- Volume 57, Issue 4, 2007

A novel Gram-positive bacterium, strain 40T, was isolated in the course of identifying bacteria from infective juveniles of the entomopathogenic nematode Steinernema thermophilum. Based on 16S rRNA gene analysis, strain 40T was found to be related to the type strains of recognized species of the genus Leucobacter, family Microbacteriaceae. The 16S rRNA gene sequence similarity values of strain 40T and Leucobacter albus IAM 14851T, Leucobacter luti LMG 23118T, Leucobacter alluvii LMG 23117T, Leucobacter komagatae DSM 8803T, Leucobacter chromiireducens CIP 108389T and Leucobacter aridicollis CIP 108388T, respectively, were 97.3, 97.5, 97.6, 97.6, 97.6 and 98.5 %. Chemotaxonomic analysis also supported the affiliation of strain 40T to the genus Leucobacter: the major menaquinone was MK-11, the peptidoglycan cross-linkage was of the B-type, the cell wall diamino acid was l-diaminobutyric acid and the major fatty acids were anteiso-C15 : 0 (42 %), anteiso-C17 : 0 (34 %) and iso-C16 : 0 (16 %). Based upon the biochemical and genomic analyses, strain 40T is sufficiently distinct from the type strains of recognized Leucobacter species to warrant the description of a novel species, for which the name Leucobacter iarius sp. nov. is proposed. The type strain is strain 40T (=DSM 17402T=CIP 108831T).

A Gram-positive, rod-shaped, non-spore-forming and strictly aerobic bacterium (Gsoil 161T) was isolated from soil of a ginseng field in Pocheon Province, South Korea. The novel isolate was characterized using a polyphasic approach in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 161T was shown to belong to the family Nocardioidaceae and was related to Aeromicrobium marinum (98.0 % similarity to the type strain), Aeromicrobium alkaliterrae (97.6 %), Aeromicrobium fastidiosum (97.0 %) and Aeromicrobium erythreum (96.7 %); the sequence similarity with other species within the family was less than 94.4 %. It was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-9(H4) as the predominant menaquinone and C16 : 0, 10-methyl C18 : 0 (tuberculostearic acid), C16 : 0 2-OH, 10-methyl C17 : 0 and 10-methyl-C16 : 0 as the major fatty acids. The G+C content of the genomic DNA was 65.5 mol%. These chemotaxonomic properties and phenotypic characteristics support the affiliation of strain Gsoil 161T to the genus Aeromicrobium. Results of physiological and biochemical tests enabled strain Gsoil 161T to be differentiated genotypically and phenotypically from currently known Aeromicrobium species. Therefore, strain Gsoil 161T represents a novel species, for which the name Aeromicrobium panaciterrae sp. nov. is proposed. The type strain is strain Gsoil 161T (=KCTC 19131T=DSM 17939T=CCUG 52476T).

A Gram-positive, aerobic, coccus-shaped, non-endospore-forming bacterium (Gsoil 633T) was isolated from soil from a ginseng field in Pocheon province in South Korea. The novel isolate was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarities, strain Gsoil 633T was shown to belong to the family Propionibacteriaceae. The closest phylogenetic relative was Microlunatus phosphovorus DSM 19555T, with 96.1 % sequence similarity; the sequence similarity to other members of the family was less than 95.4 %. The isolate was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-9(H4) as the predominant menaquinone and anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0 as the major fatty acids. The G+C content of the genomic DNA was 69.8 mol%. The morphological and chemotaxonomic properties of the isolate were consistent with those of M. phosphovorus, but the results of physiological and biochemical tests allowed the phenotypic differentiation of strain Gsoil 633T from this species. Therefore, strain Gsoil 633T represents a novel species, for which the name Microlunatus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 633T (=KCTC 13940T=DSM 17942T).

A Gram-positive bacterium, strain GW8-1761T, was isolated from soil close to the Marmore waterfalls, Terni, Italy. 16S rRNA gene sequence similarity studies showed that strain GW8-1761T belonged to the genus Actinoplanes, being most closely related to Actinoplanes italicus JCM 3165T (98.9 %), A. rectilineatus IFO 13941T (98.5 %), A. palleronii JCM 7626T (97.8 %), A. utahensis IFO 13244T (97.6 %) and A. cyaneus DSM 46137T (97.6 %). Strain GW8-1761T could be distinguished from any other Actinoplanes species with validly published names by 16S rRNA gene sequence similarity values of less than 97.5 %. Chemotaxonomic data [major menaquinone MK-9(H4); major polar lipids diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol, with phosphatidylcholine and aminoglycolipids absent; major fatty acids C15 : 0, C16 : 0, C16 : 0 iso, C17 : 1 ω8c and summed feature 3 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH)] supported the affiliation of strain GW8-1761T to the genus Actinoplanes. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW8-1761T from the most closely related species. Strain GW8-1761T therefore merits species status, and we propose the name Actinoplanes couchii sp. nov., with the type strain GW8-1761T (=DSM 45050T=CIP 109316T).

A Gram-positive bacterium, designated strain PG-02T, was isolated by serial dilution from aerobic granules obtained from a laboratory-scale sequencing batch reactor for bioremediation of phenolic wastewater. Strain PG-02T grew axenically as cocci and is an oxidase-negative and catalase-positive, non-motile facultative anaerobe. It does not reduce nitrate and grows between 15 and 37 °C, with an optimum temperature of 30 °C. The pH range for growth is between 5.0 and 8.5, with an optimum pH of 7.0. Strain PG-02T contains type A3γ peptidoglycan (ll-A2pm←Gly with alanine at position 1 of the peptide subunit). The G+C content of the DNA is 69 mol%. Menaquinone MK-9(H4) was the major isoprenoid quinone. The polar lipids included diphosphatidylglycerol and phosphatidylglycerol, while 13-methyltetradecanoic acid (i-C15 : 0) and 1,1-dimethoxy-iso-pentadecane (i-C15 : 0 DMA) were the major components in whole-cell methanolysates. PG-02T stained positively for intracellular polyphosphate granules but not poly-β-hydroxyalkanoates. It produces capsular material and possesses an autoaggregation capability. Phenotypic and 16S rRNA gene sequence analyses showed that PG-02T differed from its closest phylogenetic relatives, namely members of the suborder Propionibacterineae, which includes the genera Tessaracoccus, Microlunatus, Luteococcus, Micropruina, Propionibacterium, Propioniferax, Nocardioides, Friedmanniella and Aeromicrobium, and that it should be placed in a new genus and species as Granulicoccus phenolivorans gen. nov., sp. nov. The type strain of Granulicoccus phenolivorans is PG-02T (=ATCC BAA-1292T=DSM 17626T).

A Gram-positive, slightly halophilic, rod-shaped bacterium, designated CL-DD14T, was isolated from seawater of the East Sea, Korea. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CL-DD14T belongs to the genus Nocardioides. Levels of 16S rRNA gene sequence similarity between strain CL-DD14T and the type strains of recognized species of the genus Nocardioides were low (94.1–97.1 %). Strain CL-DD14 T grew over the pH range 6–9 and temperature range 10–40 °C. The strain grew at NaCl concentrations of 0.5–8 % (w/v) with optimum growth at 1–3 % and no growth was observed after 3 weeks on nutrient agar without any salts. It contained ll-diaminopimelic acid as the diamino acid in the cell wall. The major isoprenoid quinone was MK-8(H4) and the major cellular fatty acids were iso-C16 : 0 and 10-methyl C17 : 0. The DNA G+C content was 72.9 mol%. On the basis of phenotypic and phylogenetic data, strain CL-DD14T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides marinus sp. nov. is proposed. The type strain is CL-DD14T (=KCCM 42321T=DSM 18248T).

A Gram-positive, coccoid, non-spore-forming bacterium, designated strain 3-6T, was isolated from farmland soil and subjected to a polyphasic taxonomic analysis. Comparative analysis of the 16S rRNA gene sequence revealed that the strain represented a novel member of the suborder Micrococcineae. Its nearest phylogenetic neighbour was the type strain of Georgenia muralis (94.2 % 16S rRNA gene sequence similarity). Chemotaxonomic characteristics of strain 3-6T were as follows: the major menaquinone was MK-8(H4); the polar lipids consisted mainly of diphosphatidylglycerol, phosphatidylglycerol and one unknown glycolipid; the predominant fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0; mycolic acids were absent. A new murein type, l-lys–gly–l-glu–l-Glu (A4α), was found in the peptidoglycan of the cell wall. The DNA G+C content was 69.8 mol%. On the basis of morphological, chemotaxonomic and phylogenetic characteristics, it is suggested that strain 3-6T represents a novel species of a new genus within the suborder Micrococcineae, for which the name Ruania albidiflava gen. nov., sp. nov. is proposed. The type strain of Ruania albidiflava is 3-6T (=CGMCC 4.3142T=DSM 18029T=JCM 13910T=PCM 2644T).

The taxonomic position of a soil isolate, strain Z6T, was established using a polyphasic approach. The organism showed a range of chemical and morphological properties consistent with its classification in the genus Lechevalieria. An almost complete 16S rRNA gene sequence determined for the strain was aligned with corresponding sequences of representatives of the genus Lechevalieria and related taxa using three tree-making algorithms. The organism formed a distinct phyletic line within the evolutionary radiation occupied by the genus Lechevalieria and was more closely related to the type strain of Lechevalieria aerocolonigenes than to that of Lechevalieria flava. Strain Z6T could be distinguished from both these strains using DNA–DNA relatedness data and by a combination of phenotypic properties. The combined genotypic and phenotypic data show that strain Z6T should be assigned to the genus Lechevalieria as a representative of a novel species. The name proposed for this new taxon is Lechevalieria fradiae sp. nov. The type strain is Z6T (=CGMCC 4.3506T=JCM 14205T).

A novel psychrotolerant, Gram-positive, yellow-pigmented, aerobic bacterium, strain 0549T, was isolated from the China No. 1 glacier. The cells of the isolate were catalase-positive, motile, irregular rods. The diamino acid content of the cell-wall peptidoglycan was determined to be 2,4-diaminobutyric acid. Strain 0549T was able to grow at 4–27 °C, with optimum growth occurring at 20–22 °C. The major fatty acids were anteiso-C15 : 0, anteiso-C15 : 1, iso-C16 : 0 and anteiso-C17 : 0. The genomic DNA G+C content was 67 mol%. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 0549T belonged to the genus Cryobacterium and exhibited 96.5 % similarity to Cryobacterium psychrophilum JCM 1463T. On the basis of the phenotypic, chemotaxonomic and phylogenetic properties and the DNA–DNA relatedness data, strain 0549T represents a novel species of the genus Cryobacterium, for which the name Cryobacterium psychrotolerans is proposed. The type strain is 0549T (=CGMCC 1.5382T=JCM 13925T).

Three strains of Gram-negative, aerobic, neutrophilic, extremely halophilic archaea, designated ZJ206T, ZJ203 and ZJ204, were isolated from a solar saltern in Zhe-Jiang Province, China. Phenotypically and on the basis of 16S rRNA gene sequences, the strains were very similar. Comparative 16S rRNA gene analysis revealed 96.4–97.4 % sequence similarity to members of the genus Haloferax. The major polar lipids were C20C20 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, diglycosyl glycerol diether and sulfated diglycosyl diether. The DNA G+C content of strain ZJ206T was 62.2 mol%. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the isolates from closely related species. Therefore the isolates should be classified as members of a novel species, for which the name Haloferax larsenii sp. nov. is proposed. The type strain is ZJ206T (=CGMCC 1.5347T=JCM 13917T).

An extremely haloalkaliphilic archaeon, strain AD2T, was isolated from Aiding salt lake in Xin-Jiang, China. Strain AD2T required at least 12 % NaCl for growth. MgCl2 was not required. The isolate was able to grow over a pH range of 8.0–10.0 and temperature range of 20–55 °C, with optimal growth at pH 8.7–9.2 and 44–47 °C. The major polar lipids of strain AD2T were phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester; glycolipids were not detected. Analysis of its 16S rRNA gene sequence indicated that strain AD2T was phylogenetically related to members of the genus Natronorubrum, with sequence similarities to the type strains of Natronorubrum bangense, Natronorubrum tibetense and Natronorubrum aibiense of 97.1, 95.9 and 96.1 %, respectively. The G+C content of its DNA was 60.9 mol% (T m). Levels of DNA–DNA relatedness between strain AD2T and the type strains of Nrr. bangense, Nrr. tibetense and Nrr. aibiense were 49, 38 and 41 %, respectively. It was concluded that strain AD2T represents a novel species of the genus Natronorubrum, for which the name Natronorubrum sulfidifaciens sp. nov. is proposed. The type strain is AD2T (=CGMCC 1.6307T=JCM 14089T).

To study biological phenomena in the Dead Sea and to simulate the effects of mixing Dead Sea water with Red Sea water, experimental mesocosms were operated at the Dead Sea Works at Sedom, Israel. Dense communities of red halophilic archaea developed in mesocosms filled with 80 % Dead Sea water and 20 % Red Sea water after enrichment with phosphate. The most common type of colonies isolated from these brines belonged to the genus Halorubrum. A few white–pinkish opaque colonies contained pleomorphic flat cells with gas vesicles. Three strains isolated from the latter colonies were characterized in depth. Their 16S rRNA gene sequences showed only 91 % similarity to the closest cultured relative (Haloferax mediterranei), indicating that the new strains represent a novel species of a new genus. The name Haloplanus natans gen. nov., sp. nov. is proposed for this novel organism. The type strain of Haloplanus natans is RE-101T (=DSM 17983T=JCM 14081T).

A novel chemolithoautotrophic and hyperthermophilic member of the genus Ignicoccus was isolated from a submarine hydrothermal system at the Kolbeinsey Ridge, to the north of Iceland. The new isolate showed high similarity to the two species described to date, Ignicoccus islandicus and Ignicoccus pacificus, in its physiological properties as well as in its unique cell architecture. However, phylogenetic analysis and investigations on the protein composition of the outer membrane demonstrated that the new isolate was clearly distinct from I. islandicus and I. pacificus. Furthermore, it is the only organism known so far which is able to serve as a host for ‘Nanoarchaeum equitans’, the only cultivated member of the ‘Nanoarchaeota’. Therefore, the new isolate represents a novel species of the genus Ignicoccus, which we name Ignicoccus hospitalis sp. nov. (type strain KIN4/IT=DSM 18386T=JCM 14125T).

A Gram-negative, non-motile, filamentous, rod-shaped, non-spore-forming bacterium (strain F2T) was isolated from the surface of an electricity-harvesting electrode incubated in marine sediments. Strain F2T does not contain c-type cytochromes, flexirubin or carotenoids. It is a facultative anaerobe that can ferment sugars by using a mixed acid fermentation pathway and it can grow over a wide range of temperatures (4–42 °C). The DNA G+C (44.9 mol%) content and chemotaxonomic characteristics (major fatty acids, a-15 : 0 and 15 : 0) were consistent with those of species within the phylum Bacteroidetes. Phylogenetic analysis of the 16S rRNA nucleotide and elongation factor G amino acid sequences indicated that strain F2T represents a unique phylogenetic cluster within the phylum Bacteroidetes. On the basis of 16S rRNA gene sequence phylogeny, the closest relative available in pure culture, Alkaliflexus imshenetskii, is only 87.5 % similar to strain F2T. Results from physiological, biochemical and phylogenetic analyses showed that strain F2T should be classified as a novel genus and species within the phylum Bacteroidetes, for which the name Prolixibacter bellariivorans gen. nov., sp. nov. is proposed. The type strain is F2T (=ATCC BAA-1284T=JCM 13498T).

The taxonomic position of a novel marine, heterotrophic, gliding, halotolerant and light-pink-pigmented bacterium, designated strain KMM 6221T, was examined by using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain KMM 6221T is affiliated with the genus Echinicola, a member of the phylum Bacteroidetes, with levels of similarity of 94.7–95.0 % to strains of Echinicola pacifica. Growth of strain KMM 6221T was observed with 0–15 % NaCl and at 6–44 °C. The DNA G+C content of strain KMM 6221T was 45.9 mol%. On the basis of molecular distinctiveness supported by phenotypic and chemotaxonomic data, strain KMM 6221T is considered to represent a novel species of the genus Echinicola, for which the name Echinicola vietnamensis sp. nov. is proposed. The type strain is KMM 6221T (=DSM 17526T=LMG 23754T).

A Gram-negative, aerobic, saffron-coloured marine bacterium, designated HST1-43T, was isolated from beach sediment on the coast in Jeju, Korea, and its taxonomic status was established in a polyphasic study. 16S rRNA gene sequence analyses revealed that the isolate belonged to the family Flavobacteriaceae. The closest phylogenetic neighbours of strain HST1-43T were members of the genera Algibacter, Gaetbulibacter and Yeosuana, with levels of sequence similarity in the range 96.3–96.5 %. The isolate was non-motile and required sea salts or natural seawater for growth. The optimum temperature and pH ranges for growth were 25–30 °C and pH 6.1–8.1, respectively. MK-6 was the major menaquinone. The dominant cellular fatty acids were iso-C15 : 0, C18 : 0, C16 : 0, iso-C15 : 1 and iso-C17 : 0 3-OH. The DNA G+C content was 36.2±0.4 mol%. On the basis of phylogenetic distance and phenotypic characteristics, the isolate is considered to represent a novel genus and species in the family Flavobacteriaceae, for which the name Tamlana crocina gen. nov., sp. nov. is proposed. The type strain is HST1-43T (=KCTC 12721T=JCM 14021T).

A novel marine, Gram-negative, yellow-pigmented, rod-shaped, strictly aerobic, gliding and oxidase- and catalase-positive bacterium (strain TD-ZE3T) was isolated from a seawater sample collected off the Pacific coastline of Japan near Enoshima Island (Fujisawa, Kanagawa). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain TD-ZE3T belonged to a distinct lineage in the family Flavobacteriaceae, with 90.5 % sequence similarity with the nearest species Robiginitalea biformata. Strain TD-ZE3T could be distinguished from other members of the family Flavobacteriaceae by a number of chemotaxonomic and phenotypic characteristics. The DNA G+C content was 46.5 mol%. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1 ω9c and menaquinone-6 was the only respiratory quinone. Zeaxanthin was the major carotenoid pigment produced; flexirubin-type pigments were not produced. Strain TD-ZE3T degraded gelatin, starch and Tween 80. Based on its unique phenotypic, genotypic and phylogenetic features, strain TD-ZE3T represents a novel taxon, for which the name Zeaxanthinibacter enoshimensis gen. nov., sp. nov. is proposed. The type strain is TD-ZE3T (=NBRC 101990T=CCUG 53613T).

Strain A54T was isolated from rhizospheric soil of turf grasses irrigated with reclaimed water in Taoranting Park, Beijing, China. Phenotypic, chemotaxonomic and polygenetic analyses established the affiliation of the isolate to the genus Dyadobacter. Strain A54T possessed 97.7, 94.4 and 94.7 % 16S rRNA gene sequence similarity with respect to the type strains of Dyadobacter fermentans, D. hamtensis and D. crusticola, respectively. Furthermore, DNA–DNA hybridization did not show significant relatedness (<25 % hybridization) between strain A54T and D. fermentans ATCC 700827T. Therefore, these results indicate that strain A54T belongs to a novel species of the genus Dyadobacter, for which the name Dyadobacter beijingensis sp. nov. is proposed. The type strain is strain A54T (=CGMCC 1.6375T=JCM 14200T).