- Volume 55, Issue 1, 2005
Volume 55, Issue 1, 2005
- New Taxa
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- Gram-Positive Bacteria
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Planococcus stackebrandtii sp. nov., isolated from a cold desert of the Himalayas, India
More LessThe taxonomic position of a bacterium isolated from a cold desert of the Himalayas, India, was analysed by using a polyphasic approach. The isolated strain, designated K22-03T, had phenotypic characteristics that matched those of the genus Planococcus and it represents a novel species. The almost-complete 16S rRNA gene sequence (1464 bases) of the novel strain was compared with those of previously studied Planococcus type strains and confirmed that the strain belongs to the genus Planococcus. 16S rRNA gene sequence analysis indicated that strain K22-03T differs from all other species of Planococcus by at least 2·5 %. DNA–DNA hybridization showed that it had low genomic relatedness with Planomicrobium mcmeekinii (MTCC 3704T, 23 %), Planococcus psychrophilus (MTCC 3812T, 61 %), Planococcus antarcticus (MTCC 3854T, 45 %) and Planomicrobium okeanokoites (MTCC 3703T, 51 %), the four species with which it was most closely related based on 16S rRNA gene sequence analysis (97–97·5 % similarity). Therefore, strain K22-03T should be recognized as a novel species, for which the name Planococcus stackebrandtii sp. nov. is proposed. The type strain is K22-03T (=MTCC 6226T=DSM 16419T=JCM 12481T).
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Tenuibacillus multivorans gen. nov., sp. nov., a moderately halophilic bacterium isolated from saline soil in Xin-Jiang, China
More LessTwo Gram-positive, rod-shaped, spore-forming and moderately halophilic bacteria (strains 28-1T, 28-4), isolated from a soil sample from a neutral salt lake in Xin-Jiang, China, were characterized polyphasically. On the basis of fasta (ungapped) analyses of 16S rRNA gene sequences, strains 28-1T and 28-4 were shown to belong to the Bacillaceae and to be closely related to Filobacillus milensis DSM 13259T (97·0 %) and Bacillus haloalkaliphilus DSM 5271T (95·7 %). 16S rRNA gene sequence similarity with other recognized species was not more than 94·1 %. Phylogenetic, chemotaxonomic, physiological and biochemical data supported the differentiation of these novel strains from F. milensis and B. haloalkaliphilus. Therefore these two previously unidentified strains are considered to represent a new genus and species, for which the name Tenuibacillus multivorans gen. nov., sp. nov. is proposed. The type strain is 28-1T (=AS 1.3442T=NBRC 100370T).
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Bacillus arenosi sp. nov., Bacillus arvi sp. nov. and Bacillus humi sp. nov., isolated from soil
More LessA group of nine Gram-positive endospore-forming bacteria was isolated from soil of the Drentse A agricultural research area in the Netherlands. Using (GTG)5-PCR genomic fingerprinting and fatty acid analysis, the nine isolates were divided into three consistent groups. On the basis of 16S rRNA gene sequence similarity of representative strains, the nine isolates were shown to belong to the genus Bacillus. The first group of four isolates was most closely related to Bacillus carboniphilus (95·5 %) and Bacillus sporothermodurans (95·5 %). The second and third groups of three and two isolates, respectively, showed highest sequence similarity to Bacillus neidei (97·0 and 97·1 %, respectively) and Bacillus pycnus (both 96·7 %). A DNA–DNA relatedness study confirmed the consistency of the three groups delineated by (GTG)5-PCR and fatty acid analysis. A small number of phenotypic characters allowed differentiation of the three groups of isolates. The three groups therefore represent novel species, for which the names Bacillus humi, Bacillus arenosi and Bacillus arvi are proposed, with LMG 22167T (=DSM 16318T), LMG 22166T (=DSM 16319T) and LMG 22165T (=DSM 16317T) as the respective type strains.
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Study of mural painting isolates, leading to the transfer of ‘Bacillus maroccanus’ and ‘Bacillus carotarum’ to Bacillus simplex, emended description of Bacillus simplex, re-examination of the strains previously attributed to ‘Bacillus macroides’ and description of Bacillus muralis sp. nov.
A group of 24 strains was isolated from deteriorated mural paintings situated in Spain (necropolis of Carmona) and Germany (church of Greene-Kreiensen). (GTG)5-PCR genomic fingerprinting was performed on these strains to assess their genomic variability and the strains were delineated into four groups. Representatives were studied by 16S rRNA gene sequencing and were found to be closely related to Bacillus simplex and the species ‘Bacillus macroides’ (strain NCIMB 8796) and ‘Bacillus maroccanus’ (names not validly published) according to a fasta search. The close similarity between B. simplex, ‘B. macroides’ NCIMB 8796, ‘B. maroccanus’ and the mural painting isolates was confirmed by additional (GTG)5-PCR, ARDRA, FAME and SDS-PAGE analyses. Furthermore, these techniques revealed that strains of ‘Bacillus carotarum’, another name that has not been validly published, also showed high similarity to this group of organisms. On the other hand, it was shown that the strains labelled ‘B. macroides’ in different collections do not all belong to the same species. Strain NCIMB 8796 can be allocated to B. simplex, while strain DSM 54 (=ATCC 12905) shares the highest 16S rRNA gene sequence similarity with Bacillus sphaericus and Bacillus fusiformis (both around 98·6 %). On the basis of further DNA–DNA hybridization data and the study of phenotypic characteristics, one group of five mural painting strains was attributed to a novel species in the genus Bacillus, for which the name Bacillus muralis sp. nov. is proposed. Finally, the remaining mural painting strains, one (LMG 18508=NCIMB 8796) of two strains belonging to ‘B. macroides’ and strains belonging to ‘B. maroccanus’ and ‘B. carotarum’ are allocated to the species B. simplex and an emended description of B. simplex is given.
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Reclassification of strain CCM 132, previously classified as Kocuria varians, as Kocuria carniphila sp. nov.
A Gram-positive actinobacterium, previously classified as Kocuria varians, was subjected to a polyphasic taxonomic study. The bacterium showed the peptidoglycan type Lys–Ala3 (variation A3α), MK-7(H2) was the major menaquinone and anteiso-C15 : 0 and anteiso-C17 : 0 were the major fatty acids. On the basis of the phylogenetic and phenotypic characteristics of the actinobacterium, a novel species, Kocuria carniphila sp. nov. (type strain, CCM 132T=DSM 16004T), is proposed.
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Agromyces salentinus sp. nov. and Agromyces neolithicus sp. nov.
More LessA polyphasic study was carried out to clarify the taxonomic position of two Gram-positive bacteria isolated from soil samples of the Grotta dei Cervi (Italy), a relatively unexplored hypogean environment. The strains, 20-5T and 23-23T, showed phenotypic and phylogenetic characteristics that were consistent with their classification in the genus Agromyces. 16S rRNA gene sequence comparisons revealed that the two strains formed distinct phyletic lines within the genus Agromyces. Based on 16S rRNA gene sequence similarity, chemotaxonomic data and the results of DNA–DNA relatedness studies, it is proposed that the two isolates represent two novel species of the genus Agromyces. Pronounced differences in a broad range of phenotypic characteristics and DNA G+C content distinguished the two strains from each other and from previously described species of the genus Agromyces. Two novel species are proposed: Agromyces salentinus sp. nov. (type strain, 20-5T=HKI 0320T=DSM 16198T=NCIMB 13990T) and Agromyces neolithicus sp. nov. (type strain, 23-23T=HKI 0321T=DSM 16197T=NCIMB 13989T).
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Bacillus saliphilus sp. nov., isolated from a mineral pool in Campania, Italy
More LessA haloalkaliphilic Gram-positive bacterium, strain 6AGT, that grew aerobically at an optimum temperature of 37 °C and at pH 7–10 (optimum 9·0), was isolated from algal mat from a mineral pool located in Malvizza in the Campania region (southern Italy). The isolate tolerated high concentrations of NaCl, up to 25 %. On the basis of 16S rRNA gene sequence similarity, the strain was shown to belong to the genus Bacillus. Analysis of the 16S rRNA gene sequence revealed high similarity between strain 6AGT and an unidentified isolate from Hailaer soda lake (China) (99·9 % identity) and two Kenyan isolates, 3E1 and WE4 (98·3 and 97·8 % identity, respectively). The G+C content of the DNA was 48·4 mol%. The predominant respiratory quinones were MK-7(H2), MK-7(H4) and DMK-7(H2); phosphatidylglycerol and diphosphatidylglycerol were the predominant polar lipids. iC15 : 0 and aiC15 : 0 were the major fatty acids. Strain 6AGT accumulated osmolytes. The phylogenetic distance of strain 6AGT (=DSM 15402T=ATCC BAA-957T) from any recognized species within the genus Bacillus allowed it to be classified as the type strain of Bacillus saliphilus sp. nov.
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Pontibacillus chungwhensis gen. nov., sp. nov., a moderately halophilic Gram-positive bacterium from a solar saltern in Korea
More LessThree moderately halophilic, spore-forming strains, designated BH030062T, BH030049 and BH030080, were isolated from a solar saltern in Korea. Phylogenetic analyses and comparative 16S rRNA gene sequence studies revealed that the isolates represent a novel distinct monophyletic lineage within the phyletic group classically defined as the genus Bacillus and are most closely related to members of the genera Gracilibacillus (93·7–95·1 % similarity), Virgibacillus (93·5–94·8 %), Halobacillus (94·8–95·9 %), Filobacillus (94·4–94·8 %) and Lentibacillus (93·3–93·7 %). Strain BH030062T was strictly aerobic, rod-shaped, Gram-positive and motile by means of peritrichous flagella. It grew in the presence of 1–15 % (w/v) NaCl and at temperatures of 15–45 °C. The cell wall peptidoglycan contained A1γ-meso-diaminopimelic acid as the diagnostic diamino acid. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. DNA G+C content was about 41 mol% and the major isoprenoid quinone was MK-7. On the basis of their physiological and molecular properties, the isolates represent a new genus, Pontibacillus gen. nov., and novel species, Pontibacillus chungwhensis sp. nov. The type strain is BH030062T (=KCTC 3890T=DSM 16287T).
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Bacillus velezensis sp. nov., a surfactant-producing bacterium isolated from the river Vélez in Málaga, southern Spain
More LessTwo Gram-positive, endospore-forming bacterial strains, CR-502T and CR-14b, which produce surfactant molecules are described. Phenotypic tests and phylogenetic analyses showed these strains to be members of the genus Bacillus and related to the species Bacillus atrophaeus, Bacillus mojavensis, Bacillus subtilis, Bacillus vallismortis and Bacillus amyloliquefaciens, although they differ from these species in a number of phenotypic characteristics. DNA–DNA hybridization confirmed that they show less than 20 % hybridization with the above-mentioned species and therefore represent a novel species of Bacillus. The DNA G+C content is 46·4 mol% in strain CR-502T and 46·1 mol% in strain CR-14b. The main fatty acids in strain CR-502T are 15 : 0 anteiso (32·70 %), 15 : 0 iso (29·86 %) and 16 : 0 (13·41 %). The main quinone in strain CR-502T is MK-7 (96·6 %). In the light of the polyphasic evidence gathered in this study, it is proposed that these strains be classified as a novel species of the genus Bacillus, with the name Bacillus velezensis sp. nov. The type strain (CR-502T=CECT 5686T=LMG 22478T) was isolated from a brackish water sample taken from the river Vélez at Torredelmar in Málaga, southern Spain.
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Cryptanaerobacter phenolicus gen. nov., sp. nov., an anaerobe that transforms phenol into benzoate via 4-hydroxybenzoate
An anaerobic bacterium that transforms phenol and 4-hydroxybenzoate (4-OHB) into benzoate, strain LR7.2T, was isolated from a culture originating from a mixture of swamp water, sewage sludge, swine waste and soil. Cells of strain LR7.2T are Gram-positive short rods (1×2 μm) that are electron-dense when observed by electron microscopy. The optimum pH and temperature for growth and transformation activity of 4-OHB are 7·5–8·0 and 30–37 °C, respectively. The bacterium does not use sulphate, thiosulphate, nitrate, nitrite, FeCl3, fumarate or arsenate as an electron acceptor. It does not normally use sulphite, although stimulation of growth and 4-OHB transformation activity at a low concentration (up to 2 mM) has been reported previously under different culture conditions. The presence of 4-OHB or phenol is essential for growth; transformation of 4-OHB or phenol into benzoate is used to produce energy for growth. Using [6D]-phenol, 4-OHB was shown to be an intermediate in the transformation of phenol into benzoate. No spore was observed. The bacterium has a DNA G+C content of 51 mol% and its major membrane fatty acid is anteiso-C15 : 0. The 16S rRNA gene sequence of strain LR7.2T shows only 90 % similarity to its closest relative (Pelotomaculum thermopropionicum). From these results, a new taxon is proposed: Cryptanaerobacter phenolicus gen. nov., sp. nov. The type strain is LR7.2T (=ATCC BAA-820T=DSM 15808T).
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Streptomyces koyangensis sp. nov., a novel actinomycete that produces 4-phenyl-3-butenoic acid
More LessA 4-phenyl-3-butenoic acid-producing actinomycete, designated strain VK-A60T, was isolated from a soil sample collected from Koyang, Korea. Morphological and chemical characteristics of the strain were consistent with those of the genus Streptomyces. The cell wall of the strain contains ll-diaminopimelic acid. The predominant fatty acids are anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. The strain formed a distinct monophyletic line within the 16S rRNA gene sequence phylogenetic tree. Analyses of its morphological, physiological and biochemical characteristics, together with random amplified polymorphic DNA and DNA–DNA relatedness data, confirmed that strain VK-A60T represents a novel Streptomyces taxon that is distinguishable from closely related reference strains. Strain VK-A60T (=KCCM 10555T=NBRC 100598T) is proposed as the type strain of a novel species, for which the name Streptomyces koyangensis sp. nov. is proposed.
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Streptococcus marimammalium sp. nov., isolated from seals
More LessTwo strains of an unidentified, Gram-positive, catalase-negative, chain-forming, coccus-shaped organism recovered from seals were characterized using phenotypic and molecular taxonomic methods. Based on morphological and biochemical criteria the strains were tentatively identified as streptococci but they did not appear to correspond to any recognized species of the genus Streptococcus. Comparative 16S rRNA gene sequencing studies showed that the strains were closely related to each other and confirmed their placement in the genus Streptococcus. Sequence divergence values of >5 % with reference streptococcal species demonstrated the organisms from seals represent a novel species. SDS-PAGE analysis of whole-cell proteins confirmed that the two organisms were closely related to each other but were different from all currently defined streptococcal species. Based on biochemical criteria, molecular chemical and molecular genetic evidence, it is proposed that the unknown isolates from seals be assigned to a novel species of the genus Streptococcus, Streptococcus marimammalium sp. nov. The type strain is M54/01/1T (=CCUG 48494T=CIP 108309T).
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‘Candidatus Phytoplasma pini’, a novel taxon from Pinus silvestris and Pinus halepensis
Pinus silvestris and Pinus halepensis trees grown in Germany and Spain, respectively, showing abnormal shoot branching, dwarfed needles and other symptoms were examined for the presence of plant-pathogenic mollicutes (phytoplasmas). While phytoplasmas could not be detected unambiguously with microscopical methods, PCR amplification using universal phytoplasma primers yielded positive results. Samples collected from symptomatic and non-symptomatic plant parts of both symptomatic Pinus silvestris and Pinus halepensis trees tested positive. Also, surrounding non-symptomatic trees proved to be phytoplasma-infected. Comparisons revealed that the 16S rRNA gene sequences of the phytoplasmas identified in Pinus silvestris and Pinus halepensis were nearly identical. However, the pine phytoplasma is only distantly related to other phytoplasmas. The closest relatives are members of the palm lethal yellowing and rice yellow dwarf groups and ‘Candidatus Phytoplasma castaneae’, which share between 94·5 and 96·6 % 16S rRNA gene sequence similarity. From these data it can be concluded that the phytoplasmas identified in the two Pinus species represent a coherent but discrete taxon; it is proposed that this taxon be distinguished at putative species level under the name ‘Candidatus Phytoplasma pini’.
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Isolation of Lentibacillus salicampi strains and Lentibacillus juripiscarius sp. nov. from fish sauce in Thailand
Eight strains of aerobic, spore-forming, Gram-positive, moderately halophilic bacteria were isolated from sauce (nam-pla and bu-du) produced in Thailand by the fermentation of fish. They grew optimally in the presence of 10 % NaCl, at 37 °C and pH 7·0. A diagnostic diamino acid, meso-diaminopimelic acid, was present in the cell-wall peptidoglycan. The predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15 : 0 and iso-C16 : 0. Phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid were found to be the major polar lipid components. The DNA G+C content was 42–43 mol%. These bacteria were further divided into two groups based on phenotypic characteristics and DNA–DNA similarities. Three strains of Group I were highly affiliated to the type strain of Lentibacillus salicampi in terms of phenotypic characterization and DNA–DNA similarities (96–102 %); accordingly, they were identified as strains of L. salicampi. A representative strain of Group II, strain IS40-3T, was most closely related to L. salicampi in terms of 16S rRNA-based phylogenetic analysis, although five strains of Group II could be distinguished from L. salicampi by means of several phenotypic properties, low 16S rRNA gene sequence similarity (95·2 %) and low DNA–DNA similarities (12–32 %). Therefore, the Group II strains should be included in a novel species of the genus Lentibacillus, for which the name Lentibacillus juripiscarius sp. nov. is proposed. The type strain is IS40-3T (=JCM 12147T=PCU 229T=TISTR 1535T).
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Marinilactibacillus piezotolerans sp. nov., a novel marine lactic acid bacterium isolated from deep sub-seafloor sediment of the Nankai Trough
A piezotolerant, mesophilic, marine lactic acid bacterium (strain LT20T) was isolated from a deep sub-seafloor sediment core collected at Nankai Trough, off the coast of Japan. Cells were Gram-positive, rod-shaped, non-sporulating and non-motile. The NaCl concentration range for growth was 0–120 g l−1, with the optimum at 10–20 g l−1. The temperature range for growth at pH 7·0 was 4–50 °C, with the optimum at 37–40 °C. The optimum pH for growth was 7·0–8·0. The optimum pressure for growth was 0·1 MPa with tolerance up to 30 MPa. The main cellular phospholipids were phosphatidylglycerols (25 %), diphosphatidylglycerols (34 %) and a group of compounds tentatively identified as ammonium-containing phosphatidylserines (32 %); phosphatidylethanolamines (9 %) were minor components. The fatty acid composition was dominated by side chains of 16 : 0, 14 : 0 and 16 : 1. The G+C content of the genomic DNA was 42 mol%. On the basis of 16S rRNA gene sequence analysis and the secondary structure of the V6 region, this organism was found to belong to the genus Marinilactibacillus and was closely related to Marinilactibacillus psychrotolerans M13-2T (99 %), Marinilactibacillus sp. strain MJYP.25.24 (99 %) and Alkalibacterium olivapovliticus strain ww2-SN4C (97 %). Despite the high similarity between their 16S rRNA gene sequences (99 %), the DNA–DNA hybridization levels were less than 20 %. On the basis of physiological and genetic characteristics, it is proposed that this organism be classified as a novel species, Marinilactibacillus piezotolerans sp. nov. The type strain is LT20T (=DSM 16108T=JCM 12337T).
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Proposal of the genus Thermoactinomyces sensu stricto and three new genera, Laceyella, Thermoflavimicrobium and Seinonella, on the basis of phenotypic, phylogenetic and chemotaxonomic analyses
More LessPhylogenetic analysis based on 16S rRNA gene sequences revealed that Thermoactinomyces species with validly published names can be assigned to four clusters or lineages. The type strains of Thermoactinomyces sacchari and Thermoactinomyces putidus were differentiated from the type strains of Thermoactinomyces vulgaris and Thermoactinomyces intermedius by the predominant menaquinone and fatty acid profiles. The type strains of Thermoactinomyces dichotomicus and Thermoactinomyces peptonophilus formed lines of descent distinct from other Thermoactinomyces species. Thermoactinomyces dichotomicus KCTC 3667T was distinguishable from the type strains of Thermoactinomyces vulgaris and Thermoactinomyces intermedius by the contents of two fatty acids, iso-C16 : 0 and iso-C17 : 0. Thermoactinomyces dichotomicus could be distinguished from other Thermoactinomyces species by DNA G+C content and some phenotypic properties, particularly its property of forming a yellow colour. The type strain of Thermoactinomyces peptonophilus was distinguishable from other Thermoactinomyces species by differences in menaquinone profile, major fatty acids, DNA G+C content and some physiological properties including optimal growth temperature. On the basis of these data, the creation of three new genera, Laceyella, Thermoflavimicrobium and Seinonella, is proposed in addition to the genus Thermoactinomyces sensu stricto. The genus Laceyella gen. nov. is proposed to accommodate Thermoactinomyces sacchari and Thermoactinomyces putidus as Laceyella sacchari comb. nov. and Laceyella putida comb. nov., the genus Thermoflavimicrobium gen. nov. is proposed for Thermoactinomyces dichotomicus as Thermoflavimicrobium dichotomicum comb. nov. and the genus Seinonella gen. nov. is proposed for Thermoactinomyces peptonophilus as Seinonella peptonophila comb. nov.
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Lactobacillus delbrueckii subsp. indicus subsp. nov., isolated from Indian dairy products
More LessFour strains isolated from Indian dairy products and initially identified as Lactobacillus delbrueckii could not be assigned to a definite subspecies because molecular identification and phenotypic traits did not agree with those of recognized subspecies of L. delbrueckii. Hybridization of total DNA (78–86 % against type strains of the other three subspecies), AFLP and RAPD-PCR fingerprints, phylogenetic analysis based on 16S rRNA gene sequences and sequence analysis of two coding genes (recA and hsp60), together with phenotypic profiles, indicated that the four strains form a coherent cluster and represent a novel subspecies, for which the name Lactobacillus delbrueckii subsp. indicus subsp. nov. is proposed. The type strain is NCC725T (=LMG 22083T=DSM 15996T).
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Paenibacillus xylanilyticus sp. nov., an airborne xylanolytic bacterium
More LessDuring a search for xylan-degrading micro-organisms, a sporulating bacterium was recovered from xylan-containing agar plates exposed to air in a research laboratory (Salamanca University, Spain). The airborne isolate (designated strain XIL14T) was identified by 16S rRNA gene sequencing as representing a Paenibacillus species most closely related to Paenibacillus illinoisensis JCM 9907T (99·3 % sequence similarity) and Paenibacillus pabuli DSM 3036T (98 % sequence similarity). Phenotypic, chemotaxonomic and DNA–DNA hybridization data indicated that the isolate belongs to a novel species of the genus Paenibacillus. Cells of strain XIL14T were motile, sporulating, rod-shaped, Gram-positive and facultatively anaerobic. The predominant cellular fatty acids were anteiso-C15 : 0 and C16 : 0. The DNA G+C content of strain XIL14T was 50·5 mol%. Growth was observed with many carbohydrates, including xylan, as the only carbon source and gas production was not observed from glucose. Catalase was positive and oxidase was negative. The airborne isolate produced a variety of hydrolytic enzymes, including xylanases, amylases, gelatinase and β-galactosidase. DNA–DNA hybridization levels between strain XIL14T and P. illinoisensis DSM 11733T and P. pabuli DSM 3036T were 43·3 and 36·3 %, respectively. According to the data obtained, strain XIL14T is considered to represent a novel species for which the name Paenibacillus xylanilyticus sp. nov. is proposed (=LMG 21957T=CECT 5839T).
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Micromonospora eburnea sp. nov., isolated from a Thai peat swamp forest
Two actinomycete strains, LK2-10T and LK2-5, which produced single, non-motile spores, were isolated from peat swamp forest soil in Yala Province, Thailand. A polyphasic study was carried out to establish the taxonomic position of these strains. Morphological and chemotaxonomic characteristics of these strains coincided with those of the genus Micromonospora. Phylogenetic analysis using 16S rRNA gene sequences also indicated that these strains should be classified in the genus Micromonospora and clearly separated from their closest relative, Micromonospora nigra DSM 43818T. Furthermore, a combination of DNA–DNA hybridization results and physiological and biochemical properties indicated that these strains were distinguished from all recognized Micromonospora species. These strains therefore represent a novel species, for which the name Micromonospora eburnea sp. nov. is proposed. The type strain is LK2-10T (=JCM 12345T=PCU 238T=DSM 44814T=TISTR 1531T).
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Actinomyces dentalis sp. nov., from a human dental abscess
More LessA previously undescribed filamentous, beaded, Gram-positive, rod-shaped bacterium was isolated from pus of a human dental abscess. Based on its cellular morphology and the results of biochemical testing the organism was tentatively identified as a member of the genus Actinomyces, but it did not correspond to any currently recognized species of this genus. Comparative 16S rRNA gene sequencing studies showed the bacterium represents a distinct subline within the genus Actinomyces, clustering within a group of species that includes Actinomyces bovis, the type species of the genus. Sequence divergence values of >8 % with other recognized species within this phylogenetic group clearly demonstrated that the organism represents a hitherto unknown species. Based on biochemical and molecular phylogenetic evidence, it is proposed that the unidentified organism recovered from a dental abscess be classified as a novel species, Actinomyces dentalis sp. nov. The type strain is R18165T (=CCUG 48064T=CIP 108337T).
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Nocardia takedensis sp. nov., isolated from moat sediment and scumming activated sludge
Chemotaxonomic and morphological characterization of two actinomycete strains, MS1-3T and AS4-2, respectively isolated from moat sediment and scumming activated sludge, was carried out. This characterization clearly demonstrated that strains MS1-3T and AS4-2 belong to the genus Nocardia. 16S rRNA gene sequencing studies showed that these isolates are most closely related to Nocardia beijingensis (98·1–98·3 % similarity), Nocardia brasiliensis (97·9–98·0 %) and Nocardia tenerifensis (97·8–97·9 %). However, the results of DNA–DNA hybridizations and physiological and biochemical tests showed that strains MS1-3T and AS4-2 could be differentiated from their closest phylogenetic relatives both genotypically and phenotypically. It is proposed that the two isolates be classified as representatives of a novel species of Nocardia, Nocardia takedensis sp. nov. The type strain is MS1-3T (=NBRC 100417T=DSM 44801T); AS4-2 (=NBRC 100418=DSM 44802) is a reference strain.
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Bacillus patagoniensis sp. nov., a novel alkalitolerant bacterium from the rhizosphere of Atriplex lampa in Patagonia, Argentina
More LessA Gram-positive, rod-shaped, spore-forming bacterium (PAT 05T) was isolated from the rhizosphere of the perennial shrub Atriplex lampa in north-eastern Patagonia, Argentina. Its overall biochemical and physiological characteristics indicated that this strain should be placed in the alkaliphilic Bacillus group. Strain PAT 05T grew at pH 7–10 (optimum pH 8), but not at pH 6. Its DNA G+C content was 39·7 mol%. Sequence analysis of the 16S rRNA gene of PAT 05T revealed the closest match (99·6 % similarity) with Bacillus sp. DSM 8714. The highest level of DNA–DNA relatedness (88·6 %) was also found with this strain. On the basis of 16S rRNA gene sequence similarity and phylogenetic analysis, G+C content and DNA–DNA hybridization data, strain PAT 05T is related at the species level to Bacillus sp. DSM 8714, a member of a group referred as phenon 4a by Nielsen et al. [Nielsen, P., Fritze, D. & Priest, F. G. (1995). Microbiology 141, 1745–1761] , which still lacks taxonomic standing. These results support the proposal of strain PAT 05T (=DSM 16117T=ATCC BAA-965T) as the type strain of Bacillus patagoniensis sp. nov.
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Arthrobacter bergerei sp. nov. and Arthrobacter arilaitensis sp. nov., novel coryneform species isolated from the surfaces of cheeses
More LessFourteen isolates of two different bacterial species isolated from the surface of smear-ripened cheeses were found to exhibit many characteristics of the genus Arthrobacter. The isolates were aerobic, Gram-positive, catalase-positive, non-spore-forming and non-motile. The cell-wall peptidoglycan contained lysine, alanine and glutamic acid. rrs sequence analysis indicated that the new isolates Re117T and Ca106T are closely related to the Arthrobacter nicotianae group and showed highest sequence similarity (>98 %) to Arthrobacter nicotianae and Arthrobacter protophormiae. However, DNA–DNA hybridization studies indicated that the strains represented two novel genomic species within the genus Arthrobacter and did not belong to A. nicotianae or A. protophormiae (<43 % DNA–DNA relatedness). On the basis of the phylogenetic and phenotypic distinctiveness of the new isolates, these bacteria should be classified as two novel Arthrobacter species, for which the names Arthrobacter bergerei sp. nov. and Arthrobacter arilaitensis sp. nov. are proposed. Type strains have been deposited in culture collections as Arthrobacter bergerei Ca106T (=CIP 108036T=DSM 16367T) and Arthrobacter arilaitensis Re117T (=CIP 108037T=DSM 16368T).
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Nesterenkonia sandarakina sp. nov. and Nesterenkonia lutea sp. nov., novel actinobacteria, and emended description of the genus Nesterenkonia
Two novel actinobacteria isolates, designated YIM 70009T and YIM 70081T, were characterized in order to determine their taxonomic position. Cells of strains YIM 70009T and YIM 70081T were cocci, although only the latter were motile. The G+C contents of their DNAs were 64·0 and 64·5 mol%, respectively. On the basis of chemotaxonomic characteristics and 16S rRNA gene sequence analysis, the two isolates were classified in the genus Nesterenkonia. DNA–DNA hybridization and comparison of phenotypic characteristics revealed that strains YIM 70009T and YIM 70081T differed from each other and from known species. Therefore, it is proposed that they represent two separate novel species of the genus Nesterenkonia: Nesterenkonia sandarakina sp. nov. (type strain, YIM 70009T=CCTCC AA 203007T=DSM 15664T=KCTC 19011T) and Nesterenkonia lutea sp. nov. (type strain, YIM 70081T=CCTCC AA 203010T=DSM 15666T=KCTC 19013T).
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Carnobacterium pleistocenium sp. nov., a novel psychrotolerant, facultative anaerobe isolated from permafrost of the Fox Tunnel in Alaska
More LessA novel, psychrotolerant, facultative anaerobe, strain FTR1T, was isolated from Pleistocene ice from the permafrost tunnel in Fox, Alaska. Gram-positive, motile, rod-shaped cells were observed with sizes 0·6–0·7×0·9–1·5 μm. Growth occurred within the pH range 6·5–9·5 with optimum growth at pH 7·3–7·5. The temperature range for growth of the novel isolate was 0–28 °C and optimum growth occurred at 24 °C. The novel isolate does not require NaCl; growth was observed between 0 and 5 % NaCl with optimum growth at 0·5 % (w/v). The novel isolate was a catalase-negative chemoorganoheterotroph that used as substrates sugars and some products of proteolysis. The metabolic end products were acetate, ethanol and CO2. Strain FTR1T was sensitive to ampicillin, tetracycline, chloramphenicol, rifampicin, kanamycin and gentamicin. 16S rRNA gene sequence analysis showed 99·8 % similarity between strain FTR1T and Carnobacterium alterfunditum, but DNA–DNA hybridization between them demonstrated 39±1·5 % relatedness. On the basis of genotypic and phenotypic characteristics, it is proposed that strain FTR1T (=ATCC BAA-754T=JCM 12174T=CIP 108033T) be assigned to the novel species Carnobacterium pleistocenium sp. nov.
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- Unicellular Eukaryotes
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Geotrichum silvicola sp. nov., a novel asexual arthroconidial yeast species related to the genus Galactomyces
Four strains of an asexual arthroconidial yeast species were isolated from Drosophila flies in two Atlantic rain forest sites in Brazil and two strains from oak tasar silkworm larvae (Antheraea proylei) in India. Analysis of the sequences of the D1/D2 large subunit rRNA gene showed that this yeast represented a novel species of the genus Geotrichum, described as Geotrichum silvicola sp. nov. The novel species was related to the ascogenous genus Galactomyces. The closest relatives of Geotrichum silvicola were Galactomyces sp. strain NRRL Y-6418 and Galactomyces geotrichum. The type culture of Geotrichum silvicola is UFMG-354-2T (=CBS 9194T=NRRL Y-27641T).
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Sporidiobolus longiusculus sp. nov. and Sporobolomyces patagonicus sp. nov., novel yeasts of the Sporidiobolales isolated from aquatic environments in Patagonia, Argentina
More LessDuring a survey of carotenogenic yeasts carried out in north-western Patagonia (Argentina), several ballistoconidia-producing strains belonging to the order Sporidiobolales were isolated from aquatic environments. Five strains were found to represent two novel species, for which the names Sporidiobolus longiusculus and Sporobolomyces patagonicus are proposed, with CBS 9654T (=PYCC 5818T=CRUB 1044T) and CBS 9657T (=PYCC 5817T=CRUB 1038T) as the type strains, respectively. The elongated basidia, which are five to six times longer that those of the remaining species of the genus Sporidiobolus, are a particular micromorphological feature of Sporidiobolus longiusculus. On the basis of the sequences of the D1/D2 domains of the 26S rRNA gene, the species most closely related to Sporidiobolus longiusculus is Sporobolomyces bannaensis, whereas Sporobolomyces marcillae is the closest relative of Sporobolomyces patagonicus. Complete internal transcribed spacer sequence analysis confirmed the separate position of Sporidiobolus longiusculus, whereas for Sporobolomyces patagonicus no nucleotide differences were found with respect to Sporidiobolus pararoseus CBS 491T. Negative mating experiments between strains of Sporobolomyces patagonicus and strains of Sporidiobolus pararoseus together with the low DNA–DNA reassociation values for the type strains of the two species validated the proposal of Sporobolomyces patagonicus as a distinct species. Information on additional Patagonian Sporobolomyces isolates is also included in this report.
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- Evolution, Phylogeny And Biodiversity
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Phylogenetic and morphological evaluation of the genera Anabaena, Aphanizomenon, Trichormus and Nostoc (Nostocales, Cyanobacteria)
The heterocytous cyanobacteria form a monophyletic group according to 16S rRNA gene sequence data. Within this group, phylogenetic and morphological studies have shown that genera such as Anabaena and Aphanizomenon are intermixed. Moreover, the phylogeny of the genus Trichormus, which was recently separated from Anabaena, has not been investigated. The aim was to study the taxonomy of the genera Anabaena, Aphanizomenon, Nostoc and Trichormus belonging to the family Nostocaceae (subsection IV.I) by morphological and phylogenetic analyses of 16S rRNA gene, rpoB and rbcLX sequences. New strains were isolated to avoid identification problems caused by morphological changes of strains during cultivation. Morphological and phylogenetic data showed that benthic and planktic Anabaena strains were intermixed. In addition, the present study confirmed that Anabaena and Aphanizomenon strains were not monophyletic, as previously demonstrated. The evolutionary distances between the strains indicated that the planktic Anabaena and Aphanizomenon strains as well as five benthic Anabaena strains in cluster 1 could be assigned to a single genus. On the basis of the 16S rRNA, rpoB and rbcLX gene sequences, the Anabaena/Aphanizomenon strains (cluster 1) were divided into nine supported subclusters which could also be separated morphologically, and which therefore might represent different species. Trichormus strains were morphologically and phylogenetically heterogeneous and did not form a monophyletic cluster. These Trichormus strains, which were representatives of three distinct species, might actually belong to three genera according to the evolutionary distances. Nostoc strains were also heterogeneous and seemed to form a monophyletic cluster, which may contain more than one genus. It was found that certain morphological features were stable and could be used to separate different phylogenetic clusters. For example, the width and the length of akinetes were useful features for classification of the Anabaena/Aphanizomenon strains in cluster 1. This morphological and phylogenetic study with fresh isolates showed that the current classification of these anabaenoid genera needs to be revised.
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Polyphasic study of wine Lactobacillus strains: taxonomic implications
A. M. Rodas, S. Ferrer and I. PardoOne hundred and seventy-eight lactobacilli isolated from wine were characterized by a polyphasic approach. Strains were phenotypically identified at genus and species level by classical tests including the analysis of cell morphology, homo/heterofermentative character, sugar fermentation patterns, growth at different temperatures and the optical nature of the isomer of lactic acid produced from glucose. Molecular techniques such as random amplification of polymorphic DNA (RAPD), amplified 16S rDNA restriction analysis (16S-ARDRA), PFGE-RFLP and ribotyping were used to characterize strains, and their potential for identification and/or typing was evaluated. The information obtained with these techniques was processed with the BioNumerics software in order to analyse relationships existing between isolated strains and various reference species of the genus. Then, taxonomic dendrograms were obtained, and this information allowed the proposal of molecular procedures suitable for the identification and typing of these wine micro-organisms. The techniques useful for both identification and typing were RAPD and ribotyping, while 16S-ARDRA was only useful for identification and PFGE-RFLP only for typing purposes. The wine strains were identified as Lactobacillus brevis (19 strains), Lactobacillus collinoides (2 strains), Lactobacillus hilgardii (71 strains), Lactobacillus paracasei (13 strains), Lactobacillus pentosus (2 strains), Lactobacillus plantarum (34 strains) and Lactobacillus mali (10 strains).
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Phylogenetic analysis of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium on the basis of 16S rRNA gene and internally transcribed spacer region sequences
A total of 128 strains was isolated from more than 23 legume hosts in Korea. Phylogenetic relationships between these Korean isolates and reference strains of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium were analysed using their 16S rRNA gene and internally transcribed spacer (ITS) region sequences. Among the Bradyrhizobium strains, dendrograms based on both the 16S rRNA gene and ITS region sequences produced two main groups. The ITS tree yielded at least two new clusters that were discernable from the seven previously delineated genospecies. Large discrepancies were revealed between phylogenetic dendrograms based on 16S rRNA gene and ITS region sequences for members of the genus Rhizobium, reflecting their taxonomic heterogeneity. The amalgamation of Rhizobium and former members of Agrobacterium was confirmed using the 16S rRNA tree. Phylogenetic analysis of ITS region sequences showed that the Rhizobium giardinii clade (group II) and the Rhizobium radiobacter/Rhizobium rubi clade (group III) could be tentatively recognized as groups that are separable from the core group (group I), which includes Rhizobium leguminosarum. Dendrograms based on the 16S rRNA gene and ITS region sequences of Mesorhizobium strains were highly conflicting due to the poor taxonomic resolution of the 16S rRNA gene sequences and the low confidence in the ITS dendrogram. Several Korean isolates within the genus Mesorhizobium are thought to represent novel taxa when considering their relatively low ITS region sequence similarities (<80 %) to the reference strains.
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A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model
More LessAdvances in DNA sequencing and the increasing number of sequences available in databases have greatly enhanced the bacterial identification process. Several species within the genus Mycobacterium cause serious human and animal diseases. In order to assess their relative positions in the evolutionary process, four gene fragments, from the 16S rRNA (564 bp), hsp65 (420 bp), rpoB (396 bp) and sod (408 bp) genes, were sequenced from 97 strains, including all available type strains of the genus Mycobacterium. The results demonstrate that, in this case, the concatenation of different genes allows significant increases in the power of discrimination and the robustness of the phylogenetic tree. The sequential and/or combined use of sequences of several genes makes it possible to refine the phylogenetic approach and provides a molecular basis for accurate species identification.
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On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes
More LessA global phylogeny of major eukaryotic lineages is a significant and ongoing challenge to molecular phylogenetics. Currently, there are five hypothesized major lineages or ‘supergroups' of eukaryotes. One of these, the chromalveolates, represents a large fraction of protist and algal diversity. The chromalveolate hypothesis was originally based on similarities between the photosynthetic organelles (plastids) found in many of its members and has been supported by analyses of plastid-related genes. However, since plastids can move between eukaryotic lineages, it is important to provide additional support from data generated from the nuclear-cytosolic host lineage. Genes coding for six different cytosolic proteins from a variety of chromalveolates (yielding 68 new gene sequences) have been characterized so that multiple gene analyses, including all six major lineages of chromalveolates, could be compared and concatenated with data representing all five hypothesized supergroups. Overall support for much of the phylogenies is decreased over previous analyses that concatenated fewer genes for fewer taxa. Nevertheless, four of the six chromalveolate lineages (apicomplexans, ciliates, dinoflagellates and heterokonts) consistently form a monophyletic assemblage, whereas the remaining two (cryptomonads and haptophytes) form a weakly supported group. Whereas these results are consistent with the monophyly of chromalveolates inferred from plastid data, testing this hypothesis is going to require a substantial increase in data from a wide variety of organisms.
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- Methods
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Application of sliding-window discretization and minimization of stochastic complexity for the analysis of fAFLP genotyping fingerprint patterns of Vibrionaceae
More LessMinimization of stochastic complexity (SC) was used as a method for classification of genotypic fingerprints. The method was applied to fluorescent amplified fragment length polymorphism (fAFLP) fingerprint patterns of 507 Vibrionaceae representatives. As the current BinClass implementation of the optimization algorithm for classification only works on binary vectors, the original fingerprints were discretized in a preliminary step using the sliding-window band-matching method, in order to maximally preserve the information content of the original band patterns. The novel classification generated using the BinClass software package was subjected to an in-depth comparison with a hierarchical classification of the same dataset, in order to acknowledge the applicability of the new classification method as a more objective algorithm for the classification of genotyping fingerprint patterns. Recent DNA–DNA hybridization and 16S rRNA gene sequence experiments proved that the classification based on SC-minimization forms separate clusters that contain the fAFLP patterns for all representatives of the species Enterovibrio norvegicus, Vibrio fortis, Vibrio diazotrophicus or Vibrio campbellii, while previous hierarchical cluster analysis had suggested more heterogeneity within the fAFLP patterns by splitting the representatives of the above-mentioned species into multiple distant clusters. As a result, the new classification methodology has highlighted some previously unseen relationships within the biodiversity of the family Vibrionaceae.
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- International Committee On Systematics Of Prokaryotes
- Opinions
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Strain NBRC (formerly IFO) 3782 is the type strain of Streptomyces rameus Shibata 1959. Opinion 76
More LessThe Judicial Commission of the International Committee for Systematics of Prokaryotes decided that strain NBRC (formerly IFO) 3782 (=No. 43797), which was the originally designated type strain, has to replace ATCC 21273 as the type strain of Streptomyces rameus. ATCC 21273 was given as the type strain in the Approved Lists 1980.
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The type species of the genus Paenibacillus Ash et al. 1994 is Paenibacillus polymyxa. Opinion 77
More LessThe Judicial Commission of the International Committee for Systematics of Prokaryotes decided that the type species of the genus Paenibacillus is Paenibacillus polymyxa.
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Rejection of the genus name Pelczaria with the species Pelczaria aurantia Poston 1994. Opinion 78
More LessThe Judicial Commission of the International Committee for Systematics of Prokaryotes has decided to place the genus Pelczaria with the species Pelczaria aurantia on the list of nomina rejicienda, due to the lack of an authentic type or neotype strain.
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The nomenclatural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79
More LessThe Judicial Commission of the International Committee on Systematics of Prokaryotes has corrected the nomenclatural types of 12 orders: Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales.
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The type species of the genus Salmonella Lignieres 1900 is Salmonella enterica (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987, with the type strain LT2T, and conservation of the epithet enterica in Salmonella enterica over all earlier epithets that may be applied to this species. Opinion 80
More LessThe Judicial Commission of the International Committee for Systematics of Prokaryotes has decided that the type species of the genus Salmonella Lignieres 1900 is Salmonella enterica (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987 and that the type strain of this species is strain LT2T. In addition, the epithet enterica in Salmonella enterica is conserved over all earlier epithets that may be applied to this species.
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- Taxonomic Note
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Nomenclature and taxonomy of the genus Salmonella
More LessThe nomenclature of the genus Salmonella has reached an unsatisfactory state of affairs, with two systems of nomenclature in circulation. One system, proposed in the 1980s by Le Minor and Popoff, has received wide acceptance, although it does not conform to the rules of the Bacteriological Code. The other system, which conforms to the rules of the Bacteriological Code, is being used by an ever-decreasing minority. As a result of a number of recent Requests for an Opinion, the Judicial Commission of the International Committee on the Systematics of Prokaryotes has issued an Opinion (Opinion 80) with the intention that it should solve these discrepancies. However, like all Opinions, it is limited to matters of nomenclature and does not help to interpret the taxonomic consequences. The Judicial Commission has therefore asked experts in the field of nomenclature and taxonomy to write a commentary on the nomenclatural and taxonomic consequences of Opinion 80. The present article explains the nomenclatural consequences of Opinion 80, together with a clear presentation of the taxonomy that results when applying the currently widely accepted interpretation that the genus Salmonella currently includes only two species.
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- Errata
Volumes and issues
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