Flooded corn field


Dr Rongzhong Ye examining field soil samplesPI: Rongzhong Ye, Assistant Professor, PhD
Department of Plant and Environmental Sciences
Pee Dee Research and Education Center
2200 Pocket Road, Florence, SC 29506
E-mail:  rongzho@clemson.edu
Office:  (843)519-0494



This soil program is to develop mechanistic understanding of soil physical, chemical, aSoil ecologynd biological processes that underpin soil health, while investigating how conservative management practices, along with climate variations, affect soil physio-biogeochemical processes and the desirable agronomic and environmental outcomes. The ultimate goal of is to better understand the ecology of soil and hence to improve management of ecosystems and their sustainability. The soil program has focuses on soil organic carbon dynamics, microbial community composition and functional groups, nutrient processes, and soil health indicators and assessment.


  1. USDA- AFRI-Organic Transition. Diversifying organic inputs to improve soils supporting organic vegetable in southeastern USA (09/2020-08/2023). Total: $499,762. PI: R. Ye.
  2. NSF-CAREER. Exploring the Unknowns: Responses of soil microbial communities to increased plant functional trait diversity in managed ecosystems. (03/2020-02/2025). Total: $500,010. PI: R. Ye.
  3. Clemson University SEED. Diversifying organic inputs to improve microbial community and soil health in sandy Coastal Plain soils (02/2020-01/2021). Total: $10,000. PI: R. Ye.
  4. USDA-AFRI-Sustainable Agricultural Systems. Enhancing the sustainability of US cropping systems through cover crops and an innovative information and technology networks. (09/2019-08/2024). Total: $9,980,439. PIs: C. Reberg-Horton and S. Mirsky.
  5. NSF-Major Research Instrumentation. Acquisition of a soil greenhouse gas flux measurement system to support research in coastal ecology and sustainable agriculture. (10/2018-09/2021). Total: $230,597. PI: T. O'Halloran.
  6. USDA-NRCS-Conservation Innovative Grants. Demonstrating the influence of cover crop termination time on nutrient provision and yield of cash crops. (05/2018-06/2021). Total: $149,863. PI: R. Ye.
  7. South Carolina Cotton Board. Cover cropping and no-till to increase soil organic matter, improve soil structure, and enhance nutrient use-efficiency in cotton. (04/2018-03/2020). Total: $23,383. PI: R Ye.
  8. South Carolina Peanut Board. Evaluation of cover crop on nutrient cycling, soil quality, and yield in peanut production system in South Carolina. (07/2017-06/2020). Total: $37,331. PI: R Ye.


  1. Parajuli, B., Luo, M., Ye, R., Ducey, T.F., Park, D., Smith, M., Sigua, G., 2021. Aggregate distribution and the associated carbon in Norfolk soils under long-term conservation tillage and short-term cover cropping. Commun. Soil Sci. Plant Anal. 1–12. https://doi.org/10.1080/00103624.2020.1869769
  2. Li, Y., Yuan, H., Chen, A., Xiao, M., Deng, Y., Ye, R., Zhu, Z., Inubushi, K., Wu, J., Ge, T., 2020. Legacy effect of elevated CO2 and N fertilization on mineralization and retention of rice (Oryza sativa L.) rhizodeposit-C in paddy soil aggregates. Soil Ecol. Lett. https://doi.org/10.1007/s42832-020-0066-y
  3. Luo, M., Zhai, Z., Ye, R., Xing, R., Huang, J., Tong, C., 2020. Carbon mineralization in tidal freshwater marsh soils at the intersection of low-level saltwater intrusion and ferric iron loading. CATENA 193, 104644. https://doi.org/https://doi.org/10.1016/j.catena.2020.104644
  4. Poudel P, Ye R, Park D, P.B., 2020. Management Practices Affecting the Nutrient Provision Capacity of Cover Crops. Clemson Coop. Extension, Land-Grant Press by Clemson Ext. 2020 Aug.
  5. Ye, R., Parajuli, B., Ducey, T.F., Novak, J.M., Bauer, P.J., Szogi, A.A., 2020. Cover cropping increased phosphorus stocks in surface sandy Ultisols under long-term conservation and conventional tillage. Agron. J. 112, 3163–3173. https://doi.org/10.1002/agj2.20227
  6. Li, L.-J., Ye, R., Zhu-Barker, X., Horwath, W.R., 2019. Soil microbial biomass size and nitrogen availability regulate the incorporation of residue carbon into dissolved organic pool and microbial biomass. Soil Science Society of America Journal.
  7. Liu, Y., Luo, M., Ye, R., Huang, J., Xiao, L., Hu, Q., Zhu, A., Tong, C., 2019. Impacts of the rhizosphere effect and plant species on organic carbon mineralization rates and pathways, and bacterial community composition in a tidal marsh. FEMS Microbiology Ecology 95. DOI:10.1093/femsec/fiz120.
  8. Xiao, M., Zang, H., Liu, S., Ye, R., Zhu, Z., Su, Y., Wu, J., Ge, T., 2019. Nitrogen fertilization alters the distribution and fates of photosynthesized carbon in rice–soil systems: a 13C-CO2 pulse labeling study. Plant and Soil. DOI:10.1007/s11104-019-04030-z.
  9. Zhang, H., Yang, R., Wang, Y., Ye, R., 2019. The evaluation and prediction of agriculture-related nitrate contamination in groundwater in Chengdu Plain, southwestern China. Hydrogeology Journal 27, 785-799.
  10. Ye, R., Parajuli, B., Sigua, G., 2019. Subsurface clay soil application improved aggregate stability, nitrogen availability, and organic carbon preservation in degraded Ultisols with cover crop mixtures. Soil Science Society of America Journal. DOI: 10.2136/sssaj2018.12.0496
  11. Li, L.-J., Zhu-Barker, X., Ye, R., Doane, T.A., Horwath, W.R., 2018. Soil microbial biomass size and soil carbon influence the priming effect from carbon inputs depending on nitrogen availability. Soil Biology and Biochemistry 119, 41-49.
  12. Zhang, H., Wang, Y., Yang, R., Ye, R., 2018. Modeling the effects of phosphate mining on groundwater at different stages of mine development. Mine Water and the Environment.
  13. Zhu, Z., Ge, T., Liu, S., Hu, Y., Ye, R., Xiao, M., Tong, C., Kuzyakov, Y., Wu, J., 2018. Rice rhizodeposits affect organic matter priming in paddy soil: The role of N fertilization and plant growth for enzyme activities, CO2 and CH4 emissions. Soil Biology and Biochemistry 116, 369-377.
  14. Dai, S.-S., Li, L.-J., Ye, R., Zhu-Barker, X., Horwath, W.R., 2017. The temperature sensitivity of organic carbon mineralization is affected by exogenous carbon inputs and soil organic carbon content. European Journal of Soil Biology 81, 69-75.
  15. Hartman, W.H., Ye, R., Horwath, W.R., Tringe, S.G., 2017. A genomic perspective on stoichiometric regulation of soil carbon cycling. ISME J.
  16. Jiang, Y., van Groenigen, K.J., Huang, S., Hungate, B.A., van Kessel, C., Hu, S., Zhang, J., Wu, L., Yan, X., Wang, L., Chen, J., Hang, X., Zhang, Y., Horwath, W.R., Ye, R., Linquist, B.A., Song, Z., Zheng, C., Deng, A., Zhang, W., 2017. Higher yields and lower methane emissions with new rice cultivars. Global Change Biology DOI: 10.1111/gcb.13737, n/a-n/a.
  17. Miao, S., Ye, R., Qiao, Y., Zhu-Barker, X., Doane, T.A., Horwath, W.R., 2017. The solubility of carbon inputs affects the priming of soil organic matter. Plant and Soil 410, 129-138.
  18. Morris, J., Ye, R., Silva, L.C., Horwath, W.R., 2017. Nitrogen fertilization had no effect on CH4 and N2O emissions in rice planted in rewetted peatlands. Soil Science Society of America Journal 81, 224-232.
  19. Xu, Y., Zhan, M., Cao, C., Ge, J., Ye, R., Tian, S., Cai, M., 2017. Effects of irrigation management during the rice growing season on soil organic carbon pools. Plant and Soil 421, 337-351.
  20. Ye, R., Horwath, W.R., 2017. Influence of rice straw on priming of soil C for dissolved organic C and CH4 production. Plant and Soil.
  21. Ye, R., Doane, T.A., Horwath, W.R., 2016. Comparison of isotope methods for partitioning methane production and soil C priming effects during anaerobic decomposition of rice residue in soil. Soil Biology and Biochemistry 95, 51-59.
  22. Ye, R., Espe, M.B., Linquist, B., Parikh, S.J., Doane, T.A., Horwath, W.R., 2016. A soil carbon proxy to predict CH4 and N2O emissions from rewetted agricultural peatlands. Agriculture, Ecosystems & Environment 220, 64-75.
  23. Ye, R., Horwath, W.R., 2016. Nitrous oxide uptake in rewetted wetlands with contrasting soil organic carbon contents. Soil Biology and Biochemistry 100, 110-117.
  24. Ye, R., Keller, J.K., Jin, Q., Bohannan, B.J., Bridgham, S.D., 2016. Peatland types influence the inhibitory effects of a humic substance analog on methane production. Geoderma 265, 131-140.
  25. Chen, W., Zhang, L., Li, X., Ye, R., Li, Q., Zhu, J., Fang, N., Wang, L., Wu, Z., Horwath, W.R., 2015. Elevated ozone increases nitrifying and denitrifying enzyme activities in the rhizosphere of wheat after 5 years of fumigation. Plant and Soil 392, 279-288.
  26. Ye, R., Doane, T.A., Morris, J., Horwath, W.R., 2015. The effect of rice straw on the priming of soil organic matter and methane production in peat soils. Soil Biology and Biochemistry 81, 98-107.
  27. Liang, X., Zhu, S., Ye, R., Guo, R., Zhu, C., Fu, C., Tian, G., Chen, Y., 2014. Biological thresholds of nitrogen and phosphorus in a typical urban river system of the Yangtz delta, China. Environmental Pollution 192, 251-258.
  28. Ye, R.Z., Jin, Q.S., Bohannan, B., Keller, J.K., Bridgham, S.D., 2014. Homoacetogenesis: A potentially underappreciated carbon pathway in peatlands. Soil Biology & Biochemistry 68, 385-391.
  29. Bridgham, S.D., Ye, R., 2013. Organic matter mineralization and decomposition, In: DeLaune, R.D., Reddy, K.R., Richardson, C.J., Megonigal, J.P. (Eds.), Methods in Biogeochemistry of Wetlands. Soil Science Society of America, pp. 385-406.
  30. Ye, R.Z., Jin, Q.S., Bohannan, B., Keller, J.K., McAllister, S.A., Bridgham, S.D., 2012. pH controls over anaerobic carbon mineralization, the efficiency of methane production, and methanogenic pathways in peatlands across an ombrotrophic-minerotrophic gradient. Soil Biology & Biochemistry 54, 36-47.
  31. Ye, R.Z., McCray, J.M., Wright, A.L., 2011. Microbial Response of a Calcareous Histosol to Sulfur Amendment. Soil Science 176, 479-486.
  32. Ye, R.Z., Wright, A.L., McCray, J.M., 2011. Seasonal changes in nutrient availability for sulfur-amended everglades soils under sugarcane. Journal of Plant Nutrition 34, 2095-2113.
  33. Ye, R.Z., Wright, A.L., 2010. Multivariate analysis of chemical and microbial properties in histosols as influenced by land-use types. Soil & Tillage Research 110, 94-100.
  34. Ye, R.Z., Wright, A.L., McCray, J.M., Reddy, K.R., Young, L., 2010. Sulfur-induced changes in phosphorus distribution in Everglades Agricultural Area soils. Nutrient Cycling in Agroecosystems 87, 127-135.
  35. Ye, R.Z., Wright, A.L., Orem, W.H., McCray, J.M., 2010. Sulfur distribution and transformations in Everglades Agricultural Area soil as influenced by sulfur amendment. Soil Science 175, 263-269.
  36. Ye, R.Z., Wright, A.L., Inglett, K., Wang, Y., Ogram, A.V., Reddy, K.R., 2009. Land-use effects on soil nutrient cycling and microbial community dynamics in the Everglades Agricultural Area, Florida. Communications in Soil Science and Plant Analysis 40, 2725-2742.

Current Lab Members:

Binaya Parajuli (PhD Student, 2020)
Charles Parker (Technician)
Charles Williamson (MS Student, 2021)
Pratima Poudel (MS Student, 2019)
Shawn West (Technician)
Zhine Wang (PhD Student, 2021)


Binaya Parajuli (MS Student, 2018-2020)
Min Luo (Visiting Scholar, 2018-2019)