Flavobacterium litorale sp. nov., isolated from red alga

Muhammad, Neak; Han, Ho Le; Lee, Yong-Jae; Ko, Jae–Ho; Nguyen, Tra T H; Kim, Song‐Gun

doi:10.1099/ijsem.0.005458

Cited by 8 publications

(6 citation statements)

References 43 publications

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“…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 ).…”

Section: Methodsmentioning

confidence: 99%

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

Muhammad,

Avila,

Nedashkovskaya

et al. 2023

Front. Microbiol.

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Three novel strains designated ABR2-5T, BKB1-1T, and WSW4-B4T belonging to the genus Reichenbachiella of the phylum Bacteroidota were isolated from algae and mud samples collected in the West Sea, Korea. All three strains were enriched for genes encoding up to 216 carbohydrate-active enzymes (CAZymes), which participate in the degradation of agar, alginate, carrageenan, laminarin, and starch. The 16S rRNA sequence similarities among the three novel isolates were 94.0%–94.7%, and against all three existing species in the genus Reichenbachiella they were 93.6%–97.2%. The genome sizes of the strains ABR2-5T, BKB1-1T, and WSW4-B4T were 5.5, 4.4, and 5.0 Mb, respectively, and the GC content ranged from 41.1%–42.0%. The average nucleotide identity and the digital DNA–DNA hybridization values of each novel strain within the isolates and all existing species in the genus Reichenbachiella were in a range of 69.2%–75.5% and 17.7–18.9%, respectively, supporting the creation of three new species. The three novel strains exhibited a distinctive fatty acid profile characterized by elevated levels of iso-C15:0 (37.7%–47.4%) and C16:1 ω5c (14.4%–22.9%). Specifically, strain ABR2-5T displayed an additional higher proportion of C16:0 (13.0%). The polar lipids were phosphatidylethanolamine, unidentified lipids, aminolipids, and glycolipids. Menaquinone-7 was identified as the respiratory quinone of the isolates. A comparative genome analysis was performed using the KEGG, RAST, antiSMASH, CRISPRCasFinder, dbCAN, and dbCAN-PUL servers and CRISPRcasIdentifier software. The results revealed that the isolates harbored many key genes involved in central metabolism for the synthesis of essential amino acids and vitamins, hydrolytic enzymes, carotenoid pigments, and antimicrobial compounds. The KEGG analysis showed that the three isolates possessed a complete pathway of dissimilatory nitrate reduction to ammonium (DNRA), which is involved in the conservation of bioavailable nitrogen within the ecosystem. Moreover, all the strains possessed genes that participated in the metabolism of heavy metals, including arsenic, copper, cobalt, ferrous, and manganese. All three isolated strains contain the class 2 type II subtype C1 CRISPR-Cas system in their genomes. The distinguished phenotypic, chemotaxonomic, and genomic characteristics led us to propose that the three strains represent three novel species in the genus Reichenbachiella: R. ulvae sp. nov. (ABR2-5T = KCTC 82990T = JCM 35839T), R. agarivorans sp. nov. (BKB1-1T = KCTC 82964T = JCM 35840T), and R. carrageenanivorans sp. nov. (WSW4-B4T = KCTC 82706T = JCM 35841T).

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Section: Methodsmentioning

confidence: 99%

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

Muhammad,

Avila,

Nedashkovskaya

et al. 2023

Front. Microbiol.

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“…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).…”

Section: Physical Biochemical and Chemotaxonomic Analysismentioning

confidence: 99%

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

Muhammad,

Avila,

Kim

2024

Preprint

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Background The phylum Bacteroidota represents a significant proportion of heterotrophic bacteria found in marine ecosystems. Members of the phylum Bacteroidota are actively involved in the degradation of biopolymers such as polysaccharides and proteins. Bacteroidota genomes exhibit a significant enrichment of various enzymes, including carbohydrate-active enzymes (CAZymes), carboxypeptidases, esterases, isomerases, peptidases, phosphatases, and sulfatases. The genus Marivirga, a member of the family Marivirgaceae within the phylum Bacteroidota, comprises six documented species. During a microbial diversity study, three novel Marivirga strains (BKB1-2T, ABR2-2, and BDSF4-3T) were isolated from the West Sea, Republic of Korea. Results To explore the taxonomic status and genomic characteristics of the novel isolates, we employed a polyphasic taxonomic approach, which included phylogenetic, chemotaxonomic and comprehensive genome analysis. The three isolates were Gram-stain-negative, aerobic, rod-shaped, moderately halophilic, and had a gliding motility. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among the two isolates, BKB1-2T and BDSF4-3T, and the six reference strains were 70.5–76.5% for ANI and 18.1–25.7% for dDDH. Interestingly, the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the strains harbor genes for a comprehensive pathway for dissimilatory nitrate reduction to ammonium (DNRA), as well as other nitrogen pathways for the reduction of nitrite, nitric oxide, and nitrous oxide. Additionally, the antiSMASH analysis indicated that the strains contained three to eight biosynthetic gene clusters (BGCs) associated with the synthesis of secondary metabolites. Furthermore, the strains carried a high number of CAZyme ranging from 53 to 152, which was also demonstrated by an in vitro analysis of degradation of the polysaccharide cellulose, chitin, laminarin, starch, and xylan. Additionally, all the strains carried genes for the metabolism of heavy metals, and exhibited tolerance to heavy metals, with minimum inhibitory concentrations (MICs) in millimoles (mM) in ranges of Co2+ (3–6), Cu2+ (0.2–0.4), Ni2+ (3–5), Zn2+ (2–4), Mn2+ (20–50), and Hg2+ (0.3). Conclusions Based on polyphasic taxonomic approach, the three isolated strains represent two novel species names Marivirga arenosa sp. nov. (BKB1-2T = KCTC 82989T = InaCC B1618T), and Marivirga salinae sp. nov. (BDSF4-3T = KCTC 82973T = InaCC B1619T).

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“…Reads were de novo assembled with Flye genome assembler version 2.9.2 with a read quality score threshold of 15 [25]. The errors in the assembled genome were corrected using Medaka version 1.7.2 (https://github.com/nanoporetech/medaka) with the model ‘r941_min_sup_g507’, and the completeness of the genome was assessed with BUSCO version 5.3.1 [26]. Genomic relatedness of GRR-S3-23 T and other species of the genus Tenacibaculum were investigated using the genomic data of 25 Tenacibaculum strains and 9 outgroup strains downloaded from the NCBI RefSeq database.…”

Section: Genomic Featuresmentioning

confidence: 99%

Tenacibaculum tangerinum sp. nov., isolated from a tidal flat sediment

Lee,

Yoo,

Kwon

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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An orange-coloured bacterium, designated as strain GRR-S3-23T, was isolated from a tidal flat sediment collected from Garorim Bay, Chuncheongbuk-do, Republic of Korea. Cells of GRR-S3-23T were aerobic, Gram-stain-negative, rod-shaped and motile. GRR-S3-23T grew at 18–40 °C (optimum, 30 °C), pH 7.0–9.0 (optimum, pH 7.0) and with 2–4 % NaCl (optimum, 2–3 % w/v). Results of 16S rRNA gene sequence analysis indicated that GRR-S3-23T was closely related to Tenacibaculum aiptasiae a4T (97.6 %), followed by Tenacibaculum aestuarii SMK-4T (97.5 %), Tenacibaculum mesophilum MBIC 1140T (97.4 %), Tenacibaculum singaporense TLL-A2T (97.3 %), Tenacibaculum crassostreae JO-1T (97.2 %),and Tenacibaculum sediminilitoris YKTF-3T (97.1 %). The average amino acid identity values between GRR-S3-23T and the related strains were 86.8–72.8 %, the average nucleotide identity values were 83.3–74.1 %, and the digital DNA–DNA hybridization values were 27.0–19.6 %. GRR-S3-23T possessed menaquinone-6 (MK-6) as major respiratory quinone and had summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 20.6 %) and iso-C15 : 1G (10.8 %) as major fatty acids (>10.0 %). The polar lipid profiles of GRR-S3-23T contained phosphatidylethanolamine, one unidentified aminolipid, one unidentified aminophospholipid, three unidentified lipids, one unidentified glycolipid and four unidentified phospholipids. The DNA G+C content of GRR-S3-23T was 33.7%. On the basis of the results of the polyphasic analysis involving phylogenetic, phylogenomic, physiological and chemotaxonomic analyses described in this study, GRR-S3-23T is considered to represent a novel species within the genus Tenacibaculum , for which the name Tenacibaculum tangerinum is proposed. The type strain is GRR-S3-23T (=KCTC 102029T=KACC 23271T=JCM 36353T).

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Flavobacterium litorale sp. nov., isolated from red alga

Cited by 8 publications

References 43 publications

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

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

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

Tenacibaculum tangerinum sp. nov., isolated from a tidal flat sediment

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