understanding natural processes for lignocellulose modification could aid the challenge of dealing with the recalcitrant human-made polymers spread worldwide. We propose to look for inspiration in the charismatic fungal-growing insects to understand multipartite degradation of plant polymers. Independently evolved in diverse insect lineages, fungiculture embraces passive or active fungal cultivation for food, protection, and structural purposes. We consider there is much to learn from these symbioses, in special from the community-level degradation of recalcitrant biomass and defensive metabolites. Microbial plant-degrading systems at the core of insect fungicultures could be promising candidates for degrading synthetic plastics. Here, we first compare the degradation of lignocellulose and plastic polymers, with emphasis in the overlapping microbial players and enzymatic activities between these processes. Second, we review the literature on diverse insect fungiculture systems, focusing on features that, while supporting insects' ecology and evolution, could also be applied in biotechnological processes. Third, taking lessons from these microbial communities, we suggest multidisciplinary strategies to identify microbial degraders, degrading enzymes and pathways, as well as microbial interactions and interdependencies. Spanning from multiomics to spectroscopy, microscopy, stable isotopes probing, enrichment microcosmos, and synthetic communities, these strategies would allow for a systemic understanding of the fungiculture ecology, driving to application possibilities. Detailing how the metabolic landscape is entangled to achieve ecological success could inspire sustainable efforts for mitigating the current environmental crisis.}, }
@article {pmid35681050, year = {2022}, author = {Andreu-Sánchez, S and Aubert, G and Ripoll-Cladellas, A and Henkelman, S and Zhernakova, DV and Sinha, T and Kurilshikov, A and Cenit, MC and Jan Bonder, M and Franke, L and Wijmenga, C and Fu, J and van der Wijst, MGP and Melé, M and Lansdorp, P and Zhernakova, A}, title = {Genetic, parental and lifestyle factors influence telomere length.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {565}, pmid = {35681050}, issn = {2399-3642}, abstract = {The average length of telomere repeats (TL) declines with age and is considered to be a marker of biological ageing. Here, we measured TL in six blood cell types from 1046 individuals using the clinically validated Flow-FISH method. We identified remarkable cell-type-specific variations in TL. Host genetics, environmental, parental and intrinsic factors such as sex, parental age, and smoking are associated to variations in TL. By analysing the genome-wide methylation patterns, we identified that the association of maternal, but not paternal, age to TL is mediated by epigenetics. Single-cell RNA-sequencing data for 62 participants revealed differential gene expression in T-cells. Genes negatively associated with TL were enriched for pathways related to translation and nonsense-mediated decay. Altogether, this study addresses cell-type-specific differences in telomere biology and its relation to cell-type-specific gene expression and highlights how perinatal factors play a role in determining TL, on top of genetics and lifestyle.}, }
@article {pmid35680917, year = {2022}, author = {Willson, AM and Trugman, AT and Powers, JS and Smith-Martin, CM and Medvigy, D}, title = {Climate and hydraulic traits interact to set thresholds for liana viability.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3332}, pmid = {35680917}, issn = {2041-1723}, support = {1241874//National Science Foundation (NSF)/ ; Graduate Research Fellowship Program//National Science Foundation (NSF)/ ; 2003205//National Science Foundation (NSF)/ ; 2017949//National Science Foundation (NSF)/ ; 2018--67012--31496//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; DE--SC0014363//U.S. Department of Energy (DOE)/ ; DE--SC0020344//U.S. Department of Energy (DOE)/ ; DE--SC0014363//U.S. Department of Energy (DOE)/ ; DE--SC0020344//U.S. Department of Energy (DOE)/ ; }, abstract = {Lianas, or woody vines, and trees dominate the canopy of tropical forests and comprise the majority of tropical aboveground carbon storage. These growth forms respond differently to contemporary variation in climate and resource availability, but their responses to future climate change are poorly understood because there are very few predictive ecosystem models representing lianas. We compile a database of liana functional traits (846 species) and use it to parameterize a mechanistic model of liana-tree competition. The substantial difference between liana and tree hydraulic conductivity represents a critical source of inter-growth form variation. Here, we show that lianas are many times more sensitive to drying atmospheric conditions than trees as a result of this trait difference. Further, we use our competition model and projections of tropical hydroclimate based on Representative Concentration Pathway 4.5 to show that lianas are more susceptible to reaching a hydraulic threshold for viability by 2100.}, }
@article {pmid35680131, year = {2022}, author = {Kim, HJ and Kim, JH and Han, S and Kim, W}, title = {Compositional alteration of the nasal microbiome and Staphylococcus aureus-characterized dysbiosis in the nasal mucosa of patients with allergic rhinitis.}, journal = {Clinical and experimental otorhinolaryngology}, volume = {}, number = {}, pages = {}, doi = {10.21053/ceo.2021.01928}, pmid = {35680131}, issn = {1976-8710}, abstract = {Objectives: Host-microbial commensalism can shape the innate immune responses in the nasal mucosa, and the microbial characteristics of the nasal mucus directly impact the mechanisms of initial allergic responses in the nasal epithelium. We sought to determine alterations of the microbial composition in the nasal mucus of patients with allergic rhinitis (AR) and to elucidate the interplay between dysbiosis of the nasal microbiome and allergic inflammation.<br><br>Methods: A total of 364,923 high-quality bacterial 16S ribosomal RNA-encoding gene sequence reads from 104 samples from the middle turbinate mucosa of healthy participants and patients with AR was obtained and analyzed using the Quantitative Insights into Microbial Ecology pipeline.<br><br>Results: We analyzed the microbiota in samples of nasal mucus from patients with AR (n = 42) and clinically healthy participants (n = 30). Proteobacteria (Ralstonia genus) and Actinobacteria (Propionibacterium genus) phyla were predominant in the nasal mucus of healthy subjects, whereas the Firmicutes (Staphylococcus genus) phylum was significantly abundant in the nasal mucus of patients with AR. Especially, Ralstonia genus were significantly dominant in the clinically healthy subjects. Additional pyrosequencing data from 32 subjects (healthy participants: N=15, AR patients: N=17) revealed a greater abundance of Staphylococcus epidermidis, Corynebacterium accolens, and Nocardia coeliaca, accounting for 41.55% of mapped sequences in the nasal mucus of healthy participants. The dysbiosis of nasal microbiome was more pronounced and Staphylococcus aureus exhibited the greatest abundance (37.69%) in the presence of microbial distribution in the nasal mucus of patients with AR depending on the positive response to house dust mites and patient age and height.<br><br>Conclusion: This study revealed alterations in the nasal microbiome that occur in the nasal mucus of patients with AR at the levels of microbial genera and species. S. aureus-dominant dysbiosis was distinctive in the nasal mucus of patients with AR, suggesting a role of host-microbial commensalism in allergic inflammation.}, }
@article {pmid35679938, year = {2022}, author = {Wu, K and Tizzani, R and Zweers, H and Rijnaarts, H and Langenhoff, A and Fernandes, TV}, title = {Removal processes of individual and a mixture of organic micropollutants in the presence of Scenedesmus obliquus.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {156526}, doi = {10.1016/j.scitotenv.2022.156526}, pmid = {35679938}, issn = {1879-1026}, abstract = {Organic micropollutants (OMPs) need to be removed from wastewater as they can negatively affect aquatic organisms. It has been demonstrated that microalgae-based technologies are efficient in removing OMPs from wastewater. In this study, the removal processes and kinetics of six persistent OMPs (diclofenac, clarithromycin, benzotriazole, metoprolol, carbamazepine and mecoprop) were studied during cultivation of Scenedesmus obliquus in batch mode. These OMPs were added as individual compounds and in a mixture. Short experiments (8 days) were performed to avoid masking of OMP removal processes by light and nutrient limitation. The results show that diclofenac, clarithromycin, and benzotriazole were mainly removed by photodegradation (diclofenac), biodegradation (benzotriazole), or a combination of these two processes (clarithromycin). Peroxidase was involved in intracellular and extracellular biodegradation when benzotriazole was present as individual compound. Carbamazepine, metoprolol and mecoprop showed no biodegradation or photodegradation, and neglectable removal (<5%) by bioadsorption and bioaccumulation. Using an OMP mixture had an adverse effect on the photodegradation of clarithromycin and diclofenac, with reduced first-order kinetic constants compared to the individual compounds. Benzotriazole biodegradation was inhibited by the presence of the OMP mixture. This indicates that the presence of OMPs inhibits the photodegradation and biodegradation of some individual OMPs. These results will improve our understanding of removal processes of individual and mixtures of OMPs by microalgae-based technologies for wastewater treatment.}, }
@article {pmid35677244, year = {2022}, author = {Ahmad, M and Imtiaz, M and Shoib Nawaz, M and Mubeen, F and Imran, A}, title = {What Did We Learn From Current Progress in Heat Stress Tolerance in Plants? Can Microbes Be a Solution?.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {794782}, doi = {10.3389/fpls.2022.794782}, pmid = {35677244}, issn = {1664-462X}, abstract = {Temperature is a significant parameter in agriculture since it controls seed germination and plant growth. Global warming has resulted in an irregular rise in temperature posing a serious threat to the agricultural production around the world. A slight increase in temperature acts as stress and exert an overall negative impact on different developmental stages including plant phenology, development, cellular activities, gene expression, anatomical features, the functional and structural orientation of leaves, twigs, roots, and shoots. These impacts ultimately decrease the biomass, affect reproductive process, decrease flowering and fruiting and significant yield losses. Plants have inherent mechanisms to cope with different stressors including heat which may vary depending upon the type of plant species, duration and degree of the heat stress. Plants initially adapt avoidance and then tolerance strategies to combat heat stress. The tolerance pathway involves ion transporter, osmoprotectants, antioxidants, heat shock protein which help the plants to survive under heat stress. To develop heat-tolerant plants using above-mentioned strategies requires a lot of time, expertise, and resources. On contrary, plant growth-promoting rhizobacteria (PGPRs) is a cost-effective, time-saving, and user-friendly approach to support and enhance agricultural production under a range of environmental conditions including stresses. PGPR produce and regulate various phytohormones, enzymes, and metabolites that help plant to maintain growth under heat stress. They form biofilm, decrease abscisic acid, stimulate root development, enhance heat shock proteins, deamination of ACC enzyme, and nutrient availability especially nitrogen and phosphorous. Despite extensive work done on plant heat stress tolerance in general, very few comprehensive reviews are available on the subject especially the role of microbes for plant heat tolerance. This article reviews the current studies on the retaliation, adaptation, and tolerance to heat stress at the cellular, organellar, and whole plant levels, explains different approaches, and sheds light on how microbes can help to induce heat stress tolerance in plants.}, }
@article {pmid35677075, year = {2022}, author = {Lai, P and Nguyen, L and Okin, D and Drew, D and Battista, V and Jesudasen, S and Kuntz, T and Bhosle, A and Thompson, K and Reinicke, T and Lo, CH and Woo, J and Caraballo, A and Berra, L and Vieira, J and Huang, CY and Adhikari, UD and Kim, M and Sui, HY and Magicheva-Gupta, M and McIver, L and Goldberg, M and Kwon, D and Huttenhower, C and Chan, A}, title = {Metagenomic assessment of gut microbial communities and risk of severe COVID-19.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-1717624/v1}, pmid = {35677075}, abstract = {The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure. We profiled 127 hospitalized patients with COVID-19 (n=79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites. 48 species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or "long COVID", suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with predicting whether stool was obtained from patients with severe vs. moderate COVID-19. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease. Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to validate these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention.}, }
@article {pmid35676296, year = {2022}, author = {Suarez, C and Sedlacek, CJ and Gustavsson, DJI and Eiler, A and Modin, O and Hermansson, M and Persson, F}, title = {Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {47}, pmid = {35676296}, issn = {2055-5008}, support = {2018-01423//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/ ; 2018-01423//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/ ; 2018-01423//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/ ; ZK76//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; }, abstract = {The resistance and resilience provided by functional redundancy, a common feature of microbial communities, is not always advantageous. An example is nitrite oxidation in partial nitritation-anammox (PNA) reactors designed for nitrogen removal in wastewater treatment, where suppression of nitrite oxidizers like Nitrospira is sought. In these ecosystems, biofilms provide microhabitats with oxygen gradients, allowing the coexistence of aerobic and anaerobic bacteria. We designed a disturbance experiment where PNA biofilms, treating water from a high-rate activated sludge process, were constantly or intermittently exposed to anaerobic sidestream wastewater, which has been proposed to inhibit nitrite oxidizers. With increasing sidestream exposure we observed decreased abundance, alpha-diversity, functional versatility, and hence functional redundancy, among Nitrospira in the PNA biofilms, while the opposite patterns were observed for anammox bacteria within Brocadia. At the same time, species turnover was observed for aerobic ammonia-oxidizing Nitrosomonas populations. The different exposure regimens were associated with metagenomic assembled genomes of Nitrosomonas, Nitrospira, and Brocadia, encoding genes related to N-cycling, substrate usage, and osmotic stress response, possibly explaining the three different patterns by niche differentiation. These findings imply that disturbances can be used to manage the functional redundancy of biofilm microbiomes in a desirable direction, which should be considered when designing operational strategies for wastewater treatment.}, }
@article {pmid35675172, year = {2022}, author = {Jammer, A and Akhtar, SS and Amby, DB and Pandey, C and Mekureyaw, MF and Bak, F and Roth, PM and Roitsch, T}, title = {Enzyme activity profiling for physiological phenotyping within functional phenomics: plant growth and stress responses.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erac215}, pmid = {35675172}, issn = {1460-2431}, abstract = {High-throughput profiling of key enzyme activities of carbon, nitrogen, and antioxidant metabolism is emerging as a valuable approach to integrate cell physiological phenotyping into a holistic functional phenomics approach. However, the analyses of the large datasets generated by this method represent a bottleneck, often keeping researchers from exploiting the full potential of their studies. We address these limitations through the exemplary application of a set of data evaluation and visualisation tools within a case study. This includes the introduction of multivariate statistical analyses which can easily be implemented in similar studies, allowing researchers to extract more valuable information to identify enzymatic biosignatures. Through a literature meta-analysis, we demonstrate how enzyme activity profiling has already provided functional information on the mechanisms regulating plant development and response mechanisms to abiotic stress and pathogen attack. The high robustness of the distinct enzymatic biosignatures observed during developmental processes and under stress conditions underpins the enormous potential of enzyme activity profiling for future applications both in basic and applied research. Enzyme activity profiling will complement molecular -omics approaches to contribute to the mechanistic understanding required to narrow the genotype-to-phenotype knowledge gap and to identify predictive biomarkers for plant breeding to develop climate-resilient crops.}, }
@article {pmid35672295, year = {2022}, author = {Catania, T and Li, Y and Winzer, T and Harvey, D and Meade, F and Caridi, A and Leech, A and Larson, TR and Ning, Z and Chang, J and Van de Peer, Y and Graham, IA}, title = {A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3150}, pmid = {35672295}, issn = {2041-1723}, support = {833522//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; BB/K018809/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, abstract = {The STORR gene fusion event is considered essential for the evolution of the promorphinan/morphinan subclass of benzylisoquinoline alkaloids (BIAs) in opium poppy as the resulting bi-modular protein performs the isomerization of (S)- to (R)-reticuline essential for their biosynthesis. Here, we show that of the 12 Papaver species analysed those containing the STORR gene fusion also contain promorphinans/morphinans with one important exception. P. californicum encodes a functionally conserved STORR but does not produce promorphinans/morphinans. We also show that the gene fusion event occurred only once, between 16.8-24.1 million years ago before the separation of P. californicum from other Clade 2 Papaver species. The most abundant BIA in P. californicum is (R)-glaucine, a member of the aporphine subclass of BIAs, raising the possibility that STORR, once evolved, contributes to the biosynthesis of more than just the promorphinan/morphinan subclass of BIAs in the Papaveraceae.}, }
@article {pmid35669957, year = {2022}, author = {Adedayo, AA and Babalola, OO and Prigent-Combaret, C and Cruz, C and Stefan, M and Kutu, F and Glick, BR}, title = {The application of plant growth-promoting rhizobacteria in Solanum lycopersicum production in the agricultural system: a review.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13405}, doi = {10.7717/peerj.13405}, pmid = {35669957}, issn = {2167-8359}, abstract = {Food safety is a significant challenge worldwide, from plantation to cultivation, especially for perishable products such as tomatoes. New eco-friendly strategies are needed, and beneficial microorganisms might be a sustainable solution. This study demonstrates bacteria activity in the tomato plant rhizosphere. Further, it investigates the rhizobacteria's structure, function, and diversity in soil. Rhizobacteria that promote the growth and development of tomato plants are referred to as plant growth-promoting bacteria (PGPR). They form a series of associations with plants and other organisms in the soil through a mutualistic relationship where both parties benefit from living together. It implies the antagonistic activities of the rhizobacteria to deter pathogens from invading tomato plants through their roots. Some PGPR are regarded as biological control agents that hinder the development of spoilage organisms and can act as an alternative for agricultural chemicals that may be detrimental to the health of humans, animals, and some of the beneficial microbes in the rhizosphere soil. These bacteria also help tomato plants acquire essential nutrients like potassium (K), magnesium (Mg), phosphorus (P), and nitrogen (N). Some rhizobacteria may offer a solution to low tomato production and help tackle food insecurity and farming problems. In this review, an overview of soil-inhabiting rhizobacteria focused on improving the sustainable production of Solanum lycopersicum.}, }
@article {pmid35669004, year = {2022}, author = {Green, GBH and Williams, MB and Chehade, SB and Morrow, CD and Watts, SA and Bej, AK}, title = {High-throughput amplicon sequencing datasets of the metacommunity DNA of the gut microbiota of Zebrafish Danio rerio fed diets with differential quantities of protein and fat contents.}, journal = {Data in brief}, volume = {42}, number = {}, pages = {108313}, doi = {10.1016/j.dib.2022.108313}, pmid = {35669004}, issn = {2352-3409}, abstract = {In this paper, we present high-throughput amplicon sequence (HTS) datasets of the gut microbiota of male and female Zebrafish Danio rerio fed diets consisting of sub-optimal and above-optimal quantities of proteins and fats. The HTS datasets were generated using an Illumina MiSeq targeting the V4 hypervariable segment of the 16S rRNA gene. The raw sequence reads were quality checked, demultiplexed into FASTQ files, denoised using DADA2 (q2-dada2 denoise-paired), and subsampled. Taxonomic ids were then assigned to amplicon sequence variants (ASVs) against the silva-138-99-nb-classifier for taxonomic output using the Quantitative Insights Into Microbial Ecology (QIIME2 v2021.4). The resultant taxa list was generated at the phylum level to confirm the applicability of the HTS dataset using the "qiime taxa collapse" command. These HTS datasets of the metagenome can be accessed through the BioSample Submission Portal (https://www.ncbi.nlm.nih.gov/bioproject/) under the BioProject IDs PRJNA772302 and PRJNA772305.}, }
@article {pmid35668112, year = {2022}, author = {Berlanga-Clavero, MV and Molina-Santiago, C and Caraballo-Rodríguez, AM and Petras, D and Díaz-Martínez, L and Pérez-García, A and de Vicente, A and Carrión, VJ and Dorrestein, PC and Romero, D}, title = {Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {35668112}, issn = {2058-5276}, support = {PE 2600/1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GBMF7622//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; BacBio 637971//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; P20_00479//Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía (Ministry of Economy, Innovation, Science and Employment, Government of Andalucia)/ ; UMA18-FEDERJA-055//Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía (Ministry of Economy, Innovation, Science and Employment, Government of Andalucia)/ ; AGL2016-78662-R//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/ ; }, abstract = {Beneficial microorganisms are used to stimulate the germination of seeds; however, their growth-promoting mechanisms remain largely unexplored. Bacillus subtilis is commonly found in association with different plant organs, providing protection against pathogens or stimulating plant growth. We report that application of B. subtilis to melon seeds results in genetic and physiological responses in seeds that alter the metabolic and developmental status in 5-d and 1-month-old plants upon germination. We analysed mutants in different components of the extracellular matrix of B. subtilis biofilms in interaction with seeds and found cooperation in bacterial colonization of seed storage tissues and growth promotion. Combining confocal microscopy with fluorogenic probes, we found that two specific components of the extracellular matrix, amyloid protein TasA and fengycin, differentially increased the concentrations of reactive oxygen species inside seeds. Further, using electron and fluorescence microscopy and metabolomics, we showed that both TasA and fengycin targeted the oil bodies in the seed endosperm, resulting in specific changes in lipid metabolism and accumulation of glutathione-related molecules. In turn, this results in two different plant growth developmental programmes: TasA and fengycin stimulate the development of radicles, and fengycin alone stimulate the growth of adult plants and resistance in the phylloplane to the fungus Botrytis cinerea. Understanding mechanisms of bacterial growth promotion will enable the design of bespoke growth promotion strains.}, }
@article {pmid35667433, year = {2022}, author = {Van Le, A and Straub, D and Planer-Friedrich, B and Hug, SJ and Kleindienst, S and Kappler, A}, title = {Microbial communities contribute to the elimination of As, Fe, Mn, and NH4+ from groundwater in household sand filters.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {156496}, doi = {10.1016/j.scitotenv.2022.156496}, pmid = {35667433}, issn = {1879-1026}, abstract = {Household sand filters (SFs) are widely applied to remove iron (Fe), manganese (Mn), arsenic (As), and ammonium (NH4+) from groundwater in the Red River delta, Vietnam. Processes in the filters probably include a combination of biotic and abiotic reactions. However, there is limited information on the microbial communities treating varied groundwater compositions and on whether biological oxidation of Fe(II), Mn(II), As(III), and NH4+ contributes to the overall performance of SFs. We therefore analyzed the removal efficiencies, as well as the microbial communities and their potential activities, of SFs fed by groundwater with varying compositions from low (3.3 μg L-1) to high (600 μg L-1) As concentrations. The results revealed that Fe(II)-, Mn(II)-, NH4+-, and NO2--oxidizing microorganisms were prevalent and contributed to the performance of SFs. Additionally, groundwater composition was responsible for the differences among the present microbial communities. We found i) microaerophilic Fe(II) oxidation by Sideroxydans in all SFs, with the highest abundance in SFs fed by low-As and high-Fe groundwater, ii) Hyphomicropbiaceae as the main Mn(II)-oxidizers in all SFs, iii) As sequestration on formed Fe and Mn (oxyhydr)oxide minerals, iv) nitrification by ammonium-oxidizing archaea (AOA) followed by nitrite-oxidizing bacteria (NOB), and v) unexpectedly, the presence of a substantial amount of methane monooxygenase genes (pmoA), suggesting microbial methane oxidation taking place in SFs. Overall, our study revealed diverse microbial communities in SFs used for purifying arsenic-contaminated groundwater and our data indicate an important contribution of microbial activities to the key functional processes in SFs.}, }
@article {pmid35666722, year = {2022}, author = {Boezen, D and Ali, G and Wang, M and Wang, X and van der Werf, W and Vlak, JM and Zwart, MP}, title = {Empirical estimates of the mutation rate for an alphabaculovirus.}, journal = {PLoS genetics}, volume = {18}, number = {6}, pages = {e1009806}, doi = {10.1371/journal.pgen.1009806}, pmid = {35666722}, issn = {1553-7404}, abstract = {Mutation rates are of key importance for understanding evolutionary processes and predicting their outcomes. Empirical mutation rate estimates are available for a number of RNA viruses, but few are available for DNA viruses, which tend to have larger genomes. Whilst some viruses have very high mutation rates, lower mutation rates are expected for viruses with large genomes to ensure genome integrity. Alphabaculoviruses are insect viruses with large genomes and often have high levels of polymorphism, suggesting high mutation rates despite evidence of proofreading activity by the replication machinery. Here, we report an empirical estimate of the mutation rate per base per strand copying (s/n/r) of Autographa californica multiple nucleopolyhedrovirus (AcMNPV). To avoid biases due to selection, we analyzed mutations that occurred in a stable, non-functional genomic insert after five serial passages in Spodoptera exigua larvae. Our results highlight that viral demography and the stringency of mutation calling affect mutation rate estimates, and that using a population genetic simulation model to make inferences can mitigate the impact of these processes on estimates of mutation rate. We estimated a mutation rate of μ = 1×10-7 s/n/r when applying the most stringent criteria for mutation calling, and estimates of up to μ = 5×10-7 s/n/r when relaxing these criteria. The rates at which different classes of mutations accumulate provide good evidence for neutrality of mutations occurring within the inserted region. We therefore present a robust approach for mutation rate estimation for viruses with stable genomes, and strong evidence of a much lower alphabaculovirus mutation rate than supposed based on the high levels of polymorphism observed.}, }
@article {pmid35665438, year = {2022}, author = {Sun, J and Li, S and Fan, C and Cui, K and Tan, H and Qiao, L and Lu, L}, title = {N-Acetylglucosamine Promotes Tomato Plant Growth by Shaping the Community Structure and Metabolism of the Rhizosphere Microbiome.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0035822}, doi = {10.1128/spectrum.00358-22}, pmid = {35665438}, issn = {2165-0497}, abstract = {Communication between plants and microorganisms is vital because it influences their growth, development, defense, propagation, and metabolism in achieving maximal fitness. N-acetylglucosamine (N-GlcNAc), the building block of bacterial and fungal cell walls, was first reported to promote tomato plant growth via stimulation of microorganisms typically known to dominate the tomato root rhizosphere, such as members of Proteobacteria and Actinobacteria. Using KEGG pathway analysis of the rhizosphere microbial operational taxonomic units, the streptomycin biosynthesis pathway was enriched in the presence of N-GlcNAc. The biosynthesis of 3-hydroxy-2-butanone (acetoin) and 2,3-butanediol, two foremost types of plant growth promotion-related volatile organic compounds, were activated in both Bacillus subtilis and Streptomyces thermocarboxydus strains when they were cocultured with N-GlcNAc. In addition, the application of N-GlcNAc increased indole-3-acetic acid production in a dose-dependent manner in strains of Bacillus cereus, Proteus mirabilis, Pseudomonas putida, and S. thermocarboxydus that were isolated from an N-GlcNAc-treated tomato rhizosphere. Overall, this study found that N-GlcNAc could function as microbial signaling molecules to shape the community structure and metabolism of the rhizosphere microbiome, thereby regulating plant growth and development and preventing plant disease through complementary plant-microbe interactions. IMPORTANCE While the benefits of using plant growth-promoting rhizobacteria (PGPRs) to enhance crop production have been recognized and studied extensively under laboratory conditions, the success of their application in the field varies immensely. More fundamentally explicit processes of positive, plant-PGPRs interactions are needed. The utilization of organic amendments, such as chitin and its derivatives, is one of the most economical and practical options for improving soil and substrate quality as well as plant growth and resilience. In this study, we observed that the chitin monomer N-GlcNAc, a key microbial signaling molecule produced through interactions between chitin, soil microbes, and the plants, positively shaped the community structure and metabolism of the rhizosphere microbiome of tomatoes. Our findings also provide a new direction for enhancing the benefits and stability of PGPRs in the field.}, }
@article {pmid35662397, year = {2022}, author = {Yu, Y and van der Zwaag, M and Wedman, JJ and Permentier, H and Plomp, N and Jia, X and Kanon, B and Eggens-Meijer, E and Buist, G and Harmsen, H and Kok, J and Salles, JF and Wertheim, B and Hayflick, SJ and Strauss, E and Grzeschik, NA and Schepers, H and Sibon, OCM}, title = {Coenzyme A precursors flow from mother to zygote and from microbiome to host.}, journal = {Molecular cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molcel.2022.05.006}, pmid = {35662397}, issn = {1097-4164}, abstract = {Coenzyme A (CoA) is essential for metabolism and protein acetylation. Current knowledge holds that each cell obtains CoA exclusively through biosynthesis via the canonical five-step pathway, starting with pantothenate uptake. However, recent studies have suggested the presence of additional CoA-generating mechanisms, indicating a more complex system for CoA homeostasis. Here, we uncovered pathways for CoA generation through inter-organismal flows of CoA precursors. Using traceable compounds and fruit flies with a genetic block in CoA biosynthesis, we demonstrate that progeny survive embryonal and early larval development by obtaining CoA precursors from maternal sources. Later in life, the microbiome can provide the essential CoA building blocks to the host, enabling continuation of normal development. A flow of stable, long-lasting CoA precursors between living organisms is revealed. This indicates the presence of complex strategies to maintain CoA homeostasis.}, }
@article {pmid35661942, year = {2022}, author = {Schmid, K and Reis-Filho, JA and Loiola, M and Harvey, ES and de Kikuchi, RKP and Giarrizzo, T}, title = {Habitat-specific fish fauna responses to different management regimes in the largest coral reef complex in the South Atlantic.}, journal = {Marine environmental research}, volume = {178}, number = {}, pages = {105661}, doi = {10.1016/j.marenvres.2022.105661}, pmid = {35661942}, issn = {1879-0291}, abstract = {While marine protected areas (MPAs) are increasing worldwide, it is still needed to assess the effectiveness of those already consolidated. Methods and ecological assessments to understanding integrated and habitat-specific management regimes are still scarce and insufficient for policy implications and biodiversity conservation. Through Baited Remote Underwater Video (BRUV), we used fish assemblages as proxy of ecological and managerial status in two reef habitat types along three protection levels at Abrolhos Bank - the largest and most biodiverse coral reef complex of the South Atlantic. We found completely distinct responses in the fish fauna between the top (shallow) and bottom (deep) habitats of the unique "chapeirões" pinnacle reef formations. In the most protected zone (no-take), higher richness and abundance of commercial fish and more diverse trophic structure was observed. Particularly, large (sharks and groupers) and small carnivores (snappers) were more abundant and distributed more homogeneously over both reef habitats in the strictly enforced no-take zone. Abundance of these top-predators decreased from the low enforcement no-take zone to the multiple use area, where they were often absent while their typical preys (primary and secondary consumers) were thriving, notably in the top habitats. These outcomes highlight the importance to focus investigations not selectively on a single habitat type or depth zone in order to properly assess MPA effectiveness. Consequently, the monitoring and protection of fish species supported by marine spatial planning may benefit from an improved understanding of ecological functioning provided by MPA performance.}, }
@article {pmid35660593, year = {2022}, author = {Pensky, J and Fisher, AT and Gorski, G and Schrad, N and Dailey, H and Beganskas, S and Saltikov, C}, title = {Enhanced cycling of nitrogen and metals during rapid infiltration: Implications for managed recharge.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {156439}, doi = {10.1016/j.scitotenv.2022.156439}, pmid = {35660593}, issn = {1879-1026}, abstract = {We present results from a series of plot-scale field experiments to quantify physical infiltration dynamics and the influence of adding a carbon-rich, permeable reactive barrier (PRB) for the cycling of nitrogen and associated trace metals during rapid infiltration for managed aquifer recharge (MAR). Recent studies suggest that adding a bio-available carbon source to soils can enhance denitrification rates and associated N load reduction during moderate-to-rapid infiltration (≤1 m/day). We examined the potential for N removal during faster infiltration (>1 m/day), through coarse and carbon-poor soils, and how adding a carbon-rich PRB (wood chips) affects subsurface redox conditions and trace metal mobilization. During rapid infiltration, plots amended with a carbon-rich PRB generally demonstrated modest increases in subsurface loads of dissolved organic carbon, nitrite, manganese and iron, decreases in loads of nitrate and ammonium, and variable changes in arsenic. These trends differed considerably from those seen during infiltration through native soil without a carbon-rich PRB. Use of a carbon-rich soil amendment increased the fraction of dissolved N species that was removed at equivalent inflowing N loads. There is evidence that N removal took place primarily via denitrification. Shifts in microbial ecology following infiltration in all of the plots included increases in the relative abundances of microbes in the families Comamonadaceae, Pseudomonadaceae, Methylophilaceae, Rhodocyclaceae and Sphingomonadaceae, all of which contain genera capable of carrying out denitrification. These results, in combination with studies that have tested other soil types, flow rates, and system scales, show how water quality can be improved during infiltration for managed recharge, even during rapid infiltration, with a carbon-rich soil amendment.}, }
@article {pmid35659305, year = {2022}, author = {Chiriac, MC and Bulzu, PA and Andrei, AS and Okazaki, Y and Nakano, SI and Haber, M and Kavagutti, VS and Layoun, P and Ghai, R and Salcher, MM}, title = {Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {84}, pmid = {35659305}, issn = {2049-2618}, abstract = {BACKGROUND: The increased use of metagenomics and single-cell genomics led to the discovery of organisms from phyla with no cultivated representatives and proposed new microbial lineages such as the candidate phyla radiation (CPR or Patescibacteria). These bacteria have peculiar ribosomal structures, reduced metabolic capacities, small genome, and cell sizes, and a general host-associated lifestyle was proposed for the radiation. So far, most CPR genomes were obtained from groundwaters; however, their diversity, abundance, and role in surface freshwaters is largely unexplored. Here, we attempt to close these knowledge gaps by deep metagenomic sequencing of 119 samples of 17 different freshwater lakes located in Europe and Asia. Moreover, we applied Fluorescence in situ Hybridization followed by Catalyzed Reporter Deposition (CARD-FISH) for a first visualization of distinct CPR lineages in freshwater samples.<br><br>RESULTS: A total of 174 dereplicated metagenome-assembled genomes (MAGs) of diverse CPR lineages were recovered from the investigated lakes, with a higher prevalence from hypolimnion samples (162 MAGs). They have reduced genomes (median size 1 Mbp) and were generally found in low abundances (0.02-14.36 coverage/Gb) and with estimated slow replication rates. The analysis of genomic traits and CARD-FISH results showed that the radiation is an eclectic group in terms of metabolic capabilities and potential lifestyles, ranging from what appear to be free-living lineages to host- or particle-associated groups. Although some complexes of the electron transport chain were present in the CPR MAGs, together with ion-pumping rhodopsins and heliorhodopsins, we believe that they most probably adopt a fermentative metabolism. Terminal oxidases might function in O2 scavenging, while heliorhodopsins could be involved in mitigation against oxidative stress.<br><br>CONCLUSIONS: A high diversity of CPR MAGs was recovered, and distinct CPR lineages did not seem to be limited to lakes with specific trophic states. Their reduced metabolic capacities resemble the ones described for genomes in groundwater and animal-associated samples, apart from Gracilibacteria that possesses more complete metabolic pathways. Even though this radiation is mostly host-associated, we also observed organisms from different clades (ABY1, Paceibacteria, Saccharimonadia) that appear to be unattached to any other organisms or were associated with 'lake snow' particles (ABY1, Gracilibacteria), suggesting a broad range of potential life-strategies in this phylum. Video Abstract.}, }
@article {pmid35655089, year = {2022}, author = {Morelli, G and Patuzzi, I and Losasso, C and Ricci, A and Contiero, B and Andrighetto, I and Ricci, R}, title = {Characterization of intestinal microbiota in normal weight and overweight Border Collie and Labrador Retriever dogs.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9199}, pmid = {35655089}, issn = {2045-2322}, mesh = {Animals ; Bacteria/genetics ; Dogs ; Feces/microbiology ; Firmicutes/genetics ; *Gastrointestinal Microbiome/genetics ; Mice ; Obesity/microbiology ; Overweight/veterinary ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Obesity in dogs is an emerging issue that affects canine health and well-being. Its development is ascribed to several factors, including genetic predisposition and dietary management, and recent evidence suggests that intestinal microbiota may be involved as well. Previous works have shown obesity to be linked to significant changes in gut microbiota composition in humans and mice, but only limited information is available on the role played by canine gut microbiota. The aim of this exploratory study was to investigate whether composition of canine faecal microbiota may be influenced by overweight condition and breed. All the enrolled companion dogs were young adults, intact, healthy, and fed commercial extruded pet food; none had received antibiotics, probiotics or immunosuppressant drugs in the previous six months. Labrador Retriever (LR) and Border Collie (BC) were chosen as reference breeds and Body Condition Score (BCS) on a 9-point scale as reference method for evaluating body fat. The faecal microbial communities of 15 lean (BCS 4-5/9; 7 LRs and 8 BCs) and 14 overweight (BCS > 5/9; 8 LRs and 6 BCs) family dogs were analysed using 16S rRNA gene sequencing. Moreover, for each dog, the daily intake of energy (kcal/d) and dietary macronutrients (g/d) were calculated according to an accurate feeding history collection. Firmicutes and Bacteroidetes resulted the predominant phyla (51.5 ± 10.0% and 33.4 ± 8.5%, respectively) in all dogs. Bioinformatic and statistical analysis revealed that no bacterial taxon differed significantly based on body condition, except for genus Allisonella (p < 0.05); BC gut microbiota was richer (p < 0.05) in bacteria belonging to phyla Actinobacteria (family Coriobacteriaceae in particular) and Firmicutes (Allobaculum and Roseburia genera). No remarkable differences were recorded either for diversity indices (i.e., alpha diversity, p > 0.10) or for divergence within the sample set (i.e., beta diversity, p > 0.05). PERMANOVA tests performed on single factors demonstrated the tendency of dietary protein to influence the recruited dogs' microbiota beta-diversity at amplicon sequence variant level (p = 0.08). In conclusion, the faecal microbiota of dogs involved in this exploratory study showed no major variations based on body condition. However, our findings suggested that certain bacterial taxa previously acknowledged in obesity-related studies may be detected in dissimilar amounts depending on canine breed.}, }
@article {pmid35655088, year = {2022}, author = {de la Fuente Cantó, C and Diouf, MN and Ndour, PMS and Debieu, M and Grondin, A and Passot, S and Champion, A and Barrachina, C and Pratlong, M and Gantet, P and Assigbetsé, K and Kane, N and Cubry, P and Diedhiou, AG and Heulin, T and Achouak, W and Vigouroux, Y and Cournac, L and Laplaze, L}, title = {Genetic control of rhizosheath formation in pearl millet.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9205}, pmid = {35655088}, issn = {2045-2322}, support = {ANR17-CE20-0022-01//Agence Nationale de la Recherche/ ; ANR17-CE20-0022-01//Agence Nationale de la Recherche/ ; ANR-l0-LABX-0001-0l//Agence Nationale de la Recherche/ ; ANR-l0-LABX-0001-0l//Agence Nationale de la Recherche/ ; ANR-l0-LABX-0001-0l//Agence Nationale de la Recherche/ ; ANR-l0-LABX-0001-0l//Agence Nationale de la Recherche/ ; ANR17-CE20-0022-01//Agence Nationale de la Recherche/ ; ANR17-CE20-0022-01//Agence Nationale de la Recherche/ ; ANR17-CE20-0022-01//Agence Nationale de la Recherche/ ; ANR17-CE20-0022-01//Agence Nationale de la Recherche/ ; ANR17-CE20-0022-01//Agence Nationale de la Recherche/ ; GLDC//Consortium of International Agricultural Research Centers/ ; GLDC//Consortium of International Agricultural Research Centers/ ; GLDC//Consortium of International Agricultural Research Centers/ ; AF 1301-015//Agropolis Fondation/ ; AF 1301-015//Agropolis Fondation/ ; AF 1301-015//Agropolis Fondation/ ; AF 1301-015//Agropolis Fondation/ ; AF 1301-015//Agropolis Fondation/ ; AF 1301-015//Agropolis Fondation/ ; AF 1301-015//Agropolis Fondation/ ; AF 1301-015//Agropolis Fondation/ ; AF 1301-015//Agropolis Fondation/ ; FC 2013-0891//Fondazione Cariplo/ ; FC 2013-0891//Fondazione Cariplo/ ; FC 2013-0891//Fondazione Cariplo/ ; FC 2013-0891//Fondazione Cariplo/ ; FC 2013-0891//Fondazione Cariplo/ ; FC 2013-0891//Fondazione Cariplo/ ; FC 2013-0891//Fondazione Cariplo/ ; FC 2013-0891//Fondazione Cariplo/ ; FC 2013-0891//Fondazione Cariplo/ ; }, mesh = {Genome-Wide Association Study ; *Pennisetum/genetics ; Quantitative Trait Loci ; Rhizosphere ; Soil/chemistry ; }, abstract = {The rhizosheath, the layer of soil that adheres strongly to roots, influences water and nutrients acquisition. Pearl millet is a cereal crop that plays a major role for food security in arid regions of sub-Saharan Africa and India. We previously showed that root-adhering soil mass is a heritable trait in pearl millet and that it correlates with changes in rhizosphere microbiota structure and functions. Here, we studied the correlation between root-adhering soil mass and root hair development, root architecture, and symbiosis with arbuscular mycorrhizal fungi and we analysed the genetic control of this trait using genome wide association (GWAS) combined with bulk segregant analysis and gene expression studies. Root-adhering soil mass was weakly correlated only to root hairs traits in pearl millet. Twelve QTLs for rhizosheath formation were identified by GWAS. Bulk segregant analysis on a biparental population validated five of these QTLs. Combining genetics with a comparison of global gene expression in the root tip of contrasted inbred lines revealed candidate genes that might control rhizosheath formation in pearl millet. Our study indicates that rhizosheath formation is under complex genetic control in pearl millet and suggests that it is mainly regulated by root exudation.}, }
@article {pmid35654854, year = {2022}, author = {Monroy, S and Larrañaga, A and Martínez, A and Pérez, J and Molinero, J and Basaguren, A and Pozo, J}, title = {Temperature Sensitivity of Microbial Litter Decomposition in Freshwaters: Role of Leaf Litter Quality and Environmental Characteristics.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35654854}, issn = {1432-184X}, support = {CGL2010-22129-C04-01//Ministry of Science and Innovation of the Spanish Government/ ; BES-2012-060743//Spanish Ministry of Economy and Competitiveness/ ; DOKBERRI 2018 I//UPV/EHU/ ; }, abstract = {Ongoing global warming is expected to alter temperature-dependent processes. Nevertheless, how co-occurring local drivers will influence temperature sensitivity of plant litter decomposition in lotic ecosystems remains uncertain. Here, we examined the temperature sensitivity of microbial-mediated decomposition, microbial respiration, fungal biomass and leaf nutrients of two plant species varying in litter quality. We also assessed whether the type of microbial community and stream water characteristics influence such responses to temperature. We incubated alder (Alnus glutinosa) and eucalypt (Eucalyptus globulus) litter discs in three streams differing in autumn-winter water temperature (range 4.6-8.9 °C). Simultaneously, in laboratory microcosms, litter discs microbially conditioned in these streams were incubated at 5, 10 and 15 °C with water from the conditioning stream and with a water control from an additional stream. Both in the field and in the laboratory, higher temperatures enhanced litter decomposition rates, except for eucalypt in the field. Leaf quality modified the response of decomposition to temperature in the field, with eucalypt leaf litter showing a lower increase, whereas it did not in the laboratory. The origin of microbial community only affected the decomposition rates in the laboratory, but it did not modify the response to temperature. Water quality only defined the phosphorus content of the leaf litter or the fungal biomass, but it did not modify the response to temperature. Our results suggest that the acceleration in decomposition by global warming will be shaped by local factors, mainly by leaf litter quality, in headwater streams.}, }
@article {pmid35657425, year = {2022}, author = {Meena, M and Yadav, G and Sonigra, P and Nagda, A and Mehta, T and Swapnil, P and Harish,  and Marwal, A and Kumar, S}, title = {Multifarious Responses of Forest Soil Microbial Community Toward Climate Change.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35657425}, issn = {1432-184X}, abstract = {Forest soils are a pressing subject of worldwide research owing to the several roles of forests such as carbon sinks. Currently, the living soil ecosystem has become dreadful as a consequence of several anthropogenic activities including climate change. Climate change continues to transform the living soil ecosystem as well as the soil microbiome of planet Earth. The majority of studies have aimed to decipher the role of forest soil bacteria and fungi to understand and predict the impact of climate change on soil microbiome community structure and their ecosystem in the environment. In forest soils, microorganisms live in diverse habitats with specific behavior, comprising bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are influenced by biotic interactions and nutrient accessibility. Soil microbiome also drives multiple crucial steps in the nutrient biogeochemical cycles (carbon, nitrogen, phosphorous, and sulfur cycles). Soil microbes help in the nitrogen cycle through nitrogen fixation during the nitrogen cycle and maintain the concentration of nitrogen in the atmosphere. Soil microorganisms in forest soils respond to various effects of climate change, for instance, global warming, elevated level of CO2, drought, anthropogenic nitrogen deposition, increased precipitation, and flood. As the major burning issue of the globe, researchers are facing the major challenges to study soil microbiome. This review sheds light on the current scenario of knowledge about the effect of climate change on living soil ecosystems in various climate-sensitive soil ecosystems and the consequences for vegetation-soil-climate feedbacks.}, }
@article {pmid35655857, year = {2022}, author = {Wang, Y and Tian, L and Sun, L and Zhou, W and Zhi, W and Qing, J and Abdi Saed, Y and Dong, L and Zhang, X and Li, Y}, title = {Gut Microbes in Immunoglobulin A Nephropathy and Their Potential Therapeutic Applications.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {823267}, doi = {10.3389/fmed.2022.823267}, pmid = {35655857}, issn = {2296-858X}, abstract = {Microbial ecosystem consists of a complex community of bacterial interactions and its host microenvironment (tissue, cell, metabolite). Because the interaction between gut microbiota and host involves many diseases and seriously affects human health, the study of the interaction mechanism between gut microbiota and host has attracted great attention. The gut microbiome is made up of 100 trillion bacteria that have both beneficial and adverse effects on human health. The development of IgA Nephropathy results in changes in the intestinal microbial ecosystem that affect host physiology and health. Similarly, changes in intestinal microbiota also affect the development of IgA Nephropathy. Thus, the gut microbiome represents a novel therapeutic target for improving the outcome of IgA Nephropathy, including hematuria symptoms and disease progression. In this review, we summarize the effect of intestinal microbiota on IgA Nephropathy in recent years and it has been clarified that the intestinal microbiota has a great influence on the pathogenesis and treatment of IgA Nephropathy.}, }
@article {pmid35652980, year = {2022}, author = {Behairi, S and Baha, N and Barakat, M and Ortet, P and Achouak, W and Heulin, T and Kaci, Y}, title = {Bacterial diversity and community structure in the rhizosphere of the halophyte Halocnemum strobilaceum in an Algerian arid saline soil.}, journal = {Extremophiles : life under extreme conditions}, volume = {26}, number = {2}, pages = {18}, pmid = {35652980}, issn = {1433-4909}, support = {14MDU907//French-Algerian Hubert Curien Partnership Program (PHC) TASSILI/ ; }, abstract = {Hypersaline ecosystems host a particular microbiota, which can be specifically recruited by halophytes. In order to broaden our knowledge of hypersaline ecosystems, an in natura study was conducted on the microbiota associated with the halophyte Halocnemum strobilaceum from alkaline-saline arid soil in Algeria. We collected and identified a total of 414 strains isolated from root tissues (RT), root-adhering soil (RAS), non-adhering rhizospheric soil (NARS) and bulk soil (BS) using different NaCl concentrations. Our data showed that halophilic and halotolerant bacterial isolates in BS and the rhizosphere belonged to 32 genera distributed in Proteobacteria (49%), Firmicutes (36%), Actinobacteria (14%) and Bacteroidetes (1%). Bacterial population size and species diversity were greatly increased in the rhizosphere (factor 100). The reservoir of diversity in BS was dominated by the genera Bacillus and Halomonas. Bacillus/Halomonas ratio decreased with the proximity to the roots from 2.2 in BS to 0.3 at the root surface. Salt screening of the strains showed that species belonging to nine genera were able to grow up to 5.1 M NaCl. Thus, we found that H. strobilaceum exerted a strong effect on the diversity of the recruited microbiota with an affinity strongly attributed to the genus Halomonas.}, }
@article {pmid35652935, year = {2022}, author = {Lürling, M and Mucci, M and Douglas, GB}, title = {Response to "Risk of Collapse in Water Quality in the Guandu River (Rio de Janeiro, Brazil)" by Bacha et al., Published Online 23 August 2021, Microbial Ecology, 10.1007/s00248-021-01,839-z.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35652935}, issn = {1432-184X}, }
@article {pmid35652664, year = {2022}, author = {Smercina, DN and Kim, YM and Lipton, MS and Velickovic, D and Hofmockel, KS}, title = {Bulk and Spatially Resolved Extracellular Metabolome of Free-Living Nitrogen Fixation.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0050522}, doi = {10.1128/aem.00505-22}, pmid = {35652664}, issn = {1098-5336}, abstract = {Soil nitrogen (N) transformations constrain terrestrial net primary productivity and are driven by the activity of soil microorganisms. Free-living N fixation (FLNF) is an important soil N transformation and key N input to terrestrial systems, but the forms of N contributed to soil by FLNF are poorly understood. To address this knowledge gap, a focus on microorganisms and microbial scale processes is needed that links N-fixing bacteria and their contributed N sources to FLNF process rates. However, studying the activity of soil microorganisms in situ poses inherent challenges, including differences in sampling scale between microorganism and process rates, which can be addressed with culture-based studies and an emphasis on microbial-scale measurements. Culture conditions can differ significantly from soil conditions, so it also important that such studies include multiple culture conditions like liquid and solid media as proxies for soil environments like soil pore water and soil aggregate surfaces. Here we characterized extracellular N-containing metabolites produced by two common, diazotrophic soil bacteria in liquid and solid media, with or without N, across two sampling scales (bulk via GC-MS and spatially resolved via MALDI mass spec imaging). We found extracellular production of inorganic and organic N during FLNF, indicating terrestrial N contributions from FLNF occur in multiple forms not only as ammonium as previously thought. Extracellular metabolite profiles differed between liquid and solid media supporting previous work indicating environmental structure influences microbial function. Metabolite profiles also differed between sampling scales underscoring the need to quantify microbial scale conditions to accurately interpret microbial function. IMPORTANCE Free-living nitrogen-fixing bacteria contribute significantly to terrestrial nitrogen availability; however, the forms of nitrogen contributed by this process are poorly understood. This is in part because of inherent challenges to studying soil microorganisms in situ, such as vast differences in scale between microorganism and ecosystem and complexities of the soil system (e.g., opacity, chemical complexity). Thus, upscaling important ecosystem processes driven by soil microorganisms, like free-living nitrogen fixation, requires microbial-scale measurements in controlled systems. Our work generated bulk and spatially resolved measurements of nitrogen released during free-living nitrogen fixation under two contrasting growth conditions analogous to soil pores and aggregates. This work allowed us to determine that diverse forms of nitrogen are likely contributed to terrestrial systems by free-living nitrogen bacteria. We also demonstrated that microbial habitat (e.g., liquid versus solid media) alters microbial activity and that measurement of microbial activity is altered by sampling scale (e.g., bulk versus spatially resolved) highlighting the critical importance of quantifying microbial-scale processes to upscaling of ecosystem function.}, }
@article {pmid35651031, year = {2022}, author = {Huang, R and Shen, L and Yu, H and Jiang, J and Qin, Y and Liu, Y and Zhang, J and Song, Y}, title = {Evaluation of rain-shelter cultivation mode effects on microbial diversity during Cabernet Sauvignon (Vitis vinifera L.) maturation in Jingyang, Shaanxi, China.}, journal = {Food research international (Ottawa, Ont.)}, volume = {156}, number = {}, pages = {111165}, doi = {10.1016/j.foodres.2022.111165}, pmid = {35651031}, issn = {1873-7145}, abstract = {Rainfall particularly under continental climates with monsoonal tendency impacts the vineyard microbial niches during grapevine growth. With microbial community shifts, vine traits (grape flavor and yield) cultivated/protected under rain-shelter may ultimately be altered. Such cultivation may influence microflora dynamics via meteorological parameter variations, however this is unclear yet. Here, we used Cabernet Sauvignon, a prevalent red cultivar among wine growing regions, to evaluate the effects of the rain-shelter cultivation on the microorganism diversity. We found that average air temperature under rain-shelter conditions was 2-3 °C higher than the non-covered group, while air humidity the maximum reduction was 5.79% (p < 0.05). After grape setting stage, similar trends were observed on soil temperature (increased) and humidity (lowered) under the treatments (p < 0.05). UV and precipitation of rain-shelter treatment were less by a total of 72% and 96%, respectively (p < 0.05). The rain-shelter management presented lower fungal and bacterial OTUs. The fungal alpha diversity on leaves and branches under rain-shelter was lower (p < 0.05) than the control as the grape ripeness, with Ascomycota, Mycosphaerella and Cladosporium as the principal fungi. Our results revealed that the fungal microbiota patterns were differentiated by the cultivations from setting stage to the entire véraison and then tended to be similar at harvesting. Only branch fungal patterns were observed asymmetrically at all stages. Meanwhile, bacterial diversity and distribution varied on colonization locations where Proteobacteria and Actinobacteria were the primary bacteria phyla. Bacterial community structures overlapped at harvest, while the differences were observed between two cultivations at other stages, excluding grape berry. The rain-shelter cultivation reduced the abundance of Alternaria and Colletotrichum that may adversely affect grapevine health. Multivariate statistical analysis suggested that the effect of vineyard microclimate on microbiota distribution and succession were influenced by cultivation modes and grapevine developmental stages. This research provides evidence to address the dynamics of microbial ecology from vineyard to grape under rain-shelter cultivation, and its benefits as a sustainable vineyard management.}, }
@article {pmid35650293, year = {2022}, author = {Ren, Z and Ma, K and Jia, X and Wang, Q and Zhang, C and Li, X}, title = {Metagenomics Unveils Microbial Diversity and Their Biogeochemical Roles in Water and Sediment of Thermokarst Lakes in the Yellow River Source Area.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35650293}, issn = {1432-184X}, abstract = {Thermokarst lakes have long been recognized as biogeochemical hotspots, especially as sources of greenhouse gases. On the Qinghai-Tibet Plateau, thermokarst lakes are experiencing extensive changes due to faster warming. For a deep understanding of internal lake biogeochemical processes, we applied metagenomic analyses to investigate the microbial diversity and their biogeochemical roles in sediment and water of thermokarst lakes in the Yellow River Source Area (YRSA). Sediment microbial communities (SMCs) had lower species and gene richness than water microbial communities (WMCs). Bacteria were the most abundant component in both SMCs and WMCs with significantly different abundant genera. The functional analyses showed that both SMCs and WMCs had low potential in methanogenesis but strong in aerobic respiration, nitrogen assimilation, exopolyphosphatase, glycerophosphodiester phosphodiesterases, and polyphosphate kinase. Moreover, SMCs were enriched in genes involved in anaerobic carbon fixation, aerobic carbon fixation, fermentation, most nitrogen metabolism pathways, dissimilatory sulfate reduction, sulfide oxidation, polysulfide reduction, 2-phosphonopropionate transporter, and phosphate regulation. WMCs were enriched in genes involved in assimilatory sulfate reduction, sulfur mineralization, phosphonoacetate hydrolase, and phosphonate transport. Functional potentials suggest the differences of greenhouse gas emission, nutrient cycling, and living strategies between SMCs and WMCs. This study provides insight into the main biogeochemical processes and their properties in thermokarst lakes in YRSA, improving our understanding of the roles and fates of these lakes in a warming world.}, }
@article {pmid35648155, year = {2022}, author = {Ma, M and Chen, X and Li, S and Luo, J and Han, R and Xu, L}, title = {Composition and Diversity of Gut Bacterial Community in Different Life Stages of a Leaf Beetle Gastrolina depressa.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35648155}, issn = {1432-184X}, abstract = {Insect gut bacteria have a significant impact on host biology, which has a favorable or negative impact on insect fitness. The walnut leaf beetle (Gastrolina depressa) is a notorious pest in China, causing severe damage to Juglandaceae trees including Juglans regia and Pterocarya rhoifolia. To date, however, we know surprisingly little about the gut microbiota of G. depressa. This study used a high-throughput sequencing platform to investigate the gut bacterial community of G. depressa throughout its life cycle, including the 1st, 2nd, and 3rd instar larvae, as well as male, female, and pre-pregnant female adults. Our results showed that the diversity of the gut bacterial community in larvae was generally higher than that in adults, and young larvae (1st and 2nd larvae) possessed the most diversified and abundant community. Principal coordinate analysis results showed that the gut microbiota of adults cluster together, which is independent of the 1st and 2nd instar larvae. The main phyla were Proteobacteria and Firmicutes in the microbial community of G. depressa, while the dominant genera were Enterobacter, Rosenbergiella, Erwinia, Pseudomonas, and Lactococcus. The gut bacteria of G. depressa were mostly enriched in metabolic pathways (carbohydrate metabolism and amino acid metabolism) as revealed by functional prediction. This study contributes to a better knowledge of G. depressa's gut microbiota and its potential interactions with the host insect, facilitating the development of a microbial-based pest management strategy.}, }
@article {pmid35648154, year = {2022}, author = {Doniger, T and Kerfahi, D and Wachtel, C and Marais, E and Maggs-Kölling, G and Sherman, C and Adams, JM and Steinberger, Y}, title = {Plant Gender Affects Soil Fungal Microbiota Associated with Welwitschia mirabilis, an Unusual Desert Gymnosperm.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35648154}, issn = {1432-184X}, abstract = {In a recent study, we found a distinct soil bacterial community associated with male and female plants of the desert gymnosperm Welwitschia mirabilis. In this subsequent study, we also found that the soil fungal community associated with Welwitschia differs between male and female plants, and between unvegetated areas and the soil under plants. Site location, pH, and soil moisture also had an important influence on the composition of the fungal community. A number of Ascomycota and Chytrid species were found to be distinct indicators of male and female plants, respectively, but there was no overall difference at the phylum level or in terms of diversity. The unvegetated areas between plants also differed in terms of several Ascomycota OTUs. Network connectivity of the fungal communities was found to be higher under both male and female Welwitschia plants than in unvegetated control areas. As with the bacterial community, it is unclear what processes produce the gender-distinct fungal community, and also the more general plant-associated community, and also what the effects on the biology of the plants are. One possibility behind the gender-related difference in fungal community is that there are differences in the production of pollen or nectar between the two plant genders, affecting the below-ground soil community.}, }
@article {pmid35647000, year = {2022}, author = {Zhi, W and Song, W and Abdi Saed, Y and Wang, Y and Li, Y}, title = {Fecal Capsule as a Therapeutic Strategy in IgA Nephropathy: A Brief Report.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {914250}, doi = {10.3389/fmed.2022.914250}, pmid = {35647000}, issn = {2296-858X}, abstract = {In this brief report, we reported an IgA nephropathy (IgAN) patient who presented in November 2020 with an acute exacerbation with massive proteinuria and diarrhea. He had the earliest onset in 2018 when his IgAN was diagnosed by renal biopsy. He has been treated with active ACEI/ARB drugs for more than 90 days, intermittent steroid therapy, combined with anti-infective therapy. Although his acute symptoms resolved with each episode, he became increasingly severe as the interval between episodes shortened. Accordingly, the immunosuppressive drugs were administered under the KDIGO guidelines and related guidelines. However, the patient and his family refused this treatment. We pondered over the possible pathogenesis of IgAN, and after a full discussion with the patient and his family, FMT was administered to him after obtaining his informed consent. During the FMT procedure, one healthy volunteer (the doctor himself) also took the FMT capsules. In the end, the patient's urine protein dropped significantly and even turned negative after treatment. Neither the patient nor the healthy volunteer experienced any serious adverse effects during the use of the capsules and the subsequent 6-month follow-up period. We also used metagenomic sequencing to analyze the intestinal flora of patients before and after treatment, and a gradual increase stood out in the abundance of the patient's intestinal flora after drug administration.}, }
@article {pmid35646730, year = {2022}, author = {Yang, I and Claussen, H and Arthur, RA and Hertzberg, VS and Geurs, N and Corwin, EJ and Dunlop, AL}, title = {Subgingival Microbiome in Pregnancy and a Potential Relationship to Early Term Birth.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {873683}, doi = {10.3389/fcimb.2022.873683}, pmid = {35646730}, issn = {2235-2988}, abstract = {Background: Periodontal disease in pregnancy is considered a risk factor for adverse birth outcomes. Periodontal disease has a microbial etiology, however, the current state of knowledge about the subgingival microbiome in pregnancy is not well understood.<br><br>Objective: To characterize the structure and diversity of the subgingival microbiome in early and late pregnancy and explore relationships between the subgingival microbiome and preterm birth among pregnant Black women.<br><br>Methods: This longitudinal descriptive study used 16S rRNA sequencing to profile the subgingival microbiome of 59 Black women and describe microbial ecology using alpha and beta diversity metrics. We also compared microbiome features across early (8-14 weeks) and late (24-30 weeks) gestation overall and according to gestational age at birth outcomes (spontaneous preterm, spontaneous early term, full term).<br><br>Results: In this sample of Black pregnant women, the top twenty bacterial taxa represented in the subgingival microbiome included a spectrum representative of various stages of biofilm progression leading to periodontal disease, including known periopathogens Porphyromonas gingivalis and Tannerella forsythia. Other organisms associated with periodontal disease reflected in the subgingival microbiome included several Prevotella spp., and Campylobacter spp. Measures of alpha or beta diversity did not distinguish the subgingival microbiome of women according to early/late gestation or full term/spontaneous preterm birth; however, alpha diversity differences in late pregnancy between women who spontaneously delivered early term and women who delivered full term were identified. Several taxa were also identified as being differentially abundant according to early/late gestation, and full term/spontaneous early term births.<br><br>Conclusions: Although the composition of the subgingival microbiome is shifted toward complexes associated with periodontal disease, the diversity of the microbiome remains stable throughout pregnancy. Several taxa were identified as being associated with spontaneous early term birth. Two, in particular, are promising targets of further investigation. Depletion of the oral commensal Lautropia mirabilis in early pregnancy and elevated levels of Prevotella melaninogenica in late pregnancy were both associated with spontaneous early term birth.}, }
@article {pmid35644105, year = {2022}, author = {Bossaert, S and Kocijan, T and Winne, V and Schlich, J and Herrera-Malaver, B and Verstrepen, KJ and Van Opstaele, F and De Rouck, G and Crauwels, S and Lievens, B}, title = {Beer ethanol and iso-α-acid level affect microbial community establishment and beer chemistry throughout wood maturation of beer.}, journal = {International journal of food microbiology}, volume = {374}, number = {}, pages = {109724}, doi = {10.1016/j.ijfoodmicro.2022.109724}, pmid = {35644105}, issn = {1879-3460}, abstract = {Sour beers produced by barrel-aging of conventionally fermented beers are becoming increasingly popular. However, as the intricate interactions between the wood, the microbes and the beer are still unclear, wood maturation often leads to inconsistent end products with undesired sensory properties. Previous research on industrial barrel-aging of beer suggests that beer parameters like the ethanol content and bitterness play an important role in the microbial community composition and beer chemistry, but their exact impact still remains to be investigated. In this study, an experimentally tractable lab-scale system based on an in-vitro community of four key bacteria (Acetobacter malorum, Gluconobacter oxydans, Lactobacillus brevis and Pediococcus damnosus) and four key yeasts (Brettanomyces bruxellensis, Candida friedrichii, Pichia membranifaciens and Saccharomyces cerevisiae) that are consistently associated with barrel-aging of beer, was used to test the hypotheses that beer ethanol and bitterness impact microbial community composition and beer chemistry. Experiments were performed using different levels of ethanol (5.2 v/v%, 8 v/v% and 11 v/v%) and bitterness (13 ppm, 35 ppm and 170 ppm iso-α-acids), and beers were matured for 60 days. Samples were taken after 0, 10, 20, 30 and 60 days to monitor population densities and beer chemistry. Results revealed that all treatments and the maturation time significantly affected the microbial community composition and beer chemistry. More specifically, the ethanol treatments obstructed growth of L. brevis and G. oxydans and delayed fungal growth. The iso-α-acid treatments hindered growth of L. brevis and stimulated growth of P. membranifaciens, while the other strains remained unaffected. Beer chemistry was found to be affected by higher ethanol levels, which led to an increased extraction of wood-derived compounds. Furthermore, the distinct microbial communities also induced changes in the chemical composition of the beer samples, leading to concentration differences in beer- and wood-derived compounds like 4-ethyl guaiacol, 4-ethyl phenol, cis-oak lactone, vanillin, furfural and 5-hydroxymethyl furfural. Altogether, our results indicate that wood-aging of beer is affected by biotic and abiotic parameters, influencing the quality of the final product. Additionally, this work provides a new, cost-effective approach to study the production of barrel-aged beers based on a simplified microbial community model.}, }
@article {pmid35644095, year = {2022}, author = {Cao, Y and Zhao, J and Wang, Q and Bai, S and Yang, Q and Wei, Y and Wang, R}, title = {Industrial aerobic composting and the addition of microbial agents largely reduce the risks of heavy metal and ARG transfer through livestock manure.}, journal = {Ecotoxicology and environmental safety}, volume = {239}, number = {}, pages = {113694}, doi = {10.1016/j.ecoenv.2022.113694}, pmid = {35644095}, issn = {1090-2414}, abstract = {Composting is an effective and necessary modality in the recycling of agricultural wastes such as livestock manure, furfural, and straw. However, the risks of heavy metals (HMs) and antibiotic resistance genes (ARGs) during industrial-scale composting process have not been adequately assessed, especially with the addition of bacterial agents. In this study, changes in HMs toxicity, ARGs propagation and microbial community structure during industrial-scale aerobic composting of livestock manure were firstly investigated with various substrates addition. Moreover, the effect of the addition of bacterial agents (Bacillus strains) was evaluated. The results showed that industrial aerobic composting process could immobilize various HMs with different extents and significantly reduce the levels of ARGs such as intl1 and oqxB genes. The addition of Bacillus strains could further reduce the levels of most detected ARGs and the bioavailability of Cu and Cr, and the relative abundance of ereA and tetA was undetectable in some materials. After composting, the main bacterial community structures were similar among different substrates irrespective of bacterial agents and indicated that the composting process was the main driver for their change. This study provides a scientific reference for the safe reuse of livestock manure.}, }
@article {pmid35643931, year = {2022}, author = {Ueckermann, V and Lebre, P and Geldenhuys, J and Hoosien, E and Cowan, D and van Rensburg, LJ and Ehlers, M}, title = {The lung microbiome in HIV-positive patients with active pulmonary tuberculosis.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {8975}, pmid = {35643931}, issn = {2045-2322}, abstract = {Tuberculosis poses one of the greatest infectious disease threats of our time, especially when associated with human immunodeficiency virus (HIV) infection. Very little data is available on the lung microbiome in pulmonary tuberculosis (PTB) in HIV-positive patients. Three patient cohorts were studied: (i) HIV-positive with no respiratory disease (control cohort), (ii) HIV-positive with pneumonia and (iii) HIV-positive with PTB. Sputum specimens were collected in all patients and where possible a paired BALF was collected. DNA extraction was performed using the QIAamp DNA mini kit (QIAGEN, Germany) and extracted DNA specimens were sent to Inqaba Biotechnical Industries (Pty) Ltd for 16S rRNA gene sequence analysis using the Illumina platform (Illumina Inc, USA). Data analysis was performed using QIMME II and R Studio version 3.6.2 (2020). The lung microbiomes of patients with PTB, in the context of HIV co-infection, were dominated by Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Loss of biodiversity and dysbiosis was found in these patients when compared to the HIV-positive control cohort. Microbial community structure was also distinct from the control cohort, with the dominance of genera such as Achromobacter, Mycobacterium, Acinetobacter, Stenotrophomonas and Pseudomonas in those patients with PTB. This is the first study to describe the lung microbiome in patients with HIV and PTB co-infection and to compare findings with an HIV-positive control cohort. The lung microbiomes of patients with HIV and PTB were distinct from the HIV-positive control cohort without PTB, with an associated loss of microbial diversity.}, }
@article {pmid35643312, year = {2022}, author = {Chen, X and Chen, J and Yu, X and Sanganyado, E and Wang, L and Li, P and Liu, W}, title = {Effects of norfloxacin, copper, and their interactions on microbial communities in estuarine sediment.}, journal = {Environmental research}, volume = {212}, number = {Pt D}, pages = {113506}, doi = {10.1016/j.envres.2022.113506}, pmid = {35643312}, issn = {1096-0953}, abstract = {The discharge of antibiotics and metals in estuaries is of great concern since they threaten microbial communities that are critical for maintaining ecosystem function. To understand single and combined effects of norfloxacin (0-20 μg g-1) and copper (40 μg g-1) on microbial ecology in estuaries, we evaluated changes in bacteria population, inhibition rates, and microbial composition in estuarine sediments over a 28-day period. Bacteria population significantly decreased following single and combined exposure to norfloxacin and copper throughout the incubation period, except on Day 28 in treatments exposed to copper, 20 μg g-1 norfloxacin, or both. These three treatment groups had lower Shannon diversity and Simpson's indices on Day 28 than other treatments and the controls suggesting recovery in bacteria population did not correspond with recovery in richness and evenness. Furthermore, functional predictions revealed that the effect of time and contaminants were significantly different on some microbial community functions on Day 28, especially the combination of Cu and high concentration NFX, including aerobic chemoheterotrophy, methanol oxidation and methylotrophy. Thus, norfloxacin and copper had significant adverse effects on microbial communities in estuarine sediments; however, the combined effects were variable and depended on exposure duration and antibiotic concentration.}, }
@article {pmid35643062, year = {2022}, author = {Reinl, KL and Harris, TD and Elfferich, I and Coker, A and Zhan, Q and De Senerpont Domis, LN and Morales-Williams, AM and Bhattacharya, R and Grossart, HP and North, RL and Sweetman, JN}, title = {The role of organic nutrients in structuring freshwater phytoplankton communities in a rapidly changing world.}, journal = {Water research}, volume = {219}, number = {}, pages = {118573}, doi = {10.1016/j.watres.2022.118573}, pmid = {35643062}, issn = {1879-2448}, abstract = {Carbon, nitrogen, and phosphorus are critical macroelements in freshwater systems. Historically, researchers and managers have focused on inorganic forms, based on the premise that the organic pool was not available for direct uptake by phytoplankton. We now know that phytoplankton can tap the organic nutrient pool through a number of mechanisms including direct uptake, enzymatic hydrolysis, mixotrophy, and through symbiotic relationships with microbial communities. In this review, we explore these mechanisms considering current and projected future anthropogenically-driven changes to freshwater systems. In particular, we focus on how naturally- and anthropogenically- derived organic nutrients can influence phytoplankton community structure. We also synthesize knowledge gaps regarding phytoplankton physiology and the potential challenges of nutrient management in an organically dynamic and anthropogenically modified world. Our review provides a basis for exploring these topics and suggests several avenues for future work on the relation between organic nutrients and eutrophication and their ecological implications in freshwater systems.}, }
@article {pmid35643037, year = {2022}, author = {Arora, K and Carafa, I and Fava, F and Tuohy, KM and Nikoloudaki, O and Gobbetti, M and Cagno, RD}, title = {Sourdough performances of the golden cereal Tritordeum: Dynamics of microbial ecology, biochemical and nutritional features.}, journal = {International journal of food microbiology}, volume = {374}, number = {}, pages = {109725}, doi = {10.1016/j.ijfoodmicro.2022.109725}, pmid = {35643037}, issn = {1879-3460}, abstract = {The novel cereal 'Tritordeum' was employed in sourdough fermentation for bread making using a traditional backslopping procedure over 10 days. Culture-dependent and culture-independent approaches were used to characterize microbial ecology during sourdough preparation and propagation. Sourdough reached the highest microbial diversity after three days of propagation. Microbial diversity decreased as sourdough reached maturity (day 5). Microbiota dominance shifted from Weissella to Lactiplantibacillus genera after 5 days of propagation. Lactic acid bacteria (LAB) showed a constant increase throughout the propagations starting from 3.9 ± 0.24 log CFU g-1 on day 0 up to 8.0 ± 0.39 log CFU g-1 on day 5. Weissella confusa/cibaria and Weissella paramesenteroides were the most prevalent LAB species until day 5 of propagation, while Lactiplantibacillus plantarum was the most prevalent thereafter. Yeasts were present in low cell density (2.0 ± 0.11 log CFU g-1) until the fourth backslopping (day 4) and then gradually increased until day 10 (5.0 ± 0.29 log CFU g-1), with Saccharomyces cerevisiae being the most prevalent and dominant species. Lactic and acetic acid concentrations increased throughout Tritordeum sourdough propagations, indicative of a proportional decrease of fermentation quotient (lactic acid/acetic acid) from 13.54 ± 1.29 to 4.08 ± 0.15. Utilization of glucose, fructose and sucrose was observed, followed a progressive increase in mannitol concentrations beginning from day 4. The nutritional potential (total phenol content, antioxidant activity, dietary fiber content and total free amino acids) remained elevated during sourdough propagations. Antinutritional factors (phytic acid and raffinose) were reduced to minimal concentrations by day 10. Finally, texture analysis of Tritordeum sourdough bread was demonstrated to have better cohesiveness, resilience and firmness compared to baker's yeast bread, confirming its potential to improve functionality and use in sourdough biotechnology.}, }
@article {pmid35642946, year = {2022}, author = {Ginnan, NA and De Anda, NI and Campos Freitas Vieira, F and Rolshausen, PE and Roper, MC}, title = {Microbial Turnover and Dispersal Events Occur in Synchrony with Plant Phenology in the Perennial Evergreen Tree Crop Citrus sinensis.}, journal = {mBio}, volume = {}, number = {}, pages = {e0034322}, doi = {10.1128/mbio.00343-22}, pmid = {35642946}, issn = {2150-7511}, abstract = {Emerging research indicates that plant-associated microbes can alter plant developmental timing. However, it is unclear if host phenology affects microbial community assembly. Microbiome studies in annual or deciduous perennial plants face challenges in separating effects of tissue age from phenological driven effects on the microbiome. In contrast, evergreen perennial trees, like Citrus sinensis, retain leaves for years, allowing for uniform sampling of similarly aged leaves from the same developmental cohort. This aids in separating phenological effects on the microbiome from impacts due to annual leaf maturation/senescence. Here, we used this system to test the hypothesis that host phenology acts as a driver of microbiome composition. Citrus sinensis leaves and roots were sampled during seven phenological stages. Using amplicon-based sequencing, followed by diversity, phylogenetic, differential abundance, and network analyses, we examined changes in bacterial and fungal communities. Host phenological stage is the main determinant of microbiome composition, particularly within the foliar bacteriome. Microbial enrichment/depletion patterns suggest that microbial turnover and dispersal were driving these shifts. Moreover, a subset of community shifts were phylogenetically conserved across bacterial clades, suggesting that inherited traits contribute to microbe-microbe and/or plant-microbe interactions during specific phenophases. Plant phenology influences microbial community composition. These findings enhance understanding of microbiome assembly and identify microbes that potentially influence plant development and reproduction. IMPORTANCE Research at the forefront of plant microbiome studies indicates that plant-associated microbes can alter the timing of plant development (phenology). However, it is unclear if host phenological stage affects microbial community assembly. Microbiome studies in annual or deciduous perennial plants can face difficulty in separating effects of tissue age from phenological driven effects on the microbiome. Evergreen perennial plants, like sweet orange, maintain mature leaves for multiple years, allowing for uniform sampling of similarly aged tissue across host reproductive stages. Using this system, multiyear sampling, and high-throughput sequencing, we identified plant phenology as a major driver of microbiome composition, particularly within the leaf-associated bacterial communities. Distinct changes in microbial patterns suggest that microbial turnover and dispersal are mechanisms driving these community shifts. Additionally, closely related bacteria have similar abundance patterns across plant stages, indicating that inherited microbial traits may influence how bacteria respond to host developmental changes. Overall, this study illustrates that plant phenology does indeed govern microbiome seasonal shifts and identifies microbial candidates that may affect plant reproduction and development.}, }
@article {pmid35641581, year = {2022}, author = {Hu, S and He, R and Zeng, J and Zhao, D and Wang, S and He, F and Yu, Z and Wu, QL}, title = {Lower Compositional Variation and Higher Network Complexity of Rhizosphere Bacterial Community in Constructed Wetland Compared to Natural Wetland.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35641581}, issn = {1432-184X}, support = {2021NIGLAS-CJH01//Project of Young Scientist Group of NIGLAS/ ; QYZDJ-SSW-DQC030//Key Research Program of Frontier Science, CAS/ ; U2040201//National Natural Science Foundation of China/ ; 32022050//National Natural Science Foundation of China/ ; 31730013//National Natural Science Foundation of China/ ; 31971478//National Natural Science Foundation of China/ ; 32171563//National Natural Science Foundation of China/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; }, abstract = {Macrophyte rhizosphere microbes, as crucial components of the wetland ecosystem, play an important role in maintaining the function and stability of natural and constructed wetlands. Distinct environmental conditions and management practices between natural and constructed wetlands would affect macrophytes rhizosphere microbial communities and their associated functions. Nevertheless, the understanding of the diversity, composition, and co-occurrence patterns of the rhizosphere bacterial communities in natural and constructed wetlands remains unclear. Here, we used 16S rRNA gene high-throughput sequencing to characterize the bacterial community of the rhizosphere and bulk sediments of macrophyte Phragmites australis in representative natural and constructed wetlands. We observed higher alpha diversity of the bacterial community in the constructed wetland than that of the natural wetland. Additionally, the similarity of bacterial community composition between rhizosphere and bulk sediments in the constructed wetland was increased compared to that of the natural wetland. We also found that plants recruit specific taxa with adaptive functions in the rhizosphere of different wetland types. Rhizosphere samples of the natural wetland significantly enriched the functional bacterial groups that mainly related to nutrient cycling and plant-growth-promoting, while those of the constructed wetland-enriched bacterial taxa with potentials for biodegradation. Co-occurrence network analysis showed that the interactions among rhizosphere bacterial taxa in the constructed wetland were more complex than those of the natural wetland. This study broadens our understanding of the distinct selection processes of the macrophytes rhizosphere-associated microbes and the co-occurrence network patterns in different wetland types. Furthermore, our findings emphasize the importance of plant-microbe interactions in wetlands and further suggest P. australis rhizosphere enriched diverse functional bacteria that might enhance the wetland performance through biodegradation, nutrient cycling, and supporting plant growth.}, }
@article {pmid35640890, year = {2022}, author = {Sadiq, FA and Hansen, MF and Burmølle, M and Heyndrickx, M and Flint, S and Lu, W and Chen, W and Zhang, H}, title = {Towards understanding mechanisms and functional consequences of bacterial interactions with members of various kingdoms in complex biofilms that abound in nature.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuac024}, pmid = {35640890}, issn = {1574-6976}, abstract = {The microbial world represents a phenomenal diversity of microorganisms from different kingdoms of life which occupy an impressive set of ecological niches. Most, if not all, microorganisms once colonise a surface develop architecturally complex surface-adhered communities which we refer to as biofilms. They are embedded in polymeric structural scaffolds serve as a dynamic milieu for intercellular communication through physical and chemical signalling. Deciphering microbial ecology of biofilms in various natural or engineered settings has revealed co-existence of microorganisms from all domains of life, including Bacteria, Archaea and Eukarya. The coexistence of these dynamic microbes is not arbitrary, as a highly coordinated architectural setup and physiological complexity show ecological interdependence and myriads of underlying interactions. In this review, we describe how species from different kingdoms interact in biofilms and discuss the functional consequences of such interactions. We highlight metabolic advances of collaboration among species from different kingdoms, and advocate that these interactions are of great importance and need to be addressed in future research. Since trans-kingdom biofilms impact diverse contexts, ranging from complicated infections to efficient growth of plants, future knowledge within this field will be beneficial for medical microbiology, biotechnology, and our general understanding of microbial life in nature.}, }
@article {pmid35640512, year = {2022}, author = {Piras, F and Nakhla, G and Murgolo, S and De Ceglie, C and Mascolo, G and Bell, K and Jeanne, T and Mele, G and Santoro, D}, title = {Optimal integration of vacuum UV with granular biofiltration for advanced wastewater treatment: Impact of process sequence on CECs removal and microbial ecology.}, journal = {Water research}, volume = {220}, number = {}, pages = {118638}, doi = {10.1016/j.watres.2022.118638}, pmid = {35640512}, issn = {1879-2448}, abstract = {This study explored process synergies attainable by integrating a vacuum ultraviolet-based advanced oxidation process with biofiltration. A comparison using granular activated carbon or granular zeolite as filtration media were examined in context of advanced wastewater treatment for potable reuse. Six biofiltration columns, three with granular activated carbon and three with granular zeolite, were operated in parallel and batch-fed daily with nitrified secondary effluent. After achieving a pseudo-steady state through the filter columns, vacuum ultraviolet treatment was applied as pre-treatment or as post-treatment, at two different applied energies (i.e., VUV-E1=1 kWh/m3 and VUV-E10=10 kWh/m3). Once granular activated carbon had transitioned to biologically activated carbon, as determined based on soluble chemical oxygen demand removal, adsorption was still observed as the main mechanism for contaminants of emerging concern and nitrate removal. Vacuum ultraviolet pre-treatment markedly improved contaminants of emerging concern removal through the integrated system, achieving 40% at VUV-E1 and 90% at VUV-E10. When applied as post-treatment to zeolite column effluents, VUV-E1 and VUV-E10 further increased contaminants of emerging concern removal by 20% and 90%, respectively. In the zeolite system, vacuum ultraviolet pre-treatment also increased soluble chemical oxygen demand removal efficiency, indicating that higher energy vacuum ultraviolet increased biodegradability. Total prokaryotes were two-fold more abundant in biologically activated carbon than in zeolite, with vacuum ultraviolet pretreatment markedly affecting microbial diversity, both in terms of richness and composition. Media type only marginally affected microbial richness in the biofilters but showed a marked impact on structural composition. No clear relationship between compositional structure and depth was observed.}, }
@article {pmid35638872, year = {2022}, author = {Jonassen, KR and Ormåsen, I and Duffner, C and Hvidsten, TR and Bakken, LR and Vick, SHW}, title = {A Dual Enrichment Strategy Provides Soil- and Digestate-Competent Nitrous Oxide-Respiring Bacteria for Mitigating Climate Forcing in Agriculture.}, journal = {mBio}, volume = {}, number = {}, pages = {e0078822}, doi = {10.1128/mbio.00788-22}, pmid = {35638872}, issn = {2150-7511}, abstract = {Manipulating soil metabolism through heavy inoculation with microbes is feasible if organic wastes can be utilized as the substrate for growth and vector as a fertilizer. This, however, requires organisms active in both digestate and soil (generalists). Here, we present a dual enrichment strategy to enrich and isolate such generalists among N2O-respiring bacteria (NRB) in soil and digestates, to be used as an inoculum for strengthening the N2O-reduction capacity of soils. The enrichment strategy utilizes sequential batch enrichment cultures alternating between sterilized digestate and soil as substrates, with each batch initiated with limited O2 and unlimited N2O. The cultures were monitored for gas kinetics and community composition. As predicted by a Lotka-Volterra competition model, cluster analysis identified generalist operational taxonomic units (OTUs) which became dominant, digestate/soil-specialists which did not, and a majority that were gradually diluted out. We isolated several NRBs circumscribed by generalist OTUs. Their denitrification genes and phenotypes predicted a variable capacity to act as N2O-sinks, while all genomes predicted broad catabolic capacity. The latter contrasts with previous attempts to enrich NRB by anaerobic incubation of unsterilized digestate only, which selected for organisms with a catabolic capacity limited to fermentation products. The two isolates with the most promising characteristics as N2O sinks were a Pseudomonas sp. with a full-fledged denitrification-pathway and a Cloacibacterium sp. carrying only N2O reductase (clade II), and soil experiments confirmed their capacity to reduce N2O-emissions from soil. The successful enrichment of NRB with broad catabolic spectra suggests that the concept of dual enrichment should also be applicable for enrichment of generalists with traits other than N2O reduction. IMPORTANCE N2O emissions from farmed soils are a major source of climate forcing. Here, denitrifying bacteria act as both source and sink for N2O, determined by regulatory traits or the absence of genes coding for the enzymes producing or reducing N2O. One approach to reducing emissions is to amend large numbers of N2O-reducing bacteria (NRB) to soil. This was shown to be feasible by growing NRB to high densities in organic wastes and then applying them as fertilizers. The effect on N2O emissions, however, was transient because the isolated NRBs were unsuited to soil. Here, we have developed an enrichment strategy selecting for organisms with generalist lifestyles, tolerant of rapid environmental changes. This was used to isolate robust NRBs that grow both in digestate and when amended to soils. This strategy opens an avenue for obtaining not just robust NRBs to reduce N2O emissions, but any organism destined for application to complex environments.}, }
@article {pmid35638840, year = {2022}, author = {Zhang, S and Xia, X and Wang, J and Li, X and Xin, Y and Bao, J and Han, L and Qin, W and Yang, Z}, title = {Biogeographic Patterns and Elevational Differentiation of Sedimentary Bacterial Communities across River Systems in China.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0059722}, doi = {10.1128/aem.00597-22}, pmid = {35638840}, issn = {1098-5336}, abstract = {Bacterial biodiversity is tightly correlated with ecological functions of natural systems, and bacterial rare and abundant subcommunities make distinct contributions to ecosystem functioning. However, the biogeographic pattern and elevational differentiation of sedimentary bacterial diversity have rarely been studied in cross-river systems at a continental scale. This study analyzed the biogeographic patterns and elevational differentiations of the entire, abundant, and rare bacterial (sub)communities as well as the underlying mechanisms across nine rivers that span distinct geographic regions and large elevational gradients in China. We found that bacterial rare and abundant subcommunities shared similar biogeographic patterns and both demonstrated strong distance-decay relationships, despite their distinct community compositions. However, both null model and variation partitioning analysis results showed that while environmental selection governed rare subcommunity assemblies (contribution: 51.9%), dispersal limitation (62.7%) controlled the assembly of abundant subcommunities. The disparity was associated with the broader threshold width of abundant taxa to water temperature and pH variations than rare taxa. Elevation-induced bacterial composition variations were more evident than latitude-induced ones. Some specific operational taxonomic units (OTUs), representing 16.4% of the total sequences, much preferentially and even exclusively lived in high-elevation or low-elevation habitats and demonstrated some adaptations to local conditions. Greater positive: negative link ratios in bacterial co-occurrence networks of low elevations than high elevations (P < 0.05) partly resulted from their harboring higher organic carbon: nitrogen ratios. Together, this study draws a biogeographic picture of sedimentary bacterial communities in a continental-scale riverine system and highlights the importance of incorporating elevation-associated patterns of microbial diversity into riverine microbial ecology studies. IMPORTANCE Bacterial diversity is tightly correlated with the nutrient cycling of river systems. However, previous studies on bacterial diversity are mainly constrained to one single river system, although microbial biogeography and its drivers exhibit strong spatial scale dependence. Moreover, elevational differentiations of bacterial communities across river systems have also rarely been studied. Bacterial rare and abundant subcommunities make distinct contributions to ecosystem functioning, and they share similar biogeographic patterns in some environments but not in others. Therefore, we explored the biogeography of the entire, abundant, and rare (sub)communities in nine rivers that cover a wide space range and large elevational gradient in China. Our results revealed that bacterial rare and abundant subcommunities shared similar biogeographic patterns but their assembly mechanisms were much different in these rivers. Moreover, bacterial communities showed evident differentiations between high elevations and low elevations. These findings will facilitate a better understanding of bacterial diversity features in river systems.}, }
@article {pmid35633375, year = {2022}, author = {Araujo, ASF and de Araujo Pereira, AP and Melo, VMM and de Medeiros, EV and Mendes, LW}, title = {Environmental DNA Sequencing to Monitor Restoration Practices on Soil Bacterial and Archaeal Communities in Soils Under Desertification in the Brazilian Semiarid.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35633375}, issn = {1432-184X}, abstract = {Soils from Brazilian semiarid regions are highly vulnerable to desertification due to their geology, climate, human actions, and intensive land use that contribute to desertification. Therefore, areas under desertification have increased in the Brazilian semiarid region and it has negatively changed the soil bacterial and archaeal communities and their functionality. On the other hand, although restoration strategies are expensive and there are few soils restoration programs, some practices have been applied to restore these soils under desertification. For instance, conservationist practices and grazing exclusion have been strategically implemented, and they created a new altered soil condition for soil microbial communities, boosting soil microbial diversity. Here, we discuss the potential of these restoration strategies to recover the richness and diversity of soil bacterial and archaeal communities that were described through environmental DNA (eDNA) sequencing of soil samples. eDNA sequencing results show that areas where restoration strategies have been applied in regions under desertification in the Brazilian semiarid have increased species richness, diversity, and structure of the bacterial and archaeal community. In addition, network connectivity and functionality of the soil microorganisms have been improved over time. Altogether, we show that management strategies for soil restoration have positive effects on soil microbial communities and these effects can be monitored using the eDNA sequencing approach.}, }
@article {pmid35633186, year = {2022}, author = {Ravegnini, G and Fosso, B and Ricci, R and Gorini, F and Turroni, S and Serrano, C and Pilco-Janeta, DF and Zhang, Q and Zanotti, F and De Robertis, M and Nannini, M and Pantaleo, MA and Hrelia, P and Angelini, S}, title = {Analysis of microbiome in GISTs: looking for different players in tumorigenesis and novel therapeutic options.}, journal = {Cancer science}, volume = {}, number = {}, pages = {}, doi = {10.1111/cas.15441}, pmid = {35633186}, issn = {1349-7006}, abstract = {Preclinical forms of Gastrointestinal stromal tumor (GIST), small asymptomatic lesions, called micro-GIST, are detected in ~30% of the general population. GIST driver mutation can be already detected in microGISTs, even if they do not progress into malignant cancer; these mutations are necessary, but insufficient events to foster tumor progression. Here we profiled the tissue microbiota of 60 gastrointestinal specimens in three different patient cohorts -micro, low-risk (LR) and high-risk or metastatic GIST (HR/MET)-, exploring the compositional structure, predicted function and microbial networks, with the aim of providing a complete overview of microbial ecology in GIST and its preclinical form. Comparing microGISTs vs GISTs, both weighted and unweighted UniFrac and Bray-Curtis dissimilarities showed significant community-level separation between them and a pronounced difference in Proteobacteria, Firmicutes and Bacteroidota was observed. Through the LEfSe tool potential microbial biomarkers associated with a specific type of lesion was identified. In particular, GIST samples were significantly enriched in the phylum Proteobacteria compared to microGISTs. Several pathways involved in sugar metabolism were also highlighted in GISTs; this was expected as cancer usually displays high aerobic glycolysis in place of oxidative phosphorylation and rise of glucose flux to promote anabolic request. Our results highlight that the specific differences do exist in the tissue microbiome community between GIST and benign lesions and that microbiome restructuration can drive the carcinogenesis process.}, }
@article {pmid35631287, year = {2022}, author = {Sauvaitre, T and Van Herreweghen, F and Delbaere, K and Durif, C and Van Landuyt, J and Fadhlaoui, K and Huille, S and Chaucheyras-Durand, F and Etienne-Mesmin, L and Blanquet-Diot, S and Van de Wiele, T}, title = {Lentils and Yeast Fibers: A New Strategy to Mitigate Enterotoxigenic Escherichia coli (ETEC) Strain H10407 Virulence?.}, journal = {Nutrients}, volume = {14}, number = {10}, pages = {}, doi = {10.3390/nu14102146}, pmid = {35631287}, issn = {2072-6643}, abstract = {Dietary fibers exhibit well-known beneficial effects on human health, but their anti-infectious properties against enteric pathogens have been poorly investigated. Enterotoxigenic Escherichia coli (ETEC) is a major food-borne pathogen that causes acute traveler's diarrhea. Its virulence traits mainly rely on adhesion to an epithelial surface, mucus degradation, and the secretion of two enterotoxins associated with intestinal inflammation. With the increasing burden of antibiotic resistance worldwide, there is an imperious need to develop novel alternative strategies to control ETEC infections. This study aimed to investigate, using complementary in vitro approaches, the inhibitory potential of two dietary-fiber-containing products (a lentil extract and yeast cell walls) against the human ETEC reference strain H10407. We showed that the lentil extract decreased toxin production in a dose-dependent manner, reduced pro-inflammatory interleukin-8 production, and modulated mucus-related gene induction in ETEC-infected mucus-secreting intestinal cells. We also report that the yeast product reduced ETEC adhesion to mucin and Caco-2/HT29-MTX cells. Both fiber-containing products strengthened intestinal barrier function and modulated toxin-related gene expression. In a complex human gut microbial background, both products did not elicit a significant effect on ETEC colonization. These pioneering data demonstrate the promising role of dietary fibers in controlling different stages of the ETEC infection process.}, }
@article {pmid35630477, year = {2022}, author = {Johnson, MS and Burns, BP and Herdean, A and Angeloski, A and Ralph, P and Morris, T and Kindler, G and Wong, HL and Kuzhiumparambil, U and Sedger, LM and Larkum, AWD}, title = {A Cyanobacteria Enriched Layer of Shark Bay Stromatolites Reveals a New Acaryochloris Strain Living in Near Infrared Light.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, doi = {10.3390/microorganisms10051035}, pmid = {35630477}, issn = {2076-2607}, abstract = {The genus Acaryochloris is unique among phototrophic organisms due to the dominance of chlorophyll d in its photosynthetic reaction centres and light-harvesting proteins. This allows Acaryochloris to capture light energy for photosynthesis over an extended spectrum of up to ~760 nm in the near infra-red (NIR) spectrum. Acaryochloris sp. has been reported in a variety of ecological niches, ranging from polar to tropical shallow aquatic sites. Here, we report a new Acarychloris strain isolated from an NIR-enriched stratified microbial layer 4-6 mm under the surface of stromatolite mats located in the Hamelin Pool of Shark Bay, Western Australia. Pigment analysis by spectrometry/fluorometry, flow cytometry and spectral confocal microscopy identifies unique patterns in pigment content that likely reflect niche adaption. For example, unlike the original A. marina species (type strain MBIC11017), this new strain, Acarychloris LARK001, shows little change in the chlorophyll d/a ratio in response to changes in light wavelength, displays a different Fv/Fm response and lacks detectable levels of phycocyanin. Indeed, 16S rRNA analysis supports the identity of the A. marina LARK001 strain as close to but distinct from from the A. marina HICR111A strain first isolated from Heron Island and previously found on the Great Barrier Reef under coral rubble on the reef flat. Taken together, A. marina LARK001 is a new cyanobacterial strain adapted to the stromatolite mats in Shark Bay.}, }
@article {pmid35630422, year = {2022}, author = {Scoma, A and Khor, WC and Coma, M and Heyer, R and Props, R and Bouts, T and Benndorf, D and Li, D and Zhang, H and Rabaey, K}, title = {Lignocellulose Fermentation Products Generated by Giant Panda Gut Microbiomes Depend Ultimately on pH Rather than Portion of Bamboo: A Preliminary Study.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, doi = {10.3390/microorganisms10050978}, pmid = {35630422}, issn = {2076-2607}, abstract = {Giant pandas feed almost exclusively on bamboo but miss lignocellulose-degrading genes. Their gut microbiome may contribute to their nutrition; however, the limited access to pandas makes experimentation difficult. In vitro incubation of dung samples is used to infer gut microbiome activity. In pandas, such tests indicated that green leaves are largely fermented to ethanol at neutral pH and yellow pith to lactate at acidic pH. Pandas may feed on either green leaves or yellow pith within the same day, and it is unclear how pH, dung sample, fermentation products and supplied bamboo relate to one another. Additionally, the gut microbiome contribution to solid bamboo digestion must be appropriately assessed. Here, gut microbiomes derived from dung samples with mixed colors were used to ferment green leaves, also by artificially adjusting the initial pH. Gut microbiomes digestion of solid lignocellulose accounted for 30-40% of the detected final fermentation products. At pH 6.5, mixed-color dung samples had the same fermentation profile as green dung samples (mainly alcohols), while adjusting the initial pH to 4.5 resulted in the profile of yellow dung samples (mainly lactate). Metaproteomics confirmed that gut microbiomes attacked hemicellulose, and that the panda's alpha amylase was the predominant enzyme (up to 75%).}, }
@article {pmid35630387, year = {2022}, author = {Smercina, D and Zambare, N and Hofmockel, K and Sadler, N and Bredeweg, EL and Nicora, C and Markillie, LM and Aufrecht, J}, title = {Synthetic Soil Aggregates: Bioprinted Habitats for High-Throughput Microbial Metaphenomics.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, doi = {10.3390/microorganisms10050944}, pmid = {35630387}, issn = {2076-2607}, abstract = {The dynamics of microbial processes are difficult to study in natural soil, owing to the small spatial scales on which microorganisms operate and to the opacity and chemical complexity of the soil habitat. To circumvent these challenges, we have created a 3D-bioprinted habitat that mimics aspects of natural soil aggregates while providing a chemically defined and translucent alternative culturing method for soil microorganisms. Our Synthetic Soil Aggregates (SSAs) retain the porosity, permeability, and patchy resource distribution of natural soil aggregates-parameters that are expected to influence emergent microbial community interactions. We demonstrate the printability and viability of several different microorganisms within SSAs and show how the SSAs can be integrated into a multi-omics workflow for single SSA resolution genomics, metabolomics, proteomics, lipidomics, and biogeochemical assays. We study the impact of the structured habitat on the distribution of a model co-culture microbial community and find that it is significantly different from the spatial organization of the same community in liquid culture, indicating a potential for SSAs to reproduce naturally occurring emergent community phenotypes. The SSAs have the potential as a tool to help researchers quantify microbial scale processes in situ and achieve high-resolution data from the interplay between environmental properties and microbial ecology.}, }
@article {pmid35628778, year = {2022}, author = {Tao, S and Zhang, Y and Tian, C and Duplessis, S and Zhang, N}, title = {Elevated Ozone Concentration and Nitrogen Addition Increase Poplar Rust Severity by Shifting the Phyllosphere Microbial Community.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {5}, pages = {}, doi = {10.3390/jof8050523}, pmid = {35628778}, issn = {2309-608X}, support = {2021ZY02//Fundamental Research Funds for the Central Universities/ ; 2021M690418//China Postdoctoral Science Foundation/ ; }, abstract = {Tropospheric ozone and nitrogen deposition are two major environmental pollutants. A great deal of research has focused on the negative impacts of elevated O3 and the complementary effect of soil N addition on the physiological properties of trees. However, it has been overlooked how elevated O3 and N addition affect tree immunity in face of pathogen infection, as well as of the important roles of phyllosphere microbiome community in host-pathogen-environment interplay. Here, we examined the effects of elevated O3 and soil N addition on poplar leaf rust [Melampsora larici-populina] severity of two susceptible hybrid poplars [clone '107': Populus euramericana cv. '74/76'; clone '546': P. deltoides Í P. cathayana] in Free-Air-Controlled-Environment plots, in addition, the link between Mlp-susceptibility and changes in microbial community was determined using Miseq amplicon sequencing. Rust severity of clone '107' significantly increased under elevated O3 or N addition only; however, the negative impact of elevated O3 could be significantly mitigated when accompanied by N addition, likewise, this trade-off was reflected in its phyllosphere microbial α-diversity responding to elevated O3 and N addition. However, rust severity of clone '546' did not differ significantly in the cases of elevated O3 and N addition. Mlp infection altered microbial community composition and increased its sensitivity to elevated O3, as determined by the markedly different abundance of taxa. Elevated O3 and N addition reduced the complexity of microbial community, which may explain the increased severity of poplar rust. These findings suggest that poplars require a changing phyllosphere microbial associations to optimize plant immunity in response to environmental changes.}, }
@article {pmid35624481, year = {2022}, author = {Tian, Z and Pu, H and Cai, D and Luo, G and Zhao, L and Li, K and Zou, J and Zhao, X and Yu, M and Wu, Y and Yang, T and Guo, P and Hu, X}, title = {Characterization of the bacterial microbiota in different gut and oral compartments of splendid japalure (Japalura sensu lato).}, journal = {BMC veterinary research}, volume = {18}, number = {1}, pages = {205}, pmid = {35624481}, issn = {1746-6148}, support = {2019QD09//Doctor Launch Project of Yibin University/ ; 2019QD10//Doctor Launch Project of Yibin University/ ; XDA 20050201//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2019QZKK05010105//Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; }, abstract = {BACKGROUND: Gut and oral microbes form complex communities and play key roles in co-evolution with their hosts. However, little is understood about the bacterial community in lizards.<br><br>RESULTS: In this study, we investigated the gut and oral bacterial communities in Japalura sensu lato from Sichuan Province, China, using 16S rRNA gene sequencing. Results showed that Bacteroidota (36.5%) and Firmicutes (32.8%) were the main phyla in the gut, while Proteobacteria, Bacteroidota, Firmicutes, and Actinobacteriota were the dominant phyla in the oral cavity. 16 S rRNA sequencing analysis of fecal samples showed that: (1) Bacteroidota was the most abundant in Japalura sensu lato, which was different from the bacterial community of insectivorous animals; (2) Bacteroidota, Firmicutes, Actinobacteriota, Fusobacteriota, and Cyanobacteria were the most abundant phylum in Japalura sensu lato. (3) Proteobacteria was the dominant phylum in Japalura sensu lato and other domestic insectivorous lizards (Shinisaurus crocodilurus, Phrynocephalus vlangalii, and Takydromus septentrionalis); (4) Comparing with the bacterial community of Shinisaurus crocodilurus, Phrynocephalus vlangalii, Takydromus septentrionalis, Liolaemus parvus, L. ruibali, and Phymaturus williamsi, Desulfobacterota was uniquely present in the gut of Japalura sensu lato. 16 S rRNA sequencing of oral samples showed that Chloroflexi and Deinococcota phyla were enriched in the oral cavity, which may have a significant influence on living in extreme environments.<br><br>CONCLUSIONS: Thus, based on 16 S rRNA sequencing analysis of the community composition of the gut and oral microbiomes, this study firstly represents a foundation for understanding the gut and oral microbial ecology of Japalura sensu lato, and constitutes a detail account of the diversity of the microbiota inhabiting the gut and oral cavity of Japalura sensu lato. Further researches will continue to reveal how gut and oral microbial communities may be impacting the ecology and evolution of lizards.}, }
@article {pmid35624343, year = {2022}, author = {Vázquez, V and León, P and Gordillo, FJL and Jiménez, C and Concepción, I and Mackenzie, K and Bresnan, E and Segovia, M}, title = {High-CO2 Levels Rather than Acidification Restrict Emiliania huxleyi Growth and Performance.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35624343}, issn = {1432-184X}, support = {FC14-RNM-27//Universidad de Málaga/ ; }, abstract = {The coccolithophore Emiliania huxleyi shows a variety of responses to ocean acidification (OA) and to high-CO2 concentrations, but there is still controversy on differentiating between these two factors when using different strains and culture methods. A heavily calcified type A strain isolated from the Norwegian Sea was selected and batch cultured in order to understand whether acclimation to OA was mediated mainly by CO2 or H+, and how it impacted cell growth performance, calcification, and physiological stress management. Emiliania huxleyi responded differently to each acidification method. CO2-enriched aeration (1200 µatm, pH 7.62) induced a negative effect on the cells when compared to acidification caused by decreasing pH alone (pH 7.60). The growth rates of the coccolithophore were more negatively affected by high pCO2 than by low pH without CO2 enrichment with respect to the control (400 µatm, pH 8.1). High CO2 also affected cell viability and promoted the accumulation of reactive oxygen species (ROS), which was not observed under low pH. This suggests a possible metabolic imbalance induced by high CO2 alone. In contrast, the affinity for carbon uptake was negatively affected by both low pH and high CO2. Photochemistry was only marginally affected by either acidification method when analysed by PAM fluorometry. The POC and PIC cellular quotas and the PIC:POC ratio shifted along the different phases of the cultures; consequently, calcification did not follow the same pattern observed in cell stress and growth performance. Specifically, acidification by HCl addition caused a higher proportion of severely deformed coccoliths, than CO2 enrichment. These results highlight the capacity of CO2 rather than acidification itself to generate metabolic stress, not reducing calcification.}, }
@article {pmid35622094, year = {2022}, author = {Zhang, Z and Zhao, H and Mou, S and Nair, S and Zhao, J and Jiao, N and Zhang, Y}, title = {Phage Infection Benefits Marine Diatom Phaeodactylum tricornutum by Regulating the Associated Bacterial Community.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35622094}, issn = {1432-184X}, support = {2020YFA0608304//National Key Research and Development Programs of China/ ; }, abstract = {The interaction between marine phyto- and bacterioplankton is regulated by multiple environmental and biological factors. Among them, phages as the major regulators of bacterial mortality are considered to have important impacts on algae-associated bacteria and algae-bacteria relationship. However, little is currently known about the actual impact of phages from this perspective. Here, we revealed that phage infection improved the maximum quantum efficiency of photosystem II of Phaeodactylum tricornutum by regulating the associated bacterial community. Specifically, phage infection weakened bacterial abundance and eliminated their negative effects on the diatom. Unexpectedly, the structure of the bacterial community co-cultured with the diatom was not significantly affected, likely because the shaping effect of the diatom on the bacterial community structure can far outcompete or mask the impact of phage infection. Our results established a link between algae, bacteria, and phages, suggesting that phage infection benefits the diatom by regulating the associated bacterial community.}, }
@article {pmid35620054, year = {2022}, author = {Yaigoub, H and Tirichen, H and Xin, X and Shi, S and Wu, C and Li, R and Li, Y}, title = {Isolation of Viable Single Cells With High Yield and Purity Using a Small Amount of Human Kidney Tissue Biopsy.}, journal = {Frontiers in cell and developmental biology}, volume = {10}, number = {}, pages = {822275}, doi = {10.3389/fcell.2022.822275}, pmid = {35620054}, issn = {2296-634X}, abstract = {Objective: Establishment of an efficient method of preparing human kidney single cell suspension, using a very small amount of tissue puncture. Methods: Samples of human kidney tissue puncture were cut into pieces, and then 80 μL of the digestive enzyme were added to each punctured tissue to induce enzymatic digestion. The enzyme combination is composed of collagenases, DNase and hyaluronidase and the sample was incubated 20 min at 37°C. The obtained cell suspension was filtered through a 70 μm cell strainer, centrifuged at 300 g for 5 min and the supernatant was removed, then the pellet was resuspended in 3 ml of DMEM (Dulbecco's Modified Eagle's Medium). Cell suspension was sorted and purified by flow sorting to remove dead cells and obtain a cell suspension with higher viability rate. Results: We found that 1) diverse single cells of human kidney can be obtained by the digestive enzyme, as observed under the light microscope, with different sizes, normal cell morphology and good dispersion. 2) (2-3) × 106 single cells can be extracted from one fresh punctured kidney tissue of about 10 mg, with a cell viability rate of more than 80%. Conclusion: In this work we generated a comprehensive and high-resolution single-cell method, which is simple and efficient for preparing single cell suspension from a minimal amount of human kidney tissue. This method can facilitate the study of renal cell biology and the pathogenesis of kidney diseases.}, }
@article {pmid35618944, year = {2022}, author = {Lau, NS and Ting, SY and Sam, KK and M, J and Wong, SC and Wu, X and Waiho, K and Fazhan, H and Shu-Chien, AC}, title = {Comparative Analyses of Scylla olivacea Gut Microbiota Composition and Function Suggest the Capacity for Polyunsaturated Fatty Acid Biosynthesis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35618944}, issn = {1432-184X}, abstract = {Although numerous studies in aquatic organisms have linked lipid metabolism with intestinal bacterial structure, the possibility of the gut microbiota participating in the biosynthesis of beneficial long-chain polyunsaturated fatty acid (LC-PUFA) remains vague. We profiled the gut microbiota of the mud crab Scylla olivacea fed with either a LC-PUFA rich (FO) or a LC-PUFA-poor but C18-PUFA substrate-rich (LOCO) diet. Additionally, a diet with a similar profile as LOCO but with the inclusion of an antibiotic, oxolinic acid (LOCOAB), was also used to further demarcate the possibility of LC-PUFA biosynthesis in gut microbiota. Compared to diet FO treatment, crabs fed diet LOCO contained a higher proportion of Proteobacteria, notably two known taxonomy groups with PUFA biosynthesis capacity, Vibrio and Shewanella. Annotation of metagenomic datasets also revealed enrichment in the KEGG pathway of unsaturated fatty acid biosynthesis and polyketide synthase-like system sequences with this diet. Intriguingly, diet LOCOAB impeded the presence of Vibrio and Shewanella and with it, the function of unsaturated fatty acid biosynthesis. However, there was an increase in the function of short-chain fatty acid production, accompanied by a shift towards the abundance of phyla Bacteroidota and Spirochaetota. Collectively, these results exemplified bacterial communities and their corresponding PUFA biosynthesis pathways in the microbiota of an aquatic crustacean species.}, }
@article {pmid35617903, year = {2022}, author = {Xiong, C and Calatayud, M and van de Wiele, T and Francesconi, K}, title = {Gut microbiota metabolize arsenolipids in a donor dependent way.}, journal = {Ecotoxicology and environmental safety}, volume = {239}, number = {}, pages = {113662}, doi = {10.1016/j.ecoenv.2022.113662}, pmid = {35617903}, issn = {1090-2414}, abstract = {Understanding the interplay between the gut microbiome and arsenolipids can help us manage the potential health risk of consuming seafood, but little is known about the bioconversion fate of arsenolipids in the gastrointestinal tract. We use an in vitro mucosal simulator of the human intestinal microbial ecosystem (M-SHIME) to mimic the digestive tract of four healthy donors during exposure to two arsenolipids (an arsenic fatty acid AsFA 362 or an arsenic hydrocarbon AsHC 332). The metabolites were analyzed by HPLC-mass spectrometry. The human gut bacteria accumulated arsenolipids in a donor-dependent way, with higher retention of AsHC 332. Colonic microbiota partly transformed both arsenolipids to their thioxo analogs, while AsFA 362 was additionally transformed into arsenic-containing fatty esters, arsenic-containing fatty alcohols, and arsenic-containing sterols. There was no significant difference in water-soluble arsenicals between arsenolipid treatments. The study shows that arsenolipids can be quickly biotransformed into several lipid-soluble arsenicals of unknown toxicity, which cannot be excluded when considering potential implications on human health.}, }
@article {pmid35615500, year = {2022}, author = {Laber, CP and Pontiller, B and Bunse, C and Osbeck, CMG and Pérez-Martínez, C and Di Leo, D and Lundin, D and Legrand, C and Pinhassi, J and Farnelid, H}, title = {Seasonal and Spatial Variations in Synechococcus Abundance and Diversity Throughout the Gullmar Fjord, Swedish Skagerrak.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {828459}, doi = {10.3389/fmicb.2022.828459}, pmid = {35615500}, issn = {1664-302X}, abstract = {The picophytoplankton Synechococcus is a globally abundant autotroph that contributes significantly to primary production in the oceans and coastal areas. These cyanobacteria constitute a diverse genus of organisms that have developed independent niche spaces throughout aquatic environments. Here, we use the 16S V3-V4 rRNA gene region and flow cytometry to explore the diversity of Synechococcus within the picophytoplankton community in the Gullmar Fjord, on the west coast of Sweden. We conducted a station-based 1-year time series and two transect studies of the fjord. Our analysis revealed that within the large number of Synechococcus amplicon sequence variants (ASVs; 239 in total), prevalent ASVs phylogenetically clustered with clade representatives in both marine subcluster 5.1 and 5.2. The near-surface composition of ASVs shifted from spring to summer, when a 5.1 subcluster dominated community developed along with elevated Synechococcus abundances up to 9.3 × 104 cells ml-1. This seasonal dominance by subcluster 5.1 was observed over the length of the fjord (25 km), where shifts in community composition were associated with increasing depth. Unexpectedly, the community shift was not associated with changes in salinity. Synechococcus abundance dynamics also differed from that of the photosynthetic picoeukaryote community. These results highlight how seasonal variations in environmental conditions influence the dynamics of Synechococcus clades in a high latitude threshold fjord.}, }
@article {pmid35610383, year = {2022}, 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 = {}, number = {}, pages = {}, pmid = {35610383}, issn = {1432-184X}, 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 {pmid35610382, year = {2022}, author = {Dhar, K and Panneerselvan, L and Subashchandrabose, SR and Venkateswarlu, K and Megharaj, M}, title = {Anaerobic Degradation of Naphthalene and Pyrene by Sulfate-Reducing Cultures Enriched from Former Manufactured Gas Plant Soil.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35610382}, issn = {1432-184X}, support = {RTP scholarship//University of Newcastle/ ; }, abstract = {Biodegradation of polycyclic aromatic hydrocarbons (PAHs) under completely anaerobic sulfate-reducing conditions is an energetically challenging process. To date, anaerobic degradations of only two-ringed naphthalene and three-ringed phenanthrene by sediment-free and enriched sulfate-reducing bacteria have been reported. In this study, sulfate-reducing enrichment cultures capable of degrading naphthalene and four-ringed PAH, pyrene, were enriched from a contaminated former gas plant site soil. Bacterial community composition analysis revealed that a naphthalene-degrading enrichment culture, MMNap, was dominated (84.90%) by a Gram-positive endospore-forming member of the genus Desulfotomaculum with minor contribution (8.60%) from a member of Clostridium. The pyrene-degrading enrichment, MMPyr, was dominated (97.40%) by a species of Desulfotomaculum. The sequences representing the Desulfotomaculum phylotypes shared 98.80% similarity to each other. After 150 days of incubation, MMNap degraded 195 µM naphthalene with simultaneous reduction of sulfate and accumulation of sulfide. Similarly, MMPyr degraded 114 µM pyrene during 180 days of incubation with nearly stochiometric sulfate consumption and sulfide accumulation. In both cases, the addition of sulfate reduction inhibitor, molybdate (20 mM), resulted in complete cessation of the substrate utilization and sulfate reduction that clearly indicated the major role of the sulfate-reducing Desulfotomaculum in biodegradation of the two PAHs. This study is the first report on anaerobic pyrene degradation by a matrix-free, strictly anaerobic, and sulfate-reducing enrichment culture.}, }
@article {pmid35608637, year = {2022}, author = {Perini, L and Gostinčar, C and Likar, M and Frisvad, JC and Kostanjšek, R and Nicholes, M and Williamson, C and Anesio, AM and Zalar, P and Gunde-Cimerman, N}, title = {Interactions of Fungi and Algae from the Greenland Ice Sheet.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35608637}, issn = {1432-184X}, support = {675546//H2020 Marie Skłodowska-Curie Actions/ ; NE/M021025/1//Natural Environment Research Council/ ; 856416//H2020 European Research Council/ ; P1-0170//Javna Agencija za Raziskovalno Dejavnost RS/ ; P1-0198//Javna Agencija za Raziskovalno Dejavnost RS/ ; J4-2549//Javna Agencija za Raziskovalno Dejavnost RS/ ; DNRF137//Danmarks Grundforskningsfond/ ; 2871//Agilent Foundation/ ; }, abstract = {Heavily pigmented glacier ice algae Ancylonema nordenskiöldii and Ancylonema alaskanum (Zygnematophyceae, Streptophyta) reduce the bare ice albedo of the Greenland Ice Sheet, amplifying melt from the largest cryospheric contributor to eustatic sea-level rise. Little information is available about glacier ice algae interactions with other microbial communities within the surface ice environment, including fungi, which may be important for sustaining algal bloom development. To address this substantial knowledge gap and investigate the nature of algal-fungal interactions, an ex situ co-cultivation experiment with two species of fungi, recently isolated from the surface of the Greenland Ice Sheet (here proposed new species Penicillium anthracinoglaciei Perini, Frisvad and Zalar, Mycobank (MB 835602), and Articulospora sp.), and the mixed microbial community dominated by glacier ice algae was performed. The utilization of the dark pigment purpurogallin carboxylic acid-6-O-β-D-glucopyranoside (C18H18O12) by the two fungi was also evaluated in a separate experiment. P. anthracinoglaciei was capable of utilizing and converting the pigment to purpurogallin carboxylic acid, possibly using the sugar moiety as a nutrient source. Furthermore, after 3 weeks of incubation in the presence of P. anthracinoglaciei, a significantly slower decline in the maximum quantum efficiency (Fv/Fm, inverse proxy of algal stress) in glacier ice algae, compared to other treatments, was evident, suggesting a positive relationship between these species. Articulospora sp. did uptake the glycosylated purpurogallin, but did not seem to be involved in its conversion to aglycone derivative. At the end of the incubation experiments and, in conjunction with increased algal mortality, we detected a substantially increasing presence of the zoosporic fungi Chytridiomycota suggesting an important role for them as decomposers or parasites of glacier ice algae.}, }
@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 = {}, number = {}, pages = {e0046822}, doi = {10.1128/aem.00468-22}, pmid = {35607968}, issn = {1098-5336}, 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 {pmid35604764, year = {2022}, author = {Benítez-Páez, A and Hartstra, AV and Nieuwdorp, M and Sanz, Y}, title = {Species- and strain-level assessment using rrn long-amplicons suggests donor's influence on gut microbial transference via fecal transplants in metabolic syndrome subjects.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2078621}, doi = {10.1080/19490976.2022.2078621}, pmid = {35604764}, issn = {1949-0984}, abstract = {Fecal microbiota transplantation (FMT) is currently used for treating Clostridium difficile infection and explored for other clinical applications in experimental trials. However, the effectiveness of this therapy could vary, and partly depend on the donor's bacterial species engraftment, whose evaluation is challenging because there are no cost-effective strategies for accurately tracking the microbe transference. In this regard, the precise identification of bacterial species inhabiting the human gut is essential to define their role in human health unambiguously. We used Nanopore-based device to sequence bacterial rrn operons (16S-ITS-23S) and to reveal species-level abundance changes in the human gut microbiota of a FMT trial. By assessing the donor and recipient microbiota before and after FMT, we further evaluated whether this molecular approach reveals strain-level genetic variation to demonstrate microbe transfer and engraftment. Strict control over sequencing data quality and major microbiota covariates was critical for accurately estimating the changes in gut microbial species abundance in the recipients after FMT. We detected strain-level variation via single-nucleotide variants (SNVs) at rrn regions in a species-specific manner. We showed that it was possible to explore successfully the donor-bacterial strain (e.g., Parabacteroides merdae) engraftment in recipients of the FMT by assessing the nucleotide frequencies at rrn-associated SNVs. Our findings indicate that the engraftment of donors' microbiota is to some extent correlated with the improvement of metabolic health in recipients and that parameters such as the baseline gut microbiota configuration, sex, and age of donors should be considered to ensure the success of FMT in humans. The study was prospectively registered at the Dutch Trial registry - NTR4488 (https://www.trialregister.nl/trial/4488).}, }
@article {pmid35604433, year = {2022}, author = {Fang, J and Jiang, W and Meng, S and He, W and Wang, G and Guo, E and Yan, Y}, title = {Polychaete Bioturbation Alters the Taxonomic Structure, Co-occurrence Network, and Functional Groups of Bacterial Communities in the Intertidal Flat.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35604433}, issn = {1432-184X}, support = {41876185//National Natural Science Foundation of China/ ; 2020TD50//Central Public-interest Scientific Institution Basal Research Fund/ ; ZR2020QC046//Shandong Province Natural Science Foundation/ ; 2018YFJH0703//Key Projects of Science and Technology Innovation of Shandong Province/ ; }, abstract = {Polychaetes are important benthic macrofauna that lives in sediments, usually in intertidal flats with high organic content and high sulfide. It has been suggested that polychaete bioturbation could perform environmental remediation. During the process, the microbial community plays important roles. Here, we used high-throughput sequencing technology to study the bioturbation effects on the bacterial community in the polychaete (Perinereis aibuhitensis) burrows at different tidal positions in intertidal flat. The results showed that the bacterial communities were dramatically influenced by the polychaete bioturbation. The ACE, Chao, and Shannon indices of the polychaete burrows increased in summer. Dominant phyla in the polychaete burrows were Proteobacteria, Campilobacterota, Desulfobacterota, Chloroflexi, and Bacteroidota, and the dominant bacterial families were Sulfurvaceae, Flavobacteriaceae, Rhodobacteraceae, Woeseiaceae, Desulfobulbaceae, and Sulfurimonadaceae. Results of linear discriminant analysis effect size (LEfSe) showed that groups that include organic matter degraders, such as Bacteroidota, Flavobacteriaceae, Rhodobacteraceae, Woeseiaceae, and groups that include sulfur oxidizers, such as Campilobacterota, Sulfurovaceae, Rhodobacteraceae, Desulfobulbaceae, and Sulfurimonadaceae, were significantly increased due to the polychaete bioturbation. The polychaete bioturbation reduced the complexity of the bacterial co-occurrence network while increased its modularity and homogeneity. The polychaete bioturbation also changed the functional groups, which significantly enhanced in functional groups of aerobic nitrite oxidation, nitration, dark thiosulfate oxidation, dark sulfur oxidation, and dark sulfite oxidation, while nitrogen respiration and nitrate respiration decreased. These results provide insight into the impact of bacterial communities under the intertidal polychaete bioturbation.}, }
@article {pmid35604432, year = {2022}, author = {Salazar, B and Ortiz, A and Keswani, C and Minkina, T and Mandzhieva, S and Pratap Singh, S and Rekadwad, B and Borriss, R and Jain, A and Singh, HB and Sansinenea, E}, title = {Bacillus spp. as Bio-factories for Antifungal Secondary Metabolites: Innovation Beyond Whole Organism Formulations.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35604432}, issn = {1432-184X}, support = {LabNOTs-21-01AB//Ministry of Science and Higher Education of the Russian Federationt/ ; }, abstract = {Several fungi act as parasites for crops causing huge annual crop losses at both pre- and post-harvest stages. For years, chemical fungicides were the solution; however, their wide use has caused environmental contamination and human health problems. For this reason, the use of biofungicides has been in practice as a green solution against fungal phytopathogens. In the context of a more sustainable agriculture, microbial biofungicides have the largest share among the commercial biocontrol products that are available in the market. Precisely, the genus Bacillus has been largely studied for the management of plant pathogenic fungi because they offer a chemically diverse arsenal of antifungal secondary metabolites, which have spawned a heightened industrial engrossment of it as a biopesticide. In this sense, it is indispensable to know the wide arsenal that Bacillus genus has to apply these products for sustainable agriculture. Having this idea in our minds, in this review, secondary metabolites from Bacillus having antifungal activity are chemically and structurally described giving details of their action against several phytopathogens. Knowing the current status of Bacillus secreted antifungals is the base for the goal to apply these in agriculture and it is addressed in depth in the second part of this review.}, }
@article {pmid35602031, year = {2022}, author = {Schultz, J and Argentino, ICV and Kallies, R and Nunes da Rocha, U and Rosado, AS}, title = {Polyphasic Analysis Reveals Potential Petroleum Hydrocarbon Degradation and Biosurfactant Production by Rare Biosphere Thermophilic Bacteria From Deception Island, an Active Antarctic Volcano.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {885557}, doi = {10.3389/fmicb.2022.885557}, pmid = {35602031}, issn = {1664-302X}, abstract = {Extreme temperature gradients in polar volcanoes are capable of selecting different types of extremophiles. Deception Island is a marine stratovolcano located in maritime Antarctica. The volcano has pronounced temperature gradients over very short distances, from as high as 100°C in the fumaroles to subzero next to the glaciers. These characteristics make Deception a promising source of a variety of bioproducts for use in different biotechnological areas. In this study, we isolated thermophilic bacteria from sediments in fumaroles at two geothermal sites on Deception Island with temperatures between 50 and 100°C, to evaluate the potential capacity of these bacteria to degrade petroleum hydrocarbons and produce biosurfactants under thermophilic conditions. We isolated 126 thermophilic bacterial strains and identified them molecularly as members of genera Geobacillus, Anoxybacillus, and Brevibacillus (all in phylum Firmicutes). Seventy-six strains grew in a culture medium supplemented with crude oil as the only carbon source, and 30 of them showed particularly good results for oil degradation. Of 50 strains tested for biosurfactant production, 13 showed good results, with an emulsification index of 50% or higher of a petroleum hydrocarbon source (crude oil and diesel), emulsification stability at 100°C, and positive results in drop-collapse, oil spreading, and hemolytic activity tests. Four of these isolates showed great capability of degrade crude oil: FB2_38 (Geobacillus), FB3_54 (Geobacillus), FB4_88 (Anoxybacillus), and WB1_122 (Geobacillus). Genomic analysis of the oil-degrading and biosurfactant-producer strain FB4_88 identified it as Anoxybacillus flavithermus, with a high genetic and functional diversity potential for biotechnological applications. These initial culturomic and genomic data suggest that thermophilic bacteria from this Antarctic volcano have potential applications in the petroleum industry, for bioremediation in extreme environments and for microbial enhanced oil recovery (MEOR) in reservoirs. In addition, recovery of small-subunit rRNA from metagenomes of Deception Island showed that Firmicutes is not among the dominant phyla, indicating that these low-abundance microorganisms may be important for hydrocarbon degradation and biosurfactant production in the Deception Island volcanic sediments.}, }
@article {pmid35601228, year = {2022}, author = {Emmanuel Sunday, O and Chinasa Valerie, O and Ndidi Ethel, N and Charles Obinwanne, O and Chidiebele Emmanuel Ikechukwu, N and Chisom Joshua, O}, title = {Microbial Ecology and Evolution is key to Pandemics: using the Coronavirus model to mitigate future Public Health Challenges.}, journal = {Heliyon}, volume = {}, number = {}, pages = {e09449}, doi = {10.1016/j.heliyon.2022.e09449}, pmid = {35601228}, issn = {2405-8440}, abstract = {Pandemics are global challenges that lead to total disruption of human activities. From the inception of human existence, all pandemics have resulted in loss of human lives. The coronavirus disease caused by SAR-CoV-2 began in China and is now at the global scale with an increase in mortality and morbidity. Numerous anthropogenic activities have been implicated in the emergence and severity of pandemics, including COVID-19. These activities cause changes in microbial ecology, leading to evolution due to mutation and recombination. This review hypothesized that an understanding of these anthropogenic activities would explain the dynamics of pandemics. We used the recent coronavirus model to study issues leading to microbial evolution, preventing future pandemics. Our review highlighted anthropogenic activities, including deforestation, mining activities, waste treatment, burning of fossil fuel, as well as international travels as drivers of microbial evolution leading to pandemics. Furthermore, human-animal interaction has also been implicated in pandemic incidents. Our study recommends substantial control of such anthropogenic activities as having been highlighted as ways to reduce the frequency of mutation, reduce pathogenic reservoirs, and the emergence of infectious disease.}, }
@article {pmid35598673, year = {2022}, author = {Abel, SM and Primpke, S and Wu, F and Brandt, A and Gerdts, G}, title = {Human footprints at hadal depths: Interlayer and intralayer comparison of sediment cores from the Kuril Kamchatka trench.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {156035}, doi = {10.1016/j.scitotenv.2022.156035}, pmid = {35598673}, issn = {1879-1026}, abstract = {Microplastic (MP) pollution affects almost all ecosystems on Earth. Given the increasing plastic production worldwide and the durability of these polymers, concerns arise about the fate of this material in the environment. A candidate to consider as a depositional final sink of MP is the sea floor and its deepest representatives, hadal trenches, as ultimate sinks. In this study, 13 sediment samples were collected with a multiple-corer at depths between 5740 and 9450 m from the Kuril Kamchatka trench (KKT), in the Northwest (NW) Pacific Ocean. These samples were analysed for MP presence in the upper sediment layer, by slicing the first 5 cm of sediment cores into 1 cm horizontal layers. These were compared against each other and between the sampling areas, in order to achieve a detailed picture of the depositional system of the trench and small-scale perturbations such as bioturbation. The analyses revealed the presence of 215 to 1596 MP particles per kg -1 sediment (dry weight), with a polymer composition represented by 14 polymer types and the prevalence of particles smaller than 25 μm. A heterogeneous microplastic distribution through the sediment column and different microplastic concentration and polymer types among sampling stations located in different areas of the trench reflects the dynamics of this environment and the numerous forces that drive the deposition processes and the in situ recast of this pollutant at the trench floor.}, }
@article {pmid35598661, year = {2022}, author = {Müller, V and Chavez-Capilla, T and Feldmann, J and Mestrot, A}, title = {Increasing temperature and flooding enhance arsenic release and biotransformations in Swiss soils.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {156049}, doi = {10.1016/j.scitotenv.2022.156049}, pmid = {35598661}, issn = {1879-1026}, abstract = {Reductive dissolution is one of the main causes for arsenic (As) mobilisation in flooded soils while biomethylation and biovolatilisation are two microbial mechanisms that greatly influence the mobility and toxicity of As. Climate change results in more extreme weather events such as flooding and higher temperatures, potentially leading to an increase in As release and biotransformations. Here, we investigated the effects of flooding and temperature on As release, biomethylation and biovolatilisation from As-rich soils with different pH and source of As (one acidic and anthropogenic (Salanfe) and one neutral and geogenic (Liesberg)). Flooded soils incubated at 23 °C for two weeks showed a ~ 3-fold (Liesberg site) and ~ 7-fold (Salanfe site) increase in the total As concentration of soil solution compared to those incubated at 18 °C. Methyl- and thio-As species were found in the acidic soil and soil solution. High temperatures enhanced thiolation and methylation although inorganic As was predominant. We also show that volatile As fluxes increased more than 4-fold between treatments, from 18 ± 5 ng/kg/d at 18 °C to 75 ± 6 ng/kg/d at 23 °C from Salanfe soil. Our results suggest that high As soils with acidic pH can become an important source of As to the surrounding environment according to realistic climatic scenarios, and that biovolatilisation is very sensitive to increases in temperature. This study provides new data and further justifies further investigations into climate-induced changes on As release and speciation and its links to important factors such as microbial ecology and sulfate or iron biogeochemistry. SYNOPSIS: In the studied Swiss soils elevated temperature increases arsenic mobility through volatilisation and methylation.}, }
@article {pmid35597889, year = {2022}, author = {Ghuneim, LJ and Raghuvanshi, R and Neugebauer, KA and Guzior, DV and Christian, MH and Schena, B and Feiner, JM and Castillo-Bahena, A and Mielke, J and McClelland, M and Conrad, D and Klapper, I and Zhang, T and Quinn, RA}, title = {Complex and unexpected outcomes of antibiotic therapy against a polymicrobial infection.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {35597889}, issn = {1751-7370}, support = {R01AI145925//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, abstract = {Antibiotics are our primary approach to treating complex infections, yet we have a poor understanding of how these drugs affect microbial communities. To better understand antimicrobial effects on host-associated microbial communities we treated cultured sputum microbiomes from people with cystic fibrosis (pwCF, n = 24) with 11 different antibiotics, supported by theoretical and mathematical modeling-based predictions in a mucus-plugged bronchiole microcosm. Treatment outcomes we identified in vitro that were predicted in silico were: 1) community death, 2) community resistance, 3) pathogen killing, and 4) fermenter killing. However, two outcomes that were not predicted when antibiotics were applied were 5) community profile shifts with little change in total bacterial load (TBL), and 6) increases in TBL. The latter outcome was observed in 17.8% of samples with a TBL increase of greater than 20% and 6.8% of samples with an increase greater than 40%, demonstrating significant increases in community carrying capacity in the presence of an antibiotic. An iteration of the mathematical model showed that TBL increase was due to antibiotic-mediated release of pH-dependent inhibition of pathogens by anaerobe fermentation. These dynamics were verified in vitro when killing of fermenters resulted in a higher community carrying capacity compared to a no antibiotic control. Metagenomic sequencing of sputum samples during antibiotic therapy revealed similar dynamics in clinical samples. This study shows that the complex microbial ecology dictates the outcomes of antibiotic therapy against a polymicrobial infection.}, }
@article {pmid35596751, year = {2022}, author = {Yu, X and Zhang, Y and Shen, M and Dong, S and Zhang, F and Gao, Q and He, P and Shen, G and Yang, J and Wang, Z and Bo, G}, title = {Soil Conditioner Affects Tobacco Rhizosphere Soil Microecology.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35596751}, issn = {1432-184X}, support = {027Y2021-011//Hubei tobacco company/ ; 201903//Qingdao (Shandong Province) Tobacco Company/ ; 6651117005, 6651121004//Qingdao Agricultural University/ ; }, abstract = {Reasonable fertilization management can increase nutrient content and enzyme activity in rhizosphere soil, and even increase soil microbial richness. However, different fertilizers could raise distinct influences on the soil properties, including soil environmental factors (physicochemical properties and enzymatic activities) and microbial community. Here, the effects of two soil amendments (microbial fertilizer and woody peat) on environmental factors and microbial community structure in tobacco rhizosphere soil were evaluated, with the correlations between microbes and environmental factors explored. As the results, microbial fertilizer could effectively alleviate soil acidification, increase available potassium and organic matter contents in soil, and was also beneficial to increase nitrate reductase activity in rhizosphere soil. Fertilizers cause changes in the abundance of certain microbes in the soil. Besides, it was shown that the candidate phyla Gal15, Acidobacterota, Latescibacterota, Mortierellommycota, Basidiomycota, and Rozellomycota in tobacco rhizosphere soil had significant correlation with soil environmental factors. Through the functional analysis of these populations, it can be deduced that the changes in the abundance of certain microorganisms may be an important reason for the differences in environmental factors. All these indicated that the differences of environmental factors in different treatments are closely related to the abundance of some special soil microorganisms. Studying the life activities of these microbes would provide good guidance for exploring the interaction among crops, soil, and microorganisms and improving crop yields.}, }
@article {pmid35596750, year = {2022}, author = {Arnolds, KL and Yamada, E and Neff, CP and Schneider, JM and Palmer, BE and Lozupone, CA}, title = {Disruption of Genes Encoding Putative Zwitterionic Capsular Polysaccharides of Diverse Intestinal Bacteroides Reduces the Induction of Host Anti-Inflammatory Factors.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35596750}, issn = {1432-184X}, support = {R01 DK104047/DK/NIDDK NIH HHS/United States ; T32 AI007405/NH/NIH HHS/United States ; }, abstract = {Bacterial zwitterionic capsular polysaccharides (ZPS), such as polysaccharide A (PSA) of the intestinal commensal Bacteroides fragilis, have been shown to modulate T cells, including inducing anti-inflammatory IL-10-secreting T regulatory cells (Tregs). We previously used a genomic screen to identify diverse host-associated bacteria with the predicted genetic capacity to produce ZPSs related to PSA of B. fragilis and hypothesized that genetic disruption (KO) of a key functional gene within these operons would reduce the anti-inflammatory activity of these bacteria. We found that ZPS-KO bacteria in two common gut commensals, Bacteroides uniformis and Bacteroides cellulosilyticus, had a reduced ability to induce Tregs and IL-10 in stimulations of human peripheral blood mononuclear cells (PBMCs). Additionally, we found that macrophage stimulated with either wildtype B. fragilis or B. uniformis produced significantly more IL-10 than KOs, indicating a potentially novel function of ZPS of shifting the cytokine response in macrophages to a more anti-inflammatory state. These findings support the hypothesis that these related ZPS may represent a shared strategy to modulate host immune responses.}, }
@article {pmid35595468, year = {2022}, author = {Rotoni, C and Leite, MFA and Pijl, A and Kuramae, EE}, title = {Rhizosphere microbiome response to host genetic variability: a trade-off between bacterial and fungal community assembly.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiac061}, pmid = {35595468}, issn = {1574-6941}, abstract = {Rhizosphere microbial community composition is strongly influenced by plant species and cultivar. However, our understanding of the impact of plant cultivar genetic variability on microbial assembly composition remains limited. Here, we took advantage of vegetatively propagated chrysanthemum (Chrysanthemum indicum L.) as a plant model and induced roots in five commercial cultivars: Barolo, Chic, Chic 45, Chic Cream, and Haydar. We observed strong rhizosphere selection for the bacterial community but weaker selection for the fungal community. The genetic distance between cultivars explained 42.83% of the total dissimilarity between the bacteria selected by the different cultivars. By contrast, rhizosphere fungal selection was not significantly linked to plant genetic dissimilarity. Each chrysanthemum cultivar selected unique bacterial and fungal genera in the rhizosphere. We also observed a trade-off in the rhizosphere selection of bacteria and fungi in which the cultivar with the strongest selection of fungal communities showed the weakest bacterial selection. Finally, bacterial and fungal family taxonomic groups consistently selected by all cultivars were identified (bacteria Chitinophagaceae, Beijerinckiaceae, and Acidobacteriaceae and fungi Pseudeurotiaceae and Chrysozymaceae). Taken together, our findings suggest that chrysanthemum cultivars select distinct rhizosphere microbiomes and share a common core of microbes partially explained by the genetic dissimilarity between cultivars.}, }
@article {pmid35590462, year = {2022}, author = {Blakney, AJC and Bainard, LD and St-Arnaud, M and Hijri, M}, title = {Brassicaceae host plants mask the feedback from the previous year's soil history on bacterial communities, except when they experience drought.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16046}, pmid = {35590462}, issn = {1462-2920}, abstract = {Soil history operates through time to influence the structure and biodiversity of soil bacterial communities. Examining how different soil histories endure will help clarify the rules of bacterial community assembly. In this study, we established three different soil histories in field trials; the following year these plots were planted with five different Brassicaceae species. We hypothesized that the previously established soil histories would continue to structure the subsequent Brassicaceae bacterial root and rhizosphere communities. We used a MiSeq 16S rRNA metabarcoding strategy to determine the impact of different soil histories on the structure and biodiversity of the bacterial root and rhizosphere communities from the five different Brassicaceae host plants. We found that the Brassicaceae hosts were consistently significant factors in structuring the bacterial communities. Four host plants (Sinapis alba, Brassica napus, B. juncea, B. carinata) formed similar bacterial communities, regardless of different soil histories. Camelina sativa host plants structured phylogenetically distinct bacterial communities compared to the other hosts, particularly in their roots. Soil history established the previous year was only a significant factor for bacterial community structure when the feedback of the Brassicaceae host plants was weakened, potentially due to limited soil moisture during a dry year. Understanding how soil history is involved in the structure and biodiversity of bacterial communities through time is a limitation in microbial ecology and is required for employing microbiome technologies in improving agricultural systems. This article is protected by copyright. All rights reserved.}, }
@article {pmid35589992, year = {2022}, author = {King, NG and Moore, PJ and Thorpe, JM and Smale, DA}, title = {Consistency and Variation in the Kelp Microbiota: Patterns of Bacterial Community Structure Across Spatial Scales.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35589992}, issn = {1432-184X}, support = {MR/S032827/1//UKRI/ ; NE/S011692/1//Natural Environment Research Council/ ; }, abstract = {Kelp species are distributed along ~ 25% of the world's coastlines and the forests they form represent some of the world's most productive and diverse ecosystems. Like other marine habitat-formers, the associated microbial community is fundamental for host and, in turn, wider ecosystem functioning. Given there are thousands of bacteria-host associations, determining which relationships are important remains a major challenge. We characterised the associated bacteria of two habitat-forming kelp species, Laminaria hyperborea and Saccharina latissima, from eight sites across a range of spatial scales (10 s of metres to 100 s of km) in the northeast Atlantic. We found no difference in diversity or community structure between the two kelps, but there was evidence of regional structuring (across 100 s km) and considerable variation between individuals (10 s of metres). Within sites, individuals shared few amplicon sequence variants (ASVs) and supported a very small proportion of diversity found across the wider study area. However, consistent characteristics between individuals were observed with individual host communities containing a small conserved "core" (8-11 ASVs comprising 25 and 32% of sample abundances for L. hyperborea and S. latissima, respectively). At a coarser taxonomic resolution, communities were dominated by four classes (Planctomycetes, Gammaproteobacteria, Alphaproteobacteria and Bacteroidia) that made up ~ 84% of sample abundances. Remaining taxa (47 classes) made up very little contribution to overall abundance but the majority of taxonomic diversity. Overall, our study demonstrates the consistent features of kelp bacterial communities across large spatial scales and environmental gradients and provides an ecologically meaningful baseline to track environmental change.}, }
@article {pmid35581020, year = {2022}, author = {Xie, J and Li, Q and Haesebrouck, F and Van Hoecke, L and Vandenbroucke, RE}, title = {The tremendous biomedical potential of bacterial extracellular vesicles.}, journal = {Trends in biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tibtech.2022.03.005}, pmid = {35581020}, issn = {1879-3096}, abstract = {Bacterial extracellular vesicles (bEVs) are nano-sized, lipid membrane-delimited particles filled with bacteria-derived components. They have important roles in the physiology and pathogenesis of bacteria, and in bacteria-bacteria and bacteria-host interactions. Interestingly, recent advances in biotechnology have made it possible to engineer the bEV surface and decorate it with diverse biomolecules and nanoparticles (NPs). bEVs have been the focus of significant interest in a range of biomedical fields and are being evaluated as vaccines, cancer immunotherapy agents, and drug delivery vehicles. However, significant hurdles in terms of their safety, efficacy, and mass production need to be addressed to enable their full clinical potential. Here, we review recent advances and remaining obstacles regarding the use of bEVs in different biomedical applications and discuss paths toward clinical translation.}, }
@article {pmid35587374, year = {2022}, author = {Kohl, KD and Dieppa-Colón, E and Goyco-Blas, J and Peralta-Martínez, K and Scafidi, L and Shah, S and Zawacki, E and Barts, N and Ahn, Y and Hedayati, S and Secor, SM and Rowe, MP}, title = {Gut Microbial Ecology of Five Species of Sympatric Desert Rodents in Relation to Herbivorous and Insectivorous Feeding Strategies.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icac045}, pmid = {35587374}, issn = {1557-7023}, abstract = {The gut microbial communities of mammals provide numerous benefits to their hosts. However, given the recent development of the microbiome field, we still lack a thorough understanding of the variety of ecological and evolutionary factors that structure these communities across species. Metabarcoding is a powerful technique that allows for multiple microbial ecology questions to be investigated simultaneously. Here, we employed DNA metabarcoding techniques, predictive metagenomics, and culture-dependent techniques to inventory the gut microbial communities of several species of rodent collected from the same environment that employ different natural feeding strategies [granivorous pocket mice (Chaetodipus penicillatus); granivorous kangaroo rats (Dipodomys merriami); herbivorous woodrats (Neotoma albigula); omnivorous cactus mice (Peromyscus eremicus), and insectivorous grasshopper mice (Onychomys torridus)]. Of particular interest were shifts in gut microbial communities in rodent species with herbivorous and insectivorous diets, given the high amounts of indigestible fibers and chitinous exoskeleton in these diets, respectively. We found that herbivorous woodrats harbored the greatest microbial diversity. Granivorous pocket mice and kangaroo rats had the highest abundances of the genus Ruminococcus and highest predicted abundances of genes related to the digestion of fiber, representing potential adaptations in these species to the fiber content of seeds and the limitations to digestion given their small body size. Insectivorous grasshopper mice exhibited the greatest inter-individual variation in the membership of their microbiomes, and also exhibited the highest predicted abundances of chitin-degrading genes. Culture-based approaches identified 178 microbial isolates (primarily Bacillus and Enterococcus) capable of degrading cellulose and chitin. We observed several instances of strain-level diversity in these metabolic capabilities across isolates, somewhat highlighting the limitations and hidden diversity underlying DNA metabarcoding techniques. However, these methods offer power in allowing the investigation of several questions concurrently, thus enhancing our understanding of gut microbial ecology.}, }
@article {pmid35586862, year = {2022}, author = {Raglin, SS and Kent, AD and Ngumbi, EN}, title = {Herbivory Protection via Volatile Organic Compounds Is Influenced by Maize Genotype, Not Bacillus altitudinis-Enriched Bacterial Communities.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {826635}, doi = {10.3389/fmicb.2022.826635}, pmid = {35586862}, issn = {1664-302X}, abstract = {Belowground, plants interact with beneficial soil microbes such as plant growth-promoting rhizobacteria (PGPR). PGPR are rhizosphere bacteria that colonize roots and elicit beneficial effects in plants such as improved plant growth, pathogen resistance, abiotic stress tolerance, and herbivore protection. Treatment of plants with PGPR has been shown to trigger the emission of volatile organic compounds (VOCs). Volatile emissions can also be triggered by herbivory, termed herbivore-induced plant volatiles (HIPV), with important ramifications for chemical-mediated plant and insect interactions. Much of our current understanding of PGPR and herbivore-induced volatiles is based on studies using one plant genotype, yet domestication and modern breeding has led to the development of diverse germplasm with altered phenotypes and chemistry. In this study, we investigated if volatile emissions triggered by PGPR colonization and herbivory varies by maize genotype and microbial community assemblages. Six maize genotypes representing three decades of crop breeding and two heterotic groups were used, with four microbiome treatments: live or sterilized soil, with or without a Bacillus inoculant. Soil sterilization was used to delay microbiome establishment, resulting in low-diversity treatments. At planting, maize seeds were inoculated with PGPR Bacillus altitudinis AP-283 and grown under greenhouse conditions. Four weeks post planting, plants were subjected to feeding by third instar Helicoverpa zea (Lepidoptera: Noctuidae) larvae. Volatiles were collected using solid phase microextraction and analyzed with gas chromatography-mass spectrometry. Illumina NovaSeq 16S rRNA amplicon sequencing was carried out to characterize the rhizosphere microbiome. Maize genotype significantly influenced total volatile emissions, and relative abundance of volatile classes. We did not document a strong influence of microbe treatment on plant VOC emissions. However, inoculating plants with PGPR improved plant growth under sterile conditions. Taken together, our results suggest that genotypic variation is the dominant driver in HIPV composition and individual HIPV abundances, and any bacterial-mediated benefit is genotype and HIPV-specific. Therefore, understanding the interplay of these factors is necessary to fully harness microbially-mediated benefits and improve agricultural sustainability.}, }
@article {pmid35581504, year = {2022}, author = {Wan, L and Caruso, G and Cao, X and Song, C and Maimone, G and Rappazzo, AC and Laganà, P and Zhou, Y}, title = {Microbial Response to Coastal-Offshore Gradients in Taiwan Straits: Community Metabolism and Total Prokaryotic Abundance as Potential Proxies.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35581504}, issn = {1432-184X}, support = {2016YFE0202100.//Ministry of Science and Technology of the People's Republic of China/ ; }, abstract = {Located between the South and the East China Sea, the Taiwan Straits (TWS) are a marine shelf-channel area, with unique hydrological and geomorphological features affected by rivers inflow and with recent algal blooms with red tide events. This study aimed at assessing microbial distribution and function and their modulation in response to environmental gradients. Surface (0.5 m) water samples from 16 stations along five north to south transects were collected; total prokaryotic abundance by epifluorescence microscope and carbon substrate utilization patterns by Biolog Ecoplates were estimated. Spatially, a patchy microbial distribution was found, with the highest microbial metabolic levels and prokaryotic abundance in the TWS area between Minjiang River estuary and Pingtan Island, and progressive decreases towards offshore stations. Complex carbon sources and carbohydrates were preferentially metabolized. This study provides a snapshot of the microbial abundance and activity in TWS as a model site of aquatic ecosystems impacted from land inputs; obtained data highlights that microbial metabolism is more sensitive than abundance to environmental changes.}, }
@article {pmid35584587, year = {2022}, author = {Kuroda, K and Narihiro, T and Shinshima, F and Yoshida, M and Yamaguchi, H and Kurashita, H and Nakahara, N and Nobu, MK and Noguchi, TQP and Yamauchi, M and Yamada, M}, title = {High-rate cotreatment of purified terephthalate and dimethyl terephthalate manufacturing wastewater by a mesophilic upflow anaerobic sludge blanket reactor and the microbial ecology relevant to aromatic compound degradation.}, journal = {Water research}, volume = {219}, number = {}, pages = {118581}, doi = {10.1016/j.watres.2022.118581}, pmid = {35584587}, issn = {1879-2448}, abstract = {Polyethylene terephthalate (PET) is produced worldwide, mainly as material for plastic drink bottles. PET is produced by polymerization of purified terephthalate (PTA) or dimethyl terephthalate (DMT) with ethylene glycol. During the synthetic manufacturing processes of PTA and DMT, high organic loading wastewater is produced, which is typically treated separately by anaerobic wastewater treatment technologies. Given the high demand for PET, manufacturing plants are expanding globally, which will result in an increase in the amounts of PTA and DMT wastewater in need of treatment. In terms of effective treatment, the cotreatment of PTA and DMT wastewater has several advantages, including lower area and energy requirements. In this study, we examined the performance of an upflow anaerobic sludge blanket (UASB) reactor in cotreating PTA and DMT wastewater with high organic loading, evaluating its removal characteristics after 518 days of continuous operation. In addition, we performed a microbiome analysis of the UASB granular sludge to uncover the microbial interactions and metabolic functions within the reactor. By continuous operation, we achieved an organic removal rate of 6.6 kg m-3 day-1. In addition, we confirmed that aromatic compounds in the complex wastewater from the PTA and DMT manufacturing processes are biodegradable in the following order: benzoate > orthophthalate > terephthalate > isophthalate > p-toluic acid. 16S rRNA gene-based network analysis shows that anaerobic Woesearchaeales belonging to phylum Nanoarchaeota has a positive correlation with Methanoregula, Candidatus Methanofastidiosum, and Methanosarcina, suggesting a symbiotic relationship with methanogens in granular sludge. Shotgun metagenomic analysis revealed that terephthalate, isophthalate/orthophthalate, and benzoate were degraded by different members of Pelotomaculaceae and Syntrophorhabdaceae. According to the genomic information, we propose two new possible routes for orthophthalate degradation by the Syntrophorhabdaceae organism.}, }
@article {pmid35583791, year = {2022}, author = {Pavan, S and Prabhu, AN and Prasad Gorthi, S and Das, B and Mutreja, A and Shetty, V and Ramamurthy, T and Ballal, M}, title = {Exploring the multifactorial aspects of Gut Microbiome in Parkinson's Disease.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {35583791}, issn = {1874-9356}, abstract = {Advanced research in health science has broadened our view in approaching and understanding the pathophysiology of diseases and has also revolutionised diagnosis and treatment. Ever since the establishment of Braak's hypothesis in the propagation of alpha-synuclein from the distant olfactory and enteric nervous system towards the brain in Parkinson's Disease (PD), studies have explored and revealed the involvement of altered gut microbiota in PD. This review recapitulates the gut microbiome associated with PD severity, duration, motor and non-motor symptoms, and antiparkinsonian treatment from recent literature. Gut microbial signatures in PD are potential predictors of the disease and are speculated to be used in early diagnosis and treatment. In brief, the review also emphasises on implications of the prebiotic, probiotic, faecal microbiota transplantation, and dietary interventions as alternative treatments in modulating the disease symptoms in PD.}, }
@article {pmid35583685, year = {2022}, author = {Wu, MH and Li, T and Zhang, GS and Wu, FS and Chen, T and Zhang, BL and Wu, XK and Liu, GX and Zhang, KC and Zhang, W}, title = {Seasonal Variation of Hypolithic Microbiomes in the Gobi Desert : Seasonal Variation of Hypolithic Microbiomes in the Gobi Desert.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35583685}, issn = {1432-184X}, support = {31870479//National Natural Science Foundation of China/ ; 2019YFE0121100//National Key R&amp;D Program of China/ ; 20YF3WA007//Scientific Project of Gansu Province, China/ ; 20JR5RA548//Scientific Project of Gansu Province, China/ ; }, abstract = {Understanding how microbial communities adapt to environmental stresses is critical for interpreting ecological patterns and microbial diversity. In the case of the Gobi Desert, little is known on the environmental factors that explain hypolithic colonization under quartz stones. By analyzing nine hypolithic communities across an arid gradient and the effects of the season of the year in the Hexi Corridor of this desert, we found a significant decrease in hypolithic colonization rates (from 47.24 to 15.73%) with the increasing drought gradient and found two distinct communities in Hot and Cold samples, which survived or proliferated after a hot or a cold period. While Cold communities showed a greater species diversity and a predominance of Cyanobacteria, Hot communities showed a predominance of members of the Proteobacteria and the Firmicutes. In comparison, Cold communities also possessed stronger functions in the photosynthesis and carbon metabolism. Based on the findings of this study, we proposed that the hypolithic communities of the Hexi Corridor of the Gobi Desert might follow a seasonal developmental cycle in which temperature play an important role. Thus after a critical thermal threshold is crossed, heterotrophic microorganisms predominate in the hot period, while Cyanobacteria predominate in the cold period.}, }
@article {pmid35577973, year = {2022}, author = {Mangola, SM and Lund, JR and Schnorr, SL and Crittenden, AN}, title = {Ethical microbiome research with Indigenous communities.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {35577973}, issn = {2058-5276}, support = {RM1HG009042//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; 9780//Wenner-Gren Foundation (Wenner-Gren Foundation for Anthropological Research, Inc.)/ ; }, abstract = {Human-microbiome interactions have been associated with evolutionary, cultural and environmental processes. With clinical applications of microbiome research now feasible, it is crucial that the science conducted, particularly among Indigenous communities, adheres to principles of inclusion. This necessitates a transdisciplinary dialogue to decide how biological samples are collected and who benefits from the research and any derived products. As a group of scholars working at the interface of biological and social science, we offer a candid discussion of the lessons learned from our own research and introduce one approach to carry out ethical microbiome research with Indigenous communities.}, }
@article {pmid35576038, year = {2022}, author = {Kuzikova, I and Andronov, E and Zaytseva, T and Metelkova, L and Zhakovskaya, Z and Medvedeva, N}, title = {A microcosm approach for evaluating the microbial nonylphenol and butyltin biodegradation and bacterial community shifts in co-contaminated bottom sediments from the Gulf of Finland, the Baltic Sea.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {35576038}, issn = {1614-7499}, abstract = {Pollution of aquatic ecosystems with nonylphenol (NP) and butyltins (BuTs) is of great concern due to their effects on endocrine activity, toxicity to aquatic organisms, and extended persistence in sediments. The impact of contamination with NP and/or BuTs on the microbial community structure in marine sediments was investigated using microcosms and high-throughput sequencing. Sediment microcosms with NP (300 mg/kg) and/or BuTs (95 mg/kg) were constructed. Complete removal of monobutyltin (MBT) occurred in the microcosms after 240 days of incubation, while a residual NP rate was 40%. The content of toxic tributyltin (TBT) and dibutyltin (DBT) in the sediments did not change notably. Co-contamination of the sediments with NP and BuTs did not affect the processes of their degradation. The pollutants in the microcosms could have been biodegraded by autochthonous microorganisms. Significantly different and less diverse bacterial communities were observed in the contaminated sediments compared to non-contaminated control. Firmicutes and Gammaproteobacteria dominated in the NP treatment, Actinobacteria and Alphaproteobacteria in the BuT treatment, and Gammaproteobacteria, Alphaproteobacteria, Firmicutes, and Acidobacteria in the NP-BuT mixture treatment. The prevalence of microorganisms from the bacterial genera Halothiobacillus, Geothrix, Methanosarcina, Dyella, Parvibaculum, Pseudomonas, Proteiniclasticum, and bacteria affiliated with the order Rhizobiales may indicate their role in biodegradation of NP and BuTs in the co-contaminated sediments. This study can provide some new insights towards NP and BuT biodegradation and microbial ecology in NP-BuT co-contaminated environment.}, }
@article {pmid35575806, year = {2022}, author = {Patil, JS and Sathish, K}, title = {Responses of Phytoplankton Benthic Propagules to Macronutrient Enrichment and Varying Light Intensities: Elucidation from Monsoon-Influenced Mandovi and Zuari Riverine System : Responses of Phytoplankton Benthic Propagules to Macronutrient Enrichment and Varying Light Intensities: Elucidation from Monsoon-Influenced Mandovi and Zuari Riverine System.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35575806}, issn = {1432-184X}, support = {//science and engineering research board/ ; }, abstract = {The ecological importance of phytoplankton-benthic-propagules (PBP) from coastal sediments, except tropical monsoon-influenced rivers and estuaries, is well documented. PBP in such systems is often transported from upstream (near freshwater) to downstream (estuary) through freshwater discharges during monsoon and thereby experiences higher salinities (>30 PSU) and nutrients with varying light conditions due to reducing discharges during the monsoon-break/withdrawal-phase. However, the PBP responses (germination and subsequent growth) to such changes are unknown and are examined here at ~35 PSU salinity. For the study, macronutrients (nitrate, phosphate, silicate, and nitrate+phosphate+silicate) and light intensities were considered to assess the response of PBP representing estuarine, brackish, and near freshwater locations of monsoon-influenced Mandovi and Zuari rivers (Goa, India). Diatoms dominated the viable PBP community, but the maximum growth and sustained photosynthetic activity were observed when all macronutrients were supplied than individually. Here, variable fluorescence technique utility in PBP resurrection (detection of viability and responses) was also explored. The PBP growth was similar for macronutrients but increased with light intensity indicating a longer growth response during monsoon. For PBP (germination and photosynthetic activity), light intensities drive the rate of improvement/development, whereas the nutrients are essential for maintaining vegetative growth upon germination in the region. The PBP dominance of common planktonic species (Skeletonema and Thalassiosira) along the river also signifies the role of seawater intrusion (up to upstream locations) in distribution. Skeletonema and Thalassiosira, which contribute significantly to the total community, are light-sensitive with a similar response and cause single species blooms during monsoon and non-monsoon, respectively, depending on the species' tolerance to salinity.}, }
@article {pmid35575486, year = {2022}, author = {Peruzzo, A and Losasso, C and Di Castri, A and Drigo, I and Bano, L and Orsini, M}, title = {Genome Sequence of Campylobacter Strain 19-13652, Isolated from Breeding Pheasants.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0118421}, doi = {10.1128/mra.01184-21}, pmid = {35575486}, issn = {2576-098X}, abstract = {We report the whole-genome sequence of a Campylobacter strain that was isolated from breeding pheasants presenting "bulgy eyes" in Italy. Traditional molecular typing methods did not return any reliable result. Whole-genome sequencing and sequence comparison with known genomes did not meet the criteria for assignment to an existing species.}, }
@article {pmid35573175, year = {2022}, author = {Ghosh, A and Saha, R and Bhadury, P}, title = {Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13169}, doi = {10.7717/peerj.13169}, pmid = {35573175}, issn = {2167-8359}, abstract = {Estuaries are one of the most productive ecosystems and their productivity is maintained by resident microbial communities. Recent alterations driven by climate change have further escalated these stressors leading to the propagation of traits such as antibiotic resistance and heavy metal resistance in microbial communities. Surface water samples from eleven stations along the Thakuran and Matla estuaries of the Sundarbans Biosphere Reserve (SBR) of Sundarbans mangrove located in South Asia were sampled in monsoon (June) 2019 to elucidate resident microbial communities based on Nanopore sequencing. Metagenomic analyses revealed the widespread dominance of Proteobacteria across all the stations along with a high abundance of Firmicutes. Other phyla, including Euryarchaeota, Thaumarchaeota, Actinobacteria, Bacteroidetes and Cyanobacteria showed site-specific trends in abundance. Further taxonomic affiliations showed Gammaproteobacteria and Alphaproteobacteria to be dominant classes with high abundances of Bacilli in SBR_Stn58 and SBR_Stn113. Among the eukaryotic communities, the most abundant classes included Prasinophyceae, Saccharyomycetes and Sardariomycetes. Functional annotation showed metabolic activities such as carbohydrate, amino acid, nitrogen and phosphorus metabolisms to be uniformly distributed across all the studied stations. Pathways such as stress response, sulphur metabolism and motility-associated genes appeared in low abundances in SBR. Functional traits such as antibiotic resistance showed overwhelming dominance of genes involved in multidrug resistance along with widespread resistance towards commonly used antibiotics including Tetracycline, glycopeptide and aminoglycoside. Metal resistance genes including arsenic, nickel and copper were found in comparable abundances across the studied stations. The prevalence of ARG and MRG might indicate presence of pollutants and hint toward deteriorating ecosystem health status of Sundarbans mangrove.}, }
@article {pmid35572632, year = {2022}, author = {Aponte, H and Galindo-Castañeda, T and Yáñez, C and Hartmann, M and Rojas, C}, title = {Microbial Community-Level Physiological Profiles and Genetic Prokaryotic Structure of Burned Soils Under Mediterranean Sclerophyll Forests in Central Chile.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {824813}, doi = {10.3389/fmicb.2022.824813}, pmid = {35572632}, issn = {1664-302X}, abstract = {Forest fires alter soil microbial communities that are essential to support ecosystem recovery following land burning. These alterations have different responses according to soil abiotic pre- and post-fire conditions and fire severity, among others, and tend to decrease along vegetation recovery over time. Thus, understanding the effects of fires on microbial soil communities is critical to evaluate ecosystem resilience and restoration strategies in fire-prone ecosystems. We studied the state of community-level physiological profiles (CLPPs) and the prokaryotic community structure of rhizosphere and bulk soils from two fire-affected sclerophyll forests (one surveyed 17 months and the other 33 months after fire occurrence) in the Mediterranean climate zone of central Chile. Increases in catabolic activity (by average well color development of CLPPs), especially in the rhizosphere as compared with the bulk soil, were observed in the most recently affected site only. Legacy of land burning was still clearly shaping soil prokaryote community structure, as shown by quantitative PCR (qPCR) and Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene, particularly in the most recent fire-affected site. The qPCR copy numbers and alpha diversity indexes (Shannon and Pielou's evenness) of sequencing data decreased in burned soils at both locations. Beta diversity analyses showed dissimilarity of prokaryote communities at both study sites according to fire occurrence, and NO3 - was the common variable explaining community changes for both of them. Acidobacteria and Rokubacteria phyla significantly decreased in burned soils at both locations, while Firmicutes and Actinobacteria increased. These findings provide a better understanding of the resilience of soil prokaryote communities and their physiological conditions in Mediterranean forests of central Chile following different time periods after fire, conditions that likely influence the ecological processes taking place during recovery of fire-affected ecosystems.}, }
@article {pmid35569711, year = {2022}, author = {Matassa, S and Pelagalli, V and Papirio, S and Zamalloa, C and Verstraete, W and Esposito, G and Pirozzi, F}, title = {Direct nitrogen stripping and upcycling from anaerobic digestate during conversion of cheese whey into single cell protein.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {127308}, doi = {10.1016/j.biortech.2022.127308}, pmid = {35569711}, issn = {1873-2976}, abstract = {The environmental impact of the dairy industry is heavily influenced by the overproduction of nitrogen- and carbon-rich effluents. The present study proposes an innovative process to recover waste contaminated nitrogen from anaerobic digestate while treating excess cheese whey (CW) and producing high-quality, clean single cell protein (SCP). By relying on direct aeration stripping techniques, employing an airflow subsequently used in the aerobic cheese whey fermentation step, the investigated process was able to strip 41-80% of the total ammonium nitrogen (N-NH4+) from liquid digestate. The stripped ammonia gas (NH3) was completely recovered as N-NH4+ in the acidic CW, and further upcycled into SCP having a total protein content of 74.7% and a balanced amino acids profile. A preliminary techno-economic analysis revealed the potential to directly recover and upcycle nitrogen into SCP at costs (4.1-8.2 €·kgN-1) and energetic inputs (90-132 MJ·kgN-1) matching those of conventional feed and nitrogen management processes.}, }
@article {pmid35569666, year = {2022}, author = {Li, K and Bi, Q and Liu, X and Wang, H and Sun, C and Zhu, Y and Lin, X}, title = {Unveiling the role of dissolved organic matter on phosphorus sorption and availability in a 5-year manure amended paddy soil.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {155892}, doi = {10.1016/j.scitotenv.2022.155892}, pmid = {35569666}, issn = {1879-1026}, abstract = {Dissolved organic matter (DOM) is an active component of organic manure that is widely used in agroecosystems to increase nutrient availability and consequently enhance crop yields. However, the ways in which soil DOM characteristics are influenced by organic manure and how it contributes to crop yield and soil P availability remains unclear. Here, we conducted a 5-year field experiment and demonstrated that partial replacement of chemical P fertilizer with swine manure could maintain high rice yield and soil available P levels and increase P fertilizer use efficiency (PUE) in comparison to chemical fertilization, even when the total P input was reduced. This suggests that organic manure application can significantly mobilize soil P and increase P availability. Structural equation modeling analysis indicated that the soil pH and humification degree of DOM, rather than DOM content, directly decreased maximum P adsorption capacity. The combined results of the optical spectroscopy and ultrahigh-resolution mass spectroscopy obtained from the laboratory validation experiment based on the DOM-removed soil demonstrated that manure-derived DOM competing with P for adsorption was one of the main reasons for the increase in soil P availability and that the effective DOM components were N-containing lignins, tannins, and condensed polycyclic aromatics with higher O/C and lower H/C ratios. Overall, our results provide solid evidence that soil DOM characteristics are influenced by manure application and facilitate soil P availability, which could help guide the sustainable P management and manure application in agroecosystems.}, }
@article {pmid35569105, year = {2022}, author = {Deng, X and Zhang, N and Li, Y and Zhu, C and Qu, B and Liu, H and Li, R and Bai, Y and Shen, Q and Falcao Salles, J}, title = {Bio-organic soil amendment promotes the suppression of Ralstonia solanacearum by inducing changes in the functionality and composition of rhizosphere bacterial communities.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.18221}, pmid = {35569105}, issn = {1469-8137}, abstract = {Stimulating the development of soil suppressiveness against certain pathogens represents a sustainable solution toward reducing pesticide use in agriculture. However, understanding the dynamics of suppressiveness and the mechanisms leading to pathogen control remain largely elusive. Here, we investigated the mechanisms used by the rhizosphere microbiome induces bacterial wilt disease suppression in a long-term field experiment where continuous application of bio-organic (BF) fertilizers triggered disease suppressiveness when compared to chemical fertilizer (CF) application. We further demonstrated in a greenhouse experiment that the suppressiveness of the rhizosphere bacterial communities was triggered mainly by changes in community composition rather than only by the abundance of the introduced biocontrol strain. Metagenomics approaches revealed that members of the families Sphingomonadaceae and Xanthomonadaceae with the ability to produce secondary metabolites were enriched in the BF plant rhizosphere but only upon pathogen invasion. We experimentally validated this observation by inoculating bacterial isolates belonging to the families Sphingomonadaceae and Xanthomonadaceae into conducive soil, which led to a significant reduction in pathogen abundance and increase in non-ribosomal peptide synthetase (NRPS) gene abundance. We conclude that priming of the soil microbiome with bio-organic fertilizer amendment fostered reactive bacterial communities in the rhizosphere of tomato plants in response to biotic disturbance.}, }
@article {pmid35567250, year = {2022}, author = {Dranseikienė, D and Balčiūnaitė-Murzienė, G and Karosienė, J and Morudov, D and Juodžiukynienė, N and Hudz, N and Gerbutavičienė, RJ and Savickienė, N}, title = {Cyano-Phycocyanin: Mechanisms of Action on Human Skin and Future Perspectives in Medicine.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {9}, pages = {}, doi = {10.3390/plants11091249}, pmid = {35567250}, issn = {2223-7747}, abstract = {Cyano-phycocyanin is one of the active pigments of the blue-green algae and is usually isolated from the filamentous cyanobacteria Arthrospira platensis Gomont (Spirulina). Due to its multiple physiological functions and non-toxicity, cyano-phycocyanin may be a potential substance for the topical treatment of various skin diseases. Considering that the conventional medicine faces drug resistance, insufficient efficacy and side effects, the plant origin compounds can act as an alternative option. Thus, the aim of this paper was to review the wound healing, antimicrobial, antioxidative, anti-inflammatory, antimelanogenic and anticancer properties and mechanisms of cyano-phycocyanin topical activities on human skin. Moreover, possible applications and biotechnological requirements for pharmaceutical forms of cyano-phycocyanin for the treatment of various skin diseases are discussed in this review.}, }
@article {pmid35567212, year = {2022}, author = {Li, Y and Wang, C and Ge, L and Hu, C and Wu, G and Sun, Y and Song, L and Wu, X and Pan, A and Xu, Q and Shi, J and Liang, J and Li, P}, title = {Environmental Behaviors of Bacillus thuringiensis (Bt) Insecticidal Proteins and Their Effects on Microbial Ecology.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {9}, pages = {}, doi = {10.3390/plants11091212}, pmid = {35567212}, issn = {2223-7747}, abstract = {Bt proteins are crystal proteins produced by Bacillus thuringiensis (Bt) in the early stage of spore formation that exhibit highly specific insecticidal activities. The application of Bt proteins primarily includes Bt transgenic plants and Bt biopesticides. Transgenic crops with insect resistance (via Bt)/herbicide tolerance comprise the largest global area of agricultural planting. After artificial modification, Bt insecticidal proteins expressed from Bt can be released into soils through root exudates, pollen, and plant residues. In addition, the construction of Bt recombinant engineered strains through genetic engineering has become a major focus of Bt biopesticides, and the expressed Bt proteins will also remain in soil environments. Bt proteins expressed and released by Bt transgenic plants and Bt recombinant strains are structurally and functionally quite different from Bt prototoxins naturally expressed by B. thuringiensis in soils. The former can thus be regarded as an environmentally exogenous substance with insecticidal toxicity that may have potential ecological risks. Consequently, biosafety evaluations must be conducted before field tests and production of Bt plants or recombinant strains. This review summarizes the adsorption, retention, and degradation behavior of Bt insecticidal proteins in soils, in addition to their impacts on soil physical and chemical properties along with soil microbial diversity. The review provides a scientific framework for evaluating the environmental biosafety of Bt transgenic plants, Bt transgenic microorganisms, and their expression products. In addition, prospective research targets, research methods, and evaluation methods are highlighted based on current research of Bt proteins.}, }
@article {pmid35562794, year = {2022}, author = {Deehan, EC and Zhang, Z and Riva, A and Armet, AM and Perez-Muñoz, ME and Nguyen, NK and Krysa, JA and Seethaler, B and Zhao, YY and Cole, J and Li, F and Hausmann, B and Spittler, A and Nazare, JA and Delzenne, NM and Curtis, JM and Wismer, WV and Proctor, SD and Bakal, JA and Bischoff, SC and Knights, D and Field, CJ and Berry, D and Prado, CM and Walter, J}, title = {Elucidating the role of the gut microbiota in the physiological effects of dietary fiber.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {77}, pmid = {35562794}, issn = {2049-2618}, support = {(FunKeyGut 741623)/ERC_/European Research Council/International ; (RN-298871-372173)//Joint Programming Initiative A healthy diet for a healthy life/ ; (APC/SFI/12/RC/2273_P2)//Science Foundation Ireland Centre/ ; }, abstract = {BACKGROUND: Dietary fiber is an integral part of a healthy diet, but questions remain about the mechanisms that underlie effects and the causal contributions of the gut microbiota. Here, we performed a 6-week exploratory trial in adults with excess weight (BMI: 25-35 kg/m2) to compare the effects of a high-dose (females: 25 g/day; males: 35 g/day) supplement of fermentable corn bran arabinoxylan (AX; n = 15) with that of microbiota-non-accessible microcrystalline cellulose (MCC; n = 16). Obesity-related surrogate endpoints and biomarkers of host-microbiome interactions implicated in the pathophysiology of obesity (trimethylamine N-oxide, gut hormones, cytokines, and measures of intestinal barrier integrity) were assessed. We then determined whether clinical outcomes could be predicted by fecal microbiota features or mechanistic biomarkers.<br><br>RESULTS: AX enhanced satiety after a meal and decreased homeostatic model assessment of insulin resistance (HOMA-IR), while MCC reduced tumor necrosis factor-α and fecal calprotectin. Machine learning models determined that effects on satiety could be predicted by fecal bacterial taxa that utilized AX, as identified by bioorthogonal non-canonical amino acid tagging. Reductions in HOMA-IR and calprotectin were associated with shifts in fecal bile acids, but correlations were negative, suggesting that the benefits of fiber may not be mediated by their effects on bile acid pools. Biomarkers of host-microbiome interactions often linked to bacterial metabolites derived from fiber fermentation (short-chain fatty acids) were not affected by AX supplementation when compared to non-accessible MCC.<br><br>CONCLUSION: This study demonstrates the efficacy of purified dietary fibers when used as supplements and suggests that satietogenic effects of AX may be linked to bacterial taxa that ferment the fiber or utilize breakdown products. Other effects are likely microbiome independent. The findings provide a basis for fiber-type specific therapeutic applications and their personalization.<br><br>TRIAL REGISTRATION: Clinicaltrials.gov, NCT02322112 , registered on July 3, 2015. Video Abstract.}, }
@article {pmid35562600, year = {2022}, author = {Greene, LK and McKenney, EA and Gasper, W and Wrampelmeier, C and Hayer, S and Ehmke, EE and Clayton, JB}, title = {Gut Site and Gut Morphology Predict Microbiome Structure and Function in Ecologically Diverse Lemurs.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35562600}, issn = {1432-184X}, support = {PRFB 1906416//Directorate for Biological Sciences/ ; }, abstract = {Most studies of wildlife gut microbiotas understandably rely on feces to approximate consortia along the gastrointestinal tract. We therefore compared microbiome structure and predicted metagenomic function in stomach, small intestinal, cecal, and colonic samples from 52 lemurs harvested during routine necropsies. The lemurs represent seven genera (Cheirogaleus, Daubentonia, Varecia, Hapalemur, Eulemur, Lemur, Propithecus) characterized by diverse feeding ecologies and gut morphologies. In particular, the hosts variably depend on fibrous foodstuffs and show correlative morphological complexity in their large intestines. Across host lineages, microbiome diversity, variability, membership, and function differed between the upper and lower gut, reflecting regional tradeoffs in available nutrients. These patterns related minimally to total gut length but were modulated by fermentation capacity (i.e., the ratio of small to large intestinal length). Irrespective of feeding strategy, host genera with limited fermentation capacity harbored more homogenized microbiome diversity along the gut, whereas those with expanded fermentation capacity harbored cecal and colonic microbiomes with greater diversity and abundant fermentative Ruminococcaceae taxa. While highlighting the value of curated sample repositories for retrospective comparisons, our results confirm that the need to survive on fibrous foods, either routinely or in hypervariable environments, can shape the morphological and microbial features of the lower gut.}, }
@article {pmid35562021, year = {2022}, author = {Mariën, Q and Ulcar, B and Verleyen, J and Vanthuyne, B and Ganigué, R}, title = {High-rate conversion of lactic acid-rich streams to caproic acid in a fermentative granular system.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {127250}, doi = {10.1016/j.biortech.2022.127250}, pmid = {35562021}, issn = {1873-2976}, abstract = {Lactic acid-driven chain elongation enables upgrading low-value organic streams into caproic acid. Recently, volumetric production rates over 0.5 g L-1 h-1 have been reported for carbohydrate-rich streams in expanded granular sludge bed (EGSB) reactors. However, many target streams contain mixtures of carbohydrates and lactic acid, and little is known about their impact on product profile and microbial ecology, or the importance of carbohydrates as substrate to achieve high rates. This manuscript investigated varying glucose-to-lactate ratios and observed that decreasing glucose-content eliminated odd-chain by-products, while glucose omission required acetic acid addition to support lactic acid conversion. Decreasing the glucose-content fed resulted in decreasing amounts of granular biomass, with the disappearance of granules when no glucose was fed. Lowering the HRT to 0.3 days while feeding only lactic and acetic acid likely triggered re-granulation, enabling the highest lactic acid-driven caproic acid production rates reported thus far at 16.4±1.7 g L-1 d-1.}, }
@article {pmid35557833, year = {2018}, author = {Zhang, R and Wang, L and Chen, P and Pu, Y}, title = {Shifts in microbial community structure and diversity in a novel waterfall biofilm reactor combined with MBBR under light and dark conditions.}, journal = {RSC advances}, volume = {8}, number = {65}, pages = {37462-37471}, doi = {10.1039/c8ra07039c}, pmid = {35557833}, issn = {2046-2069}, abstract = {In this study, a novel, low-cost, easy-maintenance and effective waterfall aeration biofilm reactor (WFBR) was designed to treat wastewater with MBBR. The chemical oxygen demand (COD), nitrogen removal efficiency, and the microbial community structure in this novel system were evaluated for 70 days under light and dark conditions. The COD and ammonium nitrogen (NH3-N) removal efficiency remained at approximately 90% and 100% respectively after 25 days, even if the influent substrate concentration and illumination condition changes. High-throughput sequencing was used to investigate the composition and function of the microbial community in different fillers in the treatment system. Dark padding, illuminate carrier and fabric play the good performance in nitrogen nitrification, denitrification and fixation respectively. The major classes present were Betaproteobacteria (30.2% on average), Cytophagia (19.8%), Gammaproteobacteria (11.7%), Alphaproteobacteria (11.2%), Sphingobacteriia (5.1%), Flavobacteriia (2.6%), Deltaproteobacteria (2.4%), Verrucomicrobiae (0.7%), Chloroplast (0.6%) and Clostridia (0.5%). These results could provide important guidance for the improvement of MBBR or other tradition wastewater treatment process, and could also enrich our theoretical understanding of microbial ecology.}, }
@article {pmid35556154, year = {2022}, author = {Billet, L and Pesce, S and Martin-Laurent, F and Devers-Lamrani, M}, title = {Experimental Evidence for Manure-Borne Bacteria Invasion in Soil During a Coalescent Event: Influence of the Antibiotic Sulfamethazine.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35556154}, issn = {1432-184X}, abstract = {The fertilization of agricultural soil by organic amendment that may contain antibiotics, like manure, can transfer bacterial pathogens and antibiotic-resistant bacteria to soil communities. However, the invasion by manure-borne bacteria in amended soil remains poorly understood. We hypothesized that this kind of process is both influenced by the soil properties (and those of its microbial communities) and by the presence of contaminants such as antibiotics used in veterinary care. To test that, we performed a microcosm experiment in which four different soils were amended or not with manure at an agronomical dose and exposed or not to the antibiotic sulfamethazine (SMZ). After 1 month of incubation, the diversity, structure, and composition of bacterial communities of the soils were assessed by 16S rDNA sequencing. The invasion of manure-borne bacteria was still perceptible 1 month after the soil amendment. The results obtained with the soil already amended in situ with manure 6 months prior to the experiment suggest that some of the bacterial invaders were established in the community over the long term. Even if differences were observed between soils, the invasion was mainly attributable to some of the most abundant OTUs of manure (mainly Firmicutes). SMZ exposure had a limited influence on soil microorganisms but our results suggest that this kind of contaminant can enhance the invasion ability of some manure-borne invaders.}, }
@article {pmid35553976, year = {2022}, author = {Lanza, M and Scuderi, SA and Filippone, A and Casili, G and Campolo, M and Paterniti, I and Cuzzocrea, S and Esposito, E}, title = {The role of SCFAs on microbiota composition in a mouse model of NTG-induced migraine.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {36 Suppl 1}, number = {}, pages = {}, doi = {10.1096/fasebj.2022.36.S1.R4645}, pmid = {35553976}, issn = {1530-6860}, abstract = {BACKGROUND: Based on global burden of headache reports, migraine is a prevalent disorder that affect approximately 15% of the adult population. Generally migraine attacks are sporadic, however, some individuals develop a chronic disease form. To date, several researches have shown that migraine is associated with some gastrointestinal disorders such as Helicobacter pylori (HP) infection, irritable bowel syndrome (IBS), and celiac disease (CD). However, the mechanisms explaining how the gut and the brain may interact in patients with migraine are not entirely clear. In this study, we aimed to evaluate the role of the short-chain fatty acids (SCFAs), such as sodium propionate (SP) and sodium butyrate (SB) as mediators and modulators of host intestinal microbial ecology, in regulating the pathophysiology of migraine in a mouse model induced by nitroglycerine (NTG).<br><br>METHODS: Mice were orally administered with SB and SP at the dose of 10, 30 and 100 mg/kg, 5 min after NTG intraperitoneal injections. Histological and molecular analysis were performed on the whole brain and small intestine and behavioral tests after 4 h from migraine induction. The composition of the intestinal microbiota was extracted from frozen fecal samples and prepared for sequencing according to the protocol for Illumina Miseq System. However, the expression of inflammatory and oxidative markers were detected by Western blot. Tail flick, hot plate, orofacial formalin and photophobia tests were used to evaluate migraine-like pain and migraine-related light sensitivity.<br><br>RESULTS: SP and SB treatment notably reduced histological damage in whole brain and small intestine in NTG-injected mice. Treatments with both SCFAs decreased the markers of inflammation and increased the protective antioxidant enzymes, suggesting an important role of SCFAs to exercise neuromodulatory action. Moreover, SCFAs reduced the headache modifying the intestinal microbiota.<br><br>CONCLUSIONS: These results provided the evidence that SCFAs exerts a protective effect on central sensitization induced by NTG through a modulation of intestinal microbiota, suggesting a new insight into the potential application of SCFAs as novel supportive therapies for migraine.}, }
@article {pmid35553108, year = {2022}, author = {Petersen, C and Adhini Kuppuswami, SB and Wankhade, U and Putich, M and Wilson, G and Saldivar-Gonzalez, M and Symons, JD and Pon Velayutham, AB}, title = {Dietary Blueberries Improve Vascular Inflammation and Alter the Composition of the Gut Microbiome in Aged Mice.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {36 Suppl 1}, number = {}, pages = {}, doi = {10.1096/fasebj.2022.36.S1.R5941}, pmid = {35553108}, issn = {1530-6860}, abstract = {BACKGROUND: Aging is a risk factor for cardiovascular diseases, which are major causes of disability and mortality in the elderly. Endothelial dysfunction and an imbalanced gut microbial ecology play a pivotal role in aging-associated vascular complications. Dietary change may be an effective strategy to improve vascular health. In this study, we tested the hypothesis that dietary blueberries ameliorate vascular complications and gut dysbiosis in aged mice.<br><br>METHODS: Aged mice (17-month-old C57BL/6J male, Jackson Laboratory) were fed a control diet (O) or freeze-dried wild blueberry powder supplemented diet (3.8% in diet) (OB) for 15 weeks. Young mice (2-month-old) consumed a control diet (Y) or blueberry supplemented diet (YB) for an identical duration. Based on normalization to body surface area, the blueberry dose is equivalent to 1.5 human servings of blueberry (~240 g) per day. Metabolic parameters, vascular function and vascular inflammation were assessed at the end of the treatment period. Vascular inflammation was assessed by measuring the binding of fluorescent labelled mouse monocytic WEHI78/24 cells to the vascular endothelium. Mesenteric arteries were used to assess vascular function using isometric procedures. Microbial profiling was done using 16s rRNA amplification.<br><br>RESULTS: Metabolic parameters such as body weight, food intake and blood glucose were similar among the groups. Old mice (O) exhibited improved glucose tolerance compared to young mice (Y). Blueberry supplementation did not alter glucose tolerance in young (YB) or old mice (OB). O vs Y had increased monocyte binding to vascular endothelium indicating enhanced vascular inflammation, but this was reduced by blueberry supplementation in OB vs O. Endothelium-dependent vasorelaxation to acetylcholine and endothelium-independent vasorelaxation to sodium nitroprusside were similar among the groups. Microbial profiling indicated changes in the composition of gut microbiome among the groups. α-diversity indices such as Chao and observed species were similar at the phylum level but were different at the genus level among groups. β-diversity, which represents compositional differences among groups, was different at the phylum and genus levels. Further, the relative abundance of gut microbes at different taxa levels were altered between O vs Y and OB vs O mice. Importantly, the relative abundance of genera Candidatus Saccharimonas and Enterorhabdus were decreased whereas Muribaculum was increased in O vs Y mice. Blueberry supplementation improved the relative abundance of these three genera in OB vs O mice.<br><br>CONCLUSION: Blueberry supplementation improves aging induced vascular inflammation in C57BL/6J mice without altering the metabolic milieu indicating the direct effect of blueberries on vasculature. Our study also provides evidence for changes in the composition of gut microbiome which might mediate some of the effects of blueberry supplementation in aged mice.}, }
@article {pmid35552795, year = {2022}, author = {Newcombe, G and Marlin, M and Barge, E and Heitmann, S and Ridout, M and Busby, PE}, title = {Plant Seeds Commonly Host Bacillus spp., Potential Antagonists of Phytopathogens.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35552795}, issn = {1432-184X}, support = {1314095//National Science Foundation/ ; 16.67//National Science Foundation/ ; }, abstract = {In agriculture, horticulture and plantation forestry, Bacillus species are the most commonly applied antagonists and biopesticides, targeting plant pathogens and insect pests, respectively. Bacillus isolates are also used as bacterial plant biostimulants, or BPBs. Such useful isolates of Bacillus are typically sourced from soil. Here, we show that Bacillus - and other antagonistic microbes - can be sourced from a broad range of plant seeds. We found that culturable Bacillus isolates are common in the seeds of 98 plant species representing 39 families (i.e., 87% of the commonly cultured bacteria belonged to Bacillales). We also found that 83% of the commonly cultured fungi from the seeds of the 98 plant species belonged to just three orders of fungi-Pleosporales, Hypocreales and Eurotiales-that are also associated with antagonism. Furthermore, we confirmed antagonism potential in agaro with seed isolates of Bacillus from Pinus monticola as a representative case. Eight isolates each of seed Bacillus, seed fungi, and foliar fungi, all from P. monticola, were paired in a total of 384 possible pair-wise interactions (with seed and foliar fungi as the targets). Seed Bacillus spp. were the strongest antagonists of the seed and foliar fungi, with a mean interaction strength 2.8 times greater than seed fungi (all either Eurotiales or Hypocreales) and 3.2 times greater than needle fungi. Overall, our study demonstrates that seeds host a taxonomically narrow group of culturable, antagonistic bacteria and fungi.}, }
@article {pmid35552794, year = {2022}, author = {Chauvet, M and Monjot, A and Moné, A and Lepère, C}, title = {Single Cell Analysis Reveals a New Microsporidia-Host Association in a Freshwater Lake.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35552794}, issn = {1432-184X}, abstract = {Microsporidia are a large group of obligate intracellular eukaryotic parasites. Recent studies suggest that their diversity can be huge in freshwater lake ecosystems especially in the < 150-µm size fraction. However, little is known about their hosts and therefore their impact on the trophic food web functioning. In this study, single cell analysis and fluorescence microscopy were used to detect new host-parasite association within rotifer communities in lake Aydat (France). Our analysis showed the existence of a potential new species belonging to the Crispospora genus able of infecting the rotifer Kellicottia with a high prevalence (42.5%) suggesting that Microsporidia could have a great impact on the rotifer populations' regulation in lakes.}, }
@article {pmid35550672, year = {2022}, author = {Samara, J and Moossavi, S and Alshaikh, B and Ortega, VA and Pettersen, VK and Ferdous, T and Hoops, SL and Soraisham, A and Vayalumkal, J and Dersch-Mills, D and Gerber, JS and Mukhopadhyay, S and Puopolo, K and Tompkins, TA and Knights, D and Walter, J and Amin, H and Arrieta, MC}, title = {Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants.}, journal = {Cell host &amp; microbe}, volume = {30}, number = {5}, pages = {696-711.e5}, doi = {10.1016/j.chom.2022.04.005}, pmid = {35550672}, issn = {1934-6069}, abstract = {Probiotics are increasingly administered to premature infants to prevent necrotizing enterocolitis and neonatal sepsis. However, their effects on gut microbiome assembly and immunity are poorly understood. Using a randomized intervention trial in extremely premature infants, we tested the effects of a probiotic product containing four strains of Bifidobacterium species autochthonous to the infant gut and one Lacticaseibacillus strain on the compositional and functional trajectory of microbiome. Daily administration of the mixture accelerated the transition into a mature, term-like microbiome with higher stability and species interconnectivity. Besides infant age, Bifidobacterium strains and stool metabolites were the best predictors of microbiome maturation, and structural equation modeling confirmed probiotics as a major determinant for the trajectory of microbiome assembly. Bifidobacterium-driven microbiome maturation was also linked to an anti-inflammatory intestinal immune milieu. This demonstrates that Bifidobacterium strains are ecosystem engineers that lead to an acceleration of microbiome maturation and immunological consequences in extremely premature infants.}, }
@article {pmid35550507, year = {2022}, author = {Jamnik, T and Flasch, M and Braun, D and Fareed, Y and Wasinger, D and Seki, D and Berry, D and Berger, A and Wisgrill, L and Warth, B}, title = {Next-generation biomonitoring of the early-life chemical exposome in neonatal and infant development.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {2653}, pmid = {35550507}, issn = {2041-1723}, support = {FunKeyGut 741623//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; PreMiBrain//Medizinische Universität Wien (Medical University of Vienna)/ ; internal//Universität Wien (University of Vienna)/ ; P33188//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; }, abstract = {Exposure to synthetic and natural chemicals is a major environmental risk factor in the etiology of many chronic diseases. Investigating complex co-exposures is necessary for a holistic assessment in exposome-wide association studies. In this work, a sensitive liquid chromatography-tandem mass spectrometry approach was developed and validated. The assay enables the analysis of more than 80 highly-diverse xenobiotics in urine, serum/plasma, and breast milk; with detection limits generally in the pg-ng mL-1 range. In plasma of extremely-premature infants, 27 xenobiotics are identified; including contamination with plasticizers, perfluorinated alkylated substances and parabens. In breast milk samples collected longitudinally over the first 211 days post-partum, 29 analytes are detected, including pyrrolizidine- and tropane alkaloids which have not been identified in this matrix before. A preliminary estimation of daily toxicant intake via breast milk is conducted. In conclusion, we observe significant early-life co-exposure to multiple toxicants, and demonstrate the method's applicability for large-scale exposomics-type cohort studies.}, }
@article {pmid35549250, year = {2022}, author = {Xu, G and Ng, HL and Chen, C and Zhao, S and He, J}, title = {Efficient and Complete Detoxification of Polybrominated Diphenyl Ethers in Sediments Achieved by Bioaugmentation with Dehalococcoides and Microbial Ecological Insights.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.2c00914}, pmid = {35549250}, issn = {1520-5851}, abstract = {Polybrominated diphenyl ethers (PBDEs) are prevalent environmental pollutants, but bioremediation of PBDEs remains to be reported. Here we report accelerated remediation of a penta-BDE mixture in sediments by bioaugmentation with Dehalococcoides mccartyi strains CG1 and TZ50. Bioaugmentation with different amounts of each Dehalococcoides strain enhanced debromination of penta-BDEs compared with the controls. The sediment microcosm spiked with 6.8 × 106 cells/mL strain CG1 showed the highest penta-BDEs removal (89.9 ± 7.3%) to diphenyl ether within 60 days. Interestingly, co-contaminant tetrachloroethene (PCE) improved bioaugmentation performance, resulting in faster and more extensive penta-BDEs debromination using less bioinoculants, which was also completely dechlorinated to ethene by introducing D. mccartyi strain 11a. The better bioaugmentation performance in sediments with PCE could be attributed to the boosted growth of the augmented Dehalococcoides and capability of the PCE-induced reductive dehalogenases to debrominate penta-BDEs. Finally, ecological analyses showed that bioaugmentation resulted in more deterministic microbial communities, where the augmented Dehalococcoides established linkages with indigenous microorganisms but without causing obvious alterations of the overall community diversity and structure. Collectively, this study demonstrates that bioaugmentation with Dehalococcoides is a feasible strategy to completely remove PBDEs in sediments.}, }
@article {pmid35547145, year = {2022}, author = {McElhinney, JMWR and Catacutan, MK and Mawart, A and Hasan, A and Dias, J}, title = {Interfacing Machine Learning and Microbial Omics: A Promising Means to Address Environmental Challenges.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {851450}, doi = {10.3389/fmicb.2022.851450}, pmid = {35547145}, issn = {1664-302X}, abstract = {Microbial communities are ubiquitous and carry an exceptionally broad metabolic capability. Upon environmental perturbation, microbes are also amongst the first natural responsive elements with perturbation-specific cues and markers. These communities are thereby uniquely positioned to inform on the status of environmental conditions. The advent of microbial omics has led to an unprecedented volume of complex microbiological data sets. Importantly, these data sets are rich in biological information with potential for predictive environmental classification and forecasting. However, the patterns in this information are often hidden amongst the inherent complexity of the data. There has been a continued rise in the development and adoption of machine learning (ML) and deep learning architectures for solving research challenges of this sort. Indeed, the interface between molecular microbial ecology and artificial intelligence (AI) appears to show considerable potential for significantly advancing environmental monitoring and management practices through their application. Here, we provide a primer for ML, highlight the notion of retaining biological sample information for supervised ML, discuss workflow considerations, and review the state of the art of the exciting, yet nascent, interdisciplinary field of ML-driven microbial ecology. Current limitations in this sphere of research are also addressed to frame a forward-looking perspective toward the realization of what we anticipate will become a pivotal toolkit for addressing environmental monitoring and management challenges in the years ahead.}, }
@article {pmid35543735, year = {2022}, author = {Merlin, BL and Moraes, GJ and Cônsoli, FL}, title = {The Microbiota of a Mite Prey-Predator System on Different Host Plants Are Characterized by Dysbiosis and Potential Functional Redundancy.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35543735}, issn = {1432-184X}, support = {2018/24768-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/12004-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, abstract = {Microbiota has diverse roles in the life cycles of their hosts, affecting their growth, development, behavior, and reproduction. Changes in physiological conditions of the host can also impact the assemblage of host-associated microorganisms. However, little is known of the effects of host plant-prey-predatory mite interactions on mite microbiota. We compared the microbial communities of eggs and adult females of the two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae), and of adult females of the predatory mite Neoseiulus californicus (McGregor) (Acari: Phytoseiidae) on four different host plants (cotton, maize, pinto bean, and tomato) by metabarcoding sequencing of the V3-V4 region of the 16S ribosomal RNA gene (16S rRNA), using the Illumina MiSeq platform. Only the egg microbiota of T. urticae was affected by the host plant. The microbiota of the predatory mite N. californicus was very different from that of its prey, and the predator microbiota was unaffected by the different host plant-prey systems tested. Only the microbiota of the eggs of T. urticae carried Serratia as a high fidelity-biomarker, but their low abundance in T. urticae adult females suggests that the association between Serratia and T. urticae is accidental. Biomarker bacteria were also detected in the microbiota of adult females of T. urticae and N. californicus, with different biomarkers in each host plant species. The microbiota associated with eggs and adult females of T. urticae and adult females of N. californicus differed in their functional potential contributions to the host mite.}, }
@article {pmid35539271, year = {2018}, author = {Zhang, H and Zhao, Z and Chen, S and Wang, Y and Feng, J and Jia, J and Kang, P and Li, S}, title = {Geographical patterns of denitrifying bacterial communities associated with different urban lakes.}, journal = {RSC advances}, volume = {8}, number = {31}, pages = {17079-17090}, doi = {10.1039/c8ra01295d}, pmid = {35539271}, issn = {2046-2069}, abstract = {The geographical variation of denitrifying bacterial communities and water quality parameters in urban lakes distributed across nine provinces in China were determined. The Illumina sequencing data of the denitrifying encoding gene nirS was examined in the samples collected from nine localities (pairwise geographical distance: 200-2600 km). The results showed that fundamental differences in water quality were observed among different urban lakes. The highest nitrate (2.02 mg L-1) and total nitrogen (3.82 mg L-1) concentrations were observed in Pingzhuang (P < 0.01). The algal cell concentration ranged from 1.29 × 108 to 3.0 × 109 cell per L. The sequencing data generated a total of 421058 high quality nirS gene reads that resulted in 6369 OTUs (97% cutoff), with Proteobacteria and Firmicutes being the dominant taxa. A co-occurrence network analysis indicated that the top five genera identified as keystone taxa were Dechlorospirillum sp., Alicycliphilus sp., Dechloromonas sp., Pseudogulbenkiania sp., and Paracoccus sp. A redundancy analysis (RDA) further revealed that distinct denitrifying bacterial communities inhabited the different urban lakes, and influenced by urban lake water ammonia nitrogen, manganese and algal cell concentrations. A variance partitioning analysis (VPA) also showed that geographic location was more important than water quality factors in structuring the denitrifying bacterial communities. Together, these results provide new insight into understanding of denitrifying bacterial communities associated with geographically distributed urban lakes on a larger scale, and these results also expand our exploration of aquatic microbial ecology in freshwater bodies.}, }
@article {pmid35538057, year = {2022}, author = {Patrono, LV and Vrancken, B and Budt, M and Düx, A and Lequime, S and Boral, S and Gilbert, MTP and Gogarten, JF and Hoffmann, L and Horst, D and Merkel, K and Morens, D and Prepoint, B and Schlotterbeck, J and Schuenemann, VJ and Suchard, MA and Taubenberger, JK and Tenkhoff, L and Urban, C and Widulin, N and Winter, E and Worobey, M and Schnalke, T and Wolff, T and Lemey, P and Calvignac-Spencer, S}, title = {Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {2314}, pmid = {35538057}, issn = {2041-1723}, abstract = {The 1918 influenza pandemic was the deadliest respiratory pandemic of the 20th century and determined the genomic make-up of subsequent human influenza A viruses (IAV). Here, we analyze both the first 1918 IAV genomes from Europe and the first from samples prior to the autumn peak. 1918 IAV genomic diversity is consistent with a combination of local transmission and long-distance dispersal events. Comparison of genomes before and during the pandemic peak shows variation at two sites in the nucleoprotein gene associated with resistance to host antiviral response, pointing at a possible adaptation of 1918 IAV to humans. Finally, local molecular clock modeling suggests a pure pandemic descent of seasonal H1N1 IAV as an alternative to the hypothesis of origination through an intrasubtype reassortment.}, }
@article {pmid35537509, year = {2022}, author = {Xu, N and Zhang, Z and Shen, Y and Zhang, Q and Liu, Z and Yu, Y and Wang, Y and Lei, C and Ke, M and Qiu, D and Lu, T and Chen, Y and Xiong, J and Qian, H}, title = {Compare the performance of multiple binary classification models in microbial high-throughput sequencing datasets.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {155807}, doi = {10.1016/j.scitotenv.2022.155807}, pmid = {35537509}, issn = {1879-1026}, abstract = {The development of machine learning and deep learning provided solutions for predicting microbiota response on environmental change based on microbial high-throughput sequencing. However, there were few studies specifically clarifying the performance and practical of two types of binary classification models to find a better algorithm for the microbiota data analysis. Here, for the first time, we evaluated the performance, accuracy and running time of the binary classification models built by three machine learning methods - random forest (RF), support vector machine (SVM), logistic regression (LR), and one deep learning method - back propagation neural network (BPNN). The built models were based on the microbiota datasets that removed low-quality variables and solved the class imbalance problem. Additionally, we optimized the models by tuning. Our study demonstrated that dataset pre-processing was a necessary process for model construction. Among these 4 binary classification models, BPNN and RF were the most suitable methods for constructing microbiota binary classification models. Using these 4 models to predict multiple microbial datasets, BPNN showed the highest accuracy and the most robust performance, while the RF method was ranked second. We also constructed the optimal models by adjusting the epochs of BPNN and the n_estimators of RF for six times. The evaluation related to performances of models provided a road map for the application of artificial intelligence to assess microbial ecology.}, }
@article {pmid35534014, year = {2022}, author = {Knapp, BD and Huang, KC}, title = {The Effects of Temperature on Cellular Physiology.}, journal = {Annual review of biophysics}, volume = {51}, number = {}, pages = {499-526}, doi = {10.1146/annurev-biophys-112221-074832}, pmid = {35534014}, issn = {1936-1238}, abstract = {Temperature impacts biological systems across all length and timescales. Cells and the enzymes that comprise them respond to temperature fluctuations on short timescales, and temperature can affect protein folding, the molecular composition of cells, and volume expansion. Entire ecosystems exhibit temperature-dependent behaviors, and global warming threatens to disrupt thermal homeostasis in microbes that are important for human and planetary health. Intriguingly, the growth rate of most species follows the Arrhenius law of equilibrium thermodynamics, with an activation energy similar to that of individual enzymes but with maximal growth rates and over temperature ranges that are species specific. In this review, we discuss how the temperature dependence of critical cellular processes, such as the central dogma and membrane fluidity, contributes to the temperature dependence of growth. We conclude with a discussion of adaptation to temperature shifts and the effects of temperature on evolution and on the properties of microbial ecosystems.}, }
@article {pmid35533832, year = {2022}, author = {Lu, S and Zhang, W and Li, X and Xian, J and Hu, Y and Zhou, Y}, title = {Skin bacterial richness and diversity in ICU patients with severe pneumonia.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijid.2022.05.006}, pmid = {35533832}, issn = {1878-3511}, abstract = {OBJECTIVES: Patients with severe pneumonia admitted to the intensive care unit (ICU) have a high risk of mortality, and the microbiome is likely to affect the outcome of ICU patients with severe pneumonia; however, the skin microbiota in ICU patients with severe pneumonia remains unclear. In this study, based on 16S rRNA sequencing, we explored the difference in skin bacterial richness and diversity between the group of ICU patients with severe pneumonia (PG) and the group of healthy controls (CG).<br><br>METHODS: The diversity index and taxonomic distribution of skin bacteria were analyzed using the Quantitative Insights Into Microbial Ecology bioinformatics pipeline. Blood, endotracheal aspirate, and bronchoalveolar lavage fluid samples were collected from the same subjects of PG for culture.<br><br>RESULTS: Compared to CG, the diversity of skin bacteria in PG decreased significantly; Staphylococcus, Acinetobacter, Stenotrophomonas, Enterococcus, Halomonas, and Brevibacillus were differentially abundant in PG, most of which were also identified in the cultures of upper respiratory tract samples of the same PG.<br><br>CONCLUSIONS: We provide evidence that healthcare-associated infection in ICU patients with severe pneumonia is strongly associated with skin microbiota, which necessitates the prevention and control of skin bacterial pathogens for these patients.}, }
@article {pmid35532036, year = {2022}, author = {Van Bonn, W and Oliaro, FJ and Pinnell, LJ}, title = {Ultraviolet light alters experimental aquarium water microbial communities.}, journal = {Zoo biology}, volume = {}, number = {}, pages = {}, doi = {10.1002/zoo.21701}, pmid = {35532036}, issn = {1098-2361}, abstract = {The effect of ultraviolet (UV) light exposure, alone and in combination with CO2 exposure, on the water microbial community composition was tested in replicate experimental aquaria using source water from an established Amazon-themed exhibit housing mixed species of fishes. Total bacterial abundance, α-diversity metrics, and β-diversity metrics were determined 3 weeks and 1 week before, and weekly during 8 weeks of continuous treatment. The UV treatment significantly lowered the overall bacterial abundance while CO2 treatment had no effect. However, the UV exposure effect was variable across phyla. Some phyla were decreased while others were increased, including some of potential clinical significance. At the genus level, there were no significant differences in the relative abundance of Mycobacteria between treatments and an increase in the relative abundance of Aeromonas spp. with UV light treatment. Further work is needed to determine if the observed effects are dose-dependent or if different exposure doses produce different results.}, }
@article {pmid35531503, year = {2019}, author = {Yan, Y and Du, Z and Zhang, L and Feng, L and Sun, D and Dang, Y and Holmes, DE and Smith, JA}, title = {Identification of parameters needed for optimal anaerobic co-digestion of chicken manure and corn stover.}, journal = {RSC advances}, volume = {9}, number = {51}, pages = {29609-29618}, doi = {10.1039/c9ra05556h}, pmid = {35531503}, issn = {2046-2069}, abstract = {While studies have shown that anaerobic co-digestion of chicken manure (CM) and corn stover (CS) is an efficient method to treat these agricultural wastes, the microbial ecology of these systems and optimal parameters for the digestion process are yet to be determined. In this study, the effects of different initial substrate concentrations and CS : CM mixture ratios on co-digestion and microbial community structure were evaluated. Results demonstrated that both the highest cumulative methane yields and methane production rates were obtained from reactors with a CS : CM ratio of 1 : 1 during hemi-solid-state anaerobic digestion (HSS-AD). Cumulative methane yields and methane production rates were 24.8% and 42% lower in solid-state anaerobic digestion (SS-AD) reactors using the same CS : CM ratios. Analysis of microbial community structures revealed that cellulolytic bacteria and a diversity of syntrophic microorganisms capable of direct interspecies electron transfer (DIET) and hydrogen interspecies transfer (HIT) were enriched in the best-performing reactors. Methanosarcina species also dominated during HSS-AD, and their presence was positively correlated with methane production in the reactors.}, }
@article {pmid35531295, year = {2022}, author = {Na, N and Qili, M and Wu, N and Sun, L and Xu, H and Zhao, Y and Wei, X and Xue, Y and Tao, Y}, title = {Bacterial Community and Fermentation Quality of Ensiling Alfalfa With Commercial Lactic Acid Bacterial Additives.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {836899}, doi = {10.3389/fmicb.2022.836899}, pmid = {35531295}, issn = {1664-302X}, abstract = {The aim of this study was to determine the effects of six common commercial lactic acid bacteria (LAB) additives [A1, Lactobacillus plantarum, L. buchneri, and Enterococcus faecalis; A2, L. plantarum and L. casei; A3, L. plantarum and L. buchneri; A4, L. plantarum, L. buchneri, L. casei, and Pediococcus acidilactici; A5, L. plantarum (producing feruloyl esterase); and A6, L. buchneri, P. acidilactici, β-glucanase, and xylanase] on the bacterial community and fermentation quality of alfalfa silage. Alfalfa was harvested at the squaring stage, wilted in the field for 24 h, and ensiled without any additives (Control) or with A1, A2, A3, A4, A5, or A6. Microbial counts, bacterial community, fermentation parameters, and nutritional composition were determined after ensiling for 90 days. The total abundance of LAB genera on alfalfa pre-ensiling was 0.38% in bacterial community. The abundances of Lactobacillus, Enterococcus, and Pediococcus in the Control silage were 42.18, 40.18, and 8.09% of abundance, respectively. The abundances of Lactobacillus in A1-, A2-, A3-, A4-, and A5-treatments were 89.32, 92.93, 92.87, 81.12, and 80.44%, respectively. The abundances of Pediococcus and Lactobacillus in A6-treatment were 70.14 and 24.86%, respectively. Compared with Control silage, LAB-treated silage had lower pH and less ammonia nitrogen and water-soluble carbohydrates concentrations (p < 0.05). Further, the A5- and A6-treatments contained lower neutral detergent fiber, acid detergent fiber, and hemicellulose than other treatments (p < 0.05). Overall, LAB genera were presented as minor taxa in alfalfa pre-ensiling and as dominant taxa in alfalfa silage. Adding LAB additives improved the fermentation quality and altered the bacterial community of alfalfa silage. The main bacterial genera in Control silage were Lactobacillus, Enterococcus, and Pediococcus. Lactobacillus dominated the bacterial communities of A1-, A2-, A3-, A4-, and A5-treatments, while Pediococcus and Lactobacillus were dominant bacterial genera in A6-treatment. Inoculating A5 and A6 degraded the fiber in alfalfa silage. It is necessary to ensile alfalfa with LAB inoculants.}, }
@article {pmid35529946, year = {2022}, author = {Franzino, T and Boubakri, H and Cernava, T and Abrouk, D and Achouak, W and Reverchon, S and Nasser, W and Haichar, FEZ}, title = {Implications of carbon catabolite repression for plant-microbe interactions.}, journal = {Plant communications}, volume = {3}, number = {2}, pages = {100272}, doi = {10.1016/j.xplc.2021.100272}, pmid = {35529946}, issn = {2590-3462}, abstract = {Carbon catabolite repression (CCR) plays a key role in many physiological and adaptive responses in a broad range of microorganisms that are commonly associated with eukaryotic hosts. When a mixture of different carbon sources is available, CCR, a global regulatory mechanism, inhibits the expression and activity of cellular processes associated with utilization of secondary carbon sources in the presence of the preferred carbon source. CCR is known to be executed by completely different mechanisms in different bacteria, yeast, and fungi. In addition to regulating catabolic genes, CCR also appears to play a key role in the expression of genes involved in plant-microbe interactions. Here, we present a detailed overview of CCR mechanisms in various bacteria. We highlight the role of CCR in beneficial as well as deleterious plant-microbe interactions based on the available literature. In addition, we explore the global distribution of known regulatory mechanisms within bacterial genomes retrieved from public repositories and within metatranscriptomes obtained from different plant rhizospheres. By integrating the available literature and performing targeted meta-analyses, we argue that CCR-regulated substrate use preferences of microorganisms should be considered an important trait involved in prevailing plant-microbe interactions.}, }
@article {pmid35528619, year = {2022}, author = {Qing, JB and Song, WZ and Li, CQ and Li, YF}, title = {The Diagnostic and Predictive Significance of Immune-Related Genes and Immune Characteristics in the Occurrence and Progression of IgA Nephropathy.}, journal = {Journal of immunology research}, volume = {2022}, number = {}, pages = {9284204}, doi = {10.1155/2022/9284204}, pmid = {35528619}, issn = {2314-7156}, abstract = {Objective: To investigate the potential diagnostic and predictive significance of immune-related genes in IgA nephropathy (IgAN) and discover the abnormal glomerular inflammation in IgAN.<br><br>Methods: GSE116626 was used as a training set to identify different immune-related genes (DIRGs) and establish machine learning models for the diagnosis of IgAN; then, a nomogram model was generated based on GSE116626, and GSE115857 was used as a test set to evaluate its clinical value. Short Time-Series Expression Miner (STEM) analysis was also performed to explore the changing trend of DIRGs with the progression of IgAN lesions. GSE141344 was used with DIRGs to establish the ceRNA network associated with IgAN progression. Finally, ssGSEA analysis was performed on the GSE141295 dataset to discover the abnormal inflammation in IgAN.<br><br>Results: Machine learning (ML) performed excellently in diagnosing IgAN using six DIRGs. A nomogram model was constructed to predict IgAN based on the six DIRGs. Three trends related to IgAN lesions were identified using STEM analysis. A ceRNA network associated with IgAN progression which contained 8 miRNAs, 14 lncRNAs, and 3 mRNAs was established. A higher macrophage ratio and lower CD4+ T cell ratio in IgAN compared to controls were observed, and the correlation between macrophages and monocytes in the glomeruli of IgAN patients was inverse compared to controls.<br><br>Conclusion: This study reveals the diagnostic and predictive significance of DIRGs in IgAN and finds that the imbalance between macrophages and CD4+ immune cells may be an important pathomechanism of IgAN. These results provide potential directions for the treatment and prevention of IgAN.}, }
@article {pmid35526797, year = {2022}, author = {Zhang, X and Jin, Z and Shen, M and Chang, Z and Yu, G and Wang, L and Xia, X}, title = {Accumulation of polyethylene microplastics induces oxidative stress, microbiome dysbiosis and immunoregulation in crayfish.}, journal = {Fish &amp; shellfish immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.fsi.2022.05.005}, pmid = {35526797}, issn = {1095-9947}, abstract = {Microplastics have become a worldwide pollutant, widely discovered in soil, air and aquatic environment. Microplastics have been found in habitats where crayfish (Procambarus clarkii) cultivated, but the impact of microplastics on crayfish remains unclear. In this study, after 21-day dietary exposure, polyethylene (PE) particles were found to accumulate in intestine, hepatopancreas, gills and hemolymph of crayfish. Furthermore, PE particles can still be detected in these tissues after a 7-day depuration in clean water. PE retained in these tissues caused oxidative stress responses, as indicated by the change of oxidative-stress-related index, such as the increase of H2O2 level and SOD activity. PE exposure also caused hemocytic encapsulation in crayfish hepatopancreas and increase of mucus secretion in intestine. Moreover, PE exposure affected the microbiota balance in crayfish, by reducing the total microbiota abundance and altering the proportions of many bacterial families. Interestingly, results showed that PE exposure led to of lower numbers of hemocytes and declination of phenoloxidase activity. Finally, PE exposure induced the expression of immune-related genes, including transcription factors and antimicrobial peptides. Taken these together, we conclude that PE microplastics exert considerable toxic effects on crayfish and are a potential threat to crayfish aquaculture and consumption. This study provides basic toxicological data toward quantifying and illuminating the impact of PE microplastics on freshwater animals.}, }
@article {pmid35525854, year = {2022}, author = {da Silva, JL and Mendes, LW and Rocha, SMB and Antunes, JEL and Oliveira, LMS and Melo, VMM and Oliveira, FAS and Pereira, APA and Costa, GDN and da Silva, VB and Gomes, RLF and de Alcantara Neto, F and Lopes, ACA and Araujo, ASF}, title = {Domestication of Lima Bean (Phaseolus lunatus) Changes the Microbial Communities in the Rhizosphere.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35525854}, issn = {1432-184X}, abstract = {Plants modulate the soil microbiota and select a specific microbial community in the rhizosphere. However, plant domestication reduces genetic diversity, changes plant physiology, and could have an impact on the associated microbiome assembly. Here, we used 16S rRNA gene sequencing to assess the microbial community in the bulk soil and rhizosphere of wild, semi-domesticated, and domesticated genotypes of lima bean (Phaseolus lunatus), to investigate the effect of plant domestication on microbial community assembly. In general, rhizosphere communities were more diverse than bulk soil, but no differences were found among genotypes. Our results showed that the microbial community's structure was different from wild and semi-domesticated as compared to domesticated genotypes. The community similarity decreased 57.67% from wild to domesticated genotypes. In general, the most abundant phyla were Actinobacteria (21.9%), Proteobacteria (20.7%), Acidobacteria (14%), and Firmicutes (9.7%). Comparing the different genotypes, the analysis showed that Firmicutes (Bacillus) was abundant in the rhizosphere of the wild genotypes, while Acidobacteria dominated semi-domesticated plants, and Proteobacteria (including rhizobia) was enriched in domesticated P. lunatus rhizosphere. The domestication process also affected the microbial community network, in which the complexity of connections decreased from wild to domesticated genotypes in the rhizosphere. Together, our work showed that the domestication of P. lunatus shaped rhizosphere microbial communities from taxonomic to a functional level, changing the abundance of specific microbial groups and decreasing the complexity of interactions among them.}, }
@article {pmid35525510, year = {2022}, author = {Zhang, Z and Wang, Y and Chen, B and Lei, C and Yu, Y and Xu, N and Zhang, Q and Wang, T and Gao, W and Lu, T and Gillings, M and Qian, H}, title = {Xenobiotic pollution affects transcription of antibiotic resistance and virulence factors in aquatic microcosms.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {119396}, doi = {10.1016/j.envpol.2022.119396}, pmid = {35525510}, issn = {1873-6424}, abstract = {Antibiotic resistance genes (ARGs) and virulence factors (VFs) are critical threats to human health. Their abundance in aquatic ecosystems is maintained and enhanced via selection driven by environmental xenobiotics. However, their activity and expression in these environments under xenobiotic stress remains unknown. Here ARG and VF expression profiles were examined in aquatic microcosms under ciprofloxacin, glyphosate and sertraline hydrochloride treatment. Ciprofloxacin increased total expression of ARGs, particularly multidrug resistance factors. Total expression of ARGs and VFs decreased significantly under glyphosate and sertraline treatments. However, in opportunistic human pathogens, these agents increased expression of both ARGs and VFs. Xenobiotic pollutants, such as the compounds we tested here, have the potential to disrupt microbial ecology, promote resistance, and increase risk to human health. This study systematically evaluated the effects of environmental xenobiotics on transcription of ARGs and VFs, both of which have direct relevance to human health. Transcription of such genes has been overlooked in previous studies.}, }
@article {pmid35524818, year = {2022}, author = {Palacios, OA and Espinoza-Hicks, JC and Camacho-Dávila, AA and López, BR and de-Bashan, LE}, title = {Differences in Exudates Between Strains of Chlorella sorokiniana Affect the Interaction with the Microalga Growth-Promoting Bacteria Azospirillum brasilense : Differences in Exudates Between Strains of Chlorella sorokiniana Affect the Interaction with the Microalga Growth-Promoting Bacteria Azospirillum brasilense.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35524818}, issn = {1432-184X}, support = {284562//CONACYT/ ; }, abstract = {The microalga Chlorella sorokiniana and the microalgae growth-promoting bacteria (MGPB) Azospirillum brasilense have a mutualistic interaction that can begin within the first hours of co-incubation; however, the metabolites participating in this initial interaction are not yet identified. Nuclear magnetic resonance (NMR) was used in the present study to characterize the metabolites exuded by two strains of C. sorokiniana (UTEX 2714 and UTEX 2805) and A. brasilense Cd when grown together in an oligotrophic medium. Lactate and myo-inositol were identified as carbon metabolites exuded by the two strains of C. sorokiniana; however, only the UTEX 2714 strain exuded glycerol as the main carbon compound. In turn, A. brasilense exuded uracil when grown on the exudates of either microalga, and both microalga strains were able to utilize uracil as a nitrogen source. Interestingly, although the total carbohydrate content was higher in exudates from C. sorokiniana UTEX 2805 than from C. sorokiniana UTEX 2714, the growth of A. brasilense was greater in the exudates from the UTEX 2714 strain. These results highlight the fact that in the exuded carbon compounds differ between strains of the same species of microalgae and suggest that the type, rather than the quantity, of carbon source is more important for sustaining the growth of the partner bacteria.}, }
@article {pmid35522265, year = {2022}, author = {Sun, Y and Shi, X and He, LY and Xing, Y and Guo, QF and Xiu, ZL and Dong, YS}, title = {Biosynthetic Profile in the Co-culture of Aspergillus sydowii and Bacillus subtilis to Produce Novel Benzoic Derivatives.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35522265}, issn = {1432-184X}, support = {2019-ZD-0143//Natural Science Foundation of Liaoning Province/ ; 202110401131YY//Science and Technology Development Program of Jilin Province of China/ ; }, abstract = {Microbial co-culture simulates the natural ecosystem through the combination of artificial microbes. This approach has been widely applied in the study of activating silent genes to reveal novel secondary metabolites. However, there are still challenges in determining the biosynthetic pathways. In this study, the effects of microbial co-culture on the morphology of the microbes were verified by the morphological observation. Subsequently, through the strategy combining substrate feeding, stable isotope labeling, and gene expression analysis, the biosynthetic pathways of five benzoic acid derivatives N1-N4 and N7 were demonstrated: the secondary metabolite 10-deoxygerfelin of A. sydowii acted as an inducer to induce B. subtilis to produce benzoic acid, which was further converted into 3-OH-benzoic acid by A. sydowii. Subsequently, A. sydowii used 3-OH-benzoic acid as the substrate to synthesize the new compound N2, and then N1, N3, N4, and N7 were biosynthesized upon the upregulation of hydrolase, hydroxylase, and acyltransferase during co-culture. The plate zone analysis suggested that the biosynthesis of the newly induced compounds N1-N4 was mainly attributed to A. sydowii, and both A. sydowii and B. subtilis were indispensable for the biosynthesis of N7. This study provides an important basis for a better understanding of the interactions among microorganisms, providing new ideas for studying the biosynthetic pathways of the newly induced secondary metabolites in co-culture.}, }
@article {pmid35513592, year = {2022}, author = {Haag, KL and Caesar, L and da Silveira Regueira-Neto, M and de Sousa, DR and Montenegro Marcelino, V and de Queiroz Balbino, V and Torres Carvalho, A}, title = {Temporal Changes in Gut Microbiota Composition and Pollen Diet Associated with Colony Weakness of a Stingless Bee.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35513592}, issn = {1432-184X}, support = {PQG 19/2551-0001860-6//Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul/ ; Associação ABELHA #400597/2018-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; PQ #302121/2017-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Compared to honeybees and bumblebees, the effect of diet on the gut microbiome of Neotropical corbiculate bees such as Melipona spp. is largely unknown. These bees have been managed for centuries, but recently an annual disease is affecting M. quadrifasciata, an endangered species kept exclusively by management in Southern Brazil. Here we report the results of a longitudinal metabarcoding study involving the period of M. quadrifasciata colony weakness, designed to monitor the gut microbiota and diet changes preceding an outbreak. We found increasing amounts of bacteria associated to the gut of forager bees 2 months before the first symptoms have been recorded. Simultaneously, forager bees showed decreasing body weight. The accelerated growth of gut-associated bacteria was uneven among taxa, with Bifidobacteriaceae dominating, and Lactobacillaceae decreasing in relative abundance within the bacterial community. Dominant fungi such as Candida and Starmerella also decreased in numbers, and the stingless bee obligate symbiont Zygosaccharomyces showed the lowest relative abundance during the outbreak period. Such changes were associated with pronounced diet shifts, i.e., the rise of Eucalyptus spp. pollen amount in forager bees' guts. Furthermore, there was a negative correlation between the amount of Eucalyptus pollen in diets and the abundance of some bacterial taxa in the gut-associated microbiota. We conclude that diet and subsequent interactions with the gut microbiome are key environmental components of the annual disease and propose the use of diet supplementation as means to sustain the activity of stingless bee keeping as well as native bee pollination services.}, }
@article {pmid35513142, year = {2022}, author = {Bulgarelli, RG and Leite, MFA and de Hollander, M and Mazzafera, P and Andrade, SAL and Kuramae, EE}, title = {Eucalypt species drive rhizosphere bacterial and fungal community assembly but soil phosphorus availability rearranges the microbiome.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {155667}, doi = {10.1016/j.scitotenv.2022.155667}, pmid = {35513142}, issn = {1879-1026}, abstract = {Soil phosphorus (P) availability may limit plant growth and alter root-soil interactions and rhizosphere microbial community composition. The composition of the rhizosphere microbial community can also be shaped by plant genotype. In this study, we examined the rhizosphere microbial communities of young plants of 24 species of eucalypts (22 Eucalyptus and two Corymbia species) under low or sufficient soil P availability. The taxonomic diversity of the rhizosphere bacterial and fungal communities was assessed by 16S and 18S rRNA gene amplicon sequencing. The taxonomic modifications in response to low P availability were evaluated by principal component analysis, and co-inertia analysis was performed to identify associations between bacterial and fungal community structures and parameters related to plant growth and nutritional status under low and sufficient soil P availability. The sequencing results showed that while both soil P availability and eucalypt species influenced the microbial community assembly, eucalypt species was the stronger determinant. However, when the plants are subjected to low P-availability, the rhizosphere selection became strongest. In response to low P, the bacterial and fungal communities in the rhizosphere of some species showed significant changes, whereas in others remained relatively constant under low and sufficient P. Co-inertia analyses revealed a significant co-dependence between plant nutrient contents and bacterial and fungal community composition only under sufficient P. By contrast, under low P, bacterial community composition was related to plant biomass production. In conclusion, our study shows that eucalypt species identity was the main factor modulating rhizosphere microbial community composition; significant shifts due to P availability were observed only for some eucalypt species.}, }
@article {pmid35507445, year = {2022}, author = {Bloxham, B and Lee, H and Gore, J}, title = {Diauxic lags explain unexpected coexistence in multi-resource environments.}, journal = {Molecular systems biology}, volume = {18}, number = {5}, pages = {e10630}, doi = {10.15252/msb.202110630}, pmid = {35507445}, issn = {1744-4292}, support = {542385//Simons Foundation (SF)/ ; }, abstract = {How the coexistence of species is affected by the presence of multiple resources is a major question in microbial ecology. We experimentally demonstrate that differences in diauxic lags, which occur as species deplete their own environments and adapt their metabolisms, allow slow-growing microbes to stably coexist with faster-growing species in multi-resource environments despite being excluded in single-resource environments. In our focal example, an Acinetobacter species (Aci2) competitively excludes Pseudomonas aurantiaca (Pa) on alanine and on glutamate. However, they coexist on the combination of both resources. Experiments reveal that Aci2 grows faster but Pa has shorter diauxic lags. We establish a tradeoff between Aci2's fast growth and Pa's short lags as their mechanism for coexistence. We model this tradeoff to accurately predict how environmental changes affect community composition. We extend our work by surveying a large set of competitions and observe coexistence nearly four times as frequently when the slow-grower is the fast-switcher. Our work illustrates a simple mechanism, based entirely on supplied-resource growth dynamics, for the emergence of multi-resource coexistence.}, }
@article {pmid35507048, year = {2022}, author = {McLain, NK and Gomez, MY and Gachomo, EW}, title = {Acetaminophen Levels Found in Recycled Wastewater Alter Soil Microbial Community Structure and Functional Diversity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35507048}, issn = {1432-184X}, support = {1018746//National Institute of Food and Agriculture, Multistate Research Fund ,/ ; }, abstract = {The practice of using recycled wastewater (RWW) has been successfully adopted to address the growing demand for clean water. However, chemicals of emerging concern (CECs) including pharmaceutical products remain in the RWW even after additional cleaning. When RWW is used to irrigate crops or landscapes, these chemicals can enter these and adjacent environments. Unfortunately, the overall composition and concentrations of CECs found in different RWW sources vary, and even the same source can vary over time. Therefore, we selected one compound that is found frequently and in high concentrations in many RWW sources, acetaminophen (APAP), to use for our study. Using greenhouse grown eggplants treated with APAP concentrations within the ranges found in RWW effluents, we investigated the short-term impacts of APAP on the soil bacterial population under agricultural settings. Using Illumina sequencing-based approaches, we showed that APAP has the potential to cause shifts in the microbial community most likely by positively selecting for bacteria that are capable of metabolizing the breakdown products of APAP such as glycosides and carboxylic acids. Community-level physiological profiles of carbon metabolism were evaluated using Biolog EcoPlate as a proxy for community functions. The Biolog plates indicated that the metabolism of amines, amino acids, carbohydrates, carboxylic acids, and polymers was significantly higher in the presence of APAP. Abundance of microorganisms of importance to plant health and productivity was altered by APAP. Our results indicate that the soil microbial community and functions could be altered by APAP at concentrations found in RWW. Our findings contribute to the knowledge base needed to guide policies regulating RWW reuse in agriculture and also highlight the need to further investigate the effects of CECs found in RWW on soil microbiomes.}, }
@article {pmid35504465, year = {2022}, author = {Li, H and Miller, T and Lu, J and Goel, R}, title = {Nitrogen fixation contribution to nitrogen cycling during cyanobacterial blooms in Utah Lake.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {134784}, doi = {10.1016/j.chemosphere.2022.134784}, pmid = {35504465}, issn = {1879-1298}, abstract = {Nitrogen (N) cycling is an essential process in lake systems and N-fixation is an important component of it. Recent studies have also found that nitrate reduction through heterotrophic denitrification in lake systems did not prevent harmful cyanobacterial blooms, but instead, may have favored the dominance of N2-fixing cyanobacteria. The overall objective of this study was to estimate nitrogen fixation rates and the expressions of associated nitrogenase (nif gene) functional gene at several sites at different occasions in freshwater Utah Lake. For comparison purposes, one time sampling was also conducted in the brackish Farmington Bay of Great Salt Lake (GSL). The microbial ecology of the top 20-cm of surface water was investigated to assess the dominant cyanobacterial communities and N-related metabolisms. Our study revealed that Dolichospermum and Nodularia were potential N2-fixers for Utah Lake and brackish Farmington Bay, respectively. The in situ N2-fixation rates were 0-0.73 nmol N hr-1L-1 for Utah Lake and 0-0.85 nmol N hr-1L-1 for Farmington Bay, and these rates positively correlated with the abundance and expressions of the nif gene. In addition, nitrate reduction was measured in sediment (0.002-0.094 mg N VSS-1 hr-1). Significantly positive correlations were found among amoA, nirS and nirK abundance (R = 0.56-0.87, p < 0.05, Spearman) in both lakes. An exception was the lower nirK gene abundance detected at one site in Farmington Bay where high ammonium retentions were also detected. Based on a mass balance approach, we concluded that the amount of inorganic N loss through denitrification still exceeded the N input by N2-fixation, much like in most lakes, rivers, and marine ecosystems. This indicates that N cycling processes such as denitrification mediated by heterotrophic bacteria contributes to N-export from the lakes resulting in N limitations.}, }
@article {pmid35504213, year = {2022}, author = {Lee, M and Liang, G and Holland, SI and O'Farrell, C and Osborne, K and Manefield, MJ}, title = {Dehalobium species implicated in 2,3,7,8-tetrachlorodibenzo-p-dioxin dechlorination in the contaminated sediments of Sydney Harbour Estuary.}, journal = {Marine pollution bulletin}, volume = {179}, number = {}, pages = {113690}, doi = {10.1016/j.marpolbul.2022.113690}, pmid = {35504213}, issn = {1879-3363}, abstract = {Polychlorinated dibenzo-p-dioxins and furans (PCDD/F) are some of the most environmentally recalcitrant and toxic compounds. They occur naturally and as by-products of anthropogenic activity. Sydney Harbour Estuary (Sydney, Australia), is heavily contaminated with PCDD/F. Analysis of sediment cores revealed that the contamination source area in Homebush Bay continues to have one of the highest levels of PCDD/F contamination in the world (5207 pg WHO-TEQ g-1) with >50% of the toxicity attributed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD), the most toxic PCDD/F congener. Comparison of congener profiles at the contamination source area with surrounding bays and historical data provided evidence for the attenuation of 2,3,7,8-TCDD and other congeners at the source area. This finding was supported by the detection of di-, mono- and unchlorinated dibenzo-p-dioxin. Microbial community analysis of sediments by 16S rRNA amplicon sequencing revealed an abundance of lineages from the class Dehalococcoidia (up to 15% of the community), including the genus Dehalobium (up to 0.5%). Anaerobic seawater enrichment cultures using perchloroethene as more biologically available growth substrate enriched the Dehalobium population by more than six-fold. The enrichment culture then proved capable of reductively dechlorinating 2,3,7,8-TCDD to 2,3,7-TriCDD and octachlorodibenzo-p-dibenzodioxin (OCDD) to hepta and hexa congeners. This work is the first to show microbial reductive dehalogenation of 2,3,7,8-TCDD with a bacterium from outside the Dehalococcoides genus, and one of only a few that demonstrates PCDD/F dechlorination in a marine environment.}, }
@article {pmid35503575, year = {2022}, author = {Dick, JM and Tan, J}, title = {Chemical Links Between Redox Conditions and Estimated Community Proteomes from 16S rRNA and Reference Protein Sequences.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35503575}, issn = {1432-184X}, abstract = {Environmental influences on community structure are often assessed through multivariate analyses in order to relate microbial abundances to separately measured physicochemical variables. However, genes and proteins are themselves chemical entities; in combination with genome databases, differences in microbial abundances directly encode for chemical variability. We predicted that the carbon oxidation state of estimated community proteomes, obtained by combining taxonomic abundances from published 16S rRNA gene sequencing datasets with reference microbial proteomes from the NCBI Reference Sequence (RefSeq) database, would reflect environmental oxidation-reduction conditions. Analysis of multiple datasets confirms the geobiochemical predictions for environmental redox gradients in hydrothermal systems, stratified lakes and marine environments, and shale gas wells. The geobiochemical signal is largest for the steep redox gradients associated with hydrothermal systems and between injected water and produced fluids from shale gas wells, demonstrating that microbial community composition can be a chemical proxy for environmental redox gradients. Although estimates of oxidation state from 16S amplicon and metagenomic sequences are correlated, the 16S-based estimates show stronger associations with redox gradients in some environments.}, }
@article {pmid35502577, year = {2022}, author = {Laveilhé, A and Fochesato, S and Lalaouna, D and Heulin, T and Achouak, W}, title = {Phytobeneficial traits of rhizobacteria under the control of multiple molecular dialogues.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.14023}, pmid = {35502577}, issn = {1751-7915}, support = {2011/1473//Association Nationale de la Recherche et de la Technologie/ ; }, abstract = {Pseudomonads play crucial roles in plant growth promotion and control of plant diseases. However, under natural conditions, other microorganisms competing for the same nutrient resources in the rhizosphere may exert negative control over their phytobeneficial characteristics. We assessed the expression of phytobeneficial genes involved in biocontrol, biostimulation and iron regulation such as, phlD, hcnA, acdS, and iron-small regulatory RNAs prrF1 and prrF2 in Pseudomonas brassicacearum co-cultivated with three phytopathogenic fungi, and two rhizobacteria in the presence or absence of Brassica napus, and in relation to iron availability. We found that the antifungal activity of P. brassicacearum depends mostly on the production of DAPG and not on HCN whose production is suppressed by fungi. We have also shown that the two-competing bacterial strains modulate the plant growth promotion activity of P. brassicacearum by modifying the expression of phlD, hcnA and acdS according to iron availability. Overall, it allows us to better understand the complexity of the multiple molecular dialogues that take place underground between microorganisms and between plants and its rhizosphere microbiota and to show that synergy in favour of phytobeneficial gene expression may exist between different bacterial species.}, }
@article {pmid35502341, year = {2022}, author = {Qing, J and Song, W and Tian, L and Samuel, SB and Li, Y}, title = {Potential Small Molecules for Therapy of Lupus Nephritis Based on Genetic Effect and Immune Infiltration.}, journal = {BioMed research international}, volume = {2022}, number = {}, pages = {2259164}, doi = {10.1155/2022/2259164}, pmid = {35502341}, issn = {2314-6141}, abstract = {Lupus nephritis (LN) is the most common and significant complication of systemic lupus erythematosus (SLE) due to its poor prognosis and mortality rates in SLE patients. There is a critical need for new drugs as the pathogenesis of LN remains to be elucidated and immunosuppressive therapy comes with many deficiencies. In this study, 23 hub genes (IFI6, PLSCR1, XAF1, IFI16, IFI44, MX1, IFI44L, IFIT3, IFIT2, IFI27, DDX58, EIF2AK2, IFITM1, RTP4, IFITM3, TRIM22, PARP12, IFIH1, OAS1, HERC6, RSAD2, DDX60, and MX2) were identified through bioinformatics and network analysis and are closely related to interferon production and function. Interestingly, immune cell infiltration analysis and correlation analysis demonstrate a positive correlation between the expression of 23 hub genes and monocyte infiltration in glomeruli and M2 macrophage infiltration in the tubulointerstitium of LN patients. Additionally, the CTD database, DsigDB database, and DREIMT database were used to explore the bridging role of genes in chemicals and LN as well as the potential influence of these chemicals on immune cells. After comparison and discussion, six small molecules (Acetohexamide, Suloctidil, Terfenadine, Prochlorperazine, Mefloquine, and Triprolidine) were selected for their potential ability in treating lupus nephritis.}, }
@article {pmid35501499, year = {2022}, author = {Liu, Y and Zhang, B and Zhang, Y and Shen, Y and Cheng, C and Yuan, W and Guo, P}, title = {Organic Matter Decomposition in River Ecosystems: Microbial Interactions Influenced by Total Nitrogen and Temperature in River Water.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35501499}, issn = {1432-184X}, support = {2018ZX07111005//the National Science and Technology Major Project of the Ministry of Science and Technology of China/ ; 20200801071GH//the Science and Technology Development Program of Jilin Province/ ; }, abstract = {Microbes contribute to the organic matter decomposition (OMD) in river ecosystems. This study considers two aspects of OMD in river ecosystems which have not been examined in scientific studies previously, and these are the microbial interactions in OMD and the influence of environmental factors on microbial interactions. Cotton strip (CS), as a substitute for organic matter, was introduced to Luanhe River Basin in China. The results of CS assay, microbial sequencing, and redundancy analysis (RDA) showed that CS selectively enriched bacterial and fungal groups related to cellulose decomposition, achieving cotton strip decomposition (CSD). Bacterial phylum Proteobacteria and fungal phyla Rozellomycota and Ascomycota were the dominant groups associated with CSD. Network analysis and Mantel test results indicated that bacteria and fungi on CS cooperatively formed an interaction network to achieve the CSD. In the network, modules 2 and 4 were significantly positively associated with CSD, which were considered as the key modules in this study. The key modules were mainly composed of phyla Proteobacteria and Ascomycota, indicating that microbes in key modules were the effective decomposers of CS. Although keystone taxa were not directly associated with CSD, they may regulate the genera in key modules to achieve the CSD, since some keystone taxa were linked with the microbial genera associated with CSD in the key modules. Total nitrogen (TN) and temperature in water were the dominant environmental factors positively influenced CSD. The key modules 2 and 4 were positively influenced by water temperature and TN in water, respectively, and two keystone taxa were positively associated with TN. This profoundly revealed that water temperature and TN influenced the OMD through acting on the keystone taxa and key modules in microbial interactions. The research findings help us to understand the microbial interactions influenced by environmental factors in OMD in river ecosystems.}, }
@article {pmid35501031, year = {2022}, author = {Gómez-Muñoz, B and Efthymiou, A and Dubey, M and Sølve, J and Nicolaisen, M and Jensen, DF and Nybroe, O and Larsen, J}, title = {Cellulose amendment promotes P solubilization by Penicillium aculeatum in non-sterilized soil.}, journal = {Fungal biology}, volume = {126}, number = {5}, pages = {356-365}, doi = {10.1016/j.funbio.2022.03.003}, pmid = {35501031}, issn = {1878-6146}, abstract = {Successful application of microbial biofertilizers, such as phosphorus (P) solubilizing fungi to agroecosystems, is constrained from the lack of knowledge about their ecology; for example in terms of how they respond to an external input of carbon (C) to get established in the soil. In two soil incubation experiments we examined the performance of the P solubilizing fungus Penicillium aculeatum in non-sterile and semi-sterile (γ-irradiated) soil with different C and P sources. Results from the first experiment with C sources showed that starch and cellulose generally improved P solubilization by P. aculeatum measured as water extractable P (Pwep), though only significantly in non-sterile soil. This coincided with an increased population density of P. aculeatum measured with a hygromycin B resistant strain of this fungus. Soil respiration used to measure soil microbial activity was overall much higher in treatments with C compounds than without C in both non-sterile and semi-sterile soil. However, soil respiration was highest with cellulose in semi-sterile soil, especially in combination with P. aculeatum. Hence, for the second experiment with P sources (tricalcium phosphate (TCP) and sewage sludge ash) cellulose was used as a C source for P. aculeatum growth in all treatments. Main results showed that P. aculeatum in combination with cellulose soil amendment increased soil Pwep independent of soil sterilization and P source treatments. Soil resin P (Pres) and microbial P (Pmic), which represents stocks of potentially plant available P, were also affected from P. aculeatum inoculation. Increased soil Pres from TCP and sewage sludge ash was observed with P. aculeatum independent of soil type. On the other hand soil Pmic was higher after P. aculeatum inoculation only in semi-sterile soil. Population density of P. aculeatum measured with qPCR was maintained or increased in non-sterile and semi-sterile soil, respectively, compared to the original inoculum load of P. aculeatum. In conclusion, our results underline the importance of C source addition for P. aculeatum if used as a biofertilizer. For this, cellulose seems to be a promising option promoting P. aculeatum growth and P solubilization also in non-sterilized soil.}, }
@article {pmid35499645, year = {2022}, author = {Anderson, KE and Ricigliano, VA and Copeland, DC and Mott, BM and Maes, P}, title = {Social Interaction is Unnecessary for Hindgut Microbiome Transmission in Honey Bees: The Effect of Diet and Social Exposure on Tissue-Specific Microbiome Assembly.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35499645}, issn = {1432-184X}, support = {2022-21000-021-00D//Agricultural Research Service/ ; }, abstract = {Honey bees are a model for host-microbial interactions with experimental designs evolving towards conventionalized worker bees. Research on gut microbiome transmission and assembly has examined only a fraction of factors associated with the colony and hive environment. Here, we studied the effects of diet and social isolation on tissue-specific bacterial and fungal colonization of the midgut and two key hindgut regions. We found that both treatment factors significantly influenced early hindgut colonization explaining similar proportions of microbiome variation. In agreement with previous work, social interaction with older workers was unnecessary for core hindgut bacterial transmission. Exposure to natural eclosion and fresh stored pollen resulted in gut bacterial communities that were taxonomically and structurally equivalent to those produced in the natural colony setting. Stressed diets of no pollen or autoclaved pollen in social isolation resulted in decreased fungal abundance and bacterial diversity, and atypical microbiome structure and tissue-specific variation of functionally important core bacteria. Without exposure to the active hive environment, the abundance and strain diversity of keystone ileum species Gilliamella apicola was markedly reduced. These changes were associated with significantly larger ileum microbiotas suggesting that extended exposure to the active hive environment plays an antibiotic role in hindgut microbiome establishment. We conclude that core hindgut microbiome transmission is facultative horizontal with 5 of 6 core hindgut species readily acquired from the built hive structure and natural diet. Our findings contribute novel insights into factors influencing assembly and maintenance of honey bee gut microbiota and facilitate future experimental designs.}, }
@article {pmid35499326, year = {2022}, author = {Rahlff, J and Bornemann, TLV and Lopatina, A and Severinov, K and Probst, AJ}, title = {Host-Associated Phages Disperse across the Extraterrestrial Analogue Antarctica.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0031522}, doi = {10.1128/aem.00315-22}, pmid = {35499326}, issn = {1098-5336}, abstract = {Extreme Antarctic conditions provide one of the closest analogues of extraterrestrial environments. Since air and snow samples, especially from polar regions, yield DNA amounts in the lower picogram range, binning of prokaryotic genomes is challenging and renders studying the dispersal of biological entities across these environments difficult. Here, we hypothesized that dispersal of host-associated bacteriophages (adsorbed, replicating, or prophages) across the Antarctic continent can be tracked via their genetic signatures, aiding our understanding of virus and host dispersal across long distances. Phage genome fragments (PGFs) reconstructed from surface snow metagenomes of three Antarctic stations were assigned to four host genomes, mainly Betaproteobacteria, including Ralstonia spp. We reconstructed the complete genome of a temperate phage with nearly complete alignment to a prophage in the reference genome of Ralstonia pickettii 12D. PGFs from different stations were related to each other at the genus level and matched similar hosts. Metagenomic read mapping and nucleotide polymorphism analysis revealed a wide dispersal of highly identical PGFs, 13 of which were detected in seawater from the Western Antarctic Peninsula at a distance of 5,338 km from the snow sampling stations. Our results suggest that host-associated phages, especially of Ralstonia sp., disperse over long distances despite the harsh conditions of the Antarctic continent. Given that 14 phages associated with two R. pickettii draft genomes isolated from space equipment were identified, we conclude that Ralstonia phages are ideal mobile genetic elements to track dispersal and contamination in ecosystems relevant for astrobiology. IMPORTANCE Host-associated phages of the bacterium Ralstonia identified in snow samples can be used to track microbial dispersal over thousands of kilometers across the Antarctic continent, which functions as an extraterrestrial analogue because of its harsh environmental conditions. Due to the presence of these bacteria carrying genome-integrated prophages on space-related equipment and the potential for dispersal of host-associated phages demonstrated here, our work has implications for planetary protection, a discipline in astrobiology interested in preventing contamination of celestial bodies with alien biomolecules or forms of life.}, }
@article {pmid35496989, year = {2022}, author = {Di Martino, P}, title = {Antimicrobial agents and microbial ecology.}, journal = {AIMS microbiology}, volume = {8}, number = {1}, pages = {1-4}, doi = {10.3934/microbiol.2022001}, pmid = {35496989}, issn = {2471-1888}, abstract = {Antimicrobials are therapeutic substances used to prevent or treat infections. Disinfectants are antimicrobial agents applied to non-living surfaces. Every year, several thousand tonnes of antimicrobials and their by-products are released into the environment and in particular into the aquatic environment. This type of xenobiotic has ecological consequences in the natural environment but also in technological environments such as wastewater treatment plants and methane fermentation sewage sludge treatment plants. The constant exposure of microbial communities not only to high concentrations but also to sub-inhibitory concentrations of antibiotics is a key element in the development of antibiotic resistance in aquatic environments and in soils. The future of antimicrobials lies in the development of biosourced or bioinspired molecules. The observation and deciphering of interactions between living organisms is the key to this development.}, }
@article {pmid35495730, year = {2022}, author = {Nagar, S and Talwar, C and Motelica-Heino, M and Richnow, HH and Shakarad, M and Lal, R and Negi, RK}, title = {Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {848010}, doi = {10.3389/fmicb.2022.848010}, pmid = {35495730}, issn = {1664-302X}, abstract = {Sulfur related prokaryotes residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expands the phylogenetic breadth of these extraordinary sulfur (S) metabolizing microorganisms as well as their complex metabolic networks and syntrophic interactions in environmental biosystems. Through this study, we explored and expanded the microbial genetic repertoire with focus on S cycling genes through metagenomic analysis of S contaminated hot spring, located at the Northern Himalayas. The analysis revealed rich diversity of microbial consortia with established roles in S cycling such as Pseudomonas, Thioalkalivibrio, Desulfovibrio, and Desulfobulbaceae (Proteobacteria). The major gene families inferred to be abundant across microbial mat, sediment, and water were assigned to Proteobacteria as reflected from the reads per kilobase (RPKs) categorized into translation and ribosomal structure and biogenesis. An analysis of sequence similarity showed conserved pattern of both dsrAB genes (n = 178) retrieved from all metagenomes while other S disproportionation proteins were diverged due to different structural and chemical substrates. The diversity of S oxidizing bacteria (SOB) and sulfate reducing bacteria (SRB) with conserved (r)dsrAB suggests for it to be an important adaptation for microbial fitness at this site. Here, (i) the oxidative and reductive dsr evolutionary time-scale phylogeny proved that the earliest (but not the first) dsrAB proteins belong to anaerobic Thiobacillus with other (rdsr) oxidizers, also we confirm that (ii) SRBs belongs to δ-Proteobacteria occurring independent lateral gene transfer (LGT) of dsr genes to different and few novel lineages. Further, the structural prediction of unassigned DsrAB proteins confirmed their relatedness with species of Desulfovibrio (TM score = 0.86, 0.98, 0.96) and Archaeoglobus fulgidus (TM score = 0.97, 0.98). We proposed that the genetic repertoire might provide the basis of studying time-scale evolution and horizontal gene transfer of these genes in biogeochemical S cycling.}, }
@article {pmid35495644, year = {2022}, author = {Rangel, F and Enes, P and Gasco, L and Gai, F and Hausmann, B and Berry, D and Oliva-Teles, A and Serra, CR and Pereira, FC}, title = {Differential Modulation of the European Sea Bass Gut Microbiota by Distinct Insect Meals.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {831034}, doi = {10.3389/fmicb.2022.831034}, pmid = {35495644}, issn = {1664-302X}, abstract = {The aquaculture industry is one of the fastest-growing sectors in animal food production. However, farming of carnivorous fish strongly relies on the use of wild fish-based meals, a practice that is environmentally and economically unsustainable. Insect-based diets constitute a strong candidate for fishmeal substitution, due to their high nutritional value and low environmental footprint. Nevertheless, data on the impact of insect meal (IM) on the gut microbiome of farmed fish are so far inconclusive, and very scarce in what concerns modulation of microbial-mediated functions. Here we use high-throughput 16S rRNA gene amplicon sequencing and quantitative PCR to evaluate the impact of different IMs on the composition and chitinolytic potential of the European sea bass gut digesta- and mucosa-associated communities. Our results show that insect-based diets of distinct origins differently impact the gut microbiota of the European sea bass (Dicentrarchus labrax). We detected clear modulatory effects of IM on the gut microbiota, which were more pronounced in the digesta, where communities differed considerably among the diets tested. Major community shifts were associated with the use of black soldier fly larvae (Hermetia illucens, HM) and pupal exuviae (HEM) feeds and were characterized by an increase in the relative abundance of the Firmicutes families Bacillaceae, Enterococcaceae, and Lachnospiraceae and the Actinobacteria family Actinomycetaceae, which all include taxa considered beneficial for fish health. Modulation of the digesta community by HEM was characterized by a sharp increase in Paenibacillus and a decrease of several Gammaproteobacteria and Bacteroidota members. In turn, a mealworm larvae-based diet (Tenebrio molitor, TM) had only a modest impact on microbiota composition. Further, using quantitative PCR, we demonstrate that shifts induced by HEM were accompanied by an increase in copy number of chitinase ChiA-encoding genes, predominantly originating from Paenibacillus species with effective chitinolytic activity. Our study reveals an HEM-driven increase in chitin-degrading taxa and associated chitinolytic activity, uncovering potential benefits of adopting exuviae-supplemented diets, a waste product of insect rearing, as a functional ingredient.}, }
@article {pmid35494622, year = {2022}, author = {Guéneau, V and Plateau-Gonthier, J and Arnaud, L and Piard, JC and Castex, M and Briandet, R}, title = {Positive biofilms to guide surface microbial ecology in livestock buildings.}, journal = {Biofilm}, volume = {4}, number = {}, pages = {100075}, doi = {10.1016/j.bioflm.2022.100075}, pmid = {35494622}, issn = {2590-2075}, abstract = {The increase in human consumption of animal proteins implies changes in the management of meat production. This is followed by increasingly restrictive regulations on antimicrobial products such as chemical biocides and antibiotics, used in particular to control pathogens that can spread zoonotic diseases. Aligned with the One Health concept, alternative biological solutions are under development and are starting to be used in animal production. Beneficial bacteria able to form positive biofilms and guide surface microbial ecology to limit microbial pathogen settlement are promising tools that could complement existing biosecurity practices to maintain the hygiene of livestock buildings. Although the benefits of positive biofilms have already been documented, the associated fundamental mechanisms and the rationale of the microbial composition of these new products are still sparce. This review provides an overview of the envisioned modes of action of positive biofilms used on livestock building surfaces and the resulting criteria for the selection of the appropriate microorganisms for this specific application. Limits and advantages of this biosecurity approach are discussed as well as the impact of such practices along the food chain, from farm to fork.}, }
@article {pmid35493735, year = {2022}, author = {Kumar, D and Sharma, SR and Adegoke, A and Kennedy, A and Tuten, HC and Li, AY and Karim, S}, title = {Recently Evolved Francisella-Like Endosymbiont Outcompetes an Ancient and Evolutionarily Associated Coxiella-Like Endosymbiont in the Lone Star Tick (Amblyomma americanum) Linked to the Alpha-Gal Syndrome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {787209}, doi = {10.3389/fcimb.2022.787209}, pmid = {35493735}, issn = {2235-2988}, abstract = {Background: Ticks are hematophagous arthropods that transmit various bacterial, viral, and protozoan pathogens of public health significance. The lone star tick (Amblyomma americanum) is an aggressive human-biting tick that transmits bacterial and viral pathogens, and its bites are suspected of eliciting the alpha-gal syndrome, a newly emerged delayed hypersensitivity following consumption of red meat in the United States. While ongoing studies have attempted to investigate the contribution of different tick-inherent factors to the induction of alpha-gal syndrome, an otherwise understudied aspect is the contribution of the tick microbiome and specifically obligate endosymbionts to the establishment of the alpha-gal syndrome in humans.<br><br>Materials and Methods: Here we utilized a high-throughput metagenomic sequencing approach to cataloging the entire microbial communities residing within different developmental stages and tissues of unfed and blood-fed ticks from laboratory-maintained ticks and three new geographical locations in the United States. The Quantitative Insights Into Microbial Ecology (QIIME2) pipeline was used to perform data analysis and taxonomic classification. Moreover, using a SparCC (Sparse Correlations for Compositional data) network construction model, we investigated potential interactions between members of the microbial communities from laboratory-maintained and field-collected ticks.<br><br>Results: Overall, Francisellaceae was the most dominant bacteria identified in the microbiome of both laboratory-raised and field-collected Am. americanum across all tissues and developmental stages. Likewise, microbial diversity was seen to be significantly higher in field-collected ticks compared with laboratory-maintained ticks as seen with a higher number of both Operational Taxonomic Units and measures of species richness. Several potential positive and negative correlations were identified from our network analysis. We observed a strong positive correlation between Francisellaceae, Rickettsiaceae, and Midichloriaceae in both developmental stages and tissues from laboratory-maintained ticks, whereas ovarian tissues had a strong positive correlation of bacteria in the family Xanthobacteraceae and Rhizobiaceae. A negative interaction was observed between Coxiellaceae and Francisellaceae in Illinois, and all the bacteria detected from ticks from Delaware were negatively correlated.<br><br>Conclusion: This study is the first to catalog the microbiome of Am. americanum throughout its developmental stages and different tissue niches and report the potential replacement of Coxiellaceae by Francisellaceae across developmental stages and tissues tested except in ovarian tissues. These unique and significant findings advance our knowledge and open a new avenue of research to further understand the role of tick microbiome in tick-borne diseases and develop a holistic strategy to control alpha-gal syndrome.}, }
@article {pmid35491817, year = {2022}, author = {Zhang, M and Whiteley, M and Lewin, GR}, title = {Polymicrobial Interactions of Oral Microbiota: a Historical Review and Current Perspective.}, journal = {mBio}, volume = {}, number = {}, pages = {e0023522}, doi = {10.1128/mbio.00235-22}, pmid = {35491817}, issn = {2150-7511}, abstract = {The oral microbiota is enormously diverse, with over 700 microbial species identified across individuals that play a vital role in the health of our mouth and our overall well-being. In addition, as oral diseases such as caries (cavities) and periodontitis (gum disease) are mediated through interspecies microbial interactions, this community serves as an important model system to study the complexity and dynamics of polymicrobial interactions. Here, we review historical and recent progress in our understanding of the oral microbiome, highlighting how oral microbiome research has significantly contributed to our understanding of microbial communities, with broad implications in polymicrobial diseases and across microbial community ecology. Further, we explore innovations and challenges associated with analyzing polymicrobial systems and suggest future directions of study. Finally, we provide a conceptual framework to systematically study microbial interactions within complex communities, not limited to the oral microbiota.}, }
@article {pmid35486140, year = {2022}, author = {Rajarajan, A and Wolinska, J and Walser, JC and Dennis, SR and Spaak, P}, title = {Host-Associated Bacterial Communities Vary Between Daphnia galeata Genotypes but Not by Host Genetic Distance.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35486140}, issn = {1432-184X}, support = {310030 L 166628//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; WO 1587/6-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Host genotype may shape host-associated bacterial communities (commonly referred to as microbiomes). We sought to determine (a) whether bacterial communities vary among host genotypes in the water flea Daphnia galeata and (b) if this difference is driven by the genetic distance between host genotypes, by using D. galeata genotypes hatched from sediments of different time periods. We used 16S amplicon sequencing to profile the gut and body bacterial communities of eight D. galeata genotypes hatched from resting eggs; these were isolated from two distinct sediment layers (dating to 1989 and 2009) of a single sediment core of the lake Greifensee, and maintained in a common garden in laboratory cultures for 5 years. In general, bacterial community composition varied in both the Daphnia guts and bodies; but not between genotypes from different sediment layers. Specifically, genetic distances between host genotypes did not correlate with beta diversity of bacterial communities in Daphnia guts and bodies. Our results indicate that Daphnia bacterial community structure is to some extent determined by a host genetic component, but that genetic distances between hosts do not correlate with diverging bacterial communities.}, }
@article {pmid35486139, year = {2022}, author = {Bacha, L and de Rezende, CE and Cosenza, C and Ottoni, A and Thompson, C and Thompson, F}, title = {Letter to Microbial Ecology.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35486139}, issn = {1432-184X}, }
@article {pmid35484416, year = {2022}, author = {Câmara, PEAS and Bones, FLV and Lopes, FAC and Oliveira, FS and Barreto, CC and Knop Henriques, D and Campos, LP and Carvalho-Silva, M and Convey, P and Rosa, LH}, title = {DNA Metabarcoding Reveals Cryptic Diversity in Forest Soils on the Isolated Brazilian Trindade Island, South Atlantic.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35484416}, issn = {1432-184X}, abstract = {Located 1140 km from the South American coastline in the South Atlantic Ocean and with an age of 4 million years, Trindade Island is the most recent volcanic component of Brazilian territory. Its original native vegetation has been severely damaged by human influence, in particular through the introduction of exotic grazing animals such as goats. However, since the complete eradication of goats and other feral animals in the late 1990s, the island's vegetation has been recovering, and even some endemic species that had been considered extinct have been rediscovered. In this study, we set out to characterize the contemporary cryptic diversity in soils of the recovering native forest of Trindade Island using metabarcoding by high throughput sequencing (HTS). The sequence diversity obtained was dominated by microorganisms, including three domains (Bacteria, Archaea, and Eukarya) and five kingdoms (Fungi, Metazoa, Protozoa, Chromista, and Viridiplantae). Bacteria were represented by 20 phyla and 116 taxa, with Archaea by only one taxon. Fungi were represented by seven phyla and 250 taxa, Viridiplantae by five phyla and six taxa, Protozoa by five phyla and six taxa, Metazoa by three phyla and four taxa and Chromista by two phyla and two taxa. Even after the considerable anthropogenic impacts and devastation of the island's natural forest, our sequence data reveal the presence of a rich and complex diversity of microorganisms, invertebrates, and plants and provide important baseline biodiversity information that will contribute to ecological restoration efforts on the island.}, }
@article {pmid35482603, year = {2022}, author = {Carrizo, D and Vignale, FA and Sánchez-García, L and Farías, ME}, title = {Ecological variability based on lipid biomarkers in astrobiologically interesting wetlands from the Argentinian central Andes.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiac049}, pmid = {35482603}, issn = {1574-6941}, abstract = {Andean wetlands hold extremophilic communities adapted to live in harsh conditions. Here, we investigated the microbial ecology of three high-altitude hypersaline ponds from La Puna region (Argentina) showing an increasing extent of desiccation by analyzing their lipid sedimentary record. We recreated the microbial community structure and the carbon metabolisms in each lacustrine system based on the molecular distribution of lipid biomarkers and their compound-specific carbon and hydrogen isotopic signatures. We detected lipid compounds considered to be biomarkers of cyanobacteria, sulfate-reducing bacteria, purple sulfur bacteria, and archaea in the three Andean ponds, as well as diatoms in the intermediate salinity system. The relative abundance of purple sulfur and sulfate-reducing bacteria decreased with salinity, whereas cyanobacteria and archaea decreased their relative abundance in the mid-saline pond to increase it again and became both prevailing at the highest salinity. Carbon fixation in the three ponds was driven by a combination of the reductive tricarboxylic acid cycle, the reductive pentose phosphate cycle, and the reductive acetyl-CoA pathway. This work is the first to describe molecular and isotopic lipid fingerprints in wetlands from the central Andean Puna, and serves as a basis for further biogeochemical studies in the area.}, }
@article {pmid35482107, year = {2022}, author = {Alemany, I and Pérez-Cembranos, A and Pérez-Mellado, V and Castro, JA and Picornell, A and Ramon, C and Jurado-Rivera, JA}, title = {Faecal Microbiota Divergence in Allopatric Populations of Podarcis lilfordi and P. pityusensis, Two Lizard Species Endemic to the Balearic Islands.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35482107}, issn = {1432-184X}, support = {CGL2015-68139-C2-1-P//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; FPI-CAIB 2017//Conselleria d'Educació, Investigació, Cultura i Esport/ ; }, abstract = {Gut microbial communities provide essential functions to their hosts and are known to influence both their ecology and evolution. However, our knowledge of these complex associations is still very limited in reptiles. Here we report the 16S rRNA gene faecal microbiota profiles of two lizard species endemic to the Balearic archipelago (Podarcis lilfordi and P. pityusensis), encompassing their allopatric range of distribution through a noninvasive sampling, as an alternative to previous studies that implied killing specimens of these IUCN endangered and near-threatened species, respectively. Both lizard species showed a faecal microbiome composition consistent with their omnivorous trophic ecology, with a high representation of cellulolytic bacteria taxa. We also identified species-specific core microbiota signatures and retrieved lizard species, islet ascription, and seasonality as the main factors in explaining bacterial community composition. The different Balearic Podarcis populations are characterised by harbouring a high proportion of unique bacterial taxa, thus reinforcing their view as unique and divergent evolutionary entities.}, }
@article {pmid35479639, year = {2022}, author = {Xing, L and Zhi, Q and Hu, X and Liu, L and Xu, H and Zhou, T and Yin, H and Yi, Z and Li, J}, title = {Influence of Association Network Properties and Ecological Assembly of the Foliar Fugal Community on Crop Quality.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {783923}, doi = {10.3389/fmicb.2022.783923}, pmid = {35479639}, issn = {1664-302X}, abstract = {Revealing community assembly and their impacts on ecosystem service is a core issue in microbial ecology. However, what ecological factors play dominant roles in phyllosphere fungal community assembly and how they link to crop quality are largely unknown. Here, we applied internal transcriptional spacer high-throughput sequencing to investigate foliar fungal community assembly across three cultivars of a Solanaceae crop (tobacco) and two planting regions with different climatic conditions. Network analyses were used to reveal the pattern in foliar fungal co-occurrence, and phylogenetic null model analysis was used to elucidate the ecological assembly of foliar fungal communities. We found that the sensory quality of crop leaves and the composition of foliar fungal community varied significantly across planting regions and cultivars. In Guangcun (GC), a region with relatively high humidity and low precipitation, there was a higher diversity and more unique fungal species than the region of Wuzhishan (WZS). Further, we found that the association network of foliar fungal communities in GC was more complex than that in WZS, and the network properties were closely related to the sensory quality of crop. Finally, the results of the phylogenetic analyses show that the stochastic processes played important roles in the foliar fungal community assembly, and their relative importance was significantly correlated with the sensory quality of crop leaves, which implies that ecological assembly processes could affect crop quality. Taken together, our results highlight that climatic conditions, and plant cultivars play key roles in the assembly of foliar fungal communities and crop quality, which enhances our understanding of the connections between the phyllosphere microbiome and ecosystem services, especially in agricultural production.}, }
@article {pmid35478286, year = {2022}, author = {Clough, SE and Jousset, A and Elphinstone, JG and Friman, VP}, title = {Combining in vitro and in vivo screening to identify efficient Pseudomonas biocontrol strains against the phytopathogenic bacterium Ralstonia solanacearum.}, journal = {MicrobiologyOpen}, volume = {11}, number = {2}, pages = {e1283}, doi = {10.1002/mbo3.1283}, pmid = {35478286}, issn = {2045-8827}, support = {CHL\R1\180031//Royal Society/ ; RSG\R1\180213//Royal Society/ ; BB/T010606/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Although plant pathogens are traditionally controlled using synthetic agrochemicals, the availability of commercial bactericides is still limited. One potential control strategy could be the use of plant growth-promoting bacteria (PGPB) to suppress pathogens via resource competition or the production of antimicrobial compounds. This study aimed to conduct in vitro and in vivo screening of eight Pseudomonas strains against Ralstonia solanacearum (the causative agent of bacterial wilt) and to investigate underlying mechanisms of potential pathogen suppression. We found that inhibitory effects were Pseudomonas strain-specific, with strain CHA0 showing the highest pathogen suppression. Genomic screening identified 2,4-diacetylphloroglucinol, pyoluteorin, and orfamides A and B secondary metabolite clusters in the genomes of the most inhibitory strains, which were investigated further. Although all these compounds suppressed R. solanacearum growth, only orfamide A was produced in the growth media based on mass spectrometry. Moreover, orfamide variants extracted from Pseudomonas cultures showed high pathogen suppression. Using the "Micro-Tom" tomato cultivar, it was found that CHA0 could reduce bacterial wilt disease incidence with one of the two tested pathogen strains. Together, these findings suggest that a better understanding of Pseudomonas-Ralstonia interactions in the rhizosphere is required to successfully translate in vitro findings into agricultural applications.}, }
@article {pmid35476456, year = {2022}, author = {Alvarado, V and Hsu, SC and Wu, Z and Zhuang, H and Lee, PH and Guest, JS}, title = {Roadmap from Microbial Communities to Individuality Modeling for Anaerobic Digestion of Sewage Sludge.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.1c05258}, pmid = {35476456}, issn = {1520-5851}, abstract = {Biological models describing anaerobic digestion (AD) of sewage sludge have been widely applied to test various control and operation strategies. Anaerobic digestion model 1 (ADM1) provides a generic platform that includes the main processes of AD, excluding homoacetogenesis and the microbial structure. Homoacetogenic bacteria have been identified as important competitors for hydrogen consumption and acetate production. Although recent advances in meta-omics techniques have improved our characterization of AD microbial communities, conventional models treat functional groups as homogeneous and overlook the physiology and behavior of microbial individuality, limiting insights into mechanisms governing process performance. A novel microbial individuality model (MIM) that integrates kinetics, energetics, and agent-based modeling to describe a microbiome's behavior as heterogenic populations, including homoacetogenesis, was developed. The MIM was validated with two datasets from previous studies through daily biogas production, methane content, compound concentrations, and microbial relative abundance changes. The MIM identified the emergence of Methanosaeta at low concentrations of acetate. Moreover, this simulation supports experimental studies confirming that the overlooked homoacetogenesis is an important hydrogen sink in AD. Validated MIMs are expected to provide insights into syntrophic and competitive interactions among microbiomes in AD systems while testing different operational parameters in a virtual environment. The MIM offers a methodological framework to other biological treatment systems and their microbial community dynamics.}, }
@article {pmid35476217, year = {2022}, author = {Xu, Z and Li, Z and Ren, F and Gao, R and Wang, Z and Zhang, J and Zhao, T and Ma, X and Pu, X and Xin, T and Rombauts, S and Sun, W and Van de Peer, Y and Chen, S and Song, J}, title = {The genome of Corydalis reveals the evolution of benzylisoquinoline alkaloid biosynthesis in Ranunculales.}, journal = {The Plant journal : for cell and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/tpj.15788}, pmid = {35476217}, issn = {1365-313X}, abstract = {Species belonging to the order Ranunculales have attracted much attention because of their phylogenetic position as a sister group to all other eudicot lineages and their ability to produce unique yet diverse benzylisoquinoline alkaloids (BIAs). The Papaveraceae family in Ranunculales is often used as a model system for studying BIA biosynthesis. Here, we report the chromosome-level genome assembly of Corydalis tomentella, a species of Fumarioideae-one of the two subfamilies of Papaveraceae. Based on the comparisons of sequenced Ranunculalean species, we present clear evidence of a shared whole-genome duplication (WGD) event that has occurred before the divergence of Ranunculales but after its divergence from other eudicot lineages. The C. tomentella genome enabled us to integrate isotopic labelling and comparative genomics to reconstruct the BIA biosynthetic pathway for both sanguinarine biosynthesis shared by papaveraceous species and the cavidine biosynthesis specific to Corydalis. Also, our comparative analysis revealed that gene duplications, especially tandem gene duplications, underlie the diversification of BIA biosynthetic pathways in Ranunculales. In particular, tandemly duplicated berberine bridge enzyme-like genes appear to be involved in cavidine biosynthesis. In conclusion, our study of the C. tomentella genome provides important insights into the occurrence of WGDs during the early evolution of eudicots as well as into the evolution of BIA biosynthesis in Ranunculales.}, }
@article {pmid35474408, year = {2022}, author = {Znidersic, E and Watson, DM}, title = {Acoustic restoration: Using soundscapes to benchmark and fast-track recovery of ecological communities.}, journal = {Ecology letters}, volume = {}, number = {}, pages = {}, doi = {10.1111/ele.14015}, pmid = {35474408}, issn = {1461-0248}, support = {//Charles Sturt University/ ; }, abstract = {We introduce a new approach-acoustic restoration-focusing on the applied utility of soundscapes for restoration, recognising the rich ecological and social values they encapsulate. Broadcasting soundscapes in disturbed areas can accelerate recolonisation of animals and the microbes and propagules they carry; long duration recordings are also ideal sources of data for benchmarking restoration initiatives and evocative engagement tools.}, }
@article {pmid35473973, year = {2022}, author = {S R, S and H P, S and Prakash, I and Khan, M and H N, PK and Om, H and Basavaraj, K and Murthy, PS}, title = {Microbial ecology and functional coffee fermentation dynamics with Pichia kudriavzevii.}, journal = {Food microbiology}, volume = {105}, number = {}, pages = {104012}, doi = {10.1016/j.fm.2022.104012}, pmid = {35473973}, issn = {1095-9998}, abstract = {Specialty coffee can be developed by the application of explicit microorganisms or starters to obtain desired fermentation. In the present study, natural fermentation (NF) of Arabica coffee was carried out spontaneously, the other set was inoculated with Pichia kudriavzevii (Y) starter culture (isolated, identified and mass cultured). The effect of microbial fermentation, metagenomics, production of functional metabolites, volatiles and their sensorial aspects were studied. The bioprocess illustrated cohesive interface of coffee nutrients and microbial communities like Mycobacterium, Acinetobacter, Gordonia, etc., in NF, Lactobacillus and Leuconostoc were prevailing in Y. The Pichia and Rhodotorula dominated in both the groups. The bioactivity of bacteria and fungi induced complex changes in physicochemical features like pH (4.2-5.2), Brix° (9.5-3.0), and metabolic transition in sugar (3.0-0.7%), alcohol (1.4-2.7%), organic acids modulating flavour precursors and organoleptics in the final brew. In the roasted bean, Y exhibited higher sugar (42%), protein (25%), polyphenol (3.5%), CGA (2.5%), caffeine (17.2%), and trigonelline (2.8%) than NF. The volatile profile exhibited increased flavour molecules like furans, ketones, and pyrazines in Y, besides lactone complexes. The organoleptics in Y were highlighted with honey, malt and berry notes. P. kudriavzevii coffee fermentation could be beneficial in specialty coffee production and enhancement of distinct characteristic flavours.}, }
@article {pmid35473303, year = {2022}, author = {Seki, D and Schauberger, C and Hausmann, B and Berger, A and Wisgrill, L and Berry, D}, title = {Individuality of the Extremely Premature Infant Gut Microbiota Is Driven by Ecological Drift.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0016322}, doi = {10.1128/msystems.00163-22}, pmid = {35473303}, issn = {2379-5077}, abstract = {The initial contact between humans and their colonizing gut microbiota after birth is thought to have expansive and long-lasting consequences for physiology and health. Premature infants are at high risk of suffering from lifelong impairments, due in part to aberrant development of gut microbiota that can contribute to early-life infections and inflammation. Despite their importance to health, the ecological assembly and succession processes governing gut microbiome composition in premature infants remained incompletely understood. Here, we quantified these ecological processes in a spatiotemporally resolved 16S rRNA gene amplicon sequencing data set of 60 extremely premature neonates using an established mathematical framework. We found that gut colonization during the first months of life is predominantly stochastic, whereby interindividual diversification of microbiota is driven by ecological drift. Dispersal limitations are initially small but have increasing influence at later stages of succession. Furthermore, we find similar trends in a cohort of 32 healthy term-born infants. These results suggest that the uniqueness of individual gut microbiota of extremely premature infants is largely due to stochastic assembly. IMPORTANCE Our knowledge concerning the initial gut microbiome assembly in human neonates is limited, and scientific progression in this interdisciplinary field is hindered due to the individuality in composition of gut microbiota. Our study addresses the ecological processes that result in the observed individuality of microbes in the gastrointestinal tract between extremely premature and term-born infants. We find that initial assembly is mainly driven by neutral ecological processes. Interestingly, while this progression is predominantly random, limitations to the dispersal of microbiota between infants become increasingly important with age and are concomitant features of gut microbiome stability. This indicates that while we cannot predict gut microbiota assembly due to its random nature, we can expect the establishment of certain ecological features that are highly relevant for neonatal health.}, }
@article {pmid35468931, year = {2022}, author = {Jangid, A and Fukuda, S and Suzuki, Y and Taylor, TD and Ohno, H and Prakash, T}, title = {Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6748}, pmid = {35468931}, issn = {2045-2322}, abstract = {In the present study, we elucidated the effect of grain-based (GB) diet containing both soluble and insoluble fibers and purified ingredients-based (PIB) diet containing only insoluble fiber, namely cellulose on mice gut microbiome using whole shotgun based metagenomic sequencing. Although the fiber content in both diet types is the same (5%) the presence of soluble fiber only in the GB diet differentiates it from the PIB diet. The taxonomic analysis of sequenced reads reveals a significantly higher enrichment of probiotic Lactobacilli in the GB group as compared to the PIB group. Further, the enhancement of energy expensive cellular processes namely, cell cycle control, cell division, chromosome partitioning, and transcription is observed in the GB group which could be due to the metabolization of the soluble fiber for faster energy production. In contrast, a higher abundance of cellulolytic bacterial community namely, the members of family Lachnospiraceae and Ruminococcaceae and the metabolism functions are found in the PIB group. The PIB group shows a significant increase in host-derived oligosaccharide metabolism functions indicating that they might first target the host-derived oligosaccharides and self-stored glycogen in addition to utilising the available cellulose. In addition to the beneficial microbial community variations, both the groups also exhibited an increased abundance of opportunistic pathobionts which could be due to an overall low amount of fiber in the diet. Furthermore, backtracing analysis identified probiotic members of Lactobacillus, viz., L. crispatus ST1, L. fermentum CECT 5716, L. gasseri ATCC 33323, L. johnsonii NCC 533 and L. reuteri 100-23 in the GB group, while Bilophila wadsworthia 3_1_6, Desulfovibrio piger ATCC 29098, Clostridium symbiosum WAL-14163, and Ruminococcaceae bacterium D16 in the PIB group. These data suggest that Lactobacilli, a probiotic community of microorganisms, are the predominant functional contributors in the gut of GB diet-fed mice, whereas pathobionts too coexisted with commensals in the gut microbiome of the PIB group. Thus at 5% fiber, GB modifies the gut microbial ecology more effectively than PIB and the inclusion of soluble fiber in the GB diet may be one of the primary factors responsible for this impact.}, }
@article {pmid35464965, year = {2022}, author = {Petrin, S and Mancin, M and Losasso, C and Deotto, S and Olsen, JE and Barco, L}, title = {Effect of pH and Salinity on the Ability of Salmonella Serotypes to Form Biofilm.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {821679}, doi = {10.3389/fmicb.2022.821679}, pmid = {35464965}, issn = {1664-302X}, abstract = {Salmonella is a major cause of food-borne infections in Europe, and the majority of human infections are caused by only a few serotypes, among them are Salmonella enterica subsp. enterica serotype Enteritidis (hereafter Salmonella Enteritidis), Salmonella Typhimurium, and the monophasic variant of S. Typhimurium. The reason for this is not fully understood, but could include virulence factors as well as increased ability to transfer via the external environment. Formation of biofilm is considered an adaptation strategy used by bacteria to overcome environmental stresses. In order to assess the capability of different Salmonella serotypes to produce biofilm and establish whether this is affected by pH and salinity, 88 Salmonella isolates collected from animal, food, and human sources and belonging to 15 serotypes, including those most frequently responsible for human infections, were tested. Strains were grown in tryptic soy broth (TSB), TSB with 4% NaCl pH 4.5, TSB with 10% NaCl pH 4.5, TSB with 4% NaCl pH 7, or TSB with 10% NaCl pH 7, and biofilm production was assessed after 24 h at 37°C using crystal violet staining. A linear mixed effect model was applied to compare results from the different experimental conditions. Among the tested serotypes, S. Dublin showed the greatest ability to form biofilm even at pH 4.5, which inhibited biofilm production in the other tested serotypes. Salmonella Senftenberg and the monophasic variant of S. Typhimurium showed the highest biofilm production in TSB with 10% NaCl pH 7. In general, pH had a high influence on the ability to form biofilm, and most of the tested strains were not able to produce biofilm at pH 4.5. In contrast, salinity only had a limited influence on biofilm production. In general, serotypes causing the highest number of human infections showed a limited ability to produce biofilm in the tested conditions, indicating that biofilm formation is not a crucial factor in the success of these clones.}, }
@article {pmid35464964, year = {2022}, author = {Haber, M and Roth Rosenberg, D and Lalzar, M and Burgsdorf, I and Saurav, K and Lionheart, R and Lehahn, Y and Aharonovich, D and Gómez-Consarnau, L and Sher, D and Krom, MD and Steindler, L}, title = {Spatiotemporal Variation of Microbial Communities in the Ultra-Oligotrophic Eastern Mediterranean Sea.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {867694}, doi = {10.3389/fmicb.2022.867694}, pmid = {35464964}, issn = {1664-302X}, abstract = {Marine microbial communities vary seasonally and spatially, but these two factors are rarely addressed together. In this study, the temporal and spatial patterns of the bacterial and archaeal community were studied along a coast-to-offshore transect in the Eastern Mediterranean Sea (EMS) over six cruises, in three seasons of 2 consecutive years. Amplicon sequencing of 16S rRNA genes and transcripts was performed to determine presence and activity, respectively. The ultra-oligotrophic status of the Southeastern Mediterranean Sea was reflected in the microbial community composition dominated by oligotrophic bacterial groups such as SAR11, even at the most coastal station sampled, throughout the year. Seasons significantly affected the microbial communities, explaining more than half of the observed variability. However, the same few taxa dominated the community over the 2-year sampling period, varying only in their degree of dominance. While there was no overall effect of station location on the microbial community, the most coastal site (16 km offshore) differed significantly in community structure and activity from the three further offshore stations in early winter and summer. Our data on the microbial community compositions and their seasonality support previous notions that the EMS behaves like an oceanic gyre.}, }
@article {pmid35464924, year = {2022}, author = {Wetherington, MT and Nagy, K and Dér, L and Noorlag, J and Galajda, P and Keymer, JE}, title = {Variance in Landscape Connectivity Shifts Microbial Population Scaling.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {831790}, doi = {10.3389/fmicb.2022.831790}, pmid = {35464924}, issn = {1664-302X}, abstract = {Understanding mechanisms shaping distributions and interactions of soil microbes is essential for determining their impact on large scale ecosystem services, such as carbon sequestration, climate regulation, waste decomposition, and nutrient cycling. As the functional unit of soil ecosystems, we focus our attention on the spatial structure of soil macroaggregates. Emulating this complex physico-chemical environment as a patchy habitat landscape we investigate on-chip the effect of changing the connectivity features of this landscape as Escherichia coli forms a metapopulation. We analyze the distributions of E. coli occupancy using Taylor's law, an empirical law in ecology which asserts that the fluctuations in populations is a power law function of the mean. We provide experimental evidence that bacterial metapopulations in patchy habitat landscapes on microchips follow this law. Furthermore, we find that increased variance of patch-corridor connectivity leads to a qualitative transition in the fluctuation scaling. We discuss these results in the context of the spatial ecology of microbes in soil.}, }
@article {pmid35464923, year = {2022}, author = {Riemann, L and Rahav, E and Passow, U and Grossart, HP and de Beer, D and Klawonn, I and Eichner, M and Benavides, M and Bar-Zeev, E}, title = {Planktonic Aggregates as Hotspots for Heterotrophic Diazotrophy: The Plot Thickens.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {875050}, doi = {10.3389/fmicb.2022.875050}, pmid = {35464923}, issn = {1664-302X}, abstract = {Biological dinitrogen (N2) fixation is performed solely by specialized bacteria and archaea termed diazotrophs, introducing new reactive nitrogen into aquatic environments. Conventionally, phototrophic cyanobacteria are considered the major diazotrophs in aquatic environments. However, accumulating evidence indicates that diverse non-cyanobacterial diazotrophs (NCDs) inhabit a wide range of aquatic ecosystems, including temperate and polar latitudes, coastal environments and the deep ocean. NCDs are thus suspected to impact global nitrogen cycling decisively, yet their ecological and quantitative importance remain unknown. Here we review recent molecular and biogeochemical evidence demonstrating that pelagic NCDs inhabit and thrive especially on aggregates in diverse aquatic ecosystems. Aggregates are characterized by reduced-oxygen microzones, high C:N ratio (above Redfield) and high availability of labile carbon as compared to the ambient water. We argue that planktonic aggregates are important loci for energetically-expensive N2 fixation by NCDs and propose a conceptual framework for aggregate-associated N2 fixation. Future studies on aggregate-associated diazotrophy, using novel methodological approaches, are encouraged to address the ecological relevance of NCDs for nitrogen cycling in aquatic environments.}, }
@article {pmid35462258, year = {2022}, author = {Garrido-Baserba, M and Barnosell, I and Molinos-Senante, M and Sedlak, DL and Rabaey, K and Schraa, O and Verdaguer, M and Rosso, D and Poch, M}, title = {The third route: A techno-economic evaluation of extreme water and wastewater decentralization.}, journal = {Water research}, volume = {218}, number = {}, pages = {118408}, doi = {10.1016/j.watres.2022.118408}, pmid = {35462258}, issn = {1879-2448}, abstract = {Water systems need to become more locally robust and sustainable in view of increased population demands and supply uncertainties. Decentralized treatment is often assumed to have the potential to improve the technical, environmental, and economic performance of current technologies. The techno-economic feasibility of implementing independent building-scale decentralized systems combining rainwater harvesting, potable water production, and wastewater treatment and recycling was assessed for six main types of buildings ranging from single-family dwellings to high-rise buildings. Five different treatment layouts were evaluated under five different climatic conditions for each type of building. The layouts considered varying levels of source separation (i.e., black, grey, yellow, brown, and combined wastewater) using the corresponding toilet types (vacuum, urine-diverting, and conventional) and the appropriate pipes and pumping requirements. Our results indicate that the proposed layouts could satisfy 100% of the water demand for the three smallest buildings in all but the aridest climate conditions. For the three larger buildings, rainwater would offset annual water needs by approximately 74 to 100%. A comprehensive economic analysis considering CapEx and OpEx indicated that the cost of installing on-site water harvesting and recycling systems would increase the overall construction cost of multi-family buildings by around 6% and single-family dwellings by about 12%, with relatively low space requirements. For buildings or combined water systems with more than 300 people, the estimated total price of on-site water provision (including harvesting, treatment, recycling, and monitoring) ranged from $1.5/m3 to $2.7/m,3 which is considerably less than the typical tariffs collected by utilities in the United States and Western Europe. Where buildings can avoid the need to connect to centralized supplies for potable water and sewage disposal, water costs could be even lower. Urine-diversion has the potential to yield the least expensive solution but is the least well developed and had higher uncertainty in the cost analysis. More mature layouts (e.g., membrane bioreactors) exhibited less cost uncertainty and were economically competitive. Our analysis indicates that existing technologies can be used to create economically viable systems that greatly reduce demands on centralized utilities and, under some conditions, eliminate the need for centralized water supply or sewage collection.}, }
@article {pmid35460373, year = {2022}, author = {Balbuena, S and Castelli, L and Zunino, P and Antúnez, K}, title = {Effect of Chronic Exposure to Sublethal Doses of Imidacloprid and Nosema ceranae on Immunity, Gut Microbiota, and Survival of Africanized Honey Bees.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35460373}, issn = {1432-184X}, support = {ANII-FCE_1_2017_1_135810//Agencia Nacional de Investigación e Innovación/ ; POS_NAC_2018_1_151557//Agencia Nacional de Investigación e Innovación/ ; For Women in Science//Fondation L'Oréal/ ; }, abstract = {Large-scale honey bee colony losses reported around the world have been associated with intoxication with pesticides, as with the presence of pests and pathogens. Among pesticides, neonicotinoid insecticides are the biggest threat. Due to their extensive use, they can be found in all agricultural environments, including soil, water, and air, are persistent in the environment, and are highly toxic for honey bees. In addition, infection by different pests and pathogens can act synergistically, weakening bees. In this study, we investigated the effects of chronic exposure to sublethal doses of imidacloprid alone or combined with the microsporidia Nosema ceranae on the immune response, deformed wing virus infection (DWV), gut microbiota, and survival of Africanized honey bees. We found that imidacloprid affected the expression of some genes associated with immunity generating an altered physiological state, although it did not favor DWV or N. ceranae infection. The pesticide alone did not affect honey bee gut microbiota, as previously suggested, but when administered to N. ceranae infected bees, it generated significant changes. Finally, both stress factors caused high mortality rates. Those results illustrate the negative impact of imidacloprid alone or combined with N. ceranae on Africanized honey bees and are useful to understand colony losses in Latin America.}, }
@article {pmid35460372, year = {2022}, author = {Mascuch, SJ and Demko, A and Viulu, S and Ginigini, J and Soapi, K and Jensen, P and Kubanek, J}, title = {Antibiotic Activity Altered by Competitive Interactions Between Two Coral Reef-Associated Bacteria.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35460372}, issn = {1432-184X}, support = {U19 TW007401/TW/FIC NIH HHS/United States ; }, abstract = {Microbes produce natural products that mediate interactions with each other and with their environments, representing a potential source of antibiotics for human use. The biosynthesis of some antibiotics whose constitutive production otherwise remains low has been shown to be induced by competing microbes. Competition among macroorganism hosts may further influence the metabolic outputs of members of their microbiomes, especially near host surfaces where hosts and microbial symbionts come into close contact. At multiple field sites in Fiji, we collected matched samples of corals and algae that were freestanding or in physical contact with each other, cultivated bacteria from their surfaces, and explored growth-inhibitory activities of these bacteria against marine and human pathogens. In the course of the investigation, an interaction was discovered between two coral-associated actinomycetes in which an Agrococcus sp. interfered with the antibiotic output of a Streptomyces sp. Several diketopiperazines identified from the antibiotic-producing bacterium could not, on their own, account for the antibiotic activity indicating that other, as yet unidentified molecule(s) or molecular blends, possibly including diketopiperazines, are likely involved. This observation highlights the complex molecular dynamics at play among microbiome constituents. The mechanisms through which microbial interactions impact the biological activities of specialized metabolites deserve further attention considering the ecological and commercial importance of bacterial natural products.}, }
@article {pmid35460285, year = {2022}, author = {Bartha, L and Mandáková, T and Kovařík, A and Bulzu, PA and Rodde, N and Mahelka, V and Lysak, MA and Fustier, MA and Šafář, J and Cápal, P and Keresztes, L and Banciu, HL}, title = {Intact rDNA arrays of Potentilla-origin detected in Erythronium nucleus suggest recent eudicot-to-monocot horizontal transfer.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.18171}, pmid = {35460285}, issn = {1469-8137}, abstract = {During our initial phylogenetic study of the monocot genus Erythronium (Liliaceae), we observed peculiar eudicot-type internal transcribed spacer (ITS) sequences in a dataset derived from genomic DNA of Erythronium dens-canis. This raised the possibility horizontal transfer of a eudicot alien ribosomal DNA (rDNA) into the Erythronium genome. In this work we aimed to support the hypothesis by carrying out genomic, molecular and cytogenetic analyses. Genome skimming coupled by PacBio HiFi sequencing of a flow-sorted bacterial artificial chromosome (BAC) clone was used to characterise the alien 45S rDNA. Integration of alien rDNA in the recipient genome was further proved by Southern blotting and fluorescence in situ hybridisation (FISH) using specific probes. Alien rDNA, nested among Potentilla species in phylogenetic analysis, likely entered Erythronium lineage in the common ancestor of E. dens-canis and E. caucasicum. Transferred eudicot-type rDNA preserved its tandemly arrayed feature on a single chromosome and was found to be transcribed in the monocot host albeit much less efficiently than the native counterpart. This study adds a new example to the rarely documented nuclear-to-nuclear jumps of DNA between eudicots and monocots while holding the scientific community continually in suspense about the mode of DNA transfer.}, }
@article {pmid35458219, year = {2022}, author = {Franck, M and de Toro-Martín, J and V Varin, T and Garneau, V and Pilon, G and Roy, D and Couture, P and Couillard, C and Marette, A and Vohl, MC}, title = {Gut Microbial Signatures of Distinct Trimethylamine N-Oxide Response to Raspberry Consumption.}, journal = {Nutrients}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/nu14081656}, pmid = {35458219}, issn = {2072-6643}, support = {MRT-168045//CIHR/ ; not applicable//WA Red Raspberry Commission (WRRC)/ ; }, abstract = {The aim of this exploratory study was to evaluate the gut microbial signatures of distinct trimethylamine N-oxide (TMAO) responses following raspberry consumption. Investigations were carried out in 24 subjects at risk of developing metabolic syndrome who received 280 g/day of frozen raspberries for 8 weeks. Blood and stool samples were collected at weeks 0 and 8. Inter-individual variability in plasma TMAO levels was analyzed, 7 subjects were excluded due to noninformative signals and 17 subjects were kept for analysis and further stratified according to their TMAO response. Whole-metagenome shotgun sequencing analysis was used to determine the impact of raspberry consumption on gut microbial composition. Before the intervention, the relative abundance of Actinobacteriota was significantly higher in participants whose TMAO levels increased after the intervention (p = 0.03). The delta TMAO (absolute differences of baseline and week 8 levels) was positively associated with the abundance of gut bacteria such as Bilophila wadsworthia (p = 0.02; r2 = 0.37), from the genus Granulicatella (p = 0.03; r2 = 0.48) or the Erysipelotrichia class (p = 0.03; r2 = 0.45). Changes in the gut microbial ecology induced by raspberry consumption over an 8-week period presumably impacted quaternary amines-utilizing activity and thus plasma TMAO levels.}, }
@article {pmid35456812, year = {2022}, author = {Van den Abbeele, P and Ghyselinck, J and Marzorati, M and Koch, AM and Lambert, W and Michiels, J and Chalvon-Demersay, T}, title = {The Effect of Amino Acids on Production of SCFA and bCFA by Members of the Porcine Colonic Microbiota.}, journal = {Microorganisms}, volume = {10}, number = {4}, pages = {}, doi = {10.3390/microorganisms10040762}, pmid = {35456812}, issn = {2076-2607}, abstract = {Functional amino acids supplementation to farm animals is considered to not only be beneficial by regulating intestinal barrier, oxidative stress, and immunity, but potentially also by impacting the gut microbiota. The impact of amino acids on a piglet-derived colonic microbiota was evaluated using a 48-h in vitro batch incubation strategy. The combination of 16S rRNA gene profiling with flow cytometry demonstrated that specific microbial taxa were involved in the fermentation of each of the amino acids resulting in the production of specific metabolites. Branched chain amino acids (leucine, isoleucine, valine) strongly increased branched-chain fatty acids (+23.0 mM) and valerate levels (+3.0 mM), coincided with a marked increase of Peptostreptococcaceae. Further, glutamine and glutamate specifically stimulated acetate (~20 mM) and butyrate (~10 mM) production, relating to a stimulation of a range of families containing known butyrate-producing species (Ruminococcaceae, Oscillospiraceae, and Christensenellaceae). Finally, while tryptophan was only fermented to a minor extent, arginine and lysine specifically increased propionate levels (~2 mM), likely produced by Muribaculaceae members. Overall, amino acids were thus shown to be selectively utilized by microbes originating from the porcine colonic microbiota, resulting in the production of health-related short-chain fatty acids, thus confirming the prebiotic potential of specific functional amino acids.}, }
@article {pmid35456724, year = {2022}, author = {Guo, Z and Bao, Y and Liu, J}, title = {Environmental Difference and Spatial Distance Affect the Fidelity of Variation Source of Microbial Community Structure in Air-Dried Soils.}, journal = {Microorganisms}, volume = {10}, number = {4}, pages = {}, doi = {10.3390/microorganisms10040672}, pmid = {35456724}, issn = {2076-2607}, abstract = {Air-dried soil archives are important for microbial ecology research, although the process of air-drying preservation inevitably destroys the original microbial information in soils. Only upon fully understanding the limitations of air-dried soil can it play a greater role. The value of air-dried soil depends on the fidelity of microbial community structure information in the air-dried soil relative to that in fresh soil. To evaluate this, high-throughput sequencing was applied to investigate the microbial community of fresh soils and 227 days air-dried archives from typical farmland under a large spatial scale, and PERMANOVA was used to analyze the explanation proportion (EP) of the spatial factor on the microbial community structure in any paired-fresh or air-dried soils. The results show that for any paired soils, the value of EP ranged from 42.4% to 97.9% (p < 0.001). Importantly, taking fresh soil as a reference, the value of EP declined in air-dried soils (effect size r = 0.79, p < 0.001). Furthermore, the standardized difference in EP between fresh and air-dried soil (NDEP) was used to characterize the fidelity of variance source of microbial community structure in air-dried soils, and correlation tests showed that NDEP was negatively correlated with spatial distance (r = -0.21, p < 0.01) and with environmental difference (r = -0.37, p < 0.001). Further analyses show that larger NDEP was observed at a spatial distance <25 km or an environmental difference <0.58. Variance partitioning analysis showed that 28.0% of the variation in NDEP could be explained, with environmental difference constituting 14.0% and the interaction between the environmental difference and spatial distance constituting the remaining 14.0%. Soil texture was the most important factor for predicting NDEP, followed by soil pH and annual average temperature. This study not only emphasizes the possible decline in EP when using air-dried soils to reveal microbial community patterns, but also implies that air-dried soil is more suitable for addressing scientific questions under a large spatial scale or environmental differences.}, }
@article {pmid35454671, year = {2022}, author = {Li, Q and Li, L and Li, Q and Wang, J and Nie, S and Xie, M}, title = {Influence of Natural Polysaccharides on Intestinal Microbiota in Inflammatory Bowel Diseases: An Overview.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {8}, pages = {}, doi = {10.3390/foods11081084}, pmid = {35454671}, issn = {2304-8158}, support = {20212BCD42016//Key Laboratory of Bioactive Polysaccharides Program of Jiangxi Province/ ; 20212AAF01005//Key Technology Project in Jiangxi Province/ ; 20212BAB215036//Natural Science Foundation of Jiangxi Province/ ; }, abstract = {The incidence of inflammatory bowel disease (IBD) has increased in recent years. Considering the potential side effects of conventional drugs, safe and efficient treatment methods for IBD are required urgently. Natural polysaccharides (NPs) have attracted considerable attention as potential therapeutic agents for IBD owing to their high efficiency, low toxicity, and wide range of biological activities. Intestinal microbiota and their fermentative products, mainly short-chain fatty acids (SCFAs), are thought to mediate the effect of NPs in IBDs. This review explores the beneficial effects of NPs on IBD, with a special focus on the role of intestinal microbes. Intestinal microbiota exert alleviation effects via various mechanisms, such as increasing the intestinal immunity, anti-inflammatory activities, and intestinal barrier protection via microbiota-dependent and microbiota-independent strategies. The aim of this paper was to document evidence of NP-intestinal microbiota-associated IBD prevention, which would be helpful for guidance in the treatment and management of IBD.}, }
@article {pmid35453798, year = {2022}, author = {Malfertheiner, L and Martínez-Pérez, C and Zhao, Z and Herndl, GJ and Baltar, F}, title = {Phylogeny and Metabolic Potential of the Candidate Phylum SAR324.}, journal = {Biology}, volume = {11}, number = {4}, pages = {}, doi = {10.3390/biology11040599}, pmid = {35453798}, issn = {2079-7737}, abstract = {The bacterial SAR324 cluster is ubiquitous and abundant in the ocean, especially around hydrothermal vents and in the deep sea, where it can account for up to 30% of the whole bacterial community. According to a new taxonomy generated using multiple universal protein-coding genes (instead of the previously used 16S rRNA single gene marker), the former Deltaproteobacteria cluster SAR324 has been classified since 2018 as its own phylum. Yet, very little is known about its phylogeny and metabolic potential. We downloaded all publicly available SAR324 genomes (65) from all natural environments and reconstructed 18 new genomes using publicly available oceanic metagenomic data and unpublished data from the waters underneath the Ross Ice Shelf. We calculated a global SAR324 phylogenetic tree and identified six clusters (namely 1A, 1B, 2A, 2B, 2C and 2D) within this clade. Genome annotation and metatranscriptome read mapping showed that SAR324 clades possess a flexible array of genes suited for survival in various environments. Clades 2A and 2C are mostly present in the surface mesopelagic layers of global oceans, while clade 2D dominates in deeper regions. Our results show that SAR324 has a very versatile and broad metabolic potential, including many heterotrophic, but also autotrophic pathways. While one surface water associated clade (2A) seems to use proteorhodopsin to gain energy from solar radiation, some deep-sea genomes from clade 2D contain the complete Calvin-Benson-Bassham cycle gene repertoire to fix carbon. This, in addition to a variety of other genes and pathways for both oxic (e.g., dimethylsulfoniopropionate degradation) and anoxic (e.g., dissimilatory sulfate reduction, anaerobic benzoate degradation) conditions, can help explain the ubiquitous presence of SAR324 in aquatic habitats.}, }
@article {pmid35453791, year = {2022}, author = {Liu, Z and Wang, J and Meng, D and Li, L and Liu, X and Gu, Y and Yan, Q and Jiang, C and Yin, H}, title = {The Self-Organization of Marine Microbial Networks under Evolutionary and Ecological Processes: Observations and Modeling.}, journal = {Biology}, volume = {11}, number = {4}, pages = {}, doi = {10.3390/biology11040592}, pmid = {35453791}, issn = {2079-7737}, support = {41877345//National Nature Science Foundation of China/ ; 91851206//National Nature Science Foundation of China/ ; QYZDBSSW-DQC043//Key Research Program of Frontier Sciences of the Chinese Academy of Sciences/ ; }, abstract = {Evolutionary and ecological processes are primary drivers of ecological network constrictions. However, the ways that these processes underpin self-organization and modularity in networks are poorly understood. Here, we performed network analyses to explore the evolutionary and ecological effects on global marine microbial co-occurrence networks across multiple network levels, including those of nodes, motifs, modules and whole networks. We found that both direct and indirect species interactions were evolutionarily and ecologically constrained across at least four network levels. Compared to ecological processes, evolutionary processes generally showed stronger long-lasting effects on indirect interactions and dominated the network assembly of particle-associated communities in spatially homogeneous environments. Regarding the large network path distance, the contributions of either processes to species interactions generally decrease and almost disappear when network path distance is larger than six. Accordingly, we developed a novel mathematical model based on scale-free networks by considering the joint effects of evolutionary and ecological processes. We simulated the self-organization of microbial co-occurrence networks and found that long-lasting effects increased network stability via decreasing link gain or loss. Overall, these results revealed that evolutionary and ecological processes played key roles in the self-organization and modularization of microbial co-occurrence networks.}, }
@article {pmid35449401, year = {2022}, author = {Li, MH and Liu, KW and Li, Z and Lu, HC and Ye, QL and Zhang, D and Wang, JY and Li, YF and Zhong, ZM and Liu, X and Yu, X and Liu, DK and Tu, XD and Liu, B and Hao, Y and Liao, XY and Jiang, YT and Sun, WH and Chen, J and Chen, YQ and Ai, Y and Zhai, JW and Wu, SS and Zhou, Z and Hsiao, YY and Wu, WL and Chen, YY and Lin, YF and Hsu, JL and Li, CY and Wang, ZW and Zhao, X and Zhong, WY and Ma, XK and Ma, L and Huang, J and Chen, GZ and Huang, MZ and Huang, L and Peng, DH and Luo, YB and Zou, SQ and Chen, SP and Lan, S and Tsai, WC and Van de Peer, Y and Liu, ZJ}, title = {Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy.}, journal = {Nature plants}, volume = {8}, number = {4}, pages = {373-388}, pmid = {35449401}, issn = {2055-0278}, support = {31870199//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {To improve our understanding of the origin and evolution of mycoheterotrophic plants, we here present the chromosome-scale genome assemblies of two sibling orchid species: partially mycoheterotrophic Platanthera zijinensis and holomycoheterotrophic Platanthera guangdongensis. Comparative analysis shows that mycoheterotrophy is associated with increased substitution rates and gene loss, and the deletion of most photoreceptor genes and auxin transporter genes might be linked to the unique phenotypes of fully mycoheterotrophic orchids. Conversely, trehalase genes that catalyse the conversion of trehalose into glucose have expanded in most sequenced orchids, in line with the fact that the germination of orchid non-endosperm seeds needs carbohydrates from fungi during the protocorm stage. We further show that the mature plant of P. guangdongensis, different from photosynthetic orchids, keeps expressing trehalase genes to hijack trehalose from fungi. Therefore, we propose that mycoheterotrophy in mature orchids is a continuation of the protocorm stage by sustaining the expression of trehalase genes. Our results shed light on the molecular mechanism underlying initial, partial and full mycoheterotrophy.}, }
@article {pmid35448576, year = {2022}, author = {Rojas, EC and Jensen, B and Jørgensen, HJL and Latz, MAC and Esteban, P and Collinge, DB}, title = {The Fungal Endophyte Penicillium olsonii ML37 Reduces Fusarium Head Blight by Local Induced Resistance in Wheat Spikes.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {4}, pages = {}, doi = {10.3390/jof8040345}, pmid = {35448576}, issn = {2309-608X}, abstract = {The fungal endophyte Penicillium olsonii ML37 is a biocontrol agent of Fusarium head blight in wheat (caused by Fusarium graminearum), which has shown a limited direct inhibition of fungal growth in vitro. We used RNA-seq and LC-MS/MS analyses to elucidate metabolic interactions of the three-way system Penicillium-wheat-Fusarium in greenhouse experiments. We demonstrated that P. olsonii ML37 colonises wheat spikes and transiently activates plant defence mechanisms, as pretreated spikes show a faster and stronger expression of the defence metabolism during the first 24 h after pathogen inoculation. This effect was transient and the expression of the same genes was lower in the pathogen-infected spikes than in those infected by P. olsonii alone. This response to the endophyte includes the transcriptional activation of several WRKY transcription factors. This early activation is associated with a reduction in FHB symptoms and significantly lower levels of the F. graminearum metabolites 15-acetyl-DON and culmorin. An increase in the Penicillium-associated metabolite asperphanamate confirms colonisation by the endophyte. Our results suggest that the mode of action used by P. olsonii ML37 is via a local defence activation in wheat spikes, and that this fungus has potential as a novel biological alternative in wheat disease control.}, }
@article {pmid35447706, year = {2022}, author = {Jeske, JT and Gallert, C}, title = {Microbiome Analysis via OTU and ASV-Based Pipelines-A Comparative Interpretation of Ecological Data in WWTP Systems.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {9}, number = {4}, pages = {}, doi = {10.3390/bioengineering9040146}, pmid = {35447706}, issn = {2306-5354}, support = {02WCL1469A-J//German Federal Ministry of Education and Research/ ; }, abstract = {Linking community composition and ecosystem function via the cultivation-independent analysis of marker genes, e.g., the 16S rRNA gene, is a staple of microbial ecology and dependent disciplines. The certainty of results, independent of the bioinformatic handling, is imperative for any advances made within the field. In this work, thermophilic anaerobic co-digestion experimental data, together with primary and waste-activated sludge prokaryotic community data, were analyzed with two pipelines that apply different principles when dealing with technical, sequencing, and PCR biases. One pipeline (VSEARCH) employs clustering methods, generating individual operational taxonomic units (OTUs), while the other (DADA2) is based on sequencing error correction algorithms and generates exact amplicon sequence variants (ASVs). The outcomes of both pipelines were compared within the framework of ecological-driven data analysis. Both pipelines provided comparable results that would generally allow for the same interpretations. Yet, the two approaches also delivered community compositions that differed between 6.75% and 10.81% between pipelines. Inconsistencies were also observed linked to biologically driven variability in the samples, which affected the two pipelines differently. These pipeline-dependent differences in taxonomic assignment could lead to different conclusions and interfere with any downstream analysis made for such mis- or not-identified species, e.g., network analysis or predictions of their respective ecosystem service.}, }
@article {pmid35447252, year = {2022}, author = {Kelly, MR and Whitworth, P and Jamieson, A and Burgess, JG}, title = {Bacterial colonisation of plastic in the Rockall Trough, North-East Atlantic: An improved understanding of the deep-sea plastisphere.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {119314}, doi = {10.1016/j.envpol.2022.119314}, pmid = {35447252}, issn = {1873-6424}, abstract = {Plastic pollution has now been found within multiple ecosystems across the globe. Characterisation of microbial assemblages associated with marine plastic, or the so-called 'plastisphere', has focused predominantly on plastic in the epipelagic zone. Whether this community includes taxa that are consistently enriched on plastic compared to surrounding non plastic surfaces is unresolved, as are the ecological implications. The deep sea is likely a final sink for most of the plastic entering the ocean, yet there is limited information on microbial colonisation of plastic at depth. The aim of this study was to investigate deep-sea microbial communities associated with polystyrene (PS) and polyurethane (PU) with Bath stone used as a control. The substrates (n = 15) were deployed in the Rockall Trough (Atlantic), and recovered 420 days later from a depth of 1796 m. To characterise the bacterial communities, 16S rRNA genes were sequenced using the Illumina MiSeq platform. A dominant core microbiome (taxa shared across all substrates) comprised 8% of total ASVs (amplicon sequence variant) and accounted for 92% of the total community reads. This suggests that many commonly reported members of the plastisphere are simply opportunistic which freely colonise any hard surface. Transiently associated species consisted of approximately 7% of the total community. Thirty genera were enriched on plastic (P < 0.05), representing 1% of the total community. The discovery of novel deep-sea enriched taxa included Aurantivirga, Algivirga, IheB3-7, Spirosoma, HTCC5015, Ekhidna and Calorithrix on PS and Candidatus Obscuribacter, Haloferula, Marine Methylotrophic Group 3, Aliivibrio, Tibeticola and Dethiosulfatarculus on PU. This small fraction of the microbiome include taxa with unique metabolic abilities and show how bacterial communities can be shaped by plastic pollution at depth. This study outlines a novel approach in categorising the plastisphere to elucidate the ecological implications of enriched taxa that show an affinity for colonising plastic.}, }
@article {pmid35446625, year = {2022}, author = {Li, S and Abdulkadir, N and Schattenberg, F and Nunes da Rocha, U and Grimm, V and Müller, S and Liu, Z}, title = {Stabilizing microbial communities by looped mass transfer.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {17}, pages = {e2117814119}, doi = {10.1073/pnas.2117814119}, pmid = {35446625}, issn = {1091-6490}, support = {100192205//EC | European Regional Development Fund (ERDF)/ ; }, abstract = {SignificanceThe population ecology of microbial communities is still poorly understood and their notorious instability makes them impossible to control. Much of the instability is caused by the stochastic assembly of microorganisms, especially in highly diverse microbiomes where structural and hence functional changes occur rapidly due to the short generation time of their members. Usually, to maintain organismic proportions in communities, their niches are deterministically reinforced, but stochasticity strongly counteracts this. Based on metacommunity theory, a looped mass transfer was developed that uses the rescue effect to stabilize communities. This study fills a long-standing gap and enables continuous and proportionally equal growth of community members using an unprecedented operational design that addresses an acute need in the healthcare and biotechnology industries.}, }
@article {pmid35443156, year = {2022}, author = {Özçam, M and Oh, JH and Tocmo, R and Acharya, D and Zhang, S and Astmann, TJ and Heggen, M and Ruiz-Ramírez, S and Li, F and Cheng, CC and Vivas, E and Rey, FE and Claesen, J and Bugni, TS and Walter, J and van Pijkeren, JP}, title = {A secondary metabolite drives intraspecies antagonism in a gut symbiont that is inhibited by cell-wall acetylation.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2022.03.033}, pmid = {35443156}, issn = {1934-6069}, abstract = {The mammalian microbiome encodes numerous secondary metabolite biosynthetic gene clusters; yet, their role in microbe-microbe interactions is unclear. Here, we characterized two polyketide synthase gene clusters (fun and pks) in the gut symbiont Limosilactobacillus reuteri. The pks, but not the fun, cluster encodes antimicrobial activity. Forty-one of 51 L. reuteri strains tested are sensitive to Pks products; this finding was independent of strains' host origin. Sensitivity to Pks was also established in intraspecies competition experiments in gnotobiotic mice. Comparative genome analyses between Pks-resistant and -sensitive strains identified an acyltransferase gene (act) unique to Pks-resistant strains. Subsequent cell-wall analysis of wild-type and act mutant strains showed that Act acetylates cell-wall components, providing resistance to Pks-mediated killing. Additionally, pks mutants lost their competitive advantage, while act mutants lost their Pks resistance in in vivo competition assays. These findings provide insight into how closely related gut symbionts can compete and co-exist in the gastrointestinal tract.}, }
@article {pmid35442877, year = {2022}, author = {Khanal, M and Timilsina, S and Bhatta, BP and Bophela, K and Coutinho, T and Cochran, K and Malla, S}, title = {Pseudomonas uvaldensis sp. nov., a bacterial pathogen causing onion bulb rot.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {4}, pages = {}, doi = {10.1099/ijsem.0.005311}, pmid = {35442877}, issn = {1466-5034}, abstract = {A Gram-stain-negative, aerobic and non-spore-forming bacterial strain, designated 20TX0172T, was isolated from a rotting onion bulb in Texas, USA. The results of phylogenetic analysis based on the 16S rRNA sequence indicated that the novel strain represented a member of the genus Pseudomonas and had the greatest sequence similarities with Pseudomonas kilonensis 520-20T (99.3 %), Pseudomonas corrugata CFBP 2431T (99.2 %), and Pseudomonas viciae 11K1T (99.2 %) but the 16S rRNA phylogenetic tree displayed a monophyletic clade with Pseudomonas mediterranea CFBP 5447T. In the phylogenetic trees based on sequences of four housekeeping genes (gap1, gltA, gyrB and rpoD), the novel strain formed a separate branch, indicating that the strain was distinct phylogenetically from known species of the genus Pseudomonas. The genome-sequence-derived average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the novel isolate and P. mediterranea DSM 16733T were 86.7 and 32.7 %, respectively. These values were below the accepted species cutoff threshold of 96 % ANI and 70 % dDDH, affirming that the strain represented a novel species. The genome size of the novel species was 5.98 Mbp with a DNA G+C content of 60.8 mol%. On the basis of phenotypic and genotypic characteristics, strain 20TX0172T represents a novel species of the genus Pseudomonas. The name Pseudomonas uvaldensis sp. nov. is proposed. The type strain is 20TX0172T (=NCIMB 15426T=CIP 112022T).}, }
@article {pmid35439561, year = {2022}, author = {Fernando Herrera Adarme, O and Eduardo Lobo Baêta, B and Cardoso Torres, M and Camilo Otalora Tapiero, F and Vinicius Alves Gurgel, L and Queiroz Silva, S and Francisco de Aquino, S}, title = {Biogas production by anaerobic co-digestion of sugarcane biorefinery byproducts: comparative analyses of performance and microbial community in novel single-and two-stage systems.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {127185}, doi = {10.1016/j.biortech.2022.127185}, pmid = {35439561}, issn = {1873-2976}, abstract = {Anaerobic co-digestion (AcD) of sugarcane biorefinery byproducts (hemicelluloses hydrolysate (HH), vinasse, yeast extract and sugarcane bagasse fly ashes was evaluated using new anaerobic reactors fed with organic loading rates (OLR) from 0.9 to 10.8gCODL-1d-1. The best results were obtained in a two-stage system when the OLR was 5.65gCODL-1d-1, leading to a total chemical oxygen demand (COD) removal of 87.6 % and methane yield of 243NmLCH4gCODr-1. Microbial community analyses of sludge from both systems (one and two-stages) revealed structural changes and relationship among the main genus found (Clostridium (62.8%), Bacteroides(11.3 %), Desulfovibrio (19.1 %), Lactobacillus(67.7 %), Lactococcus (22.5%), Longilinea (78%), Methanosaeta (19.2 %) and Syntrophus (18.9 %)) with processes performance, kinetic and hydrodynamic parameters. Moreover, biomass granulation was observed in the novel structured anaerobic reactor operated at single stage due to sugarcane bagasse fly ash addition.}, }
@article {pmid35438534, year = {2022}, author = {Tiedje, JM and Bruns, MA and Casadevall, A and Criddle, CS and Eloe-Fadrosh, E and Karl, DM and Nguyen, NK and Zhou, J}, title = {Microbes and Climate Change: a Research Prospectus for the Future.}, journal = {mBio}, volume = {}, number = {}, pages = {e0080022}, doi = {10.1128/mbio.00800-22}, pmid = {35438534}, issn = {2150-7511}, abstract = {Climate change is the most serious challenge facing humanity. Microbes produce and consume three major greenhouse gases-carbon dioxide, methane, and nitrous oxide-and some microbes cause human, animal, and plant diseases that can be exacerbated by climate change. Hence, microbial research is needed to help ameliorate the warming trajectory and cascading effects resulting from heat, drought, and severe storms. We present a brief summary of what is known about microbial responses to climate change in three major ecosystems: terrestrial, ocean, and urban. We also offer suggestions for new research directions to reduce microbial greenhouse gases and mitigate the pathogenic impacts of microbes. These include performing more controlled studies on the climate impact on microbial processes, system interdependencies, and responses to human interventions, using microbes and their carbon and nitrogen transformations for useful stable products, improving microbial process data for climate models, and taking the One Health approach to study microbes and climate change.}, }
@article {pmid35437690, year = {2022}, author = {Li, H and Li, Z and Tang, Q and Li, R and Lu, L}, title = {Local-Scale Damming Impact on the Planktonic Bacterial and Eukaryotic Assemblages in the upper Yangtze River.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35437690}, issn = {1432-184X}, support = {51861125204//National Natural Science Foundation of China/ ; 52039006//National Natural Science Foundation of China/ ; cstc2020jscx-msxmX0121//Chongqing Science and Technology Commission/ ; cstc2020jcyj-jqX0010//Chongqing Science and Technology Commission/ ; }, abstract = {Dam construction and impoundment cause discontinuities in the natural biophysical gradients in rivers. These discontinuities may alter distinctive habitats and different microbial community assembly mechanisms upstream and downstream of dams, which reflect the potential impacts of damming on riverine aquatic ecosystems. In this study, we investigated the planktonic microbial assemblages of three large dams in the upper Yangtze River by using high-throughput sequencing. The results revealed that the alpha diversity indexes increased downstream of the dams. In addition, more eukaryotic ASVs solely occurred downstream of the dams, which indicated that a large proportion of eukaryotes appeared downstream of the dams. The nonmetric multidimensional scaling analysis indicated that there was no obvious geographic clustering of the planktonic microbial assemblages among the different locations or among the different dams. However, the dam barriers changed dam-related variables (maximum dam height and water level) and local environmental variables (water temperature, DOC, etc.) that could possibly affect the assembly of the planktonic microbial communities that are closest to the dams. A co-occurrence network analysis demonstrated that the keystone taxa of the planktonic bacteria and eukaryotes decreased downstream of the dams. In particular, the keystone taxa of the eukaryotes disappeared downstream of the dams. The robustness analysis indicated that the natural connectivity of the microbial networks decreased more rapidly upstream of the dams, and the downstream eukaryotic network was more stable. In conclusion, damming has a greater impact on planktonic eukaryotes than on bacteria in near-dam areas, and planktonic microbial assemblages were more susceptible to the environmental changes. Our study provides a better understanding of the ecological effects of river damming.}, }
@article {pmid35433514, year = {2022}, author = {Franklin, S and Aitken, SL and Shi, Y and Sahasrabhojane, PV and Robinson, S and Peterson, CB and Daver, N and Ajami, NA and Kontoyiannis, DP and Shelburne, SA and Galloway-Peña, J}, title = {Oral and Stool Microbiome Coalescence and Its Association With Antibiotic Exposure in Acute Leukemia Patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {848580}, doi = {10.3389/fcimb.2022.848580}, pmid = {35433514}, issn = {2235-2988}, abstract = {Failure to maintain segregation of oral and gut microbial communities has been linked to several diseases. We sought to characterize oral-fecal microbiome community coalescence, ectopic extension of oral bacteria, clinical variables contributing to this phenomenon, and associated infectious consequences by analyzing the 16S rRNA V4 sequences of longitudinal fecal (n=551) and oral (n=737) samples from 97 patients with acute myeloid leukemia (AML) receiving induction chemotherapy (IC). Clustering observed in permutation based multivariate analysis of variance (PERMANOVA) of Bray-Curtis dissimilarity and PCoA plot of UniFrac distances between intra-patient longitudinal oral-stool sample pairs suggested potential oral-stool microbial community coalescence. Bray-Curtis dissimilarities and UniFrac distances were used to create an objective definition of microbial community coalescence. We determined that only 23 of the 92 patients exhibited oral-stool community coalescence. This was validated through a linear mixed model which determined that patients who experienced coalescence had an increased proportion of shared to unique OTUs between their oral-stool sample pairs over time compared to non-coalesced patients. Evaluation of longitudinal microbial characteristics revealed that patients who experienced coalescence had increased stool abundance of Streptococcus and Stenotrophomonas compared to non-coalesced patients. When treated as a time-varying covariate, each additional day of linezolid (HR 1.15, 95% CI 1.06 - 1.24, P <0.001), meropenem (HR 1.13, 95% CI 1.05 - 1.21, P = 0.001), metronidazole (HR 1.13, 95% CI 1.05 - 1.21, P = 0.001), and cefepime (HR 1.10, 95% CI 1.01 - 1.18, P = 0.021) increased the hazard of oral-stool microbial community coalescence. Levofloxacin receipt was associated with a lower risk of microbiome community coalescence (HR 0.75, 95% CI 0.61 - 0.93, P = 0.009). By the time of neutrophil recovery, the relative abundance of Bacteroidia (P<0.001), Fusobacteria (P=0.012), and Clostridia (P=0.013) in the stool were significantly lower in patients with oral-gut community coalescence. Exhibiting oral-stool community coalescence was associated with the occurrence of infections prior to neutrophil recovery (P=0.002), as well as infections during the 90 days post neutrophil recovery (P=0.027). This work elucidates specific antimicrobial effects on microbial ecology and furthers the understanding of oral/intestinal microbial biogeography and its implications for adverse clinical outcomes.}, }
@article {pmid35432228, year = {2022}, author = {Cerbin, S and Pérez, G and Rybak, M and Wejnerowski, Ł and Konowalczyk, A and Helmsing, N and Naus-Wiezer, S and Meima-Franke, M and Pytlak, Ł and Raaijmakers, C and Nowak, W and Bodelier, PLE}, title = {Methane-Derived Carbon as a Driver for Cyanobacterial Growth.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {837198}, doi = {10.3389/fmicb.2022.837198}, pmid = {35432228}, issn = {1664-302X}, abstract = {Methane, a potent greenhouse gas produced in freshwater ecosystems, can be used by methane-oxidizing bacteria (MOB) and can therefore subsidize the pelagic food web with energy and carbon. Consortia of MOB and photoautotrophs have been described in aquatic ecosystems and MOB can benefit from photoautotrophs which produce oxygen, thereby enhancing CH4 oxidation. Methane oxidation can account for accumulation of inorganic carbon (i.e., CO2) and the release of exometabolites that may both be important factors influencing the structure of phytoplankton communities. The consortium of MOB and phototroph has been mainly studied for methane-removing biotechnologies, but there is still little information on the role of these interactions in freshwater ecosystems especially in the context of cyanobacterial growth and bloom development. We hypothesized that MOB could be an alternative C source to support cyanobacterial growth in freshwater systems. We detected low δ13C values in cyanobacterial blooms (the lowest detected value -59.97‰ for Planktothrix rubescens) what could be the result of the use of methane-derived carbon by cyanobacteria and/or MOB attached to their cells. We further proved the presence of metabolically active MOB on cyanobacterial filaments using the fluorescein isothiocyanate (FITC) based activity assay. The PCR results also proved the presence of the pmoA gene in several non-axenic cultures of cyanobacteria. Finally, experiments comprising the co-culture of the cyanobacterium Aphanizomenon gracile with the methanotroph Methylosinus sporium proved that cyanobacterial growth was significantly improved in the presence of MOB, presumably through utilizing CO2 released by MOB. On the other hand, 13C-CH4 labeled incubations showed the uptake and assimilation of MOB-derived metabolites by the cyanobacterium. We also observed a higher growth of MOB in the presence of cyanobacteria under a higher irradiance regime, then when grown alone, underpinning the bidirectional influence with as of yet unknown environmental consequences.}, }
@article {pmid35428940, year = {2022}, author = {Ganorkar, R and Jadeja, NB and Shanware, A and Ingle, AB}, title = {Characterisation of novel microbial strains Proteus mirabilis and Bordetella avium for heavy metal bioremediation and dye degradation.}, journal = {Archives of microbiology}, volume = {204}, number = {5}, pages = {262}, pmid = {35428940}, issn = {1432-072X}, abstract = {The entitled study focuses on exploring the microbial diversity and its applicability in the remediation of metal contaminated soil using microbes, which is a reliable and cost effective technique. Tungsten enriched soil of Kuhi-Agargaon-Khobna region (Nagpur, India) were analysed by XRF method to detect heavy metals. The traditional microbiological techniques were used to isolate tungsten tolerant microbes. Applicability of these microbes in bioremediation and Azo dye degradation was mainly studied. The two novel bacterial strains, Proteus mirabilis (RS2K) and Bordetella avium (RS3K), were isolated and identified to show the tolerance to tungsten, using 16S rDNA and phylogenetic analysis. These novel strains have also shown the tolerance to other metallic salts viz., (sodium) tungsten, tungstic acid, ammonium metaparatungstate, mercuric chloride, cobalt chloride and azo dye. These microbes were found to accumulate tungsten intracellularly as confirmed through ICP-MS and SEM-EDS analyses. Microbes exhibited well-equipped cellular mechanisms for metal tolerance to survive in heavy metal-laden ecology. Current study contains substantial potential in bioleaching of heavy metals and green mining along with Nano bioremediation for heavy metal pollution.}, }
@article {pmid35427643, year = {2022}, author = {Steinbauer, P and Monje, FJ and Kothgassner, O and Goreis, A and Eva, C and Wildner, B and Schned, H and Deindl, P and Seki, D and Berger, A and Olischar, M and Giordano, V}, title = {The consequences of neonatal pain, stress and opiate administration in animal models: an extensive meta-analysis concerning neuronal cell death, motor and behavioral outcomes.}, journal = {Neuroscience and biobehavioral reviews}, volume = {}, number = {}, pages = {104661}, doi = {10.1016/j.neubiorev.2022.104661}, pmid = {35427643}, issn = {1873-7528}, abstract = {This systematic review and meta-analysis aimed to investigate the association of neonatal exposure to pain, stress, opiate administration alone, as well as opiate administration prior to a painful procedure on neuronal cell death, motor, and behavioral outcomes in rodents. In total, 36 studies investigating the effect of pain (n=18), stress (n=15), opiate administration (n=13), as well as opiate administration prior to a painful event (n=7) in rodents were included in our meta-analysis. The results showed a large effect of pain (g = 1.37, 95% CI 1.00-1.74, p <.001) on neuronal cell death. Moreover, higher number of neonatal pain events were significantly associated with increased neuronal cell death, increased anxiety (b = -1.18, SE = 0.43, p =.006), and depressant-like behavior (b = 1.74, SE = 0.51, p =.027) in rodents. Both opiates and pain had no impact on motor function (g = 0.26, 95% CI 0.18-0.70, p =.248).}, }
@article {pmid35426077, year = {2022}, author = {Oliveira, NC and Rodrigues, PAP and Cônsoli, FL}, title = {Host-Adapted Strains of Spodoptera frugiperda Hold and Share a Core Microbial Community Across the Western Hemisphere.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35426077}, issn = {1432-184X}, support = {2011/50877-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/24377-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 462140-2014/8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 403851/2013-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {The fall armyworm Spodoptera frugiperda is an important polyphagous agricultural pest in the Western Hemisphere and currently invasive to countries of the Eastern Hemisphere. This species has two host-adapted strains named "rice" and "corn" strains. Our goal was to identify the occurrence of core members in the gut bacterial community of fall armyworm larvae from distinct geographical distribution and/or host strain. We used next-generation sequencing to identify the microbial communities of S. frugiperda from corn fields in Brazil, Colombia, Mexico, Panama, Paraguay, and Peru, and rice fields from Panama. The larval gut microbiota of S. frugiperda larvae did not differ between the host strains nor was it affected by the geographical distribution of the populations investigated. Our findings provide additional support for Enterococcus and Pseudomonas as core members of the bacterial community associated with the larval gut of S. frugiperda, regardless of the site of collection or strain. Further investigations are required for a deeper understanding of the nature of this relationship.}, }
@article {pmid35420423, year = {2022}, author = {Li, Q and Van Herreweghen, F and Onyango, SO and De Mey, M and Van de Wiele, T}, title = {In Vitro Microbial Metabolism of (+)-Catechin Reveals Fast and Slow Converters with Individual-Specific Microbial and Metabolite Markers.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.2c00551}, pmid = {35420423}, issn = {1520-5118}, abstract = {The bioavailability of catechin highly relies on gut microbiota which may determine its metabolic profile, resulting in different health outcomes. Here, we investigated in vitro (+)-catechin metabolism by human microbial communities. There were substantial interindividual differences in the metabolic profiles of (+)-catechin, with 5-(3',4'-dihydroxyphenyl)-γ-valerolactone being the major contributor. Furthermore, the microbial metabolic rate of catechin enabled stratification of 12 participants (fast, medium, and slow converters), despite the interference from the strong intrinsic interindividual variability in fecal microbiota. Correlations were established between this stratified population and microbiota features, such as ecosystem diversity. Additionally, fast converters had significantly higher prevalences of amplicon sequence variants (ASVs) with potential capacity of C-ring cleavage (ASV233_Eggerthella and ASV402_Eubacterium), B-ring dihydroxylation (ASV402_Eubacterium), and short-chain fatty acid (SCFA)-producing ASVs. In conclusion, metabolic-capability-based stratification allows us to uncover differences in microbial composition between fast and slow converters, which could help to elucidate interindividual variabilities in the health benefits of catechins.}, }
@article {pmid35420314, year = {2022}, author = {Fan, X and Chen, H and Yan, G and Ye, M and Yin, C and Li, T and Wakelin, SA and Liang, Y}, title = {Niche Differentiation Among Canonical Nitrifiers and N2O Reducers Is Linked to Varying Effects of Nitrification Inhibitors DCD and DMPP in Two Arable Soils.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35420314}, issn = {1432-184X}, support = {2017YFD0200707//National Key Research and Development Programs of China/ ; 42007083//National Natural Science Foundation of China/ ; 2020M671736//China Postdoctoral Science Foundation/ ; }, abstract = {The efficacy of nitrification inhibitors (NIs) dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) varies with soil types. Understanding the microbial mechanisms for this variation may lead to better modelling of NI efficacy and therefore on-farm adoption. This study addressed the response patterns of mineral nitrogen, nitrous oxide (N2O) emission, abundances of N-cycling functional guilds and soil microbiota characteristics, in relation to urea application with or without DCD or DMPP in two arable soils (an alkaline and an acid soil). The inhibition of nitrification rate and N2O emission by NI application occurred by suppressing ammonia-oxidizing bacteria (AOB) abundances and increasing the abundances of nosZI-N2O reducers; however, abundances of ammonia-oxidizing archaea (AOA) were also stimulated with NIs-added in these two arable soils. DMPP generally had stronger inhibition efficiency than DCD, and both NIs' addition decreased Nitrobacter, while increased Nitrospira abundance only in alkaline soil. N2O emissions were positively correlated with AOB and negatively correlated with nosZI in both soils and AOA only in acid soil. Moreover, N2O emissions were also positively correlated with nirK-type denitrifiers in alkaline soil, and clade A comammox in acid soil. Amendment with DCD or DMPP altered soil microbiota community structure, but had minor effect on community composition. These results highlight a crucial role of the niche differentiation among canonical ammonia oxidizers (AOA/AOB), Nitrobacter and Nitrospira, as well as nosZI- and nosZII-N2O reducers in determining the varying efficacies of DCD and DMPP in different arable soils.}, }
@article {pmid35419656, year = {2022}, author = {Xu, F and Zhu, L and Wang, J and Xue, Y and Liu, K and Zhang, F and Zhang, T}, title = {Nonpoint Source Pollution (NPSP) Induces Structural and Functional Variation in the Fungal Community of Sediments in the Jialing River, China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35419656}, issn = {1432-184X}, support = {19E061//Science Research Program of China West Normal University/ ; CJZDZYJ47//Environmental Protection Research Program of the Yangtze River/ ; 41907132//National Science Foundation of China/ ; }, abstract = {Nonpoint source pollution (NPSP) from human production and life activities causes severe destruction in river basin environments. In this study, three types of sediment samples (A, NPSP tributary samples; B, non-NPSP mainstream samples; C, NPSP mainstream samples) were collected at the estuary of the NPSP tributaries of the Jialing River. High-throughput sequencing of the fungal-specific internal transcribed spacer (ITS) gene region was used to identify fungal taxa. The impact of NPSP on the aquatic environment of the Jialing River was revealed by analysing the community structure, community diversity, and functions of sediment fungi. The results showed that the dominant phylum of sediment fungi was Rozellomycota, followed by Ascomycota and Basidiomycota (relative abundance > 5%). NPSP caused a significant increase in the relative abundances of Exosporium, Phialosimplex, Candida, Inocybe, Tausonia, and Slooffia, and caused a significant decrease in the relative abundances of Cercospora, Cladosporium, Dokmaia, Setophaeosphaeria, Paraphoma, Neosetophoma, Periconia, Plectosphaerella, Claviceps, Botrytis, and Papiliotrema. These fungal communities therefore have a certain indicator role. In addition, NPSP caused significant changes in the physicochemical properties of Jialing River sediments, such as pH and available nitrogen (AN), which significantly increased the species richness of fungi and caused significant changes in the fungal community β-diversity (P < 0.05). pH, total phosphorus (TP), and AN were the main environmental factors affecting fungal communities in sediments of Jialing River. The functions of sediment fungi mainly involved three types of nutrient metabolism (symbiotrophic, pathotrophic, and saprotrophic) and 75 metabolic circulation pathways. NPSP significantly improved the pentose phosphate pathway, pentose phosphate pathway, and fatty acid beta-oxidation V metabolic circulation pathway functions (P < 0.05) and inhibited the chitin degradation to ethanol, super pathway of heme biosynthesis from glycine, and adenine and adenosine salvage III metabolic circulation pathway functions (P < 0.05). Hence, NPSP causes changes in the community structure and functions of sediment fungi in Jialing River and has adversely affected for the stability of the Jialing River Basin ecosystem.}, }
@article {pmid35416682, year = {2022}, author = {Wu, J and Jiang, X and Yang, Q and Zhang, Y and Wang, C and Huang, R}, title = {Inhibition of Streptococcus mutans Biofilm Formation by the Joint Action of Oxyresveratrol and Lactobacillus casei.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0243621}, doi = {10.1128/aem.02436-21}, pmid = {35416682}, issn = {1098-5336}, abstract = {Microbial dysbiosis in dental plaque contributes to the occurrence of dental caries, to which Streptococcus mutans is a major contributor. Lactobacillus casei can be used as probiotic therapy to treat caries by replacing S. mutans within the dental plaque. However, the effects of probiotic treatment are not always stable. Oxyresveratrol (ORV), a plant-derived polyphenol, displays opposite effects in that it inhibits cariogenic and promotes commensal bacteria. Thus, the objectives of this study are to investigate the effects of ORV on bacterial proportions in S. mutans-L. casei biofilm and to elucidate how ORV weakens the competitiveness of S. mutans. Quantitative real-time PCR confirms a decreased S. mutans-L. casei ratio in dual-species biofilm by action of ORV. The culture supernatant of L. casei after being incubated with ORV (ORVLC) is prepared to explore the joint action of ORV and L. casei. ORVLC displays the strongest anti-biofilm effect against S. mutans when compared with the effects of L. casei supernatant or ORV alone. As a result of this treatment, both exopolysaccharides and bacteria contents in the biofilm are greatly reduced. The biofilm is transformed from water-insoluble glucan-dominant to water-soluble glucan-dominant by ORVLC through the modulation of the glycometabolism-related genes of S. mutans. As for the interactions between ORV and L. casei, ORV promotes L. casei to produce acetic acid, which provides L. casei with a competitive advantage against S. mutans. Taken together, ORV may be very suitable as an adjuvant medicine for probiotic therapy in the control of dental caries. IMPORTANCE The homeostatic imbalance in dental plaque associated with a sharp increase in the number of cariogenic bacteria such as Streptococcus mutans is critical for the occurrence and development of caries. Probiotic therapy can restore ecological balance by replacing cariogenic pathogens with probiotics. The current study innovatively finds that oxyresveratrol, a natural polyphenol, can provide probiotic Lactobacillus casei with competitive dominance in its dual-species biofilm with S. mutans. The joint action of oxyresveratrol and L. casei strongly inhibits the biofilm formation of S. mutans. Additionally, oxyresveratrol promotes L. casei to produce acetic acid, which facilitates L. casei to compete with S. mutans. Through the effects of these two mechanisms, oxyresveratrol leads to a significantly decreased S. mutans-L. casei ratio in their dual-species biofilm. Thus, oxyresveratrol is speculated to be an ideal medicine for the prevention and treatment of caries by regulating oral flora balance.}, }
@article {pmid35415771, year = {2022}, author = {Graça, D and Fernandes, I and Cássio, F and Pascoal, C}, title = {Eco-physiological Responses of Aquatic Fungi to Three Global Change Stressors Highlight the Importance of Intraspecific Trait Variability.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35415771}, issn = {1432-184X}, support = {PTDC/CTA-AMB/31245/2017//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/140761/2018//Fundação para a Ciência e a Tecnologia/ ; UIDB/04050/2020//Fundação para a Ciência e a Tecnologia/ ; }, abstract = {Anthropogenic change at a global scale is affecting life on Earth with impacts on freshwaters. Aquatic hyphomycetes are fungi that drive organic matter decomposition in freshwaters and mediate energy transfer to higher trophic levels. Intraspecific trait variability affects ecological processes and can account for species adaptations to environmental change. To ascertain how aquatic hyphomycetes respond to global change related stressors, we selected 20 strains (7 species), based on their co-occurrence in streams and phylogenetic relatedness. We measured fungal growth rates at different temperatures (7 levels), nutrient concentrations (6 levels) and medium moisture (6 levels). Our results indicate that all stressors affected fungal growth, and responses to nutrient enrichment and moisture were strain specific. Fungal responses to the stressors were not explained by their phylogenetic relatedness. In the absence of stressors, interspecific diversity best explained the variance in fungal traits, while the increase in the stress gradient increased the importance of intraspecific diversity.}, }
@article {pmid35414897, year = {2022}, author = {Suleiman, M and Pennekamp, F and Choffat, Y and Petchey, OL}, title = {Contrasting resistance and resilience to light variation of the coupled oxic and anoxic components of an experimental microbial ecosystem.}, journal = {Ecology and evolution}, volume = {12}, number = {4}, pages = {e8793}, doi = {10.1002/ece3.8793}, pmid = {35414897}, issn = {2045-7758}, abstract = {Understanding how microbial communities of aquatic ecosystems respond to environmental change remains a critical challenge in microbial ecology. In this study, we used light-dependent oxic-anoxic micro-ecosystems to understand how the functioning and diversity of aerobic and anaerobic lake analog communities are affected by a pulse light deprivation. Continuous measurements of oxygen concentration were made and a time series of full-length 16S rRNA sequencing was used to quantify changes in alpha- and beta diversity. In the upper oxic layer, oxygen concentration decreased significantly under light reduction, but showed resilience in daily mean, minimum, and maximum after light conditions were restored to control level. Only the amplitude of diurnal fluctuations in oxygen concentrations did not recover fully, and instead tended to remain lower in treated ecosystems. Alpha diversity of the upper oxic layer communities showed a delayed increase after light conditions were restored, and was not resilient in the longer term. In contrast, alpha diversity of the anoxic lower layer communities increased during the light reduction, but was resilient in the longer term. Community composition changed significantly during light reduction, and showed resilience in the oxic layer and lack of resilience in the anoxic layer. Alpha diversity and the amplitude of daily oxygen fluctuations within and among treatments were strongly correlated, suggesting that higher diversity could lead to less variable oxygen concentrations, or vice versa. Our experiment showed that light deprivation induces multifaceted responses of community function (oxygen respiration) and structure, hence focusing on a single stability component could potentially be misleading.}, }
@article {pmid35412096, year = {2022}, author = {Passarini, MRZ and Ottoni, JR and Costa, PEDS and Hissa, DC and Falcão, RM and Melo, VMM and Balbino, VQ and Mendonça, LAR and Lima, MGS and Coutinho, HDM and Verde, LCL}, title = {Fungal community diversity of heavy metal contaminated soils revealed by metagenomics.}, journal = {Archives of microbiology}, volume = {204}, number = {5}, pages = {255}, pmid = {35412096}, issn = {1432-072X}, support = {DCR-0024-01438.01.00/12//funcap/ ; }, abstract = {The inappropriate disposal of toxic compounds generated by industrial activity has been impacting the environment considerably. Microbial communities inhabiting contaminated sites may represent interesting ecological alternatives for the decontamination of environments. The present work aimed to investigate the fungal diversity and its functionality contained in stream sediments with industrial waste contaminated with heavy metals by using metagenomic approach. A total of 12 fungal orders were retrieved from datasets and, at phylum level, Ascomycota was the most abundant, followed by Basidiomycota, Chytridiomycota and Blastocladiomycota. Higher abundance of sequences was encountered within the less contaminated site, while the lower abundance was found in the sample with the higher contamination with lead. Gene sequences related to DNA repair and heavy metals biosorption processes were found in the four samples analyzed. The genera Aspergillus and Chaetomium, and Saccharomycetales order were highly present within all samples, showing their potential to be used for bioremediation studies. The present work demonstrated the importance of using the metagenomic approach to understand the dynamics and the possible metabolic pathways associated with fungal communities related to environmental samples containing heavy metals, as well as evidenced the importance of improving culturomics techniques for isolating strains with potential application in bioremediation processes of environments contaminated with heavy metals.}, }
@article {pmid35411306, year = {2022}, author = {Bibbal, D and Ruiz, P and Sapountzis, P and Mazuy-Cruchaudet, C and Loukiadis, E and Auvray, F and Forano, E and Brugère, H}, title = {Persistent Circulation of Enterohemorrhagic Escherichia coli (EHEC) O157:H7 in Cattle Farms: Characterization of Enterohemorrhagic Escherichia coli O157:H7 Strains and Fecal Microbial Communities of Bovine Shedders and Non-shedders.}, journal = {Frontiers in veterinary science}, volume = {9}, number = {}, pages = {852475}, doi = {10.3389/fvets.2022.852475}, pmid = {35411306}, issn = {2297-1769}, abstract = {Cattle are carriers, without clinical manifestations, of enterohemorrhagic Escherichia coli (EHEC) O157:H7 responsible for life-threatening infections in humans. A better identification of factors playing a role in maintaining persistence of such strains in cattle is required to develop more effective control measures. Hence, we conducted a study to identify farms with a persistent circulation of EHEC O157:H7. The EHEC O157:H7 herd status of 13 farms, which had previously provided bovine EHEC O157:H7 carriers at slaughter was investigated. Two farms were still housing positive young bulls, and this was true over a 1-year period. Only one fecal sample could be considered from a supershedder, and 60% of the carriers shed concentrations below 10 MPN/g. Moreover, EHEC O157:H7 represented minor subpopulations of E. coli. PFGE analysis of the EHEC O157:H7 strains showed that persistent circulation was due either to the persistence of a few predominant strains or to the repeated exposure of cattle to various strains. Finally, we compared fecal microbial communities of shedders (S) (n = 24) and non-shedders (NS) (n = 28), including 43 young bulls and nine cows, from one farm. Regarding alpha diversity, no significant difference between S vs. NS young bulls (n = 43) was observed. At the genus level, we identified 10 amplicon sequence variant (ASV) indicators of the S or NS groups. The bacterial indicators of S belonged to the family XIII UCG-001, Slackia, and Campylobacter genera, and Ruminococcaceae NK4A21A, Lachnospiraceae-UGC-010, and Lachnospiraceae-GCA-900066575 groups. The NS group indicator ASVs were affiliated to Pirellulaceae-1088-a5 gut group, Anaerovibrio, Victivallis, and Sellimonas genera. In conclusion, the characteristics enhancing the persistence of some predominant strains observed here should be explored further, and studies focused on mechanisms of competition among E. coli strains are also needed.}, }
@article {pmid35406804, year = {2022}, author = {Chidambaram, SB and Rathipriya, AG and Mahalakshmi, AM and Sharma, S and Hediyal, TA and Ray, B and Sunanda, T and Rungratanawanich, W and Kashyap, RS and Qoronfleh, MW and Essa, MM and Song, BJ and Monaghan, TM}, title = {The Influence of Gut Dysbiosis in the Pathogenesis and Management of Ischemic Stroke.}, journal = {Cells}, volume = {11}, number = {7}, pages = {}, doi = {10.3390/cells11071239}, pmid = {35406804}, issn = {2073-4409}, abstract = {Recent research on the gut microbiome has revealed the influence of gut microbiota (GM) on ischemic stroke pathogenesis and treatment outcomes. Alterations in the diversity, abundance, and functions of the gut microbiome, termed gut dysbiosis, results in dysregulated gut-brain signaling, which induces intestinal barrier changes, endotoxemia, systemic inflammation, and infection, affecting post-stroke outcomes. Gut-brain interactions are bidirectional, and the signals from the gut to the brain are mediated by microbially derived metabolites, such as trimethylamine N-oxide (TMAO) and short-chain fatty acids (SCFAs); bacterial components, such as lipopolysaccharide (LPS); immune cells, such as T helper cells; and bacterial translocation via hormonal, immune, and neural pathways. Ischemic stroke affects gut microbial composition via neural and hypothalamic-pituitary-adrenal (HPA) pathways, which can contribute to post-stroke outcomes. Experimental and clinical studies have demonstrated that the restoration of the gut microbiome usually improves stroke treatment outcomes by regulating metabolic, immune, and inflammatory responses via the gut-brain axis (GBA). Therefore, restoring healthy microbial ecology in the gut may be a key therapeutic target for the effective management and treatment of ischemic stroke.}, }
@article {pmid35404785, year = {2022}, author = {Ho, PY and Good, BH and Huang, KC}, title = {Competition for fluctuating resources reproduces statistics of species abundance over time across wide-ranging microbiotas.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, doi = {10.7554/eLife.75168}, pmid = {35404785}, issn = {2050-084X}, support = {F32 GM143859-01/NH/NIH HHS/United States ; R01 AI147023/NH/NIH HHS/United States ; NIH RM1 GM135102/NH/NIH HHS/United States ; FG-2021-15708//Alfred P. Sloan Foundation/ ; EF-2125383//National Science Foundation/ ; }, abstract = {Across diverse microbiotas, species abundances vary in time with distinctive statistical behaviors that appear to generalize across hosts, but the origins and implications of these patterns remain unclear. Here, we show that many of these macroecological patterns can be quantitatively recapitulated by a simple class of consumer-resource models, in which the metabolic capabilities of different species are randomly drawn from a common statistical distribution. Our model parametrizes the consumer-resource properties of a community using only a small number of global parameters, including the total number of resources, typical resource fluctuations over time, and the average overlap in resource-consumption profiles across species. We show that variation in these macroscopic parameters strongly affects the time series statistics generated by the model, and we identify specific sets of global parameters that can recapitulate macroecological patterns across wide-ranging microbiotas, including the human gut, saliva, and vagina, as well as mouse gut and rice, without needing to specify microscopic details of resource consumption. These findings suggest that resource competition may be a dominant driver of community dynamics. Our work unifies numerous time series patterns under a simple model, and provides an accessible framework to infer macroscopic parameters of effective resource competition from longitudinal studies of microbial communities.}, }
@article {pmid35403892, year = {2022}, author = {Marozzi, G and Benucci, GMN and Turchetti, B and Massaccesi, L and Baciarelli Falini, L and Bonito, G and Buzzini, P and Agnelli, A and Donnini, D and Albertini, E}, title = {Correction to: Fungal and Bacterial Diversity in the Tuber magnatum Ecosystem and Microbiome.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-022-02010-y}, pmid = {35403892}, issn = {1432-184X}, }
@article {pmid35403856, year = {2022}, author = {Yang, S and Li, L and Peng, X and Zhang, R and Song, L}, title = {Eukaryotic community composition and dynamics during solid waste decomposition.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {35403856}, issn = {1432-0614}, abstract = {Consortia of microbial community are involved in organic waste decomposition in municipal solid waste (MSW) landfill via competition, syntropy, and predation. Bacterial and archaeal community structure and function have been extensively studied in this process, whereas the eukaryotic community structure and function are largely unidentified. This gap stands for one of the fundamental researches of microbial ecology, that is, "what is the importance of variation in eukaryotic community structure and function to solid waste decomposition? The main idea of this work is to characterize changes in eukaryotic community composition and the associated driver during solid waste decomposition. Using high throughput sequencing targeting 18S rRNA genes, community composition and dynamics of eukaryotic during solid wasted decomposition were studied, as well as the differences with solid waste and leachate physiochemical parameters. Concomitant to the expected changes in physiochemical factors, eukaryotic community composition and diversity changed along solid waste decomposition indicated by aerobic phase (AP), anaerobic acid phase (ACP), and methanogenic phase (MP) and the structure was shaped by the nutrients (BOD5, total phosphorus, and nitrate) in leachate. Ascomycota, the predominant eukaryote, showed significant (p < 0.05) different structure among AP, ACP, and MP in phylum, genera, and species levels. Abundant Freshwater Opisthokonta was present in MP, suggesting a methane carbon cycling via grazing methane oxidation microorganism. Amoebozoa, Alveolata, Rhizaria, and Stramenopiles showed successional pattern during solid waste decomposition, indicating a short food chain establishment. Characterization on eukaryotic community composition and dynamics during solid waste decomposition are crucial for understanding of microbial consortia ecological function on solid waste decomposition and are also helpful for MSW management.Key points• Abundant Ascomycota significantly differed at AP, ACP, and MP.• Eukaryotic succession indicated a short food chain establishment.• Entire eukaryotic community structure was associated to nutrients in leachate.}, }
@article {pmid35402312, year = {2022}, author = {Nardos, R and Leung, ET and Dahl, EM and Davin, S and Asquith, M and Gregory, WT and Karstens, L}, title = {Network-Based Differences in the Vaginal and Bladder Microbial Communities Between Women With and Without Urgency Urinary Incontinence.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {759156}, doi = {10.3389/fcimb.2022.759156}, pmid = {35402312}, issn = {2235-2988}, mesh = {Bacteria/genetics ; Female ; Humans ; Lactobacillus/genetics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Urinary Bladder/microbiology ; *Urinary Incontinence/microbiology ; Vagina/microbiology ; }, abstract = {Background: Little is known about the relationship of proximal urogenital microbiomes in the bladder and the vagina and how this contributes to bladder health. In this study, we use a microbial ecology and network framework to understand the dynamics of interactions/co-occurrences of bacteria in the bladder and vagina in women with and without urgency urinary incontinence (UUI).<br><br>Methods: We collected vaginal swabs and catheterized urine specimens from 20 women with UUI (cases) and 30 women without UUI (controls). We sequenced the V4 region of the bacterial 16S rRNA gene and evaluated using alpha and beta diversity metrics. We used microbial network analysis to detect interactions in the microbiome and the betweenness centrality measure to identify central bacteria in the microbial network. Bacteria exhibiting maximum betweenness centrality are considered central to the microbe-wide networks and likely maintain the overall microbial network structure.<br><br>Results: There were no significant differences in the vaginal or bladder microbiomes between cases and controls using alpha and beta diversity. Silhouette metric analysis identified two distinct microbiome clusters in both the bladder and vagina. One cluster was dominated by Lactobacillus genus while the other was more diverse. Network-based analyses demonstrated that vaginal and bladder microbial networks were different between cases and controls. In the vagina, there were similar numbers of genera and subgroup clusters in each network for cases and controls. However, cases tend to have more unique bacterial co-occurrences. While Bacteroides and Lactobacillus were the central bacteria with the highest betweenness centrality in controls, Aerococcus had the highest centrality in cases and correlated with bacteria commonly associated with bacterial vaginosis. In the bladder, cases have less than half as many network clusters compared to controls. Lactobacillus was the central bacteria in both groups but associated with several known uropathogens in cases. The number of shared bacterial genera between the bladder and the vagina differed between cases and controls, with cases having larger overlap (43%) compared to controls (29%).<br><br>Conclusion: Our study shows overlaps in microbial communities of bladder and vagina, with higher overlap in cases. We also identified differences in the bacteria that are central to the overall community structure.}, }
@article {pmid35396623, year = {2022}, author = {Koide, RT}, title = {On Holobionts, Holospecies, and Holoniches: the Role of Microbial Symbioses in Ecology and Evolution.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35396623}, issn = {1432-184X}, abstract = {My goal in writing this is to increase awareness of the roles played by microbial symbionts in eukaryote ecology and evolution. Most eukaryotes host one or more species of symbiotic microorganisms, including prokaryotes and fungi. Many of these have profound impacts on the biology of their hosts. For example, microbial symbionts may expand the niches of their hosts, cause rapid adaptation of the host to the environment and re-adaptation to novel conditions via symbiont swapping, facilitate speciation, and fundamentally alter our concept of the species. In some cases, microbial symbionts and multicellular eukaryote hosts have a mutual dependency, which has obvious conservation implications. Hopefully, this contribution will stimulate a reevaluation of important ecological and evolutionary concepts including niche, adaptation, the species, speciation, and conservation of multicellular eukaryotes.}, }
@article {pmid35395701, year = {2022}, author = {van der Loos, LM and D'Hondt, S and Engelen, AH and Pavia, H and Toth, GB and Willems, A and Weinberger, F and De Clerck, O and Steinhagen, S}, title = {Salinity and host drive Ulva associated bacterial communities across the Atlantic-Baltic Sea gradient.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16462}, pmid = {35395701}, issn = {1365-294X}, abstract = {The green seaweed Ulva is a model system to study seaweed-bacteria interactions, but the impact of environmental drivers on the dynamics of these interactions is little understood. In this study, we investigated the stability and variability of the seaweed-associated bacteria across the Atlantic-Baltic Sea salinity gradient. We characterised the bacterial communities of 15 Ulva sensu lato species along 2000 km coastline in a total of 481 samples. Our results demonstrate that Ulva-associated bacterial composition was strongly structured by both salinity and host species (together explaining between 34-91% of the variation in the abundance of the different bacterial genera). The largest shift in the bacterial consortia coincided with the horohalinicum (5-8 PSU, known as the transition zone from freshwater to marine conditions). Low salinity communities especially contained high relative abundances of Luteolibacter, Cyanobium, Pirellula, Lacihabitans and an uncultured Spirosomaceae, whereas high salinity communities were predominantly enriched in Litorimonas, Leucothrix, Sulfurovum, Algibacter, and Dokdonia. We identified a small taxonomic core community (consisting of Paracoccus, Sulfitobacter, and an uncultured Rhodobacteraceae), which together contributed to 14% of the reads per sample, on average. Additional core taxa followed a gradient model, as more core taxa were shared between neighbouring salinity ranges than between ranges at opposite ends of the Atlantic-Baltic Sea gradient. Our results contradict earlier statements that Ulva-associated bacterial communities are taxonomically highly variable across individuals and largely stochastically defined. Characteristic bacterial communities associated with distinct salinity regions may therefore facilitate the host's adaptation across the environmental gradient.}, }
@article {pmid35394422, year = {2022}, author = {Meyer, BH and Adam, PS and Wagstaff, BA and Kolyfetis, GE and Probst, AJ and Albers, SV and Dorfmueller, HC}, title = {Agl24 is an ancient archaeal homolog of the eukaryotic N-glycan chitobiose synthesis enzymes.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, doi = {10.7554/eLife.67448}, pmid = {35394422}, issn = {2050-084X}, support = {109357/Z/15/Z//The Wellcome Trust and Royal Society Grant/ ; 403222702-SFB 1381//SFG/ ; Nachwuchsgruppe Dr. Alexander Probst//Ministerium für Kultur und Wissenschaft des Landes Nordrhein-Westfalen/ ; Postdoctoral fellowship//Alexander von Humboldt Foundation/ ; }, abstract = {Protein N-glycosylation is a post-translational modification found in organisms of all domains of life. The crenarchaeal N-glycosylation begins with the synthesis of a lipid-linked chitobiose core structure, identical to that in Eukaryotes, although the enzyme catalyzing this reaction remains unknown. Here, we report the identification of a thermostable archaeal β-1,4-N-acetylglucosaminyltransferase, named archaeal glycosylation enzyme 24 (Agl24), responsible for the synthesis of the N-glycan chitobiose core. Biochemical characterization confirmed its function as an inverting β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol glycosyltransferase. Substitution of a conserved histidine residue, found also in the eukaryotic and bacterial homologs, demonstrated its functional importance for Agl24. Furthermore, bioinformatics and structural modeling revealed similarities of Agl24 to the eukaryotic Alg14/13 and a distant relation to the bacterial MurG, which are catalyzing the same or a similar reaction, respectively. Phylogenetic analysis of Alg14/13 homologs indicates that they are ancient in Eukaryotes, either as a lateral transfer or inherited through eukaryogenesis.}, }
@article {pmid35389344, year = {2022}, author = {Villanueva, EMF and Lim, PK and Lim, JJJ and Lim, SC and Lau, PY and Koh, KTS and Tan, E and Kairon, RS and See, WA and Liao, JX and Hee, KM and Vijay, V and Maitra, I and Boon, CJ and Fo, K and Wang, YT and Jaya, R and Hew, LA and Lim, YY and Lee, WQ and Lee, ZQ and Foo, H and Dos Santos, AL and Mutwil, M}, title = {Protist.guru: A Comparative Transcriptomics Database for Protists.}, journal = {Journal of molecular biology}, volume = {}, number = {}, pages = {167502}, doi = {10.1016/j.jmb.2022.167502}, pmid = {35389344}, issn = {1089-8638}, abstract = {During the last few decades, the study of microbial ecology has been enabled by molecular and genomic data. DNA sequencing has revealed the surprising extent of microbial diversity and how microbial processes run global ecosystems. However, significant gaps in our understanding of the microbial world remain, and one example is that microbial eukaryotes, or protists, are still largely neglected. To address this gap, we used gene expression data from 17 protist species to create protist.guru: an online database equipped with tools for identifying co-expressed genes, gene families, and co-expression clusters enriched for specific biological functions. Here, we show how our database can be used to reveal genes involved in essential pathways, such as the synthesis of secondary carotenoids in Haematococcus lacustris. We expect protist.guru to serve as a valuable resource for protistologists, as well as a catalyst for discoveries and new insights into the biological processes of microbial eukaryotes. AVAILABILITY: The database and co-expression networks are freely available from http://protist.guru/. The expression matrices and sample annotations are found in the supplementary data.}, }
@article {pmid35389249, year = {2022}, author = {Ramond, JB and Jordaan, K and Díez, B and Heinzelmann, SM and Cowan, DA}, title = {Microbial Biogeochemical Cycling of Nitrogen in Arid Ecosystems.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {}, number = {}, pages = {e0010921}, doi = {10.1128/mmbr.00109-21}, pmid = {35389249}, issn = {1098-5557}, abstract = {Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N2O), a potent greenhouse gas.}, }
@article {pmid35389085, year = {2022}, author = {Steinigeweg, C and Alkassab, AT and Erler, S and Beims, H and Wirtz, IP and Richter, D and Pistorius, J}, title = {Impact of a Microbial Pest Control Product Containing Bacillus thuringiensis on Brood Development and Gut Microbiota of Apis mellifera Worker Honey Bees.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35389085}, issn = {1432-184X}, abstract = {To avoid potential adverse side effects of chemical plant protection products, microbial pest control products (MPCP) are commonly applied as biological alternatives. This study aimed to evaluate the biosafety of a MPCP with the active organism Bacillus thuringiensis ssp. aizawai (strain: ABTS-1857). An in-hive feeding experiment was performed under field-realistic conditions to examine the effect of B. thuringiensis (B. t.) on brood development and the bacterial abundance of the core gut microbiome (Bifidobacterium asteroids, Gilliamella apicola, the group of Lactobacillus and Snodgrasella alvi) in Apis mellifera worker bees. We detected a higher brood termination rate and a non-successful development into worker bees of treated colonies compared to those of the controls. For the gut microbiome, all tested core members showed a significantly lower normalized abundance in bees of the treated colonies than in those of the controls; thus, a general response of the gut microbiome may be assumed. Consequently, colony exposure to B. t. strain ABTS-1857 had a negative effect on brood development under field-realistic conditions and caused dysbiosis of the gut microbiome. Further studies with B. t.-based products, after field-realistic application in bee attractive crops, are needed to evaluate the potential risk of these MPCPs on honey bees.}, }
@article {pmid35388893, year = {2022}, author = {Águila, B and Yanez-Montalvo, A and Mercado-Juárez, RA and Montejano, GA and Becerra-Absalón, I and Falcón, LI}, title = {Microbialites show a distinct cyanobacterial phylogenetic structure and functional redundancy in Bacalar lagoon and Cenote Azul sinkhole, Yucatan peninsula, Mexico.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiac039}, pmid = {35388893}, issn = {1574-6941}, abstract = {Cyanobacterial components of microbialites from two geographically close systems, the Bacalar lagoon (BL) and the Cenote Azul sinkhole (CA) in Quintana Roo, Mexico, were characterized. BL and CA systems were studied along a longitudinal gradient (north to south) and a depth gradient (5 to 30 m), respectively. Microscopic observations, 16S rRNA amplicon sequencing, and shotgun metagenomics were used to characterize Cyanobacteria. Both systems showed similar metabolic/functional profiles but harbored completely different cyanobacterial taxa. BL was dominated by Nostocales, including a population of previously undescribed Chakia sp., while CA was dominated by an unknown taxon of Chroococcales, comprising 70% of relative abundance through all depths. Interestingly, cyanobacterial assemblages in microbialites exhibited phylogenetic overdispersion in most of the BL sites, while CA sites exhibited phylogenetic clustering, these differences were attributed to depth/light conditions and possibly different times of geological formation for BL and CA systems.}, }
@article {pmid35388110, year = {2022}, author = {Zhang, S and Yang, Q and Fu, S and Janssen, CR and Eggermont, M and Defoirdt, T}, title = {Indole decreases the virulence of the bivalve model pathogens Vibrio tasmaniensis LGP32 and Vibrio crassostreae J2-9.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {5749}, pmid = {35388110}, issn = {2045-2322}, support = {1500219N//Fonds Wetenschappelijk Onderzoek/ ; }, abstract = {Indole signaling plays an important role in bacterial pathogenesis. In this study, the impact of indole on biofilm formation, swimming and swarming motility were explored in Vibrio tasmaniensis LGP32 and Vibrio crassostreae J2-9, two model pathogens of bivalves. The results showed that indole decreased swimming and swarming motility in both strains, and decreased biofilm formation in V. crassostreae J2-9. Furthermore, indole affected a large number of genes at RNA level, including genes related to metabolism, ABC transporters, flagellar assembly, chemotaxis, and response regulators. Finally, the bacterial virulence towards mussel larvae was decreased by pretreatment with indole in both V. tasmaniensis LGP32 and V. crassostreae J2-9. After 5 days, the survival rate of mussel larvae increased 2.4-fold and 2.8-fold in mussel larvae challenged with V. tasmaniensis LGP32 pretreated with 200 µM and 500 µM indole, respectively. The survival rate of mussel larvae increased 1.5-fold and 1.9-fold in mussel larvae challenged with V. crassostreae J2-9 pretreated with 200 µM and 500 µM indole, respectively. These data indicate that indole has a significant impact on the virulence of V. tasmaniensis LGP32 and V. crassostreae J2-9, and indole signaling could be a promising target for antivirulence therapy.}, }
@article {pmid35388078, year = {2022}, author = {Wahl, A and Huptas, C and Neuhaus, K}, title = {Comparison of rRNA depletion methods for efficient bacterial mRNA sequencing.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {5765}, pmid = {35388078}, issn = {2045-2322}, support = {1401/1-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Current methods of high-throughput RNA sequencing of prokaryotes, including transcriptome analysis or ribosomal profiling, need deep sequencing to achieve sufficient numbers of effective reads (e.g., mapping to mRNA) in order to also find weakly expressed genetic elements. The fraction of high-quality reads mapping to coding RNAs (i.e., mRNA) is mainly influenced by the large content of rRNA and, to a lesser extent, tRNA in total RNA. Thus, depletion of rRNA increases coverage and thus sequencing costs. RiboZero, a depletion kit based on probe hybridisation and rRNA-removal was found to be most efficient in the past, but it was discontinued in 2018. To facilitate comparability with previous experiments and to help choose adequate replacements, we compare three commercially available rRNA depletion kits also based on hybridization and magnetic beads, i.e., riboPOOLs, RiboMinus and MICROBExpress, with the former RiboZero. Additionally, we constructed biotinylated probes for magnetic bead capture and rRNA depletion in this study. Based on E. coli, we found similar efficiencies in rRNA depletion for riboPOOLs and the self-made depletion method; both comparable to the former RiboZero, followed by RiboMinus, succeeded by MICROBExpress. Further, our in-house protocol allows customized species-specific rRNA or even tRNA depletion or depletion of other RNA targets. Both, the self-made biotinylated probes and riboPOOLs, were most successful in reducing the rRNA content and thereby increasing sequencing depth concerning mRNA reads. Additionally, the number of reads matching to weakly expressed genes are increased. In conclusion, the self-made specific biotinylated probes and riboPOOLs are an adequate replacement for the former RiboZero. Both are very efficient in depleting rRNAs, increasing mRNA reads and thus sequencing efficiency.}, }
@article {pmid35388041, year = {2022}, author = {Dwużnik-Szarek, D and Mierzejewska, EJ and Kiewra, D and Czułowska, A and Robak, A and Bajer, A}, title = {Update on prevalence of Babesia canis and Rickettsia spp. in adult and juvenile Dermacentor reticulatus ticks in the area of Poland (2016-2018).}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {5755}, pmid = {35388041}, issn = {2045-2322}, support = {2014/14/E/NZ7/00153//Narodowe Centrum Nauki/ ; }, abstract = {Ornate dog tick, Dermacentor reticulatus is an important vector of Babesia canis, and Rickettsia spp. and other pathogens of veterinary and public health interest. The current study is the first to investigate the long-term changes in prevalence of these pathogens in expanding tick populations in Central Europe. Molecular techniques (PCR, sequencing) were applied for the detection of pathogen DNA in adult (n = 2497) and juvenile ticks (1096 larvae and 410 nymphs). DNA of Rickettsia spp. was identified in 35% of adults and 12.6% of juvenile ticks. DNA of B. canis was detected in 3% of adult ticks and only in ticks from the Eastern region (regional prevalence 6%). As previously, no B. canis-positive ticks were found in Western Poland, including ticks from Wrocław area (n = 298). DNA of B. canis was identified in 0.33% of juvenile ticks (in 3 pools of larvae and 2 nymphs) from the Eastern region. In the current study we confirmed high occurrence of R. raoultii in adults ticks from all four zones and relatively high prevalence of B. canis in the Eastern population of D. reticulatus, corresponding well with high incidence of canine babesiosis in this area of Poland. Finally, we confirmed R. raoultii and B. canis infection in all life stages of D. reticulatus ticks.}, }
@article {pmid35385973, year = {2022}, author = {Alba, C and Sansano-Maestre, J and Cid Vázquez, MD and Martínez-Herrero, MDC and Garijo-Toledo, MM and Azami-Conesa, I and Moraleda Fernández, V and Gómez-Muñoz, MT and Rodríguez, JM}, title = {Captive Breeding and Trichomonas gallinae Alter the Oral Microbiome of Bonelli's Eagle Chicks.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35385973}, issn = {1432-184X}, support = {Grant PR26/16-20328//Santander-UCM/ ; LIFE12 NAT/ES/000701-Integral recovery of Bonelli's eagle population in Spain//LIFE programme/ ; ACIF/2013/055//Conselleria d'Educació, Investigació, Cultura i Esport/ ; }, abstract = {Bonelli's eagle (Aquila fasciata) is an endangered raptor species in Europe, and trichomonosis is one of the menaces affecting chicks at nest. In this paper, we attempt to describe the oral microbiome of Bonelli's eagle nestlings and evaluate the influence of several factors, such as captivity breeding, Trichomonas gallinae infection, and the presence of lesions at the oropharynx. The core oral microbiome of Bonelli's eagle is composed of Firmicutes, Bacteroidota, Fusobacteria and Proteobacteria as the most abundant phyla, and Megamonas and Bacteroides as the most abundant genera. None of the factors analysed showed a significant influence on alfa diversity, but beta diversity was affected for some of them. Captivity breeding exerted a high influence on the composition of the oral microbiome, with significant differences in the four most abundant phyla, with a relative increase of Proteobacteria and a decrease of the other three phyla in comparison with chicks bred at nest. Some genera were more abundant in captivity bred chicks, such as Escherichia-Shigella, Enterococcus, Lactobacillus, Corynebacterium, Clostridium and Staphylococcus, while Bacteroides, Oceanivirga, Peptostreptococcus, Gemella, Veillonella, Mycoplasma, Suttonella, Alloscardovia, Varibaculum and Campylobacter were more abundant in nest raised chicks. T. gallinae infection slightly influenced the composition of the microbiome, but chicks displaying trichomonosis lesions had a higher relative abundance of Bacteroides and Gemella, being the last one an opportunistic pathogen of abscess complications in humans. Raptor's microbiomes are scarcely studied. This is the first study on the factors that influence the oral microbiome of Bonelli's eagle.}, }
@article {pmid35384214, year = {2022}, author = {Régimbeau, A and Budinich, M and Larhlimi, A and Pierella Karlusich, JJ and Aumont, O and Memery, L and Bowler, C and Eveillard, D}, title = {Contribution of genome-scale metabolic modelling to niche theory.}, journal = {Ecology letters}, volume = {}, number = {}, pages = {}, doi = {10.1111/ele.13954}, pmid = {35384214}, issn = {1461-0248}, support = {//Fonds Français pour l'Environnement Mondial/ ; 80 PRIME//Centre National de la Recherche Scientifique/ ; ANR-10-LABX-54//MEMO LIFE/ ; ANR-19-CE20-0020//BrownCut/ ; ANR-11-IDEX-0001-02//Université de Recherche Paris Sciences et Lettres/ ; 835067//H2020 Environment/ ; 862923//H2020 Environment/ ; ANR-10-INBS-09-08//OCEANOMICS/ ; ANR-10-INBS-09-08//FRANCE GENOMIQUE/ ; }, abstract = {Standard niche modelling is based on probabilistic inference from organismal occurrence data but does not benefit yet from genome-scale descriptions of these organisms. This study overcomes this shortcoming by proposing a new conceptual niche that resumes the whole metabolic capabilities of an organism. The so-called metabolic niche resumes well-known traits such as nutrient needs and their dependencies for survival. Despite the computational challenge, its implementation allows the detection of traits and the formal comparison of niches of different organisms, emphasising that the presence-absence of functional genes is not enough to approximate the phenotype. Further statistical exploration of an organism's niche sheds light on genes essential for the metabolic niche and their role in understanding various biological experiments, such as transcriptomics, paving the way for incorporating better genome-scale description in ecological studies.}, }
@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 = {}, doi = {10.7554/eLife.76970}, pmid = {35380107}, issn = {2050-084X}, support = {GBMF#9324//Gordon and Betty Moore Foundation/ ; GBMF#9324//Gordon and Betty Moore Foundation/ ; imons Early Career Investigator in Marine Microbial Ecology and Evolution Award (822981)//Simons Foundation/ ; imons Early Career Investigator in Marine Microbial Ecology and Evolution Award (822981)//Simons Foundation/ ; Packard Fellowships for Science and Engineering//David and Lucile Packard Foundation/ ; Searle Scholars Program//Searle Scholars Program/ ; Beckman Young Investigator Program//Arnold and Mabel Beckman Foundation/ ; }, 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 {pmid35379841, year = {2022}, author = {Saeed, M and Rais, M and Akram, A and Williams, MR and Kellner, KF and Hashsham, SA and Davis, DR}, title = {Development and validation of an eDNA protocol for monitoring endemic Asian spiny frogs in the Himalayan region of Pakistan.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {5624}, pmid = {35379841}, issn = {2045-2322}, support = {8566//Higher Education Commision, Pakistan/ ; 3170//Higher Education Commision, Pakistan/ ; }, abstract = {Wildlife monitoring programs are instrumental for the assessment of species, habitat status, and for the management of factors affecting them. This is particularly important for species found in freshwater ecosystems, such as amphibians, as they have higher estimated extinction rates than terrestrial species. We developed and validated two species-specific environmental DNA (eDNA) protocols and applied them in the field to detect the Hazara Torrent Frog (Allopaa hazarensis) and Murree Hills Frog (Nanorana vicina). Additionally, we compared eDNA surveys with visual encounter surveys and estimated site occupancy. eDNA surveys resulted in higher occurrence probabilities for both A. hazarensis and N. vicina than for visual encounter surveys. Detection probability using eDNA was greater for both species, particularly for A. hazarensis. The top-ranked detection model for visual encounter surveys included effects of both year and temperature on both species, and the top-ranked occupancy model included effects of elevation and year. The top-ranked detection model for eDNA data was the null model, and the top-ranked occupancy model included effects of elevation, year, and wetland type. To our knowledge, this is the first time an eDNA survey has been used to monitor amphibian species in the Himalayan region.}, }
@article {pmid35378966, year = {2022}, author = {Liu, X and Lu, S and Shao, Y and Zhang, D and Tu, J and Chen, J}, title = {Disorders of gut microbiota in children with Tetralogy of Fallot.}, journal = {Translational pediatrics}, volume = {11}, number = {3}, pages = {385-395}, doi = {10.21037/tp-22-33}, pmid = {35378966}, issn = {2224-4344}, abstract = {Background: Gut microbiota plays an important role in cardiovascular health and disease, including congenital heart disease (CHD). Tetralogy of Fallot (TOF) is the most common form of cyanotic CHD characterized by systemic chronic hypoxia and sustained pressure overload of the right ventricle. It is well-known that hypoxia and pressure overload can affect gut microbiota. However, the effects of TOF on the gut microbiota remain little understood. This study explored the profile of the gut microbiota in children with unrepaired TOF.<br><br>Methods: A total of 12 pediatric patients diagnosed with TOF and 9 healthy age- and gender-matched children were enrolled in this study. Fecal samples were collected from every participant and subjected to 16S rDNA gene sequencing. The raw sequencing data were processed using the Quantitative Insights Into Microbial Ecology pipeline.<br><br>Results: A comparison of the gut microbiota revealed that pediatric patients with TOF had developed dysbiosis as reflected by the altered taxonomic composition and impaired functional profile. A total of 14 indicative bacterial genera were identified as differential biomarkers capable of distinguishing between healthy children and TOF patients. Furthermore, functional annotations revealed that the gut microbiota in TOF patients was characterized by increased levels of inflammatory, oxidative, and immune responses, and decreased activities of adaptation, synthesis, and metabolism.<br><br>Conclusions: Pediatric patients with unrepaired TOF have intestinal dysbacteriosis that is characterized by altered taxonomic composition and impaired functional profile. These findings suggested that the interplay between gut microbiota and the host may be dysregulated in patients with TOF.}, }
@article {pmid35378620, year = {2022}, author = {Kerfahi, D and Harvey, BP and Kim, H and Yang, Y and Adams, JM and Hall-Spencer, JM}, title = {Whole community and functional gene changes of biofilms on marine plastic debris in response to ocean acidification.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35378620}, issn = {1432-184X}, abstract = {Plastics are accumulating in the world's oceans, while ocean waters are becoming acidified by increased CO2. We compared metagenome of biofilms on tethered plastic bottles in subtidal waters off Japan naturally enriched in CO2, compared to normal ambient CO2 levels. Extending from an earlier amplicon study of bacteria, we used metagenomics to provide direct insights into changes in the full range of functional genes and the entire taxonomic tree of life in the context of the changing plastisphere. We found changes in the taxonomic community composition of all branches of life. This included a large increase in diatom relative abundance across the treatments but a decrease in diatom diversity. Network complexity among families decreased with acidification, showing overall simplification of biofilm integration. With acidification, there was decreased prevalence of genes associated with cell-cell interactions and antibiotic resistance, decreased detoxification genes, and increased stress tolerance genes. There were few nutrient cycling gene changes, suggesting that the role of plastisphere biofilms in nutrient processes within an acidified ocean may not change greatly. Our results suggest that as ocean CO2 increases, the plastisphere will undergo broad-ranging changes in both functional and taxonomic composition, especially the ecologically important diatom group, with possible wider implications for ocean ecology.}, }
@article {pmid35377164, year = {2022}, author = {Gorski, L and Cooley, MB and Oryang, D and Carychao, D and Nguyen, K and Luo, Y and Weinstein, L and Brown, E and Allard, M and Mandrell, RE and Chen, Y}, title = {Prevalence and Clonal Diversity of over 1,200 Listeria monocytogenes Isolates Collected from Public Access Waters near Produce Production Areas on the Central California Coast during 2011 to 2016.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0035722}, doi = {10.1128/aem.00357-22}, pmid = {35377164}, issn = {1098-5336}, abstract = {A 5-year survey of public access surface waters in an agricultural region of the Central California Coast was done to assess the prevalence of the foodborne pathogen Listeria monocytogenes. In nature, L. monocytogenes lives as a saprophyte in soil and water, which are reservoirs for contamination of preharvest produce. Moore swabs were deployed biweekly in lakes, ponds, streams, and rivers during 2011 to 2016. L. monocytogenes was recovered in 1,224 of 2,922 samples, resulting in 41.9% prevalence. Multiple subtypes were isolated from 97 samples, resulting in 1,323 L. monocytogenes isolates. Prevalence was higher in winter and spring and after rain events in some waterways. Over 84% of the isolates were serotype 4b. Whole-genome sequencing was done on 1,248 isolates, and in silico multilocus sequence typing revealed 74 different sequence types (STs) and 39 clonal complexes (CCs). The clones most isolated, CC639, CC183, and CC1, made up 27%, 19%, and 13%, respectively, of the sequenced isolates. Other types were CC663, CC6, CC842, CC4, CC2, CC5, and CC217. All sequenced isolates contained intact copies of core L. monocytogenes virulence genes, and pathogenicity islands LIPI-3 and LIPI-4 were identified in 73% and 63%, respectively, of the sequenced isolates. The virulence factor internalin A was predicted to be intact in all but four isolates, while genes important for sanitizer and heavy metal resistance were found in <5% of the isolates. These waters are not used for crop irrigation directly, but they are available to wildlife and can flood fields during heavy rains. IMPORTANCE Listeria monocytogenes serotype 4b and 1/2a strains are implicated in most listeriosis, and hypervirulent listeriosis stems from strains containing pathogenicity islands LIPI-3 and LIPI-4. The waters and sediments in the Central California Coast agricultural region contain widespread and diverse L. monocytogenes populations, and all the isolates contain intact virulence genes. Emerging clones CC183 and CC639 were the most abundant clones, and major clones CC1, CC4, and CC6 were well represented. CC183 was responsible for three produce-related outbreaks in the last 7 years. Most of the isolates in the survey differ from those of lesser virulence that are often isolated from foods and food processing plants because they contain genes encoding an intact virulence factor, internalin A, and most did not contain genes for sanitizer and heavy metal resistance. This isolate collection is important for understanding L. monocytogenes populations in agricultural and natural regions.}, }
@article {pmid35372103, year = {2022}, author = {Halaweish, HF and Boatman, S and Staley, C}, title = {Encapsulated Fecal Microbiota Transplantation: Development, Efficacy, and Clinical Application.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {826114}, doi = {10.3389/fcimb.2022.826114}, pmid = {35372103}, issn = {2235-2988}, abstract = {Fecal microbiota transplantation (FMT) has been established as a highly restorative therapeutic approach for treating recurrent Clostridioides difficile infection (rCDI). Recently, the use of capsule-based fecal microbiota transplantation (cFMT) has been shown to be a clinically effective approach to restore intestinal microbiota composition. This convenient, oral delivery provides an easy route of administration and a newfound flexibility for clinicians and patients. In this review, we discuss the development of cFMT, paying particular attention to lyophilized cFMT products. We review the available published clinical studies comparing cFMT with lower endoscopic FMT (eFMT) or placebo. We further discuss the pharmacokinetics of FMT, which should be understood in a framework of microbial ecology that considers the complex and dynamic interactions of gut microbiota with host factors and other microorganisms. Promisingly, the results of multiple trials investigating cFMT vs. eFMT in rCDI show cFMT to be as effective as eFMT at preventing rCDI. However, its efficacy in non-rCDI conditions, including obesity and metabolic syndrome, inflammatory bowel disease, HIV, and neurologic conditions, is less clear and more research is needed in these areas. Standardization of formulation, dose, and timing of administration to ensure optimal microbiota engraftment and clinical response is also a challenge to be addressed. Overall, cFMT is a practical method for fecal microbiota transplantation, with similar efficacy to eFMT in the resolution of rCDI, that holds therapeutic potential in a variety of other diseases.}, }
@article {pmid35370685, year = {2022}, author = {Spisni, E and Turroni, S and Alvisi, P and Spigarelli, R and Azzinnari, D and Ayala, D and Imbesi, V and Valerii, MC}, title = {Nutraceuticals in the Modulation of the Intestinal Microbiota: Current Status and Future Directions.}, journal = {Frontiers in pharmacology}, volume = {13}, number = {}, pages = {841782}, doi = {10.3389/fphar.2022.841782}, pmid = {35370685}, issn = {1663-9812}, abstract = {Pharmaceutical interest in the human intestinal microbiota has increased considerably, because of the increasing number of studies linking the human intestinal microbial ecology to an increasing number of non-communicable diseases. Many efforts at modulating the gut microbiota have been made using probiotics, prebiotics and recently postbiotics. However, there are other, still little-explored opportunities from a pharmaceutical point of view, which appear promising to obtain modifications of the microbiota structure and functions. This review summarizes all in vitro, in vivo and clinical studies demonstrating the possibility to positively modulate the intestinal microbiota by using probiotics, prebiotics, postbiotics, essential oils, fungus and officinal plants. For the future, clinical studies investigating the ability to impact the intestinal microbiota especially by using fungus, officinal and aromatic plants or their extracts are required. This knowledge could lead to effective microbiome modulations that might support the pharmacological therapy of most non-communicable diseases in a near future.}, }
@article {pmid35370677, year = {2022}, author = {Liu, L and Lu, Y and Xu, C and Chen, H and Wang, X and Wang, Y and Cai, B and Li, B and Verstrepen, L and Ghyselinck, J and Marzorati, M and Yao, Q}, title = {The Modulation of Chaihu Shugan Formula on Microbiota Composition in the Simulator of the Human Intestinal Microbial Ecosystem Technology Platform and its Influence on Gut Barrier and Intestinal Immunity in Caco-2/THP1-Blue™ Cell Co-Culture Model.}, journal = {Frontiers in pharmacology}, volume = {13}, number = {}, pages = {820543}, doi = {10.3389/fphar.2022.820543}, pmid = {35370677}, issn = {1663-9812}, abstract = {The traditional Chinese medicine (TCM)-Chaihu Shugan Formula (CSF), consisting of several Chinese botanical drugs like Bupleurum, is derived from the ancient Chinese pharmacopeia. It has been used for more than thousands of years in various suboptimal health statuses and diseases induced by chronic stress based on empirical therapy. Recent studies confirm the role of CSF in the development of many diseases, including depression, stress-induced hepatic injury and tumors. However, little has been known about the mechanisms behind the health effects of CSF. Here, we investigate the influence of CSF on the modulation of the simulated colonic microbiota of five healthy donors, gut barrier integrity, and intestinal immunity by combining the simulator of the human intestinal microbial ecosystem (SHIME®) technology platform with co-culture of intestinal and immune cells. This approach revealed that CSF stimulated the production of SCFA (acetate, propionate and butyrate) across donors while significantly lowering the production of branched SCFA (bSCFA). In terms of community composition, CSF stimulated a broad spectrum of health-related Bifidobacterium species, which are potent acetate and lactate producers. At the same time, it lowered the abundance of opportunistic pathogenic Escherichia coli. Later, we explore the effect of colonic fermentation of CSF on the gut barrier and intestinal immunity in the Caco-2/THP1-blue™ cell co-culture model. Based on the study using SHIME technology platform, CSF showed protective effects on inflammation-induced intestinal epithelial barrier disruption in all donors. Also, the treatment of CSF showed pronounced anti-inflammatory properties by strongly inducing anti-inflammatory cytokines IL-6 and IL-10 and reducing pro-inflammatory cytokine TNF-α. These findings demonstrate a significant modulatory effect of CSF on intestinal gut microbiota. CSF-microbial fermentation products improved the gut barrier and controlled intestinal inflammation.}, }
@article {pmid35367883, year = {2022}, author = {Zhu, M and Duan, X and Zeng, Q and Liu, Y and Qiu, Z}, title = {He-Ne laser irradiation ameliorates cadmium toxicity in wheat by modulating cadmium accumulation, nutrient uptake and antioxidant defense system.}, journal = {Ecotoxicology and environmental safety}, volume = {236}, number = {}, pages = {113477}, doi = {10.1016/j.ecoenv.2022.113477}, pmid = {35367883}, issn = {1090-2414}, abstract = {Cadmium (Cd) is one of the most hazardous heavy metals that negatively affect the growth and yield of wheat. He-Ne laser irradiation is known to ameliorate cadmium (Cd) stress in wheat. However, the underlying mechanism of He-Ne laser irradiation on protecting wheat against Cd stress is not well recognized. In present study, Cd-treated wheat showed significant reduction in growth, root morphology and total chlorophyll content, but notably increase of Cd accumulation in both roots and shoots. However, He-Ne laser irradiation dramatically reduced concentrations of malondialdehyde (MDA) and hydrogen peroxide (H2O2), and increased total chlorophyll content and activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX) in roots of wheat plants under Cd stress. Further, He-Ne laser irradiation significantly upregulated the transcripts of TaGR (glutathione reductase) and TaGST (glutathione-S-transferase) genes along with the increased activities of GR and GST and glutathione (GSH) concentration in roots of wheat seedlings under Cd stress. In addition, He-Ne laser irradiation enhanced the uptake of mineral elements (N, P, Mg, Fe, Zn and Cu), and significantly decreased Cd uptake and transport mainly through down-regulating the expressions of Cd transport genes (TaHMA2 and TaHMA3) in roots of wheat seedlings under Cd stress. Overall, these findings suggested that He-Ne laser irradiation alleviated the adverse effects of Cd on wheat growth by enhancing antioxidant defense system, improving mineral nutrient status, and decreasing the Cd uptake and transport. This study provides new insights into the roles of He-Ne laser irradiation in the amelioration of Cd stress in wheat and indicates the potential application of this irradiation in crop breeding and growth under Cd stress conditions.}, }
@article {pmid35367386, year = {2022}, author = {de Lapena, SAB and Terra-Garcia, M and Ward, RADC and Rossoni, RD and Melo, VMM and Junqueira, JC}, title = {Enhancing effect of chitosan on methylene blue-mediated photodynamic therapy against C. albicans: a study in planktonic growth, biofilms, and persister cells.}, journal = {Photodiagnosis and photodynamic therapy}, volume = {}, number = {}, pages = {102837}, doi = {10.1016/j.pdpdt.2022.102837}, pmid = {35367386}, issn = {1873-1597}, abstract = {Chitosan (CS) is a natural polymer extracted from the exoskeleton of crustaceans. Due to its cationic structure, CS has been studied as a possible enhancer of antimicrobial photodynamic therapy (aPDT). The objective was to evaluate the association of CS with methylene blue (MB)-mediated aPDT on Candida albicans, investigating its effects on planktonic growth, biofilms, and cells persistent to fluconazole. The ability of CS to interfere with MB absorption by Candida cells was also evaluated. For the assays, planktonic cells of C. albicans were cultivated for 24 h, and the biofilms were formed for 48 h. For the induction of persister cells, C. albicans was cultivated with high concentration of fluconazole for 48 h. Treatments were performed with MB, CS or MB+CS, followed by irradiation with LED (660 nm). As results, aPDT with MB (300 µm) reduced the planktonic cells by 1.6 log10 CFU, while the MB+CS association led to a reduction of 4.8 log10 CFU. For aPDT in biofilms, there was a microbial reduction of 2.9 log10 CFU for the treatment with MB (600 µm) and 5.3 log10 CFU for MB+CS. In relation to persister cells, the fungal reductions were 0.4 log10 CFU for MB and 1.5 log10 CFU for MB+CS. In the absorption assays, the penetration of MB into Candida cells was increased in the presence of CS. It was concluded that CS enhanced the antimicrobial activity of aPDT in planktonic growth, biofilms, and persister cells of C. albicans, probably by facilitating the penetration of MB into fungal cells.}, }
@article {pmid35366684, year = {2022}, author = {Bashir, A and Ahmad, T and Farooq, S and Lone, WI and Manzoor, MM and Nalli, Y and Sultan, P and Chaubey, A and Ali, A and Riyaz-Ul-Hassan, S}, title = {A Secondary Metabolite of Cercospora sp., Associated with Rosa damascena Mill., Inhibits Proliferation, Biofilm Production, Ergosterol Synthesis and Other Virulence Factors in Candida albicans.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35366684}, issn = {1432-184X}, abstract = {Here we describe the antimicrobial potential of secondary metabolites, fulvic acid (F.A.) and anhydrofulvic acid (AFA), produced by RDE147, an endophyte of Rosa damascena Mill. The endophyte was identified as Cercospora piaropi by ITS and β-tubulin-based phylogenetic analyses, while chemoprofiling of the endophyte by column chromatography and spectroscopy yielded two pure compounds, F.A. and AFA. The compounds demonstrated different antimicrobial profiles, with AFA suppressing the growth of C. albicans at 7.3 µg ml-1 IC50. Further studies revealed that AFA strongly restricted the biofilm production and hyphae formation in C. albicans by down-regulating several biofilm and morphogenesis-related genes. The time-kill assays confirmed the fungicidal activity of AFA against C. albicans, killing 83.6% of the pathogen cells in 24 h at the MIC concentration, and the post-antibiotic effect (PAE) experiments established the suppression of C. albicans growth for extended time periods. The compound acted synergistically with amphotericin B and nystatin and reduced ergosterol biosynthesis by the pathogen, confirmed by ergosterol estimation and comparative expression profiling of selected genes and molecular docking of AFA with C. albicans squalene epoxidase. AFA also suppressed the expression of several other virulence genes of the fungal pathogen. The study determines the anti-C. albicans potential of AFA and its impact on the biology of the pathogen. It also indicates that Cercospora species may yield potential bioactive molecules, especially fulvic acid derivatives. However, it is imperative to conduct in vivo studies to explore this molecule's therapeutic potential further.}, }
@article {pmid35366074, year = {2022}, author = {Li, W and Zhou, Z and Li, H and Wang, S and Ren, L and Hu, J and Liu, Q and Wu, C and Tang, C and Hu, F and Zeng, L and Zhao, R and Tao, M and Zhang, C and Qin, Q and Liu, S}, title = {Successional Changes of Microbial Communities and Host-Microbiota Interactions Contribute to Dietary Adaptation in Allodiploid Hybrid Fish.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35366074}, issn = {1432-184X}, support = {NT2021008//the Laboratory of Lingnan Modern Agriculture Project/ ; 21B0053//the Research Foundation of Education Bureau of Hunan Province/ ; U19A2040//National Natural Science Foundation of China/ ; 31730098//National Natural Science Foundation of China/ ; 31802287//National Natural Science Foundation of China/ ; CARS-45//Earmarked Fund for China Agriculture Research System/ ; }, abstract = {Host-microbiota interactions play critical roles in host development, immunity, metabolism, and behavior. However, information regarding host-microbiota interactions is limited in fishes due to their complex living environment. In the present study, an allodiploid hybrid fish derived from herbivorous Megalobrama amblycephala (♀) × carnivorous Culter alburnus (♂) was used to investigate the successional changes of the microbial communities and host-microbiota interactions during herbivorous and carnivorous dietary adaptations. The growth level was not significantly different in any developmental stage between the two diet groups of fish. The diversity and composition of the dominant microbial communities showed similar successional patterns in the early developmental stages, but significantly changed during the two dietary adaptations. A large number of bacterial communities coexisted in all developmental stages, whereas the abundance of some genera associated with metabolism, including Acinetobacter, Gemmobacter, Microbacterium, Vibrio, and Aeromonas, was higher in either diet groups of fish. Moreover, the abundance of phylum Firmicutes, Actinobacteria, and Chloroflexi was positively correlated with the host growth level. In addition, Spearman's correlation analysis revealed that the differentially expressed homologous genes in the intestine associated with cell growth, immunity, and metabolism were related to the dominant gut microbiota. Our results present evidence that host genetics-gut microbiota interactions contribute to dietary adaptation in hybrid fish, which also provides basic data for understanding the diversity of dietary adaptations and evolution in fish.}, }
@article {pmid35365572, year = {2022}, author = {Effenberger, M and Widjaja, AA and Grabherr, F and Schaefer, B and Grander, C and Mayr, L and Schwaerzler, J and Enrich, B and Moser, P and Fink, J and Pedrini, A and Jaschke, N and Kirchmair, A and Pfister, A and Hausmann, B and Bale, R and Putzer, D and Zoller, H and Schafer, S and Pjevac, P and Trajanoski, Z and Oberhuber, G and Adolph, T and Cook, S and Tilg, H}, title = {Interleukin-11 drives human and mouse alcohol-related liver disease.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2021-326076}, pmid = {35365572}, issn = {1468-3288}, abstract = {OBJECTIVE: Alcoholic hepatitis (AH) reflects acute exacerbation of alcoholic liver disease (ALD) and is a growing healthcare burden worldwide. Interleukin-11 (IL-11) is a profibrotic, proinflammatory cytokine with increasingly recognised toxicities in parenchymal and epithelial cells. We explored IL-11 serum levels and their prognostic value in patients suffering from AH and cirrhosis of various aetiology and experimental ALD.<br><br>DESIGN: IL-11 serum concentration and tissue expression was determined in a cohort comprising 50 patients with AH, 110 patients with cirrhosis and 19 healthy volunteers. Findings were replicated in an independent patient cohort (n=186). Primary human hepatocytes exposed to ethanol were studied in vitro. Ethanol-fed wildtype mice were treated with a neutralising murine IL-11 receptor-antibody (anti-IL11RA) and examined for severity signs and markers of ALD.<br><br>RESULTS: IL-11 serum concentration and hepatic expression increased with severity of liver disease, mostly pronounced in AH. In a multivariate Cox-regression, a serum level above 6.4 pg/mL was a model of end-stage liver disease independent risk factor for transplant-free survival in patients with compensated and decompensated cirrhosis. In mice, severity of alcohol-induced liver inflammation correlated with enhanced hepatic IL-11 and IL11RA expression. In vitro and in vivo, anti-IL11RA reduced pathogenic signalling pathways (extracellular signal-regulated kinases, c-Jun N-terminal kinase, NADPH oxidase 4) and protected hepatocytes and murine livers from ethanol-induced inflammation and injury.<br><br>CONCLUSION: Pathogenic IL-11 signalling in hepatocytes plays a crucial role in the pathogenesis of ALD and could serve as an independent prognostic factor for transplant-free survival. Blocking IL-11 signalling might be a therapeutic option in human ALD, particularly AH.}, }
@article {pmid35364696, year = {2022}, author = {Liu, N and Hu, H and Ma, W and Deng, Y and Dimitrov, D and Wang, Q and Shrestha, N and Su, X and Feng, K and Liu, Y and Hao, B and Zhang, X and Feng, X and Wang, Z}, title = {Relationships Between Soil Microbial Diversities Across an Aridity Gradient in Temperate Grasslands : Soil Microbial Diversity Relationships.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35364696}, issn = {1432-184X}, support = {2017YFA0605101//national key research development program of china/ ; XDB31000000//the Strategic Priority Research Program of Chinese Academy of Sciences/ ; 32125026//the National Natural Science Foundation of China/ ; 31988102//the National Natural Science Foundation of China/ ; LESP201702//the Youth Fund of Ministry of Education Laboratory for Earth Surface Processes of Peking University/ ; }, abstract = {Soil microbes assemble in highly complex and diverse microbial communities, and microbial diversity patterns and their drivers have been studied extensively. However, diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between microbial functional groups in arid regions remain poorly understood. Here we assessed the relationships between the diversity and abundance of bacteria, fungi, and archaea and explored how environmental factors influence these relationships. We sampled soil along a 1500-km-long aridity gradient in temperate grasslands of Inner Mongolia (China) and sequenced the 16S rRNA gene of bacteria and archaea and the ITS2 gene of fungi. The diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between different microbial functional groups were evaluated using α-diversity and co-occurrence networks based on microbial abundance. Our results indicate insignificant correlations among the diversity patterns of bacterial, fungal, and archaeal domains using α-diversity but mostly positive correlations among diversity patterns of microbial functional groups based on α-diversity and co-occurrence networks along the aridity gradient. These results suggest that studying microbial diversity patterns from the perspective of functional groups and co-occurrence networks can provide additional insights on patterns that cannot be accessed using only overall microbial α-diversity. Increase in aridity weakens the diversity correlations between bacteria and fungi and between bacterial and archaeal functional groups, but strengthens the positive diversity correlations between bacterial functional groups and between fungal functional groups and the negative diversity correlations between bacterial and fungal functional groups. These variations of the diversity correlations are associated with the different responses of microbes to environmental factors, especially aridity. Our findings demonstrate the complex responses of microbial community structure to environmental conditions (especially aridity) and suggest that understanding diversity correlations and co-occurrence patterns between soil microbial groups is essential for predicting changes in microbial communities under future climate change in arid regions.}, }
@article {pmid35363772, year = {2022}, author = {Zaoli, S and Grilli, J}, title = {The stochastic logistic model with correlated carrying capacities reproduces beta-diversity metrics of microbial communities.}, journal = {PLoS computational biology}, volume = {18}, number = {4}, pages = {e1010043}, doi = {10.1371/journal.pcbi.1010043}, pmid = {35363772}, issn = {1553-7358}, abstract = {The large taxonomic variability of microbial community composition is a consequence of the combination of environmental variability, mediated through ecological interactions, and stochasticity. Most of the analysis aiming to infer the biological factors determining this difference in community structure start by quantifying how much communities are similar in their composition, trough beta-diversity metrics. The central role that these metrics play in microbial ecology does not parallel with a quantitative understanding of their relationships and statistical properties. In particular, we lack a framework that reproduces the empirical statistical properties of beta-diversity metrics. Here we take a macroecological approach and introduce a model to reproduce the statistical properties of community similarity. The model is based on the statistical properties of individual communities and on a single tunable parameter, the correlation of species' carrying capacities across communities, which sets the difference of two communities. The model reproduces quantitatively the empirical values of several commonly-used beta-diversity metrics, as well as the relationships between them. In particular, this modeling framework naturally reproduces the negative correlation between overlap and dissimilarity, which has been observed in both empirical and experimental communities and previously related to the existence of universal features of community dynamics. In this framework, such correlation naturally emerges due to the effect of random sampling.}, }
@article {pmid35362197, year = {2022}, author = {Lal, R and Singh, BK and Sar, P and Phale, P}, title = {The Assessment of Microbial Ecology: A Special Emphasis on the Indian Scenario.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.13067}, pmid = {35362197}, issn = {1758-2229}, }
@article {pmid35361906, year = {2022}, author = {Zhang, C and Merana, GR and Harris-Tryon, T and Scharschmidt, TC}, title = {Skin immunity: dissecting the complex biology of our body's outer barrier.}, journal = {Mucosal immunology}, volume = {}, number = {}, pages = {}, pmid = {35361906}, issn = {1935-3456}, abstract = {Our skin contributes critically to health via its role as a barrier tissue, carefully regulating passage of key substrates while also providing defense against exogenous threats. Immunological processes are integral to almost every skin function and paramount to our ability to live symbiotically with skin commensal microbes and other environmental stimuli. While many parallels can be drawn to immunobiology at other mucosal sites, skin immunity demonstrates unique features that relate to its distinct topography, chemical composition and microbial ecology. Here we provide an overview of skin as an immune organ, with reference to the broader context of mucosal immunology. We review paradigms of innate as well as adaptive immune function and highlight how skin-specific structures such as hair follicles and sebaceous glands interact and contribute to these processes. Finally, we highlight for the mucosal immunology community a few emerging areas of interest for the skin immunity field moving forward.}, }
@article {pmid35361625, year = {2022}, author = {Lee, TJ and Liu, Y and Liu, WA and Lin, YF and Lee, HH and Ke, HM and Huang, JP and Lu, MJ and Hsieh, CL and Chung, KF and Liti, G and Tsai, IJ}, title = {Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.276286.121}, pmid = {35361625}, issn = {1549-5469}, abstract = {The ecology and genetic diversity of model yeast Saccharomyces cerevisiae prior to human domestication remain poorly understood. Taiwan is regarded as part of this yeast's geographic birthplace where the most divergent natural lineage was discovered. Here, we extensively sampled the broad-leaf forests across this continental island to probe the ancestral species diversity. We found that S. cerevisiae is distributed ubiquitously at low abundance in the forests. Whole-genome sequencing of 121 isolates revealed nine distinct lineages that diverged from Asian lineages during the Pleistocene, when a transient continental shelf land bridge connected Taiwan to other major landmasses. Three lineages are endemic to Taiwan and six are widespread in Asia, making this region a focal biodiversity hotspot. Both ancient and recent admixture events were detected between natural lineages and a genetic ancestry component associated with isolates from fruits was detected in most admixed isolates. Collectively, Taiwanese isolates harbor genetic diversity comparable to that of the whole Asia continent, and different lineages have coexisted at a fine spatial scale even on the same tree. Patterns of variations within each lineage revealed that S. cerevisiae is highly clonal and predominantly reproduces asexually in nature. We identified different selection patterns shaping the coding sequences of natural lineages and found fewer gene family expansion and contractions which contrast with domesticated lineages. This study establishes that S. cerevisiae has rich natural diversity sheltered from human influences, making it a powerful model system in microbial ecology.}, }
@article {pmid35360922, year = {2022}, author = {Kaiser, T and Jahansouz, C and Staley, C}, title = {Network-based approaches for the investigation of microbial community structure and function using metagenomics-based data.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {}, doi = {10.2217/fmb-2021-0219}, pmid = {35360922}, issn = {1746-0921}, abstract = {Network-based approaches offer a powerful framework to evaluate microbial community organization and function as it relates to a variety of environmental processes. Emerging studies are exploring network theory as a method for data integration that is likely to be critical for the integration of 'omics' data using systems biology approaches. Intricacies of network theory and methodological and computational complexities in network construction, however, impede the use of these tools for translational science. We provide a perspective on the methods of network construction, interpretation and emerging uses for these techniques in understanding host-microbiota interactions.}, }
@article {pmid35359714, year = {2022}, author = {Rogiers, T and Van Houdt, R and Williamson, A and Leys, N and Boon, N and Mijnendonckx, K}, title = {Molecular Mechanisms Underlying Bacterial Uranium Resistance.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {822197}, doi = {10.3389/fmicb.2022.822197}, pmid = {35359714}, issn = {1664-302X}, abstract = {Environmental uranium pollution due to industries producing naturally occurring radioactive material or nuclear accidents and releases is a global concern. Uranium is hazardous for ecosystems as well as for humans when accumulated through the food chain, through contaminated groundwater and potable water sources, or through inhalation. In particular, uranium pollution pressures microbial communities, which are essential for healthy ecosystems. In turn, microorganisms can influence the mobility and toxicity of uranium through processes like biosorption, bioreduction, biomineralization, and bioaccumulation. These processes were characterized by studying the interaction of different bacteria with uranium. However, most studies unraveling the underlying molecular mechanisms originate from the last decade. Molecular mechanisms help to understand how bacteria interact with radionuclides in the environment. Furthermore, knowledge on these underlying mechanisms could be exploited to improve bioremediation technologies. Here, we review the current knowledge on bacterial uranium resistance and how this could be used for bioremediation applications.}, }
@article {pmid35358890, year = {2022}, author = {Gui, Y and Sun, Z and Kazmi, SSUH and Rahman, MS and Xu, H}, title = {Insights for monitoring surveys into influence of tidal events on protozoan periphyton fauna along the tidelines of Yellow Sea, Northern China.}, journal = {Marine pollution bulletin}, volume = {178}, number = {}, pages = {113586}, doi = {10.1016/j.marpolbul.2022.113586}, pmid = {35358890}, issn = {1879-3363}, abstract = {To explore the influence of tidal events on protozoan periphyton fauna along tidelines, a 1-month baseline survey for bioassessment was conducted in an intertidal zone of the Yellow Sea, Northern China. A total of 27 protozoans species were identified among five sampling sites along five tidelines (sites A-E). The periphytic protozoans showed a significant variation in species distribution and community pattern along five tidelines. Species richness decreased from the high tideline (site A) and reached the minimum value at the middle tideline (site C), followed by an increase up to the low tideline (site E). Individual abundances peaked at site C and leveled off at the other four tidelines. Species richness, evenness, and diversity showed low value at site C compared with those at the other four sites. These findings suggest that periphytic protozoan fauna was shaped by tidal events along the tidelines of marine ecosystems.}, }
@article {pmid35358518, year = {2022}, author = {Shahbaz, M and Bengtson, P and Mertes, JR and Kulessa, B and Kljun, N}, title = {Spatial heterogeneity of soil carbon exchanges and their drivers in a boreal forest.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {154876}, doi = {10.1016/j.scitotenv.2022.154876}, pmid = {35358518}, issn = {1879-1026}, abstract = {Boreal forests have a large impact on the global greenhouse gas balance and their soils constitute an important carbon (C) reservoir. Mature boreal forests are typically a net CO2 sink, but there are also examples of boreal forests that are persistent CO2 sources. The reasons remain often unknown, presumably due to a lack of understanding of how biotic and abiotic drivers interact to determine the microbial respiration of soil organic matter (SOM). This study aimed at identifying the main drivers of microbial SOM respiration and CO2 and CH4 soil chamber-fluxes within dry and wet sampling areas at the mature boreal forest of Norunda, Sweden, a persistent net CO2 source. The spatial heterogeneity of the drivers was assessed with a geostatistical approach combined with stepwise multiple regression. We found that heterotrophic soil respiration increased with SOM content and nitrogen (N) availability, while the SOM reactivity, i.e., SOM specific respiration, was determined by soil moisture and N availability. The latter suggests that microbial activity was N rather than C limited and that microbial N mining might be driving old-SOM decomposition, which was observed through a positive correlation between soil respiration and its δ13C values. SOM specific heterotrophic respiration was lower in wet than in dry areas, while no such dependencies were found for chamber-based soil CO2 fluxes, implying that oxygen depletion resulted in lower SOM reactivity. The chamber-based soil CH4 flux differed significantly between the wet and dry areas. In the wet area, we observed net CH4 emission that was positively related to soil moisture and NH4+-N content. Taken together, our findings suggest that N availability has a strong regulatory effect on soil CO2 and CH4 emissions at Norunda, and that microbial decomposition of old-SOM to release bioavailable N might be partly responsible for the net CO2 emission at the site.}, }
@article {pmid35357520, year = {2022}, author = {Castillo-Esparza, JF and Mora-Velasco, KA and Rosas-Saito, GH and Rodríguez-Haas, B and Sánchez-Rangel, D and Ibarra-Juárez, LA and Ortiz-Castro, R}, title = {Microorganisms Associated with the Ambrosial Beetle Xyleborus affinis with Plant Growth-Promotion Activity in Arabidopsis Seedlings and Antifungal Activity Against Phytopathogenic Fungus Fusarium sp. INECOL_BM-06.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35357520}, issn = {1432-184X}, support = {PDCPN-2015-882//CONACYT/ ; FORDECYT-PRONACES 292399//CONACYT/ ; }, abstract = {Plants interact with a great diversity of microorganisms or insects throughout their life cycle in the environment. Plant and insect interactions are common; besides, a great variety of microorganisms associated with insects can induce pathogenic damage in the host, as mutualist phytopathogenic fungus. However, there are other microorganisms present in the insect-fungal association, whose biological/ecological activities and functions during plant interaction are unknown. In the present work evaluated, the role of microorganisms associated with Xyleborus affinis, an important beetle species within the Xyleborini tribe, is characterized by attacking many plant species, some of which are of agricultural and forestry importance. We isolated six strains of microorganisms associated with X. affinis shown as plant growth-promoting activity and altered the root system architecture independent of auxin-signaling pathway in Arabidopsis seedlings and antifungal activity against the phytopathogenic fungus Fusarium sp. INECOL_BM-06. In addition, evaluating the tripartite interaction plant-microorganism-fungus, interestingly, we found that microorganisms can induce protection against the phytopathogenic fungus Fusarium sp. INECOL_BM-06 involving the jasmonic acid-signaling pathway and independent of salicylic acid-signaling pathway. Our results showed the important role of this microorganisms during the plant- and insect-microorganism interactions, and the biological potential use of these microorganisms as novel agents of biological control in the crops of agricultural and forestry is important.}, }
@article {pmid35357187, year = {2022}, author = {Holohan, BC and Duarte, MS and Szabo-Corbacho, MA and Cavaleiro, AJ and Salvador, AF and Pereira, MA and Ziels, RM and Frijters, CTMJ and Pacheco-Ruiz, S and Carballa, M and Sousa, DZ and Stams, AJM and O'Flaherty, V and van Lier, JB and Alves, MM}, title = {Principles, Advances, and Perspectives of Anaerobic Digestion of Lipids.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.1c08722}, pmid = {35357187}, issn = {1520-5851}, abstract = {Several problems associated with the presence of lipids in wastewater treatment plants are usually overcome by removing them ahead of the biological treatment. However, because of their high energy content, waste lipids are interesting yet challenging pollutants in anaerobic wastewater treatment and codigestion processes. The maximal amount of waste lipids that can be sustainably accommodated, and effectively converted to methane in anaerobic reactors, is limited by several problems including adsorption, sludge flotation, washout, and inhibition. These difficulties can be circumvented by appropriate feeding, mixing, and solids separation strategies, provided by suitable reactor technology and operation. In recent years, membrane bioreactors and flotation-based bioreactors have been developed to treat lipid-rich wastewater. In parallel, the increasing knowledge on the diversity of complex microbial communities in anaerobic sludge, and on interspecies microbial interactions, contributed to extend the knowledge and to understand more precisely the limits and constraints influencing the anaerobic biodegradation of lipids in anaerobic reactors. This critical review discusses the most important principles underpinning the degradation process and recent key discoveries and outlines the current knowledge coupling fundamental and applied aspects. A critical assessment of knowledge gaps in the field is also presented by integrating sectorial perspectives of academic researchers and of prominent developers of anaerobic technology.}, }
@article {pmid35355087, year = {2022}, author = {Zhang, W and Wan, W and Liu, X and Yang, Y and Liu, M}, title = {Stronger Geographic Limitations Shape a Rapid Turnover and Potentially Highly Connected Network of Core Bacteria on Microplastics.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35355087}, issn = {1432-184X}, support = {32071614//National Natural Science Foundation of China/ ; }, abstract = {Core microbiota is shared microbial taxa within the same habitat, which is important for understanding the stable and consistent components of the complex microbial assembly. However, information on the microplastic core bacteria from the river ecosystems is poor. Here, we investigated the composition and function of microplastic core bacteria from the Three Gorges Reservoir area along the approximate 662 km of the Yangtze River via full-length 16S rRNA gene sequencing, compared with those in water, sediment, and soil. The results showed that the spatial turnover of bacterial communities in four habitats supported deterministic processes dominated by niche differentiation, which shaped their core bacteria. The composition and function of microplastic core bacteria were significantly different from those in the other three habitats. Rhodobacteraceae was the main component of microplastic core bacteria, while the main component of core bacteria in water, sediment, and soil were Burkholderiaceae (21.90%), Burkholderiaceae (5.01%), Nitrosomonadaceae (4.61%), respectively. Furthermore, microplastic core bacteria had stronger geographic limitations along the Yangtze River in the Three Gorges Reservoir area. Stronger geographic limitations shaped the rapid community turnover and a potentially more connected network for the microplastic core bacteria than water, sediment, and soil. More importantly, microplastic core bacteria had strong potential functions of drug resistance and could cause risks to ecosystems and human health. Microplastic core bacteria were mainly influenced by sediment core bacteria, although the bacteria colonizing on microplastics could be from all the contact environments and original sources. These findings provide important insights into the composition, function, and association of microplastic core bacteria with their surrounding environment.}, }
@article {pmid35355086, year = {2022}, author = {Li, S and Peng, H and Shi, X and Gu, Q and Shen, Z and Wang, M}, title = {Significant Effects of Associated Microorganisms on the Community of Photosynthetic Picoeukaryotes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35355086}, issn = {1432-184X}, support = {31800388//National Natural Science Foundation of China/ ; 32071573//National Natural Science Foundation of China/ ; }, abstract = {Photosynthetic picoeukaryotes (PPEs) form associations with other microorganisms. However, whether and how the associated microbes affect PPE communities remain unknown. We used flow cytometric cell sorting combined with parallel high-throughput sequencing of the 18S and 16S rRNA genes to simultaneously investigate PPEs and their associated microbial communities in the Yangtze-connected Lake Dongting. The lake harbors a great diversity of PPEs. PPE communities exhibited significant temporal rather than spatial variations. Two distinct PPE taxa affiliated with Discostella nipponica and Poterioochromonas malhamensis were dominant during winter/spring and summer, respectively. Parallel high-throughput sequencing revealed a great diversity of associated bacteria and non-pigmented eukaryotes (NPEs) in PPEs sorts. Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria among the associated bacteria and fungi among the associated NPEs were dominant. PPEs were more apparently associated with bacteria than with NPEs. The co-occurrence network of PPEs and associated microbes formed five major modules, which exhibited distinct temporal patterns, being specific to a certain period. Variations in PPEs communities were significantly correlated with both environmental factors and associated microbial communities. In variation partitioning analysis, the associated bacteria explained the greatest variations in PPE communities, and associated bacteria and NPEs co-explained a large portion of environmental effects on PPE communities. Our results highlight the significance of associated microbes in shaping PPE communities.}, }
@article {pmid35353006, year = {2022}, author = {Emmons, AL and Mundorff, AZ and Hoeland, KM and Davoren, J and Keenan, SW and Carter, DO and Campagna, SR and DeBruyn, JM}, title = {Postmortem Skeletal Microbial Community Composition and Function in Buried Human Remains.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0004122}, doi = {10.1128/msystems.00041-22}, pmid = {35353006}, issn = {2379-5077}, abstract = {Bones and teeth can provide a lasting resource to identify human remains following decomposition. Bone can support dynamic communities of micro- and macroscopic scavengers and incidental taxa, which influence the preservation of bone over time. Previously we identified key microbial taxa associated with survivability of DNA in bones of surface-decomposed human remains, observing high intra- and interindividual variation. Here we characterized the postmortem bone microbiome of skeletal remains in a multi-individual burial to better understand subsurface bone colonization and preservation. To understand microbial community origins and assembly, 16S rRNA amplicon sequences from 256 bone and 27 soil samples were compared to bone from individuals who decomposed on the ground surface, and human gut sequences from the American Gut Project. Untargeted metabolomics was applied to a subset of 41 bone samples from buried remains to examine potential microbe-metabolite interactions and infer differences related to community functionality. Results show that postmortem bone microbial communities are distinct from those of the oxic surface soils and the human gut. Microbial communities from surface-deposited bone and shallow buried bone were more similar to those from soils, while bones recovered from saturated areas deeper in the grave showed increased similarity with human gut samples with higher representation of anaerobic taxa, suggesting that the depositional environment affected the established bone microbiome. Correlations between metabolites and microbes indicate that phosphate solubilization is likely an important mechanism of microbially mediated skeletal degradation. This research expands our knowledge of microbial bone colonizers, including colonizers important in a burial environment. IMPORTANCE Understanding the microbes that colonize and degrade bone has important implications for preservation of skeletal elements and identification of unknown human remains. Current research on the postmortem bone microbiome is limited and largely focuses on archaeological or marine contexts. Our research expands our understanding of bone microbiomes in buried remains by characterizing the taxonomic and metabolic diversity of microbes that are colonizing bone after a 4-year postmortem burial interval and examines the potential impact of microbial colonization on human skeletal DNA preservation. Our results indicate that the postmortem bone microbiome is distinct from the human gut and soil. Evidence from combined metabolomic and amplicon sequencing analysis suggests that Pseudomonas and phosphate solubilization likely play a role in skeletal degradation. This work provides important insight into the types and activities of microbes controlling the preservation of buried skeletal remains.}, }
@article {pmid35352861, year = {2022}, author = {Rousk, J and C Brangarí, A}, title = {Do the respiration pulses induced by drying-rewetting matter for the soil-atmosphere carbon balance?.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.16163}, pmid = {35352861}, issn = {1365-2486}, support = {2018-01315//Svenska Forskningsrådet Formas/ ; KAW 2017.0171//Knut och Alice Wallenbergs Stiftelse/ ; 2020-04083//Vetenskapsrådet/ ; }, abstract = {We show that the explosive microbial and biogeochemical dynamics triggered by rewetting dry soil in laboratory experiments also has relevance in intact ecosystems. This highlights an opportunity to use predictions derived from laboratory studies to provide targets in ecosystem-scale biogeochemical studies.}, }
@article {pmid35352237, year = {2022}, author = {Vissenaekens, H and Grootaert, C and Raes, K and De Munck, J and Smagghe, G and Boon, N and Van Camp, J}, title = {Quercetin Mitigates Endothelial Activation in a Novel Intestinal-Endothelial-Monocyte/Macrophage Coculture Setup.}, journal = {Inflammation}, volume = {}, number = {}, pages = {}, pmid = {35352237}, issn = {1573-2576}, support = {1S18417N//FWO-Vlaanderen/ ; }, abstract = {Atherosclerosis initiation is associated with a pro-inflammatory state of the endothelium. Quercetin is a flavonoid abundantly present in plant-based foods, with a possible impact on cardiovascular health. In this study, the effects of quercetin on lipopolysaccharide (LPS)-mediated endothelial inflammation and monocyte adhesion and migration, which are initial steps of the atherogenic process, are studied. Novel in vitro multicellular models simulating the intestinal-endothelial-monocytes/macrophages axis allowed to combine relevant intestinal flavonoid absorption, metabolism and efflux, and the consequent bioactivity towards peripheral endothelial cells. In this triple coculture, quercetin exposure decreased monocyte adhesion to and macrophage migration through an LPS-stressed endothelium, and this was associated with significantly lower levels of soluble vascular cell adhesion molecule-1 (sVCAM-1). Furthermore, quercetin decreased the pro-inflammatory cell environment upon LPS-induced endothelial activation, in terms of tumor necrosis factor- α (TNF-α), interleukin-6 (IL-6), interleukin-8 (IL-8), and sVCAM-1 expression. These findings highlight a mode-of-action by which quercetin may positively impact the initial states of atherosclerosis under more physiologically relevant conditions in terms of quercetin concentrations, metabolites, and intercellular crosstalk.}, }
@article {pmid35350577, year = {2022}, author = {Song, H and Xiao, K and Chen, Z and Long, Q}, title = {Analysis of Conjunctival Sac Microbiome in Dry Eye Patients With and Without Sjögren's Syndrome.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {841112}, doi = {10.3389/fmed.2022.841112}, pmid = {35350577}, issn = {2296-858X}, abstract = {Purpose: To analyze the conjunctival sac microbial communities in patients with Sjögren's syndrome-associated dry eyes (SSDE) and non-Sjögren's syndrome-associated dry eyes (NSSDE), compared with normal controls (NC).<br><br>Methods: Conjunctival sac swab samples from 23 eyes of SSDE, 36 eyes of NSSDE, and 39 eyes of NC were collected. The V3-V4 region of the 16S ribosomal RNA (rRNA) gene high-throughput sequencing was performed on an Illumina MiSeq platform and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Alpha diversity was employed to analyze microbiome diversity through Chao1 and Shannon indexes. Beta diversity was demonstrated by the principal coordinates analysis (PCoA) and Partial Least Squares Discrimination Analysis (PLS-DA). The relative abundance was bioinformatically analyzed at the phylum and genus levels.<br><br>Results: The alpha diversity was lower in patients with dry eye disease (Shannon index: NC vs. SSDE: P = 0.020, NC vs. NSSDE: P = 0.029). The beta diversity showed divergent microbiome composition in different groups (NC vs. SSDE: P = 0.001, NC vs. NSSDE: P = 0.001, NSSDE vs. SSDE: P = 0.005). The top 5 abundant phyla were Firmicutes, Proteobacteria, Actinobacteriota, Bacteroidota, and Cyanobacteria in all three groups. The top five abundant genera included Acinetobacter, Staphylococcus, Bacillus, Corynebacterium, and Clostridium_sensu_stricto_1. The relative microbiome abundance was different between groups. The Firmicutes/Bacteroidetes (F/B) ratio was 6.42, 7.31, and 9.71 in the NC, NSSDE, and SSDE groups, respectively (NC vs. SSDE: P = 0.038, NC vs. NSSDE: P = 0.991, SSDE vs. NSSDE: P = 0.048).<br><br>Conclusion: The diversity of conjunctival sac microbiome in patients with NSSDE and SSDE was diminished compared with NC. The main microbiome at the phylum and genus level were similar between groups, but the relative abundance had variations. The Firmicutes/Bacteroidetes ratio was higher in the SSDE group.}, }
@article {pmid35348389, year = {2022}, author = {Jiménez, RR and Carfagno, A and Linhoff, L and Gratwicke, B and Woodhams, DC and Chafran, LS and Bletz, MC and Bishop, B and Muletz-Wolz, CR}, title = {Inhibitory Bacterial Diversity and Mucosome Function Differentiate Susceptibility of Appalachian Salamanders to Chytrid Fungal Infection.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0181821}, doi = {10.1128/aem.01818-21}, pmid = {35348389}, issn = {1098-5336}, abstract = {Mucosal defenses are crucial in animals for protection against pathogens and predators. Host defense peptides (antimicrobial peptides, AMPs) as well as skin-associated microbes are key components of mucosal immunity, particularly in amphibians. We integrate microbiology, molecular biology, network-thinking, and proteomics to understand how host and microbially derived products on amphibian skin (referred to as the mucosome) serve as pathogen defenses. We studied defense mechanisms against chytrid pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), in four salamander species with different Batrachochytrium susceptibilities. Bd infection was quantified using qPCR, mucosome function (i.e., ability to kill Bd or Bsal zoospores in vitro), skin bacterial communities using 16S rRNA gene amplicon sequencing, and the role of Bd-inhibitory bacteria in microbial networks across all species. We explored the presence of candidate-AMPs in eastern newts and red-backed salamanders. Eastern newts had the highest Bd prevalence and mucosome function, while red-back salamanders had the lowest Bd prevalence and mucosome function, and two-lined salamanders and seal salamanders were intermediates. Salamanders with highest Bd infection intensity showed greater mucosome function. Bd infection prevalence significantly decreased as putative Bd-inhibitory bacterial richness and relative abundance increased on hosts. In co-occurrence networks, some putative Bd-inhibitory bacteria were found as hub-taxa, with red-backs having the highest proportion of protective hubs and positive associations related to putative Bd-inhibitory hub bacteria. We found more AMP candidates on salamanders with lower Bd susceptibility. These findings suggest that salamanders possess distinct innate mechanisms that affect chytrid fungi. IMPORTANCE How host mucosal defenses interact, and influence disease outcome is critical in understanding host defenses against pathogens. A more detailed understanding is needed of the interactions between the host and the functioning of its mucosal defenses in pathogen defense. This study investigates the variability of chytrid susceptibility in salamanders and the innate defenses each species possesses to mediate pathogens, thus advancing the knowledge toward a deeper understanding of the microbial ecology of skin-associated bacteria and contributing to the development of bioaugmentation strategies to mediate pathogen infection and disease. This study improves the understanding of complex immune defense mechanisms in salamanders and highlights the potential role of the mucosome to reduce the probability of Bd disease development and that putative protective bacteria may reduce likelihood of Bd infecting skin.}, }
@article {pmid35347426, year = {2022}, author = {Dyczko, D and Kiewra, D and Kolanek, A and Błażej, P}, title = {The influence of local environmental factors in southwestern Poland on the abundance of Ixodes ricinus and prevalence of infection with Borrelia burgdorferi s.l. and B. miyamotoi.}, journal = {Parasitology research}, volume = {}, number = {}, pages = {}, pmid = {35347426}, issn = {1432-1955}, abstract = {Ticks are important ectoparasites and vectors of pathogens that cause disease in humans and animals. The natural habitat of Ixodes ricinus ticks is forests, which are convenient habitats to search for hosts, including reservoir hosts, and therefore can be an important habitat source of tick-borne pathogens. The aim of the study was to assess the usefulness of detailed forest habitat-type maps to estimate the tick-borne risk at a local scale (Lower Silesia, SW Poland). For the purposes of estimating tick abundance, we used the land cover maps available from the Forest Data Bank. For I. ricinus collection, nine sites located in three forest habitat types were chosen: broadleaf forest, mixed broadleaf and coniferous forest and coniferous forest. Ticks were collected once a month from April to June 2018 and 2019 using the standard flagging method. At each of the nine sites, ticks were collected in four plots, of 100 m2 each. Tick abundance was analysed using general linear mixed models (GLMM). A total of 2196 (10.1/100 m2) ticks were collected, including 2093 Ixodes ricinus (95.3%; 9.6/100 m2), 46 Dermacentor reticulatus (2.1%; 0.2/100 m2) and 57 Haemaphysalis concinna (2.6%; 0.3/100 m2). Among the collected I. ricinus were 589 larvae (28.1%; 2.7/100 m2), 1261 nymphs (60.3%; 5.8/100 m2), 128 females (6.1%; 0.6/100 m2) and 115 males (5.5%; 0.5/100 m2). We found a highly significant effect of forest habitat type on the density of ticks for broadleaf forest (coefficient = 1.87267, p-value = 2.79e - 07). Additionally, a significant influence of air temperature and relative humidity on the abundance of ticks was observed. During spring, the peak activity of I. ricinus was recorded in May and June. For DNA amplification of Borrelia burgdorferi s.l., a nested PCR method was used. Out of 494 I. ricinus, 83 (16.8%) were positive for Borrelia spp. The RFLP method showed the occurrence of five species including four belonging to the B. burgdorferi s.l. complex: B. afzelii (30.1%), B. garinii (38.6%), B. valaisiana (2.4%) and B. lusitaniae (18.1%). Furthermore, B. miyamotoi (9.6%), a species belonging to bacteria that cause relapsing fever as well as co-infection of B. miyamotoi/B.lusitaniae (1.2%) were found. The differences in the infection level of Borrelia spp. between broadleaf forest and mixed broadleaf and coniferous forest were statistically significant.}, }
@article {pmid35347370, year = {2022}, author = {Vipindas, PV and Venkatachalam, S and Jabir, T and Yang, EJ and Cho, KH and Jung, J and Lee, Y and Krishnan, KP}, title = {Water Mass Controlled Vertical Stratification of Bacterial and Archaeal Communities in the Western Arctic Ocean During Summer Sea-Ice Melting.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35347370}, issn = {1432-184X}, abstract = {The environmental variations and their interactions with the biosphere are vital in the Arctic Ocean during the summer sea-ice melting period in the current scenario of climate change. Hence, we analysed the vertical distribution of bacterial and archaeal communities in the western Arctic Ocean from sea surface melt-ponds to deep water up to a 3040 m depth. The distribution of microbial communities showed a clear stratification with significant differences among different water depths, and the water masses in the Arctic Ocean - surface mixed layer, Atlantic water mass and deep Arctic water - appeared as a major factor explaining their distribution in the water column. A total of 34 bacterial phyla were detected in the seawater and 10 bacterial phyla in melt-ponds. Proteobacteria was the dominant phyla in the seawater irrespective of depth, whereas Bacteroidota was the dominant phyla in the melt-ponds. A fast expectation-maximization microbial source tracking analysis revealed that only limited dispersion of the bacterial community was possible across the stratified water column. The surface water mass contributed 21% of the microbial community to the deep chlorophyll maximum (DCM), while the DCM waters contributed only 3% of the microbial communities to the deeper water masses. Atlantic water mass contributed 37% to the microbial community of the deep Arctic water. Oligotrophic heterotrophic bacteria were dominant in the melt-ponds and surface waters, whereas chemoautotrophic and mixotrophic bacterial and archaeal communities were abundant in deeper waters. Chlorophyll and ammonium were the major environmental factors that determined the surface microbial communities, whereas inorganic nutrient concentrations controlled the deep-water communities.}, }
@article {pmid35347228, year = {2022}, author = {Zoccarato, L and Sher, D and Miki, T and Segrè, D and Grossart, HP}, title = {A comparative whole-genome approach identifies bacterial traits for marine microbial interactions.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {276}, pmid = {35347228}, issn = {2399-3642}, support = {RGB 0020/2016//Human Frontier Science Program (HFSP)/ ; }, abstract = {Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10% of genomes), phytohormones (3-8%) and different B vitamins (57-70%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.}, }
@article {pmid35346496, year = {2022}, author = {Dittoe, DK and Olson, EG and Ricke, SC}, title = {Impact of the gastrointestinal microbiome and fermentation metabolites on broiler performance.}, journal = {Poultry science}, volume = {}, number = {}, pages = {101786}, doi = {10.1016/j.psj.2022.101786}, pmid = {35346496}, issn = {1525-3171}, abstract = {Optimal broiler performance is dependent on several factors such as bird genetics, environment management, and nutrition. The gastrointestinal tract microbial ecology and metabolic activities have long been considered factors contributing to broiler performance responses. However, until recently, it was difficult to define the impact of the gastrointestinal microorganisms on the broiler host. With advances in microbiome sequencing technology, there has been a rapid increase in data generated using both experimental and commercial broiler operations. As the gastrointestinal microbiome data becomes more in-depth, opportunities to link microbiota composition to broiler performance metrics such as broiler growth rate and feed conversion efficiency have emerged. In parallel, with the increased understanding of the microbiota, there has been a shift to modulate the microbiome in order to alter metabolic patterns such as fermentation products. In this review, fermentation pathways and metabolites and the relationship with the microbiome will be discussed. Additionally, this review will connect these patterns and interpretations with current broiler performance data and the potential future directions these relationships could take the broiler industry.}, }
@article {pmid35346495, year = {2022}, author = {Ricke, SC and Dittoe, DK and Olson, EG}, title = {Microbiome applications for laying hen performance and egg production.}, journal = {Poultry science}, volume = {}, number = {}, pages = {101784}, doi = {10.1016/j.psj.2022.101784}, pmid = {35346495}, issn = {1525-3171}, abstract = {Management of laying hens has undergone considerable changes in the commercial egg industry. Shifting commercial production from cage-based systems to cage-free has impacted the housing environment and created issues not previously encountered. Sources of microorganisms that become established in the early stages of layer chick development may originate from the hen and depend on the microbial ecology of the reproductive tract. Development of the layer hen GIT microbiota appears to occur in stages as the bird matures. Several factors can impact the development of the layer hen GIT, including pathogens, environment, and feed additives such as antibiotics. In this review, the current status of the laying hen GIT microbial consortia and factors that impact the development and function of these respective microbial populations will be discussed, as well as future research directions.}, }
@article {pmid35346494, year = {2022}, author = {Olson, EG and Dittoe, DK and Jendza, JA and Stock, DA and Ricke, SC}, title = {Application of microbial analyses to feeds and potential implications for poultry nutrition.}, journal = {Poultry science}, volume = {}, number = {}, pages = {101789}, doi = {10.1016/j.psj.2022.101789}, pmid = {35346494}, issn = {1525-3171}, abstract = {Poultry nutrition and feed manufacturing are interrelated for a variety of reasons. Diet formulation is essential for optimizing bird growth and feed conversion, but compositional differences and the presence of certain feed additives can alter the gastrointestinal microbial composition and functionality. Not only does dietary composition and digestibility influence poultry performance, but specific physical characteristics such as feed particle size and thermal treatments can impact the avian gastrointestinal tract (GIT) microbiota. Poultry feeds also have a characteristic microbial ecology consisting of pathogenic and nonpathogenic microorganisms. Some feed-borne pathogens such as Salmonella are well studied and linked with the colonization of birds consuming the feed. However, much less is known about the nonpathogenic feed microbiome and what impact that might have on the bird's GIT. This review discusses the potential interaction between poultry feed and the GIT microbiome, microbial ecology of feed, application of microbiome analyses to feed, and approaches for communicating these complex data sets to the poultry industry.}, }
@article {pmid35346493, year = {2022}, author = {Ricke, SC and Dittoe, DK and Brown, JA and Thompson, DR}, title = {Practical opportunities for microbiome analyses and bioinformatics in poultry processing.}, journal = {Poultry science}, volume = {}, number = {}, pages = {101787}, doi = {10.1016/j.psj.2022.101787}, pmid = {35346493}, issn = {1525-3171}, abstract = {Poultry processing is undergoing changes both in operations as well as microbial methodologies. Traditionally, microbial data has been gathered through a series of culturing methods using liquid media and plating for isolation and enumeration. Both foodborne pathogens and nonpathogenic bacterial populations are estimated to assess food safety risks as well as the potential for spoilage. Bacterial loads from carcasses are important for estimating processing control and the effectiveness of antimicrobial applications. However, these culture-based approaches may only provide part of the microbial ecology landscape associated with chicken carcasses and the subsequent changes that occur in these populations during processing. Newer molecular-based approaches, such as 16S sequencing of the microbiota, offer a means to retrieve a more comprehensive microbial compositional profile. However, such approaches also result in large data sets which must be analyzed and interpreted. As more data is generated, this will require not only bioinformatic programs to process the data but appropriate educational forums to present the processed data to a broad audience.}, }
@article {pmid35343797, year = {2022}, author = {Busby, TJ and Miller, CR and Moran, NA and Van Leuven, JT}, title = {Global Composition of the Bacteriophage Community in Honey Bees.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0119521}, doi = {10.1128/msystems.01195-21}, pmid = {35343797}, issn = {2379-5077}, abstract = {The microbial communities in animal digestive systems are critical for host development and health. They stimulate the immune system during development, synthesize important chemical compounds like hormones, aid in digestion, competitively exclude pathogens, etc. Compared to the bacterial and fungal components of the microbiome, we know little about the temporal and spatial dynamics of bacteriophage communities in animal digestive systems. Recently, the bacteriophages of the honey bee gut were characterized in two European bee populations. Most of the bacteriophages described in these two reports were novel, harbored many metabolic genes in their genomes, and had a community structure that suggests coevolution with their bacterial hosts. To describe the conservation of bacteriophages in bees and begin to understand their role in the bee microbiome, we sequenced the virome of Apis mellifera from Austin, TX, and compared bacteriophage compositions among three locations around the world. We found that most bacteriophages from Austin are novel, sharing no sequence similarity with anything in public repositories. However, many bacteriophages are shared among the three bee viromes, indicating specialization of bacteriophages in the bee gut. Our study, along with the two previous bee virome studies, shows that the bee gut bacteriophage community is simple compared to that of many animals, consisting of several hundred types of bacteriophages that primarily infect four of the dominant bacterial phylotypes in the bee gut. IMPORTANCE Viruses that infect bacteria (bacteriophages) are abundant in the microbial communities that live on and in plants and animals. However, our knowledge of the structure, dynamics, and function of these viral communities lags far behind our knowledge of their bacterial hosts. We sequenced the first bacteriophage community of honey bees from the United States and compared the U.S. honey bee bacteriophage community to those of samples from Europe. Our work is an important characterization of an economically critical insect species and shows how bacteriophage communities can contain highly conserved individuals and be highly variable in composition across a wide geographic range.}, }
@article {pmid35343791, year = {2022}, author = {Zhu, YX and Chang, YW and Wen, T and Yang, R and Wang, YC and Wang, XY and Lu, MX and Du, YZ}, title = {Species Identity Dominates over Environment in Driving Bacterial Community Assembly in Wild Invasive Leaf Miners.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0026622}, doi = {10.1128/spectrum.00266-22}, pmid = {35343791}, issn = {2165-0497}, abstract = {The microbiota of invasive animal species may be pivotal to their adaptation and spread, yet the processes driving the assembly and potential sources of host-microbiota remain poorly understood. Here, we characterized microbiota of four Liriomyza leaf miner fly species totaling 310 individuals across 43 geographical populations in China and assessed whether the microbiota of the wild leaf miner was acquired from the soil microbiota or the host plant microbiota, using high-throughput 16S rRNA sequencing. Bacterial communities differed significantly among four leaf miner species but did not mirror host phylogeny. Microbiota diversity in the native L. chinensis was significantly higher than in three invasive leaf miners (i.e., L. trifolii, L. huidobrensis, and L. sativae), yet the microbial community of the invasive species exhibited a more connected and complex network structure. Structural equation models revealed that host species identity was more important than environmental factors (e.g., geography, climate, or plants) in shaping microbiota composition. Using neutral and null model analyses, we found that deterministic processes like variable selection played a primary role in driving microbial community assembly, with some influence by stochastic processes like drift. The relative degree of these processes governing microbiota was likely correlated with host species but independent of either geographical or climatic factors. Finally, source tracking analysis showed that leaf miners might acquire microbes from their host plant rather than the soil. Our results provide a robust assessment of the ecological processes governing bacterial community assembly and potential sources of microbes in invasive leaf miners. IMPORTANCE The invasion of foreign species, including leaf miners, is a major threat to world biota. Host-associated microbiota may facilitate host adaption and expansion in a variety of ways. Thus, understanding the processes that drive leaf miner microbiota assembly is imperative for better management of invasive species. However, how microbial communities assemble during the leaf miner invasions and how predictable the processes remain unexplored. This work quantitatively deciphers the relative importance of deterministic process and stochastic process in governing the assembly of four leaf miner microbiotas and identifies potential sources of leaf miner-colonizing microbes from the soil-plant-leaf miner continuum. Our study provides new insights into the mechanisms underlying the drive of leaf miner microbiota assembly.}, }
@article {pmid35340445, year = {2022}, author = {Parks, ST and Taylor, C}, title = {Development of a Remote, Course-Based Undergraduate Experience to Facilitate In Silico Study of Microbial Metabolic Pathways.}, journal = {Journal of microbiology &amp; biology education}, volume = {23}, number = {1}, pages = {}, doi = {10.1128/jmbe.00318-21}, pmid = {35340445}, issn = {1935-7877}, abstract = {Course-based undergraduate research experiences (CUREs) often occur in a physical lab space, but they can also be offered remotely while maintaining course expectations and providing opportunity for authentic student engagement in research. Using a novel framework, remote Microbial Ecology CURE students used microbes isolated via antimicrobial-challenged Winogradsky columns to investigate phylogeny and metabolism through a hypothesis-driven meta-analysis (MA). Students used 16S rRNA and key metabolic enzymes to compare phylogeny; enzymes were modeled and evaluated for putative conserved domains, culminating in primer design and analysis. Using in silico tools facilitated student development of bioinformatics skills. The MA was subdivided into discrete sections in order to (i) provide a timeline for students to remain on schedule throughout a remote-learning lab experience, (ii) encourage feedback throughout the project, and (iii) facilitate student understanding of the experimental design. MA deliverables were designed to be specific figures with individual titles, legends, and analyses to enable their feedback for subsequent presentations. The six key formative deliverables included a word cloud (used to develop the works cited list and hypothesis), a 16S rRNA phylogenetic tree, an annotated metabolic pathway and three-dimensional model of the key metabolic enzyme, a phylogenetic tree based on the key metabolic enzyme, design and analysis of a primer set for the key metabolic enzyme, and a summative poster and graphical abstract. The MA project yielded poster presentations at virtual conferences, lab presentations, and written reports. Using the hypothesis-based MA model encouraged an authentic research experience, enabling students to develop, discuss, and progress in meaningful experiments.}, }
@article {pmid35338380, year = {2022}, author = {Yuan, B and Guo, M and Wu, W and Zhou, X and Li, M and Xie, S}, title = {Spatial and Seasonal Patterns of Sediment Bacterial Communities in Large River Cascade Reservoirs: Drivers, Assembly Processes, and Co-occurrence Relationship.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35338380}, issn = {1432-184X}, support = {91747206//national natural science foundation of china/ ; 42107493//National Natural Science Foundation of China/ ; }, abstract = {Sediment bacteria play an irreplaceable role in promoting the function and biogeochemical cycle of the freshwater ecosystem; however, little is known about their biogeographical patterns and community assembly mechanisms in large river suffering from cascade development. Here, we investigated the spatiotemporal distribution patterns of bacterial communities employing next-generation sequencing analysis and multivariate statistical analyses from the Lancang River cascade reservoirs during summer and winter. We found that sediment bacterial composition has a significant seasonal turnover due to the modification of cascade reservoirs operation mode, and the spatial consistency of biogeographical models (including distance-decay relationship and covariation of community composition with geographical distance) also has subtle changes. The linear regression between the dissimilarity of bacterial communities in sediments, geographical and environmental distance showed that the synergistic effects of geographical and environmental factors explained the influence on bacterial communities. Furthermore, the environmental difference explained little variations (19.40%) in community structure, implying the homogeneity of environmental conditions across the cascade reservoirs of Lancang River. From the quantification of the ecological process, the homogeneous selection was recognized as the dominating factor of bacterial community assembly. The co-occurrence topological network analyses showed that the key genera were more important than the most connected genera. In general, the assembly of bacterial communities in sediment of cascade reservoirs was mediated by both deterministic and stochastic processes and is always dominated by homogeneous selection with the seasonal switching, but the effects of dispersal limitation and ecological drift cannot be ignored.}, }
@article {pmid35337832, year = {2022}, author = {Monteiro Venturini, A and Silvestre Dias, NM and Gontijo, JB and Yoshiura, CA and da Silva Paula, F and Meyer, KM and Nakamura, FM and da França, AG and Borges, CD and Barlow, J and Berenguer, E and Nüsslein, K and Mazza Rodrigues, JL and Bohannan, BJM and Tsai, SM}, title = {Increased soil moisture intensifies the impacts of forest-to-pasture conversion on methane emissions and methane-cycling communities in the Eastern Amazon.}, journal = {Environmental research}, volume = {}, number = {}, pages = {113139}, doi = {10.1016/j.envres.2022.113139}, pmid = {35337832}, issn = {1096-0953}, abstract = {Climatic changes are altering precipitation patterns in the Amazon and may influence soil methane (CH4) fluxes due to the differential responses of methanogenic and methanotrophic microorganisms. However, it remains unclear if these climate feedbacks can amplify land-use-related impacts on the CH4 cycle. To better predict the responses of soil CH4-cycling microorganisms and emissions under altered moisture levels in the Brazilian Eastern Amazon, we performed a 30-day microcosm experiment manipulating the moisture content (original moisture; 60%, 80%, and 100% of field capacity - FC) of forest and pasture soils. Gas samples were collected periodically for gas chromatography analysis, and methanogenic archaeal and methanotrophic bacterial communities were assessed using quantitative PCR and metagenomics. Positive and negative daily CH4 fluxes were observed for forest and pasture, indicating that these soils can act as both CH4 sources and sinks. Cumulative emissions and the abundance of methanogenesis-related genes and taxonomic groups were affected by land use, moisture, and their interaction. Pasture soils at 100% FC had the highest abundance of methanogens and CH4 emissions, 22 times higher than forest soils under the same treatment. Higher ratios of methanogens to methanotrophs were found in pasture than in forest soils, even at field capacity conditions. Land use and moisture were significant factors influencing the composition of methanogenic and methanotrophic communities. The diversity and evenness of methanogens did not change throughout the experiment. In contrast, methanotrophs exhibited the highest diversity and evenness in pasture soils at 100% FC. Taken together, our results suggest that increased moisture exacerbates soil CH4 emissions and microbial responses driven by land-use change in the Amazon. This is the first report on the microbial CH4 cycle in Amazonian upland soils that combined one-month gas measurements with advanced molecular methods.}, }
@article {pmid35335680, year = {2022}, author = {Morris, CE and Ramirez, N and Berge, O and Lacroix, C and Monteil, C and Chandeysson, C and Guilbaud, C and Blischke, A and Sigurbjörnsdóttir, MA and Vilhelmsson, OÞ}, title = {Pseudomonas syringae on Plants in Iceland Has Likely Evolved for Several Million Years Outside the Reach of Processes That Mix This Bacterial Complex across Earth's Temperate Zones.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/pathogens11030357}, pmid = {35335680}, issn = {2076-0817}, abstract = {Here we report, for the first time, the occurrence of the bacteria from the species complex Pseudomonas syringae in Iceland. We isolated this bacterium from 35 of the 38 samples of angiosperms, moss, ferns and leaf litter collected across the island from five habitat categories (boreal heath, forest, subalpine and glacial scrub, grazed pasture, lava field). The culturable populations of P. syringae on these plants varied in size across 6 orders of magnitude, were as dense as 107 cfu g-1 and were composed of strains in phylogroups 1, 2, 4, 6, 7, 10 and 13. P. syringae densities were significantly greatest on monocots compared to those on dicots and mosses and were about two orders of magnitude greater in grazed pastures compared to all other habitats. The phylogenetic diversity of 609 strains of P. syringae from Iceland was compared to that of 933 reference strains of P. syringae from crops and environmental reservoirs collected from 27 other countries based on a 343 bp sequence of the citrate synthase (cts) housekeeping gene. Whereas there were examples of identical cts sequences across multiple countries and continents among the reference strains indicating mixing among these countries and continents, the Icelandic strains grouped into monophyletic lineages that were unique compared to all of the reference strains. Based on estimates of the time of divergence of the Icelandic genetic lineages of P. syringae, the geological, botanical and land use history of Iceland, and atmospheric circulation patterns, we propose scenarios whereby it would be feasible for P. syringae to have evolved outside the reach of processes that tend to mix this bacterial complex across the planet elsewhere.}, }
@article {pmid35335670, year = {2022}, author = {Chitlapilly Dass, S and Wang, R}, title = {Biofilm through the Looking Glass: A Microbial Food Safety Perspective.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/pathogens11030346}, pmid = {35335670}, issn = {2076-0817}, support = {USDA-NIFA 2020-67017-30776.//United States Department of Agriculture/ ; }, abstract = {Food-processing facilities harbor a wide diversity of microorganisms that persist and interact in multispecies biofilms, which could provide an ecological niche for pathogens to better colonize and gain tolerance against sanitization. Biofilm formation by foodborne pathogens is a serious threat to food safety and public health. Biofilms are formed in an environment through synergistic interactions within the microbial community through mutual adaptive response to their long-term coexistence. Mixed-species biofilms are more tolerant to sanitizers than single-species biofilms or their planktonic equivalents. Hence, there is a need to explore how multispecies biofilms help in protecting the foodborne pathogen from common sanitizers and disseminate biofilm cells from hotspots and contaminate food products. This knowledge will help in designing microbial interventions to mitigate foodborne pathogens in the processing environment. As the global need for safe, high-quality, and nutritious food increases, it is vital to study foodborne pathogen behavior and engineer new interventions that safeguard food from contamination with pathogens. This review focuses on the potential food safety issues associated with biofilms in the food-processing environment.}, }
@article {pmid35333990, year = {2022}, author = {Sugiyama, N and Uehara, O and Morikawa, T and Paudel, D and Ebata, K and Hiraki, D and Harada, F and Yoshida, K and Kato, S and Nagasawa, T and Miura, H and Abiko, Y and Furuichi, Y}, title = {Gut flora alterations due to lipopolysaccharide derived from Porphyromonas gingivalis.}, journal = {Odontology}, volume = {}, number = {}, pages = {}, pmid = {35333990}, issn = {1618-1255}, support = {20H03867//Grant-in-Aid for Scientific Research (B)/ ; }, abstract = {Gut dysbiosis induces 'leaky gut,' a condition associated with diabetes, NASH, and various auto-immune diseases. Porphyromonas gingivalis is a periodontopathic bacterium which causes periodontal tissue breakdown, and often enters the systemic blood flow. Oral administration of P. gingivalis induced gut dysbiosis in mice model, but no systemic administration of P. gingivalis has been reported thus far. In the present study, we investigated the effect of P. gingivalis-derived lipopolysaccharide (Pg-LPS) on the intestinal flora of our established mouse model. Eight-week-old C57BL/6J mice were intraperitoneally administered Pg-LPS. Three months later, DNA was extracted from stool, and RNA from the small and large intestines. After euthanizing the mice, pathological sections of the intestinal tract were prepared and stained with hematoxylin and eosin (H&amp;E). Tumor necrosis factor alpha (TNF-α), interleukin (IL)-1β, and IL-6 expression levels were evaluated using quantitative PCR. 16S rRNA gene PCR amplicon analysis data were acquired using NGS. Microbial diversity and composition were analyzed using Quantitative Insights into Microbial Ecology 2. Furthermore, alterations in microbial function were performed by PICRUSt2. No significant inflammatory changes were observed in the H&amp;E. No significant differences in the mRNA levels of IL-1β, IL-6, and TNF-α were observed between the groups. Pg-LPS administration decreased the abundance of Allobacterium in the gut. A predictive metagenomic analysis by PICRUSt2 and STAMP showed that 47 pathways increased and 17 pathways decreased after Pg-LPS administration. Systemic application of periodontal pathogens may cause changes in the intestinal flora which may affect the physiological functions of the intestinal tract.}, }
@article {pmid35333950, year = {2022}, author = {Angra, V and Sehgal, R and Gupta, R}, title = {Trends in PHA Production by Microbially Diverse and Functionally Distinct Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35333950}, issn = {1432-184X}, support = {09/237(0168)/2018-EMR-I//Council of Scientific and Industrial Research, India/ ; }, abstract = {Along with the wide applications of conventional plastics, they have a large number of disadvantages like their non-biodegradable nature, dependency on fossil fuels and the release of large amounts of toxic materials in the environment. Therefore, to resolve these problems, a number of bioplastics are studied, out of which polyhydroxyalkanoates are considered as the best alternatives. Polyhydroxyalkanoates (PHAs) are produced by microorganisms as intracellular granules during stressful conditions. Though a wide range of organisms can naturally produce PHAs, only a few of them can be used for commercial production. Therefore, more diverse organisms that accumulate a considerable amount of PHAs and also reduce the production cost need to be exploited. Transgenic plants, recombinant bacteria, algae and extremophiles are some diverse organisms that produce a high amount of PHAs at a low cost. So, if potential organisms are used for PHA production, bioplastics will be able to completely replace petroleum-based polymers. Therefore, our review mainly focuses on production of PHAs using potential organisms so that amount of PHAs produced is high and cost-effective which would further help in the commercialization of PHAs.}, }
@article {pmid35332832, year = {2022}, author = {Crits-Christoph, A and Hallowell, HA and Koutouvalis, K and Suez, J}, title = {Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2055944}, doi = {10.1080/19490976.2022.2055944}, pmid = {35332832}, issn = {1949-0984}, abstract = {A global rise in antimicrobial resistance among pathogenic bacteria has proved to be a major public health threat, with the rate of multidrug-resistant bacterial infections increasing over time. The gut microbiome has been studied as a reservoir of antibiotic resistance genes (ARGs) that can be transferred to bacterial pathogens via horizontal gene transfer (HGT) of conjugative plasmids and mobile genetic elements (the gut resistome). Advances in metagenomic sequencing have facilitated the identification of resistome modulators, including live microbial therapeutics such as probiotics and fecal microbiome transplantation that can either expand or reduce the abundances of ARG-carrying bacteria in the gut. While many different gut microbes encode for ARGs, they are not uniformly distributed across, or transmitted by, various members of the microbiome, and not all are of equal clinical relevance. Both experimental and theoretical approaches in microbial ecology have been applied to understand differing frequencies of ARG horizontal transfer between commensal microbes as well as between commensals and pathogens. In this commentary, we assess the evidence for the role of commensal gut microbes in encoding antimicrobial resistance genes, the degree to which they are shared both with other commensals and with pathogens, and the host and environmental factors that can impact resistome dynamics. We further discuss novel sequencing-based approaches for identifying ARGs and predicting future transfer events of clinically relevant ARGs from commensals to pathogens.}, }
@article {pmid35332366, year = {2022}, author = {Xiang, X and Wang, H and Man, B and Xu, Y and Gong, L and Tian, W and Yang, H}, title = {Diverse Bathyarchaeotal Lineages Dominate Archaeal Communities in the Acidic Dajiuhu Peatland, Central China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35332366}, issn = {1432-184X}, support = {41572325//National Natural Science Foundation of China/ ; CUGQY1922//Fundamental Research Funds for the Central Universities, China University of Geosciences (Wuhan)/ ; 2021F10//Open Research Fund of Hubei Key Laboratory of Critical Zone Evolution, China University of Geosciences, Wuhan, China/ ; }, abstract = {Bathyarchaeota are believed to have roles in the carbon cycle in marine systems. However, the ecological knowledge of Bathyarchaeota is limited in peatland ecosystems. Here, we investigated the vertical distribution of Bathyarchaeota community structure using quantitative PCR and high-throughput sequencing technology of ribosomal 16S rRNA gene integrated with detailed chemical profiling in the Dajiuhu Peatland, central China. Eight archaeal phyla were observed in peat samples, which mainly composed of Bathyarchaeota with a mean relative abundance about 88%, followed by Thaumarchaeota (9%). Bathyarchaeota were further split into 17 subgroups, and some subgroups showed habitat specificity to peat horizons with distinct lithological and physicochemical properties, for example, Bathy-6 and Bathy-15 had preference for the acrotelm, Bathy-5b, Bathy-16, and Bathy-19 were enriched in the catotelm, Bathy-5a, Bathy-8, and Bathy-11 were specific for the clay horizon. This spatial distribution pattern of archaeal communities along peat profile was mainly influenced by water content as indicated by RDA ordination and permutational MANOVA, whereas organic matter content exclusively affected Bathyarchaeota distribution along the peat profile significantly. The abundance of archaeal 16S rRNA genes ranged from 105 to 107 copies per gram dry sediment, and the highest archaeal biomass was observed in the periodically oxic mesotelm horizon with more dynamic archaeal interaction relationship as indicated by the network analysis. Bathyarchaeota dominated the archaeal interaction network with 82% nodes, 96% edges, and 71% keystone species. Our results provide an overview of the archaeal population, community structure, and relationship with environmental factors that affect the vertical distribution of archaeal communities and emphasize the ecology of bathyarchaeotal lineages in terrestrial peatland ecosystems.}, }
@article {pmid35331758, year = {2022}, author = {Fang, W and Lin, M and Shi, J and Liang, Z and Tu, X and He, Z and Qiu, R and Wang, S}, title = {Organic carbon and eukaryotic predation synergistically change resistance and resilience of aquatic microbial communities.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {154386}, doi = {10.1016/j.scitotenv.2022.154386}, pmid = {35331758}, issn = {1879-1026}, abstract = {With rapid global urbanization, anthropogenic activities alter aquatic biota in urban rivers through inputs of dissolved organic carbon (DOC) and nutrients. Microorganisms-mediated global element cycles provide functions in maintaining microbial ecology stability. The DOC (bottom-up control) and microbial predation (top-down control) may synergistically drive the competition and evolution of aquatic microbial communities, as well as their resistance and resilience, for which experimental evidences remain scarce. In this study, laboratory sediment-water column experiments were employed to mimic the organic carbon-driven water blackening and odorization process in urban rivers and to elucidate the impact of DOC on microbial ecology stability. Results showed that low (25-75 mg/L) and high DOC (100-150 mg/L) changed the aquatic microbial community assemblies in different patterns: (1) the low DOC enriched K-selection microorganisms (e.g., C39, Tolumonas and CR08G) with low biomass and low resilience, as well as high resistance to perturbations in changing microbial community assemblies; (2) the high DOC was associated with r-selection microorganisms (e.g., PSB-M-3 and Clostridium) with high biomass and improved resilience, together with low resistance detrimental to microbial ecology stability. Overall, this study provided new insight into the impact of DOC on aquatic microbial community stability, which may help guide sustainable urban river management.}, }
@article {pmid35330304, year = {2022}, author = {Fatemi, S and Haelewaters, D and Urbina, H and Brown, S and Houston, ML and Aime, MC}, title = {Sporobolomyces lactucae sp. nov. (Pucciniomycotina, Microbotryomycetes, Sporidiobolales): An Abundant Component of Romaine Lettuce Phylloplanes.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {3}, pages = {}, doi = {10.3390/jof8030302}, pmid = {35330304}, issn = {2309-608X}, support = {8072-42000-077-00D//Agricultural Research Service/ ; 1010662//National Institute of Food and Agriculture/ ; }, abstract = {Shifts in food microbiomes may impact the establishment of human pathogens, such as virulent lineages of Escherichia coli, and thus are important to investigate. Foods that are often consumed raw, such as lettuce, are particularly susceptible to such outbreaks. We have previously found that an undescribed Sporobolomyces yeast is an abundant component of the mycobiome of commercial romaine lettuce (Lactuca sativa). Here, we formally describe this species as Sporobolomyces lactucae sp. nov. (Pucciniomycotina, Microbotryomycetes, and Sporidiobolales). We isolated multiple strains of this yeast from commercial romaine lettuce purchased from supermarkets in Illinois and Indiana; additional isolates were obtained from various plant phylloplanes in California. S. lactucae is a red-pigmented species that is similar in appearance to other members of the genus Sporobolomyces. However, it can be differentiated by its ability to assimilate glucuronate and D-glucosamine. Gene genealogical concordance supports S. lactucae as a new species. The phylogenetic reconstruction of a four-locus dataset, comprising the internal transcribed spacer and large ribosomal subunit D1/D2 domain of the ribosomal RNA gene, translation elongation factor 1-α, and cytochrome B, places S. lactucae as a sister to the S. roseus clade. Sporobolomyces lactucae is one of the most common fungi in the lettuce microbiome.}, }
@article {pmid35320603, year = {2022}, author = {Kohler, TJ and Fodelianakis, S and Michoud, G and Ezzat, L and Bourquin, M and Peter, H and Busi, SB and Pramateftaki, P and Deluigi, N and Styllas, M and Tolosano, M and de Staercke, V and Schön, M and Brandani, J and Marasco, R and Daffonchio, D and Wilmes, P and Battin, TJ}, title = {Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.16169}, pmid = {35320603}, issn = {1365-2486}, abstract = {The shrinking of glaciers is among the most iconic consequences of climate change. Despite this, the downstream consequences for ecosystem processes and related microbiome structure and function remain poorly understood. Here, using a space-for-time substitution approach across 101 glacier-fed streams (GFSs) from six major regions worldwide, we investigated how glacier shrinkage is likely to impact the organic matter decomposition rates of benthic biofilms. To do this, we measured the activities of five common extracellular enzymes and estimated decomposition rates by using enzyme allocation equations based on stoichiometry. We found decomposition rates to average 0.0129 (% d-1), and that decreases in glacier influence (estimated by percent glacier catchment coverage, turbidity, and a glacier index) accelerates decomposition rates. To explore mechanisms behind these relationships, we further compared decomposition rates with biofilm and streamwater characteristics. We found that chlorophyll-a, temperature, and streamwater N:P together explained 61% of the variability in decomposition. Algal biomass, which is also increasing with glacier shrinkage, showed a particularly strong relationship with decomposition, likely indicating their importance in contributing labile organic compounds to these carbon-poor habitats. We also found high relative abundances of chytrid fungi in GFS sediments, which putatively parasitize these algae, promoting decomposition through a fungal shunt. Exploring the biofilm microbiome, we then sought to identify bacterial phylogenetic clades significantly associated with decomposition, and found numerous positively- (e.g. Saprospiraceae) and negatively- (e.g. Nitrospira) related clades. Lastly, using metagenomics, we found evidence of different bacterial classes possessing different proportions of EEA-encoding genes, potentially informing some of the microbial associations with decomposition rates. Our results, therefore, present new mechanistic insights into organic matter decomposition in GFSs by demonstrating that an algal-based 'green food web' is likely to increase in importance in the future, and will promote important biogeochemical shifts in these streams as glaciers vanish.}, }
@article {pmid35316575, year = {2022}, author = {Timmis, K and Verstraete, W}, title = {Multiple intertwined crises facing humanity necessitate a European Environmental Research Organization.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.14054}, pmid = {35316575}, issn = {1751-7915}, }
@article {pmid35316402, year = {2022}, author = {Tiwari, N and Bansal, M and Santhiya, D and Sharma, JG}, title = {Insights into microbial diversity on plastisphere by multi-omics.}, journal = {Archives of microbiology}, volume = {204}, number = {4}, pages = {216}, pmid = {35316402}, issn = {1432-072X}, abstract = {Plastic pollution is a major concern in marine environment as it takes many years to degrade and is one of the greatest threats to marine life. Plastic surface, referred to as plastisphere, provides habitat for growth and proliferation of various microorganisms. The discovery of these microbes is necessary to identify significant genes, enzymes and bioactive compounds that could help in bioremediation and other commercial applications. Conventional culture techniques have been successful in identifying few microbes from these habitats, leaving majority of them yet to be explored. As such, to recognize the vivid genetic diversity of microbes residing in plastisphere, their structure and corresponding ecological roles within the ecosystem, an emerging technique, called metagenomics has been explored. The technique is expected to provide hitherto unknown information on microbes from the plastisphere. Metagenomics along with next generation sequencing provides comprehensive knowledge on microbes residing in plastisphere that identifies novel microbes for plastic bioremediation, bioactive compounds and other potential benefits. The following review summarizes the efficiency of metagenomics and next generation sequencing technology over conventionally used methods for culturing microbes. It attempts to illustrate the workflow mechanism of metagenomics to elucidate diverse microbial profiles. Further, importance of integrated multi-omics techniques has been highlighted in discovering microbial ecology residing on plastisphere for wider applications.}, }
@article {pmid35316343, year = {2022}, author = {Dallas, JW and Warne, RW}, title = {Captivity and Animal Microbiomes: Potential Roles of Microbiota for Influencing Animal Conservation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35316343}, issn = {1432-184X}, abstract = {During the ongoing biodiversity crisis, captive conservation and breeding programs offer a refuge for species to persist and provide source populations for reintroduction efforts. Unfortunately, captive animals are at a higher disease risk and reintroduction efforts remain largely unsuccessful. One potential factor in these outcomes is the host microbiota which includes a large diversity and abundance of bacteria, fungi, and viruses that play an essential role in host physiology. Relative to wild populations, the generalized pattern of gut and skin microbiomes in captivity are reduced alpha diversity and they exhibit a significant shift in community composition and/or structure which often correlates with various physiological maladies. Many conditions of captivity (antibiotic exposure, altered diet composition, homogenous environment, increased stress, and altered intraspecific interactions) likely lead to changes in the host-associated microbiome. To minimize the problems arising from captivity, efforts can be taken to manipulate microbial diversity and composition to be comparable with wild populations through methods such as increasing dietary diversity, exposure to natural environmental reservoirs, or probiotics. For individuals destined for reintroduction, these strategies can prime the microbiota to buffer against novel pathogens and changes in diet and improve reintroduction success. The microbiome is a critical component of animal physiology and its role in species conservation should be expanded and included in the repertoire of future management practices.}, }
@article {pmid35316342, year = {2022}, author = {Zhao, X and Fan, X and Gong, Z and Gao, X and Wang, Y and Ni, B}, title = {The Toxic Effects of Cu and CuO Nanoparticles on Euplotes aediculatus.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35316342}, issn = {1432-184X}, support = {31672249//national natural science foundation of china/ ; }, abstract = {The single-celled eukaryote Euplotes aediculatus was chosen to test and compare the toxic effects of Cu and CuO nanoparticles (NPs). The antioxidant enzymatic activity, morphological changes, and functional groups on the membrane were determined using spectrophotometry, microscopy, and Fourier transform infrared spectroscopy after NPs treatment. The toxicity of the NPs to cells was dose-dependent, and the 24 h-LC50 values of the CuNPs and CuONPs were 0.46 µg/L and 1.24 × 103 µg/L, respectively. These NPs increased the activities of superoxide dismutase, glutathione peroxidase, and catalase and destroyed the cell structure; moreover, the CuNPs were more toxic than the CuONPs. In addition to the higher enzymatic activity, CuNPs also caused nucleoli disappearance, chromatin condensation, and mitochondrial and pellicle damage. The oxidization of the functional groups of the membrane (PO2 - , C-O-C, and δ(COH) of carbohydrates) also confirmed the severe damage caused by CuNPs. Our study showed that oxidative stress and organelle destruction played important roles in the toxic effects of these NPs on this protozoan. Compared with other aquatic organisms, E. aediculatus can be considered a potential indicator at the preliminary stage of environmental pollution.}, }
@article {pmid35314061, year = {2022}, author = {Girardi, NS and Sosa, AL and Etcheverry, MG and Passone, MA}, title = {In vitro characterization bioassays of the nematophagous fungus Purpureocillium lilacinum: Evaluation on growth, extracellular enzymes, mycotoxins and survival in the surrounding agroecosystem of tomato.}, journal = {Fungal biology}, volume = {126}, number = {4}, pages = {300-307}, doi = {10.1016/j.funbio.2022.02.001}, pmid = {35314061}, issn = {1878-6146}, abstract = {The effects of water stress and temperature on in vitro growth and enzymatic activity of Purpureocillium lilacinum (Sordariomycetes, Hypocreales, Ophiocordycipitaceae) isolates with demonstrated capacity to control Nacobbus aberrans (Secernentea, Tylenchida, Pratylenchidae) were evaluated in this study. Also, saprophytic and endophytic colonization in tomato plants were determined. P. lilacinum was able to grow under the evaluated levels of osmotic and matric stress, but the increase in water stress caused reductions in radial growth rates. Moreover, the fungal isolates produced chitinases, proteases, and leucinostatins under inductive conditions. The nematophagous fungi were able to develop saprophytically (104 CFU g-1 of soil). Meanwhile, only P. lilacinum SR38 demonstrated endophytic capacity. The results suggest that P. lilacinum can be effectively applied as biocontrol agents of phytoparasitic nematodes in tomatoes under variable agroecological conditions.}, }
@article {pmid35313934, year = {2022}, author = {Merino, I and de la Fuente, A and Domínguez-Gil, M and Eiros, JM and Tedim, AP and Bermejo-Martín, JF}, title = {Digital PCR applications for the diagnosis and management of infection in critical care medicine.}, journal = {Critical care (London, England)}, volume = {26}, number = {1}, pages = {63}, pmid = {35313934}, issn = {1466-609X}, support = {PI19/00590//Instituto de Salud Carlos III/ ; CD18/00123//Instituto de Salud Carlos III/ ; CM18/00157//Instituto de Salud Carlos III/ ; FI20/00278//Instituto de Salud Carlos III/ ; APT//European Society of Clinical Microbiology and Infectious Diseases/ ; }, abstract = {Infection (either community acquired or nosocomial) is a major cause of morbidity and mortality in critical care medicine. Sepsis is present in up to 30% of all ICU patients. A large fraction of sepsis cases is driven by severe community acquired pneumonia (sCAP), which incidence has dramatically increased during COVID-19 pandemics. A frequent complication of ICU patients is ventilator associated pneumonia (VAP), which affects 10-25% of all ventilated patients, and bloodstream infections (BSIs), affecting about 10% of patients. Management of these severe infections poses several challenges, including early diagnosis, severity stratification, prognosis assessment or treatment guidance. Digital PCR (dPCR) is a next-generation PCR method that offers a number of technical advantages to face these challenges: it is less affected than real time PCR by the presence of PCR inhibitors leading to higher sensitivity. In addition, dPCR offers high reproducibility, and provides absolute quantification without the need for a standard curve. In this article we reviewed the existing evidence on the applications of dPCR to the management of infection in critical care medicine. We included thirty-two articles involving critically ill patients. Twenty-three articles focused on the amplification of microbial genes: (1) four articles approached bacterial identification in blood or plasma; (2) one article used dPCR for fungal identification in blood; (3) another article focused on bacterial and fungal identification in other clinical samples; (4) three articles used dPCR for viral identification; (5) twelve articles quantified microbial burden by dPCR to assess severity, prognosis and treatment guidance; (6) two articles used dPCR to determine microbial ecology in ICU patients. The remaining nine articles used dPCR to profile host responses to infection, two of them for severity stratification in sepsis, four focused to improve diagnosis of this disease, one for detecting sCAP, one for detecting VAP, and finally one aimed to predict progression of COVID-19. This review evidences the potential of dPCR as a useful tool that could contribute to improve the detection and clinical management of infection in critical care medicine.}, }
@article {pmid35312808, year = {2022}, author = {Caballero, JRI and Lalande, BM and Hanna, JW and Klopfenstein, NB and Kim, MS and Stewart, JE}, title = {Genomic Comparisons of Two Armillaria Species with Different Ecological Behaviors and Their Associated Soil Microbial Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35312808}, issn = {1432-184X}, abstract = {Armillaria species show considerable variation in ecological roles and virulence, from mycorrhizae and saprophytes to important root pathogens of trees and horticultural crops. We studied two Armillaria species that can be found in coniferous forests of northwestern USA and southwestern Canada. Armillaria altimontana not only is considered as a weak, opportunistic pathogen of coniferous trees, but it also appears to exhibit in situ biological control against A. solidipes, formerly North American A. ostoyae, which is considered a virulent pathogen of coniferous trees. Here, we describe their genome assemblies and present a functional annotation of the predicted genes and proteins for the two Armillaria species that exhibit contrasting ecological roles. In addition, the soil microbial communities were examined in association with the two Armillaria species within a 45-year-old plantation of western white pine (Pinus monticola) in northern Idaho, USA, where A. altimontana was associated with improved tree growth and survival, while A. solidipes was associated with reduced growth and survival. The results from this study reveal a high similarity between the genomes of the beneficial/non-pathogenic A. altimontana and pathogenic A. solidipes; however, many relatively small differences in gene content were identified that could contribute to differences in ecological lifestyles and interactions with woody hosts and soil microbial communities.}, }
@article {pmid35312065, year = {2022}, author = {Ceron-Chafla, P and García-Timermans, C and de Vrieze, J and Ganigué, R and Boon, N and Rabaey, K and van Lier, JB and Lindeboom, REF}, title = {Pre-incubation conditions determine the fermentation pattern and microbial community structure in fermenters at mild hydrostatic pressure.}, journal = {Biotechnology and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1002/bit.28085}, pmid = {35312065}, issn = {1097-0290}, abstract = {Fermentation at elevated hydrostatic pressure is a novel strategy targeting product selectivity. However, the role of inoculum history and cross-resistance, i.e., acquired tolerance from incubation under distinctive environmental stress, remains unclear in high-pressure operation. In our here presented work, we studied fermentation and microbial community responses of halotolerant marine sediment inoculum (MSI) and anaerobic digester inoculum (ADI), pre-incubated in serum bottles at different temperatures and subsequently exposed to mild hydrostatic pressure (MHP <10 MPa) in stainless steel reactors. Results showed that MHP effects on microbial growth, activity and community structure were strongly temperature-dependent. At moderate temperature (20°C), biomass yield and fermentation were not limited by MHP; suggesting a cross-resistance effect from incubation temperature and halotolerance. Low temperatures (10°C) and MHP imposed kinetic and bioenergetic limitations, constraining growth and product formation. Fermentation remained favorable in MSI at 28°C and ADI at 37°C, despite reduced biomass yield resulting from maintenance and decay proportionally increasing with temperature. Microbial community structure was modified by temperature during the enrichment, and slight differences observed after MHP-exposure did not compromise functionality. Results showed that the relation incubation temperature - halotolerance proved to be a modifier of microbial responses to MHP and could be potentially exploited in fermentations to modulate product/biomass ratio. This article is protected by copyright. All rights reserved.}, }
@article {pmid35311515, year = {2022}, author = {Linney, MD and Eppley, JM and Romano, AE and Luo, E and DeLong, EF and Karl, DM}, title = {Microbial Sources of Exocellular DNA in the Ocean.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0209321}, doi = {10.1128/aem.02093-21}, pmid = {35311515}, issn = {1098-5336}, abstract = {Exocellular DNA is operationally defined as the fraction of the total DNA pool that passes through a membrane filter (0.1 μm). It is composed of DNA-containing vesicles, viruses, and free DNA and is ubiquitous in all aquatic systems, although the sources, sinks, and ecological consequences are largely unknown. Using a method that provides separation of these three fractions, we compared open ocean depth profiles of DNA associated with each fraction. Pelagibacter-like DNA dominated the vesicle fractions for all samples examined over a depth range of 75 to 500 m. Viral DNA consisted predominantly of myovirus-like and podovirus-like DNA and contained the highest proportion of unannotated sequences. Euphotic zone free DNA (75 to 125 m) contained primarily bacterial and viral sequences, with bacteria dominating samples from the mesopelagic zone (500 to 1,000 m). A high proportion of mesopelagic zone free DNA sequences appeared to originate from surface waters, including a large amount of DNA contributed by high-light Prochlorococcus ecotypes. Throughout the water column, but especially in the mesopelagic zone, the composition of free DNA sequences was not always reflective of cooccurring microbial communities that inhabit the same sampling depth. These results reveal the composition of free DNA in different regions of the water column (euphotic and mesopelagic zones), with implications for dissolved organic matter cycling and export (by way of sinking particles and/or migratory zooplankton) as a delivery mechanism. IMPORTANCE With advances in metagenomic sequencing, the microbial composition of diverse environmental systems has been investigated, providing new perspectives on potential ecological dynamics and dimensions for experimental investigations. Here, we characterized exocellular free DNA via metagenomics, using a newly developed method that separates free DNA from cells, viruses, and vesicles, and facilitated the independent characterization of each fraction. The fate of this free DNA has both ecological consequences as a nutrient (N and P) source and potential evolutionary consequences as a source of genetic transformation. Here, we document different microbial sources of free DNA at the surface (0 to 200 m) versus depths of 250 to 1,000 m, suggesting that distinct free DNA production mechanisms may be present throughout the oligotrophic water column. Examining microbial processes through the lens of exocellular DNA provides insights into the production of labile dissolved organic matter (i.e., free DNA) at the surface (likely by viral lysis) and processes that influence the fate of sinking, surface-derived organic matter.}, }
@article {pmid35309262, year = {2022}, author = {Amit,  and Jamwal, R and Kumari, S and Kelly, S and Cannavan, A and Singh, DK}, title = {Assessment of geographical origin of virgin coconut oil using inductively coupled plasma mass spectrometry along with multivariate chemometrics.}, journal = {Current research in food science}, volume = {5}, number = {}, pages = {545-552}, pmid = {35309262}, issn = {2665-9271}, abstract = {Recently, Virgin coconut oil (VCO) has emerged as one of the most favorable edible oils because of its application in cooking, frying as well as additive used in food, pharmaceuticals, and cosmetic goods. These qualities have established VCO in high consumer demand and there is a great need of establishing a reliable method for the identification of its geographical origin. Through this present study, for the first time, it has been established that Inductively Coupled Plasma-Mass-Spectrometry (ICP-MS) combined with multivariate chemometrics can be used for the identification of the geographical origin of the VCO samples of various provinces. Principal Component Analysis (PCA), and Linear Discriminant Analysis (LDA) were able to differentiate and classify the VCO samples of different geographical origins. Further, calibration models (Principal Component Regression and Partial Least Square Regression) were developed on the calibration dataset of the elemental concentration obtained from the ICP-MS analysis. An external dataset was used to develop the prediction model to predict the geographical origin of an unknown sample. Both PCR and PLS-R models were successfully able to predict the geographical origin with a high R2 value (0.999) and low RMSEP value 0.074 and 0.075% v/v of prediction respectively. In conclusion, ICP-MS combined with regression modelling can be used as an excellent tool for the identification of the geographical origin of the VCO samples of various provinces. This whole technique is the most suitable as it has high sensitivity as well as provides easy multi-metal analysis for a single sample of edible oil.}, }
@article {pmid35306576, year = {2022}, author = {Hanashiro, FTT and De Meester, L and Vanhamel, M and Mukherjee, S and Gianuca, AT and Verbeek, L and van den Berg, E and Souffreau, C}, title = {Bacterioplankton Assembly Along a Eutrophication Gradient Is Mainly Structured by Environmental Filtering, Including Indirect Effects of Phytoplankton Composition.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35306576}, issn = {1432-184X}, support = {PF/2010/07//KU Leuven Research Fund Excellence Center/ ; 245968/2012-1//Science Without Borders/ ; }, abstract = {Biotic interactions are suggested to be key factors structuring bacterioplankton community assembly but are rarely included in metacommunity studies. Eutrophication of ponds and lakes provides a useful opportunity to evaluate how bacterioplankton assembly is affected by specific environmental conditions, especially also by biotic interactions with other trophic levels such as phytoplankton and zooplankton. Here, we evaluated the importance of deterministic and stochastic processes on bacterioplankton community assembly in 35 shallow ponds along a eutrophication gradient in Belgium and assessed the direct and indirect effects of phytoplankton and zooplankton community variation on bacterioplankton assembly through a path analysis and network analysis. Environmental filtering by abiotic factors (suspended matter concentration and pH) explained the largest part of the bacterioplankton community variation. Phytoplankton community structure affected bacterioplankton structure through its effect on variation in chlorophyll-a and suspended matter concentration. Bacterioplankton communities were also spatially structured through pH. Overall, our results indicate that environmental variation is a key component driving bacterioplankton assembly along a eutrophication gradient and that indirect biotic interactions can also be important in explaining bacterioplankton community composition. Furthermore, eutrophication led to divergence in community structure and more eutrophic ponds had a higher diversity of bacteria.}, }
@article {pmid35305980, year = {2022}, author = {Kim, SJ and Kang, S and Xu, H and Bhaskar, P and Chenoli, S}, title = {Special issue: AFoPS on climate and life in poles.}, journal = {Environmental research}, volume = {}, number = {}, pages = {113125}, doi = {10.1016/j.envres.2022.113125}, pmid = {35305980}, issn = {1096-0953}, }
@article {pmid35138931, year = {2022}, author = {Bjorndahl, P and Bielawski, JP and Liu, L and Zhou, W and Gu, H}, title = {Novel Application of Survival Models for Predicting Microbial Community Transitions with Variable Selection for Environmental DNA.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {6}, pages = {e0214621}, doi = {10.1128/AEM.02146-21}, pmid = {35138931}, issn = {1098-5336}, support = {//Genome Canada (Génome Canada)/ ; RGPIN-2017-05108//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; ASPIRE CREATE//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; DG04109//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; }, abstract = {Survival analysis is a prolific statistical tool in medicine for inferring risk and time to disease-related events. However, it is underutilized in microbiome research to predict microbial community-mediated events, partly due to the sparsity and high-dimensional nature of the data. We advance the application of Cox proportional hazards (Cox PH) survival models to environmental DNA (eDNA) data with feature selection suitable for filtering irrelevant and redundant taxonomic variables. Selection methods are compared in terms of false positives, sensitivity, and survival estimation accuracy in simulation and in a real data setting to forecast harmful cyanobacterial blooms. A novel extension of a method for selecting microbial biomarkers with survival data (SuRFCox) reliably outperforms other methods. We determine that Cox PH models with SuRFCox-selected predictors are more robust to varied signal, noise, and data correlation structure. SuRFCox also yields the most accurate and consistent prediction of blooms according to cross-validated testing by year over eight different bloom seasons. Identification of common biomarkers among validated survival forecasts over changing conditions has clear biological significance. Survival models with such biomarkers inform risk assessment and provide insight into the causes of critical community transitions. IMPORTANCE In this paper, we report on a novel approach of selecting microorganisms for model-based prediction of the time to critical microbially modulated events (e.g., harmful algal blooms, clinical outcomes, community shifts, etc.). Our novel method for identifying biomarkers from large, dynamic communities of microbes has broad utility to environmental and ecological impact risk assessment and public health. Results will also promote theoretical and practical advancements relevant to the biology of specific organisms. To address the unique challenge posed by diverse environmental conditions and sparse microbes, we developed a novel method of selecting predictors for modeling time-to-event data. Competing methods for selecting predictors are rigorously compared to determine which is the most accurate and generalizable. Model forecasts are applied to show suitable predictors can precisely quantify the risk over time of biological events like harmful cyanobacterial blooms.}, }
@article {pmid35302890, year = {2022}, author = {Koldaeva, A and Tsai, HF and Shen, AQ and Pigolotti, S}, title = {Population genetics in microchannels.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {12}, pages = {e2120821119}, doi = {10.1073/pnas.2120821119}, pmid = {35302890}, issn = {1091-6490}, abstract = {SignificanceMany microbial populations proliferate in small channels. In such environments, reproducing cells organize in parallel lanes. Reproducing cells shift these lanes, potentially expelling other cells from the channel. In this paper, we combine theory and experiments to understand how these dynamics affects the diversity of a microbial population. We theoretically predict that genetic diversity is quickly lost along lanes of cells. Our experiments confirm that a population of proliferating Escherichia coli in a microchannel organizes into lanes of genetically identical cells within a few generations. Our findings elucidate the effect of lane formation on populations evolution, with potential applications ranging from microbial ecology in soil to dynamics of epithelial tissues in higher organisms.}, }
@article {pmid35300488, year = {2022}, author = {Frey, B and Varliero, G and Qi, W and Stierli, B and Walthert, L and Brunner, I}, title = {Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {828977}, doi = {10.3389/fmicb.2022.828977}, pmid = {35300488}, issn = {1664-302X}, abstract = {Soil microorganisms such as Bacteria and Archaea play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of soil metagenomes to a depth of 1.5 m in Swiss forests of European beech and oak species on calcareous bedrock. We explored the functional genetic potential of soil microorganisms with the aim to disentangle the effects of tree genus and soil depth on the genetic repertoire, and to gain insight into the microbial C and N cycling. The relative abundance of reads assigned to taxa at the domain level indicated a 5-10 times greater abundance of Archaea in the deep soil, while Bacteria showed no change with soil depth. In the deep soil there was an overrepresentation of genes for carbohydrate-active enzymes, which are involved in the catalyzation of the transfer of oligosaccharides, as well as in the binding of carbohydrates such as chitin or cellulose. In addition, N-cycling genes (NCyc) involved in the degradation and synthesis of N compounds, in nitrification and denitrification, and in nitrate reduction were overrepresented in the deep soil. Consequently, our results indicate that N-transformation in the deep soil is affected by soil depth and that N is used not only for assimilation but also for energy conservation, thus indicating conditions of low oxygen in the deep soil. Using shotgun metagenomics, our study provides initial findings on soil microorganisms and their functional genetic potential, and how this may change depending on soil properties, which shift with increasing soil depth. Thus, our data provide novel, deeper insight into the "dark matter" of the soil.}, }
@article {pmid35298685, year = {2022}, author = {Zhang, Z and Han, P and Zheng, Y and Jiao, S and Dong, H and Liang, X and Gao, D and Niu, Y and Yin, G and Liu, M and Hou, L}, title = {Spatiotemporal Dynamics of Bacterial Taxonomic and Functional Profiles in Estuarine Intertidal Soils of China Coastal Zone.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35298685}, issn = {1432-184X}, support = {41725002//China National Funds for Distinguished Young Scientists/ ; }, abstract = {Bacteria play an important role in regulating carbon (C), nitrogen (N), and sulfur (S) in estuarine intertidal wetlands. To gain insights into the ecological and metabolic modes possessed by bacteria in estuarine intertidal wetlands, a total of 78 surface soil samples were collected from China's coastal intertidal wetlands to examine the spatial and seasonal variations of bacterial taxonomic composition, assembly processes, and ecological system functions through shotgun metagenomic and 16S rRNA gene sequencing. Obvious spatiotemporal dynamic patterns in the bacterial community structure were identified, with more pronounced seasonal rather than spatial variations. Dispersion limitation was observed to act as a critical factor affecting community assembly, explaining approximately half of the total variation in the bacterial community. Functional bacterial community structure exhibited a more significant latitudinal change than seasonal variability, highlighting that functional stability of the bacterial communities differed with their taxonomic variability. Identification of biogeochemically related links between C, N, and S cycles in the soils showed the adaptive routed metabolism of the bacterial communities and the strong interactions between coupled metabolic pathways. Our study broadens the insights into the taxonomic and functional profiles of bacteria in China's estuarine intertidal soils and helps us understand the effects exerted by environmental factors on the ecological health and microbial diversity of estuarine intertidal flats.}, }
@article {pmid35295290, year = {2022}, author = {Zioutis, C and Seki, D and Bauchinger, F and Herbold, C and Berger, A and Wisgrill, L and Berry, D}, title = {Ecological Processes Shaping Microbiomes of Extremely Low Birthweight Infants.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {812136}, doi = {10.3389/fmicb.2022.812136}, pmid = {35295290}, issn = {1664-302X}, abstract = {The human microbiome has been implicated in affecting health outcomes in premature infants, but the ecological processes governing early life microbiome assembly remain poorly understood. Here, we investigated microbial community assembly and dynamics in extremely low birth weight infants (ELBWI) over the first 2 weeks of life. We profiled the gut, oral cavity and skin microbiomes over time using 16S rRNA gene amplicon sequencing and evaluated the ecological forces shaping these microbiomes. Though microbiomes at all three body sites were characterized by compositional instability over time and had low body-site specificity (PERMANOVA, r 2 = 0.09, p = 0.001), they could nonetheless be clustered into four discrete community states. Despite the volatility of these communities, deterministic assembly processes were detectable in this period of initial microbial colonization. To further explore these deterministic dynamics, we developed a probabilistic approach in which we modeled microbiome state transitions in each ELBWI as a Markov process, or a "memoryless" shift, from one community state to another. This analysis revealed that microbiomes from different body sites had distinctive dynamics as well as characteristic equilibrium frequencies. Time-resolved microbiome sampling of premature infants may help to refine and inform clinical practices. Additionally, this work provides an analysis framework for microbial community dynamics based on Markov modeling that can facilitate new insights, not only into neonatal microbiomes but also other human-associated or environmental microbiomes.}, }
@article {pmid35294588, year = {2022}, author = {Guarin, TC and Li, L and Pagilla, KR}, title = {Microbial community characterization in advanced water reclamation for potable reuse.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {35294588}, issn = {1432-0614}, abstract = {This study investigated the microbial community structure and composition across two treatment steps used in advanced water reclamation for potable reuse applications, namely Coagulation/Flocculation/Clarification/Granular Media Filtration (CFCGMF) and Ozone-Biological Activated Carbon filtration (O3/BAC). The study examined the richness, variations, and similarities of the microorganisms involved at each treatment step to better understand the role of ecology and the dynamics on unit process performance and the microbial community developed within it. The bacterial microbiomes at each treatment step were independently characterized using 16S metagenomic sequencing. Combining both treatment steps, a total of 3801 species were detected. From the total species detected, 38% and 98% were identified at CFCGMF and O3/BAC, respectively. The most abundant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes in both treatment steps. The identified species were classified based on their preferences to free-living style (59%) vs attached-living style (22%) showing a relatively low richness in the BAC media, but higher diversities. At the taxonomic class level, Betaproteobacteria was the predominant in both system processes. Additionally, a list of eight genera were identified as potential bacterial pathogens present in both process effluents. They are Aeromonas, Clostridium, Enterobacter, Escherichia, Flavobacterium, Legionella, Mycobacterium, and Pseudomonas. CFCGMF effluent yielded less pathogenic bacteria than both the ozone and BAC filter effluent from the O3/BAC process unit; their relative abundance accounted for about 2% and 8% for CFCGMF and O3/BAC, respectively. Detailed studies to characterize the microbial communities are crucial in interpreting the mechanisms and synergies between processes performance and microorganisms by identifying the needs and best practices to ensure public health protection. Key points • Microbial communities of two treatment processes are characterized using 16S rRNA sequencing. • Organisms that can tolerate ozone and form biofilms define microbial community in subsequent biofilters. • In relatively low abundances, potential pathogenic bacteria are detected in the treated water.}, }
@article {pmid35292274, year = {2022}, author = {Chai, G and Wang, D and Shan, J and Jiang, C and Yang, Z and Liu, E and Meng, H and Wang, H and Wang, Z and Qin, L and Xi, J and Ma, Y and Li, H and Qian, Y and Li, J and Lin, Y}, title = {Accumulation of high-molecular-weight polycyclic aromatic hydrocarbon impacted the performance and microbial ecology of bioretention systems.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {134314}, doi = {10.1016/j.chemosphere.2022.134314}, pmid = {35292274}, issn = {1879-1298}, abstract = {Bioretention has been considered as an effective management practice for urban stormwater in the removal of pollutants including polycyclic aromatic hydrocarbons (PAHs). However, the accumulation of high-molecular-weight (HMW) PAHs in bioretention systems and their potential impact on the pollutants removal performance and microbial ecology are still not fully understood. In this study, comparisons of treatment effectiveness, enzyme activity and microbial community in bioretention systems with different types of media amendments were carried out at different spiking levels of pyrene (PYR). The results showed that the removal efficiencies of chemical oxygen demand (COD) and total nitrogen in the bioretention systems were negatively impacted by the PYR levels. The relative activities of soil dehydrogenase and urease were increasingly inhibited by the elevated PYR level, indicating the declining microbial activity regarding organic matter decomposition. The spiking of PYR negatively affected microbial diversity, and distinct time- and influent-dependent changes in microbial communities were observed. The relative abundance of PAH-degrading microorganisms increased in PYR-spiked systems, while the abundance of nitrifiers decreased. The addition of media amendments was beneficial for the enrichment of microorganisms that are more resistant to PYR-related stress, therefore elevating the COD concentration removal rate by ∼50%. This study gives new insight into the multifaceted impacts of HMW PAH accumulation on microbial fingerprinting and enzyme activities, which may provide guidance on better stormwater management practices via bioretention in terms of improved system longevity and performance.}, }
@article {pmid35290040, year = {2022}, author = {Patzner, MS and Kainz, N and Lundin, E and Barczok, M and Smith, C and Herndon, E and Kinsman-Costello, L and Fischer, S and Straub, D and Kleindienst, S and Kappler, A and Bryce, C}, title = {Seasonal Fluctuations in Iron Cycling in Thawing Permafrost Peatlands.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.1c06937}, pmid = {35290040}, issn = {1520-5851}, abstract = {In permafrost peatlands, up to 20% of total organic carbon (OC) is bound to reactive iron (Fe) minerals in the active layer overlying intact permafrost, potentially protecting OC from microbial degradation and transformation into greenhouse gases (GHG) such as CO2 and CH4. During the summer, shifts in runoff and soil moisture influence redox conditions and therefore the balance of Fe oxidation and reduction. Whether reactive iron minerals could act as a stable sink for carbon or whether they are continuously dissolved and reprecipitated during redox shifts remains unknown. We deployed bags of synthetic ferrihydrite (FH)-coated sand in the active layer along a permafrost thaw gradient in Stordalen mire (Abisko, Sweden) over the summer (June to September) to capture changes in redox conditions and quantify the formation and dissolution of reactive Fe(III) (oxyhydr)oxides. We found that the bags accumulated Fe(III) under constant oxic conditions in areas overlying intact permafrost over the full summer season. In contrast, in fully thawed areas, conditions were continuously anoxic, and by late summer, 50.4 ± 12.8% of the original Fe(III) (oxyhydr)oxides were lost via dissolution. Periodic redox shifts (from 0 to +300 mV) were observed over the summer season in the partially thawed areas. This resulted in the dissolution and loss of 47.2 ± 20.3% of initial Fe(III) (oxyhydr)oxides when conditions are wetter and more reduced, and new formation of Fe(III) minerals (33.7 ± 8.6% gain in comparison to initial Fe) in the late summer under more dry and oxic conditions, which also led to the sequestration of Fe-bound organic carbon. Our data suggest that there is seasonal turnover of iron minerals in partially thawed permafrost peatlands, but that a fraction of the Fe pool remains stable even under continuously anoxic conditions.}, }
@article {pmid35287817, year = {2022}, author = {Mota-Gutierrez, J and Lis, L and Lasagabaster, A and Nafarrate, I and Ferrocino, I and Cocolin, L and Rantsiou, K}, title = {Campylobacter spp. prevalence and mitigation strategies in the broiler production chain.}, journal = {Food microbiology}, volume = {104}, number = {}, pages = {103998}, doi = {10.1016/j.fm.2022.103998}, pmid = {35287817}, issn = {1095-9998}, abstract = {This study aims to discuss the microbial ecology of the broiler gut environment, Campylobacter prevalence across the broiler production chain with a follow-up focus on a possible mitigation strategy, based on the use of bacteriophages. Scientific literature published from the last two decades was reviewed and data were collected to establish the ranges of Campylobacter loads from different samples. Results showed that the pathogen load in the sample is likely to increase from the different stages of the production chain. Contamination of water and feed represents the most notable source of contamination during the primary production, while cross-contamination of broiler carcasses, skin, and meat occurs during the slaughter, dressing, and processing via machinery, work surfaces, water, and air partially due to the leaking of contaminated feces from visceral rupture. Knowledge gaps were identified and included: a lack of studies detecting Campylobacter in broilers in most of the European countries over the last decade and a low number of studies determining the bacterial load in crates used to transport broilers to the slaughterhouse. Determining the prevalence of Campylobacter in the broiler industry will enable us to set critical control points to produce broiler flocks and meat products with a low risk of Campylobacter contamination.}, }
@article {pmid35286940, year = {2022}, author = {Safi, LSL and Tang, KW and Carnegie, RB}, title = {Investigating the epibiotic peritrich Zoothamnium intermedium Precht, 1935: Seasonality and distribution of its relationships with copepods in Chesapeake Bay (USA).}, journal = {European journal of protistology}, volume = {84}, number = {}, pages = {125880}, doi = {10.1016/j.ejop.2022.125880}, pmid = {35286940}, issn = {1618-0429}, abstract = {Zoothamnium intermedium is an obligate epibiont ciliate and has been found in a diverse array of hosts and environments. Different studies have reported conflicting distribution patterns and host preferences, even though studies in Chesapeake Bay have suggested that the ciliate has a strong host specificity for two calanoid copepod species. We examined the life cycle, host preferences, and ecological conditions conducive to Z. intermedium presence on copepods in Chesapeake Bay, the largest estuary in North America. The York River tributary was sampled biweekly from fall 2014 through summer 2015 for plankton, peritrichs and bacteria in the water column. Bacterial abundance in the water column peaked in fall and late spring, coinciding with increased abundance and species richness of non-epibiont peritrichs. Among the plankton, only the calanoid copepods Acartia tonsa and Centropages hamatus were colonized by Z. intermedium. The peritrich epibiont displayed higher colonization rates on C. hamatus even when A. tonsa was far more abundant. Multivariate correlation analysis of infestation prevalence on A. tonsa showed a strong correlation with dissolved oxygen, salinity and water temperature. Such correlations, along with differences in host species biology, might be driving the seasonality of this epibiotic relationship.}, }
@article {pmid35285907, year = {2022}, author = {Nunes, I and Hansen, V and Bak, F and Bonnichsen, L and Su, J and Hao, X and Raymond, NS and Nicolaisen, MH and Jensen, LS and Nybroe, O}, title = {Succession of the wheat seed-associated microbiome as affected by soil fertility level and introduction of Penicillium and Bacillus inoculants in the field.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiac028}, pmid = {35285907}, issn = {1574-6941}, abstract = {During germination, the seed releases nutrient-rich exudates into the spermosphere, thereby fostering competition between resident microorganisms. However, insight into the composition and temporal dynamics of seed-associated bacterial communities under field conditions is currently lacking. This field study determined the temporal changes from 11 to 31 days after sowing in the composition of seed-associated bacterial communities of winter wheat as affected by long-term soil fertilization history, and by introduction of the plant growth-promoting microbial inoculants Penicillium bilaiae and Bacillus simplex. The temporal dynamics was the most important factor affecting the composition of the seed-associated communities. An increase in the relative abundance of genes involved in organic nitrogen metabolism (ureC and gdhA), and in ammonium oxidation (amoA) suggested increased mineralization of plant-derived nitrogen compounds over time. Dynamics of the phosphorus cycling genes ppt, ppx and cphy indicated inorganic phosphorus and polyphosphate cycling, as well as phytate hydrolysis by the seed-associated bacteria early after germination. Later, an increase in genes for utilization of organic phosphorus sources (phoD, phoX and phnK) indicated phosphorus limitation. The results indicate that community temporal dynamics are partly driven by changed availability of major nutrients, and reveal no functional consequences of the added inoculants during seed germination.}, }
@article {pmid35285696, year = {2022}, author = {Song, W and Liu, J and Qin, W and Huang, J and Yu, X and Xu, M and Stahl, D and Jiao, N and Zhou, J and Tu, Q}, title = {Functional Traits Resolve Mechanisms Governing the Assembly and Distribution of Nitrogen-Cycling Microbial Communities in the Global Ocean.}, journal = {mBio}, volume = {}, number = {}, pages = {e0383221}, doi = {10.1128/mbio.03832-21}, pmid = {35285696}, issn = {2150-7511}, abstract = {Microorganisms drive much of the marine nitrogen (N) cycle, which jointly controls the primary production in the global ocean. However, our understanding of the microbial communities driving the global ocean N cycle remains fragmented. Focusing on "who is doing what, where, and how?", this study draws a clear picture describing the global biogeography of marine N-cycling microbial communities by utilizing the Tara Oceans shotgun metagenomes. The marine N-cycling communities are highly variable taxonomically but relatively even at the functional trait level, showing clear functional redundancy properties. The functional traits and taxonomic groups are shaped by the same set of geo-environmental factors, among which, depth is the major factor impacting marine N-cycling communities, differentiating mesopelagic from epipelagic communities. Latitudinal diversity gradients and distance-decay relationships are observed for taxonomic groups, but rarely or weakly for functional traits. The composition of functional traits is strongly deterministic as revealed by null model analysis, while a higher degree of stochasticity is observed for taxonomic composition. Integrating multiple lines of evidence, in addition to drawing a biogeographic picture of marine N-cycling communities, this study also demonstrated an essential microbial ecological theory-determinism governs the assembly of microbial communities performing essential biogeochemical processes; the environment selects functional traits rather than taxonomic groups; functional redundancy underlies stochastic taxonomic community assembly. IMPORTANCE A critical question in microbial ecology is how the complex microbial communities are formed in natural ecosystems with the existence of thousands different species, thereby performing essential ecosystem functions and maintaining ecosystem stability. Previous studies disentangling the community assembly mechanisms mainly focus on microbial taxa, ignoring the functional traits they carry. By anchoring microbial functional traits and their carrying taxonomic groups involved in nitrogen cycling processes, this study demonstrated an important mechanism associated with the complex microbial community assembly. Evidence shows that the environment selects functional traits rather than taxonomic groups, and functional redundancy underlies stochastic taxonomic community assembly. This study is expected to provide valuable mechanistic insights into the complex microbial community assembly in both natural and artificial ecosystems.}, }
@article {pmid35284961, year = {2022}, author = {Almeida, EL and Ribiere, C and Frei, W and Kenny, D and Coffey, MF and O'Toole, PW}, title = {Geographical and Seasonal Analysis of the Honeybee Microbiome.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35284961}, issn = {1432-184X}, support = {12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; }, abstract = {We previously showed that colonies of thriving and non-thriving honeybees co-located in a single geographically isolated apiary harboured strikingly different microbiomes when sampled at a single time point in the honey season. Here, we profiled the microbiome in returning forager bees from 10 to 12 hives in each of 6 apiaries across the southern half of Ireland, at early, middle, and late time points in the 2019 honey production season. Despite the wide range of geographical locations and forage available, apiary site was not the strongest determinant of the honeybee microbiome. However, there was clear clustering of the honeybee microbiome by time point across all apiaries, independent of which apiary was sampled. The clustering of microbiome by time was weaker although still significant in three of the apiaries, which may be connected to their geographic location and other external factors. The potential forage effect was strongest at the second timepoint (June-July) when the apiaries also displayed greatest difference in microbiome diversity. We identified bacteria in the forager bee microbiome that correlated with hive health as measured by counts of larvae, bees, and honey production. These findings support the hypothesis that the global honeybee microbiome and its constituent species support thriving hives.}, }
@article {pmid35282279, year = {2022}, author = {Amillano-Cisneros, JM and Hernández-Rosas, PT and Gomez-Gil, B and Navarrete-Ramírez, P and Ríos-Durán, MG and Martínez-Chávez, CC and Johnston-Monje, D and Martínez-Palacios, CA and Raggi, L}, title = {Loss of gut microbial diversity in the cultured, agastric fish, Mexican pike silverside (Chirostoma estor: Atherinopsidae).}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13052}, doi = {10.7717/peerj.13052}, pmid = {35282279}, issn = {2167-8359}, abstract = {Teleost fish are the most diverse group of extant vertebrates and have varied digestive anatomical structures and strategies, suggesting they also possess an array of different host-microbiota interactions. Differences in fish gut microbiota have been shown to affect host development, the process of gut colonization, and the outcomes of gene-environment or immune system-microbiota interactions. There is generally a lack of studies on the digestive mechanisms and microbiota of agastric short-intestine fish however, meaning that we do not understand how changes in gut microbial diversity might influence the health of these types of fish. To help fill these gaps in knowledge, we decided to study the Mexican pike silverside (Chirostoma estor) which has a simplified alimentary canal (agastric, short-intestine, 0.7 gut relative length) to observe the diversity and metabolic potential of its intestinal microbiota. We characterized gut microbial populations using high-throughput sequencing of the V3 region in bacterial 16S rRNA genes while searching for population shifts resulting associated with fish development in different environments and cultivation methods. Microbiota samples were taken from the digesta, anterior and posterior intestine (the three different intestinal components) of fish that grew wild in a lake, that were cultivated in indoor tanks, or that were raised in outdoor ponds. Gut microbial diversity was significantly higher in wild fish than in cultivated fish, suggesting a loss of diversity when fish are raised in controlled environments. The most abundant phyla observed in these experiments were Firmicutes and Proteobacteria, particularly of the genera Mycoplasma, Staphylococcus, Spiroplasma, and Aeromonas. Of the 14,161 OTUs observed in this experiment, 133 were found in all groups, and 17 of these, belonging to Acinetobacter, Aeromonas, Pseudomonas, and Spiroplasma genera, were found in all samples suggesting the existence of a core C. estor microbiome. Functional metagenomic prediction of bacterial ecological functions using PICRUSt2 suggested that different intestinal components select for functionally distinct microbial populations with variation in pathways related to the metabolism of amino acids, vitamins, cofactors, and energy. Our results provide, for the first time, information on the bacterial populations present in an agastric, short-gut teleost with commercial potential and show that controlled cultivation of this fish reduces the diversity of its intestinal microbiota.}, }
@article {pmid35281910, year = {2022}, author = {Zou, C and Chen, Y and Li, H and Li, W and Wei, J and Li, Z and Wang, X and Chen, T and Huang, H}, title = {Engineered Bacteria EcN-MT Alleviate Liver Injury in Cadmium-Exposed Mice via its Probiotics Characteristics and Expressing of Metallothionein.}, journal = {Frontiers in pharmacology}, volume = {13}, number = {}, pages = {857869}, doi = {10.3389/fphar.2022.857869}, pmid = {35281910}, issn = {1663-9812}, abstract = {Cadmium (Cd) exposure is a widespread problem in many parts of the world, but effective means to treat Cd exposure is still lacking. Hence, an engineered strain expressing metallothionein (MT) named Escherichia coli Nissle 1917 (EcN)-MT was constructed, and its potential in the treatment of Cd exposure was evaluated. The in vitro studies showed that metallothionein expressed by EcN-MT could significantly bind Cd. Further, the in vivo results indicated that EcN-MT strain could reduce 26.3% Cd in the liver and increase 24.7% Cd in the feces, which greatly decreased malondialdehyde (MDA) levels and increased catalase (CAT), glutathione (GSH), and superoxide dismutase (SOD) levels in liver, and reduced the expression of toll-like receptor4 (TLR4), nuclear factor-κB (NF-κB), the myeloid differentiation factor 88 (Myd88) andincreased B-cell lymphoma 2 (Bcl-2)/Bcl-2-Associated X (Bax). Moreover, high throughput sequencing results indicated that EcN-MT strain greatly enhanced the beneficial bacteria of Ruminococcaceae, Lactobacillaceae, Akkermansia, Muribaculaceae, Lachnospiraceae, Dubosiella and restored the disturbed microbial ecology to the normal level. Therefore, the high Cd binding capacity of the expressed metallothionein, together with the beneficial characteristics of the host bacteria EcN, makes EcN-MT a sound reagent for the treatment of subchronic Cd exposure-induced liver injury.}, }
@article {pmid35279466, year = {2022}, author = {Huang, YM and Jakus, N and Straub, D and Konstantinidis, KT and Blackwell, N and Kappler, A and Kleindienst, S}, title = {'Candidatus ferrigenium straubiae' sp. nov., 'Candidatus ferrigenium bremense' sp. nov., 'Candidatus ferrigenium altingense' sp. nov., are autotrophic Fe(II)-oxidizing bacteria of the family Gallionellaceae.}, journal = {Systematic and applied microbiology}, volume = {45}, number = {3}, pages = {126306}, doi = {10.1016/j.syapm.2022.126306}, pmid = {35279466}, issn = {1618-0984}, abstract = {Iron(II) [Fe(II)] oxidation coupled to denitrification is recognized as an environmentally important process in many ecosystems. However, the Fe(II)-oxidizing bacteria (FeOB) dominating autotrophic nitrate-reducing Fe(II)-oxidizing enrichment cultures, affiliated with the family Gallionellaceae, remain poorly taxonomically defined due to lack of representative isolates. We describe the taxonomic classification of three novel FeOB based on metagenome-assembled genomes (MAGs) acquired from the autotrophic nitrate-reducing enrichment cultures KS, BP and AG. Phylogenetic analysis of nearly full-length 16S rRNA gene sequences demonstrated that these three FeOB were most closely affiliated to the genera Ferrigenium, Sideroxydans and Gallionella, with up to 96.5%, 95.4% and 96.2% 16S rRNA gene sequence identities to representative isolates of these genera, respectively. In addition, average amino acid identities (AAI) of the genomes compared to the most closely related genera revealed highest AAI with Ferrigenium kumadai An22 (76.35-76.74%), suggesting that the three FeOB are members of this genus. Phylogenetic analysis of conserved functional genes further supported that these FeOB represent three novel species of the genus Ferrigenium. Moreover, the three novel FeOB likely have characteristic features, performing partial denitrification coupled to Fe(II) oxidation and carbon fixation. Scanning electron microscopy of the enrichment cultures showed slightly curved rod-shaped cells, ranging from 0.2-0.7 μm in width and 0.5-2.3 μm in length. Based on the phylogenetic, genomic and physiological characteristics, we propose that these FeOB represent three novel species, 'Candidatus Ferrigenium straubiae' sp. nov., 'Candidatus Ferrigenium bremense' sp. nov. and 'Candidatus Ferrigenium altingense' sp. nov. that might have unique metabolic features among the genus Ferrigenium.}, }
@article {pmid35278970, year = {2022}, author = {Yao, X and Liu, Y and Liu, X and Qiao, Z and Sun, S and Li, X and Wang, J and Zhang, F and Jiang, X}, title = {Effects of thifluzamide on soil fungal microbial ecology.}, journal = {Journal of hazardous materials}, volume = {431}, number = {}, pages = {128626}, doi = {10.1016/j.jhazmat.2022.128626}, pmid = {35278970}, issn = {1873-3336}, abstract = {Thifluzamide, a succinate dehydrogenase inhibitor fungicide, has been used extensively for many diseases control and has the risk of accumulation in soil ecology. In order to study the ecotoxicity of thifluzamide to soil fungal communities, typical corn field soils in north (Tai'an) and south (Guoyang) China were treated with thifluzamide (0, 0.1, 1.0 and 10.0 mg/kg) and incubated for 60 days. Thifluzamide exposure promoted soil basal respiration, and significantly reduced the number of soil culturable fungi and the abundance of soil fungi (RT-qPCR) in middle and late treatment period (15, 30, 60 days). Illumina Mi-Seq sequencing revealed that thifluzamide could reduce fungal alpha diversity (Sobs, Shannon, Simpson indexes) and change fungal community structure. FUN Guild analysis showed that the relative abundance of Undefined Saprotroph increased after the thifluzamide treatment, whereas that of Plant Pathogen decreased, and we concluded that exposure to thifluzamide could change the function of soil fungi. This study evaluated the soil ecological risk caused by thifluzamide's release into soil, providing a basis for its