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Vertical transmission of bacterial endosymbionts is accompanied by virtually irreversible gene loss that results in a progressive reduction in genome size. While the evolutionary processes of genome reduction have been well described in some terrestrial symbioses, they are less understood in marine systems where vertical transmission is rarely observed. The association between deep-sea vesicomyid clams and chemosynthetic Gammaproteobacteria is one example of maternally inherited symbioses in the ocean. Here, we assessed the contributions of drift, recombination and selection to genome evolution in two extant vesicomyid symbiont clades by comparing 15 representative symbiont genomes (1.017–1.586 Mb) to those of closely related bacteria and the hosts' mitochondria. Our analyses suggest that drift is a significant force driving genome evolution in vesicomyid symbionts, though selection and interspecific recombination appear to be critical for maintaining symbiont functional integrity and creating divergent patterns of gene conservation. Notably, the two symbiont clades possess putative functional differences in sulfide physiology, anaerobic respiration and dependency on environmental vitamin B12, which probably reflect adaptations to different ecological habitats available to each symbiont group. Overall, these results contribute to our understanding of the eco-evolutionary processes shaping reductive genome evolution in vertically transmitted symbioses.

Many foundation species in chemosynthesis-based ecosystems rely on environmentally acquired symbiotic bacteria for their survival. Hence, understanding the biogeographic distributions of these symbionts at regional scales is key to understanding patterns of connectivity and predicting resilience of their host populations (and thus whole communities). However, such assessments are challenging because they necessitate measuring bacterial genetic diversity at fine resolutions. For this purpose, the recently discovered clustered regularly interspaced short palindromic repeats (CRISPR) constitutes a promising new genetic marker. These DNA sequences harboured by about half of bacteria hold their viral immune memory, and as such, might allow discrimination of different lineages or strains of otherwise indistinguishable bacteria. In this study, we assessed the potential of CRISPR as a hypervariable phylogenetic marker in the context of a population genetic study of an uncultured bacterial species. We used high-throughput CRISPR-based typing along with multi-locus sequence analysis (MLSA) to characterize the regional population structure of the obligate but environmentally acquired symbiont species Candidatus Endoriftia persephone on the Juan de Fuca Ridge. Mixed symbiont populations of Ca. Endoriftia persephone were sampled across individual Ridgeia piscesae hosts from contrasting habitats in order to determine if environmental conditions rather than barriers to connectivity are more important drivers of symbiont diversity. We showed that CRISPR revealed a much higher symbiont genetic diversity than the other housekeeping genes. Several lines of evidence imply this diversity is indicative of environmental strains. Finally, we found with both CRISPR and gene markers that local symbiont populations are strongly differentiated across sites known to be isolated by deep-sea circulation patterns. This research showed the high power of CRISPR to resolve the genetic structure of un

To date, 13 biologically active hydrothermal vent (HTV) fields have been described on the West Indian Ocean ridges. Knowledge of benthic communities of these vent ecosystems serves as scientific bases for assessing the resilience of these ecosystems under the global effort to strike an elegant balance between future deep-sea mining and biodiversity conservation. This review aims to summarize our up-to-date knowledge of the benthic community structure and connectivity of these Indian vents and to identify knowledge gaps and key research questions to be prioritized in order to assess the resilience of these communities. The HTVs in the West Indian Ocean are home to many unique invertebrate species such as the remarkable scaly-foot snail. While distinct in composition, the macrofaunal communities of the Indian HTVs share many characteristics with those of other HTVs, including high endemism, strong zonation at the local scale, and a simple food web structure. Furthermore, Indian vent benthic communities are mosaic compositions of Atlantic, Pacific, and Antarctic HTV fauna possibly owning to multiple waves of past colonization. Phylogeographic studies have shed new light into these migratory routes. Current animal connectivity across vent fields appears to be highly influenced by distance and topological barriers. However, contrasting differences in gene flow have been documented across species. Thus, a better understanding of the reproductive biology of the Indian vent animals and the structure of their population at the local scale is crucial for conservation purposes. In addition, increased effort should be given to characterizing the vents’ missing diversity (at both the meio and micro-scale) and elucidating the functional ecology of these vents.