DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification

Abstract

Competition between nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) for resources in anoxic environments is generally thought to be governed largely by thermodynamics. It is now recognized that intermediates of nitrogen and sulfur cycling (e.g., hydrogen sulfide, nitrite, etc.) can also directly impact NRB and SRB activities in freshwater, wastewater, and sediment and therefore may play important roles in competitive interactions. Here, through comparative transcriptomic and metabolomic analyses, we have uncovered mechanisms of hydrogen sulfide- and cysteine-mediated inhibition of nitrate respiratory growth for the NRB Intrasporangium calvum C5. Specifically, the systems analysis predicted that cysteine and hydrogen sulfide inhibit growth of I. calvum C5 by disrupting distinct steps across multiple pathways, including branched-chain amino acid (BCAA) biosynthesis, utilization of specific carbon sources, and cofactor metabolism. We have validated these predictions by demonstrating that complementation with BCAAs and specific carbon sources relieves the growth inhibitory effects of cysteine and hydrogen sulfide. We discuss how these mechanistic insights give new context to the interplay and stratification of NRB and SRB in diverse environments. IMPORTANCE Nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) colonize diverse anoxic environments, including soil subsurface, groundwater, and wastewater. NRB and SRB compete for resources, and their interplay has majormore » implications on the global cycling of nitrogen and sulfur species, with undesirable outcomes in some contexts. For instance, the removal of reactive nitrogen species by NRB is desirable for wastewater treatment, but in agricultural soils, NRB can drive the conversion of nitrates from fertilizers into nitrous oxide, a potent greenhouse gas. Similarly, the hydrogen sulfide produced by SRB can help sequester and immobilize toxic heavy metals but is undesirable in oil wells where competition between SRB and NRB has been exploited to suppress hydrogen sulfide production. By characterizing how reduced sulfur compounds inhibit growth and activity of NRB, we have gained systems-level and mechanistic insight into the interplay of these two important groups of organisms and drivers of their stratification in diverse environments.« less

Authors:
 [1];  [1];  [2];  [3];  [4];  [5];  [5];  [3]; ORCiD logo [1]; ORCiD logo [4];  [6];  [5]; ORCiD logo [1]
  1. Institute for Systems Biology, Seattle, WA (United States); Univ. of Washington, Seattle, WA (United States)
  2. The Scripps Research Inst., La Jolla, CA (United States); State Univ. of New York (SUNY), Syracuse, NY (United States)
  3. Institute for Systems Biology, Seattle, WA (United States)
  4. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  5. The Scripps Research Inst., La Jolla, CA (United States)
  6. Univ. of Washington, Seattle, WA (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF)
OSTI Identifier:
1767862
Alternate Identifier(s):
OSTI ID: 1773755
Grant/Contract Number:  
AC05-00OR22725; AC02-05CH11231; OCE-1558924; CBET-1606206; MCB-1518261; DBI-1565166; MCB-1616955
Resource Type:
Accepted Manuscript
Journal Name:
mSystems
Additional Journal Information:
Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2379-5077
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; cysteine; denitrification; environmental microbiology; hydrogen sulfide; metabolomics; microbial ecology; nitrate-reducing bacteria; systems biology; transcriptomics

Citation Formats

Otwell, Anne E., Carr, Alex V., Majumder, Erica L. W., Ruiz, Maryann K., Wilpiszeski, Regina L., Hoang, Linh T., Webb, Bill, Turkarslan, Serdar, Gibbons, Sean M., Elias, Dwayne A., Stahl, David A., Siuzdak, Gary, and Baliga, Nitin S. Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification. United States: N. p., 2021. Web. doi:10.1128/msystems.01025-20.
Otwell, Anne E., Carr, Alex V., Majumder, Erica L. W., Ruiz, Maryann K., Wilpiszeski, Regina L., Hoang, Linh T., Webb, Bill, Turkarslan, Serdar, Gibbons, Sean M., Elias, Dwayne A., Stahl, David A., Siuzdak, Gary, & Baliga, Nitin S. Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification. United States. https://doi.org/10.1128/msystems.01025-20
Otwell, Anne E., Carr, Alex V., Majumder, Erica L. W., Ruiz, Maryann K., Wilpiszeski, Regina L., Hoang, Linh T., Webb, Bill, Turkarslan, Serdar, Gibbons, Sean M., Elias, Dwayne A., Stahl, David A., Siuzdak, Gary, and Baliga, Nitin S. Tue . "Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification". United States. https://doi.org/10.1128/msystems.01025-20. https://www.osti.gov/servlets/purl/1767862.
@article{osti_1767862,
title = {Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification},
author = {Otwell, Anne E. and Carr, Alex V. and Majumder, Erica L. W. and Ruiz, Maryann K. and Wilpiszeski, Regina L. and Hoang, Linh T. and Webb, Bill and Turkarslan, Serdar and Gibbons, Sean M. and Elias, Dwayne A. and Stahl, David A. and Siuzdak, Gary and Baliga, Nitin S.},
abstractNote = {Competition between nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) for resources in anoxic environments is generally thought to be governed largely by thermodynamics. It is now recognized that intermediates of nitrogen and sulfur cycling (e.g., hydrogen sulfide, nitrite, etc.) can also directly impact NRB and SRB activities in freshwater, wastewater, and sediment and therefore may play important roles in competitive interactions. Here, through comparative transcriptomic and metabolomic analyses, we have uncovered mechanisms of hydrogen sulfide- and cysteine-mediated inhibition of nitrate respiratory growth for the NRB Intrasporangium calvum C5. Specifically, the systems analysis predicted that cysteine and hydrogen sulfide inhibit growth of I. calvum C5 by disrupting distinct steps across multiple pathways, including branched-chain amino acid (BCAA) biosynthesis, utilization of specific carbon sources, and cofactor metabolism. We have validated these predictions by demonstrating that complementation with BCAAs and specific carbon sources relieves the growth inhibitory effects of cysteine and hydrogen sulfide. We discuss how these mechanistic insights give new context to the interplay and stratification of NRB and SRB in diverse environments. IMPORTANCE Nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) colonize diverse anoxic environments, including soil subsurface, groundwater, and wastewater. NRB and SRB compete for resources, and their interplay has major implications on the global cycling of nitrogen and sulfur species, with undesirable outcomes in some contexts. For instance, the removal of reactive nitrogen species by NRB is desirable for wastewater treatment, but in agricultural soils, NRB can drive the conversion of nitrates from fertilizers into nitrous oxide, a potent greenhouse gas. Similarly, the hydrogen sulfide produced by SRB can help sequester and immobilize toxic heavy metals but is undesirable in oil wells where competition between SRB and NRB has been exploited to suppress hydrogen sulfide production. By characterizing how reduced sulfur compounds inhibit growth and activity of NRB, we have gained systems-level and mechanistic insight into the interplay of these two important groups of organisms and drivers of their stratification in diverse environments.},
doi = {10.1128/msystems.01025-20},
journal = {mSystems},
number = 1,
volume = 6,
place = {United States},
year = {Tue Feb 09 00:00:00 EST 2021},
month = {Tue Feb 09 00:00:00 EST 2021}
}

Works referenced in this record:

Using Thermodynamics to Predict the Outcomes of Nitrate-Based Oil Reservoir Souring Control Interventions
journal, December 2017


Mutant phenotypes for thousands of bacterial genes of unknown function
journal, May 2018


Denitrification and environmental factors influencing nitrate removal in Guaymas Basin hydrothermally altered sediments
journal, January 2012

  • Bowles, Marshall W.; Nigro, Lisa M.; Teske, Andreas P.
  • Frontiers in Microbiology, Vol. 3
  • DOI: 10.3389/fmicb.2012.00377

Sulfide Homeostasis and Nitroxyl Intersect via Formation of Reactive Sulfur Species in Staphylococcus aureus
journal, June 2017


STAR: ultrafast universal RNA-seq aligner
journal, October 2012


Systems biology guided by XCMS Online metabolomics
journal, April 2017

  • Huan, Tao; Forsberg, Erica M.; Rinehart, Duane
  • Nature Methods, Vol. 14, Issue 5
  • DOI: 10.1038/nmeth.4260

Inhibition by sulfide of nitric and nitrous oxide reduction by denitrifying Pseudomonas fluorescens.
journal, January 1980


Boruta – A System for Feature Selection
journal, January 2010

  • Kursa, Miron B.; Jankowski, Aleksander; Rudnicki, Witold R.
  • Fundamenta Informaticae, Vol. 101, Issue 4
  • DOI: 10.3233/FI-2010-288

Glutathione analogs in prokaryotes
journal, May 2013


Microbial Ecology of the Dark Ocean above, at, and below the Seafloor
journal, June 2011

  • Orcutt, B. N.; Sylvan, J. B.; Knab, N. J.
  • Microbiology and Molecular Biology Reviews, Vol. 75, Issue 2
  • DOI: 10.1128/MMBR.00039-10

Selective carbon sources influence the end products of microbial nitrate respiration
journal, May 2020


Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses
journal, June 2014

  • Gowda, Harsha; Ivanisevic, Julijana; Johnson, Caroline H.
  • Analytical Chemistry, Vol. 86, Issue 14
  • DOI: 10.1021/ac500734c

Use of photocatalytic reduction to hasten preparation of culture media for saccharolytic Clostridium species
journal, January 2003


Low-Molecular-Weight Thiols in Thiol–Disulfide Exchange
journal, May 2013

  • Van Laer, Koen; Hamilton, Chris J.; Messens, Joris
  • Antioxidants & Redox Signaling, Vol. 18, Issue 13
  • DOI: 10.1089/ars.2012.4964

Trimmomatic: a flexible trimmer for Illumina sequence data
journal, April 2014


The global nitrogen cycle in the twenty-first century
journal, July 2013

  • Fowler, David; Coyle, Mhairi; Skiba, Ute
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 368, Issue 1621
  • DOI: 10.1098/rstb.2013.0164

Sulfide-Induced Dissimilatory Nitrate Reduction to Ammonium Supports Anaerobic Ammonium Oxidation (Anammox) in an Open-Water Unit Process Wetland
journal, May 2017

  • Jones, Zackary L.; Jasper, Justin T.; Sedlak, David L.
  • Applied and Environmental Microbiology, Vol. 83, Issue 15
  • DOI: 10.1128/AEM.00782-17

Influence of Sulfide Inhibition of Nitrification on Nitrogen Regeneration in Sediments
journal, October 1995


Mycothiol-dependent mycobacterial response to oxidative stress
journal, April 2006


The life sulfuric: microbial ecology of sulfur cycling in marine sediments: Microbial sulfur cycling in marine sediments
journal, May 2017

  • Wasmund, Kenneth; Mußmann, Marc; Loy, Alexander
  • Environmental Microbiology Reports, Vol. 9, Issue 4
  • DOI: 10.1111/1758-2229.12538

Sulfate-Reducing Bacteria as an Effective Tool for Sustainable Acid Mine Bioremediation
journal, August 2018

  • Ayangbenro, Ayansina S.; Olanrewaju, Oluwaseyi S.; Babalola, Olubukola O.
  • Frontiers in Microbiology, Vol. 9
  • DOI: 10.3389/fmicb.2018.01986

Gene Ontology: tool for the unification of biology
journal, May 2000

  • Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
  • Nature Genetics, Vol. 25, Issue 1
  • DOI: 10.1038/75556

Functional Analysis of Three Sulfide:Quinone Oxidoreductase Homologs in Chlorobaculum tepidum
journal, November 2008

  • Chan, Leong-Keat; Morgan-Kiss, Rachael M.; Hanson, Thomas E.
  • Journal of Bacteriology, Vol. 191, Issue 3
  • DOI: 10.1128/JB.01154-08

Control of Microbial Sulfide Production with Biocides and Nitrate in Oil Reservoir Simulating Bioreactors
journal, December 2015


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

XCMS Online: A Web-Based Platform to Process Untargeted Metabolomic Data
journal, June 2012

  • Tautenhahn, Ralf; Patti, Gary J.; Rinehart, Duane
  • Analytical Chemistry, Vol. 84, Issue 11
  • DOI: 10.1021/ac300698c

Resource Concentration Modulates the Fate of Dissimilated Nitrogen in a Dual-Pathway Actinobacterium
journal, January 2019


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


Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online
journal, March 2018

  • Forsberg, Erica M.; Huan, Tao; Rinehart, Duane
  • Nature Protocols, Vol. 13, Issue 4
  • DOI: 10.1038/nprot.2017.151

Cysteine and growth inhibition of Escherichia coli: threonine deaminase as the target enzyme.
journal, January 1981


SciPy 1.0: fundamental algorithms for scientific computing in Python
journal, February 2020


Autonomous Metabolomics for Rapid Metabolite Identification in Global Profiling
journal, December 2014

  • Benton, H. Paul; Ivanisevic, Julijana; Mahieu, Nathaniel G.
  • Analytical Chemistry, Vol. 87, Issue 2
  • DOI: 10.1021/ac5025649

Physiological and Proteomic Analysis of Escherichia coli Iron-Limited Chemostat Growth
journal, May 2014

  • Folsom, J. P.; Parker, A. E.; Carlson, R. P.
  • Journal of Bacteriology, Vol. 196, Issue 15
  • DOI: 10.1128/JB.01606-14

Physiological Roles and Adverse Effects of the Two Cystine Importers of Escherichia coli
journal, September 2015

  • Chonoles Imlay, Karin R.; Korshunov, Sergey; Imlay, James A.
  • Journal of Bacteriology, Vol. 197, Issue 23
  • DOI: 10.1128/JB.00277-15

Impact of elevated nitrate on sulfate-reducing bacteria: a comparative Study of Desulfovibrio vulgaris
journal, May 2010

  • He, Qiang; He, Zhili; Joyner, Dominique C.
  • The ISME Journal, Vol. 4, Issue 11
  • DOI: 10.1038/ismej.2010.59

Multiple influences of nitrate on uranium solubility during bioremediation of uranium-contaminated subsurface sediments
journal, September 2002


The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
journal, September 2005


Impacts of chemical gradients on microbial community structure
journal, January 2017

  • Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E.
  • The ISME Journal, Vol. 11, Issue 4
  • DOI: 10.1038/ismej.2016.175

New Targets and Inhibitors of Mycobacterial Sulfur Metabolism
journal, August 2013


Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors
journal, May 2015


HTSeq--a Python framework to work with high-throughput sequencing data
journal, September 2014


Sulfide-induced dissimilatory nitrate reduction to ammonia in anaerobic freshwater sediments
journal, October 1996


Effect of H 2 S on N 2 O Reduction and Accumulation during Denitrification by Methanol Utilizing Denitrifiers
journal, July 2013

  • Pan, Yuting; Ye, Liu; Yuan, Zhiguo
  • Environmental Science & Technology
  • DOI: 10.1021/es401632r

METLIN: A Technology Platform for Identifying Knowns and Unknowns
journal, January 2018

  • Guijas, Carlos; Montenegro-Burke, J. Rafael; Domingo-Almenara, Xavier
  • Analytical Chemistry, Vol. 90, Issue 5
  • DOI: 10.1021/acs.analchem.7b04424

Kinetics of Indigenous Nitrate Reducing Sulfide Oxidizing Activity in Microaerophilic Wastewater Biofilms
journal, February 2016


Bacterial Cysteine-Inducible Cysteine Resistance Systems
journal, February 2016

  • Takumi, Kazuhiro; Nonaka, Gen
  • Journal of Bacteriology, Vol. 198, Issue 9
  • DOI: 10.1128/JB.01039-15

BLAST+: architecture and applications
journal, January 2009

  • Camacho, Christiam; Coulouris, George; Avagyan, Vahram
  • BMC Bioinformatics, Vol. 10, Issue 1
  • DOI: 10.1186/1471-2105-10-421

Integrating multiple 'omics' analysis for microbial biology: application and methodologies
journal, November 2009


Aerobic denitrification in permeable Wadden Sea sediments
journal, December 2009


Array programming with NumPy
journal, September 2020

  • Harris, Charles R.; Millman, K. Jarrod; van der Walt, Stéfan J.
  • Nature, Vol. 585, Issue 7825
  • DOI: 10.1038/s41586-020-2649-2

The selective pressures on the microbial community in a metal-contaminated aquifer
journal, December 2018


Cystine import is a valuable but risky process whose hazards Escherichia coli minimizes by inducing a cysteine exporter
journal, November 2019

  • Korshunov, Sergey; Imlay, Karin R. Chonoles; Imlay, James A.
  • Molecular Microbiology, Vol. 113, Issue 1
  • DOI: 10.1111/mmi.14403

The microbial nitrogen-cycling network
journal, February 2018

  • Kuypers, Marcel M. M.; Marchant, Hannah K.; Kartal, Boran
  • Nature Reviews Microbiology, Vol. 16, Issue 5
  • DOI: 10.1038/nrmicro.2018.9

Cytochrome c Reduction by H 2 S Potentiates Sulfide Signaling
journal, July 2018


The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
journal, November 2013

  • Caspi, Ron; Altman, Tomer; Billington, Richard
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1103

METLIN MS2 molecular standards database: a broad chemical and biological resource
journal, August 2020


An accelerated workflow for untargeted metabolomics using the METLIN database
journal, September 2012

  • Tautenhahn, Ralf; Cho, Kevin; Uritboonthai, Winnie
  • Nature Biotechnology, Vol. 30, Issue 9
  • DOI: 10.1038/nbt.2348

Dissimilatory nitrate reduction to ammonium (DNRA) plays an important role in soil nitrogen conservation in neutral and alkaline but not acidic rice soil
journal, December 2014

  • Zhang, Jinbo; Lan, Ting; Müller, Christoph
  • Journal of Soils and Sediments, Vol. 15, Issue 3
  • DOI: 10.1007/s11368-014-1037-7

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014


Comparative metagenomics reveals impact of contaminants on groundwater microbiomes
journal, October 2015


NCBI BLAST+ integrated into Galaxy
journal, August 2015