Functional genomics and phenotypic characterization of PGP and biocontrol traits of rhizospheric Streptomyces spp. from Mexican milpa agroecosystem

The traditional Mesoamerican milpa is an ancient agroecosystem with significant cultural and economic importance, commonly practiced by indigenous and rural communities for subsistence agriculture. Recognized for their diversity and sustainability, milpas utilize local resources and help preserve biodiversity. This ecosystem includes various plants of American origin, which establish numerous beneficial ecological relationships and promote interactions between plants and microbes. In this study, a collection of Streptomyces strains was isolated from the rhizosphere of native Cacahuacintle maize, squash, fava bean, and huauzontle. These strains exhibited various in vitro plant growth-promoting (PGP) activities, including ammonium production, phosphate solubilization, and siderophore production. Notably, Streptomyces sp. FR-108, isolated from the fava bean rhizosphere, and Streptomyces griseus MR-45, isolated from maize, increased maize biomass in a short-term greenhouse assay. Among the other strains, Streptomyces anulatus SR-10 from squash and Streptomyces albidoflavus MR-37 from maize demonstrated in vitro extracellular enzyme secretion and antagonistic activities against phytopathogenic fungi. Comparative and functional genomic analyses of these strains revealed their typical size, topology, and G + C content characteristic of Streptomyces genomes. Additionally, a substantial repertoire of genes involved in plant growth promotion was identified, contributing to nutrient acquisition, tolerance to osmotic, drought, chemical, and temperature stresses, as well as mutualistic interactions with plants and biocontrol of fungi, bacteria, insects, and protists. While no studies have previously focused on Streptomyces as plant growth-promoting bacteria (PGPB) in milpa agroecosystems, this genus shows potential as a bioinoculant for sustainable or extensive agriculture. This underscores the significance of traditional agroecosystems as sources of beneficial microorganisms.