Aquimixticola soesokkakensis gen. nov., sp. nov., a novel lipolytic alphaproteobacterium isolated from the junction between the ocean and a freshwater spring, and reclassification of Roseovarius marinus as Pacificibacter marinus comb. nov. and emended description of the genus Pacificibacter

Abyssibius alkaniclasticus gen. nov., sp. nov., a novel member of the family Rhodobacteraceae, isolated from the Mariana Trench

A Gram-stain-negative bacterium with rod-shaped or irregular cells approximately 0.5-0.9×2.0-3.8 µm in size, designated as 960558^T, was isolated from sediment sampled in the Mariana Trench. Strain 960558^T grows at 4-37 °C (optimum, 28 °C), pH 6-7 (optimum, pH 7) and in the presence of 1-5 % (w/v) NaCl (optimum, 3 %). Strain 960558^T utilizes tetradecane or hexadecane as a sole carbon and energy source, respectively. Phylogenetic trees based on 16S rRNA gene sequences and phylogenomic reconstruction revealed a close phylogenetic relationship between strain 960558^T and members of the family Rhodobacteraceae by forming a separate branch within the type species of closely related genera. The validly published species that is most closely related to strain 960558^T is Planktotalea lamellibrachiae JAM 119^T, which has the highest 16S rRNA gene sequence similarity (93.47 %). Ubiquinone 10 is the predominant ubiquinone, while C_16 : 0, 11-methyl C_18 : 1  ω7c and C_18 : 1  ω7c and/or C_18 : 1  ω6c are the predominant fatty acids (>10 %). Additionally, phosphatidylglycerol, glycolipids, diphosphatidylglycerol, unidentified polar lipids and unidentified aminolipids are the major polar lipids. The DNA G+C content of strain 960558^T is 61 %. Average nucleotide identity and digital DNA-DNA hybridization results of strain 960558^T with other type strains are <70.2 and 22.1 %, respectively. Based on its phylogenetic, chemotaxonomic and other phenotypic properties, strain 960558^T is considered to represent a novel genus and species within the family Rhodobacteraceae, for which the name Abyssibius alkaniclasticus gen. nov., sp. nov. is proposed. The type strain of Abyssibius alkaniclasticus is 960558^T (=KCTC 82619^T=MCCC 1K04727^T).

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Roseovarius faecimaris sp. nov., isolated from a tidal flat

A Gram-stain-negative, obligate aerobic, non-motile and rod-shaped bacterium, designated MME-070^T, was isolated from a tidal flat near Muui-do, Incheon, Republic of Korea. This bacterium belonged to the Roseobacterclade within the family Rhodobacteraceae. The isolate grew at 20-40 °C, pH 7.0-9.0 with 1-5 % (w/v) NaCl. Optimal growth required 2-3 % (w/v) NaCl at 25-30 °C and pH 8.0. The 16S rRNA gene sequence of strain MME-070^T was most closely related to Roseovarius aestuarii SMK-122^T (96.9 %). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain MME-070^T clustered with the genus Roseovarius. The sole respiratory quinone was Q-10. Polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, unidentified aminolipid and some unidentified lipids. Major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), 11-methyl C18 : 1ω7c and C16 : 0. The genomic DNA G+C content of the type strain was 63.6 mol%. Based on polyphasic taxonomic analysis, strain MME-070^T is proposed to represent a novel species of the genus Roseovarius, for which the name Roseovarius faecimaris sp. nov. is proposed. The type strain is MME-070^T (=KCCM 43142^T=JCM 30757^T).

Pacificibacter aestuarii sp. nov., isolated from a tidal flat

A Gram-stain-negative, strictly aerobic bacterium, designated KJ21T, was isolated from a tidal flat in South Korea. Cells were non-motile rods showing oxidase- and catalase-positive activities. Growth of strain KJ21T was observed at 10-35 °C (optimum, 30 °C), at pH 6.0-8.5 (optimum, pH 7.0) and in the presence of 1-5 % (w/v) NaCl (optimum, 2 %). Strain KJ21T contained summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c), C16 : 0, 10-methyl C19 : 0 and C10 : 0 3-OH as the major fatty acids and ubiquinone-10 as the major isoprenoid quinone. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unknown aminolipid and an unknown lipid were detected as the major polar lipids. The G+C content of the genomic DNA was 53.9 mol%. Phylogenic analysis based on 16S rRNA gene sequences showed that strain KJ21T formed a tight phylogenetic lineage with the members of the genus Pacificibacter with a 100 % bootstrap value. Strain KJ21T was most closely related to Pacificibacter maritimus KMM 9031T (98.7 %) and Pacificibacter marinus HDW-9T (98.4 %), and the DNA-DNA relatedness values between strain KJ21T and the type strains of P. maritimus and P. marinus were 46.9±4.2 % and 39.8±5.7, respectively. On the basis of phenotypic, chemotaxonomic and molecular properties, it is clear that strain KJ21T represents a novel species of the genus Pacificibacter, for which the name Pacificibacter aestuarii sp. nov. is proposed. The type strain is KJ21T (=KACC 19098T=JCM 31805T).

Primorskyibacter insulae sp. nov., isolated from the junction between the ocean and a freshwater spring

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and rod-shaped bacterial strain, designated SSK3-2T, was isolated from the locality where the ocean and a freshwater spring meet at Jeju island, South Korea, and subjected to a polyphasic taxonomic study. Strain SSK3-2T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain SSK3-2T clustered with the type strain of Primorskyibacter sedentarius, with which it exhibited 97.3 % sequence similarity. Strain SSK3-2T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids detected in strain SSK3-2T were phosphatidylcholine, phosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. The DNA G+C content of strain SSK3-2T was 60.6 mol% and its mean DNA–DNA relatedness value with P. sedentarius JCM 16874T was 19 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain SSK3-2T is separated from P. sedentarius. On the basis of the data presented, strain SSK3-2T is considered to represent a novel species of the genus Primorskyibacter, for which the name Primorskyibacter insulae sp. nov. is proposed. The type strain is SSK3-2T ( = KCTC 42602T = CECT 8871T).

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

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.

Roseovarius scapharcae sp. nov., isolated from ark shell Scapharca broughtonii

A Gram-stain-negative, non-motile, aerobic and ovoid or rod-shaped bacterium, designated MA4-5T, was isolated from ark shell (Scapharca broughtonii) collected from the South Sea, South Korea. The novel strain grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2.0 % (w/v) NaCl. Neighbour-joining and maximum-likelihood phylogenetic trees based on 16S rRNA gene sequences showed that strain MA4-5T forms a coherent cluster with the type strains of Roseovarius albus, Roseovarius aestuarii and Roseovarius nubinhibens, sharing 97.0-99.2 % sequence similarity. It exhibited 16S rRNA gene sequence similarity of 93.1-96.1 % to the type strains of other Roseovarius species. Strain MA4-5T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids of strain MA4-5T were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain MA4-5T was 53.8 mol% and its mean DNA-DNA relatedness values with the type strains of R. albus, R. aestuarii and R. nubinhibens were 11-26 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, indicated that strain MA4-5T is separate from recognized species of the genus Roseovarius. On the basis of the data presented, strain MA4-5T is considered to represent a novel species of the genus Roseovarius, for which the name Roseovarius scapharcae sp. nov. is proposed. The type strain is MA4-5T ( = KCTC 42703T = NBRC 111226T).

Aliiroseovarius pelagivivens gen. nov., sp. nov., isolated from seawater, and reclassification of three species of the genus Roseovarius as Aliiroseovarius crassostreae comb. nov., Aliiroseovarius halocynthiae comb. nov. and Aliiroseovarius sediminilitoris comb. nov

A Gram-stain-negative, non-motile, aerobic and ovoid or rod-shaped bacterium, designated GYSW-22T, was isolated from seawater off Geoje Island in the South Sea, South Korea. Strain GYSW-22T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain GYSW-22T and the type strains of Roseovarius crassostreae, Roseovarius halocynthiae and Roseovarius sediminilitoris form a coherent cluster, independent of phylogenetic lineages or clusters comprising the type strains of other species of the genus Roseovarius. Strain GYSW-22T exhibited 16S rRNA gene sequence similarities of 97.2, 96.6 and 96.3 % to R. halocynthiae MA1-10T, R. crassostreae CV919-312T and R. sediminilitoris M-M10T, respectively, and of 92.6–94.7 % to the type strains of other species of the genus Roseovarius. Strain GYSW-22T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain GYSW-22T was 59.0 mol% and its mean DNA–DNA relatedness value with R. halocynthiae MA1-10T was 15 %. On the basis of the data presented, we propose strain GYSW-22T represents a novel species of a new genus, Aliiroseovarius pelagivivens gen. nov., sp. nov. The type strain of the type species is GYSW-22T ( = KCTC 42459T = CECT 8811T). In this study, it is also proposed that Roseovarius crassostreae, Roseovarius halocynthiae and Roseovarius sediminilitoris be reclassified into the new genus as Aliiroseovarius crassostreae comb. nov. (type strain CV919-312T = ATCC BAA-1102T = DSM 16950T), Aliiroseovarius halocynthiae comb. nov. (type strain MA1-10T = KCTC 23462T = CCUG 60745T) and Aliiroseovarius sediminilitoris comb. nov. (type strain M-M10T = KCTC 23959T = CCUG 62413T), respectively.

Notification of changes in taxonomic opinion previously published outside the IJSEM

The Bacteriological Code deals with the nomenclature of prokaryotes. This may include existing names (the Approved Lists of Bacterial Names) as well as new names and new combinations. In this sense the Code is also dealing indirectly with taxonomic opinions. However, as with most codes of nomenclature there are no mechanisms for formally recording taxonomic opinions that do not involve the creation of new names or new combinations. In particular, it would be desirable for taxonomic opinions resulting from the creation of synonyms or emended descriptions to be made widely available to the public. In 2004, the Editorial Board of the International Journal of Systematic and Evolutionary Microbiology (IJSEM) agreed unanimously that it was desirable to cover such changes in taxonomic opinions (i.e. the creation of synonyms or the emendation of circumscriptions) previously published outside the IJSEM, and to introduce a List of Changes in Taxonomic Opinion [Notification of changes in taxonomic opinion previously published outside the IJSEM; Euzéby et al. (2004). Int J Syst Evol Microbiol 54, 1429-1430]. Scientists wishing to have changes in taxonomic opinion included in future lists should send one copy of the pertinent reprint or a photocopy or a PDF file thereof to the IJSEM Editorial Office or to the Lists Editor.

It must be stressed that the date of proposed taxonomic changes is the date of the original publication not the date of publication of the list. Taxonomic opinions included in the List of Changes in Taxonomic Opinion cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission. The names that are to be used are those that are the ‘correct names’ (in the sense of Principle 6) in the opinion of the bacteriologist, with a given circumscription, position and rank. A particular name, circumscription, position and rank does not have to be adopted in all circumstances. Consequently, the List of Changes in Taxonomic Opinion must be considered as a service to bacteriology and it has no ‘official character’, other than providing a centralized point for registering/indexing such changes in a way that makes them easily accessible to the scientific community.