Jun 2026· PLoS ONE· Vol 21, pp. e0350885· 0 citations· 83 references
Medicine
TL;DR
Together, these findings identify CACC1094 as a rumen-associated P. polymyxa strain with broad-spectrum antifungal activity and experimentally validated fusaricidin production, highlighting its potential as a source of antifungal metabolites for agricultural and veterinary applications.
Abstract
While Paenibacillus polymyxa is widely recognized for its biocontrol capabilities, most characterized strains originate from soil or rhizosphere environments, leaving animal-associated populations largely unexplored. In this study, we report the isolation of P. polymyxa strain CACC1094 from the bovine rumen and its genome-guided characterization to investigate its biosynthetic potential and antifungal activity. Whole-genome sequencing yielded a complete circular chromosome of 5.55 Mb with a GC content of 45.36%, comprising 5,099 coding sequences, 39 rRNA genes, and 111 tRNA genes. Comparative phylogenomic analysis placed CACC1094 within the P. polymyxa species complex, clustering most closely with the rumen-associated strain ND24 (ANI: 98.31%) and strain 188 (ANI: 96.92%), while forming a distinct branch within the species. Genome mining identified 13 biosynthetic gene clusters, including those associated with fusaricidin and tridecaptin biosynthesis, a paenicidin-like lanthipeptide cluster, and a hybrid NRPS–PKS cluster. In dual-culture assays, CACC1094 showed broad in vitro antifungal activity against multiple plant-pathogenic fungi and oomycetes, as well as selected fungal and yeast pathogens of clinical and veterinary relevance. LC-QTOF/MS analysis of culture supernatants confirmed the production of fusaricidin A and fusaricidin B, providing direct experimental validation of genome-derived predictions. Additionally, genome annotation revealed a complete CRISPR-Cas adaptive immune system, suggesting an integrated ecological strategy that combines antimicrobial biosynthesis with defense against mobile genetic elements. Together, these findings identify CACC1094 as a rumen-associated P. polymyxa strain with broad-spectrum antifungal activity and experimentally validated fusaricidin production, highlighting its potential as a source of antifungal metabolites for agricultural and veterinary applications.
The Phytophthora blight of
Panax notoginseng
, caused by
Phytophthora cactorum
, is a devastating oomycete disease. Biocontrol strategies hold immense potential for inhibiting the spread of
P. cactorum
. We isolated 72 actinobacteria from soil and screened their antagonistic activity against
P. cactorum
. Both strain J36 and its cell-free filtrate exhibited strong antagonistic activity against
P. cactorum
and were therefore selected. Based on the 16S rRNA gene phylogenetic tree, strain J36 formed a well supported subclade with
Streptomyces zaomyceticus
NRRL B-2038 (bootstrap value 100%). However, because 16S rRNA sequences often lack sufficient resolution for species-level discrimination, we performed multilocus sequence analysis (MLSA) using three housekeeping genes (rpoB, recA, and atpD). The MLSA results consistently placed strain J36 within the same cluster as
S. zaomyceticus
NRRL B-2038, with a bootstrap support of 99%, indicating a close phylogenetic relationship. To further clarify the taxonomic status, we calculated the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain J36 and the type strain of
S. zaomyceticus
NBC-00415
T
. The ANI value was 90.91% and the dDDH value was 39.30%, both well below the accepted thresholds for species demarcation (ANI < 95%, dDDH < 70%). These genomic indices therefore strongly support that strain J36 represents a novel species within the genus
Streptomyces
. Through whole-genome sequencing and CAZymes analysis, a total of 98 carbohydrate-active enzymes (CAZymes) were detected, including 2 cellulase and 2 β-1,3-glucanases. The cell-free filtrate, which exhibited strong antagonistic activity against
P. cactorum
, also showed high activities of cellulase and β-1,3-glucanase, suggesting that these enzymes may be involved in its anti-oomycete activity. These findings suggest that J36 has potential as a biocontrol candidate, although further
in vivo
evaluation is needed to confirm its efficacy against
Phytophthora
blight of
P. notoginseng
.
Shuang Ma, Lisha Jiang, Die Yang et al.· Frontiers in Microbiology· 0 citations
Pseudomonas sp. MUP55, isolated from rainfall water in Western Australia, was characterized by polyphasic taxonomy and functional assays. Whole-genome and 16S rRNA phylogeny placed Pseudomonas sp. MUP55 in the Pseudomonas fluorescens species group. Massetolide A/D was identified as the leading candidate bioactive compound(s), consistent with its biosynthetic gene cluster, GNPS library matching, and loss of activity in regulatory mutants. The strain showed broad-spectrum antimicrobial activity against bacterial (Escherichia coli and Xanthomonas campestris) and fungal (Fusarium oxysporum and Rhizoctonia solani) plant pathogens. GacA regulates Massetolide production: a P58L mutation abolished synthesis and reduced biocontrol efficacy. Metabolomic and transcriptomic analysis of a ΔpvfC mutant revealed that the pvf cluster regulates specialized metabolism while also contributing to secreted growth-inhibitory activity. The pvf cluster differentially regulates dual siderophore systems and uncouples the co-regulated small RNAs rsmY and rsmZ in the Gac/Rsm cascade. Deletion of pvfC partially reduced the growth-inhibitory activity of Pseudomonas sp. MUP55 supernatants against bacterial pathogens, indicating that pvfC also influences secreted antimicrobial activity beyond its global regulatory role. These findings establish Pseudomonas sp. MUP55 as a taxonomically novel, mechanistically characterized biocontrol agent with potential for sustainable agriculture.
Hussain Alattas, Samuele Sala, Joseph Boctor et al.· International Journal of Mol...· 0 citations
Findings establish B. velezensis strains BP5 and BP103 as highly promising biocontrol agents, combining high genetic stability with diverse secondary metabolite profiles, suitable for development into sustainable microbial bio-bactericides.
Lê Uyển Thanh, Vu Nhat Tan, T. Huyen et al.· Frontiers in Microbiology· 0 citations
An integrated omics study provides foundational insights into the endophytic potential and genomic distinctiveness of AwOcstreb1, isolated from halophytic rice, and opens new avenues for exploring A. welwitschiae for sustainable agriculture and fungal biology.
Nishat Tamanna, Md Nafis Ul Alam, Arifa Akhter Airin et al.· Microbial Genomics· 0 citations
Subcuticular bacteria (SCB) are widespread symbionts of echinoderms and often dominate the body-wall microbiome, suggesting important roles in host physiology. However, their diversity, metabolic properties, and host associations remain poorly characterized. Here, we report a novel dominant SCB lineage associated with deep-sea holothurians, Scotoplanes spp. collected from the Northwest Pacific. We recovered two high-quality genomes, including a 649-kb complete circular genome, and propose a new genus and species, “Candidatus Abyssoplasma scotoplanesicola”, within Mycoplasmatota. The two genomes showed a highly reduced metabolic repertoire, lacking central pathways including glycolysis. In contrast, acidic cell-surface-associated proteins, including large proteins exceeding 5,000 amino acids, accounted for 27.6% of the complete genome and clustered near defense islands. Localized genome plasticity in these regions, revealed by comparison between the two closely related genomes, suggests a possible mechanism for diversification of cell-surface proteins at the host-symbiont interface. “Candidatus Abyssoplasma scotoplanesicola” occupied 76.4–98.9% of the body-wall microbiome of the Scotoplanes specimens. Fluorescence in situ hybridization analysis confirmed that these bacteria formed aggregates on the epidermal side of the body wall. Overall, this study provides genome-and spatially resolved views of dominant SCB in holothurians and offers evolutionary insights into host-interface diversification in the deep-sea holothurian body wall.