Complete genome sequence and mass spectrometry assist mining siderophore turnerbactin analogs in a non-model Pseudoduganella strain with biocontrol potential

Complete genome sequence of Streptomyces californicus ADR1, an anti-infective, anti-biofilm and anti-oxidant producing endophyte isolated from the medicinal plant Datura metel.

OBJECTIVE Streptomyces californicus strain ADR1 is an endophytic actinobacterium isolated from Datura metel that produces secondary metabolites with potent antibacterial and anti-biofilm activities against WHO-listed high-priority Gram-positive pathogens. While anti-bacterial and antioxidant potential of the strain ADR1 has been extensively characterized, its complete genome sequence remains to be investigated for further insights into its biosynthetic potential. This study presents the complete genome sequence analysis of the strain ADR1 to provide a robust genomic foundation for understanding its metabolic versatility and biosynthesis of compounds with therapeutic significance. DATA DESCRIPTION The ADR1 genome was sequenced using Illumina HiSeq. The assembly comprised 262 scaffolds with a total genome size of 8.4 Mb and G + C content of 72.5%, containing 7427 protein-coding genes. AntiSMASH and IIT-Hyderabad novelBGC analysis revealed 39 biosynthetic gene clusters, including non-ribosomal peptide synthetases, type I polyketide synthases, terpene and melanin clusters, correlating with the diverse therapeutic compounds previously identified through GC-MS analysis. This high-quality genome provides crucial insights into the biosynthetic potential underlying potent antimicrobial and antioxidant activities of the strain ADR1.

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.

Genome-wide exploration of biosynthetic gene clusters and their association with virulence in the entomopathogenic fungus Beauveria

Species of the genus Beauveria are widely used as biological control agents due to their ability to infect and kill a broad range of arthropod pests. Despite their agricultural importance, the genomic diversity underlying virulence and secondary metabolism across the genus remains uncharacterized. In this study, we performed a comprehensive phylogenomic and biosynthetic gene cluster (BGC) analysis of 322 high-quality Beauveria genomes, including one newly sequenced Beauveria bassiana isolate (AS272) obtained from soil in southern Brazil. The genome of AS272 comprises 32.9 Mb with 9,778 predicted genes and high completeness (96.7% BUSCO). Comparative analysis revealed extensive conservation of orthogroups but indicated that the increased gene repertoire of AS272 is primarily associated with the expansion of existing gene families, particularly transporters belonging to the major facilitator superfamily (MFS) and ATP-binding cassette (ABC) families. Phylogenomic reconstruction based on single-copy orthologs resolved major species clades within the genus and identified potential misidentified genomes in public databases. Genome mining using antiSMASH identified 14,160 BGCs across the dataset, with NRPS and PKS clusters dominating the biosynthetic landscape. Clustering with BiG-SCAPE revealed a mixture of highly conserved gene cluster families (GCFs) and numerous lineage-specific clusters, highlighting both evolutionary stability and diversification of secondary metabolism within Beauveria. Notably, B. bassiana lacked strictly conserved core GCFs across all isolates, instead exhibiting a heavy-tailed distribution of cluster frequencies consistent with substantial intraspecific genomic plasticity. Protein–protein interaction network analysis further indicated that several conserved BGCs are embedded within networks enriched for proteins associated with host–pathogen interactions. Together, these findings reveal a dynamic genomic architecture underlying secondary metabolism and pathogenic potential in Beauveria, providing a comparative framework for understanding virulence evolution and identifying candidate pathways for future functional and biotechnological studies.

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

Genome mining and comparative genome analysis of Pseudomonas fluorescens revealed diverse biosynthetic and metabolic potential

Bacterial genome sequencing has been used to identify a myriad of bioactive compounds that have yet to be characterised. Pseudomonas fluorescens is a widely distributed Gram-negative bacterium known for its plant growth-promoting traits and production of diverse secondary metabolites. P. fluorescens genome harbours several biosynthetic gene clusters (BGCs), and it is challenging to link many of these BGCs with their respective product under laboratory conditions. The current study employed a bioinformatic approach to gain in-depth genomic insight into the distribution, evolution, and diversity of these BGCs in P. fluorescens, facilitating the exploration of cryptic biosynthetic capabilities. In addition, to understand the genomic landscape and evolutionary dynamics, core pan-genome analysis was conducted for P. fluorescens species. We identified a total of 2098 BGCs across the high-quality targeted genomes (n = 174), including non-ribosomal peptide synthetases (NRPSs), ribosomal-synthesised and post-translationally modified peptides (RiPPs), polyketides (PKSs), Terpenes, siderophores, and arylpolyenes, which were the most prevalent. Several low similarity clusters (n = 14) were identified that encode putative novel metabolites. Core Pan-genome analysis revealed an “open pan-genome” and large accessory genome enriched in secondary metabolism genes, supporting the biosynthetic versatility of P. fluorescens. This work enhances our understanding of the metabolic capabilities and genomic landscape of the P. fluorescens species, providing a foundation for natural product discovery using bioinformatic approaches.

A Novel Indigoidine-like NRPS Gene from Arthrobacter antioxidans QL17 Enhances Oxidative Stress Resistance Through Radical Scavenging and Transcriptional Reprogramming

Water-soluble blue microbial pigments with antioxidant activity remain rare, and their host-level protective mechanisms are poorly understood. Here, we identified the genetic basis of blue pigment biosynthesis in the glacier-derived strain Arthrobacter antioxidans QL17. Heavy-ion mutagenesis yielded a hyperpigmented mutant (M157) and a pigment-deficient mutant (M186), and pigment yield was positively associated with hydrogen peroxide (H2O2) tolerance. Genome mining identified MWM45_RS16760 as the sole core biosynthetic gene in a candidate nonribosomal peptide synthetase (NRPS)-like cluster. The encoded protein displayed an adenylation–peptidyl carrier protein–thioesterase (A-PCP-TE) architecture with a predicted L-glutamine-specific A domain, and its transcript abundance paralleled pigment production across the three strains. Phylogenetic analysis placed MWM45_RS16760 in a distinct actinomycete-associated indigoidine-like lineage separated from the characterized BpsA and IndC branches. Heterologous expression in Escherichia coli reconstructed a blue-pigment-producing phenotype, increased H2O2 tolerance, and was accompanied by enhanced extracellular DPPH and ABTS radical-scavenging activities in the culture supernatant. Comparative transcriptomics further revealed coordinated activation of oxidative-stress and proteostasis responses alongside repression of tryptophan biosynthesis and flagellar assembly. These findings identify MWM45_RS16760 as a candidate indigoidine-like NRPS associated with blue pigment biosynthesis and oxidative-stress resistance, with heterologous expression linked to enhanced radical scavenging and coordinated transcriptional reprogramming, expanding the phylogenetic and functional diversity of indigoidine-like systems.