The plant-parasitic root-knot nematode Meloidogyne exigua causes significant damage and is an important threat in Coffea arabica plantations. The utilization of plant-beneficial microbes as biological control agents against sedentary endoparasitic nematodes has been a longstanding strategy. However, their application in field conditions to control root-knot nematodes and their interaction with the rhizospheric microbiota of coffee plants remain largely unexplored. This study aimed to investigate the effects of biological control agent-based bioproducts and a chemical nematicide, used in various combinations, on the control of root-knot nematodes and the profiling of the coffee plant rhizomicrobiome in a field trial. The commercially available biological products, including Trichoderma asperellum URM 5911 (Quality), Bacillus subtilis UFPEDA 764 (Rizos), Bacillus methylotrophicus UFPEDA 20 (Onix), and nematicide Cadusafos (Rugby), were applied to adult coffee plants. The population of second-stage juveniles (J2) and eggs, as well as plant yield, were evaluated over three consecutive years. However, no significant differences were observed between the control group and the groups treated with bioproducts and the nematicide. Furthermore, the diversity and community composition of bacteria, fungi, and eukaryotes in the rhizosphere soil of bioproduct-treated plants were evaluated. The dominant phyla identified in the 16 S, ITS2, and 18 S communities included Proteobacteria, Acidobacteria, Actinobacteria, Ascomycota, Mortierellomycota, and Cercozoa in both consecutive years. There were no significant differences detected in the Shannon diversity of 16 S, ITS2, and 18 S communities between the years of data. The application of a combination of T. asperellum, B. subtilis, and B. methylotrophicus, as well as the use of Cadusafos alone and in combination with T. asperellum, B. subtilis, and B. methylotrophicus, resulted in a significant reduction (26.08%, 39.13%, and 21.73%, respectively) in the relative abundance of Fusarium spp. Moreover, the relative abundance of Trichoderma spp. significantly increased by 500%, 200%, and 100% at the genus level, respectively, compared to the control treatment. By constructing a co-occurrence network, we discovered a complex network structure among the species in all the bioproduct-treated groups. However, our findings indicate that the introduction of exogenous beneficial microbes into field conditions was unable to modulate the existing microbiota significantly. These findings suggest that the applied bioproducts had no significant impact on the reshaping of the overall microbial diversity in the rhizosphere microbiome but rather recruited selected microrganisms and assured net return to the grower. The results underscore the intricate nature of the rhizosphere microbiome and suggest the necessity for alternate biocontrol strategies and a re-evaluation of agricultural practices to improve nematode control by aligning with the complex ecological interactions in the rhizosphere.

The accumulation of microplastics in agricultural soil brings unexpected adverse effects on crop growth and soil quality, which is threatening the sustainability of agriculture. Biochar is an emerging soil amendment material of interest as it can remediate soil pollutants. However, the mechanisms underlying biochar alleviated the toxic effects of microplastics in crops and soil were largely unknown. Using a common economic crop, peanut as targeted species, the present study evaluated the plant physiologica and molecular response and rhizosphere microbiome when facing microplastic contamination and biochar amendment. Transcriptome and microbiome analyses were conducted on peanut root and rhizosphere soil treated with CK (no microplastic and no biochar addition), MP (1.5% polystyrene microplastic addition) and MB (1.5% polystyrene microplastic+2% peanut shell biochar addition). The results indicated that microplastics had inhibitory effects on plant root development and rhizosphere bacterial diversity and function. However, biochar application could significantly promote the expressions of key genes associated with antioxidant activities, lignin synthesis, nitrogen transport and energy metabolism to alleviate the reactive oxygen species stress, root structure damage, nutrient transport limitation, and energy metabolism inhibition induced by microplastic contamination on the root. In addition, the peanut rhizosphere microbiome results showed that biochar application could restore the diversity and richness of microbial communities inhibited by microplastic contamination and promote nutrient availability of rhizosphere soil by regulating the abundance of nitrogen cycling-related and organic matter decomposition-related microbial communities. Consequently, the application of biochar could enhance root development by promoting oxidative stress resistance, nitrogen transport and energy metabolism and benefit the rhizosphere microecological environment for root development, thereby improved the plant-soil system health of microplastic-contaminated agroecosystem.