Herbicide resistance in Echinochloa species and soil microbial diversity: perspectives for sustainable weed management

The withdrawal of many plant protection products (PPPs) from the EU market due to Reg. EC/1107/2009 and the lack of new modes of action (MoAs) have led to the evolution of herbicide resistance (HeR) that represents a very serious problem particularly for those territories traditionally dedicated to rice cultivation in Northern Italy. In this area, a survey on the spread of herbicide resistance is underway through monitoring studies and laboratory tests with the aim of highlighting the causes favoring the phenomenon. In our study we evaluated the relationship between the soil microbial composition of paddy fields in Lombardy and the incidence of resistance to acetolactate synthase (ALS) and acetyl- CoA carboxylase (ACCase) inhibitors in Echinochloa species. Soil samples were collected in 32 rice farms, located in the provinces of Pavia and Milano and managed according to the Directive 2009/128 EC, where Echinochloa species surviving herbicide treatments were recognized. The incidence of surviving specimens was recorded through cover/abundance values in accordance with Braun-Blanquet. Seeds were collected and controlled green-house growth trials were performed applying the same herbicides used in fields. Three weeks after treatment, the sensitivity/resistance of plants to herbicides was tested following EPPO standards. Total DNA was extracted from soil samples and was amplified. Metagenomic amplicons of bacterial and fungal communities were sequenced and bioinformatic analysis was performed. Specimens of Echinochloa crus-galli (L.) P. Beauv and Echinochloa oryzicola (Vasinger) Vasinger resistant to herbicide treatments were detected. A relation between the soil microbiomes diversity and the herbicide resistance incidence was observed. A low microbial diversity was recorded in highly infested paddies (resistant Echinochloa coverage ≥ 60%) while a high microbial diversity was recorded in poorly infested paddies (resistant Echinochloa coverage ≤ 5%). Fungal communities appeared to be more involved in the phenomenon than Bacteria and Archaea. Two diDerent microbial profiles related to the high or low incidence of herbicide resistance in Echinochloa species were identified: Lactobacillales, Malasseziales and Diaporthales resulted in a positive relation with high HeR incidence, otherwise Rhizobiales and Solibacterales resulted in a positive relation with low HeR incidence. The relation between HeR incidence variability and diDerent microbial communities allows us to make hypotheses on the greater or lesser probability of herbicide resistance occurrence, based on the composition and α-diversity of the soil microbiome. Understanding complex interactions of weeds with soil microorganisms and improving the biodiversity of soil microbial communities could be strategic in developing more eDective approaches to herbicide- resistant weed management and plant protection, with the final aim of optimizing precision weed management (PWM) technologies.