Soil microbiome analysis of Uruguayan grasslands and croplands reveals losses of microbial diversity and necromass recycling traits.

BACKGROUND

Soil microbiomes are critical regulators of nutrient biogeochemical cycles, contributing significantly to ecosystem services that support plant productivity. In this study, we investigated the effects of agricultural rotations on soil microbial communities in Uruguayan grasslands, comparing cropland soils with native grasslands grazed by livestock. By employing advanced metagenomic techniques, we characterized the diversity and functional potential of the soil microbiome, with particular emphasis on its roles in carbon, nitrogen, and phosphorus cycling. Additionally, we assessed functional genes associated with microbial necromass recycling, a key process for maintaining soil health and fertility.

RESULTS

Our analysis revealed a significant decrease in fungal diversity and a restructuring of the fungal community in agricultural soils, highlighting the profound impact of farming practices on soil biology. In contrast, while we did not observe a similar decline in bacterial diversity, there was a noticeable shift in its composition. Agricultural soils showed a reduced abundance of bacteriophages, which are associated with bacterial necromass formation, as well as a decline in enzymes involved in microbial necromass decomposition. This suggests potential long-term consequences for soil carbon dynamics and crop productivity. Additionally, croplands exhibited a marked decrease in genes and enzymes involved in nitrogen and phosphorus cycling, indicating diminished functionality and resilience for these essential nutrient processes compared to grassland soils.

CONCLUSIONS

Our findings emphasize the need for a sustainable approach to agriculture that preserves microbial diversity and functionality, ensuring the resilience of soil ecosystems. By comparing soil microbiomes across different land use types, this research provides novel insights into the mechanisms through which agriculture alters soil ecosystems and offers guidance for enhancing soil management practices to support environmental sustainability and agricultural productivity.