Agricultural intensification, microbial homogenization and loss of rare microbiota

To meet the needs of a growing human population, agricultural management practices have undergone substantial intensification, specialization and industrialization. This has contributed to biotic homogenization and a loss of diversity in microbial communities within agricultural systems. In this Perspective, we summarize recent studies that report microbial homogenization due to agricultural intensification. We propose a definition of microbial homogenization and explore how intensive agricultural practices can cause taxonomic, physiological, genetic and functional homogenization of microbial communities. Our analysis indicates that globally the diversity of rare taxa is lower in intensively managed agricultural lands compared with less-intensive lands and that agricultural intensification suppresses beneficial microorganisms and promotes pathogenic taxa. We identify microbial taxa that are sensitive to intensification and discuss how the disproportionate impact on rare microbiota can threaten agro-ecosystem functions and food security. Finally, we outline key challenges and suggest areas that require further research.