@article {pmid38627822,
year = {2024},
author = {Williams, J and Pettorelli, N and Hartmann, AC and Quinn, RA and Plaisance, L and O'Mahoney, M and Meyer, CP and Fabricius, KE and Knowlton, N and Ransome, E},
title = {Decline of a distinct coral reef holobiont community under ocean acidification.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {75},
pmid = {38627822},
issn = {2049-2618},
support = {NE/R012229/1//Natural Environment Research Council/ ; 2022717//National Science Foundation/ ; 1558868//National Science Foundation/ ; 1558868//National Science Foundation/ ; },
abstract = {BACKGROUND: Microbes play vital roles across coral reefs both in the environment and inside and upon macrobes (holobionts), where they support critical functions such as nutrition and immune system modulation. These roles highlight the potential ecosystem-level importance of microbes, yet most knowledge of microbial functions on reefs is derived from a small set of holobionts such as corals and sponges. Declining seawater pH - an important global coral reef stressor - can cause ecosystem-level change on coral reefs, providing an opportunity to study the role of microbes at this scale. We use an in situ experimental approach to test the hypothesis that under such ocean acidification (OA), known shifts among macrobe trophic and functional groups may drive a general ecosystem-level response extending across macrobes and microbes, leading to reduced distinctness between the benthic holobiont community microbiome and the environmental microbiome.

RESULTS: We test this hypothesis using genetic and chemical data from benthic coral reef community holobionts sampled across a pH gradient from CO2 seeps in Papua New Guinea. We find support for our hypothesis; under OA, the microbiome and metabolome of the benthic holobiont community become less compositionally distinct from the sediment microbiome and metabolome, suggesting that benthic macrobe communities are colonised by environmental microbes to a higher degree under OA conditions. We also find a simplification and homogenisation of the benthic photosynthetic community, and an increased abundance of fleshy macroalgae, consistent with previously observed reef microbialisation.

CONCLUSIONS: We demonstrate a novel structural shift in coral reefs involving macrobes and microbes: that the microbiome of the benthic holobiont community becomes less distinct from the sediment microbiome under OA. Our findings suggest that microbialisation and the disruption of macrobe trophic networks are interwoven general responses to environmental stress, pointing towards a universal, undesirable, and measurable form of ecosystem changed. Video Abstract.},
}

@article {pmid38366712,
year = {2024},
author = {Pillai, P and Gouhier, TC},
title = {Metamicrobiome diversity promotes the evolution of host-microbial mutualisms.},
journal = {Journal of evolutionary biology},
volume = {37},
number = {4},
pages = {414-428},
doi = {10.1093/jeb/voae019},
pmid = {38366712},
issn = {1420-9101},
support = {OCE-1458158//National Science Foundation/ ; },
abstract = {Ecological theory suggests that a host organism's internal spatial structure can promote the persistence of mutualistic microbes by allowing for the turnover of tissue occupied by non-beneficial or cheating microbes. This type of regulation, whereby a host preferentially rewards tissue occupied by beneficial members of its microbiome but sanctions tissue occupied by non-beneficial cheaters, is expected to generate a competition-extinction trade-off by allowing beneficial microbes to experience a lower extinction rate than competitively dominant cheaters. Using an adaptive dynamics approach, we demonstrate that although ecologically stable, microbial regulation via sanctioning is not stable in any evolutionary sense, as each individual host will be under pressure to reduce the costs incurred from cheater suppression in order to maximize its own fitness at the expense of the rest of the host population. However, increasing the diversity of non-beneficial cheaters in the host population metamicrobiome can lead to an increase in the relative fitness of hosts that actively sanction non-performing tissue, thus facilitating the evolutionary emergence and persistence of such strategies in host-microbial systems. These counter-intuitive results demonstrate how diversity at multiple levels of biological organization and spatiotemporal scales can interact to facilitate the establishment and maintenance of mutualistic relationships.},
}

@article {pmid38607980,
year = {2024},
author = {Partida-Martínez, LP},
title = {Fungal holobionts as blueprints for synthetic endosymbiotic systems.},
journal = {PLoS biology},
volume = {22},
number = {4},
pages = {e3002587},
doi = {10.1371/journal.pbio.3002587},
pmid = {38607980},
issn = {1545-7885},
abstract = {Rhizopus microsporus is an example of a fungal holobiont. Strains of this species can harbor bacterial and viral endosymbionts inherited by the next generation. These microbial allies increase pathogenicity and defense and control asexual and sexual reproduction.},
}

@article {pmid38606974,
year = {2024},
author = {Cardoso, PM and Hill, LJ and Villela, HDM and Vilela, CLS and Assis, JM and Rosado, PM and Rosado, JG and Chacon, MA and Majzoub, ME and Duarte, GAS and Thomas, T and Peixoto, RS},
title = {Localization and symbiotic status of probiotics in the coral holobiont.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0026124},
doi = {10.1128/msystems.00261-24},
pmid = {38606974},
issn = {2379-5077},
abstract = {UNLABELLED: Corals establish symbiotic relationships with microorganisms, especially endosymbiotic photosynthetic algae. Although other microbes have been commonly detected in coral tissues, their identity and beneficial functions for their host are unclear. Here, we confirm the beneficial outcomes of the inoculation of bacteria selected as probiotics and use fluorescence in situ hybridization (FISH) to define their localization in the coral Pocillopora damicornis. Our results show the first evidence of the inherent presence of Halomonas sp. and Cobetia sp. in native coral tissues, even before their inoculation. Furthermore, the relative enrichment of these coral tissue-associated bacteria through their inoculation in corals correlates with health improvements, such as increases in photosynthetic potential, and productivity. Our study suggests the symbiotic status of Halomonas sp. and Cobetia sp. in corals by indicating their localization within coral gastrodermis and epidermis and correlating their increased relative abundance through active inoculation with beneficial outcomes for the holobiont. This knowledge is crucial to facilitate the screening and application of probiotics that may not be transient members of the coral microbiome.

IMPORTANCE: Despite the promising results indicating the beneficial outcomes associated with the application of probiotics in corals and some scarce knowledge regarding the identity of bacterial cells found within the coral tissue, the correlation between these two aspects is still missing. This gap limits our understanding of the actual diversity of coral-associated bacteria and whether these symbionts are beneficial. Some researchers, for example, have been suggesting that probiotic screening should only focus on the very few known tissue-associated bacteria, such as Endozoicomonas sp., assuming that the currently tested probiotics are not tissue-associated. Here, we provide specific FISH probes for Halomonas sp. and Cobetia sp., expand our knowledge of the identity of coral-associated bacteria and confirm the probiotic status of the tested probiotics. The presence of these beneficial microorganisms for corals (BMCs) inside host tissues and gastric cavities also supports the notion that direct interactions with the host may underpin their probiotic role. This is a new breakthrough; these results argue against the possibility that the positive effects of BMCs are due to factors that are not related to a direct symbiotic interaction, for example, that the host simply feeds on inoculated bacteria or that the bacteria change the water quality.},
}

@article {pmid38605712,
year = {2024},
author = {Garrido, M and Minard, G and Veiga, J and Martínez-de la Puente, J},
title = {Editorial: Ecological interactions between mosquitoes and their microbiota: implications for pathogen transmission.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1395348},
pmid = {38605712},
issn = {1664-302X},
}

@article {pmid38602593,
year = {2024},
author = {Maslin, M and Paix, B and van der Windt, N and Ambo-Rappe, R and Debitus, C and Gaertner-Mazouni, N and Ho, R and de Voogd, NJ},
title = {Prokaryotic communities of the French Polynesian sponge Dactylospongia metachromia display a site-specific and stable diversity during an aquaculture trial.},
journal = {Antonie van Leeuwenhoek},
volume = {117},
number = {1},
pages = {65},
pmid = {38602593},
issn = {1572-9699},
support = {08858/VP/DRMM//Direction des Ressources Marines/ ; 08858/VP/DRMM//Direction des Ressources Marines/ ; 08858/VP/DRMM//Direction des Ressources Marines/ ; 3299/MTF//Government of French Polynesia/ ; 3299/MTF//Government of French Polynesia/ ; 16.161.301//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 16.161.301//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
abstract = {Dynamics of microbiomes through time are fundamental regarding survival and resilience of their hosts when facing environmental alterations. As for marine species with commercial applications, such as marine sponges, assessing the temporal change of prokaryotic communities allows us to better consider the adaptation of sponges to aquaculture designs. The present study aims to investigate the factors shaping the microbiome of the sponge Dactylospongia metachromia, in a context of aquaculture development in French Polynesia, Rangiroa, Tuamotu archipelago. A temporal approach targeting explants collected during farming trials revealed a relative high stability of the prokaryotic diversity, meanwhile a complementary biogeographical study confirmed a spatial specificity amongst samples at different longitudinal scales. Results from this additional spatial analysis confirmed that differences in prokaryotic communities might first be explained by environmental changes (mainly temperature and salinity), while no significant effect of the host phylogeny was observed. The core community of D. metachromia is thus characterized by a high spatiotemporal constancy, which is a good prospect for the sustainable exploitation of this species towards drug development. Indeed, a microbiome stability across locations and throughout the farming process, as evidenced by our results, should go against a negative influence of sponge translocation during in situ aquaculture.},
}

@article {pmid38601888,
year = {2024},
author = {Sherwani, MK and Gopalakrishnan, S},
title = {A systematic literature review: deep learning techniques for synthetic medical image generation and their applications in radiotherapy.},
journal = {Frontiers in radiology},
volume = {4},
number = {},
pages = {1385742},
pmid = {38601888},
issn = {2673-8740},
abstract = {The aim of this systematic review is to determine whether Deep Learning (DL) algorithms can provide a clinically feasible alternative to classic algorithms for synthetic Computer Tomography (sCT). The following categories are presented in this study: ∙ MR-based treatment planning and synthetic CT generation techniques. ∙ Generation of synthetic CT images based on Cone Beam CT images. ∙ Low-dose CT to High-dose CT generation. ∙ Attenuation correction for PET images. To perform appropriate database searches, we reviewed journal articles published between January 2018 and June 2023. Current methodology, study strategies, and results with relevant clinical applications were analyzed as we outlined the state-of-the-art of deep learning based approaches to inter-modality and intra-modality image synthesis. This was accomplished by contrasting the provided methodologies with traditional research approaches. The key contributions of each category were highlighted, specific challenges were identified, and accomplishments were summarized. As a final step, the statistics of all the cited works from various aspects were analyzed, which revealed that DL-based sCTs have achieved considerable popularity, while also showing the potential of this technology. In order to assess the clinical readiness of the presented methods, we examined the current status of DL-based sCT generation.},
}

@article {pmid38589941,
year = {2024},
author = {Liu, F and Ryu, T and Ravasi, T and Wang, X and Wang, G and Li, Z},
title = {Niche-dependent sponge hologenome expression profiles and the host-microbes interplay: a case of the hawaiian demosponge Mycale Grandis.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {22},
pmid = {38589941},
issn = {2524-6372},
support = {31861143020, 41776138//This work was supported by the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Most researches on sponge holobionts focus primarily on symbiotic microbes, yet data at the level of the sponge hologenome are still relatively scarce. Understanding of the sponge host and its microbial gene expression profiles and the host-microbes interplay in different niches represents a key aspect of sponge hologenome. Using the Hawaiian demosponge Mycale grandis in different niches as a model, i.e. on rocks, on the surface of coral Porites compressa, under alga Gracilaria salicornia, we compared the bacterial and fungal community structure, functional gene diversity, expression pattern and the host transcriptome by integrating open-format (deep sequencing) and closed-format (GeoChip microarray) high-throughput techniques.

RESULTS: Little inter-niche variation in bacterial and fungal phylogenetic diversity was detected for M. grandis in different niches, but a clear niche-dependent variability in the functional gene diversity and expression pattern of M. grandis host and its symbiotic microbiota was uncovered by GeoChip microarray and transcriptome analyses. Particularly, sponge host genes related to innate immunity and microbial recognition showed a strong correlation with the microbial symbionts' functional gene diversity and transcriptional richness in different niches. The cross-niche variability with respect to the symbiont functional gene diversity and the transcriptional richness of M. grandis holobiont putatively reflects the interplay of niche-specific selective pressure and the symbiont functional diversity.

CONCLUSIONS: Niche-dependent gene expression profiles of M. grandis hologenome and the host-microbes interplay were suggested though little inter-niche variation in bacterial and fungal diversity was detected, particularly the sponge innate immunity was found to be closely related to the symbiotic microbes. Altogether, these findings provide novel insights into the black box of one sponge holobiont in different niches at the hologenome level.},
}

@article {pmid38589605,
year = {2024},
author = {Mazzella, V and Dell'Anno, A and Etxebarría, N and González-Gaya, B and Nuzzo, G and Fontana, A and Núñez-Pons, L},
title = {High microbiome and metabolome diversification in coexisting sponges with different bio-ecological traits.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {422},
pmid = {38589605},
issn = {2399-3642},
abstract = {Marine Porifera host diverse microbial communities, which influence host metabolism and fitness. However, functional relationships between sponge microbiomes and metabolic signatures are poorly understood. We integrate microbiome characterization, metabolomics and microbial predicted functions of four coexisting Mediterranean sponges -Petrosia ficiformis, Chondrosia reniformis, Crambe crambe and Chondrilla nucula. Microscopy observations reveal anatomical differences in microbial densities. Microbiomes exhibit strong species-specific trends. C. crambe shares many rare amplicon sequence variants (ASV) with the surrounding seawater. This suggests important inputs of microbial diversity acquired by selective horizontal acquisition. Phylum Cyanobacteria is mainly represented in C. nucula and C. crambe. According to putative functions, the microbiome of P. ficiformis and C. reniformis are functionally heterotrophic, while C. crambe and C. nucula are autotrophic. The four species display distinct metabolic profiles at single compound level. However, at molecular class level they share a "core metabolome". Concurrently, we find global microbiome-metabolome association when considering all four sponge species. Within each species still, sets of microbe/metabolites are identified driving multi-omics congruence. Our findings suggest that diverse microbial players and metabolic profiles may promote niche diversification, but also, analogous phenotypic patterns of "symbiont evolutionary convergence" in sponge assemblages where holobionts co-exist in the same area.},
}

@article {pmid38587594,
year = {2024},
author = {Van Gerrewey, T and Chung, HS},
title = {MAPK Cascades in Plant Microbiota Structure and Functioning.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {38587594},
issn = {1976-3794},
support = {2021R1F1A1048959//Ministry of Science and ICT, South Korea/ ; BOF/STA/202002/007//Bijzonder Onderzoeksfonds UGent/ ; },
abstract = {Mitogen-activated protein kinase (MAPK) cascades are highly conserved signaling modules that coordinate diverse biological processes such as plant innate immunity and development. Recently, MAPK cascades have emerged as pivotal regulators of the plant holobiont, influencing the assembly of normal plant microbiota, essential for maintaining optimal plant growth and health. In this review, we provide an overview of current knowledge on MAPK cascades, from upstream perception of microbial stimuli to downstream host responses. Synthesizing recent findings, we explore the intricate connections between MAPK signaling and the assembly and functioning of plant microbiota. Additionally, the role of MAPK activation in orchestrating dynamic changes in root exudation to shape microbiota composition is discussed. Finally, our review concludes by emphasizing the necessity for more sophisticated techniques to accurately decipher the role of MAPK signaling in establishing the plant holobiont relationship.},
}

@article {pmid38575584,
year = {2024},
author = {Messer, LF and Bourne, DG and Robbins, SJ and Clay, M and Bell, SC and McIlroy, SJ and Tyson, GW},
title = {A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2902},
pmid = {38575584},
issn = {2041-1723},
abstract = {Microbial diversity has been extensively explored in reef-building corals. However, the functional roles of coral-associated microorganisms remain poorly elucidated. Here, we recover 191 bacterial and 10 archaeal metagenome-assembled genomes (MAGs) from the coral Acropora kenti (formerly A. tenuis) and adjacent seawater, to identify microbial functions and metabolic interactions within the holobiont. We show that 82 MAGs were specific to the A. kenti holobiont, including members of the Pseudomonadota, Bacteroidota, and Desulfobacterota. A. kenti-specific MAGs displayed significant differences in their genomic features and functional potential relative to seawater-specific MAGs, with a higher prevalence of genes involved in host immune system evasion, nitrogen and carbon fixation, and synthesis of five essential B-vitamins. We find a diversity of A. kenti-specific MAGs encode the biosynthesis of essential amino acids, such as tryptophan, histidine, and lysine, which cannot be de novo synthesised by the host or Symbiodiniaceae. Across a water quality gradient spanning 2° of latitude, A. kenti microbial community composition is correlated to increased temperature and dissolved inorganic nitrogen, with corresponding enrichment in molecular chaperones, nitrate reductases, and a heat-shock protein. We reveal mechanisms of A. kenti-microbiome-symbiosis on the Great Barrier Reef, highlighting the interactions underpinning the health of this keystone holobiont.},
}

@article {pmid38564842,
year = {2024},
author = {Chatterjee, S and Leach, ST and Lui, K and Mishra, A},
title = {Symbiotic symphony: Understanding host-microbiota dialogues in a spatial context.},
journal = {Seminars in cell & developmental biology},
volume = {161-162},
number = {},
pages = {22-30},
doi = {10.1016/j.semcdb.2024.03.001},
pmid = {38564842},
issn = {1096-3634},
abstract = {Modern precision sequencing techniques have established humans as a holobiont that live in symbiosis with the microbiome. Microbes play an active role throughout the life of a human ranging from metabolism and immunity to disease tolerance. Hence, it is of utmost significance to study the eukaryotic host in conjunction with the microbial antigens to obtain a complete picture of the host-microbiome crosstalk. Previous attempts at profiling host-microbiome interactions have been either superficial or been attempted to catalogue eukaryotic transcriptomic profile and microbial communities in isolation. Additionally, the nature of such immune-microbial interactions is not random but spatially organised. Hence, for a holistic clinical understanding of the interplay between hosts and microbiota, it's imperative to concurrently analyze both microbial and host genetic information, ensuring the preservation of their spatial integrity. Capturing these interactions as a snapshot in time at their site of action has the potential to transform our understanding of how microbes impact human health. In examining early-life microbial impacts, the limited presence of communities compels analysis within reduced biomass frameworks. However, with the advent of spatial transcriptomics we can address this challenge and expand our horizons of understanding these interactions in detail. In the long run, simultaneous spatial profiling of host-microbiome dialogues can have enormous clinical implications especially in gaining mechanistic insights into the disease prognosis of localised infections and inflammation. This review addresses the lacunae in host-microbiome research and highlights the importance of profiling them together to map their interactions while preserving their spatial context.},
}

@article {pmid38560995,
year = {2024},
author = {Stiller, J and Feng, S and Chowdhury, AA and Rivas-González, I and Duchêne, DA and Fang, Q and Deng, Y and Kozlov, A and Stamatakis, A and Claramunt, S and Nguyen, JMT and Ho, SYW and Faircloth, BC and Haag, J and Houde, P and Cracraft, J and Balaban, M and Mai, U and Chen, G and Gao, R and Zhou, C and Xie, Y and Huang, Z and Cao, Z and Yan, Z and Ogilvie, HA and Nakhleh, L and Lindow, B and Morel, B and Fjeldså, J and Hosner, PA and da Fonseca, RR and Petersen, B and Tobias, JA and Székely, T and Kennedy, JD and Reeve, AH and Liker, A and Stervander, M and Antunes, A and Tietze, DT and Bertelsen, M and Lei, F and Rahbek, C and Graves, GR and Schierup, MH and Warnow, T and Braun, EL and Gilbert, MTP and Jarvis, ED and Mirarab, S and Zhang, G},
title = {Complexity of avian evolution revealed by family-level genomes.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41586-024-07323-1},
pmid = {38560995},
issn = {1476-4687},
abstract = {Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method, and the choice of genomic regions [1-3]. Here, we address these issues by analyzing genomes of 363 bird species [4] (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a remarkable degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Paleogene (K-Pg) boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that challenge modeling due to extreme GC content, variable substitution rates, incomplete lineage sorting, or complex evolutionary events such as ancient hybridization. Assessment of the impacts of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates, and relative brain size following the K-Pg extinction event, supporting the hypothesis that emerging ecological opportunities catalyzed the diversification of modern birds. The resulting phylogenetic estimate offers novel insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.},
}

@article {pmid38560465,
year = {2024},
author = {Auclert, LZ and Chhanda, MS and Derome, N},
title = {Interwoven processes in fish development: microbial community succession and immune maturation.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17051},
doi = {10.7717/peerj.17051},
pmid = {38560465},
issn = {2167-8359},
abstract = {Fishes are hosts for many microorganisms that provide them with beneficial effects on growth, immune system development, nutrition and protection against pathogens. In order to avoid spreading of infectious diseases in aquaculture, prevention includes vaccinations and routine disinfection of eggs and equipment, while curative treatments consist in the administration of antibiotics. Vaccination processes can stress the fish and require substantial farmer's investment. Additionally, disinfection and antibiotics are not specific, and while they may be effective in the short term, they have major drawbacks in the long term. Indeed, they eliminate beneficial bacteria which are useful for the host and promote the raising of antibiotic resistance in beneficial, commensal but also in pathogenic bacterial strains. Numerous publications highlight the importance that plays the diversified microbial community colonizing fish (i.e., microbiota) in the development, health and ultimately survival of their host. This review targets the current knowledge on the bidirectional communication between the microbiota and the fish immune system during fish development. It explores the extent of this mutualistic relationship: on one hand, the effect that microbes exert on the immune system ontogeny of fishes, and on the other hand, the impact of critical steps in immune system development on the microbial recruitment and succession throughout their life. We will first describe the immune system and its ontogeny and gene expression steps in the immune system development of fishes. Secondly, the plurality of the microbiotas (depending on host organism, organ, and development stage) will be reviewed. Then, a description of the constant interactions between microbiota and immune system throughout the fish's life stages will be discussed. Healthy microbiotas allow immune system maturation and modulation of inflammation, both of which contribute to immune homeostasis. Thus, immune equilibrium is closely linked to microbiota stability and to the stages of microbial community succession during the host development. We will provide examples from several fish species and describe more extensively the mechanisms occurring in zebrafish model because immune system ontogeny is much more finely described for this species, thanks to the many existing zebrafish mutants which allow more precise investigations. We will conclude on how the conceptual framework associated to the research on the immune system will benefit from considering the relations between microbiota and immune system maturation. More precisely, the development of active tolerance of the microbiota from the earliest stages of life enables the sustainable establishment of a complex healthy microbial community in the adult host. Establishing a balanced host-microbiota interaction avoids triggering deleterious inflammation, and maintains immunological and microbiological homeostasis.},
}

@article {pmid38553475,
year = {2024},
author = {McGrath, AH and Lema, K and Egan, S and Wood, G and Gonzalez, SV and Kjelleberg, S and Steinberg, PD and Marzinelli, EM},
title = {Disentangling direct vs indirect effects of microbiome manipulations in a habitat-forming marine holobiont.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {33},
pmid = {38553475},
issn = {2055-5008},
support = {Holsworth Wildlife Endowment//Ecological Society of Australia (ESA)/ ; DP180104041//Department of Education and Training | Australian Research Council (ARC)/ ; DP180104041//Department of Education and Training | Australian Research Council (ARC)/ ; DP180104041//Department of Education and Training | Australian Research Council (ARC)/ ; },
abstract = {Host-associated microbiota are critical for eukaryotic host functioning, to the extent that hosts and their associated microbial communities are often considered "holobionts". Most studies of holobionts have focused on descriptive approaches or have used model systems, usually in the laboratory, to understand host-microbiome interactions. To advance our understanding of host-microbiota interactions and their wider ecological impacts, we need experimental frameworks that can explore causation in non-model hosts, which often have highly diverse microbiota, and in their natural ecological setting (i.e. in the field). We used a dominant habitat-forming seaweed, Hormosira banksii, to explore these issues and to experimentally test host-microbiota interactions in a non-model holobiont. The experimental protocols were aimed at trying to disentangle microbially mediated effects on hosts from direct effects on hosts associated with the methods employed to manipulate host-microbiota. This was done by disrupting the microbiome, either through removal/disruption using a combination of antimicrobial treatments, or additions of specific taxa via inoculations, or a combination of thew two. The experiments were done in mesocosms and in the field. Three different antibiotic treatments were used to disrupt seaweed-associated microbiota to test whether disturbances of microbiota, particularly bacteria, would negatively affect host performance. Responses of bacteria to these disturbances were complex and differed substantially among treatments, with some antibacterial treatments having little discernible effect. However, the temporal sequence of responses antibiotic treatments, changes in bacterial diversity and subsequent decreases in host performance, strongly suggested an effect of the microbiota on host performance in some treatments, as opposed to direct effects of the antibiotics. To further test these effects, we used 16S-rRNA-gene sequencing to identify bacterial taxa that were either correlated, or uncorrelated, with poor host performance following antibiotic treatment. These were then isolated and used in inoculation experiments, independently or in combination with the previously used antibiotic treatments. Negative effects on host performance were strongest where specific microbial antimicrobials treatments were combined with inoculations of strains that were correlated with poor host performance. For these treatments, negative host effects persisted the entire experimental period (12 days), even though treatments were only applied at the beginning of the experiment. Host performance recovered in all other treatments. These experiments provide a framework for exploring causation and disentangling microbially mediated vs. direct effects on hosts for ecologically important, non-model holobionts in the field. This should allow for better predictions of how these systems will respond to, and potentially mitigate, environmental disturbances in their natural context.},
}

@article {pmid38548931,
year = {2024},
author = {Friedländer, MR and Gilbert, MTP},
title = {How ancient RNA survives and what we can learn from it.},
journal = {Nature reviews. Molecular cell biology},
volume = {},
number = {},
pages = {},
pmid = {38548931},
issn = {1471-0080},
}

@article {pmid38543670,
year = {2024},
author = {Tosado-Rodríguez, E and Alvarado-Vélez, I and Romaguera, J and Godoy-Vitorino, F},
title = {Vaginal Microbiota and HPV in Latin America: A Narrative Review.},
journal = {Microorganisms},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/microorganisms12030619},
pmid = {38543670},
issn = {2076-2607},
support = {U54MD007600/MD/NIMHD NIH HHS/United States ; P20GM103475/GM/NIGMS NIH HHS/United States ; U54MD007587/GM/NIGMS NIH HHS/United States ; CA096297/CA/NCI NIH HHS/United States ; },
abstract = {With the expansion of human microbiome studies in the last 15 years, we have realized the immense implications of microbes in human health. The human holobiont is now accepted, given the commensal relationships with bacteria, fungi, parasites, viruses, and human cells. The cervicovaginal microbiota is a specific case within the human microbiome where diversity is lower to maintain a chemical barrier of protection against infections. This narrative review focuses on the vaginal microbiome. It summarizes key findings on how native bacteria protect women from disease or predispose them to damaging inflammatory processes with an emphasis on the role of HPV infections in Latin America, one of the world's regions with the highest cervical cancer prevalence.},
}

@article {pmid38537113,
year = {2024},
author = {Beza-Beza, CF and Wiegmann, BM and Ware, JA and Petersen, M and Gunter, N and Cole, ME and Schwarz, M and Bertone, MA and Young, D and Mikaelyan, A},
title = {Chewing through challenges: Exploring the evolutionary pathways to wood-feeding in insects.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e2300241},
doi = {10.1002/bies.202300241},
pmid = {38537113},
issn = {1521-1878},
abstract = {Decaying wood, while an abundant and stable resource, presents considerable nutritional challenges due to its structural rigidity, chemical recalcitrance, and low nitrogen content. Despite these challenges, certain insect lineages have successfully evolved saproxylophagy (consuming and deriving sustenance from decaying wood), impacting nutrient recycling in ecosystems and carbon sequestration dynamics. This study explores the uneven phylogenetic distribution of saproxylophagy across insects and delves into the evolutionary origins of this trait in disparate insect orders. Employing a comprehensive analysis of gut microbiome data, from both saproxylophagous insects and their non-saproxylophagous relatives, including new data from unexplored wood-feeding insects, this Hypothesis paper discusses the broader phylogenetic context and potential adaptations necessary for this dietary specialization. The study proposes the "Detritivore-First Hypothesis," suggesting an evolutionary pathway to saproxylophagy through detritivory, and highlights the critical role of symbiotic gut microbiomes in the digestion of decaying wood.},
}

@article {pmid38536705,
year = {2024},
author = {Kriaa, A and Mariaule, V and De Rudder, C and Jablaoui, A and Sokol, H and Wilmes, P and Maguin, E and Rhimi, M},
title = {From animal models to gut-on-chip: the challenging journey to capture inter-individual variability in chronic digestive disorders.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2333434},
doi = {10.1080/19490976.2024.2333434},
pmid = {38536705},
issn = {1949-0984},
abstract = {Chronic digestive disorders are of increasing incidence worldwide with expensive treatments and no available cure. Available therapeutic schemes mainly rely on symptom relief, with large degrees of variability in patients' response to such treatments, underlining the need for new therapeutic strategies. There are strong indications that the gut microbiota's contribution seems to be a key modulator of disease activity and patients' treatment responses. Hence, efforts have been devoted to understanding host-microbe interactions and the mechanisms underpinning such variability. Animal models, being the gold standard, provide valuable mechanistic insights into host-microbe interactions. However, they are not exempt from limitations prompting the development of alternative methods. Emerging microfluidic technologies and gut-on-chip models were shown to mirror the main features of gut physiology and disease state, reflect microbiota modification, and include functional readouts for studying host responses. In this commentary, we discuss the relevance of animal models in understanding host-microbe interactions and how gut-on-chip technology holds promises for addressing patient variability in responses to chronic digestive disease treatment.},
}

@article {pmid38535570,
year = {2024},
author = {Arnholdt-Schmitt, B and Sircar, D and Aziz, S and Germano, TA and Thiers, KLL and Noceda, C and Bharadwaj, R and Mohanapriya, G and Costa, JH},
title = {Transcriptome Analyses in Adult Olive Trees Indicate Acetaldehyde Release and Cyanide-Mediated Respiration Traits as Critical for Tolerance against Xylella fastidiosa and Suggest AOX Gene Family as Marker for Multiple-Resilience.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/pathogens13030227},
pmid = {38535570},
issn = {2076-0817},
abstract = {Xylella fastidiosa (Xf) is a global bacterial threat for a diversity of plants, including olive trees. However, current understanding of host responses upon Xf-infection is limited to allow early disease prediction, diagnosis, and sustainable strategies for breeding on plant tolerance. Recently, we identified a major complex trait for early de novo programming, named CoV-MAC-TED, by comparing early transcriptome data during plant cell survival with SARS-CoV-2-infected human cells. This trait linked ROS/RNS balancing during first hours of stress perception with increased aerobic fermentation connected to alpha-tubulin-based cell restructuration and control of cell cycle progression. Furthermore, our group had advanced concepts and strategies for breeding on plant holobionts. Here, we studied tolerance against Xf-infection by applying a CoV-MAC-TED-related gene set to (1) progress proof-of-principles, (2) highlight the importance of individual host responses for knowledge gain, (3) benefit sustainable production of Xf-threatened olive, (4) stimulate new thinking on principle roles of secondary metabolite synthesis and microbiota for system equilibration and, (5) advance functional marker development for resilience prediction including tolerance to Xf-infections. We performed hypothesis-driven complex analyses in an open access transcriptome of primary target xylem tissues of naturally Xf-infected olive trees of the Xf-tolerant cv. Leccino and the Xf-susceptible cv. Ogliarola. The results indicated that cyanide-mediated equilibration of oxygen-dependent respiration and carbon-stress alleviation by the help of increased glycolysis-driven aerobic fermentation paths and phenolic metabolism associate to tolerance against Xf. Furthermore, enhanced alternative oxidase (AOX) transcript levels through transcription Gleichschaltung linked to quinic acid synthesis appeared as promising trait for functional marker development. Moreover, the results support the idea that fungal endophytes strengthen Xf-susceptible genotypes, which lack efficient AOX functionality. Overall, this proof-of-principles approach supports the idea that efficient regulation of the multi-functional AOX gene family can assist selection on multiple-resilience, which integrates Xf-tolerance, and stimulates future validation across diverse systems.},
}

@article {pmid38535568,
year = {2024},
author = {Fan, MZ and Kim, SW},
title = {Modulation of Porcine Gut Microbiota and Microbiome: Hologenomic, Dietary, and Endogenous Factors.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/pathogens13030225},
pmid = {38535568},
issn = {2076-0817},
support = {na//the Natural Science and Engineering Research Council (NSERC) of Canada; Agriculture, Agri-Food Canada (AAFC) Swine Innovation Porc (SIP) Swine Cluster Program; and the Metagen Enzyme Corporation. North Carolina Agricultural Foundation (Raleigh, NC, USA) a/ ; },
abstract = {Global pig production contributes to about 35% of the world's meat production and consumption [...].},
}

@article {pmid38534358,
year = {2024},
author = {Andrews, K and Landeryou, T and Sicheritz-Pontén, T and Nale, JY},
title = {Diverse Prophage Elements of Salmonella enterica Serovars Show Potential Roles in Bacterial Pathogenicity.},
journal = {Cells},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/cells13060514},
pmid = {38534358},
issn = {2073-4409},
abstract = {Nontyphoidal salmonellosis is an important foodborne and zoonotic infection that causes significant global public health concern. Diverse serovars are multidrug-resistant and encode several virulence indicators; however, little is known on the role prophages play in driving these traits. Here, we extracted prophages from seventy-five Salmonella genomes which represent the fifteen important serovars in the United Kingdom. We analyzed the intact prophages for the presence of virulence genes and established their genomic relationships. We identified 615 prophages from the Salmonella strains, from which 195 prophages are intact, 332 are incomplete, while 88 are questionable. The average prophage carriage was found to be 'extreme' in S. Heidelberg, S. Inverness, and S. Newport (10.2-11.6 prophages/strain), 'high' in S. Infantis, S. Stanley, S. Typhimurium, and S. Virchow (8.2-9.0 prophages/strain), 'moderate' in S. Agona, S. Braenderup, S. Bovismorbificans, S. Choleraesuis, S. Dublin, and S. Java (6.0-7.8 prophages/strain), and 'low' in S. Javiana and S. Enteritidis (5.8 prophages/strain). Cumulatively, 61 virulence genes (1500 gene copies) were detected from representative intact prophages and linked to Salmonella delivery/secretion system (42.62%), adherence (32.7%), magnesium uptake (3.88%), regulation (5%), stress/survival (1.6%), toxins (10%), and antivirulence (1.6%). Diverse clusters were formed among the intact prophages and with bacteriophages of other enterobacteria, suggesting different lineages and associations. Our work provides a strong body of data to support the contributions diverse prophages make to the pathogenicity of Salmonella, including thirteen previously unexplored serovars.},
}

@article {pmid38529721,
year = {2024},
author = {Pankey, MS and Gochfeld, DJ and Gastaldi, M and Macartney, KJ and Clayshulte Abraham, A and Slattery, M and Lesser, MP},
title = {Phylosymbiosis and metabolomics resolve phenotypically plastic and cryptic sponge species in the genus Agelas across the Caribbean basin.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17321},
doi = {10.1111/mec.17321},
pmid = {38529721},
issn = {1365-294X},
support = {1632333//Division of Ocean Sciences/ ; 1632348//Division of Ocean Sciences/ ; 1638289//Division of Ocean Sciences/ ; 1638296//Division of Ocean Sciences/ ; },
abstract = {Fundamental to holobiont biology is recognising how variation in microbial composition and function relates to host phenotypic variation. Sponges often exhibit considerable phenotypic plasticity and also harbour dense microbial communities that function to protect and nourish hosts. One of the most prominent sponge genera on Caribbean coral reefs is Agelas. Using a comprehensive set of morphological (growth form, spicule), chemical and molecular data on 13 recognised species of Agelas in the Caribbean basin, we were able to define only five species (=clades) and found that many morphospecies designations were incongruent with phylogenomic and population genetic analyses. Microbial communities were also strongly differentiated between phylogenetic species, showing little evidence of cryptic divergence and relatively low correlation with morphospecies assignment. Metagenomic analyses also showed strong correspondence to phylogenetic species, and to a lesser extent, geographical and morphological characters. Surprisingly, the variation in secondary metabolites produced by sponge holobionts was explained by geography and morphospecies assignment, in addition to phylogenetic species, and covaried significantly with a subset of microbial symbionts. Spicule characteristics were highly plastic, under greater impact from geographical location than phylogeny. Our results suggest that while phenotypic plasticity is rampant in Agelas, morphological differences within phylogenetic species affect functionally important ecological traits, including the composition of the symbiotic microbial communities and metabolomic profiles.},
}

@article {pmid38526019,
year = {2024},
author = {Duchêne, DA and Duchêne, S and Stiller, J and Heller, R and Ho, SYW},
title = {ClockstaRX: Testing molecular clock hypotheses with genomic data.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae064},
pmid = {38526019},
issn = {1759-6653},
abstract = {Phylogenomic data provide valuable opportunities for studying evolutionary rates and timescales. These analyses require theoretical and statistical tools based on molecular clocks. We present ClockstaRX, a flexible platform for exploring and testing evolutionary rate signals in phylogenomic data. Here, information about evolutionary rates in branches across gene trees is placed in Euclidean space, allowing data transformation, visualization, and hypothesis testing. ClockstaRX implements formal tests for identifying groups of loci and branches that make a large contribution to patterns of rate variation. This information can then be used to test for drivers of genomic evolutionary rates or to inform models for molecular dating. Drawing on the results of a simulation study, we recommend forms of data exploration and filtering that might be useful prior to molecular-clock analyses.},
}

@article {pmid38525076,
year = {2024},
author = {Pineda-Mendoza, RM and Gutiérrez-Ávila, JL and Salazar, KF and Rivera-Orduña, FN and Davis, TS and Zúñiga, G},
title = {Comparative metabarcoding and biodiversity of gut-associated fungal assemblages of Dendroctonus species (Curculionidae: Scolytinae).},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1360488},
pmid = {38525076},
issn = {1664-302X},
abstract = {The genus Dendroctonus is a Holarctic taxon composed of 21 nominal species; some of these species are well known in the world as disturbance agents of forest ecosystems. Under the bark of the host tree, these insects are involved in complex and dynamic associations with phoretic ectosymbiotic and endosymbiotic communities. Unlike filamentous fungi and bacteria, the ecological role of yeasts in the bark beetle holobiont is poorly understood, though yeasts were the first group to be recorded as microbial symbionts of these beetles. Our aim was characterize and compare the gut fungal assemblages associated to 14 species of Dendroctonus using the internal transcribed spacer 2 (ITS2) region. A total of 615,542 sequences were recovered yielding 248 fungal amplicon sequence variants (ASVs). The fungal diversity was represented by 4 phyla, 16 classes, 34 orders, 54 families, and 71 genera with different relative abundances among Dendroctonus species. The α-diversity consisted of 32 genera of yeasts and 39 genera of filamentous fungi. An analysis of β-diversity indicated differences in the composition of the gut fungal assemblages among bark beetle species, with differences in species and phylogenetic diversity. A common core mycobiome was recognized at the genus level, integrated mainly by Candida present in all bark beetles, Nakazawaea, Cladosporium, Ogataea, and Yamadazyma. The bipartite networks confirmed that these fungal genera showed a strong association between beetle species and dominant fungi, which are key to maintaining the structure and stability of the fungal community. The functional variation in the trophic structure was identified among libraries and species, with pathotroph-saprotroph-symbiotroph represented at the highest frequency, followed by saprotroph-symbiotroph, and saprotroph only. The overall network suggested that yeast and fungal ASVs in the gut of these beetles showed positive and negative associations among them. This study outlines a mycobiome associated with Dendroctonus nutrition and provides a starting point for future in vitro and omics approaches addressing potential ecological functions and interactions among fungal assemblages and beetle hosts.},
}

@article {pmid38517169,
year = {2024},
author = {Paulay, A and Grimaud, GM and Caballero, R and Laroche, B and Leclerc, M and Labarthe, S and Maguin, E},
title = {Design of a proteolytic module for improved metabolic modeling of Bacteroides caccae.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0015324},
doi = {10.1128/msystems.00153-24},
pmid = {38517169},
issn = {2379-5077},
abstract = {The gut microbiota plays a crucial role in health and is significantly modulated by human diets. In addition to Western diets which are rich in proteins, high-protein diets are used for specific populations or indications, mainly weight loss. In this study, we investigated the effect of protein supplementation on Bacteroides caccae, a Gram-negative gut symbiont. The supplementation with whey proteins led to a significant increase in growth rate, final biomass, and short-chain fatty acids production. A comprehensive genomic analysis revealed that B. caccae possesses a set of 156 proteases with putative intracellular and extracellular localization and allowed to identify amino acid transporters and metabolic pathways. We developed a fully curated genome-scale metabolic model of B. caccae that incorporated its proteolytic activity and simulated its growth and production of fermentation-related metabolites in response to the different growth media. We validated the model by comparing the predicted phenotype to experimental data. The model accurately predicted B. caccae's growth and metabolite production (R[2] = 0.92 for the training set and R[2] = 0.89 for the validation set). We found that accounting for both ATP consumption related to proteolysis, and whey protein accessibility is necessary for accurate predictions of metabolites production. These results provide insights into B. caccae's adaptation to a high-protein diet and its ability to utilize proteins as a source of nutrition. The proposed model provides a useful tool for understanding the feeding mechanism of B. caccae in the gut microbiome.IMPORTANCEMicrobial proteolysis is understudied despite the availability of dietary proteins for the gut microbiota. Here, the proteolytic potential of the gut symbiont Bacteroides caccae was analyzed for the first time using pan-genomics. This sketches a well-equipped bacteria for protein breakdown, capable of producing 156 different proteases with a broad spectrum of cleavage targets. This functional potential was confirmed by the enhancement of growth and metabolic activities at high protein levels. Proteolysis was included in a B. caccae metabolic model which was fitted with the experiments and validated on external data. This model pinpoints the links between protein availability and short-chain fatty acids production, and the importance for B. caccae to gain access to glutamate and asparagine to promote growth. This integrated approach can be generalized to other symbionts and upscaled to complex microbiota to get insights into the ecological impact of proteins on the gut microbiota.},
}

@article {pmid38506531,
year = {2024},
author = {Sivaprakasam, S and Mohd Azim Khan, NA and Yee Fan, T and Kumarasan, Y and Sicheritz-Pontén, T and Petersen, B and Mohd Hata, E and Vadamalai, G and Parimannan, S and Rajandas, H},
title = {Complete genome sequence of plant growth-promoting Bacillus stratosphericus AIMST-CREST02 isolated from bulk soil of a paddy field.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0113723},
doi = {10.1128/mra.01137-23},
pmid = {38506531},
issn = {2576-098X},
abstract = {Here, we present the complete genome of a plant growth-promoting strain, Bacillus stratosphericus AIMST-CREST02 isolated from the bulk soil of a high-yielding paddy plot. The genome is 3,840,451 bp in size with a GC content of 41.25%. Annotation predicted the presence of 3,907 coding sequences, including genes involved in auxin biosynthesis regulation and gamma-aminobutyric acid (GABA) metabolism.},
}

@article {pmid38505556,
year = {2024},
author = {Chakraborty, N},
title = {Metabolites: a converging node of host and microbe to explain meta-organism.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1337368},
pmid = {38505556},
issn = {1664-302X},
abstract = {Meta-organisms encompassing the host and resident microbiota play a significant role in combatting diseases and responding to stress. Hence, there is growing traction to build a knowledge base about this ecosystem, particularly to characterize the bidirectional relationship between the host and microbiota. In this context, metabolomics has emerged as the major converging node of this entire ecosystem. Systematic comprehension of this resourceful omics component can elucidate the organism-specific response trajectory and the communication grid across the ecosystem embodying meta-organisms. Translating this knowledge into designing nutraceuticals and next-generation therapy are ongoing. Its major hindrance is a significant knowledge gap about the underlying mechanisms maintaining a delicate balance within this ecosystem. To bridge this knowledge gap, a holistic picture of the available information has been presented with a primary focus on the microbiota-metabolite relationship dynamics. The central theme of this article is the gut-brain axis and the participating microbial metabolites that impact cerebral functions.},
}

@article {pmid38500001,
year = {2024},
author = {Jiang, W and Cheng, Z and Zhai, W and Ma, X and Gao, J and Liu, X and Liu, D and Zhou, Z and Wang, P},
title = {Oxytetracycline Increases the Residual Risk of Imidacloprid in Radish (Raphanus sativus) and Disturbs the Plant-Rhizosphere Microbiome Holobiont Homeostasis.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c00271},
pmid = {38500001},
issn = {1520-5118},
abstract = {Antibiotics can be accidentally introduced into farmland by wastewater irrigation, and the environmental effects are still unclear. In this study, the effects of oxytetracycline on the residue of imidacloprid in soil and radishes were investigated. Besides, the rhizosphere microbiome and radish metabolome were analyzed. It showed that the persistence of imidacloprid in soil was unchanged, but the content of olefin-imidacloprid was increased by oxytetracycline. The residue of imidacloprid in radishes was increased by nearly 1.5 times, and the hazard index of imidacloprid was significantly raised by 1.5-4 times. Oxytetracycline remodeled the rhizosphere microbiome, including Actinobe, Elusimic, and Firmicutes, and influenced the metabolome of radishes. Especially, some amino acid metabolic pathways in radish were downregulated, which might be involved in imidacloprid degradation. It can be assumed that oxytetracycline increased the imidacloprid residue in radish through disturbing the plant-rhizosphere microbiome holobiont and, thus, increased the pesticide dietary risk.},
}

@article {pmid38499447,
year = {2024},
author = {Piccini, C and Martínez de la Escalera, G and Segura, A and Croci, C and Kruk, C},
title = {The Microcystis-microbiome interactions: origins of the colonial lifestyle.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae035},
pmid = {38499447},
issn = {1574-6941},
abstract = {Species of the Microcystis genus are the most common bloom-forming toxic cyanobacteria worldwide. They belong to a clade of unicellular cyanobacteria whose ability to reach high biomasses during blooms is linked to the formation of colonies. Colonial lifestyle provides several advantages under stressing conditions of light intensity, ultraviolet light, toxic substances and grazing. The progression from a single-celled organism to multicellularity in Microcystis has usually been interpreted as individual phenotypic responses of the cyanobacterial cells to the environment. Here, we synthesize current knowledge about Microcystis colonial lifestyle and its role in the organism ecology. We then briefly review the available information on Microcystis microbiome and propose that changes leading from single cells to colonies are the consequence of specific and tightly regulated signals between the cyanobacterium and its microbiome through a biofilm-like mechanism. The resulting colony is a multi-specific community of interdependent microorganisms.},
}

@article {pmid38497271,
year = {2024},
author = {Destoumieux-Garzón, D and Montagnani, C and Dantan, L and Nicolas, NS and Travers, MA and Duperret, L and Charrière, GM and Toulza, E and Mitta, G and Cosseau, C and Escoubas, JM},
title = {Cross-talk and mutual shaping between the immune system and the microbiota during an oyster's life.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1901},
pages = {20230065},
doi = {10.1098/rstb.2023.0065},
pmid = {38497271},
issn = {1471-2970},
abstract = {The Pacific oyster Crassostrea gigas lives in microbe-rich marine coastal systems subjected to rapid environmental changes. It harbours a diversified and fluctuating microbiota that cohabits with immune cells expressing a diversified immune gene repertoire. In the early stages of oyster development, just after fertilization, the microbiota plays a key role in educating the immune system. Exposure to a rich microbial environment at the larval stage leads to an increase in immune competence throughout the life of the oyster, conferring a better protection against pathogenic infections at later juvenile/adult stages. This beneficial effect, which is intergenerational, is associated with epigenetic remodelling. At juvenile stages, the educated immune system participates in the control of the homeostasis. In particular, the microbiota is fine-tuned by oyster antimicrobial peptides acting through specific and synergistic effects. However, this balance is fragile, as illustrated by the Pacific Oyster Mortality Syndrome, a disease causing mass mortalities in oysters worldwide. In this disease, the weakening of oyster immune defences by OsHV-1 µVar virus induces a dysbiosis leading to fatal sepsis. This review illustrates the continuous interaction between the highly diversified oyster immune system and its dynamic microbiota throughout its life, and the importance of this cross-talk for oyster health. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.},
}

@article {pmid38497265,
year = {2024},
author = {Klimovich, A and Bosch, TCG},
title = {Novel technologies uncover novel 'anti'-microbial peptides in Hydra shaping the species-specific microbiome.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1901},
pages = {20230058},
doi = {10.1098/rstb.2023.0058},
pmid = {38497265},
issn = {1471-2970},
abstract = {The freshwater polyp Hydra uses an elaborate innate immune machinery to maintain its specific microbiome. Major components of this toolkit are conserved Toll-like receptor (TLR)-mediated immune pathways and species-specific antimicrobial peptides (AMPs). Our study harnesses advanced technologies, such as high-throughput sequencing and machine learning, to uncover a high complexity of the Hydra's AMPs repertoire. Functional analysis reveals that these AMPs are specific against diverse members of the Hydra microbiome and expressed in a spatially controlled pattern. Notably, in the outer epithelial layer, AMPs are produced mainly in the neurons. The neuron-derived AMPs are secreted directly into the glycocalyx, the habitat for symbiotic bacteria, and display high selectivity and spatial restriction of expression. In the endodermal layer, in contrast, endodermal epithelial cells produce an abundance of different AMPs including members of the arminin and hydramacin families, while gland cells secrete kazal-type protease inhibitors. Since the endodermal layer lines the gastric cavity devoid of symbiotic bacteria, we assume that endodermally secreted AMPs protect the gastric cavity from intruding pathogens. In conclusion, Hydra employs a complex set of AMPs expressed in distinct tissue layers and cell types to combat pathogens and to maintain a stable spatially organized microbiome. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.},
}

@article {pmid38497257,
year = {2024},
author = {Maritan, E and Quagliariello, A and Frago, E and Patarnello, T and Martino, ME},
title = {The role of animal hosts in shaping gut microbiome variation.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1901},
pages = {20230071},
doi = {10.1098/rstb.2023.0071},
pmid = {38497257},
issn = {1471-2970},
abstract = {Millions of years of co-evolution between animals and their associated microbial communities have shaped and diversified the nature of their relationship. Studies continue to reveal new layers of complexity in host-microbe interactions, the fate of which depends on a variety of different factors, ranging from neutral processes and environmental factors to local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics and mathematical modelling to disentangle the individual contribution of ecological factors to microbiome evolution. Within this framework, host factors are known to be among the dominant drivers of microbiome composition in different animal species. However, the extent to which they shape microbiome assembly and evolution remains unclear. In this review, we summarize our understanding of how host factors drive microbial communities and how these dynamics are conserved and vary across taxa. We conclude by outlining key avenues for research and highlight the need for implementation of and key modifications to existing theory to fully capture the dynamics of host-associated microbiomes. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.},
}

@article {pmid38495510,
year = {2024},
author = {Yang, L and Guo, Y and Yang, H and Li, S and Zhang, Y and Gao, C and Wei, T and Hao, L},
title = {Distinct microbiota assembly and functional patterns in disease-resistant and susceptible varieties of tobacco.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1361883},
doi = {10.3389/fmicb.2024.1361883},
pmid = {38495510},
issn = {1664-302X},
abstract = {The plant microbiota is believed to be an accessory genome that extends plant functions, forming holobionts together with the host plant. Plant disease resistance, therefore, is inextricably linked with plant microbiota, which play important roles in plant growth and health. To explore the relationship between plant microbiota and disease resistance, we investigated the tobacco microbiome of two varieties with contrasting disease-resistance levels to bacterial wilt and black shank diseases. Comparative microbiome analysis indicated that the resistant variety assembled a distinct microbiota with higher network complexity and diversity. While Pseudomonas and Ensifer, which contain biocontrol and beneficial members, were enriched in the rhizosphere of the resistant variety, Ralstonia, a genus including the known causative pathogen, was enriched in the susceptible variety. Metagenome sequencing revealed that biocontrol functions, such as hydrogen cyanide synthase, pyochelin biosynthesis, and arthrofactin-type cyclic lipopeptide synthetase, were more abundant in the resistant variety. Further analysis indicated that contigs encoding the corresponding genes were mostly assigned to Pseudomonas. Among all the metagenome-assembled genomes, positive selection was suggested in the genome assigned to Pseudomonas only in the rhizosphere of the resistant variety. The search of biosynthetic gene clusters in the Pseudomonas genome revealed a non-ribosomal peptide synthetase, the compound of which was brabantamide A, with known antimicrobial activity. Collectively, our study suggests that the plant microbiota might be involved in microbe-mediated disease resistance. Particularly, our results highlight Pseudomonas in the rhizosphere of the disease-resistant variety as a promising biocontrol candidate. Our study may facilitate further screening of bacterial isolates and the targeted design of microbial communities.},
}

@article {pmid38493232,
year = {2024},
author = {Moreno-Pino, M and Manrique-de-la-Cuba, MF and López-Rodríguez, M and Parada-Pozo, G and Rodríguez-Marconi, S and Ribeiro, CG and Flores-Herrera, P and Guajardo, M and Trefault, N},
title = {Unveiling microbial guilds and symbiotic relationships in Antarctic sponge microbiomes.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {6371},
pmid = {38493232},
issn = {2045-2322},
support = {3210656//ANID FONDECYT Postdoctoral Grant/ ; 21211164//ANID Doctoral Fellowships/ ; 21192150//ANID Doctoral Fellowships/ ; 21190286//ANID Doctoral Fellowships/ ; DG_02-22//INACH Grants/ ; DG_15-20//INACH Grants/ ; DG_12-20//INACH Grants/ ; RT_34-17//INACH Grants/ ; 1230758//ANID FONDECYT Grant/ ; },
mesh = {Animals ; *Porifera/microbiology ; Antarctic Regions ; Ammonia ; Archaea/genetics ; Bacteria/genetics ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Marine sponges host diverse microbial communities. Although we know many of its ecological patterns, a deeper understanding of the polar sponge holobiont is still needed. We combine high-throughput sequencing of ribosomal genes, including the largest taxonomic repertoire of Antarctic sponge species analyzed to date, functional metagenomics, and metagenome-assembled genomes (MAGs). Our findings show that sponges harbor more exclusive bacterial and archaeal communities than seawater, while microbial eukaryotes are mostly shared. Furthermore, bacteria in Antarctic sponge holobionts establish more cooperative interactions than in sponge holobionts from other environments. The bacterial classes that established more positive relations were Bacteroidia, Gamma- and Alphaproteobacteria. Antarctic sponge microbiomes contain microbial guilds that encompass ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and sulfur-oxidizing bacteria. The retrieved MAGs showed a high level of novelty and streamlining signals and belong to the most abundant members of the main microbial guilds in the Antarctic sponge holobiont. Moreover, the genomes of these symbiotic bacteria contain highly abundant functions related to their adaptation to the cold environment, vitamin production, and symbiotic lifestyle, helping the holobiont survive in this extreme environment.},
}

Animals
*Porifera/microbiology
Antarctic Regions
Ammonia
Archaea/genetics
Bacteria/genetics
*Microbiota/genetics
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid38491515,
year = {2024},
author = {Wentzien, NM and Fernández-González, AJ and Valverde-Corredor, A and Lasa, AV and Villadas, PJ and Wicaksono, WA and Cernava, T and Berg, G and Fernández-López, M and Mercado-Blanco, J},
title = {Pitting the olive seed microbiome.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {17},
pmid = {38491515},
issn = {2524-6372},
abstract = {BACKGROUND: The complex and co-evolved interplay between plants and their microbiota is crucial for the health and fitness of the plant holobiont. However, the microbiota of the seeds is still relatively unexplored and no studies have been conducted with olive trees so far. In this study, we aimed to characterize the bacterial, fungal and archaeal communities present in seeds of ten olive genotypes growing in the same orchard through amplicon sequencing to test whether the olive genotype is a major driver in shaping the seed microbial community, and to identify the origin of the latter. Therefore, we have developed a methodology for obtaining samples from the olive seed's endosphere under sterile conditions.

RESULTS: A diverse microbiota was uncovered in olive seeds, the plant genotype being an important factor influencing the structure and composition of the microbial communities. The most abundant bacterial phylum was Actinobacteria, accounting for an average relative abundance of 41%. At genus level, Streptomyces stood out because of its potential influence on community structure. Within the fungal community, Basidiomycota and Ascomycota were the most abundant phyla, including the genera Malassezia, Cladosporium, and Mycosphaerella. The shared microbiome was composed of four bacterial (Stenotrophomonas, Streptomyces, Promicromonospora and Acidipropionibacterium) and three fungal (Malassezia, Cladosporium and Mycosphaerella) genera. Furthermore, a comparison between findings obtained here and earlier results from the root endosphere of the same trees indicated that genera such as Streptomyces and Malassezia were present in both olive compartments.

CONCLUSIONS: This study provides the first insights into the composition of the olive seed microbiota. The highly abundant fungal genus Malassezia and the bacterial genus Streptomyces reflect a unique signature of the olive seed microbiota. The genotype clearly shaped the composition of the seed's microbial community, although a shared microbiome was found. We identified genera that may translocate from the roots to the seeds, as they were present in both organs of the same trees. These findings set the stage for future research into potential vertical transmission of olive endophytes and the role of specific microbial taxa in seed germination, development, and seedling survival.},
}

@article {pmid38488860,
year = {2024},
author = {Freddi, S and Rajabal, V and Tetu, SG and Gillings, MR and Penesyan, A},
title = {Microbial biofilms on macroalgae harbour diverse integron gene cassettes.},
journal = {Microbiology (Reading, England)},
volume = {170},
number = {3},
pages = {},
doi = {10.1099/mic.0.001446},
pmid = {38488860},
issn = {1465-2080},
mesh = {*Integrons/genetics ; *Bacteria/genetics/metabolism ; Genes, Bacterial/genetics ; Drug Resistance, Microbial ; Biofilms ; },
abstract = {Integrons are genetic platforms that capture, rearrange and express mobile modules called gene cassettes. The best characterized gene cassettes encode antibiotic resistance, but the function of most integron gene cassettes remains unknown. Functional predictions suggest that many gene cassettes could encode proteins that facilitate interactions with other cells and with the extracellular environment. Because cell interactions are essential for biofilm stability, we sequenced gene cassettes from biofilms growing on the surface of the marine macroalgae Ulva australis and Sargassum linearifolium. Algal samples were obtained from coastal rock platforms around Sydney, Australia, using seawater as a control. We demonstrated that integrons in microbial biofilms did not sample genes randomly from the surrounding seawater, but harboured specific functions that potentially provided an adaptive advantage to both the bacterial cells in biofilm communities and their macroalgal host. Further, integron gene cassettes had a well-defined spatial distribution, suggesting that each bacterial biofilm acquired these genetic elements via sampling from a large but localized pool of gene cassettes. These findings suggest two forms of filtering: a selective acquisition of different integron-containing bacterial species into the distinct biofilms on Ulva and Sargassum surfaces, and a selective retention of unique populations of gene cassettes at each sampling location.},
}

*Integrons/genetics
*Bacteria/genetics/metabolism
Genes, Bacterial/genetics
Drug Resistance, Microbial
Biofilms

@article {pmid38478382,
year = {2024},
author = {Zenteno-Alegría, CO and Yarzábal Rodríguez, LA and Ciancas Jiménez, J and Álvarez Gutiérrez, PE and Gunde-Cimerman, N and Batista-García, RA},
title = {Fungi beyond limits: The agricultural promise of extremophiles.},
journal = {Microbial biotechnology},
volume = {17},
number = {3},
pages = {e14439},
pmid = {38478382},
issn = {1751-7915},
support = {389616//National Council of Humanities, Sciences and Technologies (CONAHCyT)/ ; //Darwin Initiative UK/ ; DARPP220//Darwin Initiative Round 27/ ; DIR30S2/1004//Darwin Initiative Round 30/ ; I0-0022//Slovenian Research Agency to Infrastructural Centre Mycosmo/ ; P4-0432//Slovenian Research Agency to Infrastructural Centre Mycosmo/ ; P1-0198//Slovenian Research Agency to Infrastructural Centre Mycosmo/ ; RYC2022-037554-I//MCIN/AEI/ ; //FSE+/ ; },
mesh = {*Extremophiles ; *Mycorrhizae ; Symbiosis ; Fungi/genetics ; Agriculture/methods ; Crops, Agricultural/microbiology ; },
abstract = {Global climate changes threaten food security, necessitating urgent measures to enhance agricultural productivity and expand it into areas less for agronomy. This challenge is crucial in achieving Sustainable Development Goal 2 (Zero Hunger). Plant growth-promoting microorganisms (PGPM), bacteria and fungi, emerge as a promising solution to mitigate the impact of climate extremes on agriculture. The concept of the plant holobiont, encompassing the plant host and its symbiotic microbiota, underscores the intricate relationships with a diverse microbial community. PGPM, residing in the rhizosphere, phyllosphere, and endosphere, play vital roles in nutrient solubilization, nitrogen fixation, and biocontrol of pathogens. Novel ecological functions, including epigenetic modifications and suppression of virulence genes, extend our understanding of PGPM strategies. The diverse roles of PGPM as biofertilizers, biocontrollers, biomodulators, and more contribute to sustainable agriculture and environmental resilience. Despite fungi's remarkable plant growth-promoting functions, their potential is often overshadowed compared to bacteria. Arbuscular mycorrhizal fungi (AMF) form a mutualistic symbiosis with many terrestrial plants, enhancing plant nutrition, growth, and stress resistance. Other fungi, including filamentous, yeasts, and polymorphic, from endophytic, to saprophytic, offer unique attributes such as ubiquity, morphology, and endurance in harsh environments, positioning them as exceptional plant growth-promoting fungi (PGPF). Crops frequently face abiotic stresses like salinity, drought, high UV doses and extreme temperatures. Some extremotolerant fungi, including strains from genera like Trichoderma, Penicillium, Fusarium, and others, have been studied for their beneficial interactions with plants. Presented examples of their capabilities in alleviating salinity, drought, and other stresses underscore their potential applications in agriculture. In this context, extremotolerant and extremophilic fungi populating extreme natural environments are muchless investigated. They represent both new challenges and opportunities. As the global climate evolves, understanding and harnessing the intricate mechanisms of fungal-plant interactions, especially in extreme environments, is paramount for developing effective and safe plant probiotics and using fungi as biocontrollers against phytopathogens. Thorough assessments, comprehensive methodologies, and a cautious approach are crucial for leveraging the benefits of extremophilic fungi in the changing landscape of global agriculture, ensuring food security in the face of climate challenges.},
}

*Extremophiles
*Mycorrhizae
Symbiosis
Fungi/genetics
Agriculture/methods
Crops, Agricultural/microbiology

@article {pmid38470181,
year = {2024},
author = {Xu, M and Cai, Z and Cheng, K and Chen, G and Zhou, J},
title = {Mitigation of Vibrio coralliilyticus-induced coral bleaching through bacterial dysbiosis prevention by Ruegeria profundi.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0227423},
doi = {10.1128/aem.02274-23},
pmid = {38470181},
issn = {1098-5336},
abstract = {Vibrio species are prevalent in ocean ecosystems, particularly Vibrio coralliilyticus, and pose a threat to corals and other marine organisms under global warming conditions. While microbiota manipulation is considered for coral disease management, understanding the role of commensal bacteria in stress resilience remains limited. Here, a single bacterial species (Ruegeria profundi) rather than a consortium of native was used to combat pathogenic V. coralliilyticus and protect corals from bleaching. R. profundi showed therapeutic activity in vivo, preventing a significant reduction in bacterial diversity in bleached corals. Notably, the structure of the bacterial community differed significantly among all the groups. In addition, compared with the bleached corals caused by V. coralliilyticus, the network analysis revealed that complex interactions and positive correlations in the bacterial community of the R. profundi protected non-bleached corals, indicating R. profundi's role in fostering synergistic associations. Many genera of bacteria significantly increased in abundance during V. coralliilyticus infection, including Vibrio, Alteromonas, Amphritea, and Nautella, contributing to the pathogenicity of the bacterial community. However, R. profundi effectively countered the proliferation of these genera, promoting potential probiotic Endozoicomonas and other taxa, while reducing the abundance of betaine lipids and the type VI section system of the bacterial community. These changes ultimately influenced the interactive relationships among symbionts and demonstrated that probiotic R. profundi intervention can modulate coral-associated bacterial community, alleviate pathogenic-induced dysbiosis, and preserve coral health. These findings elucidated the relationship between the behavior of the coral-associated bacterial community and the occurrence of pathological coral bleaching.IMPORTANCEChanges in the global climate and marine environment can influence coral host and pathogen repartition which refers to an increased likelihood of pathogen infection in hosts. The risk of Vibrio coralliilyticus-induced coral disease is significantly heightened, primarily due to its thermos-dependent expression of virulent and populations. This study investigates how coral-associated bacterial communities respond to bleaching induced by V. coralliilyticus. Our findings demonstrate that Ruegeria profundi exhibits clear evidence of defense against pathogenic bacterial infection, contributing to the maintenance of host health and symbiont homeostasis. This observation suggests that bacterial pathogens could cause dysbiosis in coral holobionts. Probiotic bacteria display an essential capability in restructuring and manipulating coral-associated bacterial communities. This restructuring effectively reduces bacterial community virulence and enhances the pathogenic resistance of holobionts. The study provides valuable insights into the correlation between the health status of corals and how coral-associated bacterial communities may respond to both pathogens and probiotics.},
}

@article {pmid38462458,
year = {2023},
author = {Libertini, G},
title = {Phenoptosis and the Various Types of Natural Selection.},
journal = {Biochemistry. Biokhimiia},
volume = {88},
number = {12},
pages = {2007-2022},
doi = {10.1134/S0006297923120052},
pmid = {38462458},
issn = {1608-3040},
mesh = {Animals ; Bees ; *Aging/genetics ; Ecosystem ; Selection, Genetic ; *Ants ; Reproduction ; Biological Evolution ; },
abstract = {In the first description of evolution, the fundamental mechanism is the natural selection favoring the individuals best suited for survival and reproduction (selection at the individual level or classical Darwinian selection). However, this is a very reductive description of natural selection that does not consider or explain a long series of known phenomena, including those in which an individual sacrifices or jeopardizes his life on the basis of genetically determined mechanisms (i.e., phenoptosis). In fact, in addition to (i) selection at the individual level, it is essential to consider other types of natural selection such as those concerning: (ii) kin selection and some related forms of group selection; (iii) the interactions between the innumerable species that constitute a holobiont; (iv) the origin of the eukaryotic cell from prokaryotic organisms; (v) the origin of multicellular eukaryotic organisms from unicellular organisms; (vi) eusociality (e.g., in many species of ants, bees, termites); (vii) selection at the level of single genes, or groups of genes; (viii) the interactions between individuals (or more precisely their holobionts) of the innumerable species that make up an ecosystem. These forms of natural selection, which are all effects and not violations of the classical Darwinian selection, also show how concepts as life, species, individual, and phenoptosis are somewhat not entirely defined and somehow arbitrary. Furthermore, the idea of organisms selected on the basis of their survival and reproduction capabilities is intertwined with that of organisms also selected on the basis of their ability to cooperate and interact, even by losing their lives or their distinct identities.},
}

Animals
Bees
*Aging/genetics
Ecosystem
Selection, Genetic
*Ants
Reproduction
Biological Evolution

@article {pmid38454513,
year = {2024},
author = {Lavecchia, A and Fosso, B and Engelen, AH and Borin, S and Manzari, C and Picardi, E and Pesole, G and Placido, A},
title = {Macroalgal microbiomes unveil a valuable genetic resource for halogen metabolism.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {47},
pmid = {38454513},
issn = {2049-2618},
support = {UIDB/04326/2020//Portuguese national funds from FCT/ ; 634486//European Commission/ ; 634486//European Commission/ ; 634486//European Commission/ ; },
mesh = {*Rhodophyta/genetics/metabolism ; *Microbiota/genetics ; Bacteria/genetics/metabolism ; *Seaweed/genetics/metabolism ; Metagenome ; *Anti-Infective Agents ; Halogens/metabolism ; },
abstract = {BACKGROUND: Macroalgae, especially reds (Rhodophyta Division) and browns (Phaeophyta Division), are known for producing various halogenated compounds. Yet, the reasons underlying their production and the fate of these metabolites remain largely unknown. Some theories suggest their potential antimicrobial activity and involvement in interactions between macroalgae and prokaryotes. However, detailed investigations are currently missing on how the genetic information of prokaryotic communities associated with macroalgae may influence the fate of organohalogenated molecules.

RESULTS: To address this challenge, we created a specialized dataset containing 161 enzymes, each with a complete enzyme commission number, known to be involved in halogen metabolism. This dataset served as a reference to annotate the corresponding genes encoded in both the metagenomic contigs and 98 metagenome-assembled genomes (MAGs) obtained from the microbiome of 2 red (Sphaerococcus coronopifolius and Asparagopsis taxiformis) and 1 brown (Halopteris scoparia) macroalgae. We detected many dehalogenation-related genes, particularly those with hydrolytic functions, suggesting their potential involvement in the degradation of a wide spectrum of halocarbons and haloaromatic molecules, including anthropogenic compounds. We uncovered an array of degradative gene functions within MAGs, spanning various bacterial orders such as Rhodobacterales, Rhizobiales, Caulobacterales, Geminicoccales, Sphingomonadales, Granulosicoccales, Microtrichales, and Pseudomonadales. Less abundant than degradative functions, we also uncovered genes associated with the biosynthesis of halogenated antimicrobial compounds and metabolites.

CONCLUSION: The functional data provided here contribute to understanding the still largely unexplored role of unknown prokaryotes. These findings support the hypothesis that macroalgae function as holobionts, where the metabolism of halogenated compounds might play a role in symbiogenesis and act as a possible defense mechanism against environmental chemical stressors. Furthermore, bacterial groups, previously never connected with organohalogen metabolism, e.g., Caulobacterales, Geminicoccales, Granulosicoccales, and Microtrichales, functionally characterized through MAGs reconstruction, revealed a biotechnologically relevant gene content, useful in synthetic biology, and bioprospecting applications. Video Abstract.},
}

*Rhodophyta/genetics/metabolism
*Microbiota/genetics
Bacteria/genetics/metabolism
*Seaweed/genetics/metabolism
Metagenome
*Anti-Infective Agents
Halogens/metabolism

@article {pmid38451230,
year = {2024},
author = {Eisenhofer, R and Nesme, J and Santos-Bay, L and Koziol, A and Sørensen, SJ and Alberdi, A and Aizpurua, O},
title = {A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0359023},
doi = {10.1128/spectrum.03590-23},
pmid = {38451230},
issn = {2165-0497},
abstract = {Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both. To assess the pros and cons of these different approaches, we used 22 fecal DNA extracts collected weekly for 11 weeks from two respective lab mice to study seven performance metrics over four combinations of sequencing depth and technology: (i) 20 Gbp of Illumina short-read data, (ii) 40 Gbp of short-read data, (iii) 20 Gbp of PacBio HiFi long-read data, and (iv) 40 Gbp of hybrid (20 Gbp of short-read +20 Gbp of long-read) data. No strategy was best for all metrics; instead, each one excelled across different metrics. The long-read approach yielded the best assembly statistics, with the highest N50 and lowest number of contigs. The 40 Gbp short-read approach yielded the highest number of refined bins. Finally, the hybrid approach yielded the longest assemblies and the highest mapping rate to the bacterial genomes. Our results suggest that while long-read sequencing significantly improves the quality of reconstructed bacterial genomes, it is more expensive and requires deeper sequencing than short-read approaches to recover a comparable amount of reconstructed genomes. The most optimal strategy is study-specific and depends on how researchers assess the trade-off between the quantity and quality of recovered genomes.IMPORTANCEMice are an important model organism for understanding the gut microbiome. When studying these gut microbiomes using DNA techniques, researchers can choose from technologies that use short or long DNA reads. In this study, we perform an extensive benchmark between short- and long-read DNA sequencing for studying mice gut microbiomes. We find that no one approach was best for all metrics and provide information that can help guide researchers in planning their experiments.},
}

@article {pmid38445866,
year = {2024},
author = {Chen, B and Wei, Y and Yu, K and Liang, Y and Yu, X and Liao, Z and Qin, Z and Xu, L and Bao, Z},
title = {The microbiome dynamics and interaction of endosymbiotic Symbiodiniaceae and fungi are associated with thermal bleaching susceptibility of coral holobionts.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0193923},
doi = {10.1128/aem.01939-23},
pmid = {38445866},
issn = {1098-5336},
abstract = {The thermal bleaching percentage of coral holobionts shows interspecific differences under heat-stress conditions, which are closely related to the coral-associated microbiome. However, the ecological effects of community dynamics and interactions between Symbiodiniaceae and fungi on coral thermal bleaching susceptibility remain unclear. In this study, we analyzed the diversity, community structure, functions, and potential interaction of Symbiodiniaceae and fungi among 18 coral species from a high thermal bleaching risk atoll using next-generation sequencing. The results showed that heat-tolerant C3u sub-clade and Durusdinium dominated the Symbiodiniaceae community of corals and that there were no core amplicon sequence variants in the coral-associated fungal community. Fungal richness and the abundance of confirmed functional animal-plant pathogens were significantly positively correlated with the coral thermal bleaching percentage. Fungal indicators, including Didymellaceae, Chaetomiaceae, Schizophyllum, and Colletotrichum, were identified in corals. Each coral species had a complex Symbiodiniaceae-fungi interaction network (SFIN), which was driven by the dominant Symbiodiniaceae sub-clades. The SFINs of coral holobionts with low thermal bleaching susceptibility exhibited low complexity and high betweenness centrality. These results indicate that the extra heat tolerance of coral in Huangyan Island may be linked to the high abundance of heat-tolerant Symbiodiniaceae. Fungal communities have high interspecific flexibility, and the increase of fungal diversity and pathogen abundance was correlated with higher thermal bleaching susceptibility of corals. Moreover, fungal indicators were associated with the degrees of coral thermal bleaching susceptibility, including both high and intermediate levels. The topological properties of SFINs suggest that heat-tolerant coral have limited fungal parasitism and strong microbial network resilience.IMPORTANCEGlobal warming and enhanced marine heatwaves have led to a rapid decline in coral reef ecosystems worldwide. Several studies have focused on the impact of coral-associated microbiomes on thermal bleaching susceptibility in corals; however, the ecological functions and interactions between Symbiodiniaceae and fungi remain unclear. We investigated the microbiome dynamics and potential interactions of Symbiodiniaceae and fungi among 18 coral species in Huangyan Island. Our study found that the Symbiodiniaceae community of corals was mainly composed of heat-tolerant C3u sub-clade and Durusdinium. The increase in fungal diversity and pathogen abundance has close associations with higher coral thermal bleaching susceptibility. We first constructed an interaction network between Symbiodiniaceae and fungi in corals, which indicated that restricting fungal parasitism and strong interaction network resilience would promote heat acclimatization of corals. Accordingly, this study provides insights into the role of microorganisms and their interaction as drivers of interspecific differences in coral thermal bleaching.},
}

@article {pmid38443414,
year = {2024},
author = {Iguchi, A and Iijima, M and Mizusawa, N and Ohno, Y and Yasumoto, K and Suzuki, A and Suga, S and Tanaka, K and Zaitsu, K},
title = {Single-polyp metabolomics for coral health assessment.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {3369},
pmid = {38443414},
issn = {2045-2322},
support = {19K22938//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; Animals ; *Anthozoa ; Ecosystem ; Tandem Mass Spectrometry ; Coral Reefs ; *Dinoflagellida ; *Polyps ; },
abstract = {Coral reef ecosystems supported by environmentally sensitive reef-building corals face serious threats from human activities. Our understanding of these reef threats is hampered by the lack of sufficiently sensitive coral environmental impact assessment systems. In this study, we established a platform for metabolomic analysis at the single-coral-polyp level using state-of-the-art mass spectrometry (probe electrospray ionization/tandem mass spectrometry; PESI/MS/MS) capable of fine-scale analysis. We analyzed the impact of the organic UV filter, benzophenone (BP), which has a negative impact on corals. We also analyzed ammonium and nitrate samples, which affect the environmental sensitivity of coral-zooxanthella (Symbiodiniaceae) holobionts, to provide new insights into coral biology with a focus on metabolites. The method established in this study breaks new ground by combining PESI/MS/MS with a technique for coral polyps that can control the presence or absence of zooxanthellae in corals, enabling functions of zooxanthellae to be assessed on a polyp-by-polyp basis for the first time. This system will clarify biological mechanisms of corals and will become an important model system for environmental impact assessment using marine organisms.},
}

Humans
Animals
*Anthozoa
Ecosystem
Tandem Mass Spectrometry
Coral Reefs
*Dinoflagellida
*Polyps

@article {pmid38441978,
year = {2024},
author = {Schwob, G and Cabrol, L and Saucède, T and Gérard, K and Poulin, E and Orlando, J},
title = {Unveiling the co-phylogeny signal between plunderfish Harpagifer spp. and their gut microbiomes across the Southern Ocean.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0383023},
doi = {10.1128/spectrum.03830-23},
pmid = {38441978},
issn = {2165-0497},
abstract = {UNLABELLED: Understanding the factors that sculpt fish gut microbiome is challenging, especially in natural populations characterized by high environmental and host genomic complexity. However, closely related hosts are valuable models for deciphering the contribution of host evolutionary history to microbiome assembly, through the underscoring of phylosymbiosis and co-phylogeny patterns. Here, we propose that the recent diversification of several Harpagifer species across the Southern Ocean would allow the detection of robust phylogenetic congruence between the host and its microbiome. We characterized the gut mucosa microbiome of 77 individuals from four field-collected species of the plunderfish Harpagifer (Teleostei, Notothenioidei), distributed across three biogeographic regions of the Southern Ocean. We found that seawater physicochemical properties, host phylogeny, and geography collectively explained 35% of the variation in bacterial community composition in Harpagifer gut mucosa. The core microbiome of Harpagifer spp. gut mucosa was characterized by a low diversity, mostly driven by selective processes, and dominated by a single Aliivibrio Operational Taxonomic Unit (OTU) detected in more than 80% of the individuals. Nearly half of the core microbiome taxa, including Aliivibrio, harbored co-phylogeny signal at microdiversity resolution with host phylogeny, indicating an intimate symbiotic relationship and a shared evolutionary history with Harpagifer. The clear phylosymbiosis and co-phylogeny signals underscore the relevance of the Harpagifer model in understanding the role of fish evolutionary history in shaping the gut microbiome assembly. We propose that the recent diversification of Harpagifer may have led to the diversification of Aliivibrio, exhibiting patterns that mirror the host phylogeny.

IMPORTANCE: Although challenging to detect in wild populations, phylogenetic congruence between marine fish and its microbiome is critical, as it highlights intimate associations between hosts and ecologically relevant microbial symbionts. Our study leverages a natural system of closely related fish species in the Southern Ocean to unveil new insights into the contribution of host evolutionary trajectory on gut microbiome assembly, an underappreciated driver of the global marine fish holobiont. Notably, we unveiled striking evidence of co-diversification between Harpagifer and its microbiome, demonstrating both phylosymbiosis of gut bacterial communities and co-phylogeny of some specific bacterial symbionts, mirroring the host diversification patterns. Given Harpagifer's significance as a trophic resource in coastal areas and its vulnerability to climatic and anthropic pressures, understanding the potential evolutionary interdependence between the hosts and its microbiome provides valuable microbial candidates for future monitoring, as they may play a pivotal role in host species acclimatization to a rapidly changing environment.},
}

@article {pmid38438489,
year = {2024},
author = {Voolstra, CR and Raina, JB and Dörr, M and Cárdenas, A and Pogoreutz, C and Silveira, CB and Mohamed, AR and Bourne, DG and Luo, H and Amin, SA and Peixoto, RS},
title = {The coral microbiome in sickness, in health and in a changing world.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {38438489},
issn = {1740-1534},
abstract = {Stony corals, the engines and engineers of reef ecosystems, face unprecedented threats from anthropogenic environmental change. Corals are holobionts that comprise the cnidarian animal host and a diverse community of bacteria, archaea, viruses and eukaryotic microorganisms. Recent research shows that the bacterial microbiome has a pivotal role in coral biology. A healthy bacterial assemblage contributes to nutrient cycling and stress resilience, but pollution, overfishing and climate change can break down these symbiotic relationships, which results in disease, bleaching and, ultimately, coral death. Although progress has been made in characterizing the spatial-temporal diversity of bacteria, we are only beginning to appreciate their functional contribution. In this Review, we summarize the ecological and metabolic interactions between bacteria and other holobiont members, highlight the biotic and abiotic factors influencing the structure of bacterial communities and discuss the impact of climate change on these communities and their coral hosts. We emphasize how microbiome-based interventions can help to decipher key mechanisms underpinning coral health and promote reef resilience. Finally, we explore how recent technological developments may be harnessed to address some of the most pressing challenges in coral microbiology, providing a road map for future research in this field.},
}

@article {pmid38425799,
year = {2024},
author = {Abd El-Daim, IA and Saad, MM},
title = {Editorial: Holobionts cross talks during microbial-mediated stress tolerance in plants.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1377919},
pmid = {38425799},
issn = {1664-462X},
}

@article {pmid38424629,
year = {2024},
author = {Toullec, G and Rädecker, N and Pogoreutz, C and Banc-Prandi, G and Escrig, S and Genoud, C and Olmos, CM and Spangenberg, J and Meibom, A},
title = {Host starvation and in hospite degradation of algal symbionts shape the heat stress response of the Cassiopea-Symbiodiniaceae symbiosis.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {42},
pmid = {38424629},
issn = {2049-2618},
support = {200021_179092//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 200021_179092//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 212614//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 200021_179092//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {Animals ; Ecosystem ; Symbiosis/physiology ; *Cnidaria ; Heat-Shock Response ; Coral Reefs ; *Dinoflagellida/physiology ; *Anthozoa/physiology ; },
abstract = {BACKGROUND: Global warming is causing large-scale disruption of cnidarian-Symbiodiniaceae symbioses fundamental to major marine ecosystems, such as coral reefs. However, the mechanisms by which heat stress perturbs these symbiotic partnerships remain poorly understood. In this context, the upside-down jellyfish Cassiopea has emerged as a powerful experimental model system.

RESULTS: We combined a controlled heat stress experiment with isotope labeling and correlative SEM-NanoSIMS imaging to show that host starvation is a central component in the chain of events that ultimately leads to the collapse of the Cassiopea holobiont. Heat stress caused an increase in catabolic activity and a depletion of carbon reserves in the unfed host, concurrent with a reduction in the supply of photosynthates from its algal symbionts. This state of host starvation was accompanied by pronounced in hospite degradation of algal symbionts, which may be a distinct feature of the heat stress response of Cassiopea. Interestingly, this loss of symbionts by degradation was concealed by body shrinkage of the starving animals, resulting in what could be referred to as "invisible" bleaching.

CONCLUSIONS: Overall, our study highlights the importance of the nutritional status in the heat stress response of the Cassiopea holobiont. Compared with other symbiotic cnidarians, the large mesoglea of Cassiopea, with its structural sugar and protein content, may constitute an energy reservoir capable of delaying starvation. It seems plausible that this anatomical feature at least partly contributes to the relatively high stress tolerance of these animals in rapidly warming oceans. Video Abstract.},
}

Animals
Ecosystem
Symbiosis/physiology
*Cnidaria
Heat-Shock Response
Coral Reefs
*Dinoflagellida/physiology
*Anthozoa/physiology

@article {pmid38395103,
year = {2024},
author = {Prathapan, P},
title = {Characterisation of the fig-fig wasp holobiont.},
journal = {Bio Systems},
volume = {237},
number = {},
pages = {105162},
doi = {10.1016/j.biosystems.2024.105162},
pmid = {38395103},
issn = {1872-8324},
mesh = {Animals ; *Wasps ; *Ficus ; Pollination ; Ecosystem ; Symbiosis ; },
abstract = {Plants and animals have long been considered distinct kingdoms, yet here a 'plant-animal' is described. An extraordinary symbiosis in which neither organism can reproduce without the other, the fig tree (Ficus) provides the habitat for its exclusive pollinator: the fig wasp (Agaonidae). Characterising the 'fig-fig wasp holobiont' acknowledges, for the first time, 'plant-animal symbiogenesis'.},
}

Animals
*Wasps
*Ficus
Pollination
Ecosystem
Symbiosis

@article {pmid38390522,
year = {2024},
author = {Bech, PK and Jarmusch, SA and Rasmussen, JA and Limborg, MT and Gram, L and Henriksen, NNSE},
title = {Succession of microbial community composition and secondary metabolism during marine biofilm development.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae006},
pmid = {38390522},
issn = {2730-6151},
abstract = {In nature, secondary metabolites mediate interactions between microorganisms residing in complex microbial communities. However, the degree to which community dynamics can be linked to secondary metabolite potential remains largely unknown. In this study, we address the relationship between community succession and secondary metabolism variation. We used 16S and 18S rRNA gene and adenylation domain amplicon sequencing, genome-resolved metagenomics, and untargeted metabolomics to track the taxons, biosynthetic gene clusters, and metabolome dynamics in situ of microorganisms during marine biofilm succession over 113 days. Two phases were identified during the community succession, with a clear shift around Day 29, where the alkaloid secondary metabolites, pseudanes, were also detected. The microbial secondary metabolite potential changed between the phases, and only a few community members, including Myxococotta spp., were responsible for the majority of the biosynthetic gene cluster potential in the early succession phase. In the late phase, bryozoans and benthic copepods were detected, and the microbial nonribosomal peptide potential drastically decreased in association with a reduction in the relative abundance of the prolific secondary metabolite producers. Conclusively, this study provides evidence that the early succession of the marine biofilm community favors prokaryotes with high nonribosomal peptide synthetase potential. In contrast, the late succession is dominated by multicellular eukaryotes and a reduction in bacterial nonribosomal peptide synthetase potential.},
}

@article {pmid38385710,
year = {2024},
author = {Xiao, Y and Gao, L and Li, Z},
title = {Unique high-temperature tolerance mechanisms of zoochlorellae Symbiochlorum hainanensis derived from scleractinian coral Porites lutea.},
journal = {mBio},
volume = {15},
number = {3},
pages = {e0278023},
doi = {10.1128/mbio.02780-23},
pmid = {38385710},
issn = {2150-7511},
support = {42176146//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Animals ; *Anthozoa ; Temperature ; Chlorophyll A ; Selenic Acid ; Antioxidants ; Thiamine ; Symbiosis/physiology ; },
abstract = {UNLABELLED: Global warming is a key issue that causes coral bleaching mainly because of the thermosensitivity of zooxanthellae. Compared with the well-studied zooxanthellae Symbiodiniaceae in coral holobionts, we rarely know about other coral symbiotic algae, let alone their thermal tolerance. In this study, a zoochlorellae, Symbiochlorum hainanensis, isolated from the coral Porites lutea, was proven to have a threshold temperature of 38°C. Meanwhile, unique high-temperature tolerance mechanisms were suggested by integrated transcriptomics and real-time quantitative PCR, physiological and biochemical analyses, and electron microscopy observation. Under heat stress, S. hainanensis shared some similar response strategies with zooxanthellae Effrenium sp., such as increased ascorbate peroxidase, glutathione peroxidase, superoxide dismutase activities and chlorophyll a, thiamine, and thiamine phosphate contents. In particular, more chloroplast internal layered structure, increased CAT activity, enhanced selenate reduction, and thylakoid assembly pathways were highlighted for S. hainanensis's high-temperature tolerance. Notably, it is the first time to reveal a whole selenate reduction pathway from SeO4[2-] to Se[2-] and its contribution to the high-temperature tolerance of S. hainanensis. These unique mechanisms, including antioxidation and maintaining photosynthesis homeostasis, efficiently ensure the high-temperature tolerance of S. hainanensis than Effrenium sp. Compared with the thermosensitivity of coral symbiotic zooxanthellae Symbiodiniaceae, this study provides novel insights into the high-temperature tolerance mechanisms of coral symbiotic zoochlorellae S. hainanensis, which will contribute to corals' survival in the warming oceans caused by global climate change.

IMPORTANCE: The increasing ocean temperature above 31°C-32°C might trigger a breakdown of the coral-Symbiodiniaceae symbioses or coral bleaching because of the thermosensitivity of Symbiodiniaceae; therefore, the exploration of alternative coral symbiotic algae with high-temperature tolerance is important for the corals' protection under warming oceans. This study proves that zoochlorellae Symbiochlorum hainanensis can tolerate 38°C, which is the highest temperature tolerance known for coral symbiotic algae to date, with unique high-temperature tolerance mechanisms. Particularly, for the first time, an internal selenium antioxidant mechanism of coral symbiotic S. hainanensis to high temperature was suggested.},
}

Animals
*Anthozoa
Temperature
Chlorophyll A
Selenic Acid
Antioxidants
Thiamine
Symbiosis/physiology

@article {pmid38376185,
year = {2024},
author = {Hassani, MA and Cui, Z and LaReau, J and Huntley, RB and Steven, B and Zeng, Q},
title = {Inter-species interactions between two bacterial flower commensals and a floral pathogen reduce disease incidence and alter pathogen activity.},
journal = {mBio},
volume = {15},
number = {3},
pages = {e0021324},
pmid = {38376185},
issn = {2150-7511},
support = {2023-51181-41319, 2023-51300-40727, 2020-67013-31794//U.S. Department of Agriculture (USDA)/ ; },
mesh = {Incidence ; Flowers/microbiology ; *Malus/genetics/microbiology ; *Erwinia amylovora/metabolism ; Plant Diseases/microbiology ; },
abstract = {UNLABELLED: Flowers are colonized by a diverse community of microorganisms that can alter plant health and interact with floral pathogens. Erwinia amylovora is a flower-inhabiting bacterium and a pathogen that infects different plant species, including Malus × domestica (apple). Previously, we showed that the co-inoculation of two bacterial strains, members of the genera Pseudomonas and Pantoea, isolated from apple flowers, reduced disease incidence caused by this floral pathogen. Here, we decipher the ecological interactions between the two flower-associated bacteria and E. amylovora in field experimentation and in vitro co-cultures. The two flower commensal strains did not competitively exclude E. amylovora from the stigma habitat, as both bacteria and the pathogen co-existed on the stigma of apple flowers and in vitro. This suggests that plant protection might be mediated by other mechanisms than competitive niche exclusion. Using a synthetic stigma exudation medium, ternary co-culture of the bacterial strains led to a substantial alteration of gene expression in both the pathogen and the two microbiota members. Importantly, the gene expression profiles for the ternary co-culture were not just additive from binary co-cultures, suggesting that some functions only emerged in multipartite co-culture. Additionally, the ternary co-culture of the strains resulted in a stronger acidification of the growth milieu than mono- or binary co-cultures, pointing to another emergent property of co-inoculation. Our study emphasizes the critical role of emergent properties mediated by inter-species interactions within the plant holobiont and their potential impact on plant health and pathogen behavior.

IMPORTANCE: Fire blight, caused by Erwinia amylovora, is one of the most important plant diseases of pome fruits. Previous work largely suggested plant microbiota commensals suppressed disease by antagonizing pathogen growth. However, inter-species interactions of multiple flower commensals and their influence on pathogen activity and behavior have not been well studied. Here, we show that co-inoculating two bacterial strains that naturally colonize the apple flowers reduces disease incidence. We further demonstrate that the interactions between these two microbiota commensals and the floral pathogen led to the emergence of new gene expression patterns and a strong alteration of the external pH, factors that may modify the pathogen's behavior. Our findings emphasize the critical role of emergent properties mediated by inter-species interactions between plant microbiota and plant pathogens and their impact on plant health.},
}

Incidence
Flowers/microbiology
*Malus/genetics/microbiology
*Erwinia amylovora/metabolism
Plant Diseases/microbiology

@article {pmid38374916,
year = {2024},
author = {McLaughlin, MS and Yurgel, SN and Abbasi, PA and Ali, S},
title = {The effects of chemical fungicides and salicylic acid on the apple microbiome and fungal disease incidence under changing environmental conditions.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1342407},
pmid = {38374916},
issn = {1664-302X},
abstract = {Epiphytic and endophytic micro-organisms associated with plants form complex communities on or in their host plant. These communities influence physiological traits, development, and host susceptibility to abiotic and biotic stresses, and these communities are theorized to have evolved alongside their hosts, forming a unit of selection known as the holobiont. The microbiome is highly variable and can be influenced by abiotic factors, including applied exogenous agents. In this study, we compared the impact of chemical fungicide and salicylic acid treatments on the fungal communities of "Honeycrisp" apples at harvest over two consecutive growing years. We demonstrated variations in fungal community structure and composition by tissue type, growing season, and treatment regimes and that fungicide treatments were associated with reduced network complexity. Finally, we show that the inclusion of salicylic acid with 50% less chemical fungicides in an integrated spray program allowed a reduction in fungicide use while maintaining effective control of disease at harvest and following storage.},
}

@article {pmid38371405,
year = {2024},
author = {Ghitti, E and Rolli, E and Vergani, L and Borin, S},
title = {Flavonoids influence key rhizocompetence traits for early root colonization and PCB degradation potential of Paraburkholderia xenovorans LB400.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1325048},
pmid = {38371405},
issn = {1664-462X},
abstract = {INTRODUCTION: Flavonoids are among the main plant root exudation components, and, in addition to their role in symbiosis, they can broadly affect the functionality of plant-associated microbes: in polluted environments, for instance, flavonoids can induce the expression of the enzymatic degradative machinery to clean-up soils from xenobiotics like polychlorinated biphenyls (PCBs). However, their involvement in root community recruitment and assembly involving non-symbiotic beneficial interactions remains understudied and may be crucial to sustain the holobiont fitness under PCB stress.

METHODS: By using a set of model pure flavonoid molecules and a natural blend of root exudates (REs) with altered flavonoid composition produced by Arabidopsis mutant lines affected in flavonoid biosynthesis and abundance (null mutant tt4, flavonoid aglycones hyperproducer tt8, and flavonoid conjugates hyperaccumulator ttg), we investigated flavonoid contribution in stimulating rhizocompetence traits and the catabolic potential of the model bacterial strain for PCB degradation Paraburkholderia xenovorans LB400.

RESULTS: Flavonoids influenced the traits involved in bacterial recruitment in the rhizoplane by improving chemotaxis and motility responses, by increasing biofilm formation and by promoting the growth and activation of the PCB-degradative pathway of strain LB400, being thus potentially exploited as carbon sources, stimulating factors and chemoattractant molecules. Indeed, early rhizoplane colonization was favored in plantlets of the tt8 Arabidopsis mutant and reduced in the ttg line. Bacterial growth was promoted by the REs of mutant lines tt4 and tt8 under control conditions and reduced upon PCB-18 stress, showing no significant differences compared with the WT and ttg, indicating that unidentified plant metabolites could be involved. PCB stress presumably altered the Arabidopsis root exudation profile, although a sudden "cry-for-help" response to recruit strain LB400 was excluded and flavonoids appeared not to be the main determinants. In the in vitro plant-microbe interaction assays, plant growth promotion and PCB resistance promoted by strain LB400 seemed to act through flavonoid-independent mechanisms without altering bacterial colonization efficiency and root adhesion pattern.

DISCUSSIONS: This study further contributes to elucidate the vast array of functions provided by flavonoids in orchestrating the early events of PCB-degrading strain LB400 recruitment in the rhizosphere and to support the holobiont fitness by stimulating the catabolic machinery involved in xenobiotics decomposition and removal.},
}

@article {pmid38371393,
year = {2024},
author = {Chuang, PS and Yu, SP and Liu, PY and Hsu, MT and Chiou, YJ and Lu, CY and Tang, SL},
title = {A gauge of coral physiology: re-examining temporal changes in Endozoicomonas abundance correlated with natural coral bleaching.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae001},
pmid = {38371393},
issn = {2730-6151},
abstract = {Bacteria contribute to many physiological functions of coral holobionts, including responses to bleaching. The bacterial genus, Endozoicomonas, dominates the microbial flora of many coral species and its abundance appears to be correlated with coral bleaching. However, evidences for decoupling of bleaching and Endozoicomonas abundance changes have also been reported. In 2020, a severe bleaching event was recorded at reefs in Taiwan, providing a unique opportunity to re-examine bleaching-Endozoicomonas association using multiple stony corals in natural environments. In this study, we monitored tissue color and microbiome changes in three coral species (Montipora sp., Porites sp., and Stylophora pistillata) in Kenting National Park, following the bleaching event. All tagged Montipora sp. and Porites sp. recovered from bleaching within 1 year, while high mortality occurred in S. pistillata. Microbiome analysis found no correlation of Endozoicomonas relative abundance and bleaching severity during the sampling period, but found a stronger correlation when the month in which bleaching occurred was excluded. Moreover, Endozoicomonas abundance increased during recovery months in Montipora sp. and Porites sp., whereas in S. pistillata it was nearly depleted. These results suggest that Endozoicomonas abundance may represent a gauge of coral health and reflect recovery of some corals from stress. Interestingly, even though different Endozoicomonas strains predominated in the three corals, these Endozoicomonas strains were also shared among coral taxa. Meanwhile, several Endozoicomonas strains showed secondary emergence during coral recovery, suggesting possible symbiont switching in Endozoicomonas. These findings indicate that it may be possible to introduce Endozoicomonas to non-native coral hosts as a coral probiotic.},
}

@article {pmid38365239,
year = {2024},
author = {Maire, J and Tsang Min Ching, SJ and Damjanovic, K and Epstein, HE and Judd, LM and Blackall, LL and van Oppen, MJH},
title = {Tissue-associated and vertically transmitted bacterial symbiont in the coral Pocillopora acuta.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38365239},
issn = {1751-7370},
support = {FL180100036//Australian Research Council/ ; //Native Australian Animals Trust/ ; //Paul G. Allen Philanthropies/ ; //James Cook University/ ; //Australian Institute of Marine Science/ ; },
mesh = {Animals ; *Anthozoa/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Metagenome ; *Gammaproteobacteria/genetics ; Coral Reefs ; Symbiosis ; },
abstract = {Coral microhabitats are colonized by a myriad of microorganisms, including diverse bacteria which are essential for host functioning and survival. However, the location, transmission, and functions of individual bacterial species living inside the coral tissues remain poorly studied. Here, we show that a previously undescribed bacterial symbiont of the coral Pocillopora acuta forms cell-associated microbial aggregates (CAMAs) within the mesenterial filaments. CAMAs were found in both adults and larval offspring, suggesting vertical transmission. In situ laser capture microdissection of CAMAs followed by 16S rRNA gene amplicon sequencing and shotgun metagenomics produced a near complete metagenome-assembled genome. We subsequently cultured the CAMA bacteria from Pocillopora acuta colonies, and sequenced and assembled their genomes. Phylogenetic analyses showed that the CAMA bacteria belong to an undescribed Endozoicomonadaceae genus and species, which we propose to name Candidatus Sororendozoicomonas aggregata gen. nov sp. nov. Metabolic pathway reconstruction from its genome sequence suggests this species can synthesize most amino acids, several B vitamins, and antioxidants, and participate in carbon cycling and prey digestion, which may be beneficial to its coral hosts. This study provides detailed insights into a new member of the widespread Endozoicomonadaceae family, thereby improving our understanding of coral holobiont functioning. Vertically transmitted, tissue-associated bacteria, such as Sororendozoicomonas aggregata may be key candidates for the development of microbiome manipulation approaches with long-term positive effects on the coral host.},
}

Animals
*Anthozoa/microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics
Bacteria/genetics
Metagenome
*Gammaproteobacteria/genetics
Coral Reefs
Symbiosis

@article {pmid38364305,
year = {2024},
author = {Berg, G and Dorador, C and Egamberdieva, D and Kostka, JE and Ryu, CM and Wassermann, B},
title = {Shared governance in the plant holobiont and implications for one health.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {3},
pages = {},
pmid = {38364305},
issn = {1574-6941},
support = {DE-SC0023297//Department of Energy/ ; RS-2022-RD010288//Rural Development Administration/ ; //National Research Foundation/ ; },
mesh = {Humans ; Aged, 80 and over ; Symbiosis ; *One Health ; *Microbiota ; Plants ; },
abstract = {The holobiont Holobiont theory is more than 80 years old, while the importance of microbial communities for plant holobionts was already identified by Lorenz Hiltner more than a century ago. Both concepts are strongly supported by results from the new field of microbiome research. Here, we present ecological and genetic features of the plant holobiont that underpin principles of a shared governance between hosts and microbes and summarize the relevance of plant holobionts in the context of global change. Moreover, we uncover knowledge gaps that arise when integrating plant holobionts in the broader perspective of the holobiome as well as one and planetary health concepts. Action is needed to consider interacting holobionts at the holobiome scale, for prediction and control of microbiome function to improve human and environmental health outcomes.},
}

Humans
Aged, 80 and over
Symbiosis
*One Health
*Microbiota
Plants

@article {pmid38360316,
year = {2024},
author = {Linsmayer, LB and Noel, SK and Leray, M and Wangpraseurt, D and Hassibi, C and Kline, DI and Tresguerres, M},
title = {Effects of bleaching on oxygen dynamics and energy metabolism of two Caribbean coral species.},
journal = {The Science of the total environment},
volume = {919},
number = {},
pages = {170753},
doi = {10.1016/j.scitotenv.2024.170753},
pmid = {38360316},
issn = {1879-1026},
mesh = {Animals ; *Anthozoa/physiology ; Oxygen/metabolism ; Caribbean Region ; *Dinoflagellida ; Energy Metabolism ; Hypoxia ; Coral Reefs ; },
abstract = {As mass coral bleaching events become more frequent, it is increasingly important to elucidate the factors underlying coral susceptibility and survival. We measured photosynthesis, respiration, and O2 concentration at the coral tissue surface, Symbiodiniaceae genotypes, and energy metabolic enzyme activities in Agaricia agaricites and Orbicella franksi throughout experimentally-induced thermal bleaching (+3 °C). A. agaricites colonies started to bleach two days into the thermal treatment and were fully bleached between Days 19-31. In contrast, O. franksi colonies only started to bleach on Day 12 and five colonies fully bleached between Days 24-38 while the remining three colonies took up 55 days. Both species experienced decreased photosynthesis and respiration rates as bleaching progressed. As a result, daytime O2 concentration at the coral surface shifted from hyperoxia in unbleached corals to normoxia in partially bleached corals, and to near hypoxia in fully bleached corals. Additionally, nighttime tissue surface O2 concentration shifted from hypoxia to normoxia, likely resulting from decreased symbiotic algae density, respiration, and photosynthates that fuel coral aerobic respiration. Genetic profiling of internal transcribed spacer 2 (ITS2) revealed differences in Symbiodiniaceae clade proportions between control and bleached colonies. Activity levels of energy metabolic enzymes did not significantly vary between control and bleached A. agaricites, but malate dehydrogenase and strombine dehydrogenase activities were significantly higher in bleached O. franksi colonies compared to controls. These differences were driven by the three O. franksi colonies that took the longest to bleach and contained >98 % Durusdinium sp. D1. The shifts in O2 dynamics within the microhabitat of bleached corals may have important implications for the metabolism of the coral holobiont while the changes in Symbiodiniaceae ITS2 profile and the upregulation of energy metabolic enzymes identify a potential factor contributing to bleaching dynamics.},
}

Animals
*Anthozoa/physiology
Oxygen/metabolism
Caribbean Region
*Dinoflagellida
Energy Metabolism
Hypoxia
Coral Reefs

@article {pmid38354884,
year = {2024},
author = {Ju, H and Zhang, J and Zou, Y and Xie, F and Tang, X and Zhang, S and Li, J},
title = {Bacteria undergo significant shifts while archaea maintain stability in Pocillopora damicornis under sustained heat stress.},
journal = {Environmental research},
volume = {250},
number = {},
pages = {118469},
doi = {10.1016/j.envres.2024.118469},
pmid = {38354884},
issn = {1096-0953},
abstract = {Global warming reportedly poses a critical risk to coral reef ecosystems. Bacteria and archaea are crucial components of the coral holobiont. The response of archaea associated with warming is less well understood than that of the bacterial community in corals. Also, there have been few studies on the dynamics of the microbial community in the coral holobiont under long-term heat stress. In order to track the dynamic alternations in the microbial communities within the heat-stressed coral holobiont, three-week heat-stress monitoring was carried out on the coral Pocillopora damicornis. The findings demonstrate that the corals were stressed at 32 °C, and showed a gradual decrease in Symbiodiniaceae density with increasing duration of heat stress. The archaeal community in the coral holobiont remained relatively unaltered by the increasing temperature, whereas the bacterial community was considerably altered. Sustained heat stress exacerbated the dissimilarities among parallel samples of the bacterial community, confirming the Anna Karenina Principle in animal microbiomes. Heat stress leads to more complex and unstable microbial networks, characterized by an increased average degree and decreased modularity, respectively. With the extension of heat stress duration, the relative abundances of the gene (nifH) and genus (Tistlia) associated with nitrogen fixation increased in coral samples, as well as the potential pathogenic bacteria (Flavobacteriales) and opportunistic bacteria (Bacteroides). Hence, our findings suggest that coral hosts might recruit nitrogen-fixing bacteria during the initial stages of suffering heat stress. An environment that is conducive to the colonization and development of opportunistic and pathogenic bacteria when the coral host becomes more susceptible as heat stress duration increases.},
}

@article {pmid38350445,
year = {2024},
author = {Laine, J and Mak, SST and Martins, NFG and Chen, X and Gilbert, MTP and Jones, FC and Pedersen, MW and Romundset, A and Foote, AD},
title = {Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation.},
journal = {Current biology : CB},
volume = {34},
number = {5},
pages = {1142-1147.e6},
doi = {10.1016/j.cub.2024.01.056},
pmid = {38350445},
issn = {1879-0445},
mesh = {Animals ; *Ecosystem ; Adaptation, Physiological/genetics ; *Smegmamorpha/genetics ; Retrospective Studies ; Lakes ; },
abstract = {Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary ancient DNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms[1][,][2][,][3] and to thereby potentially provide an understanding of the evolutionary histories of past populations.[4][,][5] To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than 1 g of sediment.[6][,][7] Here, we maximize sequence coverage by extracting DNA from ∼50× more sediment per sample than the majority of previous studies[1][,][2][,][3] to achieve genotype resolution. From a time series of Late Pleistocene sediments spanning from a marine to freshwater ecosystem, we compare adaptive genotypes reconstructed from the environmental genomes of three-spined stickleback at key time points of this transition. We find a staggered temporal dynamic in which freshwater alleles at known loci of large effect in marine-freshwater divergence of three-spined stickleback (e.g., EDA)[8] were already established during the brackish phase of the formation of the isolation basin. However, marine alleles were still detected across the majority of marine-freshwater divergence-associated loci, even after the complete isolation of the lake from marine ingression. Our retrospective approach to studying adaptation from environmental genomes of three-spined sticklebacks at the end of the last glacial period complements contemporary experimental approaches[9][,][10][,][11] and highlights the untapped potential for retrospective "evolve and resequence" natural experiments using sedaDNA.},
}

Animals
*Ecosystem
Adaptation, Physiological/genetics
*Smegmamorpha/genetics
Retrospective Studies
Lakes

@article {pmid38347271,
year = {2024},
author = {Suárez, J},
title = {Scrutinizing microbiome determinism: why deterministic hypotheses about the microbiome are conceptually ungrounded.},
journal = {History and philosophy of the life sciences},
volume = {46},
number = {1},
pages = {12},
pmid = {38347271},
issn = {1742-6316},
support = {2019/35/B/HS1/01998//Narodowe Centrum Nauki/ ; SV-23-FBBVA-1//Fundación BBVA/ ; PID2022-137993NA-I00//Spanish National Plan for Scientific and Technical Research and Innovation/ ; },
mesh = {*Biological Evolution ; Symbiosis ; *Microbiota/genetics ; Phenotype ; },
abstract = {This paper addresses the topic of determinism in contemporary microbiome research. I distinguish two types of deterministic claims about the microbiome, and I show evidence that both types of claims are present in the contemporary literature. First, the idea that the host genetics determines the composition of the microbiome which I call "host-microbiome determinism". Second, the idea that the genetics of the holobiont (the individual unit composed by a host plus its microbiome) determines the expression of certain phenotypic traits, which I call "microbiome-phenotype determinism". Drawing on the stability of traits conception of individuality (Suárez in Hist Philos Life Sci 42:11, 2020) I argue that none of these deterministic hypotheses is grounded on our current knowledge of how the holobiont is transgenerationally assembled, nor how it expresses its phenotypic traits.},
}

*Biological Evolution
Symbiosis
*Microbiota/genetics
Phenotype

@article {pmid38345665,
year = {2024},
author = {Sasaki, S and Mori, T and Enomoto, H and Nakamura, S and Yokota, H and Yamashita, H and Goto-Inoue, N},
title = {Assessing Molecular Localization of Symbiont Microalgae in Coral Branches Through Mass Spectrometry Imaging.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {},
number = {},
pages = {},
pmid = {38345665},
issn = {1436-2236},
support = {21H04742//Japan Society for the Promotion of Science/ ; },
abstract = {Reef-building corals are a fundamental pillar of coral reef ecosystems in tropical and subtropical shallow environments. Corals harbor symbiotic dinoflagellates belonging to the family Symbiodiniaceae, commonly known as zooxanthellae. Extensive research has been conducted on this symbiotic relationship, yet the fundamental information about the distribution and localization of Symbiodiniaceae cells in corals is still limited. This information is crucial to understanding the mechanism underlying the metabolite exchange between corals and their algal symbionts, as well as the metabolic flow within holobionts. To examine the distribution of Symbiodiniaceae cells within corals, in this study, we used fluorescence imaging and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MS-Imaging) on branches of the Acropora tenuis coral. We successfully prepared frozen sections of the coral for molecular imaging without fixing or decalcifying the coral branches. By combining the results of MS-Imaging with that of the fluorescence imaging, we determined that the algal Symbiodiniaceae symbionts were not only localized in the tentacle and surface region of the coral branches but also inhabited the in inner parts. Therefore, the molecular imaging technique used in this study could be valuable to further investigate the molecular dynamics between corals and their symbionts.},
}

@article {pmid38340371,
year = {2024},
author = {Wang, S and Lu, C and Zhang, Q and He, X and Wang, W and Li, J and Su, H},
title = {Microbial community and transcriptional responses to V. coralliilyticus stress in coral Favites halicora and Pocillopora damicornis holobiont.},
journal = {Marine environmental research},
volume = {196},
number = {},
pages = {106394},
doi = {10.1016/j.marenvres.2024.106394},
pmid = {38340371},
issn = {1879-0291},
abstract = {Variability in coral hosts susceptibility to Vibrio coralliilyticus is well-documented; however, the comprehensive understanding of tolerance of response to pathogen among coral species is lacked. Herein, we investigated the microbial communities and transcriptome dynamics of two corals in response to Vibrio coralliilyticus. Favites halicora displayed greater resistance to Vibrio coralliilyticus challenge than Pocillopora damicornis. Furthermore, the relative abundances of Flavobacteriaceae, Vibrionacea, Rhodobacteraceae, and Roseobacteraceae increased significantly in Favites halicora following pathogen stress, whereas that of Akkermansiaceae increased significantly in Pocillopora damicornis, leading to bacterial community imbalance. In contrast to the previous results, pathogen infection did not have much effect on the community structures of Symbiodiniaceae and fungi, but led to a decrease in the density of Symbiodiniaceae. Transcriptome analysis indicated that Vibrio infection triggered a coral immune response, resulting in higher expression of immune-related genes, which appeared to have higher transcriptional plasticity in Favites halicora than in Pocillopora damicornis. Specifically, the upregulated genes of Favites halicora were predominantly involved in the apoptosis pathway, whereas Pocillopora damicornis were significantly enriched in the nucleotide excision repair and base excision repair pathways. These findings suggest that coral holobionts activate different mechanisms across species in response to pathogens through shifts in microbial communities and transcriptomes, which provides novel insight into assessing the future coral assemblages suffering from disease outbreaks.},
}

@article {pmid38339825,
year = {2024},
author = {Welsh, BL and Eisenhofer, R},
title = {The prevalence of controls in phyllosphere microbiome research: a methodological review.},
journal = {The New phytologist},
volume = {242},
number = {1},
pages = {23-29},
doi = {10.1111/nph.19573},
pmid = {38339825},
issn = {1469-8137},
support = {//Wine Australia/ ; },
mesh = {Prevalence ; Systematic Reviews as Topic ; *Microbiota/genetics ; },
abstract = {DNA contamination can critically confound microbiome studies. Here, we take a systematic approach to review the current literature and investigate the prevalence of contamination controls in phyllosphere microbiome research over the past decade. By utilising systematic review principles for this review, we were able to conduct a thorough investigation, screening 450 articles from three databases for eligibility and extracting data in a controlled and methodical manner. Worryingly, we observed a surprisingly low usage of both positive and negative contamination controls in phyllosphere research. As a result, we propose a set of minimum standards to combat the effects of contamination in future phyllosphere research.},
}

Prevalence
Systematic Reviews as Topic
*Microbiota/genetics

@article {pmid38334273,
year = {2024},
author = {Olofsson, JK and Tyler, T and Dunning, LT and Hjertson, M and Rühling, Å and Hansen, AJ},
title = {Morphological and genetic evidence suggest gene flow among native and naturalized mint species.},
journal = {American journal of botany},
volume = {111},
number = {2},
pages = {e16280},
doi = {10.1002/ajb2.16280},
pmid = {38334273},
issn = {1537-2197},
mesh = {Humans ; *Mentha/genetics ; Gene Flow ; Phylogeny ; *Oils, Volatile/pharmacology ; Hybridization, Genetic ; },
abstract = {PREMISE: Cultivation and naturalization of plants beyond their natural range can bring previously geographically isolated taxa together, increasing the opportunity for hybridization, the outcomes of which are not predictable. Here, we explored the phenotypic and genomic effects of interspecific gene flow following the widespread cultivation of Mentha spicata (spearmint), M. longifolia, and M. suaveolens.

METHODS: We morphologically evaluated 155 herbarium specimens of three Mentha species and sequenced the genomes of a subset of 93 specimens. We analyzed the whole genomes in a population and the phylogenetic framework and associated genomic classifications in conjunction with the morphological assessments.

RESULTS: The allopolyploid M. spicata, which likely evolved in cultivation, had altered trichome characters, that is possibly a product of human selection for a more palatable plant or a byproduct of selection for essential oils. There were signs of genetic admixture between mints, including allopolyploids, indicating that the reproductive barriers between Mentha species with differences in ploidy are likely incomplete. Still, despite gene flow between species, we found that genetic variants associated with the cultivated trichome morphology continue to segregate.

CONCLUSIONS: Although hybridization, allopolyploidization, and human selection during cultivation can increase species richness (e.g., by forming hybrid taxa), we showed that unless reproductive barriers are strong, these processes can also result in mixing of genes between species and the potential loss of natural biodiversity.},
}

Humans
*Mentha/genetics
Gene Flow
Phylogeny
*Oils, Volatile/pharmacology
Hybridization, Genetic

@article {pmid38322319,
year = {2024},
author = {Czajkowski, R and Zhu, L and Kuo, CH and Li, Z},
title = {Editorial: Insights in microbial symbioses: 2022/2023.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1367452},
pmid = {38322319},
issn = {1664-302X},
}

@article {pmid38320428,
year = {2024},
author = {Estaque, T and Basthard-Bogain, S and Bianchimani, O and Blondeaux, V and Cheminée, A and Fargetton, M and Richaume, J and Bally, M},
title = {Investigating the outcomes of a threatened gorgonian in situ transplantation: Survival and microbiome diversity in Paramuricea clavata (Risso, 1827).},
journal = {Marine environmental research},
volume = {196},
number = {},
pages = {106384},
doi = {10.1016/j.marenvres.2024.106384},
pmid = {38320428},
issn = {1879-0291},
abstract = {Gorgonian octocorals are threatened by global and local stressors that can act synergistically to affect their health. In recent years, mass mortality events triggered by marine heatwaves have caused demographic declines in Mediterranean gorgonian populations that may lead to their collapse. Potential changes in microbiome composition under stressful conditions may further increase the susceptibility of the gorgonian holobiont to disease. Given the low recovery capacity of gorgonians, restoration approaches using transplantation are becoming an increasingly attractive option to counteract their decline. Here, we compared the survival and microbiome diversity of Paramuricea clavata colonies transplanted to sites differing in depth and local environmental conditions. Gorgonians sampled at a greater depth than the transplantation site were more likely to suffer necrosis after 1 year of monitoring. Gorgonian transplantation into environments disturbed by an anthropogenic source of pollution resulted in an imbalance of the microbiome with potential consequences on the success of restoration initiatives.},
}

@article {pmid38308082,
year = {2024},
author = {Reigel, AM and Easson, CG and Apprill, A and Freeman, CJ and Bartley, MM and Fiore, CL},
title = {Sponge-derived matter is assimilated by coral holobionts.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {146},
pmid = {38308082},
issn = {2399-3642},
support = {1924540//National Science Foundation (NSF)/ ; 1923962//National Science Foundation (NSF)/ ; },
mesh = {Animals ; *Anthozoa/physiology ; Coral Reefs ; Biodiversity ; Nutrients ; },
abstract = {Coral reef biodiversity is maintained by a complex network of nutrient recycling among organisms. Sponges assimilate nutrients produced by other organisms like coral and algae, releasing them as particulate and dissolved matter, but to date, only a single trophic link between sponge-derived dissolved matter and a macroalgae has been identified. We sought to determine if sponge-coral nutrient exchange is reciprocal using a stable isotope 'pulse-chase' experiment to trace the uptake of [13]C and [15]N sponge-derived matter by the coral holobiont for three coral species (Acropora cervicornis, Orbicella faveolata, and Eunicea flexuosa). Coral holobionts incorporated 2.3-26.8x more [15]N than [13]C from sponge-derived matter and A. cervicornis incorporated more of both C and N than the other corals. Differential isotopic incorporation among coral species aligns with their ecophysiological characteristics (e.g., morphology, Symbiodiniaceae density). Our results elucidate a recycling pathway on coral reefs that has implications for improving coral aquaculture and management approaches.},
}

Animals
*Anthozoa/physiology
Coral Reefs
Biodiversity
Nutrients

@article {pmid38304271,
year = {2024},
author = {Hartvig, I and Kosawang, C and Rasmussen, H and Kjær, ED and Nielsen, LR},
title = {Co-occurring orchid species associated with different low-abundance mycorrhizal fungi from the soil in a high-diversity conservation area in Denmark.},
journal = {Ecology and evolution},
volume = {14},
number = {2},
pages = {e10863},
pmid = {38304271},
issn = {2045-7758},
abstract = {Plant-fungal interactions are ubiquitous across ecosystems and contribute significantly to plant ecology and evolution. All orchids form obligate symbiotic relationships with specific fungi for germination and early growth, and the distribution of terrestrial orchid species has been linked to occurrence and abundance of specific orchid mycorrhizal fungi (OMF) in the soil. The availability of OMF can therefore be a habitat requirement that is relevant to consider when establishing management and conservation strategies for threatened orchid species, but knowledge on the spatial distribution of OMF in soil is limited. We here studied the mycorrhizal associations of three terrestrial orchid species (Anacamptis pyramidalis, Orchis purpurea and Platanthera chlorantha) found in a local orchid diversity hotspot in eastern Denmark, and investigated the abundance of the identified mycorrhizal fungi in the surrounding soil. We applied ITS metabarcoding to samples of orchid roots, rhizosphere soil and bulk soil collected at three localities, supplemented with standard barcoding of root samples with OMF specific primers, and detected 22 Operational Taxonomic Units (OTUs) putatively identified as OMF. The three orchid species displayed different patterns of OMF associations, supporting the theory that association with specific fungi constitutes part of an orchid's ecological niche allowing co-occurrence of many species in orchid-rich habitats. The identified mycorrhizal partners in the basidiomycete families Tulasnellaceae and Ceratobasidiaceae (Cantharallales) were detected in low abundance in rhizosphere soil, and appeared almost absent from bulk soil at the localities. This finding highlights our limited knowledge of the ecology and trophic mode of OMF outside orchid tissues, as well as challenges in the detection of specific OMF with standard methods. Potential implications for management and conservation strategies are discussed.},
}

@article {pmid38294254,
year = {2024},
author = {Brealey, JC and Kodama, M and Rasmussen, JA and Hansen, SB and Santos-Bay, L and Lecaudey, LA and Hansen, M and Fjære, E and Myrmel, LS and Madsen, L and Bernhard, A and Sveier, H and Kristiansen, K and Gilbert, MTP and Martin, MD and Limborg, MT},
title = {Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon.},
journal = {mSystems},
volume = {9},
number = {2},
pages = {e0104323},
pmid = {38294254},
issn = {2379-5077},
support = {901436//Fiskeri - og havbruksnæringens forskningsfond (FHF)/ ; CEH-DNRF143//Danmarks Grundforskningsfond (DNRF)/ ; 817729//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; 311913//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; CF21-0356//Carlsbergfondet (Carlsberg Foundation)/ ; 325589//Norges Forskningsråd (Forskningsrådet)/ ; },
mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/genetics ; *Salmo salar ; Aquaculture ; Dysbiosis/veterinary ; *Parasitic Diseases ; *Cestode Infections ; },
abstract = {Animals and their associated microbiota share long evolutionary histories. However, it is not always clear how host genotype and microbiota interact to affect phenotype. We applied a hologenomic approach to explore how host-microbiota interactions shape lifetime growth and parasite infection in farmed Atlantic salmon (Salmo salar). Multi-omics data sets were generated from the guts of 460 salmon, 82% of which were naturally infected with an intestinal cestode. A single Mycoplasma bacterial strain, MAG01, dominated the gut metagenome of large, non-parasitized fish, consistent with previous studies showing high levels of Mycoplasma in the gut microbiota of healthy salmon. While small and/or parasitized salmon also had high abundance of MAG01, we observed increased alpha diversity in these individuals, driven by increased frequency of low-abundance Vibrionaceae and other Mycoplasma species that carried known virulence genes. Colonization by one of these cestode-associated Mycoplasma strains was associated with host individual genomic variation in long non-coding RNAs. Integrating the multi-omic data sets revealed coordinated changes in the salmon gut mRNA transcriptome and metabolome that correlated with shifts in the microbiota of smaller, parasitized fish. Our results suggest that the gut microbiota of small and/or parasitized fish is in a state of dysbiosis that partly depends on the host genotype, highlighting the value of using a hologenomic approach to incorporate the microbiota into the study of host-parasite dynamics.IMPORTANCEStudying host-microbiota interactions through the perspective of the hologenome is gaining interest across all life sciences. Intestinal parasite infections are a huge burden on human and animal health; however, there are few studies investigating the role of the hologenome during parasite infections. We address this gap in the largest multi-omics fish microbiota study to date using natural cestode infection of farmed Atlantic salmon. We find a clear association between cestode infection, salmon lifetime growth, and perturbation of the salmon gut microbiota. Furthermore, we provide the first evidence that the genetic background of the host may partly determine how the gut microbiota changes during parasite-associated dysbiosis. Our study therefore highlights the value of a hologenomic approach for gaining a more in-depth understanding of parasitism.},
}

Humans
Animals
*Gastrointestinal Microbiome/genetics
*Salmo salar
Aquaculture
Dysbiosis/veterinary
*Parasitic Diseases
*Cestode Infections

@article {pmid38289136,
year = {2024},
author = {Vergani, L and Patania, J and Riva, V and Nerva, L and Nuzzo, F and Gambino, G and Borin, S and Mapelli, F},
title = {Deciphering the interaction of bacteria inoculants with the recipient endophytic community in grapevine micropropagated plants.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {2},
pages = {e0207823},
pmid = {38289136},
issn = {1098-5336},
support = {20172TZHYX//Ministero dell'Istruzione, dell'Università e della Ricerca (MIUR)/ ; },
mesh = {*Agricultural Inoculants ; Phylogeny ; Plant Roots/microbiology ; Bacteria/genetics ; Enterobacteriaceae ; Endophytes/physiology ; },
abstract = {Engineering the plant microbiome with beneficial endophytic bacteria can improve the growth, health, and productivity of the holobiont. Here, we administered two beneficial bacterial strains, Kosakonia VR04 sp. and Rhizobium GR12 sp., to micropropagated grapevine cuttings obtained via somatic embryogenesis. While both strains colonized the plant endosphere, only Rhizobium GR12 sp. increased root biomass under nutritional-deficit conditions, as supported by the plant growth promotion traits detected in its genome. Phylogenetic and co-occurrence analyses revealed that the plant native bacterial community, originally dominated by Streptococcaceae and Micrococcaceae, dramatically changed depending on the inoculation treatments, as invading strains differently affected the relative abundance and the interactions of pre-existing taxa. After 30 days of plantlets' growth, Pantoea became a predominant taxon, and considering untreated plantlets as references, Rhizobium sp. GR12 showed a minor impact on the endophytic bacterial community. On the other hand, Kosakonia sp. VR04 caused a major change in community composition, suggesting an opportunistic colonization pattern. Overall, the results corroborate the importance of preserving the native endophytic community structure and functions during plant microbiome engineering.IMPORTANCEA better comprehension of bacterial colonization processes and outcomes could benefit the use of plant probiotics in the field. In this study, we applied two different beneficial bacteria to grapevine micropropagated plantlets and described how the inoculation of these strains impacts endophytic microbiota assembly. We showed that under nutritional deficit conditions, the response of the receiving endophytic bacterial communities to the invasion of the beneficial strains related to the manifestation of plant growth promotion effects by the inoculated invading strains. Rhizobium sp. GR12 was able to preserve the native microbiome structure despite its effective colonization, highlighting the importance of the plant-endophyte associations for the holobiont performance. Moreover, our approach showed that the use of micropropagated plantlets could be a valuable strategy to study the interplay among the plant, its native microbiota, and the invader on a wider portfolio of species besides model plants, facilitating the application of new knowledge in agriculture.},
}

*Agricultural Inoculants
Phylogeny
Plant Roots/microbiology
Bacteria/genetics
Enterobacteriaceae
Endophytes/physiology

@article {pmid38287457,
year = {2024},
author = {Nweze, JE and Šustr, V and Brune, A and Angel, R},
title = {Functional similarity, despite taxonomical divergence in the millipede gut microbiota, points to a common trophic strategy.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {16},
pmid = {38287457},
issn = {2049-2618},
support = {19-24309Y//Grantová Agentura České Republiky/ ; 19-24309Y//Grantová Agentura České Republiky/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Bacteria ; *Arthropods/genetics ; Metagenome ; Bacteroidetes/genetics ; Proteobacteria/genetics ; Metagenomics ; Carbohydrates ; Nitrogen/metabolism ; Sulfates/metabolism ; },
abstract = {BACKGROUND: Many arthropods rely on their gut microbiome to digest plant material, which is often low in nitrogen but high in complex polysaccharides. Detritivores, such as millipedes, live on a particularly poor diet, but the identity and nutritional contribution of their microbiome are largely unknown. In this study, the hindgut microbiota of the tropical millipede Epibolus pulchripes (large, methane emitting) and the temperate millipede Glomeris connexa (small, non-methane emitting), fed on an identical diet, were studied using comparative metagenomics and metatranscriptomics.

RESULTS: The results showed that the microbial load in E. pulchripes is much higher and more diverse than in G. connexa. The microbial communities of the two species differed significantly, with Bacteroidota dominating the hindguts of E. pulchripes and Proteobacteria (Pseudomonadota) in G. connexa. Despite equal sequencing effort, de novo assembly and binning recovered 282 metagenome-assembled genomes (MAGs) from E. pulchripes and 33 from G. connexa, including 90 novel bacterial taxa (81 in E. pulchripes and 9 in G. connexa). However, despite this taxonomic divergence, most of the functions, including carbohydrate hydrolysis, sulfate reduction, and nitrogen cycling, were common to the two species. Members of the Bacteroidota (Bacteroidetes) were the primary agents of complex carbon degradation in E. pulchripes, while members of Proteobacteria dominated in G. connexa. Members of Desulfobacterota were the potential sulfate-reducing bacteria in E. pulchripes. The capacity for dissimilatory nitrate reduction was found in Actinobacteriota (E. pulchripes) and Proteobacteria (both species), but only Proteobacteria possessed the capacity for denitrification (both species). In contrast, some functions were only found in E. pulchripes. These include reductive acetogenesis, found in members of Desulfobacterota and Firmicutes (Bacillota) in E. pulchripes. Also, diazotrophs were only found in E. pulchripes, with a few members of the Firmicutes and Proteobacteria expressing the nifH gene. Interestingly, fungal-cell-wall-degrading glycoside hydrolases (GHs) were among the most abundant carbohydrate-active enzymes (CAZymes) expressed in both millipede species, suggesting that fungal biomass plays an important role in the millipede diet.

CONCLUSIONS: Overall, these results provide detailed insights into the genomic capabilities of the microbial community in the hindgut of millipedes and shed light on the ecophysiology of these essential detritivores. Video Abstract.},
}

Animals
*Gastrointestinal Microbiome/genetics
Phylogeny
Bacteria
*Arthropods/genetics
Metagenome
Bacteroidetes/genetics
Proteobacteria/genetics
Metagenomics
Carbohydrates
Nitrogen/metabolism
Sulfates/metabolism

@article {pmid38273492,
year = {2024},
author = {Vompe, AD and Epstein, HE and Speare, KE and Schmeltzer, ER and Adam, TC and Burkepile, DE and Sharpton, TJ and Vega Thurber, R},
title = {Microbiome ecological memory and responses to repeated marine heatwaves clarify variation in coral bleaching and mortality.},
journal = {Global change biology},
volume = {30},
number = {1},
pages = {e17088},
doi = {10.1111/gcb.17088},
pmid = {38273492},
issn = {1365-2486},
support = {2006244//Directorate for Biological Sciences/ ; 1637396//Division of Ocean Sciences/ ; 2023424//Division of Ocean Sciences/ ; 2023701//Division of Ocean Sciences/ ; },
mesh = {Animals ; Coral Reefs ; Coral Bleaching ; *Anthozoa/physiology ; *Microbiota ; Heat-Shock Response ; },
abstract = {Microbiomes are essential features of holobionts, providing their hosts with key metabolic and functional traits like resistance to environmental disturbances and diseases. In scleractinian corals, questions remain about the microbiome's role in resistance and resilience to factors contributing to the ongoing global coral decline and whether microbes serve as a form of holobiont ecological memory. To test if and how coral microbiomes affect host health outcomes during repeated disturbances, we conducted a large-scale (32 exclosures, 200 colonies, and 3 coral species sampled) and long-term (28 months, 2018-2020) manipulative experiment on the forereef of Mo'orea, French Polynesia. In 2019 and 2020, this reef experienced the two most severe marine heatwaves on record for the site. Our experiment and these events afforded us the opportunity to test microbiome dynamics and roles in the context of coral bleaching and mortality resulting from these successive and severe heatwaves. We report unique microbiome responses to repeated heatwaves in Acropora retusa, Porites lobata, and Pocillopora spp., which included: microbiome acclimatization in A. retusa, and both microbiome resilience to the first marine heatwave and microbiome resistance to the second marine heatwave in Pocillopora spp. Moreover, observed microbiome dynamics significantly correlated with coral species-specific phenotypes. For example, bleaching and mortality in A. retusa both significantly increased with greater microbiome beta dispersion and greater Shannon Diversity, while P. lobata colonies had different microbiomes across mortality prevalence. Compositional microbiome changes, such as changes to proportions of differentially abundant putatively beneficial to putatively detrimental taxa to coral health outcomes during repeated heat stress, also correlated with host mortality, with higher proportions of detrimental taxa yielding higher mortality in A. retusa. This study reveals evidence for coral species-specific microbial responses to repeated heatwaves and, importantly, suggests that host-dependent microbiome dynamics may provide a form of holobiont ecological memory to repeated heat stress.},
}

Animals
Coral Reefs
Coral Bleaching
*Anthozoa/physiology
*Microbiota
Heat-Shock Response

@article {pmid38265168,
year = {2024},
author = {Huang, W and Meng, L and Xiao, Z and Tan, R and Yang, E and Wang, Y and Huang, X and Yu, K},
title = {Heat-tolerant intertidal rock pool coral Porites lutea can potentially adapt to future warming.},
journal = {Molecular ecology},
volume = {33},
number = {5},
pages = {e17273},
doi = {10.1111/mec.17273},
pmid = {38265168},
issn = {1365-294X},
support = {42090041//National Natural Science Foundation of China/ ; 41866006//National Natural Science Foundation of China/ ; 42030502//National Natural Science Foundation of China/ ; 2023GXNSFAA026510//Natural Science Foundation of Guangxi Province/ ; },
mesh = {Animals ; *Anthozoa/physiology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Coral Reefs ; *Rhodobacteraceae/genetics ; Symbiosis ; },
abstract = {The growing threat of global warming on coral reefs underscores the urgency of identifying heat-tolerant corals and discovering their adaptation mechanisms to high temperatures. Corals growing in intertidal rock pools that vary markedly in daily temperature may have improved heat tolerance. In this study, heat stress experiments were performed on scleractinian coral Porites lutea from subtidal habitat and intertidal rock pool of Weizhou Island in the northern South China Sea. Thermotolerance differences in corals from the two habitats and their mechanisms were explored through phenotype, physiological indicators, ITS2, 16S rRNA, and RNA sequencing. At the extremely high temperature of 34°C, rock pool P. lutea had a stronger heat tolerance than those in the subtidal habitat. The strong antioxidant capacity of the coral host and its microbial partners was important in the resistance of rock pool corals to high temperatures. The host of rock pool corals at 34°C had stronger immune and apoptotic regulation, downregulated host metabolism and disease-infection-related pathways compared to the subtidal habitat. P. lutea, in this habitat, upregulated Cladocopium C15 (Symbiodiniaceae) photosynthetic efficiency and photoprotection, and significantly increased bacterial diversity and coral probiotics, including ABY1, Ruegeria, and Alteromonas. These findings indicate that rock pool corals can tolerate high temperatures through the integrated response of coral holobionts. These corals may be 'touchstones' for future warming. Our research provides new insights into the complex mechanisms by which corals resist global warming and the theoretical basis for coral reef ecosystem restoration and selection of stress-resistant coral populations.},
}

Animals
*Anthozoa/physiology
Ecosystem
RNA, Ribosomal, 16S/genetics
Coral Reefs
*Rhodobacteraceae/genetics
Symbiosis

@article {pmid38258023,
year = {2024},
author = {Dor-Roterman, YR and Benayahu, Y and Reshef, L and Gophna, U},
title = {Host-Microbiome Interactions in a Changing Sea: The Gill Microbiome of an Invasive Oyster under Drastic Temperature Changes.},
journal = {Microorganisms},
volume = {12},
number = {1},
pages = {},
pmid = {38258023},
issn = {2076-2607},
abstract = {The gill tissue of bivalve mollusks hosts rich symbiotic microbial communities that may contribute to host health. Spondylus spinosus is an invasive Lessepsian oyster in the Eastern Mediterranean Sea that has become highly abundant while constantly expanding its range northwestward. Using 16S rRNA gene amplicon sequencing, we examined how temperature affects S. spinosus oysters and their gill microbiota in a series of experiments: exposing them to the current annual seawater temperature range, to the colder temperature of the Western Mediterranean Sea, and to the elevated temperature as predicted under global warming scenarios. The bacterial genus Endozoicomonas dominated the communities of the S. spinosus, mainly upon exposure to winter-like (16 °C) temperatures. Exposure to the elevated seawater temperature resulted in a significant change in the bacterial communities, while the oysters maintained normal functioning, suggesting that the oyster may survive a seawater warming scenario. Exposure to 11 °C led to the health deterioration of the oysters, the emergence of opportunistic pathogens, such as Arcobacter, Vibrio, Colwelliaceae, and Pseudoalteromonas, and a decline in the relative abundance of Endozoicomonas, suggesting that S. spinosus might not survive Western Mediterranean Sea winters. Both the host and its gill bacteria are thus greatly affected by temperature, which could consequently restrict the range of expansion of this and other invasive oysters.},
}

@article {pmid38246375,
year = {2024},
author = {Efremova, J and Mazzella, V and Mirasole, A and Teixidó, N and Núñez-Pons, L},
title = {Divergent morphological and microbiome strategies of two neighbor sponges to cope with low pH in Mediterranean CO2 vents.},
journal = {The Science of the total environment},
volume = {916},
number = {},
pages = {170171},
doi = {10.1016/j.scitotenv.2024.170171},
pmid = {38246375},
issn = {1879-1026},
mesh = {Humans ; *Seawater/chemistry ; Carbon Dioxide ; RNA, Ribosomal, 16S/genetics ; Dysbiosis ; Hydrogen-Ion Concentration ; *Microbiota/physiology ; Phylogeny ; },
abstract = {Ocean Acidification (OA) profoundly impacts marine biochemistry, resulting in a net loss of biodiversity. Porifera are often forecasted as winner taxa, yet the strategies to cope with OA can vary and may generate diverse fitness status. In this study, microbial shifts based on the V3-V4 16S rRNA gene marker were compared across neighboring Chondrosia reniformis sponges with high microbial abundance (HMA), and Spirastrella cunctatrix with low microbial abundance (LMA) microbiomes. Sponge holobionts co-occurred in a CO2 vent system with low pH (pHT ~ 7.65), and a control site with Ambient pH (pHT ~ 8.05) off Ischia Island, representing natural analogues to study future OA, and species' responses in the face of global environmental change. Microbial diversity and composition varied in both species across sites, yet at different levels. Increased numbers of core taxa were detected in S. cunctatrix, and a more diverse and flexible core microbiome was reported in C. reniformis under OA. Vent S. cunctatrix showed morphological impairment, along with signs of putative stress-induced dysbiosis, manifested by: 1) increases in alpha diversity, 2) shifts from sponge related microbes towards seawater microbes, and 3) high dysbiosis scores. Chondrosia reniformis in lieu, showed no morphological variation, low dysbiosis scores, and experienced a reduction in alpha diversity and less number of core taxa in vent specimens. Therefore, C. reniformis is hypothesized to maintain an state of normobiosis and acclimatize to OA, thanks to a more diverse, and likely metabolically versatile microbiome. A consortium of differentially abundant microbes was identified associated to either vent or control sponges, and chiefly related to carbon, nitrogen and sulfur-metabolisms for nutrient cycling and vitamin production, as well as probiotic symbionts in C. reniformis. Diversified symbiont associates supporting functional convergence could be the key behind resilience towards OA, yet specific acclimatization traits should be further investigated.},
}

Humans
*Seawater/chemistry
Carbon Dioxide
RNA, Ribosomal, 16S/genetics
Dysbiosis
Hydrogen-Ion Concentration
*Microbiota/physiology
Phylogeny

@article {pmid38244627,
year = {2024},
author = {Adomako, MO and Wu, J and Lu, Y and Adu, D and Seshie, VI and Yu, FH},
title = {Potential synergy of microplastics and nitrogen enrichment on plant holobionts in wetland ecosystems.},
journal = {The Science of the total environment},
volume = {915},
number = {},
pages = {170160},
doi = {10.1016/j.scitotenv.2024.170160},
pmid = {38244627},
issn = {1879-1026},
mesh = {*Ecosystem ; Wetlands ; Microplastics ; Plastics ; Nitrogen/metabolism ; Soil/chemistry ; *Microbiota ; },
abstract = {Wetland ecosystems are global hotspots for environmental contaminants, including microplastics (MPs) and nutrients such as nitrogen (N) and phosphorus (P). While MP and nutrient effects on host plants and their associated microbial communities at the individual level have been studied, their synergistic effects on a plant holobiont (i.e., a plant host plus its microbiota, such as bacteria and fungi) in wetland ecosystems are nearly unknown. As an ecological entity, plant holobionts play pivotal roles in biological nitrogen fixation, promote plant resilience and defense chemistry against pathogens, and enhance biogeochemical processes. We summarize evidence based on recent literature to elaborate on the potential synergy of MPs and nutrient enrichment on plant holobionts in wetland ecosystems. We provide a conceptual framework to explain the interplay of MPs, nutrients, and plant holobionts and discuss major pathways of MPs and nutrients into the wetland milieu. Moreover, we highlight the ecological consequences of loss of plant holobionts in wetland ecosystems and conclude with recommendations for pending questions that warrant urgent research. We found that nutrient enrichment promotes the recruitment of MPs-degraded microorganisms and accelerates microbially mediated degradation of MPs, modifying their distribution and toxicity impacts on plant holobionts in wetland ecosystems. Moreover, a loss of wetland plant holobionts via long-term MP-nutrient interactions may likely exacerbate the disruption of wetland ecosystems' capacity to offer nature-based solutions for climate change mitigation through soil organic C sequestration. In conclusion, MP and nutrient enrichment interactions represent a severe ecological risk that can disorganize plant holobionts and their taxonomic roles, leading to dysbiosis (i.e., the disintegration of a stable plant microbiome) and diminishing wetland ecosystems' integrity and multifunctionality.},
}

*Ecosystem
Wetlands
Microplastics
Plastics
Nitrogen/metabolism
Soil/chemistry
*Microbiota

@article {pmid38238538,
year = {2024},
author = {Allentoft, ME and Sikora, M and Refoyo-Martínez, A and Irving-Pease, EK and Fischer, A and Barrie, W and Ingason, A and Stenderup, J and Sjögren, KG and Pearson, A and Sousa da Mota, B and Schulz Paulsson, B and Halgren, A and Macleod, R and Jørkov, MLS and Demeter, F and Sørensen, L and Nielsen, PO and Henriksen, RA and Vimala, T and McColl, H and Margaryan, A and Ilardo, M and Vaughn, A and Fischer Mortensen, M and Nielsen, AB and Ulfeldt Hede, M and Johannsen, NN and Rasmussen, P and Vinner, L and Renaud, G and Stern, A and Jensen, TZT and Scorrano, G and Schroeder, H and Lysdahl, P and Ramsøe, AD and Skorobogatov, A and Schork, AJ and Rosengren, A and Ruter, A and Outram, A and Timoshenko, AA and Buzhilova, A and Coppa, A and Zubova, A and Silva, AM and Hansen, AJ and Gromov, A and Logvin, A and Gotfredsen, AB and Henning Nielsen, B and González-Rabanal, B and Lalueza-Fox, C and McKenzie, CJ and Gaunitz, C and Blasco, C and Liesau, C and Martinez-Labarga, C and Pozdnyakov, DV and Cuenca-Solana, D and Lordkipanidze, DO and En'shin, D and Salazar-García, DC and Price, TD and Borić, D and Kostyleva, E and Veselovskaya, EV and Usmanova, ER and Cappellini, E and Brinch Petersen, E and Kannegaard, E and Radina, F and Eylem Yediay, F and Duday, H and Gutiérrez-Zugasti, I and Merts, I and Potekhina, I and Shevnina, I and Altinkaya, I and Guilaine, J and Hansen, J and Aura Tortosa, JE and Zilhão, J and Vega, J and Buck Pedersen, K and Tunia, K and Zhao, L and Mylnikova, LN and Larsson, L and Metz, L and Yepiskoposyan, L and Pedersen, L and Sarti, L and Orlando, L and Slimak, L and Klassen, L and Blank, M and González-Morales, M and Silvestrini, M and Vretemark, M and Nesterova, MS and Rykun, M and Rolfo, MF and Szmyt, M and Przybyła, M and Calattini, M and Sablin, M and Dobisíková, M and Meldgaard, M and Johansen, M and Berezina, N and Card, N and Saveliev, NA and Poshekhonova, O and Rickards, O and Lozovskaya, OV and Gábor, O and Uldum, OC and Aurino, P and Kosintsev, P and Courtaud, P and Ríos, P and Mortensen, P and Lotz, P and Persson, P and Bangsgaard, P and de Barros Damgaard, P and Vang Petersen, P and Martinez, PP and Włodarczak, P and Smolyaninov, RV and Maring, R and Menduiña, R and Badalyan, R and Iversen, R and Turin, R and Vasilyev, S and Wåhlin, S and Borutskaya, S and Skochina, S and Sørensen, SA and Andersen, SH and Jørgensen, T and Serikov, YB and Molodin, VI and Smrcka, V and Merts, V and Appadurai, V and Moiseyev, V and Magnusson, Y and Kjær, KH and Lynnerup, N and Lawson, DJ and Sudmant, PH and Rasmussen, S and Korneliussen, TS and Durbin, R and Nielsen, R and Delaneau, O and Werge, T and Racimo, F and Kristiansen, K and Willerslev, E},
title = {Publisher Correction: Population genomics of post-glacial western Eurasia.},
journal = {Nature},
volume = {626},
number = {7997},
pages = {E3},
doi = {10.1038/s41586-024-07044-5},
pmid = {38238538},
issn = {1476-4687},
}

@article {pmid38233870,
year = {2024},
author = {Tabassum, N and Ahmed, HI and Parween, S and Sheikh, AH and Saad, MM and Krattinger, SG and Hirt, H},
title = {Host genotype, soil composition, and geo-climatic factors shape the fonio seed microbiome.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {11},
pmid = {38233870},
issn = {2049-2618},
mesh = {*Soil/chemistry ; Genome-Wide Association Study ; Seeds/genetics/microbiology ; *Microbiota/genetics ; Plants ; Endophytes ; Genotype ; Bacteria/genetics ; },
abstract = {BACKGROUND: Fonio (Digitaria exilis), an orphan millet crop, is the oldest indigenous crop in West Africa. Although the yield is low due to pre-domestication characteristics, the quick maturation time, drought tolerance, and the ability to thrive on poor soils make fonio a climate-smart crop. Being holobionts, plants evolve in close interaction with microbial partners, which is crucial for plant phenology and fitness. As seeds are the bottleneck of vertically transmitting plant microbiota, we proposed to unravel the seed microbiome of the under-domesticated and resilient crop fonio. Our study investigated the bacterial seed endophyte diversity across 126 sequenced fonio accessions from distinct locations in West Africa. We conducted a correlation study of the structures and functions of the seed-associated microbiomes with the native geo-climate and soil structure data. We also performed Genome-wide association studies (GWAS) to identify genetic loci associated with seed endophyte diversity.

RESULT: We report that fonio millet has diverse heritable seed endophytic taxa. We analyzed the seed microbiomes of 126 fonio accessions and showed that despite the diversity of microbiomes from distinct geographical locations, all fonio genetic groups share a core microbiome. In addition, we observed that native soil composition, geo-climatic factors, and host genotype correlate with the seed microbiomes. GWAS analysis of genetic loci associated with endophyte seed bacterial diversity identified fonio SNPs associated with genes functioning in embryo development and stress/defense response.

CONCLUSION: Analysis of the seed endophyte of the climate-smart crop fonio indicated that despite possessing a heritable core microbiome, native conditions may shape the overall fonio seed microbiomes in different populations. These distinct microbiomes could play important roles in the adaptation of fonio to different environmental conditions. Our study identified the seed microbiome as a potential target for enhancing crop resilience to climate stress in a sustainable way. Video Abstract.},
}

*Soil/chemistry
Genome-Wide Association Study
Seeds/genetics/microbiology
*Microbiota/genetics
Plants
Endophytes
Genotype
Bacteria/genetics

@article {pmid38230446,
year = {2024},
author = {Castro, LC and Vergés, A and Straub, SC and Campbell, AH and Coleman, MA and Wernberg, T and Steinberg, P and Thomas, T and Dworjanyn, S and Cetina-Heredia, P and Roughan, M and Marzinelli, EM},
title = {Effect of marine heatwaves and warming on kelp microbiota influence trophic interactions.},
journal = {Molecular ecology},
volume = {33},
number = {5},
pages = {e17267},
doi = {10.1111/mec.17267},
pmid = {38230446},
issn = {1365-294X},
support = {DP160100114//Australian Research Council/ ; DP170100023//Australian Research Council/ ; DP180104041//Australian Research Council/ ; LP150100064//Australian Research Council/ ; },
mesh = {*Kelp/physiology ; Ecosystem ; Climate Change ; Oceans and Seas ; *Seaweed ; *Microbiota ; },
abstract = {The range-expansion of tropical herbivores due to ocean warming can profoundly alter temperate reef communities by overgrazing the seaweed forests that underpin them. Such ecological interactions may be mediated by changes to seaweed-associated microbiota in response to warming, but empirical evidence demonstrating this is rare. We experimentally simulated ocean warming and marine heatwaves (MHWs) to quantify effects on two dominant temperate seaweed species and their microbiota, as well as grazing by a tropical herbivore. The kelp Ecklonia radiata's microbiota in sustained warming and MHW treatments was enriched with microorganisms associated with seaweed disease and tissue degradation. In contrast, the fucoid Sargassum linearifolium's microbiota was unaffected by temperature. Consumption by the tropical sea-urchin Tripneustes gratilla was greater on Ecklonia where the microbiota had been altered by higher temperatures, while Sargassum's consumption was unaffected. Elemental traits (carbon, nitrogen), chemical defences (phenolics) and tissue bleaching of both seaweeds were generally unaffected by temperature. Effects of warming and MHWs on seaweed holobionts (host plus its microbiota) are likely species-specific. The effect of increased temperature on Ecklonia's microbiota and subsequent increased consumption suggest that changes to kelp microbiota may underpin kelp-herbivore interactions, providing novel insights into potential mechanisms driving change in species' interactions in warming oceans.},
}

*Kelp/physiology
Ecosystem
Climate Change
Oceans and Seas
*Seaweed
*Microbiota

@article {pmid38228019,
year = {2024},
author = {Li, J and Guo, A and Huang, S and Azam, F and Sun, X and Zhang, J and Long, L and Zhang, S},
title = {Outer membrane vesicles produced by coral-associated Vibrio coralliilyticus inhibit bacteriophage infection and its ecological implications.},
journal = {Microbiological research},
volume = {281},
number = {},
pages = {127607},
doi = {10.1016/j.micres.2024.127607},
pmid = {38228019},
issn = {1618-0623},
mesh = {Animals ; *Anthozoa/microbiology ; *Bacteriophages ; *Vibrio ; },
abstract = {The potential to produce and release outer membrane vesicles (OMVs) is evolutionarily conserved among bacteria, facilitating interactions between microbes. OMV release and its ecological significance have rarely been reported in coral holobionts. Here, via transmission electron microscopy (TEM), we discovered that the coral-associated strain Vibrio coralliilyticus DSM 19607 produced OMVs in culture. OMVs purified from V. coralliilyticus DSM 19607 inhibited the bacteriophage (phage) SBM1 infection of the V. coralliilyticus host, which was impaired by elevated temperature. Observation via TEM showed that sequestrating phages was a potential approach for V. coralliilyticus OMVs protection against phage infection. Furthermore, detection in coral mucus showed that interactions between membrane vesicles and phages potentially occurred in the natural environment. These results imply that OMVs regulate the coral microbiome and may have important implications for our mechanistic understanding of coral health and disease in the face of climate change.},
}

Animals
*Anthozoa/microbiology
*Bacteriophages
*Vibrio

@article {pmid38216372,
year = {2023},
author = {Pogoreutz, C and Ziegler, M},
title = {Frenemies on the reef? Resolving the coral-Endozoicomonas association.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2023.11.006},
pmid = {38216372},
issn = {1878-4380},
abstract = {Stony corals are poster child holobionts due to their intimate association with diverse microorganisms from all domains of life. We are only beginning to understand the diverse functions of most of these microbial associates, including potential main contributors to holobiont health and resilience. Among these, bacteria of the elusive genus Endozoicomonas are widely perceived as beneficial symbionts based on their genomic potential and their high prevalence and ubiquitous presence in coral tissues. Simultaneously, evidence of pathogenic and parasitic Endozoicomonas lineages in other marine animals is emerging. Synthesizing the current knowledge on the association of Endozoicomonas with marine holobionts, we challenge the perception of a purely mutualistic coral-Endozoicomonas relationship and propose directions to elucidate its role along the symbiotic spectrum.},
}

@article {pmid38200295,
year = {2024},
author = {Allentoft, ME and Sikora, M and Refoyo-Martínez, A and Irving-Pease, EK and Fischer, A and Barrie, W and Ingason, A and Stenderup, J and Sjögren, KG and Pearson, A and Sousa da Mota, B and Schulz Paulsson, B and Halgren, A and Macleod, R and Jørkov, MLS and Demeter, F and Sørensen, L and Nielsen, PO and Henriksen, RA and Vimala, T and McColl, H and Margaryan, A and Ilardo, M and Vaughn, A and Fischer Mortensen, M and Nielsen, AB and Ulfeldt Hede, M and Johannsen, NN and Rasmussen, P and Vinner, L and Renaud, G and Stern, A and Jensen, TZT and Scorrano, G and Schroeder, H and Lysdahl, P and Ramsøe, AD and Skorobogatov, A and Schork, AJ and Rosengren, A and Ruter, A and Outram, A and Timoshenko, AA and Buzhilova, A and Coppa, A and Zubova, A and Silva, AM and Hansen, AJ and Gromov, A and Logvin, A and Gotfredsen, AB and Henning Nielsen, B and González-Rabanal, B and Lalueza-Fox, C and McKenzie, CJ and Gaunitz, C and Blasco, C and Liesau, C and Martinez-Labarga, C and Pozdnyakov, DV and Cuenca-Solana, D and Lordkipanidze, DO and En'shin, D and Salazar-García, DC and Price, TD and Borić, D and Kostyleva, E and Veselovskaya, EV and Usmanova, ER and Cappellini, E and Brinch Petersen, E and Kannegaard, E and Radina, F and Eylem Yediay, F and Duday, H and Gutiérrez-Zugasti, I and Merts, I and Potekhina, I and Shevnina, I and Altinkaya, I and Guilaine, J and Hansen, J and Aura Tortosa, JE and Zilhão, J and Vega, J and Buck Pedersen, K and Tunia, K and Zhao, L and Mylnikova, LN and Larsson, L and Metz, L and Yepiskoposyan, L and Pedersen, L and Sarti, L and Orlando, L and Slimak, L and Klassen, L and Blank, M and González-Morales, M and Silvestrini, M and Vretemark, M and Nesterova, MS and Rykun, M and Rolfo, MF and Szmyt, M and Przybyła, M and Calattini, M and Sablin, M and Dobisíková, M and Meldgaard, M and Johansen, M and Berezina, N and Card, N and Saveliev, NA and Poshekhonova, O and Rickards, O and Lozovskaya, OV and Gábor, O and Uldum, OC and Aurino, P and Kosintsev, P and Courtaud, P and Ríos, P and Mortensen, P and Lotz, P and Persson, P and Bangsgaard, P and de Barros Damgaard, P and Vang Petersen, P and Martinez, PP and Włodarczak, P and Smolyaninov, RV and Maring, R and Menduiña, R and Badalyan, R and Iversen, R and Turin, R and Vasilyev, S and Wåhlin, S and Borutskaya, S and Skochina, S and Sørensen, SA and Andersen, SH and Jørgensen, T and Serikov, YB and Molodin, VI and Smrcka, V and Merts, V and Appadurai, V and Moiseyev, V and Magnusson, Y and Kjær, KH and Lynnerup, N and Lawson, DJ and Sudmant, PH and Rasmussen, S and Korneliussen, TS and Durbin, R and Nielsen, R and Delaneau, O and Werge, T and Racimo, F and Kristiansen, K and Willerslev, E},
title = {Population genomics of post-glacial western Eurasia.},
journal = {Nature},
volume = {625},
number = {7994},
pages = {301-311},
pmid = {38200295},
issn = {1476-4687},
support = {207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; U19 AG023122/AG/NIA NIH HHS/United States ; R35 GM142916/GM/NIGMS NIH HHS/United States ; UH2 AG064706/AG/NIA NIH HHS/United States ; U24 AG051129/AG/NIA NIH HHS/United States ; R01 GM138634/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Agriculture/history ; Asia, Western ; Black Sea ; Diploidy ; Europe/ethnology ; *Genetics, Population ; *Genome, Human ; Genotype ; History, Ancient ; *Human Migration/history ; Hunting/history ; *Metagenomics ; Ice Cover ; },
abstract = {Western Eurasia witnessed several large-scale human migrations during the Holocene[1-5]. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes-mainly from the Mesolithic and Neolithic periods-from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a 'great divide' genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 BP, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a 'Neolithic steppe' cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.},
}

Humans
Agriculture/history
Asia, Western
Black Sea
Diploidy
Europe/ethnology
*Genetics, Population
*Genome, Human
Genotype
History, Ancient
*Human Migration/history
Hunting/history
*Metagenomics
Ice Cover

@article {pmid38198924,
year = {2024},
author = {Cha, J and Kim, TG and Bhae, E and Gwak, HJ and Ju, Y and Choe, YH and Jang, IH and Jung, Y and Moon, S and Kim, T and Lee, W and Park, JS and Chung, YW and Yang, S and Kang, YK and Hyun, YM and Hwang, GS and Lee, WJ and Rho, M and Ryu, JH},
title = {Skin microbe-dependent TSLP-ILC2 priming axis in early life is co-opted in allergic inflammation.},
journal = {Cell host & microbe},
volume = {32},
number = {2},
pages = {244-260.e11},
doi = {10.1016/j.chom.2023.12.006},
pmid = {38198924},
issn = {1934-6069},
mesh = {Humans ; Adult ; Infant, Newborn ; *Thymic Stromal Lymphopoietin ; Immunity, Innate ; Lymphocytes ; Cytokines/metabolism ; Skin/metabolism ; *Dermatitis, Atopic ; Inflammation ; },
abstract = {Although early life colonization of commensal microbes contributes to long-lasting immune imprinting in host tissues, little is known regarding the pathophysiological consequences of postnatal microbial tuning of cutaneous immunity. Here, we show that postnatal exposure to specific skin commensal Staphylococcus lentus (S. lentus) promotes the extent of atopic dermatitis (AD)-like inflammation in adults through priming of group 2 innate lymphoid cells (ILC2s). Early postnatal skin is dynamically populated by discrete subset of primed ILC2s driven by microbiota-dependent induction of thymic stromal lymphopoietin (TSLP) in keratinocytes. Specifically, the indole-3-aldehyde-producing tryptophan metabolic pathway, shared across Staphylococcus species, is involved in TSLP-mediated ILC2 priming. Furthermore, we demonstrate a critical contribution of the early postnatal S. lentus-TSLP-ILC2 priming axis in facilitating AD-like inflammation that is not replicated by later microbial exposure. Thus, our findings highlight the fundamental role of time-dependent neonatal microbial-skin crosstalk in shaping the threshold of innate type 2 immunity co-opted in adulthood.},
}

Humans
Adult
Infant, Newborn
*Thymic Stromal Lymphopoietin
Immunity, Innate
Lymphocytes
Cytokines/metabolism
Skin/metabolism
*Dermatitis, Atopic
Inflammation

@article {pmid38196363,
year = {2024},
author = {Howe, J and Cornwallis, CK and Griffin, AS},
title = {Conflict-reducing innovations in development enable increased multicellular complexity.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2014},
pages = {20232466},
pmid = {38196363},
issn = {1471-2954},
mesh = {Animals ; Phylogeny ; *Cognition ; Cell Division ; *Stem Cells ; },
abstract = {Obligately multicellular organisms, where cells can only reproduce as part of the group, have evolved multiple times across the tree of life. Obligate multicellularity has only evolved when clonal groups form by cell division, rather than by cells aggregating, as clonality prevents internal conflict. Yet obligately multicellular organisms still vary greatly in 'multicellular complexity' (the number of cells and cell types): some comprise a few cells and cell types, while others have billions of cells and thousands of types. Here, we test whether variation in multicellular complexity is explained by two conflict-suppressing mechanisms, namely a single-cell bottleneck at the start of development, and a strict separation of germline and somatic cells. Examining the life cycles of 129 lineages of plants, animals, fungi and algae, we show using phylogenetic comparative analyses that an early segregation of the germline stem-cell lineage is key to the evolution of more cell types, driven by a strong correlation in the Metazoa. By contrast, the presence of a strict single-cell bottleneck was not related to either the number of cells or the number of cell types, but was associated with early germline segregation. Our results suggest that segregating the germline earlier in development enabled greater evolutionary innovation, although whether this is a consequence of conflict reduction or other non-conflict effects, such as developmental flexibility, is unclear.},
}

Animals
Phylogeny
*Cognition
Cell Division
*Stem Cells

@article {pmid38186589,
year = {2023},
author = {Pellissier, L and Gaudry, A and Vilette, S and Lecoultre, N and Rutz, A and Allard, PM and Marcourt, L and Ferreira Queiroz, E and Chave, J and Eparvier, V and Stien, D and Gindro, K and Wolfender, JL},
title = {Comparative metabolomic study of fungal foliar endophytes and their long-lived host Astrocaryum sciophilum: a model for exploring the chemodiversity of host-microbe interactions.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1278745},
pmid = {38186589},
issn = {1664-462X},
abstract = {INTRODUCTION: In contrast to the dynamics observed in plant/pathogen interactions, endophytic fungi have the capacity to establish enduring associations within their hosts, leading to the development of a mutually beneficial relationship that relies on specialized chemical interactions. Research indicates that the presence of endophytic fungi has the ability to significantly modify the chemical makeup of the host organism. Our hypothesis proposes the existence of a reciprocal exchange of chemical signals between plants and fungi, facilitated by specialized chemical processes that could potentially manifest within the tissues of the host. This research aimed to precisely quantify the portion of the cumulative fungal endophytic community's metabolome detectable within host leaves, and tentatively evaluate its relevance to the host-endophyte interplay. The understory palm Astrocaryum sciophilum (Miq.) Pulle was used as a interesting host plant because of its notable resilience and prolonged life cycle, in a tropical ecosystem.

METHOD: Using advanced metabolome characterization, including UHPLC-HRMS/MS and molecular networking, the study explored enriched metabolomes of both host leaves and 15 endophytic fungi. The intention was to capture a metabolomic "snapshot" of both host and endophytic community, to achieve a thorough and detailed analysis.

RESULTS AND DISCUSSION: This approach yielded an extended MS-based molecular network, integrating diverse metadata for identifying host- and endophyte-derived metabolites. The exploration of such data (>24000 features in positive ionization mode) enabled effective metabolome comparison, yielding insights into cultivable endophyte chemodiversity and occurrence of common metabolites between the holobiont and its fungal communities. Surprisingly, a minor subset of features overlapped between host leaf and fungal samples despite significant plant metabolome enrichment. This indicated that fungal metabolic signatures produced in vitro remain sparingly detectable in the leaf. Several classes of primary metabolites were possibly shared. Specific fungal metabolites and/or compounds of their chemical classes were only occasionally discernible in the leaf, highlighting endophytes partial contribution to the overall holobiont metabolome. To our knowledge, the metabolomic study of a plant host and its microbiome has rarely been performed in such a comprehensive manner. The general analytical strategy proposed in this paper seems well-adapted for any study in the field of microbial- or microbiome-related MS and can be applied to most host-microbe interactions.},
}

@article {pmid38174936,
year = {2024},
author = {Wei, Y and Chen, B and Yu, K and Liao, Z and Yu, X and Qin, Z and Bao, Z and Xu, L and Wang, Y},
title = {Evolutionary radiation and microbial community dynamics shape the thermal tolerance of Fungiidae in the southern South China Sea.},
journal = {Microbiology spectrum},
volume = {12},
number = {2},
pages = {e0243623},
pmid = {38174936},
issn = {2165-0497},
support = {42030502, 42090041//MOST | National Natural Science Foundation of China (NSFC)/ ; GXLSCRSCS2021103//Self-Topic Project of Guangxi Laboratory on the Study of Coral Reefs in the South China Sea/ ; PM-zx703-202105-176, PM-zx703-202004-143//Central Public-interest Scientific Institution Basal Research Fund/ ; 42306165//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Animals ; *Anthozoa/microbiology/physiology ; Coral Reefs ; Acclimatization ; Bacteria ; *Microbiota ; China ; *Dinoflagellida/physiology ; },
abstract = {Fungiidae have shown increased thermal adaptability in coral reef ecosystems under global warming. This study analyzes the evolutionary divergence and microbial communities of Fungiidae in the Sanjiao Reef of the southern South China Sea and explores the impact of coral evolution radiation and microbial dynamics on the heat tolerance of Fungiidae. The results found that Cycloseris was an ancient branch of Fungiidae, dating back approximately 147.8953 Mya, and Fungiidae differentiated into two ancestral clades (clades I and II) before 107.0312 Ma. Fungiidae exhibited specific symbioses with the Cladocopium C27 sub-clade. Notably, the Cladocopium C1 sub-clade has a high relative abundance in clade I, whereas the heat-tolerant Cladocopium C40 and C3u sub-clades subdominante in clade II. Regarding bacterial communities, Cycloseris costulata, the earliest divergent species, had higher bacterial β-diversity, while the latest divergent species, Lithophyllon scabra, displayed lower bacterial α-diversity and higher community stability. Beneficial bacteria dominante Fungiidae's bacterial community (54%). The co-occurrence network revealed that microbial networks in clade II exhibited lower complexity and greater resilience than those in clade I. Our study highlights that host evolutionary radiation and microbial communities shaped Fungiidae's thermal tolerance. The variability in subdominant Symbiodiniaceae populations may contribute to interspecific differences in thermal tolerance along the evolutionary branches of Fungiidae. The presence of abundant beneficial bacteria may further enhance the thermal ability of the Fungiidae. Furthermore, the later divergent species of Fungiidae have stronger heat tolerance, possibly driven by the increased regulation ability of the host on the bacterial community, greater microbial community stability, and interaction network resistance.IMPORTANCECoral reefs are facing significant threats due to global warming. The heat tolerance of coral holobionts depends on both the coral host and its microbiome. However, the association between coral evolutionary radiation and interspecific differences in microbial communities remains unclear. In this study, we investigated the role of evolutionary radiation and microbial community dynamics in shaping the thermal acclimation potential of Fungiidae in the Sanjiao Reef of the southern South China Sea. The study's results suggest that evolutionary radiation enhances the thermal tolerance of Fungiidae. Fungiidae species that have diverged more recently have exhibited a higher presence of heat-tolerant Symbiodiniaceae taxa, more stable bacterial communities, and a robust and resilient microbial interaction network, improving the thermal adaptability of Fungiidae. In summary, this study provides new insights into the thermal adaptation patterns of corals under global warming conditions.},
}

Animals
*Anthozoa/microbiology/physiology
Coral Reefs
Acclimatization
Bacteria
*Microbiota
China
*Dinoflagellida/physiology

@article {pmid38153910,
year = {2023},
author = {Khurana, MP and Scheidwasser-Clow, N and Penn, MJ and Bhatt, S and Duchêne, DA},
title = {The limits of the constant-rate birth-death prior for phylogenetic tree topology inference.},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syad075},
pmid = {38153910},
issn = {1076-836X},
abstract = {Birth-death models are stochastic processes describing speciation and extinction through time and across taxa, and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under the constant-rate birth-death (crBD) model tend to differ from empirical trees, for example with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between the crBD model and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which the crBD model differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD model trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used Bayesian methods and crBD priors with those that used other non-crBD priors and non-Bayesian methods (i.e., maximum likelihood methods), we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolutionary rates, and re-inferred the trees under maximum likelihood and using the crBD model in a Bayesian setting. We find that when the substitution rate is low, the crBD prior results in overly balanced trees, but the tendency is negligible when substitution rates are sufficiently high. Overall, our findings demonstrate the general robustness of crBD priors across a broad range of phylogenetic inference scenarios, but also highlights that empirically observed phylogenetic imbalance is highly improbable under the crBD model, leading to systematic bias in data sets with limited information content.},
}

@article {pmid38150785,
year = {2024},
author = {Bauermeister, A and Furtado, LC and Ferreira, EG and Moreira, EA and Jimenez, PC and Lopes, NP and Araújo, WL and Olchanheski, LR and Monteiro da Cruz Lotufo, T and Costa-Lotufo, LV},
title = {Chemical and microbial diversity of a tropical intertidal ascidian holobiont.},
journal = {Marine environmental research},
volume = {194},
number = {},
pages = {106303},
doi = {10.1016/j.marenvres.2023.106303},
pmid = {38150785},
issn = {1879-0291},
mesh = {Animals ; Phylogeny ; *Urochordata ; RNA, Ribosomal, 16S/genetics ; Tandem Mass Spectrometry ; Bacteria/genetics ; },
abstract = {The tropical ascidian Eudistoma vannamei, endemic to the northeastern coast of Brazil, is considered a prolific source of secondary metabolites and hosts Actinomycetota that produce bioactive compounds. Herein, we used an omics approach to study the ascidian as a holobiont, including the microbial diversity through 16S rRNA gene sequencing and metabolite production using mass spectrometry-based metabolomics. Gene sequencing analysis revealed all samples of E. vannamei shared about 50% of the observed ASVs, and Pseudomonadota (50.7%), Planctomycetota (9.58%), Actinomycetota (10.34%), Bacteroidota (12.05%) were the most abundant bacterial phyla. Analysis of tandem mass spectrometry (MS/MS) data allowed annotation of compounds, including phospholipids, amino acids, and pyrimidine alkaloids, such as staurosporine, a member of a well-known chemical class recognized as a microbial metabolite. Isolated bacteria, mainly belonging to Streptomyces and Micromonospora genera, were cultivated and extracted with ethyl acetate. MS/MS analysis of bacterial extracts allowed annotation of compounds not detected in the ascidian tissue, including marineosin and dihydroergotamine, yielding about 30% overlapped ions between host and isolated bacteria. This study reveals E. vannamei as a rich source of microbial and chemical diversity and, furthermore, highlights the importance of omic tools for a comprehensive investigation of holobiont systems.},
}

Animals
Phylogeny
*Urochordata
RNA, Ribosomal, 16S/genetics
Tandem Mass Spectrometry
Bacteria/genetics

@article {pmid38148332,
year = {2023},
author = {Boonmak, C and Kettongruang, S and Buranathong, B and Morikawa, M and Duangmal, K},
title = {Duckweed-associated bacteria as plant growth-promotor to enhance growth of Spirodela polyrhiza in wastewater effluent from a poultry farm.},
journal = {Archives of microbiology},
volume = {206},
number = {1},
pages = {43},
pmid = {38148332},
issn = {1432-072X},
support = {FF(KU)4.64//Kasetsart University Research and Development Institute (KURDI)/ ; FF(KU)4.64//Kasetsart University Research and Development Institute (KURDI)/ ; },
mesh = {Animals ; *Araceae/microbiology ; Farms ; Poultry ; *Wastewater ; },
abstract = {Duckweed has been highlighted as an invaluable resource because of its abilities to remove nitrogen and phosphorus from wastewater coupling with the production of high starch/protein-containing plant biomass. Duckweed recruits microbes and particularly forms a stable "core" bacterial microbiota, which greatly reduces the colonization efficiency of plant growth-promoting bacteria (PGPB). In this study, natural duckweeds were enriched in a sterilized-partially treated wastewater effluent from a poultry farm. After 24 days of cultivation, the duckweed-associated bacteria (DAB) were isolated and evaluated for their plant growth-promoting (PGP) potentials by co-cultivation with axenic Spirodela polyrhiza. Ten species were found in more than one location and could be considered candidates for the stable "core" DAB. Among them, all isolates of Acinetobacter soli, Acidovorax kalamii, Brevundimonas vesicularis, Pseudomonas toyotomiensis, and Shinella curvata increased duckweed growth in Hoagland medium. The highest PGP ability was observed in Sh. curvata W12-8 (with EPG value of 208.72%), followed by Paracoccus marcusii W7-16 (171.31%), Novosphingobium subterraneum W5-13 (156.96%), and Ac. kalamii W7-18 (156.96%). However, the highest growth promotion in the wastewater was observed when co-cultured with W7-16, which was able to increase biomass dry weight and root length of duckweed by 3.17 and 2.26 folds, respectively.},
}

Animals
*Araceae/microbiology
Farms
Poultry
*Wastewater

@article {pmid38144201,
year = {2023},
author = {Clerissi, C and Huot, C and Portet, A and Gourbal, B and Toulza, E},
title = {Covariation between microeukaryotes and bacteria associated with Planorbidae snails.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16639},
pmid = {38144201},
issn = {2167-8359},
mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics ; Eukaryota/genetics ; *Microbiota/genetics ; Snails/genetics ; },
abstract = {BACKGROUND: Microbial communities associated with macroorganisms might affect host physiology and homeostasis. Bacteria are well studied in this context, but the diversity of microeukaryotes, as well as covariations with bacterial communities, remains almost unknown.

METHODS: To study microeukaryotic communities associated with Planorbidae snails, we developed a blocking primer to reduce amplification of host DNA during metabarcoding analyses. Analyses of alpha and beta diversities were computed to describe microeukaryotes and bacteria using metabarcoding of 18S and 16S rRNA genes, respectively.

RESULTS: Only three phyla (Amoebozoa, Opisthokonta and Alveolata) were dominant for microeukaryotes. Bacteria were more diverse with five dominant phyla (Proteobacteria, Bacteroidetes, Tenericutes, Planctomycetes and Actinobacteria). The composition of microeukaryotes and bacteria were correlated for the Biomphalaria glabrata species, but not for Planorbarius metidjensis. Network analysis highlighted clusters of covarying taxa. Among them, several links might reflect top-down control of bacterial populations by microeukaryotes, but also possible competition between microeukaryotes having opposite distributions (Lobosa and Ichthyosporea). The role of these taxa remains unknown, but we believe that the blocking primer developed herein offers new possibilities to study the hidden diversity of microeukaryotes within snail microbiota, and to shed light on their underestimated interactions with bacteria and hosts.},
}

Animals
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics
Eukaryota/genetics
*Microbiota/genetics
Snails/genetics

@article {pmid38140133,
year = {2023},
author = {Machado, ACHR and Marinheiro, LJ and Benson, HAE and Grice, JE and Martins, TDS and Lan, A and Lopes, PS and Andreo-Filho, N and Leite-Silva, VR},
title = {A Novel Handrub Tablet Loaded with Pre- and Post-Biotic Solid Lipid Nanoparticles Combining Virucidal Activity and Maintenance of the Skin Barrier and Microbiome.},
journal = {Pharmaceutics},
volume = {15},
number = {12},
pages = {},
pmid = {38140133},
issn = {1999-4923},
support = {UNIFESP Process Nº 23089.125507 / 2020-08, Project Code PFSP-2101.0005//Embrapii - Empresa Brasileira de Pesquisa e Inovação Industrial/ ; },
abstract = {OBJECTIVE: This study aimed to develop a holobiont tablet with rapid dispersibility to provide regulation of the microbiota, virucidal activity, and skin barrier protection.

METHODS: A 2[3] factorial experiment was planned to define the best formulation for the development of the base tablet, using average weight, hardness, dimensions, swelling rate, and disintegration time as parameters to be analyzed. To produce holobiont tablets, the chosen base formulation was fabricated by direct compression of prebiotics, postbiotics, and excipients. The tablets also incorporated solid lipid nanoparticles containing postbiotics that were obtained by high-pressure homogenization and freeze-drying. The in vitro virucidal activity against alpha-coronavirus particles (CCoV-VR809) was determined in VERO cell culture. In vitro analysis, using monolayer cells and human equivalent skin, was performed by rRTq-PCR to determine the expression of interleukins 1, 6, 8, and 17, aquaporin-3, involucrin, filaggrin, FoxO3, and SIRT-1. Antioxidant activity and collagen-1 synthesis were also performed in fibroblast cells. Metagenomic analysis of the skin microbiome was determined in vivo before and after application of the holobiont tablet, during one week of continuous use, and compared to the use of alcohol gel. Samples were analyzed by sequencing the V3-V4 region of the 16S rRNA gene.

RESULTS: A handrub tablet with rapid dispersibility was developed for topical use and rinse off. After being defined as safe, the virucidal activity was found to be equal to or greater than that of 70% alcohol, with a reduction in interleukins and maintenance or improvement of skin barrier gene markers, in addition to the reestablishment of the skin microbiota after use.

CONCLUSIONS: The holobiont tablets were able to improve the genetic markers related to the skin barrier and also its microbiota, thereby being more favorable for use as a hand sanitizer than 70% alcohol.},
}

@article {pmid38135048,
year = {2023},
author = {Boggio, GM and Monteiro, HF and Lima, FS and Figueiredo, CC and Bisinotto, RS and Santos, JEP and Mion, B and Schenkel, FS and Ribeiro, ES and Weigel, KA and Peñagaricano, F},
title = {Host and rumen microbiome contributions to feed efficiency traits in Holstein cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2023-23869},
pmid = {38135048},
issn = {1525-3198},
abstract = {It is now widely accepted that dairy cow performance is influenced by both the host genome and rumen microbiome composition. The contributions of the genome and the microbiome to the phenotypes of interest are quantified by heritability (h[2]) and microbiability (m[2]), respectively. However, if the genome and microbiome are included in the model, then the heritability reflects only the contribution of the direct genetic effects quantified as direct heritability (hd[2]), and the holobiont effect reflects the joint action of the genome and the microbiome, quantified as the holobiability (ho[2]). The objectives of this study were to estimate h[2], hd[2],m[2], and ho[2] for dry matter intake, milk energy, and residual feed intake; and to evaluate the predictive ability of different models, including genome, microbiome, and their interaction. Data consisted of feed efficiency records, SNP genotype data, and 16S rRNA rumen microbial abundances from 448 mid-lactation Holstein cows from 2 research farms. Three kernel models were fit to each trait: one with only the genomic effect (model G), one with the genomic and microbiome effects (model GM), and one with the genomic, microbiome, and interaction effects (model GMO). The model GMO, or holobiont model, showed the best goodness-of-fit. The hd[2] estimates were always 10 to 15% lower than h[2] estimates for all traits, suggesting a mediated genetic effect through the rumen microbiome, and m[2] estimates were moderate for all traits, and up to 26% for milk energy. The ho[2] was greater than the sum of hd[2] and m[2], suggesting that the genome-by-microbiome interaction had a sizeable effect on feed efficiency. Kernel models fitting the rumen microbiome, i.e., models GM and GMO, showed larger predictive correlations and smaller prediction bias than the model G. These findings reveal a moderate contribution of the rumen microbiome to feed efficiency traits in lactating Holstein cows and strongly suggest that the rumen microbiome mediates part of the host genetic effect.},
}

@article {pmid38132295,
year = {2023},
author = {Barker, T and Bulling, M and Thomas, V and Sweet, M},
title = {The Effect of Pollen on Coral Health.},
journal = {Biology},
volume = {12},
number = {12},
pages = {},
pmid = {38132295},
issn = {2079-7737},
abstract = {Corals are facing a range of threats, including rises in sea surface temperature and ocean acidification. Some now argue that keeping corals ex situ (in aquaria), may be not only important but necessary to prevent local extinction, for example in the Florida Reef Tract. Such collections or are already becoming common place, especially in the Caribbean, and may act as an ark, preserving and growing rare or endangered species in years to come. However, corals housed in aquaria face their own unique set of threats. For example, hobbyists (who have housed corals for decades) have noticed seasonal mortality is commonplace, incidentally following months of peak pollen production. So, could corals suffer from hay fever? If so, what does the future hold? In short, the answer to the first question is simple, and it is no, corals cannot suffer from hay fever, primarily because corals lack an adaptive immune system, which is necessary for the diagnosis of such an allergy. However, the threat from pollen could still be real. In this review, we explore how such seasonal mortality could play out. We explore increases in reactive oxygen species, the role of additional nutrients and how the microbiome of the pollen may introduce disease or cause dysbiosis in the holobiont.},
}

@article {pmid38129884,
year = {2023},
author = {Troitsky, TS and Laine, VN and Lilley, TM},
title = {When the host's away, the pathogen will play: the protective role of the skin microbiome during hibernation.},
journal = {Animal microbiome},
volume = {5},
number = {1},
pages = {66},
pmid = {38129884},
issn = {2524-4671},
support = {202300065//Maj ja Tor Nesslingin Säätiö/ ; 329250//Academy of Finland/ ; 329250//Academy of Finland/ ; },
abstract = {The skin of animals is enveloped by a symbiotic microscopic ecosystem known as the microbiome. The host and microbiome exhibit a mutualistic relationship, collectively forming a single evolutionary unit sometimes referred to as a holobiont. Although the holobiome theory highlights the importance of the microbiome, little is known about how the skin microbiome contributes to protecting the host. Existing studies focus on humans or captive animals, but research in wild animals is in its infancy. Specifically, the protective role of the skin microbiome in hibernating animals remains almost entirely overlooked. This is surprising, considering the massive population declines in hibernating North American bats caused by the fungal pathogen Pseudogymnoascus destructans, which causes white-nose syndrome. Hibernation offers a unique setting in which to study the function of the microbiome because, during torpor, the host's immune system becomes suppressed, making it susceptible to infection. We conducted a systematic review of peer-reviewed literature on the protective role of the skin microbiome in non-human animals. We selected 230 publications that mentioned pathogen inhibition by microbes residing on the skin of the host animal. We found that the majority of studies were conducted in North America and focused on the bacterial microbiome of amphibians infected by the chytrid fungus. Despite mentioning pathogen inhibition by the skin microbiome, only 30.4% of studies experimentally tested the actual antimicrobial activity of symbionts. Additionally, only 7.8% of all publications studied defensive cutaneous symbionts during hibernation. With this review, we want to highlight the knowledge gap surrounding skin microbiome research in hibernating animals. For instance, research looking to mitigate the effects of white-nose syndrome in bats should focus on the antifungal microbiome of Palearctic bats, as they survive exposure to the Pseudogymnoascus destructans -pathogen during hibernation. We also recommend future studies prioritize lesser-known microbial symbionts, such as fungi, and investigate the effects of a combination of anti-pathogen microbes, as both areas of research show promise as probiotic treatments. By incorporating the protective skin microbiome into disease mitigation strategies, conservation efforts can be made more effective.},
}

@article {pmid38123486,
year = {2024},
author = {Lee, JH},
title = {Host-Microbe Interactions Regulate Intestinal Stem Cells and Tissue Turnover in Drosophila.},
journal = {International journal of stem cells},
volume = {17},
number = {1},
pages = {51-58},
pmid = {38123486},
issn = {2005-3606},
abstract = {With the activity of intestinal stem cells and continuous turnover, the gut epithelium is one of the most dynamic tissues in animals. Due to its simple yet conserved tissue structure and enteric cell composition as well as advanced genetic and histologic techniques, Drosophila serves as a valuable model system for investigating the regulation of intestinal stem cells. The Drosophila gut epithelium is in constant contact with indigenous microbiota and encounters externally introduced "non-self" substances, including foodborne pathogens. Therefore, in addition to its role in digestion and nutrient absorption, another essential function of the gut epithelium is to control the expansion of microbes while maintaining its structural integrity, necessitating a tissue turnover process involving intestinal stem cell activity. As a result, the microbiome and pathogens serve as important factors in regulating intestinal tissue turnover. In this manuscript, I discuss crucial discoveries revealing the interaction between gut microbes and the host's innate immune system, closely associated with the regulation of intestinal stem cell proliferation and differentiation, ultimately contributing to epithelial homeostasis.},
}

@article {pmid38096292,
year = {2023},
author = {Lin, AT and Hammond-Kaarremaa, L and Liu, HL and Stantis, C and McKechnie, I and Pavel, M and Pavel, SSM and Wyss, SSÁ and Sparrow, DQ and Carr, K and Aninta, SG and Perri, A and Hartt, J and Bergström, A and Carmagnini, A and Charlton, S and Dalén, L and Feuerborn, TR and France, CAM and Gopalakrishnan, S and Grimes, V and Harris, A and Kavich, G and Sacks, BN and Sinding, MS and Skoglund, P and Stanton, DWG and Ostrander, EA and Larson, G and Armstrong, CG and Frantz, LAF and Hawkins, MTR and Kistler, L},
title = {The history of Coast Salish "woolly dogs" revealed by ancient genomics and Indigenous Knowledge.},
journal = {Science (New York, N.Y.)},
volume = {382},
number = {6676},
pages = {1303-1308},
pmid = {38096292},
issn = {1095-9203},
support = {CC2109/WT_/Wellcome Trust/United Kingdom ; CC2109/CRUK_/Cancer Research UK/United Kingdom ; 852558/ERC_/European Research Council/International ; 217223/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; CC2109/MRC_/Medical Research Council/United Kingdom ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; },
mesh = {Animals ; *Dogs/anatomy & histology/classification/genetics ; Genomics ; Northwestern United States ; Breeding ; *Wool ; *Selection, Genetic ; },
abstract = {Ancestral Coast Salish societies in the Pacific Northwest kept long-haired "woolly dogs" that were bred and cared for over millennia. However, the dog wool-weaving tradition declined during the 19th century, and the population was lost. In this study, we analyzed genomic and isotopic data from a preserved woolly dog pelt from "Mutton," collected in 1859. Mutton is the only known example of an Indigenous North American dog with dominant precolonial ancestry postdating the onset of settler colonialism. We identified candidate genetic variants potentially linked with their distinct woolly phenotype. We integrated these data with interviews from Coast Salish Elders, Knowledge Keepers, and weavers about shared traditional knowledge and memories surrounding woolly dogs, their importance within Coast Salish societies, and how colonial policies led directly to their disappearance.},
}

Animals
*Dogs/anatomy & histology/classification/genetics
Genomics
Northwestern United States
Breeding
*Wool
*Selection, Genetic

@article {pmid38088556,
year = {2024},
author = {Toullec, G and Lyndby, NH and Banc-Prandi, G and Pogoreutz, C and Martin Olmos, C and Meibom, A and Rädecker, N},
title = {Symbiotic nutrient exchange enhances the long-term survival of cassiosomes, the autonomous stinging-cell structures of Cassiopea.},
journal = {mSphere},
volume = {9},
number = {1},
pages = {e0032223},
pmid = {38088556},
issn = {2379-5042},
support = {200021_179092//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 212614//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; ANR-22-CPJ2-0113-01//French National Research Agency (ANR)/ ; },
mesh = {*Symbiosis ; Nitrogen/metabolism ; *Dinoflagellida ; Carbon/metabolism ; Photosynthesis ; },
abstract = {Medusae of the widely distributed upside-down jellyfish Cassiopea release autonomous, mobile stinging structures. These so-called cassiosomes play a role in predator defense and prey capture, and are major contributors to "contactless" stinging incidents in (sub-)tropical shallow waters. While the presence of endosymbiotic dinoflagellates in cassiosomes has previously been observed, their potential contribution to the metabolism and long-term survival of cassiosomes is unknown. Combining stable isotope labeling and correlative scanning electron microscopy and nanoscale secondary ion mass spectrometry imaging with a long-term in vitro experiment, our study reveals a mutualistic symbiosis based on nutritional exchanges in dinoflagellate-bearing cassiosomes. We show that organic carbon input from the dinoflagellates fuels the metabolism of the host tissue and enables anabolic nitrogen assimilation. This symbiotic nutrient exchange enhances the life span of cassiosomes for at least one month in vitro. Overall, our study demonstrates that cassiosomes, in analogy with Cassiopea medusae, are photosymbiotic holobionts. Cassiosomes, which are easily accessible under aquarium conditions, promise to be a powerful new miniaturized model system for in-depth ultrastructural and molecular investigation of cnidarian photosymbioses.IMPORTANCEThe upside-down jellyfish Cassiopea releases autonomous tissue structures, which are a major cause of contactless stinging incidents in (sub-) tropical coastal waters. These so-called cassiosomes frequently harbor algal symbionts, yet their role in cassiosome functioning and survival is unknown. Our results show that cassiosomes are metabolically active and supported by algal symbionts. Algal photosynthesis enhances the cassiosomes long-term survival in the light. This functional understanding of cassiosomes thereby contributes to explaining the prevalence of contactless stinging incidents and the ecological success of some Cassiopea species. Finally, we show that cassiosomes are miniaturized symbiotic holobionts that can be used to study host-microbe interactions in a simplified system.},
}

*Symbiosis
Nitrogen/metabolism
*Dinoflagellida
Carbon/metabolism
Photosynthesis

@article {pmid38087002,
year = {2023},
author = {Montaño-Salazar, S and Quintanilla, E and Sánchez, JA},
title = {Microbial shifts associated to ENSO-derived thermal anomalies reveal coral acclimation at holobiont level.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {22049},
pmid = {38087002},
issn = {2045-2322},
mesh = {Animals ; *Anthozoa/microbiology ; El Nino-Southern Oscillation ; Biodiversity ; Acclimatization ; Cold Temperature ; Bacteria ; Coral Reefs ; },
abstract = {The coral microbiome conforms a proxy to study effects of changing environmental conditions. However, scarce information exists regarding microbiome dynamics and host acclimation in response to environmental changes associated to global-scale disturbances. We assessed El Niño Southern Oscillation (ENSO)-derived thermal anomalies shifts in the bacterial microbiome of Pacifigorgia cairnsi (Gorgoniidae: Octocorallia) from the remote island of Malpelo in the Tropical Eastern Pacific. Malpelo is a hot spot of biodiversity and lacks direct coastal anthropogenic impacts. We evaluated the community composition and predicted functional profiles of the microbiome during 2015, 2017 and 2018, including different phases of ENSO cycle. The bacterial community diversity and composition between the warming and cooling phase were similar, but differed from the neutral phase. Relative abundances of different microbiome core members such as Endozoicomonas and Mycoplasma mainly drove these differences. An acclimated coral holobiont is suggested not just to warm but also to cold stress by embracing similar microbiome shifts and functional redundancy that allow maintaining coral's viability under thermal stress. Responses of the microbiome of unperturbed sea fans such as P. cairnsi in Malpelo could be acting as an extended phenotype facilitating the acclimation at the holobiont level.},
}

Animals
*Anthozoa/microbiology
El Nino-Southern Oscillation
Biodiversity
Acclimatization
Cold Temperature
Bacteria
Coral Reefs

@article {pmid38085949,
year = {2023},
author = {Penn, MJ and Scheidwasser, N and Penn, J and Donnelly, CA and Duchêne, DA and Bhatt, S},
title = {Leaping through Tree Space: Continuous Phylogenetic Inference for Rooted and Unrooted Trees.},
journal = {Genome biology and evolution},
volume = {15},
number = {12},
pages = {},
pmid = {38085949},
issn = {1759-6653},
mesh = {Phylogeny ; *Models, Genetic ; Computer Simulation ; *Algorithms ; },
abstract = {Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains challenging. To address this problem, for the first time, we perform both tree exploration and inference in a continuous space where the computation of gradients is possible. This continuous relaxation allows for major leaps across tree space in both rooted and unrooted trees, and is less susceptible to convergence to local minima. Our approach outperforms the current best methods for inference on unrooted trees and, in simulation, accurately infers the tree and root in ultrametric cases. The approach is effective in cases of empirical data with negligible amounts of data, which we demonstrate on the phylogeny of jawed vertebrates. Indeed, only a few genes with an ultrametric signal were generally sufficient for resolving the major lineages of vertebrates. Optimization is possible via automatic differentiation and our method presents an effective way forward for exploring the most difficult, data-deficient phylogenetic questions.},
}

Phylogeny
*Models, Genetic
Computer Simulation
*Algorithms