Deep sequencing of subseafloor eukaryotic rRNA reveals active Fungi across marine subsurface provinces

PLoS One. 2013;8(2):e56335. doi: 10.1371/journal.pone.0056335. Epub 2013 Feb 13.


The deep marine subsurface is a vast habitat for microbial life where cells may live on geologic timescales. Because DNA in sediments may be preserved on long timescales, ribosomal RNA (rRNA) is suggested to be a proxy for the active fraction of a microbial community in the subsurface. During an investigation of eukaryotic 18S rRNA by amplicon pyrosequencing, unique profiles of Fungi were found across a range of marine subsurface provinces including ridge flanks, continental margins, and abyssal plains. Subseafloor fungal populations exhibit statistically significant correlations with total organic carbon (TOC), nitrate, sulfide, and dissolved inorganic carbon (DIC). These correlations are supported by terminal restriction length polymorphism (TRFLP) analyses of fungal rRNA. Geochemical correlations with fungal pyrosequencing and TRFLP data from this geographically broad sample set suggests environmental selection of active Fungi in the marine subsurface. Within the same dataset, ancient rRNA signatures were recovered from plants and diatoms in marine sediments ranging from 0.03 to 2.7 million years old, suggesting that rRNA from some eukaryotic taxa may be much more stable than previously considered in the marine subsurface.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Carbon / metabolism
  • Diatoms / genetics
  • Eukaryotic Cells / metabolism
  • Fungi / genetics*
  • Fungi / growth & development
  • Fungi / metabolism
  • Geography
  • Geologic Sediments / microbiology*
  • High-Throughput Nucleotide Sequencing / methods*
  • Insecta / genetics
  • Nitrates / metabolism
  • Plants / genetics
  • Population Dynamics
  • RNA, Ribosomal / genetics*
  • Seawater / microbiology
  • Sulfides / metabolism


  • Nitrates
  • RNA, Ribosomal
  • Sulfides
  • Carbon

Grant support

This work was performed with funding from the Center for Dark Energy Biosphere Investigations (C-DEBI) to William Orsi (OCE-0939564) and The Ocean Life Institute (WHOI) to Virginia Edgcomb (OLI-27071359). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.