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Title: Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere

Abstract

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected super-critical (sc) CO2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO2 harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO2- water separators at a natural scCO2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO2 and N2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. In conclusion, the existence of a microbial ecosystem associated with the McElmo Dome scCO2 reservoir indicates that potential impacts of the deep biosphere on CO2 fate and transport should be taken into consideration as a component of GCS planning and modelling.

Authors:
 [1];  [2];  [3]
+ Show Author Affiliations
  1. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Civil and Environmental Engineering
  2. Singapore-MIT Alliance for Research and Technology (Singapore). Center for Environmental Sensing and Modeling
  3. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Civil and Environmental Engineering; Singapore-MIT Alliance for Research and Technology (Singapore). Center for Environmental Sensing and Modeling
Publication Date:
Research Org.:
Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
Sponsoring Org.:
USDOE; National Institutes of Health (NIH); National Research Foundation of Singapore
OSTI Identifier:
1425642
Grant/Contract Number:  
SC0012555; P30-ES002109
Resource Type:
Accepted Manuscript
Journal Name:
Environmental Microbiology
Additional Journal Information:
Journal Volume: 19; Journal Issue: 6; Journal ID: ISSN 1462-2912
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES

Citation Formats

Freedman, Adam J. E., Tan, BoonFei, and Thompson, Janelle R. Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere. United States: N. p., 2017. Web. doi:10.1111/1462-2920.13706.
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Freedman, Adam J. E., Tan, BoonFei, & Thompson, Janelle R. Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere. United States. https://doi.org/10.1111/1462-2920.13706
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Freedman, Adam J. E., Tan, BoonFei, and Thompson, Janelle R. Tue . "Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere". United States. https://doi.org/10.1111/1462-2920.13706. https://www.osti.gov/servlets/purl/1425642.
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@article{osti_1425642,
title = {Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere},
author = {Freedman, Adam J. E. and Tan, BoonFei and Thompson, Janelle R.},
abstractNote = {Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected super-critical (sc) CO2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO2 harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO2- water separators at a natural scCO2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO2 and N2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. In conclusion, the existence of a microbial ecosystem associated with the McElmo Dome scCO2 reservoir indicates that potential impacts of the deep biosphere on CO2 fate and transport should be taken into consideration as a component of GCS planning and modelling.},
doi = {10.1111/1462-2920.13706},
journal = {Environmental Microbiology},
number = 6,
volume = 19,
place = {United States},
year = {Tue May 02 00:00:00 EDT 2017},
month = {Tue May 02 00:00:00 EDT 2017}
}
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https://doi.org/10.1111/1462-2920.13706
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Works referenced in this record:

The active site of the [FeFe]-hydrogenase from Desulfovibrio desulfuricans. II. Redox properties, light sensitivity and CO-ligand exchange as observed by infrared spectroscopy
journal, December 2005

  • Roseboom, Winfried; De Lacey, Antonio L.; Fernandez, Victor M.
  • JBIC Journal of Biological Inorganic Chemistry, Vol. 11, Issue 1
  • DOI: 10.1007/s00775-005-0040-2

Characterization of bacterial diversity to a depth of 1500 m in the Outokumpu deep borehole, Fennoscandian Shield: Deep terrestrial biodiversity
journal, May 2011

Incomplete Wood-Ljungdahl pathway facilitates one-carbon metabolism in organohalide-respiring Dehalococcoides mccartyi
journal, April 2014

  • Zhuang, W. -Q.; Yi, S.; Bill, M.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 17
  • DOI: 10.1073/pnas.1321542111

Investigating Deep Phylogenetic Relationships among Cyanobacteria and Plastids by Small Subunit rRNA Sequence Analysis
journal, July 1999

Oxidation of primary aliphatic alcohols by Acetobacterium carbinolicum sp. nov., a homoacetogenic anaerobe
journal, December 1984

  • Eichler, Barbara; Schink, Bernhard
  • Archives of Microbiology, Vol. 140, Issue 2-3
  • DOI: 10.1007/BF00454917

Variation in Energy Available to Populations of Subsurface Anaerobes in Response to Geological Carbon Storage
journal, August 2011

  • Kirk, Matthew F.
  • Environmental Science & Technology, Vol. 45, Issue 15
  • DOI: 10.1021/es201279e

Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle
journal, July 2014

  • Nakayama, T.; Kamikawa, R.; Tanifuji, G.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 31
  • DOI: 10.1073/pnas.1405222111

Soil microbial community changes as a result of long-term exposure to a natural CO2 vent
journal, May 2010

  • Oppermann, B. I.; Michaelis, W.; Blumenberg, M.
  • Geochimica et Cosmochimica Acta, Vol. 74, Issue 9
  • DOI: 10.1016/j.gca.2010.02.006

Carbamoylphosphate synthetase activity is essential for the optimal growth of Streptococcus thermophilus in milk
journal, July 2009

Resilience of planktonic and biofilm cultures to supercritical CO2
journal, December 2008

  • Mitchell, Andrew C.; Phillips, Adrienne J.; Hamilton, Marty A.
  • The Journal of Supercritical Fluids, Vol. 47, Issue 2
  • DOI: 10.1016/j.supflu.2008.07.005

Desulfovibrio vulgaris bacterioferritin uses H2O2 as a co-substrate for iron oxidation and reveals DPS-like DNA protection and binding activities
journal, July 2012

  • Timóteo, Cristina G.; Guilherme, Márcia; Penas, Daniela
  • Biochemical Journal, Vol. 446, Issue 1
  • DOI: 10.1042/BJ20111439

A novel arsenate respiring isolate that can utilize aromatic substrates
journal, June 2004

Solubility trapping in formation water as dominant CO2 sink in natural gas fields
journal, April 2009

  • Gilfillan, Stuart M. V.; Lollar, Barbara Sherwood; Holland, Greg
  • Nature, Vol. 458, Issue 7238
  • DOI: 10.1038/nature07852

Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
journal, June 2007

  • Wang, Q.; Garrity, G. M.; Tiedje, J. M.
  • Applied and Environmental Microbiology, Vol. 73, Issue 16
  • DOI: 10.1128/AEM.00062-07

Multiple Rubisco forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle
journal, February 2008

  • Badger, Murray Ronald; Bek, Emily Jane
  • Journal of Experimental Botany, Vol. 59, Issue 7
  • DOI: 10.1093/jxb/erm297

Functional Gene Analysis Suggests Different Acetogen Populations in the Bovine Rumen and Tammar Wallaby Forestomach
journal, October 2010

  • Gagen, E. J.; Denman, S. E.; Padmanabha, J.
  • Applied and Environmental Microbiology, Vol. 76, Issue 23
  • DOI: 10.1128/AEM.01679-10

Desulfosporosinus youngiae sp. nov., a spore-forming, sulfate-reducing bacterium isolated from a constructed wetland treating acid mine drainage
journal, July 2009

  • Lee, Y. -J.; Romanek, C. S.; Wiegel, J.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 11
  • DOI: 10.1099/ijs.0.007336-0

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
journal, November 2014

Denitrification: An Important Pathway for Nitrous Oxide Production in Tropical Mangrove Sediments (Goa, India)
journal, January 2010

  • Fernandes, Sheryl Oliveira; Bharathi, P. A. Loka; Bonin, Patricia C.
  • Journal of Environment Quality, Vol. 39, Issue 4
  • DOI: 10.2134/jeq2009.0477

The noble gas geochemistry of natural CO2 gas reservoirs from the Colorado Plateau and Rocky Mountain provinces, USA
journal, February 2008

  • Gilfillan, Stuart M. V.; Ballentine, Chris J.; Holland, Greg
  • Geochimica et Cosmochimica Acta, Vol. 72, Issue 4
  • DOI: 10.1016/j.gca.2007.10.009

Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit
journal, August 2013

  • Preheim, Sarah P.; Perrotta, Allison R.; Martin-Platero, Antonio M.
  • Applied and Environmental Microbiology, Vol. 79, Issue 21
  • DOI: 10.1128/AEM.00342-13

Correlating carbon monoxide oxidation with cox genes in the abundant Marine Roseobacter Clade
journal, November 2010

Comparison between geochemical and biological estimates of subsurface microbial activities
journal, January 1994

  • Phelps, T. J.; Murphy, E. M.; Pfiffner, S. M.
  • Microbial Ecology, Vol. 28, Issue 3
  • DOI: 10.1007/BF00662027

Influence of Acidic pH on Hydrogen and Acetate Production by an Electrosynthetic Microbiome
journal, October 2014

  • LaBelle, Edward V.; Marshall, Christopher W.; Gilbert, Jack A.
  • PLoS ONE, Vol. 9, Issue 10, Article No. e109935
  • DOI: 10.1371/journal.pone.0109935

Fast and sensitive protein alignment using DIAMOND
journal, November 2014

  • Buchfink, Benjamin; Xie, Chao; Huson, Daniel H.
  • Nature Methods, Vol. 12, Issue 1
  • DOI: 10.1038/nmeth.3176

Carbon sequestration
journal, August 2007

  • Lal, Rattan
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 363, Issue 1492
  • DOI: 10.1098/rstb.2007.2185

Characterization of the [NiFe] Hydrogenase from the Sulfate ReducerDesulfovibrio vulgarisHildenborough
journal, November 1997

  • Romão, Célia V.; Pereira, Inês A. C.; Xavier, António V.
  • Biochemical and Biophysical Research Communications, Vol. 240, Issue 1
  • DOI: 10.1006/bbrc.1997.7598

Long-term Operation of Microbial Electrosynthesis Systems Improves Acetate Production by Autotrophic Microbiomes
journal, May 2013

  • Marshall, Christopher W.; Ross, Daniel E.; Fichot, Erin B.
  • Environmental Science & Technology, Vol. 47, Issue 11, p. 6023-6029
  • DOI: 10.1021/es400341b

Sterilization using high-pressure carbon dioxide
journal, October 2006

  • Zhang, Jian; Davis, Thomas A.; Matthews, Michael A.
  • The Journal of Supercritical Fluids, Vol. 38, Issue 3
  • DOI: 10.1016/j.supflu.2005.05.005

Microbial Growth under Supercritical CO 2
journal, February 2015

  • Peet, Kyle C.; Freedman, Adam J. E.; Hernandez, Hector H.
  • Applied and Environmental Microbiology, Vol. 81, Issue 8
  • DOI: 10.1128/AEM.03162-14

Deep subsurface microbial processes
journal, January 1995

  • Lovley, Derek R.; Chapelle, Francis H.
  • Reviews of Geophysics, Vol. 33, Issue 3
  • DOI: 10.1029/95RG01305

UPARSE: highly accurate OTU sequences from microbial amplicon reads
journal, August 2013

Arsenic in an As-contaminated abandoned mine was mobilized from fern-rhizobium to frond-bacteria via the ars gene
journal, October 2010

  • Chang, Jin-Soo; Lee, Se-Yong; Kim, Kyoung-Woong
  • Biotechnology and Bioprocess Engineering, Vol. 15, Issue 5
  • DOI: 10.1007/s12257-009-3154-5

Complete genome sequence of Oscillibacter valericigenes Sjm18-20T (=NBRC 101213T)
journal, July 2012

  • Katano, Yoko; Fujinami, Shun; Kawakoshi, Akatsuki
  • Standards in Genomic Sciences, Vol. 6, Issue 3
  • DOI: 10.4056/sigs.2826118

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
journal, November 2012

  • Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1219

Potential impact of CO2 storage on subsurface microbial ecosystems and implications for groundwater quality
journal, January 2011

Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla: High CO
journal, April 2015

  • Emerson, Joanne B.; Thomas, Brian C.; Alvarez, Walter
  • Environmental Microbiology, Vol. 18, Issue 6
  • DOI: 10.1111/1462-2920.12817

Oil Field Souring Control by Nitrate-Reducing Sulfurospirillum spp. That Outcompete Sulfate-Reducing Bacteria for Organic Electron Donors
journal, February 2007

  • Hubert, C.; Voordouw, G.
  • Applied and Environmental Microbiology, Vol. 73, Issue 8
  • DOI: 10.1128/AEM.02332-06

Interspecies electron transfer in methanogenic propionate degrading consortia
journal, March 2004

Microbial syntrophy: interaction for the common good
journal, May 2013

  • Morris, Brandon E. L.; Henneberger, Ruth; Huber, Harald
  • FEMS Microbiology Reviews, Vol. 37, Issue 3
  • DOI: 10.1111/1574-6976.12019

Cysteine-mediated electron transfer in syntrophic acetate oxidation by cocultures of Geobacter sulfurreducens and Wolinella succinogenes
journal, July 2002

  • Kaden, Jan; S. Galushko, Alexander; Schink, Bernhard
  • Archives of Microbiology, Vol. 178, Issue 1
  • DOI: 10.1007/s00203-002-0425-3

Microbial diversity and methanogenic activity of Antrim Shale formation waters from recently fractured wells
journal, January 2013

Effective terminal sterilization using supercritical carbon dioxide
journal, June 2006

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
journal, May 2013

  • Albertsen, Mads; Hugenholtz, Philip; Skarshewski, Adam
  • Nature Biotechnology, Vol. 31, Issue 6
  • DOI: 10.1038/nbt.2579

Saturated CO 2 inhibits microbial processes in CO 2 -vented deep-sea sediments
journal, January 2013

Retentive Memory of Bacteria: Long-Term Regulation of Dehalorespiration in Sulfurospirillum multivorans
journal, December 2008

  • John, M.; Rubick, R.; Schmitz, R. P. H.
  • Journal of Bacteriology, Vol. 191, Issue 5
  • DOI: 10.1128/JB.00597-08

Supercritical carbon dioxide inactivation of Escherichia coli and Saccharomyces cerevisiae in different growth stages
journal, March 2012

  • Ortuño, Carmen; Martínez-Pastor, María Teresa; Mulet, Antonio
  • The Journal of Supercritical Fluids, Vol. 63
  • DOI: 10.1016/j.supflu.2011.12.022

An oligarchic microbial assemblage in the anoxic bottom waters of a volcanic subglacial lake
journal, December 2008

  • Gaidos, Eric; Marteinsson, Viggo; Thorsteinsson, Thorsteinn
  • The ISME Journal, Vol. 3, Issue 4
  • DOI: 10.1038/ismej.2008.124

Microbial diversity in long-term water-flooded oil reservoirs with different in situ temperatures in China
journal, October 2012

  • Zhang, Fan; She, Yue-Hui; Chai, Lu-Jun
  • Scientific Reports, Vol. 2, Issue 1
  • DOI: 10.1038/srep00760

Isolation and characterisation of sulfur-oxidising bacteria, including strains of Rhizobium, from calcareous sandy soils and their effects on nutrient uptake and growth of maize (Zea mays L.)
journal, January 2006

  • El-Tarabily, Khaled A.; Soaud, Abdou A.; Saleh, Maher E.
  • Australian Journal of Agricultural Research, Vol. 57, Issue 1
  • DOI: 10.1071/AR04237

Lithotrophic growth ofSulfurospirillum deleyianum with sulfide as electron donor coupled to respiratory reduction of nitrate to ammonia
journal, September 1995

  • Eisenmann, Effi; Beuerle, Joachim; Sulger, Klaus
  • Archives of Microbiology, Vol. 164, Issue 3
  • DOI: 10.1007/BF02529969

Prokaryotic carbonic anhydrases
journal, October 2000

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
journal, August 2009

  • Hamady, Micah; Lozupone, Catherine; Knight, Rob
  • The ISME Journal, Vol. 4, Issue 1
  • DOI: 10.1038/ismej.2009.97

Involvement of formate as an interspecies electron carrier in a syntrophic acetate-oxidizing anaerobic microorganism in coculture with methanogens
journal, January 2001

Bacterioplankton Community Shifts in an Arctic Lake Correlate with Seasonal Changes in Organic Matter Source
journal, April 2003

Hydrogen as an electron donor for sulfate-reducing bacteria in slurries of salt marsh sediment
journal, December 1981

  • Nedwell, David B.; Banat, Ibrahim M.
  • Microbial Ecology, Vol. 7, Issue 4
  • DOI: 10.1007/BF02341425

Non-thermal bacterial inactivation with dense CO2
journal, October 2003

  • Spilimbergo, S.; Bertucco, A.
  • Biotechnology and Bioengineering, Vol. 84, Issue 6
  • DOI: 10.1002/bit.10783

Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota
journal, April 2010

Fracture Sealing with Microbially-Induced Calcium Carbonate Precipitation: A Field Study
journal, March 2016

  • Phillips, Adrienne J.; Cunningham, Alfred B.; Gerlach, Robin
  • Environmental Science & Technology, Vol. 50, Issue 7
  • DOI: 10.1021/acs.est.5b05559

Microbial Transformations of Arsenic in the Environment: From Soda Lakes to Aquifers
journal, April 2006

Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments
journal, August 2012

  • Engelhardt, Tim; Sahlberg, Monika; Cypionka, Heribert
  • The ISME Journal, Vol. 7, Issue 1
  • DOI: 10.1038/ismej.2012.92

Monitoring of the microbial community composition in deep subsurface saline aquifers during CO2 storage in Ketzin, Germany
journal, January 2011

Changes in the deep subsurface microbial biosphere resulting from a field-scale CO2 geosequestration experiment
journal, May 2014

Stimulation of growth by proteorhodopsin phototrophy involves regulation of central metabolic pathways in marine planktonic bacteria
journal, August 2014

  • Palovaara, J.; Akram, N.; Baltar, F.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 35
  • DOI: 10.1073/pnas.1402617111

Comparison of denitrification by Pseudomonas stutzeri, Pseudomonas aeruginosa, and Paracoccus denitrificans.
journal, January 1983

Reductive Dechlorination of Tetrachloroethene to Ethene by a Two-Component Enzyme Pathway
journal, April 1998

Note: Sulfurospirillum barnesii sp. nov. and Sulfurospirillum arsenophilum sp. nov., new members of the Sulfurospirillum clade of the  -Proteobacteria
journal, July 1999

  • Stolz, J. F.; Ellis, D. J.; Blum, J. S.
  • International Journal of Systematic Bacteriology, Vol. 49, Issue 3
  • DOI: 10.1099/00207713-49-3-1177
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