Publications

4366

A strictly aerobic, Gram-stain-negative, ovoid-shaped and non-motile bacterium, designated as strain MJ-SS7T, was isolated from tidal mudflat sediment collected at a macro-tidal clam farm in Gochang, Republic of Korea. Strain MJ-SS7T exhibited oxidase- and catalase-positive activities. Growth occurred at 20–37 °C (optimum: 30 °C), pH 6–8 (optimum: pH 7) and in the presence of 0–9% (w/v) NaCl (optimum: 3%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that MJ-SS7T belonged to the family Roseobacteraceae. Its closest relatives, based on sequence similarity, were Rhodophyticola porphyridii KACC 18805T (95.9%), Kangsaoukella pontilimi KCTC 72224T (95.8%) and Actibacterium pelagium JN33T (95.5%). The major fatty acids included summed feature 8 (C18:1  ω7c/C18:1  ω6c), C16:0, C16:0 2OH and C18:0. The major polar lipids consisted of phosphatidylglycerol, five unidentified phospholipids, four unidentified aminolipids, two unidentified aminophospholipids and four unidentified lipids. The major respiratory quinone was ubiquinone-10. The genome size was 5.20 Mb, with a DNA G+C content of 63.4 mol%, encoding 5,031 protein-coding genes, 3 rRNA genes and 46 tRNA genes. Comparative genomic analyses confirmed its novelty, with average nucleotide identity (<73%) and average amino acid identity (<70%) values below the species delineation thresholds. Based on polyphasic taxonomic data, strain MJ-SS7T represents a novel species of a new genus within the family Roseobacteraceae, for which the name Ovoidimarina sediminis gen. nov., sp. nov. is proposed. The type strain is MJ-SS7T (=KEMB 21436T=KCTC 8329T=JCM 36750T).

Genomic information can yield new insights into the molecular and physiological mechanisms that underpin pathogen virulence and transmission. We decode the genome of Spirobacillus cienkowskii Metchnikoff 1889, a gram-negative bacterium and one of the first described parasites of Daphnia. We use long-read sequencing and extensive annotation to assemble the complete circular genome of 2.81 Mbp with 2,486 protein-coding genes. In addition to antiviral systems, including CRISPR-Cas and restriction-modification systems, we describe the likely molecular basis of the unusual red phenotype of S. cienkowskii, which results from carotenoid production. We further describe genetic modules that may mediate this bacterium’s interactions with its host and environment. Our study provides insight into the metabolic and functional capacities of a parasite through the assessment of its genome. More generally, it demonstrates what can be learnt by applying recent advances in high-throughput sequencing to the study of parasites.

ABSTRACT The stolbur disease associated with “ Candidatus Phytoplasma solani” (CaPsol) is very common in Europe and the Mediterranean regions and adversely affects perennial or annual plants but is rarely reported on cucurbits. We report the first multilocus genetic characterisation of CaPsol strains infecting cucurbit plants and the presence of some RNA viruses prevalent in cucurbits. Between 2019 and 2020, 156 symptomatic and nine asymptomatic plant samples were collected during surveys in cucurbit‐growing areas. Symptomatic plants exhibited leaf deformation, growth retardation, yellowing, flower deformation and other virus‐like symptoms. Molecular testing detected potyviruses, tobamoviruses and Cucumis melo endornavirus (CmEV) as single and double infections in 108 samples, but CaPsol was determined only in seven plants as a single infection. CaPsol strains infecting squash and watermelon in the Marmara region of Türkiye were genetically characterised by describing their tuf, vmp1 and stamp gene sequences. All cucurbit‐associated CaPsol strains were of the tuf ‐b1 genotype and five different stamp genotypes previously reported in other crops and wild plant reservoirs in Europe. Cucurbit CaPsol strains had vmp1 gene sequences corresponding to RFLP types V4 and V14, previously detected in the Mediterranean basin. These strains were not novel cucurbit‐specific genotypes but shared similarities with genotypes from diverse plant hosts across Europe. This indicated that CaPsol is not restricted to cucurbits and may persist in alternative plant hosts. Thus, disease management should include monitoring alternative plant reservoirs, rather than focusing solely on cucurbit production areas. Viral infections showed significantly higher prevalence compared to phytoplasma infections in the region.