Agricultural land use induces broader homogenization of soil microbial functional composition than taxonomic composition in sub-Saharan Africa

Land-use changes from natural ecosystems to farmlands substantially alter soil functioning worldwide, particularly in sub-Saharan Africa, where rapid population growth and intensive agriculture pose serious challenges. Soil microbial diversity is vital in supporting ecosystem multifunctionality and preventing pathogen growth. Recent studies have revealed that farming activities homogenize microbial communities across distant sites, which may lead to functional homogenization on that scale. However, given the redundancy of microbial functions—where different taxa can perform similar functions—farming may drive functional homogenization over broader spatial scales than taxonomic homogenization. We compared the taxonomic and functional compositions of soil prokaryotic and fungal communities between natural lands and farmlands across spatial scales ranging from within-site (∼200 m) to across-site (∼1500 km) in Kenya and Malawi, using amplicon sequencing of 16S rRNA and ITS genes and the prediction of microbial functions. Soil microbial predicted-functional compositions were homogenized more broadly than taxonomic compositions in farmlands compared to natural lands, suggesting that similar functional responses to farming occur across scales where different taxa thrive. Furthermore, environmental factors (soil pH, carbon, nitrogen, and moisture) were predominantly related to within-site homogeneity, whereas farming itself was a significant contributor to across-site homogeneity, indicating an overriding influence of farming compared to environmental variations. Additionally, pathogenic fungi were relatively more abundant in farmlands, likely due to reduced species competition and farming-induced environmental changes such as low soil pH. Our findings highlight the need to investigate microbial functional diversity alongside taxonomic diversity when assessing land-use impacts on soil health for sustainable land management.