Oceanicola litoreus sp. nov., an alphaproteobacterium isolated from the seashore sediment

Pseudooceanicola endophyticus sp. nov., a novel endophytic bacterium isolated from bark Aegiceras corniculatum

A Gram-stain-negative, aerobic, short-rod-shaped bacterium, designated strain CBS1P-1^T, was isolated from a surface-sterilized bark of Aegiceras corniculatum. Growth of strain CBS1P-1^T was observed with between 0 and 12.0 % (w/v) NaCl (optimally with 5.0 %) and at between pH 6.0-9.0. It grew at temperatures between 25-37 °C (optimum, 30 °C). Chemotaxonomic analysis showed that ubiquinone-10 was the respiratory quinone. The lipids comprised diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid, an unidentified phospholipid and an unidentified aminolipid. The major fatty acids of strain CBS1P-1^T were C_18 : 1  ω7c, C_16 : 0 and C_19 : 0 cyclo ω8c. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CBS1P-1^T was most related to Pseudooceanicola antarcticus CGMCC 1.12662^T with a sequence similarity of 96.5 %. The average nucleotide identity and digital DNA-DNA hybridization values between strain CBS1P-1^T and P. antarcticus 1.12662^T were 77.5 and 21.1 %, respectively. The G+C content of the genomic DNA was 67.3 mol%. Based on phylogenetic, chemotaxonomic and phenotypic data, strain CBS1P-1^T is considered to represent a novel species of the genus Pseudooceanicola, for which the name Pseudooceanicola endophyticus is proposed. The type strain is CBS1P-1^T (=KCTC 62836^T=CGMCC 1.13743^T).

Harenicola maris gen. nov., sp. nov. isolated from the Sea of Japan shallow sediments

A Gram-negative, non-motile bacterium КMM 3653^T was isolated from a sediment sample from the Sea of Japan seashore, Russia. On the basis of the 16S rRNA gene sequence analysis the strain КMM 3653^T was positioned within the family Rhodobacteraceae (class Alphaproteobacteria) forming a distinct lineage with the highest gene sequence similarities to the members of the genera Pacificibacter (95.2-94.7%) and Nioella (95.1-94.5%), respectively. According to the phylogenomic tree based on 400 conserved protein sequences, strain КMM 3653^T was placed in the cluster comprising Vannielia litorea, Nioella nitratireducens, Litoreibacter albidus and Pseudoruegeria aquimaris as a separate lineage adjacent to V. litorea KCTC 32083^T. The average nucleotide identity values between strain КMM 3653^T and V. litorea KCTC 32083^T, N. nitratireducens KCTC 32417^T, L. albidus KMM 3851^T, and P. aquimaris CECT 7680^T were 71.1, 70.3, 69.6, and 71.0%, respectively. Strain КMM 3653^T contained Q-10 as the predominant ubiquinone and C_18:1ω7c as the major fatty acid followed by C_16:0. The polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid, two unidentified aminolipids, and five unidentified lipids. The DNA G+C content of 61.8% was calculated from the genome sequence. Based on the phylogenetic evidence and distinctive phenotypic characteristics, we proposed strain KMM 3653^T (= KCTC 82575^T) to be classified as a novel genus and species Harenicola maris gen. nov., sp. nov.

Pelagovum pacificum gen. nov., sp. nov., a novel member of the family Rhodobacteraceae isolated from surface seawater of the Mariana Trench

A Gram-stain-negative, aerobic, ovoid-rod-shaped bacterium, designated strain SM1903^T, was isolated from surface seawater of the Mariana Trench. The strain grew at 15-37 °C (optimum, 35 °C) and with 1-15 % (optimum, 4 %) NaCl. It hydrolysed aesculin but did not reduce nitrate to nitrite and hydrolyse Tween 80. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SM1903^T formed a separate lineage within the family Rhodobacteraceae, sharing the highest 16S rRNA gene sequence similarity with type strains of Pseudooceanicola antarcticus (95.7 %) and Roseisalinus antarcticus (95.7 %). In phylogenetic trees based on single-copy OCs and whole proteins sequences, strain SM1903^T fell within a sub-cluster encompassed by Oceanicola granulosus, Roseisalinus antarcticus and Histidinibacterium lentulum and formed a branch adjacent to Oceanicola granulosus. The major cellular fatty acids were summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c), C_16 : 0 and 11-methyl-C_18 : 1  ω7c. The polar lipids mainly comprised phosphatidylglycerol, phosphatidylcholine, one unidentified lipid, one unidentified aminolipid, and one unidentified glycolipid. The solo respiratory quinone was ubiquinone-10. The genomic DNA G+C content of strain SM1903^T was 66.0 mol%. Based on the results of phenotypic, chemotaxonomic, and phylogenetic characterization for strain SM1903^T, it is considered to represent a novel species of a novel genus in the family Rhodobacteraceae, for which the name Pelagovum pacificum gen. nov., sp. nov. is proposed. The type strain is SM1903^T (=MCCC 1K03608^T=KCTC 72046^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.

Complete Genome Sequence of a Quorum-Sensing Bacterium, Oceanicola sp. Strain D3, Isolated from a Microplastic Surface in Coastal Water of Qingdao, China

Oceanicola sp. strain D3 was isolated from the plastisphere of polyvinyl chloride (PVC) in coastal water of Qingdao, China. Here, we present the complete genome sequence of strain D3, which consists of a chromosome of 3,926,685 bp with a G+C content of 64.49% and 4,964 coding DNA sequences. This is the first report of a quorum-sensing (QS) system in an Oceanicola sp. strain.

Pseudopontivivens aestuariicola gen. nov., sp. nov., a Novel Bacterium of the Class Alphaproteobacteria Isolated from a Tidal Flat

A Gram-stain-negative, non-motile and coccoid, ovoid or rod-shaped bacterial strain, OITF-57^T, which was isolated from a tidal flat sediment in South Korea, was characterized taxonomically. Strain OITF-57^T grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2.0% (w/v) NaCl. Strain OITF-57^T exhibited the highest 16S rRNA gene sequence similarity value (94.2%) to the type strain of Pontivivens insulae forming a cluster in the neighbour-joining phylogenetic tree. In the maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences and the phylogenetic tress based on gyrB sequences, strain OITF-57^T formed evolutionary lineages independent of those of other taxa. Strain OITF-57^T contained Q-10 as the predominant ubiquinone and C_18:1 ω7c as the major fatty acid. The major polar lipids of strain OITF-57^T were phosphatidylcholine and phosphatidylglycerol. The DNA G + C content of strain OITF-57^T was 66.0 mol%. The chemotaxonomic data and other differential phenotypic properties made it possible to distinguish strain OITF-57^T from the genus Pontivivens and other phylogenetically related genera. On the basis of the data presented, strain OITF-57^T constitutes a new genus and species within the class Alphaproteobacteria, for which the name Pseudopontivivens aestuariicola gen. nov., sp. nov. is proposed. The type strain is OITF-57^T (= KACC 19570^T = CGMCC 1.13481^T).

Psychromarinibacter halotolerans gen. nov., sp. nov., isolated from seawater of the Yellow Sea

A Gram-stain-negative, strictly aerobic, motile, non-gliding, oxidase-positive, catalase-positive, rod-shaped bacterium, designated strain YBW34T, was isolated from seawater from the bottom of the Yellow Sea at station H12 (-73m in depth). Growth occurred at 10-45 °C (optimum 28 °C), in the presence of 1-12 % NaCl (w/v, optimum 4 %) and at pH 6.0-8.0 (optimum pH 7.0). The major fatty acids (>10 %) were C18 : 1 ω7c and C16 : 0. The major polar lipids comprised phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and three unidentified aminolipids. The major respiratory quinone was ubiquinone-10 (Q-10). The DNA G+C content of strain YBW34T was 64.2 mol%. The most closely related species was Tropicimonas isoalkanivorans JCM 14837T with 95.8 % sequence similarity in Alphaproteobacteria. It showed 16S rRNA gene sequence similarities of 93.03-95.49, 93.03-95.49 and 95.31-95.32 % to species of genera Rhodovulum, Lutimaribacter and Oceanicola, respectively. Nevertheless, strain YBW34T formed a distinct lineage in the trees which did not join the genera mentioned above in the phylogenetic dendrogram based on 16S rRNA gene sequences. The phenotypic, chemotaxonomic and phylogenetic data indicated that strain YBW34T represents a novel genus and species, for which the name Psychromarinibacter halotolerans gen. nov., sp. nov. is proposed. The type strain is YBW34T (=JCM 31462T=KCTC 52366T=MCCC 1K03203T).

Lacimonas salitolerans gen. nov., sp. nov., isolated from surface water of a saline lake

A Gram-stain-negative bacterium, strain TS-T30T, was isolated from a saline lake (Lake Tuosu) in Qaidam basin, Qinghai province, China, and its taxonomic position was determined by using a polyphasic approach. Cells were non-spore-forming rods, non-motile, 0.8–1.4 μm wide and 1.9–4.0 μm long. Strain TS-T30T was strictly heterotrophic and aerobic. Catalase- and oxidase-positive. Growth was observed in the presence of 0.5–11.0 % (w/v) NaCl (optimum 3.0 %), and at 10–35 °C (optimum 25 °C) and pH 6.5–10.0 (optimum pH 8.5). Strain TS-T30T contained C18 : 1ω7c as the only predominant fatty acid. The major respiratory quinone was Q-10. The DNA G+C content was 62 mol% (T m). Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T30T formed a distinct lineage that was independent of other most closely related genera: Lutimaribacter (95.2–95.9 % 16S rRNA gene sequence similarities), Poseidonocella (95.4 %), Ruegeria (92.8–94.9 %), Marivita (93.6–94.9 %), Seohaeicola (94.7 %), Sediminimonas (94.7 %), Shimia (93.9–94.7 %), Oceanicola (92.6–94.5 %) and Roseicyclus (94.5 %). The major polar lipids were phosphatidylglycerol, one unidentified phospholipid and an unknown aminolipid; phosphatidylcholine was not detected. These data demonstrated that strain TS-T30T represents a novel species of a new genus in the family Rhodobacteraceae, for which the name Lacimonas salitolerans gen. nov., sp. nov. is proposed. The type strain of the type species is TS-T30T ( = CGMCC 1.12477T = NBRC 110969T).

Pontivivens insulae gen. nov., sp. nov., isolated from seawater

A Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated GYSW-23T, was isolated from seawater off Geoje island in the South Sea, South Korea. Strain GYSW-23T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of approximately 2.0–3.0   % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain GYSW-23T forms a distinct evolutionary lineage independent of other taxa of the family Rhodobacteraceae. It exhibited 16S rRNA gene sequence similarity values of 94.0, 93.5, 93.4 and 93.4 % to the type strains of Roseovarius aestuarii, Ruegeria marina, Roseovarius pacificus and Oceanicola litoreus, respectively, and 93.6 % to ‘Actibacterium atlanticum’ 22II-S11-z10. Strain GYSW-23T contained Q-10 as the predominant ubiquinone and C18  :  1ω7c as the major fatty acid. The major polar lipids of strain GYSW-23T were phosphatidylcholine, phosphatidylglycerol and one unidentified aminolipid. The fatty acid and polar lipid profiles of strain GYSW-23T were distinguishable from those of the phylogenetically related taxa. The DNA G+C content of strain GYSW-23T was 60.6 mol%. On the basis of the phylogenetic, chemotaxonomic and other phenotypic properties, strain GYSW-23T is considered to represent a novel species of a new genus in the family Rhodobacteraceae, for which the name Pontivivens insulae gen. nov., sp. nov. is proposed. The type strain of Pontivivens insulae is GYSW-23T ( = KCTC 42458T = CECT 8812T).

Nioella nitratireducens gen. nov., sp. nov., a novel member of the family Rhodobacteraceae isolated from Azorean Island

A novel Gram-negative, non-spore forming, rod-shaped aerobic bacterium, designated SSW136(T), was isolated from a surface seawater sample collected at Espalamaca (in Faial Island), Azores. Growth was found to occur from 10 to 37 °C, pH 6.0-8.0, and with 2-11 % of NaCl. 16S rRNA gene sequence indicated that the strain SSW136(T) belongs to the family Rhodobacteraceae. Strain SSW136(T) exhibited 96.3, 95.9, 95.7 and 95.5 sequence similarity to the type strains Oceanicola litoreus M-M22(T), Roseovarius aestuarii SMK-122(T), Marivita geojedonensis DPG-138(T), and Pseudoruegeria aquimaris SW-255(T) respectively. Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain SSW136(T) was affiliated to the family Rhodobacteraceae and formed a separate branch. The G+C content was 63.5 mol%. The major respiratory quinone was found to be Q-10. The polar lipids of strain SSW136(T) consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids and three unidentified phospholipids. The major fatty acids were C18:1 ω7c (46.5 %), Cyclo-C19:0 ω8c (16.0 %) and C16:0 (12.8 %). On the basis of the morphological, genotypic, chemotaxonomic characteristics and low DNA-DNA relatedness, strain SSW136(T) is proposed to represent a novel genus and novel species, Nioella nitratireducens gen. nov., sp. nov., in the family Rhodobacteraceae. The type strain is SSW136(T) (=KCTC 32417(T) = NCIM 5499(T)).

Oceanicola antarcticus sp. nov. and Oceanicola flagellatus sp. nov., moderately halophilic bacteria isolated from seawater

Two Gram-stain-negative, aerobic, moderately halophilic, rod-shaped bacteria (strains Ar-45T and DY470T) were isolated from seawater collected from the Southern Ocean and the Pacific Ocean, respectively. Growth of strain Ar-45T was observed with between 0.5 and 10.0 % (w/v) NaCl (optimally with 0.5–3.0 %) and between pH 5.5 and 9.5. Strain DY470T grew in the presence of 0.5–7.5 % (w/v) NaCl (optimally with 2.0 %) and at pH 5.5–8.5. Chemotaxonomic analysis showed Q-10 as the respiratory quinone for both strains. The major fatty acids (>5 %) of strain Ar-45T were C16 : 0, C19 : 0 cyclo ω8c and C18 : 1ω7c, while those of strain DY470T were C18 : 1ω7c, C16 : 0 and 11-methyl C18 : 1ω7c. The DNA G+C contents of the two strains were 62.0 and 61.8 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains Ar-45T and DY470T were related most closely to the genus Oceanicola , with sequence similarities of 97.4–94.0 and 97.7–94.7 %, respectively. The DNA–DNA hybridization value between strain Ar-45T and Oceanicola marinus LMG 23705T was 22.0 %. Levels of DNA–DNA relatedness between strain DY470T and Oceanicola nitratireducens LMG 24663T and Oceanicola batsensis DSM 15984T were 32.5 and 26.1 %, respectively. Based on phylogenetic, chemotaxonomic and phenotypic data, strains Ar-45T and DY470T are considered to represent two novel species of the genus Oceanicola , for which the names Oceanicola antarcticus (type strain Ar-45T = CGMCC 1.12662T = LMG 27868T) and Oceanicola flagellatus (type strain DY470T = CGMCC 1.12664T = LMG 27871T) are proposed.

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, and these authors’ names will be included in the author index of the present issue. 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.