Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome

Nelson, William C.; Graham, Emily B.; Crump, Alex R.; Fansler, Sarah J.; Arntzen, Evan V.; Kennedy, David W.; Stegen, James C.; Liu, ed., Wenzhi

doi:10.1371/journal.pone.0228165

Title: Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome

Journal Article · 26 January 2020 · PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0228165 · OSTI ID:1595181

; Graham, Emily B.;

; Fansler, Sarah J.; Arntzen, Evan V.; Kennedy, David W.; Stegen, James C.; Liu, ed., Wenzhi

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC05-76RL01830; AC06-76RL01830

OSTI ID:: 1595181

Report Number(s):: PNNL-SA--125632; 10.1371/journal.pone.0228165

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 1 Vol. 15; ISSN 1932-6203

Publisher:: Public Library of Science (PLoS)Copyright Statement

Country of Publication:: United States

Language:: English

References (40)

Ecosystem Consequences of Microbial Diversity and Community Structure Schimel, J. Ecological Studies https://doi.org/10.1007/978-3-642-78966-3_17	book	January 1995
Characteristics of aerobic and anaerobic ammonium-oxidizing bacteria in the hyporheic zone of a contaminated river Wang, Ziyuan; Qi, Yun; Wang, Jun World Journal of Microbiology and Biotechnology, Vol. 28, Issue 9 https://doi.org/10.1007/s11274-012-1090-6	journal	June 2012
Microbial diversity and function in soil: from genes to ecosystems Torsvik, Vigdis; Øvreås, Lise Current Opinion in Microbiology, Vol. 5, Issue 3, p. 240-245 https://doi.org/10.1016/S1369-5274(02)00324-7	journal	June 2002
Microbial diversity — exploration of natural ecosystems and microbiomes Gibbons, Sean M.; Gilbert, Jack A. Current Opinion in Genetics & Development, Vol. 35 https://doi.org/10.1016/j.gde.2015.10.003	journal	December 2015
Do we need to understand microbial communities to predict ecosystem function? A comparison of statistical models of nitrogen cycling processes Graham, Emily B.; Wieder, William R.; Leff, Jonathan W. Soil Biology and Biochemistry, Vol. 68 https://doi.org/10.1016/j.soilbio.2013.08.023	journal	January 2014
Hydrologic Controls on Nitrogen Cycling Processes and Functional Gene Abundance in Sediments of a Groundwater Flow-Through Lake Stoliker, Deborah L.; Repert, Deborah A.; Smith, Richard L. Environmental Science & Technology, Vol. 50, Issue 7 https://doi.org/10.1021/acs.est.5b06155	journal	March 2016
Fine-Scale in Situ Measurement of Riverbed Nitrate Production and Consumption in an Armored Permeable Riverbed Lansdown, Katrina; Heppell, Catherine M.; Dossena, Matteo Environmental Science & Technology, Vol. 48, Issue 8 https://doi.org/10.1021/es4056005	journal	March 2014
Functional redundancy in ecology and conservation Rosenfeld, Jordan S. Oikos, Vol. 98, Issue 1 https://doi.org/10.1034/j.1600-0706.2002.980116.x	journal	July 2002
Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale Bru, D.; Ramette, A.; Saby, N. P. A. The ISME Journal, Vol. 5, Issue 3 https://doi.org/10.1038/ismej.2010.130	journal	August 2010
Complete nitrification by Nitrospira bacteria Daims, Holger; Lebedeva, Elena V.; Pjevac, Petra Nature, Vol. 528, Issue 7583 https://doi.org/10.1038/nature16461	journal	November 2015
Recently identified microbial guild mediates soil N2O sink capacity Jones, Christopher M.; Spor, Ayme; Brennan, Fiona P. Nature Climate Change, Vol. 4, Issue 9 https://doi.org/10.1038/nclimate2301	journal	July 2014
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms13219	journal	October 2016
Division of labour in microorganisms: an evolutionary perspective West, Stuart A.; Cooper, Guy A. Nature Reviews Microbiology, Vol. 14, Issue 11 https://doi.org/10.1038/nrmicro.2016.111	journal	September 2016
Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology Stegen, James C.; Johnson, Tim; Fredrickson, James K. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-02922-9	journal	February 2018
Biodiversity and Ecological Redundancy Walker, Brian H. Conservation Biology, Vol. 6, Issue 1 https://doi.org/10.1046/j.1523-1739.1992.610018.x	journal	March 1992
Genomic insights that advance the species definition for prokaryotes Konstantinidis, K. T.; Tiedje, J. M. Proceedings of the National Academy of Sciences, Vol. 102, Issue 7 https://doi.org/10.1073/pnas.0409727102	journal	February 2005
Resistance, resilience, and redundancy in microbial communities Allison, S. D.; Martiny, J. B. H. Proceedings of the National Academy of Sciences, Vol. 105, Issue Supplement 1 https://doi.org/10.1073/pnas.0801925105	journal	August 2008
Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils Sanford, R. A.; Wagner, D. D.; Wu, Q. Proceedings of the National Academy of Sciences, Vol. 109, Issue 48 https://doi.org/10.1073/pnas.1211238109	journal	November 2012
Global biogeography of microbial nitrogen-cycling traits in soil Nelson, Michaeline B.; Martiny, Adam C.; Martiny, Jennifer B. H. Proceedings of the National Academy of Sciences, Vol. 113, Issue 29 https://doi.org/10.1073/pnas.1601070113	journal	July 2016
Biodiversity and ecosystem productivity in a fluctuating environment: The insurance hypothesis Yachi, S.; Loreau, M. Proceedings of the National Academy of Sciences, Vol. 96, Issue 4 https://doi.org/10.1073/pnas.96.4.1463	journal	February 1999
Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming Song, Hyun-Seob; Goldberg, Noam; Mahajan, Ashutosh Bioinformatics, Vol. 33, Issue 15 https://doi.org/10.1093/bioinformatics/btx171	journal	March 2017
Organismal and spatial partitioning of energy and macronutrient transformations within a hypersaline mat Mobberley, Jennifer M.; Lindemann, Stephen R.; Bernstein, Hans C. FEMS Microbiology Ecology, Vol. 93, Issue 4 https://doi.org/10.1093/femsec/fix028	journal	March 2017
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability Katoh, K.; Standley, D. M. Molecular Biology and Evolution, Vol. 30, Issue 4 https://doi.org/10.1093/molbev/mst010	journal	January 2013
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform Katoh, K. Nucleic Acids Research, Vol. 30, Issue 14 https://doi.org/10.1093/nar/gkf436	journal	July 2002
Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes: Deterministic assembly of hyporheic microbiomes Graham, Emily B.; Crump, Alex R.; Resch, Charles T. Environmental Microbiology, Vol. 19, Issue 4 https://doi.org/10.1111/1462-2920.13720	journal	March 2017
Bacterial diversity promotes community stability and functional resilience after perturbation Girvan, M. S.; Campbell, C. D.; Killham, K. Environmental Microbiology, Vol. 7, Issue 3 https://doi.org/10.1111/j.1462-2920.2005.00695.x	journal	March 2005
Influence of land-use intensity on the spatial distribution of N-cycling microorganisms in grassland soils: Spatial distribution of N-cycling soil microorganisms Keil, Daniel; Meyer, Annabel; Berner, Doreen FEMS Microbiology Ecology, Vol. 77, Issue 1 https://doi.org/10.1111/j.1574-6941.2011.01091.x	journal	April 2011
VEGAN, a package of R functions for community ecology Dixon, Philip Journal of Vegetation Science, Vol. 14, Issue 6 https://doi.org/10.1111/j.1654-1103.2003.tb02228.x	journal	April 2003
Impacts of Biodiversity Loss on Ocean Ecosystem Services Worm, B.; Barbier, E. B.; Beaumont, N. Science, Vol. 314, Issue 5800 https://doi.org/10.1126/science.1132294	journal	November 2006
The Influence of Functional Diversity and Composition on Ecosystem Processes Tilman, D. Science, Vol. 277, Issue 5330 https://doi.org/10.1126/science.277.5330.1300	journal	August 1997
Cell biology and molecular basis of denitrification. Zumft, W. G. Microbiology and molecular biology reviews : MMBR, Vol. 61, Issue 4 https://doi.org/10.1128/.61.4.533-616.1997	journal	January 1997
Linking Uncultivated Microbial Populations and Benthic Carbon Turnover by Using Quantitative Stable Isotope Probing Coskun, Ömer K.; Pichler, Monica; Vargas, Sergio Applied and Environmental Microbiology, Vol. 84, Issue 18 https://doi.org/10.1128/AEM.01083-18	journal	July 2018
Nitrogen Cycling Potential of a Grassland Litter Microbial Community Nelson, Michaeline B.; Berlemont, Renaud; Martiny, Adam C. Applied and Environmental Microbiology, Vol. 81, Issue 20 https://doi.org/10.1128/AEM.02222-15	journal	July 2015
Xander: employing a novel method for efficient gene-targeted metagenomic assembly Wang, Qiong; Fish, Jordan A.; Gilman, Mariah Microbiome, Vol. 3, Issue 1 https://doi.org/10.1186/s40168-015-0093-6	journal	August 2015
Accelerated Profile HMM Searches Eddy, Sean R. PLoS Computational Biology, Vol. 7, Issue 10 https://doi.org/10.1371/journal.pcbi.1002195	journal	October 2011
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
Habitat Loss, Trophic Collapse, and the Decline of Ecosystem Services Dobson, Andrew; Lodge, David; Alder, Jackie Ecology, Vol. 87, Issue 8 https://doi.org/10.1890/0012-9658(2006)87[1915:HLTCAT]2.0.CO;2	journal	August 2006
Effects of Biodiversity on Ecosystem Functioning: a Consensus of Current Knowledge Hooper, D. U.; Chapin, F. S.; Ewel, J. J. Ecological Monographs, Vol. 75, Issue 1 https://doi.org/10.1890/04-0922	journal	February 2005
Fundamentals of Microbial Community Resistance and Resilience Shade, Ashley; Peter, Hannes; Allison, Steven D. Frontiers in Microbiology, Vol. 3 https://doi.org/10.3389/fmicb.2012.00417	journal	January 2012
Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes? Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00214	journal	February 2016

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59 BASIC BIOLOGICAL SCIENCES
denitrification
hyporheic zone
metagenomics
microbial ecology
nitrification

Title: Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome

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