Our understanding of how plant-microbe interactions regulate carbon (C) and nitrogen (N) retention in soil organic matter (SOM) remains uncertain. Conflicting evidence suggests that microbial decomposition can lead to the loss of unprotected particulate SOM, but also that microbial decomposition produces simpler compounds that preferentially form more persistent aggregate- or mineral-protected SOM pools. Further, uncertainty remains in how plant-microbe interactions alter SOM retention in these different pools through litter chemistry controls on microbial decomposition traits and rhizosphere priming. As a result, this uncertainty limits our ability to sustainably manage ecosystems and understand future feedbacks between terrestrial ecosystems and the global climate. In this dissertation, I address these uncertainties to answer the following research questions: 1) How do plant-microbe interactions between plant litter and microbial decomposition traits influence the formation of new soil C for different bioenergy crop litters in the lab?; 2) How do rhizosphere plant-microbe interactions influence soil organic matter stabilization and destabilization depending on nutrient levels in-situ?; and 3) Can empirical measurements help constrain, parameterize, and validate modeled plant-microbe interactions to improve representations of forest ecosystem responses to global change?
For question 1, I examined differences between two bioenergy feedstocks, corn and miscanthus, in the ability of their litter to form new unprotected SOM vs. mineral-protected SOM. I traced the fate of isotopically enriched litter C into microbial respiration and SOM pools in the lab and found that chemically simple corn litter promoted higher microbial uptake and carbon use efficiency, forming less unprotected SOM and more mineral-protected SOM than more complex miscanthus litters. I also demonstrated the potential for our measurements to parameterize a microbial SOM model and improve predictions of soil C formation. This link between litter quality, microbial efficiency, and SOM formation bridges empirical uncertainty in how bioenergy crops build soil C. For question 2, I investigated whether living roots and their associated fungi increase or decrease new SOM formation from litter. I traced isotopically enriched litter C and N into SOM pools in root ingrowth cores incubated in a miscanthus field. I found that roots stimulated litter decomposition but balanced this loss by transferring carbon into aggregate-protected SOM. Further, roots selectively mobilized N from litter without additional C release, suggesting that roots efficiently mine N and build persistent soil C. This work expands our mechanistic understanding of how living roots shape agricultural ecosystem processes. For question 3, I investigated if modelling plant-microbe interactions and microbially-explicit N cycling could improve representations of forest soil C and N retention under changes in anthropogenic N deposition. I leveraged decades of C and N cycling data from a whole-watershed N fertilization experiment to run a microbially-explicit plant-microbe interactions model. The model accurately represented key ecosystem C responses to enhanced N availability, including a decline in plant C cost for N acquisition and an increase in soil C. By incorporating new, microbially-explicit N cycling, the model could also capture how enhanced N availability altered N cycling and streamwater N losses. When we ran the model forward under declining N deposition, the model predicted that N losses recovered faster than soil C pools. However, the C sequestered due to N deposition may be vulnerable to future loss, particularly in a warming climate. Collectively, my research shows that vital ecosystem services like soil C and N retention depend on microbially-mediated processes that are regulated by plant-microbe interactions
