Comparative single-cell genomics of Atribacterota JS1 in the Japan Trench hadal sedimentary biosphere

• DOI: 10.1128/msphere.00337-23
• Publication Date: 2024-01-03T22:00:56Z
• Authors: Kana Jitsuno; Tatsuhiko Hoshino; Yohei Nishikawa; Masato Kogawa; Katsuhiko Mineta; Michael Strasser; Ken Ikehara; Jeremy Everest; Lena Maeda; Fumio Inagaki; Haruko Takeyama; ; Piero Bellanova; Morgane Brunet; Zhirong Cai; Antonio Cattaneo; Katharina Hochmuth; Kanhsi Hsiung; Takashi Ishizawa; Takuya Itaki; Kana Jitsuno; Joel Johnson; Toshiya Kanamatsu; Myra Keep; Arata Kioka; Christian Maerz; Cecilia McHugh; Aaron Micallef; Luo Min; Dhananjai Pandey; Jean Noel Proust; Troy Rasbury; Natascha Riedinger; Rui Bao; Yasufumi Satoguchi; Derek Sawyer; Chloe Seibert; Maxwell Silver; Susanne Straub; Joonas Virtasalo; Yonghong Wang; Ting-Wei Wu; Sarah Zellers; Martin Kölling; Jyh-Jaan Steven H...; Yoshitaka Nagahashi
• Keywords: Environmental DNA

ABSTRACT Deep-sea and subseafloor sedimentary environments host heterotrophic microbial communities that contribute to Earth’s carbon cycling. However, the potential metabolic functions of individual microorganisms their biogeographical distributions in hadal ocean sediments remain largely unexplored. In this study, we conducted single-cell genome sequencing on sediment samples collected from six sites (7,445–8,023 m water depth) along an approximately 500 km transect Japan Trench during International Ocean Discovery Program Expedition 386. A total 1,886 amplified genomes (SAGs) were obtained, offering comprehensive genetic insights into surface (<1 above sulfate-methane transition zone Trench. Our data set included 269 SAGs Atribacterota JS1, predominant bacterial clade these environments. Phylogenetic analysis classified nine distinct phylotypes, whereas metagenome-assembled categorized only two advancing JS1 diversity coverage through a single cell-based approach. Comparative genomic lineages different habitats revealed frequent detection genes related organic utilization, such as extracellular enzymes like clostripain α-amylase, ABC transporters oligopeptide members. Furthermore, specific phylotypes exhibited strong correlation with situ methane concentrations contained involved glycine betaine metabolism. These findings suggest phylogenomically diverse novel is widely distributed sediment, playing crucial roles cycling within biosphere. IMPORTANCE The represents tectonically active associated Pacific plate subduction beneath northeastern arc. This for first time, documented large-scale metagenomic survey Trench, obtaining high-quality information communities. Single-cell genomics predominance not recoverable conventional binning. Their includes degradation matter, which contributes methanogenesis deeper layers. enhance understanding at depths exceeding 7,000 provide new ecological role biogeochemical