Chondrinema litorale gen. nov., sp. nov., of the phylum Bacteroidota, carrying multiple megaplasmids isolated from a tidal flat in the West Sea, Korea

Abstract

A Gram-stain-negative, long rod, oxidase and catalase-positive strain WSW3-B12T was isolated from red algae on tidal flats in the West Sea, Korea. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain WSW3-B12T had the highest sequence similarity, 92.7%, to Flexithrix dorotheae DSM 6795T, followed by Rapidithrix thailandica TISTR 1750T at 90.8% in the family Flammeovirgaceae of the phylum Bacteroidota. The whole genome sequence determined using both the Nanopore and Illumina platforms revealed that the complete genome consists of 29 contigs, among which contig 1 was a circular chromosome, while the remaining 28 contigs were plasmids. The size of the genome was 10.1 Mbp and the G+C content was 34.1%. The average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), average amino acid identity (AAI), and percentage of conserved proteins (POCP), phylogenomic-related indexes between the strain WSW3-B12T and the closest strain Flexithrix dorotheae DSM 6795T, were 76.6%, 19.9%, 57.2%, and 55.6%, respectively, which were all lower than the threshold values to support the creation of a novel genus. A comprehensive genome analysis revealed that the strain WSW3-B12T harbored many of the key genes involved in central metabolism in the main chromosome and also carried important genes for the production of vitamins, quinone, and antimicrobial resistance on the plasmids. The strain also carried genes that are involved in the metabolism of heavy metals such as arsenic, cobalt, copper, and iron on both the chromosome and plasmids. Furthermore, the genome of the strain was highly enriched with carbohydrate-active enzymes (CAZymes), carrying a total of 241 CAZymes. Moreover, a complete CRISPR/Cas system was detected on plasmid 20. The major fatty acids of the strain were iso-C15:0 and C16:1 ω5. The polar lipids contained phosphatidylethanolamine, four unidentified lipids, and four glycolipids. The respiratory quinone was menaquinone 7. Based on the phenotypic, chemotaxonomic, and genomic analyses, the strain WSW3-B12T could be assigned to a novel species and novel genus within the family Flammeovirgaceae, for which the name Chondrinema litorale gen. nov., sp. nov. (type strain WSW3-B12T = KCTC 82707T = GDMCC 1.3198T) is proposed.

Three novel marine species of the genus Reichenbachiella exhibiting degradation of complex polysaccharides

“…Motility was observed by using a hanging-drop technique, and gliding activity was observed by growing the strain on low-nutrient media composed of sea water and 0.7% (w/v) agar ( Tittsler and Sandholzer, 1936 ). The optimal temperature and salt tolerance for the growth was determined by using MA ( Muhammad et al, 2022 ) while the optimal pH for the growth was tested in MB ( Muhammad et al, 2023 ). To determine the growth under an anaerobic condition, all three strains were tested on a solid medium composed of 0.2% (w/v) glucose, 2% (w/v) NaCl, 0.1% (w/v) polypeptone, 0.1% (w/v) KH 2 PO 4, 0.1% (w/v) K 2 HPO 4 , 0.2% (w/v) NH 4 Cl, 0.14% (w/v) MgSO4, NaNO 3 (w/v) 0.17, 1.5% (w/v) agar, 0.1% (w/v) resazurin, 0.05% (w/v) cysteine HCl, 1 mL trace elements, and 1 mL multivitamins ( Wolin et al, 1963 ; Kim et al, 2001 ; Bae et al, 2020 ).…”

“…While investigating the microbial diversity of the tidal flats in the West Sea, Korea, a high number of novel bacteria capable of degrading complex polysaccharides were isolated ( Muhammad et al, 2023 ; Nguyen et al, 2023 ). Three novel strains, ABR2-5 T , BKB1-1 T , and WSW4-B4 T , were isolated from macroalgae and sea mud.…”

Comparative genome analysis of the genus Marivirga and proposal of two novel marine species: Marivirga arenosa sp. nov., and Marivirga salinae sp. nov

“…All isolates were checked for gliding motility through the hanging-drop technique and using soft agar media [27]. The optimum temperature and salt concentration for growth were assessed by using MA as the growth medium [2], while the optimum pH was examined using pH adjusted marine broth (MB, BD) as the testing medium [28]. For the determination of growth under anaerobic conditions, all isolates were inoculated within an anaerobic chamber (Coy Labs, USA) and the cells were cultivated on MA in an anaerobic jar at 30 °C (BD GasPak Systems).…”

“…After Pseudomonatoda and Cyanobacteria, members of the phylum Bacteroidota rank as the ocean's most abundant bacterial group [1]. Bacteroidota strains have been isolated from a wide range of marine environments, including tidal flats [2], coastal sediments [3], deep sea [4], and hydrothermal vents [5]. By analyzing metagenomic data obtained from global ocean sampling and conducting a CARD-FISH study across the North Atlantic Ocean it was revealed that, subsequent to Cyanobacteria and Pelagibacter, Bacteroidota are the prevailing bacteria in marine environments [6].…”