A facultatively chemolithoautotrophic, thiosulfate-oxidizing, Gram-negative, aerobic, motile, rod-shaped bacterial strain, designated ATSB16T, was isolated from rhizosphere soils of sesame (Sesamum indicum L.). 16S rRNA gene sequence analysis demonstrated that this strain was closely related to Pandoraea pnomenusa LMG 18087T (96.7 % similarity), P. pulmonicola LMG 18016T (96.5 %), P. apista LMG 16407T (96.2 %), P. norimbergensis LMG 18379T (96.1 %) and P. sputorum LMG 18819T (96.0 %). Strain ATSB16T shared 96.0–96.4 % sequence similarity with four unnamed genomospecies of Pandoraea. The major cellular fatty acids of the strain ATSB16T were C17 : 0 cyclo (33.0 %) and C16 : 0 (30.6 %). Q-8 was the predominant respiratory quinone. The major polar lipids were phosphatidylmethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified aminophospholipids. Hydroxyputrescine and putrescine were the predominant polyamines. The genomic DNA G+C content of the strain was 64.0 mol%. On the basis of the results obtained from this study, strain ATSB16T represents a novel species of the genus Pandoraea, for which the name Pandoraea thiooxydans sp. nov. is proposed. The type strain is ATSB16T (=KACC 12757T =LMG 24779T).
Gram-negative, coccoid, non-motile bacteria that are catalase-, urease- and indole-negative, facultatively anaerobic and oxidase-positive were isolated from the bovine rumen using an improved selective medium for members of the Pasteurellaceae. All strains produced significant amounts of succinic acid under anaerobic conditions with glucose as substrate. Phenotypic characterization and multilocus sequence analysis (MLSA) using 16S rRNA, rpoB, infB and recN genes were performed on seven independent isolates. All four genes showed high sequence similarity to their counterparts in the genome sequence of the patent strain MBEL55E, but less than 95 % 16S rRNA gene sequence similarity to any other species of the Pasteurellaceae. Genetically these strains form a very homogeneous group in individual as well as combined phylogenetic trees, clearly separated from other genera of the family from which they can also be separated based on phenotypic markers. Genome relatedness as deduced from the recN gene showed high interspecies similarities, but again low similarity to any of the established genera of the family. No toxicity towards bovine, human or fish cells was observed and no RTX toxin genes were detected in members of the new taxon. Based on phylogenetic clustering in the MLSA analysis, the low genetic similarity to other genera and the phenotypic distinction, we suggest to classify these bovine rumen isolates as Basfia succiniciproducens gen. nov., sp. nov. The type strain is JF4016T (=DSM 22022T =CCUG 57335T).
A Gram-negative, rod-shaped, facultatively anaerobic, halotolerant bacterial strain, designated YIM YD3T, was isolated from a salt mine in Yunnan, south-west China. The taxonomy of strain YIM YD3T was investigated by a polyphasic approach. Strain YIM YD3T was motile, formed pink colonies and was positive for catalase and oxidase activities. Q-10 was the predominant respiratory ubiquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine and two unknown phospholipids. The major fatty acids (>10 % of total fatty acids) were C18 : 1 ω7c, C18 : 1 ω9c, C16 : 0 and C19 : 0 cyclo ω8c. The DNA G+C content was 71.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct line within a clade containing the genera Balneimonas, Bosea, Chelatococcus and Microvirga in the order Rhizobiales, with highest levels of 16S RNA gene sequence similarity to the type strain of Balneimonas flocculans (93.5 %). On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain YIM YD3T represents a novel species in a new genus, for which the name Salinarimonas rosea gen. nov., sp. nov. is proposed, with strain YIM YD3T (=KCTC 22346T=CCTCC AA208038T) as the type strain.
A Gram-stain-negative, facultatively anaerobic bacterial strain, designated 717T, was isolated from a water sample collected from the Muga river, Girona, north-east Spain. Preliminary analysis of the 16S rRNA gene sequence showed that this strain belonged to the genus Aeromonas, the nearest species being Aeromonas veronii (99.5 % similarity, with seven different nucleotides). A polyphasic study based on a multilocus phylogenetic analysis of five housekeeping genes (gyrB, rpoD, recA, dnaJ and gyrA; 3684 bp) showed isolate 717T to be an independent phylogenetic line, with Aeromonas sobria, Aeromonas veronii and Aeromonas allosaccharophila as the closest neighbour species. DNA–DNA reassociation experiments and phenotypic analysis identified that strain 717T represents a novel species, for which the name Aeromonas fluvialis sp. nov. is proposed, with type strain 717T (=CECT 7401T =LMG 24681T).
A gas-vacuolate bacterium, strain 174T, was isolated from a sea-ice core collected from Point Barrow, Alaska, USA. Comparative analysis of 16S rRNA gene sequences showed that this bacterium was most closely related to Psychromonas ingrahamii 37T, with a similarity of >99 %. However, strain 174T could be clearly distinguished from closely related species by DNA–DNA hybridization; relatedness values determined by two different methods between strain 174T and P. ingrahamii 37T were 58.4 and 55.7 % and those between strain 174T and Psychromonas antarctica DSM 10704T were 46.1 and 33.1 %, which are well below the 70 % level used to define a distinct species. Phenotypic analysis, including cell size (strain 174T is the largest member of the genus Psychromonas, with rod-shaped cells, 8–18 μm long), further differentiated strain 174T from other members of the genus Psychromonas. Strain 174T could be distinguished from its closest relative, P. ingrahamii, by its utilization of d-mannose and d-xylose as sole carbon sources, its ability to ferment myo-inositol and its inability to use fumarate and glycerol as sole carbon sources. In addition, strain 174T contained gas vacuoles of two distinct morphologies and grew at temperatures ranging from below 0 to 10 °C and its optimal NaCl concentration for growth was 3.5 %. The DNA G+C content was 40 mol%. Whole-cell fatty acid analysis showed that 16 : 1ω7c and 16 : 0 comprised 44.9 and 26.4 % of the total fatty acid content, respectively. The name Psychromonas boydii sp. nov. is proposed for this novel species, with strain 174T (=DSM 17665T =CCM 7498T) as the type strain.
Novel aerobic, Gram-negative bacteria with DNA G+C contents below 50 mol% were isolated from the culturable microbiota associated with the Mediterranean seagrass Posidonia oceanica. 16S rRNA gene sequence analyses revealed that they belong to the genus Marinomonas. Strain IVIA-Po-186 is a strain of the species Marinomonas mediterranea, showing 99.77 % 16S rRNA gene sequence similarity with the type strain, MMB-1T, and sharing all phenotypic characteristics studied. This is the first description of this species forming part of the microbiota of a marine plant. A second strain, designated IVIA-Po-101T, was closely related to M. mediterranea based on phylogenetic studies. However, it differed in characteristics such as melanin synthesis and tyrosinase, laccase and antimicrobial activities. In addition, strain IVIA-Po-101T was auxotrophic and unable to use acetate. IVIA-Po-101T shared 97.86 % 16S rRNA gene sequence similarity with M. mediterranea MMB-1T, but the level of DNA–DNA relatedness between the two strains was only 10.3 %. On the basis of these data, strain IVIA-Po-101T is considered to represent a novel species of the genus Marinomonas, for which the name Marinomonas balearica sp. nov. is proposed. The type strain is IVIA-Po-101T (=CECT 7378T =NCIMB 14432T). A third novel strain, IVIA-Po-185T, was phylogenetically distant from all recognized Marinomonas species. It shared the highest 16S rRNA gene sequence similarity (97.4 %) with the type strain of Marinomonas pontica, but the level of DNA–DNA relatedness between the two strains was only 14.5 %. A differential chemotaxonomic marker of this strain in the genus Marinomonas is the presence of the fatty acid C17 : 0 cyclo. Strain IVIA-Po-185T is thus considered to represent a second novel species of the genus, for which the name Marinomonas pollencensis sp. nov. is proposed. The type strain is IVIA-Po-185T (=CECT 7375T =NCIMB 14435T). An emended description of the genus Marinomonas is given based on the description of these two novel species, as well as other Marinomonas species described after the original description of the genus.
A bacterium, designated strain DC-196T, isolated from kitchen refuse compost was analysed by using a polyphasic approach. Strain DC-196T was characterized as a Gram-negative short rod that was catalase- and oxidase-positive, and able to grow at 10–40 °C, pH 6–9 and in NaCl concentrations as high as 3 %. Chemotaxonomically, C18 : 1 was observed to be the predominant cellular fatty acid and ubiquinone 10 (Q10) was the predominant respiratory quinone. The G+C content of the genomic DNA was determined to be 66 mol%. On the basis of the genotypic, phenotypic and chemotaxonomic characteristics, strain DC-196T was assigned to the genus Shinella, although with distinctive features. At the time of writing, 16S rRNA gene sequence similarities of 97.6–96.8 % and the low DNA–DNA hybridization values of 38.2–32.2 % with the type strains of the three recognized Shinella species confirmed that strain DC-196T represents a novel species of the genus, for which the name Shinella fusca sp. nov. is proposed (type strain DC-196T=CCUG 55808T=LMG 24714T).
Five heterotrophic, aerobic, catalase- and oxidase-positive, non-motile strains were characterized from freshwater habitats located in Austria, France, Uganda, P. R. China and New Zealand. The strains shared 16S rRNA gene similarities of ≥99.3 %. The novel strains grew on NSY medium over a temperature range of 10–35 °C (two strains also grew at 5 °C and one strain grew at 38 °C) and a NaCl tolerance range of 0.0–0.3 % (four strains grew up to 0.5 % NaCl). The predominant fatty acids were C16 : 0, C18 : 1 ω7c, C12 : 0 3-OH, and summed feature 3 (including C16 : 1 ω7c). The DNA G+C content of strain MWH-MoIso2T was 44.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that the five new strains formed a monophyletic cluster closely related to Polynucleobacter necessarius (96–97 % sequence similarity). This cluster also harboured other isolates as well as environmental sequences which have been obtained from several habitats. Investigations with taxon-specific FISH probes demonstrated that the novel bacteria dwell as free-living, planktonic cells in freshwater systems. Based on the revealed phylogeny and pronounced chemotaxonomic differences to P. necessarius (presence of >7 % C12 : 0 3-OH and absence of C12 : 0 and C12 : 0 2-OH), the new strains are suggested to represent a novel species, for which the name Polynucleobacter cosmopolitanus sp. nov. is proposed. The type strain is MWH-MoIso2T (=DSM 21490T=CIP 109840T=LMG 25212T). The novel species belongs to the minority of described species of free-living bacteria for which both in situ data from their natural environments and culture-based knowledge are available.
The taxonomic positions of two bacterial strains, ir6-1T and ir6-4T, isolated from soil collected in Iriomote Island in Japan, were determined by using a polyphasic taxonomic approach. The strains were facultatively anaerobic, motile and Gram-stain-negative rods and their optimum pH for growth was pH 4.0. Their major respiratory quinone was ubiquinone-8 and the predominant cellular fatty acids were C14 : 0, C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. The G+C content of the genomic DNA of ir6-1T and ir6-4T was 59.9 and 57.5 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strains clustered with the genus Silvimonas in the class Betaproteobacteria. DNA–DNA similarities were lower than 53 % among ir6-1T, ir6-4T and Silvimonas terrae NBRC 100961T, and these strains could be differentiated from each other by several phenotypic characters. Based on these results, we propose the emendation of the genus Silvimonas and inclusion of two novel species, Silvimonas iriomotensis sp. nov. (type strain ir6-1T=NBRC 103188T =CGMCC 1.8859T =KCTC 22513T) and Silvimonas amylolytica sp. nov. (ir6-4T =NBRC 103189T =CGMCC 1.8860T =KCTC 22514T).
A facultatively anaerobic, nitrogen-fixing bacterium, strain MSSRF40T, was isolated from roots of mangrove-associated wild rice (Porteresia coarctata Tateoka). On the basis of 16S rRNA gene sequence similarities, strain MSSRF40T was shown to belong to the family Enterobacteriaceae, most closely related to Cronobacter muytjensii E603T (97.2 % sequence similarity), Enterobacter cloacae subsp. dissolvens LMG 2683T (97.1 %), E. radicincitans D5/23T (97.1 %) and E. ludwigii EN-119T (97.0 %). Sequence analysis of rpoB, gyrB and hsp60 genes showed that strain MSSRF40T had relatively low sequence similarity (<91, <84 and <90 %) to recognized species of different genera of the family Enterobacteriaceae and formed an independent phyletic lineage in all phylogenetic analyses using the 16S rRNA, rpoB, gyrB and hsp60 genes, clearly indicating that strain MSSRF40T could not be affiliated to any of the recognized genera within the family Enterobacteriaceae. The dominant cellular fatty acids were C16 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and C18 : 1 ω7c, similar to those of other members of the Enterobacteriaceae. The DNA G+C content was 50.1 mol%. Phylogenetic distinctiveness and phenotypic differences from its phylogenetic neighbours indicated that strain MSSRF40T represents a novel species and genus within the family Enterobacteriaceae, for which the name Mangrovibacter plantisponsor gen. nov., sp. nov. is proposed. The type strain of Mangrovibacter plantisponsor is strain MSSRF40T (=LMG 24236T =DSM 19579T).
A Gram-negative, motile and pleomorphic bacterial strain, SMK-146T, was isolated from a tidal flat sediment of the Yellow Sea, Korea, and its taxonomic position was investigated. Strain SMK-146T grew optimally at pH 7.0–8.0 and 30 °C. It contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c and 11-methyl C18 : 1 ω7c as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 68.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SMK-146T belongs to the genus Jannaschia. Strain SMK-146T exhibited 16S rRNA gene sequence similarity values of 95.3–97.0 % to the type strains of the five recognized Jannaschia species. The mean DNA–DNA relatedness value between strain SMK-146T and Jannaschia seosinensis KCCM 42114T, the closest phylogenetic neighbour, was 17 %. Differential phenotypic properties also revealed that strain SMK-146T differs from the recognized Jannaschia species. On the basis of phenotypic, phylogenetic and genetic data, strain SMK-146T represents a novel species of the genus Jannaschia, for which the name Jannaschia seohaensis sp. nov. is proposed. The type strain is SMK-146T (=KCTC 22172T =CCUG 55326T).
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).
A Gram-negative, non-motile, psychrotolerant bacterium exhibiting high catalase activity, designated strain T-3-2T, was isolated from a drain of a fish-processing plant. Its catalase activity was 12 000 U (mg protein)−1, much higher than the activity of the other Psychrobacter strains tested. The strain grew at 0–30 °C and in the presence of 0–12 % NaCl. The predominant isoprenoid quinone was ubiquinone-8 (Q-8), and C16 : 1 ω9c and C18 : 1 ω9c were the predominant cellular fatty acids. The DNA G+C content of strain T-3-2T was 43.9 mol%. 16S rRNA gene sequence phylogeny suggested that strain T-3-2T is a member of the genus Psychrobacter, with the closest relatives being the type strains of Psychrobacter nivimaris (99.2 % similarity), P. aquimaris (98.7 %) and P. proteolyticus (98.5 %). DNA–DNA hybridization showed less than 65 % relatedness with these strains. A phylogenetic tree based on gyrB gene sequences was more reliable, with higher bootstrap values than the 16S rRNA gene sequence-based tree. The result also differentiated the isolate from previously reported Psychrobacter species. Owing to the significant differences in phenotypic and chemotaxonomic characteristics and the phylogenetic and DNA–DNA relatedness data, the isolate merits classification within a novel species, for which the name Psychrobacter piscatorii sp. nov. is proposed. The type strain is T-3-2T (=JCM 15603T =NCIMB 14510T).
A novel Gram-negative bacteria, named CZ41_10aT, was isolated from coastal surface waters of the north-western Mediterranean Sea. Cells were motile, pleomorphic rods, 1.6 μm long and 0.7 μm wide and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 65 mol%. Phylogenetic analysis of 16S rRNA gene sequences placed the new isolate in the genus Thalassobaculum, a member of the family Rhodospirillaceae, class Alphaproteobacteria. Unlike Thalassobaculum litoreum CL-GR58T, its closest relative, strain CZ41_10aT was unable to grow anaerobically and did not exhibit nitrate reductase activity. On the basis of DNA–DNA hybridization, fatty acid content and physiological and biochemical characteristics, this isolate represents a novel species for which the name Thalassobaculum salexigens sp. nov. is proposed. The type strain is CZ41_10aT (=DSM 19539T=CIP 109064T=MOLA 84T). An emended description of the genus Thalassobaculum is also given.
A taxonomic study was carried out on strain LMC2up-L3T, which was isolated from a polycyclic aromatic hydrocarbon-degrading consortium enriched with a sediment sample collected from a hydrothermal field of the south-west Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LMC2up-L3T belonged to the genus Oceanibaculum, with the highest sequence similarity of 98.4 % to Oceanibaculum indicum P24T; similarity to other strains was below 93.1 %. DNA–DNA hybridization between strain LMC2up-L3T and O. indicum P24T was 31 %. rep-PCR fingerprints also differentiated strain LMC2up-L3T from O. indicum P24T. The G+C content of the chromosomal DNA was 67.7 mol%. The principal fatty acids were C16 : 1 (17.8 %), C16 : 0 (21.2 %), C18 : 1 ω7c (23.6 %), C18 : 0 (4.1 %), C18 : 1 2-OH (4.5 %) and C19 : 0 cyclo ω8c (17.4 %). The combined genotypic and phenotypic data show that strain LMC2up-L3T represents a novel species of the genus Oceanibaculum, for which the name Oceanibaculum pacificum sp. nov. is proposed, with the type strain LMC2up-L3T (=CCTCC AB 209059T =LMG 24859T =MCCC 1A02656T). An emended description of the genus Oceanibaculum is also provided.
Four strains isolated from cultured Manila clam, Ruditapes philippinarum, in the north-western coast of Spain were characterized phenotypically and genotypically. Phylogenetic analyses based on the 16S rRNA gene sequences indicated that these bacteria were closely related to Aliivibrio wodanis, Aliivibrio salmonicida, Aliivibrio fischeri and Aliivibrio logei with sequence similarities between 98.1 and 96.0 %. Phylogenetic analysis based on the RNA polymerase alpha chain (rpoA), RecA protein (recA), the α-subunit of bacterial ATP synthase (atpA) and the uridine monophosphate (UMP) kinase (pyrH) genes and fluorescent amplified fragment length polymorphism experiments clearly showed that these novel isolates form a tight genomic group different from any currently known Aliivibrio species. On the basis of phylogenetic analysis and phenotypic data, the four strains represent a novel taxon, for which the name Aliivibrio finisterrensis sp. nov. is proposed. Several phenotypic features were revealed that discriminate A. finisterrensis from other Aliivibrio species. The type strain is CMJ 11.1T (=CECT 7228T=LMG 23869T).