Soil Microbial Community Shifts and Ecosystem Multifunctionality in Response to Integrated Cover Cropping and Nitrogen Management in Mississippi Corn Production Systems

ORCID

Chinthalapudi: https://orcid.org/0000-0002-4377-1097; Shanmugam: https://orcid.org/0000-0001-5598-309X

MSU Affiliation

College of Agriculture and Life Sciences; Department of Plant and Soil Sciences; Institute of Genomics, Biocomputing and Biotechnology

Creation Date

2026-09-30

Abstract

Integrating cover crops (CCs) with nitrogen (N) management can enhance soil health, yet their combined effects on soil microbiomes and multifunctionality remain insufficiently characterized in short-term, multi-location corn systems in Mississippi. We evaluated how CC identity (single species and mixtures) and reduced N fertilization shape soil microbial communities and soil multifunctionality across a three-year field experiment (2021–2025) conducted at two locations in Mississippi, USA (Starkville and Newton). Treatments included six CCs with a no-cover control under two N rates (0 and 112 kg N ha−1). At corn V4 growth stage, soil samples (0–15 cm) were analyzed for physicochemical and biological indicators (pH, total C and N, POXC, glomalin, and enzyme activities), bacterial and fungal communities (16S rRNA V4 and ITS2 amplicon sequencing), and N-cycling functional genes (amoA and nifH via qPCR). Across years and locations, CCs, especially ryegrass, consistently increased soil biological indicators and elevated a composite multifunctionality index, while N fertilization reduced soil pH and exerted comparatively smaller effects on multifunctionality. Microbial community structure was primarily driven by interannual variation and location factors, with N fertilization consistently increasing bacterial α-diversity, and CC effects were most evident in specific years and were strongest under ryegrass. Network analyses indicated higher bacterial network complexity under 0 N, whereas fungal networks showed greater connectivity under N addition. Bacterial diversity and key bacterial taxa were positively associated with multifunctionality, and structural equation modeling indicated that microbial diversity and N-cycling functional groups mediate management effects on multifunctionality. Overall, ryegrass enhanced microbial-linked ecosystem services under reduced N inputs, though these shifts did not translate into consistent corn yield gains.

Keywords

ryegrass, soil health, maize, structural equation modelling (SEM), nitrogen cycling, N-cycling genes, co-occurrence networks, rhizosphere, bacterial communities, fungal communities, qPCR

Publication Date

8-1-2026

Publication Title

Microbiological Research

Publisher

Elsevier

Creative Commons License

Creative Commons Attribution 4.0 International License
This work is licensed under a Creative Commons Attribution 4.0 International License.

Rights

© 2026 The Authors

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Digital Object Identifier (DOI)

https://doi.org/10.1016/j.micres.2026.128651