U.S. Department of EnergyOffice of Scientific and Technical Information
Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes
Abstract
Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA sequencing-based studies is recognition of the enormous variety of little known and previously unknown microorganisms that mediate recycling of these vast stores of buried carbon in subsoil compartments of the terrestrial system. More importantly, the genome resolution achieved in these studies has enabled association of specific members of these microbial communities with carbon compound transformations and other linked biogeochemical processes–such as the nitrogen cycle–that can impact the quality of groundwater, surface water, and atmospheric trace gas concentrations. The emerging view also emphasizes the importance of organism interactions through exchange of metabolic byproducts (e.g., within the carbon, nitrogen, and sulfur cycles) and via symbioses since many novel organisms exhibit restricted metabolic capabilities and an associated extremely small cell size. New, genome-resolved information reshapes our view of subsurface microbial communities and provides critical new inputs for advanced reactive transport models. Finally, these inputs are needed for accurate prediction of feedbacks in watershed biogeochemical functioning and their influence on the climate via the fluxes ofmore »
- Authors:
-
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1471018
- Alternate Identifier(s):
- OSTI ID: 1398007
- Grant/Contract Number:
- AC02-05CH11231; SC0004918; AC06-76RLO 1830
- Resource Type:
- Journal Article: Accepted Manuscript
- Journal Name:
- Trends in Microbiology
- Additional Journal Information:
- Journal Volume: 24; Journal Issue: 8; Journal ID: ISSN 0966-842X
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; metagenome; subsurface biogeochemistry; reaction pathway; greenhouse gases
Citation Formats
Long, Philip E., Williams, Kenneth H., Hubbard, Susan S., and Banfield, Jillian F. Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes. United States: N. p., 2016.
Web. doi:10.1016/j.tim.2016.04.006.
Long, Philip E., Williams, Kenneth H., Hubbard, Susan S., & Banfield, Jillian F. Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes. United States. https://doi.org/10.1016/j.tim.2016.04.006
Long, Philip E., Williams, Kenneth H., Hubbard, Susan S., and Banfield, Jillian F. 2016.
"Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes". United States. https://doi.org/10.1016/j.tim.2016.04.006. https://www.osti.gov/servlets/purl/1471018.
@article{osti_1471018,
title = {Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes},
author = {Long, Philip E. and Williams, Kenneth H. and Hubbard, Susan S. and Banfield, Jillian F.},
abstractNote = {Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA sequencing-based studies is recognition of the enormous variety of little known and previously unknown microorganisms that mediate recycling of these vast stores of buried carbon in subsoil compartments of the terrestrial system. More importantly, the genome resolution achieved in these studies has enabled association of specific members of these microbial communities with carbon compound transformations and other linked biogeochemical processes–such as the nitrogen cycle–that can impact the quality of groundwater, surface water, and atmospheric trace gas concentrations. The emerging view also emphasizes the importance of organism interactions through exchange of metabolic byproducts (e.g., within the carbon, nitrogen, and sulfur cycles) and via symbioses since many novel organisms exhibit restricted metabolic capabilities and an associated extremely small cell size. New, genome-resolved information reshapes our view of subsurface microbial communities and provides critical new inputs for advanced reactive transport models. Finally, these inputs are needed for accurate prediction of feedbacks in watershed biogeochemical functioning and their influence on the climate via the fluxes of greenhouse gases, CO2, CH4, and N2O.},
doi = {10.1016/j.tim.2016.04.006},
url = {https://www.osti.gov/biblio/1471018},
journal = {Trends in Microbiology},
issn = {0966-842X},
number = 8,
volume = 24,
place = {United States},
year = {Tue May 03 00:00:00 EDT 2016},
month = {Tue May 03 00:00:00 EDT 2016}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 28 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Microorganisms and climate change: terrestrial feedbacks and mitigation options
journal, October 2010
- Singh, Brajesh K.; Bardgett, Richard D.; Smith, Pete
- Nature Reviews Microbiology, Vol. 8, Issue 11
Enhancing metaproteomics-The value of models and defined environmental microbial systems
journal, January 2016
- Herbst, Florian-Alexander; Lünsmann, Vanessa; Kjeldal, Henrik
- PROTEOMICS, Vol. 16, Issue 5
Bicarbonate impact on U(VI) bioreduction in a shallow alluvial aquifer
journal, February 2015
- Long, Philip E.; Williams, Kenneth H.; Davis, James A.
- Geochimica et Cosmochimica Acta, Vol. 150
Stimulating the In Situ Activity of Geobacter Species To Remove Uranium from the Groundwater of a Uranium-Contaminated Aquifer
journal, October 2003
- Anderson, R. T.; Vrionis, H. A.; Ortiz-Bernad, I.
- Applied and Environmental Microbiology, Vol. 69, Issue 10
Ecology and exploration of the rare biosphere
journal, March 2015
- Lynch, Michael D. J.; Neufeld, Josh D.
- Nature Reviews Microbiology, Vol. 13, Issue 4
Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics
journal, October 2015
- Evans, P. N.; Parks, D. H.; Chadwick, G. L.
- Science, Vol. 350, Issue 6259
Accurate, multi-kb reads resolve complex populations and detect rare microorganisms
journal, February 2015
- Sharon, Itai; Kertesz, Michael; Hug, Laura A.
- Genome Research, Vol. 25, Issue 4
Capturing prokaryotic dark matter genomes
journal, December 2015
- Gasc, Cyrielle; Ribière, Céline; Parisot, Nicolas
- Research in Microbiology, Vol. 166, Issue 10
Subterranean microbial populations metabolize hydrogen and acetate under in situ conditions in granitic groundwater at 450 m depth in the Äspö Hard Rock Laboratory, Sweden
journal, April 2012
- Pedersen, Karsten
- FEMS Microbiology Ecology, Vol. 81, Issue 1
Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla
journal, September 2012
- Wrighton, K. C.; Thomas, B. C.; Sharon, I.
- Science, Vol. 337, Issue 6102
High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats
journal, January 2015
- Zhou, Jizhong; He, Zhili; Yang, Yunfeng
- mBio, Vol. 6, Issue 1
From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems
journal, August 2015
- Garza, Daniel R.; Dutilh, Bas E.
- Cellular and Molecular Life Sciences, Vol. 72, Issue 22
Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria
journal, April 2015
- Baker, Brett J.; Lazar, Cassandre Sara; Teske, Andreas P.
- Microbiome, Vol. 3, Issue 1
Classifying the uncultivated microbial majority: A place for metagenomic data in the Candidatus proposal
journal, June 2015
- Konstantinidis, Konstantinos T.; Rosselló-Móra, Ramon
- Systematic and Applied Microbiology, Vol. 38, Issue 4
Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer
journal, March 2016
- Jewell, Talia N. M.; Karaoz, Ulas; Brodie, Eoin L.
- The ISME Journal, Vol. 10, Issue 9
Microbiology: Create a global microbiome effort
journal, October 2015
- Dubilier, Nicole; McFall-Ngai, Margaret; Zhao, Liping
- Nature, Vol. 526, Issue 7575
Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum
journal, January 2016
- Anantharaman, Karthik; Brown, Christopher T.; Burstein, David
- PeerJ, Vol. 4
Unraveling interactions in microbial communities - from co-cultures to microbiomes
journal, May 2015
- Tan, Justin; Zuniga, Cristal; Zengler, Karsten
- Journal of Microbiology, Vol. 53, Issue 5
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990
- Woese, C. R.; Kandler, O.; Wheelis, M. L.
- Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
N2-dependent growth and nitrogenase activity in the metal-metabolizing bacteria, Geobacter and Magnetospirillum species
journal, June 2000
- Bazylinski, Dennis A.; Dean, Annette J.; Schuler, Dirk
- Environmental Microbiology, Vol. 2, Issue 3
Pocket DNA sequencers make real-time diagnostics a reality
journal, February 2016
- Pennisi, E.
- Science, Vol. 351, Issue 6275
Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents
journal, February 2015
- Reed, Daniel C.; Breier, John A.; Jiang, Houshuo
- The ISME Journal, Vol. 9, Issue 8
Uranium Bioreduction Rates across Scales: Biogeochemical Hot Moments and Hot Spots during a Biostimulation Experiment at Rifle, Colorado
journal, August 2014
- Bao, Chen; Wu, Hongfei; Li, Li
- Environmental Science & Technology, Vol. 48, Issue 17
Anthropogenic warming has increased drought risk in California
journal, March 2015
- Diffenbaugh, Noah S.; Swain, Daniel L.; Touma, Danielle
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 13
Aquifer environment selects for microbial species cohorts in sediment and groundwater
journal, February 2015
- Hug, Laura A.; Thomas, Brian C.; Brown, Christopher T.
- The ISME Journal, Vol. 9, Issue 8
In-depth study of Mollivirus sibericum , a new 30,000-y-old giant virus infecting Acanthamoeba
journal, September 2015
- Legendre, Matthieu; Lartigue, Audrey; Bertaux, Lionel
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 38
Workshop to develop deep-life continental scientific drilling projects
journal, January 2015
- Kieft, T. L.; Onstott, T. C.; Ahonen, L.
- Scientific Drilling, Vol. 19
Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
journal, March 2015
- Castelle, Cindy J.; Wrighton, Kelly C.; Thomas, Brian C.
- Current Biology, Vol. 25, Issue 6
Systems-based approaches to unravel multi-species microbial community functioning
journal, January 2015
- Abram, Florence
- Computational and Structural Biotechnology Journal, Vol. 13
Nanopore-based Fourth-generation DNA Sequencing Technology
journal, February 2015
- Feng, Yanxiao; Zhang, Yuechuan; Ying, Cuifeng
- Genomics, Proteomics & Bioinformatics, Vol. 13, Issue 1
Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes
journal, March 2015
- Hultman, Jenni; Waldrop, Mark P.; Mackelprang, Rachel
- Nature, Vol. 521, Issue 7551
Evidence of Geobacter-associated phage in a uranium-contaminated aquifer
journal, August 2014
- Holmes, Dawn E.; Giloteaux, Ludovic; Chaurasia, Akhilesh K.
- The ISME Journal, Vol. 9, Issue 2
The microbial ecology of permafrost
journal, May 2014
- Jansson, Janet K.; Taş, Neslihan
- Nature Reviews Microbiology, Vol. 12, Issue 6
Unusual biology across a group comprising more than 15% of domain Bacteria
journal, June 2015
- Brown, Christopher T.; Hug, Laura A.; Thomas, Brian C.
- Nature, Vol. 523, Issue 7559
Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils
journal, June 2015
- Stefani, Franck O. P.; Bell, Terrence H.; Marchand, Charlotte
- PLOS ONE, Vol. 10, Issue 6
Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA
journal, November 2014
- Osburn, Magdalena R.; LaRowe, Douglas E.; Momper, Lily M.
- Frontiers in Microbiology, Vol. 5
A new view of the tree of life
journal, April 2016
- Hug, Laura A.; Baker, Brett J.; Anantharaman, Karthik
- Nature Microbiology, Vol. 1, Issue 5
Influence of hydrological, biogeochemical and temperature transients on subsurface carbon fluxes in a flood plain environment
journal, February 2016
- Arora, Bhavna; Spycher, Nicolas F.; Steefel, Carl I.
- Biogeochemistry, Vol. 127, Issue 2-3
Past water management affected GHG production and microbial community pattern in Italian rice paddy soils
journal, February 2016
- Lagomarsino, A.; Agnelli, A. E.; Pastorelli, R.
- Soil Biology and Biochemistry, Vol. 93
Environmental forcing does not induce diel or synoptic variation in the carbon isotope content of forest soil respiration
journal, January 2015
- Bowling, D. R.; Egan, J. E.; Hall, S. J.
- Biogeosciences, Vol. 12, Issue 16
High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments
journal, January 2014
- Engelhardt, Tim; Kallmeyer, Jens; Cypionka, Heribert
- The ISME Journal, Vol. 8, Issue 7
Diverse uncultivated ultra-small bacterial cells in groundwater
journal, February 2015
- Luef, Birgit; Frischkorn, Kyle R.; Wrighton, Kelly C.
- Nature Communications, Vol. 6, Issue 1
Microbial evolution in extreme environments: microbial migration, genomic highways, and geochemical barriers in hydrothermal ecosystems
journal, August 2015
- Raymond, Jason; Alsop, Eric B.
- Environmental Systems Research, Vol. 4, Issue 1
The promises and challenges of solid-state sequencing
journal, February 2016
- Lindsay, Stuart
- Nature Nanotechnology, Vol. 11, Issue 2
Methane dynamics regulated by microbial community response to permafrost thaw
journal, October 2014
- McCalley, Carmody K.; Woodcroft, Ben J.; Hodgkins, Suzanne B.
- Nature, Vol. 514, Issue 7523
Influence of Heterogeneous Ammonium Availability on Bacterial Community Structure and the Expression of Nitrogen Fixation and Ammonium Transporter Genes during in Situ Bioremediation of Uranium-Contaminated Groundwater
journal, June 2009
- Mouser, Paula J.; N’Guessan, A. Lucie; Elifantz, Hila
- Environmental Science & Technology, Vol. 43, Issue 12
Viral dark matter and virus–host interactions resolved from publicly available microbial genomes
journal, July 2015
- Roux, Simon; Hallam, Steven J.; Woyke, Tanja
- eLife, Vol. 4
Soil physics meets soil biology: Towards better mechanistic prediction of greenhouse gas emissions from soil
journal, April 2012
- Blagodatsky, Sergey; Smith, Pete
- Soil Biology and Biochemistry, Vol. 47
A unified initiative to harness Earth's microbiomes
journal, October 2015
- Alivisatos, A. P.; Blaser, M. J.; Brodie, E. L.
- Science, Vol. 350, Issue 6260
Methane production from protozoan endosymbionts following stimulation of microbial metabolism within subsurface sediments
journal, August 2014
- Holmes, Dawn E.; Giloteaux, Ludovic; Orellana, Roberto
- Frontiers in Microbiology, Vol. 5
Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes
journal, February 2015
- Worden, A. Z.; Follows, M. J.; Giovannoni, S. J.
- Science, Vol. 347, Issue 6223
Gene-centric approach to integrating environmental genomics and biogeochemical models
journal, January 2014
- Reed, Daniel C.; Algar, Christopher K.; Huber, Julie A.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 5
Discovery of a novel methanogen prevalent in thawing permafrost
journal, February 2014
- Mondav, Rhiannon; Woodcroft, Ben J.; Kim, Eun-Hae
- Nature Communications, Vol. 5, Issue 1
Coupled soil oxygen and greenhouse gas dynamics under variable hydrology
journal, April 2016
- Jarecke, Karla M.; Loecke, Terrance D.; Burgin, Amy J.
- Soil Biology and Biochemistry, Vol. 95
Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater
journal, February 2013
- Holmes, Dawn E.; Giloteaux, Ludovic; Williams, Kenneth H.
- The ISME Journal, Vol. 7, Issue 7
Works referencing / citing this record:
Comparison of Microbiomes and Resistomes in Two Karst Groundwater Sites in Chongqing, China
journal, June 2019
- Zhang, Yuan; Zhang, Yuanzhu; Kuang, Zhongmei
- Groundwater, Vol. 57, Issue 5
The influence of substrate concentration on the culturability of heterotrophic soil microbes isolated by high-throughput dilution-to-extinction cultivation
journal, December 2019
- Bartelme, Ryan P.; Custer, Joy M.; Dupont, Christopher L.
- mSphere
Iron-oxidizer hotspots formed by intermittent oxic–anoxic fluid mixing in fractured rocks
journal, January 2020
- Bochet, Olivier; Bethencourt, Lorine; Dufresne, Alexis
- Nature Geoscience, Vol. 13, Issue 2
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
journal, October 2016
- Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.
- Nature Communications, Vol. 7, Issue 1
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
journal, October 2016
- Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.
- Nature Communications, Vol. 7, Issue 1
MetaTOR: A Computational Pipeline to Recover High-Quality Metagenomic Bins From Mammalian Gut Proximity-Ligation (meta3C) Libraries
journal, August 2019
- Baudry, Lyam; Foutel-Rodier, Théo; Thierry, Agnès
- Frontiers in Genetics, Vol. 10
Diversity, Ecology, and Prevalence of Antimicrobials in Nature
journal, November 2019
- Mullis, Megan M.; Rambo, Ian M.; Baker, Brett J.
- Frontiers in Microbiology, Vol. 10