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Microbial Genomics logo Microbial Genomics

Volume 11, Issue 3

Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific Open Access

Abstract

Marine sediments are vast, underexplored habitats and represent one of the largest carbon deposits on our planet. Microbial communities drive nutrient cycling in these sediments, but the full extent of their taxonomic and metabolic diversity remains to be explored. Here, we analysed shallow coastal and deep subseafloor sediment cores from 0.01 to nearly 600 metres below the seafloor, in the Western Pacific Region. Applying metagenomics, we identified several taxonomic clusters across all samples, which mainly aligned with depth and sediment type. Inferring functional patterns provided insights into possible ecological roles of the main microbial taxa. These included , the most abundant phylum across all samples, whereby the classes and dominated deep-subsurface and most shallow coastal sediments, respectively. and were the most abundant phyla among Archaea, contributing to high relative abundances of Archaea reaching over 50% in some samples. We recovered high-quality metagenome-assembled genomes for all main prokaryotic lineages and proposed names for three phyla, i.e. phyl. nov. (former RBG-13-66-14), phyl. nov. (former UBA6262) and phyl. nov. (former UBA8248). Metabolic capabilities across all samples ranged from aerobic respiration and photosynthesis in the shallowest sediment layers to heterotrophic carbon utilization, sulphate reduction and methanogenesis in deeper anoxic sediments. We also identified taxa with the potential to be involved in nitrogen and sulphur cycling and heterotrophic carbon utilization. In summary, this study contributes to our understanding of the taxonomic and functional diversity in benthic prokaryotic communities across marine sediments in the Western Pacific Region.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): deep biosphere , deep subseafloor , DNA extraction , marine sediment , metagenomics and Pacific
Funding
This study was supported by the:
  • MEXT KAKENHI (Award JP19H05684)
    • Principal Award Recipient: TakuroNunoura
  • Australian Research Council (Award DP180101506)
    • Principal Award Recipient: ChristianRinke
  • Australian Research Council (Award FT170100213)
    • Principal Award Recipient: ChristianRinke
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific
M Gen 11, 001351 (2025); https://doi.org/10.1099/mgen.0.001351
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