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1. Pseudovibrio ascidiaceicola 5337, a marine bacterial symbiont of the ascidian gut with unusual genome features

   https://doi.org/10.1128/mra.00594-25  

   Young, Morgan; Natarajan, Ojas; Lim, Shen Jean; Dishaw, Larry J (September 2025, Microbiology Resource Announcements)

   Stedman, Kenneth M (Ed.)

   ABSTRACT We isolatedPseudovibrio ascidiaceicolastrain 5337, a gut bacterium of the ascidianCiona robusta,from Mission Bay, San Diego. The genomic assembly is 6.94 Mb and 99.99% complete, comprising 22 contigs and 6,613 protein-coding genes. Unicycler identified seven circular contigs, and PHASTEST identified 11 prophage regions, including two gene transfer agents. 

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2. The Agrobacterium fabrum efflux pump PecM is produced in response to the plant exudate 4-hydroxybenzaldehyde to avoid disruption of central metabolism

   https://doi.org/10.1128/jb.00150-25  

   Ghosh, Arpita; Grove, Anne (July 2025, Journal of Bacteriology)

   Becker, Anke (Ed.)

   ABSTRACT Agrobacterium fabrum is a phytopathogen that causes crown gall disease. In the rhizosphere, it encounters plant exudates, some of which are toxic, such as 4-hydroxybenzaldehyde (4HBA). Others, including 4-hydroxybenzoate (4HB), participate in the induction of virulence genes.A. fabrum encodes the transcription factor PecS, which has been reported to enhance bacterial fitness in the rhizosphere. The gene encoding PecS is divergent from pecM, which encodes an efflux pump. PecS represses both pecS and pecM, as evidenced by increased expression in the presence of the PecS ligand urate and by elevated pecM expression in a pecS disruption strain. We report here that the expression ofpecM is induced selectively by 4HBA. Expression of genes encoding enzymes involved in the degradation of 4HB is induced by both 4HBA and 4HB, as expected; however, overexpression ofpecM attenuates the induction by 4HBA, suggesting that 4HBA is a substrate for PecM. Consistent with this inference, untargeted metabolomics shows that 4HBA accumulates intracellularly whenpecM is disrupted. Analysis of PecS by thermal stability assay and DNase I footprinting suggests that 4HBA is not a ligand for PecS. Taken together, our data suggest that 4HBA is a substrate for PecM.IMPORTANCEPlant roots secrete a number of compounds that may be toxic to bacteria residing in the surrounding soil. One such bacterium is Agrobacterium fabrum, which infects plants and induces tumor formation. We show here that an A. fabrum strain in which the efflux pump PecM has been disrupted accumulates 4-hydroxybenzaldehyde, and that this plant root exudate induces the expression of pecM. Our data suggest that PecM and PecS, a transcription factor that regulates pecM expression, both function to promote A. fabrum fitness in the rhizosphere. As a competitive advantage in the rhizosphere is a prerequisite for subsequent plant infection, our data contribute to a more complete understanding of the A. fabrum infection process. 

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3. The biocontrol potential of endophyte Bacillus velezensis to reduce post-harvest tomato infection caused by Rhizopus microsporus

   https://doi.org/10.1128/spectrum.01064-25  

   Kock, Alicia; Napo, Mmanoko; Viviers, Dionné; Akinmoladun, Oluwakemi V; Alayande, Kazeem A; Yusuf, Abdullahi; Uehling, Jessie; Pawlowska, Teresa E; Adeleke, Rasheed A (October 2025, Microbiology Spectrum)

   Hockett, Kevin Loren (Ed.)

   ABSTRACT Rhizopus microsporusis a necrotrophic post-harvest pathogen that causes significant economic losses in the agricultural sector. To explore alternatives to conventional management strategies for the mitigation of post-harvest infections, we investigated the potential of two previously identified endophyticBacillus velezensisstrains as biological control agents. Throughin vitroandin vivoexperiments, we examined the mechanisms of biocontrol displayed by twoB. velezensisstrains (KV10 and KV15) against threeR. microsporusstrains (W2-50, W2-51, and W2-58).In vitroassays assessed co-cultivability and the inhibitory effects ofB. velezensisagainstR. microsporus. The results demonstrated strain-specific antifungal activity with a reduction in fungal growth across treatments. Further analysis revealed that volatile organic compounds produced byB. velezensiscontributed to its antifungal properties. To evaluate the biocontrol efficacyin vivo, tomato fruits were inoculated withR. microsporusand subsequently treated withB. velezensis. The results support the strain-specific reduction in tomato spoilage, yielding various spoilage rates observed across treatments. Our findings highlight the potential ofB. velezensisas a promising biocontrol agent for the management ofR. microsporuspost-harvest infections in tomatoes. Further research is warranted to optimize the applicationof B. velezensisas a sustainable and environmentally friendly approach for controlling post-harvest diseases in tomatoes.IMPORTANCEOur study shows the significance of improving sustainable agriculture by offering an alternative to the use of chemical fungicides in post-harvest applications. Opportunistic fungal pathogens likeRhizopus microsporuscan have detrimental effects on post-harvest commodities like tomatoes. Post-harvest fungal infections are mainly controlled by chemical fungicides that pose health risks to humans and the environment. Utilizing biocontrol agents provides an environmentally safe alternative. Understanding the mechanisms of biocontrol employed by beneficial bacteria likeBacillus velezensison fungal pathogens gives insight into safer, more environmentally friendly alternatives to protect food crops. Our results suggest that targeted microbial solutions can mitigate post-harvest losses. 

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4. Draft genome sequence of Paenibacillus turicensis DSM 14349 ^T from cerebrospinal fluid of a patient in Switzerland

   https://doi.org/10.1128/mra.01373-25  

   Berzansky, Marion; Handojo, Mia; Pukall, Rüdiger; Göker, Markus; Woyke, Tanja; Seshadri, Rekha; Luna_Lopez, Carlos; Read, Betsy (April 2026, Microbiology Resource Announcements)

   Van_Tyne, Daria (Ed.)

   ABSTRACT We report the draft genome of the gram-positive bacteriumPaenibacillus turicensisDSM 14349^T,isolated from the cerebrospinal fluid of a male patient. The 4.8 Mbp genome encodes 4,551 genes, including 4,423 protein-coding sequences, some of which may contribute to its ability to survive in a nutrient-poor environment. 

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5. Genome evolution of Acinetobacter baylyi ADP1 during laboratory domestication: acquired mutations impact competence and metabolism

   https://doi.org/10.1128/aem.00936-25  

   Gifford, Isaac; Vergis, Meghna R; Barrick, Jeffrey E (August 2025, Applied and Environmental Microbiology)

   Nikel, Pablo Ivan (Ed.)

   ABSTRACT The bacteriumAcinetobacter baylyiis a model organism known for its extreme natural competence and metabolic versatility. It is capable of taking up environmental DNA at a high rate across all growth phases. The type strain ADP1 was created by random mutagenesis of a precursor strain, BD4, to prevent it from forming cell chains in culture. ADP1 has since been distributed between research groups over several decades and acquired subsequent mutations during this time. In this study, we compare the genome sequences ofA. baylyiBD4 and its modern descendants to identify and understand the effects of mutations acquired and engineered during its domestication. We demonstrate that the ADP1 variants in use today differ in their competence, growth on different carbon sources, and autoaggregation. In addition, we link the global carbon storage regulator CsrA and a transposon insertion that removes its C-terminal domain specifically to changes in both overall competence and an almost complete loss of competence during the stationary phase. Reconstructing the history of ADP1 and the diversity that has evolved in the variants currently in use improves our understanding of the desirable properties of this experimentally and industrially important bacterium and suggests ways that its reliability can be improved through further genome engineering.IMPORTANCEAcinetobacter baylyiADP1 is a bacterial chassis of interest to microbiologists in academia and industry due to its extreme natural competence and wide metabolic range. Its ability to take up DNA from its environment makes it straightforward to efficiently edit its chromosome. We identify and characterize mutations that have been passed down to modern strains of ADP1 from the initial work in the 1960s, as well as subsequent mutations and genome edits separating strains in use by different research groups today. These mutations, including one in a global regulator (CsrA), have significant phenotypic consequences that have affected the reproducibility and consistency of experiments reported in the literature. We link a mutation in this global regulator to unexpected changes in natural competence. We also show that domesticatedA. baylyistrains have impaired growth on a variety of carbon sources. 

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