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BER Research Highlights

Metabolic Handoffs Among Microbial Community Members Drive Biogeochemical Cycles
Published: October 24, 2016
Posted: October 27, 2016

Tree showing all of bacterial diversity that is now represented by genomes, with the major lineages indicated by wedges. Research on the microbiology of the Rifle aquifer has provided new genomic information within previously identified groups (black wedges). In addition, many major bacterial groups were first identified and via study of the Rifle site (red and purple wedges). Red wedges indicate many major lineages that were first identified in the current study. Colored dots indicate the genomically predicted roles of members of these newly defined bacterial lineages in geochemical cycling. Remarkably, few major bacterial lineages have not been genomically sampled at this site (olive green wedges). [Image courtesy of Anantharaman et al. 2016. DOI: 10.1038/ncomms13219. Reprinted under CC by 4.0.]

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system.

The Science
2,540 genomes that represent the majority of known bacterial phyla and 47 new phylum-level lineages were reconstructed from sediment and groundwater collected from a semi-arid floodplain near Rifle, CO. Analyses showed that inter-organism interactions are required to turn the carbon, sulfur and nitrogen biogeochemical cycles and revealed that complex patterns of community assembly are likely key to ecosystem functioning and resilience.

The Impact
The research almost doubled the number of major bacterial groups and provided detailed information about the ecosystem roles of organisms from these groups. The research dramatically increased understanding of subsurface biology and motivates new approaches to ecosystem modeling. The genomes represent a treasure-trove that will be mined for biotechnology.

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. Terabase-scale cultivation-independent metagenomics was applied to aquifer sediments and groundwater and 2,540 high-quality near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla were constructed.  Some of these genomes derive from 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system were used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, it was shown that few organisms within the community conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.

BER PM Contact
David Lesmes, SC-23.1, 301-903-2977

Susan Hubbard
Lawrence Berkeley National Laboratory

Funding: This work was supported by Lawrence Berkeley National Laboratory’s Sustainable Systems Scientific Focus Area funded by the US Department of Energy, Office of Science, Office of Biological and Environmental Research.  Terabase-scale sequencing critical for this work was provided by the Joint Genome Institute via Community Science Program allocations.

K. Anantharaman, C. T. Brown, L. A. Hug, I.Sharon, C. J. Castelle, A. J. Probst, B. C. Thomas, A. Singh, M. J. Wilkins, U. Karaoz, E. L. Brodie, K. H. Williams, S. S. Hubbard, and J. F. Banfield. “Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system”. Nature Communications 7, ncomms13219 (2016). [DOI: 10.1038/ncomms13219]. (Reference link)

Topic Areas:

  • Research Area: Subsurface Biogeochemical Research
  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Microbes and Communities
  • Research Area: Sustainable Biofuels and Bioproducts
  • Research Area: DOE Joint Genome Institute (JGI)

Division: SC-33.1 Earth and Environmental Sciences Division, BER


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