Abstract
The deep sea is home to a vast and largely unexplored microbial biosphere, along with large amounts of complex organic matter (COM). However, the functional capacity of the deep-sea microbiome to metabolize organic matter across diverse regions remains poorly understood. Here, we combine 16S rRNA gene amplicon sequencing, metagenomics, and metatranscriptomics to comprehensively characterize prokaryotic communities across different years (2018 and 2022) and habitats (cold seeps, hydrothermal vents, and seamounts). Our results reveal spatio-temporal community heterogeneity driven by geochemical gradients, alongside a widespread genetic potential for organic matter metabolism. Notably, the PVC (Planctomycetota–Verrucomicrobiota–Chlamydiota) superphylum exhibits extensive polysaccharide degradation capabilities, exemplified by the isolation of Planctomycetota strain WC338 and Lentisphaerota strain WC36 via laminarin enrichment. Growth experiments and transcriptomics confirm their strict laminarin dependence and characterize the underlying catabolic machinery—specifically, the deployment of different glycoside hydrolase (GH) families, which are broadly distributed and prevalent across the PVC superphylum. Furthermore, we demonstrate that laminarin acts as an effective selective substrate for enriching and isolating the deep-sea PVC superphylum bacteria. Collectively, these findings reveal that PVC bacteria—an overlooked group in laminarin degradation—possess specialized adaptations for polysaccharide breakdown and actively participate in laminarin turnover in deep-sea environments.
Subjects
- Bacteriology
- Metagenomics
- Microbial ecology
- Water microbiology
Acknowledgements
We extend special appreciation to the captain and crew of the RV KEXUE, as well as the FAXIAN ROV team for assistance with sample collection.
Funding
This work was supported by the Key R&D Program of Shandong Province of China (Grant No. 2026CXPT225), National Key R&D Program of China (Grant No. 2025YFF0516902), National Natural Science Foundation of China (Grant Nos. 42221005 and 42530409), Science and Technology Innovation Project of Laoshan Laboratory (Grant Nos. LSKJ202203103 and 2022QNLM030004-3), Shandong Provincial Natural Science Foundation (Grant Nos. ZR2024ZD49 and ZR2023QD010), Major Research Plan of the National Natural Science Foundation (Grant No. 92351301), Qingdao West Coast New District University Presidents Fund (Grant No. E42424101N), Taishan Scholars Program (Grant Nos. tstp20230637 and tsqn202312264), and Huiquan Young Scholars Program (Grant Nos. E6KY23101Q and E6KY19101Q).
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Zheng, R., Wang, C. & Sun, C. Multi-omics and cultivation reveal laminarin-degrading PVC bacteria in the deep sea.
Nat Commun (2026). https://doi.org/10.1038/s41467-026-76253-5
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DOI: https://doi.org/10.1038/s41467-026-76253-5
Source: Ecology - nature.com
