Agricultural land use determines functional genetic diversity of soil microbial communities

•Land-use management affected the genetic potential of microbes to degrade SOM.•Microbial functions highly correlated to soil N, while their taxonomy was more to C.•Functional diversity of microbes did not correlate to their taxonomic diversity.•Captured metagenomics had higher resolution in deducing the effects of land-use.

Microbial communities play a major role in the degradation of soil organic matter (SOM) in soils. Despite its significance, the functional diversity of the highly diverse microbial communities is poorly understood. To address this, we applied a recently developed technique, captured metagenomics, to determine the effects of land-use on the functional genetic diversity of genes involved in the carbon degradation of SOM in five pairs of agricultural soils with either winter wheat or grass as management. In addition, 16S rRNA based amplicon sequencing was used to study the taxonomic composition in the same soils. The functional genes resulting from the captured metagenomes had a higher abundance and diversity of sequences coding for enzymes degrading SOM in the grasslands compared to the wheat soils. Though the taxonomic diversity did not correlate with the land use. Amounts of C and N (organic matter content) in the soils affected both functional and taxonomic diversity of the microbial communities, where N was highly correlated to their functions and C was highly correlated to their taxonomy. Captured metagenomic analyses of the functional genes may provide a measure of the potential SOM degradation capacity by soil microbial communities at a high resolution. This can be used for assessments of how agricultural management affects the functioning of soil communities.