skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Active sulfur cycling in the terrestrial deep subsurface

Abstract

The deep terrestrial subsurface remains an environment where there is limited understanding of the extant microbial metabolisms. At Olkiluoto, Finland, a deep geological repository is under construction for the final storage of spent nuclear fuel. It is therefore critical to evaluate the potential impact microbial metabolism, including sulfide generation, could have upon the safety of the repository. As such, we investigated a deep groundwater where sulfate is present, but groundwater geochemistry suggests limited microbial sulfate-reducing activity. Examination of the microbial community at the genome-level revealed microorganisms with the metabolic capacity for both oxidative and reductive sulfur transformations. Deltaproteobacteria are shown to have the genetic capacity for sulfate reduction and possibly sulfur disproportionation, while Rhizobiaceae, Rhodocyclaceae, Sideroxydans, and Sulfurimonas oxidize reduced sulfur compounds. Further examination of the proteome confirmed an active sulfur cycle, serving for microbial energy generation and growth. Our results reveal that this sulfide-poor groundwater harbors an active microbial community of sulfate-reducing and sulfide-oxidizing bacteria, together mediating a sulfur cycle that remained undetected by geochemical monitoring alone. The ability of sulfide-oxidizing bacteria to limit the accumulation of sulfide was further demonstrated in groundwater incubations and highlights a potential sink for sulfide that could be beneficial for geological repository safety.

Authors:
ORCiD logo [1];  [2];  [3]; ORCiD logo [3];  [4]; ORCiD logo [4]; ORCiD logo [5];  [6]; ORCiD logo [6]
  1. Ecole Polytechnique Federale Lausanne (Switzlerland); Univ. of Calgary, AB (Canada)
  2. Posiva Oy, Eurajoki (Finland)
  3. KTH Royal Inst. of Technology, Stockholm (Sweden)
  4. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Chemical Sciences Division
  5. (Bob) L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Chemical Sciences Division
  6. Ecole Polytechnique Federale Lausanne (Switzlerland)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Sponsoring Org.:
Posiva Oy; The Census of Deep Life within the Deep Carbon Observatory; USDOE Office of Science (SC)
OSTI Identifier:
1606636
Grant/Contract Number:  
AC05-00OR22725; 2015-06-17; AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
The ISME Journal
Additional Journal Information:
Journal Volume: 14; Journal Issue: 5; Journal ID: ISSN 1751-7362
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 58 GEOSCIENCES; Biogeochemistry; Ecosystem ecology; Environmental sciences; Microbial ecology

Citation Formats

Bell, Emma, Lamminmäki, Tiina, Alneberg, Johannes, Andersson, Anders F., Qian, Chen, Xiong, Weili, Hettich, Robert, Frutschi, Manon, and Bernier-Latmani, Rizlan. Active sulfur cycling in the terrestrial deep subsurface. United States: N. p., 2020. Web. https://doi.org/10.1038/s41396-020-0602-x.
Bell, Emma, Lamminmäki, Tiina, Alneberg, Johannes, Andersson, Anders F., Qian, Chen, Xiong, Weili, Hettich, Robert, Frutschi, Manon, & Bernier-Latmani, Rizlan. Active sulfur cycling in the terrestrial deep subsurface. United States. https://doi.org/10.1038/s41396-020-0602-x
Bell, Emma, Lamminmäki, Tiina, Alneberg, Johannes, Andersson, Anders F., Qian, Chen, Xiong, Weili, Hettich, Robert, Frutschi, Manon, and Bernier-Latmani, Rizlan. Tue . "Active sulfur cycling in the terrestrial deep subsurface". United States. https://doi.org/10.1038/s41396-020-0602-x. https://www.osti.gov/servlets/purl/1606636.
@article{osti_1606636,
title = {Active sulfur cycling in the terrestrial deep subsurface},
author = {Bell, Emma and Lamminmäki, Tiina and Alneberg, Johannes and Andersson, Anders F. and Qian, Chen and Xiong, Weili and Hettich, Robert and Frutschi, Manon and Bernier-Latmani, Rizlan},
abstractNote = {The deep terrestrial subsurface remains an environment where there is limited understanding of the extant microbial metabolisms. At Olkiluoto, Finland, a deep geological repository is under construction for the final storage of spent nuclear fuel. It is therefore critical to evaluate the potential impact microbial metabolism, including sulfide generation, could have upon the safety of the repository. As such, we investigated a deep groundwater where sulfate is present, but groundwater geochemistry suggests limited microbial sulfate-reducing activity. Examination of the microbial community at the genome-level revealed microorganisms with the metabolic capacity for both oxidative and reductive sulfur transformations. Deltaproteobacteria are shown to have the genetic capacity for sulfate reduction and possibly sulfur disproportionation, while Rhizobiaceae, Rhodocyclaceae, Sideroxydans, and Sulfurimonas oxidize reduced sulfur compounds. Further examination of the proteome confirmed an active sulfur cycle, serving for microbial energy generation and growth. Our results reveal that this sulfide-poor groundwater harbors an active microbial community of sulfate-reducing and sulfide-oxidizing bacteria, together mediating a sulfur cycle that remained undetected by geochemical monitoring alone. The ability of sulfide-oxidizing bacteria to limit the accumulation of sulfide was further demonstrated in groundwater incubations and highlights a potential sink for sulfide that could be beneficial for geological repository safety.},
doi = {10.1038/s41396-020-0602-x},
journal = {The ISME Journal},
number = 5,
volume = 14,
place = {United States},
year = {2020},
month = {2}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

Nitrate reduction in sulfate-reducing bacteria
journal, June 2016


Sulfur Oxidation Genes in Diverse Deep-Sea Viruses
journal, May 2014


Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth
journal, October 2008


eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
journal, November 2015

  • Huerta-Cepas, Jaime; Szklarczyk, Damian; Forslund, Kristoffer
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1248

Complete genome sequence of Desulfocapsa sulfexigens, a marine deltaproteobacterium specialized in disproportionating inorganic sulfur compounds
journal, April 2013

  • Finster, Kai Waldemar; Kjeldsen, Kasper Urup; Kube, Michael
  • Standards in Genomic Sciences, Vol. 8, Issue 1
  • DOI: 10.4056/sigs.3777412

Prokaryotic sulfur oxidation
journal, June 2005

  • Friedrich, Cornelius G.; Bardischewsky, Frank; Rother, Dagmar
  • Current Opinion in Microbiology, Vol. 8, Issue 3
  • DOI: 10.1016/j.mib.2005.04.005

A minimalistic microbial food web in an excavated deep subsurface clay rock
journal, November 2015

  • Bagnoud, Alexandre; de Bruijn, Ino; Andersson, Anders F.
  • FEMS Microbiology Ecology, Vol. 92, Issue 1
  • DOI: 10.1093/femsec/fiv138

Molecular mechanism of energy conservation in polysulfide respiration
journal, June 2008

  • Jormakka, Mika; Yokoyama, Ken; Yano, Takahiro
  • Nature Structural & Molecular Biology, Vol. 15, Issue 7
  • DOI: 10.1038/nsmb.1434

The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration
journal, June 2009

  • Marcia, M.; Ermler, U.; Peng, G.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 24
  • DOI: 10.1073/pnas.0904165106

Active Microbial Communities Inhabit Sulphate-Methane Interphase in Deep Bedrock Fracture Fluids in Olkiluoto, Finland
journal, January 2015

  • Bomberg, Malin; Nyyssönen, Mari; Pitkänen, Petteri
  • BioMed Research International, Vol. 2015
  • DOI: 10.1155/2015/979530

Pathways and Microbiology of Thiosulfate Transformations and Sulfate Reduction in a Marine Sediment (Kattegat, Denmark) †
journal, January 1991


Biological reduction of uranium coupled with oxidation of ammonium by Acidimicrobiaceae bacterium A6 under iron reducing conditions
journal, November 2015


Microbial diversity involved in iron and cryptic sulfur cycling in the ferruginous, low-sulfate waters of Lake Pavin
journal, February 2019


Dominance of sulfur-fueled iron oxide reduction in low-sulfate freshwater sediments
journal, April 2015

  • Hansel, Colleen M.; Lentini, Chris J.; Tang, Yuanzhi
  • The ISME Journal, Vol. 9, Issue 11
  • DOI: 10.1038/ismej.2015.50

Rapid Reactivation of Deep Subsurface Microbes in the Presence of C-1 Compounds
journal, February 2015


Isotope fractionation and sulfur metabolism by pure and enrichment cultures of elemental sulfur-disproportionating bacteria
journal, March 1998


Disproportionation of elemental sulfur by haloalkaliphilic bacteria from soda lakes
journal, September 2013


The “bacterial heterodisulfide” DsrC is a key protein in dissimilatory sulfur metabolism
journal, July 2014

  • Venceslau, S. S.; Stockdreher, Y.; Dahl, C.
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1837, Issue 7
  • DOI: 10.1016/j.bbabio.2014.03.007

Biogenesis of cbb3-type cytochrome c oxidase in Rhodobacter capsulatus
journal, June 2012

  • Ekici, Seda; Pawlik, Grzegorz; Lohmeyer, Eva
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1817, Issue 6
  • DOI: 10.1016/j.bbabio.2011.10.011

WebMGA: a customizable web server for fast metagenomic sequence analysis
journal, September 2011


Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones
journal, December 2011

  • Grote, J.; Schott, T.; Bruckner, C. G.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 2
  • DOI: 10.1073/pnas.1111262109

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments
journal, March 2017

  • Hernsdorf, Alex W.; Amano, Yuki; Miyakawa, Kazuya
  • The ISME Journal, Vol. 11, Issue 8
  • DOI: 10.1038/ismej.2017.39

Disguised as a Sulfate Reducer: Growth of the Deltaproteobacterium Desulfurivibrio alkaliphilus by Sulfide Oxidation with Nitrate
journal, July 2017


cbb3-Type Cytochrome c Oxidases, Aerobic Respiratory Enzymes, Impact the Anaerobic Life of Pseudomonas aeruginosa PAO1
journal, September 2014

  • Hamada, M.; Toyofuku, M.; Miyano, T.
  • Journal of Bacteriology, Vol. 196, Issue 22
  • DOI: 10.1128/JB.01978-14

Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment
journal, September 2017


Stable Sulfur and Oxygen Isotope Fractionation of Anoxic Sulfide Oxidation by Two Different Enzymatic Pathways
journal, July 2014

  • Poser, Alexander; Vogt, Carsten; Knöller, Kay
  • Environmental Science & Technology, Vol. 48, Issue 16
  • DOI: 10.1021/es404808r

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences
journal, February 2016

  • Kanehisa, Minoru; Sato, Yoko; Morishima, Kanae
  • Journal of Molecular Biology, Vol. 428, Issue 4
  • DOI: 10.1016/j.jmb.2015.11.006

Geochemical evidence for cryptic sulfur cycling in salt marsh sediments
journal, November 2016

  • Mills, Jennifer V.; Antler, Gilad; Turchyn, Alexandra V.
  • Earth and Planetary Science Letters, Vol. 453
  • DOI: 10.1016/j.epsl.2016.08.001

The biomass and biodiversity of the continental subsurface
journal, September 2018


KEGG for integration and interpretation of large-scale molecular data sets
journal, November 2011

  • Kanehisa, M.; Goto, S.; Sato, Y.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr988

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015

  • Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.
  • Genome Research, Vol. 25, Issue 7
  • DOI: 10.1101/gr.186072.114

Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations
journal, October 2015

  • Wu, Xiaofen; Holmfeldt, Karin; Hubalek, Valerie
  • The ISME Journal, Vol. 10, Issue 5
  • DOI: 10.1038/ismej.2015.185

A Cryptic Sulfur Cycle in Oxygen-Minimum-Zone Waters off the Chilean Coast
journal, November 2010


Sulphate-controlled Diversity of Subterranean Microbial Communities over Depth in Deep Groundwater with Opposing Gradients of Sulphate and Methane
journal, July 2014


Sulfur isotope fractionation during bacterial reduction and disproportionation of thiosulfate and sulfite
journal, August 1998

  • Habicht, Kirsten S.; Canfield, Donald E.; Rethmeier, J̈org
  • Geochimica et Cosmochimica Acta, Vol. 62, Issue 15
  • DOI: 10.1016/S0016-7037(98)00167-7

A cryptic sulfur cycle driven by iron in the methane zone of marine sediment (Aarhus Bay, Denmark)
journal, June 2011

  • Holmkvist, Lars; Ferdelman, Timothy G.; Jørgensen, Bo Barker
  • Geochimica et Cosmochimica Acta, Vol. 75, Issue 12
  • DOI: 10.1016/j.gca.2011.03.033

Acetate Activates Deep Subsurface Fracture Fluid Microbial Communities in Olkiluoto, Finland
journal, November 2018


Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2T, a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes
journal, September 2016

  • Melton, Emily Denise; Sorokin, Dimitry Y.; Overmars, Lex
  • Standards in Genomic Sciences, Vol. 11, Issue 1
  • DOI: 10.1186/s40793-016-0184-4

H2-fuelled microbial metabolism in Opalinus Clay
journal, June 2019


Sulfur-Driven Iron Reduction Coupled to Anaerobic Ammonium Oxidation
journal, June 2017


Microbial life in deep granitic rock
journal, July 1997


Biogeochemical Cycling by a Low-Diversity Microbial Community in Deep Groundwater
journal, September 2018


Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock
journal, October 2016

  • Bagnoud, Alexandre; Chourey, Karuna; Hettich, Robert L.
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms12770

Disproportionation of inorganic sulfur compounds by the sulfate-reducing bacterium Desulfocapsa thiozymogenes gen. nov., sp. nov.
journal, September 1996

  • Janssen, P. H.; Schuhmann, Alexandra; Bak, F.
  • Archives of Microbiology, Vol. 166, Issue 3
  • DOI: 10.1007/s002030050374

Distribution of culturable microorganisms in Fennoscandian Shield groundwater
journal, February 2002


HydDB: A web tool for hydrogenase classification and analysis
journal, September 2016

  • Søndergaard, Dan; Pedersen, Christian N. S.; Greening, Chris
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep34212

Heterotrophic Communities Supplied by Ancient Organic Carbon Predominate in Deep Fennoscandian Bedrock Fluids
journal, September 2014


Binning metagenomic contigs by coverage and composition
journal, September 2014

  • Alneberg, Johannes; Bjarnason, Brynjar Smári; de Bruijn, Ino
  • Nature Methods, Vol. 11, Issue 11
  • DOI: 10.1038/nmeth.3103

Oxygen minimum zone cryptic sulfur cycling sustained by offshore transport of key sulfur oxidizing bacteria
journal, April 2018

  • Callbeck, Cameron M.; Lavik, Gaute; Ferdelman, Timothy G.
  • Nature Communications, Vol. 9, Issue 1
  • DOI: 10.1038/s41467-018-04041-x

Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids
journal, January 2016

  • Purkamo, Lotta; Bomberg, Malin; Kietäväinen, Riikka
  • Biogeosciences, Vol. 13, Issue 10
  • DOI: 10.5194/bg-13-3091-2016

Sulfide-Quinone Reductase from Rhodobacter capsulatus: Requirement for Growth, Periplasmic Localization, and Extension of Gene Sequence Analysis †
journal, January 1999


Intensive cryptic microbial iron cycling in the low iron water column of the meromictic Lake Cadagno: A cryptic microbial iron cycle
journal, November 2016

  • Berg, Jasmine S.; Michellod, Dolma; Pjevac, Petra
  • Environmental Microbiology, Vol. 18, Issue 12
  • DOI: 10.1111/1462-2920.13587

IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering
journal, August 2009

  • Ma, Ze-Qiang; Dasari, Surendra; Chambers, Matthew C.
  • Journal of Proteome Research, Vol. 8, Issue 8
  • DOI: 10.1021/pr900360j

Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield
journal, August 2013

  • Nyyssönen, Mari; Hultman, Jenni; Ahonen, Lasse
  • The ISME Journal, Vol. 8, Issue 1
  • DOI: 10.1038/ismej.2013.125

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
journal, November 2018


Sulfide production and oxidation by heterotrophic bacteria under aerobic conditions
journal, August 2017


Potential for primary productivity in a globally-distributed bacterial phototroph
journal, March 2018


Electron Shuttles Enhance Anaerobic Ammonium Oxidation Coupled to Iron(III) Reduction
journal, August 2016

  • Zhou, Guo-Wei; Yang, Xiao-Ru; Li, Hu
  • Environmental Science & Technology, Vol. 50, Issue 17
  • DOI: 10.1021/acs.est.6b02077

Identifying and Quantifying the Intermediate Processes during Nitrate-Dependent Iron(II) Oxidation
journal, April 2018

  • Jamieson, James; Prommer, Henning; Kaksonen, Anna H.
  • Environmental Science & Technology, Vol. 52, Issue 10
  • DOI: 10.1021/acs.est.8b01122

Enzymatic and Genetic Characterization of Carbon and Energy Metabolisms by Deep-Sea Hydrothermal Chemolithoautotrophic Isolates of Epsilonproteobacteria
journal, November 2005


An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers
journal, November 2016

  • Lau, Maggie C. Y.; Kieft, Thomas L.; Kuloyo, Olukayode
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 49
  • DOI: 10.1073/pnas.1612244113

The MetaCyc database of metabolic pathways and enzymes
journal, October 2017

  • Caspi, Ron; Billington, Richard; Fulcher, Carol A.
  • Nucleic Acids Research, Vol. 46, Issue D1
  • DOI: 10.1093/nar/gkx935

Gene expression in the deep biosphere
journal, June 2013

  • Orsi, William D.; Edgcomb, Virginia P.; Christman, Glenn D.
  • Nature, Vol. 499, Issue 7457
  • DOI: 10.1038/nature12230

MyriMatch:  Highly Accurate Tandem Mass Spectral Peptide Identification by Multivariate Hypergeometric Analysis
journal, February 2007

  • Tabb, David L.; Fernando, Christopher G.; Chambers, Matthew C.
  • Journal of Proteome Research, Vol. 6, Issue 2
  • DOI: 10.1021/pr0604054

Nitrite reductase activity of sulphate-reducing bacteria prevents their inhibition by nitrate-reducing, sulphide-oxidizing bacteria
journal, July 2003


Slow Microbial Life in the Seabed
journal, January 2016


Sulfate formation via ATP sulfurylase in thiosulfate- and sulfite-disproportionating bacteria
journal, February 1989

  • Kr�mer, Michael; Cypionka, Heribert
  • Archives of Microbiology, Vol. 151, Issue 3
  • DOI: 10.1007/BF00413135

Weighing the deep continental biosphere
journal, September 2013


Microbiological disproportionation of inorganic sulfur compounds
journal, August 2008


Methanogenic and Sulphate-Reducing Microbial Communities in Deep Groundwater of Crystalline Rock Fractures in Olkiluoto, Finland
journal, December 2012