- Volume 54, Issue 3, 2004
Volume 54, Issue 3, 2004
- Validation List No. 97
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Validation of publication of new names and new combinations previously effectively published outside the IJSEM
The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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- Notification List
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Notification that new names and new combinations have appeared in volume 54, part 1, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles).
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- New Taxa
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- Archaea
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Methanobacterium aarhusense sp. nov., a novel methanogen isolated from a marine sediment (Aarhus Bay, Denmark)
More LessStrain H2-LRT, a 5–18 μm long and 0·7 μm wide filamentous, mesophilic, moderately halophilic, non-motile hydrogenotrophic methanogen, was isolated from marine sediment of Aarhus Bay, Denmark, 1·7 m below the sediment surface. On the basis of 16S rRNA gene comparison with sequences of known methanogens, strain H2-LRT could be affiliated to the genus Methanobacterium. The strain forms a distinct line of descent within this genus, with Methanobacterium oryzae (95·9 % sequence identity) and Methanobacterium bryantii (95·7 % sequence identity) as its closest relatives. The 16S rRNA-based affiliation was supported by comparison of the mcrA gene, which encodes the α-subunit of methyl-coenzyme M reductase. Strain H2-LRT grew only on H2/CO2. The DNA G+C content is 34·9 mol%. Optimum growth temperature was 45 °C. The strain grew equally well at pH 7·5 and 8. No growth or methane production was observed below pH 5 or above pH 9. Strain H2-LRT grew well within an NaCl concentration range of 100 and 900 mM. No growth or methane production was observed at 1 M NaCl. At 50 mM NaCl, growth and methane production were reduced. Based on 16S rRNA gene sequence analysis, the isolate is proposed to represent a novel taxon within the genus Methanobacterium, namely Methanobacterium aarhusense sp. nov. The type strain is H2-LRT (=DSM 15219T=ATCC BAA-828T).
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- Other Bacteria
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Kordia algicida gen. nov., sp. nov., an algicidal bacterium isolated from red tide
More LessA bacterium (named OT-1T) that showed algicidal activity was isolated from sea water of Masan Bay, Korea, during an outbreak of red tide. Phylogenetic analysis based on 16S rDNA sequences showed that the isolate formed a distinct phyletic lineage within the family Flavobacteriaceae of the Cytophaga–Flavobacterium–Bacteroides group. No species with a validly published name showed ⩾93 % 16S rRNA gene sequence similarity to strain OT-1T. The isolate had major amounts of iso-branched and 3-hydroxy iso-branched fatty acids and menaquinone 6 and a DNA G+C content of 34 mol%; these chemotaxonomic characters also supported the placement of the organism in the family Flavobacteriaceae. The strain was Gram-negative, yellow-pigmented, non-motile, non-gliding, flexirubin-negative, strictly aerobic, catalase-negative, oxidase-positive and halophilic. Na+, Ca2+ and Mg2+ ions were obligately required for growth. The strain utilized various sugars as sole carbon sources and degraded gelatin, skimmed milk and starch. Several phenotypic characters can be used to differentiate the test strain from phylogenetically related marine bacterial genera. On the basis of polyphasic evidence, it is proposed that strain OT-1T should be assigned to the family Flavobacteriaceae as Kordia algicida gen. nov., sp. nov. The type strain is OT-1T (=KCTC 8814PT=NBRC 1000336T).
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Phylogeny of the ring-forming bacterium Arcicella aquatica gen. nov., sp. nov. (ex Nikitin et al. 1994), from a freshwater neuston biofilm
More LessArcicella aquatica NO-502T, obtained from a neuston film on a freshwater lake and belonging to the phylum Bacteroidetes, is characterized by ring-forming cells. The bacterium is a strict aerobe, with optimal growth between 28 and 30 °C. Carbohydrates, but no organic acids or amino acids, are used as substrates. The G+C content of strain NO-502T is 34·5 mol%; its genome size is 2·9×109 Da. The genus Arcicella and its type species Arcicella aquatica (type strain NO-502T=LMG 21963T=CIP 107990T) are proposed, and descriptions of this genus and species are given.
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Formosa algae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae
Four light-yellow-pigmented, Gram-negative, short-rod-shaped, non-motile isolates were obtained from enrichment culture during degradation of the thallus of the brown alga Fucus evanescens. The isolates studied were chemo-organotrophic, alkalitolerant and mesophilic. Polar lipids were analysed and phosphatidylethanolamine was the only phospholipid identified. The predominant cellular fatty acids were 15 : 0, i15 : 0, ai15 : 0, i15 : 1 and 15 : 1(n-6). The DNA G+C contents of the four strains were 34·0–34·4 mol%. The level of DNA relatedness of the four isolates was conspecific (88–98 %), indicating that they belong to the same species. The 16S rDNA sequence of strain KMM 3553T was determined. Phylogenetic analysis revealed that KMM 3553T formed a distinct phyletic line in the phylum Bacteroidetes, class Flavobacteria in the family Flavobacteriaceae and that, phylogenetically, this strain could be placed almost equidistant from the genera Gelidibacter and Psychroserpens (16S rRNA gene sequence similarities of 94 %). On the basis of significant differences in phenotypic and chemotaxonomic characteristics, it is suggested that the isolates represent a novel species in a new genus; the name Formosa algae gen. nov., sp. nov. is proposed. The type strain is KMM 3553T (=CIP 107684T).
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Prevotella shahii sp. nov. and Prevotella salivae sp. nov., isolated from the human oral cavity
More LessTwo bacterial strains, EHS11T and EPSA11T, which were isolated from the human oral cavity, were characterized in terms of phenotypic and biochemical characteristics, cellular fatty acid profiles and phylogenetic position based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that each of the isolates belonged to a novel species of the genus Prevotella. Strain EHS11T was related to Prevotella loescheii (about 95 % similarity), whereas strain EPSA11T was related to Prevotella oris (about 94 % similarity). Both strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. The cellular fatty acid composition of strain EPSA11T was very similar to that of P. oris JCM 8540T. On the other hand, the cellular fatty acid composition of strain EHS11T was significantly different from those of other Prevotella species. The predominant fatty acids in strain EHS11T are C18 : 1 ω9c, C16 : 0 and C16 : 0 3-OH, whereas other Prevotella species, except for P. loescheii JCM 8530T, possess anteiso-C15 : 0, iso-C17 : 0 3-OH and C18 : 1 ω9c. The predominant fatty acids in P. loescheii JCM 8530T are anteiso-C15 : 0, C16 : 0 and C18 : 1 ω9c. DNA–DNA hybridization experiments revealed a genomic distinction of strains EHS11T and EPSA11T from P. loescheii JCM 8530T and P. oris JCM 8540T. On the basis of these data, two novel Prevotella species are proposed: Prevotella shahii sp. nov. and Prevotella salivae sp. nov. The type strains of P. shahii and P. salivae are EHS11T (=JCM 12083T=DSM 15611T) and EPSA11T (=JCM 12084T=DSM 15606T), respectively.
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Psychroflexus tropicus sp. nov., an obligately halophilic Cytophaga–Flavobacterium–Bacteroides group bacterium from an Hawaiian hypersaline lake
More LessA Gram-negative bacterium designated LA1T was isolated from water collected in hypersaline Lake Laysan on Laysan Island in the Northwestern Hawaiian Islands. Cells occurred singly as fine rods to short filaments. Growth in 50 % strength marine broth occurred optimally when the medium contained 7·5–10 % (w/v) NaCl. The major fatty acids in LA1T grown at 15 and 30 °C were 12-methyl tetradecanoic acid and 13-methyl tetradecanoic acid, respectively. The nucleotide sequence of the 16S rRNA gene showed that LA1T belonged in the Cytophaga–Flavobacterium–Bacteroides (CFB) group in the domain Bacteria. The closest described neighbour in terms of 16S rRNA gene sequence identity was Psychroflexus torquis ACAM 623T (94·4 % over 1423 bases), an obligate psychrophile from Antarctic sea-ice. The G+C content of 35·0 mol% was consistent with this affiliation. Phenotypic and genotypic analyses, including DNA hybridization, indicated that LA1T could be assigned to the genus Psychroflexus but, based on significant differences, including growth at 43 °C, it constitutes a novel species, Psychroflexus tropicus sp. nov., for which LA1T (=ATCC BAA-734T=DSM 15496T) is the type strain.
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Propionispora hippei sp. nov., a novel Gram-negative, spore-forming anaerobe that produces propionic acid
More LessA Gram-negative, spore-forming anaerobe, KST, was isolated from an enrichment culture that was set up for anaerobic degradation of the aliphatic polyester poly(propylene adipate). The strain had the cellular organization of Sporomusa, vibrio-shaped cells and terminal round spores, and fermented sugars and sugar alcohols to propionic and acetic acid. Based on the morphological and physiological features as well as on a 16S rRNA gene similarity of 98 %, it was grouped with Propionispora vibrioides. A relatively low DNA–DNA hybridization value with the type strain of this species (47 %), and differences in substrate utilization and spore morphology, suggested that the strain should be classified in a separate species, Propionispora hippei sp. nov., with KST as the type strain (=DSM 15287T=ATCC BAA-665T).
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Characterization of a ‘Bacteroidetes’ symbiont in Encarsia wasps (Hymenoptera: Aphelinidae): proposal of ‘Candidatus Cardinium hertigii’
More LessPreviously, analysis of 16S rDNA sequences placed a newly discovered lineage of bacterial symbionts of arthropods in the ‘Bacteroidetes’. This symbiont lineage is associated with a number of diverse host reproductive manipulations, including induction of parthenogenesis in several Encarsia parasitoid wasps (Hymenoptera: Aphelinidae). In this study, electron microscopy and phylogenetic analysis of the 16S rRNA and gyrB genes of symbionts from Encarsia hispida and Encarsia pergandiella are used to describe and further characterize these bacteria. Phylogenetic analyses based on these two genes showed that the Encarsia symbionts are allied with the Cytophaga aurantiaca lineage within the ‘Bacteroidetes’, with their closest described relative being the acanthamoeba symbiont ‘Candidatus Amoebophilus asiaticus’. The Encarsia symbionts share 97 % 16S rDNA sequence similarity with Brevipalpus mite and Ixodes tick symbionts and 88 % sequence similarity with ‘Candidatus A. asiaticus’. Electron microscopy revealed that many of the bacteria found in the ovaries of the two Encarsia species contained a regular, brush-like array of microfilament-like structures that appear to be characteristic of the symbiont. Finally, the role of this bacterium in parthenogenesis induction in E. hispida was confirmed. Based on phylogenetic analyses and electron microscopy, classification of the symbionts from Encarsia as ‘Candidatus Cardinium hertigii’ is proposed.
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- Proteobacteria
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Petrobacter succinatimandens gen. nov., sp. nov., a moderately thermophilic, nitrate-reducing bacterium isolated from an Australian oil well
A novel Gram-negative, aerobic and moderately thermophilic bacterium, strain 4BONT, was isolated from a non-water-flooded Australian terrestrial oil reservoir. Cells were non-spore-forming straight rods, which were motile by means of a polar flagellum. The optimum growth conditions were 55 °C, pH 6·9 and 0·5 % NaCl. Strain 4BONT was oxidase- and catalase-positive; it grew on fumarate, pyruvate, succinate, formate, ethanol and yeast extract in the presence of oxygen or nitrate as terminal electron acceptor. Nitrate was reduced to nitrous oxide. The DNA G+C content of the strain was 58·6 mol%. The closest phylogenetic relative of strain 4BONT was Hydrogenophilus thermoluteolus (similarity of 91·8 %), of the β-Proteobacteria. As strain 4BONT is physiologically and phylogenetically different from H. thermoluteolus, it is proposed that it be assigned to a novel species of a novel genus, Petrobacter succinatimandens gen. nov., sp. nov. The type strain is 4BONT (=DSM 15512T=CIP 107790T).
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Phylogenetic relationships of the genera Stella, Labrys and Angulomicrobium within the ‘Alphaproteobacteria’ and description of Angulomicrobium amanitiforme sp. nov.
More LessThe unusually shaped bacteria of the genera Stella, Labrys and Angulomicrobium have been described based on their cell morphology and biochemistry. However, their phylogenetic relationships remain unresolved. An earlier study that was based on 5S rRNA gene sequences placed the genus Stella within the ‘Alphaproteobacteria’. In the present report, polar lipids and 16S rRNA genes of the type strains of the two species in the genus Stella, Stella humosa DSM 5900T and Stella vacuolata DSM 5901T, are studied, as well as the type strains of the monospecific genera Labrys (Labrys monachus VKM B-1479T) and Angulomicrobium (Angulomicrobium tetraedrale DSM 5895T). It was found that the genus Stella belongs to the order Rhodospirillales in the family Rhodospirillaceae, and not to the Acetobacteraceae. Whilst the position of the genus Angulomicrobium in the family Hyphomicrobiaceae was confirmed, the genus Labrys could not be placed into any known family, but was adjacent to the family ‘Beijerinckiaceae’. In addition, data were obtained for strain VKM B-1336, which was shown not to belong to the genus Angulomicrobium, and strain NCIMB 1785T (=DSM 15561T), for which the name Angulomicrobium amanitiforme sp. nov. is proposed.
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Reinekea marinisedimentorum gen. nov., sp. nov., a novel gammaproteobacterium from marine coastal sediments
More LessA Gram-negative, oxidase- and catalase-positive, rod-shaped bacterium, designated strain KMM 3655T, was isolated from a coastal marine sediment sample. The novel bacterium required sodium ions for growth and grew between 0·5 and 5 % NaCl and at 4–37 °C, but not at 40 °C. It reduced nitrate, formed acids from glucose under aerobic and anaerobic conditions, utilized a limited spectrum of organic substrates and did not produce gelatinase, caseinase, amylase or chitinase. The major isoprenoid quinone was Q8. Polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and an unknown phospholipid. Fatty acid analysis of strain KMM 3655T revealed C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c as predominant components. The G+C content of the DNA was 51·1 mol%. Phylogenetic analysis of the 16S rDNA sequence placed the new isolate within the γ-Proteobacteria as a separate deep branch, with about 90 % sequence similarity to representatives of the genus Oceanospirillum and other remotely related genera. Combined phylogenetic and physiological data show that the new marine sediment isolate, KMM 3655T, represents a novel genus and species, for which the name Reinekea marinisedimentorum gen. nov., sp. nov. is proposed. The type strain is KMM 3655T (=DSM 15388T).
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Proposal to accommodate Burkholderia cepacia genomovar VI as Burkholderia dolosa sp. nov.
More LessPhenotypic and genotypic studies revealed new tools for differentiating Burkholderia cepacia genomovar VI from Burkholderia multivorans and other B. cepacia-complex species. Hence, the name Burkholderia dolosa sp. nov. is proposed, with LMG 18943T (=CCUG 47727T) as the type strain. B. dolosa can be differentiated from other B. cepacia-complex bacteria by its inability to assimilate tryptamine, azelaic acid and salicin and by its failure to grow on the B. cepacia-selective medium PCAT. Both 16S rDNA and recA RFLP analysis revealed unique B. dolosa restriction patterns. In addition, new 16S rDNA- and recA-based PCR assays allowed its specific identification.
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Agarivorans albus gen. nov., sp. nov., a γ-proteobacterium isolated from marine animals
More LessSix bacterial strains were isolated from healthy marine organisms that were collected from the coast of the Kanto area in Japan. Phylogenetic analysis based on 16S rDNA sequence similarity showed that the six isolates formed a separate cluster in the γ-Proteobacteria and were related to the genera Alteromonas and Glaciecola (<91·6 % similarity). The isolates were related closely to each other (DNA–DNA reassociation values of 74–93 %). The isolates had a polar flagellum and were Gram-negative, mesophilic, strictly aerobic rods that required salt for growth. Distinct phenotypic features of this group included the ability to hydrolyse agar and white pigmentation of colonies. The DNA G+C content of the isolates was 48–50 mol%. The major quinone was Q-8. Phenotypic characteristics of the isolates differed from those of members of the genera Alteromonas and Glaciecola. The name Agarivorans albus gen. nov., sp. nov. is proposed for the six isolates; the type strain is MKT 106T (=IAM 14998T=LMG 21761T).
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Legionella drancourtii sp. nov., a strictly intracellular amoebal pathogen
A Legionella-like amoebal pathogen (LLAP), formerly named LLAP12T, was characterized on the basis of microscopic appearance, staining characteristics, growth in Acanthamoeba polyphaga at different temperatures, DNA G+C content, serological cross-reactivity and 16S rRNA and macrophage infectivity potentiator (mip) gene sequence analysis. LLAP12T was found to be a motile, Gram-negative bacterium that grew within cytoplasmic vacuoles in infected amoebae. The infecting bacteria induced lysis of their amoebal hosts and time taken to do so was dependent on incubation temperature. Recovery of LLAP12T from amoebae onto axenic media could not be achieved. Phylogenetic analysis of LLAP12T, based on 16S rRNA and mip gene sequence analysis, indicated that it lay within the radiation of the Legionellaceae and that it clustered specifically with Legionella lytica and Legionella rowbothamii. The divergence observed between LLAP12T and these two species was of a degree equal to, or greater than, that observed between other members of the family. In support of this delineation, LLAP12T was found not to cross-react serologically with any other Legionella species. The mip and 16S rRNA gene sequence-based analyses also indicated that LLAP12T was related very closely to two other previously identified LLAP isolates, LLAP4 and LLAP11. Taken together, these results support the proposal of LLAP12T as the type strain of Legionella drancourtii sp. nov.
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Psychrophilic pseudomonads from Antarctica: Pseudomonas antarctica sp. nov., Pseudomonas meridiana sp. nov. and Pseudomonas proteolytica sp. nov.
More LessThirty-one bacteria that belonged to the genus Pseudomonas were isolated from cyanobacterial mat samples that were collected from various water bodies in Antarctica. All 31 isolates were psychrophilic; they could be divided into three groups, based on their protein profiles. Representative strains of each of the three groups, namely CMS 35T, CMS 38T and CMS 64T, were studied in detail. Based on 16S rRNA gene sequence analysis, it was established that the strains were related closely to the Pseudomonas fluorescens group. Phenotypic and chemotaxonomic characteristics further confirmed their affiliation to this group. The three strains could also be differentiated from each other and the closely related species Pseudomonas orientalis, Pseudomonas brenneri and Pseudomonas migulae, based on phenotypic and chemotaxonomic characteristics and the level of DNA–DNA hybridization. Therefore, it is proposed that strains CMS 35T (=MTCC 4992T=DSM 15318T), CMS 38T (=MTCC 4993T=DSM 15319T) and CMS 64T (=MTCC 4994T=DSM 15321T) should be assigned to novel species of the genus Pseudomonas as Pseudomonas antarctica sp. nov., Pseudomonas meridiana sp. nov. and Pseudomonas proteolytica sp. nov., respectively.
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Halomonas boliviensis sp. nov., an alkalitolerant, moderate halophile isolated from soil around a Bolivian hypersaline lake
More LessHalomonas boliviensis sp. nov. is proposed for two moderately halophilic, psychrophilic, alkalitolerant bacteria, LC1T (=DSM 15516T=ATCC BAA-759T) and LC2 (=DSM 15517=ATCC BAA-760), both of which were isolated from a soil sample around the lake Laguna Colorada, located at 4300 m above sea level in the south-west region of Bolivia. The bacteria are aerobic, motile, Gram-negative rods that produce colonies with a cream pigment. Moreover, they are heterotrophs that are able to utilize various carbohydrates as carbon sources. The organisms reduce nitrate and show tryptophan deaminase activity. The genomic DNA G+C contents were 51·4 mol% for isolate LC1T and 52·6 mol% for isolate LC2. Based on 16S rDNA sequence analysis, isolates LC1T and LC2 were identified as members of the genus Halomonas and clustered closely with Halomonas variabilis DSM 3051T and Halomonas meridiana DSM 5425T. However, DNA–DNA relatedness between the new isolates and the closest related Halomonas species was low.
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Halomonas ventosae sp. nov., a moderately halophilic, denitrifying, exopolysaccharide-producing bacterium
More LessHalomonas ventosae sp, nov. includes three moderately halophilic, exopolysaccharide-producing strains isolated from saline soils in Jaén (south-eastern Spain). These strains can grow anaerobically using either nitrate or nitrite as terminal electron acceptor and hydrolyse both tyrosine and phenylalanine. Their G+C content varies between 72·6 and 74·3 mol%. The affiliation of the isolates with the genus Halomonas was confirmed by 16S rRNA gene sequence comparison. DNA–DNA hybridization shows 70·4–82·7 % relatedness among the three strains. Nevertheless, their relatedness is less than 43 % compared to related reference strains. The proposed type strain for Halomonas ventosae is strain Al12T (=CECT 5797T=DSM 15911T). It grows best at 8 % (w/v) sea salts and requires the presence of Na+. Its major fatty acids are 18 : 1 ω7c, 16 : 0, 16 : 1 ω7c, and 15 : 0 iso 2-OH. The predominant respiratory lipoquinone found in strain Al12T is ubiquinone with nine isoprene units (Q-9).
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Reclassification of Bisgaard taxon 33, with proposal of Volucribacter psittacicida gen. nov., sp. nov. and Volucribacter amazonae sp. nov. as new members of the Pasteurellaceae
More LessA total of 25 strains isolated from parrots, budgerigars, parakeets (Psittaciformes) and a chicken, mostly associated with respiratory disease or septicaemia, were classified as a new genus, Volucribacter gen. nov., within the family Pasteurellaceae, on the basis on unique phenotypic characteristics and clear monophyly as determined by 16S rRNA gene sequence comparison. Comparison of 16S rRNA gene sequences from six strains showed at least 98·8 % similarity and the closest similarity outside the genus was found to Bisgaard taxon 34 and to Pasteurella avium, at 94·6 and 94·5 %, respectively. Phenotypes that separate the new genus from other genera of the Pasteurellaceae included at least two characters. The genus includes two species, Volucribacter psittacicida sp. nov. and Volucribacter amazonae sp. nov., corresponding to the two biovars previously outlined, underlining that most isolates have been obtained from psittacine birds. The two species can be separated by fermentation of meso-inositol, (−)-l-fucose, maltose and dextrin and a positive ONPG test. The type strains for Volucribacter psittacicida and Volucribacter amazonae are respectively Gerl. 236/81T (=CCUG 47536T=DSM 15534T) and 146/S8/89T (=CCUG 47537T=DSM 15535T).
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Sphingomonas yabuuchiae sp. nov. and Brevundimonas nasdae sp. nov., isolated from the Russian space laboratory Mir
On the basis of phenotypic and genotypic characteristics and 16S rRNA gene sequence analysis, novel species belonging to the genera Sphingomonas and Brevundimonas were identified from samples taken from the Russian space laboratory Mir. Strain A1-18T was isolated from the air. 16S rDNA sequence analysis showed that strain A1-18T formed a coherent cluster with Sphingomonas sanguinis, Sphingomonas parapaucimobilis, Sphingomonas paucimobilis and Sphingomonas roseiflava with sequence similarity of 97·5–98·6 %. Similar to other Sphingomonas species, the G+C content was 66·1 mol%, but DNA–DNA hybridization rates at optimal temperatures among these related species were only 24·7–51·7 %. Strain A1-18T can be differentiated biochemically from related species. Strain W1-2BT was isolated from condensation water. It forms a distinct lineage within the genus Brevundimonas, forming a coherent cluster with Brevundimonas vesicularis, Brevundimonas aurantiaca and Brevundimonas intermedia. 16S rDNA sequence similarities were 98·6–99·5 % and the G+C content was 66·5 mol%, similar to other Brevundimonas species, but DNA–DNA relatedness was only 50·2–54·8 %. Strain W1-2BT also showed some differential biochemical properties from its related species. A series of polyphasic taxonomic studies led to the proposal of two novel species, Sphingomonas yabuuchiae sp. nov. (type strain A1-18T=GTC 868T=JCM 11416T=DSM 14562T) and Brevundimonas nasdae sp. nov. (type strain W1-2BT=GTC 1043T=JCM 11415T=DSM 14572T).
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Vibrio gallicus sp. nov., isolated from the gut of the French abalone Haliotis tuberculata
Five alginolytic, facultatively anaerobic, non-motile bacteria were isolated from the gut of the abalone Haliotis tuberculata. Phylogenetic analyses based on 16S rDNA data indicated that these strains are related to Vibrio wodanis, Vibrio salmonicida, Vibrio logei and Vibrio fischeri (but with <97 % 16S rRNA gene sequence similarity). DNA–DNA hybridization and fluorescence amplified fragment length polymorphism fingerprinting demonstrated that the five strains constituted a single species that was different from all currently known vibrios. The name Vibrio gallicus sp. nov. (type strain, CIP 107863T=LMG 21878T=HT2-1T; DNA G+C content, 43·6–44·3 mol%) is proposed for this novel taxon. Several phenotypic features were disclosed that discriminated V. gallicus from other Vibrio species: V. gallicus can be differentiated from Vibrio halioticoli on the basis of four traits (β-galactosidase test and assimilation of three carbon compounds) and from Vibrio superstes by 16 traits.
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Pseudomonas lutea sp. nov., a novel phosphate-solubilizing bacterium isolated from the rhizosphere of grasses
A phosphate-solubilizing bacterial strain designated OK2T was isolated from rhizospheric soil of grasses growing spontaneously in a soil from Spain. Cells of the strain were Gram-negative, strictly aerobic, rod-shaped and motile. Phylogenetic analysis of the 16S rRNA gene indicated that this bacterium belongs to the γ-subclass of Proteobacteria within the genus Pseudomonas and that the closest related species is Pseudomonas graminis. The strain produced catalase but not oxidase. Cellulose, casein, starch, gelatin and urea were not hydrolysed. Aesculin was hydrolysed. Growth was observed with many carbohydrates as carbon sources. The main non-polar fatty acids detected were hexadecenoic acid (16 : 1), hexadecanoic acid (16 : 0) and octadecenoic acid (18 : 1). The hydroxy fatty acids detected were 3-hydroxydecanoic acid (3-OH 10 : 0), 3-hydroxydodecanoic acid (3-OH 12 : 0) and 2-hydroxydodecanoic acid (2-OH 12 : 0). The G+C DNA content determined was 59·3 mol%. DNA–DNA hybridization showed 48·7 % relatedness between strain OK2T and P. graminis DSM 11363T and 26·2 % with respect to Pseudomonas rhizosphaerae LMG 21640T. Therefore, these results indicate that strain OK2T (=LMG 21974T=CECT 5822T) belongs to a novel species of the genus Pseudomonas, and the name Pseudomonas lutea sp. nov. is proposed.
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Herbaspirillum chlorophenolicum sp. nov., a 4-chlorophenol-degrading bacterium
More LessA 4-chlorophenol-degrading bacterial strain, formerly designated as a strain of Comamonas testosteroni, was reclassified as a member of the genus Herbaspirillum based on its phenotypic and chemotaxonomic characteristics, as well as phylogenetic analysis using 16S rDNA sequences. Phylogenetic inference based on 16S rDNA sequences showed that strain CPW301T clusters in a phylogenetic branch that contains Herbaspirillum species. 16S rDNA sequence similarity of strain CPW301T to species of the genus Herbaspirillum with validly published names is in the range 98·7–98·9 %. Despite the considerably high 16S rDNA sequence similarity, strain CPW301T could be distinguished clearly from type strains of Herbaspirillum species with validly published names by DNA–DNA relatedness values, which were <15·7 %. The genomic DNA G+C content of strain CPW301T is 61·3 mol%. The predominant ubiquinone is Q-8 and the major cellular fatty acids are C16 : 0 and cyclo-C17 : 0. The strain does not fix nitrogen and is not plant-associated. It is an aerobic rod with one unipolar flagellum. On the basis of these characteristics, a novel Herbaspirillum species, Herbaspirillum chlorophenolicum sp. nov., is proposed. The type strain of the novel species is strain CPW301T (=KCTC 12096T=IAM 15024T).
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Collimonas fungivorans gen. nov., sp. nov., a chitinolytic soil bacterium with the ability to grow on living fungal hyphae
A polyphasic approach was used to describe the phylogenetic position of 22 chitinolytic bacterial isolates that were able to grow at the expense of intact, living hyphae of several soil fungi. These isolates, which were found in slightly acidic dune soils in the Netherlands, were strictly aerobic, Gram-negative rods. Cells grown in liquid cultures were flagellated and possessed pili. A wide range of sugars, alcohols, organic acids and amino acids could be metabolized, whereas several di- and trisaccharides could not be used as substrates. The major cellular fatty acids were C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. DNA G+C contents were 57–62 mol%. Analysis of nearly full-length 16S rDNA sequences showed that the isolates were related closely to each other (>98·6 % sequence similarity) and could be assigned to the β-Proteobacteria, family ‘Oxalobacteraceae’, order ‘Burkholderiales’. The most closely related species belonged to the genera Herbaspirillum and Janthinobacterium, exhibiting 95·9–96·7 % (Herbaspirillum species) and 94·3–95·6 % (Janthinobacterium species) 16S rDNA sequence similarity to the isolates. Several physiological and biochemical properties indicated that the isolates could be distinguished clearly from both of these genera. Therefore, it is proposed that the isolates described in this study are representatives of a novel genus, Collimonas gen. nov. Genomic fingerprinting (BOX-PCR), detailed analysis of 16S rDNA patterns and physiological characterization (Biolog) of the isolates revealed the existence of four subclusters. The name Collimonas fungivorans gen. nov., sp. nov. has been given to one subcluster (four isolates) that appears to be in the centre of the novel genus; isolates in the other subclusters have been tentatively named Collimonas sp. The type strain of Collimonas fungivorans gen. nov., sp. nov. is Ter6T (=NCCB 100033T=LMG 21973T).
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Emendation of the genus Acidomonas Urakami, Tamaoka, Suzuki and Komagata 1989
More LessThe genus Acidomonas and the species Acidomonas methanolica were recharacterized by using the type strain (NRIC 0498T), three reference strains and 10 methanol-utilizing bacteria that were isolated from activated sludge from three different sewage-treatment plants in Tokyo. Based on 16S rDNA sequences, all strains formed a single cluster within the Acetobacteraceae that was clearly different from the genera Acetobacter, Gluconobacter, Gluconacetobacter, Asaia and Kozakia. The 14 strains were identified as a single species, Acidomonas methanolica, by DNA–DNA similarities, showed DNA G+C contents that ranged from 62 to 63 mol% and had Q-10 as the major quinone, accounting for >87 % of total ubiquinones. Cells of Acidomonas methanolica had a single polar flagellum (or occasionally polar tuft flagella); this differs from a previous study that described peritrichous flagella. Oxidation of acetate was positive for all strains, but oxidation of lactate was weakly positive and varied with strains. Dihydroxyacetone was not produced from glycerol. Pantothenic acid was an essential requirement for growth. The strains tested grew at mostly the same extent at pH 3·0–8·0. Therefore, Acidomonas methanolica should be regarded as acidotolerant, not acidophilic. The descriptions of the genus Acidomonas and the species Acidomonas methanolica Urakami, Tamaoka, Suzuki and Komagata 1989 are emended with newly obtained data.
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Catellibacterium nectariphilum gen. nov., sp. nov., which requires a diffusible compound from a strain related to the genus Sphingomonas for vigorous growth
A bacterial strain, designated AST4T, was isolated from activated sludge. The bacterium did not show significant growth on nutrient broth, but growth was clearly stimulated by addition of supernatant from other bacterial cultures. Culture filtrate of a strain related to the genus Sphingomonas in particular increased the cell yield and growth rate of strain AST4T. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain AST4T is located within the ‘Rhodobacter group’ in the α-3 subclass of Proteobacteria, but is clearly distant from related genera in this group such as Paracoccus, Rhodobacter and Rhodovulum. Strain AST4T is a Gram-negative, non-motile, rod-shaped (0·6–0·8×1·3–2·0 μm) and aerobic bacterium. It was not able to reduce nitrate to nitrite or N2. No phototrophic growth was observed. Optimal growth occurred at 30 °C and pH 6·5–7·5. The dominant cellular fatty acid in the isolate was C18 : 1 cis11. Ubiquinone-10 was the major respiratory quinone. The G+C content was 64·5 mol% (by HPLC). Based on the phylogenetic and phenotypic traits, the name Catellibacterium nectariphilum gen. nov., sp. nov. is proposed for this isolate; the type strain is AST4T (=NBRC 100046T=JCM 11959T=DSM 15620T).
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- Gram-Positive Bacteria
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Mycobacterium saskatchewanense sp. nov., a novel slowly growing scotochromogenic species from human clinical isolates related to Mycobacterium interjectum and Accuprobe-positive for Mycobacterium avium complex
A pigmented, slowly growing Mycobacterium avium complex AccuProbe-positive organism was isolated from the sputum and pleural fluid of a 72-year-old female with bronchiectasis. The unusual morphology of the organism prompted further identification by 16S rRNA gene sequencing, revealing a perfect identity with previously uncharacterized strain Mycobacterium sp. MCRO 8 (GenBank accession no. X93034), with the closest established species by 16S rDNA analysis being Mycobacterium interjectum. HPLC of the organism corresponded to previously obtained patterns identified as M. interjectum-like and, upon sequence evaluation of a selection of strains with a similar profile, more were subsequently identified as MCRO 8. A total of 16 strains isolated from human respiratory samples were evaluated in the characterization of this novel species, for which the name Mycobacterium saskatchewanense sp. nov. is proposed. The type strain is strain 00-250T (=ATCC BAA-544T=DSM 44616T=CIP 108114T).
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Reclassification of Cellulosimicrobium variabile Bakalidou et al. 2002 as Isoptericola variabilis gen. nov., comb. nov.
More LessAs already depicted in the original publication, the type strain of the species Cellulosimicrobium variabile Bakalidou et al. 2002 , DSM 10177T, does not cluster unambiguously with the type species, Cellulosimicrobium cellulans DSM 43879T, in phylogenetic analysis. Strain DSM 10177T is moderately related to the recently described species Xylanimonas cellulosilytica, Promicromonospora pachnodae and Xylanibacterium ulmi, forming a lineage that branches between C. cellulans and members of the genus Promicromonospora in most dendrograms generated on the basis of different algorithms and reference strains. The type strains of the two Cellulosimicrobium species resemble each other in morphology, composition of fatty acids, DNA G+C content, phospholipids and the presence of lysine in position 3 of the peptide subunit of peptidoglycan. However, the two strains differ from each other in cell-wall sugars and in the amino acid composition of the A4α-type peptidoglycan, which contains serine and aspartic acid in C. cellulans, whereas only aspartic acid is present in the interpeptide bridge of C. variabile. This type is also present in Xylanimonas cellulosilytica XIL07T, but not in the neighbouring species P. pachnodae DSM 12657T, which exhibits the l-lys–l-ser–d-Glu type. On the basis of distinct phylogenetic position and the amino acid composition of peptidoglycan, a novel genus and combination for C. variabile, Isoptericola variabilis gen. nov., comb. nov., is proposed.
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Streptomyces hebeiensis sp. nov.
More LessA novel actinomycete strain, YIM 001T, was isolated from a soil sample collected from Hebei province, People's Republic of China. The strain was characterized by white to grey aerial mycelium. Long spore chains, borne on the aerial mycelium, were straight to Rectiflexibiles; the spore chains were composed of non-motile and coccoid spores with a warty surface. The cell wall of strain YIM 001T contained ll-diaminopimelic acid (A2pm) and traces of meso-A2pm. Whole-cell hydrolysates contained mainly glucose and small amounts of xylose, galactose and arabinose. The menaquinones were MK-9(H4) (4·6 %), MK-9(H6) (60 %), MK-9(H8) (30·7 %) and MK-9(H10) (4·7 %). Phosphatidylethanolamine was the diagnostic phospholipid. The DNA G+C content of strain YIM 001T was 71·4 mol%. Phylogenetic analysis indicated that strain YIM 001T belongs to the genus Streptomyces. Based on its phenotypic and genotypic characteristics, strain YIM 001T (=CCTCC AA 203005T=CIP 107974T=DSM 41837T) is proposed as the type strain of a novel species, Streptomyces hebeiensis sp. nov.
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Anaerobranca californiensis sp. nov., an anaerobic, alkalithermophilic, fermentative bacterium isolated from a hot spring on Mono Lake
A novel, obligately anaerobic, alkalithermophilic, chemo-organotrophic bacterium was isolated from the sediment of an alkaline hot spring located on Paoha Island in Mono Lake, California, USA. This rod-shaped bacterium was motile via peritrichous flagella. Isolated strains grew optimally in 5–25 g NaCl l−1, at pH 9·0–9·5 and at a temperature of 58°C and were fermentative and mainly proteolytic, utilizing peptone, Casamino acids and yeast extract. Optimal growth was seen in the presence of elemental sulfur, polysulfide or thiosulfate with concomitant reduction to hydrogen sulfide. Sulfite was also formed in an equal ratio to sulfide during reduction of thiosulfate. The novel isolate could also reduce Fe(III) and Se(IV) in the presence of organic matter. On the basis of physiological properties, 16S rRNA gene sequence and DNA–DNA hybridization data, strain PAOHA-1T (=DSM 14826T=UNIQEM 227T) belongs to the genus Anaerobranca and represents a novel species, Anaerobranca californiensis sp. nov.
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Jeotgalicoccus pinnipedialis sp. nov., from a southern elephant seal (Mirounga leonina)
More LessA previously unknown Gram-positive, catalase-positive, facultatively anaerobic, non-spore-forming, coccus-shaped bacterium (A/G14/99/10T), originating from the mouth of a female southern elephant seal, was subjected to a taxonomic analysis. Comparative 16S rRNA gene-sequencing showed that the organism formed a hitherto unknown subline within the catalase-positive, low-G+C, Gram-positive cocci, exhibiting a specific association with species of the genus Jeotgalicoccus. Sequence divergence values of approximately 7 %, together with phenotypic differences, showed the unknown bacterium to be distinct from the two described species of this genus, Jeotgalicoccus halotolerans and Jeotgalicoccus psychrophilus. Based on phenotypic and phylogenetic considerations, it is proposed that strain A/G14/99/10T=CCUG 42722T=CIP 107946T from the mouth of a seal be classified as the type strain of a novel species of the genus Jeotgalicoccus, Jeotgalicoccus pinnipedialis sp. nov.
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Pseudonocardia benzenivorans sp. nov.
More LessA Gram-positive, rod-shaped, non-spore-forming bacterium (B5T) was isolated from an enrichment culture that contained 1,2,3,5-tetrachlorobenzene as the sole source of carbon. On the basis of 16S rRNA gene sequence similarity studies, strain B5T was shown to belong to the family Pseudonocardiaceae and was related most closely to Pseudonocardia sulfidoxydans (98·8 %) and Pseudonocardia hydrocarbonoxydans (98·3 %). 16S rRNA gene sequence similarity to other Pseudonocardia species was <97 %. Chemotaxonomic data [major menaquinone, MK-8(H4); major polar lipids, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol; major fatty acids, C16 : 0, iso-C16 : 0 and iso-C15 : 0] supported the affiliation of strain B5T to the genus Pseudonocardia. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain B5T from P. sulfidoxydans and P. hydrocarbonoxydans. Strain B5T therefore represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia benzenivorans sp. nov. is proposed, with the type strain B5T (=DSM 44703T=CIP 107928T).
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Arthrobacter nitroguajacolicus sp. nov., a novel 4-nitroguaiacol-degrading actinobacterium
Three bacterial isolates from soil, capable of degradation or transformation of nitroaromatic compounds and displaying a rod–coccus growth cycle, were studied by a polyphasic approach. On the basis of 16S rRNA sequence analysis and of chemotaxonomic characteristics, such as type A3α peptidoglycan with an interpeptide bridge Ala–Thr–Ala, the major menaquinone MK-9(H2) and fatty acid composition, the isolates were assigned to the genus Arthrobacter. DNA–DNA hybridization, riboprinting and phenotypic studies revealed that the three strains constitute a single species, distinct from phylogenetically neighbouring Arthrobacter aurescens and Arthrobacter ilicis. A novel species, Arthrobacter nitroguajacolicus sp. nov., with the type strain G2-1T (=CCM 4924T=DSM 15232T) is proposed.
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Corynebacterium halotolerans sp. nov., isolated from saline soil in the west of China
A halotolerant, non-spore-forming actinobacterium was isolated from a soil sample from the west of China. The strain, designated YIM 70093T (=CCTCC AA 001024T=DSM 44683T), comprised Gram-positive, non-motile, diphtheroid and irregular rods. It grew in 0–25 % KCl (KCl could be substituted by NaCl or MgCl2.6H2O), with optimum growth at 10 % KCl, and its optimal pH and cultivation temperature were 7·2 and 28 °C, respectively. On the basis of its morphological, physiological and phylogenetic characteristics, strain YIM 70093T should be classified in the genus Corynebacterium. However, it is sufficiently different from hitherto described Corynebacterium species to be considered as a novel species, for which the name Corynebacterium halotolerans sp. nov. is proposed.
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Gulosibacter molinativorax gen. nov., sp. nov., a molinate-degrading bacterium, and classification of ‘Brevibacterium helvolum’ DSM 20419 as Pseudoclavibacter helvolus gen. nov., sp. nov.
More LessA Gram-positive, molinate-degrading bacterium, strain ON4T (=DSM 13485T=LMG 21909T), was isolated from a mixed bacterial culture able to mineralize the herbicide molinate. The strain was strictly aerobic, oxidase- and catalase-positive and non-acid-fast, with a growth temperature of 10–41 °C. It contained the major menaquinone MK-9 and a cell-wall peptidoglycan based on d-ornithine. 16S rDNA sequence analysis revealed that the strain formed a distinct line of descent in the family Microbacteriaceae, showing the highest 16S rDNA similarity (∼95 %) to members of the genus Curtobacterium and ‘Brevibacterium helvolum’ DSM 20419 (=ATCC 13715). The latter was reported to have the cell-wall peptidoglycan type B2γ and the major menaquinone MK-9, which are typical of Clavibacter, but it is clearly separated from this genus at the phylogenetic level. Based on low values of 16S rDNA sequence similarity to previously described genera and their distinctive phenotypic characteristics, it is proposed that strains ON4T and ‘B. helvolum’ DSM 20419 be classified as two novel genera and species, with the respective names Gulosibacter molinativorax gen. nov., sp. nov. and Pseudoclavibater helvolus gen. nov., sp. nov.
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Bacillus hwajinpoensis sp. nov. and an unnamed Bacillus genomospecies, novel members of Bacillus rRNA group 6 isolated from sea water of the East Sea and the Yellow Sea in Korea
More LessTwo Gram-positive or -variable, endospore-forming, slightly halophilic strains (SW-72T and SW-93) were isolated from sea water of the East Sea and the Yellow Sea in Korea, respectively, and subjected to polyphasic taxonomic study. Both strains had cell-wall peptidoglycan that was based on meso-diaminopimelic acid and MK-7 as the predominant menaquinone. The two strains contained large amounts of saturated and branched fatty acids, with anteiso-C15 : 0 as the major fatty acid. The DNA G+C contents of strains SW-72T and SW-93 were 40·9 and 41·0 mol%, respectively. Phylogenetic analysis based on 16S rDNA sequences showed that strains SW-72T and SW-93 fall within the radiation of the cluster that comprises members of the genus Bacillus, particularly Bacillus rRNA group 6. There were five nucleotide differences between the 16S rDNA sequences of strains SW-72T and SW-93. The mean level of DNA–DNA relatedness between strains SW-72T and SW-93 was 21·5 %. Strains SW-72T and SW-93 showed 93·1–95·2 % 16S rDNA sequence similarity to the type strains of Bacillus species that are assigned to rRNA group 6. Strains SW-72T and SW-93 could not be differentiated clearly by using their phenotypic properties. On the basis of phenotypic properties, phylogeny and genomic data, it is proposed that strain SW-72T (=KCCM 41641T=JCM 11807T) should be placed in the genus Bacillus as the type strain of a novel species, Bacillus hwajinpoensis sp. nov., and that strain SW-93 (=KCCM 41640=JCM 11806) should be placed in the genus Bacillus as an unnamed Bacillus genomospecies.
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Reclassification of Lactobacillus cellobiosus Rogosa et al. 1953 as a later synonym of Lactobacillus fermentum Beijerinck 1901
More LessThe name Lactobacillus cellobiosus is validly published, but the species is often neglected in taxonomic studies, due to its high similarity to Lactobacillus fermentum. In the present paper, literature data concerning the two species were reviewed. Phylogenetic placement of L. cellobiosus was obtained based on 16S rDNA sequences, and genetic similarity was further investigated by comparing partial recA gene sequences for the type strains of L. cellobiosus and L. fermentum. Based on the high identity values for 16S rDNA (99 %) and recA gene (98 %) sequences, the results of DNA–DNA hybridization assays and phenotypic traits available from the literature, it is proposed that L. cellobiosus be reclassified and, as a rule of priority, renamed as L. fermentum, the first described species.
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Rothia aeria sp. nov., Rhodococcus baikonurensis sp. nov. and Arthrobacter russicus sp. nov., isolated from air in the Russian space laboratory Mir
Four Gram-positive bacteria, strains A1-17BT, A1-22T, A1-3T and A1-8, isolated from the air in the Russian space laboratory Mir, were subjected to a polyphasic taxonomic study. Phylogenetic analysis of the bacteria based on their 16S rDNA sequence showed that they belong to the genera Rothia (A1-17BT), Rhodococcus (A1-22T) and Arthrobacter (A1-3T and A1-8). Morphological, physiological, chemotaxonomic and genomic characteristics supported the assignments of these strains to these genera, but they could not be classified as any existing species within each respective genus. 16S rDNA similarity values between strain A1-17BT and its neighbours, Rothia dentocariosa genomovar II, Rothia dentocariosa, Rothia mucilaginosa and Rothia nasimurium, were respectively 99·8, 98·0, 96·4 and 95·4 %. Polyphasic taxonomic evidence indicated that strain A1-17BT should be categorized together with the unofficially named Rothia dentocariosa genomovar II, but clearly differentiated them from the established species of the genus Rothia. Strain A1-22T formed a coherent cluster with Rhodococcus erythropolis, Rhodococcus globerulus, Rhodococcus marinonascens and Rhodococcus percolatus in 16S rDNA sequence analysis, but DNA–DNA relatedness values were only 45·5, 35·3, 18·9 and 21·9 %. Strains A1-3T and A1-8 shared 99·9 % 16S rDNA sequence similarity, and strain A1-3T showed the highest level of 16S rDNA similarity, 96·6 %, to Arthrobacter polychromogenes. Contrasting biochemical characteristics were also identified. Finally, as a result of the polyphasic taxonomic study, three of the strains are proposed as type strains of novel species: Rothia aeria sp. nov. (A1-17BT=GTC 867T=JCM 11412T=DSM 14556T), Rhodococcus baikonurensis sp. nov. (A1-22T=GTC 1041T=JCM 11411T=DSM 44587T) and Arthrobacter russicus sp. nov. (A1-3T=GTC 863T=JCM 11414T=DSM 14555T).
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Nesterenkonia halotolerans sp. nov. and Nesterenkonia xinjiangensis sp. nov., actinobacteria from saline soils in the west of China
The taxonomic position of two Gram-positive strains, YIM 70084T and YIM 70097T, isolated from hypersaline soils was determined by a polyphasic approach. Cells of strain YIM 70084T are motile cocci, whereas those of strain YIM 70097T are non-motile rods. The G+C contents of their DNA are 64·4 and 66·7 mol%. Both strains had chemotaxonomic markers typical of the genus Nesterenkonia and formed a coherent cluster with Nesterenkonia species in a phylogenetic inference based on 16S rDNA sequence analysis, exhibiting less than 97 % similarity to each other and to the other two type strains of the genus. Phylogenetic distinction and differences in the peptidoglycan type, composition of cell-wall sugars, phospholipid patterns, the major menaquinones and other phenotypic characteristics indicate that the strains under study represent two novel species, Nesterenkonia halotolerans sp. nov. (type strain YIM 70084T=CCTCC AA 001022T=DSM 15474T) and Nesterenkonia xinjiangensis sp. nov. (type strain YIM 70097T=CCTCC AA 001025T=DSM 15475T).
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Paenibacillus lactis sp. nov., isolated from raw and heat-treated milk
Endospore-forming bacteria were recovered from individual packages from different processing lines in a dairy plant during a tenacious periodical contamination of their UHT-milk production. Two colony types were seen, one of which was identified as Bacillus sporothermodurans. Analysis of the 16S rRNA gene of the second colony type placed these isolates within the genus Paenibacillus, with Paenibacillus lautus as the closest known relative. Moreover, over 99 % similarity was observed to the 16S rDNA sequence of MB 2035, a strain isolated previously from raw milk during a survey at dairy farms for very heat-resistant spore-forming bacteria. Nine other potentially closely related strains among the dairy farm isolates were found using rep-PCR typing. The taxonomic positions of these 19 isolates were further investigated using 16S rRNA gene sequencing and DNA–DNA hybridizations of representative strains. All 19 isolates shared a high degree of phenotypic similarity and were easily distinguished from closely related members of the genus. Anteiso-C15 : 0, C16 : 0 and iso-C15 : 0 were among the major fatty acids and the genomic DNA G+C content was 51·6–51·7 mol%. Therefore, based on their phenotypic, phylogenetic and genomic distinctiveness, these 19 strains, isolated from both raw and heat-treated milk, are placed in the genus Paenibacillus as Paenibacillus lactis sp. nov. The type strain is MB 1871T (=LMG 21940T=DSM 15596T).
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Corynebacterium caspium sp. nov., from a Caspian seal (Phoca caspica)
More LessA previously unknown Gram-positive, non-spore-forming, non-lipophilic, catalase-positive, irregular rod-shaped bacterium (M/106/00/5T) was isolated, in mixed culture, from the penis of a Caspian seal (Phoca caspica). The strain was a facultative anaerobe that was able to grow at 22 and 42 °C. Comparative 16S rRNA gene sequencing showed that the organism formed a hitherto unknown subline within the genus Corynebacterium. Sequence divergence values of more than 5 % from other described Corynebacterium species, together with phenotypic differences, showed that the unidentified bacterium represents a previously unrecognized member of this genus. On the basis of phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium isolated from a Caspian seal (strain M/106/00/5T=CCUG 44566T=CIP 107965T) be classified as the type strain of a novel species of the genus Corynebacterium, Corynebacterium caspium sp. nov.
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Transfer of Bacillus ehimensis and Bacillus chitinolyticus to the genus Paenibacillus with emended descriptions of Paenibacillus ehimensis comb. nov. and Paenibacillus chitinolyticus comb. nov.
More LessThe taxonomic status of Bacillus ehimensis and Bacillus chitinolyticus was examined, based on their 16S rDNA sequences, DNA–DNA hybridization and other taxonomic characteristics. A phylogenetic analysis using 16S rDNA sequences revealed that the two species belong to the genus Paenibacillus. In particular, B. ehimensis KCTC 3748T and B. chitinolyticus KCTC 3791T were found to be phylogenetically closely related to Paenibacillus koreensis YC300T (98·3 % sequence similarity) and Paenibacillus chinjuensis WN9T (95·2 % sequence similarity), respectively. DNA–DNA hybridization values between B. ehimensis KCTC 3748T and P. koreensis YC300T were less than 26 %. An experiment using Paenibacillus-specific PCR primers, PAEN515F and 1377R, revealed that B. ehimensis and B. chitinolyticus had the same amplified 16S rDNA fragment as members of the genus Paenibacillus. Accordingly, it is proposed that B. ehimensis and B. chitinolyticus be transferred to the genus Paenibacillus as Paenibacillus ehimensis comb. nov. and Paenibacillus chitinolyticus comb. nov., respectively.
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Anoxybacillus contaminans sp. nov. and Bacillus gelatini sp. nov., isolated from contaminated gelatin batches
Aerobic, endospore-forming bacteria that are attributed to the genus Bacillus or related genera constitute a hazard to the quality of gelatin. During repetitive extragenic palindromic DNA (rep)-PCR screening of gelatin isolates, a group of five isolates (group 1) and a group of 66 isolates (group 2) that did not match any pattern in our database were found. On the basis of 16S rDNA sequence analysis, representative strains of the different rep-PCR fingerprint types of group 1 were shown to be related most closely to Anoxybacillus species, but with sequence similarity of <97 %. Likewise, representative strains of group 2 were shown to be related most closely to Bacillus species, with 16S rDNA sequence similarity of <97 %. DNA–DNA reassociation values of isolates that displayed the most divergent rep-PCR profiles revealed that strains within each group belonged to a single species, according to recommendations for species delineation. A mean fatty acid profile could be calculated for each group. Isolates within a single group had similar patterns of results in API and other phenotypic tests; no correlation of patterns of results with rep-PCR groups was seen. Physiological characterization of group 1 isolates allows their distinction from other Anoxybacillus species. Despite the weak reaction of group 2 isolates in API tests, physiological characterization allows distinction between Bacillus species that react weakly in API tests. Two novel species are therefore proposed, with the names Anoxybacillus contaminans sp. nov. (type strain, LMG 21881T=DSM 15866T) and Bacillus gelatini sp. nov. (type strain, LMG 21880T=DSM 15865T).
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Clostridium hastiforme is a later synonym of Tissierella praeacuta
More LessThe previously proposed species Clostridium hastiforme and Tissierella praeacuta appear to be similar from their published descriptions. Accordingly, the aim of the current study was to perform phenotypic and genetic analyses of the type strains of both species, in order to clarify their taxonomic positions. The type strains of C. hastiforme (DSM 5675T) and T. praeacuta (NCTC 11158T) exhibited identical biochemical profiles and their 16S rRNA gene sequences displayed 99·9 % similarity. DNA–DNA hybridization was also estimated to be 96·5 %. Thus, it was concluded that C. hastiforme and T. praeacuta are synonyms, where T. praeacuta has priority. An emended description of the genus Tissierella is also given.
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Syntrophomonas curvata sp. nov., an anaerobe that degrades fatty acids in co-culture with methanogens
More LessA strict anaerobe (strain GB8-1T) that degraded straight-chain fatty acids with C4–C18 in syntrophic association with methanogens was isolated from an up-flow anaerobic sludge blanket reactor treating beer wastewater. Strain GB8-1T degraded 1 mol butyrate into about 2 mol acetate and 1 mol (presumably) H2 in co-culture with a methanogen. Neither branched-chain fatty acids nor benzoate could be degraded. Strain GB8-1T could grow on crotonate in pure culture and converted 1 mol crotonate to 0·5 mol butyrate and 1 mol acetate. Generation time was about 11 h when grown on crotonate at 37 °C. Fumarate, sulfate, thiosulfate, sulfur and nitrate could not serve as electron acceptors for strain GB8-1T to degrade butyrate. Cells of strain GB8-1T were curved rods with Gram-negative cell walls; no spores were observed. The DNA G+C content was 46·6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GB8-1T was related most closely to the fatty acid-oxidizing, syntrophic bacterium Syntrophomonas sapovorans DSM 3441T; however, the relationship was not very close (95·4 % sequence similarity). Some phenotypic features also differentiated strain GB8-1T from Syntrophomonas sapovorans DSM 3441T. Therefore, a novel species, Syntrophomonas curvata sp. nov., is proposed. The type strain is GB8-1T (=CGMCC 1.5010T=DSM 15682T).
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- Unicellular Eukaryotes
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Systematics of the anamorphic basidiomycetous yeast genus Trichosporon Behrend with the description of five novel species: Trichosporon vadense, T. smithiae, T. dehoogii, T. scarabaeorum and T. gamsii
More LessPhylogenetic trees of the anamorphic basidiomycetous yeast genus Trichosporon Behrend, based on molecular sequence analysis of the internal transcribed spacer region and the D1/D2 region of the large subunit of ribosomal (26S) DNA, are presented. This study includes three novel species from soils, Trichosporon vadense sp. nov. (type strain, CBS 8901T), Trichosporon smithiae sp. nov. (type strain, CBS 8370T) and Trichosporon gamsii sp. nov. (type strain, CBS 8245T), one novel species from an insect, Trichosporon scarabaeorum sp. nov. (type strain, CBS 5601T) and one species of unknown origin, Trichosporon dehoogii sp. nov. (type strain, CBS 8686T). The phylogenetic positions and physiological characteristics that distinguish the new taxa from related species, based partly on growth tests that are not traditionally used in yeast taxonomy (uric acid, ethylamine, l-4-hydroxyproline, tyramine and l-phenylalanine as sources of carbon and nitrogen, and polygalacturonate, quinate, 4-ethylphenol, phloroglucinol, 2,3-dihydroxybenzoate and orcinol as sole carbon sources), are discussed. Assimilation of l-rhamnose and erythritol and maximum growth temperature were also used to delineate species.
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Auriculibuller fuscus gen. nov., sp. nov. and Bullera japonica sp. nov., novel taxa in the Tremellales
Seven phylloplane yeast strains that were collected in the Arrábida Natural Park, Portugal, and identified preliminarily as Bullera alba, the anamorphic stage of Bulleromyces albus, were investigated. In contrast to Bulleromyces albus, these isolates produced a brownish pigment when grown on potato dextrose agar. The pigment caused darkening of the cultures and diffused into the culture medium. Mating studies revealed that the Arrábida isolates did not react with the different mating types of Bulleromyces albus, but were sexually compatible with them and produced mycelium with clamp connections, haustoria and transversally septate basidia that ejected the basidiospores. Various taxonomic criteria that were evaluated during the present study and comparison with other sexual taxa of the Tremellales indicated that this teleomorph should be classified in a novel genus. Therefore, Auriculibuller fuscus gen. nov., sp. nov. (type strain, PYCC 5690T=CBS 9648T) is proposed. In addition, during the course of this investigation, a member of a novel Bullera species, Bullera japonica sp. nov. (type strain, PYCC 4534T=CBS 2013T), was found among collection isolates that were identified formerly as Bullera alba. In molecular phylogenetic analysis of the D1/D2 domains of the 26S rDNA and the internal transcribed spacer region, the two taxa were found to be closely related, but distinct at the species level.
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Reassignment of the basidiomycetous yeasts Trichosporon pullulans to Guehomyces pullulans gen. nov., comb. nov. and Hyalodendron lignicola to Trichosporon lignicola comb. nov.
More LessNucleotide sequence analyses of the hymenomycetous yeasts demonstrated that Hyalodendron lignicola should be considered as a member of the genus Trichosporon within the Trichosporonales and that Trichosporon pullulans is associated closely with the Cystofilobasidiales, rather than the Trichosporonales. Accordingly, the following proposals are made: Trichosporon lignicola comb. nov. and Guehomyces gen. nov., to accommodate Guehomyces pullulans comb. nov. in the Cystofilobasidiales.
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- Evolution, Phylogeny And Biodiversity
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Delineation of the genus Actinobacillus by comparison of partial infB sequences
More LessA 426 bp fragment of infB, a housekeeping gene that encodes translation initiation factor 2, was sequenced from 59 clinical isolates and type strains of Actinobacillus species and sequences were compared. Partial sequences of 16S rRNA genes were also obtained. By comparing infB sequences, Actinobacillus pleuropneumoniae, Actinobacillus equuli, Actinobacillus suis, Actinobacillus ureae, Actinobacillus arthritidis, Actinobacillus hominis and two unnamed genomospecies showed more than 85 % similarity to the type strain of the type species of the genus, Actinobacillus lignieresii. The taxonomic position of Actinobacillus capsulatus was unresolved; this species is more remotely related to A. lignieresii. The two species A. lignieresii and A. pleuropneumoniae could not be clearly separated by infB sequence analysis. The phylogeny of the genus Actinobacillus based on infB analysis was essentially congruent with relationships inferred from 16S rRNA sequence comparisons and DNA hybridization studies. Discrepancies were encountered with single strains or taxa at the periphery of the genus. Greater intraspecies variation was observed with infB sequences than with 16S rRNA gene sequences, with notable exceptions. The apparent subdivision of some species by 16S rRNA analysis was most likely caused by RNA operon heterogeneity.
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Volumes and issues
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Volume 74 (2024)
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