Polyphasic Taxonomic Analysis of Pontitalea aquivivens gen. nov., sp. nov., Isolated from Seawater

A Gram-stain-negative, rod-shaped, strictly aerobic, non-motile, and chemo-organoheterotrophic alphaproteobacterium, designated KMU-169T, was isolated from coastal seawater in the Republic of Korea. The novel isolate was able to grow at 0-2.0% NaCl concentrations (w/v), pH 6.0-9.5, and 15-40 °C. The analysis based on 16S rRNA gene sequences indicated that strain KMU-169T belongs to the family Paracoccaceae and shared the highest similarity (97.0%) with "Defluviimonas salinarum" CAU 1641T. The major (> 10%) cellular fatty acids were C18:1 ω7c and summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c). The predominant respiratory quinone was ubiquinone-10. Strain KMU-169T comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, an unidentified phospholipid, and an unidentified lipid. The assembled draft genome size of strain KMU-169T was 4.1 Mbp with a DNA G + C content of 65.0%. The average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values between the genomes of strain KMU-169T and its closely related taxa were 71.9-76.8%, 60.9-76.1%, and 18.4-21.0%, respectively. The genome of the strain KMU-169T revealed the presence of numerous genes involved in bio-macromolecule degradation, indicating a high potential for producing industrially valuable enzymes. Based on the polyphasic taxonomic data reported in this study, a novel genus and a new species of the family Paracoccaceae, for which the name Pontitalea aquivivens gen. nov., sp. nov., is proposed with the type strain KMU-169T (= KCCM 90598T = NBRC 117093T).

Genomic potential for inorganic carbon sequestration and xenobiotic degradation in marine bacterium Youngimonas vesicularis CC-AMW-ET affiliated to family Paracoccaceae

Ecological studies on marine microbial communities largely focus on fundamental biogeochemical processes or the most abundant constituents, while minor biological fractions are frequently neglected. Youngimonas vesicularis CC-AMW-ET, isolated from coastal surface seawater in Taiwan, is an under-represented marine Paracoccaceae (earlier Rhodobacteraceae) member. The CC-AMW-ET genome was sequenced to gain deeper insights into its role in marine carbon and sulfur cycles. The draft genome (3.7 Mb) contained 63.6% GC, 3773 coding sequences and 51 RNAs, and displayed maximum relatedness (79.06%) to Thalassobius litoralis KU5D5T, a Roseobacteraceae member. While phototrophic genes were absent, genes encoding two distinct subunits of carbon monoxide dehydrogenases (CoxL, BMS/Form II and a novel form III; CoxM and CoxS), and proteins involved in HCO3- uptake and interconversion, and anaplerotic HCO3- fixation were found. In addition, a gene coding for ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO, form II), which fixes atmospheric CO2 was found in CC-AMW-ET. Genes for complete assimilatory sulfate reduction, sulfide oxidation (sulfide:quinone oxidoreductase, SqrA type) and dimethylsulfoniopropionate (DMSP) cleavage (DMSP lyase, DddL) were also identified. Furthermore, genes that degrade aromatic hydrocarbons such as quinate, salicylate, salicylate ester, p-hydroxybenzoate, catechol, gentisate, homogentisate, protocatechuate, 4-hydroxyphenylacetic acid, N-heterocyclic aromatic compounds and aromatic amines were present. Thus, Youngimonas vesicularis CC-AMW-ET is a potential chemolithoautotroph equipped with genetic machinery for the metabolism of aromatics, and predicted to play crucial roles in the biogeochemical cycling of marine carbon and sulfur.

Sedimentimonas flavescens gen. nov., sp. nov., isolated from sediment of Clam Island, Liaoning Province

A novel Gram-stain negative, aerobic and ovoid to short rod shaped bacterium with a single polar flagellum, named strain B57^T, was isolated from sediment of Clam Island, Liaoning Province, China. The optimal growth of this strain was found to occur at 37 °C, pH 6-6.5, and in the presence of 2% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B57^T forms a distinct lineage within the family Rhodobacteraceae, sharing high 16S rRNA gene sequence similarity with Sinirhodobacter populi sk2b1^T (97.4%). The average amino acid identity of B57^T and the closely related species were lower than the threshold level for genus delineation. The dominant respiratory quinone of strain B57^T was identified as Q-10. The major fatty acids were found to be Summed Feature 8 (C_18:1ω7c and/or C_18:1ω6c), Summed Feature 3 (C_16:1ω7c and/or C_16:1ω6c) and C_16: 0. The polar lipids were identified as phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, two unidentified phospholipids, one unidentified glycolipid, and one unidentified lipid. The DNA G + C content of strain B57^T was determined to be 64.1 mol%. Based on the biochemical, phylogenetic and chemotaxonomic analysis, strain B57^T is concluded to represent a novel species of a novel genus, for which the name Sedimentimonas flavescens gen. nov., sp. nov.is proposed. The type strain is B57^T (= CGMCC1.19488^T = KCTC 92053^T).

Szabonella alba gen. nov., sp. nov., a motile alkaliphilic bacterium of the family Rhodobacteraceae isolated from a soda lake

A Gram-stain-negative, oxidase- and catalase-positive, rod-shaped, creamy white coloured bacterial strain, DMG-N-6T, was isolated from a water sample of Lake Fertő/Neusiedler See (Hungary). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain forms a distinct linage within the family Rhodobacteraceae . Its closest relatives are Tabrizicola alkalilacus DJCT (96.76% similarity) and Tabrizicola piscis K13M18T (96.76%), followed by Tabrizicola sediminis DRYC-M-16T (96.69 %), Rhodobacter sediminicola JA983T (96.62 %), Tabrizicola aquatica RCRI19T (96.47 %) and Cereibacter johrii JA192T (96.18 %). The novel bacterial strain favours an alkaline environment (pH 8.0-12.0) and grows optimally at 18–28°C in the presence of 2–4 % (w/v) NaCl. Cells of DMG-N-6T were motile by a single subpolar flagellum. Bacteriochlorophyll a was not detected. The predominant respiratory quinone was ubiquinone Q-10. The major cellular fatty acid was C18:1 ω7c. The polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, phosphatidylcholine, an unidentified phospholipid and five unidentified lipids. The assembled draft genome of strain DMG-N-6T had 52 contigs with a total length of 4 219 778 bp and a G+C content of 64.3 mol%. Overall genome-related indices (ANI <77.8 %, AAI <69.0 %, dDDH <19.6 %) with respect to close relatives were all significantly below the corresponding threshold to demarcate bacterial genus and species. Strain DMG-N-6T (=DSM 108208T=NCAIM B.02645T) is strongly different from its closest relatives and is suggested as the type strain of a novel species of a new genus in the family Rhodobacteraceae , for which the name Szabonella alba gen. nov., sp. nov. is proposed.

Roseitranquillus sediminis gen. nov., sp. nov. a novel genus and species of the family Rhodobacteraceae, isolated from sediment of an Arctic fjord

A Gram-negative, aerobic, non-motile, oxidase-positive, catalase-positive, rod-shaped bacterium, designated strain MCCB 386^T was isolated from sediment samples collected from Kongsfjorden, an Arctic fjord. The strain MCCB 386^T showed growth at 4-37 °C (optimum 27°C) in the presence of 1-8% NaCl (w/v, optimum 3.5%) and at pH 6.0-8.0 (optimum pH 7.0). The major fatty acids were C_18:1ω7c (54.0%) and 11-methyl C_18:1ω7c (22.6%). The dominant respiratory quinone was Q-10. The major polar lipids comprised of phosphatidylcholine (PC), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphoglycolipid (PGL), one unidentified aminolipid, two glycolipids and two unidentified lipids. The genomic G+C content of the strain MCCB 386^T was 68.1 mol%. The 16 S rRNA gene sequences based phylogenetic analysis of MCCB 386^T showed that Psychromarinibacter halotolerans YBW34^T (95.88%) is the most closely related species. In addition, overall genome relatedness indices (OGRI) of MCCB 386^T with closely related strains were lower than threshold level for species and genus delineation. The analysis of Biosynthetic Gene clusters (BGCs) revealed the potential of this strain for production of novel bioactive secondary metabolites. As per polyphasic taxonomic characterisation, strain MCCB 386^T represents a novel species of a novel genus for which the name Roseitranquillus sediminis gen. nov., sp. nov. is suggested. The type strain of the species is MCCB 386^T (= JCM 33,538^T= KACC 21,531^T).

Proposal for transfer of Defluviimonas alba to the genus Frigidibacter as Frigidibacter mobilis nom. nov

A polyphasic taxonomic study was undertaken to clarify the exact position of the type strain cai42^T of the species Defluviimonas alba Pan et al. 2015. The results of the 16S rRNA gene sequence analysis indicated that the two sequences from cai42^T shared 99.6 and 99.7 % similarity to that of the type strain SP32^T of the species Frigidibacter albus and formed a coherent clade in the phylogenetic tree. Whole genomic comparison between cai42^T and SP32^T yielded a digital DNA-DNA hybridization estimate of 36.3 %, an average nucleotide identity of 88.8 % and an average amino acid identity of 89.8 %, clearly indicating that the two strains should belong to two genospecies of the same genus. The close relationship between the two strains was underpinned by the results of genome-based phylogenetic analysis. Although cai42^T and SP32^T shared similar physiological and biochemical properties, some striking differences, such as mobility, the temperature range for growth and the polar lipid components, could distinguish them as separate species. Therefore, the comparative phenotypic and genotypic analyses supported the incorporation of Defluviimonas alba into the genus Frigidibacter as Frigidibacter mobilis nom. nov. with the type strain cai42^T (=CGMCC 1.12518^T=LMG 27406^T).

Frigidibacter oleivorans sp. nov., isolated from a deep well with oil reservoir water

A Gram-stain-negative, rod-shaped bacterium, designated XJ4^T, was isolated from oil-contaminated water, collected from Xinjiang Province, north-west PR China (45° 1' 27″ N, 85° 6' 14″ E). Growth occurred at 20-45 °C (optimum, 30 °C) and pH 6.0-10.0 (optimum, pH 6.0-7.0). Strain XJ4^T could tolerate up to 7 % (w/v) NaCl and grow optimally in the absence of NaCl. Phylogenetic analysis based on comparative sequence analysis of 16S rRNA gene sequences indicated that strain XJ4^T belonged to the genus Frigidibacter, and that was closely related to Frigidibacter mobilis cai42^T (97.2 %), Frigidibacter albus SP32^T (97.0 %) and Rhodobacter aestuarii JA296^T (97.0 %). The average nucleotide identity values between XJ4^T and three type strains were 77.9, 77.6 and 71.9 %, respectively. The DNA G+C content of strain XJ4^T was 69.5 mol%. The sole respiratory quinone was Q-10. The major cellular fatty acid was summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c), C_18 : 0 and 11-methyl C_18 : 1  ω7c. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids, an unidentified aminolipid and unidentified lipids. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, strain XJ4^T represents a novel species of the genus Frigidibacter, for which the name Frigidibacter oleivorans sp. nov. is proposed. The type strain is XJ4^T (=CGMCC 1.13778^T=LMG 30952^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.

Tabrizicola alkalilacus sp. nov., isolated from alkaline Lake Dajiaco on the Tibetan Plateau

A novel Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium was isolated from Lake Dajiaco on the Tibetan Plateau. Strain DJC^T grew without NaCl and tolerated up to 3 % (w/v) NaCl. Growth occurred at pH 6.0-10.0 (optimum, pH 7.0-8.0) and 15-37 °C (optimum, 25-30 °C). Vitamins were not required for growth. The main polar lipids of strain DJC^T were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant respiratory quinone was Q-10. The major fatty acid was C_18 : 1ω7c. Genome sequencing revealed a genome size of 4.61 Mbp and a G+C content of 62.9 mol%. Analysis of 16S rRNA sequences showed that strain DJC^T belonged to the genus Tabrizicola, with the closest neighbour Tabrizicola aquatica RCRI19^T (97.5 %). DNA-DNA relatedness between strain DJC^T and the closest phylogenetically related strain T. aquatica RCRI19^T was 40.8 %. Stain DJC^T was clearly distinguished from the type strain mentioned above through phylogenetic analysis, DNA-DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristic comparisons. Based on its phenotypic and chemotaxonomic characteristics, strain DJC^T could be classified as a representative of a novel species of the genus for which the name Tabrizicola alkalilacus sp. nov. is proposed. The type strain is DJC^T (=CICC 24242^T=KCTC 62173^T).

Associated bacteria of Botryococcus braunii (Chlorophyta)

Botryococcus braunii (Chlorophyta) is a green microalga known for producing hydrocarbons and exopolysaccharides (EPS). Improving the biomass productivity of B. braunii and hence, the productivity of the hydrocarbons and of the EPS, will make B. braunii more attractive for industries. Microalgae usually cohabit with bacteria which leads to the formation of species-specific communities with environmental and biological advantages. Bacteria have been found and identified with a few B. braunii strains, but little is known about the bacterial community across the different strains. A better knowledge of the bacterial community of B. braunii will help to optimize the biomass productivity, hydrocarbons, and EPS accumulation. To better understand the bacterial community diversity of B. braunii, we screened 12 strains from culture collections. Using 16S rRNA gene analysis by MiSeq we described the bacterial diversity across 12 B. braunii strains and identified possible shared communities. We found three bacterial families common to all strains: Rhizobiaceae, Bradyrhizobiaceae, and Comamonadaceae. Additionally, the results also suggest that each strain has its own specific bacteria that may be the result of long-term isolated culture.

Pelagivirga sediminicola gen. nov., sp. nov. isolated from the Bohai Sea

A Gram-stain-negative bacterium, strain BH-SD19^T, that was isolated from a marine sediment sample collected from the Bohai Sea, was subjected to a polyphasic taxonomic study. Cells of BH-SD19^T are non-flagellated, non-gliding, oval-shaped rods, 0.5-1.0 µm wide and 1.0-2.0 µm long. BH-SD19^T is strictly aerobic, and oxidase- and catalase-positive. Growth occurs at 15-40 °C (optimum 35 °C), at pH 6.0-8.5 (optimum 7.0-7.5) and with 1-10 % (w/v) NaCl (optimum 2 %). The predominant fatty acids are C19 : 0cyclo ω8c (46.5 %), C16 : 0 (20.3 %) and C18 : 1ω7c and/or C18 : 1ω6c (10.6 %). The major respiratory quinone is Q-10. The major polar lipids are phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The DNA G+C content is 64.0 mol%. BH-SD19^T shows the highest 16S rRNA sequence similarity to Pontibaca methylaminivorans (95.2 %) and strains of species of the genus Roseovarius(93.4-95.2 %). Sequence similarity values between BH-SD19^T and other phylogenetically related species are all below 95.0 %. Phylogenetic trees based on 16S rRNA gene sequences indicate that BH-SD19^T forms a distinct lineage and does not join any known genera in the trees. Phenotypic, chemotaxonomic and phylogenetic data indicate that BH-SD19^T represents a novel genus and species in the family Rhodobacteraceae, for which the name Pelagivirga sediminicola gen. nov., sp. nov. is proposed. The type strain is BH-SD19^T (=CCTCC AB 2017074^T=KCTC 62202^T).

Rhodosalinus sediminis gen. nov., sp. nov., isolated from marine saltern

A novel Gram-stain-negative, moderately halophilic, motile, facultatively anaerobic and rod-shaped strain, designated WDN1C137^T, was isolated from a marine saltern at Wendeng, PR China. Optimal growth occurred at 40 °C, pH 7.5 and with 7.0 % (w/v) NaCl. Q-10 was the sole respiratory quinone. The major cellular fatty acids (>10.0 %) in WDN1C137^T were C18 : 1ω7c (46.2 %), cyclo C19 : 0ω8c (18.7 %) and C16 : 0 (12.3 %). The major polar lipids were phosphatidylglycerol, phosphoglycolipid, phosphatidylcholine, one unidentified glycolipid, one unidentified lipid, one unidentified aminolipid and two unidentified phospholipids. The genomic DNA G+C content was 70.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that WDN1C137^T shared the highest similarity (94.5 %) to Roseivivax jejudonensis KCTC 42110^T, followed by Roseivivax halodurans JCM 10272^T (94.2 %) and Roseivivax roseus DSM 23042^T (94.1 %). WDN1C137^T formed a separate branch from the closely related genera Roseivivax, Loktanella, Paracoccus and Cribrihabitans within the family Rhodobacteraceae, which indicated that it represented a novel genus in the phylogenetic tree. On the basis of the data from the current polyphasic study, the isolate is proposed to represent a novel species of a novel genus within the family Rhodobacteraceae, with the name Rhodosalinus sediminis gen. nov., sp. nov. The type strain of the type species is WDN1C137^T (=KCTC 52478^T=MCCC 1H00170^T).

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).

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).

Amylibacter cionae sp. nov., isolated from the sea squirt Ciona savignyi

A Gram-stain-negative, non-motile, aerobic and rod-shaped bacterial strain, designated H-12T, was isolated from a sea squirt (Ciona savignyi) collected from Tsingtao Port, Jiaozhou Bay, China, and its taxonomic position was investigated. Strain H-12T grew optimally at 25-30 °C, at pH 7.0-8.0 and in the presence of 3.0-4.0 % (w/v) NaCl. The 16S rRNA gene sequence of strain H-12T exhibited the highest similarity to that of the type strain of Amylibacter marinus (95.3 %). A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain H-12T clustered with the type strain of A. marinus. The predominant ubiquinone in strain H-12T was identified as Q-10. The major fatty acids of strain H-12T were C18 : 1ω7c and C18 : 1ω7c 11-methyl. The major polar lipids detected in strain H-12T were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, one unidentified aminolipid, two unidentified phospholipids and five unidentified lipids. The DNA G+C content of strain H-12T was 52.7 mol%. On the basis of phylogenetic, chemotaxonomic and phenotypic properties, strain H-12T is considered to represent a novel species within the genus Amylibacter, for which the name Amylibacter cionae sp. nov. is proposed. The type strain is H-12T (=KCTC 52581T=CGMCC 1.15880T).