Discovery and Comprehensive Characterization of Pseudomonas sp. MUP55: Taxonomy, Massetolide-Mediated Biocontrol, and Regulatory and Antimicrobial Contributions of the pvf Cluster

Interactions Between Bacillus atrophaeus 100 MTN1 and Fusarium oxysporum f. sp. lycopersici Reprogram the Transcriptomic and Metabolomic Profile to Combat Tomato (cv. Kalyan) Wilt

This research evaluated the biocontrol potential of the bacterial flora from cured sugarcane bagasse (SCB) against Fusarium oxysporum f. sp. lycopersici (Fol), the causal agent of tomato Fusarium wilt. Screenings of twenty SCB-derived isolates revealed consistent antagonistic activity, inhibiting mycelial growth from 32.08% to 55.00%. The most effective isolate, 100MTN1, was identified via 16S rRNA sequencing (GenBank: PX506225) as Bacillus atrophaeus. Interaction between B. atrophaeus 100MTN1 and Fol FOLViF has revealed a distinct profile of bioactive metabolites produced specifically during co-cultivation. Transcriptomic profiling of Fol FOLViF exposure to 100MTN1 identified 189 differentially expressed genes, with downregulation of genes involved in DNA replication, translation, and membrane transport, and upregulation of those linked to secondary metabolism and oxidative stress. KEGG pathway mapping further supported the possible causes of disruptions within the pathogen. Molecular docking suggested that the B. atrophaeus 100MTN1 derived metabolite, 6-Hydroxy-3′-methoxyflavone and exhibits binding affinity for key Fol proteins that compares favorably with the commercial fungicides. Greenhouse trials using tomato cv. Kalyan confirmed that treatment with strain 100MTN1 was associated with reduced disease severity and enhanced plant growth. These findings suggest that B. atrophaeus 100MTN1 suppresses Fol FOLViF through a combination of metabolite-driven inhibition and transcriptional interference, signifying its potential as a biological control agent for managing Fusarium wilt.

Phenotypic and genomic insights into Stenotrophomonas sepilia SMBL8: metabolic versatility, antibiotic resistance and pathogenic potential

The genome, transcriptome and metabolome of Aspergillus welwitschiae Ocstreb1 from wild halophytic rice, Oryza coarctata, indicates its distinctiveness.

Aspergillus welwitschiae is a widespread fungus with diverse roles as a plant mutualist, opportunistic human pathogen and industrial enzyme producer. The endophytic strain AwOcstreb1, isolated from halophytic rice (Oryza coarctata), promotes growth in commercial rice under normal and saline conditions. Despite its significance, genomic and metabolic resources for A. welwitschiae remain limited, with no complete genome information available for endophytic strains within the species. Moreover, the close relationship of this species to Aspergillus niger complicates its taxonomic resolution. We performed whole-genome and transcriptomic sequencing of AwOcstreb1 cultured on potato dextrose agar, along with -MS-based volatile metabolite profiling. Comparative analyses included simple sequence repeat (SSR), transposable element (TE; including starships) and carbohydrate-active enzyme (CAZyme) profiling across A. welwitschiae strains. Evolutionary relationships with A. niger were examined using average nucleotide identity (ANI) and orthologous gene clustering, supported by phylogenomic reconstruction. Genes for mycotoxin production and plant growth-promoting traits were also searched in this strain. The AwOcstreb1 genome is 37.7 Mb with 13,242 predicted genes, of which 66.6% were actively expressed under potato dextrose agar growth. The genome harbours 5,126 SSRs, 19,434 TEs and a CAZyme composition similar to other A. welwitschiae strains. Although established marker genes such as CaM and β-tubulin identify AwOcstreb1 as A. welwitschiae, whole-genome ANI and orthologous gene-based analyses place A. welwitschiae strains within the broader A. niger species complex, suggesting that it represents a population-level group rather than a clearly separated species, a view that is still not widely adopted. Synteny analysis showed that the AwOcstreb1 genes are highly collinear with those of A. niger. Genes involved in phosphate and zinc solubilization and siderophore biosynthesis were detected, whereas ochratoxin A biosynthetic genes were absent. Although the presence of fumonisin genes was detected, only a trace amount of the toxin was detected both in culture as well as rice grains. Among 172 strain-specific orthogroups, several encode intrinsically disordered, secreted or membrane-associated proteins that are potentially linked to endophytic lifestyle adaptations. Volatile metabolite profiling identified compounds such as 17-pentatriacontene, eicosane and octanal, each linked to known biological sources and potential functions, such as antifungal, antibacterial and anti-inflammatory activities. Several additional metabolites were also identified, whose biological roles need further investigation. This integrated omics study provides foundational insights into the endophytic potential and genomic distinctiveness of AwOcstreb1. This work opens new avenues for exploring A. welwitschiae for sustainable agriculture and fungal biology.

Whole-genome sequencing and characterization of Pseudomonas stutzeri P1 endophyte isolated from potato unveils plant growth-promoting and other traits

Endophytic bacteria play an important role in plant growth promotion and stress tolerance, offering sustainable alternatives to chemical inputs in agriculture. In this study, an endophytic bacterial strain P1 was isolated and identified as Pseudomonas stutzeri , a plant-associated bacterium exhibiting multiple plant growth–promoting traits (PGPTs). Biochemical (qualitative and quantitative) and in vitro analyses demonstrated nitrogen fixation, phosphate solubilization, ammonia production, indole-3-acetic acid (IAA) production, biofilm formation, and tolerance to abiotic stresses, including salinity and drought. Furthermore, the P1 strain displayed strong biocontrol activity against the fungal pathogen Fusarium oxysporum f. sp. cumini, indicating its potential to mitigate biotic stress. Whole-genome sequencing generated a high-quality complete genome of 4,758,235 bp. Functional annotation showed enrichment of metabolic pathways associated with plant-microbe interactions and environmental adaptation. Further analyses using KEGG and PGPT-pred data confirmed the presence of genes associated with direct and indirect PGPT, such as nitrogen fixation, phosphate solubilization, biofilm formation, and stress tolerance. The genome also contained genes related to CAZymes, adhesion, and motility, highlighting a strong plant association, whereas the genome lacked major virulence factors and antimicrobial traits, supporting the non-pathogenic nature of the P1 strain. Overall, these findings demonstrate the potential of P1 as a promising bioinoculant candidate for sustainable agriculture in the potato sector.

Genomic insights into the bioremediation potential of Paenibacillus taichungensis strain 53b: a multi-resistant plant growth-promoting bacterium

Characterization of a quorum-sensing communication based on gamma-butyrolactones in Rhodococcus erythropolis

Quorum sensing (QS) enables bacteria to coordinate collective behaviors, including the production of secondary metabolites with potential biotechnological applications, through the synthesis and detection of small signaling molecules. In Streptomyces, QS is well-described and mainly mediated by 2,3-disubstituted γ-butyrolactones (GBLs), which play key roles in the regulation of secondary metabolism and spore production. Despite their importance, GBL-based QS systems remain poorly characterized in other actinomycetal genera. Here, we investigated the distribution, structure, and function of GBL biosynthetic and regulatory systems within the genus Rhodococcus, focusing on the biocontrol strain Rhodococcus erythropolis R138. Comparative genomic analyses revealed that the scbA and scbR homologs, which are involved in GBL biosynthesis and detection, respectively, are widely conserved among Rhodococcus species and are organized within a conserved GBL gene cluster. Structural modeling using AlphaFold showed a high degree of conservation between ScbA and ScbR from Streptomyces coelicolor and their homologs in R. erythropolis R138. By combining liquid chromatography–mass spectrometry analyses with a GBL-specific reporter assay, we demonstrated that R. erythropolis R138 produces biologically active GBL(−like) molecules. Production of the investigated GBL molecules required the scbA gene, which restored spore production and promoted colony development in the scbA-deleted S. coelicolor strain during interaction with R. erythropolis R138. Transcriptional analyses further showed that both ScbR and a LuxR-like regulator may contribute to the fine-tuned regulation of scbA expression, revealing a complex regulatory network controlling GBL biosynthesis. This study provides novel and unexpected insights into the involvement of a LuxR homolog in regulating a QS system in Gram-positive bacteria. Together, these results demonstrate that functional GBL-based QS systems are conserved and active in R. erythropolis and likely widespread in the genus. This study expands current knowledge of QS in Actinomycetota and highlights the potential role of GBL signaling in regulating biotechnologically and ecologically relevant traits in Rhodococcus.