- Volume 55, Issue 6, 2005

Two Gram-negative, rod-shaped, non-spore-forming bacterial strains designated C42T and C52T were isolated in the Medical Clinic for Small Animals and Ungulates at the University for Veterinary Medicine Vienna, Austria. On the basis of 16S rRNA gene sequence similarity, both strains were shown to belong to the genus Sphingomonas. Strain C42T showed the greatest levels of sequence similarity with Sphingomonas melonis DSM 14444T and Sphingomonas aquatilis KCTC 2881T (both 97·7 %). Strain C52T showed the greatest levels of sequence similarity with Sphingomonas koreensis KCTC 2882T (97·2 %), Sphingomonas aquatilis KCTC 2881T (97·1 %) and S. melonis DSM 14444T (97·0 %). The presence of Q-10 as the main ubiquinone, the predominance of the compound sym-homospermidine in the polyamine patterns, the presence of a Sphingomonadaceae-specific sphingoglycolipid in the polar lipid patterns, the presence of the fatty acid 2-OH C14 : 0 and the lack of 3-hydroxy fatty acids supported the identification of the two novel strains as members of the genus Sphingomonas sensu stricto. Unique physiological characteristics, protein patterns, quantitative differences in their fatty acid profiles and the results of genomic fingerprinting and DNA–DNA hybridizations differentiated strains C42T and C52T from closely related Sphingomonas species. Hence, the two strains are described as novel species of the genus Sphingomonas sensu stricto. The names Sphingomonas abaci sp. nov. (type strain C42T=LMG 21978T=DSM 15867T) and Sphingomonas panni sp. nov. (type strain C52T=LMG 21979T=DSM 15761T) are proposed.

Four nitrite-dissimilating strains, isolated from Weser Estuary sediments, were investigated using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belong to the ‘Betaproteobacteria’ and are related to the genus Alcaligenes. The highest level of sequence similarity (100 %) was found with strain M3A (=ATCC 700596), a dimethyl sulfide-producing marine isolate that was included in this study. DNA–DNA hybridizations between the five strains and related Alcaligenes faecalis strains confirmed that the former belong to a single and novel species within the genus Alcaligenes. The isolates are Gram-negative, motile, rod-shaped cells with a DNA G+C content of about 56 mol%. The whole-cell fatty acid profiles of the isolates were very similar and included C16 : 0, C17 : 0 cyclo, C18 : 1 ω7c, summed feature 2 (comprising any combination of C12 : 0 aldehyde, an unknown fatty acid of equivalent chain length 10·928, C16 : 1 iso I and C14 : 0 3-OH) and summed feature 3 (C15 : 0 iso 2-OH and/or C16 : 1 ω7c) as the major fatty acid components. On the basis of their phylogenetic, genomic and phenotypic properties, the five novel strains can be assigned to the genus Alcaligenes as a novel species, for which the name Alcaligenes aquatilis sp. nov. is proposed. The type strain is LMG 22996T (=CCUG 50924T).

Twenty alkaliphilic bacterial strains from industrial applications or enzyme studies were subjected to a polyphasic taxonomic investigation, including 16S rRNA gene sequencing, determination of genomic DNA G+C content, DNA–DNA hybridization, fatty acid analysis and standard bacteriological characterization. By comparing the groupings obtained based on the genomic DNA G+C content and the construction of a phylogenetic tree based on the 16S rRNA gene sequence, 12 clusters of similar strains were recognized. DNA–DNA hybridization revealed that these clusters represented five novel genospecies. Further analysis supported the proposal of five novel species in the genus Bacillus: Bacillus wakoensis sp. nov. (type strain N-1T=JCM 9140T=DSM 2521T), Bacillus hemicellulosilyticus sp. nov. (type strain C-11T=JCM 9152T=DSM 16731T), Bacillus cellulosilyticus sp. nov. (type strain N-4T=JCM 9156T=DSM 2522T), Bacillus akibai sp. nov. (type strain 1139T=JCM 9157T=ATCC 43226T) and Bacillus mannanilyticus sp. nov. (type strain AM-001T=JCM 10596T=DSM 16130T).

A Gram-positive, rod-shaped, motile and endospore-forming bacterial strain, KSL-134T, was isolated from an alkaline soil in Korea, and its taxonomic position was investigated by a polyphasic study. Strain KSL-134T grew optimally at pH 7·5 and 30 °C. Its cell wall peptidoglycan contained meso-diaminopimelic acid. Strain KSL-134T was characterized as having MK-7 as the predominant menaquinone and anteiso-C15 : 0 as the major fatty acid. The DNA G+C content was 49·4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KSL-134T formed a distinct lineage within the evolutionary radiation encompassed by the genus Paenibacillus. Similarity levels between the 16S rRNA gene sequence of strain KSL-134T and those of the type strains of recognized Paenibacillus species ranged from 90·4 to 96·5 %. DNA–DNA relatedness levels and some differential phenotypic properties were enough to distinguish strain KSL-134T from several phylogenetically related Paenibacillus species. On the basis of phenotypic and phylogenetic data, strain KSL-134T (=KCTC 3956T=DSM 17040T) was classified in the genus Paenibacillus as a member of a novel species, for which the name Paenibacillus alkaliterrae sp. nov. is proposed.

A Gram-variable, facultatively anaerobic, endospore-forming bacterium was isolated from surface-sterilized seeds of the garden pea and characterized with phenotypic and molecular methods. A PCR with the Paenibacillus-specific primer PAEN515F and the 16S rRNA gene sequence indicated that strain C/2T belongs to the genus Paenibacillus and is closely related to Paenibacillus phyllosphaerae (94·0 % sequence similarity). Strain C/2T generated a unique phenotypic profile, in particular for the production of acid from substrates. The DNA G+C content (50·8 mol%) and the major fatty acid (anteiso-C15 : 0) are consistent with the genus Paenibacillus. DNA–DNA hybridization distinguished strain C/2T from other phylogenetically related Paenibacillus species and, therefore, strain C/2T (=CCM 4839T=LMG 23002T) is here described as the type strain of a novel species, for which the name Paenibacillus mendelii sp. nov. is proposed.

A halo-alkaliphilic, Gram-positive, non-motile bacterium, designated strain 4AGT, was isolated from a mineral pool located in Malvizza, Campania, southern Italy. On the basis of 16S rRNA gene sequence analysis, strain 4AGT was shown to belong to the genus Alkalibacillus within the phylum Firmicutes; its phylogenetic distance from recognized Alkalibacillus species was <95·0 %. Chemotaxonomic data (MK-7 as the major menaquinone; directly cross-linked meso-diaminopimelic acid in the cell wall; phosphatidylglycerol and diphosphatidylglycerol as major polar lipids; iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 as major fatty acids; and glycine betaine and glutamate as major compatible solutes) supported the affiliation of the strain to the genus Alkalibacillus. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 4AGT from the two recognized Alkalibacillus species. Strain 4AGT therefore represents a novel species, for which the name Alkalibacillus filiformis sp. nov. is proposed. The type strain is 4AGT (=DSM 15448T=ATCC BAA-956T).

A Gram-positive or Gram-variable, motile, endospore-forming, halophilic bacterial strain, MSS-402T, was isolated from a marine solar saltern in Korea, and subjected to a polyphasic taxonomic study. Some cells of strain MSS-402T were long filamentous rods. The isolate grew optimally at 37 °C and in the presence of 3–5 % (w/v) NaCl. Strain MSS-402T had cell-wall peptidoglycan based on l-orn–d-Asp, MK-7 as the predominant menaquinone and anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 as major fatty acids. The DNA G+C content was 42·9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain MSS-402T falls within the evolutionary radiation of species of the genus Halobacillus. Levels of 16S rRNA gene sequence similarity between strain MSS-402T and the type strains of recognized Halobacillus species ranged from 98·0 % (with Halobacillus halophilus) to 99·2 % (with Halobacillus litoralis and Halobacillus trueperi). Levels of DNA–DNA binding indicated that strain MSS-402T represents a genomic species that is distinct from recognized Halobacillus species. Strain MSS-402T was differentiated from Halobacillus species by means of several phenotypic characteristics. On the basis of its phenotypic properties and phylogenetic and genetic distinctiveness, strain MSS-402T (=KCTC 3957T=DSM 17110T) should be classified as the type strain of a novel Halobacillus species, for which the name Halobacillus yeomjeoni sp. nov. is proposed.

Eleven novel strains of marine-inhabiting lactic acid bacteria that were isolated from living and decaying marine organisms collected from a temperate area of Japan are described. The isolates were motile with peritrichous flagella and non-sporulating. They lacked catalase, quinones and cytochromes. Fermentation products from glucose were lactate, formate, acetate and ethanol. Lactate yield as percentage conversion from glucose was affected by the pH of the fermentation medium: ∼55 % at the optimal growth pH of 8·0, greater than ∼70 % at pH 7·0 and less than ∼30 % at pH 9·0. The molar ratio of the other three products was the same at each cultivation pH, approximately 2 : 1 : 1. Carbohydrates and related compounds were aerobically metabolized to acetate and pyruvate as well as lactate. The isolates were slightly halophilic, highly halotolerant and alkaliphilic. The optimum NaCl concentration for growth was 2·0–3·0 % (w/v), with a range of 0–25·5 %. The optimum pH for growth was 8·0–9·5, with a range of 6·0–10·0. The G+C content of the DNA was 38·5–40·7 mol%. The isolates constituted two genomic species (DNA–DNA relatedness of less than 41 %) each characterized by sugar fermentation profiles. The cell-wall peptidoglycan of both phenotypes contained meso-diaminopimelic acid. The major cellular fatty acids were C16 : 0 and a-C13 : 0. Comparative sequence analysis of the 16S rRNA genes revealed that these isolates represent novel species constituting a phylogenetic unit outside the radiation of typical lactic acid bacteria and an independent line of descent within the group composed of the halophilic/halotolerant/alkaliphilic and/or alkalitolerant species in Bacillus rRNA group 1, with 94·8–95·1 % similarity to the genus Paraliobacillus, 93·7–94·1 % to the genus Gracilibacillus and 93·8–94·2 % to Virgibacillus marismortui. On the basis of possession of physiological and biochemical characteristics common to typical lactic acid bacteria within Bacillus rRNA group 1, chemotaxonomic characteristics and phylogenetic independence, a new genus and two species, Halolactibacillus halophilus gen. nov., sp. nov. and Halolatibacillus miurensis sp. nov., are proposed. The type strains are Halolactibacillus halophilus M2-2T (=DSM 17073T=IAM 15242T=NBRC 100868T=NRIC 0628T) (G+C content 40·2 mol%) and Halolactibacillus miurensis M23-1T (=DSM 17074T=IAM 15247T=NBRC 100873T=NRIC 0633T) (G+C content 38·5 mol%).

Seventeen anaerobic, Gram-negative, tiny coccobacilli were collected in France from various human clinical samples. Biochemical analyses as well as molecular studies, including 16S rRNA and dnaK gene sequencing, affiliated all the isolates to the genus Dialister. However, 16S rRNA and dnaK gene sequence similarities were below 95·2 and 79·7 %, respectively, when comparisons were performed with the currently described species Dialister pneumosintes and Dialister invisus. Two clusters consisting of 13 and four isolates could be differentiated. 16S rRNA- and dnaK-based phylogeny confirmed that these two clusters represent two novel and distinct lineages within the genus Dialister. Finally, phenotypic, genotypic and phylogenetic data supported the proposal of the two novel species Dialister micraerophilus sp. nov. (type strain ADV 04.01T=AIP 25.04T=CIP 108278T=CCUG 48837T) and Dialister propionicifaciens sp. nov. (type strain ADV 1053.03T=AIP 26.04T=CIP 108336T=CCUG 49291T). The G+C content of the DNA of the D. micraerophilus type strain is 36·3 mol%. On the basis of 16S rRNA gene sequence analysis, 11 isolates originating from Canada could also be affiliated to D. micraerophilus sp. nov., and were included in the species description.

The taxonomic position of two bovine strains, LMG 13603 and LMG 14595, assigned to the species Enterococcus raffinosus on the basis of biochemical features, was reinvestigated. Both reference strains and two other isolates, 6/1 (=LMG 22829) originating from a charcoal-broiled river lamprey and IE38.4 (=LMG 22830) from the air of a poultry slaughter by-product processing plant, occupied a clearly separate position, on the basis of sequence analysis of the housekeeping gene pheS (encoding the phenylalanyl-tRNA synthase α-subunit), relative to the type strain of E. raffinosus and all other enterococcal species with validly published names. 16S rRNA gene sequencing of strains LMG 13603, LMG 14595, 6/1 and IE38.4 confirmed their phylogenetic position in the Enterococcus avium species group, there being more than 99 % 16S rRNA gene sequence similarity to most members of the group, including E. raffinosus, and revealed Enterococcus pseudoavium as the closest phylogenetic relative (99·8–99·9 %). Further phenotypic and genotypic analyses using whole-cell-protein electrophoresis, (GTG)5-PCR fingerprinting, ribotyping and DNA–DNA hybridization experiments demonstrated that all four strains represent a novel enterococcal species, for which the name Enterococcus devriesei sp. nov. is proposed. The type strain is LMG 14595T (=CCM 7299T).

The ‘Lactobacillus plantarum group’ encompasses the taxa Lactobacillus plantarum subsp. plantarum, Lactobacillus plantarum subsp. argentoratensis, Lactobacillus paraplantarum, Lactobacillus pentosus and Lactobacillus arizonensis. In this study, the phylogenetic position of L. arizonensis was examined using 16S rRNA gene-specific methodologies (16S rRNA sequencing and ribotyping) and genomic DNA-based investigations [repetitive extragenic palindromic DNA (rep)-PCR and DNA–DNA hybridization]. Our results show that the L. arizonensis type strain could not be distinguished from the type strain of L. plantarum or from various L. plantarum reference strains. Therefore, it is proposed that the species L. arizonensis should be reclassified as a heterotypic synonym of L. plantarum.

A Gram-positive, aerobic, long-rod-shaped, non-spore-forming bacterium (strain PPLBT) was isolated from soil mixed with Iberian pig hair. This actinomycete showed keratinase activity in vitro when chicken feathers were added to the culture medium. Strain PPLBT was oxidase-negative and catalase-positive and produced lipase and esterase lipase. This actinomycete grew at 40 °C on nutrient agar and in the same medium containing 5 % (w/v) NaCl. Growth was observed with many different carbohydrates as the sole carbon source. On the basis of 16S rRNA gene sequence similarity, strain PPLBT was shown to belong to the genus Terrabacter of the family Intrasporangiaceae. Strain PPLBT showed 98·8 % 16S rRNA gene sequence similarity to Terrabacter tumescens. Chemotaxonomic data, such as the main ubiquinone (MK-8), the main polar lipids (phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylinositol) and the main fatty acids (i-C15 : 0, ai-C15 : 0, i-C16 : 0 and ai-C17 : 0) supported the affiliation of strain PPLBT to the genus Terrabacter. The G+C content of the DNA was 71 mol%. The results of DNA–DNA hybridization (36·6 % relatedness between Terrabacter tumescens and strain PPLBT) and physiological and biochemical tests suggested that strain PPLBT belongs to a novel species of the genus Terrabacter, for which the name Terrabacter terrae sp. nov. is proposed. The type strain is PPLBT (=CECT 3379T=LMG 22921T).

Four novel ellipsoidal spore-forming Bacillus isolates with swollen sporangia, isolated from raw milk and feed concentrate, showed a high level of similarity in SDS-PAGE, fatty acid methyl esters and routine phenotypic tests. However, 16S rRNA gene sequence comparisons showed that this taxon was different from other related Bacillus species, and only a low level of DNA relatedness was found with the closest phylogenetic and phenotypic relative, Bacillus galactosidilyticus. This taxon could be differentiated from B. galactosidilyticus on the basis of morphological differences, stronger acid reactions with a wide range of substrates after 48 h incubation, and qualitative and quantitative differences in fatty acid content. On the basis of these data, a novel species, Bacillus ruris sp. nov., is proposed, with LMG 22866T (=DSM 17057T) as the type strain.

Three novel strains were isolated from a soil sample collected in Japan using GPM agar plates supplemented with superoxide dismutase and/or catalase. The strains were Gram-positive, catalase-positive, irregular rod-shaped bacteria with meso-diaminopimelic acid as a peptidoglycan diagnostic diamino acid, and the acyl type of the peptidoglycan was acetyl. The major menaquinone was MK-8(H4). Mycolic acids were not detected. The G+C content of the DNA was 72–73 mol%. On the basis of morphological and chemotaxonomic properties and a phylogenetic analysis using 16S rRNA gene sequences, these strains were classified as a novel genus and species, Oryzihumus leptocrescens gen. nov., sp. nov., in the family Intrasporangiaceae of the order Actinomycetales. The type strain is KV-628T (=NRRL B-24347T=JCM 12835T=NBRC 100762T).

An actinobacterial strain, RMV-1378T, isolated from a cold desert of the Indian Himalayas, was subjected to polyphasic taxonomic characterization. The strain formed branching, non-fragmenting vegetative hyphae and did not produce diffusible pigments. Neither aerial mycelium nor spore formation was observed. The G+C content of the DNA was 72·0 mol%. The strain had chemotaxonomic characteristics typical of the genus Actinoalloteichus and was closely related (99·3 % 16S rRNA gene sequence similarity) to Actinoalloteichus cyanogriseus, currently the only Actinoalloteichus species with a validly published name. However, the results of DNA–DNA hybridization experiments showed 51·9 % relatedness with the type strain of A. cyanogriseus. On the basis of the above data and the physiological and biochemical distinctiveness of RMV-1378T (=MTCC 6194T=JCM 12472T=DSM 44848T), this strain should be classified as the type strain of a novel species of Actinoalloteichus, for which the name Actinoalloteichus spitiensis sp. nov. is proposed.

A polyphasic approach was used to characterize a bacterium, GPTSA 11T, isolated from a warm spring located in a reserve forest in Assam, India. The cells are Gram-variable, strictly aerobic, sporulating motile rods. The major fatty acids of the strain are C15 : 0 anteiso (48·42 %), C16 : 0 iso (11·59 %), C16 : 1 ω11c (6·16 %), C15 : 0 iso (6·03 %), C17 : 0 anteiso (5·68 %) and C16 : 1 ω7c alcohol (5·01 %). The presence of the fatty acid C16 : 1 ω7c alcohol distinguishes this strain from other closely related species of the genus Paenibacillus. The strain contains MK-7 as the diagnostic menaquinone. The G+C content of the genomic DNA is 41·2 mol%. Analysis of the 16S rRNA gene sequence (1466 nt) revealed the presence of signature sequences PAEN 515F (5′-GAGTAACTGCTCTCGGAATGACGGTACTTGAGAAGAAAGCCCC-3′) and PAEN 862F (5′-TCGATACCCTTGGTGCCGAAGT-3′), which were found in the species of the genus Paenibacillus surveyed by Shida et al. [ Shida, O., Takagi, H., Kadowaki, K., Nakamura, L. K. & Komagata, K. (1997) . Int J Syst Bacteriol 47, 289–298]. The sequence shows closest similarity (95·85 %) to that of Paenibacillus apiarius, followed by Paenibacillus alvei (94·34 %), Paenibacillus cineris (93·87 %), Paenibacillus favisporus (93·80 %), Paenibacillus chibensis (93·47 %) and Paenibacillus azoreducens (93·40 %). Biochemical, physiological, chemotaxonomic and phylogenetic analyses justify placement of the strain in the genus Paenibacillus but not within any existing species. It should, therefore, be considered as representing a novel species, for which the name Paenibacillus assamensis sp. nov. is proposed. The type strain is GPTSA 11T (=MTCC 6934T=JCM 13186T).

Telonema is a widely distributed group of phagotrophic flagellates with two known members. In this study, the structural identity and molecular phylogeny of Telonema antarcticum was investigated and a valid description is proposed. Molecular phylogeny was studied using small-subunit rRNA (SSU rRNA) gene sequences. The pear-shaped cell had two subequal flagella that emerged laterally on the truncated antapical tail. One flagellum had tripartite hairs. The cell was naked, but had subsurface vesicles containing angular paracrystalline bodies of an unknown nature. A unique complex cytoskeletal structure, the subcortical lamina, was found to be an important functional and taxonomic feature of the genus. Telonema has an antero-ventral depression where food particles are ingested and then transferred to a conspicuous anterior food vacuole. The molecular phylogeny inferred from the SSU rRNA gene sequence suggested that Telonema represents an isolated and deep branch among the tubulocristate protists.

Environmental molecular surveys of microbial diversity have uncovered a vast number of novel taxonomic units in the eukaryotic tree of life that are exclusively known by their small-subunit (SSU) rRNA gene signatures. In this study, we reveal the cellular and taxonomic identity of a novel eukaryote SSU rRNA gene sequence clade within the Kinetoplastea. Kinetoplastea are ubiquitously distributed flagellated protists of high ecological and medical importance. We isolated an organism from the oxic–anoxic interface of the anoxic Framvaren Fjord (Norway), which branches within an unidentified kinetoplastean sequence clade. Ultrastructural studies revealed a typical cellular organization that characterized the flagellated isolate as a member of the order Neobodonida Vickerman 2004, which contains five genera. The isolate differed in several distinctive characters from Dimastigella, Cruzella, Rhynchobodo and Rhynchomonas. The arrangement of the microtubular rod that supports the apical cytostome and the cytopharynx differed from the diagnosis of the fifth described genus (Neobodo Vickerman 2004) within the order Neobodonida. On the basis of both molecular and microscopical data, a novel genus within the order Neobodonida, Actuariola gen. nov., is proposed. Here, we characterize its type species, Actuariola framvarensis sp. nov., and provide an in situ tool to access the organism in nature and study its ecology.