Bacterial Core Gene Research Articles

A positive correlation between GC content and growth temperature in prokaryotes

BackgroundGC pairs are generally more stable than AT pairs; GC-rich genomes were proposed to be more adapted to high temperatures than AT-rich genomes. Previous studies consistently showed positive correlations between growth temperature and the GC contents of structural RNA genes. However, for the whole genome sequences and the silent sites of the codons in protein-coding genes, the relationship between GC content and growth temperature is in a long-lasting debate.ResultsWith a dataset much larger than previous studies (681 bacteria and 155 archaea with completely assembled genomes), our phylogenetic comparative analyses showed positive correlations between optimal growth temperature (Topt) and GC content both in bacterial and archaeal structural RNA genes and in bacterial whole genome sequences, chromosomal sequences, plasmid sequences, core genes, and accessory genes. However, in the 155 archaea, we did not observe a significant positive correlation of Topt with whole-genome GC content (GCw) or GC content at four-fold degenerate sites. We randomly drew 155 samples from the 681 bacteria for 1000 rounds. In most cases (> 95%), the positive correlations between Topt and genomic GC contents became statistically nonsignificant (P > 0.05). This result suggested that the small sample sizes might account for the lack of positive correlations between growth temperature and genomic GC content in the 155 archaea and the bacterial samples of previous studies. Comparing the GC content among four categories (psychrophiles/psychrotrophiles, mesophiles, thermophiles, and hyperthermophiles) also revealed a positive correlation between GCw and growth temperature in bacteria. By including the GCw of incompletely assembled genomes, we expanded the sample size of archaea to 303. Positive correlations between GCw and Topt appear especially after excluding the halophilic archaea whose GC contents might be strongly shaped by intense UV radiation.ConclusionsThis study explains the previous contradictory observations and ends a long debate. Prokaryotes growing in high temperatures have higher GC contents. Thermal adaptation is one possible explanation for the positive association. Meanwhile, we propose that the elevated efficiency of DNA repair in response to heat mutagenesis might have the by-product of increasing GC content like that happens in intracellular symbionts and marine bacterioplankton.

Spiractinospora alimapuensis gen. nov., sp. nov., isolated from marine sediment of Valparaíso Bay (Chile) and proposal for reclassification of two species of the genus Nocardiopsis.

An alkaliphilic actinobacterium, designated VN6-2T, was isolated from marine sediment collected from Valparaíso Bay, Chile. Strain VN6-2T formed yellowish-white branched substrate mycelium without fragmentation. Aerial mycelium was well developed, forming wavy or spiral spore chains. Strain VN6-2T exhibited a 16S rRNA gene sequence similarity of 93.9 % to Salinactinospora qingdaonensis CXB832T, 93.7 % to Murinocardiopsis flavida 14-Be-013T, and 93.7 % to Lipingzhangella halophila 14-Be-013T. Genome sequencing revealed a genome size of 5.9 Mb and an in silico G+C content of 69.3 mol%. Both of the phylogenetic analyses based on 16S rRNA gene sequences and the up-to-date bacterial core gene sequences revealed that strain VN6-2T formed a distinct monophyletic clade within the family Nocardiopsaceae. Chemotaxonomic assessment of strain VN6-2T showed that the major fatty acids were iso-C16 : 0, anteiso-C17 : 0 and 10-methyl-C18 : 0, and the predominant respiratory quinones were MK-9, MK-9(H2) and MK-9(H4). Whole-cell hydrolysates contained meso-diaminopimelic acid as the cell-wall diamino acid, and ribose and xylose as the diagnostic sugars. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, aminophospholipids, glycolipid and phospholipid. Based on the results of this polyphasic study, a novel genus, Spiractinospora gen. nov., is proposed within the family Nocardiopsaceae and the type species Spiractinospora alimapuensis gen. nov., sp. nov. The type strain is VN6-2T (CECT 30026T, CCUG 66258T). On the basis of the phylogenetic results herein, we also propose that Nocardiopsis arvandica and Nocardiopsis litoralis are later heterotypic synonyms of Nocardiopsis sinuspersici and Nocardiopsis kunsanensis, respectively, for which emended descriptions are given.

Salegentibacter lacus sp. nov. and Salegentibacter tibetensis sp. nov., isolated from hypersaline lakes on the Tibetan Plateau.

Two Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and non-motile strains (LM13ST and JZCK2T) were isolated from hypersaline lakes in China. The colonies of both strains were yellow-pigmented and convex. Both strains could grow at 4-34 °C, pH 6.5-9.0 and with 1.0-13.0 % (w/v) NaCl. Comparisons based on 16S rRNA gene sequences showed that strains LM13ST and JZCK2T share less than 98.3 % similarity with species of the genus Salegentibacter. The phylogenetic tree reconstructed based on 16S rRNA gene sequences also showed that Salegentibacter species are the most closely related neighbours of strains LM13ST and JZCK2T. The sequenced draft genome sizes of strains LM13ST and JZCK2T are 4.06 and 4.22 Mbp with G+C contents of 37.0 and 37.8 mol%, respectively. The phylogenomic tree reconstructed using the Up-to-date Bacterial Core Gene set pipeline also demonstrated that both strains belong to the genus Salegentibacter. The calculated pairwise average nucleotide identity values and digital DNA-DNA hybridization values between strains LM13ST and JZCK2T and Salegentibacter species were less than 86.4 and 32.0 %, respectively. The respiratory quinone in both strains was MK-6. Their major fatty acids were iso-C12 : 0, iso-C14 : 0, C15 : 1 ω10c, iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and C17 : 1 ω10c. Their major polar lipids included phosphatidylethanolamine, one unidentified lipid and one unidentified aminolipid, but strain LM13ST also contained one more unidentified aminolipid, one more unidentified lipid and one unidentified phospholipid. Combining the above descriptions, strains LM13ST and JZCK2T should represent two independent novel species of the genus Salegentibacter, for which the names Salegentibacter lacus sp. nov. (type strain LM13ST=GDMCC 1.2643T=KCTC 82861T) and Salegentibacter tibetensis sp. nov. (type strain JZCK2T=GDMCC 1.2621T=KCTC 82862T) are proposed.

Microcella flavibacter sp. nov., isolated from marine sediment, and reclassification of Chryseoglobus frigidaquae, Chryseoglobus indicus, and Yonghaparkia alkaliphila as Microcella frigidaquae comb.nov., Microcella indica nom. nov., and Microcella alkalica nom. nov.

A novel Gram-staining positive, aerobic, rod-shaped, non-motile and yellow-pigmented actinobacterium, designated strain WY83T, was isolated from a marine sediment of Indian Ocean. Strain WY83T grew optimally at 30-35°C, pH 7-8 and with 0-3% (w/v) NaCl. The predominant menaquinones were MK-10, MK-11 and MK-12, and the major fatty acids were C19:1 ω9c/C19:1 ω11c, anteiso-C15:0, C17:0 3OH, and iso-C16:0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid. The cell-wall peptidoglycan contained lysine as a diamino acid. The DNA G + C content was 72.3mol%. Phylogenetic analysis based on 16S rRNA gene sequences and ninety-two bacterial core genes indicated that strain WY83T formed an evolutionary lineage with Chryseoglobus frigidaquae JCM 14730T, Chryseoglobus indicus CTD02-10-2T, Yonghaparkia alkaliphila JCM 15138T, Microcellaalkaliphila DSM 18851T andMicrocella putealisDSM 19627T within the radiation enclosing members of the family Microbacteriaceae. All pairwise percentage of conserved proteins between strain WY83T and the closely related phylogenetic neighbors were greater than 65%. The average nucleotide identity and in silico DNA-DNA hybridization values were both below the thresholds used for the delineation of a new species. On the basis of the evidence presented, strains WY83T, Y. alkaliphilaJCM 15138T, C. frigidaquaeJCM 14730T, M.alkaliphilaDSM 18851TandM. putealisDSM 19627T should belong to different species of the same genus. Strain WY83T represents a novel species of the genus Microcella, for which the name Microcella flavibacter sp. nov. is proposed. The type strain is WY83T (= KCTC 39637T = MCCC 1A07099T). Furthermore, Chryseoglobus frigidaquae, Chryseoglobus indicus, and Yonghaparkia alkaliphila were reclassified as Microcella frigidaquae comb.nov., Microcella indica nom.nov., and Microcella alkalica nom.nov., respectively.

Isolation, Phylogenetic and Gephyromycin Metabolites Characterization of New Exopolysaccharides-Bearing Antarctic Actinobacterium from Feces of Emperor Penguin.

A new versatile actinobacterium designated as strain NJES-13 was isolated from the feces of the Antarctic emperor penguin. This new isolate was found to produce two active gephyromycin analogues and bioflocculanting exopolysaccharides (EPS) metabolites. Phylogenetic analysis based on pairwise comparison of 16S rRNA gene sequences showed that strain NJES-13 was closely related to Mobilicoccus pelagius Aji5-31T with a gene similarity of 95.9%, which was lower than the threshold value (98.65%) for novel species delineation. Additional phylogenomic calculations of the average nucleotide identity (ANI, 75.9–79.1%), average amino acid identity (AAI, 52.4–66.9%) and digital DNA–DNA hybridization (dDDH, 18.6–21.9%), along with the constructed phylogenomic tree based on the up-to-date bacterial core gene (UBCG) set from the bacterial genomes, unequivocally separated strain NJES-13 from its close relatives within the family Dermatophilaceae. Hence, it clearly indicated that strain NJES-13 represented a putative new actinobacterial species isolated from the gut microbiota of mammals inhabiting the Antarctic. The obtained complete genome of strain NJES-13 consisted of a circular 3.45 Mb chromosome with a DNA G+C content of 67.0 mol%. Furthering genome mining of strain NJES-13 showed the presence of five biosynthetic gene clusters (BGCs) including one type III PKS responsible for the biosynthesis of the core of gephyromycins, and a series of genes encoding for bacterial EPS biosynthesis. Thus, based on the combined phylogenetic and active metabolites characterization presented in this study, we confidently conclude that strain NJES-13 is a novel, fresh actinobacterial candidate to produce active gephyromycins and microbial bioflocculanting EPS, with potential pharmaceutical, environmental and biotechnological implications.

Flavobacterium difficile sp. nov., isolated from a freshwater waterfall.

A bacterial strain designated KDG-16T is isolated from a freshwater waterfall in Taiwan and characterized to determine its taxonomic affiliation. Cells of strain KDG-16T are Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and form light yellow colonies. Optimal growth occurs at 20-25°C, pH 6-7, and with 0% NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set reveal that strain KDG-16T is affiliated with species in the genus Flavobacterium. Analysis of 16S rRNA gene sequences shows that strain KDG-16T shares the highest similarity with Flavobacterium terrigena DSM 17934T (97.7%). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain KDG-16T and the closely related Flavobacterium species are below the cut-off values of 95-96, 90 and 70%, respectively, used for species demarcation. Strain KDG-16T contains iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH as the predominant fatty acids. The polar lipid profile consists of phosphatidylethanolamine, one uncharacterized aminophospholipid, one uncharacterized phospholipid, two uncharacterized aminolipids and two uncharacterized lipids. The major polyamine is homospermidine. The major isoprenoid quinone is MK-6. Genomic DNA G + C content of strain KDG-16T is 31.6%. Based on the polyphasic taxonomic data obtained, strain KDG-16T is considered to represent a novel species in the genus Flavobacterium, for which the name Flavobacterium difficile sp. nov. is proposed. The type strain is KDG-16T (= BCRC 81194T = LMG 31332T).

UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis

Phylogenomic tree reconstruction has recently become a routine and critical task to elucidate the evolutionary relationships among bacterial species. The most widely used method utilizes the concatenated core genes, universally present in a single-copy throughout the bacterial domain. In our previous study, a bioinformatics pipeline termed Up-to-date Bacterial Core Genes (UBCG) was developed with a set of bacterial core genes selected from 1,429 species covering 28 phyla. In this study, we revised a new bacterial core gene set, named UBCG2, that was selected from the more extensive genome sequence set belonging to 3,508 species spanning 43 phyla. UBCG2 comprises 81 genes with nine Clusters of Orthologous Groups of proteins (COGs) functional categories. The new gene set and complete pipeline are available at http://leb.snu.ac.kr/ubcg2.

Pontixanthobacter rizhaonensis sp. nov., a marine bacterium isolated from surface seawater of the Yellow Sea, and proposal of Pseudopontixanthobacter gen. nov., Pseudopontixanthobacter confluentis comb. nov. and Pseudopontixanthobacter sediminis comb. nov.

A bacterial strain designated RZ02T was isolated from surface seawater collected from the Yellow Sea in PR China and characterized by polyphasic taxonomy. Cells of strain RZ02T were Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive rods forming ochre-pigmented colonies. Growth occurred at 7-36 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0) and with 1-5 % (optimum, 2 %) NaCl. The major cellular fatty acids (>10 %) of strain RZ02T were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol and sphingoglycolipid. The genome size of strain RZ02T was 2.79 Mbp with a G+C content of 55.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RZ02T was mostly related to Pontixanthobacter luteolus SW-109T and Pontixanthobacter aestiaquae HDW-31T (97.3 and 97.1% sequence similarity, respectively), and formed a phyletic lineage with members of the genus Pontixanthobacter. The phylogenetic analysis based on the up-to-date bacterial core gene sequences confirmed that strain RZ02T clustered within the genus Pontixanthobacter. The average nucleotide identity and in silico DNA-DNA hybridization values between strain RZ02T and P. luteolus SW-109T and P. aestiaquae HDW-31T were 72.8 and 72.9 % and 18.7 and 18.5%, respectively. Based on these evidences, strain RZ02T is proposed to represent a novel species of the genus Pontixanthobacter under the name Pontixanthobacter rizhaonensis sp. nov. The type strain is RZ02T (=KCTC 62828T=MCCC 1K04521T). In addition, based on the results of whole genome analyses, proposals of Pseudopontixanthobacter gen. nov., Pseudopontixanthobacter confluentis comb. nov. and Pseudopontixanthobacter sediminis comb. nov. are also included.

Reclassification of Algibacter wandonensis as a Later Heterotypic Synonym of Algibacter lectus Based on Whole-Genome Sequence Analysis.

The genus Algibacter belongs to the family Flavobacteriaceae of the Bacteroidetes, and all members of this genus were isolated from marine environments. Among the Algibacter species, two members, Algibacter lectus KMM 3902T and Algibacter wandonensis WS-MY22T, were isolated from green algae and sediment around a brown algae respectively. The 16S rRNA gene sequences of these two type strains possess 99.4% sequence similarity. In this study, further studies were undertaken to clarify the taxonomic assignments of the two species. Whole-genome sequence analysis showed that the similarities for other phylogenetic markers are also very high (i.e. 99.9% for gyrB, 99.6% for recA and 99.9% for rpoD). Average nucleotide identity, average amino acids identity and digital DNA-DNA hybridization value between A. lectus KMM 3902T and A. wandonensis WS-MY22T are 98.3%, 98.6% and 89.4% respectively, all clearly exceed suggested species delineation thresholds. Furthermore, phylogenetic trees based on sequences of 16S rRNA gene and up-to-date bacterial core gene set (UBCG) consisting of 92 genes provided additional evidence that A. lectus KMM 3902T and A. wandonensis WS-MY22T are very closely related. In addition, a review of their profiles indicated that A. lectus KMM 3902T and A. wandonensis WS-MY22T did not present pronounced differences at phenotypic and chemotaxonomic levels. Based on these evidence, we propose that A. wandonensis should be reclassified as later heterotypic synonyms of A. lectus.

Martelella alba sp. nov., isolated from mangrove rhizosphere soil within the Beibu Gulf

Strain BGMRC 2036T was isolated from rhizosphere soil of Bruguiear gymnorrhiza collected from the Beibu Gulf of China. Optimum growth occurred at 28 °C, pH 7.0, and under the conditions of 3–5% (w/v) NaCl. The phylogenetic comparisons of 16S rRNA gene sequences displayed that strain BGMRC 2036T was closely related to Martelella limonii NBRC109441T (96.6% sequence similarity), M. mediterranea CGMCC 1.12224T (96.5%), M. lutilitoris GH2-6T (96.5%), M. radicis BM5-7T (96.2%), and M. mangrove BM9-1T (95.9%), M. suaedae NBRC109440T (95.8%). The phylogenomic tree based on the up-to-date bacterial core gene set indicated that the strain BGMRC 2036T form a clade formed with members of the genera Martelella. The major polar lipids include phosphatidylmethylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphotidylinositol, two unidentified phospholipids, and three unidentified ninhydrin positive phospholipids. The major respiratory quinone is Q-10, which is similar to those of genera Martelella. The main cellular fatty acids are C18:1ω7c, C16:0, and C12:0 aldehyde. Genome sequencing revealed a genome size of 4.99 Mbp and a G + C content of 62.3 mol%. Pairwise comparison of the genomes of the new strain BGMRC 2036T and the three reference strains M. endophytica YC 6887T, M. mediterranea CGMCC 1.12224T, and M. mangrovi USBA-857 indicated that gANI value was lower than 81% and a digital DNA–DNA hybridization value was lower than 27%. The strain BGMRC 2036T possessed genes putatively encoding riboflavin synthesis and flavodoxin A polyphasic taxonomic study suggested that strain BGMRC 2036T represented a novel species belonging to the genus Martelella, and it was named Martelella alba sp. nov. The type strain is BGMRC 2036T (=KCTC 52121T =NBRC 111908T).

Zongyanglinia huanghaiensis gen. nov., sp. nov., a novel denitrifying bacterium isolated from the yellow sea, and transfer of Pelagicola marinus to Zongyanglinia gen. nov. as Zongyanglinia marinus comb. nov.

Two Gram-stain-negative, oxidase- and catalase-positive, aerobic strains (CY05T and H18S-6) were isolated from sediment samples of the Yellow Sea, China. The strains were positive for denitrification. Optimum growth was observed at 20°C, pH 7.5-8.0 and with 2.0%-3.0% NaCl. The predominant cellular fatty acids (> 10%) were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), major respiratory quinone was ubiquinone-10 and main polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and one unidentified aminolipid. The approximate genome size of strains CY05T and H18S-6 were 4.86 and 5.04 Mbp, the genomic G + C content of them were 54.2 and 54.5%, respectively. Both of the phylogenetic analysis based on 16S rRNA gene sequences and the up-to-date bacterial core gene (UBCG) sequences revealed that strains CY05T, H18S-6 and Pelagicola marinus DSW4-44T formed a distinct monophyletic clade within the family Rhodobacteraceae. The ANI and isDDH values between strains CY05T and H18S-6 were 94.0% and 56.5%, between CY05T and Pelagicola marinus DSW4-44T were 94.1% and 59.8%, respectively, all below the accepted threshold value for species delineation. But the ANI and isDDH values between strains H18S-6 and Pelagicola marinus DSW4-44T were 96.8% and 76.7% respectively, indicating that strains H18S-6 and Pelagicola marinus DSW4-44T belong to the same species. Based on the distinctive polyphasic evidence, CY05T represent a novel species of a novel genus of the family Rhodobacteraceae, for which the name Zongyanglinia huanghaiensis gen. nov., sp. nov. is proposed. The type strain is CY05T (= MCCC 1K04409T = KCTC 62200T). Moreover, the reclassification of Pelagicola marinus Choi et al. 2019 as Zongyanglinia marinus comb. nov. (type strain DSW4-44T = KCTC 62762T = KCCM 43261T = JCM 33637T) is proposed based on the polyphasic taxonomic data obtained in this study.

Comparative Analysis of Core and Accessory Genes in Coexpression Network.

Prokaryotes harbor a various proportion of accessory genes in their genomes. The integration of accessory functions with the core regulation network is critical for environmental adaptation, particularly considering a theoretically unlimited number of niches on the earth for microorganisms. Comparative genomics can reveal a co-occurrence pattern between a subset of accessory genes (or variations in core genes) and an adaptation trait, while comparative transcriptomics can further uncover whether a coordinated regulation of gene expression is involved. In this chapter, we introduce a protocol for weighted gene coexpression network construction by using well-developed open source tools, and a further application of such a network in comparative analysis of bacterial core and accessory genes.

Kushneria phosphatilytica sp. nov., a phosphate-solubilizing bacterium isolated from a solar saltern.

A Gram-stain-negative, motile, rod-shaped, non-endospore-forming, aerobic and halophilic bacterium, designated strain YCWA18T, was isolated from the sediment of Jimo-Daqiao saltern in China. This strain was able to grow at NaCl concentrations in the range 0.5-20 % (w/v) with optimum growth at 6 % (w/v) NaCl. Growth occurred at temperatures of 4-40 °C (optimum 28 °C) and pH 4.0-9.0 (optimum 7.0). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YCWA18T belonged to the genus Kushneria and shared the highest sequence similarity of 98.7 % with Kushneria sinocarnis DSM 23229T. Moreover, the phylogenetic analysis based on the 23S rRNA gene sequence also confirmed the phylogenetic position of this novel strain. The predominant fatty acids were C16 : 0, C17 : 0 cyclo and C12 : 0 3-OH. The major isoprenoid quinone was Q-9 (94.2 %) and the polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), an unidentified aminolipid (AL), an unidentified phospholipids (PL) and two unidentified lipids (L). The complete genome of strain YCWA18T consisted of a single, circular chromosome of 3 624 619 bp, with an average G+C content of 59.1 mol%. A genome-based phylogenetic tree constructed using an up-to-date bacterial core gene set (UBCG) showed that strain YCWA18T formed a clade with K. sinocarnis DSM 23229T. However, the level of the ANI and dDDH values between strain YCWA18T and K. sinocarnis DSM 23229T were 82.3 and 24.6 %, respectively, which were low enough to distinguish strain YCWA18T from K. sinocarnis DSM 23229T. Overall, based on the phenotypic, chemotaxonomic, phylogenetic and genomic analyses, strain YCWA18T represents a novel species of genus Kushneria. The name Kushneria phosphatilytica sp. nov. is proposed, with the type strain YCWA18T (=CGMCC 1.9149T=NCCB 100306T).

Oricola thermophila sp. nov., a marine bacterium isolated from tidal flat sediment and emended description of the genus Oricola Hameed et al. 2015

A Gram-stain-negative, facultatively anaerobic, rod-shaped (1.8-4.4×0.5-0.7 µm) and motile marine bacterium, designated as MEBiC13590T, was isolated from tidal flat sediment sampled at Incheon City, on the west coast of the Republic of Korea. The 16S rRNA gene sequence analysis revealed that strain MEBiC13590T showed high similarity to Oricola cellulosilytica CC-AMH-0T (98.2 %), followed by Oceaniradius stylonematis StC1T (97.5 %); however, it clustered with Oricola cellulosilytica. The phylogenomic tree inferred by the up-to-date bacterial core gene set suggested that strain MEBiC13590T shared a phyletic line with Oricola cellulosilytica. Average nucleotide identity and digital DNA-DNA hybridization values (75.0 and 19.3 %, respectively) between strain MEBiC13590T and Oricola cellulosilytica CC-AMH-0T were below the respective species delineation cutoffs. Growth was observed at 22-50 °C (optimum, 45 °C), at pH 5-9 (optimum, pH 7) and with 1-6 % (optimum, 3 %) NaCl. The predominant cellular fatty acids were C16 : 0 (7.6 %), C18 : 0 (12.2 %), 11-methyl C18 : 1 ω7c (5.7 %), C19 : 0 cyclo ω6c and summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c; 38 %). The DNA G+C content was 63.5 mol%. The major respiratory quinone was Q-10. Several phenotypic characteristics such as growth temperature, oxygen requirement, enzyme activities of urease, gelatinase, lipase (C14), α-chymotrypsin, acid phosphatase, β-galactosidase, β-glucosidase etc. differentiate strain MEBiC13590T from Oricola cellulosilytica CC-AMH-0T. Based on this polyphasic taxonomic data, strain MEBiC13590T should be classified as representing a novel species in the genus Oricola for which the name Oricola thermophila sp. nov. is proposed . The type strain is MEBiC13590T (=KCCM 43313T=JCM 33661T).

Tabrizicola oligotrophica sp. nov. and Rhodobacter tardus sp. nov., two new species of bacteria belonging to the family Rhodobacteraceae.

Two Gram-stain-negative, aerobic, non-motile bacteria, designated KMS-5T and CYK-10T, were isolated from freshwater environments. 16S rRNA gene sequence similarity results indicated that these two novel strains belong to the family Rhodobacteraceae. Strain KMS-5T is closely related to species within the genus Tabrizicola (96.1-96.8 % sequence similarity) and Cypionkella (96.5-97.0 %). Strain CYK-10T is closest to Rhodobacter thermarum YIM 73036T with 96.6 % sequence similarity. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set showed that strain KMS-5T is affiliated with species in the genus Tabrizicola and strain CYK-10T is placed in a distinct clade with Rhodobacter blasticus ATCC 33485T, Rhodobacter thermarum YIM 73036T and Rhodobacter flagellatus SYSU G03088T. These two strains shared common chemotaxonomic features comprising Q-10 as the major quinone, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine as the principal polar lipids, and C18 : 1 ω7c as the main fatty acid. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between these two novel isolates and their closest relatives were below the cut-off values of 95-96, 90 and 70 %, respectively, used for species demarcation. The obtained polyphasic taxonomic data suggested that strain KMS-5T represents a novel species within the genus Tabrizicola, for which the name Tabrizicola oligotrophica sp. nov. is proposed with KMS-5T (=BCRC 81196T=LMG 31337T) as the type strain, and strain CYK-10T should represent a novel species of the genus Rhodobacter, for which the name Rhodobacter tardus sp. nov. is proposed with CYK-10T (=BCRC 81191T=LMG 31336T) as the type strain.

Orrella amnicola sp. nov., isolated from a freshwater river, reclassification of Algicoccus marinus as Orrella marina comb. nov., and emended description of the genus Orrella.

A novel Gram-negative, aerobic, non-motile, ovoid to rod-shaped bacterium, designated NBD-18T, was isolated from a freshwater river in Taiwan. Optimal growth occurred at 30 °C, at pH 6 and in the absence of NaCl. The predominant fatty acids of strain NBD-18T were C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C17 : 0 cyclo and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidyldimethylethanolamine. The major polyamine was putrescine. The major isoprenoid quinone was Q-8. The genomic DNA G+C content of strain NBD-18T was 50.9 %. Strain NBD-18T was most closely related to Orrella dioscoreae LMG 29303T and Algicoccus marinus HZ20T at a 16S rRNA gene sequence similarity of 97.7 %. 16S rRNA gene sequence similarity between O. dioscoreae LMG 29303T and A. marinus HZ20T was 97.7 %. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set indicated that strain NBD-18T, O. dioscoreae LMG 29303T and A. marinus HZ20T are affiliated with the same genus. Digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values among these three strains supported that they belong to the same genus and that strain NBD-18T represents a novel species. Thus, A. marinus HZ20T should be reclassified as Orrella marina comb. nov. based on the rules for priority of publication and validation. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain NBD-18T represents a novel species in the genus Orrella, for which the name Orrella amnicola sp. nov. is proposed. The type strain is NBD-18T (=BCRC 81197T=LMG 31338T).

Roseovarius gahaiensis sp. nov., isolated from Gahai Saline Lake, PR China.

A Gram-stain-negative, aerobic, non-motile and ovoid- to rod-shaped bacterial strain, designated GH877T, was isolated from a water sample of Gahai saline lake in Qaidam Basin,PR China. The isolate grew at 5-45 °C, pH 6.0-9.0 (optima, 37 °C and pH 7.5) and with 0.5-20 % (w/v) NaCl (optimum, 2.0 %). The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain GH877T belonged to the genus Roseovarius, and had highest 16S rRNA gene sequence similarity of 97.7 % to Roseovarius pacificus 81-2T, followed by Roseovarius halotolerans HJ50T (97.5 %) and Roseovarius litoreus GSW-M15T (96.8 %). Genome sequencing revealed a genome size of 3 378 519 bp and a G+C content of 59.8 mol %. Up-to-date bacterial core gene set analysis indicated that strain GH877T represents one independent lineage with R. pacificus DSM29589T. The average nucleotide identity values of GH877T with R. pacificus 81-2T and R. halotolerans HJ50T are 80.7 and 77.3 %, respectively. In silico DNA-DNA hybridization values between strain GH877T and R. pacificus 81-2T and R. halotolerans HJ50T are 23.2 and 20.0 %, respectively. Q-10 was the predominant respiratory quinone and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0 were the major cellular fatty acids. The polar lipids of strain GH877T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and two unidentified phosphoglycolipids. Based on polyphasic taxonomic analysis, strain GH877T is proposed to represent a novel species of the genus Roseovarius, for which the name Roseovarius gahaiensis sp. nov. is proposed. (type strain GH877T=CGMCC 1.13971T=KCTC 72576T).

Rhodovarius crocodyli sp. nov., isolated from a crocodile pond.

Bacterial strain CCP-6T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain CCP-6T is affiliated with species in the genus Rhodovarius. Strain CCP-6T was most closely related to Rhodovarius lipocyclicus CCUG 44693T with a 98.9% 16S rRNA gene sequence similarity. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and formed light pink-coloured colonies. Optimal growth occurred at 30 °C, pH 6 and in the absence of NaCl. The major fatty acids of strain CCP-6T were C18 : 1 ω7c, C16 : 0 and C19 : 0 cyclo ω8c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol, three unidentified aminophospholipids and an unidentified phospholipid. The predominant polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content of the genomic DNA was 69.3 mol%. Strain CCP-6T showed 85.8% average nucleotide identity and 14.5% digital DNA-DNA hybridization identity with Rhodovarius lipocyclicus CCUG 44693T. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain CCP-6T represents a novel species in the genus Rhodovarius, for which the name Rhodovarius crocodyli sp. nov. is proposed. The type strain is CCP-6T (=BCRC 81095T=LMG 30310T=KCTC 62188T).

Alteromonas profundi sp. nov., isolated from the Indian Ocean.

A Gram-staining-negative bacterium, designated 345S023T, was isolated from a sea water sample from the Indian Ocean. The results of 16S rRNA gene sequence analysis revealed that 345S023T represents a member of the genus Alteromonas, with closely related type strains Alteromonas fortis 1T (98.7 %), Alteromonas hispanica F-32T (98.6 %) and Alteromonas genovensis LMG 24078T (98.6 %). Up-to-date bacterial core gene set analysis revealed that 345S023T formed a phyletic lineage with Alteromonas australica H 17T. The case for 345S023T representing a novel species was supported by genomic results. Pairwise in silico DNA-DNA hybridization and average nucleotide identity values were much lower than the proposed and generally accepted species boundaries. Strain 345S023T contains ubiquinone-8 (Q-8) as the sole isoprenoid quinone, summed featured 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the dominant cellular fatty acids (>10 %), and phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genome of strain 345S023T consisted of a 4.4 Mb chromosome with a DNA G+C content of 44.4 %. On the basis of these genomic, chemotaxonomic and phenotypic characteristics, we propose a novel species: Alteromonas profundi sp. nov. The type strain is 345S023T(=JCM 33893T=MCCC 1K04570T).

Methylobacterium symbioticum sp. nov., a new species isolated from spores of Glomus iranicum var. tenuihypharum.

Strain SB0023/3T, isolated from spores of the arbuscular mycorrhizal fungus Glomus iranicum var. tenuihypharum, was analysed to determine whether it represents a new species. It was studied for its applicability in the field of agriculture to reduce the input of nitrogen fertilizers. Comparative analysis of the 16S rRNA gene sequence shows the strain to be affiliated to the genus Methylobacterium, the closest similarities (98.7%) being shared with Methylobacterium dankookense. Further phylogenomic analysis through Up-to-date Bacterial Core Gene (UBCG) confirmed Methylobacterium dankookense as its closest relative. Average Nucleotide Identity (ANI) and in silico DNA-DNA hybridization (DDH) were lower than 92% and 44%, respectively, of the values shown by its phylogenetic relatives. Its genome had an approximate length of 6.05Mb and the G + C content of the genome was 70.1mol%. The main cellular fatty acid was Summed Feature 8 (C18:1ω7c and/or C18:1ω6c). It is a Gram-staining-negative, pink-pigmented, strictly aerobic and facultative methylotroph; it grows at 28 ºC and can grow at up to 3% salinity in the presence of sodium chloride. All the data collected support the naming of a novel species to accommodate the strain SB0023/3T, for which the name Methylobacterium symbioticum sp. nov. is proposed. The type strain is SB0023/3T (=CECT 9862T =PYCC 8351T).