Herbicide-treated soil as a reservoir of beneficial bacteria: microbiome analysis and PGP bioinoculants in maize.

Background: Herbicides are integral to agricultural weed management but can adversely affect non-target organisms, soil health, and microbiome. We investigated the effects of herbicides on the total soil bacterial community composition using 16S rRNA gene amplicon community profiling. Further, we aimed to identify herbicide-tolerant bacteria with plant growth-promoting (PGP) capabilities as a mitigative strategy for these negative effects, thereby promoting sustainable agricultural practices.

Results: A bacterial community analysis explored the effects of long-term S-metolachlor application on soil bacterial diversity, revealing that the herbicide's impact on microbial communities is less significant than the effects of temporal factors (summer vs. winter) or agricultural practices (continuous maize cultivation vs. maize-winter wheat rotation). Although S-metolachlor did not markedly alter the overall bacteriome structure in our environmental context, the application of enrichment techniques enabled the selection of genera such as Pseudomonas, Serratia, and Brucella, which were rare in metagenome analysis of soil samples. Strain isolation revealed a rich source of herbicide-tolerant PGP bacteria within the culturable microbiome fraction, termed the high herbicide concentration tolerant (HHCT) bacterial culture collection. Within the HHCT collection, we isolated 120 strains that demonstrated significant in vitro PGP and biocontrol potential, and soil quality improvement abilities. The most promising HHCT isolates were combined into three consortia, each exhibiting a comprehensive range of plant-beneficial traits. We evaluated the efficacy and persistence of these multi-strain consortia during 4-week in pot experiments on maize using both agronomic parameters and 16S rRNA gene community analysis assessing early-stage plant development, root colonization, and rhizosphere persistence. Notably, 7 out of 10 inoculated consortia partners successfully established themselves and persisted in the maize root microbiome without significantly altering host root biodiversity. Our results further evidenced that all three consortia positively impacted both seed germination and early-stage plant development, increasing shoot biomass by up to 47%.

Conclusions: Herbicide-treated soil bacterial community analysis revealed that integrative agricultural practices can suppress the effects of continuous S-metolachlor application on soil microbial diversity and stabilize microbiome fluctuations. The HHCT bacterial collection holds promise as a source of beneficial bacteria that promote plant fitness while maintaining herbicide tolerance.