Gene expression in the deep biosphere

Abstract

Scientific ocean drilling has revealed a deep biosphere of widespread microbial life in sub-seafloor sediment. Microbial metabolism in the marine subsurface probably has an important role in global biogeochemical cycles1,2,3, but deep biosphere activities are not well understood1. Here we describe and analyse the first sub-seafloor metatranscriptomes from anaerobic Peru Margin sediment up to 159 metres below the sea floor, represented by over 1 billion complementary DNA (cDNA) sequence reads. Anaerobic metabolism of amino acids, carbohydrates and lipids seem to be the dominant metabolic processes, and profiles of dissimilatory sulfite reductase (dsr) transcripts are consistent with pore-water sulphate concentration profiles1. Moreover, transcripts involved in cell division increase as a function of microbial cell concentration, indicating that increases in sub-seafloor microbial abundance are a function of cell division across all three domains of life. These data support calculations1 and models4 of sub-seafloor microbial metabolism and represent the first holistic picture of deep biosphere activities.

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Figure 1: Biogeochemical and gene-expression profiles of the deep biosphere from Peru Margin sediment, Ocean Drilling Program Site 1229D.
Figure 2: Profiles of deep biosphere metabolic activities in Peru Margin sediment.
Figure 3: Transcripts involved in cell motility and DNA repair.
Figure 4: A comparison of gene-expression data to existing metagenomic studies13,29 from Ocean Drilling Program Site 1229.

Accession codes

Accessions

Sequence Read Archive

Data deposits

Data has been deposited in the NCBI Short Read Archive under accession number SRA058813 and in MG RAST (metagenomics.anl.gov) under accession numbers 4515478.3, 4515477.3, 4515476.3, 4510337.3, 4510336.3 and 4510335.3.

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Acknowledgements

This work was fostered by a Center for Dark Energy Biosphere Investigations (CDEBI) grant OCE-0939564 to W.D.O. and a National Science Foundation IOS grant 1238801 to J.F.B. We thank C. House and A. Teske for providing samples. We also thank M. Sogin and R. Fox at the Josephine Bay Paul Center for providing access to computing resources. E. Leadbetter and S. Hallam provided comments on the manuscript, and we also thank S. D’Hondt for discussions on the deep biosphere. This is CDEBI contribution 137.

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W.D.O. performed experiments, analysed data and wrote the paper; W.D.O., J.F.B. and V.P.E. designed experiments and developed ideas. W.D.O. and G.D.C. developed analytical tools. All authors participated in data interpretation and provided editorial comments on the manuscript.

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Correspondence to William D. Orsi.

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The authors declare no competing financial interests.

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Orsi, W., Edgcomb, V., Christman, G. et al. Gene expression in the deep biosphere. Nature 499, 205–208 (2013). https://doi.org/10.1038/nature12230

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