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PubMed2026

Biocontrol Potential of a Novel Bacillus velezensis Strain Against Major Soft Rot Bacteria Pectobacterium and Dickeya.

Management of soft rot Pectobacteriaceae (SRP) remains a major challenge because effective control options such as bactericides, chemical treatments, or resistant commercial varieties are currently lacking. In a quest for an effective control measure against SRP, we isolated bacteria from soil and potato samples from potato fields across Montana. The bacterial isolates were screened for their effective suppression of major soft rot and blackleg pathogens Pectobacterium brasiliense strain Pb1692 and Dickeya dianthicola strain ME23. We screened more than 3,000 bacterial isolates using inhibition-zone assays on nutrient agar plates. From this collection, we identified a strong antagonist effective against Pb1692 and ME23. This isolate successfully suppressed potato soft rot and blackleg disease in both laboratory and greenhouse evaluations. Genome sequencing identified the bacterial antagonist as Bacillus velezensis strain DN539, which can survive well at 8°C, a potato postharvest storage temperature. We enriched the B. velezensis DN539 supernatant in bioactive fractions, and mass spectrometry analysis identified the bioactive compound as isomers of surfactin. Scanning electron microscopy identified that surfactin-enriched fraction resulted in the leakage of the cellular content of phytobacteria tested in our study in as little as 10 min, followed by complete degradation of bacterial cells within 1 h. The surfactin-enriched fraction also had antimicrobial effects against other economically important phytobacteria such as Erwinia amylovora, Xanthomonas campestris, and Pseudomonas syringae. These indicate that surfactin synthesized by Bacillus velezensis DN539 has potential to be developed as a biocontrol agent against broad range of phytobacteria.

Pectobacterium↗
PubMed2026

Comparative essentialome analysis of six Pectobacteriaceae strains using the TNSEEK pipeline identifies conserved and strain-specific fitness determinants.

Transposon sequencing (Tn-seq) is a powerful technique for defining the essential genes required for bacterial survival. However, gene essentiality can vary significantly across taxonomic levels, and comparing large Tn-seq datasets from multiple strains presents considerable analytical challenges. To address this, we developed TNSEEK, a fully automated bioinformatics pipeline for the systematic and comparative analysis of Tn-seq experiments. We applied TNSEEK to analyse newly generated data for six soft rot Pectobacteriaceae strains, encompassing species from the Dickeya and Pectobacterium genera, grown in a rich medium. This approach identified a core essentialome of 225 genes, primarily involved in fundamental cellular maintenance, conserved across all 6 strains, a set comparable in size to that of the neighbouring Enterobacteriaceae family. Only a few genus-specific essential genes were found, highlighting interesting distinct metabolic capabilities between Dickeya and Pectobacterium genera. In striking contrast, we discovered a large variable essentialome comprising 181 strain-specific genes, many of which are of unknown function. A portion of these strain-specific essential genes are components of defence systems and prophage genomic regions. The unexpected essentiality of selected components of these modules is consistent with cellular dependency on cognate toxic, restriction or immunity functions encoded by defence-associated loci under the tested growth condition. Furthermore, a comparison with the Escherichia coli essentialome demonstrates that discrepancies in gene essentiality can often be attributed to differences in growth conditions, particularly temperature, as well as variations in genetic redundancy. In conclusion, the TNSEEK pipeline provides a reproducible framework for comparative analysis of mariner/Himar1 Tn-seq datasets across multiple strains.

Pectobacterium↗
PubMed2025

Phenotypic profiling of carbon utilization of Pectobacterium brasiliense (Pbr1692).

Pectobacterium brasiliense 1692 (Pbr1692) is a necrotrophic pathogen that infects many crops such as potatoes and ornamental plants and derives nutrients from degraded plant tissue. Previous studies have identified Pbr1692 genes required for ecological fitness and virulence, however there is a lack of information on nutrient utilization in Pbr1692. Carbon source utilization profiling in Pbr1692 could provide a platform to decipher its metabolic flexibility and adaptation. This study assessed the nutrient utilization of Pbr1692 in different carbon sources, using Biolog Phenotypic Microarray (PM). An array of carbon sources utilized by Pbr1692 were identified, 32 carbohydrates and 8 carboxylic acids were among the preferred carbon nutrients utilized by Pbr1692. The PM results also revealed that the citric acid cycle, amino acid metabolism, and pentose phosphate metabolic pathways might be used to produce energy for Pbr1692. In addition, growth of Pbr1692 cells in minimal medium supplemented with citric acid, glucose, and aspartic acid retained the typical rod shape, suggesting that nutrient variation did not influence Pbr1692 cell morphology adaptation. This study provides an understanding on the adaptation of Pbr1692 and lays a foundation for understanding carbon metabolism of Pbr1692.

Carbon↗