Abstract
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.
Highlights
The deep marine subsurface harbors an immense number of microbes, initially observed by microscopy and later confirmed by nucleic acid and lipid studies [1,2,3,4,5]
Most sequence-based studies of microbial diversity within environmental samples, including the marine subsurface, have utilized PCR amplification of target genes, most commonly small subunit ribosomal RNA (SSU rRNA), from DNA extracted from the environmental sample as a starting material e.g. [9,17]
Amplicon libraries of eukaryotic V4 rRNA were prepared from sediments from the Eastern Equatorial Pacific (45.3 mbsf), Peru Margin (48.1 mbsf), Hydrate Ridge (1.8 mbsf), North Pond (1.6 mbsf), the Benguela Continental Slope (4.6 mbsf), and Sippewissett Salt Marsh (0.01 and 0.08 mbsf) (Table 1)
Summary
The deep marine subsurface harbors an immense number of microbes, initially observed by microscopy and later confirmed by nucleic acid and lipid studies [1,2,3,4,5]. To identify contaminants we performed additional RT-PCR amplifications at 55 cycles using RNAse free sterile water and RNA extraction blanks (resulting from RNA extractions in which no sample was added) as template.
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