- Volume 58, Issue 2, 2008

An aerobic, Gram-negative bacterium, strain KMM 329T, was isolated from a deep-sea sponge specimen from the Philippine Sea and subjected to a polyphasic taxonomic investigation. Comparative 16S rRNA gene sequence analysis showed that strain KMM 329T clustered with the species of the genus Lysobacter. The highest level of 16S rRNA gene sequence similarity (97.0 %) was found with respect to Lysobacter concretionis KCTC 12205T; lower values (96.4–95.2 %) were obtained with respect to the other recognized Lysobacter species. The value for DNA–DNA relatedness between strain KMM 329T and L. concretionis KCTC 12205T was 47 %. Branched fatty acids 16 : 0 iso, 15 : 0 iso, 11 : 0 iso 3-OH and 17 : 1 iso were found to be predominant. Strain KMM 329T had a DNA G+C content of 69.0 mol%. On the basis of the phenotypic, chemotaxonomic, DNA–DNA hybridization and phylogenetic data, strain KMM 329T represents a novel species of the genus Lysobacter, for which the name Lysobacter spongiicola sp. nov. is proposed. The type strain is KMM 329T (=NRIC 0728T =JCM 14760T).

Two Gram-negative, non-motile, non-spore-forming, coccoid bacteria (strains CCM 4915T and CCM 4916), isolated from clinical specimens of the common vole Microtus arvalis during an epizootic in the Czech Republic in 2001, were subjected to a polyphasic taxonomic study. On the basis of 16S rRNA (rrs) and recA gene sequence similarities, both isolates were allocated to the genus Brucella. Affiliation to Brucella was confirmed by DNA–DNA hybridization studies. Both strains reacted equally with Brucella M-monospecific antiserum and were lysed by the bacteriophages Tb, Wb, F1 and F25. Biochemical profiling revealed a high degree of enzyme activity and metabolic capabilities not observed in other Brucella species. The omp2a and omp2b genes of isolates CCM 4915T and CCM 4916 were indistinguishable. Whereas omp2a was identical to omp2a of brucellae from certain pinniped marine mammals, omp2b clustered with omp2b of terrestrial brucellae. Analysis of the bp26 gene downstream region identified strains CCM 4915T and CCM 4916 as Brucella of terrestrial origin. Both strains harboured five to six copies of the insertion element IS711, displaying a unique banding pattern as determined by Southern blotting. In comparative multilocus VNTR (variable-number tandem-repeat) analysis (MLVA) with 296 different genotypes, the two isolates grouped together, but formed a separate cluster within the genus Brucella. Multilocus sequence typing (MLST) analysis using nine different loci also placed the two isolates separately from other brucellae. In the IS711-based AMOS PCR, a 1900 bp fragment was generated with the Brucella ovis-specific primers, revealing that the insertion element had integrated between a putative membrane protein and cboL, encoding a methyltransferase, an integration site not observed in other brucellae. Isolates CCM 4915T and CCM 4916 could be clearly distinguished from all known Brucella species and their biovars by means of both their phenotypic and molecular properties, and therefore represent a novel species within the genus Brucella, for which the name Brucella microti sp. nov. with the type strain CCM 4915T (=BCCN 07-01T=CAPM 6434T) is proposed.

Two novel marine, Gram-negative, non-motile, catalase- and oxidase-positive, aerobic bacteria were isolated from coastal seawater in Tokyo Bay. Analysis of almost-complete 16S rRNA gene sequences showed that the two isolates are members of the genus Paracoccus, sharing highest 16S rRNA gene sequence similarity (96.5 %) with Paracoccus aminophilus NBRC 16710T. The DNA–DNA reassociation values between P. aminophilus NBRC 16710T and these isolates were only 10–20 %, in contrast to the high DNA relatedness between the two isolates (89 %). At least 1 % (w/v) NaCl was required for growth. Cellular fatty acid profiles revealed C18 : 1 ω7c as the major component and C10 : 0 3-OH as the major hydroxy fatty acid. Ubiquinone-10 was detected as the major respiratory quinone. The G+C content of the genomic DNA of both strains was 69 mol%. On the basis of DNA–DNA hybridization data and physiological and chemotaxonomic characteristics, it is proposed that these strains should be placed in a novel species, Paracoccus marinus sp. nov. The type strain is KKL-A5T (=NBRC 100637T =CIP 108500T); KKL-B9 (=NBRC 100640) is a reference strain.

The taxonomic position of a novel bacterial strain, YC5194T, with antimicrobial activity, isolated from the rhizosphere of pepper in Jinju, South Korea, was studied using a polyphasic approach. Cells of the strain were Gram-negative, rod-shaped, facultative anaerobes. It grew at a temperature of 15–37 °C (optimum 28 °C). Growth of the strain occurred between pH 5.5 and 8.5, with an optimum of pH 7.0–7.5. The strain inhibited mycelial growth of Pythium ultimum, Colletotrichum gloeosporioides, Fusarium oxysporum, Botrytis cinerea, Rhizoctonia solani and Botryosphaeria dothidea and growth of Bacillus subtilis. The G+C content of the total DNA was 65.4 mol%. The 16S rRNA gene sequence of the strain was most closely related to species of the genus Lysobacter (<94.0 to >99.0 % sequence similarity). Chemotaxonomic data (major quinone, Q-8; major polar lipids, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidyl-N-methylethanolamine; major fatty acids, iso-C15 : 0, summed feature 3, C16 : 0, iso-C17 : 1 ω9c and C18 : 1 ω7c) supported the affiliation of strain YC5194T to the genus Lysobacter. Phylogenetic analysis based on 16S rRNA gene sequences, DNA–DNA hybridization data and biochemical and physiological characteristics strongly supported the genotypic and phenotypic differentiation of strain YC5194T from species of Lysobacter with validly published names. Strain YC5194T therefore represents a novel species, for which the name Lysobacter capsici sp. nov. is proposed. The type strain is YC5194T (=KCTC 22007T =DSM 19286T).

A Gram-negative, non-spore-forming, rod-shaped, Hydrogenophaga-like bacterial strain, K102T, was isolated from wastewater collected from a textile dye works in Korea and subjected to a polyphasic taxonomic study. Strain K102T grew optimally at pH 7.0–8.0 and 30–37 °C in the presence of 0.5 % (w/v) NaCl. It contained Q-8 as the predominant ubiquinone and C16 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and C18 : 1 ω7c as the major fatty acids. The DNA G+C content was 64.8 mol%. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain K102T fell within the radiation of the cluster comprising species of the genus Hydrogenophaga. Strain K102T exhibited 16S rRNA gene sequence similarity values of 95.9–98.9 % to the type strains of recognized Hydrogenophaga species. Levels of DNA–DNA relatedness between strain K102T and the type strains of its four phylogenetically most closely related species, together with differential phenotypic properties, revealed that strain K102T could be distinguished from all recognized species of the genus Hydrogenophaga. On the basis of phenotypic, phylogenetic and genetic data, strain K102T is considered to represent a novel species of the genus Hydrogenophaga, for which the name Hydrogenophaga bisanensis sp. nov. is proposed. The type strain is K102T (=KCTC 12980T =CCUG 54518T).

An ovoid to rod-shaped, phototrophic, purple sulfur bacterium, designated strain JA136T, was isolated in pure culture from brackish water near Kakinada, India, in a medium that contained 2 % NaCl (w/v). Cells were Gram-negative and motile by means of a single polar flagellum. Strain JA136T had no absolute salt requirement for growth but was able to tolerate up to 4 % NaCl (w/v). Intracellular photosynthetic membranes were of the vesicular type. Bacteriochlorophyll a and the carotenoid lycopene of the rhodopinal series were present as photosynthetic pigments. Strain JA136T was able to grow photolithoautotrophically and photolithoheterotrophically. There was no vitamin requirement for growth of strain JA136T. Phylogenetic analysis on the basis of 16S rRNA gene sequences indicated that strain JA136T clustered with species of the genus Allochromatium in the class Gammaproteobacteria. Strain JA136T showed highest 16S rRNA gene sequence similarity with the type strains of Allochromatium vinosum (97.0 %), Allochromatium minutissimum (95.8 %) and Allochromatium warmingii (90.0 %). Based on 16S rRNA gene sequence similarity data and morphological and physiological characteristics, strain JA136T was sufficiently distinct from recognized Allochromatium species to be described as representing a novel species of the genus, for which the name Allochromatium renukae sp. nov. is proposed. The type strain is JA136T (=JCM 14262T =DSM 18713T).

A polyphasic taxonomic study was performed to compare 26 novel bacterial isolates obtained from (semi-)natural grassland soils and a heathland soil in the Netherlands with 16 strains that had previously been assigned to the genus Collimonas. Genomic fingerprinting (BOX-PCR), whole-cell protein electrophoresis, matrix-assisted laser desorption ionization time-of-flight mass spectrometry of intact cells and physiological characterization (Biolog) of the isolates confirmed the existence of different strain clusters (A–D) within the genus Collimonas. Until now, only cluster C strains have been formally classified, as Collimonas fungivorans. In this study, DNA–DNA hybridizations were performed with a selection of strains representing the four clusters. The results showed that cluster B strains also belong to C. fungivorans and that strains of clusters A and D represent two novel species within the genus Collimonas. The latter novel species could be differentiated by means of phenotypic and genotypic characteristics and are classified as Collimonas arenae sp. nov. (cluster A; type strain Ter10T =LMG 23964T =CCUG 54727T) and Collimonas pratensis sp. nov. (cluster D; type strain Ter91T =LMG 23965T =CCUG 54728T).

A Gram-negative, rod-shaped, aerobic bacterium, designated strain RP007T, was isolated from a polycyclic aromatic hydrocarbon-contaminated soil in New Zealand. Two additional strains were recovered from a compost heap in Belgium (LMG 18808) and from the rhizosphere of maize in the Netherlands (LMG 24204). The three strains had virtually identical 16S rRNA gene sequences and whole-cell protein profiles, and they were identified as members of the genus Burkholderia, with Burkholderia phenazinium as their closest relative. Strain RP007T had a DNA G+C content of 63.5 mol% and could be distinguished from B. phenazinium based on a range of biochemical characteristics. Strain RP007T showed levels of DNA–DNA relatedness towards the type strain of B. phenazinium and those of other recognized Burkholderia species of less than 30 %. The results of 16S rRNA gene sequence analysis, DNA–DNA hybridization experiments and physiological and biochemical tests allowed the differentiation of strain RP007T from all recognized species of the genus Burkholderia. Strains RP007T, LMG 18808 and LMG 24204 are therefore considered to represent a single novel species of the genus Burkholderia, for which the name Burkholderia sartisoli sp. nov. is proposed. The type strain is RP007T (=LMG 24000T =CCUG 53604T =ICMP 13529T).

A Gram-negative, facultatively anaerobic strain with slightly curved and straight rod-shaped cells, strain CL-GR58T, was isolated from coastal seawater (near Gori, Korea). Analyses of the 16S rRNA gene sequence revealed that strain CL-GR58T belonged to the family Rhodospirillaceae with Azospirillum lipoferum as its closest relative (gene sequence similarity of 90.9 %). Phylogenetic analyses of the 16S rRNA gene sequences showed that strain CL-GR58T was not associated with any known genera in the family Rhodospirillaceae. The novel strain grew in the presence of 1–10 % sea salts, optimally at 30–35 °C and pH 8. The major cellular fatty acids consisted of C18 : 1 ω7c (48.5 %), C16 : 0 (14.8 %), C17 : 0 (12.2 %), C19 : 0 cyclo ω8c (6.3 %) and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH, 6.0 %). Among the phylogenetically related genera, the fatty acid C17 : 0 was found only in strain CL-GR58T. The DNA G+C content of the novel strain was 68.0 mol%. According to phylogenetic analyses of the 16S rRNA gene sequence, fatty acid content and the physiological data, strain CL-GR58T represents a novel species in a new genus of the family Rhodospirillaceae, for which the name Thalassobaculum litoreum gen. nov., sp. nov. is proposed. The type strain of the type species is CL-GR58T (=KCCM 42674T=DSM 18839T).

A Gram-negative, short rod-shaped, nitrogen-fixing bacterium (CC-21T) was isolated from a soil sample collected from the regional agricultural research station in Kaohsiung County (Taiwan). Using 16S rRNA gene sequence analysis, it could be clearly demonstrated that this isolate was novel: it showed <97 % similarity to species of the genera Acidovorax, Alicycliphilus, Giesbergeria, Simplicispira and Diaphorobacter. The organism used several organic acids, but only a few sugars as substrates. The fatty acid profile differed from those reported for members of the genera Acidovorax, Alicycliphilus, Giesbergeria, Simplicispira and Diaphorobacter. On the basis of 16S rRNA gene sequence analysis in combination with physiological data, strain CC-21T represents a novel species in a new genus, for which the name Pseudacidovorax intermedius gen. nov., sp. nov. is proposed; the type strain is CC-21T (=CCUG 54492T=CIP 109510T).

A Gram-negative, aerobic bacterium, H1-M8T, was isolated from seashore sand in Korea and then characterized using a polyphasic approach. Cells were short rods (0.7–1.0×1.5–2.0 μm) and were motile (each cell having at least one flagellum). Colonies were light-brown, non-pigmented, circular and convex with clear margins. Growth of the strain was observed at 5–35 °C, pH 6.0–9.0 and NaCl concentrations up to 8.4 % (w/v). Phylogenetic analysis of the 16S rRNA gene sequence revealed a clear affiliation between the novel strain and members of the genus Jannaschia. The sequence similarities between H1-M8T and type strains of the genus Jannaschia ranged from 97.0 to 97.8 %. However, DNA–DNA hybridizations between the isolate and type strains of other related species produced low values (21–38 %). The major isoprenoid quinone was Q-10 and the predominant cellular fatty acids were 18 : 1ω7c (68.2 %) and 18 : 0 (10.5 %). The G+C content of the DNA was 63.6 mol%. On the basis of physiological, biochemical and chemotaxonomic traits and data from the comparative 16S rRNA sequence analysis, strain H1-M8T represents a novel species of the genus Jannaschia, for which the name Jannaschia pohangensis sp. nov. is proposed. The type strain is H1-M8T (=KACC 11609T =DSM 19073T).

Three ascomycetous yeast strains, H-6T, ZX-15 and ZX-20, isolated from the bark of two tree species of the family Fagaceae collected from different regions of China, formed unconjugated and persistent asci containing two to four globose ascospores. 26S rDNA D1/D2 domain and internal transcribed spacer (ITS) region (including 5.8S rDNA) sequence analysis showed that they were closely related to the currently accepted Saccharomyces species with strong support. Comparisons of the rDNA sequences, electrophoretic karyotypes and physiological characters indicated that the three strains represent a novel species in the genus Saccharomyces. The name Saccharomyces arboricolus sp. nov. was proposed for the novel species, with H-6T (=AS 2.3317T=CBS 10644T) isolated from the bark of Quercus fabri as the type strain.

Two yeast strains (TM2-16 and PT1-17T) were isolated by membrane filtration from samples of estuarine water collected from two mangrove forests, in Khao Lumpee-Haad Thaimueang National Park and Mu Ko Ra-Ko Prathong National Park, Phang-Nga Province, Thailand. Analysis of the D1/D2 domain of the large-subunit rDNA sequences revealed that the sequences of the two strains were identical. The closest species in terms of pairwise sequence similarity was Candida galli, but the level of nucleotide substitutions (13.2 %) was sufficient to justify the description of a separate species. Phylogenetic analysis demonstrated that the two strains occupy a basal position with respect to Yarrowia lipolytica and C. galli of the Yarrowia clade, supported by a high bootstrap value. The two strains showed identical phenotypic characteristics, including proliferation by multilateral budding, absence of ascospores and ballistoconidia and negative Diazonium blue B and urease reactions. The major ubiquinone was Q-9. On the basis of the above findings, these two strains were assigned to a single novel species of the genus Candida, for which the name Candida phangngensis sp. nov. is proposed. The type strain is PT1-17T (=BCC 21231T =NBRC 101967T =CBS 10407T).

The teleomorph of Candida cleridarum was discovered through the detection of conjugation between isolates of a large collection from the nitidulid beetles of the genus Carpophilus found in the flowers of various cacti in Arizona, USA. The previous oversight of the sexual cycle of this yeast is attributed to the inequality (ca. 5 : 1) of the two mating types. Extensive conjugation between compatible mating types is observed after overnight incubation on 5 % malt agar, followed after 3–5 days by the formation of mature asci. The hat-shaped ascospores are reminiscent of those seen in Kodamaea species, which are members of the same guild. However, published analyses of D1/D2 large subunit rDNA sequences indicate an affinity with the genus Debaryomyces. As the latter is polyphyletic and morphologically heterogeneous, and in view of the distinct life cycle of the new teleomorph, the new genus Kurtzmaniella is described with a novel species, Kurtzmaniella cleridarum sp. nov. Given the close relatedness of Kurtzmaniella cleridarum sp. nov. to Candida quercitrusa, Candida oleophila and Candida railenensis, for which several natural isolates were available, strains of these species were mixed in pairs under the conditions found favourable for the former. Conjugation was not detected in those species. The type strain of Kurtzmaniella cleridarum sp. nov. is UWOPS 99-101.1T (=CBS 8793T=NRRL Y-48386T, h+ ), type of Candida cleridarum. The allotype is UWOPS 07-123.1 (=CBS 10688=NRRL Y-48387, h− ).

A nitrogen-fixing bacterium, designated strain T98T, was isolated from rhizosphere soil of Forsythia mira. Phylogenetic analysis based on a fragment of the nifH gene and the full-length 16S rRNA gene sequence revealed that strain T98T was a member of the genus Paenibacillus. High levels of 16S rRNA gene similarity were found between strain T98T and Paenibacillus durus ATCC 35681T (97.0 %), Paenibacillus sabinae DSM 17841T (98.3 %) and Paenibacillus zanthoxyli DSM 18202T (96.8 %). Levels of 16S rRNA gene sequence similarity between strain T98T and the type strains of other recognized members of the genus Paenibacillus were below 97.0 %. Levels of DNA–DNA relatedness between strain T98T and P. durus ATCC 35681T, P. sabinae DSM 17841T and P. zanthoxyli DSM 18202T were 27.6, 30.0 and 32.1 %, respectively. The DNA G+C content of strain T98T was 50.4 mol%. The major fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. On the basis of its phenotypic characteristics and levels of DNA–DNA hybridization, strain T98T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus forsythiae sp. nov. is proposed. The type strain is T98T (=CCBAU 10203T =DSM 17842T).

A Gram-positive, motile, endospore-forming, irregular rod-shaped (0.7–0.9×2.5–5.0 μm), halophilic bacterial strain, NTU-101T, was isolated from Chigu saltern in southern Taiwan, previously used as a salt production field. The isolate was characterized taxonomically based on biochemical and molecular approaches. It grows optimally at 40 °C and in the presence of 5–10 % NaCl. Strain NTU-101T has cell-wall peptidoglycan based on meso-diaminopimelic acid and MK-7 as the predominant menaquinone. Major polar lipids are phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. Anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0 are the major fatty acids. The DNA G+C content was 37.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed its affiliation to the genus Virgibacillus. DNA–DNA relatedness values between strain NTU-101T and Virgibacillus dokdonensis and Virgibacillus pantothenticus were 17.5 and 21.5 %, respectively. Based on the phenotypic and phylogenetic properties, strain NTU-101T (=BCRC 17637T=CGMCC 1.6496T) was classified as a novel strain of Virgibacillus species, for which the name Virgibacillus chiguensis sp. nov. is proposed.

Four bacterial strains, designated K9T, K105, K1012A and K101, were isolated from soil in Lithuania. All these strains could use n-butanol as a sole carbon source. The strains grew in a medium containing 12–120 mM n-butanol. The strains were strictly aerobic, Gram-positive endospore-formers. The best growth was achieved at 25 °C and pH 7.0 in medium containing 1 % (w/v) NaCl. The strains showed identical profiles of 16S–23S rRNA internal transcribed spacer PCR and nearly identical 16S rRNA gene PCR-RFLP electrophoretic patterns and physiological characteristics, demonstrating their relationship at the species level. The cellular fatty acid profile of K9T consisted of significant amounts of the C15 branched-chain fatty acids iso-C15 : 0 (16.78 %) and anteiso-C15 : 0 (45.80 %). The diagnostic cell-wall diamino acid was meso-diaminopimelic acid. The 16S rRNA gene sequence of K9T showed the highest similarity to the sequences of Bacillus simplex DSM 1321T and Bacillus muralis LMG 20238T (98.3 and 97.7 %, respectively). The DNA G+C content was 37.4 mol%. Studies of DNA–DNA relatedness, morphological, physiological and chemotaxonomic analyses and phylogenetic data based on 16S rRNA gene sequencing allowed strains K9T, K105, K1012A and K101 to be described as members of a novel species of the genus Bacillus, for which the name Bacillus butanolivorans sp. nov. is proposed. The type strain is K9T (=DSM 18926T =LMG 23974T).