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Metazoans comprise multiple physical niches ("microenvironments"), each colonized by unique microbiomes that contribute to their hosts' evolutionary dynamics, influencing their health, physiology, and adaptation to changing environments. Most wildlife microbiome studies focus on higher metazoans and multiple host microenvironments, while studies of lower species often concentrate on a single microenvironment, sometimes pooling whole bodies or specimens. This is particularly evident in small-sized animals, such as freshwater meiofaunal invertebrates, thus impeding a holistic understanding of microbiome assembly across host microenvironments and its relation with host population genetics. Leveraging the anostracan fairy shrimp Branchinecta , which has easily discernible organs and expected high levels of intraspecific genetic divergence, we aimed to investigate the microbiome assembly processes and test the phylosymbiosis signal in two microenvironments (gill and intestine) across four host populations of Branchinecta gaini within Maritime Antarctica, using 16S rRNA metabarcoding. Our results showed that the gill and intestine harbor strikingly different microbiomes resulting from the B. gaini ecological filtering of the surrounding environment microbial community. Both microenvironments exhibit their respective core microbiomes, yet the gill's core microbiome is narrower and constitutes a smaller proportion of the overall bacterial community compared to that of the intestine. Within each host population (i.e. each sampling site), the microbiome assembles through distinct eco-evolutionary processes in both microenvironments, mostly stochastically (ecological drift) in the gill and deterministically (variable selection) in the intestine. Across different B. gaini populations, variable selection dominates in driving compositional divergence of both microenvironment microbiomes, although to a lesser extent in the gill. Lastly, our study reveals robust correlation between host intraspecific genetic structure and intestine microbiome composition, providing evidence of phylosymbiosis in anostracans. Contrastingly, phylosymbiosis was less pronounced in the gill microbiome. We discuss the potential differences in ecological filtering between each host microenvironment that may underlie the difference in the strength of phylosymbiosis. Our study highlights the relevance of considering host microenvironment and intraspecific levels in testing the phylosymbiosis hypothesis to better understand the intricate eco-evolutionary relationships between hosts and their microbiomes. [ABSTRACT FROM AUTHOR]

Conceptual biogeographic frameworks have proposed that the relative contribution of environmental and geographical factors on microbial distribution depends on several characteristics of the habitat (e.g. environmental heterogeneity, species diversity, and proportion of specialist/generalist taxa), all of them defining the degree of habitat specificity, but few experimental demonstrations exist. Here, we aimed to determine the effect of habitat specificity on bacterial biogeographic patterns and assembly processes in benthic coastal ecosystems of the Southern Ocean (Patagonia, Falkland/Malvinas, Kerguelen, South Georgia, and King George Islands), using 16S rRNA gene metabarcoding. The gradient of habitat specificity resulted from a 'natural experimental design' provided by the Abatus sea urchin model, from the sediment (least specific habitat) to the intestinal tissue (most specific habitat). The phylogenetic composition of the bacterial communities showed a clear differentiation by site, driven by a similar contribution of geographic and environmental distances. However, the strength of this biogeographic pattern decreased with increasing habitat specificity: sediment communities showed stronger geographic and environmental divergence compared to gut tissue. The proportion of stochastic and deterministic processes contributing to bacterial assembly varied according to the geographic scale and the habitat specificity level. For instance, an increased contribution of dispersal limitation was observed in gut tissue habitat. Our results underscore the importance of considering different habitats with contrasting levels of specificity to better understand bacterial biogeography and assembly processes over oceanographic scales. [ABSTRACT FROM AUTHOR]

Background: Lichens are micro-ecosystems relying on diverse microorganisms for nutrient cycling, environmental adaptation, and structural support. We investigated the spatial-scale dependency of factors shaping the ecological processes that govern lichen-associated bacteria. We hypothesize that lichens function as island-like habitats hosting divergent microbiomes and promoting landscape gamma-diversity. Three microenvironments —thalli, substrates, and neighboring soils— were sampled from four geographically overlapping species of Peltigera cyanolichens, spanning three bioclimatic zones in the Chilean Patagonia, to determine how bacterial diversity, assembly processes, ecological drivers, interaction patterns, and niche breadth vary among Peltigera microenvironments on a broad geographical scale. Results: The hosts' phylogeny, especially that of the cyanobiont, alongside climate as a secondary factor, impose a strong ecological filtering of bacterial communities within Peltigera thalli. This results in deterministically assembled, low diverse, and phylogenetically convergent yet structurally divergent bacterial communities. Host evolutionary and geographic distances accentuate the divergence in bacterial community composition of Peltigera thalli. Compared to soil and substrate, Peltigera thalli harbor specialized and locally adapted bacterial taxa, conforming sparse and weak ecological networks. Conclusions: The findings suggest that Petigera thalli create fragmented habitats that foster landscape bacterial gamma-diversity. This underscores the importance of preserving lichens for maintaining a potential reservoir of specialized bacteria. [ABSTRACT FROM AUTHOR]

Animals have a deep evolutionary relationship with microbial symbionts, such that individual microbes or an entire microbial community can diverge alongside the host. Here, we explore these host-microbe relationships in Echinometra, a sea urchin genus that speciated with the Isthmus of Panama and throughout the Indo-West Pacific. We find that the eggs from five Echinometra species generally associate with a species-specific bacterial community and that the relatedness of these communities is largely congruent with host phylogeny. Microbiome divergence per million years was higher in more recent speciation events than in older ones. We, however, did not find any bacterial groups that displayed co-phylogeny with Echinometra. Together, these findings suggest that the evolutionary relationship between Echinometra and their microbiota operates at the community level. We find no evidence suggesting that the associated microbiota is the evolutionary driver of Echinometra speciation. Instead, divergence between Echinometra and their microbiota is likely the byproduct of ecological, geographic, and reproductive isolations. [ABSTRACT FROM AUTHOR]

Purpose: The ecological interdependence between macroorganisms and their microbial communities promotes stable associations over time, potentially leading to their evolutionary co-diversification. The detection of intricate eco-evolutionary interactions between animals and their microbiota is challenging, primarily due to complex bacterial communities related to poorly resolved host population structure. Strikingly, co-diversification in invertebrates, characterized by generally less complex microbiota, remains largely unexplored. Here, we compared the bacterial communities associated with two distinct lineages of Nacella limpets, a dominant shallow water patellogastropod of the Southern Ocean shores with a well-described population structure. Our goals were to elucidate the uniqueness of Nacella microbiota, resulting from an ecological filter that selectively favors certain bacterial taxa. Additionally, we aimed to depict the genetic structure of bacterial symbiont seeking evidence of co-diversification with Nacella. Methods: We sequence the V4-V5 regions of the bacterial 16S rRNA gene in three distinct microenvironments associated with Nacella: rock substrate, radula, and whole intestine. These samples were collected from two populations of Nacella deaurata and Nacella concinna, located in the West Antarctic Peninsula and Falkland/Malvinas Islands, respectively. Results: We assessed ecological filtering patterns in the limpet microbiota, uncovering unique bacterial communities in both radulas and intestines, with specifically enriched bacterial taxa compared to the surrounding environment. By examining microdiversity patterns of core bacterial taxa, we revealed a deep phylogeographic structure of Psychrilyobacter in Nacella intestines. Conclusion: We highlight the Southern Ocean limpets of the Nacella genus as a novel and promising model for studying co-diversification between marine mollusks and their resident microbiota. [ABSTRACT FROM AUTHOR]

Most of the microbial biogeographic patterns in the oceans have been depicted at the whole community level, leaving out finer taxonomic resolution (i.e., microdiversity) that is crucial to conduct intra-population phylogeographic study, as commonly done for macroorganisms. Here, we present a new approach to unravel the bacterial phylogeographic patterns combining community-wide survey by 16S rRNA gene metabarcoding and intra-species resolution through the oligotyping method, allowing robust estimations of genetic and phylogeographic indices, and migration parameters. As a proof-of-concept, we focused on the bacterial genus Spirochaeta across three distant biogeographic provinces of the Southern Ocean; maritime Antarctica, sub-Antarctic Islands, and Patagonia. Each targeted Spirochaeta operational taxonomic units were characterized by a substantial intrapopulation microdiversity, and significant genetic differentiation and phylogeographic structure among the three provinces. Gene flow estimations among Spirochaeta populations support the role of the Antarctic Polar Front as a biogeographic barrier to bacterial dispersal between Antarctic and sub-Antarctic provinces. Conversely, the Antarctic Circumpolar Current appears as the main driver of gene flow, connecting sub-Antarctic Islands with Patagonia and maritime Antarctica. Additionally, historical processes (drift and dispersal limitation) govern up to 86% of the spatial turnover among Spirochaeta populations. Overall, our approach bridges the gap between microbial and macrobial ecology by revealing strong congruency with macroorganisms distribution patterns at the populational level, shaped by the same oceanographic structures and ecological processes. [ABSTRACT FROM AUTHOR]

Abatus agassizii is an irregular sea urchin species that inhabits shallow waters of South Georgia and South Shetlands Islands. As a deposit-feeder, A. agassizii nutrition relies on the ingestion of the surrounding sediment in which it lives barely burrowed. Despite the low complexity of its feeding habit, it harbors a long and twice-looped digestive tract suggesting that it may host a complex bacterial community. Here, we characterized the gut microbiota of specimens from two A. agassizii populations at the south of the King George Island in the West Antarctic Peninsula. Using a metabarcoding approach targeting the 16S rRNA gene, we characterized the Abatus microbiota composition and putative functional capacity, evaluating its differentiation among the gut content and the gut tissue in comparison with the external sediment. Additionally, we aimed to define a core gut microbiota between A. agassizii populations to identify potential keystone bacterial taxa. Our results show that the diversity and the composition of the microbiota, at both genetic and predicted functional levels, were mostly driven by the sample type, and to a lesser extent by the population location. Specific bacterial taxa, belonging mostly to Planctomycetacia and Spirochaetia , were differently enriched in the gut content and the gut tissue, respectively. Predictive functional profiles revealed higher abundance of specific pathways, as the sulfur cycle in the gut content and the amino acid metabolism, in the gut tissue. Further, the definition of a core microbiota allowed to obtain evidence of specific localization of bacterial taxa and the identification of potential keystone taxa assigned to the Desulfobacula and Spirochaeta genera as potentially host selected. The ecological relevance of these keystone taxa in the host metabolism is discussed. [ABSTRACT FROM AUTHOR]

Summary: We investigated whether the diversity, endemicity and specificity of alder symbionts could be changed by isolation in a Mediterranean glacial refugium. We studied both ectomycorrhizal (EM) fungi and nitrogen‐fixing actinobacteria associated with alders, and compared their communities in Corsica and on the European continent. Nodules and root tips were sampled on the three alder species present in Corsica and continental France and Italy. Phylogenies based on internal transcribed spacer (ITS) and a multilocus sequence analysis approach were used to characterize fungal and Frankia species, respectively. Patterns of diversity, endemism and specialization were compared between hosts and regions for each symbiont community. In Corsica, communities were not generally richer than on the mainland. The species richness per site depended mainly on host identity: Alnus glutinosa and Alnus cordata hosted richer Frankia and EM communities, respectively. Half of the Frankia species were endemic to Corsica against only 4% of EM species. Corsica is not a hotspot of diversity for all alder symbionts but sustains an increased frequency of poor‐dispersers such as hypogeous fungi. Generalist EM fungi and host‐dependent profusely sporulating (Sp+) Frankia were abundantly associated with Corsican A. cordata, a pattern related to a more thermophilic and xerophylic climate and to the co‐occurrence with other host trees. [ABSTRACT FROM AUTHOR]

Molecular Ecology, 30 (23), 6193 - 6210. https://doi.org/10.1111/mec.16066 20 Cordier, T., Alonso-Sáez, L., Apothéloz-Perret-Gentil, L., Aylagas, E., Bohan, D. A., Bouchez, A., Chariton, A., Creer, S., Frühe, L., Keck, F., Keeley, N., Laroche, O., Leese, F., Pochon, X., Stoeck, T., Pawlowski, J., & Lanzén, A. (2021). Molecular Ecology, 30 (23), 6211 - 6228. https://doi.org/10.1111/mec.16099 30 Ficetola, G. F., Boyer, F., Valentini, A., Bonin, A., Meyer, A., Dejean, T., Gaboriaud, C., Usseglio-Polatera, P., & Taberlet, P. (2021). Molecular Ecology, 30 (13), 3111 - 3126. https://doi.org/10.1111/mec.15644 69 Meyer, A., Boyer, F., Valentini, A., Bonin, A., Ficetola, G. F., Beisel, J.-N., Bouquerel, J., Wagner, P., Gaboriaud, C., Leese, F., Dejean, T., Taberlet, P., & Usseglio-Polatera, P. (2021). Molecular Ecology, 30 (13), 3189 - 3202. https://doi.org/10.1111/mec.15632 31 Foote, A. D., Hooper, R., Alexander, A., Baird, R. W., Baker, C. S., Ballance, L., Barlow, J., Brownlow, A., Collins, T., Constantine, R., Dalla Rosa, L., Davison, N. J., Durban, J. W., Esteban, R., Excoffier, L., Martin, S. L. F., Forney, K. A., Gerrodette, T., Gilbert, M. T. P., ... Morin, P. A. (2021) Runs of homozygosity in killer whale genomes provide a global record of demographic histories. [Extracted from the article]

Since bacterial consortia involved in conventional wastewater treatment processes are not efficient in removing diclofenac (DCF), an emerging pollutant frequently detected in water bodies, the identification of microorganisms able to metabolise this pharmaceutical compound is relevant. Thus, DCF removal was investigated using bacteria isolated from aqueous stock solutions of this micropollutant and identified as Bacillus and Brevibacillus species using 16S rRNA gene sequencing. A 100% DCF removal was achieved after 17 hours of experiment at 20°C in a nutrient medium; the biodegradation kinetic followed a pseudo-first order (kbiol = 11 L·gSS−1·d−1). Quantitative assessment of DCF removal showed that its main route was biotic degradation. The main degradation product of DCF, 4′-hydroxy-diclofenac (4′-OH-DCF), was identified using liquid chromatography-electrospray ionisation high-resolution mass spectrometry. Since the ecotoxicological impact of 4′-hydroxy-diclofenac was not reported in the literature, the ecotoxicity of DCF and its metabolite were tentatively evaluated using Vibrio fischeri bioassays. Results from these tests showed that this metabolite is not more toxic than its parent compound and may hopefully be an intermediate product in the DCF transformation. Indeed, no significant difference in ecotoxicity was observed after 30 min between DCF (50 should be writtten in subscript all along the manuscript in EC50 = 23 ± 4 mg·L−1) and 4′-hydroxy-diclofenac (EC50 = 19 ± 2 mg·L−1). Besides, the study highlighted a limit of the Microtox® bioassay, which is largely used to assess ecotoxicity. The bioluminescence of Vibrio fischeri was impacted due to the production of microbial activity and the occurrence of some carbon source in the studied medium. [ABSTRACT FROM AUTHOR]