Whole genome analysis calls for a taxonomic rearrangement of the genus Colwellia

Liu, Ang; Zhang, Yan-Jiao; Peng, Cheng; Peng, Yajie; Blom, Jochen; Xue, Qing-Jie

doi:10.1007/s10482-020-01405-6

Cited by 47 publications

(19 citation statements)

References 40 publications

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“…Although a proposed genus boundary of the POCP value for prokaryotic lineages was assigned as 50%, many studies later showed exceptions at the inter-genera comparison. The universal cut-off of 50% is considered conservative, as being only an index of relatedness (Liu et al, 2020) as reflected in its ineffectiveness in delineating different genera of the family Methylococcaceae (Orata et al, 2018), Bacillaceae (Aliyu et al, 2016), Burkholderiaceae (Lopes-Santos et al, 2017), and Rhodobacteraceae (Wirth and Whitman, 2018). Luo et al (2014) have shown that AAI values of related but different genera ranged from 60 to 80%.…”

Section: Coccoidmentioning

confidence: 99%

Phylotaxogenomics for the Reappraisal of the Genus Roseomonas With the Creation of Six New Genera

et al. 2021

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The genus Roseomonas is a significant group of bacteria which is invariably of great clinical and ecological importance. Previous studies have shown that the genus Roseomonas is polyphyletic in nature. Our present study focused on generating a lucid understanding of the phylogenetic framework for the re-evaluation and reclassification of the genus Roseomonas. Phylogenetic studies based on the 16S rRNA gene and 92 concatenated genes suggested that the genus is heterogeneous, forming seven major groups. Existing Roseomonas species were subjected to an array of genomic, phenotypic, and chemotaxonomic analyses in order to resolve the heterogeneity. Genomic similarity indices (dDDH and ANI) indicated that the members were well-defined at the species level. The Percentage of Conserved Proteins (POCP) and the average Amino Acid Identity (AAI) values between the groups of the genus Roseomonas and other interspersing members of the family Acetobacteraceae were below 65 and 70%, respectively. The pan-genome evaluation depicted that the pan-genome was an open type and the members shared 958 core genes. This claim of reclassification was equally supported by the phenotypic and chemotaxonomic differences between the groups. Thus, in this study, we propose to re-evaluate and reclassify the genus Roseomonas and propose six novel genera as Pararoseomonas gen. nov., Falsiroseomonas gen. nov., Paeniroseomonas gen. nov., Plastoroseomonas gen. nov., Neoroseomonas gen. nov., and Pseudoroseomonas gen. nov.

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Section: Coccoidmentioning

confidence: 99%

Phylotaxogenomics for the Reappraisal of the Genus Roseomonas With the Creation of Six New Genera

et al. 2021

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“…Furthermore, Mason et al (2014) suggested that the high abundance of Colwellia in the sediments below the oil plume was due to its transport by MOS. Many species of Colwellia are psychrophilic and/or piezophilic (Bowman, 2014;Liu et al, 2020), and one strain, RC25 was able to degrade 75% of MC-252 oil at 5 • C (Baelum et al, 2012). While some of this loss can be attributed to evaporation, Colwellia species are probably important hydrocarbon degraders in deep-sea MOS (e.g., MC-252 at 4 to 6 • C and 15 MPa).…”

Section: Colwelliaceaementioning

confidence: 99%

“…While some of this loss can be attributed to evaporation, Colwellia species are probably important hydrocarbon degraders in deep-sea MOS (e.g., MC-252 at 4 to 6 • C and 15 MPa). As an aside, phylogenetic analysis of strain RC25 (Supplementary Figure 1) reveals that it clusters within Colwelliaceae Clade 1, which according to Liu et al (2020) should be renamed as Cognaticolwellia.…”

Section: Colwelliaceaementioning

confidence: 99%

Marine Oil Snow, a Microbial Perspective

Gregson

McKew

Holland³

et al. 2021

Front. Mar. Sci.

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Under certain conditions, dispersed crude oil in the sea combines with organisms, organic matter, and minerals to form marine oil snow (MOS), thereby contributing to the sinking of oil to the seafloor. Marine microbes are the main players in MOS formation, particularly via the production of extracellular polymeric substances. Distinct groups of microbes also consume the majority of the hydrocarbons during descent, leading to enrichment of the less bioavailable hydrocarbons and asphaltenes in the residue. Here we discuss the dynamics of microbial communities in MOS together with their impacts on MOS evolution. We explore the effects of dispersant application on MOS formation, and consider ways in which laboratory experiments investigating MOS formation can be more representative of the situation in the marine environment, which in turn will improve our understanding of the contribution of MOS to the fate of spilled oil.

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“…AAI is considered as a powerful tool to delimit taxonomic ranks at the genus level, in particular the Roseobacter group [41, 42]. AAI cutoff values for delineating genera are within the range of 60–80% [43].…”

Section: Whole-genome Sequencing Analysismentioning

confidence: 99%

Cochlodiniinecator piscidefendens gen. nov., sp. nov., an algicidal bacterium against the ichthyotoxic dinoflagellate Cochlodinium polykrikoides

Lee

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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Harmful algal blooms caused by Cochlodinium polykrikoides result in enormous economic damage to the aquaculture industry. Biological control methods have attracted wide attention due to their environmental-friendliness. In this study, a novel algicidal bacterium, designated strain M26A2MT, was determined for its taxonomic position and was evaluated for its potential to mitigate C. polykrikoides blooms. Strain M26A2MT exhibited the highest 16S rRNA gene sequence similarity to the type strains of Planktotalea lamellibrachiae (97.3%), Halocynthiibacter namhaensis (97.2%), Pseudohalocynthiibacter aestuariivivens (96.8%) and Halocynthiibacter arcticus (96.4%) in the family Rhodobacteraceae . The predominant fatty acids were C10 : 0 3-OH and summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c). The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and three unidentified lipids. Q-10 was the respiratory quinone. Strain M26A2MT exerted significant algicidal activity against C. polykrikoides cells by destroying the membrane integrity and the photosynthetic system. Our findings suggest that strain M26A2MT shows a high potential to control outbreaks of C. polykrikoides. Based on the polyphasic characterization, strain M26A2MT is considered to represent a novel species within a novel genus of the family Rhodobacteraceae , for which the name Cochlodiniinecator piscidefendens gen. nov., sp. nov. is proposed. The type strain is M26A2MT (=KCTC 82083T=JCM 34119T).

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Whole genome analysis calls for a taxonomic rearrangement of the genus Colwellia

Cited by 47 publications

References 40 publications

Phylotaxogenomics for the Reappraisal of the Genus Roseomonas With the Creation of Six New Genera

Phylotaxogenomics for the Reappraisal of the Genus Roseomonas With the Creation of Six New Genera

Marine Oil Snow, a Microbial Perspective

Cochlodiniinecator piscidefendens gen. nov., sp. nov., an algicidal bacterium against the ichthyotoxic dinoflagellate Cochlodinium polykrikoides

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