- Volume 56, Issue 1, 2006
Volume 56, Issue 1, 2006
- Validation List No. 107
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List of new names and new combinations previously effectively, but not validly, published
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 55, part 5, 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). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
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- List Of Changes In Taxonomic Opinion No. 3
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Notification of changes in taxonomic opinion previously published outside the IJSEM
The Bacteriological Code deals with the nomenclature of prokaryotes. This may include existing names (the Approved Lists of Bacterial Names) as well as new names and new combinations. In this sense the Code is also dealing indirectly with taxonomic opinions. However, as with most codes of nomenclature there are no mechanisms for formally recording taxonomic opinions that do not involve the creation of new names or new combinations. In particular, it would be desirable for taxonomic opinions resulting from the creation of synonyms or emended descriptions to be made widely available to the public. In 2004, the Editorial Board of the International Journal of Systematic and Evolutionary Microbiology (IJSEM) agreed unanimously that it was desirable to cover such changes in taxonomic opinions (i.e. the creation of synonyms or the emendation of circumscriptions) previously published outside the IJSEM, and to introduce a List of Changes in Taxonomic Opinion [Notification of changes in taxonomic opinion previously published outside the IJSEM; Euzéby et al. (2004). Int J Syst Evol Microbiol 54, 1429–1430]. Scientists wishing to have changes in taxonomic opinion included in future lists should send one copy of the pertinent reprint or a photocopy or a PDF file thereof to the IJSEM Editorial Office or to the Lists Editor. It must be stressed that the date of proposed taxonomic changes is the date of the original publication not the date of publication of the list. Taxonomic opinions included in the List of Changes in Taxonomic Opinion cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission. The names that are to be used are those that are the ‘correct names' (in the sense of Principle 6) in the opinion of the bacteriologist, with a given circumscription, position and rank. A particular name, circumscription, position and rank does not have to be adopted in all circumstances. Consequently, the List of Changes in Taxonomic Opinion must be considered as a service to bacteriology and it has no ‘official character’, other than providing a centralized point for registering/indexing such changes in a way that makes them easily accessible to the scientific community.
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- New Taxa
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- Actinobacteria
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rpoB gene sequence-based characterization of emerging non-tuberculous mycobacteria with descriptions of Mycobacterium bolletii sp. nov., Mycobacterium phocaicum sp. nov. and Mycobacterium aubagnense sp. nov.
More LessOver the past 10 years, 16S rRNA gene sequencing has contributed to the establishment of more than 45 novel species of non-tuberculous mycobacteria and to the description of emerging mycobacterial infections. Cumulative experience has indicated that this molecular tool underestimates the diversity of this group and does not distinguish between all recognized mycobacterial taxa. In order to improve the recognition of emerging rapidly growing mycobacteria (RGM), rpoB gene sequencing has been developed. Our previous studies have shown that an RGM isolate is a member of a novel species if it exhibits >3 % sequence divergence in the rpoB gene from the type strains of established species. When applied to a collection of 59 clinical RGM isolates, rpoB gene sequencing revealed nine novel isolates (15·3 %) whereas only two isolates (3·4 %) were deemed to be novel by conventional 16S rRNA gene sequence analysis. A polyphasic approach, including biochemical tests, antimicrobial susceptibility analyses, hsp65, sodA and recA gene sequence analysis, DNA G+C content determination and cell-wall fatty acid composition analysis, supported the evidence that these nine isolates represent three novel species. Whereas Mycobacterium phocaicum sp. nov. (type strain N4T=CIP 108542T=CCUG 50185T) and Mycobacterium aubagnense sp. nov. (type strain U8T=CIP 108543T=CCUG 50186T; Mycobacterium mucogenicum group) were susceptible to most antibiotics, Mycobacterium bolletii sp. nov. (type strain BDT=CIP 108541T=CCUG 50184T; Mycobacterium chelonae–abscessus group) was resistant to the quinolones, tetracycline, macrolides and imipenem. Only M. bolletii was resistant to clarithromycin. These data illustrate that rpoB gene sequence-based identification is a powerful tool to characterize emerging RGM and mycobacterial infections and provides valuable help in differentiating RGM at both the intra- and interspecies level, thus contributing to a faster and more efficient diagnosis and epidemiological follow-up.
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Williamsia deligens sp. nov., isolated from human blood
More LessThe taxonomic status of two bacterial strains isolated from human blood was characterized using a polyphasic approach. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV, short-chain mycolic acids that co-migrated with those extracted from members of the genus Williamsia and that produce C16 : 0 and C18 : 0 fatty acids on pyrolysis GC, and dihydrogenated menaquinone with nine isoprene units as the predominant isoprenologue. The generic assignment was confirmed by 16S rRNA gene sequencing. Comparative analysis of the 16S rRNA gene sequence showed that these isolates constitute a distinct phyletic line within the genus Williamsia, displaying 96·2 and 97·2 % sequence similarities to Williamsia muralis and Williamsia maris, respectively. The two isolates could be distinguished from the type strains of the latter species on the basis of several phenotypic traits. The genotypic and phenotypic data show that the strains merit classification as a novel species of Williamsia, for which the name Williamsia deligens sp. nov. is proposed, with type strain IMMIB RIV-956T (=DSM 44902T=CCUG 50873T).
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Reclassification of Amycolatopsis orientalis DSM 43387 as Amycolatopsis benzoatilytica sp. nov.
More LessAmycolatopsis orientalis DSM 43387, a clinical isolate from submandibular mycetoma tissue, is one of three plasmid-bearing strains of the genus Amycolatopsis. It degrades aromatic compounds such as m-hydroxybenzoate, but does not produce any antibiotics, in contrast to Amycolatopsis orientalis NBRC 12806T. Phylogenetic analysis based on a complete 16S rRNA gene sequence placed the strain in the clade of Amycolatopsis albidoflavus IMSNU 22139T, distant from the clade of A. orientalis NBRC 12806T. The strain showed low DNA–DNA hybridization values of 24·1 and 45·7 % with A. orientalis NBRC 12806T and A. albidoflavus DSM 44639T (=IMSNU 22139T), respectively. It could also be readily distinguished from A. orientalis NBRC 12806T and all species with validly published names classified in the genus Amycolatopsis, by using a combination of chemical and physiological markers such as utilization of lactose, degradation of xanthine, hypoxanthine, gelatin and casein and hydrolysis of Tween 80, indicating that it represents a novel species. Strain DSM 43387 could also be differentiated from A. orientalis NBRC 12806T and its nearest neighbour A. albidoflavus IMSNU 22139T on the basis of fatty acid and phospholipid profiles. Based on genotypic and phenotypic differences, the name Amycolatopsis benzoatilytica sp. nov. is proposed for strain DSM 43387 that was previously classified as Amycolatopsis orientalis. The type strain is AK 16/65T (=DSM 43387T=ATCC 55165T=IMRU 1389T).
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Actinomadura hallensis sp. nov., a novel actinomycete isolated from Mt. Halla in Korea
More LessA novel actinomycete, strain H647-1T, which was isolated from soil of Mt. Halla, Jeju Island, Republic of Korea, was subjected to phenotypic and genotypic characterization. The organism, which produces warty spore chains arranged in hooks or spirals on the aerial mycelium, was shown to have chemotaxonomic characteristics consistent with assignment to the genus Actinomadura. A comparative analysis of 16S rRNA gene sequences indicated that the organism formed a distinct clade within the evolutionary radiation of the family Thermomonosporaceae and that it was closely associated with members of the genus Actinomadura, but possessed a 22 nt extended loop between positions 453 and 479 of the 16S rRNA gene sequence (Escherichia coli numbering). A broad range of phenotypic and genetic data supported the suggestion that this organism represents a novel species of the genus Actinomadura, for which the name Actinomadura hallensis sp. nov. is proposed. The type strain is strain H647-1T (=IMSNU 50760T=KCTC 9992T=KCCM 42245T=NRRL B-24436T).
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Amycolatopsis minnesotensis sp. nov., isolated from a prairie soil
More LessTwo actinomycete strains, 32U-2T and 32U-4, were isolated from a prairie soil in Minnesota and subjected to characterization by means of polyphasic taxonomy. The 16S rRNA gene sequences were determined following PCR amplification and cloning. A phylogenetic analysis, based on comparative analysis of 16S rRNA gene sequences, indicated that the organisms consistently formed a well-separated, distinct sub-branch within the radiation of the genus Amycolatopsis of the family Pseudonocardiaceae. The levels of 16S rRNA sequence similarity between the isolates and the type strains of recognized Amycolatopsis species ranged from 94·1 to 97·9 %. The highest levels of sequence similarity were found between the isolates and Amycolatopsis coloradensis (97·6–97·9 %), Amycolatopsis alba and Amycolatopsis orientalis (97·3–97·6 %) and Amycolatopsis lurida (97·2–97·5 %). Chemotaxonomic characteristics supported the phylogenetic relationships between the organisms and members of the genus Amycolatopsis. However, a broad range of phenotypic and genetic data revealed that the isolates should be classified as novel species of the genus Amycolatopsis, for which the name Amycolatopsis minnesotensis sp. nov. is proposed. The type strain is 32U-2T (=KCCM 42246T=NRRL B-24435T).
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Nocardioides lentus sp. nov., isolated from an alkaline soil
More LessGram-positive, rod- or coccoid-shaped bacterial strains KSL-17T, KSL-18 and KSL-19 were isolated from an alkaline soil in Korea. They were subjected to analysis using polyphasic taxonomy. Strains KSL-17T, KSL-18 and KSL-19 grew optimally at pH 8·0 and 28 °C and in the presence of 0·5 % (w/v) NaCl. They were characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and iso-C16 : 0 as the major fatty acid. Their DNA G+C contents were in the range 74·6–74·8 mol%. Strains KSL-17T, KSL-18 and KSL-19 were identical in terms of their 16S rRNA gene sequences and exhibited a mean level of DNA–DNA relatedness of 85–90 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains KSL-17T, KSL-18 and KSL-19 formed a distinct phylogenetic lineage within the genus Nocardioides. The levels of 16S rRNA gene sequence similarity between the three strains and the type strains of Nocardioides species were in the range 92·6–95·2 %. On the basis of phenotypic, genetic and phylogenetic data, strains KSL-17T (=KCTC 19039T=DSM 16315T), KSL-18 and KSL-19 should be classified as members of a novel species of the genus Nocardioides, for which the name Nocardioides lentus sp. nov. is proposed.
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Myceligenerans crystallogenes sp. nov., isolated from Roman catacombs
Three xylan-degrading actinobacterial strains were isolated from different sampling sites in the Roman catacombs of Domitilla and San Callisto. The organisms showed morphological and chemotaxonomic properties such as peptidoglycan type A4α, l-lys–l-thr–d-Glu; whole-cell sugars (glucose, mannose and galactose); octa-, hexa- and tetrahydrogenated menaquinones with nine isoprene units; phosphatidylglycerol and diphosphatidylglycerol as the major phospholipids; anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0 as the predominant fatty acids; and a DNA G+C content of 72 mol%. These features are consistent with affiliation of these isolates to the genus Myceligenerans. The three isolates shared a 16S rRNA gene similarity of 99·9 % and were most closely related to Myceligenerans xiligouense DSM 15700T (97·9 % sequence similarity). The low level of DNA–DNA relatedness (about 14 %) and the differences in phenotypic characteristics between the novel strains and M. xiligouense DSM 15700T justify the proposal of a novel species of the genus Myceligenerans, Myceligenerans crystallogenes sp. nov., with CD12E2-27T (=HKI 0369T=DSM 17134T=NCIMB 14061T=VTT E-032285T) as the type strain.
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- Archaea
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Methanosaeta harundinacea sp. nov., a novel acetate-scavenging methanogen isolated from a UASB reactor
Kai Ma, Xiaoli Liu and Xiuzhu DongTwo methanogenic strains, 8AcT and 6Ac, were isolated from an upflow anaerobic sludge blanket reactor treating beer-manufacture wastewater in Beijing, China. Cells of strains 8AcT and 6Ac were rod-shaped (0·8–1·0×3–5 μm) and non-motile, occurring singly or in pairs; however, at high cell density the cells were arranged in long chains within a common sheath. The two strains used acetate exclusively for growth and methane production. The specific growth rate of strain 8AcT was 0·030 h−1 when growing in acetate (20 mM) at 37 °C. The temperature range for growth was 25–45 °C, with the fastest growth at 34–37 °C. The pH range for growth and methane production was 6·5–9·0, with the fastest growth at pH 7·2–7·6. The G+C content of genomic DNA of strain 8AcT was 55·7 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that the novel strains clustered with Methanosaeta species; the 16S rRNA gene sequence similarities between strain 8AcT and Methanosaeta concilii DSM 3013 and ‘Methanosaeta thermophila’ DSM 6194 were 92·5 and 87·3 %, respectively. The sequence similarity levels of mcrA, the gene encoding the α-subunit of methyl-coenzyme M reductase, and of the deduced amino acids of mcrA, between strain 8AcT and Methanosaeta concilii DSM 3671T were 36 and 78·9 %, respectively. Based on the phylogenetic and phenotypic analyses, the novel species Methanosaeta harundinacea sp. nov. is proposed, with strain 8AcT (=JCM 13211T=CGMCC 1.5026T) as the type strain.
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- Bacteroidetes
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Paludibacter propionicigenes gen. nov., sp. nov., a novel strictly anaerobic, Gram-negative, propionate-producing bacterium isolated from plant residue in irrigated rice-field soil in Japan
More LessA strictly anaerobic, propionate-producing bacterial strain (WB4T) isolated from rice plant residue in anoxic rice-field soil in Japan was characterized phenotypically and phylogenetically. Cells were Gram-negative, non-motile, non-spore-forming, short rods. The strain utilized various sugars and produced propionate and acetate as major fermentation products with a small amount of succinate. The optimum growth temperature was 30 °C. Oxidase, catalase and nitrate-reducing activities were negative. The major cellular fatty acids were anteiso-C15 : 0, C15 : 0 and anteiso-C17 : 0 3-OH. Menaquinone MK-8(H4) was the major respiratory quinone. The genomic DNA G+C content was 39·3 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence placed the strain in the phylum ‘Bacteroidetes’. The closest relative to strain WB4T was an environmental clone from water contaminated with equine manure (sequence similarity of 99·7 %) and the strain formed a distinct cluster with other environmental clones mainly from freshwater sediments. The closest recognized species were members of the genus Dysgonomonas, with 16S rRNA gene sequence similarities of 90·9–89·8 %. Bacteroides merdae was the next closest recognized species (similarity of 88·7 % to the type strain). Given that the ecological, physiological and chemotaxonomic characteristics of strain WB4T were different from those of any related species, a new genus and species Paludibacter propionicigenes gen. nov., sp. nov., is proposed to accommodate it. The type strain is WB4T (=JCM 13257T=DSM 17365T).
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Gaetbulimicrobium brevivitae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a tidal flat of the Yellow Sea in Korea
More LessA Gram-negative, non-spore-forming and rod-shaped gliding bacterium, designated strain SMK-19T, was isolated from a tidal flat sediment of the Yellow Sea, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain SMK-19T grew optimally at 37 °C, in the presence of 2–3 % (w/v) NaCl and at pH 7·0–8·0. It contained MK-6 as the predominant menaquinone, and iso-C17 : 0 3-OH and iso-C15 : 0 as the major fatty acids. Major polar lipids were phosphatidylethanolamine, unidentified phospholipids and an amino-group-containing lipid that is ninhydrin-positive. The DNA G+C content was 36·0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that strain SMK-19T formed a distinct evolutionary lineage within the family Flavobacteriaceae. The 16S rRNA gene sequence of strain SMK-19T exhibited similarity values of <94·4 % to those of other members of the family Flavobacteriaceae. Strain SMK-19T was distinguished from phylogenetically related genera by differences in several phenotypic properties. On the basis of phenotypic, phylogenetic and chemotaxonomic data, SMK-19T (=KCTC 12390T=DSM 17196T) was classified at the type strain of a novel genus and species, Gaetbulimicrobium brevivitae gen. nov., sp. nov.
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Bacteroides intestinalis sp. nov., isolated from human faeces
More LessDuring studies of the microbiota of human faeces, five strains of Gram-negative anaerobic rods were isolated following growth in a polyamine-deficient medium. These strains belonged to the genus Bacteroides on the basis of 16S rRNA gene sequence data. 16S rRNA gene sequence similarity between one of the strains, 341T, and recognized species within the genus Bacteroides was <95 %. The DNA G+C content (44 mol%) and major fatty acid composition (anteiso-C15 : 0, 32·0 %) supported the affiliation of strain 341T to the genus Bacteroides. Biochemical tests and DNA–DNA hybridization analysis demonstrated that strain 341T was distinct from Bacteroides uniformis and Bacteroides helcogenes, to which it was related most closely. On the basis of these data, a novel Bacteroides species, Bacteroides intestinalis sp. nov., is proposed with strain 341T (=JCM 13265T=DSM 17393T) as the type strain.
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Arenibacter palladensis sp. nov., a novel marine bacterium isolated from the green alga Ulva fenestrata, and emended description of the genus Arenibacter
The taxonomic position of three novel, marine, heterotrophic, aerobic, pigmented, gliding bacteria, isolated from the green alga Ulva fenestrata in the Sea of Japan, was determined. 16S rRNA gene sequence analysis revealed that the strains belong to the genus Arenibacter. The results of DNA–DNA hybridization experiments supported by phenotypic and chemotaxonomic data showed that the isolates represent a novel species of the genus Arenibacter, for which the name Arenibacter palladensis sp. nov. is proposed. The type strain is KMM 3961T (=LMG 21972T=CIP 108849T).
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Formosa agariphila sp. nov., a budding bacterium of the family Flavobacteriaceae isolated from marine environments, and emended description of the genus Formosa
Two marine, heterotrophic, aerobic, yellow-pigmented, agarolytic bacterial strains that are motile by means of gliding were isolated from the green alga Acrosiphonia sonderi and from sea water. Comparative 16S rRNA gene sequence analysis revealed an affiliation between the strains studied and the genus Formosa, a member of the family Flavobacteriaceae. The level of sequence similarity between strain KMM 3901T and Formosa algae KMM 3553T was 99·1 %. The results of DNA–DNA hybridization experiments and phenotypic analysis indicated that the strains represent a novel species of the genus Formosa, for which the name Formosa agariphila sp. nov. is proposed, with KMM 3901T (=KCTC 12365T=LMG 23005T=DSM 15362T) as the type strain. The description of the genus Formosa is emended with newly obtained data.
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Culturable phylogenetic diversity of the phylum ‘Bacteroidetes’ from river epilithon and coastal water and description of novel members of the family Flavobacteriaceae: Epilithonimonas tenax gen. nov., sp. nov. and Persicivirga xylanidelens gen. nov., sp. nov.
More LessMembers of the phylum ‘Bacteroidetes’ are important heterotrophs involved in cycling organic carbon in aquatic habitats. Their diversity has been studied by molecular methods in both freshwater and marine habitats and many novel genera and species within this phylum have been characterized in recent years. In this study, we examined the diversity of members of the ‘Bacteroidetes’ that could be readily isolated on solid media from river epilithon and coastal sea water. Most (93 %) of the 55 isolates confirmed as members of the ‘Bacteroidetes’ and examined by phylogenetic analysis of 16S rRNA gene sequences belonged to the Flavobacteriaceae. Furthermore, most (62 %) of these were almost certainly members of the genus Flavobacterium and all but one were from river epilithon. Conversely, the sea-water isolates were more widely distributed in clades containing other genera. Some of the isolates were deep-branching within phylogenetic trees and so could not be assigned to putative genera. Two of these deep-branching isolates were characterized by polyphasic taxonomy and are proposed as novel species within two new genera of the family Flavobacteriaceae. These are Epilithonimonas tenax gen. nov., sp. nov. (type strain EP105T=NCIMB 14026T=DSM 16811T) and Persicivirga xylanidelens gen. nov., sp. nov. (type strain SW256T=NCIMB 14027T=DSM 16809T).
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Stenothermobacter spongiae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a marine sponge in the Bahamas, and emended description of Nonlabens tegetincola
A bacterial strain, UST030701-156T, was isolated from a marine sponge in the Bahamas. Strain UST030701-156T was orange-pigmented, Gram-negative, rod-shaped with tapered ends, slowly motile by gliding and strictly aerobic. The predominant fatty acids were a15 : 0, i15 : 0, i15 : 0 3-OH, i17 : 0 3-OH, i17 : 1ω9c and summed feature 3, comprising i15 : 0 2-OH and/or 16 : 1ω7c. MK-6 was the only respiratory quinone. Flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequences placed UST030701-156T within a distinct lineage in the family Flavobacteriaceae, with 93·3 % sequence similarity to the nearest neighbour, Nonlabens tegetincola. The DNA G+C content of UST030701-156T was 41·0 mol% and was much higher than that of N. tegetincola (33·6 mol%). Strain UST030701-156T can be distinguished from other members of the Flavobacteriaceae by means of a number of chemotaxonomic and phenotypic characteristics. It is proposed, therefore, that UST030701-156T represents a novel taxon designated Stenothermobacter spongiae gen. nov., sp. nov. The type strain is UST030701-156T (=NRRL B-41138T=JCM 13191T). Carbon-source utilization by N. tegetincola was re-examined and an emended description is therefore included.
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Donghaeana dokdonensis gen. nov., sp. nov., isolated from sea water
More LessA Gram-negative, non-motile, non-spore-forming and rod-shaped bacterial strain, DSW-6T, was isolated from sea water and subjected to a polyphasic study. Strain DSW-6T grew optimally at 25 °C, in the presence of 2 % (w/v) NaCl and at pH 7·0–8·0. It was characterized chemotaxonomically as having MK-6 as the predominant menaquinone and iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and C15 : 0 as the major fatty acids (>10 % of total fatty acids). Major polar lipids were phosphatidylethanolamine, unidentified phospholipids and amino-group-containing lipids that are ninhydrin-positive. The DNA G+C content was 36·9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DSW-6T forms an independent line of descent within the family Flavobacteriaceae. The 16S rRNA gene sequence of strain DSW-6T exhibited similarity values of less than 94·7 % to the sequences of other members of the family Flavobacteriaceae. Strain DSW-6T could be distinguished from other phylogenetically related genera by differences in several phenotypic properties. Therefore, in view of the combined phenotypic and phylogenetic data, it is proposed that strain DSW-6T (=KCTC 12402T=DSM 17205T) represents a novel genus and species, Donghaeana dokdonensis gen. nov., sp. nov.
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Larkinella insperata gen. nov., sp. nov., a bacterium of the phylum ‘Bacteroidetes’ isolated from water of a steam generator
A Gram-negative bacterium, designated strain LMG 22510T, was isolated from water of a pharmaceutical company steam generator. The cells had a ring-like and horseshoe-shaped morphology and possessed gliding motility. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain was a member of the Flexibacter group within the phylum ‘Bacteroidetes’; its nearest neighbour was Spirosoma linguale (88·8 % sequence similarity). DNA base content, fatty acid composition and biochemical characteristics were determined. Genotypic and phenotypic data indicated that strain LMG 22510T could not be assigned to any recognized genus; therefore, a novel genus and species is proposed, Larkinella insperata gen. nov., sp. nov., with LMG 22510T (=NCIMB 14103T) as the type strain.
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- Proteobacteria
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Acetobacter oeni sp. nov., isolated from spoiled red wine
A bacterial strain, designated B13T, was isolated from spoiled red wine from the Dão region, Portugal. The strain was Gram-negative, strictly aerobic, rod-shaped and motile. Phylogenetic analysis on the basis of 16S rRNA gene sequences indicated that B13T belonged to the genus Acetobacter within the Alphaproteobacteria. The closest related species was Acetobacter aceti, with 98·4 % 16S rRNA gene sequence similarity. DNA–DNA hybridization showed that B13T constituted a taxon separate from the Acetobacter species with validly published names. The DNA G+C content of B13T was 58·1 mol%. Phenotypic characteristics of B13T allowed its differentiation from the recognized Acetobacter species. B13T produced 5-ketogluconic acid from glucose, but no 2-ketogluconic acid. It produced catalase, but no oxidase. It utilized glycerol, but not maltose, ethanol or methanol as carbon sources. On the basis of the results obtained, B13T represents a novel species for which the name Acetobacter oeni sp. nov. is proposed. The type strain is B13T (=LMG 21952T=CECT 5830T).
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Roseomonas lacus sp. nov., isolated from freshwater lake sediment
More LessAn aerobic, Gram-negative bacterial strain, TH-G33T, was isolated from freshwater sediment of Taihu Lake in China. The taxonomy of strain TH-G33T was studied by using phenotypic and phylogenetic methods. Cells of strain TH-G33T were coccoid rods or rods and formed colourless to pale-pink colonies on nutrient agar. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences showed that strain TH-G33T was related to Roseomonas mucosa (94·4 %), Roseomonas gilardii subsp. gilardii (94·1 %), Roseomonas gilardii subsp. rosea (94·8 %) and Roseomonas cervicalis (93·9 %). Cells contained ubiquinone 10 (Q-10) as the major quinone and the G+C content was 71·9 mol%. Thus, strain TH-G33T represents a novel species of the genus Roseomonas, for which the name Roseomonas lacus sp. nov. is proposed. The type strain is TH-G33T (=CGMCC 1.3617T=JCM 13283T).
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Colwellia aestuarii sp. nov., isolated from a tidal flat sediment in Korea
More LessA novel Colwellia-like bacterial strain, SMK-10T, was isolated from a tidal flat sediment in Korea and subjected to a polyphasic taxonomic analysis. Cells of strain SMK-10T were Gram-negative, motile, greyish yellow-pigmented, curved rods. Optimal growth occurred at 25–30 °C and in the presence of 2–3 % (w/v) NaCl. Strain SMK-10T contained Q-8 as the predominant ubiquinone and C16 : 1 ω7c and/or iso-C15 : 0 2-OH, C17 : 1, C15 : 1 and iso-C16 : 0 as major fatty acids. The DNA G+C content was 39·3 mol%. Phylogenetic trees based on 16S rRNA gene sequence analysis showed that strain SMK-10T belonged to the genus Colwellia. 16S rRNA gene sequence similarity values (94·7–96·7 %) to the type strains of all other Colwellia species and various differential phenotypic properties were sufficient to distinguish strain SMK-10T from recognized Colwellia species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain SMK-10T (=KCTC 12480T=DSM 17314T) is classified as the type strain of a novel Colwellia species, for which the name Colwellia aestuarii sp. nov. is proposed.
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Jannaschia seosinensis sp. nov., isolated from hypersaline water of a solar saltern in Korea
More LessA slightly halophilic alphaproteobacterium, designated CL-SP26T, was isolated from hypersaline water of a solar saltern located in Seosin, Korea. 16S rRNA gene sequence analysis revealed an affiliation with the genus Jannaschia. Sequence similarities between CL-SP26T and type strains of members of the genus Jannaschia were 94·9–97·2 %. Cells were rod-shaped and motile with one or more monopolar flagella. Strain CL-SP26T grew on solid media as circular red colonies. It was able to grow in 3–10 % sea salt; however, no growth occurred in media containing NaCl as the only salt. Strain CL-SP26T grew at 5–35 °C and pH 7–10. The major fatty acids were 18 : 1ω7c (64 %) and 18 : 0 (12·0 %). Three fatty acids, 3-OH 14 : 0/iso 16 : 1 (3·6 %), 18 : 3ω6c (2·2 %) and 10-methyl 19 : 0 (1·9 %), found in minor quantities in CL-SP26T, are unique among Jannaschia species. The DNA G+C content was 63 mol%. According to physiological data, fatty acid composition and 16S rRNA gene sequence analysis, CL-SP26T was assigned to the genus Jannaschia, but could be distinguished from recognized species of the genus. Strain CL-SP26T (=KCCM 42114T=JCM 13035T) therefore represents a novel species, for which the name Jannaschia seosinensis sp. nov. is proposed.
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Belnapia moabensis gen. nov., sp. nov., an alphaproteobacterium from biological soil crusts in the Colorado Plateau, USA
More LessStrain CP2CT was isolated from biological soil crusts in the Colorado Plateau, USA. The isolate was aerobic, facultatively fermentative, Gram-negative, non-motile and red-pigmented (due to the presence of carotenoids), but did not contain bacteriochlorophyll a. The strain tested positive for catalase, oxidase and urease and was negative for lysine and ornithine decarboxylases and arginine dihydrolase. The major fatty acids present were C18 : 1 ω7c and C16 : 0. It had a high DNA G+C content of 75 mol%. Comparisons of 16S rRNA gene sequences identified bacteriochlorophyll a-producing strains of Paracraurococcus ruber (94·9 %), Craurococcus roseus (92·2 %) and Roseococcus thiosulfatophilus (92·3 %), as well as non-bacteriochlorophyll a-producing bacteria Muricoccus roseus (94·9 %), Roseomonas gilardii (94·2 %) and Roseomonas mucosa (93·8 %), as the bacteria most closely related to strain CP2CT. Phylogenetically, CP2CT was placed roughly equidistantly from the above organisms. Based on its phylogenetic placement and morphological and physiological characteristics, strain CP2CT is assigned to a new genus in the α-1 subgroup of the Proteobacteria, for which the name Belnapia gen. nov. is proposed. Strain CP2CT (=ATCC BAA-1043T=DSM 16746T) is proposed as the type strain of the type species of this genus, with the name Belnapia moabensis gen. nov., sp. nov.
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Stappia marina sp. nov., a marine bacterium isolated from the Yellow Sea
A Gram-negative, aerobic and halophilic bacterium designated strain mano18T was isolated from a tidal flat area of Dae-Chun, Chung-Nam, Korea. This strain was motile by means of polar flagella, occasionally forming rosette-like aggregates, reduced nitrate to nitrite, required sodium ions for growth, exhibited catalase and oxidase activities and contained Q-10 as the major quinone and C18 : 1 ω7c as the dominant cellular fatty acid. Analysis of the 16S rRNA gene sequence revealed that this strain is affiliated with a cluster within the Alphaproteobacteria. Strain mano18T synthesized bacteriochlorophyll under aerobic conditions. The 16S rRNA gene sequence similarity between strain mano18T and the most closely related species, Stappia aggregata DSM 13394T, was 98·5 %. Levels of DNA–DNA relatedness between strain mano18T and the type strains of S. aggregata and Stappia stellulata were respectively 6·2–11·2 and 3·3–7·6 %. Strain mano18T, like other Stappia strains, possesses carbon monoxide dehydrogenase genes. The results of DNA–DNA hybridization and the polyphasic data confirmed that strain mano18T can be considered to represent a novel taxon in the genus Stappia. The name Stappia marina sp. nov. is proposed for the tidal flat isolate; the type strain is strain mano18T (=KCTC 12288T=DSM 17023T).
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Stenotrophomonas koreensis sp. nov., isolated from compost in South Korea
More LessA Gram-negative, rod-shaped, non-spore-forming bacterium (TR6-01T) was isolated from compost near Daejeon city in South Korea. On the basis of 16S rRNA gene sequence similarity, strain TR6-01T was shown to belong to the class Gammaproteobacteria, related to Stenotrophomonas acidaminiphila (97·1 %) and Stenotrophomonas maltophilia (96·9 %); the phylogenetic distance from any other established species within the genus Stenotrophomonas was less than 97·0 %. Phenotypic and chemotaxonomic data (major ubiquinone Q-8; fatty acid profile) supported the affiliation of strain TR6-01T to the genus Stenotrophomonas. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain TR6-01T from the five Stenotrophomonas species with validly published names. TR6-01T therefore represents a novel species, for which the name Stenotrophomonas koreensis sp. nov. is proposed, with the type strain TR6-01T (=KCTC 12211T=JCM 13256T).
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Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium
Three strains of bacteria that degrade the cyanobacterial hepatotoxin microcystin, Y2T, MDB2 and MDB3, were isolated from a eutrophic lake, Lake Suwa, and the Tenryu River, Japan, and characterized. These strains were aerobic and chemo-organotrophic and their cells were Gram-negative, non-spore-forming rods, motile by means of single polar flagella. Yellow-pigmented colonies were formed on nutrient agar media. The strains assimilated only citrate among the organic compounds tested as carbon sources. The G+C content of genomic DNA ranged from 63·6 to 63·7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolates formed a tight cluster within the family Sphingomonadaceae but were clearly separate from established genera of this family, e.g. Sphingomonas, Sphingobium, Novosphingobium and Sphingopyxis; sequence similarities between the new isolates and type strains from established genera ranged from 90·9 to 94·9 %. Chemotaxonomic and phenotypic data supported the conclusion that these strains were members of the family Sphingomonadaceae. The major components of the cellular fatty acids were 18 : 1ω7c (36–41 %) and 16 : 1ω7c (33–36 %). Hydroxy fatty acids were mainly 2-OH 14 : 0 (11–13 %), and 3-OH fatty acids were absent. Glycosphingolipids were detected. Ubiquinone-10 and homospermidine were present as the major quinine and polyamine, respectively. Thus, it is proposed that the three strains represent a new genus and species of the family Sphingomonadaceae with the name Sphingosinicella microcystinivorans gen. nov., sp. nov. The type strain is Y2T (=KCTC 12019T=JCM 13185T).
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Mesorhizobium thiogangeticum sp. nov., a novel sulfur-oxidizing chemolithoautotroph from rhizosphere soil of an Indian tropical leguminous plant
More LessThe bacterial strain SJTT, along with 15 other mesophilic, neutrophilic and facultatively sulfur-oxidizing chemolithotrophic isolates, was isolated by enrichment on reduced sulfur compounds as the sole energy and electron source from soils immediately adjacent to the roots of Clitoria ternatea, a slender leguminous herb of the Lower Gangetic plains of India. Strain SJTT was able to oxidize thiosulfate and elemental sulfur for chemolithoautotrophic growth. 16S rRNA and recA gene sequence-based phylogenetic analyses showed that the Gram-negative rod-shaped bacterium belonged to the genus Mesorhizobium and was most closely related to Mesorhizobium loti, Mesorhizobium plurifarium, Mesorhizobium amorphae and Mesorhizobium chacoense. Unequivocally low 16S rRNA (<97 %) and recA (⩽88 %) gene sequence similarities to all existing species of the most closely related genera, a unique fatty acid profile, a distinct G+C content (59·6 mol%) and phenotypic characteristics all suggested that strain SJTT represents a novel species. DNA–DNA hybridization and SDS-PAGE analysis of whole-cell proteins also confirmed the taxonomic uniqueness of SJTT. It is therefore proposed that isolate SJTT (=LMG 22697T=MTCC 7001T) be classified as the type strain of a novel species, Mesorhizobium thiogangeticum sp. nov.
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Methylobacter tundripaludum sp. nov., a methane-oxidizing bacterium from Arctic wetland soil on the Svalbard islands, Norway (78° N)
More LessA Gram-negative, rod-shaped, non-motile, non-spore forming bacterium (SV96T) was isolated from wetland soil near Ny-Ålesund, Svalbard. On the basis of 16S rRNA gene sequence similarity, strain SV96T was shown to belong to the Gammaproteobacteria, related to Methylobacter psychrophilus Z-0021T (99·1 %), Methylobacter luteus ATCC 49878T (97·3 %), Methylobacter marinus A45T (97·0 %) and Methylobacter whittenburyi ATCC 51738T (95·8 %); the closest related species within the genus Methylomicrobium with a validly published name was Methylomicrobium album ATCC 33003T (95·0 %). Chemotaxonomic data (including the major fatty acids: 16 : 1ω8, 16 : 1ω7 and 16 : 1ω5t) supported the affiliation of strain SV96T to the genus Methylobacter. The results of DNA–DNA hybridization, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain SV96T from the four Methylobacter species mentioned above. Strain SV96T therefore represents a novel species, for which the name Methylobacter tundripaludum sp. nov. is proposed (type strain SV96T=DSM 17260T=ATCC BAA-1195T).
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Polyphasic study of Zymomonas mobilis strains revealing the existence of a novel subspecies Z. mobilis subsp. francensis subsp. nov., isolated from French cider
More LessZymomonas mobilis strains recently isolated from French ‘framboisé’ ciders were compared with collection strains of the two defined subspecies, Z. mobilis subsp. mobilis and Z. mobilis subsp. pomaceae, using a polyphasic approach. Six strains isolated from six different regions of France were compared with three strains of Z. mobilis subsp. mobilis, including the type strain LMG 404T, and four strains of Z. mobilis subsp. pomaceae, including the type strain LMG 448T, using phenotypic and genotypic methods. For phenotypic characterization, both physiological tests and SDS-PAGE protein profiles revealed significant differences between the two known subspecies and the French isolates; three distinct groups were observed. These findings were further confirmed by random amplified polymorphic DNA and repetitive extragenic palindromic-PCR genotyping methods in which the French isolates were clearly distinguished from the other two subspecies. Sequence analysis of a fragment ranging from 604 to 617 nucleotides corresponding to the 16S–23S rRNA gene intergenic spacer region (ISR), a 592 nucleotide HSP60 gene fragment and a 1044 nucleotide gyrB gene fragment confirmed the presence of three distinct groups. The French strains exhibited almost 94 % similarity to the ISR, 90 % to HSP60 and 86 % to gyrB sequences of the three collection strains of Z. mobilis subsp. mobilis and 87, 84 and 80 % sequence similarity, respectively, was observed with the four Z. mobilis subsp. pomaceae strains. Based on both the phenotypic and genotypic results, the French strains are proposed to represent a novel subspecies, Zymomonas mobilis subsp. francensis subsp. nov. Strain AN0101T (=LMG 22974T=CIP 108684T) was designated as the type strain.
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Dokdonella koreensis gen. nov., sp. nov., isolated from soil
More LessTwo Gram-negative, motile, non-spore-forming and rod-shaped bacterial strains, DS-123T and DS-140, were isolated from soil and their taxonomic positions were investigated by a polyphasic study. Strains DS-123T and DS-140 grew optimally at 30 °C and pH 6·5 without NaCl. They contained Q-8 as the predominant ubiquione and iso-C17 : 1 ω9c, iso-C17 : 0 and iso-C15 : 0 as the major fatty acids. Major polar lipids detected in the two strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an amino-group-containing lipid that was ninhydrin-positive. Their DNA G+C contents were 71·0 mol%. Strains DS-123T and DS-140 exhibited no difference in their 16S rRNA gene sequences and possessed a mean DNA–DNA relatedness level of 92 %. Phylogenetic trees based on 16S rRNA gene sequences showed that strains DS-123T and DS-140 formed a distinct evolutionary lineage within the Gammaproteobacteria. The 16S rRNA gene sequences of strains DS-123T and DS-140 exhibited similarity values of less than 94·1 % to members of the Gammaproteobacteria. Strains DS-123T and DS-140 were distinguished from phylogenetically related genera by differences in some phenotypic properties. On the basis of phenotypic, phylogenetic and genetic data, it is proposed that strains DS-123T (=KCTC 12396T=DSM 17203T) and DS-140 be classified in a novel genus and species, Dokdonella koreensis gen. nov., sp. nov.
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Shewanella halifaxensis sp. nov., a novel obligately respiratory and denitrifying psychrophile
More LessIndigenous bacteria found in the sediment of the Emerald Basin (depth of 215 m, Atlantic Ocean) located offshore of Halifax Harbour (Nova Scotia, Canada) were previously found to be able to degrade the explosive compound hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). In the present study, a novel obligately respiratory, denitrifying and RDX-mineralizing bacterium, designated strain HAW-EB4T, was isolated from the marine sediment. This bacterium utilized peptone, yeast extract, Casamino acids, esters (Tweens 20, 40 and 80), sugars (N-acetyl-d-glucosamine, ribose), several C2 and C3 acids (acetate, pyruvate, lactate, propionate) and amino acids (serine, proline) as sole carbon and energy sources. Aerobically grown cells (in marine broth 2216 at 10 °C) contained C14 : 0 (6 %), iso-C15 : 0 (12 %), C16 : 0 (20 %), C16 : 1 ω7 (37 %), C18 : 1 ω7 (7 %) and C20 : 5 ω3 (7 %) as major membrane fatty acids, and Q7 (28·1 %) and MK-7 (60·9 %) as dominant respiratory quinones, consistent with deep-sea species of Shewanella. The novel bacterium had a DNA G+C content of 45 mol% and showed similarity to Shewanella species in terms of 16S rRNA and gyrB gene sequences (93–99 and 67·3–88·4 % similarity, respectively), with Shewanella pealeana being the most closely related species. Genomic DNA–DNA hybridization between strain HAW-EB4T and S. pealeana revealed a level of relatedness of 17·9 %, lower than the 70 % species cut-off value, indicating that strain HAW-EB4T (=NCIMB 14093T=DSM 17350T) is the type strain of a novel species of Shewanella, for which the name Shewanella halifaxensis sp. nov. is proposed.
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Lysobacter koreensis sp. nov., isolated from a ginseng field
More LessStrain Dae16T, a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from the soil of a ginseng field in South Korea and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain Dae16T belongs to the Gammaproteobacteria and had the highest degree of sequence similarity to Lysobacter gummosus ATCC 29489T (97·1 %), Lysobacter antibioticus DSM 2044T (96·6 %), Lysobacter enzymogenes DSM 2043T (96·2 %), Lysobacter concretionis KCTC 12205T (94·7 %) and Lysobacter brunescens ATCC 29482T (93·7 %). Chemotaxonomic data revealed that strain Dae16T possesses a quinone system with Q-8 as the predominant compound and C15 : 0 iso, C16 : 0 iso and C17 : 1 iso ω9c as the predominant iso-branched fatty acids, all of which corroborated the assignment of the strain to the genus Lysobacter. Results of DNA–DNA hybridization and physiological and biochemical tests clearly demonstrated that strain Dae16T represents a distinct species. Based on these data, it is proposed that Dae16T (=KCTC 12204T=NBRC 101156T) should be classified as the type strain of a novel Lysobacter species, Lysobacter koreensis sp. nov.
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Shewanella hafniensis sp. nov. and Shewanella morhuae sp. nov., isolated from marine fish of the Baltic Sea
More LessTwo novel species belonging to the genus Shewanella are described on the basis of their phenotypic characteristics, phylogenetic analyses of 16S rRNA and gyrB gene sequences and levels of DNA–DNA hybridization. A total of 47 strains belonging to two novel Gram-negative, psychrotolerant, H2S-producing bacterial species were isolated from marine fish (cod and flounder) caught from the Baltic Sea off Denmark. The phenotypic characteristics of strains belonging to group 1 (14 strains) indicated that these represented a non-sucrose-assimilating variant of Shewanella baltica with a DNA G+C content of 47·0 mol%. Strains of group 2 (33 isolates) did not utilize the carbon substrates assimilated by S. baltica except gluconate, N-acetylglucosamine and malate. Their DNA G+C content was 44·0 mol%. Phylogenetic analysis of the 16S rRNA gene sequence data placed the two novel species within the genus Shewanella. Group 1 strains showed greatest sequence similarity to Shewanella putrefaciens ATCC 8071T (99·0 %) and with S. baltica NCTC 10375T (98·3 %). However, gyrB gene sequence analysis showed these isolates to share only 90·0 % sequence similarity with S. putrefaciens ATCC 8071T and 93·9 % with S. baltica NCTC 10375T. Similarly, DNA–DNA hybridization experiments revealed DNA relatedness levels of 38 % between the group 1 isolates and S. putrefaciens ATCC 8071T and 43 % with S. baltica NCTC 10375T. The group 2 strains shared less than 97 % 16S rRNA gene sequence similarities with recognized Shewanella species. Comparisons between the two novel species indicated 16S rRNA gene sequence similarity of ∼98 %, gyrB gene sequence similarity of ∼89 % and DNA–DNA reassociation values of 20–34 %. Based on the evidence presented, two novel species, Shewanella hafniensis sp. nov. (type strain P010T=ATCC BAA-1207T=NBRC 100975T) and Shewanella morhuae sp. nov. (type strain U1417T=ATCC BAA-1205T=NBRC 100978T), are described.
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- Eukaryotic Micro-Organisms
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Pseudozyma hubeiensis sp. nov. and Pseudozyma shanxiensis sp. nov., novel ustilaginomycetous anamorphic yeast species from plant leaves
More LessAmong basidiomycetous yeast strains isolated from wilting leaves of various plants in China, two groups of Pseudozyma strains were distinguished from the others by morphological and physiological characterization. Molecular taxonomic analysis based on sequencing of the large subunit (26S) rRNA gene D1/D2 domain and internal transcribed spacer (ITS) region confirmed that the two groups represent two novel species. They are proposed as Pseudozyma hubeiensis sp. nov. (type strain WS 6.4T=AS 2.2493T=CBS 10077T) and Pseudozyma shanxiensis sp. nov. (type strain SH 64T=AS 2.2523T=CBS 10075T). The phylogenetic relationships of the novel species with described Pseudozyma species and related ustilagomycetous teleomorphs were analysed based on the combined sequences of ITS and D1/D2. The phenotypic diagnosis of Pseudozyma was emended because of the negative inositol assimilation reaction of P. hubeiensis sp. nov., which was closely related to the type species of the genus, Pseudozyma prolifica.
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Rhodotorula pacifica sp. nov., a novel yeast species from sediment collected on the deep-sea floor of the north-west Pacific Ocean
More LessA novel species of the genus Rhodotorula was isolated from sediments collected on the deep-sea floor in the north-west Pacific Ocean. Strains SY-96T, isolated from the Yap Trench, and SY-246, isolated from the Iheya Ridge, had almost identical nucleotide sequences for their internal transcribed spacers and their 5·8S rDNA. Their physiological characteristics were also almost identical. The strains were assumed to be related to Rhodotorula mucilaginosa and Rhodotorula dairenensis based on sequence similarities in the D1/D2 region of the 26S rDNA. The low DNA–DNA relatedness and sequence similarity between strain SY-96T and related species revealed that strains SY-96T and SY-246 represent a hitherto unknown species. As ballistoconidia and sexual reproduction were not observed in strains SY-96T and SY-246, these strains are described as Rhodotorula pacifica sp. nov. The type strain is SY-96T (=JCM 10908T=CBS 10070T).
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Geotrichum vulgare sp. nov., a novel asexual arthroconidial yeast
More LessTwo strains of a novel yeast species were isolated from different habitats, from soil in an alluvial zone national park in Austria and from a drain in a Turkish soft drinks factory. Analysis of the nucleotide sequences of the D1/D2 region of their large-subunit rDNAs and PCR fingerprints show that the strains are members of the same species, described as Geotrichum vulgare sp. nov. Analysis of nucleotide sequences showed that this species is related to the ascogenous genus Galactomyces. The closest phylogenetic relative is Geotrichum silvicola, a recently described species. The type strain of Geotrichum vulgare is HA1379T (=CBS 10073T=NRRL Y-27915T).
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Affiliation of Cochlosoma to trichomonads confirmed by phylogenetic analysis of the small-subunit rRNA gene and a new family concept of the order Trichomonadida
More LessThe protozoan genus Cochlosoma includes parasitic intestinal flagellates of birds and mammals of uncertain taxonomic classification. The presence of an adhesive disc, superficially similar to that of Giardia, led to a proposal that Cochlosoma should be classified as diplomonads. Careful morphological and ultrastructural observations, however, revealed conspicuous homologies to trichomonads. We addressed the question of classification and phylogenetic affiliation of Cochlosoma using the methods of molecular phylogenetics. Analyses based on the 16S rRNA gene sequence of the species Cochlosoma anatis very robustly placed Cochlosoma in the clade of the parabasalid subfamilies Trichomonadinae, Trichomitopsiinae and Pentatrichomonoidinae of the order Trichomonadida (bootstraps >94 %). The data did not provide robust support for any particular position of Cochlosoma within this clade because the sequence suffered from mutational saturation and produced a long branch. The most probable sister taxon of Cochlosoma is the genus Pentatrichomonas, because their relationship was supported specifically by the slowest-mutating, least-saturated positions as determined using the method slow–fast. Classification of the order Trichomonadida was revised to accommodate knowledge about its phylogeny – the family Cochlosomatidae and subfamilies Trichomitopsiinae and Pentatrichomonoidinae were abandoned, Trichomonadidae was amended and new families Tritrichomonadidae (formerly a subfamily) and Trichomitidae were proposed.
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Candida bracarensis sp. nov., a novel anamorphic yeast species phenotypically similar to Candida glabrata
More LessTwo yeast strains, 153MT and NCYC 3133, isolated from clinical sources in separate hospitals were found to be almost identical in the sequences of the D1/D2 domain of large-subunit rDNA, the PCR fingerprinting profiles and physiological characteristics. The isolates are phenotypically similar, although not identical, to Candida glabrata and Kluyveromyces delphensis (recently renamed Nakaseomyces delphensis). Sequence analysis of the 26S rDNA D1/D2 gene variable region revealed that the two clinical isolates were closely related phylogenetically to C. glabrata and K. delphensis, but differed sufficiently to justify their assignment as representatives of a separate species. The name Candida bracarensis sp. nov. is proposed for the novel species with the type strain 153MT (=CBS 10154T=NCYC D3853T=CECT 12000T).
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- Other Gram-Positive Bacteria
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Pilibacter termitis gen. nov., sp. nov., a lactic acid bacterium from the hindgut of the Formosan subterranean termite (Coptotermes formosanus)
More LessA previously undescribed anaerobic, heterofermentative, non-spore-forming, Gram-positive rod was isolated from the hindgut of the Formosan subterranean termite Coptotermes formosanus Shiraki. The DNA G+C content of this bacterium was 37·8 mol%. Sequence analysis of the 16S rRNA gene revealed that this organism is related to, but distinct from, several genera of lactic acid bacteria, principally several species of the genus Enterococcus. Phenotypic traits that serve to separate this organism from related genera include high levels of the cellular fatty acid C18 : 1ω9c and the production of ethanol along with lactic acid as fermentation products. Based on the collected phylogenetic and phenotypic evidence, it is proposed that the unknown organism represents a novel species in a new genus, Pilibacter termitis gen. nov., sp. nov. The type strain is TI-1T (=ATCC BAA-1030T=CCUG 49613T).
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Lactobacillus sobrius sp. nov., abundant in the intestine of weaning piglets
To obtain porcine isolates related to Lactobacillus amylovorus, we screened strains from piglet intestine grown on Lactobacillus-specific MRS agar for hybridization to a fluorescent 16S rRNA-targeted DNA probe. Six strains were isolated and further characterized by phenotypic and molecular taxonomic methods. The isolates were Gram-positive, catalase-negative, facultatively anaerobic rods. They had similar phenotypic characteristics and displayed genomic DNA–DNA relatedness values of >78 % to each other, indicating that they belong to a single species. Comparative 16S rRNA gene sequence analysis demonstrated that the novel isolates were members of Lactobacillus rRNA group I, which includes Lactobacillus delbrueckii, the type species of the genus. Based on 16S rRNA gene sequence similarity, Lactobacillus kitasatonis (99 %), Lactobacillus crispatus (98 %) and Lactobacillus amylovorus (97 %) were the nearest relatives of the novel isolates, but their DNA–DNA relatedness was found to be lower than 49 %. One of the isolates, strain OTU171-001T, was further characterized using physiological and biochemical tests. Together, the results enabled genotypic and phenotypic differentiation of strain OTU171-001T from the other species that showed 16S rRNA gene sequence similarity values greater than 97 %. Strain OTU171-001T merits species status and the name Lactobacillus sobrius sp. nov. is proposed. The type strain is OTU171-001T (=DSM 16698T=NCCB 100067T).
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Bacillus koreensis sp. nov., a spore-forming bacterium, isolated from the rhizosphere of willow roots in Korea
More LessAn endospore-forming, rod-shaped bacterium was isolated from the rhizosphere of willow roots in Korea. The bacterium, designated strain BR030T, was a strictly aerobic, motile rod. The cell wall contained type A1γ peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The major cellular phospholipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and unknown phospholipids (PL1, PL2). The genomic DNA G+C content was 36 mol%. Comparative 16S rRNA gene sequence analyses showed that strain BR030T formed a distinct phyletic line within the genus Bacillus and was most closely related to Bacillus flexus DSM 1320T, with 16S rRNA gene sequence similarity of 96·8 %. Sequence similarities to other type strains were lower than 96·2 %. On the basis of physiological and molecular properties, the isolate represents a novel species within the genus Bacillus, for which the name Bacillus koreensis sp. nov. is proposed. The type strain is BR030T (=KCTC 3914T=DSM 16467T).
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Reclassification of Leuconostoc argentinum as a later synonym of Leuconostoc lactis
Leuconostoc argentinum, Leuconostoc lactis and ten related strains from Romanian dairy products formed a single cluster, clearly separated from other Leuconostoc species, after numerical analysis of repetitive extragenic palindromic-PCR patterns, whole-cell protein profiles (SDS-PAGE) and fluorescent amplified fragment length polymorphism (FAFLP) band patterns. 16S rRNA gene sequence analysis confirmed a very high similarity between both type strains and representative dairy isolates (>99·6 %). DNA–DNA hybridization experiments revealed high relatedness values between the type strains of L. argentinum and L. lactis and between these strains and representative Romanian strains. These data and the lack of phenotypic distinctive characteristics demonstrate that L. argentinum and L. lactis are synonymous.
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Virgibacillus koreensis sp. nov., a novel bacterium from a salt field, and transfer of Virgibacillus picturae to the genus Oceanobacillus as Oceanobacillus picturae comb. nov. with emended descriptions
More LessA novel Virgibacillus strain, BH30097T, was isolated from a salt field near Taean-Gun on the Yellow Sea in Korea. Cells were Gram-positive rods and bore ellipsoidal endospores in terminal positions. The optimum pH and temperature for growth of this organism were pH 7 and 25 °C, respectively. The main respiratory quinone was MK-7 and the major cellular fatty acids were anteiso-C15 : 0 and iso-C16 : 0. Analysis based on 16S rRNA gene sequence data revealed that the isolate formed an evolutionary lineage distinct from other Virgibacillus species. Levels of sequence similarity between the isolate and other Virgibacillus species ranged from 93·8 to 96·7 %. DNA–DNA relatedness values between strain BH30097T and a phylogenetically closely related strain, Virgibacillus halodenitrificans KCTC 3790T, were less than 24 %. On the basis of morphological, physiological and chemotaxonomic characteristics, 16S rRNA gene sequence comparison and DNA–DNA hybridization, a novel species, Virgibacillus koreensis sp. nov., is proposed, with the type strain BH30097T (=KCTC 3823T=JCM 12387T). It is also proposed that Virgibacillus picturae be transferred to the genus Oceanobacillus as Oceanobacillus picturae comb. nov. based on its 16S rRNA gene sequences and other taxonomic characteristics.
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‘Candidatus Phytoplasma fragariae’, a novel phytoplasma taxon discovered in yellows diseased strawberry, Fragaria×ananassa
More LessSymptoms of general stunting and yellowing of leaves were observed in diseased cultivated strawberry (Fragaria×ananassa Duchesne) in Lithuania. Analysis of 16S rRNA gene sequences amplified by PCR indicated that the symptoms were associated with infection by a phytoplasma, designated strawberry yellows (StrawY) phytoplasma. Phylogenetic analysis of 16S rRNA gene sequences indicated that StrawY phytoplasma, ‘Candidatus Phytoplasma australiense’, ‘Candidatus Phytoplasma asteris’, stolbur phytoplasma and ‘Candidatus Phytoplasma japonicum’ shared a common ancestor, but were mutually distinct. Nucleotide sequence alignments of a 1·3 kb 16S rRNA gene sequence fragment revealed that StrawY phytoplasma shared 97·4 % or less similarity with previously described ‘Candidatus Phytoplasma’ species. These results, in addition to natural host and geographical occurrence, support the recognition of StrawY phytoplasma as a representative of a novel taxon, ‘Candidatus Phytoplasma fragariae’.
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- Evolution, Phylogeny And Biodiversity
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Molecular evolution of the nif gene cluster carrying nifI 1 and nifI 2 genes in the Gram-positive phototrophic bacterium Heliobacterium chlorum
More LessA major nif cluster was detected in the strictly anaerobic, Gram-positive phototrophic bacterium Heliobacterium chlorum. The cluster consisted of 11 genes arranged within a 10 kb region in the order nifI 1, nifI 2, nifH, nifD, nifK, nifE, nifN, nifX, fdx, nifB and nifV. The phylogenetic position of Hbt. chlorum was the same in the NifH, NifD, NifK, NifE and NifN trees; Hbt. chlorum formed a cluster with Desulfitobacterium hafniense, the closest neighbour of heliobacteria based on the 16S rRNA phylogeny, and two species of the genus Geobacter belonging to the Deltaproteobacteria. Two nifI genes, known to occur in the nif clusters of methanogenic archaea between nifH and nifD, were found upstream of the nifH gene of Hbt. chlorum. The organization of the nif operon and the phylogeny of individual and concatenated gene products showed that the Hbt. chlorum nif operon carrying nifI genes upstream of the nifH gene was an intermediate between the nif operon with nifI downstream of nifH (group II and III of the nitrogenase classification) and the nif operon lacking nifI (group I). Thus, the phylogenetic position of Hbt. chlorum nitrogenase may reflect an evolutionary stage of a divergence of the two nitrogenase groups, with group I consisting of the aerobic diazotrophs and group II consisting of strictly anaerobic prokaryotes.
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Molecular signatures in protein sequences that are characteristics of the phylum Aquificae
More LessSpecies of the phylum Aquificae are of great interest due to their strict extreme thermophilic growth characteristics. Presently, there is no known molecular characteristic which is unique to this group of bacteria. This work describes six conserved inserts and deletions (indels or signature sequences) in four widely distributed proteins that are distinctive features of species from the phylum Aquificae. These include three signatures consisting of a 2 aa insert, a 5–6 aa insert and a 6 aa deletion in DNA polymerase I (PolA), a 6–7 aa insert in glucose-inhibited protein A (GidA), a 52 aa insert in the RNA polymerase β′-subunit (RpoC) and a 4 aa insert in elongation factor Tu (EF-Tu). Fragments of these genes were amplified in most cases from Hydrogenobacter hydrogenophilus, Hydrogenothermus marinus and Thermocrinis ruber and combined with available sequence data from ‘Aquifex aeolicus’ and Sulfurihydrogenibium azorense. The presence of the PolA, GidA and RpoC indels in all of the species sequenced provides evidence that they are probably distinctive characteristics of the entire phylum. The indel in EF-Tu, which is shared by Aquifex species and Hydrogenobacter but not Hydrogenothermus and Sulfurihydrogenibium, may provide a molecular marker for the family Aquificaceae. We have also identified a 51 aa insert in SecA preprotein translocase that is commonly shared by various species of the Aquificae as well as two Thermotoga species (Thermotoga maritima and Thermotoga neapolitana) which may be due to lateral gene transfer between these groups. In phylogenetic trees based on a concatenated dataset of fragments from eight different proteins as well as 16S rRNA, the observed branching pattern of these species was very similar and it was consistent with the relationships inferred from various indels. The identified indels provide a novel means for distinguishing species of the Aquificae from all other bacteria in molecular terms and may prove useful for functional studies aimed at understanding the unique biochemical and physiological characteristics of the Aquificae.
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RFLP analysis of the rRNA operon of a Brazilian collection of bradyrhizobial strains from 33 legume species
More LessGenetic diversity in tropical rhizobial species is still poorly known. With the aim of increasing this knowledge, three ribosomal regions of 119 strains belonging to the official Brazilian culture collection of rhizobia and classified as Bradyrhizobium based on morphological and physiological characteristics in vitro were analysed by RFLP-PCR. The strains were isolated from 33 legume species, representing nine tribes and all three subfamilies; they all form very effective N2-fixing nodules and 43 of them are recommended for use in Brazilian commercial inoculants as the most effective for their hosts. For the 16S rRNA gene, type and reference strains of Bradyrhizobium japonicum fell into two major clusters, joined at a level of similarity of 50 %, which included 52 strains, 90 % of which were isolated from soybean. Two other clusters, joined at a similarity of 53 %, included reference strains of Bradyrhizobium elkanii, but not USDA 76T; furthermore, two other major clusters were identified and all strains were clustered at a final level of similarity of only 28 %. For the intergenic spacer (IGS) between genes coding for the 16S and 23S rRNA, strains were clustered at a final level of similarity of 27 %. Reference strains of B. japonicum fell into a major group with 51 strains, 84 % isolated from soybean, with a similarity of 59 %, while strains of B. elkanii fell into another major group, with a similarity of 55 %, clustering 44 strains, 59 % of which were isolated from hosts other than soybean. New clusters were also observed for the IGS region. The largest number of differences was detected in the analysis of the 23S rRNA gene, and 16 groups and isolated strains were joined at a very low level of similarity (16 %). In a combined analysis with the three ribosomal regions, the majority of strains isolated from soybean clustered with a similarity of 54 % with type and reference strains of B. japonicum, while most strains isolated from Brazilian indigenous legume species grouped with B. elkanii at a level of similarity of 46 %. All strains were clustered at a very low level of similarity (27 %), and at least two new clusters were clearly defined. These new clusters might be related to intraspecific differences or to novel subspecies, or even to novel species; indeed, strains from one of these clusters show higher 16S rRNA gene sequence similarity to members of the genus Burkholderia. The results obtained in this study emphasize the high level of diversity of symbiotic diazotrophic bacteria in the tropics that still remains to be determined.
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