Promotion of healthy crop growth by cover crops-based steering of the soil microbiome

Conventional food production is often accompanied by elevated nutrient inputs, pesticide applications and frequent tillage, often leading to nutrient leakage, a decrease of soil organic matter content, soil erosion and biodiversity loss. Cover crops are non-economic crops grown between cropping seasons that could help to reverse the aforementioned effects. In addition, cover crops can be grown to stimulate and steer the soil microbial community to optimize healthy crop growth. However, despite their relatively widespread use, little is known about the impact of cover crops on the composition and activity of the microbiome and the persistence of such effects over time.

We conducted a field experiment that comprised of ten commonly used cover crop species with representatives from five plant families. Cover crops (plus fallow control) were grown as monocultures in bottomless 70 l containers under field conditions. To characterize both the resident and the active fractions of the bacterial, fungal and protist communities, total DNA and RNA were isolated from soil sampled at three time points: (1) during cover crop growth (rhizosphere), (2) after cover crop incorporation in soil, and (3) after cash crop harvest (bulk soil). The three organismal groups were characterized using the Illumina MiSeq platform.

The analysis of the rhizosphere samples revealed that cover crops impacted significantly the local soil microbiome, explaining up to 50% of the variation in the microbial communities. Cover crops showed distinct selection strengths on their rhizosphere, and they induced qualitatively different changes in the microbial assemblies. Oilseed radish provoked the strongest microbial shifts, whereas black oat, hybrid ryegrass and marigold (Tagetes sp.) induced milder changes.

A legacy effect of the cover crop treatments was determined for the soil bacterial community (for fungi and protists data analysis in progress). Cover crop treatment explained respectively up to 27% and 14%, of the overall bacterial variation in the two subsequent sampling time points. A selection of taxa highly enriched in the rhizosphere of oilseed radish, including the families Pseudomonadaceae and Alcaligenaceae, was found to be persistently enhanced in the bulk soil after the treatment.

The current data set is a starting point for the application of specific cover crop species or mixtures thereof to steer the soil microbiome in a predictable direction to optimize healthy crop growth.