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.

中文翻译：

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利用 CRISPR 揭示深海细菌共生体种群结构


以化学合成为基础的生态系统中的许多基础物种依赖于环境中获得的共生细菌来生存。因此，了解这些共生体在区域尺度上的生物地理分布是了解连接模式和预测其宿主种群（以及整个社区）的恢复力的关键。然而，此类评估具有挑战性，因为它们需要以高分辨率测量细菌遗传多样性。为此，最近发现的成簇规则间隔短回文重复序列（CRISPR）构成了一种有前途的新遗传标记。大约一半的细菌所携带的这些DNA序列保留了它们的病毒免疫记忆，因此，可能允许区分不同谱系或原本无法区分的细菌的菌株。在这项研究中，我们在未培养的细菌物种的群体遗传学研究中评估了 CRISPR 作为高变系统发育标记的潜力。我们使用基于 CRISPR 的高通量分型和多位点序列分析 (MLSA) 来表征胡安德富卡山脊上专性但环境获得的共生物种Candidatus Endoriftia persephone 的区域种群结构。 Ca的混合共生群体。对来自对比栖息地的个体Ridgeia piscesae宿主的 Endoriftia persephone 进行了采样，以确定环境条件而不是连通性障碍是否是共生体多样性更重要的驱动因素。我们发现 CRISPR 揭示了比其他管家基因更高的共生体遗传多样性。多项证据表明，这种多样性表明了环境压力。 最后，我们通过 CRISPR 和基因标记发现，当地共生体种群在已知被深海环流模式隔离的地点之间存在强烈差异。这项研究展示了 CRISPR 在解决未培养细菌种群遗传结构方面的强大能力，并代表着朝着使关键微生物物种成为即将进行的海底采矿作业保护政策的一个组成部分迈出了一步。