Metagenomic profiling of tomato rhizosphere delineates the diverse nature of uncultured microbes as influenced by Bacillus velezensis VB7 and Trichoderma koningiopsis TK towards the suppression of root-knot nematode under field conditions.

The plant-parasitic Root Knot Nematodes (Meloidogyne spp.,) play a pivotal role to devastate vegetable crops across the globe. Considering the significance of plant-microbe interaction in the suppression of Root Knot Nematode, we investigated the diversity of microbiome associated with bioagents-treated and nematode-infected rhizosphere soil samples through metagenomics approach. The wide variety of organisms spread across different ecosystems showed the highest average abundance within each taxonomic level. In the rhizosphere, Proteobacteria, Firmicutes, and Actinobacteria were the dominant bacterial taxa, while Ascomycota, Basidiomycota, and Mucoromycota were prevalent among the fungal taxa. Regardless of the specific treatments, bacterial genera like Bacillus, Sphingomonas, and Pseudomonas were consistently found in high abundance. Shannon diversity index vividly ensured that, bacterial communities were maximum in B. velezensis VB7-treated soil (1.4-2.4), followed by Root Knot Nematode-associated soils (1.3-2.2), whereas richness was higher with Trichoderma konigiopsis TK drenched soils (1.3-2.0). The predominant occurrence of fungal genera such as Aspergillus Epicoccum, Choanephora, Alternaria and Thanatephorus habituate rhizosphere soils. Shannon index expressed the abundant richness of fungal species in treated samples (1.04-0.90). Further, refraction and species diversity curve also depicted a significant increase with maximum diversity of fungal species in B. velezensis VB7-treated soil than T. koningiopsis and nematode-infested soil. In field trial, bioagents-treated tomato plant (60% reduction of Meloidogyne incognita infection) had reduced gall index along with enhanced plant growth and increased fruit yield in comparison with the untreated plant. Hence, B. velezensis VB7 and T. koingiopsis can be well explored as an antinemic bioagents against RKN. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03851-1.

Metagenomic Approach Deciphers the Role of Community Composition of Mycobiome Structured by Bacillus velezensis VB7 and Trichoderma koningiopsis TK in Tomato Rhizosphere to Suppress Root-Knot Nematode Infecting Tomato.

The soil microbiome is crucial for maintaining the sustainability of the agricultural environment. Concerning the role of diverse mycobiomes and their abundance toward the suppression of root-knot nematode (RKN) infection in vegetable crops, our understanding is unclear. To unveil this issue, we examined the fungal microbiome in tomato rhizosphere augmented with bioagents challenged against RKN at taxonomic and functional levels. Composition of the mycobiome in tomato rhizosphere treated with Bacillus velezensis VB7 and Trichoderma koningiopsis TK differed significantly from the infected tomato rhizosphere. The abundance and diversity of fungal species, however, were significantly higher in the combined treatments of bioagents than for individual treatments. Fungal microbiome diversity was negatively correlated in the RKN-associated soil. Network analysis of the fungal biome indicated a larger and complex network of fungal biome diversity in bioagent-treated soil than in nematode-associated tomato rhizosphere. The diversity index represented by that challenging the RKN by drenching with consortia of B. velezensis VB7 and T. koningiopsis TK, or applying them individually, constituted the maximum abundance and richness of the mycobiome compared to the untreated control. Thus, the increased diverse nature and relative abundance of the mycobiome in tomato rhizosphere was mediated through the application of either T. koningiopsis TK or B. velezensis VB7, individually or as a consortium comprising both fungal and bacterial antagonists, which facilitated engineering the community composition of fungal bioagents. This in turn inhibited the infestation of RKN in tomato. It would be interesting to explore further the possibility of combined applications of B. velezensis VB7 and T. koningiopsis TK to manage root-knot nematodes as an integrated approach for managing plant parasitic nematodes at the field level.

Flagellin and elongation factor of Bacillus velezensis (VB7) reprogramme the immune response in tomato towards the management of GBNV infection.

The present study investigates the reprogramming of plant defense system, upon interaction with MAMP (Microbe Associated Molecular Pattern) gene products including, flagellin (Flg) and elongation factor (EF-Tu) of Bacillus velezensis (VB7) and groundnut bud necrosis virus (GBNV) in tomato (Shivam). The MAMP gene products induced the plant defense genes including, PAL, PPO, LOX, JAR, MYC2 and PDF 1.2. Secondary metabolites of Bacillus spp. at 1000 parts per million (ppm) concentration effectively reduced GBNV symptom expression in cowpea (CO7) up to 83.1 % compared to untreated, GBNV inoculated, control. The secondary metabolites from B. velezensis (VB7) and B. licheniformis (Soya 1) reduced GBNV symptoms in cowpea (CO7) up to 1.7 lesions/cm2 leaf area compared to 8.6 lesions/cm2 in virus inoculated control. Further, field study revealed that the combined application of B. velezensis (VB7) and B. licheniformis (Soya1) at 1% (10 mL/L) as, soil and foliar application reduced the percent disease incidence (PDI) up to 10.5 (PDI) compared to 28.4 (PDI) in untreated control plants. Besides, it also improved the plant growth and yield up to 23.5 tonnes/ha compared to 13.8 tonnes/ha in untreated control.