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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]

Species that form complex biogenic structures may increase niche space for many others and are assumed to be paramount for whole‐assemblage stability and ecosystem functioning. Because they often ameliorate physical conditions, ecosystem engineering species are also predicted to become more important with environmental stress. Testing this hypothesis, however, has proven difficult because isolating facilitation effects along the entire stress gradient is challenging. Here we addressed motile invertebrate assemblages associated to the mid‐intertidal chthamalid barnacle cover at four rocky shores, either with ('facilitated') or without ('control') a secondary natural cover of small mussels (Mytilaster solisianus and Brachidontes darwinianus). Following a factorial balanced design, replicate samples were taken at three tidal heights in all sites, encompassing a clear gradient of thermal stress and desiccation potential along the vertical range of the mussel‐enriched zone. While observations on general abundance were mostly consistent with stress‐independent facilitation, results for richness, diversity and assemblage structure indicated overarching stress‐dependent responses. All these later three response variables steadily declined from the low to the high level in the control barnacle habitat but remained unaltered in the mussel‐facilitated habitat. Increased facilitation higher on the shore is mostly due to retention of stress‐vulnerable groups such as polychaetes, flatworms and large nematodes which virtually collapse in the higher control habitat, further indicating that mechanisms of mussel facilitation involve relief of environmental stress rather than protection from higher‐order consumers. Our results suggest that mussel ecosystem engineering was fully preserved during the summer season when sampling took place. Ongoing research simulating heat waves compatible to climate‐change scenarios will test whether mussel facilitation would hold over the coming decades. [ABSTRACT FROM AUTHOR]

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 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.