Evolution of Protein Molecules

Manual for the Identification of Medical Bacteria.

The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.

List of new names and new combinations previously effectively, but not validly, published.

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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Genome-Based Taxonomic Classification of the Phylum Actinobacteria

DNA base composition was determined by reversed-phase high-performance liquid chromatography (HPLC). DNA was hydrolysed into nucleosides with nuclease P1 and bacterial alkaline phosphatase. The mixture of nucleosides was applied to HPLC without any further purification. One determination by chromatography needed 2 μg of hydrolysed nucleosides and took only 8 min. The relative standard error of nucleoside analysis was less than 1%. The system described here gives a direct and precise method for determining DNA base composition.

Research letterDetermination of DNA base composition by reversed-phase high-performance liquid chromatography

A novel Gram-stain-negative, non-gliding, facultatively anaerobic and rod-shaped bacterium, designated X7T, was isolated from marine sediment taken from the coast of Weihai, China. Strain X7T grew optimally at 28–30 °C, at pH 7.0 and in the presence of 2–3 % (w/v) NaCl. Based on the 16S rRNA gene sequence analysis, strain X7T was a member of the genus 
Salinimicrobium
and was most closely related to the species 
Salinimicrobium gaetbulicola
with a 96.3 % 16S rRNA gene sequence similarity value. The major cellular fatty acids of strain X7T were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 1ω9c, iso-C17 : 1ω9c, C17 : 0 2-OH and iso-C17 : 0 3-OH. The major polar lipids of strain X7T were phosphatidylethanolamine, one unidentified phospholipid, two unidentified aminolipids and five unidentified lipids. The predominant respiratory quinone was MK-6, and the genomic DNA G+C content was 46.7 mol%. Phylogenetic, phenotypic, chemotaxonomic and genotypic results indicated that strain X7T represents a novel species of the genus 
Salinimicrobium
, for which the name Salinimicrobium flavum sp. nov. is proposed. The type strain is X7T (=KCTC 42585T=MCCC 1H00115T).

Salinimicrobium flavum sp. nov., isolated from coastal sediment.

A novel bacterial strain, JDX94T, was isolated from tundra soil sampled north of the Yellow River station, Arctic. Cells were Gram-stain-negative, non-spore-forming, short rod-shaped and aerobic. The strain displayed growth at 4–37 °C with an optimum at 28 °C, with 0–1.0 % (w/v) NaCl (optimum, 0%) and at pH 6.0–9.0 (optimum, pH 7.0–7.5). Cells contained summed feature 3 (comprising C16 : 1
ω7c and/or C16 : 1
ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH as its major cellular fatty acids and menaquinone-7 as the only respiratory quinone. The polar lipid profile of strain JDX94T consisted of phosphatidylethanolamine, two unidentified aminolipids and four unknown polar lipids. The DNA G+C content was 37.5 mol%. On the basis 16S rRNA gene sequence comparison, strain JDX94T showed the highest sequence similarity (96.7 %) to Pedobacteragri JCM 15120T, followed by 
Pedobacteralluvionis
DSM 19624T (96.3 %). Furthermore, the average nucleotide identity and digital DNA–DNA hybridization values between strain JDX94T and related species of the genus 
Pedobacter
were 74.6–79.2 % and 18.9–24.5 %, respectively. Based on the presented results, we propose a novel species for which the name 
Pedobacter
chinensis sp. nov. is suggested, with the type strain JDX94T (=MCCC 1H00335T= KCTC 62850T).

Pedobacter chinensis sp. nov., a cellulose-decomposing bacterium from Arctic tundra soil.

A Gram-stain-negative, non-spore-forming, non-motile, short-rod-shaped and aerobic bacterial strain (designated lm1T) was isolated from propylene oxide saponification wastewater activated sludge obtained from a wastewater treatment facility in Binzhou (Shandong province, PR China). Strain lm1T grew between 15 and 45 °C (optimum, 40 °C). The pH range for growth was at pH 4.0–10.0 (optimum growth at pH 8.0). The range of NaCl concentration for the growth of strain lm1T was 0–4.0 % (w/v), with optimum growth at 1.0–2.0 % (w/v). Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain lm1T belonged to the genus Rhodoligotrophos and was closely related to Rhodoligotrophos appendicifer JCM 16873T (96.7 % 16S rRNA gene sequence similarity) and Rhodoligotrophos jinshengii CCTCC AB2013083T (96.2 %). The average nucleotide identity value and the digital DNA–DNA hybridization value between strain lm1T and R. appendicifer JCM 16873T were 73.4 and 14.3 %, respectively. The major cellular fatty acids of strain lm1T were C19 : 0cyclo ω8c, C18 : 1ω7c and C16 : 0. Strain lm1T contained Q-10 as the predominant respiratory quinone. The polar lipid profile was composed of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, three unidentified aminolipids, one unidentified glycolipid and five unknown lipids. The G+C content of the genomic DNA was 64.4 mol%. Based on polyphasic taxonomic data, strain lm1T could be classified as a representative of a novel species of the genus Rhodoligotrophos , for which the name Rhodoligotrophos defluvii sp. nov. is proposed. The type strain is lm1T (=CCTCC AB2019071T=KCTC 72156T).

Rhodoligotrophos defluvii sp. nov., isolated from activated sludge

A novel Gram-stain-negative, non-spore-forming, non-motile, facultatively anaerobic, rod-shaped strain, designated XDB06T, was isolated from coastal sediment of Xiaoshi Island, Weihai, China. Optimal growth occurred at 37 °C, pH 7.5 and with 4.0 % (w/v) NaCl. Q-8 was the sole respiratory quinone. The major cellular fatty acids in strain XDB06T were iso-C15 : 0 and iso-C16 : 0. The polar lipids of strain XDB06T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified glycolipids and four unidentified phospholipids. The genomic DNA G+C content of the strain was 65.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain XDB06T clusters within the genus Wenzhouxiangella and is most closely related to Wenzhouxiangella. marina MCCC 1K00261T, with a 16S rRNA gene sequence similarity of 96.50 %. Based on data from the current polyphasic study, strain XDB06T represents a novel species of the genus Wenzhouxiangella, for which the name Wenzhouxiangella sediminis sp. nov. is proposed. The type strain is XDB06T (=KCTC 52041T=MCCC 1K02285T).

Wenzhouxiangella sediminis sp. nov., isolated from coastal sediment.

A novel Gram-stain-negative, aerobic, rod-shaped, non-flagellated and agar-digesting marine bacterium, designated as HZ1T, was isolated from the marine alga Porphyra yezoensis Ueda (AST58-103) collected from the coastal area of Weihai, PR China. Phylogenetic analysis based on 16S rRNA gene sequences placed HZ1T in the genus 
Tenacibaculum
, and it formed a distinct clade in the phylogenetic tree with the type strains of 
Tenacibaculum amylolyticum
and 
Tenacibaculum skagerrakense
, with 97.0 % and 96.7 % 16S rRNA gene sequence similarities, respectively. The DNA G+C content of the isolate was 31.8 mol%. HZ1T contained MK-6 as the predominant menaquinone and iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH and iso-C15 : 1G as the major fatty acids. The major polar lipids were phosphatidylethanolamine, four unidentified lipids and five unidentified aminolipids. On the basis of the results of the phylogenetic analysis and phenotypic properties, it is concluded that HZ1T represents a novel species of the genus 
Tenacibaculum
, for which the name 
Tenacibaculum
agarivorans sp. nov. is proposed. The type strain is HZ1T (=MCCC 1H00174T=KCTC 52476T).

Zong-Jun Du

Papers

Salinimicrobium flavum sp. nov., isolated from coastal sediment.

Pedobacter chinensis sp. nov., a cellulose-decomposing bacterium from Arctic tundra soil.

Rhodoligotrophos defluvii sp. nov., isolated from activated sludge

Wenzhouxiangella sediminis sp. nov., isolated from coastal sediment.

Tenacibaculum agarivorans sp. nov., an agar-degrading bacterium isolated from marine alga Porphyra yezoensis Ueda.