İhsan Yaşa

Aquaculture environments are dynamic ecosystems that may influence the evolution and adaptive potential of bacterial pathogens. In this study, a locally isolated Vibrio anguillarum strain VK1 (PRJNA1452808) from Türkiye was characterized using 16S rDNA phylogenetic analysis and whole-genome-based approaches. The high-quality draft genome (4.23 Mb; GC content 44.31%) comprised 194 contigs and 4,102 coding sequences, including 1,057 hypothetical proteins. Functional analyses revealed putative stress response mechanisms and iron acquisition systems, suggesting metabolic versatility and environmental adaptability. Genome-based screening identified 33 putative antimicrobial resistance-associated determinants, including multidrug efflux-related genes and genes linked to antibiotics commonly used in aquaculture. In addition, genes associated with Type III and Type VI secretion systems were detected, potentially indicating adaptive traits related to host interaction and environmental persistence. Overall, the findings suggest that strain VK1 possesses a flexible genomic structure that may support adaptation to fluctuating aquaculture conditions. However, further functional studies are needed to biologically validate the potential virulence and AMR related features.

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.

The root nodule symbiosis between legumes and rhizobia plays a fundamental role in biological nitrogen fixation and ecosystem sustainability. Genista acanthoclada, a perennial woody legume native to arid and rocky slopes of Western Türkiye, has not previously been investigated regarding to its symbiotic microsymbionts. In this study, five bacterial isolates were obtained from root nodules of G. acanthoclada collected from Yamanlar Mountain (İzmir, Türkiye) on Yeast Extract Mannitol Agar (YEMA) and rhizobial strains (GA.7.1 and GA.9) were rapidly selected by colony PCR targeting the nodC gene. Both isolates exhibited typical rhizobial phenotypic characteristics, including Gram-negative rod-shaped morphology, positive catalase and oxidase activities, and weak Congo red absorption on YEMA medium. Taxonomic analyses based on 16S rRNA, recA, and atpD gene sequences revealed that both isolates belong to the genus Mesorhizobium. The incongruence between the phylogenetic analysis based on nodC amino acid sequences and the core gene phylogenies suggests that horizontal gene transfer may play a role in the evolution of nodulation-related genes. In contrast, the nifH-based phylogeny was largely congruent with housekeeping gene phylogenies, indicating a more conserved evolutionary history of nitrogen fixation genes. These findings provide the first data on the rhizobia associated with the nodules of G. acanthoclada and contribute to a better understanding of the evolutionary dynamics of legume–rhizobium interactions.

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.

Bitki özleri, geleneksel tıpta yıllardır yaygın olarak kullanılmaktadır. Lamiaceae familyası, tıp, gıda, ilaç endüstrisinde kullanılan aromatik bitkileri içerir. Bu türler gıda olarak tüketilirken, aromatik özellikleriyle de geleneksel tıbbın vazgeçilmez parçası olarak değerlendirilmektedir. Sağlık ve endüstriyel ürünlerde GRAS (Güvenli) kabul edilen Lamiaceae türleri ekonomik botanik açısından da önemlidir. İzmir kekiği (Origanum onites), Anadolu adaçayı (Salvia fruticosa), Mercanköşk (Origanum majorana) gibi Lamiaceae bitkilerinin güçlü bakterisidal, antifungal özellikleri bilinirken, bu bitkilerden sağlanan yağ ve hidrosol formdaki ekstraktların anti-biyofilm, antiquorum sensing özellikleri dikkat çekmektedir. Çalışmada bu ekstraktların; kimyasal içerik analizleri, bakteriyel virülansın temelini oluşturan Quorum sensing (QS) ve biyofilm aktivitelerinin inhibisyonuna odaklanılmıştır. Sonuç olarak İzmir kekiği, Anadolu adaçayı ve Mercanköşk bitki ekstraktlarının hidrosol formlarına karşı Vibrio spp.’nin dirençli olduğu belirlenmiştir. Vibrio spp.’ye karşı en etkili formun İzmir kekiği ve mercanköşk yağ ekstraktı olduğu ortaya konmuş ve ½ MIC (Subletal) konsantrasyonunda biyofilm inhibisyonu %85 tespit edilmiştir. İzmir Kekiği ve Mercanköşk’ün çalışmadaki tüm Vibrio türleri üzerinde antimikrobiyal, anti-biyofilm etkisi gösterirken ayrıca AHL biyosensör suşu CV026’da QS mekanizmasını inhibe etmiştir. Akuakültür çiftliklerinde toplu balık ölümleriyle ilişkilendirilen Vibrio spp. patojen suşlarıyla mücadelede doğal bir yaklaşım olarak bitki ekstraktlarının etkinliği gösterilmiştir. Bulgular bu yaklaşımın antimikrobiyallere dirençli balık patojenlerine yönelik, bitkisel ekstraktların kemoterapötiklere alternatif tedavi edici araçlar olarak kullanılmasını desteklemektedir.

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.