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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]

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]