Soil Health and Microbial Community Response to a Cover Crop Rotation in Puerto Rico

Cover cropping can be a promising management strategy to improve soil health in the tropics. Our study evaluated physical, chemical, and microbiological indicators of soil health three years after implementing a maize and cowpea cover crop rotation with five fertilizer rates in replicated plots on a Torrifluventic Haplustepts in the southern semiarid coast of Puerto Rico. The Soil Management Assessment Framework (SMAF) was used to integrate different soil parameters to provide a comprehensive overview of soil health changes. Water aggregate stability (WAS) was not affected by cover crops. Soil pH significantly decreased with increasing nitrogen (N) fertilization rate and with cover crop rotation. Chemical and microbial indicators of soil health related to organic matter dynamics and nutrient cycling potential [e.g., microbial biomass nitrogen (MBN), potentially mineralizable N (PMN), β-glucosidase activity, combined enzyme activity for carbon (C), N, and phosphorus (P) cycling (β-glucosidase, β-glucosaminidase, and acid phosphatase] were significantly (p < 0.1) improved by cover crop but were not affected by fertilizer rate or cover crop x fertilizer rate. Fatty acid methyl esters (FAME) analysis showed that only G+ bacteria were significantly higher due to cover cropping. Principal component analysis revealed that total FAMEs and markers for G+ bacteria, G− bacteria, actinobacteria, and saprophytic fungi responded similarly to management and were generally influenced by cover cropping. Overall, improvements in microbial communities led to significant increases in key functions supporting soil health and sustainability within just three years of cover cropping adoption. The SMAF, as a well-known soil quality/health index, detected early benefits of using cover crops. Our study provided evidence that these indicators can serve as tools to assist farmers in selecting sustainable management practices such as cover crops in the tropics, yet long-term monitoring is still needed.