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.

/pdf/genome-based-taxonomic-classification-of-the-phylum-4uc1zrzg88.pdf

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 Gram-stain-negative, rod-shaped bacterium (designated strain M1309T), with slow gliding motility, was isolated from marine sediment obtained off the coast of Weihai, PR China. The growth of M1309T was observed at 16–42 °C (optimum, 37 °C) and pH 6.5–8.0 (optimum, 7.0–7.5) in the presence of 2.0–6.0 % (w/v) NaCl (optimum, 2.0–3.0 %). Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the strain represented a member of the genus 
Winogradskyella
. M1309T exhibited the highest 16S rRNA gene sequence similarity, of 95.5 %, to Winogradskyella poriferorum JCM 12885T. Chemotaxonomic analysis revealed that the sole respiratory quinone was menaquinone 6 (MK-6) and the major fatty acids included iso-C15 : 0, iso-C15 : 1G and iso-C17 : 0 3-OH. The major polar lipids included phosphatidylethanolamine, two aminolipids, and three unidentified lipids. The DNA G+C content of the strain was 36.1 mol%. On the basis of phenotypic distinctiveness and phylogenetic divergence, strain M1309T is considered to represent a novel species of the genus 
Winogradskyella
, for which the name Winogradskyella tangerina sp. nov. is proposed. The type strain is M1309T (=KCTC 52896T=MCCC 1K03310T).

Winogradskyella tangerina sp. nov., a member of the Flavobacteriaceae isolated from coastal sediment.

A Gram-stain-negative, aerobic, rod-shaped, non-gliding and non-motile bacterium designated as N1E253T, was isolated from marine sediments collected from the coast of Weihai, PR China. N1E253T was found to grow at pH 7.0–9.0 (optimum, pH 7.5), 15–37 °C (optimum, 30 °C) in the presence of 1.5–5.0% (w/v) NaCl (optimum, 3.0%). The major polar lipids of strain N1E253T were phosphatidylethanolamine, diphosphatidylglycerol and one unidentified phospholipid. The sole respiratory quinone was MK-9. The major cellular fatty acids (> 10.0%) were iso-C14: 0, C16: 0 and Summed Feature 3 (C16:1 ω7c and/or C16:1 ω6c). The result of the 16S rRNA gene sequence analysis confirmed the affiliation of this novel isolate to the family Verrucomicrobiaceae, with Persicirhabdus sediminis KCTC 22039 T being its closest relative with 92.1% sequence similarity. Genome sequencing revealed a genome size of 5,073,947 bp, DNA G + C content of 52.0% and two protein-coding genes related to the resistance of fluoroquinolones. Based on physiological, genomic, biochemical and chemotaxonomic characteristics, we propose that strain N1E253T represents a novel species of a novel genus within the family Verrucomicrobiaceae, for which the name Oceaniferula marina gen. nov., sp. nov. is proposed. The type strain is N1E253T (= KCTC 72800 T = MCCC 1H00405T).

Oceaniferula marina gen.nov., sp.nov., an anti-fluoroquinolone bacterium isolated from marine sediment

A Gram-stain-negative, strictly aerobic, oxidase- and catalase-positive, non-gliding, motile with a single polar flagellum, and short rod-shaped bacterial strain, designated XYN52T, was isolated from a freshwater lake in the west of China. Phylogenetic analysis of the 16S rRNA gene determined that strain XYN52T was a member of the genus 
Pelagibacterium
within the family 
Hyphomicrobiaceae
. Strain XYN52T was able to grow at 4–37 °C (optimum, 30 °C), pH 6.0–9.0 (pH 7.5) and in the presence of up to 7.0 % w/v NaCl (0.5 %).The major quinone was ubiquinone 10. The major cellular fatty acids were C18 : 1ω6c/C18 : 1ω7c, C19 : 0ω8c cyclo and 11-methyl C18 : 1ω7c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and three kinds of glycolipids. The genomic DNA G+C content was 64.5 mol%. On the basis of these data, strain XYN52T represents a novel species in the genus 
Pelagibacterium
, for which the name Pelagibacterium lacus sp. nov. is proposed. The type strain is XYN52T (=KCTC 62845T=MCCC 1H00348T).

Pelagibacterium lacus sp. nov., isolated from lake water.

A Gram-stain-negative, aerobic, yellow, non-motile, rod-shaped and alginate-degrading bacterium, designated Dm15T, was isolated from marine alga collected in Weihai, PR China Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Dm15T represents a distinct line of the family Flavobacteriaceae Strain Dm15T had the highest 16S rRNA gene sequence similarity to its closest phylogenetic neighbour Arcticiflavibacter luteus (967 %) and 937-964 % sequence similarity to other phylogenetic neighbours (Bizionia paragorgiae, Winogradskyella thalassocola, Ichthyenterobacterium magnum, Psychroserpens burtonensis and Arcticiflavibacter luteus) in the family Flavobacteriaceae The novel isolate was able to grow at 10-40 °C (optimum, 30-33 °C), pH 70-90 (optimum, pH 70-75) and with 05-60 % NaCl (optimum 20-30 %, w/v) It could grow at 40 °C, and degrade alginate and cellulose, which were different from the neighbour genera The draft genome consisted of 3395 genes with a total length of 3 798 431 bp and 341mol% G+C content Especially, there were some specific genes coding for cellulase and alginate lyase, which provided a basis for the above phenotypic characteristics The strain's genome sequence showed 711-802 % average amino acid identity values and 718-777 % average nucleotide identity values compared to the type strains of related genera within the family Flavobacteriaceae It shared digital DNA-DNA hybridization identity of 198 and 209 % with I magnum and A luteus, respectively The sole menaquinone was MK-6 The major fatty acids were iso-C15 : 0 and iso-C15 : 1 G The polar lipids included six unidentified polar lipids, four unidentified aminolipids and phosphatidylethanolamine Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain Dm15T represents a novel species of a new genus in the family Flavobacteriaceae, phylum Bacteroidetes, for which the name Flavihalobacter algicola gen nov, sp nov is proposed The type strain is Dm15T (KCTC 42256T=CICC 23815T)

Flavihalobacter algicola gen. nov. sp. nov., a member of the family Flavobacteriaceae with alginate-degradation activity, isolated from marine alga Saccharina japonica.

A Gram-stain-negative, rod-shaped bacterium (designated strain N24T) with gliding motility was isolated from thermal spring water sampled at Xi’an, PR China. Cells were 0.4–0.8 µm wide and 1.8–7.8 µm long. Optimal growth occurred at 33 °C and pH 7.0 on Reasoner's 2A (R2A) agar. Strain N24T could produce exopolysaccharide on R2A agar at 33 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain N24T formed a distinct phyletic lineage within the family 
Chitinophagaceae
and was most closely related to members of the genera 
Flavisolibacter
, 
Cnuella
, 
Niveitalea
, 
Flavitalea
, 
Flaviaesturariibacter
and 
Niastella
with 91.7–93.9 % 16S rRNA gene sequence similarities. The major fatty acids of strain N24T were iso-C15 : 0 (31.8 %), iso-C17 : 0 3-OH (16.1 %) and iso-C15 : 1 G (12.9 %). The polar lipid profile consisted of phosphatidylethanolamine, two aminolipids and six unknown lipids; the quinone system consisted of menaquinone-7 (MK-7). The genomic G+C content was 49.3 mol%. On the basis of the evidence presented in this study, strain N24T represents a novel species of a new genus in the family 
Chitinophagaceae
, for which the name Paracnuella aquatica gen. nov., sp. nov. is proposed. The type species is N24T (=KCTC 62083T=MCCC 1H00301T).

Zong-Jun Du

Papers

Winogradskyella tangerina sp. nov., a member of the Flavobacteriaceae isolated from coastal sediment.

Oceaniferula marina gen.nov., sp.nov., an anti-fluoroquinolone bacterium isolated from marine sediment

Pelagibacterium lacus sp. nov., isolated from lake water.

Flavihalobacter algicola gen. nov. sp. nov., a member of the family Flavobacteriaceae with alginate-degradation activity, isolated from marine alga Saccharina japonica.

Paracnuella aquatica gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a hot spring