Psychroserpens damuponensis sp. nov., isolated from seawater

Lee, Dong-Heon; Cho, Sun Ja; Kim, Suk Min; Lee, Sun Bok

doi:10.1099/ijs.0.041632-0

Cited by 16 publications

(16 citation statements)

References 19 publications

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“…S1). This composition was similar to that of type strains of species of the genus Psychroserpens with respect to the presence of phosphatidylethanolamine, unidentified aminolipids, an unidentified phospholipid and unidentified lipids (Bowman et al , 1997; Kwon et al , 2006; Lee et al , 2013). However, the presence of an unidentified aminophospholipid in PAMC 27130 T distinguished it from the reference strains.…”

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confidence: 66%

“…The genus Psychroserpens was first proposed with a description of Psychroserpens burtonensis that was isolated from Burton Lake, Antarctica (Bowman et al , 1997). Two other species, Psychroserpens mesophilus and Psychroserpens damuponensis , were isolated from a young marine biofilm formed on an acrylic surface (Kwon et al , 2006) and from a seawater sample collected from the coast at Damupo beach, Republic of Korea (Lee et al , 2013), respectively. Members of the genus Psychroserpens are characterized as being Gram-staining-negative, yellow to yellowish-orange, oxidase-positive and obligately aerobic with rod-shaped cells and MK-6 as the major respiratory quinone.…”

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confidence: 99%

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Psychroserpens jangbogonensis sp. nov., a psychrophilic bacterium isolated from Antarctic marine sediment

Baek

Lee

Hwang

et al. 2015

International Journal of Systematic and Evolutionary Microbiology

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A Gram-staining-negative, yellow-pigmented, aerobic, rod-shaped and non-motile bacterium, PAMC 27130 T , was isolated from the marine sediment of the Ross Sea, Antarctica. The temperature, pH and NaCl tolerance ranges for growth were 4-20 6C, pH 6.0-9.0 and 0.5-5.0 % (w/v) NaCl, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PAMC 27130 T belonged to the genus Psychroserpens and was closely related to Psychroserpens mesophilus, Psychroserpens damuponensis and Psychroserpens burtonensis with 97.2, 94.7 and 94.2 % sequence similarities, respectively. Genomic relatedness analyses based on average nucleotide identity and genome-to-genome distance showed that strain PAMC 27130 T could be clearly distinguished from other species of the genus Psychroserpens . The genomic DNA G+C content was 32.7 mol%. The major fatty acids (.10 %) were C 20 : 4 v6c (13.2 %), iso-C 15 : 0 (12.3 %), iso-C 15 : 1 G (11.7 %) and iso-C 15 : 0 3-OH (10.0 %). The major respiratory isoprenoid quinone was menaquinone-6 (MK-6) and the polar lipids were phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid, an unidentified aminophospholipid and three unidentified lipids. On the basis of genotypic and phenotypic data collected in this study, it is proposed that strain PAMC 27130 T represents a novel species of the genus Psychroserpens, for which the name Psychroserpens jangbogonensis sp. nov. is proposed. The type strain is PAMC 27130 T (5KCTC 42128 T 5JCM 30228 T ).

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confidence: 66%

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confidence: 99%

Psychroserpens jangbogonensis sp. nov., a psychrophilic bacterium isolated from Antarctic marine sediment

Baek

Lee

Hwang

et al. 2015

International Journal of Systematic and Evolutionary Microbiology

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“…The description is as before (Lee D.-H. et al, 2013) with the following modification. The G+C content of the type-strain genome is 32.5%, its approximate size 3.95 Mbp, its GenBank deposit SAMN02929384.…”

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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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“…S1c). B. paragorgiae KMM 6029 T , Psychroserpens burtonensis ACAM 188 T and F. algae KMM 3553 T contained phosphatidylethanolamine as the major polar lipid (Ivanova et al , 2004; Lee et al , 2013; present study). Menaquinone 6 (MK-6) was the predominant respiratory quinone in strain AK20 T and the reference type strains.…”

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confidence: 49%

Xanthomarina gelatinilytica gen. nov., sp. nov., isolated from seawater

Vaidya

Kumar

Sharma

et al. 2015

International Journal of Systematic and Evolutionary Microbiology

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A novel Gram-stain-negative, rod-shaped, yellow-pigmented, non-sporulating, non-motile bacterium, designated strain AK20 T , was isolated from seawater collected from Kochi city, Kerala state, India. Colonies on marine agar were circular, yellow, shiny, translucent, 2-3 mm in diameter, convex and with entire margin. Flexirubin-type pigment was present. The fatty acids were dominated by iso-branched units with a high abundance of iso-C 15 : 0 , iso-C 15 : 1 G, iso-C 17 : 0 3-OH, summed feature 3 (C 16 : 1 v7c and/or iso-C 15 : 0 2-OH) and iso-C 15 : 0 3-OH. Polar lipids included phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids and four unidentified lipids. Menaquinone 6 (MK-6) was the predominant respiratory quinone. The DNA G+C content of strain AK20T was 38.8 mol%.Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AK20 T was closely related to Formosa spongicola A2 T and Bizionia paragorgiae KMM 6029 T (pair-wise sequence similarities of 95.9 and 95.7 %, respectively), forming a distinct branch within the family Flavobacteriaceae and clustering with the clade comprising species of the genus Bizionia. Based on phenotypic and chemotaxonomic characteristics and phylogenetic analysis, strain AK20 T is different from the existing genera in the family Flavobacteriaceae, and is therefore considered to represent a novel species of a new genus, for which the name Xanthomarina gelatinilytica gen. nov., sp. nov. is proposed. The type strain of Xanthomarina gelatinilytica is AK20 T (5MTCC 11705 T 5JCM 18821 T ).

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Psychroserpens damuponensis sp. nov., isolated from seawater

Cited by 16 publications

References 19 publications

Psychroserpens jangbogonensis sp. nov., a psychrophilic bacterium isolated from Antarctic marine sediment

Psychroserpens jangbogonensis sp. nov., a psychrophilic bacterium isolated from Antarctic marine sediment

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

Xanthomarina gelatinilytica gen. nov., sp. nov., isolated from seawater

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