- Volume 53, Issue 5, 2003
Volume 53, Issue 5, 2003
- New Taxa
-
- Gram-Positive Bacteria
-
-
Promicromonospora vindobonensis sp. nov. and Promicromonospora aerolata sp. nov., isolated from the air in the medieval ‘Virgilkapelle’ in Vienna
Two airborne bacterial isolates designated V45T and V54AT were characterized in order to determine their taxonomic position. 16S rDNA sequence analysis showed that the two isolates shared 98·1 % sequence similarity. Highest sequence similarities (98·0–98·5 %) were found to Promicromonospora citrea DSM 43110T and Promicromonospora sukumoe IFO 14650T. Detection of a quinone system with the predominant compound MK-9(H4), a polar lipid pattern containing phosphatidylglycerol, a fatty acid profile with the predominant acids C15 : 0 iso and C15 : 0 anteiso and the diagnostic cell-wall diamino acid l-lysine supported the assignment of the novel isolates to the genus Promicromonospora. The two isolates could be distinguished from P. sukumoe by the presence of glycine in the peptidoglycan, and the detection of the cell-wall sugar galactose differentiates them from the two established species of the genus Promicromonospora. Each of the two isolates displayed a unique biochemical profile. Results from DNA–DNA hybridizations clearly demonstrated that V45T and V54AT represent separate species. Based on these data, it is proposed that V45T (=IFO 16525T=CCM 7044T) and V54AT (=IFO 16526T =CCM 7043T) be classified as the type strains of two novel Promicromonospora species, for which the names Promicromonospora vindobonensis sp. nov. and Promicromonospora aerolata sp. nov. are proposed.
-
-
-
Garciella nitratireducens gen. nov., sp. nov., an anaerobic, thermophilic, nitrate- and thiosulfate-reducing bacterium isolated from an oilfield separator in the Gulf of Mexico
A novel Gram-positive, anaerobic and thermophilic bacterium, strain MET79T, was isolated from an oil well located in the Gulf of Mexico. Cells were straight rods, motile by a subpolar flagellum. Spores were formed in old cultures. Inner gas vacuoles swelled the cells when exposed to air. The optimum growth conditions were 55 °C, pH 7·5 and 1 % NaCl. Yeast extract was required for growth. Strain MET79T fermented several sugars, some organic acids and Casamino acids. Glucose was fermented into lactate, acetate, butyrate, H2 and CO2. Strain MET79T reduced thiosulfate to hydrogen sulfide and nitrate to ammonium. The DNA G+C content was 30·9 mol%. The closest phylogenetic relative of strain MET79T was Caloranaerobacter azorensis (88·7 % 16S rDNA sequence similarity). As strain MET79T (=DSM 15102T=CIP 107615T) was physiologically and phylogenetically different from its closest relatives, it is assigned as the type strain of a novel species of a new genus, Garciella nitratireducens gen. nov., sp. nov.
-
-
-
Actinomyces oricola sp. nov., from a human dental abscess
A previously undescribed Actinomyces-like bacterium was isolated from 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 hitherto unknown subline within the genus Actinomyces, clustering within a group of species, which includes Actinomyces bovis, the type species of the genus. Based on biochemical and molecular phylogenetic evidence, it is proposed that the unknown organism recovered from a dental abscess be classified as a new species, Actinomyces oricola sp. nov. The type strain of Actinomyces oricola is R5292T (=CCUG 46090T=CIP 107639T).
-
-
-
Taxonomic re-evaluation of whorl-forming Streptomyces (formerly Streptoverticillium) species by using phenotypes, DNA–DNA hybridization and sequences of gyrB, and proposal of Streptomyces luteireticuli (ex Katoh and Arai 1957) corrig., sp. nov., nom. rev.
More LessThe taxonomic status of 64 strains of whorl-forming Streptomyces (formerly Streptoverticillium) species was re-evaluated and strains were reclassified on the basis of their phenotypes, DNA–DNA hybridization data and partial sequences of gyrB, the structural gene of the B subunit of DNA gyrase. These strains, which consisted of 46 species and eight subspecies with validly published names and 13 species whose names have not been validly published [including 10 strains examined by the International Streptomyces Project (ISP)], were divided into two groups, namely typical and atypical whorl-forming Streptomyces species, based on their phenotypes and gyrB gene sequences. The typical whorl-forming species (59 strains) were divided into six major clusters of three or more species, seven minor clusters of two species and five single-member clusters, based on the threshold value of 97 % gyrB sequence similarity. Major clusters were typified by Streptomyces abikoensis, Streptomyces cinnamoneus, Streptomyces distallicus, Streptomyces griseocarneus, Streptomyces hiroshimensis and Streptomyces netropsis. Phenotypically, members of each cluster resembled each other closely except for the S. distallicus cluster, which was divided phenotypically into the S. distallicus and Streptomyces stramineus subclusters, and the S. netropsis cluster, which was divided into the S. netropsis and Streptomyces eurocidicus subclusters. Strains in each minor cluster closely resembled each other phenotypically. DNA–DNA relatedness between the representative species and others in each major cluster and/or subcluster, and between strains in the minor clusters, was >70 %, indicating that the major clusters and/or subclusters and the minor clusters each comprise a single species. It was concluded that 59 strains of typical whorl-forming Streptomyces species consisted of the following 18 species, including subjective synonym(s): S. abikoensis, Streptomyces ardus, Streptomyces blastmyceticus, S. cinnamoneus, S. eurocidicus, S. griseocarneus, S. hiroshimensis, Streptomyces lilacinus, ‘Streptomyces luteoreticuli’, Streptomyces luteosporeus, Streptomyces mashuensis, Streptomyces mobaraensis, Streptomyces morookaense, S. netropsis, Streptomyces orinoci, S. stramineus, Streptomyces thioluteus and Streptomyces viridiflavus.
-
-
-
Bacillus krulwichiae sp. nov., a halotolerant obligate alkaliphile that utilizes benzoate and m-hydroxybenzoate
Obligate alkaliphilic strains, AM31DT and AM11D, that utilize benzoate and m-hydroxybenzoate were isolated from soil obtained from Tsukuba, Ibaraki, Japan. The isolates grew at pH 8–10, but not at neutral pH. They were Gram-positive, facultatively anaerobic, straight rods with peritrichous flagella and produced ellipsoidal spores. The isolates reduced nitrate to nitrite and grew in 0–14 % NaCl, but not in higher concentrations. The major isoprenoid quinones were menaquinone-5, -6 and -7, and the cellular fatty acid profile consisted of significant amounts of 15-C branched-chain acids, isoC15 : 0 and anteisoC15 : 0. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain AM31DT was a member of group 6 (alkaliphiles) in the genus Bacillus. DNA–DNA hybridization revealed a low relatedness of the isolates with several phylogenetically close neighbours, including Bacillus alcalophilus and Bacillus pseudalcaliphilus (less than 19·3 %). Based on phenotypic characteristics, phylogenetic data and DNA–DNA relatedness data, it was concluded that these isolates merited classification as a new species, for which the name Bacillus krulwichiae is proposed. The type strain of this species is AM31DT (=NCIMB 13904T=JCM 11691T=IAM 15000T).
-
-
-
Alicyclobacillus pomorum sp. nov., a novel thermo-acidophilic, endospore-forming bacterium that does not possess ω-alicyclic fatty acids, and emended description of the genus Alicyclobacillus
More LessA thermo-acidophilic endospore-forming bacterium was isolated from a mixed fruit juice. The organism, strain 3AT, was rod-shaped, grew aerobically at 30–60 °C (optimum 45–50 °C), pH 3·0–6·0 (optimum pH 4·0–4·5) and produced acid from various sugars. It contained menaquinone-7 as the major isoprenoid quinone. The G+C content of the DNA was 53·1 mol%. The predominant cellular fatty acids of the strain were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and anteiso-C17 : 0, but ω-alicyclic fatty acids, which are characteristic of the genus Alicyclobacillus, were not found in the strain. Phylogenetic analyses based on both 16S rRNA and gyrB (DNA gyrase B subunit gene) gene sequences showed that strain 3AT falls into the Alicyclobacillus cluster, validated by significant bootstrap values. However, strain 3AT did not show a close relationship to the other species of the cluster. The level of 16S rDNA similarity between strain 3AT and other strains of the cluster was between 92·5 and 95·5 %. The level of gyrB sequence similarity between strain 3AT and other strains of the cluster was between 68·5 and 74·4 %. DNA–DNA hybridization values between strain 3AT and phylogenetically related strains of the genera Alicyclobacillus, Bacillus and Sulfobacillus were under 13 %, indicating that strain 3AT represents a distinct species. On the basis of these results, strain 3AT should be classified as a novel Alicyclobacillus species. The name Alicyclobacillus pomorum is proposed for this organism. The type strain of Alicyclobacillus pomorum is strain 3AT (=DSM 14955T=IAM 14988T).
-
-
-
Prauserella halophila sp. nov. and Prauserella alba sp. nov., moderately halophilic actinomycetes from saline soil
The actinomycete strains YIM 90001T and YIM 90005T were isolated on starch-casein agar [20 % (w/v) NaCl, pH 7·0] from a soil sample collected from Xinjiang Province in the west of China. The two isolates were aerobic and Gram-positive. The substrate mycelium was fragmented and an aerial mycelium was well developed on Czapek medium. The aerial mycelium formed long spore chains with branched short or long spore chains at maturity, which were straight to flexuous, and spores were non-motile. Based on the results of metabolic, chemotaxonomic and molecular analyses, the two isolates were identified as two new species of the genus Prauserella, for which the names Prauserella halophila for strain YIM 90001T (=DSM 44617T=CCTCC AA001015T) and Prauserella alba for strain YIM 90005T (=DSM 44590T=CCTCC AA001016T) are proposed.
-
-
-
Longispora albida gen. nov., sp. nov., a novel genus of the family Micromonosporaceae
More LessA novel actinomycete strain was isolated from a soil sample collected in Japan by using gellan gum as a solidifying agent. Spore-chains from the short sporophores were straight and each had more than 20 spores per chain. Spores possessed no motility. Cell-wall peptidoglycan contained meso-diaminopimelic acid, glycine, alanine and glutamic acid; whole-cell hydrolysates contained arabinose, galactose and xylose. The acyl type of the peptidoglycan was glycolyl. The predominant menaquinones were MK-10(H4) and MK-10(H6); MK-10(H8) was a minor component. Mycolic acids were not detected. The diagostic phospholipid was phosphatidylethanolamine. Cellular fatty acids included heptadecenoic (C17 : 1), 14-methylpentadecanoic (i-C16 : 0) and octadecenoic (C18 : 1) acids. The G+C content of the DNA was 70 mol%. On the basis of morphogical and chemotaxonomic properties and phylogenetic analysis based on 16S rDNA sequence data, it is proposed that this strain should be classified in a novel genus and species, Longispora albida gen. nov., sp. nov., in the family Micromonosporaceae. The type strain is K97-0003T (=NRRL B-24201T=JCM 11711T).
-
-
-
Aerobic growth of Anoxybacillus pushchinoensis K1T: emended descriptions of A. pushchinoensis and the genus Anoxybacillus
More LessIn this work, corrections are made to the descriptions of the species Anoxybacillus pushchinoensis corrig. and the genus Anoxybacillus. Experiments to determine the relationship of A. pushchinoensis K1T to oxygen showed that it was capable of aerobic growth, but preferred to grow anaerobically. During aerobic growth, the redox indicator resazurin was reduced as a result of hydrogen gas production. The facultatively anaerobic nature of K1T was ascertained by cultivation in aerobic liquid medium, where growth began at the bottom of the tube. The anaerobic nature of K1T was also indicated by a negative catalase reaction. This work is submitted to correct the description of the species A. pushchinoensis from obligate anaerobe to aerotolerant anaerobe and to emend the description of the genus Anoxybacillus from obligate anaerobes or facultative anaerobes to aerotolerant anaerobes or facultative anaerobes.
-
-
-
Saccharomonospora paurometabolica sp. nov., a moderately halophilic actinomycete isolated from soil in China
A novel, moderately halophilic actinomycete, strain YIM 90007T, was isolated from a soil sample collected from the Xinjiang Province, China, and characterized. The optimum growth temperature of the strain was between 35 and 37 °C and growth occurred optimally in 10 % (w/v) NaCl. The cell wall of strain YIM 90007T contained meso-diaminopimelic acid. Whole-cell sugars were galactose, arabinose and ribose. The principal menaquinone was MK-9(H4), while MK-9(H2) was found in smaller amounts. The phospholipids were phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and hydroxyphosphatidylethanolamine. The predominant cellular fatty acids were of the iso- and anteiso-branched and unbranched types; significant amounts of 2-hydroxy fatty acids were also found but 10-methyl-branched fatty acids were missing. The DNA G+C content of strain YIM 900007T was 71 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed strain YIM 90007T to be closely related to Saccharomonospora halophila (98·7 % similarity). DNA–DNA hybridization revealed a relatedness of 53·8 % between strain YIM 90007T and S. halophila DSM 44411T. Based on physiological and biochemical characteristics, phylogenetic analysis (based on 16S rRNA gene sequences) and DNA–DNA relatedness, it is concluded that strain YIM 90007T represents a novel species of the genus Saccharomonospora, for which the name Saccharomonospora paurometabolica (type strain YIM 90007T=CCTCC AA001018T=CCRC 16315T=DSM 44619T) is proposed.
-
-
-
Nocardia puris sp. nov.
More LessA bacterial isolate (IMMIB R-145T) from a human abscess was subjected to a polyphasic taxonomic study. Chemotaxonomic investigations revealed the isolate to have cell wall chemotype IV and mycolic acids consistent with characteristics of the genus Nocardia. Comparative 16S rRNA gene sequencing showed that the isolate constituted a distinct subline within the genus Nocardia, displaying greater than 1·7 % sequence divergence with established species. However, a DNA–DNA hybridization study demonstrated unambiguously that the isolate was genealogically distinct from closely related species, namely, Nocardia abscessus, Nocardia cyriacigeorgica and Nocardia farcinica, with which it showed high levels of 16S rDNA sequence similarity (97·8, 97·9 and 98·3 %, respectively). Based on phenotypic and phylogenetic data, it is proposed that this isolate be classified as a new species of the genus Nocardia, for which the name Nocardia puris (type strain IMMIB R-145T=DSM 44599T=NRRL B-24204T) is proposed.
-
-
-
Amycolatopsis kentuckyensis sp. nov., Amycolatopsis lexingtonensis sp. nov. and Amycolatopsis pretoriensis sp. nov., isolated from equine placentas
More LessActinomycete strains isolated from lesions on equine placentas from two horses in Kentucky and one in South Africa were subjected to a polyphasic taxonomic study. Chemotaxonomic and morphological characteristics indicated that the isolates are members of the genus Amycolatopsis. On the basis of phylogenetic analysis of 16S rDNA sequences, the isolates are related most closely to Amycolatopsis mediterranei. Physiological characteristics of these strains indicated that they do not belong to A. mediterranei and DNA relatedness determinations confirmed that these strains represent three novel species of the genus Amycolatopsis, for which the names Amycolatopsis kentuckyensis (type strain, NRRL B-24129T=LDDC 9447-99T=DSM 44652T), Amycolatopsis lexingtonensis (type strain, NRRL B-24131T=LDDC 12275-99T=DSM 44653T) and Amycolatopsis pretoriensis (type strain, NRRL B-24133T=ARC OV1 0181T=DSM 44654T) are proposed.
-
-
-
Species identification of genus Bifidobacterium based on partial HSP60 gene sequences and proposal of Bifidobacterium thermacidophilum subsp. porcinum subsp. nov.
Lin Zhu, Wei Li and Xiuzhu DongSequence homology of partial 60 kDa heat-shock protein (HSP60) genes was analysed for 50 Bifidobacterium strains that represent 12 Bifidobacterium species and subspecies with validly published names. Sequence similarities were 96·5–100 % within the same species, 95·5–97 % at the subspecies level and 80–96 % (mean, 88 %) at the interspecies level among the 10 Bifidobacterium species. Hence, the HSP60 gene was a more accurate tool for species identification within the genus Bifidobacterium than 16S rDNA. Two new Bifidobacterium strains isolated from piglet faeces were shown to be closely related to the thermophilic bifidobacterial group, based on 16S rDNA sequence analysis: strain P3-14T (=AS 1.3009T=LMG 21689T) exhibited 97·9 % similarity to Bifidobacterium boum JCM 1211T, 97·2 % similarity to Bifidobacterium thermacidophilum AS 1.2282T and 97 % similarity to Bifidobacterium thermophilum JCM 1207T. However, higher levels of DNA–DNA relatedness (83 %) and HSP60 gene sequence similarity (97 %) were determined between B. thermacidophilum AS 1.2282T and strain P3-14T, indicating a closer relationship between them. The new strains differed from B. thermacidophilum AS 1.2282T in some phenotypic characteristics, such as growth at a lower temperature (46·5 °C), as well as different sugar-fermentation patterns. Hence, a novel Bifidobacterium subspecies, Bifidobacterium thermacidophilum subsp. porcinum subsp. nov., is designated.
-
-
-
Gordonia paraffinivorans sp. nov., a hydrocarbon-degrading actinomycete isolated from an oil-producing well
More LessThe taxonomic position of an actinomycete, strain HD321T, isolated from an oil-producing well of Daqing oilfield, was clarified using a polyphasic taxonomic approach. The strain possessed cell-wall chemotype IV, MK-9(H2) as the predominant menaquinone, relatively long-chain mycolic acids (52–62 carbon atoms) of the Gordonia type, straight-chain saturated and monounsaturated fatty acids and tuberculostearic acid. The G+C content of the DNA was 66 mol%. 16S rDNA analyses as well as chemotaxonomic and physiological properties indicated that strain HD321T represents a novel species within the genus Gordonia, for which the name Gordonia paraffinivorans sp. nov. is proposed; the type strain is HD321T (=AS 4.1730T=DSM 44604T).
-
-
-
Macrococcus brunensis sp. nov., Macrococcus hajekii sp. nov. and Macrococcus lamae sp. nov., from the skin of llamas
Eight strains of Gram-positive, catalase- and oxidase-positive cocci were isolated from the skin of llamas (Lama glama L.) and characterized using a polyphasic approach. These strains were assigned to the genus Macrococcus on the basis of their phenotypic properties (resistance to bacitracin and sensitivity to furazolidone) and DNA base content (40–42 mol% G+C). Phylogenetic analysis based on 16S rDNA confirmed that the strains are members of the genus Macrococcus. They differed from all hitherto described macrococcal species in their production of phosphatase and reduction of nitrate (most strains) and the inability to produce acid from glycerol or to grow in 7·5 % NaCl. Ribotyping (EcoRI), macrorestriction analysis (XbaI) and fatty acid methyl ester analysis divided the strains from llamas into three stable clusters. Moreover, ribotyping differentiated the strains analysed not only from previously described macrococcal species but also from oxidase-positive staphylococci. DNA–DNA hybridization confirmed that the three clusters represent separate genomic groups (similarity values<54 %). All the results showed that the strains represent three novel species, for which the names Macrococcus hajekii sp. nov. (type strain CCM 4809T=LMG 21711T), Macrococcus brunensis sp. nov. (type strain CCM 4811T=LMG 21712T) and Macrococcus lamae sp. nov. (type strain CCM 4815T=LMG 21713T) are proposed.
-
- Unicellular Eukaryotes
-
-
Novel anamorphic mite-associated fungi belonging to the Ustilaginomycetes: Meira geulakonigii gen. nov., sp. nov., Meira argovae sp. nov. and Acaromyces ingoldii gen. nov., sp. nov.
Three novel mite-associated basidiomycetous species are described in two new anamorph genera as Meira geulakonigii gen. nov., sp. nov. (type CBS 110052T=NRRL Y-27483T=AS 004T), Meira argovae sp. nov. (type CBS 110053T=NRRL Y-27482T=AS 005T) and Acaromyces ingoldii gen. nov., sp. nov. (type CBS 110050T=NRRL Y-27484T=AS 001T). Morphologically, these fungi are similar to the yeast-like fungi classified in the Ustilaginales, such as Pseudozyma species. However, analysis of the D1/D2 domain of the LSU rDNA suggests that they belong to two different lineages within the Exobasidiomycetidae of the Ustilaginomycetes (Basidiomycota). Furthermore, these fungi may be of interest for the biocontrol of mites, as they reduced mite numbers by approximately 80 % after inoculation.
-
-
-
Metschnikowia vanudenii sp. nov. and Metschnikowia lachancei sp. nov., from flowers and associated insects in North America
More LessTwo new species of the ascosporic yeast genus Metschnikowia were isolated from nectaries and associated muscoid flies of flowers from the common milkweed (Asclepias syriaca) in North America, and are described as Metschnikowia vanudenii [type strain=PYCC 4650T=CBS 9134T=NRRL Y-27243T=UWO(PS) 86A4.1T] and Metschnikowia lachancei [type strain=PYCC 4605T=CBS 9131T=NRRL Y-27242T=UWO(PS) 7ASB2.3T]. As with the previously described Metschnikowia gruessii, M. vanudenii has vegetative cells with an ‘aeroplane’ or cross-like configuration, produces ovoid chlamydospores and forms ellipsoidopedunculate asci with two acicular ascospores. Metschnikowia lachancei is distinguished from other Metschnikowia species by formation of club-shaped asci with 1–2 thick clavate ascospores. The phylogenetic positions of the proposed new species within Metschnikowia were determined from sequence analysis of the D1/D2 domain of 26S rDNA. The new species show low nuclear DNA relatedness with neighbouring taxa.
-
-
-
Hanseniaspora meyeri sp. nov., Hanseniaspora clermontiae sp. nov., Hanseniaspora lachancei sp. nov. and Hanseniaspora opuntiae sp. nov., novel apiculate yeast species
More LessFourteen apiculate yeast strains isolated from various sources in South Africa, North America and the Hawaiian islands were found to be genetically divergent from other Hanseniaspora–Kloeckera species by using randomly amplified polymorphic DNA (RAPD)-PCR. After cluster analysis of the RAPD-PCR fingerprints, five groups were recognized. DNA reassociation values among representatives of these groups and strains of Hanseniaspora–Kloeckera species revealed that the strains represent five novel species. Four are described here as novel species of Hanseniaspora: Hanseniaspora meyeri sp. nov. (type CBS 8734T), Hanseniaspora clermontiae sp. nov. (type CBS 8821T), Hanseniaspora lachancei sp. nov. (type CBS 8818T) and Hanseniaspora opuntiae sp. nov. (type CBS 8733T). The fifth novel species, which is represented by only a single strain, CBS 8772, is not introduced as a new taxon. Phylogenetic analyses of the D1/D2 region of the 26S rDNA and internal transcribed spacer (ITS) regions with 5·8S rDNA sequences placed H. meyeri, H. clermontiae, H. lachancei, H. opuntiae and strain CBS 8772 close to Hanseniaspora uvarum and Hanseniaspora guilliermondii. The key characteristics for standard physiological identification of H. clermontiae and H. lachancei were respectively maximal growth temperature and assimilation of 2-keto-d-gluconate. However, physiological characteristics did not allow the distinction of H. opuntiae and strain CBS 8772 from H. guilliermondii or H. meyeri from H. uvarum. These three novel taxa can be identified by either ITS sequencing or PCR-RFLP of ITS regions using restriction enzymes MboII and HinfI.
-
- Evolution, Phylogeny And Biodiversity
-
-
-
Phylogenetic and physiological characterization of a heterotrophic, chemolithoautotrophic Thiothrix strain isolated from activated sludge
More LessThe sheathed filamentous bacterium known as strain CT3, isolated by micromanipulation from an activated sludge treatment plant in Italy, is a member of the genus Thiothrix in the γ-Proteobacteria according to 16S rDNA sequence analysis. The closest phylogenetic neighbours of strain CT3 are strains I and QT, which were also isolated from activated sludge and belong to the species Thiothrix fructosivorans. These strains have respectively 99·2 and 99·4 % similarity to CT3 by 16S rDNA sequence comparison. CT3 shows 63–67 % DNA–DNA hybridization with strain I, which is the only currently viable strain of T. fructosivorans. CT3 is the second strain in the genus Thiothrix that has been shown to be capable of growing autotrophically with reduced sulfur compounds as the sole energy source; autotrophy was also confirmed in strain I. The first reported chemolithoautotrophic isolate of this genus was a strain of ‘Thiothrix ramosa’ that was isolated from a hydrogen sulfide spring and is morphologically distinguishable from all other described strains of Thiothrix, including CT3. CT3 is an aerobic organism that is non-fermentative, not capable of denitrification and able to grow heterotrophically. Autotrophy in the genus Thiothrix should be investigated more fully to better define the taxonomy of this genus.
-
-
-
-
16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: extension of the dataset and proposal of a new lineage within the nitrosomonads
The phylogenetic relationship of 12 ammonia-oxidizing isolates (eight nitrosospiras and four nitrosomonads), for which no gene sequence information was available previously, was investigated based on their genes encoding 16S rRNA and the active site subunit of ammonia monooxygenase (AmoA). Almost full-length 16S rRNA gene sequences were determined for the 12 isolates. In addition, 16S rRNA gene sequences of 15 ammonia-oxidizing bacteria (AOB) published previously were completed to allow for a more reliable phylogeny inference of members of this guild. Moreover, sequences of 453 bp fragments of the amoA gene were determined from 15 AOB, including the 12 isolates, and completed for 10 additional AOB. 16S rRNA gene and amoA-based analyses, including all available sequences of AOB pure cultures, were performed to determine the position of the newly retrieved sequences within the established phylogenetic framework. The resulting 16S rRNA gene and amoA tree topologies were similar but not identical and demonstrated a superior resolution of 16S rRNA versus amoA analysis. While 11 of the 12 isolates could be assigned to different phylogenetic groups recognized within the betaproteobacterial AOB, the estuarine isolate Nitrosomonas sp. Nm143 formed a separate lineage together with three other marine isolates whose 16S rRNA sequences have not been published but have been deposited in public databases. In addition, 17 environmentally retrieved 16S rRNA gene sequences not assigned previously and all originating exclusively from marine or estuarine sites clearly belong to this lineage.
-
-
-
Flow cytometric sorting, phylogenetic analysis and in situ detection of Oscillospira guillermondii, a large, morphologically conspicuous but uncultured ruminal bacterium
Flow cytometric sorting based on its large cell size enabled an enriched fraction of Oscillospira guillermondii cells to be obtained from the rumen contents of a sheep. Phylogenetic analysis based on cloned 16S rDNA sequences indicated that the bacterium is a member of the low-G+C Gram-positive bacterial cluster. Sporobacter termitidis and Papillibacter cinnamivorans were the most closely related known species, with sequence similarities of only 86·3–88·1 %. Fluorescently labelled 16S rRNA-targeted oligonucleotide probes specific for Oscillospira were designed and applied to the rumen sample from which the enriched fraction was obtained. The probes hybridized specifically with the large, morphologically conspicuous Oscillospira cells.
-
- International Committee On Systematics Of Prokaryotes
-
- Taxonomic Notes
-
-
Agrobacterium is a definable genus of the family Rhizobiaceae
More LessMembers of the genus Agrobacterium constitute a diverse group of organisms, all of which, when harbouring the appropriate plasmids, are capable of causing neoplastic growths on susceptible host plants. The agrobacteria, which are members of the family Rhizobiaceae, can be differentiated into at least three biovars, corresponding to species divisions based on differential biochemical and physiological tests. Recently, Young et al. [Int J Syst Evol Microbiol 51 (2003), 89–103] proposed to incorporate all members of the genus Agrobacterium into the genus Rhizobium. We present evidence from classical and molecular comparisons that supports the conclusion that the biovar 1 and biovar 3 agrobacteria are sufficiently different from members of the genus Rhizobium to warrant retention of the genus Agrobacterium. The biovar 2 agrobacteria cluster more closely to the genus Rhizobium, but some studies suggest that these isolates differ from species of Rhizobium with respect to their capacity to interact with plants. We conclude that there is little scientific support for the proposal to group the agrobacteria into the genus Rhizobium and consequently recommend retention of the genus Agrobacterium.
-
-
-
Classification and nomenclature of Agrobacterium and Rhizobium – a reply to Farrand et al. (2003)
More LessFarrand et al. [Int J Syst Evol Microbiol 53 (2003), 1681–1687] have presented a critique of the proposal of Young et al. [Int J Syst Evol Microbiol 51 (2001), 89–103] to revise the nomenclature and classification of Rhizobium. They argued that Young et al. (2001) are mistaken in their reclassification of all Agrobacterium species within Rhizobium, and that the resulting nomenclatural revision is ‘unnecessary and unwarranted’. These objections arise because the authors appear not to understand the role of formal nomenclature, and fail to distinguish between formal and special-purpose nomenclatures (Bacteriological Code, 1990 Revision). The arguments set out by Farrand et al. (2003) can be addressed in terms of (1) the taxonomic status of the genera Agrobacterium and Rhizobium; (2) the status of species and biovars and their nomenclature; and (3) the role of transmissible genomic elements in classification and nomenclature. Finally, an attempt is made to unravel the confusion underpinning their discussion with a consideration of the relationship between formal and special-purpose nomenclatures.
-
-
-
Taxonomic problems arising in the genera Haloterrigena and Natrinema
More LessData currently available on members of the genera Haloterrigena and Natrinema suggest that some strains of the species Haloterrigena turkmenica that have been shown by DNA–DNA hybridization to belong to this species show a high degree of 16S rDNA sequence similarity to members of the genus Natrinema. However, closer examination of the data presented in the original publications and in subsequent publications suggests that there may be a number of problems associated with some of the published data.
-
-
-
The nomenclatural type of the genus Deleya and the consequences of Deleya aesta and Alcaligenes aquamarinus being synonyms
More LessThe genus Deleya was created to encompass a number of marine organisms that had previously been classified in diverse genera. Deleya aesta was designated as the type species of the genus. Subsequent work indicated that Deleya aesta, Alcaligenes aquamarinus and Alcaligenes faecalis subsp. homari were heterotypic synonyms. Consequently, Akagawa & Yamasato (Int J Syst Bacteriol 39, 462–466, 1989) concluded that, based on Rules 23a and 51b of the Bacteriological Code (1975 Revision), the oldest legitimate species epithet was aquamarinus and the type species of the genus Deleya should therefore be changed to Deleya aquamarina. Dobson & Franzmann (Int J Syst Bacteriol 46, 550–558, 1996) concluded that it was not possible to distinguish between members of the genus Deleya and members of the genus Halomonas Vreeland et al. 1980 , leading them to transfer members of the genus Deleya to the genus Halomonas and resulting in the creation of a new combination, Halomonas aquamarina. Closer examination of some of these changes indicates that they are not all in accordance with the Rules of the Bacteriological Code (1975 or 1990 Revisions).
-
Volumes and issues
-
Volume 74 (2024)
-
Volume 73 (2023)
-
Volume 72 (2022 - 2023)
-
Volume 71 (2020 - 2021)
-
Volume 70 (2020)
-
Volume 69 (2019)
-
Volume 68 (2018)
-
Volume 67 (2017)
-
Volume 66 (2016)
-
Volume 65 (2015)
-
Volume 64 (2014)
-
Volume 63 (2013)
-
Volume 62 (2012)
-
Volume 61 (2011)
-
Volume 60 (2010)
-
Volume 59 (2009)
-
Volume 58 (2008)
-
Volume 57 (2007)
-
Volume 56 (2006)
-
Volume 55 (2005)
-
Volume 54 (2004)
-
Volume 53 (2003)
-
Volume 52 (2002)
-
Volume 51 (2001)
-
Volume 50 (2000)
-
Volume 49 (1999)
-
Volume 48 (1998)
-
Volume 47 (1997)
-
Volume 46 (1996)
-
Volume 45 (1995)
-
Volume 44 (1994)
-
Volume 43 (1993)
-
Volume 42 (1992)
-
Volume 41 (1991)
-
Volume 40 (1990)
-
Volume 39 (1989)
-
Volume 38 (1988)
-
Volume 37 (1987)
-
Volume 36 (1986)
-
Volume 35 (1985)
-
Volume 34 (1984)
-
Volume 33 (1983)
-
Volume 32 (1982)
-
Volume 31 (1981)
-
Volume 30 (1980)
-
Volume 29 (1979)
-
Volume 28 (1978)
-
Volume 27 (1977)
-
Volume 26 (1976)
-
Volume 25 (1975)
-
Volume 24 (1974)
-
Volume 23 (1973)
-
Volume 22 (1972)
-
Volume 21 (1971)
-
Volume 20 (1970)
-
Volume 19 (1969)
-
Volume 18 (1968)
-
Volume 17 (1967)
-
Volume 16 (1966)
-
Volume 15 (1965)
-
Volume 14 (1964)
-
Volume 13 (1963)
-
Volume 12 (1962)
-
Volume 11 (1961)
-
Volume 10 (1960)
-
Volume 9 (1959)
-
Volume 8 (1958)
-
Volume 7 (1957)
-
Volume 6 (1956)
-
Volume 5 (1955)
-
Volume 4 (1954)
-
Volume 3 (1953)
-
Volume 2 (1952)
-
Volume 1 (1951)