Repository for CLM-Microbe and other associated modeling work within the Ecological Modeling and Integration Laboratory at SDSU. https://xulab.sdsu.edu/. The CLM-Microbe is branched from CLM4.5 in 2013. It is developed under an open-source license, all codes are publically accessible. Anyone who wants to use this model needs to contact Xiaofeng Xu at xxu@sdsu.edu for coordinating different efforts on model development and application.
Publications with the CLM-Microbe model.
1). Xu X., Schimel J. P., Thornton P. E., Song X., Yuan F.H., Goswami S., (2014) Substrate and environmental controls on microbial assimilation of soil organic carbon: a framework for Earth system models. Ecology Letters 17:547-555. (The modeling framework for microbial carbon assimilation)
2). Xu X., Elias D. A., Graham D. E., Phelps T. J., Carrol S. L., Wullschleger S. D., Thornton P. E. (2015) A microbial functional group based module for simulating methane production and consumption: application to an incubation permafrost soil. Journal of Geophysical Research-Biogeosciences 120:1315-1333. (The microbial functional-group based methane module)
3). Xu X., Yuan F., Hanson P.J., Wullschleger S.D., Thornton P.E., Riley W.J., Song X., Graham D.E., Song C.C., Tian H. (2016) Review and Synthesis: Four decades of modeling methane cycling within terrestrial ecosystems. Biogeosciences 13:3735-3755. (A review paper on different types of methane models including the CLM-Microbe; the CLM-Microbe represents the new direction of microbial model on methane processes)
4). Wang Y., Yuan F.M., Yuan F.H., Gu B., Hahn M.S., Torn M.S., Ricciuto D.M., Kumar J., He L., Zona D., Lipson D.L., Wagner R., Oechel W.C., Wullschleger S.D., Thornton P.E., Xu X. (2019) Mechanistic Modeling of microtopographic impact on CH4 processes in an Alaskan tundra ecosystem using the CLM-Microbe model. Journal of Advances in Modeling Earth Systems 11:4228-4304. (Site-level application of the CLM-Microbe in simulating methane flux in the Arctic)
5). He L., Lipson D.L., Rodrigues J.L., Mayes M.A., Bjork R.G., Glaser B., Thornton P.E., Xu X. (2021). Dynamics of Fungal and Bacterial Biomass Carbon in Natural Ecosystems: Site-level Applications of the CLM-Microbe Model. Journal of Advance in Modeling Earth Systems, DOI: 10.1029/2020MS002283. (Site-level application of the CLM-Microbe in simulating bacterial and fungal biomass in major biomes)
6). He, L, Lai C.T., Mayes M.A., Murayama S., Xu X. (2021) Microbial seasonality promotes soil respiratory carbon emission in natural ecosystems: a modeling study. Global Change Biology. DOI:10.1111/gcb.15627. (Site-level model application to confirm microbial seasonality has stimulation impacts on soil carbon emission)
7). Zuo Y.J., Wang Y.H., He L.Y., Wang N.N., Liu J.Z., Yuan F.H., Li K.X., Guo Z.Y., Sun Y., Zhu X.H., Zhang L.H., Song C.C., Sun L., Xu X.F. (2022) Modeling methane dynamics in three wetlands in northeastern China by using the CLM-Microbe model. Ecosystem Health and Sustainability. DOI:10.1080/20964129.2022.2074895. (Site-level application of the CLM-Microbe model to CH4 dynamics in Asian temperate wetlands)
8). Wang, Y., Yuan F.M., Anrt K., Liu J.Z., He L.Y., Zuo Y.J., Zona D., Lipson D.A., Oechel W.C., Ricciuto D.M., Wullschleger S.D., Thornton P.E., Xu X.F. (2022) Upscaling methane flux from plot-level to eddy covariance tower domains by combining the CLM-Microbe model with three footprint algorithms. Frontier in Environmental Sciences. 10， DOI: 10.3389/fenvs.2022.939238 (Regional model application to simulate metane flux within eddy tower domain in the Arctic tundra ecosystems)
9). Dissertation: He, Liyuan. (2022) Multi-scale modeling of soil microbial control on terrestrial carbon cycle. Joint doctoral program - San Diego State University & University of California Davis.
10). Dissertation: Wang, Yihui. (2022) Multi-scale modeling of Arctic methane cycling using the CLM-Microbe model. Joint doctoral program - San Diego State University & University of California Davis.
11). He L., Rodrigues J., Mayes M., Lao C.T., Xu X.F. (2023) Historical dynamics of terrestrial carbon during 1901-2016 as simulated by the CLM-Microbe model. Biogeosciences Discuss. [preprint], https://doi.org/10.5194/bg-2023-15, in review, 2023. (Global application of the CLM-Microbe model to estimate the historical dynamics of terrestrial carbon including the carbon components in vegetation, soils, and microbes)
12). He. L., Viovy N., Xu X.F. (2023) Differentiation of soil bacterial and fungal macroecology in the United States. Global Biogeochemical Cycles (Under review) (Site-level application of the CLM-Microbe to investigate the bacterial and fungal macroecology across the US)
13). Wang Y.H., He L.Y., Liu J.Z., Arndt K.A., Rodrigues J.L.M., Zona D., Lipson D.A., Oechel W.C., Ricciuto D.M., Wullschleger S.D., Xu X.F. (2023) Projecting methane emissions in Arctic tundra ecosystems under different climate scenarios. Journal of Advances in Modeling Earth Systems (Under revision). (Regional application of the CLM-Microbe model in projecting methane flux within five eddy covarance domain at a 4m resolution)