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Allison, S. D., Romero-Olivares, A. L., Lu, L., Taylor, J., & Treseder, K. K. (2018). Temperature acclimation and adaptation of enzyme physiology in Neurospora discreta. Fungal Ecology, 35, 78–86. [Author final version]


He, Y., S. E. Trumbore, M. S. Torn, J. W. Harden, L. J. S. Vaughn, S. D. Allison, and J. T. Randerson. 2016. Radiocarbon constraints imply reduced carbon uptake by soils during the 21st century. Science in press.

Sistla, S. A., A. B. Roddy, N. E. Williams, D. B. Kramer, K. Stevens, and S. D. Allison. 2016. Agroforestry practices promote biodiversity and natural resource diversity in Atlantic Nicaragua. PLoS One in press.

Martiny, J. B. H., C. Weihe, Y. Lu, R. Berlemont, E. L. Brodie, M. L. Goulden, K. K. Treseder, and S. D. Allison. 2016. Microbial legacies alter decomposition in response to simulated global change. ISME Journal in press.

Evans, S., J. B. H. Martiny, and S. D. Allison. 2016. Effects of dispersal and selection on stochastic assembly in microbial communities. ISME Journal in press.

Widder, S., R. J. Allen, T. Pfeiffer, T. P. Curtis, C. Wiuf, W. T. Sloan, O. X. Cordero, S. P. Brown, B. Momeni, W. Shou, H. Kettle, H. J. Flint, A. F. Haas, B. Laroche, J.-U. Kreft, P. B. Rainey, S. Freilich, S. Schuster, K. Milferstedt, J. R. van der Meer, T. Grokopf, J. Huisman, A. Free, C. Picioreanu, C. Quince, I. Klapper, S. Labarthe, B. F. Smets, H. Wang, Isaac Newton Institute Fellows, and O. S. Soyer. 2016. Challenges in microbial ecology: building predictive understanding of community function and dynamics. ISME Journal: in press.

Khalili, B., O. A. Ogunseitan, M. L. Goulden, and S. D. Allison. 2016. Interactive effects of precipitation manipulation and nitrogen addition on soil properties in California grassland and shrubland. Applied Soil Ecology 107:144–153.

Vereecken, H., A. Schnepf, J. W. Hopmans, M. Javaux, D. Or, T. Roose, J. Vanderborght, M. Young, W. Amelung, M. Aitkenhead, S. D. Allison, S. Assouline, P. Baveye, M. Berli, N. Brüggemann, P. Finke, M. Flury, T. Gaiser, G. Govers, T. Ghezzehei, P. Hallett, and K. Lamorski. 2016. Modeling soil processes: review, key challenges and new perspectives. Vadose Zone Journal 15:doi:10.2136/vzj2015.09.0131.

Liu, W., S. D. Allison, J. Xia, L. Liu, and S. Wan. 2016. Precipitation regime drives warming responses of microbial biomass and activity in temperate steppe soils. Biology and Fertility of Soils 52:469–477.

Luo, Y., A. Ahlström, S. D. Allison, N. H. Batjes, V. Brovkin, N. Carvalhais, A. Chappell, P. Ciais, E. A. Davidson, A. Finzi, K. Georgiou, B. Guenet, O. Hararuk, J. W. Harden, Y. He, F. Hopkins, L. Jiang, C. Koven, R. B. Jackson, C. D. Jones, M. J. Lara, J. Liang, A. D. McGuire, W. Parton, C. Peng, J. T. Randerson, A. Salazar, C. A. Sierra, M. J. Smith, H. Tian, K. E. O. Todd-Brown, M. Torn, K. J. van Groenigen, Y. P. Wang, T. O. West, Y. Wei, W. R. Wieder, J. Xia, X. Xu, X. Xu, and T. Zhou. 2016. Toward more realistic projections of soil carbon dynamics by Earth system models. Global Biogeochemical Cycles 30:40–56.


Wieder, W. R., S. D. Allison, E. A. Davidson, K. Georgiou, O. Hararuk, Y. He, F. Hopkins, Y. Luo, M. Smith, B. Sulman, K. Todd-Brown, Y.-P. Wang, J. Xia, and X. Xu. 2015. Explicitly representing soil microbial processes in Earth system models. Global Biogeochemical Cycles 29:1782–1800.

Hynson, N. A., S. D. Allison, and K. K. Treseder. 2015. Quantum dots reveal shifts in organic nitrogen uptake by fungi exposed to long-term nitrogen enrichment. PLoS One 10:e0138158.

Mouginot, C., A. E. Zimmerman, J. A. Bonachela, H. Fredricks, S. D. Allison, B. A. S. Van Mooy, and A. C. Martiny. 2015. Resource allocation by the marine cyanobacterium Synechococcus WH8102 in response to different nutrient supply ratios. Limnology and Oceanography 60:1634-1641.

Amend, A. S., A. C. Martiny, S. D. Allison, R. Berlemont, M. L. Goulden, Y. Lu, K. K. Treseder, C. Weihe, and J. B. H. Martiny. 2016. Microbial response to simulated global change is phylogenetically conserved and linked with functional potential. ISME Journal 10:109-118.

Matulich, K. L., C. Weihe, S. D. Allison, A. S. Amend, R. Berlemont, M. L. Goulden, S. Kimball, A. C. Martiny, and J. B. H. Martiny. 2015. Temporal variation overshadows the response of leaf litter microbial communities to simulated global change. ISME Journal 9:2477-2489.

Baker, N. R., and S. D. Allison. 2015. Ultraviolet photodegradation facilitates microbial decomposition of litter in a Mediterranean climate. Ecology 96:1994-2003. [pdf]

German, D. P., and S. D. Allison. 2015. Drying and substrate concentrations interact to inhibit decomposition of carbon substrates added to combusted Inceptisols from a boreal forest. Biology and Fertility of Soils 51:525-533. [pdf]


Berlemont, R., S. D. Allison, C. Weihe, Y. Lu, E. L. Brodie, J. B. H. Martiny, and A. C. Martiny. 2014. Cellulolytic potential under environmental changes in microbial communities from grassland litter. Frontiers in Microbiology 5:639.

Allison, S. D. 2014. Modeling adaptation of carbon use efficiency in microbial communities. Frontiers in Microbiology 5:571.

Hagerty, S. B., K. J. van Groenigen, S. D. Allison, B. A. Hungate, E. Schwartz, G. W. Koch, R. K. Kolka, and P. Dijkstra. 2014. Accelerated microbial turnover but constant growth efficiency with warming in soil. Nature Climate Change 4:903-906. [pdf proof]

Allison, S. D., S. S. Chacon, and D. P. German. 2014. Substrate concentration constraints on microbial decomposition. Soil Biology & Biochemistry 79:43-49. [pdf]

Mouginot, C., R. Kiwamura, K. Matulich, R. Berlemont, S. D. Allison, A. S. Amend, and A. C. Martiny. 2014. Elemental stoichiometry of Fungi and Bacteria strains from grassland leaf litter. Soil Biology & Biochemistry 76:278-285. [pdf]

Allison, S. D., Y. Lu, A. G. Kent, and A. C. Martiny. 2014. Extracellular enzyme production and cheating in Pseudomonas fluorescens depend on diffusion rates. Frontiers in Microbiology 5:169.

Todd-Brown, K. E. O., J. T. Randerson, F. Hopkins, V. Arora, T. Hajima, C. Jones, E. Shevliakova, J. Tjiputra, E. Volodin, T. Wu, Q. Zhang, and S. D. Allison. 2014. Changes in soil organic carbon storage predicted by Earth system models during the 21st century. Biogeosciences 11:2341-2356.

Zimmerman, A. E., A. C. Martiny, M. W. Lomas, and S. D. Allison. 2014. Phosphate supply explains variation in nucleic acid allocation but not C:P stoichiometry in the Western North Atlantic. Biogeosciences 11:1599-1611.

Li, J., G. Wang, S. D. Allison, M. A. Mayes, and Y. Luo. 2014. Soil carbon sensitivity to temperature and carbon use efficiency compared across microbial-ecosystem models of varying complexity. Biogeochemistry 119:67-84. [pdf]

Zimmerman, A. E., S. D. Allison, and A. C. Martiny. 2014. Phylogenetic constraints on elemental stoichiometry and resource allocation in heterotrophic marine bacteria. Environmental Microbiology 16:1398-1410. [pdf]


Bach, C. E., D. D. Warnock, D. J. Van Horn, M. N. Weintraub, R. L. Sinsabaugh, S. D. Allison, and D. P. German. 2013. Measuring phenol oxidase and peroxidase activities with pyrogallol, l-DOPA, and ABTS: Effect of assay conditions and soil type. Soil Biology & Biochemistry 67:183-191. [pdf]

Wieder, W. R., G. B. Bonan, and S. D. Allison. 2013. Global soil carbon predictions are improved by modelling microbial processes. Nature Climate Change 3:909-912. [proof pdf]. News and Views by Schimel.

McGuire, K. L., S. D. Allison, N. Fierer, and K. K. Treseder 2013. Ectomycorrhizal-dominated boreal and tropical forests have distinct fungal communities, but analogous spatial patterns across soil horizons. PLoS One 8:e68278.

Aronson, E, S. D. Allison, and B. R. Helliker. 2013. Environmental impacts on the diversity of methane-cycling microbes and their resultant function. Frontiers in Microbiology 4:225.

Bonachela, J. A., S. D. Allison, A. C. Martiny, and S. A. Levin. 2013. A model for variable phytoplankton stoichiometry based on cell protein regulation. Biogeosciences 10:4341-4356.

Alster, C. J., D. P. German, Y. Lu, and S. D. Allison. 2013. Microbial enzymatic responses to drought and to nitrogen addition in a southern California grassland. Soil Biology & Biochemistry 64:68-79. [pdf]

Allison, S. D., Y. Lu, C. Weihe, M. L. Goulden, A. C. Martiny, K. K. Treseder, and J. B. H. Martiny. 2013. Microbial abundance and composition influence litter decomposition response to environmental change. Ecology 94:714-725. [pdf]

Zimmerman, A. E., A. C. Martiny, and S. D. Allison. 2013. Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes. ISME Journal 7:1187-1199. [pdf]

Todd-Brown, K. E. O., J. T. Randerson, W. M. Post, F. M. Hoffman, C. Tarnocai, E. A. G. Schuur, and S. D. Allison. 2013. Causes of variation in soil carbon simulations from CMIP5 Earth system models and comparison with observations. Biogeosciences 10:1717-1736.


Shade, A., H. Peter, S. D. Allison, D. Baho, M. Berga, H. Buergmann, D. H. Huber, S. Langenheder, J. T. Lennon, J. B. Martiny, K. L. Matulich, T. M. Schmidt, J. Handelsman. 2012. Fundamentals of microbial community resistance and resilience. Frontiers in Microbiology 3:417.

Folse, H. J., III, and S. D. Allison. 2012. Cooperation, competition, and coalitions in enzyme-producing microbes: Social evolution and nutrient mineralization rates. Frontiers in Microbiology 3:338.

Allison, S.D., Y. Chao, J. D. Farrara, S. Hatosy, and A. C. Martiny. 2012. Fine-scale temporal variation in marine extracellular enzymes of coastal southern California. Frontiers in Microbiology 3:301.

Aronson, E., and S. D. Allison. 2012. Meta-analysis of environmental impacts on nitrous oxide release in response to N amendment. Frontiers in Microbiology 3:272.

Allison, S. D. 2012. A trait-based approach for modeling microbial litter decomposition. Ecology Letters 15:1058-1070. [.zip file with model code]

Todd-Brown, K. E. O., F. M. Hopkins, S. N. Kivlin, J. M. Talbot, and S. D. Allison. 2012. A framework for representing microbial decomposition in coupled climate models. Biogeochemistry in press. [pdf]

German, D. P., K. B. R. Marcelo, M. M. Stone, and S. D. Allison. 2012. The Michaelis-Menten kinetics of soil extracellular enzymes in response to temperature: a cross-latitudinal study. Global Change Biology 2012:1468-1479. [pdf]

Stone, M. M., M. S. Weiss, C. L. Goodale, M. B. Adams, I. J. Fernandez, D. P. German, and S. D. Allison. 2012. Temperature sensitivity of soil enzyme kinetics under N-fertilization in two temperate forests. Global Change Biology 18:1173-1184. [pdf]

German, D. P., M. N. Weintraub, A. S. Grandy, C. L. Lauber, Z. L. Rinkes, and S. D. Allison. 2012. Response to Steen and Ziervogel’s comment on “Optimization of hydrolytic and oxidative enzyme methods to ecosystem studies” [Soil Biology & Biochemistry 43: 1387-1397]. Soil Biology & Biochemistry 48:198-199. [pdf]


Allison, S. D. and K. K Treseder. 2011. Climate change feedbacks to microbial decomposition in boreal soils. Fungal Ecology 4:362-374. [pdf]

German, D. P., S. S. Chacon, and S. D. Allison. 2011. Substrate concentration and enzyme allocation can affect rates of microbial decomposition. Ecology 92:1471-1480. [pdf]

Martiny, J. B. H., J. A. Eisen, K. Penn, S. D. Allison, and M. C. Horner-Devine. 2011. Drivers of bacterial β-diversity depend on spatial scale. Proceedings of the National Academy of Sciences of the United States of America 108:7850-7854. [pdf]

German, D. P., M. N. Weintraub, A. S. Grandy, C. L. Lauber, Z. L. Rinkes, and S. D. Allison. 2011. Optimization of extracellular enzyme assay methods for ecosystem studies. Soil Biology & Biochemistry 43:1387-1397. [pdf] Corrigendum: [pdf]

Allison, S. D., M. N. Weintraub, T. B. Gartner, and M. P. Waldrop. 2011. Evolutionary-economic principles as regulators of soil enzyme production and ecosystem function. pp. 229-243 in G. C. Shukla and A. Varma, editors. Soil Enzymology. Springer-Verlag. [pdf]

Wallenstein, M., S. Allison, J. Ernakovich, J. M. Steinweg, and R. Sinsabaugh. 2011. Controls on the temperature sensitivity of soil enzymes:  A key driver of in-situ enzyme activity rates. pp. 245-258 in G. C. Shukla and A. Varma, editors. Soil Enzymology. Springer-Verlag. [pdf]


Allison, S. D., K. L. McGuire, and K. K. Treseder. 2010. Resistance of microbial and soil properties to warming treatment seven years after boreal fire. Soil Biology & Biochemistry 42:1872-1878. [pdf]

McGuire, K. L., E. Bent, J. Borneman, A. Majumder, S. D. Allison, and K. K. Treseder. 2010. Functional diversity in resource use by fungi. Ecology 91:2324-2332. [pdf]

Allison, S. D., M. D. Wallenstein, and M. A. Bradford. 2010. Soil-carbon response to warming dependent on microbial physiology. Nature Geoscience 3:336-340. [pdf] [press release]

Allison, S. D., T. B. Gartner, M. C. Mack, K. L. McGuire, and K. K. Treseder. 2010. Nitrogen alters C dynamics during early succession in boreal forest. Soil Biology & Biochemistry 42:1157-1164. [pdf]


Cornwell, W. K., J. H. C. Cornelissen, S. D. Allison, J. Bauhus, P. Eggleton, C. M. Preston, F. Scarff, J. T. Weedon, C. Wirth, A. E. Zanne. 2009. Plant traits and wood fates across the globe—rotted, burned, or consumed? Global Change Biology 15:2431-2449. [pdf]

Bradford, M. A., M. D. Wallenstein, S. D. Allison, K. K. Treseder, S. D. Frey, B. W. Watts, C. A. Davies, T. R. Maddox, J. M. Melillo, J. E. Mohan, and J. F. Reynolds. 2009. Decreased mass specific respiration under experimental warming is robust to the microbial biomass method employed. Ecology Letters 12:E15-E18. [pdf]

Allison, S. D., D. S. LeBauer, M. R. Ofrecio, R. Reyes, A.-M. Ta, T. M. Tran. 2009. Low levels of nitrogen addition stimulate decomposition by boreal forest fungi. Soil Biology & Biochemistry 41:293-302. [pdf]


Allison, S. D., and K. K. Treseder. 2008. Warming and drying suppress microbial activity and carbon cycling in boreal forest soils. Global Change Biology 14:2898-2909. [pdf] [press release]

Hanson, C. A., S. D. Allison, M. A. Bradford, M. D. Wallenstein, and K. K. Treseder. 2008. Fungal taxa target different carbon sources in forest soil. Ecosystems 11:1157-1167. [pdf]

Talbot, J. M., S. D. Allison, and K. K. Treseder. 2008. Decomposers in disguise: mycorrhizal fungi as regulators of soil C dynamics in ecosystems under global change. Functional Ecology 22:955-963. [pdf]

Sinsabaugh, R. L., C. L. Lauber, M. N. Weintraub, B. Ahmed, S. D. Allison, C. Crenshaw, A. R. Contosta, D. Cusack, S. Frey, M. E. Gallo, T. B. Gartner, S. E. Hobbie, K. Holland, B. L. Keeler, J. S. Powers, M. Stursova, C. Takacs-Vesbach, M. P. Waldrop, M. D. Wallenstein, D. R. Zak, and L. H. Zeglin. 2008. Stoichiometry of soil enzyme activity at global scale. Ecology Letters 11:1252-1264. [pdf]

Cornwell, W. K., J. H. C. Cornelissen, K. Amatangelo, E. Dorrepaal, V. T. Eviner, O. Godoy, S. E. Hobbie, B. Hoorens, H. Kurokawa, N. Perez Harguindeguy, H. M. Quested, L. S. Santiago, D. A. Wardle, I. J. Wright, R. Aerts, S. D. Allison, P. van Bodegom, V. Brovkin, A. Chatain, T. Callaghan, S. Díaz, E. Garnier, D. E. Gurvich, E. Kazakou, J. A. Klein, J. Read, P. B. Reich, N. A. Soudzilovskaia, M. V. Vaieretti, and M. Westoby. 2008. Plant species traits are the predominant control on litter decomposition rates within biomes worldwide. Ecology Letters 11:1065-1071. [pdf]

Allison, S. D., and J. B. H. Martiny. 2008. Resistance, resilience, and redundancy in microbial communities. PNAS 105(Suppl. 1):11512-11519. [pdf]

Treseder, K. K., C. I. Czimczik, S. E. Trumbore, and S. D. Allison. 2008. Uptake of an amino acid by ectomycorrhizal fungi in a boreal forest. Soil Biology & Biochemistry 40:1964-1966. [pdf]

Allison, S. D., C. I. Czimczik, and K. K. Treseder. 2008. Microbial activity and soil respiration under nitrogen addition in Alaskan boreal forest. Global Change Biology 14:1156-1168. [pdf]


Allison, S. D., C. A. Hanson, and K. K. Treseder. 2007. Nitrogen fertilization reduces diversity and alters community structure of active fungi in boreal ecosystems. Soil Biology & Biochemistry 39:1878-1887. [pdf]

Allison, S. D., T. B. Gartner, K. Holland, M. Weintraub, and R. L. Sinsabaugh. 2007. Soil enzymes: linking proteomics and ecological process. Manual of Environmental Microbiology, 3rd Edition. pp 704-711. ASM Press. [pdf]


Allison, S. D. 2006. Brown ground: a soil carbon analog for the Green World Hypothesis? American Naturalist 167:619-627. [pdf]

Allison, S. D. 2006. Soil minerals and humic acids alter enzyme stability: implications for ecosystem processes. Biogeochemistry 81:361-373. [pdf]

Allison, S. D., and J. D. Jastrow. 2006. Activities of extracellular enzymes in physically isolated fractions of restored grassland soils. Soil Biology & Biochemistry 38:3245-3256. [pdf]

Allison, S. D., C. B. Nielsen, and R. F. Hughes. 2006. Elevated enzyme activities in soils under the invasive nitrogen-fixing tree Falcataria moluccana. Soil Biology & Biochemistry 38:1537-1544. [pdf]


Allison, S. D. 2005. Cheaters, diffusion, and nutrients constrain decomposition by microbial enzymes in spatially structured environments. Ecology Letters 8:626-635. [pdf] [Supplementary Material]

Allison, S. D., and P. M. Vitousek. 2005. Responses of extracellular enzymes to simple and complex nutrient inputs. Soil Biology & Biochemistry 37:937-944. [pdf]

Allison, S. D. 2005. Tropical Forest Diversity and Dynamism - Book Review. Quarterly Review of Biology 80:262. [pdf]

Allison, S. D., and J. C. Schultz. 2005. Biochemical responses of chestnut oak to a galling cynipid. Journal of Chemical Ecology 31:151-166. [pdf]


Allison, S. D., and P. M. Vitousek. 2004. Rapid nutrient cycling in leaf litter from invasive species in Hawai’i . Oecologia 141:612-619. [pdf]

Allison, S. D., and P. M. Vitousek. 2004. Extracellular enzyme activities and carbon chemistry as drivers of tropical plant litter decomposition. Biotropica 36:285-296. [pdf]

Allison, S. D., and J. C. Schultz. 2004. Differential activity of peroxidase isozymes in response to wounding, gypsy moth, and plant hormones in northern red oak (Quercus rubra L.). Journal of Chemical Ecology 30:1363-1379. [pdf]

Pauw, A., S. A. Van Bael, H. A. Peters, S. D. Allison, J. L. C. Camargo, M. Cifuentes-Jara, A. Conserva, T. G. Restom, T. Heartsill-Scalley, S. A. Mangan, G. Nunez-Iturri, E. Rivera-Ocasio, M. Rountree, S. Vetter, and C. V. de Castilho. 2004. Physical damage in relation to carbon allocation strategies of tropical forest tree saplings. Biotropica 63:410-413. [pdf]


Vitousek, P. M., O. A. Chadwick, P. A. Matson, S. Allison, L. A. Derry, L. Kettley, A. Luers, E. Mecking, V. Monastra, and S. Porder. 2003. Erosion and the rejuvenation of weathering-derived nutrient supply in an old tropical landscape. Ecosystems 6:762-772. [pdf]


Vitousek, P. M., S. Hättenschwiler, L. Olander, and S. Allison. 2002. Nitrogen and nature. Ambio 31:97-101. [pdf]

© Steven Allison 2012