- Volume 60, Issue 7, 2010

A Gram-stain-positive, obligately alkaliphilic bacterium designated strain GMBE 72T was isolated from mushroom compost from Yalova, located in the Marmara region of Turkey. Cells were aerobic, straight rods and they formed subterminal to terminal ellipsoidal endospores. The isolate was catalase-positive, oxidase-negative and motile and contained a type A1γ peptidoglycan based on meso-diaminopimelic acid. The strain grew at pH 8.0–12.5. The major cellular fatty acid was anteiso-C15 : 0. The genomic DNA G+C content was 40.2 mol%. Phylogenetic analyses based on 16S rRNA gene sequencing showed that strain GMBE 72T belonged to the genus Bacillus and exhibited 98.2 % sequence similarity to Bacillus pseudofirmus DSM 8715T. DNA–DNA reassociation was 56 % between GMBE 72T and B. pseudofirmus DSM 8715T. According to our polyphasic characterization, strain GMBE 72T represents a novel species of the genus Bacillus, for which the name Bacillus marmarensis sp. nov. is proposed. The type strain is GMBE 72T (=DSM 21297T =JCM 15719T).

Identification of a bacterial strain, designated CJ71T, was carried out using a polyphasic taxonomic approach. Strain CJ71T was isolated from sediment from the estuarine wetland of the Han River, South Korea, by enrichment culture using pyrene as the sole carbon and energy source. The isolate was white-pigmented, rod-shaped, Gram-positive, strictly aerobic and motile. 16S rRNA gene sequence analysis revealed that strain CJ71T had the highest sequence similarity (96.9 %) to Brevibacillus formosus DSM 9885T. The predominant cellular fatty acids in strain CJ71T were anteiso-C15 : 0 (49.5 %), iso-C15 : 0 (16.9 %), iso-C14 : 0 (16.9 %) and iso-C16 : 0 (4.9 %). The major isoprenoid quinone was MK-7. The G+C content of the genomic DNA was 52.4 mol%. Results from the polyphasic taxonomic study suggest that strain CJ71T represents a novel species of the genus Brevibacillus for which the name Brevibacillus fluminis sp. nov. is proposed; the type strain is CJ71T (=KACC 13381T=JCM 15716T)

Although Anoxybacillus and Geobacillus, two genera of thermophilic bacteria close to the genus Bacillus, have only been described recently, the number of species in these genera has increased rapidly. Four thermophilic, lipolytic strains (DR01, DR02, DR03 and DR04) isolated from a hot spring in Veracruz (Mexico), which could not be identified phenotypically, were subjected to 16S rRNA gene sequence analysis. Three strains were identified as belonging to the genus Anoxybacillus, but strain DR03 was identified as Geobacillus pallidus. This result led us to perform a phylogenetic analysis of the genera Anoxybacillus and Geobacillus based on 16S rRNA gene sequences from all the type strains of these genera. Phylogenetic trees showed three major clusters, Anoxybacillus–Geobacillus tepidamans, Geobacillus sensu stricto and Geobacillus pallidus, while the 16S rRNA gene sequences of G. pallidus (DR03 and the type strain) showed low similarity to sequences of Anoxybacillus (92.5–95.1 %) and Geobacillus (92.8–94.5 %) species, as well as to Bacillus subtilis (92.2–92.4 %). In addition, G. pallidus could be differentiated from Anoxybacillus and Geobacillus on the basis of DNA G+C content and fatty acid and polar lipid profiles. From these results, it is proposed that Geobacillus pallidus should be classified in a novel genus, for which we propose the name Aeribacillus, as Aeribacillus pallidus gen. nov., comb. nov. The type strain of Aeribacillus pallidus is H12T (=ATCC 51176T =DSM 3670T =LMG 19006T).

A novel strain, HY-22RT, was isolated from soil of a Euphrates poplar forest in Xinjiang, China. The cells were Gram-positive-staining, rod-shaped and motile by means of peritrichous flagella. Growth occurred at 10–37 °C (optimum 30 °C), at pH 7.0–8.0 (optimum pH 7.0) and with 0–1 % NaCl. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HY-22RT was closely related to Cohnella phaseoli GSPC1T (96.3 % sequence similarity). The major respiratory quinone was MK-7 and the predominant fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 49.6 mol%. On the basis of the phylogenetic, physiological and chemotaxonomic data, strain HY-22RT represents a novel species in the genus Cohnella, for which the name Cohnella luojiensis sp. nov. is proposed. The type strain is HY-22RT (=CCTCC AB 208254T =NRRL B-59213T).

A Gram-negative, aerobic, rod-shaped, motile Brevundimonas-like bacterial strain, J22T, was isolated from black sand collected from Soesoggak, Jeju Island, Korea. Growth of strain J22T was observed in R2A medium at temperatures between 10 and 42 °C (optimum 30 °C), between pH 6.5 and 10.5 (optimum pH 7.5) and at a NaCl concentration between 0 and 4 % (w/v) (optimum 0–1 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain J22T belonged to the genus Brevundimonas, with high sequence similarities of >97 % to the sequence of the type strains Brevundimonas alba CB88T, Brevundimonas lenta DS-18T, Brevundimonas variabilis CB17T, Mycoplana bullata TK0051T, Brevundimonas kwangchunensis KSL-102T, Brevundimonas intermedia CB63T, Brevundimonas subvibrioides CB81T and Brevundimonas bacteroides CB7T. Strain J22T exhibited DNA–DNA relatedness values of less than 22.2 % with the phylogenetically related species of the genus Brevundimonas. The DNA G+C content of strain J22T was 66.3 mol%. The predominant cellular fatty acids were C18 : 1 ω7c, C16 : 0 and C16 : 1 ω9c; C12 : 0 3-OH was present, which chemotaxonomically characterizes the members of the genus Brevundimonas. Phylogenetic, genomic and biochemical characteristics served to differentiate this isolate from recognized members of the genus Brevundimonas. Strain J22T (=KCTC 22177T=JCM 15911T) should be classified as a novel species in the genus Brevundimonas, for which the name Brevundimonas basaltis sp. nov. is proposed.

A Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (Sa25T) was isolated from air of a duck barn. 16S rRNA gene and recA sequence analyses clearly placed the isolate in the vicinity of the Brucella–Ochrobactrum–Pseudochrobactrum group, with the closest relative being Pseudochrobactrum glaciei KMM 3858T. This allocation was confirmed by analyses of the quinone system (ubiquinone Q-10), fatty acid data (major fatty acids C18 : 1 ω7c and C19 : 0 cyclo ω8c) and polar lipid profile (major components diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and unknown aminolipid AL1; moderate amounts of three unknown polar lipids, L1–L3, an unknown aminolipid and an unknown aminophospholipid APL2). The polyamine pattern of Sa25T exhibited the major compound putrescine and moderate amounts of spermidine; a similar polyamine pattern with the major compound putrescine was also detected in Pseudochrobactrum glaciei KMM 3858T. DNA–DNA hybridization of strain Sa25T with Pseudochrobactrum glaciei KMM 3858T and the type strains of the other Pseudochrobactrum species showed values ranging from 50.3 to 24.8 %, and physiological and biochemical data clearly differentiated this isolate from the described Pseudochrobactrum species. Since Sa25T and Pseudochrobactrum glaciei KMM 3858T form a distinct lineage in the 16S rRNA gene sequence-based phylogenetic tree, and this separate position is supported by unique characteristics of their polyamine patterns and polar lipid profiles, we propose the novel genus Paenochrobactrum gen. nov., with the type species Paenochrobactrum gallinarii sp. nov. (type strain Sa25T =CCUG 57736T =CCM 7656T) and the reclassification of Pseudochrobactrum glaciei as Paenochrobactrum glaciei comb. nov. (type strain Pi26T =KMM 3858T =NRIC 0733T =JCM 15115T).

A Gram-negative, non-spore-forming, rod-shaped bacterium, designated strain DCY01T, was isolated from soil from a ginseng field in South Korea and was characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain DCY01T belonged to the Gammaproteobacteria and was most closely related to Stenotrophomonas koreensis KCTC 12211T (98.4 % similarity), Stenotrophomonas humi R-32729T (97.2 %), Stenotrophomonas terrae R-32768 (97.1 %), Stenotrophomonas maltophilia DSM 50170T (96.9 %) and Stenotrophomonas nitritireducens DSM 12575T (96.8 %). Chemotaxonomic analyses revealed that strain DCY01T possessed a quinone system with Q-8 as the predominant compound, and iso-C15 : 0 (28.2 %), C16 : 0 10-methyl (13.2 %), iso-C15 : 1 F (10.8 %) and C15 : 0 (7.5 %) as major fatty acids, corroborating assignment of strain DCY01T to the genus Stenotrophomonas. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The results of DNA–DNA hybridization and physiological and biochemical tests clearly demonstrated that strain DCY01T represents a species distinct from recognized Stenotrophomonas species. Based on these data, DCY01T (=KCTC 12539T=NBRC 101154T) should be classified as the type strain of a novel species of the genus Stenotrophomonas, for which the name Stenotrophomonas ginsengisoli sp. nov. is proposed.

A beige-pigmented bacterium (strain CCUG 53761AT) was isolated from human blood from an 85-year-old man in Göteborg, Sweden. Comparative analysis of 16S rRNA gene sequences showed that this bacterium displayed <95 % similarity to all described species of the genera of the family Alcaligenaceae. It grouped within the radiation of the genus Alcaligenes, but showed only 93.0–94.8 % similarity to type strains of members of this genus (Alcaligenes faecalis subsp. parafaecalis, 94.8 %; Alcaligenes faecalis subsp. faecalis, 94.2 %; Alcaligenes faecalis subsp. phenolicus, 93.4 %). This discrimination was supported by chemotaxonomic differences. The polyamine pattern consisted of the predominant compound putrescine, moderate amounts of spermidine and minor to trace amounts of spermine and cadaverine; 2-hydroxyputrescine was not detectable. The quinone system was ubiquinone Q-8 with minor amounts of Q-7. The polar lipid profile was composed of the major lipids diphosphatidylglycerol and phosphatidylethanolamine and moderate amounts of phosphatidylglycerol and an unknown phospholipid; minor lipids were also detected. The fatty acid profile, with large amounts of C16 : 0 and C17 : 0 cyclo and the absence of C12 : 0 2-OH as hydroxylated fatty acid, also differed significantly from those reported for Alcaligenes species. On the basis of these data, it is proposed that strain CCUG 53761AT represents a novel genus and species, for which the name Paenalcaligenes hominis gen. nov., sp. nov. is proposed. The type strain of Paenalcaligenes hominis is CCUG 53761AT =CCM 7698T.

Strain DCY21T, a Gram-negative, gliding and rod-shaped aerobic bacterium was isolated from soil of a ginseng field in the Republic of Korea and characterized using a polyphasic approach in order to determine its taxonomic position. Comparative 16S rRNA gene sequence analysis revealed that strain DCY21T clustered with the species of the genus Lysobacter. It was closely related to Lysobacter gummosus LMG 8763T (97.9 %), Lysobacter capsici YC5194T (97.6 %), Lysobacter antibioticus DSM 2044T (97.5 %), Lysobacter niastensis DSM 18481T (97.2 %) and Lysobacter enzymogenes DSM 2043T (96.9 %). The major cellular fatty acids of strain DCY21T were iso-C15 : 0 (34.3 %), iso-C17 : 1 ω9c (19.5 %) and iso-C17 : 0 (17.2 %) and the major isoprenoid quinone was Q-8. The major polar lipids of strain DCY21T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidyl-N-methylethanolamine. The G+C content of the total DNA was 65.4 mol%. The DNA–DNA relatedness values, and biochemical and physiological characteristics strongly supported the genotypic and phenotypic differentiation of strain DCY21T from species of the genus Lysobacter. Strain DCY21T therefore represents a novel species, for which the name Lysobacter soli sp. nov. is proposed. The type strain is DCY21T (=KCTC 22011T =LMG 24126T).

A Gram-staining-negative, aerobic, rod-shaped, non-spore-forming bacterial strain, Ca-34T, was isolated from nodules of chickpea (Cicer arietinum) in Pakistan and studied for its taxonomic affiliation. The almost full-length 16S rRNA gene sequence showed highest similarities to those of strains of the genus Ochrobactrum. Based on results of MALDI-TOF MS and 16S rRNA gene sequence similarity (98.6 %), strain Ca-34T and Ochrobactrum intermedium LMG 3301T are phylogenetic neighbours; the two strains shared DNA–DNA relatedness of 64 %. The fatty acid profile [predominantly C18 : 1 ω7c (67.7 %) and C19 : 0 cyclo ω8c (19.6 %)] also supported the genus affiliation. Metabolically, strain Ca-34T differed from other type strains of Ochrobactrum in many reactions and from all type strains in testing positive for gelatin hydrolysis and in testing negative for assimilation of alaninamide and l-threonine. Based on phenotypic and genotypic data, we conclude that strain Ca-34T represents a novel species, for which we propose the name Ochrobactrum ciceri sp. nov. (type strain Ca-34T =DSM 22292T =CCUG 57879T).

A methylotrophic nitrogen-fixing bacterial strain, Ah-143T, isolated from the rhizosphere soil of field-grown groundnut was analysed by a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis combined with rpoB gene sequence analysis allocated strain Ah-143T to the family Enterobacteriaceae, with Enterobacter radicincitans and Enterobacter cowanii as the closest relatives. The strain is Gram-stain-negative, non-spore-forming, aerobic and motile, having straight rod-shaped cells with a DNA G+C content of approximately 53.2 mol%. The strain utilizes methanol as a carbon source and the mxaF gene was closely related to the mxaF gene of members of the genus Methylobacterium. The fatty acid profile consisted of C16 : 0, C17 : 0 cyclo, C18 : 1 ω7c, summed feature 2 (iso-C16 : 1 I and/or C14 : 0 3-OH) and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c) as the major components. DNA–DNA relatedness of strain Ah-143T with its close relatives was less than 20 %. On the basis of the phylogenetic analyses, DNA–DNA hybridization data, and unique physiological and biochemical characteristics, it is proposed that the strain represents a novel species of the genus Enterobacter and should be named Enterobacter arachidis sp. nov. The type strain is Ah-143T (=NCIMB 14469T =KCTC 22375T).

A Gram-negative, aerobic or facultatively anaerobic, non-spore-forming, motile, rod-shaped bacterium (strain Gsoil 3165T) was isolated from soil of a ginseng field in Pocheon, South Korea. Its taxonomic position was determined by using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain Gsoil 3165T was shown to belong to the family Comamonadaceae, class Betaproteobacteria, and was related most closely to the type strains of Variovorax boronicumulans (98.9 % similarity), Variovorax paradoxus (98.3 %), Variovorax soli (98.2 %) and Variovorax dokdonensis (96.6 %). Levels of 16S rRNA gene sequence similarity between strain Gsoil 3165T and the type strains of other species in the family Comamonadaceae were less than 97.0 %. The G+C content of the genomic DNA of strain Gsoil 3165T was 66 mol%. Phenotypic and chemotaxonomic data (Q-8 as the major ubiquinone; C16 : 0 and C17 : 0 cyclo as major fatty acids) supported the affiliation of strain Gsoil 3165T to the genus Variovorax. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain Gsoil 3165T from recognized Variovorax species. Gsoil 3165T is therefore considered to represent a novel species of the genus Variovorax, for which the name Variovorax ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3165T (=KCTC 12583T =LMG 23392T).

Two facultatively anaerobic, budding bacterial strains, designated W1215-PCA4T and SRNK-1, were isolated from water from Lake Michigan, USA. The two strains showed identical ERIC-PCR-generated genomic fingerprints and shared 99.9 % 16S rRNA gene sequence similarity. Strain W1215-PCA4T showed highest 16S rRNA gene sequence similarities to Labrys monachus VKM B-1479T (95.8 %), Labrys methylaminiphilus DSM 16812T (95.1 %), Labrys okinawensis MAFF 210191T (96.0 %), Labrys miyagiensis G24103T (95.4 %), Labrys neptuniae BCRC 17578T (95.7 %) and Labrys portucalensis DSM 17916T (95.8 %). Data suggested that the two strains were members of a single novel species of the genus Labrys. The major cellular fatty acids of the two isolates were C18 : 1 ω7c, C19 : 0 cyclo ω8c and C16 : 0. Their polar lipid profiles were highly similar to that of Labrys monachus DSM 5896T. The primary quinone was ubiquinone Q-10, with minor amounts of Q-9 and Q-11. sym-Homospermidine was the predominant polyamine, with putrescine present in moderate amounts. The two strains were identical in terms of their biochemical and physiological traits, but were distinguishable from other species of the genus Labrys. Hence, the description of a novel species in this genus appears to be justified. The name Labrys wisconsinensis sp. nov. is proposed; the type strain is W1215-PCA4T (=DSM 19619T=NRRL B-51088T).

Strain BZ92rT was isolated from hydrocarbon-contaminated soil. Cells were Gram-negative, aerobic, rod-shaped and cold-adapted (growth at 1–25 °C). The major fatty acids were iso-C15 : 0 (25.6 %), iso-C17 : 1 ω9c (24.9 %), iso-C11 : 0 (18.4 %) and iso-C11 : 0 3-OH (16.2 %). The predominant ubiquinone was ubiquinone-8. The genomic DNA G+C content was 72.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BZ92rT was a member of the genus Luteimonas (94.5–95.2 % 16S rRNA gene sequence similarity). On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain BZ92rT was considered to represent a novel species of the genus Luteimonas. The name Luteimonas terricola sp. nov. is proposed, with BZ92rT (=DSM 22344T =CGMCC 1.8985T) as the type strain.

A Gram-negative, motile, rod-shaped bacterium, strain S4T, was isolated from coastal sediment collected off Xiamen, China. The physiological and biochemical features of strain S4T, determined using the API 20NE, API ZYM and Biolog GN2 systems, were similar to those of members of the genus Shewanella. Phylogenetic analyses based on 16S rRNA and gyrB gene sequences placed strain S4T in the genus Shewanella, and it was most closely related to Shewanella oneidensis and related species. DNA–DNA hybridization demonstrated only 11.9–30.4 % relatedness between S4T and the type strains of related Shewanella species. On the basis of phylogenetic and phenotypic characteristics, strain S4T is classified in the genus Shewanella as a representative of a distinct novel species, for which the name Shewanella xiamenensis sp. nov. is proposed. The type strain is S4T (=CCTCC M 209017T =JCM 16212T).

A Gram-negative, aerobic, greyish–yellowish-pigmented, stenohaline, rod-shaped, non-motile bacterium, strain KMM 3900T, was isolated from a coastal seawater sample collected from the Sea of Japan. Based on phylogenetic analysis, strain KMM 3900T was positioned within the Gammaproteobacteria on a separate branch adjacent to members of the genera Reinekea and Kangiella, sharing less than 88 % 16S rRNA gene sequence similarity with all recognized species of the Gammaproteobacteria. The major isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unknown phospholipids. Fatty acid analysis revealed iso-C15 : 0, C16 : 1 ω7c and C16 : 0 as the dominant components. The DNA G+C content was 43.8 mol%. Based on its unique phenotypic characteristics and phylogenetic remoteness, marine isolate KMM 3900T is considered to represent a novel genus and species, for which the name Marinicella litoralis gen. nov., sp. nov. is proposed. The type strain of Marinicella litoralis is KMM 3900T (=NRIC 0758T =JCM 16154T).

A whitish Gram-negative, motile, aerobic bacterium, designated strain H 14T, was isolated from seawater collected at St Kilda beach in Port Phillip Bay, Melbourne, Australia. Analysis of 16S rRNA gene sequences revealed that the organism belonged to the Roseobacter lineage of the class Alphaproteobacteria, forming a distinct evolutionary lineage at the genus level. Strain H 14T was distantly related to the genera Nautella, Ruegeria and Pseudoruegeria (family Rhodobacteraceae). Strain H 14T was unable to degrade gelatin, casein, chitin, agar and starch, did not produce any carotenoids, did not possess bacteriochlorophyll a and had a limited ability to utilize carbon sources. Strain H 14T grew with concentrations of 1–8 % (w/v) NaCl and over a temperature range of 5–35 °C. Phosphatidylglycerol was the major phospholipid (90 %); phosphatidylcholine (7.9 %) and phosphatidylethanolamine (2.0 %) were present in minor quantities. The predominant fatty acids were C18 : 1 ω7c (82.4 %), C18 : 1 ω9c (5.1 %) and C18 : 0 (3.8 %). The DNA G+C composition for strain H 14T was 59.1 mol%. Based on the results of physiological, biochemical, chemotaxonomic and phylogenetic investigations, a new genus, Celeribacter gen. nov., with the type species Celeribacter neptunius sp. nov. is proposed. The type strain of the type species is H 14T (=KMM 6012T=CIP 109922T).

A Gram-negative, rod-shaped, sulfate-reducing bacterium (strain JS_SRB250LacT) was isolated from a tidal sand-flat in the German Wadden Sea. 16S rRNA gene sequence analysis showed that strain JS_SRB250LacT belonged to the Desulfobulbaceae (Deltaproteobacteria), with Desulfopila aestuarii MSL86T being the closest recognized relative (94.2 % similarity). Higher similarity (96.6 %) was shared with ‘Desulfobacterium corrodens’ IS4, but this name has not been validly published. The affiliation of strain JS_SRB250LacT to the genus Desulfopila was further supported by analysis of aprBA gene sequences and shared physiological characteristics, in particular the broad range of organic electron donors used for sulfate reduction. Compared with Desulfopila aestuarii MSL86T, strain JS_SRB250LacT additionally utilized butyrate and succinate and grew chemolithoautotrophically with hydrogen as an electron donor. CO dehydrogenase activity was demonstrated, indicating that the reductive acetyl-CoA pathway (Wood–Ljungdahl pathway) was used for CO2 fixation. Results of cellular fatty acid analysis allowed chemotaxonomic differentiation of strain JS_SRB250LacT from Desulfopila aestuarii MSL86T by the presence of C17 : 0 cyclo and the absence of hydroxy and unsaturated branched-chain fatty acids. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain JS_SRB250LacT represents a novel species of the genus Desulfopila, for which the name Desulfopila inferna sp. nov. is proposed. The type strain is JS_SRB250LacT (=DSM 19738T =NBRC 103921T).

A Gram-negative-staining, non-motile, non-spore-forming and strictly aerobic bacterial strain, SC35T, was isolated from tidal flat sediment collected from the South Sea, Korea, and subjected to a taxonomic study using a polyphasic approach. The organism grew optimally at 20–30 °C and with 1–2 % (w/v) NaCl. Strain SC35T contained ubiquinone-8 as the predominant respiratory lipoquinone and C18 : 1 ω9c as the major fatty acid. The DNA G+C content was 48.5 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain SC35T formed a lineage within the genus Psychrobacter (94.3–96.5 % sequence similarity), forming a distinct branch in a clade also containing Psychrobacter pacificensis NIBH P2K6T and Psychrobacter celer SW-238T. On the basis of phenotypic and phylogenetic data, strain SC35T (=KCTC 22503T=JCM 16343T) was placed in the genus Psychrobacter as the type strain of a novel species, for which the name Psychrobacter aestuarii sp. nov. is proposed.