Synthetic microbial communities (SynComs) could potentially enhance some functions of the plant microbiome and emerge as a promising inoculant for improving crop performance. Here, we characterized a collection of bacteria, previously isolated from the wheat rhizosphere, for their antifungal activity against soilborne fungal pathogens. Ten SynComs with different compositions from 14 bacterial strains were created. Seven SynComs protected wheat from Rhizoctonia solani AG8 infection, although SynComs were not more effective than single strains in reducing wheat root rot disease. Further, the mechanisms of interaction of the tested bacteria with each other and plants were explored. We found that nine bacteria and nine SynComs impacted the root growth of Arabidopsis. Nine bacteria and four SynComs significantly inhibited the growth of AG8 by producing volatiles. The cell-free supernatants from six bacteria inhibited the growth of AG8. Together, this study provided the potential for improving crop resilience by creating SynComs.

Plant fungal pathogens can rapidly evolve and adapt to new environmental conditions in response to sudden changes of host populations in agro-ecosystems. However, the genomic basis of their host adaptation, especially at the forma specialis level, remains unclear. We sequenced two isolates each representing Puccinia striiformis f. sp. tritici (Pst) and P. striiformis f. sp. hordei (Psh), different formae speciales of the stripe rust fungus P. striiformis highly adapted to wheat and barley, respectively. The divergence of Pst and Psh, estimated to start 8.12 million years ago, has been driven by high nucleotide mutation rates. The high genomic variation within dikaryotic urediniospores of P. striiformis has provided raw genetic materials for genome evolution. No specific gene families have enriched in either isolate, but extensive gene loss events have occurred in both Pst and Psh after the divergence from their most recent common ancestor. A large number of isolate-specific genes were identified, with unique genomic features compared to the conserved genes, including 1) significantly shorter in length; 2) significantly less expressed; 3) significantly closer to transposable elements; and 4) redundant in pathways. The presence of specific genes in one isolate (or forma specialis) was resulted from the loss of the homologues in the other isolate (or forma specialis) by the replacements of transposable elements or losses of genomic fragments. In addition, different patterns and numbers of telomeric repeats were observed between the isolates. Host adaptation of P. striiformis at the forma specialis level is a complex pathogenic trait, involving not only virulence-related genes but also other genes. Gene loss, which might be adaptive and driven by transposable element activities, provides genomic basis for host adaptation of different formae speciales of P. striiformis.

Soybean (Glycine max [L.] Merr.) is an important oilseed crop with a high economic value. However, three damaging soybean diseases, soybean cyst nematode (SCN; Heterodera glycines Ichinohe), Sclerotinia stem rot caused by the fungus Sclerotinia sclerotiorum (Lid.) de Bary, and soybean root rot caused by Fusarium spp., are major constraints to soybean production in the Great Plains. Current disease management options, including resistant or tolerant varieties, fungicides, nematicides, and agricultural practices (crop rotation and tillage), have limited efficacy for these pathogens or have adverse effects on the ecosystem. Microbes with antagonistic activity are a promising option to control soybean diseases with the advantage of being environmentally friendly and sustainable. In this study, 61 bacterial strains isolated from wheat rhizospheres were used to examine their antagonistic abilities against three soybean pathogens. Six bacterial strains significantly inhibited the growth of Fusarium graminearum in the dual-culture assay. These bacterial strains were identified as Chryseobacterium ginsengisoli, C. indologenes, Pseudomonas poae, two Pseudomonas spp., and Delftia acidovorans by 16S rRNA gene sequencing. Moreover, C. ginsengisoli, C. indologenes, and P. poae significantly increased the mortality of SCN second-stage juveniles (J2), and two Pseudomonas spp. inhibited the growth of S. sclerotiorum in vitro. Further growth chamber tests found that C. ginsengisoli and C. indologenes reduced soybean Fusarium root rot disease. C. ginsengisoli and P. poae dramatically decreased SCN egg number on SCN-susceptible soybean ‘Williams 82’. Two Pseudomonas spp. protected soybean plants from leaf damage and collapse after being infected by S. sclerotiorum. These bacteria exhibit versatile antagonistic potential. This work lays the foundation for further research on the field control of soybean pathogens.

Plant is one of the primary drivers of microbial communities in the rhizosphere. The consistent presence of the same plant species over time such as monocropping in agriculture can drive significant changes in plant-associated microbiomes. Most of the studies with monocropping have focused on bacteria, which are involved in the natural suppression of a number of soilborne diseases, including Rhizoctonia root rot and take-all. However, few studies have examined how monocropping and root rot pathogens jointly affect the structure of fungal communities in the rhizosphere. In this greenhouse study, rhizosphere fungal communities from successive wheat plantings infected with the fungal pathogen Rhizoctonia solani AG8 were characterized using MiSeq sequencing targeting the internal transcribed spacer 1 region of the ribosomal RNA gene. Sequence analyses revealed that distinct fungal groups clustered by planting cycles with or without strain AG8 inoculation but infection with strain AG8 enhanced the separation of fungal communities. Clusters of fungal communities were also observed in strain-AG8-infected and noninfected rhizospheres, whereas there was no difference in fungal communities between the rhizospheres with the least root disease and those with the worst root disease. Planting cycles significantly reduced fungal α diversity. The most abundant fungal genus was Mortierella which increased in relative abundance with planting cycles in strain-AG8-infected samples. In contrast, fungal genera that included Pseudogymnoascus, Gibberella, Fusarium, Fusicolla, Exophiala, and Waitea were reduced in relative abundance with successive plantings and strain AG8 infection. Together, this study revealed how fungal communities change with successive wheat growth under the pressure of a soilborne fungal pathogen.

Introducing cover crops is a conservation practice that diversifies cropping systems and counteracts the detrimental consequences of simplified cropping systems. However, the legacy effects of cover crops on cash crop rhizosphere microbiota are poorly understood. We investigated the response of cash crop rhizosphere microbiota following 5 years of cover crops (winter rye for maize and a mixture of winter rye, forage turnip, clover, Berseem, and Crimson for soybean) introduced into a long-term maize–soybean rotation. Five years of cover crop integration significantly increased the average soybean yields and marginally increased maize yields between 2018 and 2022. Cover crops had significant effects on soybean rhizosphere microbiota selecting bacterial genera within Actinobacteria and Thaumarchaeota phyla and some potentially pathogenic fungi species. There was no significant effect of cover crops on maize rhizosphere microbiota. Cash crop growth stage had consistent, significant effects on both soybean and maize rhizosphere microbiota and accounted for a higher percentage of variation in the rhizosphere microbiota compared with cover crops. Crop growth stage effects were notably strong at the flowering stage for soybean and the seedling stage for maize. The soybean rhizosphere was enriched with nitrogen-fixing bacteria in the flowering stage, whereas the maize rhizosphere recruited a high abundance of plant growth-promoting bacteria in the seedling stage. Cover crops did not significantly improve six selected soil health indicators, with the weak responses linked with cash crop identity. Cover crop legacies may promote beneficial changes in cash crop rhizosphere microbiota, but legacy assessments should account for cash crop identity and growth stage. [ ] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Fusarium head blight (FHB) is a devastating disease of wheat (Triticum aestivum) worldwide. This disease is caused by Fusarium species including Fusarium graminearum Schwabe sensu stricto, F. culmo...