Diversity of original and culture enrichment samples of hadal sediments from the Mariana Trench

Culture enrichment is an approach to discover the uncharted microbial species in environmental microbiota, yet this strategy has not been widely used to study microbes from deep-sea environments. Here we report the cultivation and genomic analyses of sediment microbiota collected from 6477 m depth of the Mariana Trench. The sediment samples were cultured anaerobically in laboratory for four months, before subjected to full-length 16S rRNA gene sequencing using the PacBio technique and metagenome sequencing using both the Illumina and Nanopore techniques. The 16S rRNA gene analyses revealed 437 operational taxonomic units that are specific for the cultured microbiota, despite the lower diversity of the cultured microbiota in comparison with the original microbiota. Metagenome analyses revealed the prevalence of functions related to respiration, energy production, and stress response in the cultured microbiota, suggesting these functions may contribute to microbial proliferation under the laboratory condition. Binning of the assembled metagenome contigs generated four nearly complete genomes, affiliated to yet unclassified species under the genera Alcanivorax, Idiomarina, Sulfitobacter, and Erythrobacter, which were enriched in the cultured microbiota but rare or undetectable in the original microbiota. Analyses of the four genomes revealed a variety of genes for carbohydrate utilization and dissimilatory nitrite reduction, pointing to an ability to respire diverse carbon sources using nitrite as the final electron acceptor. Taken together, we showed that coupling culture enrichment and long-read sequencing is probably an ideal way to mine novel microbial species in the hadal environment, particularly the rare species in their native environment niches, and thus expand our understanding of the hadal microbial diversity.

培养富集法是发掘环境微生物群落中未知微生物物种的有效手段，但该策略尚未被广泛应用于深海环境微生物的研究。本研究针对采自马里亚纳海沟6477米深度的沉积物微生物群落，开展了培养与基因组学分析，相关结果报道如下。我们将沉积物样品置于实验室厌氧环境中培养四个月，随后采用PacBio测序技术开展全长16S核糖体RNA基因（16S rRNA gene）测序，并联合Illumina与Nanopore测序技术完成宏基因组（metagenome）测序。16S rRNA基因分析结果显示，培养后的微生物群落共包含437个特异性操作分类单元（operational taxonomic units），尽管其群落多样性相较于原始沉积物微生物群落更低。宏基因组分析表明，培养后的微生物群落中，与呼吸作用、能量产生及应激反应相关的功能通路显著富集，提示这类功能可能助力微生物在实验室培养条件下实现增殖。对组装得到的宏基因组重叠群进行宏基因组分箱，共获得4个近乎完整的基因组，它们分别隶属于Alcanivorax、Idiomarina、Sulfitobacter及Erythrobacter四个属中尚未被分类鉴定的物种——这类物种在培养后的微生物群落中显著富集，但在原始群落中极为罕见甚至无法被检测到。对这4个基因组的分析显示，其携带多种碳水化合物利用基因与异化亚硝酸盐还原基因，表明这些微生物能够以亚硝酸盐作为最终电子受体，通过呼吸作用利用多种碳源。综上，本研究证实，将培养富集法与长读长测序技术相结合，或是发掘深渊环境中新型微生物物种的理想策略——尤其针对原生境生态位中的稀有物种，该策略将有助于我们进一步拓展对深渊微生物多样性的认知。