Cropping system drives microbial community response to simulated climate change and plant inputs

The soil microbiome’s role in regulating biogeochemical processing is critical to the cycling and storage of soil organic carbon (C). The function of the microbiome under different land management uses has become a focal area of research due to the interest in managing soil C to mitigate climate change. This study investigates the structural and functional response of soil microbiomes from annual monoculture (corn [Zea mays L.]) and perennial diversified (prairie) cropping systems, both under no-till management for bioenergy production. We used a full factorial soil incubation study to understand the influence of temperature and moisture on microbial C decomposition in these soils, with and without addition of cellulose as a model plant residue. Overall, perennial prairie soil supported distinct microbiomes with more diverse prokaryotic and fungal communities compared to annual corn soil. The less diverse corn microbiome was sensitive to the addition of C, resulting in significantly higher respiration compared to prairie, and this increased respiration was amplified under warmer temperatures. In contrast to C loss from the corn soil as carbon dioxide (CO2), prairie soil had significantly higher extracellular enzyme activities and small increases in microbial biomass, illustrating cropping system-specific tradeoffs between microbial C allocation. Specific community structure shifts occurred with added cellulose, where fast-growing, motile decomposers became more abundant under wet conditions, while a small subset of fungi dominated under dry conditions. These differential responses of fungi and bacteria reflect microbial traits important for accessing substrates like plant residues. These changes in community structure due to moisture and cellulose amendment were not necessarily reflected in community function, as potential enzyme activities of most hydrolases were insensitive to temperature and C amendment on this short time scale. Lower respiration occurred in prairie compared to corn soil in response to increased available C and temperature, indicating a more resistant prairie microbiome that may be beneficial when confronted with climate change. These findings support deploying perennial and diversified systems in place of annual monocultures as bioenergy feedstocks, cover crops, buffer strips, or urban greenspaces as part of a land management strategy and highlight the importance of microbial activity in developing sustainable agroecosystems.