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 novel Gram-stain-positive, motile and facultatively anaerobic strain, designated NC2-31T, was isolated from sediment from the coast of Weihai, PR China. Optimal growth occurred at 37 °C, pH 7.5 and with 2.0–3.0 % (w/v) NaCl. MK-7 was the major respiratory quinone. Meso-diaminopimelic acid was a diagnostic diamino acid in the peptidoglycan. The major polar lipids of NC2-31T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). The genomic DNA G+C content of the strain was 46.3 mol%. The predominant cellular fatty acids (>10.0 %) of NC2-31T were iso-C15 : 0 (18.9 %), anteiso-C15 : 0 (15.8 %), summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) (15.3 %) and iso-C16 : 0 (10.3 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that NC2-31T should be classified as representing a member of the genus 
Bacillus
. Based on data from the current polyphasic study, NC2-31T represents a novel species within the genus 
Bacillus
, for which the name 
Bacillus
marinisedimentorum sp. nov. is proposed with type strain NC2-31T (=KCTC 33721T=MCCC 1K01239T).

Bacillus marinisedimentorum sp. nov., isolated from marine sediment.

Pseudohalioglobus sediminis sp. nov., isolated from coastal sediment

A novel strain, U0105T, was isolated from marine sediment of the coast of Weihai, China. The bacterium was aerobic, Gram-stain-negative, oxidase-positive, catalase-positive, rod-shaped and motile. Growth was observed at salinities of 1.0–6.0 % (w/v) NaCl (optimum with 2.0–3.0 %), temperatures of 20–40 °C (optimum at 37 °C) and pH of 6.5–9.5 (optimum at pH 7.0–7.5). The isolate could not reduce nitrate to nitrite. It could hydrolyse starch and Tweens 20, 40 and 60, but not casein or cellulose. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain U0105T belonged to the genus 
Alteromonas
, with highest sequence similarity to 
Alteromonas aestuariivivens
KCTC 52655T (97.1 %). The average nucleotide identity value and the digital DNA–DNA hybridization value between strain U0105T and 
A. aestuariivivens
KCTC 52655T were 69.2 % and 21.2 %, respectively. Strain U0105T was found to contain Q-8 as the sole menaquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the major fatty acids. The major polar lipids were identified as phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the chromosomal DNA was 45.3 mol%. The combined genotypic and phenotypic data show that strain U0105T represents a novel species of the genus 
Alteromonas
, for which the name 
Alteromonas
sediminis sp. nov. is proposed. The type strain is U0105T (=KCTC 62080T=MCCC 1H00299T).

Alteromonas sediminis sp. nov., isolated from sediment in a sea cucumber culture pond.

Bradyrhizobium aeschynomenes sp. nov., a root and stem nodule microsymbiont of Aeschynomene indica.

A Gram-stain-negative, facultative anaerobic, motile, slightly bent rod-shaped bacterium, designated strain E4404T, was isolated from coastal sediment sampled Weihai, China. According to phylogenetic analysis based on its 16S rRNA gene sequence, strain E4404T shared the highest similarity with the type strain of 
Vibrio
variabilis
(97.0 %), followed by the type strains of 
Vibrio
maritimus
(96.1 %) and 
Vibrio
europaeus
(96.0 %). Multilocus sequence analysis based on the 16S rRNA gene and eight housekeeping genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA and topA) showed that strain E4404T formed a unique clade in the genus 
Vibrio
. The average nucleotide identity and digital DNA–DNA hybridization values between strain E4404T and some other species in the genus 
Vibrio
were 71.0–72.7 % and 20.4–22.4 %, respectively. Cells grew at 15–37 °C and pH 6.0–8.5 in the presence of 1.0–6.0 % (w/v) NaCl, with optimal growth at 33 °C and pH 7.0–7.5 in the presence of 3.0–3.5 % (w/v) NaCl. No growth was observed on thiosulfate citrate bile salts sucrose medium. The major fatty acids of strain E4404T were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The genomic DNA G+C content of strain E4404T was 46.1 mol%. Based on the phylogenetic, genotypic, phenotypic, biochemical and chemotaxonomic characteristics, strain E4404T represented a novel species of the genus 
Vibrio
, for which the name 
Vibrio
albus sp. nov. is proposed. The type strain is E4404T (=MCCC 1H00197T=KCTC 52890T).

Zong-Jun Du

Papers

Bacillus marinisedimentorum sp. nov., isolated from marine sediment.

Pseudohalioglobus sediminis sp. nov., isolated from coastal sediment

Alteromonas sediminis sp. nov., isolated from sediment in a sea cucumber culture pond.

Bradyrhizobium aeschynomenes sp. nov., a root and stem nodule microsymbiont of Aeschynomene indica.

Vibrio albus sp. nov., isolated from marine sediment.