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

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]
  1. Department of Biology and PhD Program in Biogeoscience, Boston University, Boston Massachusetts USA, Climate Sciences Department, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley California USA
  2. Appalachian Laboratory, University of Maryland Center for Environmental Sciences, Frostburg Maryland USA
  3. Department of Biology and PhD Program in Biogeoscience, Boston University, Boston Massachusetts USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1393732
Grant/Contract Number:  
SC0006916; SC0012288; AC02-05CH11231
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
Journal of Geophysical Research. Biogeosciences
Additional Journal Information:
Journal Name: Journal of Geophysical Research. Biogeosciences Journal Volume: 122 Journal Issue: 9; Journal ID: ISSN 2169-8953
Publisher:
American Geophysical Union (AGU)
Country of Publication:
United States
Language:
English

Citation Formats

Abramoff, Rose Z., Davidson, Eric A., and Finzi, Adrien C. A parsimonious modular approach to building a mechanistic belowground carbon and nitrogen model: Parsimonious, Modular Model of Belowground C and N Cycling. United States: N. p., 2017. Web. doi:10.1002/2017JG003796.
Abramoff, Rose Z., Davidson, Eric A., & Finzi, Adrien C. A parsimonious modular approach to building a mechanistic belowground carbon and nitrogen model: Parsimonious, Modular Model of Belowground C and N Cycling. United States. doi:10.1002/2017JG003796.
Abramoff, Rose Z., Davidson, Eric A., and Finzi, Adrien C. Thu . "A parsimonious modular approach to building a mechanistic belowground carbon and nitrogen model: Parsimonious, Modular Model of Belowground C and N Cycling". United States. doi:10.1002/2017JG003796.
@article{osti_1393732,
title = {A parsimonious modular approach to building a mechanistic belowground carbon and nitrogen model: Parsimonious, Modular Model of Belowground C and N Cycling},
author = {Abramoff, Rose Z. and Davidson, Eric A. and Finzi, Adrien C.},
abstractNote = {},
doi = {10.1002/2017JG003796},
journal = {Journal of Geophysical Research. Biogeosciences},
number = 9,
volume = 122,
place = {United States},
year = {2017},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1002/2017JG003796

Citation Metrics:
Cited by: 8 works
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Works referenced in this record:

Soil CO 2 efflux in a beech forest: the contribution of root respiration
journal, January 1999

  • Epron, Daniel; Farque, Laetitia; Lucot, Eric
  • ANNALS OF FOREST SCIENCE, Vol. 56, Issue 4
  • DOI: 10.1051/forest:19990403

Representing life in the Earth system with soil microbial functional traits in the MIMICS model
journal, January 2015

  • Wieder, W. R.; Grandy, A. S.; Kallenbach, C. M.
  • Geoscientific Model Development Discussions, Vol. 8, Issue 2
  • DOI: 10.5194/gmdd-8-2011-2015

A theoretical analysis of microbial eco-physiological and diffusion limitations to carbon cycling in drying soils
journal, June 2014


A Theoretical Model of Litter Decay and Microbial Interaction
journal, May 2006


Incorporating microbial dormancy dynamics into soil decomposition models to improve quantification of soil carbon dynamics of northern temperate forests
journal, December 2015

  • He, Yujie; Yang, Jinyan; Zhuang, Qianlai
  • Journal of Geophysical Research: Biogeosciences, Vol. 120, Issue 12
  • DOI: 10.1002/2015JG003130

Mineral protection of soil carbon counteracted by root exudates
journal, March 2015

  • Keiluweit, Marco; Bougoure, Jeremy J.; Nico, Peter S.
  • Nature Climate Change, Vol. 5, Issue 6
  • DOI: 10.1038/nclimate2580

Substrate supply, fine roots, and temperature control proteolytic enzyme activity in temperate forest soils
journal, April 2011

  • Brzostek, Edward R.; Finzi, Adrien C.
  • Ecology, Vol. 92, Issue 4
  • DOI: 10.1890/10-1803.1

Moisture modulates rhizosphere effects on C decomposition in two different soil types
journal, September 2007


Priming effects: Interactions between living and dead organic matter
journal, September 2010


A big-microsite framework for soil carbon modeling
journal, September 2014

  • Davidson, Eric A.; Savage, Kathleen E.; Finzi, Adrien C.
  • Global Change Biology, Vol. 20, Issue 12
  • DOI: 10.1111/gcb.12718

A note on the reverse Michaelis–Menten kinetics
journal, February 2013


Differences in fungal and bacterial physiology alter soil carbon and nitrogen cycling: insights from meta-analysis and theoretical models
journal, May 2013

  • Waring, Bonnie G.; Averill, Colin; Hawkes, Christine V.
  • Ecology Letters, Vol. 16, Issue 7
  • DOI: 10.1111/ele.12125

Analysis of Factors Controlling Soil Organic Matter Levels in Great Plains Grasslands1
journal, January 1987


Stoichiometry of dissolved organic matter dynamics on the continental shelf of the northeastern U.S.A.
journal, April 1997


Root carbon inputs to the rhizosphere stimulate extracellular enzyme activity and increase nitrogen availability in temperate forest soils
journal, December 2012


Labile soil carbon inputs mediate the soil microbial community composition and plant residue decomposition rates
journal, September 2010


Priming effects in soils after combined and repeated substrate additions
journal, September 2005


Models of soil organic matter decomposition: the SoilR package, version 1.0
journal, January 2012

  • Sierra, C. A.; Müller, M.; Trumbore, S. E.
  • Geoscientific Model Development, Vol. 5, Issue 4
  • DOI: 10.5194/gmd-5-1045-2012

Three scales of temporal resolution from automated soil respiration measurements
journal, November 2009


Contribution of sorption, DOC transport and microbial interactions to the 14C age of a soil organic carbon profile: Insights from a calibrated process model
journal, September 2015


The Dual Arrhenius and Michaelis-Menten kinetics model for decomposition of soil organic matter at hourly to seasonal time scales
journal, October 2011


Microbial models with data-driven parameters predict stronger soil carbon responses to climate change
journal, March 2015

  • Hararuk, Oleksandra; Smith, Matthew J.; Luo, Yiqi
  • Global Change Biology, Vol. 21, Issue 6
  • DOI: 10.1111/gcb.12827

Substrate and environmental controls on microbial assimilation of soil organic carbon: a framework for Earth system models
journal, February 2014

  • Xu, Xiaofeng; Schimel, Joshua P.; Thornton, Peter E.
  • Ecology Letters, Vol. 17, Issue 5
  • DOI: 10.1111/ele.12254

The dependence of soil CO2 efflux on temperature
journal, February 2001


Seasonal dynamics of soil respiration and N mineralization in chronically warmed and fertilized soils
journal, March 2011


Stoichiometry constrains microbial response to root exudation- insights from a model and a field experiment in a temperate forest
journal, January 2013


Rhizosphere priming can promote mobilisation of N-rich compounds from soil organic matter
journal, February 2015


On the Temperature Dependence of Soil Respiration
journal, June 1994

  • Lloyd, J.; Taylor, J. A.
  • Functional Ecology, Vol. 8, Issue 3
  • DOI: 10.2307/2389824

CLM4-BeTR, a generic biogeochemical transport and reaction module for CLM4: model development, evaluation, and application
journal, January 2013

  • Tang, J. Y.; Riley, W. J.; Koven, C. D.
  • Geoscientific Model Development, Vol. 6, Issue 1
  • DOI: 10.5194/gmd-6-127-2013

Long-Term Nitrogen Additions and Nitrogen Saturation in Two Temperate Forests
journal, May 2000

  • Magill, Alison H.; Aber, John D.; Berntson, Glenn M.
  • Ecosystems, Vol. 3, Issue 3
  • DOI: 10.1007/s100210000023

Interactions between soil and tree roots accelerate long-term soil carbon decomposition
journal, November 2007


Scaling of C:N:P Stoichiometry in Forests Worldwide: Implications of Terrestrial Redfield-Type Ratios
journal, September 2004

  • McGroddy, Megan E.; Daufresne, Tanguy; Hedin, Lars O.
  • Ecology, Vol. 85, Issue 9
  • DOI: 10.1890/03-0351

The Michaelis-Menten kinetics of soil extracellular enzymes in response to temperature: a cross-latitudinal study
journal, January 2012


Intra-annual and interannual variability of ecosystem processes in shortgrass steppe
journal, August 2000

  • Kelly, R. H.; Parton, W. J.; Hartman, M. D.
  • Journal of Geophysical Research: Atmospheres, Vol. 105, Issue D15
  • DOI: 10.1029/2000JD900259

Carbon input to soil may decrease soil carbon content: Carbon input in soil carbon sequestration
journal, March 2004


Causes of variation in soil carbon simulations from CMIP5 Earth system models and comparison with observations
journal, January 2013

  • Todd-Brown, K. E. O.; Randerson, J. T.; Post, W. M.
  • Biogeosciences, Vol. 10, Issue 3
  • DOI: 10.5194/bg-10-1717-2013

C:N:P stoichiometry in soil: is there a “Redfield ratio” for the microbial biomass?
journal, July 2007


Responses and feedbacks of coupled biogeochemical cycles to climate change: examples from terrestrial ecosystems
journal, February 2011

  • Finzi, Adrien C.; Austin, Amy T.; Cleland, Elsa E.
  • Frontiers in Ecology and the Environment, Vol. 9, Issue 1
  • DOI: 10.1890/100001

Weaker soil carbon–climate feedbacks resulting from microbial and abiotic interactions
journal, November 2014


Plant-derived compounds stimulate the decomposition of organic matter in arctic permafrost soils
journal, May 2016

  • Wild, Birgit; Gentsch, Norman; Čapek, Petr
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep25607

Development of microbial-enzyme-mediated decomposition model parameters through steady-state and dynamic analyses
journal, January 2013

  • Wang, Gangsheng; Post, Wilfred M.; Mayes, Melanie A.
  • Ecological Applications, Vol. 23, Issue 1
  • DOI: 10.1890/12-0681.1

The effect of soil drying on humus decomposition and nitrogen availability
journal, September 1958


The Biogeochemistry of Carbon at Hubbard Brook
journal, August 2005


Vegetation and climate controls on potential CO2, DOC and DON production in northern latitude soils
journal, September 2002


Biogeochemical model of Lake Zürich: sensitivity, identifiability and uncertainty analysis
journal, July 2001


Thermal adaptation of soil microbial respiration to elevated temperature
journal, December 2008


Sensitivity of decomposition rates of soil organic matter with respect to simultaneous changes in temperature and moisture
journal, February 2015

  • Sierra, Carlos A.; Trumbore, Susan E.; Davidson, Eric A.
  • Journal of Advances in Modeling Earth Systems, Vol. 7, Issue 1
  • DOI: 10.1002/2014MS000358

The hysteresis response of soil CO 2 concentration and soil respiration to soil temperature
journal, August 2015

  • Zhang, Quan; Katul, Gabriel G.; Oren, Ram
  • Journal of Geophysical Research: Biogeosciences, Vol. 120, Issue 8
  • DOI: 10.1002/2015JG003047

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

A Matlab toolbox for Global Sensitivity Analysis
journal, August 2015


Carbon cycling under 300 years of land use change: Importance of the secondary vegetation sink: CARBON CYCLING AND LAND USE IN LM3V
journal, June 2009

  • Shevliakova, Elena; Pacala, Stephen W.; Malyshev, Sergey
  • Global Biogeochemical Cycles, Vol. 23, Issue 2
  • DOI: 10.1029/2007GB003176

A potential loss of carbon associated with greater plant growth in the European Arctic
journal, June 2012

  • Hartley, Iain P.; Garnett, Mark H.; Sommerkorn, Martin
  • Nature Climate Change, Vol. 2, Issue 12
  • DOI: 10.1038/nclimate1575

Unifying soil respiration pulses, inhibition, and temperature hysteresis through dynamics of labile soil carbon and O 2 : Soil C and O2 regulate soil respiration
journal, April 2014

  • Oikawa, P. Y.; Grantz, D. A.; Chatterjee, A.
  • Journal of Geophysical Research: Biogeosciences, Vol. 119, Issue 4
  • DOI: 10.1002/2013JG002434

A theoretical model of C- and N-acquiring exoenzyme activities, which balances microbial demands during decomposition
journal, October 2012


Activation Energy of Extracellular Enzymes in Soils from Different Biomes
journal, March 2013


Temperature Coefficient of soil Nitrogen Mineralization
journal, January 1973


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


Interacting effects of temperature, soil moisture and plant biomass production on ecosystem respiration in a northern temperate grassland
journal, June 2005


Seasonality and partitioning of root allocation to rhizosphere soils in a midlatitude forest
journal, November 2016

  • Abramoff, Rose Z.; Finzi, Adrien C.
  • Ecosphere, Vol. 7, Issue 11
  • DOI: 10.1002/ecs2.1547

How Roots Control the flux of Carbon to the Rhizosphere
journal, April 2003


Nitrogen fertilization decreases forest soil fungal and bacterial biomass in three long-term experiments
journal, February 2006

  • Wallenstein, Matthew D.; McNulty, Steven; Fernandez, Ivan J.
  • Forest Ecology and Management, Vol. 222, Issue 1-3
  • DOI: 10.1016/j.foreco.2005.11.002

Changes to particulate versus mineral-associated soil carbon after 50 years of litter manipulation in forest and prairie experimental ecosystems
journal, March 2014


The turnover of organic carbon in subsoils. Part 2. Modelling carbon turnover
journal, April 2008


Modelling temperature and moisture effects on C–N transformations in soils: comparison of nine models
journal, October 1997


Thermodynamic theory explains the temperature optima of soil microbial processes and high Q 10 values at low temperatures
journal, May 2014

  • Schipper, Louis A.; Hobbs, Joanne K.; Rutledge, Susanna
  • Global Change Biology, Vol. 20, Issue 11
  • DOI: 10.1111/gcb.12596

Nitrogen Mineralization-Water Relations in Soils1
journal, January 1974


Short-term soil respiration and nitrogen immobilization response to nitrogen applications in control and nitrogen-enriched temperate forests
journal, July 2004


Plant, microbial and ecosystem carbon use efficiencies interact to stabilize microbial growth as a fraction of gross primary production
journal, February 2017

  • Sinsabaugh, Robert L.; Moorhead, Daryl L.; Xu, Xiaofeng
  • New Phytologist, Vol. 214, Issue 4
  • DOI: 10.1111/nph.14485

Diel patterns of autotrophic and heterotrophic respiration among phenological stages
journal, January 2013

  • Savage, K.; Davidson, E. A.; Tang, J.
  • Global Change Biology, Vol. 19, Issue 4
  • DOI: 10.1111/gcb.12108

Simulation of carbon and nitrogen transformations in soil: Microbial biomass and metabolic products
journal, October 1993


Soil respiration in a northeastern US temperate forest: a 22-year synthesis
journal, November 2013

  • Giasson, M. -A.; Ellison, A. M.; Bowden, R. D.
  • Ecosphere, Vol. 4, Issue 11
  • DOI: 10.1890/ES13.00183.1

Rhizosphere priming effects on soil carbon and nitrogen mineralization
journal, September 2014


Practical identifiability analysis of large environmental simulation models
journal, April 2001

  • Brun, Roland; Reichert, Peter; Künsch, Hans R.
  • Water Resources Research, Vol. 37, Issue 4
  • DOI: 10.1029/2000WR900350

Global soil carbon projections are improved by modelling microbial processes
journal, July 2013

  • Wieder, William R.; Bonan, Gordon B.; Allison, Steven D.
  • Nature Climate Change, Vol. 3, Issue 10
  • DOI: 10.1038/nclimate1951

Linear Analysis of soil Decomposition: Insights from the Century Model
journal, May 1998


The temperature response of soil microbial efficiency and its feedback to climate
journal, January 2013

  • Frey, Serita D.; Lee, Juhwan; Melillo, Jerry M.
  • Nature Climate Change, Vol. 3, Issue 4
  • DOI: 10.1038/nclimate1796

Reconciling the temperature dependence of respiration across timescales and ecosystem types
journal, June 2012

  • Yvon-Durocher, Gabriel; Caffrey, Jane M.; Cescatti, Alessandro
  • Nature, Vol. 487, Issue 7408
  • DOI: 10.1038/nature11205

Different soil respiration responses to litter manipulation in three subtropical successional forests
journal, December 2015

  • Han, Tianfeng; Huang, Wenjuan; Liu, Juxiu
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep18166

Integrating microbial physiology and physio-chemical principles in soils with the MIcrobial-MIneral Carbon Stabilization (MIMICS) model
journal, January 2014


Microbial community dynamics alleviate stoichiometric constraints during litter decay
journal, March 2014

  • Kaiser, Christina; Franklin, Oskar; Dieckmann, Ulf
  • Ecology Letters, Vol. 17, Issue 6
  • DOI: 10.1111/ele.12269

Rhizosphere processes are quantitatively important components of terrestrial carbon and nutrient cycles
journal, January 2015

  • Finzi, Adrien C.; Abramoff, Rose Z.; Spiller, Kimberly S.
  • Global Change Biology, Vol. 21, Issue 5
  • DOI: 10.1111/gcb.12816

Does adding microbial mechanisms of decomposition improve soil organic matter models? A comparison of four models using data from a pulsed rewetting experiment
journal, September 2009


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

A Method for Scaling Vegetation Dynamics: the Ecosystem Demography Model (ed)
journal, November 2001


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

Variance based sensitivity analysis of model output. Design and estimator for the total sensitivity index
journal, February 2010

  • Saltelli, Andrea; Annoni, Paola; Azzini, Ivano
  • Computer Physics Communications, Vol. 181, Issue 2
  • DOI: 10.1016/j.cpc.2009.09.018

Large-scale forest girdling shows that current photosynthesis drives soil respiration
journal, June 2001

  • Högberg, Peter; Nordgren, Anders; Buchmann, Nina
  • Nature, Vol. 411, Issue 6839
  • DOI: 10.1038/35081058

Long-term doubling of litter inputs accelerates soil organic matter degradation and reduces soil carbon stocks
journal, December 2015


Partitioning sources of soil respiration in boreal black spruce forest using radiocarbon
journal, February 2006