Cnuibacter physcomitrellae gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from the moss of Physcomitrella patens

Zhou, Xun; Guan, Guo; Wang, Le Qi; Bai, Su Lan; Li, Yan Hong

doi:10.1099/ijsem.0.000775

Cited by 10 publications

(1 citation statement)

References 28 publications

(14 reference statements)

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“…The description is as before (Zhou et al, 2016 ) with the following modification. The G+C content of the type-strain genome is 70.8%, its approximate size 4.35 Mbp, its GenBank deposit SAMN06622498 .…”

Section: Discussionmentioning

confidence: 99%

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

et al. 2018

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The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

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Section: Discussionmentioning

confidence: 99%

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

et al. 2018

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A gromyces

Evtushenko¹,

Ariskina²,

Prisyazhnaya³

et al. 2017

Bergey's Manual of Systematics of Archaea and Bacteria

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Ag.ro.my'ces. Gr. n. agros field or soil; N.L. masc. n. myces (from Gr. masc. n. mykes ‐etis ) fungus; N.L. masc. n. Agromyces soil fungus. Actinobacteria / Actinobacteria / Micrococcales / Microbacteriaceae / Agromyces Young cultures usually produce thin ( mostly 0.3–0 . 6 μ m in diameter ) branched vegetative hyphae, short branching filaments, and occasionally form irregular rods that subsequently break up into diphtheroid, rod like to coccoid elements . Scant aerial hyphae occur on rare occasions. Nonmotile. Nonsporeforming. Gram‐stain‐positive type of cell wall. Non‐acid fast. Lysozyme sensitive. Colonies are generally yellow or white , circular, 1–2 mm in diameter, opaque, often penetrating into the agar. Chemo‐organotrophs , having a respiratory type of metabolism. Aerobic to microaerophilic . Catalase and oxidase test reactions intensities vary among species. Most strains grow well on standard laboratory media and use a wide range of organic compounds as sole sources of carbon for growth and energy. Some species are nutritionally exacting. Mesophilic; optimal growth at ∼24–30°C; growth range ∼7–40°C, some species show weak growth at 1–5°C. Grow optimally at near neutral or slightly alkaline pH, some can grow at initial pH values up to pH 12. Generally nonhalophilic, some species prefer low salt concentrations. The cell‐wall peptidoglycan is a group B type, based on 2,4‐diaminobutyric acid ( l ‐isomer predominating). Menaquinones are the sole respiratory quinones; the predominant component is typically an unsaturated menaquinone with 12 isoprene units ( MK‐12 ); the next most common components are MK‐11 and MK‐13. Major cellular fatty acids are C 15:0 anteiso, C 17:0 anteiso, and C 16:0 iso Mycolic acids are absent. Principal polar lipids are diphosphatidylglycerol, phosphatidylglycerol, and characteristic glycolipids. The usual natural habitat is soil; occur in other diverse terristrial and aquatic environments and in microbial assemblages associated with plants, animals, and humans. Isolation from unequivocally pathological materials is uncommon; a single case of bacteremia associated with Agromyces mediolanus is reported. DNA G + C content ( mol% ): 65 ( T m )–73 (HPLC). Type species : Agromyces ramosus Gledhill and Casida 1969, 346 AL .

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Molecular Detection of Diverse Leifsonia Strains Associated With Sugarcane

Young

Nock

2017

Plant Disease

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Leifsonia xyli subsp. xyli, causal agent of ratoon stunting disease (RSD) of sugarcane (Saccharum interspecific hybrids), is the most well-known member of the Microbacteriaceae genus Leifsonia. However, the presence of other Leifsonia strains associated with sugarcane has not been reported. A total of 697 Australian and 40 Indonesian sugarcane fields were screened by leaf sheath biopsy (LSB) PCR using primers specific for L. xyli subsp. xyli, in addition to primers designed to amplify DNA from other members of the genus Leifsonia. While L. xyli subsp. xyli was detected in 126 fields, a total of 37 distinct and novel Leifsonia and non-Leifsonia strains were detected in 116 fields. Representatives of these strains were also detected in multiple samples of expressed xylem sap. Sequencing and phylogenetic analyses demonstrated the presence of a broad complex of novel Leifsonia strains, in addition to strains closely related to the recently erected Cnuibacter genus. Attempts to isolate Leifsonia strains were unsuccessful; however, one strain related to Cnuibacter was recovered from expressed xylem sap. Among the genetically diverse lineages discovered, identical genotypes were present in multiple sugarcane varieties growing in disparate regions in different years, strongly suggesting an ongoing association with sugarcane. The epidemiological significance of these strains is unknown, but there is evidence that they can interfere with serological and microscopic RSD diagnostics, and there is the potential that they may represent new and distinct pathologies of sugarcane.

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Cnuibacter physcomitrellae gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from the moss of Physcomitrella patens

Cited by 10 publications

References 28 publications

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

A gromyces

Molecular Detection of Diverse Leifsonia Strains Associated With Sugarcane

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