On the legacy of cover crop-specific microbial footprints

Apart from improving the physical and chemical condition of arable soils, cover crops have the potential to boost and activate selected soil microbiota that could contribute to improved nutrient cycling and strengthened disease suppressiveness. However, a main crop can only benefit from cover crop-induced microbial shifts if these persist until the onset of the main growing season. Here, we map the persistence of microbiome changes by cover crops over time. We performed a field experiment on a sandy soil with ten different cover crop monocultures belonging to five plant families, one cover crop mixture and a fallow control. Cover crops were grown for 4.5 months under field conditions in 70-L bottomless containers in a random block design with eight replications. We studied the total (DNA-based) and the potentially active (RNA-based) microbial fractions at the onset of the main growing season, and just after the harvest of the main crop, potato (respectively 3.5 and 10 months after cover crop termination), through MiSeq sequencing. All cover crops tested induced shifts in the soil microbiome that lasted at least until the onset of the main growing season. Cover crop treatments gave rise to species and even cultivar-specific microbial footprints, and - although roughly the same trends were observed - DNA-based microbial shifts were not necessarily paralleled by similar changes at RNA level. We conclude that cover crops have the potential to act as handles to steer the soil microbiome in a way that is supportive of sustainable crop production.