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.