Two agarolytic strains of Gram-negative, heterotrophic, facultatively anaerobic, marine bacteria, designated AAM1T and AAT1T, were isolated from seawater samples collected in the shallow coastal region of An-Ping Harbour, Tainan, Taiwan. Cells grown in broth cultures were straight rods that were motile by means of a single polar flagellum. The two isolates required NaCl for growth and grew optimally at about 25–30 °C, in 2–4 % NaCl and at pH 8. They grew aerobically and could achieve anaerobic growth by fermenting d-glucose or other sugars. The major isoprenoid quinone was Q-8 (79.8–92.0 %) and the major cellular fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 26.4–35.6 %), C18 : 1 ω7c (27.1–31.4 %) and C16 : 0 (14.8–16.3 %) in the two strains. Strains AAM1T and AAT1T had DNA G+C contents of 52.9 and 52.4 mol%, respectively. The two strains had a 16S rRNA gene sequence similarity of 98.6 % and shared 84.9–92.4 % sequence similarity with the type strains of Agarivorans albus (91.2–92.4 %), eight Alteromonas species (84.9–87.1 %), two Aestuariibacter species (86.0–87.0 %), Bowmanella denitrificans (86.1–86.7 %), eight Glaciecola species (85.0–87.9 %) and Salinimonas chungwhensis (85.9–86.1 %). Despite their high sequence similarity, strains AAM1T and AAT1T had a DNA–DNA relatedness value of only 4.5 %. The data obtained from these polyphasic taxonomic studies revealed that the two agarolytic isolates could be classified as representatives of two novel species in a new genus, Aliagarivorans gen. nov., with Aliagarivorans marinus sp. nov. [type strain is AAM1T (=BCRC 17888T=JCM 15522T)] as the type species and Aliagarivorans taiwanensis sp. nov. [type strain is AAT1T (=BCRC 17889T=JCM 15537T)] as a second species.
A motile, rod-shaped, pale-brown-pigmented bacterium, designated strain C4T, was isolated from seawater collected from the South Sea (Republic of Korea). Cells were Gram-negative, facultatively anaerobic, and catalase- and oxidase-positive. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 19.4 %), C16 : 0 (16.3 %), C17 : 1 ω8c (9.5 %) and iso-C15 : 0 (7.7 %). The DNA G+C content was 40.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain C4T formed a lineage within the genus Shewanella (92.7–96.1 % sequence similarity to representative strains of the genus Shewanella) and was part of a distinct branch with the clade comprising Shewanella haliotis DW01T and Shewanella algae ATCC 51192T. Phenotypic characteristics enabled strain C4T to be distinguished from S. haliotis and S. algae. On the basis of the data presented in this study, strain C4T represents a novel species, for which the name Shewanella marina sp. nov. is proposed. The type strain is C4T (=KCTC 22185T=JCM 15074T).
The taxonomic position of the genera Advenella and Tetrathiobacter was examined. 16S rRNA gene sequence analysis revealed that the two genera are closely related, representing a monophyletic cluster with high sequence similarity (98.1–99.7 %) within the family Alcaligenaceae. The phenotypic characteristics of the type strains of Advenella incenata, Tetrathiobacter kashmirensis and Tetrathiobacter mimigardefordensis were re-examined using the API 20NE, API ZYM and API 50CH systems. Phylogenetic data together with similarities in phenotypic characteristics, G+C content and cellular acid composition suggest that they should be classified in the same genus. On the basis of the data presented, the two species of the genus Tetrathiobacter should be transferred to the genus Advenella, since this genus has nomenclatural priority. Therefore, Tetrathiobacter kashmirensis and Tetrathiobacter mimigardefordensis should be transferred to the genus Advenella as Advenella kashmirensis comb. nov. (type strain WT001T =LMG 22695T =MTCC7002T) and Advenella mimigardefordensis comb. nov. (type strain DPN7T =DSM 17166T =LMG 22922T). Emended descriptions of Advenella incenata and the genus Advenella are also presented.
Thirteen novel strains were isolated from root nodules of three different leguminous plants of the genera Albizia, Kummerowia and Dalbergia grown in China. Cells of these strains were Gram-negative, strictly aerobic, non-spore-forming, motile rods. Phylogenetic analysis of 16S rRNA gene sequences revealed that they belong to the genus Rhizobium. A representative strain, CCBAU 25010T, showed 98.8 % 16S rRNA gene sequence similarity to its closest phylogenetic relative, Rhizobium sullae IS123T. The 16S–23S intergenic spacer (ITS) sequence of CCBAU 25010T shared 91.5 and 87.2 % sequence similarity, respectively, with those of Rhizobium etli CFN 42T and Rhizobium leguminosarum LMG 14904T. Analysis of the sequences of the housekeeping genes atpD and recA was in agreement with the results of ITS sequence analysis. The nodC gene sequence of CCBAU 25010T was identical to that of Rhizobium tropici CFN 299. DNA–DNA hybridization values for strain CCBAU 25010T ranged from 20.7 % (with Rhizobium mongolense USDA 1844T) to 34.4 % (with R. leguminosarum USDA 2370T). Cell protein SDS-PAGE, BOX-PCR and several phenotypic characteristics, such as use of sole carbon sources and antibiotic resistance, could differentiate the novel strains from defined Rhizobium species. We therefore propose that the novel strains reported in this study form a novel species, Rhizobium mesosinicum sp. nov., with the type strain CCBAU 25010T (=LMG 24135T =JCM 14777T).
A Gram-negative, coccoid to short rod-shaped, non-spore-forming, moderately halophilic bacterium, designated strain YIM 90738T, was isolated from a salt lake in Xinjiang province, north-west China, and was subjected to a polyphasic taxonomic study. The strain was non-motile and grew at pH 6.0–8.0 (optimal growth at pH 7.0), 10–55 °C (optimal growth at 37 °C) and salinities of 1–15 % NaCl (w/v, optimal growth at 8 % NaCl). Ubiquinone 10 was detected as the major respiratory quinone. The cellular fatty acid profile had C18 : 1 ω7c (80.4 % of the total) as the major component, similar to those of members of the genus Paracoccus. The nearest phylogenetic neighbour of strain YIM 90738T was the type strain of Paracoccus homiensis, as determined by 16S rRNA gene sequence analysis (97.5 % similarity). The level of DNA–DNA relatedness between P. homiensis DSM 17862T and strain YIM 90738T was 51.5 %. The G+C content of the genomic DNA of strain YIM 90738T was 60.3 mol%. On the basis of phenotypic and phylogenetic data and its genotypic distinctiveness, strain YIM 90738T (=CCTCC AB 206074T =KCTC 22163T) is proposed as the type strain of a novel species of the genus Paracoccus, Paracoccus saliphilus sp. nov.
Several strains isolated from the legume Pachyrhizus erosus were characterized on the basis of diverse genetic, phenotypic and symbiotic approaches. These novel strains formed two groups closely related to Bradyrhizobium elkanii according to their 16S rRNA gene sequences. Strains PAC48T and PAC68T, designated as the type strains of these two groups, presented 99.8 and 99.1 % similarity, respectively, in their 16S rRNA gene sequences with respect to B. elkanii USDA 76T. In spite of these high similarity values, the analysis of additional phylogenetic markers such as atpD and glnII genes and the 16S–23S intergenic spacer (ITS) showed that strains PAC48T and PAC68T represented two separate novel species of the genus Bradyrhizobium with B. elkanii as their closest relative. Phenotypic differences among the novel strains isolated from Pachyrhizus and B. elkanii were found regarding the assimilation of carbon sources and antibiotic resistance. All these differences were congruent with DNA–DNA hybridization analysis which revealed 21 % genetic relatedness between strains PAC48T and PAC68T and 46 % and 25 %, respectively, between these strains and B. elkanii LMG 6134T. The nodD and nifH genes of strains PAC48T and PAC68T were phylogenetically divergent from those of bradyrhizobia species that nodulate soybean. Soybean was not nodulated by the novel Pachyrhizus isolates. Based on the genotypic and phenotypic data obtained in this study, the new strains represent two novel species for which the names Bradyrhizobium pachyrhizi sp. nov. (type strain PAC48T=LMG 24246T=CECT 7396T) and Bradyrhizobium jicamae sp. nov. (type strain PAC68T=LMG 24556T=CECT 7395T) are proposed.
A Gram-negative, aerobic rod was isolated from the hypersaline, heliothermal and meromictic Ekho Lake (East Antarctica) at a depth of 6 m. The novel strain (designated EL-50T) was oxidase-positive and weakly catalase-positive and metabolized a variety of carboxylic acids, alcohols, sugars and lipids. Cells of strain EL-50T had an absolute requirement for artificial seawater or NaCl. Optimum growth occurred at 16 °C and at pH values ranging from 7.0 to 9.5. A large in vivo absorption band at 865–866 nm indicated the production of bacteriochlorophyll (bchl) a. The predominant cellular fatty acid of strain EL-50T was 18 : 1ω7c, with 3-OH 14 : 1, 16 : 1ω9c, 16 : 0 and 18 : 1ω9c present in lower amounts. Fatty acids 16 : 0 and 18 : 1ω9c were probably amide-linked. The main polar lipids were diphosphatidylglycerol, phospatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. Ubiquinone 10 was produced. The cell-wall diamino acid was meso-diaminopimelic acid. The DNA G+C content of strain EL-50T was 61 mol%. 16S rRNA gene sequence comparisons indicated that the novel isolate was phylogenetically most closely related to alkaliphilic Rhodobaca and Roseinatronobacter species (approximately 96 % 16S rRNA gene similarity). The organism had no particular relationship to any other cultivated members within the Alphaproteobacteria. The distinct morphological, physiological and genotypic differences from the previously described taxa studied supported the description of a new genus and novel species, for which the name Roseibaca ekhonensis gen. nov., sp. nov. is proposed. The type strain is EL-50T (=DSM 11469T=CECT 7235T).
Strain 1a22T, a nitrogen-fixing bacterium, was isolated from soil associated with the rhizosphere of a perennial grass growing in a fallow agricultural field in Ithaca, New York, USA. Analysis of the 16S rRNA gene sequence placed the strain in the Rubrivivax–Roseateles–Leptothrix–Azohydromonas–Aquincola–Ideonella branch of the Betaproteobacteria and the closest characterized relative was the type strain of Ideonella dechloratans (97.7 % 16S rRNA sequence similarity). Cells of strain 1a22T were Gram-negative, motile, straight rods, which formed polyhydroxybutyrate-like granules and were positive for oxidase and weakly positive for catalase. Cells were chemo-organotrophic, unable to grow by reduction of chlorate or nitrate and grew exclusively through aerobic respiration. Growth with mannitol on N-free solid media caused the strain to produce copious amounts of slime. The G+C content of the genomic DNA was 67.4 mol%. The major cellular fatty acids were C16 : 1 cis-9 and C16 : 0 and cells contained significant amounts of the hydroxy fatty acids C10 : 0 3-OH, C12 : 0 2-OH and C12 : 0 3-OH. Based on DNA–DNA hybridization studies, 16S rRNA gene sequence analysis, fatty acid analysis, and morphological and physiological characteristics, strain 1a22T represents a novel species in the genus Ideonella, for which the name Ideonella azotifigens sp. nov. is proposed. The type strain of Ideonella azotifigens is 1a22T (=JCM 15503T=DSM 21438T).
A Gram-negative, aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated Gsoil 191T, was isolated from a soil sample from a ginseng field in Pocheon Province, South Korea, and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 191T belongs to the family Xanthomonadaceae and is related to Dokdonella fugitiva LMG 23001T (97.8 % sequence similarity) and Dokdonella koreensis KCTC 12396T (96.9 %). The G+C content of the genomic DNA was 68.7 mol%. The major respiratory quinone was Q-8 and the major fatty acids were iso-C17 : 1 ω9c (30.6 %), iso-C17 : 0 (21.6 %) and iso-C15 : 0 (13.0 %), supporting the affiliation of strain Gsoil 191T to the genus Dokdonella. DNA–DNA hybridization experiments showed that the DNA–DNA relatedness values between strain Gsoil 191T and its closest phylogenetic neighbours were below 40 %. The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain Gsoil 191T from recognized species of the genus Dokdonella. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 191T represents a novel species of the genus Dokdonella, for which the name Dokdonella ginsengisoli sp. nov. is proposed. The type strain is Gsoil 191T (=KCTC 12564T=DSM 17954T=CCUG 52462T).
An aerobic, Gram-negative, yellow-coloured, rod-shaped bacterial strain, designated KIS28-6T, was isolated from soil from Ulleung, an island located in the East Sea of Korea. A phylogenetic analysis revealed that strain KIS28-6T was a member of the genus Dokdonella, having 16S rRNA gene sequence similarities of 98.1 and 96.9 % with respect to Dokdonella fugitiva CIP 108692T and Dokdonella koreensis DSM 17203T, respectively. Strain KIS28-6T showed DNA–DNA hybridization values of 38 and 32 % with respect to D. fugitiva CIP 108692T and D. koreensis DSM 17203T, respectively. The major fatty acids (>10 %) were iso-C17 : 1 ω9c (35.7 %), iso-C17 : 0 (26.9 %) and iso-C15 : 0 (11.7 %), the major respiratory quinone was Q-8 and the DNA G+C content was 73.0 mol%. On the basis of the results obtained in this polyphasic taxonomic analysis, strain KIS28-6T represents a novel species of the genus Dokdonella, for which the name Dokdonella soli sp. nov. is proposed. The type strain is KIS28-6T (=KACC 12741T =JCM 15421T).
A Gram-negative-staining bacterium, designated strain 25BT, was isolated from a soil sample from a rice field in Guangxi Province, China, and its taxonomic position was investigated by using a polyphasic approach. Cells were rod-shaped, non-spore-forming, non-motile and strictly aerobic. Strain 25BT grew optimally at 37 °C and pH 7.0. The predominant fatty acids of this soil isolate were C18 : 1 ω7c, C19 : 0 cyclo ω8c and C16 : 0. Phylogenetic analysis based on the almost-complete 16S rRNA gene sequence showed that strain 25BT formed a monophyletic clade with the type strain of Microvirga subterranea; the two organisms shared 97.2 % 16S rRNA gene sequence similarity. However, the two strains shared low DNA–DNA relatedness. Strain 25BT was also readily distinguishable from Microvirga subterranea DSM 14364T by various phenotypic characteristics. The combination of genotypic and phenotypic data suggests that the isolate represents a novel species of the genus Microvirga, for which the name Microvirga guangxiensis sp. nov. is proposed. The type strain is 25BT (=CGMCC 1.7666T=JCM 15710T).
Heckmann and Schmidt described the genus Polynucleobacter for bacterial endosymbionts of freshwater ciliates affiliated with the genus Euplotes, and the species Polynucleobacter necessarius for obligate endosymbionts living in the cytoplasm of Euplotes aediculatus. Pure cultures of the type strain could not be established due to the obligate nature of the symbiotic relationship between the endosymbionts and their hosts. Therefore, Polynucleobacter necessarius is one of a few bacterial species with validly published names that lack a deposited pure culture. Meanwhile, it was demonstrated that the endosymbionts used for the description of the type of Polynucleobacter necessarius are closely related to obligately free-living strains. Similarity values of the 16S rRNA gene sequences obtained from the endosymbionts in the ciliate culture and free-living isolates in the range 99.1–99.4 % indicate that these organisms belong to the same species. Here, we have emended the description of Polynucleobacter necessarius by characterization of free-living strains maintained as pure cultures. The species Polynucleobacter necessarius was characterized as having low G+C contents of the DNA (44–46 mol%), small genome sizes (1.5–2.5 Mbp) and a lack of motility. Because of distinct differences in lifestyle and the genome size of Polynucleobacter necessarius strains, we propose that two novel subspecies should be established, Polynucleobacter necessarius subsp. necessarius subsp. nov. [with a type, which is a description based on endosymbionts in the culture ‘stock 15’ of the ciliate E. aediculatus (ATCC 30859)] and Polynucleobacter necessarius subsp. asymbioticus subsp. nov. [with the type strain QLW-P1DMWA-1T (=DSM 18221T=CIP 109841T)], for the obligate endosymbionts of E. aediculatus and Euplotes harpa and obligately free-living strains, respectively.
The taxonomic status of a Gram-negative-staining bacterium, isolated from the faeces of a seal, was investigated using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that the novel isolate formed a distinct phyletic line within the genus Psychrobacter, displaying >3.3 % sequence divergence with other known Psychrobacter species. The generic assignment was confirmed by chemotaxonomic data, which revealed a fatty acid profile that included straight-chain saturated, unsaturated and 3-hydroxylated fatty acids, with C18 : 1 ω9c as the major fatty acid. A ubiquinone with eight isoprene units (Q-8) was the predominant respiratory quinone and spermidine was the predominant polyamine. The novel isolate was distinguished from other members of the genus Psychrobacter by using a set of phenotypic properties. On the basis of phenotypic and phylogenetic considerations, it is proposed that the new isolate represents a novel species, for which the name Psychrobacter lutiphocae sp. nov. is proposed. Strain IMMIB L-1110T (=DSM 21542T=CCUG 56590T) is the type strain.
A novel polycyclic aromatic hydrocarbon (PAH)-degrading bacterium, strain H25T, which was isolated from deep-sea water of the Indian Ocean, was studied phenotypically, genotypically and phylogenetically. Strain H25T can utilize several PAHs including phenanthrene and fluoranthene as sole carbon sources. The 16S rRNA gene sequence of strain H25T showed the highest similarity with that of Novosphingobium naphthalenivorans TUT562T (96.3 %), and showed lower similarities (92.1–96.0 %) with other members of the genus Novosphingobium. The major fatty acids of strain H25T were C14 : 0 2-OH (3.2 %), C16 : 0 (13.6 %), C16 : 1 ω7c (5.2 %), C18 : 0 (13.4 %) and C18 : 1 ω7c (57.0 %), which accounted for 92.3 % of the total fatty acids. It had ubiquinone 10 as the major respiratory quinone and spermidine as the major polyamine. All these characteristics were consistent with those of recognized Novosphingobium species. Results of DNA–DNA hybridization experiments and BOX-PCR fingerprint comparisons also indicate that strain H25T represents a novel Novosphingobium species, for which the name Novosphingobium indicum sp. nov. is proposed. The type strain is H25T (=MCCC 1A01080T =CGMCC 1.6784T =LMG 24713T).
A Gram-negative, spiral-shaped, phototrophic, purple non-sulfur bacterial strain, designated JA145T, was isolated from a freshwater habitat. Cells of strain JA145T were motile by means of a monopolar flagellum. Intracellular photosynthetic membranes were of the stacked type. Bacteriochlorophyll a and the carotenoid lycopene and its glucosides were present as photosynthetic pigments. There was no vitamin requirement for strain JA145T. The predominant cellular fatty acids were C16 : 1 ω7c/C16 : 1 ω6c (22.24 %), C16 : 0 (22.97 %) and C18 : 1 ω7c (43.24 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JA145T clustered with species of the genus Phaeospirillum, in the class Alphaproteobacteria. The highest sequence similarities of strain JA145T were found with the type strains of Phaeospirillum fulvum (96.12 %) and Phaeospirillum molischianum (96.19 %). Based on the 16S rRNA gene sequence analysis and the morphological and physiological characteristics, strain JA145T is considered to represent a novel species, for which the name Phaeospirillum chandramohanii sp. nov. is proposed. The type strain is JA145T (=JCM 14933T=KCTC 5703T=NBRC 104961T).
Strain CN83T, a Gram-negative, aerobic, rod-shaped bacterium, was isolated from sediment of the East China Sea. The isolate was catalase- and oxidase-positive and cells were motile by means of polar flagella. The DNA G+C content was 44.9 mol%. The major fatty acids were C16 : 1 ω7c and/or iso-C15 : 0 2-OH, C16 : 0, C18 : 1 ω7c, C14 : 0 and C12 : 0. 16S rRNA gene sequence analysis showed that strain CN83T belonged to the genus Vibrio and had the highest sequence similarity to Vibrio agarivorans (98.4 %) and Vibrio campbellii (97.8 %). Phylogenetic analysis revealed that strain CN83T formed a monophyletic clade adjacent to the type strain of V. agarivorans. The DNA–DNA hybridization values of strain CN83T with V. agarivorans DSM 13756T and V. campbellii DSM 19270T were 44.6 and 25.5 %, respectively. On the basis of the phenotypic and genotypic data, strain CN83T represents a novel species of the genus Vibrio, for which the name Vibrio hangzhouensis sp. nov. is proposed. The type strain is CN83T (=CGMCC 1.7062T=JCM 15146T).