Half of the microbial cells in the Earth’s oceans are found in sediments1. Many of these cells are members of the Archaea2, single-celled prokaryotes in a domain of life separate from Bacteria and Eukaryota. However, most of these archaea lack cultured representatives, leaving their physiologies and placement on the tree of life uncertain. Here we show that the uncultured miscellaneous crenarchaeotal group (MCG) and marine benthic group-D (MBG-D) are among the most numerous archaea in the marine sub-sea floor. Single-cell genomic sequencing of one cell of MCG and three cells of MBG-D indicated that they form new branches basal to the archaeal phyla Thaumarchaeota3 and Aigarchaeota4, for MCG, and the order Thermoplasmatales, for MBG-D. All four cells encoded extracellular protein-degrading enzymes such as gingipain and clostripain that are known to be effective in environments chemically similar to marine sediments. Furthermore, we found these two types of peptidase to be abundant and active in marine sediments, indicating that uncultured archaea may have a previously undiscovered role in protein remineralization in anoxic marine sediments.
At a glance
- Global distribution of microbial abundance and biomass in subseafloor sediment. Proc. Natl Acad. Sci. USA 109, 16213–16216 (2012) , , , &
- Quantification of microbial communities in forearc sediment basins off Sumatra. Geomicrobiol. J. 27, 170–182 (2010) , , &
- Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nature Rev. Microbiol. 6, 245–252 (2008) , , &
- Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res. 39, 3204–3223 (2011) et al.
- Major players on the microbial stage: why archaea are important. Microbiology 157, 919–936 (2011) et al.
- Heterotrophic archaea dominate sedimentary subsurface ecosystems off Peru. Proc. Natl Acad. Sci. USA 103, 3846–3851 (2006) et al.
- Molecular indicators of diagenetic status in marine organic matter. Geochim. Cosmochim. Acta 61, 5363–5369 (1997) , , , &
- Bacterial influence on amino acid enantiomerization in a coastal marine sediment. Limnol. Oceanogr. 46, 1358–1369 (2001) , , &
- Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments. ISME J. 6, 1949–1965 (2012) et al.
- A cryptic sulfur cycle driven by iron in the methane zone of marine sediment (Aarhus Bay, Denmark). Geochim. Cosmochim. Acta 75, 3581–3599 (2011) , &
- Genomic DNA amplification from a single bacterium. Appl. Environ. Microbiol. 71, 3342–3347 (2005) et al.
- Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proc. Natl Acad. Sci. USA 104, 9052–9057 (2007) &
- Genetic structure of three fosmid-fragments encoding 16S rRNA genes of the Miscellaneous Crenarchaeotic Group (MCG): implications for physiology and evolution of marine sedimentary archaea. Environ. Microbiol. 14, 467–479 (2012) et al.
- MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res. 40, D343–D350 (2012) , &
- Evolutionary lines of cysteine peptidases. Biol. Chem. 382, 727–733 (2001) &
- The structure–function relationship in the clostripain family of peptidases. Eur. J. Biochem. 271, 983–992 (2004) &
- A ubiquitous thermoacidophilic archaeon from deep-sea hydrothermal vents. Nature 442, 444–447 (2006) et al.
- The Pfam protein families database. Nucleic Acids Res. 40, D290–D301 (2012) et al.
- Clostripain: characterization of the active site. FEBS Lett. 283, 277–280 (1991) , &
- Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment. Nature 484, 101–104 (2012) , , , &
- IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res. 40, D123–D129 (2012) et al.
- 2-keto acid oxidoreductases from Pyrococcus furiosus and Thermococcus litoralis. Methods Enzymol. 331, 144–158 (2001) , &
- Role for ferredoxins in the origin of life and biological evolution. Nature 233, 136–138 (1971) , &
- Tungstoenzymes. Chem. Rev. 96, 2817–2840 (1996) , &
- Seasonal dynamics of the depth and rate of anaerobic oxidation of methane in Aarhus Bay (Denmark) sediments. J. Mar. Res. 66, 127–155 (2008) et al.
- A simple energy-conserving system: Proton reduction copuled to proton translocation. Proc. Natl Acad. Sci. USA 100, 7545–7550 (2003) , &
- Methanogenic archaea: ecologically relevant differences in energy conservation. Nature Rev. Microbiol. 6, 579–591 (2008) , , , &
- Functional exoenzymes as indicators of metabolically active bacteria in 124,000-year-old sapropel layers of the Eastern Mediterranean Sea. Appl. Environ. Microbiol. 66, 2589–2598 (2000) &
- Sedimentary organic matter preservation: an assessment and speculative synthesis. Mar. Chem. 49, 81–115 (1995) &
- Spotlight on the Thaumarchaeota. ISME J. 6, 227–230 (2012) , &
- Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863–864 (2011) &
- Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics 11, 187 (2010) , , &
- SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012) et al.
- GenDB-an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 31, 2187–2195 (2003) et al.
- JCoast—A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes. BMC Bioinformatics 9, 177 (2008) et al.
- ARB: a software environment for sequence data. Database 32, 1363–1371 (2004) et al.
- Assembling the marine metagenome, one cell at a time. PLoS ONE 4, e5299 (2009) et al.
- The integrated microbial genomes (IMG) system. Nucleic Acids Res. 34, D344–D348 (2006) et al.
- tRNAscan-SE: A Program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 0955–0964 (1997) &
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997) et al.
- Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333, 1296–1300 (2011)
- Archaeal phylogeny based on ribosomal proteins. Mol. Biol. Evol. 19, 631–639 (2002) , , &
- An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences. BMC Evol. Biol. 5, 36 (2005) , &
- Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinform. 9, 286–298 (2008) &
- A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 57, 758–771 (2008) , &
- Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Gateway Computing Environments Workshop. 1–8 (2010) , &
- 1996) Case study—Århus Bay. Eutrophication in Coastal Marine Systems 137–154 (American Geophysical Union,
- Diversity of sulfate-reducing bacteria from an extreme hypersaline sediment, Great Salt Lake (Utah). FEMS Microbiol. Ecol. 60, 287–298 (2007) et al.
- Archaea in coastal marine environments. Proc. Natl Acad. Sci. USA 89, 5685–5689 (1992)
- 1991) & Development and Application of Nucleic Acid Probes (Wiley,
- Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes. Appl. Environ. Microbiol. 66, 5066–5072 (2000) &
- Uncultured archaea in deep marine subsurface sediments: have we caught them all? ISME J. 2, 3–18 (2008) &
- Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS ONE 5, e9085 (2010) et al.
- Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Society 75, 7537–7541 (2009) et al.
- SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188–7196 (2007) et al.
- PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Res. 30, 3481–3489 (2002) , &
- Characterization of β-glucosidase activity in intertidal marine sediments. Appl. Environ. Microbiol. 51, 373–380 (1986)
- Construction and characterization of arginine-specific cysteine proteinase (Arg-gingipain)-deficient mutants of Porphyromonas gingivalis: Evidence for significant contribution of Arg-gingipain to virulence. J. Biol. Chem. 270, 23619–23626 (1995) , , &
- Synthesis of lysine-containing sulphonium salts and their properties as proteinase inhibitors. Biochem. J. 250, 871 (1988) , , &
- R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing http://www.rproject.org (2012)
- Supplementary Information (1.7 MB)
This file contains Supplementary Materials and Methods, Supplementary Tables 1-7 and 9-12 (see separate file for Supplementary Table 8), Supplementary Figures 1-10 and additional references.
- Supplementary Tables (44 KB)
This file contains Supplementary Table 8.