Population genomics and pathotypic evaluation of the bacterial leaf blight pathogen of rice reveals rapid evolutionary dynamics of a plant pathogen.

The Xanthomonas oryzae pv. oryzae (Xoo) is a bacterial pathogen causing bacterial blight disease in rice, resulting in significant yield reductions of up to 50% in rice production. Despite its serious threat to food production globally, knowledge of its population structure and virulence evolution is relatively limited. In this study, we employed whole-genome sequencing to explore the diversity and evolution of Xoo in the main rice-growing areas of China over the past 30 years. Using phylogenomic analysis, we revealed six lineages. CX-1 and CX-2 primarily contained Xoo isolates from South China, while CX-3 represented Xoo isolates from North China. Xoo isolates belonging to CX-5 and CX-6 were the most prevalent across all studied areas, persisting as dominant lineages for several decades. Recent sporadic disease outbreaks were primarily caused by Xoo isolates derived from the two major lineages, CX-5 and CX-6, although Xoo isolates from other lineages also contributed to these outbreaks. The lineage and sub-lineage distributions of Xoo isolates were strongly correlated with their geographical origin, which was found to be mainly determined by the planting of the two major rice subspecies, indica and japonica. Moreover, large-scale virulence testing was conducted to evaluate the diversity of pathogenicity for Xoo. We found rapid virulence evolution against rice, and its determinant factors included the genetic background of Xoo, rice resistance genes, and planting environment of rice. This study provides an excellent model for understanding the evolution and dynamics of plant pathogens in the context of their interactions with their hosts, which are shaped by a combination of geographical conditions and farming practices. The findings of this study may have important implications for the development of effective strategies for disease management and crop protection in rice production systems.

Heritability of tomato rhizobacteria resistant to Ralstonia solanacearum.

BACKGROUND: Ralstonia solanacearum (Rs) is a soilborne phytopathogen that causes bacterial wilt and substantial yield losses in many plants, such as tomatoes. A resistant tomato cultivar can recruit a beneficial microbiome from soil to resist Rs. However, whether this recruitment is inheritable from resistant parent to progeny has not been determined. RESULTS: In the present study, we investigated the rhizosphere microbiomes of tomatoes with clear kinship and different resistance against Rs. Resistant tomatoes grown with the additions of natural soil or its extract showed lower disease indexes than those grown in the sterile soil, demonstrating the importance of soil microbiome in resisting Rs. The results of 16S ribosomal RNA gene amplicon sequencing revealed that the resistant cultivars had more robust rhizosphere microbiomes than the susceptible ones. Besides, the resistant progeny HF12 resembled its resistant parent HG64 in the rhizosphere microbiome. The rhizosphere microbiome had functional consistency between HF12 and HG64 as revealed by metagenomics. Based on multi-omics analysis and experimental validation, two rhizobacteria (Sphingomonas sp. Cra20 and Pseudomonas putida KT2440) were enriched in HF12 and HG64 with the ability to offer susceptible tomatoes considerable protection against Rs. Multiple aspects were involved in the protection, including reducing the virulence-related genes of Rs and reshaping the transcriptomes of the susceptible tomatoes. CONCLUSIONS: We found promising bacteria to suppress the tomato bacterial wilt in sustainable agriculture. And our research provides insights into the heritability of Rs-resistant tomato rhizobacteria, echoing the inheritance of tomato genetic material. Video Abstract.

Precision Probiotics in Agroecosystems: Multiple Strategies of Native Soil Microbiotas for Conquering the Competitor Ralstonia solanacearum.

Ralstonia solanacearum (Rs), a soilborne phytopathogen, causes bacterial wilt disease in a broad range of hosts. Common approaches, for example, the direct reduction of the pathogen using classic single broad-spectrum probiotics, suffer from poor colonization efficiency, interference by resident microbiota, and nonnative-microorganism invasion. The soil microbiota plays an important role in plant health. Revealing the intrinsic linkage between the microbiome and the occurrence of disease and then applying it to agroecosystems for the precise control of soilborne diseases should be an effective strategy. Here, we surveyed the differences in the microbiome between healthy and diseased soils used for tomato planting across six climatic regions in China by using 16S rRNA amplicon and metagenomic sequencing. The roles of species associated with disease symptoms were further validated. Healthy soil possessed more diverse bacterial communities and more potential plant probiotics than diseased soil. Healthy soil simultaneously presented multiple strategies, including specifically antagonizing Rs, decreasing the gene expression of the type III secretion system of Rs, and competing for nutrition with Rs. Bacteria enriched in diseased samples promoted the progression of tomato bacterial wilt by strengthening the chemotaxis of pathogens. Therefore, Rs and its collaborators should be jointly combatted for disease suppression. Our research provides integrated insights into a multifaceted strategy for the biocontrol of tomato bacterial wilt based on the individual network of local microbiota. IMPORTANCE In the current work, the relationship between the soil microbiota and tomato bacterial wilt on a large scale offered us a comprehensive understanding of the disease. The delicate strategy of the microbiota in soil used for growing tomatoes to conquer the strong competitor, Rs, was revealed by microbiome research. The collaborators of Rs that coexist in a common niche with Rs strengthened our understanding of the pathogenesis of bacterial wilt. Bacteria enriched in healthy soil that antagonized pathogens with high specificity provide a novel view for ecofriendly probiotics mining. Our study offers new perspectives on soilborne-pathogen biocontrol in agroecosystems by decoding the rule of the natural ecosystem.

Engineered glyphosate oxidase coupled to spore-based chemiluminescence system for glyphosate detection.

The extensive and intensive utilization of glyphosate (Glyp) caused public concerns on the potential risk of environment and health resulted from the chemical residues. Therefore, the development of a high-selective, low-cost and easy-operation Glyp detection methods is highly desired. Screening highly selective enzymes by directed evolution is important in practical applications. Herein, a glyphosate oxidase (GlypO) preferring substrate Glyp to produce H2O2 was obtained via directed evolution from glycine oxidase obtained from Bacillus cereus (BceGO). The catalytic efficiency, specificity constant, and affinity enhancement factor of GlypO toward Glyp were increased by 2.85 × 103-fold; 2.25 × 105-fold; and 9.64 × 104-fold, respectively, compared with those of BceGO. The catalytic efficiency toward glycine decreased by 78.60-fold. The spores of Bacillus subtilis (B. subtilis) effectively catalyzed luminol-H2O2 reaction to create excellent chemiluminescence (CL) signal because CotA-laccase exists on their surface. Based on these findings, a new CL biosensor via coupling to biological reaction system was presented for Glyp detection. The CL biosensor exhibited several advantages, such as eco-friendliness, low cost, high selectivity and sensitivity, and good practical application prospects for environmental pollution control.

Enrichment of potentially beneficial bacteria from the consistent microbial community confers canker resistance on tomato.

The soil microbiota interacts with plants closely and exerts strong influences on plant health and productivity. However, the relationship between the microbiota and the bacterial canker of tomato that is caused by Clavibacter michiganensis subsp. michiganensis (Cmm) is still unclear. In order to establish causal relationship between the microbiota and plant phenotypes, the microbial communities of 49 tomato samples (including 15 cultivars) with different canker symptoms collected from the greenhouse in Gansu province, China were investigated via 16S ribosomal RNA sequencing. Roots exhibited a strong filter effect in the process of root colonization by microorganisms according to the α-diversity and the separation patterns of the microbiota in bulk soil, rhizosphere and endosphere. In addition, the gradually decreased cluster extent from bulk soil to endosphere indicating the selective effect of tomato on microbiota. Although the composition of the microbiota is similar, the potential beneficial bacteria and functions (e.g. antibiotics production, pollution degradation, nutrition acquisition) enriched in the rhizosphere and endosphere of healthy samples compared to those in the diseased ones. Furthermore, more robust networks occurred in the rhizosphere and endosphere of healthy samples compared to the diseased ones. Our research provided substantial evidence that although the plant genotype is the dominant factor of phenotype, the rhizosphere and endosphere microbiota, as part of phytobiomes or holobiont, could contribute to the host's phenotype. This causal relationship between microbiota and host phenotypes could guide us in rationally designing novel synthetic communities (SynComs) for tomato canker biocontrol in the near future.