Publications

4889

Abstract Bdellovibrio are predatory bacteria with potential applications in treating multidrug-resistant bacterial infections. We isolated Bdellovibrio sp. kdesi from sewage in Reynosa, Mexico, and performed comprehensive genomic characterization. The complete genome (3,343,978bp; 48.5% GC content; 3,208 coding sequences) contains a single rRNA operon with two identical 16S rRNA genes at distinct loci. While 16S rRNA analysis showed 99.3% identity to B. bacteriovorus SSB218315, polyphasic genomic analysis revealed kdesi as a distinct species. Core-genome phylogeny, average nucleotide identity (ANI ~ 89%), average amino acid identity (AAI ~ 82%), and digital DNA-DNA hybridization (dDDH < 70%) clearly demonstrated that Kdesi along with several other strains currently classified as B. bacteriovorus represents novel genomospecies requiring formal taxonomic revision. Comparative genomic analysis of 29 Bdellovibrio genomes revealed an open pan-genome (~ 25,000 genes) with limited transposable elements, absence of SecB in the Sec secretion system, and strain-specific adaptations in Type IV secretion systems. These findings underscore the need for genome-based taxonomic revision of the genus and highlight the importance of using multiple molecular criteria beyond 16S rRNA for bacterial species delineation.

Abstract The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy for prokaryotic genomes sourced from the NCBI Assembly database. GTDB release 10 (R10-RS226) spans 715 230 bacterial and 17 245 archaeal genomes organized into 136 646 bacterial and 6968 archaeal species clusters. Fewer new major branches of prokaryotic life are being discovered with each release of GTDB, suggesting that we are beginning to saturate readily discoverable microbial diversity through culture-independent analyses. However, species discovery continues unabated as >95% of bacterial and archaeal species remain to be genomically elucidated based on conservative projections. We present additions to the GTDB website, methodological improvements, policy changes, notable nomenclatural updates, and user applications. We conclude with a summary of future plans for the resource including a fungal taxonomy and a nomenclatural extension to classify pathogens.

Abstract BACKGROUND Huanglongbing (HLB) is the most devastating citrus disease worldwide, with no resistant commercial citrus varieties identified and no effective chemical treatments currently available on the market. The main challenge in developing effective strategies for controlling HLB is the inability to culture its associated pathogen, the fastidious Candidatus Liberibacter asiaticus ( C Las), in defined media or axenic cultures. RESULTS In this study, we developed an effective method for screening antimicrobials against C Las using periwinkle as a model plant. Compared with citrus, periwinkle offers notable advantages, including reduced time, increased efficiency, and lower costs. This method consists of two main components: screening exogenously applied antimicrobials and evaluating overexpressed endogenous antimicrobial peptides. Using this method, we demonstrated that bromothalonil and cyproconazole effectively inhibit the proliferation of C Las in hydroponically grown periwinkle. Further analyses revealed that bromothalonil and cyproconazole were also highly toxic to other citrus pathogens, including Xanthomonas citri subsp. citri ( Xcc ), Alternaria alternata tangerine pathotype (Z7), and Penicillium digitatum (KH8). In addition, we established an Agrobacterium rhizogenes ‐mediated hairy root genetic transformation system for periwinkle and demonstrated that the proliferation of C Las was significantly inhibited in transgenic roots overexpressing antimicrobial peptide (SAMP). CONCLUSION An efficient antimicrobial screening system for C Las and several other citrus pathogens has been established. By addressing challenges such as high costs, prolonged experimental periods, and heavy workloads, we anticipate that this developed method will serve as a useful tool for the identification of antimicrobials effective against C Las and other citrus pathogens. © 2025 Society of Chemical Industry.

ABSTRACT X‐disease, caused by strains in the 16SrIII‐A subgroup of ‘ Candidatus Phytoplasma pruni’, is a devastating disease of Prunus species (stone fruits). Multiple outbreaks of this disease have occurred across much of North America for more than a century, with the most recent one beginning around 2010 in the Pacific Northwest of the United States, causing severe damage to the stone fruit industry. Sensitive and specific detection of X‐disease is critical to prevent the propagation and spread of infected plant material; however, current PCR‐based detection workflows lack specificity to X‐disease and require one or more PCR assays followed by additional testing to confirm the species identity. In this study, two real‐time PCR assays, one targeting the secY gene and the other targeting the tuf gene, were developed for specific detection of X‐disease in stone fruits. The CPH‐TXD assay targeting the tuf gene provided high‐sensitivity target detection of as few as five target copies with significantly reduced cross‐reactivity compared to current methods. The CPH‐SXD assay targeting the secY gene detected a minimum of 30 target copies and showed no cross‐reaction with closely related strains. The repeatability and reproducibility of both assays were verified with acceptable results. Together, these assays provide efficient and high‐specificity detection methods to combat the growing threat of X‐disease in North America.

First sugar beet varieties with reasonable yield stability under infection with Candidatus Arsenophonus phytopathogenicus (ARSEPH), the causal agent of the syndrome “Basses Richesses” (SBR), were discovered, but the mechanisms behind this have not been described yet. Thus, this research aimed at analyzing different morphological, physiological and quality related traits of ARSEPH infected sugar beet taproots to identify methods for SBR variety screening. In a greenhouse experiment, one susceptible and two tolerant varieties were infected with ARSEPH via the vector Pentastiridius leporinus (reed glass-winged cicada) under controlled conditions. In the susceptible variety, an infection with ARSEPH caused an average reduction in volume (~40%), length (~6%), width (~21%), fresh mass (~41%) and an increase in dry matter content (~5%). The tolerant varieties exhibited a lower effect on these parameters but showed a greater increase in alcohol insoluble residues (cellulose, hemicellulose, pectin, lignin) and marc content. The significant enhancement in flexural taproot tissue strength observed in the tolerant varieties may be linked to increased levels of structural cell components. The susceptible and one tolerant variety exhibited reduced periderm puncture resistance after infection. This first study of physiological and morphological traits provides deeper insights into host-pathogen interaction and potential variety response. To confirm the relevance and implications of the results as new parameters for screening of SBR-tolerant varieties, further analysis with additional varieties across a larger number of samples is necessary.