Unveiling rhizobacterial diversity in rice-maize systems in response to penoxsulam-pendimethalin application

The rice-maize system is crucial for Asia for improving productivity and resilience. The conventional puddled transplanting (CT) of rice, while prevalent, is resource-intensive and environmentally unsustainable. Zero-tillage direct-seeded rice (ZT-DSR) provides a conservation-oriented alternative, but greater weed pressure demands efficient herbicide applications. The ready-mix penoxsulam (PEN) and pendimethalin (PND) are widely used soil-applied pre-emergence herbicides, but their combined effects on soil microbial communities under different crop establishment practices remain unclear. Therefore, the current study was carried out to evaluate the effect of the ready-mix herbicides on rice rhizosphere under rice-maize agroecosystem. A 16 S rRNA amplicon sequencing study was conducted in the rice rhizosphere to assess herbicidal efficacy and soil bacterial responses under conventional tillage and ZT–DSR in a completely randomized block design. A total of 50 bacterial species were identified in the rice rhizosphere under different establishment methods and herbicide (PEN + PND) application. Soils under zero-till (ZT) with PEN + PND showed higher nutrient levels and enhanced enzymatic activities, including urease, DHA and ALP, compared to control and conventional tillage (CT) soils. Although PEN + PND initially reduced the microbial population by 14 days after the application of herbicides, bacterial, fungal and actinomycete counts recovered by harvest, with ZT showing the highest rebound. Species such as Occallatibacter riparius, Candidatus Korobacter versatilis, Raoultibacter timonensis, Thermoleophilum album and Bacillus velezensis demonstrated tolerance to the herbicides. Based on relative abundance patterns in microbial community, certain bacterial taxa, including Occallatibacter riparius, Candidatus Korobacter versatilis, Raoultibacter timonensis, Thermoleophilum album and Bacillus velezensis, were observed to persist under pendimethalin and penoxsulam application. Some newly emerged species, Bacillus velezensis (under zero-till) and Xanthomonas albilineans, Pseudolabrys taiwanensis, Clostridium beijerinckii, Clostridium thermarum and Romboutsia sp. 13,368 (under conventional tillage) with herbicide application showed higher relative abundance following herbicide application in comparison to non-application. The study showed potential changes in microbial abundance patterns and shifts under penoxsulam and pendimethalin application. The findings support preliminary insights into microbial dynamics under the use of zero-tillage with herbicide application to sustain soil health in rice-maize systems. However, the functional validation is required to elucidate resistance mechanisms including biochemical, morphological and genetic processes, along with their interactions.