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Title: Microbial carbon use efficiency predicted from genome-scale metabolic models

Authors:
; ORCiD logo; ORCiD logo;
Publication Date:
Research Org.:
Univ. of Illinois, Champaign, IL (United States). Center for Advanced Bioenergy and Bioproducts Innovation
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1619681
Alternate Identifier(s):
OSTI ID: 1558097
Grant/Contract Number:  
502206221; SC0018420
Resource Type:
Published Article
Journal Name:
Nature Communications
Additional Journal Information:
Journal Name: Nature Communications Journal Volume: 10 Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Carbon use efficiency; soil bacteria

Citation Formats

Saifuddin, Mustafa, Bhatnagar, Jennifer M., Segrè, Daniel, and Finzi, Adrien C. Microbial carbon use efficiency predicted from genome-scale metabolic models. United Kingdom: N. p., 2019. Web. doi:10.1038/s41467-019-11488-z.
Saifuddin, Mustafa, Bhatnagar, Jennifer M., Segrè, Daniel, & Finzi, Adrien C. Microbial carbon use efficiency predicted from genome-scale metabolic models. United Kingdom. doi:10.1038/s41467-019-11488-z.
Saifuddin, Mustafa, Bhatnagar, Jennifer M., Segrè, Daniel, and Finzi, Adrien C. Thu . "Microbial carbon use efficiency predicted from genome-scale metabolic models". United Kingdom. doi:10.1038/s41467-019-11488-z.
@article{osti_1619681,
title = {Microbial carbon use efficiency predicted from genome-scale metabolic models},
author = {Saifuddin, Mustafa and Bhatnagar, Jennifer M. and Segrè, Daniel and Finzi, Adrien C.},
abstractNote = {},
doi = {10.1038/s41467-019-11488-z},
journal = {Nature Communications},
number = 1,
volume = 10,
place = {United Kingdom},
year = {2019},
month = {8}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1038/s41467-019-11488-z

Citation Metrics:
Cited by: 1 work
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Works referenced in this record:

Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria
journal, April 2014

  • Barberán, Albert; Ramirez, Kelly S.; Leff, Jonathan W.
  • Ecology Letters, Vol. 17, Issue 7
  • DOI: 10.1111/ele.12282

Impact of wheat straw decomposition on successional patterns of soil microbial community structure
journal, February 2009


In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
journal, February 2001

  • Edwards, Jeremy S.; Ibarra, Rafael U.; Palsson, Bernhard O.
  • Nature Biotechnology, Vol. 19, Issue 2
  • DOI: 10.1038/84379

Bacterial genomic G+C composition-eliciting environmental adaptation
journal, January 2010


BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
journal, October 2015

  • King, Zachary A.; Lu, Justin; Dräger, Andreas
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1049

Soil carbon sensitivity to temperature and carbon use efficiency compared across microbial-ecosystem models of varying complexity
journal, January 2014


High-throughput generation, optimization and analysis of genome-scale metabolic models
journal, August 2010

  • Henry, Christopher S.; DeJongh, Matthew; Best, Aaron A.
  • Nature Biotechnology, Vol. 28, Issue 9
  • DOI: 10.1038/nbt.1672

A Brief History of Seed Size
journal, January 2005


Global spatiotemporal distribution of soil respiration modeled using a global database
journal, January 2015


Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics
journal, May 2014


Soil carbon and nitrogen mineralization: Theory and models across scales
journal, July 2009


Efficiently gap-filling reaction networks
journal, June 2014


Streamlining and Simplification of Microbial Genome Architecture
journal, October 2006


Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.
journal, January 1994


Rapid peptide metabolism: A major component of soil nitrogen cycling?: PEPTIDE METABOLISM BY SOIL MICROBES
journal, August 2011

  • Farrell, Mark; Hill, Paul W.; Wanniarachchi, Sudas D.
  • Global Biogeochemical Cycles, Vol. 25, Issue 3
  • DOI: 10.1029/2010GB003999

Environmental and stoichiometric controls on microbial carbon-use efficiency in soils: Research review
journal, July 2012


Stoichiometry of microbial carbon use efficiency in soils
journal, May 2016

  • Sinsabaugh, Robert L.; Turner, Benjamin L.; Talbot, Jennifer M.
  • Ecological Monographs, Vol. 86, Issue 2
  • DOI: 10.1890/15-2110.1

Phylogenetic organization of bacterial activity
journal, March 2016

  • Morrissey, Ember M.; Mau, Rebecca L.; Schwartz, Egbert
  • The ISME Journal, Vol. 10, Issue 9
  • DOI: 10.1038/ismej.2016.28

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010


The physiology and ecological implications of efficient growth
journal, January 2015


Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
journal, August 2011

  • Schellenberger, Jan; Que, Richard; Fleming, Ronan M. T.
  • Nature Protocols, Vol. 6, Issue 9
  • DOI: 10.1038/nprot.2011.308

Phylogenetic conservatism of functional traits in microorganisms
journal, December 2012

  • Martiny, Adam C.; Treseder, Kathleen; Pusch, Gordon
  • The ISME Journal, Vol. 7, Issue 4
  • DOI: 10.1038/ismej.2012.160

Dynamics and identification of soil microbial populations actively assimilating carbon from 13 C-labelled wheat residue as estimated by DNA- and RNA-SIP techniques
journal, March 2007


phytools: an R package for phylogenetic comparative biology (and other things): phytools: R package
journal, December 2011


Microbial carbon use efficiency: accounting for population, community, and ecosystem-scale controls over the fate of metabolized organic matter
journal, February 2016

  • Geyer, Kevin M.; Kyker-Snowman, Emily; Grandy, A. Stuart
  • Biogeochemistry, Vol. 127, Issue 2-3
  • DOI: 10.1007/s10533-016-0191-y

Bacterial carbon use plasticity, phylogenetic diversity and the priming of soil organic matter
journal, April 2017

  • Morrissey, Ember M.; Mau, Rebecca L.; Schwartz, Egbert
  • The ISME Journal, Vol. 11, Issue 8
  • DOI: 10.1038/ismej.2017.43

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe
journal, August 2015

  • Leff, Jonathan W.; Jones, Stuart E.; Prober, Suzanne M.
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 35
  • DOI: 10.1073/pnas.1508382112

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
journal, December 2012

  • Fierer, N.; Leff, J. W.; Adams, B. J.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 52
  • DOI: 10.1073/pnas.1215210110

A protocol for generating a high-quality genome-scale metabolic reconstruction
journal, January 2010


Exploiting rRNA operon copy number to investigate bacterial reproductive strategies
journal, September 2016

  • Roller, Benjamin R. K.; Stoddard, Steven F.; Schmidt, Thomas M.
  • Nature Microbiology, Vol. 1, Issue 11
  • DOI: 10.1038/nmicrobiol.2016.160

Soil organic nitrogen mineralization across a global latitudinal gradient: NITROGEN MINERALIZATION VERSUS LATITUDE
journal, March 2009

  • Jones, D. L.; Kielland, K.; Sinclair, F. L.
  • Global Biogeochemical Cycles, Vol. 23, Issue 1
  • DOI: 10.1029/2008GB003250

KBase: The United States Department of Energy Systems Biology Knowledgebase
journal, July 2018

  • Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S.
  • Nature Biotechnology, Vol. 36, Issue 7
  • DOI: 10.1038/nbt.4163

Using Genome-scale Models to Predict Biological Capabilities
journal, May 2015


Soil microbial organic nitrogen uptake is regulated by carbon availability
journal, October 2014


Phylocom: software for the analysis of phylogenetic community structure and trait evolution
journal, August 2008


Towards predicting the environmental metabolome from metagenomics with a mechanistic model
journal, March 2018

  • Garza, Daniel R.; van Verk, Marcel C.; Huynen, Martijn A.
  • Nature Microbiology, Vol. 3, Issue 4
  • DOI: 10.1038/s41564-018-0124-8

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
journal, November 2016

  • Magnúsdóttir, Stefanía; Heinken, Almut; Kutt, Laura
  • Nature Biotechnology, Vol. 35, Issue 1
  • DOI: 10.1038/nbt.3703

The genomic basis of trophic strategy in marine bacteria
journal, September 2009

  • Lauro, F. M.; McDougald, D.; Thomas, T.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 37, p. 15527-15533
  • DOI: 10.1073/pnas.0903507106

A parsimonious modular approach to building a mechanistic belowground carbon and nitrogen model: Parsimonious, Modular Model of Belowground C and N Cycling
journal, September 2017

  • Abramoff, Rose Z.; Davidson, Eric A.; Finzi, Adrien C.
  • Journal of Geophysical Research: Biogeosciences, Vol. 122, Issue 9
  • DOI: 10.1002/2017JG003796

Trends between gene content and genome size in prokaryotic species with larger genomes
journal, February 2004

  • Konstantinidis, K. T.; Tiedje, J. M.
  • Proceedings of the National Academy of Sciences, Vol. 101, Issue 9
  • DOI: 10.1073/pnas.0308653100

Responses of a tundra system to warming using SCAMPS: a stoichiometrically coupled, acclimating microbe–plant–soil model
journal, February 2014

  • Sistla, Seeta A.; Rastetter, Edward B.; Schimel, Joshua P.
  • Ecological Monographs, Vol. 84, Issue 1
  • DOI: 10.1890/12-2119.1

Long-term forest soil warming alters microbial communities in temperate forest soils
journal, February 2015

  • DeAngelis, Kristen M.; Pold, Grace; TopçuoÄŸlu, Begüm D.
  • Frontiers in Microbiology, Vol. 6
  • DOI: 10.3389/fmicb.2015.00104

A global relationship between the heterotrophic and autotrophic components of soil respiration?
journal, October 2004


Sustainable bioenergy production from marginal lands in the US Midwest
journal, January 2013

  • Gelfand, Ilya; Sahajpal, Ritvik; Zhang, Xuesong
  • Nature, Vol. 493, Issue 7433
  • DOI: 10.1038/nature11811

Physicochemical study of curcumin in oil driven nanoemulsions with surfactants
journal, August 2016


Soil-carbon response to warming dependent on microbial physiology
journal, April 2010

  • Allison, Steven D.; Wallenstein, Matthew D.; Bradford, Mark A.
  • Nature Geoscience, Vol. 3, Issue 5
  • DOI: 10.1038/ngeo846

APE: Analyses of Phylogenetics and Evolution in R language
journal, January 2004


The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
journal, November 2013

  • Overbeek, Ross; Olson, Robert; Pusch, Gordon D.
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1226

The Phylogenetic Regression
journal, December 1989

  • Grafen, A.
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 326, Issue 1233
  • DOI: 10.1098/rstb.1989.0106

The Uptake of Amino Acids by Microbes and Trees in Three Cold-Temperate Forests
journal, December 2005

  • Finzi, Adrien C.; Berthrong, Sean T.
  • Ecology, Vol. 86, Issue 12
  • DOI: 10.1890/04-1460

Microbial biomass, functional capacity, and community structure after 12 years of soil warming
journal, November 2008


Rapid microbial uptake and mineralization of amino acids and peptides along a grassland productivity gradient
journal, May 2014


Differences in substrate use efficiency: impacts of microbial community composition, land use management, and substrate complexity
journal, February 2016

  • Bölscher, Tobias; Wadsö, Lars; Börjesson, Gunnar
  • Biology and Fertility of Soils, Vol. 52, Issue 4
  • DOI: 10.1007/s00374-016-1097-5

Testing for Phylogenetic Signal in Comparative Data: Behavioral Traits are more Labile
journal, April 2003


Picante: R tools for integrating phylogenies and ecology
journal, April 2010


Carbon use efficiency of microbial communities: stoichiometry, methodology and modelling
journal, April 2013

  • Sinsabaugh, Robert L.; Manzoni, Stefano; Moorhead, Daryl L.
  • Ecology Letters, Vol. 16, Issue 7
  • DOI: 10.1111/ele.12113

Adjustment of microbial nitrogen use efficiency to carbon:nitrogen imbalances regulates soil nitrogen cycling
journal, April 2014

  • Mooshammer, Maria; Wanek, Wolfgang; Hämmerle, Ieda
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms4694

Temperature-associated increases in the global soil respiration record
journal, March 2010


High carbon use efficiency in soil microbial communities is related to balanced growth, not storage compound synthesis
journal, October 2015


Toward an Ecological Classification of soil Bacteria
journal, June 2007

  • Fierer, Noah; Bradford, Mark A.; Jackson, Robert B.
  • Ecology, Vol. 88, Issue 6
  • DOI: 10.1890/05-1839