- Volume 58, Issue 12, 2008

A novel bacterial strain, designated Gsoil 954T, showing β-glucosidase activity was isolated from a soil sample from a ginseng field in Pocheon Province, South Korea. The isolate was a Gram-positive, aerobic, motile, coccus-shaped, non-endospore-forming bacterium. Comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil 954T belonged to the family Propionibacteriaceae, the highest levels of sequence similarity being found with the type strains of Microlunatus ginsengisoli (96.4 %) and Microlunatus phosphovorus (96.2 %). The strain showed <95.9 % similarity with respect to other species within the family Propionibacteriaceae. In addition, the presence of ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-9(H4) as the major menaquinone and anteiso-C15 : 0 and iso-C15 : 0 as the major cellular fatty acids suggested its affiliation with the genus Microlunatus. The G+C content of the genomic DNA was 65.1 mol%. On the basis of its phenotypic characteristics and phylogenetic distinctiveness, strain Gsoil 954T represents a novel species within the genus Microlunatus, for which the name Microlunatus panaciterrae sp. nov. is proposed. The type strain is Gsoil 954T (=KCTC 13058T=DSM 18662T).

A novel psychrophilic, Gram-positive, yellow-pigmented and aerobic bacterium, strain 0543T, was isolated from the China No. 1 glacier. Strain 0543T was able to grow at 4–23 °C, with optimum growth at 18–19 °C. The major fatty acids were anteiso-C15 : 0 (58.36 %), iso-C16 : 0 (21.13 %), iso-C14 : 0 (10.25 %) and anteiso-C17 : 0 (7.16 %). The genomic DNA G+C content was 63.5 mol% and the major menaquinone was MK-10. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 0543T represented a lineage within the family Microbacteriaceae, with the highest similarity of 97.4 % with Salinibacterium amurskyense KMM 3673T. On the basis of polyphasic, chemotaxonomic, physiological and biochemical evidence from this study, the novel species Salinibacterium xinjiangense sp. nov. is proposed; the type strain is 0543T(=CGMCC 1.5381T =JCM 13926T).

Six mycobacterial isolates from haemodialysis water, conforming a homogeneous phylogenetic group in a previous multigenic analysis, were classified taxonomically. Physiological and biochemical characterization, as well as DNA–DNA hybridizations, demonstrated that the isolates were facultatively autotrophic, aerobic and hydrogen-oxidizing bacteria, representing a novel species in the rapid growing Mycobacterium group, for which the name Mycobacterium llatzerense sp. nov. is proposed. The type strain is MG13T (=CECT 7273T=CCUG 54744T).

A novel chitinolytic actinomycete isolated from a Brazilian cerrado soil, designated strain RCQ1071T, was assigned to the genus Streptomyces on the basis of chemical and morphological characteristics. The almost-complete nucleotide sequence of the 16S rRNA gene of strain RCQ1071T was determined and also placed this strain in the genus Streptomyces. Phylogenetic analyses of 16S rRNA gene sequences showed that strain RCQ1071T formed a long branch in a group related to Streptomyces albulus, sharing approximately 98 % sequence similarity. Levels of DNA–DNA relatedness between strain RCQ1071T and members of this group, namely S. albulus DSM 40492T, Streptomyces noursei DSM 40635T and Streptomyces yunnanensis DSM 41793T, were 38.3, 27.8 and 46 %, respectively, strongly indicating that strain RCQ1071T was not a member of any of these species. The relatively long branch length within a stable clade together with the phenotypic data strongly supported that strain RCQ1071T represented a novel species. Based on the combination of physiological, phylogenetic and genomic data, strain RCQ1071T is suggested to represent a novel species of the genus Streptomyces, for which the name Streptomyces lunalinharesii sp. nov. is proposed. The type strain is RCQ1071T (=ATCC BAA-1231T =CIP 108852T =DSM 41876T).

An actinobacterium, designated strain 44C3T, was isolated in Michigan, USA, from the hindgut of the larvae of Tipula abdominalis, an aquatic crane fly, and was subjected to a polyphasic taxonomic investigation. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain represented a separate clade within the family Microbacteriaceae. It showed highest 16S rRNA gene sequence similarity with Cryobacterium psychrotolerans 0549T (96.5 %). Strain 44C3T had a novel B-type peptidoglycan. The peptidoglycan contained the diamino acid lysine, the peptide Gly–d-Glu was detected in the partial hydrolysate and alanine was the N terminus of the interpeptide bridge. No other amino acids found in other B-type peptidoglycans (including diaminobutyric acid, ornithine, homoserine and hydroxyglutamic acid) could be detected. The major menaquinones were MK-12 and MK-11, the major fatty acids were ai-C15 : 0, ai-C17 : 0 and i-C16 : 0 and the DNA G+C content was 60.9 mol%. Analysis of the chemotaxonomic and phylogenetic data suggested that strain 44C3T represented a novel species of a new genus within the family Microbacteriaceae, for which the name Klugiella xanthotipulae gen. nov., sp. nov. is proposed. The type strain of Klugiella xanthotipulae is 44C3T (=DSM 18031T =ATCC BAA-1524T).

A chromomycin-producing actinomycete, strain AP19, was isolated from a sample of faeces collected from Foping national nature reserve in China. Chemotaxonomic and morphological properties indicated that the novel isolate was a member of the genus Streptomyces. Phylogenetic analyses based on an almost complete 16S rRNA gene sequence of the strain and on the 120-nt nucleotide variable γ-region of this molecule revealed that it was closely related to Streptomyces griseus ISP 5236T and Streptomyces cavourensis subsp. washingtonensis ATCC 27732T. DNA–DNA relatedness values among these strains were above 70 %. Streptomyces cavourensis subsp. washingtonensis could be readily distinguished from Streptomyces cavourensis ATCC 14889T by differing BOX-PCR fingerprinting patterns, relatively low 16S rRNA gene sequence similarity and a low DNA–DNA relatedness value. It is proposed, therefore, that Streptomyces cavourensis subsp. washingtonensis is a later synonym of Streptomyces griseus.

Previous studies have proposed that Streptomyces caeruleus is an earlier heterotypic synonym for Streptomyces niveus and Streptomyces spheroides. In this study, phylogenetic analysis of the almost complete 16S rRNA gene sequences of the Streptomyces caeruleus type strains NBRC 13344T, JCM 4014T and NRRL B-2194T revealed that S. caeruleus was closely related to Actinoalloteichus cyanogriseus and not to S. niveus, S. spheroides or any other species of the genus Streptomyces. Moreover, the diagnostic cell-wall diamino acid was found to be meso-diaminopimelic acid in S. caeruleus and DNA–DNA hybridization studies revealed that S. caeruleus NBRC 13344T was a member of the same species as A. cyanogriseus NBRC 14455T. Based on these chemotaxonomic and phylogenetic data, it is proposed that Streptomyces caeruleus ( Baldacci 1944 ) Pridham et al. 1958 be reclassified as a heterotypic synonym of Actinalloteichus cyanogriseus Tamura et al. 2000 . Furthermore, based on phylogenetic, morphological and MALDI-TOF MS analyses, it is proposed that the species Streptomyces laceyi Manfio et al. 2004 and Streptomyces spheroides Wallick et al. 1956 are reclassified as later heterotypic synonyms of Streptomyces niveus Smith et al. 1956 .

Slowly growing, non-chromogenic mycobacteria were isolated from striped barombi mbo cichlids (Stomatepia mariae) maintained at the London Zoo Aquarium, UK. The isolates could be differentiated from other slowly growing, non-pigmented mycobacteria by a combination of phenotypic features including their inability to grow at 37 °C, positive tests for heat-stable catalase, tellurite reduction and arylsulfatase activity, and the absence of urease activity, Tween 80 hydrolysis, nitrate reductase, iron uptake and semiquantitative catalase. The almost full-length 16S rRNA gene sequence, together with partial sequences from the 65 kDa heat-shock protein (hsp65) and the β-subunit of the bacterial RNA polymerase (rpoB) genes and the 16S–23S internal transcribed spacer 1 (ITS 1) region were identical for all three novel strains, but distinct from those of all known mycobacterial species. Phylogenetic analysis based on 16S rRNA gene sequences placed the novel isolates within the slowly growing mycobacteria group in close proximity to Mycobacterium florentinum. Based on genotypic and phenotypic findings, it is proposed that these isolates represent a novel species of the genus Mycobacterium, for which the name Mycobacterium stomatepiae sp. nov. is proposed with strain T11T (=DSM 45059T=CIP 109275T=NCIMB 14252T) as the type strain.

The taxonomic position of a group of actinobacterial strains isolated from the phyllosphere of potato plants was investigated by using a polyphasic approach. Although the similarity values for their 16S rRNA gene sequences suggested an intermediate position between Microbacterium and Agrococcus, the phylogenetic tree demonstrated a clear clustering of the representative strain, K 114/01T, within the genus Agrococcus. The presence of 2,4-diaminobutyric acid as the diagnostic diamino acid in the cell-wall peptidoglycan of strain K 114/01T substantiated the affiliation to the genus Agrococcus. An analysis performed using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry revealed highly similar spectral patterns for the isolated strains, which, together with their conformity regarding a multitude of phenotypic features, supported their affiliation to the same species. Differences in several physiological features, peptidoglycan and menaquinone composition and whole-cell fatty acid profiles enabled discrimination of the phyllosphere isolates with respect to recognized Agrococcus species. As the 16S rRNA gene sequence similarity values were below 97 %, the strains isolated from the phyllosphere of potato plants represent a novel species of the genus Agrococcus, for which the name Agrococcus versicolor sp. nov. is proposed. The type strain is K 114/01T (=DSM 19812T =LMG 24386T).

A coryneform bacterium isolated from the sputum of a patient with pneumonia was characterized by phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and short chain mycolic acids consistent with the genus Corynebacterium. Comparative 16S rRNA gene sequencing studies confirmed this assignment, with the organism forming a hitherto unknown subline within the genus associated with a subcluster containing Corynebacterium hansenii, Corynebacterium freneyi, Corynebacterium xerosis, Corynebacterium amycolatum and Corynebacterium sphenisci. Sequence divergence values of >2.7 % from established corynebacterial species suggested that the new isolate represented a novel species. This was also supported by the results of the biochemical tests. On the basis of phenotypic and phylogenetic evidence, it is proposed that the unknown bacterium be classified as a novel species of the genus Corynebacterium, Corynebacterium sputi sp. nov. (type strain IMMIB L-999T=DSM 45148T=CCUG 55795T).

A Gram-positive, aerobic, motile, coccoid or short rod-shaped bacterium, 5420S-23T, was isolated from an air sample collected in the Republic of Korea. According to phylogenetic analysis based on 16S rRNA gene sequences, strain 5420S-23T revealed 97.5, 97.3, 97.3 and 97.2 % similarity, respectively, to Cellulomonas biazotea DSM 20112T, Cellulomonas cellasea DSM 20118T, Cellulomonas fimi DSM 20113T and Cellulomonas chitinilytica X.bu-bT. The peptidoglycan type of strain 5420S-23T was A4β, containing l-ornithine–d-glutamic acid. The cell-wall sugars were galactose, glucose and xylose. The major fatty acids were anteiso-C15 : 0 (49.7 %) and C16 : 0 (20.0 %). The major menaquinone was MK-9(H4) and major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content was 74 mol%. The results of DNA–DNA hybridization with strains of closely related Cellulomonas species, in combination with chemotaxonomic and physiological data, demonstrated that isolate 5420S-23T represents a novel Cellulomonas species, for which the name Cellulomonas aerilata sp. nov. is proposed, with strain 5420S-23T (=KACC 20692T =DSM 18649T) as the type strain.

A Gram-positive, aerobic, neutrophilic and rod-shaped bacterium, strain Shh49T, was isolated from a deep-sea sediment sample collected from the East Pacific polymetallic nodule region. The strain was able to grow within a temperature range of 4–35 °C and tolerated up to 7.5 % (w/v) NaCl. Strain Shh49T was characterized chemotaxonomically by having MK-12 and MK-13 as predominant isoprenoid quinones, anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as major fatty acids and ornithine as cell-wall diamino acid. The genomic DNA G+C content was 66.8 mol%. On the basis of 16S rRNA gene sequence similarities, the closest phylogenetic neighbours were the type strains of Microbacterium phyllosphaerae (98.3 %) and Microbacterium keratanolyticum (98.0 %), but strain Shh49T could be clearly distinguished from its phylogenetic relatives with reference to a broad range of physiological and biochemical markers. DNA–DNA relatedness of strain Shh49T with M. phyllosphaerae DSM 13468T and M. keratanolyticum DSM 8606T was 56 and 31 %, respectively. On the basis of phenotypic and genotypic data presented in this study, strain Shh49T represents a novel species of the genus Microbacterium, for which the name Microbacterium profundi sp. nov. is proposed. The type strain is Shh49T (=CGMCC 1.6777T =JCM 14840T).

A motile, rod-shaped, pink-pigmented, extremely halophilic archaeon, strain SF3-213T, was isolated from a crystallizer pond at the Cargill Solar Salt Plant, Newark, California (USA). Analysis of the almost-complete 16S rRNA gene sequence showed that the isolate was phylogenetically related to species of the genus Halorubrum, with a close relationship to Halorubrum trapanicum NRC 34021T (98.6 % similarity), Halorubrum sodomense ATCC 33755T (98.3 %) and Halorubrum xinjiangense AS 1.3527T (98.2 %). The polar lipids of strain SF3-213T were C20C20 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and a sulfated diglycosyl-diether. Strain SF3-213T grew in 2.5–5.0 M NaCl. The temperature and pH ranges for growth were 25–42 °C and 6.8–8.5, respectively. Optimal growth occurred at 3.5–4.5 M NaCl, 37 °C and pH 7.3. Mg2+ was required for growth. The DNA G+C content was 69.4 mol%. DNA–DNA hybridization values lower than 70 % were obtained between strain SF3-213T and the closely related species of the genus Halorubrum. Based on the data presented in this study, strain SF3-213T represents a novel species for which the name Halorubrum californiense sp. nov. is proposed; the type strain is SF3-213T (=CECT 7256T=DSM 19288T=JCM 14715T).

A novel extremely halophilic strain, designated XH-65T, isolated from the salt lake Xilinhot in Inner Mongolia, PR China, was subjected to a polyphasic taxonomic characterization. Strain XH-65T is neutrophilic, non-motile and requires at least 2.5 M NaCl for growth, with an optimum at 3.4 M NaCl, and grows at pH 6.0–9.0, with optimum growth at pH 7.5. Strain XH-65T grows at 25–50 °C, with optimal growth at 37 °C. Magnesium is not required for growth. On the basis of 16S rRNA gene sequence analysis, strain XH-65T was shown to belong to the genus Haloterrigena and was related to Haloterrigena turkmenica VKM B-1734T (98.1 % sequence similarity), Haloterrigena saccharevitans AB14T (96.9 %), Haloterrigena thermotolerans PR5T (96.3 %), Haloterrigena limicola AX-7T (95.8 %) and Haloterrigena hispanica FP1T (95.7 %). DNA–DNA hybridization revealed 37 % relatedness between strain XH-65T and Htg. turkmenica VKM B-1734T. The polar lipid composition revealed the presence of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and mannose-2,6-disulfate (1→2)-glucose glycerol diether (S2-DGD). The results of the DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain XH-65T from the six Haloterrigena species with validly published names. Therefore, strain XH-65T represents a novel species, for which the name Haloterrigena salina sp. nov. is proposed, with the type strain XH-65T (=CGMCC 1.6203T =JCM 13891T).

Two heterotrophic, aerobic, yellow-pigmented, Gram-negative, non-gliding bacteria, designated AKS293T and AKS432T, isolated from a red alga, were analysed using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis revealed that the novel strains were affiliated to the genus Lacinutrix, a member of the family Flavobacteriaceae, showing sequence similarities of 96.1–96.4 % with respect to the type strain of Lacinutrix copepodicola. The two novel isolates shared 99.5 % 16S rRNA gene sequence similarity and 55.0 % DNA–DNA relatedness. They grew optimally at 17.5 °C and pH 6.5. The main cellular fatty acids of strain AKS293T were iso-C15 : 0, iso-C15 : 0 3-OH and iso-C16 : 0 3-OH, while those of strain AKS432T were anteiso-C15 : 0, iso-C15 : 0, iso-C15 : 1 and iso-C15 : 0 3-OH. In both cases, the major isoprenoid quinone was MK-6. The DNA G+C contents were 34.7 and 37.0 mol% for strains AKS293T and AKS432T, respectively. The phylogenetic evidence, phenotypic data and DNA–DNA hybridization results support the differentiation of strains AKS293T and AKS432T from each other and from their closest relative, L. copepodicola DJ3T. Therefore, strains AKS293T and AKS432T represent two novel species, for which the names Lacinutrix algicola sp. nov. and Lacinutrix mariniflava sp. nov. are proposed, respectively. The type strain of L. algicola sp. nov. is AKS293T (=KCCM 42313T=JCM 13825T) and the type strain of L. mariniflava sp. nov. is AKS432T (=KCCM 42306T=JCM 13824T). An emended description of the genus Lacinutrix is also proposed.

The taxonomic position of a strain isolated from kerosene-contaminated soil in Hungary and formerly misidentified as Brevundimonas vesicularis was examined using a polyphasic approach. The isolate, designated CHB-20pT, could be clearly assigned to the genus Chryseobacterium (family Flavobacteriaceae) on the basis of 16S rRNA gene sequence similarity. Strain CHB-20pT, a moderate oil degrader, was a Gram-negative, aerobic, mesophilic microbe with a temperature optimum of 28–30 °C. Predominant fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1 ω7c and/or iso-C15 : 0 2-OH) and iso-C17 : 0 3-OH. Menaquinone-6 (MK-6) was the predominant respiratory quinone; MK-5 was present as a minor component. The almost complete 16S rRNA gene sequence of strain CHB-20pT shared 94–97 % similarity with sequences of the type strains of species of the genus Chryseobacterium. DNA–DNA relatedness between strain CHB-20pT and its closest relative, Chryseobacterium caeni, was lower than 46 %. Moreover, several diagnostic phenotypic properties distinguished strain CHB-20pT from C. caeni. On the basis of biochemical, chemotaxonomic and genotypic data, isolate CHB-20pT represents a novel species within the genus Chryseobacterium, Chryseobacterium hungaricum sp. nov.; the type strain is CHB-20pT (=NCAIM B2269T=DSM 19684T).

A facultatively anaerobic, marine spirochaete, designated strain SIP1T, was isolated from interstitial water from a cyanobacteria-containing microbial mat. Cells of strain SIP1T were 0.3–0.4×10–12 μm in size, helical with a body pitch of approximately 1.4 μm and motile by means of two to four periplasmic flagella (one, or occasionally two, being inserted near each end of the cell). Cells were catalase-negative and used a variety of monosaccharides and disaccharides and pectin as energy sources, growing especially well on cellobiose. Neither organic acids nor amino acids were utilized as energy sources. One or more amino acids in tryptone and one or more components of yeast extract were required for growth. Growth was observed at 9–37 °C (optimally at or near 37 °C), at initial pH 5–8 (optimally at initial pH 7.5) and in media prepared with 20–100 % (v/v) seawater (optimally at 60–80 %) or 0.10–1.00 M NaCl (optimally at 0.30–0.40 M). The products of cellobiose fermentation were acetate, ethanol, CO2, H2 and small amounts of formate. Aerated cultures performed incomplete oxidation of cellobiose to acetate (and, presumably, CO2) plus small amounts of ethanol and formate, but exhibited a Y cellobiose that was only slightly greater than that of cellobiose-fermenting anoxic cultures. The G+C content of the genomic DNA of strain SIP1T was 41.4 mol%, the lowest among known spirochaetas. On the basis of its 16S rRNA gene sequence, strain SIP1T was grouped among other members of the genus Spirochaeta, but it bore only 89 % similarity with respect to its closest known relatives, Spirochaeta litoralis and Spirochaeta isovalerica, two marine obligate anaerobes. On the basis of its phenotypic properties and phylogenetic position, strain SIP1T represents a novel species of the genus Spirochaeta, for which the name Spirochaeta cellobiosiphila sp. nov. is proposed. The type strain is SIP1T (=ATCC BAA-1285T =DSM 17781T).

A pale-pink strain (CCUG 53370T) from water was investigated by a polyphasic taxonomic approach. The cells stained Gram-positive and were rod-shaped and non-spore-forming. Analyses using the 16S rRNA gene sequence of the isolate showed that the organism belongs to the genus Deinococcus, with the highest sequence similarities to the type strains of Deinococcus ficus (94.4 %), Deinococcus navajonensis (94.3 %) and Deinococcus mumbaiensis (94.3 %). Chemotaxonomic data revealed that CCUG 53370T contains exclusively menaquinone MK-8 as the respiratory quinone and a complex polar lipid profile consisting of different unidentified glycolipids and polar lipids, two unknown phospholipids and three unknown phosphoglycolipids. As in other deinococci, one of these phosphoglycolipids was predominant in the profile, and it was identified in Deinococcus radiodurans as 2′-O-(1,2-diacyl-sn-glycero-3-phospho)-3′-O-(α-galactosyl)-N-d-glyceroyl alkylamine. Predominant fatty acids were C16 : 1 ω7c, C17 : 1 ω8c and C17 : 1 ω9c. Biochemical and chemotaxonomic properties demonstrate that strain CCUG 53370T represents a novel species, for which the name Deinococcus aquatilis sp. nov. is proposed. The type strain is CCUG 53370T (=CCM 7524T).