Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system View Full Text


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Article Info

DATE

2016-10-24

AUTHORS

Karthik Anantharaman, Christopher T. Brown, Laura A. Hug, Itai Sharon, Cindy J. Castelle, Alexander J. Probst, Brian C. Thomas, Andrea Singh, Michael J. Wilkins, Ulas Karaoz, Eoin L. Brodie, Kenneth H. Williams, Susan S. Hubbard, Jillian F. Banfield

ABSTRACT

The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth’s biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles. More... »

PAGES

13219

References to SciGraph publications

  • 2014-08-14. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences in NATURE REVIEWS MICROBIOLOGY
  • 2014-03-13. Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2009-08-21. Community-wide analysis of microbial genome sequence signatures in GENOME BIOLOGY
  • 2016-03-04. Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2013-08-05. Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling in MICROBIOME
  • 2015-06. Interaction networks for identifying coupled molecular processes in microbial communities in BIODATA MINING
  • 2015-06-15. Unusual biology across a group comprising more than 15% of domain Bacteria in NATURE
  • 2011-12-15. Nitrite oxidation in the Namibian oxygen minimum zone in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2007-01-15. Prediction of effective genome size in metagenomic samples in GENOME BIOLOGY
  • 2015-03-02. Ecology and exploration of the rare biosphere in NATURE REVIEWS MICROBIOLOGY
  • 2014-09-14. Binning metagenomic contigs by coverage and composition in NATURE METHODS
  • 2013-08-27. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment in NATURE COMMUNICATIONS
  • 2011-01-13. Microbial seed banks: the ecological and evolutionary implications of dormancy in NATURE REVIEWS MICROBIOLOGY
  • 2011-05-19. EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data in GENOME BIOLOGY
  • 2010-03-08. Prodigal: prokaryotic gene recognition and translation initiation site identification in BMC BIOINFORMATICS
  • 2016-04-11. A new view of the tree of life in NATURE MICROBIOLOGY
  • 2015-02-27. Diverse uncultivated ultra-small bacterial cells in groundwater in NATURE COMMUNICATIONS
  • 2012-03-04. Fast gapped-read alignment with Bowtie 2 in NATURE METHODS
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    URI

    http://scigraph.springernature.com/pub.10.1038/ncomms13219

    DOI

    http://dx.doi.org/10.1038/ncomms13219

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1035143030

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/27774985


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