Integrative microbiome and transcriptome analyses reveal Telluria sp. 100-57A as a candidate for aphid suppression in pepper

Cadmium tolerance and taxonomic diversity of cultivable bacteria isolated from Inga sp. nodules, Quararibea sp. roots and rhizosphere soil in cocoa agroforestry systems of the Peruvian Amazon

Cadmium (Cd) contamination in the Peruvian Amazon cocoa soils threatens production sustainability and international market access. This study characterized the taxonomic and genomic diversity of bacteria isolated from Inga sp. nodules, Quararibea sp. roots, and rhizosphere soil in cocoa agroforestry systems in Bagua, Amazonas, Peru (1.02–3.54 mg Cd kg−1), and evaluated the Cd tolerance phenotypes in vitro. From 93 initial isolates, 53 grew under cadmium screening; 23 were selected for Sanger sequencing, yielding 12 high-quality 16S rRNA sequences suitable for downstream phylogenetic analysis (GenBank: PZ012327–PZ012338). These strains were identified via 16S rRNA gene sequencing and BOX-PCR fingerprinting, revealing distribution across three bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria) and five classes. Notably, no rhizobia sensu stricto were recovered from Inga sp. nodules; all nodule-derived isolates were non-rhizobial endophytes (NREs) belonging to Achromobacter, Pseudomonas, Klebsiella, Priestia, and Glutamicibacter. BOX-PCR identified 12 unique genotypes (Shannon H′ = 2.485) distributed in four genomic clusters unrelated to phylogenetic affiliation. The Cd tolerance (25–200 ppm) was assessed via OD₆₀₀ in TY medium. Tolerance indices (0.190–0.643) classified strains into quartiles: highly tolerant (n = 3), tolerant (n = 3), sensitive (n = 3), and highly sensitive (n = 3). JSRA_S05 (K. variicola) showed clear hormesis (TI = 1.235 at 25 ppm), whereas JSRA_S08 (Glutamicibacter sp.) exhibited a possible hormetic tendency (TI = 1.012 at 50 ppm). IC₅₀ values (0.18–719.7 ppm) showed low correlation with TI (ρ < 0.1), indicating complementary dimensions of tolerance. Tolerance was strain-specific, as evidenced by opposite responses of two K. variicola strains (highly tolerant JSRA_S05 versus highly sensitive JSRA_N14). Strains associated with Quararibea sp. were consistently among the most tolerant. Three strains (JSRA_S05, JSRA_S08, and JSRA_R15), combining high physiological tolerance with taxonomic and source diversity, are proposed as priority candidates for functional evaluation in biosorption, bioaccumulation, and plant-inoculation assays. These culture-dependent findings indicate that, under the cultivation conditions employed, the cultivable bacterial fraction recovered from Cd-impacted Inga sp. nodules in Amazonian cocoa agroecosystems is dominated by non-rhizobial endophytes, representing a promising biological resource for further bioremediation studies. Whether classical rhizobia are truly absent or simply not retrieved under these conditions requires culture-independent confirmation.

Integrative functional profiling of rhizospheric and endophytic bacteria reveals Lelliottia aquatilis as a multifunctional PGPR in Himalayan ecosystems

This study introduces L. aquatilis strain MC3 as an emerging candidate for bioinoculant development and one of the first reports for identification of L. aquatilis as multifunctional PGPR from Himalayan ecosystems.

Integrated metabarcoding and culturomics reveal the rot-suppressive rhizoplane mycobiome of cassava across contrasting agroecological habitats

Introduction Cassava stem and root rot caused by Fusarium falciforme (Fusarium solani species complex) constrains production in waterlogged tropical systems. In Kerala, India, disease endemicity differs markedly between wetlands and uplands, yet the ecological basis of this variation remains unresolved. We tested whether rhizoplane mycobiome structure and functional stability govern pathogen suppression across these habitats. Methods Rhizoplane fungal communities from healthy and diseased plants in endemic wetlands and non-endemic uplands were profiled using Internal Transcribed Spacer amplicon sequencing, complemented by culture-dependent isolation and soil physicochemical analyses. Core taxa were identified through microbiome modeling and validated by ITS sequencing of isolates. Antagonistic activity against F. falciforme was assessed using dual-culture assays and greenhouse validation. Results Quality filtering retained 847,760, 1,037,834, and 539,722 high-quality paired-end reads from the upland, wetland diseased, and wetland healthy rhizoplane samples, respectively. Healthy wetland rhizoplanes exhibited higher diversity and stability than diseased counterparts (Shannon +20%; inverse Simpson +60%). Disease was associated with diversity collapse and enrichment of opportunistic taxa, whereas upland communities remained distinct and stable. A conserved core mycobiome dominated by the members of Pichia, Aspergillus, Sugiyamaella, and Fusarium was identified, with Penicillium and Talaromyces forming an extended functional core. Isolates of Penicillium oxalicum and Talaromyces pinophilus inhibited F. falciforme by >90% in vitro and reduced disease incidence to 0% in greenhouse assays, matching chemical control. Soil acidity and nutrient imbalance were strongly associated with mycobiome disruption and disease. Discussion Disease emergence coincided with loss of rhizoplane diversity and depletion of key antagonists, indicating failure of microbial resistance under edaphic stress. The consistent identification and validation of P. oxalicum and T. pinophilus as keystone antagonists support their functional role in pathogen suppression. Integrating microbiome conservation with soil health restoration offers a robust, climate-resilient strategy for managing cassava stem and root rot in tropical agroecosystems.

From diversity to function: microbiome-mediated plant growth promotion, secondary metabolism, and antimicrobial resistance in Rauwolfia serpentina

These distinct functional profiles demonstrates that the protected root endomicrobiome specializes in plant signalling and nutrient assimilation, while the rhizosphere microbiome, facing higher competition, specializes in nutrient acquisition and stress resilience.

Comparative Insights into Bacterial Endophytome and Antifungal Metabolites in Fusarium Wilt-Resistant and -Susceptible Banana Cultivars Unveil the Resistance Toward Fusarium oxysporum f. sp. cubense

India contributes 26% of global banana production, yet cultivation is severely threatened by Fusarium wilt (Fusarium oxysporum f. sp. cubense, Foc), necessitating sustainable, eco-friendly management strategies. This study evaluated the biocontrol potential of endophytic bacteria isolated from Foc-resistant and -susceptible banana cultivars. Isolates from the pseudostem, corm, and root of the resistant cultivar showed significantly greater inhibitory activity than those from the susceptible cultivar, underscoring the role of host genotype in shaping functionally competent endophytic communities. Among all isolates, Bacillus sp. from the corm of cv. Rose (AB) showed the highest mycelial inhibition of Foc (70.37–76.54%) in vitro. GC-MS-based metabolite profiling revealed a chemically diverse array of secondary metabolites, fatty acid esters, steroids, terpenoids, siloxanes, and nitrogenous compounds. Corm-associated endophytes exhibited membrane-disruptive and cytotoxic activity, while root-associated endophytes contributed protective, defense-modulatory effects. Halomonas sp. RoRo2 and B. subtilis RoC1 showed the highest inhibition in both agar-well and in planta assays, with unsaturated fatty acids and organic acid derivatives implicated as key antifungal effectors acting through multiple biochemical pathways. These findings identify metabolically versatile endophytes as promising candidates for developing efficient, environmentally compatible bioinoculants as sustainable alternatives to chemical control of Fusarium wilt in banana.

Microbial diversity and insights into feeding behavior of the two-spot cotton leaf hopper (Amrasca biguttula)