Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer
Abstract
Groundwater ecosystems are conventionally thought to be fueled by surface-derived allochthonous organic matter and dominated by heterotrophic microbes living under often-oligotrophic conditions. However, in a 2-month study of nitrate amendment to a perennially suboxic aquifer in Rifle (CO), strain-resolved metatranscriptomic analysis revealed pervasive and diverse chemolithoautotrophic bacterial activity relevant to C, S, N and Fe cycling. Before nitrate injection, anaerobic ammonia-oxidizing (anammox) bacteria accounted for 16% of overall microbial community gene expression, whereas during the nitrate injection, two other groups of chemolithoautotrophic bacteria collectively accounted for 80% of the metatranscriptome: (1) members of the Fe(II)-oxidizing Gallionellaceae family and (2) strains of the S-oxidizing species, Sulfurimonas denitrificans. Notably, the proportion of the metatranscriptome accounted for by these three groups was considerably greater than the proportion of the metagenome coverage that they represented. Transcriptional analysis revealed some unexpected metabolic couplings, in particular, putative nitrate-dependent Fe(II) and S oxidation among nominally microaerophilic Gallionellaceae strains, including expression of periplasmic (NapAB) and membrane-bound (NarGHI) nitrate reductases. The three most active groups of chemolithoautotrophic bacteria in this study had overlapping metabolisms that allowed them to occupy different yet related metabolic niches throughout the study. Overall, these results highlight the important role that chemolithoautotrophy can have inmore »
- Authors:
-
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth and Environmental Sciences
- 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); National Inst. of Health (NIH) (United States)
- OSTI Identifier:
- 1377452
- Grant/Contract Number:
- AC02-05CH11231; S10RR029668; S10RR027303
- Resource Type:
- Accepted Manuscript
- Journal Name:
- The ISME Journal
- Additional Journal Information:
- Journal Volume: 10; Journal Issue: 9; Journal ID: ISSN 1751-7362
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES
Citation Formats
Jewell, Talia N. M., Karaoz, Ulas, Brodie, Eoin L., Williams, Kenneth H., and Beller, Harry R. Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer. United States: N. p., 2016.
Web. doi:10.1038/ismej.2016.25.
Jewell, Talia N. M., Karaoz, Ulas, Brodie, Eoin L., Williams, Kenneth H., & Beller, Harry R. Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer. United States. https://doi.org/10.1038/ismej.2016.25
Jewell, Talia N. M., Karaoz, Ulas, Brodie, Eoin L., Williams, Kenneth H., and Beller, Harry R. Fri .
"Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer". United States. https://doi.org/10.1038/ismej.2016.25. https://www.osti.gov/servlets/purl/1377452.
@article{osti_1377452,
title = {Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer},
author = {Jewell, Talia N. M. and Karaoz, Ulas and Brodie, Eoin L. and Williams, Kenneth H. and Beller, Harry R.},
abstractNote = {Groundwater ecosystems are conventionally thought to be fueled by surface-derived allochthonous organic matter and dominated by heterotrophic microbes living under often-oligotrophic conditions. However, in a 2-month study of nitrate amendment to a perennially suboxic aquifer in Rifle (CO), strain-resolved metatranscriptomic analysis revealed pervasive and diverse chemolithoautotrophic bacterial activity relevant to C, S, N and Fe cycling. Before nitrate injection, anaerobic ammonia-oxidizing (anammox) bacteria accounted for 16% of overall microbial community gene expression, whereas during the nitrate injection, two other groups of chemolithoautotrophic bacteria collectively accounted for 80% of the metatranscriptome: (1) members of the Fe(II)-oxidizing Gallionellaceae family and (2) strains of the S-oxidizing species, Sulfurimonas denitrificans. Notably, the proportion of the metatranscriptome accounted for by these three groups was considerably greater than the proportion of the metagenome coverage that they represented. Transcriptional analysis revealed some unexpected metabolic couplings, in particular, putative nitrate-dependent Fe(II) and S oxidation among nominally microaerophilic Gallionellaceae strains, including expression of periplasmic (NapAB) and membrane-bound (NarGHI) nitrate reductases. The three most active groups of chemolithoautotrophic bacteria in this study had overlapping metabolisms that allowed them to occupy different yet related metabolic niches throughout the study. Overall, these results highlight the important role that chemolithoautotrophy can have in aquifer biogeochemical cycling, a finding that has broad implications for understanding terrestrial carbon cycling and is supported by recent studies of geochemically diverse aquifers.},
doi = {10.1038/ismej.2016.25},
journal = {The ISME Journal},
number = 9,
volume = 10,
place = {United States},
year = {Fri Mar 04 00:00:00 EST 2016},
month = {Fri Mar 04 00:00:00 EST 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: 73 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:
The bacterial cytochrome cbb3 oxidases
journal, April 2004
- Pitcher, Robert S.; Watmough, Nicholas J.
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1655
Composition and Activity of an Autotrophic Fe(II)-Oxidizing, Nitrate-Reducing Enrichment Culture
journal, September 2009
- Blothe, M.; Roden, E. E.
- Applied and Environmental Microbiology, Vol. 75, Issue 21
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
Origin and Fate of Industrial Ammonium in Anoxic Ground Water- 15 N Evidence for Anaerobic Oxidation (Anammox)
journal, June 2008
- Clark, Ian; Timlin, Robert; Bourbonnais, Annie
- Ground Water Monitoring & Remediation, Vol. 28, Issue 3
High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment
journal, April 2012
- Handley, Kim M.; Wrighton, Kelly C.; Piceno, Yvette M.
- FEMS Microbiology Ecology, Vol. 81, Issue 1
Natural denitrification in the saturated zone: A review
journal, June 1992
- Korom, Scott F.
- Water Resources Research, Vol. 28, Issue 6
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
journal, August 2012
- Sharon, I.; Morowitz, M. J.; Thomas, B. C.
- Genome Research, Vol. 23, Issue 1
Relative influences of DOC flux and subterranean fauna on microbial abundance and activity in aquifer sediments: new insights from 13C-tracer experiments: Role of carbon supply and subterranean fauna on aquifer microorganisms
journal, June 2009
- Foulquier, Arnaud; Simon, Laurent; Gilbert, Franck
- Freshwater Biology, Vol. 55, Issue 7
Microbial sulfur transformations in sediments from Subglacial Lake Whillans
journal, November 2014
- Purcell, Alicia M.; Mikucki, Jill A.; Achberger, Amanda M.
- Frontiers in Microbiology, Vol. 5
Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome
journal, June 2008
- Urich, Tim; Lanzén, Anders; Qi, Ji
- PLoS ONE, Vol. 3, Issue 6
Physiological characterization of anaerobic ammonium oxidizing bacterium ‘ C andidatus Jettenia caeni’ : Physiology of ‘
journal, December 2014
- Ali, Muhammad; Oshiki, Mamoru; Awata, Takanori
- Environmental Microbiology, Vol. 17, Issue 6
Biogeochemistry and natural attenuation of nitrate in groundwater at an explosives test facility
journal, September 2004
- Beller, Harry R.; Madrid, Vic; Bryant Hudson, G.
- Applied Geochemistry, Vol. 19, Issue 9
The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs
journal, June 2012
- Lesniewski, Ryan A.; Jain, Sunit; Anantharaman, Karthik
- The ISME Journal, Vol. 6, Issue 12
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
Archaeal and bacterial community composition of a pristine coastal aquifer in Doñana National Park, Spain
journal, May 2007
- López-Archilla, Ai; Moreira, D.; Velasco, S.
- Aquatic Microbial Ecology, Vol. 47
Microbial community gene expression in ocean surface waters
journal, March 2008
- Frias-Lopez, J.; Shi, Y.; Tyson, G. W.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 10
Resistance, resilience, and redundancy in microbial communities
journal, August 2008
- Allison, S. D.; Martiny, J. B. H.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue Supplement 1
Analysis of Microbial Gene Transcripts in Environmental Samples
journal, July 2005
- Poretsky, R. S.; Bano, N.; Buchan, A.
- Applied and Environmental Microbiology, Vol. 71, Issue 7
Inhibition of anaerobic ammonium oxidizing (anammox) enrichment cultures by substrates, metabolites and common wastewater constituents
journal, March 2013
- Carvajal-Arroyo, José M.; Sun, Wenjie; Sierra-Alvarez, Reyes
- Chemosphere, Vol. 91, Issue 1
Insight into the evolution of the iron oxidation pathways
journal, February 2013
- Ilbert, Marianne; Bonnefoy, Violaine
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1827, Issue 2
How to make a living from anaerobic ammonium oxidation
journal, May 2013
- Kartal, Boran; de Almeida, Naomi M.; Maalcke, Wouter J.
- FEMS Microbiology Reviews, Vol. 37, Issue 3
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
Metatranscriptome of marine bacterioplankton during winter time in the North Sea assessed by total RNA sequencing
journal, February 2015
- Kopf, Anna; Kostadinov, Ivaylo; Wichels, Antje
- Marine Genomics, Vol. 19
Acetate Availability and its Influence on Sustainable Bioremediation of Uranium-Contaminated Groundwater
journal, June 2011
- Williams, Kenneth H.; Long, Philip E.; Davis, James A.
- Geomicrobiology Journal, Vol. 28, Issue 5-6
Metagenomics meets time series analysis: unraveling microbial community dynamics
journal, June 2015
- Faust, Karoline; Lahti, Leo; Gonze, Didier
- Current Opinion in Microbiology, Vol. 25
Denitrification and Organic Carbon Availability in Two Aquifers
journal, November 1993
- Starr, Robert C.; Gillham, Robert W.
- Ground Water, Vol. 31, Issue 6
Deduced amino acid sequence, functional expression, and unique enzymatic properties of the form I and form II ribulose bisphosphate carboxylase/oxygenase from the chemoautotrophic bacterium Thiobacillus denitrificans.
journal, January 1996
- Hernandez, J. M.; Baker, S. H.; Lorbach, S. C.
- Journal of Bacteriology, Vol. 178, Issue 2
Diversity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Large-Subunit Genes from Groundwater and Aquifer Microorganisms
journal, June 2003
- Alfreider, A.; Vogt, C.; Hoffmann, D.
- Microbial Ecology, Vol. 45, Issue 4
Anammox Bacterial Diversity in Various Aquatic Ecosystems Based on the Detection of Hydrazine Oxidase Genes (hzoA/hzoB)
journal, September 2010
- Hirsch, Matthew D.; Long, Zachery T.; Song, Bongkeun
- Microbial Ecology, Vol. 61, Issue 2
Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea
journal, November 2009
- Ghosh, Wriddhiman; Dam, Bomba
- FEMS Microbiology Reviews, Vol. 33, Issue 6
Another multiheme protein, hydroxylamine oxidoreductase, abundantly produced in an anammox bacterium besides the hydrazine-oxidizing enzyme
journal, March 2008
- Shimamura, Munetaka; Nishiyama, Takashi; Shinya, Kazutaka
- Journal of Bioscience and Bioengineering, Vol. 105, Issue 3
Field evidence of selenium bioreduction in a uranium-contaminated aquifer: Field evidence of selenium bioreduction
journal, February 2013
- Williams, Kenneth H.; Wilkins, Michael J.; N'Guessan, A. Lucie
- Environmental Microbiology Reports, Vol. 5, Issue 3
The effect of sulfide inhibition on the ANAMMOX process
journal, March 2013
- Jin, Ren-Cun; Yang, Guang-Feng; Zhang, Qian-Qian
- Water Research, Vol. 47, Issue 3
The complete genome sequence for putative H 2 - and S-oxidizer C andidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome : Complete genome of
journal, April 2014
- Handley, Kim M.; Bartels, Daniela; O'Loughlin, Edward J.
- Environmental Microbiology, Vol. 16, Issue 11
The Genome Sequence of the Obligately Chemolithoautotrophic, Facultatively Anaerobic Bacterium Thiobacillus denitrificans
journal, February 2006
- Beller, H. R.; Chain, P. S. G.; Letain, T. E.
- Journal of Bacteriology, Vol. 188, Issue 4
Persistence of uranium groundwater plumes: Contrasting mechanisms at two DOE sites in the groundwater–river interaction zone
journal, April 2013
- Zachara, John M.; Long, Philip E.; Bargar, John
- Journal of Contaminant Hydrology, Vol. 147
Vertical migration and distribution of added dissolved iron in Carex lasiocarpa marsh soil
journal, July 2012
- Zou, Yuan-chun; Yu, Xiao-fei; Lu, Xian-guo
- Ecological Engineering, Vol. 44
Heterotrophic denitrification potential as an adaptive response in groundwater bacteria
journal, April 1995
- Bengtsson, Göran; Bergwall, Christer
- FEMS Microbiology Ecology, Vol. 16, Issue 4
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
Gene transcript analysis of assimilatory iron limitation in Geobacteraceae during groundwater bioremediation
journal, May 2008
- O'Neil, Regina A.; Holmes, Dawn E.; Coppi, Maddalena V.
- Environmental Microbiology, Vol. 10, Issue 5
Deciphering the evolution and metabolism of an anammox bacterium from a community genome
journal, April 2006
- Strous, Marc; Pelletier, Eric; Mangenot, Sophie
- Nature, Vol. 440, Issue 7085
Distribution and diversity of autotrophic bacteria in groundwater systems based on the analysis of RubisCO genotypes
journal, April 2009
- Alfreider, Albin; Vogt, Carsten; Geiger-Kaiser, Margot
- Systematic and Applied Microbiology, Vol. 32, Issue 2
Comparative genomics of freshwater Fe-oxidizing bacteria: implications for physiology, ecology, and systematics
journal, January 2013
- Emerson, David; Field, Erin K.; Chertkov, Olga
- Frontiers in Microbiology, Vol. 4
Genetic Evidence for Bacterial Chemolithoautotrophy Based on the Reductive Tricarboxylic Acid Cycle in Groundwater Systems
journal, January 2012
- Alfreider, Albin; Vogt, Carsten
- Microbes and Environments, Vol. 27, Issue 2
Mo and W bis-MGD enzymes: nitrate reductases and formate dehydrogenases
journal, August 2004
- Moura, Jos� J. G.; Brondino, Carlos D.; Trinc�o, Jos�
- JBIC Journal of Biological Inorganic Chemistry, Vol. 9, Issue 7
Field tracer test for denitrification in a pyrite-bearing schist aquifer
journal, August 1998
- Pauwels, Hélène; Kloppmann, Wolfram; Foucher, Jean-Claude
- Applied Geochemistry, Vol. 13, Issue 6
Whole-Genome Transcriptional Analysis of Chemolithoautotrophic Thiosulfate Oxidation by Thiobacillus denitrificans under Aerobic versus Denitrifying Conditions
journal, September 2006
- Beller, H. R.; Letain, T. E.; Chakicherla, A.
- Journal of Bacteriology, Vol. 188, Issue 19
Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre
journal, June 2009
- Poretsky, Rachel S.; Hewson, Ian; Sun, Shulei
- Environmental Microbiology, Vol. 11, Issue 6
Genome dynamics in a natural archaeal population
journal, January 2007
- Allen, E. E.; Tyson, G. W.; Whitaker, R. J.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 6
Reduction of nitric oxide catalyzed by hydroxylamine oxidoreductase from an anammox bacterium
journal, December 2014
- Irisa, Tatsuya; Hira, Daisuke; Furukawa, Kenji
- Journal of Bioscience and Bioengineering, Vol. 118, Issue 6
Organic Carbon Supply and Metabolism in a Shallow Groundwater Ecosystem
journal, November 2000
- Baker, Michelle A.; Valett, H. Maurice; Dahm, Clifford N.
- Ecology, Vol. 81, Issue 11
Unraveling the Stratification of an Iron-Oxidizing Microbial Mat by Metatranscriptomics
journal, July 2014
- Quaiser, Achim; Bodi, Xavier; Dufresne, Alexis
- PLoS ONE, Vol. 9, Issue 7
ConStrains identifies microbial strains in metagenomic datasets
journal, September 2015
- Luo, Chengwei; Knight, Rob; Siljander, Heli
- Nature Biotechnology, Vol. 33, Issue 10
Structural Basis of Biological NO Generation by Octaheme Oxidoreductases
journal, December 2013
- Maalcke, Wouter J.; Dietl, Andreas; Marritt, Sophie J.
- Journal of Biological Chemistry, Vol. 289, Issue 3
Ecological Aspects of the Distribution of Different Autotrophic CO 2 Fixation Pathways
journal, January 2011
- Berg, Ivan A.
- Applied and Environmental Microbiology, Vol. 77, Issue 6
Transcriptional activity of paddy soil bacterial communities
journal, April 2009
- Shrestha, Pravin Malla; Kube, Michael; Reinhardt, Richard
- Environmental Microbiology, Vol. 11, Issue 4
Detection and Quantification of Bacteria Involved in Aerobic and Anaerobic Ammonium Oxidation in an Ammonium-Contaminated Aquifer
journal, March 2009
- Smits, Theo H. M.; Hüttmann, Arne; Lerner, David N.
- Bioremediation Journal, Vol. 13, Issue 1
Biochemistry and molecular biology of anammox bacteria
journal, June 2009
- Jetten, Mike S. M.; Niftrik, Laura van; Strous, Marc
- Critical Reviews in Biochemistry and Molecular Biology, Vol. 44, Issue 2-3
The High-Molecular-Weight Cytochrome c Cyc2 of Acidithiobacillus ferrooxidans Is an Outer Membrane Protein
journal, March 2002
- Yarzábal, Andrés; Brasseur, Gaël; Ratouchniak, Jeanine
- Journal of Bacteriology, Vol. 184, Issue 5
Diversity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Large-Subunit Genes from Groundwater and Aquifer Microorganisms
journal, June 2003
- Alfreider, A.; Vogt, C.; Hoffmann, D.
- Microbial Ecology, Vol. 45, Issue 4
Anammox Bacterial Diversity in Various Aquatic Ecosystems Based on the Detection of Hydrazine Oxidase Genes (hzoA/hzoB)
journal, September 2010
- Hirsch, Matthew D.; Long, Zachery T.; Song, Bongkeun
- Microbial Ecology, Vol. 61, Issue 2
Mo and W bis-MGD enzymes: nitrate reductases and formate dehydrogenases
journal, August 2004
- Moura, Jos� J. G.; Brondino, Carlos D.; Trinc�o, Jos�
- JBIC Journal of Biological Inorganic Chemistry, Vol. 9, Issue 7
The bacterial cytochrome cbb3 oxidases
journal, April 2004
- Pitcher, Robert S.; Watmough, Nicholas J.
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1655
Insight into the evolution of the iron oxidation pathways
journal, February 2013
- Ilbert, Marianne; Bonnefoy, Violaine
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1827, Issue 2
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
Inhibition of anaerobic ammonium oxidizing (anammox) enrichment cultures by substrates, metabolites and common wastewater constituents
journal, March 2013
- Carvajal-Arroyo, José M.; Sun, Wenjie; Sierra-Alvarez, Reyes
- Chemosphere, Vol. 91, Issue 1
Metagenomics meets time series analysis: unraveling microbial community dynamics
journal, June 2015
- Faust, Karoline; Lahti, Leo; Gonze, Didier
- Current Opinion in Microbiology, Vol. 25
The effect of sulfide inhibition on the ANAMMOX process
journal, March 2013
- Jin, Ren-Cun; Yang, Guang-Feng; Zhang, Qian-Qian
- Water Research, Vol. 47, Issue 3
Denitrifying genes in bacterial and Archaeal genomes
journal, September 2002
- Philippot, Laurent
- Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, Vol. 1577, Issue 3
The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs
journal, June 2012
- Lesniewski, Ryan A.; Jain, Sunit; Anantharaman, Karthik
- The ISME Journal, Vol. 6, Issue 12
Deciphering the evolution and metabolism of an anammox bacterium from a community genome
journal, April 2006
- Strous, Marc; Pelletier, Eric; Mangenot, Sophie
- Nature, Vol. 440, Issue 7085
ConStrains identifies microbial strains in metagenomic datasets
journal, September 2015
- Luo, Chengwei; Knight, Rob; Siljander, Heli
- Nature Biotechnology, Vol. 33, Issue 10
Genome dynamics in a natural archaeal population
journal, January 2007
- Allen, E. E.; Tyson, G. W.; Whitaker, R. J.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 6
Microbial community gene expression in ocean surface waters
journal, March 2008
- Frias-Lopez, J.; Shi, Y.; Tyson, G. W.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 10
Biochemistry and molecular biology of anammox bacteria
journal, June 2009
- Jetten, Mike S. M.; Niftrik, Laura van; Strous, Marc
- Critical Reviews in Biochemistry and Molecular Biology, Vol. 44, Issue 2-3
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
journal, August 2012
- Sharon, I.; Morowitz, M. J.; Thomas, B. C.
- Genome Research, Vol. 23, Issue 1
Gene transcript analysis of assimilatory iron limitation in Geobacteraceae during groundwater bioremediation
journal, May 2008
- O'Neil, Regina A.; Holmes, Dawn E.; Coppi, Maddalena V.
- Environmental Microbiology, Vol. 10, Issue 5
Transcriptional activity of paddy soil bacterial communities
journal, April 2009
- Shrestha, Pravin Malla; Kube, Michael; Reinhardt, Richard
- Environmental Microbiology, Vol. 11, Issue 4
Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre
journal, June 2009
- Poretsky, Rachel S.; Hewson, Ian; Sun, Shulei
- Environmental Microbiology, Vol. 11, Issue 6
High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment
journal, April 2012
- Handley, Kim M.; Wrighton, Kelly C.; Piceno, Yvette M.
- FEMS Microbiology Ecology, Vol. 81, Issue 1
Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea
journal, November 2009
- Ghosh, Wriddhiman; Dam, Bomba
- FEMS Microbiology Reviews, Vol. 33, Issue 6
New Insight into Microbial Iron Oxidation as Revealed by the Proteomic Profile of an Obligate Iron-Oxidizing Chemolithoautotroph
journal, June 2015
- Barco, Roman A.; Emerson, David; Sylvan, Jason B.
- Applied and Environmental Microbiology, Vol. 81, Issue 17
Genome of the Epsilonproteobacterial Chemolithoautotroph Sulfurimonas denitrificans
journal, December 2007
- Sievert, S. M.; Scott, K. M.; Klotz, M. G.
- Applied and Environmental Microbiology, Vol. 74, Issue 4
Suspension Array Analysis of 16S rRNA from Fe- and SO42-Reducing Bacteria in Uranium-Contaminated Sediments Undergoing Bioremediation
journal, July 2006
- Chandler, D. P.; Jarrell, A. E.; Roden, E. R.
- Applied and Environmental Microbiology, Vol. 72, Issue 7
Large Fractions of CO 2 -Fixing Microorganisms in Pristine Limestone Aquifers Appear To Be Involved in the Oxidation of Reduced Sulfur and Nitrogen Compounds
journal, January 2015
- Herrmann, Martina; Rusznyák, Anna; Akob, Denise M.
- Applied and Environmental Microbiology, Vol. 81, Issue 7
Effects of aerobic and microaerobic conditions on anaerobic ammonium-oxidizing (anammox) sludge.
journal, January 1997
- Strous, M.; Van Gerven, E.; Kuenen, J. G.
- Applied and environmental microbiology, Vol. 63, Issue 6
Draft Genome Sequence of an Anaerobic Ammonium-Oxidizing Bacterium, “ Candidatus Brocadia sinica”
journal, April 2015
- Oshiki, Mamoru; Shinyako-Hata, Kaori; Satoh, Hisashi
- Genome Announcements, Vol. 3, Issue 2
Deduced amino acid sequence, functional expression, and unique enzymatic properties of the form I and form II ribulose bisphosphate carboxylase/oxygenase from the chemoautotrophic bacterium Thiobacillus denitrificans.
journal, January 1996
- Hernandez, J. M.; Baker, S. H.; Lorbach, S. C.
- Journal of Bacteriology, Vol. 178, Issue 2
The High-Molecular-Weight Cytochrome c Cyc2 of Acidithiobacillus ferrooxidans Is an Outer Membrane Protein
journal, January 2002
- Yarzabal, A.; Brasseur, G.; Ratouchniak, J.
- Journal of Bacteriology, Vol. 184, Issue 1
Another multiheme protein, hydroxylamine oxidoreductase, abundantly produced in an anammox bacterium besides the hydrazine-oxidizing enzyme
journal, March 2008
- Shimamura, Munetaka; Nishiyama, Takashi; Shinya, Kazutaka
- Journal of Bioscience and Bioengineering, Vol. 105, Issue 3
Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome
journal, June 2008
- Urich, Tim; Lanzén, Anders; Qi, Ji
- PLoS ONE, Vol. 3, Issue 6
Comparative genomics of freshwater Fe-oxidizing bacteria: implications for physiology, ecology, and systematics
journal, January 2013
- Emerson, David; Field, Erin K.; Chertkov, Olga
- Frontiers in Microbiology, Vol. 4
Microbial sulfur transformations in sediments from Subglacial Lake Whillans
journal, November 2014
- Purcell, Alicia M.; Mikucki, Jill A.; Achberger, Amanda M.
- Frontiers in Microbiology, Vol. 5
Works referencing / citing this record:
Geochemical Exports to River From the Intrameander Hyporheic Zone Under Transient Hydrologic Conditions: East River Mountainous Watershed, Colorado
journal, October 2018
- Dwivedi, Dipankar; Steefel, Carl I.; Arora, Bhavna
- Water Resources Research, Vol. 54, Issue 10
Hidden diversity revealed by genome-resolved metagenomics of iron-oxidizing microbial mats from Lō’ihi Seamount, Hawai’i
journal, April 2017
- Fullerton, Heather; Hager, Kevin W.; McAllister, Sean M.
- The ISME Journal, Vol. 11, Issue 8
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
High reactivity of deep biota under anthropogenic CO2 injection into basalt
journal, October 2017
- Trias, Rosalia; Ménez, Bénédicte; le Campion, Paul
- Nature Communications, Vol. 8, Issue 1
H2S events in the Peruvian oxygen minimum zone facilitate enhanced dissolved Fe concentrations
journal, August 2018
- Schlosser, Christian; Streu, Peter; Frank, Martin
- Scientific Reports, Vol. 8, Issue 1
Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer
journal, July 2019
- Mailloux, Brian J.; Kim, Carol; Kichuk, Tess
- Scientific Reports, Vol. 9, Issue 1
Microbial anaerobic Fe(II) oxidation - Ecology, mechanisms and environmental implications: Microbial anaerobic Fe(II) oxidation
journal, October 2018
- Bryce, Casey; Blackwell, Nia; Schmidt, Caroline
- Environmental Microbiology, Vol. 20, Issue 10
Comparison of sulfide‐oxidizing Sulfurimonas strains reveals a new mode of thiosulfate formation in subsurface environments
journal, January 2020
- Lahme, Sven; Callbeck, Cameron M.; Eland, Lucy E.
- Environmental Microbiology, Vol. 22, Issue 5
Insights into Carbon Metabolism Provided by Fluorescence In Situ Hybridization-Secondary Ion Mass Spectrometry Imaging of an Autotrophic, Nitrate-Reducing, Fe(II)-Oxidizing Enrichment Culture
journal, March 2018
- Tominski, Claudia; Lösekann-Behrens, Tina; Ruecker, Alexander
- Applied and Environmental Microbiology, Vol. 84, Issue 9
Growth and Population Dynamics of the Anaerobic Fe(II)-Oxidizing and Nitrate-Reducing Enrichment Culture KS
journal, March 2018
- Tominski, Claudia; Heyer, Helene; Lösekann-Behrens, Tina
- Applied and Environmental Microbiology, Vol. 84, Issue 9
Transient O2 pulses direct Fe crystallinity and Fe(III)-reducer gene expression within a soil microbiome
journal, October 2018
- Wilmoth, Jared Lee; Moran, Mary Ann; Thompson, Aaron
- Microbiome, Vol. 6, Issue 1
Short-term effect of simulated salt marsh restoration by sand-amendment on sediment bacterial communities
journal, April 2019
- Thomas, François; Morris, James T.; Wigand, Cathleen
- PLOS ONE, Vol. 14, Issue 4
Snowmelt Induced Hydrologic Perturbations Drive Dynamic Microbiological and Geochemical Behaviors across a Shallow Riparian Aquifer
journal, May 2016
- Danczak, Robert E.; Yabusaki, Steven B.; Williams, Kenneth H.
- Frontiers in Earth Science, Vol. 4
Evidence for Microbial Mediated NO3− Cycling Within Floodplain Sediments During Groundwater Fluctuations
journal, July 2019
- Bouskill, Nicholas J.; Conrad, Mark E.; Bill, Markus
- Frontiers in Earth Science, Vol. 7
Metatranscriptomic Analysis Reveals Unexpectedly Diverse Microbial Metabolism in a Biogeochemical Hot Spot in an Alluvial Aquifer
journal, January 2017
- Jewell, Talia N. M.; Karaoz, Ulas; Bill, Markus
- Frontiers in Microbiology, Vol. 8, Article No. 40
FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies
journal, January 2020
- Garber, Arkadiy I.; Nealson, Kenneth H.; Okamoto, Akihiro
- Frontiers in Microbiology, Vol. 11
Hidden diversity revealed by genome-resolved metagenomics of iron-oxidizing microbial mats from Lō’ihi Seamount, Hawai’i
journal, April 2017
- Fullerton, Heather; Hager, Kevin W.; McAllister, Sean M.
- The ISME Journal, Vol. 11, Issue 8
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
Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer
journal, July 2019
- Mailloux, Brian J.; Kim, Carol; Kichuk, Tess
- Scientific Reports, Vol. 9, Issue 1
Evidence for the Existence of Autotrophic Nitrate-Reducing Fe(II)-Oxidizing Bacteria in Marine Coastal Sediment
journal, October 2016
- Laufer, Katja; Røy, Hans; Jørgensen, Bo Barker
- Applied and Environmental Microbiology, Vol. 82, Issue 20
Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents
journal, February 2020
- McAllister, Sean M.; Polson, Shawn W.; Butterfield, David A.
- mSystems, Vol. 5, Issue 1
Snowmelt Induced Hydrologic Perturbations Drive Dynamic Microbiological and Geochemical Behaviors across a Shallow Riparian Aquifer
journal, May 2016
- Danczak, Robert E.; Yabusaki, Steven B.; Williams, Kenneth H.
- Frontiers in Earth Science, Vol. 4
Metatranscriptomic Analysis Reveals Unexpectedly Diverse Microbial Metabolism in a Biogeochemical Hot Spot in an Alluvial Aquifer
journal, January 2017
- Jewell, Talia N. M.; Karaoz, Ulas; Bill, Markus
- Frontiers in Microbiology, Vol. 8, Article No. 40
Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle
journal, January 2019
- Eveillard, Damien; Bouskill, Nicholas J.; Vintache, Damien
- Frontiers in Microbiology, Vol. 9