- Volume 56, Issue 11, 2006

A Gram-positive, non-motile, slightly halophilic actinomycete, strain JG-241T, was isolated from jeotgal, a traditional Korean fermented seafood, and its taxonomic position was investigated by using a polyphasic approach. Strain JG-241T grew optimally at 25–30 °C and in the presence of 2–5 % (w/v) NaCl. The physiological and biochemical properties of strain JG-241T were distinguishable from those of recognized Nesterenkonia species. Strain JG-241T had a peptidoglycan type based on l-lys–gly–d-Asp. It contained MK-7, MK-8 and MK-9 as the predominant menaquinones and anteiso-C15 : 0 and anteiso-C17 : 0 as the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. The DNA G+C content was 68.0 mol%. Comparative 16S rRNA gene sequence analysis showed that strain JG-241T falls within the radiation of the cluster comprising Nesterenkonia species. Similarity values between the 16S rRNA gene sequence of strain JG-241T and those of the type strains of Nesterenkonia species ranged from 96.7 to 99.7 %. DNA–DNA relatedness data and repetitive extragenic palindromic DNA-PCR genomic fingerprinting patterns showed that strain JG-241T differs genetically from recognized Nesterenkonia species. On the basis of its phenotypic properties and phylogenetic and genetic distinctiveness, strain JG-241T represents a novel species of the genus Nesterenkonia, for which the name Nesterenkonia jeotgali sp. nov. is proposed. The type strain is JG-241T (=KCTC 19053T=JCM 12610T).

A soil isolate, strain CC-AB07T, was characterized using a polyphasic approach. This organism had chemotaxonomic and morphological properties consistent with its classification in the genus Gordonia. 16S rRNA gene sequence analysis showed that the novel strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Gordonia, its closest neighbours being the type strains of Gordonia alkanivorans, Gordonia amicalis, Gordonia bronchialis, Gordonia desulfuricans, Gordonia polyisoprenivorans and Gordonia rhizosphera. The novel isolate was distinguished from all of these type strains using a range of phenotypic properties and by gyrB gene sequence analysis. It was evident from the genotypic and phenotypic data that strain CC-AB07T should be classified as representing a novel species in the genus Gordonia, for which the name Gordonia soli sp. nov. is proposed. The type strain is CC-AB07T (=BCRC 16810T=DSM 44995T).

A motile, pleomorphic, red-pigmented archaeon, strain EJ-52T, was isolated from water from Lake Ejinor, a saline lake in Inner Mongolia, China. Analysis of the almost-complete 16S rRNA gene sequence showed that the isolate was phylogenetically related to species of the genus Halorubrum, being most closely related to Halorubrum saccharovorum ATCC 29252T (96.1 % sequence similarity), Halorubrum lacusprofundi JCM 8891T (95.9 %), Halorubrum tibetense AS 1.3239T (95.2 %), Halorubrum alcaliphilum AS 1.3528T (95.2 %) and Halorubrum vacuolatum JCM 9060T (95.1 %). The polar lipids of strain EJ-52T were C20C20 derivatives of phosphatidylglycerol phosphate and phosphatidylglycerol phosphate methyl ester and a sulfated diglycosyl diether. Strain EJ-52T requires at least 2.5 M NaCl for growth and grows optimally at 3.4 M NaCl. The strain grows at 25–50 °C, with optimal growth occurring at 35–45 °C. Mg2+ is not required. The DNA G+C content is 64.2 mol%. On the basis of the data obtained in this study, strain EJ52T represents a novel species, for which the name Halorubrum orientale sp. nov. is proposed. The type strain is EJ-52T (=CECT 7145T=JCM 13889T=CGMCC 1.6295T).

A Gram-negative, non-motile, neutrophilic, pleomorphic and extremely halophilic archaeon, strain EJ-57T, was isolated from saline Lake Ejinor in Inner Mongolia, China. Strain EJ-57T was able to grow at 25–50 °C, required at least 1.8 M NaCl for growth (optimum at 3.4 M NaCl) and grew over a pH range from 6.0 to 8.5 (optimum at pH 7.0). Hypotonic treatment with less than 1.5 M NaCl caused cell lysis. Analysis of the almost complete 16S rRNA gene sequence indicated that the isolate represented a member of the genus Natrinema in the family Halobacteriaceae. Strain EJ-57T was most closely related to Natrinema versiforme JCM 10478T (96.2 % sequence similarity), Natrinema pallidum NCIMB 777T (95.9 % sequence similarity), Natrinema altunense JCM 12890T (95.8 % sequence similarity) and Natrinema pellirubrum NCIMB 786T (95.5 % sequence similarity). However, DNA–DNA hybridization experiments showed that strain EJ-57T was not related to these species, with levels of DNA–DNA relatedness equal to or below 39 %. The major polar lipids of the isolate were C20C20 and C20C25 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and the disulfated glycolipid S2-DGA-1. The G+C content of the genomic DNA was 64.7 mol%. Comparative analysis of phenotypic characteristics between strain EJ-57T and recognized Natrinema species supported the conclusion that EJ-57T represents a novel species within this genus, for which the name Natrinema ejinorense sp. nov. is proposed. The type strain is EJ-57T (=CECT 7144T=JCM 13890T=CGMCC 1.6202T).

A Gram-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated Gsoil 104T, was isolated from a soil sample from a ginseng field in Pocheon Province (South Korea) and was characterized taxonomically by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities, strain Gsoil 104T was shown to belong to the family Sphingobacteriaceae, being related to Pedobacter africanus DSM 12126T (97.0 %), Pedobacter caeni LMG 22862T (96.9 %), Pedobacter cryoconitis DSM 14825T (96.8 %) and Pedobacter heparinus DSM 2366T (96.6 %). The phylogenetic distance from any other Pedobacter species with a validly published name was greater than 3.4 % (i.e. <96.6 % 16S rRNA gene sequence similarity). DNA–DNA hybridization experiments showed that values for DNA–DNA relatedness between strain Gsoil 104T and its phylogenetically closest neighbours were below 37 %. The G+C content of the genomic DNA was 43.6 mol%. The predominant respiratory quinone was MK-7. The major fatty acids were C16 : 1 ω7c, iso-C15 : 0, C16 : 0, iso-C17 : 0 3-OH and iso-C15 : 0 2-OH. These chemotaxonomic data support the affiliation of strain Gsoil 104T to the genus Pedobacter. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 104T represents a novel species in the genus Pedobacter, for which the name Pedobacter ginsengisoli sp. nov. is proposed. The type strain is Gsoil 104T (=KCTC 12576T=LMG 23399T).

A polyphasic taxonomic approach was employed to characterize a strain designated GPTSA100-9T, which was isolated from water sampled from a warm spring. The micro-organism, comprising Gram-negative, strictly aerobic rods, could not grow on nutritionally rich media such as tryptic soy broth. Analysis of the 16S rRNA gene sequence (1396 nt) of strain GPTSA100-9T revealed that it is a member of the genus Flavobacterium, sharing 99.8 % sequence similarity with the CFB group bacterium strain A0653 (AF236016), 93.4 % with ‘[Flexibacter] aurantiacus subsp. excathedrus’ and 93.2–92.0 % with Flavobacterium saliperosum, Flavobacterium soli, Flavobacterium aquatile and Flavobacterium columnare. The G+C content of the genomic DNA was 31.0 mol%. The major fatty acids of the strain grown on modified R2A agar were iso-C15 : 0 (18.5 %), iso-C15 : 1 G (18.0 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c, 16.6 %) and iso-C17 : 0 3-OH (9.0 %). On the basis of phenotypic and genotypic characteristics, strain GPTSA100-9T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium indicum sp. nov. is proposed. The type strain is GPTSA100-9T (=MTCC 6936T=DSM 17447T).

A halophilic, Gram-negative, motile, non-sporulating bacterium designated strain FB1T was isolated from a wine-barrel-decalcification wastewater. The organism comprises straight rods and has a strictly respiratory metabolism with O2. Strain FB1T grows optimally at 20–30 °C and 5–6 % NaCl. The predominant fatty acids were found to be C18 : 1 ω9c (30.4 %), C16 : 0 (25.7 %), C12 : 0 3-OH (10.3 %), C16 : 1 ω9c (9.7 %) and C16 : 1 ω7c (8.4 %). A phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain forms a coherent cluster within the genus Marinobacter. The highest level of 16S rRNA gene sequence similarity (97.9 %) exhibited by strain FB1T was with the type strain of Marinobacter excellens. However, the level of DNA–DNA relatedness between the novel strain and M. excellens CIP 107686T was only 31.2 %. The DNA G+C content of strain FB1T was 58.7 mol%. On the basis of phenotypic and genotypic characteristics, and also phylogenetic evidence, strain FB1T is considered to represent a novel species of the genus Marinobacter, for which the name Marinobacter vinifirmus sp. nov. is proposed. The type strain is FB1T (=DSM 17747T=CCUG 52119T).

The taxonomic positions and phylogenetic relationships of two new methylotrophic isolates from Lake Washington (USA) sediment, FAM5T and 500, and the previously described methylotrophic strain EHg5 isolated from contaminated soil in Estarreja (Portugal) were investigated. All three strains were facultative methylotrophs capable of growth on a variety of C1 and multicarbon compounds. Optimal growth occurred at pH 7.5–8 and 30–37 °C. The major fatty acids were C16 : 1 ω7c and C16 : 0. The major quinone was ubiquinone Q8. Neither methanol dehydrogenase nor methanol oxidase activities were detectable in cells grown on methanol, suggesting an alternative, as-yet unknown, mechanism for methanol oxidation. The isolates assimilated C1 units at the level of formaldehyde, via the serine cycle. The DNA G+C content of the strains ranged between 64 and 65 mol%. 16S rRNA gene sequence similarity between the three new isolates was 99.85–100 %, but was below 94 % with other members of the Betaproteobacteria, indicating that the isolates represent a novel taxon. Based on physiological, phenotypic and genomic characteristics of the three isolates, a new genus, Methyloversatilis gen. nov., is proposed within the family Rhodocyclaceae. The type strain of Methyloversatilis universalis gen. nov., sp. nov. is FAM5T (=CCUG 52030T=JCM 13912T).

A bacterial strain (designated KMY03T) that possesses β-glucosidase activity was isolated from soil from a ginseng field in South Korea and was characterized in order to determine its taxonomic position. The bacterium was found to comprise Gram-negative, rod-shaped, motile cells with unipolar polytrichous flagella. On the basis of 16S rRNA gene sequence similarity, strain KMY03T was shown to belong to the family Burkholderiaceae of the Betaproteobacteria, being most closely related to Burkholderia caledonica LMG 19076T (97.8 %), Burkholderia terricola LMG 20594T (97.5 %), Burkholderia xenovorans LMG 21463T (97.4 %) and Burkholderia phytofirmans LMG 22146T (97.3 %). Chemotaxonomic data (major ubiquinone, Q-8; major fatty acids, C17 : 0 cyclo, C16 : 0, C19 : 0 cyclo ω8c and summed feature 2) supported the affiliation of the novel strain with the genus Burkholderia. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed the strain to be differentiated genotypically and phenotypically from Burkholderia species with validly published names. On the basis of these data, strain KMY03T represents a novel species of the genus Burkholderia, for which the name Burkholderia ginsengisoli sp. nov. is proposed. The type strain is KMY03T (=KCTC 12389T=NBRC 100965T).

An intracellular bacterium with the unique ability to enter mitochondria exists in the European vector of Lyme disease, the hard tick Ixodes ricinus. Previous phylogenetic analyses based on 16S rRNA gene sequences suggested that the bacterium formed a divergent lineage within the Rickettsiales (Alphaproteobacteria). Here, we present additional phylogenetic evidence, based on the gyrB gene sequence, that confirms the phylogenetic position of the bacterium. Based on these data, as well as electron microscopy (EM), in situ hybridization and other observations, we propose the name ‘Candidatus Midichloria mitochondrii’ for this bacterium. The symbiont appears to be ubiquitous in females of I. ricinus across the tick's distribution, while lower prevalence is observed in males (44 %). Based on EM and in situ hybridization studies, the presence of ‘Candidatus M. mitochondrii’ in females appears to be restricted to ovarian cells. The bacterium was found to be localized both in the cytoplasm and in the intermembrane space of the mitochondria of ovarian cells. ‘Candidatus M. mitochondrii’ is the first bacterium to be identified that resides within animal mitochondria.

The transfer of Thiobacillus delicatus to the genus Thiomonas as a distinct species, Thiomonas delicata (type strain NBRC 14566T), is confirmed by its morphological and physiological properties, DNA–DNA hybridization and the grouping of its 16S rRNA gene sequence with those of other species of the genus. An emended formal description of Thiomonas delicata is given. The status of Thiomonas cuprina DSM 5495T as a member of the genus is reconsidered.

A bacterial strain, S21BT, was isolated from Altamira Cave (Cantabria, Spain). The cells were Gram-negative, short rods growing aerobically. Comparative 16S rRNA gene sequence analysis revealed that strain S21BT represented a separate subline of descent within the family ‘Aurantimonadaceae’ (showing 96 % sequence similarity to Aurantimonas coralicida) in the order Rhizobiales (Alphaproteobacteria). The major fatty acids detected were C16 : 0 and C18 : 1 ω7c. The G+C content of the DNA from strain S21BT was 71.8 mol%. Oxidase and catalase activities were present. Strain S21BT utilized a wide range of substrates for growth. On the basis of the results of this polyphasic study, isolate S21BT represents a novel species of the genus Aurantimonas, for which the name Aurantimonas altamirensis sp. nov. is proposed. The type strain is S21BT (=CECT 7138T=LMG 23375T).

A Gram-negative, aerobic bacterium, designated strain FR1439T, was isolated from the soil of Dokdo in the Republic of Korea. The cells of strain FR1439T were catalase- and oxidase-positive, motile and rod-shaped. Phylogenetic analysis of the 16S rRNA gene sequence revealed that it represents a distinct line of descent within the genus Pseudomonas. The levels of DNA–DNA relatedness between strain FR1439T and type strains of phylogenetically related species, namely Pseudomonas flavescens, Pseudomonas mendocina, Pseudomonas pseudoalcaligenes and Pseudomonas straminea, ranged from 28 to 37 %. Several phenotypic characteristics, together with the cellular fatty acid composition, can be used to differentiate strain FR1439T from related pseudomonads. On the basis of the polyphasic taxonomic evidence presented in this study, strain FR1439T represents a novel species, for which the name Pseudomonas segetis sp. nov. is proposed. The type strain is FR1439T (=IMSNU 14101T=CIP 108523T=KCTC 12331T).

A Gram-negative, aerobic, coccobacillus to rod-shaped bacterium was isolated from three patients with chronic granulomatous disease. The organism was subjected to a polyphasic taxonomic study. A multilocus phylogenetic analysis based on the 16S rRNA gene, the internal transcribed spacer (ITS) region and the RecA protein demonstrated that the organism belongs to a new sublineage within the acetic acid bacteria in the family Acetobacteraceae. Phenotypic features are summarized as follows: the organism grew at an optimum temperature of 35–37 °C and optimum pH of 5.0–6.5. It produced a yellow pigment, oxidized lactate and acetate, the latter weakly, produced little acetic acid from ethanol and could use methanol as a sole carbon source. The two major fatty acids were a straight-chain unsaturated acid (C18 : 1ω7c) and C16 : 0. The DNA base composition was 59.1 mol% G+C. The very weak production of acetic acid from ethanol, the ability to use methanol, the yellow pigmentation and high optimum temperature for growth distinguished this organism from other acetic acid bacteria. The unique phylogenetic and phenotypic characteristics suggest that the bacterium should be classified within a separate genus, for which the name Granulibacter bethesdensis gen. nov., sp. nov. is proposed. The type strain is CGDNIH1T (=ATCC BAA-1260T=DSM 17861T).

The species Phaseolus vulgaris is a promiscuous legume nodulated by several species of the family Rhizobiaceae. During a study of rhizobia nodulating this legume in Portugal, we isolated several strains that nodulate P. vulgaris effectively and also Macroptilium atropurpureum and Leucaena leucocephala, but they form ineffective nodules in Medicago sativa. According to phylogenetic analysis of the 16S rRNA gene sequence, the strains from this study belong to the genus Rhizobium, with Rhizobium rhizogenes and Rhizobium tropici as the closest related species, with 99.9 and 99.2 % similarity, respectively, between the type strains of these species and strain P1-7T. The nodD and nifH genes carried by strain P1-7T are phylogenetically related to those of other species nodulating Phaseolus. This strain does not carry virulence genes present in the type strain of R. rhizogenes, ATCC 11325T. Analysis of the recA and atpD genes confirms this phylogenetic arrangement, showing low similarity with respect to those of R. rhizogenes ATCC 11325T (91.9 and 94.1 % similarity, respectively) and R. tropici IIB CIAT 899T (90.6 % and 91.8 % similarity, respectively). The intergenic spacer (ITS) of the strains from this study is phylogenetically divergent from those of R. rhizogenes ATCC 11235T and R. tropici CIAT 899T, with 85.9 and 82.8 % similarity, respectively, with respect to strain P1-7T. The tRNA profile and two-primer random amplified polymorphic DNA pattern of strain P1-7T are also different from those of R. rhizogenes ATCC 11235T and R. tropici CIAT 899T. The strains isolated in this study can be also differentiated from R. rhizogenes and R. tropici by several phenotypic characteristics. The results of DNA–DNA hybridization showed means of 28 and 25 % similarity between strain P1-7T and R. rhizogenes ATCC 11235T and R. tropici CIAT 899T, respectively. All these data showed that the strains isolated in this study belong to a novel species of the genus Rhizobium, for which we propose the name Rhizobium lusitanum sp. nov.; the type strain is P1-7T (=LMG 22705T=CECT 7016T).

Two novel mesophilic, facultatively anaerobic, selenate-reducing bacteria, designated strains FUT3661T and Asr22-7T, were isolated from a sediment sample and the alimentary tract of littleneck clams, respectively. Both sources of the samples were collected from the coast of Tokyo Bay, Japan. Cells were Gram-negative rods and motile by means of a polar flagellum. The strains reduced selenate to elemental selenium (Se0) and also reduced iron(III) oxyhydroxide, iron(III) citrate, arsenate, manganese(IV) oxide, elemental sulfur and oxygen and used lactate, pyruvate, yeast extract, tryptone and Casamino acids as electron donors and carbon sources. The strains contained both menaquinone (MK-7) and ubiquinones (Q-7 and Q-8) as isoprenoid quinones. The major fatty acids were C16 : 0 and C16 : 1 ω9c. The G+C content of the genomic DNA was 58.1 mol% for strain FUT3661T and 57.2 mol% for strain Asr22-7T. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strains were related to members of the genus Ferrimonas (<94.0 % similarities), although the two novel strains formed a separate lineage. 16S rRNA gene sequence similarity between strains FUT3661T and Asr22-7T was 96 %. On the basis of this polyphasic analysis, it was concluded that strains FUT3661T and Asr22-7T represent two novel species within the genus Ferrimonas, for which the names Ferrimonas futtsuensis sp. nov. (type strain FUT3661T=NBRC 101558T=DSM 18154T) and Ferrimonas kyonanensis sp. nov. (type strain Asr22-7T=NBRC 101286T=DSM 18153T) are proposed.

A novel, extremely halophilic bacterium was isolated from brine samples collected from Ezzemoul sabkha in north-east Algeria. Cells of this isolate, designated B2T, were Gram-negative, rod-shaped and motile. Growth occurred between 10 and 25 % (w/v) NaCl and the isolate grew optimally at 15–20 % (w/v) NaCl. The pH range for growth was 6.0–9.0 with an optimum at pH 7.0–7.5. The predominant fatty acids were C16 : 0 and C18 : 1 ω9c. Other fatty acids present were C16 : 1 ω9c, C18 : 0 10-methyl, C12 : 0 3-OH, C10 : 0 and C12 : 0. The G+C content of the genomic DNA was 56.0 mol%. 16S rRNA gene sequence analysis indicated that strain B2T was closely related to Salicola marasensis in the Gammaproteobacteria. The level of 16S rRNA gene sequence similarity between strain B2T and the type strain of Salicola marasensis was 99 %. DNA–DNA hybridization experiments between strain B2T and Salicola marasensis indicated a level of relatedness of 52 %. The phenotypic characteristics of strain B2T allowed its differentiation from recognized species of the genus Salicola. Strain B2T was able to hydrolyse starch but not aesculin. It was unable to use carbohydrates and could not use citrate, pyruvate or succinate as sole carbon and energy sources. On the basis of the polyphasic data presented, strain B2T is considered to represent a novel species of the genus Salicola, for which the name Salicola salis sp. nov. is proposed. The type strain is B2T (=CECT 7106T=LMG 23122T).