Thalassobius mediterraneus gen. nov., sp. nov., and reclassification of Ruegeria gelatinovorans as Thalassobius gelatinovorus comb. nov

Proposal of Thalassovita gen. nov. and Alloyangia gen. nov. as replacement names for the illegitimate prokaryotic generic names Thalassobius and Yangia, respectively

The prokaryotic generic names Thalassobius Arahal et al. 2005 and Yangia Dai et al. 2006 are illegitimate because they are later homonyms of the genus names Thalassobius Solier 1849 (Coleoptera) and Yangia Zheng 1997 (fossil Rodentia), respectively Principle two and Rule 51b(4) of the International Code of Nomenclature of Prokaryotes]. We therefore propose the replacement generic names Thalassovita and Alloyangia, with type species Thalassovita gelatinovora and Alloyangia pacifica, respectively.

Characterization of Host-Associated Microbiota and Isolation of Antagonistic Bacteria from Greater Amberjack (Seriola dumerili, Risso, 1810) Larvae

Greater amberjack (Seriola dumerili) is a new species in marine aquaculture with high mortalities at the larval stages. The microbiota of amberjack larvae was analyzed using 16S rDNA sequencing in two groups, one added copepod nauplii (Acartia tonsa) in the diet, and one without copepods (control). In addition, antagonistic bacteria were isolated from amberjack larvae and live food cultures. Proteobacteria was the most abundant phylum followed by Bacteroidota in amberjack larvae. The composition and diversity of the microbiota were influenced by age, but not by diet. Microbial community richness and diversity significantly increased over time. Rhodobacteraceae was the most dominant family followed by Vibrionaceae, which showed the highest relative abundance in larvae from the control group 31 days after hatching. Alcaligenes and Thalassobius genera exhibited a significantly higher relative abundance in the copepod group. Sixty-two antagonistic bacterial strains were isolated and screened for their ability to inhibit four fish pathogens (Aeromonas veronii, Vibrio harveyi, V. anguillarum, V. alginolyticus) using a double-layer test. Phaeobacter gallaeciensis, Phaeobacter sp., Ruegeria sp., and Rhodobacter sp. isolated from larvae and Artemia sp. inhibited the fish pathogens. These antagonistic bacteria could be used as host-derived probiotics to improve the growth and survival of the greater amberjack larvae.

Thiosulfatihalobacter marinus gen. nov. sp. nov., a novel member of the family Roseobacteraceae, isolated from the West Pacific Ocean

Two strains (GL-11-2T and ZH2-Y79) were isolated from the seawater collected from the West Pacific Ocean and the East China Sea, respectively. Cells were Gram-stain-negative, strictly aerobic, non-motile and rod-shaped. Cells grew in the medium containing 0.5–7.5 % NaCl (w/v, optimum, 1.0–3.0 %), at pH 6.0–8.0 (optimum, pH 6.5–7.0) and at 4–40 °C (optimum, 30 °C). H2S production occurred in marine broth supplemented with sodium thiosulphate. The almost-complete 16S rRNA gene sequences of the two isolates were identical, and exhibited the highest similarity to Pseudoruegeria aquimaris JCM 13603T (97.5 %), followed by Ruegeria conchae TW15T (97.2%), Shimia aestuarii DSM 15283T (97.1 %) and Ruegeria lacuscaerulensis ITI-1157T (97.0 %). Phylogenetic analysis revealed that the isolates were affiliated with the family Roseobacteraceae and represented an independent lineage. The sole isoprenoid quinone was ubiquinone 10. The principal fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c) and cyclo-C19 : 0  ω8c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol. The DNA G+C content was 62.3 mol%. The orthologous average nucleotide identity, in silico DNA–DNA hybridization and average amino acid identity values among the genomes of strain GL-11-2T and the reference strains were 73.2–79.0, 20.3–22.5 and 66.0–80.8 %, respectively. Strains GL-11-2ᵀ and ZH2-Y79 possessed complete metabolic pathways for thiosulphate oxidation, dissimilatory nitrate reduction and denitrification. Phylogenetic distinctiveness, chemotaxonomic differences and phenotypic properties revealed that the isolates represent a novel genus and species of the family Roseobacteraceae , belonging to the class Alphaproteobacteria , for which the name Thiosulfatihalobacter marinus gen. nov., sp. nov. (type strain, GL-11–2T=KCTC 82723T=MCCC M20691T) is proposed.

Isolation of Thalassobius mangrovi sp. nov., a novel bacterium in the family Rhodobacteraceae, from marine mangrove sediment

A Gram-stain-negative, strictly aerobic and oval-shaped bacterial strain with a flagellum, designated GS-10^T, was isolated from mangrove wetland sediment. GS-10^T grew at 20-40 °C (optimum, 37 °C), in the pH range of 5.0-11.0 (optimum, 6.0-8.0) and under various NaCl concentrations from 1 to 11 % (w/v) (optimum, 5-6 %). The respiratory quinone was ubiquinone-10, and the predominant polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids (>10 % of the total fatty acids) were summed feature 4 (C_17 : 1iso I/anteiso B) and summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c). The G+C content of the genomic DNA was 63.71 %. On the basis of the results from comparative analysis of the 16S rRNA gene sequence, GS-10^T represents a member of the family Rhodobacteraceae and had the highest sequence similarity to Thalassobius gelatinovorus CECT 4357^T (97.47 %), followed by Lutimaribacter pacificus W11-2B^T (97.03 %), Marivita cryptomonadis CL-SK44^T (96.83 %), Thalassobius autumnalis CECT 5118^T (96.75 %) and Thalassobius mediterraneus CECT 5383^T (96.68 %). Phylogenetic trees based on 16S rRNA gene sequences, multilocus sequence analysis (MLSA) and whole genome sequences revealed that GS-10^T clustered with species within the genus Thalassobius. The average nucleotide identity (ANI) and the average amino acid identity (AAI) values were calculated from complete genome sequences and indicated that GS-10^T represented a novel species of the genus Thalassobius, and the name Thalassobius mangrovi sp. nov. is proposed for this species. The type strain of Thalassobius mangrovi is GS-10^T (=MCCC 1K03624^T=KCTC 82131^T).

Thalassobius aquimarinus sp. nov., isolated from the Sea of Japan seashore

An aerobic, Gram-negative, non-pigmented non-motile bacterium designed КMM 8518^T was isolated from a seawater sampled from the Sea of Japan seashore. Strain КMM 8518^T grew at 7-42 °C and in the presence of 1-7% NaCl. The phylogenetic analyses based on 16S rRNA gene and whole-genome sequences placed the novel strain КMM 8518^T into the genus Thalassobius as a separate lineage. Strain КMM 8518^T shared the highest 16S rRNA gene sequence similarity of 98% to Thalassobius gelatinovorus KCTC 22092^T and similarity values of ≤ 97% to other recognized Thalassobius species. The average nucleotide identity and digital DNA-DNA hybridization values between strain КMM 8518^T and T. gelatinovorus KCTC 22092^T were 79.6% and 23.5%, respectively. The major respiratory quinone was ubiquinone-10. The major fatty acid was C_18:1ω7c followed by 11-methyl C_18:1ω7c. Polar lipids comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid, an unidentified phospholipid, and three unidentified lipids. The DNA G+C content of 62.7% was calculated from genome sequence analysis. Based on the phylogenetic analyses and distinctive phenotypic characteristics, the marine bacterium КMM 8518^T is concluded to represent a novel species of the genus Thalassobius for which the name Thalassobius aquimarinus sp. nov. is proposed. The type strain of the species is strain KMM 8518^T (= KCTC 82576^T).

Ruegeria haliotis sp. nov., Isolated from the Gut of the Abalone Haliotis rubra

A Gram-stain-negative, aerobic, non-motile, white-pigmented, short rod-shaped, and alginate-degrading bacterium, designated B1Z28^T, was isolated from the gut of the abalone Haliotis rubra obtained at Weihai, China. Strain B1Z28^T was found to grow at 4-35 °C, pH 6.5-9.0, and in the presence of 0.5-8.0% (w/v) NaCl. Cells were positive for oxidase and catalase activity. The 16S rRNA-based phylogenetic analysis revealed that the nearest phylogenetic neighbors of strain B1Z28^T were Tritonibacter scottomollicae MCCC 1A06440^T (98.1%), Ruegeria faecimaris KCTC 23044^T (98.0%), and Ruegeria meonggei KCTC 32450^T (97.8%). Based on phylogenomic analysis, the average nucleotide identity (ANI) values between strain B1Z28^T and the neighbor strains were 71.6, 77.2, and 78.1%, respectively; the digital DNA-DNA hybridization (dDDH) values based on the draft genomes between strain B1Z28^T and its closest neighbors were 20.5, 20.8, and 21.6%, respectively. Ubiquinone-10 (Q-10) was detected as the predominant respiratory quinone. The dominant cellular fatty acids were Summed feature 8 (contained C_18:1 ω7c and/or C_18:1 ω6c). The polar lipids included phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phospholipid (PL), aminolipid (AL), and three unidentified lipids. Based on the phylogenetic and phenotypic characteristics, strain B1Z28^T is considered to represent a novel species of the genus Ruegeria, for which the name Ruegeria haliotis sp. nov. is proposed. The type strain is B1Z28^T (= KCTC 72686^T = MCCC 1H00393^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.

Ruegeria lutea sp. nov., isolated from marine sediment, Masan Bay, South Korea

A Gram-stain-negative, non-motile, mesophilic, short rod-shaped, aerobic bacterium designated as 318-1^T was isolated from a marine sediment collected from Masan Bay, South Korea. Strain 318-1^T grew optimally at pH 6-7, at 30 °C and in the presence of 2-3 % (w/v) NaCl, tolerant of up to 8 % (w/v) NaCl, and accumulated poly-β-hydroxybutyrate (PHB). A comparative analysis of 16S rRNA gene sequences revealed that strain 318-1^T formed a distinct phyletic lineage in the genus Ruegeria (family Rhodobacteraceae, class Alphaproteobacteria) and showed high sequence similarity to Ruegeria halocynthiae DSM 27839^T (96.5 %) and Shimia haliotis DSM 28453^T (96.3 %). Comparing the genome sequence of 318-1^T with those of the type strains of seven species of the genus Rugeria and two species of the genus Shimia, the values obtained were below the thresholds with analysis of average nucleotide identities (ANI, 71.6-76.8 %) and in silico DNA-DNA hybridisation, Genome-to-Genome Distance Calculator (GGDC, 18.5-20.6 %). The DNA G+C content was 65.75 mol%. Chemotaxonomic data [predominant quinone ubiquinone Q10; polar lipid profile consisting of major compounds phosphatidylcholine (PC), phosphatidylglycerol (PG), an unidentified aminolipid and an unidentified lipid; major fatty acids summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c)] supported the affiliation of strain 318-1^T to the genus Ruegeria. Genomic, chemotaxonomic, and phenotypic differentiation of strain 318-1^T from the members of the genus Ruegeria support it as a novel species. On the basis of the results in this study, a novel species, Ruegeria lutea sp. nov., is proposed. The type strain is 318-1^T (=JCM 30927^T=KEMB 7306-525^T=KCTC 72105^T).

Litorivita pollutaquae gen. nov., sp. nov., a marine bacterium in the family Rhodobacteraceae isolated from surface seawater of Xiamen Port, China

A Gram-stain-negative Rhodobacterales strain, designated as FSX-11^T, was isolated from surface seawater of Xiamen port in China. Strain FSX-11^T showed less than 96.5 % 16S rRNA gene sequence similarity to the type strains of species with validly published names. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel isolate formed a distinct monophyletic clade within the family Rhodobacteriaceae and clustered distantly with the genera Thalassobius and Marivita. Cells of strain FSX-11^T were non-motile, oval-shaped and facultative anaerobic. Optimal growth occurred at 20-30 °C, at pH 7.0-8.0 and in the presence of 2-3 % NaCl (w/v). The major respiratory quinone was ubiquinone-10. Summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), 11-methyl C18 : 1ω7c and C16 : 0 were the major fatty acids. The DNA G+C content of strain FSX-11^T was 58.7 mol%. On the basis of phylogenetic analysis, phenotypic and chemotaxonomic characteristics and 16S rRNA gene signature nucleotide patterns, strain FSX-11^T represents a novel species in a novel genus within the family Rhodobacteraceae, for which the name Litorivita pollutaquae gen. nov., sp. nov. is proposed. The type strain is FSX-11^T (=JCM 32715^T=MCCC 1K03503^T).

Differential incorporation of one-carbon substrates among microbial populations identified by stable isotope probing from the estuary to South China Sea

Methanol (MOH) and monomethylamine (MMA) are two typical one-carbon (C₁) compounds found in natural environments. They play an important role in marine and atmospheric chemistry, cloud formation, and global climate. The main biological sink of MOH and MMA is rapid consumption by marine microbes. Here, field-based time-series incubations with supplemental ¹³C-labelled MOH and MMA and isotope ratio analyses were performed. A substantial difference in the MOH and MMA incorporation rates and bacterial taxa were observed between the South China Sea (SCS) and the Pearl River estuary. C₁ substrates were assimilated more quickly in the estuary than the SCS shelf where MOH and MMA had similar bio-availability. However, microbial responses to MMA may be faster than to MOH in the coastal and basin surface water of the SCS despite similar active bacterial populations. Three ecological types of bacteria, in terms of response to supplemented MOH and MMA, were identified: rapid incorporation (I, dominant C₁-incorporating group), slow incorporation (II, minor C₁-incorporating group), and no incorporation (III, C₁-non-incorporating group). Members of the families Methylophilaceae (β-Proteobacteria) and Piscirickettsiaceae (γ-Proteobacteria) belonged to type I and actively incorporated substrates in the estuary and SCS, respectively. Diverse MOH and MMA-incorporating type II bacteria were identified by stable isotope probing in the SCS, and could play a more important role in the transformation of C₁ compounds in marine environments than hitherto assumed.

Ruegeria kandeliae sp. nov., isolated from the rhizosphere soil of a mangrove plant Kandelia candel

A Gram-negative, rod-shaped and motile bacterium, designated strain J95^T, was isolated from the rhizosphere soil of a mangrove plant Kandeliacandel (L.) Druce in Mai Po Nature Reserve, Hong Kong. Growth of strain J95^T was observed at pH 5.0-8.5 (optimum, 6.0-7.0), between 10-40 °C (30-37 °C) and in the presence of 0-9 % (w/v) NaCl (0.5-3 %). Chemotaxonomic analysis showed ubiquinone-10 as the predominant respiratory quinone and C18 : 1ω7c and C19 : 0 cycloω8c as the major fatty acids. The major polar lipids were lipid, aminolipid, phospholipid, phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The genomic contained a circular chromosome of 5.48 Mb with a DNA G+C content of 65.7 mol%. The genome included 5299 genes. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain J95^T belongs to the genus Ruegeria with highest sequence similarity (96.8 %) to the type strain Ruegeria marina ZH17^T. The combined phenotypic, chemotaxonomic and phylogenetic data suggested that strain J95^T represents a novel species of the genus Ruegeria, for which the name Ruegeria kandeliae sp. nov. is proposed. The type strain is J95^T (=MCCC 1K03284^T=DSM 104293^T).

Comparative Genomics of Thalassobius Including the Description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp. nov

A taxogenomic study was conducted to describe two new Thalassobius species and to analyze the internal consistency of the genus Thalassobius along with Shimia and Thalassococcus. Strains CECT 5113^T, CECT 5114, CECT 5118^T, and CECT 5120 were isolated from coastal Mediterranean seawater, Spain. Cells were Gram-negative, non- motile coccobacilli, aerobic chemoorganotrophs, with an optimum temperature of 26°C and salinity of 3.5-5%. Major cellular fatty acids of strains CECT 5113^T and CECT 5114 were C_{18 : 1} ω7c/ω6c and C_{10 : 0} 3OH, G+C content was 54.4-54.5 mol% and were able to utilize propionate, L-threonine, L- arginine, and L-aspartate as carbon sources. They exhibited 98.3% 16S rRNA gene sequence similarity, 75.0-75.1 ANIb and 19.5-20.9 digital DDH to type strain of their closest species, Thalassobius maritimus. Based on these data, strains CECT 5113^T and CECT 5114 are recognized as a new species, for which the name Thalassobius activus is proposed, with strain CECT 5113^T (=LMG 29900^T) as type strain. Strains CECT 5118^T and CECT 5120 were found to constitute another new species, with major cellular fatty acids C_{18 : 1} ω7c/ω6c and C_{18 : 1} ω7c 11-methyl and a G+C content of 59.8 mol%; they were not able to utilize propionate, L-threonine, L- arginine or L-aspartate. Their closest species was Thalassobius mediterraneus, with values of 99.6% 16S rRNA gene sequence similarity, 79.1% ANIb and 23.2% digital DDH compared to the type strain, CECT 5383^T. The name Thalassobius autumnalis is proposed for this second new species, with strain CECT 5118^T (=LMG 29904^T) as type strain. To better determine the phylogenetic relationship of the two new species, we submitted 12 genomes representing species of Thalassobius, Shimia, and Thalassoccocus, to a phylogenomic analysis based on 54 single protein-encoding genes (BCG54). The resulting phylogenomic tree did not agree with the current genera classification, as Thalassobius was divided in three clades, Thalassobius sensu stricto (T. mediterraneus, T. autumnalis sp. nov., and T. gelatinovorus), Thalassobius aestuarii plus the three Shimia spp (S. marina, S. haliotis, and Shimia sp. SK013) and finally, Thalasobius maritimus plus T. activus sp. nov. Thalassococcus halodurans remained apart from the two genera. Phenotypic inferences from explored genomes are presented.

Ruegeria profundi sp. nov. and Ruegeria marisrubri sp. nov., isolated from the brine-seawater interface at Erba Deep in the Red Sea

Two moderately halophilic marine bacterial strains of the family Rhodobacteraceae, designated ZGT108^T and ZGT118^T, were isolated from the brine-seawater interface at Erba Deep in the Red Sea (Saudi Arabia). Cells of both strains were aerobic, rod-shaped, non-motile, and Gram-stain-negative. The sequence similarity of the 16S rRNA genes of strains ZGT108^T and ZGT118^T was 94.9 %. The highest 16S rRNA gene sequence similarity of strain ZGT108^T to its closest relative, Ruegeria conchae JCM 17315^T, was 98.9 %, while the 16S rRNA gene of ZGT118^T was most closely related to that of Ruegeria intermedia LMG 25539^T (97.7 % similarity). The sizes of the draft genomes as presented here are 4 258 055 bp (strain ZGT108^T) and 4 012 109 bp (strain ZGT118^T), and the G+C contents of the draft genomes are 56.68 mol% (ZGT108^T) and 62.94 mol% (ZGT108^T). The combined physiological, biochemical, phylogenetic and genotypic data supported placement of both strains in the genus Ruegeria and indicated that the two strains are distinct from each other as well as from all other members in the genus Ruegeria. This was also confirmed by low DNA-DNA hybridization values (<43.6 %) and low ANI values (<91.8 %) between both strains and the most closely related Ruegeria species. Therefore, we propose two novel species in the genus Ruegeria to accommodate these novel isolates: Ruegeriaprofundi sp. nov. (type strain ZGT108^T=JCM 19518^T=ACCC 19861^T) and Ruegeriamarisrubri sp. nov. (type strain ZGT118^T=JCM 19519^T=ACCC 19862^T).

Diversity of bacteria in ships ballast water as revealed by next generation DNA sequencing

The bacterial diversity in ballast water from five general cargo ships calling at the Port of Houston was determined with ion semiconductor DNA sequencing (Ion Torrent PGM) of PCR amplified 16S rRNA genes. Phylogenetic analysis revealed that the composition of bacteria in ballast water did not resemble that of typical marine habitats or even open ocean waters where BWEs occur. The predominant group of bacteria in ships conducting BWEs was the Roseobacter clade within the Alphaproteobacteria. In contrast, Gammaproteobacteria were predominant in the ship that did not conduct a BWE. All the ships contained human, fish, and terrestrial plant pathogens as well as bacteria indicative of fecal or activated sludge contamination. Most of the 60 pathogens had not been detected in ballast water previously. Among these were the human pathogens Corynebacterium diptheriae and several Legionella species and the fish pathogens Francisella piscicida and Piscirickettsia salmonis.

Nitropelagius marinus gen. nov., sp. nov., Isolated From Seawater, Je-bu island, South Korea [corrected]

A Gram-stain-negative, non-spore forming, non-motile and aerobic strain, designated JB22(T), was isolated from seawater, Je-bu Island, South Korea. Strain JB22(T) was catalase and oxidase positive. Optimal growth of JB22(T) was observed at 30 °C and pH 7.0. NaCl tolerance range was 1-9 % (w/v) with an optimum of 2.0 % concentration. The phylogenetic analysis based on 16S rRNA gene sequence of strain JB22(T) showed the highest sequence similarity to those of Pelagicola litorisediminis D1-W8(T) (95.8 %), Roseovarius litoreus GSW-M15(T) (95.2 %), Roseovarius aestuarii SMK-122(T) (95.0 %), Donghicola eburmeus SW-277(T) (95.0 %), and Roseovarius halotolerans HJ50(T) (94.9 %). It contained ubiquine-10 as the major respiratory quinone and C18:1 ω7c (69.3 %), :0 (9.9 %), C18:1 ω7c 11-methyl (9.6 %) as the major fatty acid. The polar lipid profile included phosphatidylcholine, phosphatidylglycerol, and unidentified aminolipid. The DNA G+C content of the strain JB22(T) was 47 mol  %. Based on physiological and chemotaxonomic characteristics, strain JB22(T) should be regarded as a new genus of the family Rhodobacteraceae, for which the Nitropelagi marinus gen. nov., sp. nov. is proposed. The type strain is JB22(T) (= KEMB 3001-101(T) = JCM 30822(T)).

Draft genome sequence of Thalassobius mediterraneus CECT 5383(T), a poly-beta-hydroxybutyrate producer

Thalassobius mediterraneus is the type species of the genus Thalassobius and a member of the Roseobacter clade, an abundant representative of marine bacteria. T. mediterraneus XSM19^T (= CECT 5383^T) was isolated from the Western Mediterranean coast near Valencia (Spain) in 1989. We present here the draft genome sequence and annotation of this strain (ENA/DDBJ/NCBI accession number CYSF00000000), which is comprised of 3,431,658 bp distributed in 19 contigs and encodes 10 rRNA genes, 51 tRNA genes and 3276 protein coding genes. Relevant findings are commented, including the complete set of genes required for poly-beta-hydroxybutyrate (PHB) synthesis and genes related to degradation of aromatic compounds.

Brevirhabdus pacifica gen. nov., sp. nov., isolated from deep-sea sediment in a hydrothermal vent field

A Gram-stain-negative, motile, aerobic bacterial strain, designated 22DY15T, was isolated from a deep-sea sediment sample collected from a hydrothermal vent field located in the East Pacific Rise. The isolate was a short rod with a single flagellum and was positive for catalase and oxidase activities. Q-10 was the predominant respiratory quinone. The major polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphoglycolipid, one aminolipid and three unidentified phospholipids. The principal fatty acid (>70 %) was C18 : 1ω7c. The genomic DNA G+C content was 64.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22DY15T represents a distinct lineage within the family Rhodobacteraceae. The closest relatives were species of the genera Aliiroseovarius (93.3–96.0 % 16S rRNA gene sequence similarity), Sulfitobacter (94.0–96.0 %) and Loktanella (92.0–95.9 %). Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain 22DY15T could be differentiated from its most closely related genera. Therefore, it is proposed that strain 22DY15T represents a novel species in a new genus of the family Rhodobacteraceae, for which the name Brevirhabdus pacifica gen. nov., sp. nov. is proposed. The type strain of the type species is 22DY15T ( = JCM 19489T = DSM 27767T = CGMCC 1.12416T = MCCC 1K00276T).

Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov

Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended.

Shimia biformata sp. nov., isolated from surface seawater, and emended description of the genus Shimia Choi and Cho 2006

A novel, Gram-staining-negative, non-flagellated, oval or short-rod-shaped, strictly aerobic and non-spore-forming marine bacterium, designated strain CC-AMW-CT, was isolated from coastal surface seawater in Kending County, Taiwan. Cells of strain CC-AMW-CT displayed unusual morphology and formed colourless or beige colonies on marine agar. The isolate shared pairwise 16S rRNA gene sequence similarities of 97.2 and 97.1 % with Shimia marina BCRC 80068T and Shimia isoporae BCRC 80085T, respectively, and established a discrete phyletic lineage closely associated with the members of the genus Shimia . DNA–DNA hybridization values indicated <18.2 % genomic relatedness with species of the genus Shimia . The polar lipid profile of strain CC-AMW-CT comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids, four unidentified lipids and an unidentified phospholipid. The predominant fatty acids were C18 : 1ω7c and/or C18 : 1ω6c (summed feature 8; 75.5 %). The DNA G+C content was 61.2 mol%. The predominant respiratory quinone was ubiquinone Q-10 and the major polyamine was cadaverine. The chemotaxonomic evidence, including extraordinary amounts of C18 : 1ω7c and/or C18 : 1ω6c, major polar lipids, polyamine, quinone and DNA G+C contents of CC-AMW-CT, was in line with that of the members of the genus Shimia . Thus, strain CC-AMW-CT should be classified as a novel species of the genus Shimia , for which the name Shimia biformata sp. nov. is proposed. The type strain is CC-AMW-CT ( = JCM 18818T = BCRC 80548T). An emended description of the genus Shimia is also proposed.

Planktomarina temperata gen. nov., sp. nov., belonging to the globally distributed RCA cluster of the marine Roseobacter clade, isolated from the German Wadden Sea

Four heterotrophic bacterial strains belonging to the globally distributed marine RCA (Roseobacter clade-affiliated) cluster (family Rhodobacteraceae , class Alphaproteobacteria ) were obtained from coastal seawater samples. Strain RCA23T was isolated from a 10−7 dilution culture inoculated with seawater from the German Wadden Sea (southern North Sea), reflecting the high abundance of RCA bacteria in this habitat. Strains IMCC1909, IMCC1923 and IMCC1933 were isolated from diluted seawater (10−3) of the Yellow Sea, South Korea. Based on 16S rRNA gene sequence comparison, Octadecabacter antarcticus 307T is the closest described relative of the RCA strains, with 95.4–95.5 % sequence similarity. Cells of RCA23T, IMCC1909, IMCC1923 and IMCC1933 are small motile rods requiring sodium ions. Optimal growth of RCA23T occurs at 25 °C and within a very narrow pH range (pH 7–8, optimum pH 7.5). The DNA G+C base content of RCA23T is 53.67 mol%. The major respiratory lipoquinone is ubiquinone-10 (Q-10) and the dominant fatty acids (>1 %) are 12 : 1 3-OH, 16 : 1ω7c, 16 : 0, 18 : 1ω7c, 18 : 0 and 11-methyl 18 : 1ω7c. The polar lipid pattern indicated the presence of phosphatidylglycerol, two unidentified aminolipids and two unidentified phospholipids. On marine agar, RCA23T forms non-pigmented, transparent to light beige, small (<1 mm), circular, convex colonies. Strain RCA23T harbours all genes for the production of bacteriochlorophyll a (BChl a). Genes encoding the light-harvesting reaction centre of BChl a (pufM) were identified in all RCA strains. No visible pigmentation was observed for any of the strains under laboratory conditions, but spectrophotometric analysis revealed weak production of BChl a by RCA23T. Morphological, physiological and genotypic features of strain RCA23T suggest that it represents a novel species of a new genus within the Rhodobacteraceae , for which we propose the name Planktomarina temperata gen. nov., sp. nov., described previously by Giebel et al. [ISME J 5 (2011), 8–19] as ‘Candidatus Planktomarina temperata’. The type strain of Planktomarina temperata is RCA23T ( = DSM 22400T = JCM 18269T).

Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring

A cream-coloured, Gram-negative, aerobic, non-motile moderately thermophilic, rod-to-irregular-shaped bacterium, CC-GIMAT-2T, was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan, on marine agar 2216. The 16S rRNA gene sequence analysis and subsequent comparisons showed that it was placed into the genus Ruegeria with 97.4 % similarity to Ruegeria lacuscaerulensis ITI-1157T, and a lower sequence similarity to all other species of the genus Ruegeria . Reconstruction of phylogenetic trees indicated that strain CC-GIMAT-2T clustered within the genus Ruegeria . Robust tree topology for the genus Ruegeria including the new strain was only obtained by including all Rhodobacteraceae type strains but not if the analysis was limited to few selected taxa. The quinone system contained exclusively ubiquinone Q-10 and the fatty acid profile consisted mainly of C18 : 1ω7c, 11-methyl C18 : 1ω7c and C12 : 0 3-OH. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminolipid. Other lipids were detected in moderate to minor amounts. The characteristic feature of the polyamine pattern was the predominant triamine spermidine. On the basis of the 16S rRNA gene sequence analysis and of the chemotaxonomic and physiological data, strain CC-GIMAT-2T represents a novel species of the genus Ruegeria , for which the name Ruegeria intermedia sp. nov. is proposed. The type strain is CC-GIMAT-2T ( = CCUG 59209T = LMG 25539T = CCM 7758T).

Description of Tropicibacter mediterraneus sp. nov. and Tropicibacter litoreus sp. nov

Four strains (M15∅_3, M17(T), M49 and R37(T)) were isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. Together with an older preserved isolate (strain 2OM6) from cultured oysters at Vinaroz, Castellón, Spain, the strains were thoroughly characterized in a polyphasic study and were placed phylogenetically within the Roseobacter clade in the family Rhodobacteraceae. Highest 16S rRNA sequence similarities of the five strains to the types of any established species corresponded to Tropicibacter multivorans (95.8-96.4%), Phaeobacter inhibens (95.9-96.3%) and Phaeobacter gallaeciensis (95.9-96.2%). On the other hand, whole genome (ANI) and protein fingerprinting (MALDI-TOF) data proved: (i) non clonality among the strains, and (ii) the existence of two genospecies, one consisting of strains M15∅_3, M17(T), M49 and 2OM6 and another one consisting of strain R37(T). Phenotypic traits determined allow differentiating both genospecies from each other and from closely related taxa. In view of all data collected we propose to accommodate these isolates in two species as members of the genus Tropicibacter, Tropicibacter mediterraneus sp. nov. (type strain M17(T)=CECT 7615(T)=KCTC 23058(T)) and Tropicibacter litoreus sp. nov. (type strain R37(T)=CECT 7639(T)=KCTC 23353(T)).

Ruegeria conchae sp. nov., isolated from the ark clam Scapharca broughtonii

A slightly halophilic, Gram-negative, strictly aerobic, non-motile rod, designated TW15T, was isolated from an ark clam in South Korea. Growth occurred at 10–37 °C, with 1–5 % (w/v) NaCl and at pH 7.0–10.0. Optimal growth occurred at 25–30 °C, with 2 % (w/v) NaCl and at pH 8.0. Strain TW15T exhibited both oxidase and catalase activities. The major fatty acids of strain TW15T were summed feature 8 (consisting of C18 : 1ω7c and/or C18 : 1ω6c) and 11-methyl C18 : 1ω7c. The predominant isoprenoid quinone was ubiquinone-10 (Q-10). The polar lipids of strain TW15T comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and five unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TW15T was most closely related to Ruegeria lacuscaerulensis DSM 11314T (98.0 % 16S rRNA gene sequence similarity). DNA–DNA relatedness with closely related strains was <52±3 %. The DNA G+C content was 55.7 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain TW15T represents a novel species of the genus Ruegeria , for which the name Ruegeria conchae sp. nov. is proposed. The type strain is TW15T ( = KACC 15115T  = JCM 17315T).

Epibacterium ulvae gen. nov., sp. nov., epibiotic bacteria isolated from the surface of a marine alga

Two Gram-reaction-negative, rod-shaped, motile bacteria, designated strains U82 and U95(T), were isolated from the marine alga Ulva australis collected at Sharks Point, Clovelly, a rocky intertidal zone near Sydney, Australia. Both strains were oxidase- and catalase-positive, formed brown- to black-pigmented colonies and required NaCl for growth. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that these strains belong to the Roseobacter clade within the Alphaproteobacteria. The 16S rRNA genes of both strains were identical across the sequenced 1326 nt, but showed differences in the intergenic spacer region (ITS) between the 16S and the 23S rRNA genes. At the genomic level the DNA G+C contents of strains U82 and U95(T) were identical (52.6 mol%) and they had a DNA-DNA hybridization value of 83.7%, suggesting that these strains belong to the same species. The closest described phylogenetic neighbour to strains U82 and U95(T) was Thalassobius aestuarii DSM 15283(T) with 95.8% 16S rRNA gene sequence similarity. Other close relatives include further species of the genera Thalassobius and Shimia. Strains U82 and U95(T) were negative for bacteriochlorophyll a production, showed antibacterial activity towards other marine bacteria, were resistant to the antibiotics gentamicin and spectinomycin and were unable to hydrolyse starch or gelatin. The major fatty acids (>1%) were 18 : 1ω7c, 16 : 0, 18 : 2, 10 : 0 3-OH, 12 : 0, 20 : 1 2-OH and 18 : 0. The polar lipid pattern indicated the presence of phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids and four unidentified phospholipids. Both strains produced ubiquinone 10 (Q-10) as the sole respiratory lipoquinone. Based on their phenotypic and phylogenetic characteristics, it is suggested that strains U82 and U95(T) are members of a novel species within a new genus for which the name Epibacterium ulvae gen. nov., sp. nov. is proposed. The type strain of the type species is U95(T) ( = DSM 24752(T) = LMG 26464(T)).

Ruegeria halocynthiae sp. nov., isolated from the sea squirt Halocynthia roretzi

A Gram-negative, non-motile, rod-shaped bacterial strain, designated MA1-6T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea, and was characterized to determine its taxonomic position. Strain MA1-6T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MA1-6T fell within the clade comprising Ruegeria species and exhibited 95.3–96.5 % similarity to the type strains of recognized Ruegeria species. Strain MA1-6T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid, which is consistent with data for Ruegeria species. The major polar lipids detected in strain MA1-6T and Ruegeria atlantica KCTC 12424T were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and an unidentified lipid. The DNA G+C content of strain MA1-6T was 58.6 mol%. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain MA1-6T can be distinguished from recognized Ruegeria species. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain MA1-6T is considered to represent a novel species of the genus Ruegeria , for which the name Ruegeria halocynthiae sp. nov. is proposed; the type strain is MA1-6T ( = KCTC 23463T = CCUG 60744T).

Thalassobius maritimus sp. nov., isolated from seawater

A Gram-stain-negative, aerobic, motile, rod-shaped bacterial strain, GSW-M6T, was isolated from seawater of Geoje island, Korea, and was subjected to a polyphasic taxonomic study. Strain GSW-M6T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain GSW-M6T clustered with Thalassobius aestuarii, Thalassobius gelatinovorus and Thalassobius mediterraneus. Strain GSW-M6T exhibited 96.2–96.9 % 16S rRNA gene sequence similarity to the type strains of these three Thalassobius species. Strain GSW-M6T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profiles of strain GSW-M6T and the type strains of the three Thalassobius species were similar, with phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid as common major components. The DNA G+C content of strain GSW-M6T was 57 mol%. The mean level of DNA–DNA relatedness between strain GSW-M6T and the type strain of Thalassobius gelatinovorus was 17 %. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, enabled strain GSW-M6T to be differentiated from recognized species of the genus Thalassobius. On the basis of the data presented, strain GSW-M6T is considered to represent a novel species of the genus Thalassobius, for which the name Thalassobius maritimus sp. nov. is proposed. The type strain is GSW-M6T ( = KCTC 23347T  = CCUG 60021T).

Primorskyibacter sedentarius gen. nov., sp. nov., a novel member of the class Alphaproteobacteria from shallow marine sediments

Two Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped bacteria, strains KMM 9015 and KMM 9018T, were isolated from a sample of shallow sediment collected from the Sea of Japan. An analysis of the nearly complete 16S rRNA gene sequences showed that the isolates were very close to each other phylogenetically (99.9 % sequence similarity) and their close relatives were Marinovum algicola FF3T (95.8 and 95.9 %, respectively) and members of the genera Leisingera (95.7–95.1 and 95.8–95.2 %), Phaeobacter (95.0–94.2 and 95.1–94.2 %) and Thalassobius (96.3–94.8 and 96.2–94.7 %) of the class Alphaproteobacteria. In phylogenetic trees based on 16S rRNA gene sequences, strains KMM 9015 and KMM 9018T were positioned as a distinct phylogenetic line adjacent to Marinovum algicola. The major isoprenoid quinone was Q-10, the polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown lipid and the major fatty acid was C18 : 1ω7c, followed by 11-methyl C18 : 1ω7c, in both strains. The DNA G+C contents of strains KMM 9015 and KMM 9018T were 60.2 and 61.9 mol%, respectively. Based on distinctive phenotypic characteristics and phylogenetic analysis, strains KMM 9015 and KMM 9018T represent a novel species in a novel genus, for which the name Primorskyibacter sedentarius gen. nov., sp. nov. is proposed. The type strain of Primorskyibacter sedentarius is strain KMM 9018T ( = NRIC 0784T  = JCM 16874T).

Hasllibacter halocynthiae gen. nov., sp. nov., a nutriacholic acid-producing bacterium isolated from the marine ascidian Halocynthia roretzi

A Gram-negative, aerobic, ovoid to rod-shaped bacterial strain, KME 002(T) was isolated from a marine ascidian, Halocynthia roretzi, off the coast of Gangneung, Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that this strain belonged to the family Rhodobacteraceae in the class Alphaproteobacteria and was closely related to the type strains of Dinoroseobacter shibae, Roseovarius crassostreae and Pseudoruegeria aquimaris with 95.0, 94.7 and 94.5% 16S rRNA gene sequence similarities, respectively. KME 002(T) was an obligately halophilic bacterium requiring 1 to 5% (w/v) NaCl, with an absolute requirement for magnesium chloride for growth. Cells were motile by means of a single polar flagellum and showed budding fission. The predominant cellular fatty acid of the isolate was C(18:1)ω7c and Q-10 was the major ubiquinone. The DNA G+C content of the strain was 71.6 mol%. The major secondary metabolites from cultures in liquid medium were cholic acid derivatives, including 3α,12α-hydroxy-3-keto-glycocholanic acid, 12-hydroxy-3-keto-glycocholanic acid, nutriacholic acid and deoxycholic acid. These characteristics determined in this polyphasic study suggest that strain KME 002(T) represents a novel species in a new genus of the family Rhodobacteraceae. The name Hasllibacter halocynthiae gen. nov., sp. nov. is proposed for this isolate, and the type strain is KME 002(T) (=JCM 16214(T)=KCCM 90082(T)).

Litoreibacter albidus gen. nov., sp. nov. and Litoreibacter janthinus sp. nov., members of the class Alphaproteobacteria isolated from the seashore

Two Gram-negative, strictly aerobic, non-motile bacteria designated strains KMM 3851T and KMM 3842T were respectively isolated from a marine snail specimen (Umbonium costatum) and from surrounding sediments collected simultaneously from the shore of the Sea of Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains KMM 3851T and KMM 3842T were affiliated with the Roseobacter lineage of the class Alphaproteobacteria as a separate phylogenetic line adjacent to the members of the genus Thalassobacter. These novel isolates shared 98.5 % 16S rRNA gene sequence similarity and 15 % DNA–DNA relatedness. The major isoprenoid quinone of both strains was Q-10 and polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and aminophospholipids. In addition, strain KMM 3851T contained two unknown lipids, whereas strain KMM 3842T contained diphosphatidylglycerol. Fatty acid analysis revealed C18 : 1 ω7c and C16 : 0 as major components and small amounts of C18 : 2. The DNA G+C contents were 60.4 mol% (KMM 3851T) and 58.5 mol% (KMM 3842T). Based on distinctive phenotypic characteristics, DNA–DNA hybridization data and phylogenetic distance, strains KMM 3851T and KMM 3842T should be classified as representatives of two novel species in a new genus, Litoreibacter gen. nov., with the type species Litoreibacter albidus sp. nov. (type strain KMM 3851T =NRIC 0773T =JCM 16493T) and a second species Litoreibacter janthinus sp. nov. (type strain KMM 3842T =NRIC 0772T =JCM 16492T).

Celeribacter neptunius gen. nov., sp. nov., a new member of the class Alphaproteobacteria

A whitish Gram-negative, motile, aerobic bacterium, designated strain H 14T, was isolated from seawater collected at St Kilda beach in Port Phillip Bay, Melbourne, Australia. Analysis of 16S rRNA gene sequences revealed that the organism belonged to the Roseobacter lineage of the class Alphaproteobacteria, forming a distinct evolutionary lineage at the genus level. Strain H 14T was distantly related to the genera Nautella, Ruegeria and Pseudoruegeria (family Rhodobacteraceae). Strain H 14T was unable to degrade gelatin, casein, chitin, agar and starch, did not produce any carotenoids, did not possess bacteriochlorophyll a and had a limited ability to utilize carbon sources. Strain H 14T grew with concentrations of 1–8 % (w/v) NaCl and over a temperature range of 5–35 °C. Phosphatidylglycerol was the major phospholipid (90 %); phosphatidylcholine (7.9 %) and phosphatidylethanolamine (2.0 %) were present in minor quantities. The predominant fatty acids were C18 : 1 ω7c (82.4 %), C18 : 1 ω9c (5.1 %) and C18 : 0 (3.8 %). The DNA G+C composition for strain H 14T was 59.1 mol%. Based on the results of physiological, biochemical, chemotaxonomic and phylogenetic investigations, a new genus, Celeribacter gen. nov., with the type species Celeribacter neptunius sp. nov. is proposed. The type strain of the type species is H 14T (=KMM 6012T=CIP 109922T).

Ruegeria faecimaris sp. nov., isolated from a tidal flat sediment

A Gram-negative-staining, non-motile and rod-shaped bacterial strain, HD-28(T), was isolated from a tidal flat of the Yellow Sea, Korea. Strain HD-28(T) grew optimally at pH 7.0-8.0 and 30 °C in the presence of 2-3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HD-28(T) was most closely related to species of the genus Ruegeria and exhibited 95.5-96.9 % 16S rRNA gene sequence similarity to the type strains of Ruegeria species. A neighbour-joining phylogenetic tree based on gyrB gene sequences also showed that strain HD-28(T) fell within the cluster comprising recognized species of the genus Ruegeria, showing 77.5-83.9 % sequence similarity. Strain HD-28(T) contained Q-10 as the predominant ubiquinone and C(18 : 1)ω7c as the major fatty acid. The major polar lipids detected in strain HD-28(T) were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. The DNA G+C content was 57.9 mol%. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain HD-28(T) could be distinguished from recognized species of the genus Ruegeria. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain HD-28(T) is considered to represent a novel species of the genus Ruegeria, for which the name Ruegeria faecimaris sp. nov. is proposed. The type strain is HD-28(T) ( = KCTC 23044(T) = CCUG 58878(T)).

Ruegeria marina sp. nov., isolated from marine sediment

A Gram-negative, neutrophilic and rod-shaped bacterium, strain ZH17(T), was isolated from a marine sediment of the East China Sea and subjected to a polyphasic taxonomic characterization. The isolate grew in the presence of 0-7.5 % (w/v) NaCl and at pH 6.5-9.0; optimum growth was observed with 0.5-3.0 % (w/v) NaCl and at pH 7.5. Chemotaxonomic analysis showed ubiquinone-10 as predominant respiratory quinone and C(18 : 1)ω7c, 11-methyl C(18 : 1)ω7c, C(16 : 0), C(12 : 0) 3-OH and C(16 : 0) 2-OH as major fatty acids. The genomic DNA G+C content was 63.5 mol%. Comparative 16S rRNA gene sequence analysis revealed that the isolate belongs to the genus Ruegeria. Strain ZH17(T) exhibited the closest phylogenetic affinity to the type strain of Ruegeria pomeroyi, with 97.2 % sequence similarity, and less than 97 % sequence similarity with respect to other described species of the genus Ruegeria. The DNA-DNA reassociation value between strain ZH17(T) and R. pomeroyi DSM 15171(T) was 50.7 %. On the basis of phenotypic and genotypic data, strain ZH17(T) represents a novel species of the genus Ruegeria, for which the name Ruegeria marina sp. nov. (type strain ZH17(T) =CGMCC 1.9108(T) =JCM 16262(T)) is proposed.

Gaetbulicola byunsanensis gen. nov., sp. nov., isolated from tidal flat sediment

A Gram-negative, non-motile and pleomorphic bacterial strain, SMK-114T, which belongs to the class Alphaproteobacteria, was isolated from a tidal flat sample collected in Byunsan, Korea. Strain SMK-114T grew optimally at pH 7.0–8.0 and 25–30 °C and in the presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain SMK-114T formed a cluster with Octadecabacter species, with which it exhibited 16S rRNA gene sequence similarity values of 95.2–95.4 %. This cluster was part of the clade comprising Thalassobius species with a bootstrap resampling value of 76.3 %. Strain SMK-114T exhibited 16S rRNA gene sequence similarity values of 95.1–96.3 % to members of the genus Thalassobius. It contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The DNA G+C content was 60.0 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain SMK-114T is considered to represent a novel species in a new genus for which the name Gaetbulicola byunsanensis gen. nov., sp. nov. is proposed. The type strain of Gaetbulicola byunsanensis is SMK-114T (=KCTC 22632T =CCUG 57612T).

Legitimacy is an essential concept of the International Code of Nomenclature of Prokaryotes - a major revision of the Code is called for

Tindall [Int J Syst Evol Microbiol 58 (2008), 1979-1986] claimed that the International Code of Nomenclature of Prokaryotes (the Code) creates a paradox in the application of the term 'legitimate' in relation to valid publication, that the term is dispensable and that the paradox would be resolved by revising the Code to avoid its use. Although it is not clearly explained in the Code, the concept of legitimacy is central to the proposal of names. Discarding the concept would fundamentally alter the conceptual structure of the Code and obscure significant distinctions in formal nomenclature. The text of the Code itself is not clear and a careful reading suggests that it would be enhanced by a critical overview involving textual revision and restructuring of some sections. The Judicial Commission is asked not to accept Tindall's suggested revision and it is proposed that the Editorial Board of the International Committee on Systematics of Prokaryotes re-examine the Code from first principles and make such revisions as will avoid in future the confusion, ambiguities and uncertainties indicated here.

Sediminimonas qiaohouensis gen. nov., sp. nov., a member of the Roseobacter clade in the order Rhodobacterales

Two aerobic bacterial strains, YIM B024(T) and YIM B025, were isolated from a salt mine in Yunnan, south-west China. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. The novel strains grew at 15-37 degrees C, pH 6.5-9.0 and 0.25-20 % (w/v) NaCl; optimum growth was observed at 28-30 degrees C, pH 7.0-8.5 and 1.5-10 % NaCl. Oxidase, catalase and nitrate-reducing activities were detected. The two strains were closely related to each other with a 16S rRNA gene sequence similarity of 100 %. DNA-DNA hybridization experiments revealed high relatedness values (90+/-0.4 %) between strains YIM B024(T) and YIM B025, which suggested that these two new strains constituted a single species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates formed a loose cluster with members of the genus Roseivivax in the Roseobacter clade, but were clearly separated from this genus. The levels of 16S rRNA gene sequence similarity between the two isolates and members of the genus Roseivivax ranged from 92.4 to 93.9 %. The major polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and four unknown phospholipids. The major cellular fatty acids were C(18 : 1)omega7c, C(16 : 0), C(18 : 1)omega9c, 11-methyl C(18 : 1)omega7c and C(19 : 0) cyclo omega8c. The sole respiratory quinone was Q-10 and the genomic DNA G+C content was 63.0-64.1 mol%. The distinct phylogenetic position and a combination of phenotypic and chemotaxonomic characteristics supported the proposal of the new isolates as representing a novel species in a new genus, for which the name Sediminimonas qiaohouensis gen. nov., sp. nov. is proposed. The type strain of the type species is YIM B024(T) (=KCTC 22349(T)=CCTCC AA 208033(T)).