Although barnyardgrass (Echinochloa crus-galli L.) is more competitive than rice (Oryza sativa L.) in the aboveground part, little is known about whether barnyardgrass is still competitive in recruiting endophytes and the root microbiota composition variation of rice under the barnyardgrass stress. Here, by detailed temporal characterization of root-associated microbiomes of rice plants during co-planted barnyardgrass stress and a comparison with the microbiomes of unplanted soil, we found that the bacterial community diversity of rice was dramatically higher while the fungal community richness was significantly lower than that of barnyardgrass at BBCH 45 and 57. More importantly, rice recruited more endophytic bacteria at BBCH 45 and 57, and more endophytic fungi at BBCH 17, 24, 37 to aginst the biotic stress from barnyardgrass. Principal coordinates analysis (PCoA) showed that rice and barnyardgrass had different community compositions of endophytic bacteria and fungi in roots. The PICRUSt predictive analysis indicated that majority of metabolic pathways of bacteria were overrepresented in barnyardgrass. However, eleven pathways were significantly presented in rice. In addition, rice and barnyardgrass harbored different fungal trophic modes using FUNGuild analysis. A negative correlation between bacteria and fungi in rice and barnyardgrass roots was found via network analysis. Actinobacteria was the vital bacteria in rice, while Proteobacteria dominated in barnyardgrass, and Ascomycota was the vital fungi in each species. These findings provided data and a theoretical basis for the in-depth understanding of the competition of barnyardgrass and endophytes and have implications relevant to weed prevention and control strategies using root microbiota.

With the expansion of saline-alkaline tolerant rice in China, the effects of salinity stress (NaCl) on quinclorac-resistant Echinochloa crus-galli (L.) Beauv (E. crus-galli) is unclear. In this study, the growth chamber experiment was conducted to test the germination and growth physiology of seven populations of E. crus-galli with quinclorac-different resistance levels which were collected from Hunan province. The results showed that a significant decrease of the germination rate and fresh weight of the plants, as well as the length of the roots and young shoots appeared, along with the increased resistance while treated with NaCl. However, no significant differences were detected between quinclorac-resistant and -susceptible E. crus-galli populations while without NaCl treatment. A further study with spectrophotometer showed that the salinity treatment resulted in the increase of the GST activity in all E. crus-galli populations, which are more obvious in those resistant biotypes, and transcriptomics revealed that salt stress reduces the adaptability of quinclorac-resistant E. crus-galli by reducing the biosynthesis, activities of antioxidant enzymes and metabolic enzyme. This study demonstrated that salinity stress (NaCl) may reduce the adaptability of quinclorac-resistant E. crus-galli.

Despite the growing knowledge concerning allelopathic interference with barnyard grass, little is understood regarding the competitive physiological mechanisms of the interaction between allelopathic rice and herbicide-resistant barnyard grass. A hydroponic system was employed to investigate the root morphological traits and different phytohormonal changes in allelopathic and non-allelopathic rice cultivars when co-planted with quinclorac-resistant and -susceptible barnyard grass, respectively. The results show that shoot and root biomass were greater in PI. Barnyard grass stress induced an increase in shoot and root biomass in PI at 7 and 14 days of co-culturing rice and barnyard grass. Especially under the stress of quinclorac-resistant barnyard grass, the shoot biomass of PI increased by 23% and 68%, respectively, and the root biomass increased by 37% and 34%, respectively. In terms of root morphology, PI exhibited a significantly higher fine-root length, in root diameters of <0.5 mm, a greater number of root tips, and longer root tips compared to LE. The response to quinclorac-resistant barnyard grass stress was consistent in terms of the SA and JA content. The obvious accumulation of SA and JA was observed in two rice cultivars under quinclorac-resistant barnyard grass stress, with greater amounts of SA and JA in PI. The significant decrease in auxin (IAA) and abscisic acid (ABA) content in rice was detected from 7 to 14 days under co-culture stress. Additionally, highly significant and positive correlations were found between SA and JA content, and the number of root tips and root tip length at root diameters of 0–0.5 mm in rice.

Allelopathic rice is increasingly recognised as a promising strategy for sustainable weed management. Resistance to the herbicide quinclorac is widespread in barnyardgrass, but it remains unclear whether allelopathic rice exerts the same defence against herbicide‐susceptible and ‐resistant barnyardgrass. We conducted integrated transcriptomic, metabolomic, and metagenomic analyses to investigate the responses of allelopathic rice to quinclorac‐susceptible (S) and ‐resistant barnyardgrass (R) lines. Distinct chemical strategies were identified in allelopathic rice: Terpenoids (e.g., carnosic acid, phytocassane B, and ipomeatetrahydrofuran) mainly suppressed S, while amino acids (e.g., pipecolic acid, L‐glutamate, and L‐histidine) were key against R. Correspondingly, terpenoid biosynthesis and nitrogen metabolism were the most enriched pathways under S and R stress, respectively. Additionally, terpenoid accumulation correlated positively with salicylic acid (SA) and jasmonic acid (JA) concentrations in roots under S. Both terpenoids and amino acids formed the stable ecological networks with rhizosheath microbiota. Functional metagenomic analysis further showed that ABC transporter and quorum sensing pathways were upregulated under S, whereas nitrogen fixation predominated under R. Notably, amino acids formed a nitrogen‐related ecological network with nitrogen‐metabolising microbiota, contributing to improved plant‐available soil nitrogen and total nitrogen content in rice plants. Bioassays showed that exogenous pipecolic acid (≥ 40 μM) and L‐histidine (80 μM) inhibited barnyardgrass seedling growth without affecting allelopathic and non‐allelopathic rice. These findings demonstrate that allelopathic rice employs divergent chemical‐microbial defence strategies against S and R barnyardgrass, highlight the dual role of amino acids, and provide a basis for precision weed management, particularly for herbicide‐resistant weeds in paddy fields.

Barnyardgrass (Echinochloa spp.) is a prevalent type of weed in rice fields worldwide. Despite the growing knowledge concerning allelopathic interference with barnyardgrass, little is understood regarding the competitive mechanisms between allelopathic rice and herbicide-resistant barnyardgrass at the plant physiological level. In this context, a hydroponic system was employed to investigate the root morphological traits and different phytohormones levels of two rice cultivars, i.e., the allelopathic rice cultivar “PI312777” (PI) and the non-allelopathic rice cultivar “Lemont” (LE), when co-planted with quinclorac-resistant and -susceptible barnyardgrass, respectively. The results showed that the shoot and root biomass were greater in the allelopathic rice cultivar. Moreover, the treatments at the two time points induced an increase in shoot and root biomass of PI when subjected to barnyardgrass stress. In terms of root morphology, PI exhibited significantly higher fine-root length in diameters <0.5 mm, a greater number of root tips, and longer root tips compared to LE. In addition, the levels of different plant hormones, including auxin (IAA), abscisic acid (ABA), jasmonic acid (JA), and salicylic acid (SA), known for their diverse adaptation strategies to biotic stress, were analysed. The response to quinclorac-resistant barnyardgrass stress was consistent in terms of the content of well-known stress-related hormones, namely SA and JA. The accumulation of SA and JA was observed in both rice cultivars under the stress of quinclorac-resistant barnyardgrass, with higher contents of these hormones in PI than that in LE. The most significant change was observed in IAA and ABA contents in rice, which decreased significantly from 7 days to 14 days under co-culture stress. Additionally, PI contained higher levels of IAA and ABA than LE in the presence of barnyardgrass stress. This research may aid in the development of strategies for reducing the environmental impact of herbicides through the prudent selection of non-chemical herbicide control tactics.