- Volume 59, Issue 5, 2009

A Gram-positive-staining, filamentous bacterial strain that developed cylindrical sporangia containing four oval- to rod-shaped spores at the ends of short sporangiophores on branched aerial mycelium was isolated from tropical rainforest soil near a hot spring. The cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine as cell-wall amino acids; the whole-cell hydrolysate contained rhamnose, madurose, glucose, galactose and 3-O-methylmannose as whole-cell sugars. The predominant menaquinone was MK-9(H4). Mycolic acids were not detected. The diagnostic phospholipid was phosphatidylethanolamine. The predominant cellular fatty acids were iso-C16 : 0 and 10-methylated C17 : 0. The G+C content of the DNA was 71.1 mol%. The phenotypic and chemotaxonomic analyses showed that the isolate had characteristics typical of members of the genus Planotetraspora. Furthermore, 16S rRNA gene sequence analysis also indicated that this strain belongs to the genus Planotetraspora, but as a putative novel species. Following phenotypic, chemotaxonomic and genotypic studies, the isolate is proposed to be a representative of a novel species, to be named Planotetraspora thailandica sp. nov. The type strain is BCC 21825T (=NBRC 104271T). An emended description of the genus Planotetraspora is also presented.

The taxonomic position of the cholesterol-degrading strain Chol-3T, isolated from a sewage sludge sample, was clarified using a polyphasic taxonomic approach. Phylogenetic analysis of its 16S rRNA gene sequence, whole-cell fatty acid profile and mycolic acid composition revealed that this isolate is a member of the genus Gordonia with the species Gordonia sihwensis, G. hydrophobica and G. shandongensis being the nearest phylogenetic neighbours. The results of DNA–DNA hybridization against its phylogenetically closest neighbours as well as the results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain Chol-3T from the other Gordonia species with validly published names. Strain Chol-3T therefore merits recognition as a member of a novel species within the genus Gordonia, for which the name Gordonia cholesterolivorans sp. nov. is proposed. The type strain is Chol-3T (=CECT 7408T =DSM 45229T).

Two strains of non-spore-forming, rod-shaped, Gram-positive bacteria, CIP 101303T and CIP 102116, were isolated from human blood in 1976 and 1977, respectively. These strains had chemotaxonomic markers that were consistent with classification in the genus Microbacterium, i.e. MK-10, MK-11 and MK-12 as the major menaquinones, predominant iso- and anteiso-branched cellular fatty acids, galactose, mannose and rhamnose as the cell-wall sugars and ornithine as the diamino acid in the cell-wall peptidoglycan. The DNA G+C content was 70–72 mol%. Comparative 16S rRNA gene sequence studies revealed that strains CIP 101303T and CIP 102116 belonged to the genus Microbacterium and that they were related closely to Microbacterium halotolerans. The level of DNA–DNA relatedness showed that the two isolates represented a separate genomic species. Based on phenotypic and genotypic results, it is proposed that strains CIP 101303T and CIP 102116 be assigned to a novel species, Microbacterium binotii sp. nov. The type strain is CIP 101303T (=DSM 19164T).

Two actinomycete strains, designated YIM 56256T and YIM 61331T, were isolated from the roots of Scoparia dulcis and Maytenus austroyunnanensis, two Chinese medicinal plants, and their taxonomic status was established based on a polyphasic investigation. The organisms were found to have chemical and morphological markers typical of members of the genus Glycomyces. 16S rRNA gene sequence analysis showed that they were closely related to each other and to Glycomyces sambucus E71T. A battery of physiological characteristics and levels of DNA–DNA relatedness indicated that strains YIM 56256T and YIM 61331T represent two novel species, clearly different from the related known Glycomyces species. On the basis of the data presented, it is evident that each of these strains represents a novel species of the genus Glycomyces, for which the names Glycomyces scopariae sp. nov. (type strain YIM 56256T =KCTC 19158T =DSM 44968T) and Glycomyces mayteni sp. nov. (type strain YIM 61331T =KCTC 19527T =CCTCC AA 208004T) are proposed.

A non-chromogenic, slowly growing Mycobacterium strain was isolated from a maxillary sinus lavage from a symptomatic patient in Riyadh, Saudi Arabia. It was initially identified as a member of the Mycobacterium tuberculosis complex by a commercial line-probe assay. Its 16S rRNA, hsp65 and rpoB gene and 16S–23S internal transcribed spacer sequences were unique; phylogenetic analysis based on the 16S rRNA gene sequence groups this organism close to Mycobacterium szulgai and Mycobacterium malmoense. Its unique biochemical properties and mycolic acid profile support separate species status. We propose the name Mycobacterium riyadhense sp. nov. to accommodate this strain. The type strain is NLA000201958T (=CIP 109808T =DSM 45176T).

A Gram-positive bacterial strain, designated YIM 56238T, was isolated from plant roots (Aquilaria sinensis), and characterized by using a polyphasic approach. Strain YIM 56238T grew optimally at pH 7.0–8.0 and at 28 °C. Analysis of the 16S rRNA gene sequence of strain YIM 56238T indicated that it belongs to the genus Micrococcus. Chemotaxonomic data strongly supported the classification of this strain within the genus Micrococcus: the cell-wall peptidoglycan contained lysine, glutamic acid, alanine and glycine; the predominant menaquinones were MK-8(H2) (63.6 %) and MK-7(H2) (21.1 %); the phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown ninhydrin-negative phospholipid; and the major cellular fatty acids were iso-C15 : 0 (30.95 %) and anteiso-C15 : 0 (53.75 %). The G+C content of the genomic DNA was 72.9 mol%. A number of physiological features were found that clearly distinguished strain YIM 56238T from recognized species of the genus Micrococcus. DNA–DNA hybridization studies suggested that the novel strain represents a separate genomic species. On the basis of the data, therefore, strain YIM 56238T represents a novel species of the genus Micrococcus, for which the name Micrococcus endophyticus sp. nov. is proposed. The type strain is YIM 56238T (=DSM 17945T=KCTC 19156T).

An actinomycete isolated from soil from a field of grass was analysed using a polyphasic taxonomic approach. The organism, designated strain W12T, was found to have a range of chemical and morphological properties consistent with its classification in the genus Saccharopolyspora. An almost-complete 16S rRNA gene sequence determined for the strain was aligned with corresponding sequences for representatives of the genus Saccharopolyspora, using two tree-making algorithms. The novel organism formed a monophyletic clade with the type strain of Saccharopolyspora antimicrobica, but the DNA–DNA relatedness value was low. Strain W12T also had a phenotypic profile that readily distinguished it from recognized representatives of the genus Saccharopolyspora. It is evident from the combined genotypic and phenotypic data that the new organism should be classified as a novel species of the genus Saccharopolyspora. The name proposed for this new taxon is Saccharopolyspora jiangxiensis sp. nov., with strain W12T (=CGMCC 4.3529T=JCM 14613T) as the type strain.

Two novel extremely acidophilic, iron-oxidizing actinobacteria were isolated, one from a mine site in North Wales, UK (isolate T23T), and the other from a geothermal site in Yellowstone National Park, Wyoming, USA (Y005T). These new actinobacteria belong to the subclass Acidimicrobidae, and in contrast to the only other classified member of the subclass (Acidimicrobium ferrooxidans), both isolates were obligate heterotrophs. The mine site isolate was mesophilic and grew as small rods, while the Yellowstone isolate was a moderate thermophile and grew as long filaments, forming macroscopic flocs in liquid media. Both isolates accelerated the oxidative dissolution of pyrite in yeast extract-amended cultures, but neither was able to oxidize reduced forms of sulfur. Ferrous iron oxidation enhanced growth yields of the novel mesophilic actinobacterium T23T, though this was not confirmed for the Yellowstone isolate. Both isolates catalysed the dissimilatory reduction of ferric iron, using glycerol as electron donor, in oxygen-free medium. Based on comparative analyses of base compositions of their chromosomal DNA and of their 16S rRNA gene sequences, the isolates are both distinct from each other and from Acidimicrobium ferrooxidans, and are representatives of two novel genera. The names Ferrimicrobium acidiphilum gen. nov., sp. nov. and Ferrithrix thermotolerans gen. nov., sp. nov. are proposed for the mesophilic and moderately thermophilic isolates, respectively, with the respective type strains T23T (=DSM 19497T=ATCC BAA-1647T) and Y005T (=DSM 19514T=ATCC BAA-1645T).

A brown–orange-pigmented, non-spore-forming, coccus-shaped actinomycete, designated S2-20T, was isolated from desert sand from Xinjiang Province in China. The isolate stains Gram-positive, is motile and produces a brownish diffusible pigment. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S2-20T was phylogenetically affiliated to the genus Kineococcus, and the sequence similarity to the type strains of Kineococcus species was less than 96 %, making it clear that strain S2-20T represents a species that is separate from recognized Kineococcus species. Its major fatty acid was anteiso-C15 : 0. The major menaquinone was MK-9(H2). Whole-cell hydrolysates of strain S2-20T contained meso-diaminopimelic acid, arabinose and galactose. The DNA G+C content was 77.8 mol%. On the basis of phylogenetic, phenotypic and chemotaxonomic characteristics, strain S2-20T should be classified within a novel species of the genus Kineococcus, for which the name Kineococcus xinjiangensis sp. nov. is proposed. The type strain is S2-20T (=CCTCC AB 207179T =KCTC 19474T).

Three Gram-positive, rod-shaped, oxidase-negative, non-spore-forming, non-motile bacteria (KSS-3SeT, KSS-4Se and KSS-10Se) were isolated from a coolant lubricant. 16S rRNA gene sequence analyses revealed almost identical sequences, with only a few (<10 positions) differences for these three isolates. Comparisons showed the highest similarities to Corynebacterium pilosum NCTC 11862T (97.6 % similarity with strain KSS-3SeT). Similarities with other established Corynebacterium species were lower than 97.0 %. Chemotaxonomic data studied for strain KSS-3SeT [polar lipids – major compounds phosphatidylglycerol and an unknown glycolipid, moderate amounts of phosphatidylinositol and diphosphatidylglycerol; polyamines (small amounts) – major compounds spermidine and spermine; quinones – significant amounts of menaquinones MK-9(H2), MK-8(H2) and MK-7(H2); and major fatty acids – tuberculostearic acid (10-methyl C18 : 0), C16 : 0 and C18 : 1 ω9c] were congruent with those reported for Corynebacterium. The strain showed differences in phenotype from C. pilosum. DNA–DNA hybridizations between KSS-3SeT and C. pilosum DSM 20521T yielded a relatedness of 22.9 % (20.4 % in the reciprocal assay). From these results, it is evident that the organisms represent a novel species, for which the name Corynebacterium lubricantis sp. nov. is proposed (type strain KSS-3SeT =DSM 45231T =CCUG 56567T =CCM 7546T).

The taxonomic status of a bacterium isolated from a patient with bronchial carcinoma was established using a polyphasic taxonomic approach. The strain had morphological and chemotaxonomic characteristics consistent with those of members of the genus Saccharopolyspora. The generic assignment was confirmed by comparative analysis of the 16S rRNA gene sequence, which showed that the strain constituted a distinct phyletic line, displaying 93.5–96.9 % sequence similarity with respect to members of the genus Saccharopolyspora. The isolate was distinguished from the type strains of recognized members of the genus Saccharopolyspora by means of various biochemical tests. The genotypic and phenotypic data obtained demonstrated that strain IMMIB L-1070T represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora rosea sp. nov. is proposed. The type strain is IMMIB L-1070T (=DSM 45226T=CCUG 56401T).

Peatlands are important sources of CH4 emissions to the atmosphere and molecular surveys have identified a diverse, but mainly uncultured, euryarchaeal community in them. Characterization of a strain, E1-9cT, associated with uncultured group E1, from a minerotrophic fen is reported. Cells were regular cocci, usually found in pairs, that stained Gram-positive and were resistant to lysis by 0.1 % SDS. Multiple flagella were observed, but motility was not observed in wet mounts. Optimal growth was obtained at moderate temperatures (28–30 °C) and slightly acidic pH (5.5). Total Na+ and NaCl were only tolerated at concentrations less than 100 mM and 0.5 %, respectively, and Na2S concentrations above 0.1 mM were inhibitory. H2/CO2 and formate were the only methanogenic substrates used by E1-9cT; formate concentrations above 50 mM were inhibitory for growth. Vitamins, coenzyme M and acetate (4 mM) were required for growth and the doubling time was about 19 h. Phylogenetic analysis of the 16S rRNA gene and inferred McrA amino acid sequences showed that E1-9cT represented an independent lineage within the order Methanomicrobiales. Physiological and phylogenetic comparisons with different members of the order supported classification of E1-9cT in a new genus in the Methanomicrobiales. The name Methanosphaerula palustris gen. nov., sp. nov. is proposed; strain E1-9cT (=ATCC BAA-1565T =DSM 19958T) is the type strain of Methanosphaerula palustris.

A methanogenic organism from the domain Archaea (SD1T) was isolated from saline water released from a coal seam located 926 m below the surface via a methane-producing well near Monroe, Louisiana, USA. Growth and methanogenesis were supported with methanol, monomethylamine, dimethylamine or trimethylamine, but not with dimethylsulfide, formate, acetate or H2/CO2. Cells grew in high-salt minimal medium but growth was stimulated with yeast extract or tryptone. Cells were single, non-motile, irregular coccoids 0.5–1.0 μm in diameter and the cell wall contained protein. Conditions for the maximum rate of growth were 40–50 °C, 0.2–0.6 M NaCl, 100–≥200 mM MgCl2, and pH 7.0–8.0. The G+C content of the genomic DNA was 42±1mol %. A comparison of 16S rRNA gene sequences indicated that strain SD1T was most closely related to Methanolobus oregonensis DSM 5435T with 96 % gene sequence similarity. It is proposed that strain SD1T represents a novel species, Methanolobus zinderi sp. nov. The type strain is SD1T (=ATCC BAA-1601T=DSM 21339T).

A novel strain, designated Jip 10T, isolated from dried rice straw, was characterized by a polyphasic approach to clarify its taxonomic position. The isolate was Gram-negative, facultatively aerobic, heterotrophic, non-motile, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate clustered with the genus Mucilaginibacter in the phylum Bacteroidetes. 16S rRNA gene sequence similarities between strain Jip 10T and the type strains of Mucilaginibacter gracilis and Mucilaginibacter paludis were 93.7 and 93.6 %, respectively. The G+C content of the genomic DNA was 48.1 mol%. Chemotaxonomic data [major menaquinone MK-7 and major fatty acids iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c)] supported the affiliation of strain Jip 10T to the genus Mucilaginibacter. However, the results of physiological and biochemical tests allowed phenotypic differentiation of strain Jip 10T from other Mucilaginibacter species with validly published names. Therefore, strain Jip 10T (=KCTC 12639T =LMG 23488T) was classified in the genus Mucilaginibacter as the type strain of a novel species, for which the name Mucilaginibacter daejeonensis sp. nov. is proposed.

A Gram-negative, strictly aerobic, motile, filamentous and viscous exopolymer-producing bacterium, designated strain YT21T, was isolated from fresh water. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain YT21T lies within a cluster containing the established genera Segetibacter, Terrimonas, Niastella and Chitinophaga in the phylum Bacteroidetes. However, the isolate represented a lineage distinct from these genera, with sequence similarities ranging from 88.9 to 91.8 %. The genomic G+C content was 45.2 mol%. The predominant isoprenoid quinone was MK-7. The major fatty acids were 15 : 0 iso, 17 : 0 iso 3-OH and 15 : 1 iso G. On the basis of morphological features and phenotypic and phylogenetic data, strain YT21T represents a novel genus and species, for which the name Filimonas lacunae gen. nov., sp. nov. is proposed. The type strain of Filimonas lacunae is strain YT21T (=NBRC 104114T =DSM 21054T).

A novel strain, NJ-8T, was isolated from sediment of the eutrophic Taihu Lake (China) and was subjected to a taxonomic study by using a polyphasic approach. The novel strain was aerobic and formed orange-pigmented colonies on R2A agar. Cells were Gram-negative single rods that were motile by means of gliding. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NJ-8T belonged to the phylum Bacteroidetes, with Niastella yeongjuensis DSM 17621T (92.3 % gene sequence similarity) and Niastella koreensis DSM 17620T (92.0 % similarity) as its closest relatives. The major fatty acids (>5 % of the total) were iso-C15 : 0 (27.8 %), iso-C15 : 1 G (15.4 %), iso-C17 : 0 3-OH (14.5 %) and summed feature 3 (comprising C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 13.9 %). The genomic DNA G+C content was 46.6 mol%. Based on molecular and phenotypic data, strain NJ-8T is considered to represent a novel species of a new genus, for which the name Lacibacter cauensis gen. nov., sp. nov. is proposed. The type strain of the type species of the genus, Lacibacter cauensis, is NJ-8T (=CGMCC 1.7271T=NBRC 104930T).

A Gram-negative, rod-shaped bacterium, designated strain YC6274T, was isolated from a stream (Sasang) carrying wastewater polluted with heavy metals in Busan, Korea. Growth was observed at 10–35 °C (optimum, 30 °C) and pH 6.0–9.5 (optimum, pH 7.5–8.0). Comparative 16S rRNA gene sequence analyses showed that the strain was most closely related to Flavobacterium cucumis R2A45-3T (96.6 % similarity), F. aquatile ATCC 11947T (93.7 %), F. croceum EMB47T (93.3 %), F. indicum GPTSA100-9T (93.3 %) and F. terrigena DS-20T (93.2 %). Sequence similarities with strains of other Flavobacterium species with validly published names were lower than 93.0 %. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain YC6274T formed a distinct phyletic lineage within the genus Flavobacterium. The predominant fatty acids of strain YC6274T were iso-C15 : 0, iso-C16 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, iso-C16 : 0 3-OH and iso-C15 : 0 3-OH. The G+C content of the genomic DNA was 32.5 mol% and the major quinone was MK-6. On the basis of phenotypic, chemotaxonomic and molecular data, it is clear that strain YC6274T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium sasangense sp. nov. is proposed. The type strain is YC6274T (=KCTC 22246T =DSM 21067T).