Winogradskyella sediminis sp. nov., isolated from marine sediment

Zhang, De-Chao; Liu, Yanxia; Huang, Hongyan; Weber, Karin; Margesin, Rosa

doi:10.1099/ijsem.0.001157

Cited by 14 publications

(4 citation statements)

References 33 publications

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“…The description is as before (Zhang et al, 2016b) with the following modification. The G+C content of the type-strain genome is 33.6%, its approximate size 3.80 Mbp, its IMG deposit 2739367661.…”

Section: Discussionmentioning

confidence: 99%

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

et al. 2019

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Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

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Section: Discussionmentioning

confidence: 99%

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

et al. 2019

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“…S4). The sole respiratory quinone of strain ZXX205 T was MK-6, which is also the major respiratory quinone in the most members of the genus Winogradskyella [2, 7–12]. The DNA G+C content of ZXX205 T was 35.5 %, a value in the range reported for recognized species of the genus Winogradskyella (30.1~39.0 mol%) [1–4, 7–12].…”

Section: Full-textmentioning

confidence: 99%

“…Besides W. psychrotolerans (the respiratory quinones of this species are MK-6 and MK-7) [6], the sole or major respiratory quinone of the species in genus Winogradskyella is MK-6 [2, 7–12]. The main cellular fatty acids are branched-chain (iso-C 15 : 0 , iso-C 15 : 1 , anteiso-C 15 : 0 ) and fatty acids with hydroxy groups (iso-C 15 : 0 3-OH, iso-C 16 : 0 3-OH, and iso-C 17 : 0 3-OH) [10, 12].…”

Section: Full-textmentioning

confidence: 99%

“…Within the genus Winogradskyella, all members have been isolated from marine environments or marine organisms [7], strictly aero-bic or facultatively anaerobic and catalase-positive. Besides W. psychrotolerans (the respiratory quinones of this species are MK-6 and MK-7) [6], the sole or major respiratory quinone of the species in genus Winogradskyella is MK-6 [2,[7][8][9][10][11][12]. The main cellular fatty acids are branched-chain (iso-C 15 : 0 , iso-C 15 : 1 , anteiso-C 15 : 0 ) and fatty acids with hydroxy groups (iso-C 15 : 0 3-OH, iso-C 16 : 0 3-OH, and iso-C 17 : 0 3-OH) [10,12].…”

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confidence: 99%

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Winogradskyella ouciana sp. nov., isolated from the hadal seawater of the Mariana Trench

Liu

Liang

et al. 2019

International Journal of Systematic and Evolutionary Microbiology

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A Gram-staining-negative, strictly aerobic, long-rod shaped with no flagellum and yellow-pigmented bacterium designated strain ZXX205T, was isolated from the hadal seawater at the depth of 7500 m in the Mariana Trench, Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences placed strain ZXX205T within the genus Winogradskyella and strain ZXX205T was most closely related to Winogradskyella flava KCTC 52348T and Winogradskyella echinorum KCTC 22026T with 96.9 % and 96.6 % sequence similarity, respectively. The sequence similarities to all other type strains were 96.3 % or less, and to the type strain Winogradskyella thalassocola LMG 22492T was 94.1 %. Growth occurred in the presence of 0–9.0 % (w/v) NaCl (optimum 3.0 %), at 4–45 °C (optimum 28 °C) and pH 6.0–9.0 (optimum pH 7.5). The sole respiratory quinone was menaquinone 6 (MK-6). The dominant cellular fatty acids (>10 %) of strain ZXX205T were iso-C15 : 0, iso-C15 : 1 G, iso-C16 : 0 3-OH and iso-C16 : 0. The polar lipids profile contained predominantly phosphatidylethanolamine, four glycolipids, four unidentified aminolipids and three unidentified lipids. The genomic DNA G+C content was 35.5 %. The DNA–DNA relatedness (DDH) values between strain ZXX205T and the most closely related species Winogradskyella flava and Winogradskyella echinorum were 21.1 and 20.4 %, respectively. Based on polyphasic taxonomic analysis, strain ZXX205T is considered to represent a novel species in the genus Winogradskyella of the family Flavobacteriaceae , for which the name Winogradskyella ouciana is proposed. The type strain is ZXX205T (=MCCC 1K03851T=JCM 33665T).

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Winogradskyella aurantia sp. nov., isolated from a marine solar saltern

Sun

Chen

2017

Antonie van Leeuwenhoek

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A Gram-stain negative, non-flagellated, facultatively anaerobic, slightly halophilic bacterium, WNB302, was isolated from a marine solar saltern in Wendeng, China (122°0'38.85″E, 36°57'56.49″N). Cells of strain WNB302 were 0.2-0.7 µm wide and 2.0-10.0 µm long, catalase- positive and oxidase-negative. Colonies were opaque, orange and approximately 1.0-2.0 mm in diameter after culture for 96 h on marine agar 2216. Growth occurs at 15-37 °C (optimum, 33-35 °C), pH 6.0-8.5 (optimum, pH 7.0-7.5), and with 0.5-7% NaCl (optimum, 2-3% NaCl). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain WNB302 belongs to the genus Winogradskyella and is closely related to Winogradskyella exilis KCTC 32356. Strain WNB302 exhibited 96.2 and 96.0% 16S rRNA gene sequence similarities with W. exilis KCTC 32356 and W. litoriviva KCTC 23972. Average nucleotide identity (ANI) value based on draft genomes between strain WNB302 and Winogradskyella thalassocola KCTC 12221 showed a relatedness of 81.1% (with 93.7% of 16S rRNA gene sequence similarity). The major respiratory quinone of strain WNB302 was found to be MK-6, and the dominant fatty acids were found to be iso-C and iso-C G. The major polar lipids of strain WNB302 were three unidentified lipids (L1, L2 and L3), one unidentified aminolipids (AL1) and phosphatidylethanolamine (PE). The genomic DNA G+C content was 37.0 mol%. On the basis of the data presented, strain WNB302 is considered to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella aurantia sp. nov. is proposed. The type strain is WNB302 (= KCTC 52614 = MCCC 1H00172).

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Winogradskyella sediminis sp. nov., isolated from marine sediment

Abstract: A Gram-stain-negative, rod-shaped, yellow-pigmented, gliding bacterial strain, designated S5-23-3 T , was isolated from a sediment sample of the Yellow Sea in China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S5-23-3 T was related to the

Cited by 14 publications

References 33 publications

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Winogradskyella ouciana sp. nov., isolated from the hadal seawater of the Mariana Trench

Winogradskyella aurantia sp. nov., isolated from a marine solar saltern

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