Systems biology approaches towards predictive microbial ecology
Abstract
Summary Through complex interspecies interactions, microbial processes drive nutrient cycling and biogeochemistry. However, we still struggle to predict specifically which organisms, communities and biotic and abiotic processes are determining ecosystem function and how environmental changes will alter their roles and stability. While the tools to create such a predictive microbial ecology capability exist, cross‐disciplinary integration of high‐resolution field measurements, detailed laboratory studies and computation is essential. In this perspective, we emphasize the importance of pursuing a multiscale, systems approach to iteratively link ecological processes measured in the field to testable hypotheses that drive high‐throughput laboratory experimentation. Mechanistic understanding of microbial processes gained in controlled lab systems will lead to the development of theory that can be tested back in the field. Using N 2 O production as an example, we review the current status of field and laboratory research and layout a plausible path to the kind of integration that is needed to enable prediction of how N‐cycling microbial communities will respond to environmental changes. We advocate for the development of realistic and predictive gene regulatory network models for environmental responses that extend from single‐cell resolution to ecosystems, which is essential to understand how microbial communities involved in N 2more »
- Authors:
-
- Institute for Systems Biology, Seattle, WA (United States)
- Institute for Systems Biology, Seattle, WA (United States);Univ. of Washington, Seattle, WA (United States)
- Institute for Systems Biology, Seattle, WA (United States);Univ. of Washington, Seattle, WA (United States) ; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- 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)
- OSTI Identifier:
- 1777943
- Alternate Identifier(s):
- OSTI ID: 1478266
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Environmental Microbiology
- Additional Journal Information:
- Journal Volume: 20; Journal Issue: 12; Journal ID: ISSN 1462-2912
- Publisher:
- Wiley
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Otwell, Anne E., López García de Lomana, Adrián, Gibbons, Sean M., Orellana, Mónica V., and Baliga, Nitin S. Systems biology approaches towards predictive microbial ecology. United States: N. p., 2018.
Web. doi:10.1111/1462-2920.14378.
Otwell, Anne E., López García de Lomana, Adrián, Gibbons, Sean M., Orellana, Mónica V., & Baliga, Nitin S. Systems biology approaches towards predictive microbial ecology. United States. https://doi.org/10.1111/1462-2920.14378
Otwell, Anne E., López García de Lomana, Adrián, Gibbons, Sean M., Orellana, Mónica V., and Baliga, Nitin S. Fri .
"Systems biology approaches towards predictive microbial ecology". United States. https://doi.org/10.1111/1462-2920.14378. https://www.osti.gov/servlets/purl/1777943.
@article{osti_1777943,
title = {Systems biology approaches towards predictive microbial ecology},
author = {Otwell, Anne E. and López García de Lomana, Adrián and Gibbons, Sean M. and Orellana, Mónica V. and Baliga, Nitin S.},
abstractNote = {Summary Through complex interspecies interactions, microbial processes drive nutrient cycling and biogeochemistry. However, we still struggle to predict specifically which organisms, communities and biotic and abiotic processes are determining ecosystem function and how environmental changes will alter their roles and stability. While the tools to create such a predictive microbial ecology capability exist, cross‐disciplinary integration of high‐resolution field measurements, detailed laboratory studies and computation is essential. In this perspective, we emphasize the importance of pursuing a multiscale, systems approach to iteratively link ecological processes measured in the field to testable hypotheses that drive high‐throughput laboratory experimentation. Mechanistic understanding of microbial processes gained in controlled lab systems will lead to the development of theory that can be tested back in the field. Using N 2 O production as an example, we review the current status of field and laboratory research and layout a plausible path to the kind of integration that is needed to enable prediction of how N‐cycling microbial communities will respond to environmental changes. We advocate for the development of realistic and predictive gene regulatory network models for environmental responses that extend from single‐cell resolution to ecosystems, which is essential to understand how microbial communities involved in N 2 O production and consumption will respond to future environmental conditions.},
doi = {10.1111/1462-2920.14378},
journal = {Environmental Microbiology},
number = 12,
volume = 20,
place = {United States},
year = {Fri Oct 19 00:00:00 EDT 2018},
month = {Fri Oct 19 00:00:00 EDT 2018}
}
Web of Science
Works referenced in this record:
Resolving N 2 O respiration pathways: a tale of two NosZ clades : Resolving N
journal, November 2017
- Stein, Lisa Y.
- Environmental Microbiology, Vol. 19, Issue 12
Denitrification in Gram-positive bacteria: an underexplored trait
journal, January 2011
- Verbaendert, Ines; De Vos, Paul; Boon, Nico
- Biochemical Society Transactions, Vol. 39, Issue 1
Habitat heterogeneity and connectivity shape microbial communities in South American peatlands
journal, May 2016
- Oloo, Felix; Valverde, Angel; Quiroga, María Victoria
- Scientific Reports, Vol. 6, Issue 1
Microbial community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia
journal, January 2010
- Zaikova, Elena; Walsh, David A.; Stilwell, Claire P.
- Environmental Microbiology, Vol. 12, Issue 1
Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures
journal, September 2017
- Chan, Thalia E.; Stumpf, Michael P. H.; Babtie, Ann C.
- Cell Systems, Vol. 5, Issue 3
cMonkey 2 : Automated, systematic, integrated detection of co-regulated gene modules for any organism
journal, April 2015
- Reiss, David J.; Plaisier, Christopher L.; Wu, Wei-Ju
- Nucleic Acids Research, Vol. 43, Issue 13
Coping with Anoxia: A Comprehensive Proteomic and Transcriptomic Survey of Denitrification
journal, September 2014
- Kohlmann, Yvonne; Pohlmann, Anne; Schwartz, Edward
- Journal of Proteome Research, Vol. 13, Issue 10
Archaea produce lower yields of N 2 O than bacteria during aerobic ammonia oxidation in soil : N
journal, April 2016
- Hink, Linda; Nicol, Graeme W.; Prosser, James I.
- Environmental Microbiology, Vol. 19, Issue 12
A modeling study on mitigation of N2O emissions and NO3 leaching at different agricultural sites across Europe using LandscapeDNDC
journal, May 2016
- Molina-Herrera, Saúl; Haas, Edwin; Klatt, Steffen
- Science of The Total Environment, Vol. 553
Metabolic modeling of a mutualistic microbial community
journal, January 2007
- Stolyar, Sergey; Van Dien, Steve; Hillesland, Kristina Linnea
- Molecular Systems Biology, Vol. 3, Issue 1
Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii
journal, December 2015
- López García de Lomana, Adrián; Schäuble, Sascha; Valenzuela, Jacob
- Biotechnology for Biofuels, Vol. 8, Issue 1
Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression
journal, July 2014
- Fisher, Charles K.; Mehta, Pankaj
- PLoS ONE, Vol. 9, Issue 7
Global metabolomic responses of Nitrosomonas europaea 19718 to cold stress and altered ammonia feeding patterns
journal, November 2015
- Lu, Huijie; Ulanov, Alexander V.; Nobu, Masaru
- Applied Microbiology and Biotechnology, Vol. 100, Issue 4
Mechanisms of Chromium and Uranium Toxicity in Pseudomonas stutzeri RCH2 Grown under Anaerobic Nitrate-Reducing Conditions
journal, August 2017
- Thorgersen, Michael P.; Lancaster, W. Andrew; Ge, Xiaoxuan
- Frontiers in Microbiology, Vol. 8
Nitrogen Cycle of the Open Ocean: From Genes to Ecosystems
journal, January 2011
- Zehr, Jonathan P.; Kudela, Raphael M.
- Annual Review of Marine Science, Vol. 3, Issue 1
Keystone taxa as drivers of microbiome structure and functioning
journal, May 2018
- Banerjee, Samiran; Schlaeppi, Klaus; van der Heijden, Marcel G. A.
- Nature Reviews Microbiology, Vol. 16, Issue 9
Regional inventory of nitric oxide and nitrous oxide emissions for forest soils of southeast Germany using the biogeochemical model PnET-N-DNDC
journal, December 2001
- Butterbach-Bahl, Klaus; Stange, Florian; Papen, Hans
- Journal of Geophysical Research: Atmospheres, Vol. 106, Issue D24
The Evolution and Future of Earth’s Nitrogen Cycle
journal, October 2010
- Canfield, Donald E.; Glazer, Alexander N.; Falkowski, Paul G.
- Science, Vol. 330, Issue 6001
Nitrous oxide emissions from soils: how well do we understand the processes and their controls?
journal, July 2013
- Butterbach-Bahl, Klaus; Baggs, Elizabeth M.; Dannenmann, Michael
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 368, Issue 1621
Trace Metal Imaging of Sulfate-Reducing Bacteria and Methanogenic Archaea at Single-Cell Resolution by Synchrotron X-Ray Fluorescence Imaging
journal, May 2017
- Glass, Jennifer B.; Chen, Si; Dawson, Katherine S.
- Geomicrobiology Journal, Vol. 35, Issue 1
The nitrate-ammonifying and nosZ -carrying bacterium B acillus vireti is a potent source and sink for nitric and nitrous oxide under high nitrate conditions
journal, May 2014
- Mania, Daniel; Heylen, Kim; van Spanning, Rob J. M.
- Environmental Microbiology, Vol. 16, Issue 10
Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor
journal, July 2017
- Parada, Alma E.; Fuhrman, Jed A.
- The ISME Journal, Vol. 11, Issue 11
Transcriptional and environmental control of bacterial denitrification and N2O emissions
journal, December 2017
- Gaimster, Hannah; Alston, Mark; Richardson, David J.
- FEMS Microbiology Letters, Vol. 365, Issue 5
Sources and sinks for N 2 O, can microbiologist help to mitigate N 2 O emissions? : Sources and sinks for N
journal, December 2017
- Bakken, Lars R.; Frostegård, Åsa
- Environmental Microbiology, Vol. 19, Issue 12
Insights into the Effect of Soil pH on N2O and N2 Emissions and Denitrifier Community Size and Activity
journal, January 2010
- Cuhel, J.; Simek, M.; Laughlin, R. J.
- Applied and Environmental Microbiology, Vol. 76, Issue 6
Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations
journal, October 2017
- Qin, Wei; Amin, Shady A.; Lundeen, Rachel A.
- The ISME Journal, Vol. 12, Issue 2
Microbial metatranscriptomics in a permanent marine oxygen minimum zone: OMZ community gene expression
journal, January 2011
- Stewart, Frank J.; Ulloa, Osvaldo; DeLong, Edward F.
- Environmental Microbiology, Vol. 14, Issue 1
Erosion of functional independence early in the evolution of a microbial mutualism
journal, September 2014
- Hillesland, K. L.; Lim, S.; Flowers, J. J.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 41
Mechanism for microbial population collapse in a fluctuating resource environment
journal, March 2017
- Turkarslan, Serdar; Raman, Arjun V.; Thompson, Anne W.
- Molecular Systems Biology, Vol. 13, Issue 3
Transcriptome of a Nitrosomonas europaea Mutant with a Disrupted Nitrite Reductase Gene (nirK)
journal, June 2006
- Cho, C. M. -H.; Yan, T.; Liu, X.
- Applied and Environmental Microbiology, Vol. 72, Issue 6
Planktonic food web structure at a coastal time-series site: I. Partitioning of microbial abundances and carbon biomass
journal, March 2017
- Caron, David A.; Connell, Paige E.; Schaffner, Rebecca A.
- Deep Sea Research Part I: Oceanographic Research Papers, Vol. 121
Phenotypic and genotypic richness of denitrifiers revealed by a novel isolation strategy
journal, July 2017
- Lycus, Pawel; Lovise Bøthun, Kari; Bergaust, Linda
- The ISME Journal, Vol. 11, Issue 10
A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell
journal, December 2007
- Bonneau, Richard; Facciotti, Marc T.; Reiss, David J.
- Cell, Vol. 131, Issue 7
Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia
journal, June 2016
- Hatzenpichler, Roland; Connon, Stephanie A.; Goudeau, Danielle
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 28
The influence of soil pH on denitrification: progress towards the understanding of this interaction over the last 50 years
journal, September 2002
- SImek, M.; Cooper, J. E.
- European Journal of Soil Science, Vol. 53, Issue 3
Tuning the modular Paracoccus denitrificans respirome to adapt from aerobic respiration to anaerobic denitrification : A Paracoccus denitrificans
journal, December 2017
- Giannopoulos, Georgios; Sullivan, Matthew J.; Hartop, Katherine R.
- Environmental Microbiology, Vol. 19, Issue 12
Marine N 2 O Emissions From Nitrification and Denitrification Constrained by Modern Observations and Projected in Multimillennial Global Warming Simulations
journal, January 2018
- Battaglia, G.; Joos, F.
- Global Biogeochemical Cycles, Vol. 32, Issue 1
Microbial ecology of expanding oxygen minimum zones
journal, May 2012
- Wright, Jody J.; Konwar, Kishori M.; Hallam, Steven J.
- Nature Reviews Microbiology, Vol. 10, Issue 6
Inference of Gene Regulatory Network Based on Local Bayesian Networks
journal, August 2016
- Liu, Fei; Zhang, Shao-Wu; Guo, Wei-Feng
- PLOS Computational Biology, Vol. 12, Issue 8
Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes
journal, July 2014
- Hawley, A. K.; Brewer, H. M.; Norbeck, A. D.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 31
Denitrification Response Patterns during the Transition to Anoxic Respiration and Posttranscriptional Effects of Suboptimal pH on Nitrogen Oxide Reductase in Paracoccus denitrificans
journal, August 2010
- Bergaust, L.; Mao, Y.; Bakken, L. R.
- Applied and Environmental Microbiology, Vol. 76, Issue 19
Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments
journal, January 2010
- Miller, Lance D.; Mosher, Jennifer J.; Venkateswaran, Amudhan
- BMC Microbiology, Vol. 10, Issue 1
Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils
journal, November 2012
- Sanford, R. A.; Wagner, D. D.; Wu, Q.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 48
Syntrophic exchange in synthetic microbial communities
journal, April 2014
- Mee, M. T.; Collins, J. J.; Church, G. M.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 20
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
Transcript profiles of Nitrosomonas europaea during growth and upon deprivation of ammonia and carbonate
journal, April 2006
- Wei, Xueming; Yan, Tingfen; Hommes, Norman G.
- FEMS Microbiology Letters, Vol. 257, Issue 1
Species co-occurrence networks: Can they reveal trophic and non-trophic interactions in ecological communities?
journal, February 2018
- Freilich, Mara A.; Wieters, Evie; Broitman, Bernardo R.
- Ecology, Vol. 99, Issue 3
Global biogeography of microbial nitrogen-cycling traits in soil
journal, July 2016
- Nelson, Michaeline B.; Martiny, Adam C.; Martiny, Jennifer B. H.
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 29
High resolution time series reveals cohesive but short-lived communities in coastal plankton
journal, January 2018
- Martin-Platero, Antonio M.; Cleary, Brian; Kauffman, Kathryn
- Nature Communications, Vol. 9, Issue 1
A multi-year time-series of N 2 O dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia
journal, September 2017
- Capelle, David W.; Hawley, Alyse K.; Hallam, Steven J.
- Limnology and Oceanography, Vol. 63, Issue 2
Nitrogen substrate–dependent nitrous oxide cycling in salt marsh sediments
journal, May 2015
- Ji, Qixing; Babbin, Andrew R.; Peng, Xuefeng
- Journal of Marine Research, Vol. 73, Issue 3
Kinetics of NH 3 -oxidation, NO-turnover, N 2 O-production and electron flow during oxygen depletion in model bacterial and archaeal ammonia oxidisers : Kinetics of NH
journal, September 2017
- Hink, Linda; Lycus, Pawel; Gubry-Rangin, Cécile
- Environmental Microbiology, Vol. 19, Issue 12
Modeling global annual N 2 O and NO emissions from fertilized fields : N
journal, November 2002
- Bouwman, A. F.; Boumans, L. J. M.; Batjes, N. H.
- Global Biogeochemical Cycles, Vol. 16, Issue 4
Predicting in situ soil N2O emission using NOE algorithm and soil database
journal, January 2005
- Henault, C.; Bizouard, F.; Laville, P.
- Global Change Biology, Vol. 11, Issue 1
Steady-State Growth under Inorganic Carbon Limitation Conditions Increases Energy Consumption for Maintenance and Enhances Nitrous Oxide Production in Nitrosomonas europaea
journal, March 2016
- Mellbye, Brett L.; Giguere, Andrew; Chaplen, Frank
- Applied and Environmental Microbiology, Vol. 82, Issue 11
Nitrogen cycling in the secondary nitrite maximum of the eastern tropical North Pacific off Costa Rica
journal, December 2015
- Buchwald, Carolyn; Santoro, Alyson E.; Stanley, Rachel H. R.
- Global Biogeochemical Cycles, Vol. 29, Issue 12
Nitrous oxide production by nitrification and denitrification in the Eastern Tropical South Pacific oxygen minimum zone: NITROUS OXIDE PRODUCTION IN OMZ
journal, December 2015
- Ji, Qixing; Babbin, Andrew R.; Jayakumar, Amal
- Geophysical Research Letters, Vol. 42, Issue 24
Microbial oceanography of anoxic oxygen minimum zones
journal, September 2012
- Ulloa, O.; Canfield, D. E.; DeLong, E. F.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 40
DAYCENT National-Scale Simulations of Nitrous Oxide Emissions from Cropped Soils in the United States
journal, January 2006
- Del Grosso, S. J.; Parton, W. J.; Mosier, A. R.
- Journal of Environment Quality, Vol. 35, Issue 4
Temperature determines the diversity and structure of N 2 O-reducing microbial assemblages
journal, March 2018
- Wu, Bo; Liu, Feifei; Weiser, Michael D.
- Functional Ecology, Vol. 32, Issue 7
Cell morphology drives spatial patterning in microbial communities
journal, December 2016
- Smith, William P. J.; Davit, Yohan; Osborne, James M.
- Proceedings of the National Academy of Sciences, Vol. 114, Issue 3
Spatial scale drives patterns in soil bacterial diversity: Spatial scale drives soil diversity
journal, March 2016
- O'Brien, Sarah L.; Gibbons, Sean M.; Owens, Sarah M.
- Environmental Microbiology, Vol. 18, Issue 6
Production of oceanic nitrous oxide by ammonia-oxidizing archaea
journal, January 2012
- Löscher, C. R.; Kock, A.; Könneke, M.
- Biogeosciences, Vol. 9, Issue 7
Linking Genes to Microbial Biogeochemical Cycling: Lessons from Arsenic
journal, June 2017
- Zhu, Yong-Guan; Xue, Xi-Mei; Kappler, Andreas
- Environmental Science & Technology, Vol. 51, Issue 13
Spreading Dead Zones and Consequences for Marine Ecosystems
journal, August 2008
- Diaz, R. J.; Rosenberg, R.
- Science, Vol. 321, Issue 5891
Functional Enzyme-Based Approach for Linking Microbial Community Functions with Biogeochemical Process Kinetics
journal, September 2017
- Li, Minjing; Qian, Wei-jun; Gao, Yuqian
- Environmental Science & Technology, Vol. 51, Issue 20
Deciphering microbial interactions in synthetic human gut microbiome communities
journal, June 2018
- Venturelli, Ophelia S.; Carr, Alex V.; Fisher, Garth
- Molecular Systems Biology, Vol. 14, Issue 6
Exploring the Denitrification Proteome of Paracoccus denitrificans PD1222
journal, May 2018
- Olaya-Abril, Alfonso; Hidalgo-Carrillo, Jesús; Luque-Almagro, Víctor M.
- Frontiers in Microbiology, Vol. 9
Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters
journal, April 2017
- Needham, David M.; Sachdeva, Rohan; Fuhrman, Jed A.
- The ISME Journal, Vol. 11, Issue 7
Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast
journal, May 2017
- Wang, Zhuo; Danziger, Samuel A.; Heavner, Benjamin D.
- PLOS Computational Biology, Vol. 13, Issue 5
Peaks of in situ N 2 O emissions are influenced by N 2 O-producing and reducing microbial communities across arable soils
journal, September 2017
- Domeignoz-Horta, Luiz A.; Philippot, Laurent; Peyrard, Celine
- Global Change Biology, Vol. 24, Issue 1
Adaptive Prediction Emerges Over Short Evolutionary Time Scales
journal, June 2017
- López García de Lomana, Adrián; Kaur, Amardeep; Turkarslan, Serdar
- Genome Biology and Evolution, Vol. 9, Issue 6
Interactions of Nitrosomonas europaea and Nitrobacter winogradskyi grown in co-culture
journal, November 2014
- Pérez, José; Buchanan, Alex; Mellbye, Brett
- Archives of Microbiology, Vol. 197, Issue 1
Predominant but Previously-overlooked Prokaryotic Drivers of Reductive Nitrogen Transformation in Paddy Soils, Revealed by Metatranscriptomics
journal, January 2017
- Masuda, Yoko; Itoh, Hideomi; Shiratori, Yutaka
- Microbes and environments, Vol. 32, Issue 2
Two dynamic regimes in the human gut microbiome
journal, February 2017
- Gibbons, Sean M.; Kearney, Sean M.; Smillie, Chris S.
- PLOS Computational Biology, Vol. 13, Issue 2
A high-resolution network model for global gene regulation in Mycobacterium tuberculosis
journal, September 2014
- Peterson, Eliza J. R.; Reiss, David J.; Turkarslan, Serdar
- Nucleic Acids Research, Vol. 42, Issue 18
The segment polarity network is a robust developmental module
journal, July 2000
- von Dassow, George; Meir, Eli; Munro, Edwin M.
- Nature, Vol. 406, Issue 6792
Nitrous Oxide (N2O): The Dominant Ozone-Depleting Substance Emitted in the 21st Century
journal, August 2009
- Ravishankara, A. R.; Daniel, J. S.; Portmann, R. W.
- Science, Vol. 326, Issue 5949
A compendium of geochemical information from the Saanich Inlet water column
journal, October 2017
- Torres-Beltrán, Mónica; Hawley, Alyse K.; Capelle, David
- Scientific Data, Vol. 4, Issue 1
High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats
journal, January 2015
- Zhou, Jizhong; He, Zhili; Yang, Yunfeng
- mBio, Vol. 6, Issue 1
Intergenomic Comparisons Highlight Modularity of the Denitrification Pathway and Underpin the Importance of Community Structure for N2O Emissions
journal, December 2014
- Graf, Daniel R. H.; Jones, Christopher M.; Hallin, Sara
- PLoS ONE, Vol. 9, Issue 12
Robustness of a model microbial community emerges from population structure among single cells of a clonal population
journal, May 2017
- Thompson, Anne W.; Turkarslan, Serdar; Arens, Christina E.
- Environmental Microbiology, Vol. 19, Issue 8
Rapid nitrous oxide cycling in the suboxic ocean
journal, June 2015
- Babbin, A. R.; Bianchi, D.; Jayakumar, A.
- Science, Vol. 348, Issue 6239
Regulation of nitrogen metabolism in the nitrate-ammonifying soil bacterium B acillus vireti and evidence for its ability to grow using N 2 O as electron acceptor : Regulation of N-metabolism and N
journal, January 2016
- Mania, Daniel; Heylen, Kim; van Spanning, Rob J. M.
- Environmental Microbiology, Vol. 18, Issue 9
Massive nitrous oxide emissions from the tropical South Pacific Ocean
journal, June 2015
- Arévalo-Martínez, D. L.; Kock, A.; Löscher, C. R.
- Nature Geoscience, Vol. 8, Issue 7
Detecting Causality in Complex Ecosystems
journal, September 2012
- Sugihara, G.; May, R.; Ye, H.
- Science, Vol. 338, Issue 6106
Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone
journal, September 2013
- Ganesh, Sangita; Parris, Darren J.; DeLong, Edward F.
- The ISME Journal, Vol. 8, Issue 1
Transcriptional and metabolic regulation of denitrification in P aracoccus denitrificans allows low but significant activity of nitrous oxide reductase under oxic conditions : Oxic N
journal, January 2016
- Qu, Zhi; Bakken, Lars R.; Molstad, Lars
- Environmental Microbiology, Vol. 18, Issue 9
Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale
journal, June 2009
- Lauber, C. L.; Hamady, M.; Knight, R.
- Applied and Environmental Microbiology, Vol. 75, Issue 15
Metagenomic analysis of nitrogen and methane cycling in the Arabian Sea oxygen minimum zone
journal, January 2016
- Lüke, Claudia; Speth, Daan R.; Kox, Martine A. R.
- PeerJ, Vol. 4
From the Ground Up: Global Nitrous Oxide Sources are Constrained by Stable Isotope Values
journal, March 2015
- Snider, David M.; Venkiteswaran, Jason J.; Schiff, Sherry L.
- PLOS ONE, Vol. 10, Issue 3
Simulating the global distribution of nitrogen isotopes in the ocean: NITROGEN ISOTOPES IN THE GLOBAL OCEAN
journal, November 2010
- Somes, Christopher J.; Schmittner, Andreas; Galbraith, Eric D.
- Global Biogeochemical Cycles, Vol. 24, Issue 4
Constraining a complex biogeochemical model for CO 2 and N 2 O emission simulations from various land uses by model–data fusion
journal, January 2017
- Houska, Tobias; Kraus, David; Kiese, Ralf
- Biogeosciences, Vol. 14, Issue 14
The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions
journal, January 2018
- Hink, Linda; Gubry-Rangin, Cécile; Nicol, Graeme W.
- The ISME Journal, Vol. 12, Issue 4
Top-down estimates of European CH 4 and N 2 O emissions based on four different inverse models
journal, January 2015
- Bergamaschi, P.; Corazza, M.; Karstens, U.
- Atmospheric Chemistry and Physics, Vol. 15, Issue 2
Modularity of nitrogen-oxide reducing soil bacteria: linking phenotype to genotype: Modularity of denitrifiers: phenotype to genotype
journal, March 2016
- Roco, Constance A.; Bergaust, Linda L.; Bakken, Lars R.
- Environmental Microbiology, Vol. 19, Issue 6
Ocean acidification conditions increase resilience of marine diatoms
journal, June 2018
- Valenzuela, Jacob J.; López García de Lomana, Adrián; Lee, Allison
- Nature Communications, Vol. 9, Issue 1
A system‐level model for the microbial regulatory genome
journal, July 2014
- Brooks, Aaron N.; Reiss, David J.; Allard, Antoine
- Molecular Systems Biology, Vol. 10, Issue 7
Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of Nitrosomonas europaea and Nitrobacter winogradskyi
journal, March 2018
- Mellbye, Brett L.; Giguere, Andrew T.; Murthy, Ganti S.
- mSystems, Vol. 3, Issue 3
Disentangling gross N2O production and consumption in soil
journal, November 2016
- Wen, Yuan; Chen, Zhe; Dannenmann, Michael
- Scientific Reports, Vol. 6, Issue 1
Patterns of thaumarchaeal gene expression in culture and diverse marine environments
journal, April 2018
- Carini, Paul; Dupont, Christopher L.; Santoro, Alyson E.
- Environmental Microbiology, Vol. 20, Issue 6
Soil food web properties explain ecosystem services across European land use systems
journal, August 2013
- de Vries, F. T.; Thebault, E.; Liiri, M.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 35
A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen
journal, October 2013
- Yoon, Sung Ho; Turkarslan, Serdar; Reiss, David J.
- Genome Research, Vol. 23, Issue 11
The response patterns of community traits of N2O emission-related functional guilds to temperature across different arable soils under inorganic fertilization
journal, May 2017
- Yin, Chang; Fan, Fenliang; Song, Alin
- Soil Biology and Biochemistry, Vol. 108
Community Composition of Nitrous Oxide Consuming Bacteria in the Oxygen Minimum Zone of the Eastern Tropical South Pacific
journal, June 2017
- Sun, Xin; Jayakumar, Amal; Ward, Bess B.
- Frontiers in Microbiology, Vol. 8
Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana
journal, April 2013
- Ashworth, J.; Coesel, S.; Lee, A.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 18
Use of stable isotope-labelled cells to identify active grazers of picocyanobacteria in ocean surface waters
journal, February 2009
- Frias-Lopez, Jorge; Thompson, Anne; Waldbauer, Jacob
- Environmental Microbiology, Vol. 11, Issue 2
Compound driven differences in N2 and N2O emission from soil; the role of substrate use efficiency and the microbial community
journal, March 2017
- Giles, Madeline E.; Daniell, Tim J.; Baggs, Elizabeth M.
- Soil Biology and Biochemistry, Vol. 106
Synthetic microbial communities
journal, April 2014
- Großkopf, Tobias; Soyer, Orkun S.
- Current Opinion in Microbiology, Vol. 18
Presence of nitrous oxide hotspots in the coastal upwelling area off central Chile: an analysis of temporal variability based on ten years of a biogeochemical time series
journal, April 2015
- Farías, L.; Besoain, V.; García-Loyola, S.
- Environmental Research Letters, Vol. 10, Issue 4
Genome-Wide Discovery of Putative sRNAs in Paracoccus denitrificans Expressed under Nitrous Oxide Emitting Conditions
journal, November 2016
- Gaimster, Hannah; Chalklen, Lisa; Alston, Mark
- Frontiers in Microbiology, Vol. 7
First 20 years of DNDC (DeNitrification DeComposition): Model evolution
journal, November 2014
- Gilhespy, Sarah L.; Anthony, Steven; Cardenas, Laura
- Ecological Modelling, Vol. 292
Nitrogen footprints: Regional realities and options to reduce nitrogen loss to the environment
journal, September 2016
- Shibata, Hideaki; Galloway, James N.; Leach, Allison M.
- Ambio, Vol. 46, Issue 2
A meta-analysis of changes in bacterial and archaeal communities with time
journal, April 2013
- Shade, Ashley; Gregory Caporaso, J.; Handelsman, Jo
- The ISME Journal, Vol. 7, Issue 8
Deciphering microbial interactions and detecting keystone species with co-occurrence networks
journal, May 2014
- Berry, David; Widder, Stefanie
- Frontiers in Microbiology, Vol. 5
Challenges in microbial ecology: building predictive understanding of community function and dynamics
journal, March 2016
- Widder, Stefanie; Allen, Rosalind J.; Pfeiffer, Thomas
- The ISME Journal, Vol. 10, Issue 11
Rapidly moving new bacteria to model-organism status
journal, June 2018
- Liu, Hualan; Deutschbauer, Adam M.
- Current Opinion in Biotechnology, Vol. 51
Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes
journal, December 2017
- Desai, Jigar S.; Sartor, Ryan C.; Lawas, Lovely Mae
- Scientific Reports, Vol. 7, Issue 1
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
journal, September 2010
- Chandrasekaran, Sriram; Price, Nathan D.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 41
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
journal, July 2010
- McKenna, A.; Hanna, M.; Banks, E.
- Genome Research, Vol. 20, Issue 9
Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone
journal, December 2017
- Fuchsman, Clara A.; Devol, Allan H.; Saunders, Jaclyn K.
- Frontiers in Microbiology, Vol. 8
Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones
journal, January 2013
- Peng, Xuefeng; Jayakumar, Amal; Ward, Bess B.
- Frontiers in Microbiology, Vol. 4
Year-Round Shotgun Metagenomes Reveal Stable Microbial Communities in Agricultural Soils and Novel Ammonia Oxidizers Responding to Fertilization
journal, November 2017
- Orellana, Luis H.; Chee-Sanford, Joanne C.; Sanford, Robert A.
- Applied and Environmental Microbiology, Vol. 84, Issue 2
Steady-State Oxygen Isotope Effects of N2O Production in Paracoccus denitrificans
journal, March 2017
- Barford, Carol; Montoya, Joseph; Altabet, Mark
- Microbial Ecology, Vol. 74, Issue 3
The contribution of manure and fertilizer nitrogen to atmospheric nitrous oxide since 1860
journal, August 2009
- Davidson, Eric A.
- Nature Geoscience, Vol. 2, Issue 9
Gene-centric approach to integrating environmental genomics and biogeochemical models
journal, January 2014
- Reed, Daniel C.; Algar, Christopher K.; Huber, Julie A.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 5
Ammonia‐oxidizing bacteria are the primary N 2 O producers in an ammonia‐oxidizing archaea dominated alkaline agricultural soil
journal, June 2018
- Meinhardt, Kelley A.; Stopnisek, Nejc; Pannu, Manmeet W.
- Environmental Microbiology, Vol. 20, Issue 6
Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities: Synthetic microbial ecosystems
journal, December 2013
- De Roy, Karen; Marzorati, Massimo; Van den Abbeele, Pieter
- Environmental Microbiology, Vol. 16, Issue 6
Regulation of denitrification at the cellular level: a clue to the understanding of N 2 O emissions from soils
journal, May 2012
- Bakken, Lars R.; Bergaust, Linda; Liu, Binbin
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 367, Issue 1593
Agriculture's impact on microbial diversity and associated fluxes of carbon dioxide and methane
journal, April 2011
- Levine, Uri Y.; Teal, Tracy K.; Robertson, G. Philip
- The ISME Journal, Vol. 5, Issue 10