Organic management and cover crop species steer soil microbial community structure and functionality along with soil organic matter properties

It is well recognized that organic soil management stimulates bacterial biomass and activity and that including cover crops in the rotation increases soil organic matter (SOM). Yet, to date the relative impact of different cover crop species and organic vs. non-organic soil management on soil bacteria and fungi and on SOM quantity and quality remains to be tested. We used a long-term (10 years) full-factorial field experiment to test the combined effects of organic vs. conventional soil management with different cover crop species (oat or rye) and the legacy effects of seven soil health treatments (SHTs: treatments with compost, chitin, marigold, grass–clover, biofumigation or anaerobic soil disinfestation (ASD), and fallow as control) on microbial community biomass, structure and catabolic activity and on SOM quantity and quality (dissolved organic carbon (DOC), aromaticity and water repellency). Microbial community traits were assessed using PLFA/NLFA analyses and multi-substrate induced respiration. We found that organic soil management enhanced total microbial biomass by increasing bacterial, saprotrophic and arbuscular mycorrhizal fungal biomass; and increased total microbial catabolic activity, associated with maintaining high microbial efficiency (low qCO2). Effects of organic management were amplified by oat as cover crop, which enhanced the abundance of saprotrophic fungi resulting in a higher fungal:bacterial ratio. Total SOM concentration was similar among treatments, however the most easily accessible fraction, i.e. DOC, was higher in organic compared to conventional soils. Also, the aromaticity of the DOC was lower in organic than in conventional systems, which was associated with lower water repellency. There was a legacy effect of SHTs on fungal:bacterial ratio in that chitin and marigold showed higher fungal:bacterial ratio compared to compost, biofumigation and ASD even 6 years after the last application. We conclude that organic soil management enhances the abundance of all microbial groups and their total catabolic activity, associated with a higher concentration and lower aromaticity of dissolved organic matter. These effects can be enlarged by the growth of specific cover crops and the application of certain soil health treatments.