Asiye Esra Eren Eroğlu

Photobacterium damselae subsp. piscicida (Pdp) is one of the major bacterial pathogens affecting marine aquaculture worldwide. This study presents, to our knowledge, the first comparative genomic characterization of a Pdp strain (KLC25) isolated in Türkiye in the context of publicly available genomes from different geographic regions. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) analyses supported the taxonomic assignment of KLC25 to P. damselae. Whole-genome phylogeny positioned KLC25 closest to the isolates MT1415 (Italian) and DI21 (Spanish), whereas core genome phylogeny clustered it with the Cypriot strain BIC8 and the Greek strain GalP1, revealing differences in clustering between whole- and core-genome approaches. Plasmid-associated sequences homologous to pPHDP10, pPHDP70 and pPHDPT3 were also detected in KLC25. Comparative analysis of the prophage regions predicted in KLC25 revealed similarities to phages from different Pdp strains, with most regions showing their highest sequence similarity to phages associated with different strains. While virulence-related determinants were highly conserved across the analyzed genomes, anti-phage defense systems and acquired antimicrobial resistance genes exhibited greater variability. Overall, this study expands our understanding of the genomic diversity and evolution of Pdp and provides a valuable resource for future investigations into its pathogenicity and epidemiology.

Nitrogen fixing Rhizobia play an important role in legume growth and sustainable agriculture, and genome based analyses have become essential for understanding the genetic basis of their symbiotic traits and functional potential. Here, Rhizobium anhuiense strain IY2 was isolated from the root nodules of the endemic legume Trifolium caudatum and characterized using 16 S rRNA and whole-genome sequencing. The genome, sequenced via the Illumina NovaSeq 6000 platform, spans 6,917,460 bp with approximately 6,900 predicted coding sequences (CDSs). Genomic analysis suggested the presence of various genetic determinants potentially linked to plant growth promotion, including those involved in iron acquisition, nitrogen metabolism, stress response, and auxin biosynthesis. While no CRISPR arrays were detected, two prophage regions were identified. Bioinformatic screening via the CARD database identified 47 AMR-related sequences, primarily comprising putative efflux systems and antibiotic targets rather than confirmed resistance determinants. The genome also harbors nod , nif , and fix gene clusters, indicating the genomic potential for symbiotic nitrogen fixation (SNF). Phylogenetic analysis of the nodC amino acid sequence supports a host-specific symbiotic relationship with Trifolium species. Notably, the presence of two distinct copies of the nodD gene suggests a potential for broad host range and strong symbiotic adaptability. This study provides the first genomic insights into the symbiotic association between a rhizobial species and T. caudatum , a legume endemic to Turkey.

Multi-drug resistant Vibrio species pose a significant threat to both public health and the global aquaculture industry. Among them, Vibrio anguillarum is one of the major causative agents of vibriosis outbreaks in farmed fish. In this study, two novel bacteriophages (vY6 and vY28) infecting V. anguillarum were isolated from water samples collected at an aquaculture farm in Türkiye and characterized to evaluate their potential as biological control agents. One-step growth curve analysis showed latent periods of 20 min for vY6 and 25 min for vY28 and both phages remained stable across a wide range of pH and temperature conditions. Whole genome sequencing revealed draft genome sizes of 84.553 bp for vY6 and 99.873 bp for vY28, encoding 57 and 55 predicted coding sequences, respectively, with no detectable antimicrobial resistance genes or virulence-associated genes. Genome annotation identified genes involved in structural assembly, DNA packaging, replication, and host cell lysis. Antibacterial activity against V. anguillarum was evaluated by monitoring optical density at 600 nm. Phage treatment significantly suppressed bacterial growth compared to the untreated control. After 24 h, vY6 and vY28 reduced bacterial growth by approximately 61% and 48%, respectively, while the phage combination resulted in approximately 69% inhibition. Viable cell count analysis confirmed strong antibacterial activity, with reductions of up to 5.62 ± 0.71 log during the early stages of infection. These findings provide a basis for further studies exploring phage-based approaches to control vibriosis.

The Gram-negative marine bacterium Photobacterium damselae subsp. piscicida (Pdp) is a pathogen responsible for pseudotuberculosis in various fish species, posing significant threats to aquaculture. Pdp employs strong virulence mechanisms, one of which is the production of the piscibactin siderophore, which plays a key role in iron acquisition from the host. In this study, we evaluated the ferrophilic properties of the Pdp strain EKL1 in relation to growth and biofilm production. In vitro iron limitation significantly suppressed biofilm formation and planktonic growth in EKL1. We then investigated the anti-biofilm activity of deferoxamine (DFO), an iron chelator used to treat transfusion-induced iron overload in thalassemia patients, against EKL1. DFO strongly inhibited EKL1 biofilm production (by 82.1%), suggesting that iron chelation therapy could be an effective strategy to prevent Pdp-induced photobacteriosis outbreaks. Finally, we characterized the iron-bound form of piscibactin through extensive spectroscopic analyses of the siderophore produced by EKL1. Our findings contribute to the development of novel piscibactin-targeted inhibitors, advancing siderophore-based anti-virulence strategies against Pdp.

Artan nüfus, şehirleşme, iklim değişikliği ve mahsul üretimi üzerindeki baskı, ekosistemin uzun vadeli sürdürülebilirliğini ve işleyişini tehdit etmektedir. Bu bağlamda, biyoçeşitliliğin ve genetik kaynakların korunması, yeşil sürdürülebilir tarım stratejilerinin önemli bir iş planını oluşturmaktadır. Bitki ile ilişkili mikroorganizmalar üzerine yapılan genom tabanlı araştırmalar hem bitki patojenleri hem de bitki gelişimini destekleyici bakterilerin (PGPB) tarımda kullanımı konusundaki bilgi birikimimizi büyük ölçüde geliştirmiştir. Mikroorganizmaların doğal ortamlardaki bazı gen ifadeleri standart laboratuvar koşullarında kültüre edildiklerinde, doğal tetikleyicilerin veya stres sinyallerinin yokluğundan dolayı baskılanabilmektedir. Bu çalışmada, sürdürülebilir tarımda bitki ile ilişkili mikrobiyom çeşitliliğinin ve işlevsel öneminin anlaşılmasında genomik yaklaşımların sunduğu fırsatlar ele alınmıştır. Bakteriyel suşların primer ve sekonder metabolitler için tam biyosentetik kapasitesi, yani doğrudan ve dolaylı PGPB mekanizmaları için anahtar belirteçler, tüm genom dizisinin analizi ile ortaya çıkarılabilmektedir. Bakteriyel tüm genom yaklaşımı simbiyotik azot fiksasyonunda rol oynayan gen kümeleri, siderofor çeşitliliği, antimikrobiyal/ağır metal direnci ile ilişkili genler başta olmak üzere birçok PGPB özelliklerinin determinantlarını açığa çıkarabilmektedir. Genomik teknolojilerin kullanımı, faydalı bitki-mikroorganizma etkileşimlerinin modülasyonunu sağlayarak sürdürülebilir tarım için umut verici ve çevre dostu yeni uygulamaların geliştirilmesine olanak tanıyacaktır.

Bacteriophages are currently considered one of the most promising alternatives to antibiotics under the ‘One Health’ approach due to their ability to effectively combat bacterial infections. This study aimed to characterize Vibrio species in hatchery water samples collected from an aquaculture farm and investigate the biocontrol potential of their bacteriophages. Vibrio spp. (n = 32) isolates confirmed by LNA probe-based qPCR were used as hosts. Three Vibrio phages were isolated. IKEM_vK exhibited a broad host range, infecting V. harveyi (n = 8), V. alginolyticus (n = 2), V. azureus (n = 1), and V. ordalii (n = 1). IKEM_v5 showed lytic activity against V. anguillarum (n = 4) and V. ordalii (n = 1), while IKEM_v14 was specific to V. scophtalmi (n = 4). The morphological appearance of phages and their lytic effects on the host were visualized using scanning electron microscopy (SEM). All three phages remained relatively stable within the pH range of 6–11 and up to 60 °C. The lytic activities and biofilm inhibition capabilities of these phages against planktonic Vibrio cells support their potential applications in controlling vibriosis in aquaculture systems.

A novel strain of Gram-negative, rod-shaped aerobic bacteria, identified as IY22, was isolated from the root nodules of Astragalus flavescens. The analysis of the 16S rDNA and recA (recombinase A) gene sequences indicated that the strain belongs to the genus Phyllobacterium. During the phylogenetic analysis, it was found that strain IY22 is closely related to P. trifolii strain PETP02^T and P. bourgognense strain STM 201^T. The genome of IY22 was determined to be 6,010,116 base pairs long with a DNA G+C ratio of 56.37 mol%. The average nucleotide identity (ANI) values showed a range from 91.7% to 93.6% when compared to its close relatives. Moreover, IY22 and related strains had digital DNA-DNA hybridization (dDDH) values ranging from 16.9% to 54.70%. Multiple genes (including nodACDSNZ, nifH/frxC, nifUS, fixABCJ, and sufABCDES) associated with symbiotic nitrogen fixation have been detected in strain IY22. Furthermore, this strain features genes that contribute to improving plant growth in various demanding environments. This study reports the first evidence of an association between A. flavescens and a rhizobial species. Native high-altitude legumes are a potential source of new rhizobia, and we believe that they act as a form of insurance for biodiversity against the threats of desertification and drought.