Molecular and functional characteristics of streptomycete communities in relation to soil factors and potato common scab

Naturally-occurring disease-suppressive soils provide control of plant pathogens via the activities of indigenous microbes. While all soils contain antagonistic microbes, there is little systematic understanding of the correlates of variation in indigenous antagonist populations and on their relationships with plant diseases. We characterized the population densities, inhibitory capacities, and phylogenetic composition of soil streptomycete communities in a potato field over time in relation to edaphic factors, antagonist inoculation, and potato common scab severities. Antagonistic Streptomyces populations were highly variable in time and space. Similarly, metagenomic analyses of streptomycete communities showed extensive spatial and temporal variation in composition. Soil characteristics (pH, potassium, organic matter, nitrate, and phosphorous) sometimes explained up to 50% of the spatial variation in Streptomyces population densities, proportion of inhibitory isolates, or pathogen suppressive capacity among locations in the field. Soil pH was positively correlated with common scab severity, and negatively correlated with the proportion of pathogen-inhibitory Streptomyces among locations in the field. This suggests that high pH may have direct beneficial effects on pathogen populations and disease development, and/or indirect effects on pathogen populations via reductions in pathogen-inhibitory Streptomyces populations. Mean pathogen suppressive capacity of antagonistic Streptomyces was negatively correlated with common scab disease. Streptomyces inoculants had no discernible effect on streptomycete community composition, antagonistic capacities, or potato common scab severities, likely reflecting poor colonization of inoculants. Further understanding of the relationships between indigenous antagonist populations and plant diseases will be important to harnessing the potential of indigenous communities to contribute to sustainable disease management.