Publications

4467

A Gram-stain-negative, anaerobic and rod-shaped bacterium was isolated from gut of rainbow trout in Japan. The temperature range for the growth of 9N8T was 10–30 °C with an optimum at 20 °C. The organism produced acetate and butyrate when grown on AccuDia™ Gifu Anaerobic Medium broth, Modified. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain 9N8T was related to the genus Fusobacterium (<92.9% similarity) and formed a distinct phylogenetic lineage from existing genera within the family Fusobacteriaceae. Strain 9N8T has a genome size of 2.60 Mb. The genomic DNA G+C content was 29.4 mol%. Average amino acid identity values between strain 9N8T and strains in the family Fusobacteriaceae ranged from 39.2 to 57.5%. The major fatty acids of strain 9N8T were C14 : 0, C16 : 1 ω7c and C16 : 0. On the basis of the morphological, physiological, biochemical and genetic information, a novel genus and species, Piscibacter tructae, is proposed, with 9N8T (=NBRC 116745T=DSM 118263T) as the type strain.

Areca palm yellow leaf phytoplasma (AYLP) and Areca palm velarivirus 1 (APV1) are two critical pathogens associated with yellow leaf in areca palm, resulting in devastating damage to areca production. However, evidence of their co-infection remains unclear. Areca palms showing yellow leaf symptoms (suspected to be caused by phytoplasma and velarivirus 1) were surveyed and sampled around Hainan Island of China and the pathogens were identified and analyzed in the study. The results showed that infectious leaf yellowing symptoms of areca palms primarily occurred in eastern and southern cities and counties of Hainan Island. Molecular identification revealed co-infection of 'Candidatus Phytoplasma asteris' (16SrI-B subgroup) and APV1 in individual areca palm samples. Among 520 samples tested by qPCR, AYLP was detected in 23.46% (n=122), APV1 in 53.46% (n=278), and a co-infection with both AYLP and APV1 in 10.96% (n=57). A statistically significant difference in APV1 detection rate was observed between asymptomatic and symptomatic plantations (P < 0.0001), suggesting APV1 infection likely represents an important risk factor for yellowing development in cultivated areca palm populations. These results confirm the co-infection of AYLP and APV1 on Hainan Island, offering epidemiological evidence for targeted disease management.

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.