Effect of Dry and Flooded Rice as Cover Crops on Soil Health and Microbial Community on Histosols

Soil loss due to subsidence is a major concern in the Everglades Agricultural Area (EAA) of South Florida. Summer is typically the fallow season in the EAA, and soil loss due to oxidation and erosion is significant. Flooding and cover cropping are common practices being adopted to conserve soil, reduce weed pressure, and enhance soil health in the EAA. Cover crops also increase the microbial biomass which are the key drivers of soil function. The objective of this study was to determine the effect of (i) fallow, (ii) dry rice as a cover crop, (iii) flooded fallow, and (iv) flooded rice as a cover crop on soil health indicators and microbial community and diversity within the EAA. Baseline (pre-planting) soil samples were collected from all fields before the application of different treatments and post-harvest soil samples were collected after rice was cut and tilled into the soil surface. Microbial community composition was determined using 16S rRNA gene amplicon and fungal ITS gene amplicon sequencing. Soil bulk density decreased, and cation exchange capacity (CEC) increased in all farming practices including fallow fields. Results showed flooded fallow, flooded rice, and rice planting increased maximum water holding capacity (MWHC) and soil protein and decreased total potassium (TK). Bulk soil microbial communities responded surprisingly quickly to the applied treatments. Taxonomic composition of prokaryotic and fungal communities at the phylum level revealed visible shifts in microbial communities in response to the treatments. Instead of leaving field fallow, planting rice or flooding is a better strategy to improve soil health.