Bacterial rrn copy numbers linked to soil function and crop yield in long-term manure-fertilized soils

Abstract

The 16S rRNA operon (rrn) copy number in bacteria has been proposed as a genomic trait linked to microbial life-history strategies and resource availability. Yet, its role in agroecosystems under different management histories is unclear. We investigated how soil microbial communities and metabolites respond to 36 years of varying manure fertilization strategies (chemical fertilizers with or without manure) using 16S rRNA gene amplicon sequencing and nontargeted metabolomics. Manure treatments favored copiotrophic bacteria, increasing the average rrn copy numbers while reducing oligotrophs. Microbial life-history strategies were primarily driven by C: N, SOC, and available phosphorus (AP). The rrn copy number was positively correlated with the abundance of genes encoding functions for C, N, and P cycling, as well as correlated enzyme activities, indicating that copiotroph-dominated communities in manure-fertilized soils exhibit a competitor strategy to utilize a broader range of resources. Significant correlations between soil metabolite profiles and rrn copy numbers, and strong interactions between copiotrophic strategists and key metabolites suggest that microbial communities with distinct life-history strategies harbor unique metabolic profiles. PLS-PM modeling and random forest analysis identified rrn copy number as a predictive trait for soil functions (metabolic profiles and enzyme activities) and maize yield. These findings highlight bacterial rrn copy number as a key trait underpinning the life-history strategies and functional potential of microbial communities in response to long-term manure fertilization.