Erythrobacter pelagi sp. nov., a member of the family 
               
                  Erythrobacteraceae
               
             isolated from the Red Sea

Wu, Huixian; Lai, Pok Yui; Lee, On On; Zhou, Xiaojian; Miao, Li; Wang, Hao; Qian, Pei‐Yuan

doi:10.1099/ijs.0.029561-0

“…In addition to the 47 Erythrobacteraceae type strains for which genome sequences were available, 27 type strains were obtained from culture collections including the China General Microbiological Culture Collection (CGMCC), the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ), the Japan Collection of Microorganisms (JCM), the Korean Collection for Type Cultures (KCTC), the Korea Environmental Microorganism Bank (KEMB), the Collection of the Laboratorium voor Microbiologie en Microbiele Genetica (LMG) and the Marine Culture Collection of China (MCCC) or received as gifts from other scholars ( and Acknowledgements). These type strains were cultivated under appropriate conditions proposed previously [3, 12, 14, 20, 28, 31–33, 36, 44, 62–77] for subsequent genomic sequencing.…”

Section: Methodsmentioning

confidence: 99%

Genomic-based taxonomic classification of the family Erythrobacteraceae

Xu

¹

,

Sun

²

,

Chen

³

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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The family Erythrobacteraceae , belonging to the order Sphingomonadales , class Alphaproteobacteria , is globally distributed in various environments. Currently, this family consist of seven genera: Altererythrobacter , Croceibacterium , Croceicoccus , Erythrobacter , Erythromicrobium , Porphyrobacter and Qipengyuania . As more species are identified, the taxonomic status of the family Erythrobacteraceae should be revised at the genomic level because of its polyphyletic nature evident from 16S rRNA gene sequence analysis. Phylogenomic reconstruction based on 288 single-copy orthologous clusters led to the identification of three separate clades. Pairwise comparisons of average nucleotide identity, average amino acid identity (AAI), percentage of conserved protein and evolutionary distance indicated that AAI and evolutionary distance had the highest correlation. Thresholds for genera boundaries were proposed as 70 % and 0.4 for AAI and evolutionary distance, respectively. Based on the phylo-genomic and genomic similarity analysis, the three clades were classified into 16 genera, including 11 novel ones, for which the names Alteraurantiacibacter, Altericroceibacterium, Alteriqipengyuania, Alteripontixanthobacter, Aurantiacibacter, Paraurantiacibacter, Parerythrobacter, Parapontixanthobacter, Pelagerythrobacter, Tsuneonella and Pontixanthobacter are proposed. We reclassified all species of Erythromicrobium and Porphyrobacter as species of Erythrobacter . This study is the first genomic-based study of the family Erythrobacteraceae , and will contribute to further insights into the evolution of this family.

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“…These strains were most closely related to Erythrobacter citreus from the western Mediterranean Sea, 24 E. flavus from the East Sea in Korea 25 and E. pelagi from the Red Sea. 26 The second most common group of strains was identical to the genus Alteromonas. In total, 29 of such strains were obtained from 9 water samples.…”

Section: Discussionmentioning

confidence: 99%

Diversity of culturable bacteria in deep-sea water from the South Atlantic Ocean

Wang

¹

,

Yan

²

,

Ma

³

et al. 2017

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The variability of culturable bacterial diversity and distribution was studied by phylogenetic analysis of 16S rRNA sequences. Seventeen water samples were examined and were collected, from different depths in the range of 5 m to 2700 m at 3 sampling sites (CTD06, CTD10 and CTD11) in the South Atlantic Ocean. Phylogenetic analysis of 16S rRNA gene sequences revealed a significant diversity of culturable bacteria. A total of 247 strains clustered into 8 classes: g-Proteobacteria, a-Proteobacteria, Actinobacteria, Actinomycetales, Bacilli, Flavobacteria, Opitutae and Sphingobacteria. The 17 water samples were dominated by populations of strains belonging to the genus Erythrobacter (16.60%). Of the 247 strains, 10 were potential new species and might form a minor population in the deep sea. To our knowledge, this is the first report to analyze the diversity of culturable bacteria in the South Atlantic Ocean from different depths across the water column.

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“…Members of this genus are Gram-stain-negative, orange- or pink-pigmented bacteria. At the time of writing, the genus Erythrobacter comprises 17 species: Erythrobacter longus (Shiba & Simidu, 1982), E. litoralis (Yurkov et al , 1994), E. citreus (Denner et al , 2002), E. flavus (Yoon et al , 2003), E. aquimaris (Yoon et al , 2004), E. gaetbuli (Yoon et al , 2005), E. seohaensis (Yoon et al , 2005), E. vulgaris (Ivanova et al , 2005), E. gangjinensis (Lee et al , 2010), E. nanhaisediminis (Xu et al , 2010), E. marinus (Jung et al , 2012), E. pelagi (Wu et al , 2012), ‘ E. westpacificensis ’ (Wei et al , 2013; name not validly published), E. jejuensis (Yoon et al , 2013), E. odishensis (Subhash et al , 2013), E. lutimaris (Jung et al , 2014) and the recently described ‘ E. luteus ’ (Lei et al , 2015). In the present study, the aim was to determine the exact taxonomic position of strain s21-N3 T using a polyphasic approach.…”

mentioning

confidence: 99%

Erythrobacter atlanticus sp. nov., a bacterium from ocean sediment able to degrade polycyclic aromatic hydrocarbons

Zhuang

¹

,

Liu

²

,

Wang

³

et al. 2015

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-negative, motile, rod-shaped, orange-pigmented bacterium able to degrade polycyclic aromatic hydrocarbons was isolated from deep-sea sediment of the Atlantic Ocean and subjected to a polyphasic taxonomic study. The strain, designated s21-N3 T , could grow at 4-37 8C (optimum 28 8C), at pH 5-10 (optimum pH 7-8) and with 1-7 % (w/v) NaCl (optimum 2-3 %). Strain s21-N3 T was positive for nitrate reduction, denitrification, aesculin hydrolysis, oxidase and catalase, but negative for indole production and urease. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain s21-N3 T formed a distinct branch within the genus Erythrobacter, sharing high similarities with three closely related strains, Erythrobacter marinus HWDM-33 T (98.67 %), 'Erythrobacter luteus' KA37 (97.80 %) and Erythrobacter gangjinensis K7-2 T (97.59 %). The similarities between strain s21-N3 T and other type strains of recognized species within the genus Erythrobacter ranged from 95.00 to 96.47 %. The digital DNA-DNA hybridization values and average nucleotide identity (ANI) values between strain s21-N3 T and the three closely related strains Erythrobacter marinus HWDM-33 T , 'Erythrobacter luteus' KA37 and Erythrobacter gangjinensis K7-2 T were 18.60, 18.00 and 18.50 % and 74.24, 72.49 and 72.54 %, respectively. The principal fatty acids were summed feature 8 (C 18 : 1 v7c/v6c) and summed feature 3 (C 16 : 1 v7c/v6c). The respiratory lipoquinone was identified as Q-10. The major polar lipids comprised sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and diphosphatidylglycerol. The G+C content of the chromosomal DNA was determined to be 58.18 mol%. The combined genotypic and phenotypic distinctiveness demonstrated that strain s21-N3 T represents a novel species of the genus Erythrobacter, for which the name Erythrobacter atlanticus sp. nov. is proposed, with the type strain s21-N3 T (5MCCC 1A00519 T 5KCTC 42697 T ).Erythrobacter, the type genus of the family Erythrobacteraceae, was originally proposed by Shiba & Simidu (1982).Members of this genus are Gram-stain-negative, orange-or pink-pigmented bacteria. At the time of writing, the genus Erythrobacter comprises 17 species: Erythrobacter longus (Shiba & Simidu, 1982), E. litoralis (Yurkov et al., 1994) (Lei et al., 2015). In the present study, the aim 3These authors contributed equally to the paper.Abbreviations: ANI, average nucleotide identity; dDDH, digital DNA-DNA hybridization; PAH, polycyclic aromatic hydrocarbon.The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene and complete genome sequences of Erythrobacter atlanticus s21-N3 T are KP994305 and CP011310, respectively. Accession numbers for the draft genome sequences of E. marinus HWDM-33 T , 'E. luteus' KA37 and E. gangjinensis K7-2 T are LBHU00000000, LBHB00000000 and LBHC00000000, respectively. was to determine the exact taxonomic position of strain s21-N3 T using a polyphasic approach.During an investigation of the polycyclic-aromatic-hydrocarbon-degrading bac...

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Erythrobacter pelagi sp. nov., a member of the family Erythrobacteraceae isolated from the Red Sea

Cited by 28 publications

References 32 publications

Genomic-based taxonomic classification of the family Erythrobacteraceae

Genomic-based taxonomic classification of the family Erythrobacteraceae

Diversity of culturable bacteria in deep-sea water from the South Atlantic Ocean

Erythrobacter atlanticus sp. nov., a bacterium from ocean sediment able to degrade polycyclic aromatic hydrocarbons

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