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.

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 sediminis sp. nov., isolated from tidal flat sediment

A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterial strain, designated CAU 1488^T, was isolated from tidal flat sediment, and its taxonomic position was investigated using a polyphasic approach. The organism grew optimally at a temperature of 30 °C, at pH 7.0-7.5 and in the presence of 0-6 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1488^T forms a lineage distinct from Ruegeria marisrubri ZGT 118^T (97.9 %), Ruegeria marina ZH17^T (97.6 %), Ruegeria lacuscaerulensis ITI 1157^T (97.5 %), Ruegeria pomeroyi DSS-3^T (97.1 %), Ruegeria profundi ZGT108^T (97.0 %), Ruegeria intermedia CC-GIMAT-2^T (96.8 %), Ruegeria atlantica CECT 4292^T (96.7 %) and Ruegeria kandeliae J95^T (95.9 %). Genome sequencing revealed that CAU 1488^T had a genome size of 4.23 Mbp and a G+C content of 63.2 mol%. Overall genome related indexes including average nucleotide identity and digital DNA-DNA hybridization values were 75.0-83.0 % and 26.2 %, which are below the cutoffs of 95 and 70 %, respectively, indicating that strain CAU 1488^T represents a distinct species from the members of the genus Ruegeria. The predominant quinone was ubiquinone-10 (Q-10). The major fatty acids were summed feature 8 (C_18 : 1  ω7c/ω6c; 60.7 %) and its polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and unidentified aminolipids. On the basis of phenotypic, chemotaxonomic and genomic data, strain CAU 1488^T constitutes a novel species of the genus Ruegeria, for which the name Ruegeria sediminis sp. nov. is proposed. The type strain is CAU 1488^T (=KCTC 62996^T=NBRC 113693^T).

Antarcticimicrobium sediminis gen. nov., sp. nov., isolated from Antarctic intertidal sediment, transfer of Ruegeria lutea to Antarcticimicrobium gen. nov. as Antarcticimicrobium luteum comb. nov

A Gram-stain-negative, aerobic, non-flagellated and rod- or ovoid-shaped bacterium, designated as strain S4J41^T, was isolated from Antarctic intertidal sediment. The isolate grew at 0-37 °C and with 0.5-10 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed Tween 80 and gelatin. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain S4J41^T constituted a distinct phylogenetic line within the family Rhodobacteraceae and was closely related with some species in the genera Ruegeria, Phaeobacter, Pseudopuniceibacterium, Sulfitobacter, Puniceibacterium and Poseidonocella with 98.6-95.7 % 16S rRNA gene sequence similarities. The major cellular fatty acids were C_16 : 0, summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c) and C_18 : 0 and the major polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid. The sole respiratory quinone was Q-10. The genomic DNA G+C content of strain S4J41^T was 60.3 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain S4J41^T is considered to represent a novel species in a new genus within the family Rhodobacteraceae, for which the name Antarcticimicrobium sediminis gen. nov., sp. nov. is proposed. The type strain is S4J41^T (=MCCC 1K03508^T=KCTC 62793^T). Moreover, the transfer of Ruegeria lutea Kim et al. 2019 to Antarcticimicrobium gen. nov. as Antarcticimicrobium luteum comb. nov. (type strain 318-1^T=JCM 30927^T=KCTC 72105^T) is also proposed.

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).

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).

Ruegeria denitrificans sp. nov., a marine bacterium in the family Rhodobacteraceae with the potential ability for cyanophycin synthesis

Strain CECT 5091^T, an aerobic, marine, Gram-reaction- and Gram-stain-negative, chemoheterotrophic bacterium was isolated from oysters harvested off the Spanish Mediterranean coast. Analysis of the 16S rRNA gene sequence placed the strain within the genus Ruegeria, in the family Rhodobacteraceae, with 16S rRNA gene similarities of 98.7, 98.7 and 98.4 % to Ruegeria conchae, Ruegeria atlanticaand Ruegeria arenilitoris, respectively. Average nucleotide identities (ANI) and in silico DNA-DNA hybridization (DDH) were determined, comparing the genome sequence of CECT 5091^T with those of the type strains of 12 species of the genus Ruegeria: the values obtained were always below the thresholds (95-96 % ANI, 70 % in silico DDH) used to define genomic species, proving that CECT 5091^T represents a novel species of the genus Ruegeria. The strain was slightly halophilic and mesophilic, with optimum growth at 26 °C, pH 7.0 and 3 % salinity, it required sodium and magnesium ions for growth and was able to reduce nitrate to dinitrogen. Carbon sources for growth include some carbohydrates (d-ribose, d-glucose, l-rhamnose, N-acetyl-d-glucosamine) and multiple organic acids and amino acids. The major cellular fatty acid was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), representing 70 % of the total fatty acids. Carbon monoxide oxidation, cyanophycin synthetic ability and phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine production are predicted from genome annotation, while bacteriochlorophyll a production was absent. The DNA G+C content of the genome was 56.7 mol%. We propose the name Ruegeriadenitrificans sp. nov. and strain CECT 5091^T (=5OM10^T=LMG 29896^T) as the type strain for the novel species.

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).

Draft genome sequence of the marine Rhodobacteraceae strain O3.65, cultivated from oil-polluted seawater of the Deepwater Horizon oil spill

The marine alphaproteobacterium strain O3.65 was isolated from an enrichment culture of surface seawater contaminated with weathered oil (slicks) from the Deepwater Horizon (DWH) oil spill and belongs to the ubiquitous, diverse and ecological relevant Roseobacter group within the Rhodobacteraceae. Here, we present a preliminary set of physiological features of strain O3.65 and a description and annotation of its draft genome sequence. Based on our data we suggest potential ecological roles of the isolate in the degradation of crude oil within the network of the oil-enriched microbial community. The draft genome comprises 4,852,484 bp with 4,591 protein-coding genes and 63 RNA genes. Strain O3.65 utilizes pentoses, hexoses, disaccharides and amino acids as carbon and energy source and is able to grow on several hydroxylated and substituted aromatic compounds. Based on 16S rRNA gene comparison the closest described and validated strain is Phaeobacter inhibens DSM 17395, however, strain O3.65 is lacking several phenotypic and genomic characteristics specific for the genus Phaeobacter. Phylogenomic analyses based on the whole genome support extensive genetic exchange of strain O3.65 with members of the genus Ruegeria, potentially by using the secretion system type IV. Our physiological observations are consistent with the genomic and phylogenomic analyses and support that strain O3.65 is a novel species of a new genus within the Rhodobacteraceae.

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)).

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).

Ruegeria meonggei sp. nov., an alphaproteobacterium isolated from ascidian Halocynthia roretzi

A Gram-negative, strictly aerobic, non-flagellated and rod-shaped bacterial strain, designated MA-E2-3(T), was isolated from an ascidian (Halocynthia roretzi) collected from the South Sea, South Korea. Strain MA-E2-3(T) was found to grow optimally at 30 °C, at pH 7.0-8.0 and in the presence of 2.0-3.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain MA-E2-3(T) fell within the clade comprising Ruegeria species, clustering consistently with the type strain of Ruegeria halocynthiae, with which it exhibited 98.2 % sequence similarity. Sequence similarities to the type strains of the other recognized Ruegeria species were 94.7-97.7 %. Strain MA-E2-3(T) was found to contain Q-10 as the predominant ubiquinone and C18:1 ω7c as the predominant fatty acid. The major polar lipids of strain MA-E2-3(T) were identified as phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain MA-E2-3(T) was determined to be 58.0 mol%. Mean DNA-DNA relatedness values between strain MA-E2-3(T) and the type strains of four phylogenetically closely related Ruegeria species were in the range of 13-23 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain MA-E2-3(T) is separated from other Ruegeria species. On the basis of the data presented, strain MA-E2-3(T) (=KCTC 32450(T) = CECT 8411(T)) represents a novel species of the genus Ruegeria, for which the name Ruegeria meonggei sp. nov. is proposed.