Cover crop suppression with glyphosate-based herbicides (GBHs) represents a common agricultural practice. The objective of this study was to compare rhizospheric microbial communities of A. sativa plants treated with a GBH relative to the mechanical suppression (mowing) in order to assess their differences and the potential implications for soil processes. Samples were obtained at 4, 10, 17 and 26 days post-suppression. Soil catabolic profiling and DNA-based methods were applied. At 26 days, higher respiration responses and functional diversity indices (Shannon index and catabolic evenness) were observed under glyphosate suppression and a neat separation of catabolic profiles was detected in multivariate analysis. Sarcosine and Tween 20 showed the highest contribution to this separation. Metabarcoding revealed a non-significant effect of suppression method on either alpha-diversity metrics or beta-diversity. Conversely, differences were detected in the relative abundance of specific bacterial taxa. Mesorhizobium sequences were detected in higher relative abundance in glyphosate-treated plants at the end of the experiment while the opposite trend was observed for Gaiella. Quantitative PCR of amoA gene from ammonia-oxidizing archaea showed a lower abundance under GBH suppression again at 26 days, while ammonia-oxidizing bacteria remained lower at all sampling times. Broad host range plasmids IncP-1β and IncP-1ε were exclusively detected in the rhizosphere of glyphosate-treated plants at 10 days and at 26 days, respectively. Overall, our study demonstrates differential effects of suppression methods on the abundance of specific bacterial taxa, on the physiology and mobile genetic elements of microbial communities while no differences were detected in taxonomic diversity.

Cover cropping (CC) is the most promising in-field practice to improve soil health and mitigate N losses from fertilizer use. Although the soil microbiota play essential roles in soil health, their response to CC has not been well characterized by bioindicators of high taxonomic resolution within typical agricultural systems. Our objective was to fill this knowledge gap with genus-level indicators for corn [Zea mays L.] monocultures with three N fertilizer rates (N0, N202, N269; kg N ha⁻¹), after introducing a CC mixture of cereal rye [Secale cereale L.] and hairy vetch [Vicia villosa Roth.], using winter fallows (BF) as controls. A 3 × 2 split-plot arrangement of N rates and CC treatments was studied in a randomized complete block design with three replicates over two years. Bacterial and archaeal 16S rRNA and fungal ITS regions were sequenced with Illumina MiSeq system. Overall, our high-resolution bioindicators were able to represent specific functional or ecological shifts within the microbial community. The abundances of indicators representing acidophiles, nitrifiers, and denitrifiers increased with N fertilization, while those of heterotrophic nitrifiers, nitrite oxidizers, and complete denitrifiers increased with N0. Introducing CC decreased soil nitrate levels by up to 50% across N rates, and CC biomass increased by 73% with N fertilization. CC promoted indicators of diverse functions and niches, including N-fixers, nitrite reducers, and mycorrhizae, while only two N-cycling genera were associated with BF. Thus, CC can enhance the soil biodiversity of simplified cropping systems and reduce nitrate leaching, but might increase the risk of nitrous oxide emission without proper nutrient management. This primary information is the first of its kind in this system and provided valuable insights into the limits and potential of CC as a strategy to improve soil health.