Abstract
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 uncultured bacterial populations and represents a step towards making keystone microbial species an integral part of conservation policies for upcoming mining operations on the seafloor.
Highlights
Marine bacteria and archaea perform vital marine ecosystem functions including primary productivity at the sunlit surface, remineralization and storage of carbon in the water column and the ocean’s interior through the biological carbon pump
We have demonstrated that the clustered regularly interspaced short palindromic repeats (CRISPR) array is a genetic marker fit-for-purpose for the uncultured chemoautrophic symbiont species Ca
The CRISPR haplotypes we identified only varied through spacer deletions and yet they revealed 30 times more diversity than any of the other gene markers selected for their polymorphism
Summary
Marine bacteria and archaea perform vital marine ecosystem functions including primary productivity at the sunlit surface, remineralization and storage of carbon in the water column and the ocean’s interior through the biological carbon pump They are primary producers within the ocean’s dark interior, inhabiting environments such as hydrothermal vents and hydrocarbon seeps, where they utilize geochemical energy rather than sunlight to fix carbon. Given their fundamental roles in marine ecosystems, understanding the processes that govern microbial biogeographic distributions, community assembly and ecosystem function is a primary pursuit of marine microbial ecology. Together with the collection of environmental data, the use of multiple hypervariable gene markers has provided a growing body of evidence suggesting that dispersal of microbes in the oceans is limited [4, 5], and that geographical isolation even affects bacteria at the local scale [6,7,8]
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