- Volume 55, Issue 3, 2005
Volume 55, Issue 3, 2005
- Validation List No. 103
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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 55, 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). 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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- New Taxa
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- Archaea
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Desulfurococcus fermentans sp. nov., a novel hyperthermophilic archaeon from a Kamchatka hot spring, and emended description of the genus Desulfurococcus
An obligately anaerobic, hyperthermophilic, organoheterotrophic archaeon, strain Z-1312T, was isolated from a freshwater hot spring of the Uzon caldera (Kamchatka Peninsula, Russia). The cells were regular cocci, 1–4 μm in diameter, with one long flagellum. The cell envelope was composed of a globular layer attached to the cytoplasmic membrane. The temperature range for growth was 63–89 °C, with an optimum between 80 and 82 °C. The pH range for growth at 80 °C was 4·8–6·8, with an optimum at pH 6·0. Strain Z-1312T grew by hydrolysis and/or fermentation of a wide range of polymeric and monomeric substrates, including agarose, amygdalin, arabinose, arbutin, casein hydrolysate, cellulose (filter paper, microcrystalline cellulose, carboxymethyl cellulose), dextran, dulcitol, fructose, lactose, laminarin, lichenan, maltose, pectin, peptone, ribose, starch and sucrose. No growth was detected on glucose, xylose, mannitol or sorbitol. Growth products when sucrose or starch were used as the substrate were acetate, H2 and CO2. Elemental sulfur, thiosulfate and nitrate added as potential electron acceptors for anaerobic respiration did not stimulate growth when tested with starch as the substrate. H2 at 100 % in the gas phase did not inhibit growth on starch or peptone. The G+C content of the DNA was 42·5 mol%. 16S rRNA gene sequence analysis placed the isolated strain Z-1312T as a member of the genus Desulfurococcus, where it represented a novel species, for which the name Desulfurococcus fermentans sp. nov. (type strain Z-1312T=DSM 16532 T=VKM V-2316T) is proposed.
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Methanogenium frittonii Harris et al. 1996 is a later synonym of Methanoculleus thermophilus (Rivard and Smith 1982) Maestrojuán et al. 1990
More LessThe 16S rRNA gene sequence of [Methanogenium] frittonii DSM 2832T was determined and was found to be 99·9 % similar to the sequence of Methanoculleus thermophilus DSM 2373T. DNA–DNA hybridizations between both strains revealed 86 % DNA–DNA binding, indicating that both strains belong to the same species. The determination of the DNA G+C content of both type strains, DSM 2832T and DSM 2373T, revealed values of 56·1 and 59·1 mol%, respectively. Based on the phenotypic and genotypic characteristics, it is proposed to unite the species [Methanogenium] frittonii and Methanoculleus thermophilus under the name Methanoculleus thermophilus, which is the earlier synonym and hence has priority. Emended descriptions of the species Methanoculleus thermophilus and the genus Methanogenium are also given.
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Natrinema altunense sp. nov., an extremely halophilic archaeon isolated from a salt lake in Altun Mountain in Xinjiang, China
More LessA novel extremely halophilic strain, AJ2T, was isolated from Ayakekum salt lake located in the Altun Mountain National Nature Reserve in Xinjiang, China. This isolate was neutrophilic, motile and grew in a wide range of MgCl2 concentrations (0·005–1·0 M). The major polar lipids of the isolate were C20C20 and C20C25 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate. A comprehensive 16S rRNA gene sequence analysis revealed that the isolate shared 96·6–97·7 % sequence identity with Natrinema species. The isolate, however, could be genetically differentiated from these species by DNA–DNA hybridization analysis and on the basis of its physiological properties. On the basis of the polyphasic evidence, strain AJ2T (=AS 1.3731T=JCM 12890T) represents the type strain of a novel species, for which the name Natrinema altunense sp. nov. is proposed.
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- Other Bacteria
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Muricauda flavescens sp. nov. and Muricauda aquimarina sp. nov., isolated from a salt lake near Hwajinpo Beach of the East Sea in Korea, and emended description of the genus Muricauda
More LessFour Gram-negative, non-spore-forming, slightly halophilic rods (strains SW-62T, SW-74, SW-63T and SW-72) with appendages were isolated from a salt lake near Hwajinpo Beach on the East Sea in Korea, and subjected to a polyphasic taxonomic analysis. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SW-62T, SW-74, SW-63T and SW-72 formed a coherent cluster with Muricauda ruestringensis. Strains SW-62T and SW-74 had the same 16S rRNA gene sequence, as did strains SW-63T and SW-72. The level of 16S rRNA gene sequence similarity between strains SW-62T and SW-63T was 97·0 %. Strains SW-62T and SW-63T exhibited 16S rRNA gene similarity levels of 96·5 and 98·3 %, respectively, with respect to M. ruestringensis DSM 13258T. The predominant isoprenoid quinone found in the four isolates and M. ruestringensis DSM 13258T was MK-6. The four strains contained iso-C17 : 0 3-OH, iso-C15 : 1 and iso-C15 : 0 as the major fatty acids. Their DNA G+C contents were 44·1–45·4 mol%. The levels of DNA–DNA relatedness indicated that strains SW-62T and SW-74 and strains SW-63T and SW-72 were members of two species that were different from M. ruestringensis. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strains SW-62T and SW-74 and strains SW-63T and SW-72 were placed in the genus Muricauda as two distinct novel species, for which the names Muricauda flavescens sp. nov. (type strain, SW-62T=KCCM 41645T=JCM 11812T) and Muricauda aquimarina sp. nov. (type strain, SW-63T=KCCM 41646T=JCM 11811T), respectively, are proposed.
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Reclassification of [Cytophaga] marinoflava Reichenbach 1989 as Leeuwenhoekiella marinoflava gen. nov., comb. nov. and description of Leeuwenhoekiella aequorea sp. nov.
Five heterotrophic, aerobic, halotolerant and pigmented bacterial strains with gliding motility were isolated from Antarctic sea water; one other isolate was collected from the sea urchin Strongylocentrotus intermedius in the Gulf of Peter the Great in the Sea of Japan. 16S rRNA gene sequence analysis indicated that the strains are members of the family Flavobacteriaceae, the nearest neighbour (with 97·1 % sequence similarity) being the misclassified species [Cytophaga] marinoflava. DNA–DNA hybridization experiments and chemotaxonomic and phenotypic analyses demonstrated that the six novel isolates represent a single species distinct from [C.] marinoflava. On the basis of its separate phylogenetic lineage (the nearest neighbours show 92 % sequence similarity), [C.] marinoflava is reclassified as Leeuwenhoekiella marinoflava gen. nov., comb. nov. A second species of this new genus, Leeuwenhoekiella aequorea sp. nov., is proposed for the six novel isolates, with strain LMG 22550T (=CCUG 50091T) as the type strain.
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Owenweeksia hongkongensis gen. nov., sp. nov., a novel marine bacterium of the phylum ‘Bacteroidetes’
An aerobic, Gram-negative, non-fermentative, rod-shaped, motile, orange-pigmented bacterium, UST20020801T, was isolated from sea-water samples collected from Port Shelter, Hong Kong, S.A.R., China, in August 2002. The full 16S rRNA gene sequence of this strain shared only 87·5 % similarity with its nearest relative, Crocinitomix catalasitica, a species of the family Cryomorphaceae. However, strain UST20020801T possessed menaquinone-6, a major respiratory quinone of members of the family Flavobacteriaceae. This strain contains unique fatty acids such as i15 : 1G, i17 : 1ω9c, 2-OH 15 : 0, 15 : 1ω6c and three unknown fatty acids of equivalent chain-length of 11·543, 13·565 and 16·582. Further analysis of its ecophysiology and biochemistry suggests that this strain represents a new genus in the phylum ‘Bacteroidetes’. The name Owenweeksia hongkongensis gen. nov., sp. nov. is proposed. The type strain is UST20020801T (=NRRL B-23963T=JCM 12287T).
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Pedobacter himalayensis sp. nov., from the Hamta glacier located in the Himalayan mountain ranges of India
More LessStrain HHS 22T was isolated from a glacial water sample from the snout of the Hamta glacier located in the Himalayan mountain ranges of India. Phenotypic, chemotaxonomic and phylogenetic analyses established the affiliation of the isolate to the genus Pedobacter. HHS 22T exhibits high 16S rRNA gene sequence similarity with Pedobacter cryoconitis (98 %). However, the level of DNA–DNA relatedness between HHS 22T and P. cryoconitis is only 42 %. Furthermore, HHS 22T differs from P. cryoconitis and the four other recognized species of Pedobacter in a number of phenotypic characteristics. These data suggest that HHS 22T represents a novel species of the genus Pedobacter, for which the name Pedobacter himalayensis sp. nov. is proposed. The type strain is HHS 22T (=JCM 12171T=MTCC 6384T).
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Petrimonas sulfuriphila gen. nov., sp. nov., a mesophilic fermentative bacterium isolated from a biodegraded oil reservoir
More LessA mesophilic, anaerobic, fermentative bacterium, strain BN3T, was isolated from a producing well of a biodegraded oil reservoir in Canada. Cells were Gram-negative, non-motile rods that did not form spores. The temperature range for growth was 15–40 °C, with optimum growth at 37–40 °C. The strain grew with up 4 % NaCl, with optimum growth in the absence of NaCl. Tryptone was required for growth. Yeast extract and elemental sulfur stimulated growth. Growth was also enhanced during fermentation of glucose, arabinose, galactose, maltose, mannose, rhamnose, lactose, ribose, fructose, sucrose, cellobiose, lactate, mannitol and glycerol. Acetate, hydrogen and CO2 were produced during glucose fermentation. Elemental sulfur and nitrate were used as electron acceptors and were reduced to sulfide and ammonium, respectively. The G+C content of the genomic DNA was 40·8 mol%. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the strain was a member of the phylum ‘Bacteroidetes’, distantly related to the genera Bacteroides and Tannerella (similarity values of less than 90 %). The chemotaxonomic data (fatty acids, polar lipids and quinones composition) also indicated that strain BN3T could be clearly distinguished from its closest cultivated relatives. This novel organism possesses phenotypic, chemotaxonomic and phylogenetic traits that do not allow its classification as a member of any previously described genus; therefore, it is proposed that this isolate should be described as a member of a novel species of a new genus, Petrimonas gen. nov., of which Petrimonas sulfuriphila sp. nov. is the type species. The type strain is BN3T (=DSM 16547T=JCM 12565T).
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Mucispirillum schaedleri gen. nov., sp. nov., a spiral-shaped bacterium colonizing the mucus layer of the gastrointestinal tract of laboratory rodents
The mammalian gastrointestinal tract is covered by a layer of mucus that can harbour a range of bacterial species specifically adapted to colonize this ecological niche. Examination of 110 bacterial isolates cultivated from the gastrointestinal tract of 23 mice revealed the presence of a subgroup of 30 isolates that did not correspond genetically with genera commonly associated with this site, i.e. members of the ε-Proteobacteria such as Helicobacter and Campylobacter species. Instead this group of isolates was found to lie within the phylum Deferribacteres, a completely distinct lineage in the domain Bacteria. There was a high level of consensus in results obtained from the phenotypic and genotypic characterization of a number of the isolates, which showed they were distinct from other members of the Deferribacteres. As such, they are proposed to constitute a new genus and species, Mucispirillum schaedleri gen. nov., sp. nov. These organisms are anaerobic, Gram-negative, spiral-shaped rods with bipolar flagella. The type strain is HRI I17T (=ATCC BAA-1009T=ACM 5223T).
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Marinitoga hydrogenitolerans sp. nov., a novel member of the order Thermotogales isolated from a black smoker chimney on the Mid-Atlantic Ridge
A novel, thermophilic, anaerobic bacterium that is able to tolerate hydrogen was isolated from a deep-sea hydrothermal chimney collected at the Rainbow field on the Mid-Atlantic Ridge. Cells were rod-shaped and surrounded by a sheath-like outer structure (toga); they were weakly motile by means of a polar flagellum. They appeared singly, in pairs or in short chains. They grew at 35–65 °C (optimum 60 °C), pH 4·5–8·5 (optimum pH 6·0) and 10–65 g sea salts l−1 (optimum 30–40 g l−1). The isolate was organotrophic, and able to grow on various carbohydrates or complex proteinaceous substrates. Growth was not inhibited under 100 % hydrogen or in the presence of 2 % oxygen in the gas phase. The isolate reduces sulfur, although sulfur reduction is not required for growth. The fermentation products identified on glucose were acetate, ethanol, formate, hydrogen and CO2. The G+C content of the genomic DNA was 28±1 mol%. Phylogenetic analysis of the 16S rRNA gene placed the strain within the genus Marinitoga, order Thermotogales, in the bacterial domain. On the basis of the 16S rRNA gene sequence comparisons and physiological characteristics, the isolate is considered to represent a novel species, for which the name Marinitoga hydrogenitolerans sp. nov. is proposed. The type strain is AT1271T (=DSM 16785T=JCM 12826T).
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Transfer of Chryseobacterium meningosepticum and Chryseobacterium miricola to Elizabethkingia gen. nov. as Elizabethkingia meningoseptica comb. nov. and Elizabethkingia miricola comb. nov.
More LessThe taxonomic positions of six strains (including the type strain) of Chryseobacterium meningosepticum ( King 1959 ) Vandamme et al. 1994 and the type strain of Chryseobacterium miricola Li et al. 2004 were re-evaluated by using a polyphasic taxonomic approach. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that the strains represent a separate lineage from the type strains of the Chryseobacterium–Bergeyella–Riemerella branch within the family Flavobacteriaceae (90·7–93·9 % similarities), which was supported by phenotypic differences. Combined phylogenetic and phenotypic data showed that C. meningosepticum and C. miricola should be transferred to a new genus, Elizabethkingia gen. nov., with the names Elizabethkingia meningoseptica comb. nov. (type strain, ATCC 13253T=NCTC 10016T=LMG 12279T=CCUG 214T) and Elizabethkingia miricola comb. nov. (type strain, DSM 14571T=JCM 11413T=GTC 862T) proposed.
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Dyadobacter crusticola sp. nov., from biological soil crusts in the Colorado Plateau, USA, and an emended description of the genus Dyadobacter Chelius and Triplett 2000
More LessBacterial strain CP183-8T was isolated from biological soil crusts collected in the Colorado Plateau, USA. Cells of this strain were aerobic, non-motile, Gram-negative, psychrotolerant and formed beaded chains in the stationary growth phase. They contained C16 : 1 ω5c and C16 : 1 ω7c as major fatty acids. 16S rRNA gene sequence analysis assigned the strain to the genus Dyadobacter. However, it shared a sequence similarity of only 95·88 % with the type strain of Dyadobacter fermentans, NS114T. Because it also exhibited a significant number of phenotypic and chemotaxonomic differences from D. fermentans, it is described as a novel second species in the genus Dyadobacter, with the name Dyadobacter crusticola sp. nov. The type strain is CP183-8T (=DSM 16708T=ATCC BAA-1036T).
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Chryseobacterium taichungense sp. nov., isolated from contaminated soil
More LessA bacterial strain (CC-TWGS1-8T) isolated from a tar-contaminated soil in Taiwan was studied in a detailed taxonomic study. The cells were Gram-negative, rod-shaped and non-spore-forming. Phylogenetic analyses using the 16S rRNA gene sequence of the strain clearly revealed an affiliation to the genus Chryseobacterium, the highest sequence similarities being to the type strain of Chryseobacterium indologenes (96·8 %), to Chryseobacterium gleum (96·8 %) and to Chryseobacterium joostei (96·4 %). The 16S rRNA gene sequence similarities to all other Chryseobacterium species were below 96 %. The major whole-cell fatty acids were 15 : 0 iso (35·4 %) and 17 : 0 iso 3OH (22·5 %). DNA–DNA hybridization values and the biochemical and chemotaxonomic properties demonstrate that strain CC-TWGS1-8T represents a novel species, for which the name Chryseobacterium taichungense sp. nov. is proposed. The type strain is CC-TWGS1-8T (=CCUG 50001T=CIP 108519T).
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Pedobacter caeni sp. nov., a novel species isolated from a nitrifying inoculum
More LessA Gram-negative, rod-shaped, non-spore-forming bacterium was isolated from a nitrifying inoculum. On the basis of 16S rRNA gene sequence similarity, LMG 22862T was shown to belong to the family Sphingobacteriaceae, related to Pedobacter africanus (98·0 %) and Pedobacter heparinus (97·6 %). The results of 16S rRNA gene sequence analysis, DNA–DNA hybridization, SDS-PAGE, analysis of the fatty acid composition and physiological and biochemical tests allowed genotypic and phenotypic differentiation of LMG 22862T from Pedobacter species with validly published names. LMG 22862T therefore represents a novel species within this genus, for which the name Pedobacter caeni sp. nov. is proposed, with the type strain LMG 22862T (=DSM 16990T).
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Bacteroides massiliensis sp. nov., isolated from blood culture of a newborn
More LessGram-negative anaerobic rods were isolated from blood culture of a healthy baby born at term. Based on phylogenetic analysis and specific phenotypic characteristics, this strain was included within the Bacteroides cluster. The novel bile-resistant anaerobic species was designated Bacteroides massiliensis and it has 92·8 % 16S rRNA similarity to Bacteroides vulgatus and a DNA G+C content of 49 mol%. The major cellular fatty acid is anteiso-branched C15 : 0. The type strain of B. massiliensis sp. nov. is B84634T (=CIP 107942T=CCUG 48901T).
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- Proteobacteria
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Desulfonatronum cooperativum sp. nov., a novel hydrogenotrophic, alkaliphilic, sulfate-reducing bacterium, from a syntrophic culture growing on acetate
More LessA novel alkaliphilic, sulfate-reducing bacterium was isolated from a syntrophic acetate-decomposing community enriched from samples of the soda lake Khadin, Tuva, Russia; the isolate was designated strain Z-7999T. Cells of strain Z-7999T were vibrioid, Gram-negative, 0·4–0·5×1·0–2·5 μm and motile by means of a polar flagellum. The temperature range for growth was 15–40 °C, with an optimum of 35–38 °C. The pH range for growth was 6·7–10·3, with an optimum of pH 8·0–9·0. The NaCl concentration range for growth was 1–80 g l−1. The novel isolate was obligately anaerobic, was alkaliphilic with a broad pH range and had an obligate requirement for carbonate ions in the growth medium. In the presence of sulfate as electron acceptor, it grew with hydrogen, formate and lactate. It was not able to ferment sugars, organic acids, amino acids or peptides. During growth on formate, strain Z-7999T reduced sulfite and thiosulfate to sulfide. It was able to grow lithoheterotrophically with sulfate and formate when acetate was added as a carbon source for biosynthesis of biomass. The G+C content of the genomic DNA of strain Z-7999T was 56·5 mol%. Results of comparative 16S rRNA gene sequence analyses revealed that strain Z-7999T was part of the δ-Proteobacteria and clustered with other members of the genus Desulfonatronum (similarity values of 95·2 and 95·3 % to Desulfonatronum lacustre and Desulfonatronum thiodismutans, respectively). DNA–DNA hybridization with D. lacustre was 37 %. On the basis of physiological and phylogenetic data, it is proposed that strain Z-7999T (=DSM 16749T=VKM B-2329T) should be placed in the genus Desulfonatronum as a representative of a novel species, Desulfonatronum cooperativum sp. nov.
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Psychrobacter aquimaris sp. nov. and Psychrobacter namhaensis sp. nov., isolated from sea water of the South Sea in Korea
More LessTwo Gram-negative, non-motile, non-spore-forming, slightly halophilic bacterial strains, SW-210T and SW-242T, were isolated from sea water of the South Sea in Korea, and were characterized taxonomically by means of a polyphasic approach. The two isolates grew optimally at 25–30 °C and in the presence of 2–3 % (w/v) NaCl. Strains SW-210T and SW-242T contained Q-8 as the predominant respiratory lipoquinone and C18 : 1 ω9c as the major fatty acid. The DNA G+C contents of strains SW-210T and SW-242T were 43·2 and 45·3 mol%, respectively. The 16S rRNA gene sequences of strains SW-210T and SW-242T were 98·9 % similar, and the mean DNA–DNA relatedness value between them was 24 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains SW-210T and SW-242T form distinct phylogenetic lineages within the radiation of the cluster comprising Psychrobacter species, having 16S rRNA gene sequence similarity levels of 95·9–99·2 % with respect to the type strains of Psychrobacter species. The levels of DNA–DNA relatedness between the two isolates and the type strains of 15 phylogenetically related Psychrobacter species were well below 70 %. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strains SW-210T and SW-242T were classified in the genus Psychrobacter as representing two distinct novel species, for which the names Psychrobacter aquimaris sp. nov. (type strain, SW-210T=KCTC 12254T=DSM 16329T) and Psychrobacter namhaensis sp. nov. (type strain, SW-242T=KCTC 12255T=DSM 16330T) are proposed, respectively.
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Thiovirga sulfuroxydans gen. nov., sp. nov., a chemolithoautotrophic sulfur-oxidizing bacterium isolated from a microaerobic waste-water biofilm
More LessA novel mesophilic, chemolithoautotrophic, sulfur-oxidizing bacterium, designated strain SO07T, was isolated from a microaerobic waste-water biofilm. Chemolithoautotrophic growth was observed with elemental sulfur, sulfide and thiosulfate as sole electron donors and oxygen as electron acceptor. Anaerobic and heterotrophic growth were not observed. Nitrate was not used as a terminal electron acceptor. The optimum pH and temperature for growth were pH 7·5 and 30 °C, respectively. The major isoprenoid quinone was Q-8. The DNA G+C content of strain SO07T was 47·1 mol%. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that strain SO07T formed a monophyletic group in the γ-Proteobacteria with only 89 % similarity to members of the genus Halothiobacillus, its nearest phylogenetic neighbours. In addition, the isolate differed from members of the genus Halothiobacillus in its requirement for and tolerance of NaCl; strain SO07T was unable to grow in NaCl concentrations of more than 180 mM. On the basis of phylogenetic, chemotaxonomic and physiological data, it is proposed that isolate SO07T (=JCM 12417T=ATCC BAA-1033T) represents the type strain of a novel species in a new genus, Thiovirga sulfuroxydans gen. nov., sp. nov.
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Alteromonas addita sp. nov.
On the basis of phenotypic, genotypic characteristics and analysis of 16S rRNA gene sequences, a novel species belonging to the genus Alteromonas is described. A non-pigmented, motile, Gram-negative bacterium designated R10SW13T was isolated from sea water samples collected in Chazhma Bay (Sea of Japan, Pacific Ocean). The novel organism mainly grew between 4 °C and 37 °C, was neutrophilic and slightly halophilic, tolerating up to 10 % NaCl. Strain R10SW13T was haemolytic and was able to degrade starch and Tween 80 and to degrade gelatin and agar weakly, but did not degrade casein. Phosphatidylethanolamine (44·3±0·9 %) and phosphatidylglycerol (55·7±0·9 %) were the predominant phospholipids. The major fatty acids formed were typical for the genus Alteromonas, including 16 : 0, 16 : 1ω-7 and 18 : 1ω-7. The G+C content of the DNA was 43·4 mol%. DNA–DNA hybridization experiments showed 38–53 % binding with the DNAs of type strains of phylogenetically related species of the genus Alteromonas, namely: Alteromonas macleodii, Alteromonas marina, Alteromonas stellipolaris, Alteromonas litorea, ‘Alteromonas macleodii subsp. fijiensis’ and ‘Alteromonas infernus’. Based on these results, a novel species, Alteromonas addita sp. nov., is proposed, with strain R10SW13T (=KMM 3600T=KCTC 12195T=LMG 22532T) as the type strain.
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Thioclava pacifica gen. nov., sp. nov., a novel facultatively autotrophic, marine, sulfur-oxidizing bacterium from a near-shore sulfidic hydrothermal area
More LessStrain TL 2T was isolated on mineral medium with thiosulfate from a near-shore sulfidic hydrothermal area in Matupi Harbour on the island of New Britain, Papua New Guinea. The cells varied from long filaments with swollen ends, often aggregated, to short rods, depending on the growth conditions. The bacterium was obligately aerobic and grew autotrophically with thiosulfate as energy source or heterotrophically with organic acids and sugars. In thiosulfate-limited continuous culture, μ max and Y max for autotrophic growth were 0·1 h−1 and 3 g protein mol−1, respectively. From the various reduced sulfur compounds tested, only thiosulfate and sulfide supported active respiration. Inorganic carbon was assimilated via the Calvin cycle. Presence of the ‘green’-type of form I RubisCO gene was detected. Growth was possible from 15 to 47 °C with an optimum at 35 °C, pH 6·5–8·5 with an optimum at pH 8·0, and between 10 and 90 g NaCl l−1 with an optimum at 35 g l−1. Phylogenetic analysis based on 16S rRNA and cbbL gene sequences demonstrated that strain TL 2T forms a separate lineage within the alpha-3 subdivision of the Proteobacteria, distantly related to the genera Rhodovulum and Rhodobacter. On the basis of these results, a novel genus and species, Thioclava pacifica gen. nov., sp. nov., is proposed to accommodate strain TL 2T (=DSM 10166T=UNIQEM 229T).
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Pusillimonas noertemannii gen. nov., sp. nov., a new member of the family Alcaligenaceae that degrades substituted salicylates
More LessThe taxonomic position of a Pseudomonas-like strain, designated BN9T, was investigated. This strain had previously been isolated as a 5-aminosalicylate-degrading organism from a 6-aminonaphthalene-2-sulphonate-degrading mixed bacterial culture. Previously, detection of ubiquinone Q-8, a polyamine pattern with putrescine, spermidine and 2-hydroxyputrescine as the major polyamines, and partial 16S rRNA gene sequencing had suggested that strain BN9T belongs to the ‘Betaproteobacteria’. This was supported by sequencing the 16S rRNA gene, which demonstrated 94–96 % sequence similarity to different species of the genera Achromobacter, Alcaligenes and Bordetella, and suggested that strain BN9T represents a member of the family Alcaligenaceae. Different methods for the construction of phylogenetic dendrograms placed the strain separately from all other genera within the Alcaligenaceae. Fatty acid analysis demonstrated the presence of high concentrations of C19 : 0 cyclo ω8c. On the basis of low 16S rRNA gene sequence similarity to other members of the Alcaligenaceae, fatty acid and polar lipid profiles, and other unique phenotypic properties of strain BN9T, the creation of a new genus and species with the name Pusillimonas noertemannii gen. nov., sp. nov. is proposed. The type strain is BN9T (=DSM 10065T=NCIMB 14020T).
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Dinoroseobacter shibae gen. nov., sp. nov., a new aerobic phototrophic bacterium isolated from dinoflagellates
A novel group of aerobic anoxygenic phototrophic bacteria was isolated from marine dinoflagellates, and two strains were characterized in detail. Cells were Gram-negative cocci or ovoid rods and were motile by means of a single, polarly inserted flagellum. They were obligate aerobes requiring 1–7 % salinity. The optimal pH range for growth was 6·5–9·0 and the temperature optimum was 33 °C. The bacteria contained bacteriochlorophyll a and spheroidenone as the only carotenoid. The in vivo absorption spectrum displayed two maxima in the infrared region at 804 and 868 nm. The distinct 804 nm band indicates the presence of light-harvesting system 2. Various organic carbon sources were assimilated, including many carboxylic acids, glucose and glycerol, but not butyrate, ethanol or methanol. Dissimilatory nitrate reduction was found for both strains. The physiological characteristics of the new strains resembled those of Roseobacter denitrificans, but there were differences in the lipid composition. Based on 16S rRNA gene sequence analysis the new strains are relatively distant from other recognized species, with the closest relatives Jannaschia helgolandensis, Ruegeria atlantica and Rhodobacter veldkampii showing 94·1–93·4 % similarity. Similarity to Roseobacter denitrificans was only 92·2 %, in line with numerous other species of the Roseobacter group. Therefore, it is proposed to classify the strains in a new genus and species within the Roseobacter clade, Dinoroseobacter shibae gen. nov., sp. nov. The type strain is DFL 12T (=DSM 16493T=NCIMB 14021T).
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Pseudomonas argentinensis sp. nov., a novel yellow pigment-producing bacterial species, isolated from rhizospheric soil in Córdoba, Argentina
More LessDuring a study in the Argentinian region of Chaco (Córdoba), some strains were isolated from the rhizosphere of grasses growing in semi-desertic arid soils. Two of these strains, one isolated from the rhizospheric soil of Chloris ciliata (strain CH01T) and the other from Pappophorum caespitosum (strain PA01), were Gram-negative, strictly aerobic rods, which formed yellow round colonies on nutrient agar. They produced a water-insoluble yellow pigment, and a fluorescent pigment was also detected. A polyphasic taxonomic approach was used to characterize the strains. Comparison of the 16S rRNA gene sequences showed a similarity of 99·3 % between them, and phylogenetic analysis revealed that the strains belong to the genus Pseudomonas, within the γ-subclass of the Proteobacteria. The closest related species is Pseudomonas straminea IAM 1598T (similarity of 99·0 % to strain CH01T and 98·8 % to strain PA01), clustering in a separate branch with the various methods of tree building used. Strains CH01T and PA01 both had a single polar flagellum, like other yellow pigment-producing pseudomonads related to them. Both strains produced catalase and oxidase. Similar to P. straminea, they did not hydrolyse gelatin or casein. The G+C DNA contents determined were 57·5 mol% for CH01T and 58·0 mol% for PA01. DNA–DNA hybridization results showed 81 % relatedness between them, and only 40–44 % relatedness with respect to the type strain of P. straminea. These results, together with other phenotypic characteristics, support the conclusion that both isolates belong to the same species, and should be described as representing a novel species within the genus Pseudomonas, for which the name Pseudomonas argentinensis sp. nov. is proposed. The type strain is CH01T (=LMG 22563T=CECT 7010T).
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Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China
A taxonomic study was performed on strain YIM 31775T, which was isolated from a soil sample collected from Yunnan Province, China. The isolate was chemo-organotrophic, aerobic and Gram-negative. Cells were short rods and motile, with one or more polar flagella. Growth temperature and pH ranged from 4 to 55 °C and 6·5 to 12·0, respectively; the optimum growth temperature and pH were 28–37 °C and 7·0–9·0, respectively. Q-8 was the predominant respiratory lipoquinone. The major fatty acids were C16 : 1 ω7c (42·4 %) and C16 : 0 (28·1 %). The DNA G+C content was 62·4±0·3 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM 31775T should be placed within the family ‘Oxalobacteraceae’, in which it formed a distinct lineage. Based on the high 16S rRNA gene sequence divergence and phenotypic characteristics, it is proposed that strain YIM 31775T should be classified as representing a novel member of the family ‘Oxalobacteraceae’, for which the name Naxibacter alkalitolerans gen. nov., sp. nov. is proposed. The type strain is YIM 31775T (=CCTCC AA 204003T=KCTC 12194T).
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Lysobacter concretionis sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket reactor
More LessThe taxonomic positions of Lysobacter species with validly published names and a novel strain Ko07T, which was newly isolated from an upflow anaerobic sludge blanket reactor treating wastewater from a brewery, were (re)estimated on the basis of results obtained by using a polyphasic taxonomy approach. Phylogenetic inference based on 16S rRNA gene sequences showed that strain Ko07T and all Lysobacter species with validly published names clustered together in a phylogenetic branch within the class ‘Gammaproteobacteria’. The sequence similarity of strain Ko07T to the type strains of established Lysobacter species was in the range 94·9–96·7 %. Ubiquinone Q-8 and branched fatty acids, C11 : 0 iso, C15 : 0 iso, C16 : 0 iso, iso C17 : 1 ω9c and C11 : 0 iso 3OH, predominantly appeared in strain Ko07T as well as in all type strains of the recognized Lysobacter species. The DNA–DNA hybridization values of strain Ko07T with those of recognized Lysobacter species were estimated to be 2–20 %. Despite sharing common taxonomic features in important phenotypic characteristics, such as gliding movement, long-rod shape and proteolytic activity, strain Ko07T could be distinguished from the Lysobacter species with validly published names by its low DNA–DNA hybridization value, a comparatively low DNA G+C content (63·8 mol%), substrate utilization and some physiochemical characteristics. On the basis of the results obtained in this study, it is proposed that strain Ko07T should be classified as representing a novel member of the genus Lysobacter, for which the name Lysobacter concretionis sp. nov. is proposed. The type strain is Ko07T (=KCTC 12205T=DSM 16239T).
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Reclassification of Agrobacterium ferrugineum LMG 128 as Hoeflea marina gen. nov., sp. nov.
More LessMembers of the species Agrobacterium ferrugineum were isolated from marine environments. The type strain of this species (=LMG 22047T=ATCC 25652T) was recently reclassified in the new genus Pseudorhodobacter, in the order ‘Rhodobacterales’ of the class ‘Alphaproteobacteria’. Strain LMG 128 (=ATCC 25654) was also initially classified as belonging to the species Agrobacterium ferrugineum; however, the nearly complete 16S rRNA gene sequence of this strain indicated that it does not belong within the genus Agrobacterium or within the genus Pseudorhodobacter. The closest related organism, with 95·5 % 16S rRNA gene similarity, was Aquamicrobium defluvii from the family ‘Phyllobacteriaceae’ in the order ‘Rhizobiales’. The remaining genera from this order had 16S rRNA gene sequence similarities that were lower than 95·1 % with respect to strain LMG 128. These phylogenetic distances suggested that strain LMG 128 belonged to a different genus. The major fatty acid present in strain LMG 128 was mono-unsaturated straight chain 18 : 1ω7c. The G+C content of the DNA was 53·1 mol%. Strain LMG 128 grew at 4 °C but not at 40 °C, and tolerated up to 5 % NaCl. The pH range for growth was 6–8. It produced urease and β-galactosidase, and hydrolysed aesculin. Denitrification was negative. Growth was observed with many carbohydrates as the only carbon source. The data from this polyphasic study indicate that this strain belongs to a new genus of the family ‘Phyllobacteriaceae’, and therefore it is proposed that strain LMG 128T should be reclassified as representing a novel species within the new genus Hoeflea gen. nov., for which the name Hoeflea marina sp. nov. is proposed.
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Erythrobacter luteolus sp. nov., isolated from a tidal flat of the Yellow Sea in Korea
More LessA Gram-negative, non-spore-forming, yellow-pigmented, slightly halophilic bacterial strain, SW-109T, was isolated from a tidal flat of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. This isolate did not produce bacteriochlorophyll a and contained ubiquinone-10 as the predominant respiratory lipoquinone and C18 : 1 ω7c as the major fatty acid. The DNA G+C content was 60·3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SW-109T is phylogenetically affiliated to the genus Erythrobacter of the family Sphingomonadaceae. Strain SW-109T exhibited levels of 16S rRNA gene sequence similarity to the type strains of Erythrobacter species of 94·0–96·3 %, making it possible to categorize strain SW-109T as a species that is separate from previously recognized Erythrobacter species. On the basis of its phenotypic properties and phylogenetic distinctiveness, SW-109T (=KCTC 12311T=JCM 12599T) was classified as the type strain of a novel Erythrobacter species, for which the name Erythrobacter luteolus sp. nov. is proposed.
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Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment
More LessTwo bacterial strains, B-5T and NO1A, were isolated from the surface water of the Bohai Sea and deep-sea sediment of the east Pacific Ocean, respectively. Both strains were halophilic, aerobic, Gram-negative, non-spore-forming, catalase- and oxidase-positive motile rods. They grew on a restricted spectrum of organic compounds, including some organic acids and alkanes. On the basis of 16S rRNA gene sequence similarity, strains B-5T and NO1A were shown to belong to the γ-Proteobacteria. Highest similarity values were found with Alcanivorax venustensis (95·2 %), Alcanivorax jadensis (94·6 %) and Alcanivorax borkumensis (94·1 %). Principal fatty acids of both strains were C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. The chemotaxonomically characteristic fatty acid C19 : 0 cyclo ω8c was also detected. On the basis of the above, together with results of physiological and biochemical tests, DNA–DNA hybridization, comparisons of 16S–23S internal transcribed spacer sequences and comparisons of the partial deduced amino acid sequence of alkane hydroxylase, both strains were affiliated to the genus Alcanivorax but were differentiated from recognized Alcanivorax species. Therefore, a novel species, Alcanivorax dieselolei sp. nov., represented by strains B-5T and NO1A is proposed, with the type strain B-5T (=DSM 16502T=CGMCC 1.3690T).
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Burkholderia phytofirmans sp. nov., a novel plant-associated bacterium with plant-beneficial properties
A Gram-negative, non-sporulating, rod-shaped, motile bacterium, with a single polar flagellum, designated strain PsJNT, was isolated from surface-sterilized onion roots. This isolate proved to be a highly effective plant-beneficial bacterium, and was able to establish rhizosphere and endophytic populations associated with various plants. Seven related strains were recovered from Dutch soils. Based on 16S rRNA gene sequence data, strain PsJNT and the Dutch strains were identified as representing a member of the genus Burkholderia, as they were closely related to Burkholderia fungorum (98·7 %) and Burkholderia phenazinium (98·5 %). Analysis of whole-cell protein profiles and DNA–DNA hybridization experiments confirmed that all eight strains belonged to a single species. Strain PsJNT had a DNA G+C content of 61·0 mol%. Only low levels of DNA–DNA hybridization to closely related species were found. Qualitative and quantitative differences in fatty acid composition between strain PsJNT and closely related species were identified. The predominant fatty acids in strain PsJNT were 16 : 0, 18 : 1ω7c and summed feature 3 (comprising 16 : 1ω7c and/or iso-15 : 0 2-OH). Isolate PsJNT showed high 1-aminocyclopropane-1-carboxylate deaminase activity and is therefore able to lower the ethylene level in a developing or stressed plant. Production of the quorum-sensing signal compound 3-hydroxy-C8-homoserine lactone was detected. Based on the results of this polyphasic taxonomic study, strain PsJNT and the seven Dutch isolates are considered to represent a single, novel species, for which the name Burkholderia phytofirmans sp. nov. is proposed. The type strain is strain PsJNT (=LMG 22146T=CCUG 49060T).
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Sphingopyxis baekryungensis sp. nov., an orange-pigmented bacterium isolated from sea water of the Yellow Sea in Korea
More LessA Gram-negative, motile, slightly halophilic bacterial strain, SW-150T, was isolated from sea water of the Yellow Sea, Korea, and was characterized by a polyphasic taxonomic approach. Strain SW-150T grew optimally at 25–30 °C and in the presence of 2 % (w/v) NaCl. The isolate could be distinguished from other Sphingopyxis species in producing an orange pigment. It contained ubiquinone-10 as the predominant respiratory lipoquinone and C18 : 1 ω7c and C17 : 1 ω6c as the major fatty acids. No 3-hydroxy fatty acids were detected. Major polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 63 mol%. Comparative 16S rRNA gene sequence analyses showed that strain SW-150T was phylogenetically affiliated to the genus Sphingopyxis of the family Sphingomonadaceae. Similarity values between the 16S rRNA gene sequences of strain SW-150T and the type strains of Sphingopyxis species ranged from 91·6 to 94·2 %, making it possible to categorize strain SW-150T as a species that is separate from previously described Sphingopyxis species. On the basis of phenotypic properties and phylogenetic distinctiveness, SW-150T (=KCTC 12231T=DSM 16222T) should be classified as the type strain of a novel Sphingopyxis species, for which the name Sphingopyxis baekryungensis sp. nov. is proposed.
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Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China
More LessA novel aromatic-compound-degrading bacterium, strain T3-B9T, was isolated from sediment of Taihu Lake, Jiangsu Province, south-east China. This bacterial isolate assimilated several aromatic compounds such as phenol, aniline, nitrobenzene, 4-chloronitrobenzene and phenanthrene. The taxonomy of strain T3-B9T was studied by polyphasic methods. The organism showed a range of phenotypic and chemotaxonomic properties consistent with those of the genus Novosphingobium. The 16S rRNA gene sequence similarity of strain T3-B9T to members of the genus Novosphingobium ranged from 91·6 to 97·5 %, and this isolate clustered phylogenetically with members of genus Novosphingobium. The DNA–DNA relatedness values of strain T3-B9T to the most phylogenetically related species, Novosphingobium subterraneum DSM 12447T, Novosphingobium aromaticivorans ATCC 700278T and Novosphingobium stygium ATCC 700280T, were 31, 33 and 14 %, respectively. The combined genotypic and phenotypic data show that strain T3-B9T represents a novel species of the genus Novosphingobium, for which the name Novosphingobium taihuense sp. nov. is proposed. The type strain is T3-B9T (=AS 1.3432T=JCM 12465T).
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Pleomorphomonas oryzae gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from paddy soil of Oryza sativa
More LessFive strains of free-living diazotrophs isolated from rice were characterized by using a polyphasic approach. The strains were found to be very closely related, with 99–100 % 16S rRNA gene sequence similarity and DNA–DNA hybridization values greater than 70 %, suggesting that they represent a single species. When compared with other recognized species, they showed not more than 93 and 89 % similarity for the 16S rRNA and nifH gene sequences, respectively. Phylogenetic distances showed that these isolates were distinct from other taxa within the α-Proteobacteria. Chemotaxonomic characteristics of these isolates included the DNA G+C content (62·1–63·1 mol%), the major quinone system (Q-10), predominant fatty acids (18 : 1ω7c, cyclo 19 : 0ω8c and 16 : 0) and major hydroxy fatty acids (14 : 0 3-OH, 18 : 0 3-OH and 16 : 0 3-OH). Based on phylogenetic and phenotypic analyses, these isolates are considered to represent a novel genus and species, for which the name Pleomorphomonas oryzae gen. nov., sp. nov. is proposed. The type strain is F-7T (=IAM 15079T=ATCC BAA-940T=DSM 16300T).
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Asticcacaulis taihuensis sp. nov., a novel stalked bacterium isolated from Taihu Lake, China
More LessA novel stalked bacterium, designated strain T3-B7T, was isolated from sediment of Taihu Lake, Jiangsu Province, China, and its taxonomy was studied by using a polyphasic approach. Cell morphology, physiological and biochemical properties, and polar lipids indicated that strain T3-B7T represented a member of the genus Asticcacaulis. Based on 16S rRNA gene sequence similarity analysis, strain T3-B7T was found to be phylogenetically related to Asticcacaulis biprosthecium DSM 4723T (98·5 %) and Asticcacaulis excentricus DSM 4724T (95·0 %), but could be differentiated from these two species on the basis of the number and position of prosthecae, assimilation of sugars, nitrate reduction and tolerance to NaCl. Levels of DNA–DNA relatedness of strain T3-B7T to A. biprosthecium DSM 4723T and A. excentricus DSM 4724T were 37·1 and 18·0 %, respectively. The G+C content of strain T3-B7T was 59 mol% (T m). It is concluded that strain T3-B7T represents a novel species of the genus Asticcacaulis, for which the name of Asticcacaulis taihuensis sp. nov. is proposed. The type strain is T3-B7T (=AS 1.3431T=JCM 12463T).
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Labrys methylaminiphilus sp. nov., a novel facultatively methylotrophic bacterium from a freshwater lake sediment
A new bacterial isolate from a methylamine enrichment culture is described, representing a novel species of facultatively methylotrophic bacteria. The non-motile bacterium is Gram-negative, replicates by budding and does not form endospores. The isolate utilizes methylated amines, as well as a variety of monosaccharides, disaccharides, amino acids, organic acids, aromatic compounds and alcohols as substrates, but does not utilize methanol. Growth factors are not required, although yeast extract stimulates growth. The major components of the fatty acid profile are C18 : 1 ω7c, C19 : 0 cyclo and C16 : 0. The dominant cellular phospholipids are phosphatidyl acid, phosphatidylcholine and phosphatidylethanolamine. The G+C content of the DNA is 65·7±0·3 mol%. 16S rRNA gene-based phylogenetic analysis revealed that the novel isolate belongs to the α-Proteobacteria and is closely related to the only representative of the genus Labrys, Labrys monachus (97·4 % sequence similarity). However, the level of DNA–DNA relatedness with L. monachus is less than 3 %, justifying the placement of this isolate into a novel species of the genus Labrys. The name Labrys methylaminiphilus sp. nov. is proposed (type strain JLW10T=ATCC BAA-1080T=DSM 16812T).
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Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov., Paenibacillus anaericanus sp. nov. and Paenibacillus terrae strain MH72, N2O-producing bacteria isolated from the gut of the earthworm Aporrectodea caliginosa
More LessEarthworms emit nitrous oxide (N2O) via the activity of bacteria in their gut. Four N2O-producing facultative aerobes, ED1T, ED5T, MH21T and MH72, were isolated from the gut of the earthworm Aporrectodea caliginosa. The isolates produced N2O under conditions that simulated the microenvironment of the earthworm gut. ED1T and ED5T were Gram-negative, motile rods that carried out complete denitrification (i.e. the reduction of nitrate to N2) and contained membranous c-type cytochromes. ED1T grew optimally at 30 °C and pH 7. ED1T oxidized organic acids and reduced (per)chlorate, sulfate, nitrate and nitrite. The closest phylogenetic relative of ED1T was Dechloromonas agitata. ED5T grew optimally at 25 °C and pH 7. ED5T grew mainly on sugars, and nitrate and nitrite were used as alternative electron acceptors. The closest phylogenetic relatives of ED5T were Flavobacterium johnsoniae and Flavobacterium flevense. MH21T and MH72 were motile, spore-forming, rod-shaped bacteria with a three-layered cell wall. Sugars supported the growth of MH21T and MH72. Cells of MH21T grew in chains, were linked by connecting filaments and contained membranous b-type cytochromes. MH21T grew optimally at 30–35 °C and pH 7·7, grew by fermentation and reduced low amounts of nitrite to N2O. The closest phylogenetic relatives of MH21T were Paenibacillus borealis and Paenibacillus chibensis. Based on morphological, physiological and phylogenetic characteristics, ED1T (=DSM 15892T=ATCC BAA-841T), ED5T (=DSM 15936T=ATCC BAA-842T) and MH21T (=DSM 15890T=ATCC BAA-844T) are proposed as type strains of the novel species Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov. and Paenibacillus anaericanus sp. nov., respectively. MH72 is considered a new strain of Paenibacillus terrae.
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Arcobacter halophilus sp. nov., the first obligate halophile in the genus Arcobacter
More LessA Gram-negative bacterium, designated LA31BT, was isolated from water collected from a hypersaline lagoon on Laysan Atoll in the north-western Hawaiian Islands. Single cells of LA31BT were slightly curved but became helical as their length increased. Preliminary characterization based on 16S rRNA gene sequence analysis showed that LA31BT shared 96·0 % identity with an Arcobacter sp. isolated from a cyanobacterial mat in hypersaline Lake Sinai, and 94 % identity with Arcobacter nitrofigilis, the type species of the genus Arcobacter. A polyphasic taxonomic study was conducted and confirmed the phylogenetic affiliation of strain LA31BT to the genus Arcobacter. However, LA31BT was found to be distinct from all recognized Arcobacter species, by a comprehensive biochemical test analysis, whole-cell fatty acid profiling, DNA G+C content (35 mol% in LA31BT) and degree of DNA–DNA reassociation. Most notably, LA31BT was found to be an obligate halophile, a hitherto undescribed feature among recognized Arcobacter species. These data indicate that LA31BT should be considered to represent a novel species in the genus Arcobacter, for which the name Arcobacter halophilus sp. nov. is proposed. This is the first obligately halophilic member of the genus. The type strain is LA31BT (=ATCC BAA-1022T=CIP 108450T).
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Syntrophobacter sulfatireducens sp. nov., a novel syntrophic, propionate-oxidizing bacterium isolated from UASB reactors
More LessTwo obligate anaerobes, TB8106T and WZH410, which degraded propionate in syntrophic association with methanogens, were isolated from two upflow anaerobic sludge blanket reactors, one treating brewery wastewater and the other bean curd wastewater. The strains were Gram-negative, non-spore-forming and non-motile. Cells were egg-shaped, with a size of 1·0–1·3×1·8–2·2 μm. Growth was observed at 20–48 °C and pH 6·2–8·8. Both strains converted propionate to acetate and methane in co-culture with methanogens, and grew on propionate plus sulfate in pure culture, with a doubling time of 52–55 h at 37 °C. Sulfate and thiosulfate both served as electron acceptors for propionate degradation. The DNA G+C contents of the two strains were 58·5 and 58·7 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strains were closely related to a propionate-oxidizing syntrophic bacterium, Syntrophobacter fumaroxidans DSM 10017T (94·7 % similarity). However, the novel strains could not ferment fumarate, and grew at a more alkaline pH range than Syntrophobacter fumaroxidans. Moreover, the novel isolates had obviously higher growth rates on propionate plus sulfate (0·12 day−1) than Syntrophobacter fumaroxidans DSM 10017T (0·024 day−1). Therefore, a novel species, Syntrophobacter sulfatireducens sp. nov., is proposed, with strain TB8106T (=AS 1.5016T=DSM 16706T) as the type strain.
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Marinobacter hydrocarbonoclasticus Gauthier et al. 1992 and Marinobacter aquaeolei Nguyen et al. 1999 are heterotypic synonyms
More LessThe genus Marinobacter was described with a single species, Marinobacter hydrocarbonoclasticus Gauthier et al. 1992 , to place a hydrocarbon-degrading marine bacterium belonging to the γ-subclass of the Proteobacteria. Marinobacter aquaeolei Nguyen et al. 1999 , the second described species of the genus, was proposed for a strain isolated from an oil-producing well on an offshore platform in southern Vietnam, on the basis of differences in the whole-cell protein pattern and lipopolysaccharide composition, although its phenotypic and genotypic characteristics were very similar to those of the type species, M. hydrocarbonoclasticus. In the present paper, literature data concerning the two species were reviewed. Fatty acid composition, G+C content and DNA–DNA hybridization studies were performed in order to clarify the taxonomic positions of these two species. Based on the results obtained in this study and phenotypic and phylogenetic traits available from the literature, it is proposed that the two species should be united under the same name; according to the rules of priority, M. hydrocarbonoclasticus, the first described species, is the earlier synonym and M. aquaeolei is the later synonym.
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- Gram-Positive Bacteria
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Pontibacillus marinus sp. nov., a moderately halophilic bacterium from a solar saltern, and emended description of the genus Pontibacillus
More LessA moderately halophilic, Gram-positive, rod-shaped bacterium (BH030004T) was isolated from a solar saltern in Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BH030004T belonged to the genus Pontibacillus. Chemotaxonomic data (DNA G+C content, 42 mol%; major isoprenoid quinone, MK-7; cell-wall type, A1γ-type meso-diaminopimelic acid; major fatty acids, iso-C15 : 0 and anteiso-C15 : 0) also supported the affiliation of the isolate to the genus Pontibacillus. Although the 16S rRNA gene sequence similarity between strain BH030004T and Pontibacillus chungwhensis DSM 16287T was relatively high (99·1 %), physiological properties and DNA–DNA hybridization (about 7 % DNA–DNA relatedness) allowed genotypic and phenotypic differentiation of strain BH030004T from the type strain of P. chungwhensis. Therefore, strain BH030004T represents a novel species of the genus Pontibacillus, for which the name Pontibacillus marinus sp. nov. is proposed. The type strain is BH030004T (=KCTC 3917T=DSM 16465T).
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Brevibacillus levickii sp. nov. and Aneurinibacillus terranovensis sp. nov., two novel thermoacidophiles isolated from geothermal soils of northern Victoria Land, Antarctica
More LessThirteen strains of endospore-forming bacteria were isolated from geothermal soils at Cryptogam Ridge, the north-west slope of Mt Melbourne, and at the vents and summit of Mt Rittmann in northern Victoria Land, Antarctica. 16S rRNA gene sequencing, SDS-PAGE and routine phenotypic characterization tests indicated that the seven isolates from the north-west slope of Mt Melbourne represent a novel species of Brevibacillus and that the six isolates from Cryptogam Ridge and the vents and summit of Mt Rittmann represent a novel species of Aneurinibacillus. Brevibacillus strains were not isolated from the sites at Mt Rittmann or Cryptogam Ridge and Aneurinibacillus strains were not isolated from the north-west slope of Mt Melbourne. Preliminary metabolic studies revealed that l-glutamic acid, although not essential for growth, was utilized by both species. The Brevibacillus species possessed an uptake system specific for l-glutamic acid, whereas the Aneurinibacillus species possessed a more general uptake system capable of transporting other related amino acids. Both species utilized a K+ antiport system and similar energy systems for the uptake of l-glutamic acid. The rate of uptake by the Brevibacillus species type strain was 20-fold greater than that shown by the Aneurinibacillus species type strain. The names Brevibacillus levickii sp. nov. and Aneurinibacillus terranovensis sp. nov. are proposed for the novel taxa; the type strains are Logan B-1657T (=LMG 22481T=CIP 108307T) and Logan B-1599T (LMG 22483T=CIP 108308T), respectively.
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Mycobacterium florentinum sp. nov., isolated from humans
Eight mycobacterial strains isolated during an 11 year period from the sputum of independent patients with various pulmonary disorders and, in one case, from a lymph node of a young girl, were found to present identical features. Phenotypic and genotypic characteristics revealed that the most closely related species to these test isolates were Mycobacterium triplex and Mycobacterium lentiflavum. However, the lipids of the cell wall of the test isolates differed from those of the latter species by TLC and presented unique profiles by both GC and HPLC. Genotypic analysis showed that they had unique 16S rRNA gene and internal transcribed spacer (ITS) sequences, and could be differentiated from all other mycobacterial strains by PCR restriction analysis of hsp65. The strains presented high resistance to antimycobacterial drugs. The name Mycobacterium florentinum sp. nov. is proposed for this taxon, with strain FI-93171T (=DSM 44852T=CIP 108409T) as the type strain.
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Bacillus arsenicus sp. nov., an arsenic-resistant bacterium isolated from a siderite concretion in West Bengal, India
More LessStrain Con a/3T is a Gram-positive, motile, endospore-forming, rod-shaped and arsenic-resistant bacterium, which was isolated from a concretion of arsenic ore obtained from a bore-hole. The bacterium grew in the presence of 20 mM arsenate and 0·5 mM arsenite. Diaminopimelic acid was present in the cell wall peptidoglycan, MK-7 was the major menaquinone, and iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and C16 : 1(δ7cis) were the major fatty acids. Based on its phenotypic, chemotaxonomic and phylogenetic characteristics, strain Con a/3T was identified as a member of the genus Bacillus. It exhibited maximum similarity (97 %) at the 16S rRNA gene level with Bacillus barbaricus (DSM 14730T); however, the DNA–DNA relatedness value with B. barbaricus was 60 %. Strain Con a/3T also exhibited a number of phenotypic differences from B. barbaricus (DSM 14730T). Strain Con a/3T was therefore identified as representing a novel species of the genus Bacillus, for which the name Bacillus arsenicus sp. nov. is proposed. The type strain is Con a/3T (=MTCC 4380T=DSM 15822T=JCM 12167T).
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Corynebacterium mooreparkense, a later heterotypic synonym of Corynebacterium variabile
Strains of a Gram-positive bacterium were isolated from the Irish smear-ripened cheese Gubbeen, and assigned to a new species, Corynebacterium mooreparkense, in 2001. During a further study on the same cheese, no additional isolates from this species could be found. Instead, multiple isolates of its nearest phylogenetic neighbour, Corynebacterium variabile, were found. A first screening with rep-PCR and SDS-PAGE pointed to a similarity between C. mooreparkense and C. variabile. Following this peculiar result, attempts were made to collect all type strains deposited at different culture collections and all strains described by Brennan et al. [Int J Syst Evol Microbiol (2001) 51, 843–852] . Subsequently, 16S rRNA gene sequencing and DNA–DNA hybridizations were performed. All C. mooreparkense strains had a 16S rRNA gene sequence similarity of at least 99·5 % with C. variabile and the DNA–DNA relatedness was 95 %. On the basis of these results, it is concluded that C. mooreparkense is a later heterotypic synonym of C. variabile.
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Rhodococcus yunnanensis sp. nov., a mesophilic actinobacterium isolated from forest soil
A Gram-positive, aerobic, non-motile, mesophilic strain, designated YIM 70056T, was isolated from a forest soil sample in Yunnan Province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that this isolate had less than 97·0 % similarity to any Rhodococcus species with validly published names, with the exception of Rhodococcus fascians (DSM 20669T), which was found to be its closest neighbour (98·9 % similarity). Chemotaxonomic data, including peptidoglycan type, diagnostic sugar compositions, fatty acid profiles, menaquinones, polar lipids and mycolic acids, were determined for this isolate; the results supported the affiliation of strain YIM 70056T to the genus Rhodococcus. The DNA G+C content was 63·5 mol%. The results of DNA–DNA hybridization with R. fascians DSM 20669T, in combination with chemotaxonomic and physiological data, demonstrated that isolate YIM 70056T represents a novel Rhodococcus species, for which the name Rhodococcus yunnanensis sp. nov. is proposed, with YIM 70056T (=CCTCC AA 204007T=KCTC 19021T=DSM 44837T) as the type strain.
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Mycobacterium pseudoshottsii sp. nov., a slowly growing chromogenic species isolated from Chesapeake Bay striped bass (Morone saxatilis)
A group of slowly growing photochromogenic mycobacteria was isolated from Chesapeake Bay striped bass (Morone saxatilis) during an epizootic of mycobacteriosis. Growth characteristics, acid-fastness and 16S rRNA gene sequencing results were consistent with those of the genus Mycobacterium. Biochemical reactions, growth characteristics and mycolic acid profiles (HPLC) resembled those of Mycobacterium shottsii, a non-pigmented mycobacterium also isolated during the same epizootic. Sequencing of the 16S rRNA genes, the gene encoding the exported repeated protein (erp) and the gene encoding the 65 kDa heat-shock protein (hsp65) and restriction enzyme analysis of the hsp65 gene demonstrated that this group of isolates is unique. Insertion sequences associated with Mycobacterium ulcerans, IS2404 and IS2606, were detected by PCR. These isolates could be differentiated from other slowly growing pigmented mycobacteria by their inability to grow at 37 °C, production of niacin and urease, absence of nitrate reductase, negative Tween 80 hydrolysis and resistance to isoniazid (1 μg ml−1), p-nitrobenzoic acid, thiacetazone and thiophene-2-carboxylic hydrazide. On the basis of this polyphasic study, it is proposed that these isolates represent a novel species, Mycobacterium pseudoshottsii sp. nov. The type strain, L15T, has been deposited in the American Type Culture Collection as ATCC BAA-883T and the National Collection of Type Cultures (UK) as NCTC 13318T.
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Clostridium sardiniense Prévot 1938 and Clostridium absonum Nakamura et al. 1973 are heterotypic synonyms: evidence from phylogenetic analyses of phospholipase C and 16S rRNA sequences, and DNA relatedness
More LessClostridium sardiniense Prévot 1938 and Clostridium absonum Nakamura et al. 1973 have long been considered similar in terms of their biological and biochemical properties, but their taxonomic positions have not been clarified by DNA–DNA hybridization studies or rigorous analysis of 16S rRNA genes. In the present study, DNA–DNA hybridization analysis revealed that C. absonum strains DSM 599T, DSM 600 and KZ 1544 shared 83·0–86·3 % DNA relatedness with C. sardiniense DSM 2632T. 16S rRNA gene sequence analysis showed that the C. absonum strains also shared high identity with C. sardiniense DSM 2632T (99·7, 99·3 and 99·8 % for DSM 599T, DSM 600 and KZ 1544, respectively), implying that C. absonum and C. sardiniense are synonyms. In addition, alignment of the inferred amino acid sequences for phospholipase C (PLC) indicated 96·5 % identity between PLCs from C. sardiniense and C. absonum, but relatively low identity with other clostridial species. These results strongly suggest that the species C. sardiniense and C. absonum should be united, with the name C. sardiniense having priority.
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Bacillus alveayuensis sp. nov., a thermophilic bacterium isolated from deep-sea sediments of the Ayu Trough
More LessTwo thermophilic, spore-forming strains, TM1T and TM5, were isolated from deep-sea sediment (4000 m below sea level) of the Ayu Trough in the western Pacific Ocean. Cells of the two strains were Gram-positive, motile and rod-shaped. Their spores were ellipsoidal, subterminal to terminal and occurred in swollen sporangia. The two strains grew at temperatures up to 65 °C and in the pH range 6·5–9·0. The NaCl concentration for optimal growth was 3·0 % (w/v) and growth was inhibited by 5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains TM1T and TM5 belonged to the genus Bacillus, and that strain TM1T was most closely related to Bacillus aeolius DSM 15084T (96·7 %), Bacillus smithii DSM 4216T (96·1 %), Bacillus methanolicus NCIMB 13113T (95·8 %) and Bacillus pallidus DSM 3670T (95·7 %). Between the 16S rRNA gene sequences of strains TM1T and TM5 there were only three nucleotide differences, implying that the two strains were of the same species. The cellular fatty acid profiles of the two strains were also very similar, with iso-C15 : 0, iso-C16 : 0, C16 : 0, iso-C17 : 0 and anteiso-C17 : 0 as the major components. The G+C content of strain TM1T was 38·7 %. On the basis of phenotypic and molecular data, strains TM1T and TM5 represent a novel species of the genus Bacillus, for which the name Bacillus alveayuensis sp. nov. is proposed. The type strain is TM1T (=KCTC 10634T=JCM 12523T).
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Slackia faecicanis sp. nov., isolated from canine faeces
Morphological, biochemical and molecular genetic studies were carried out on an unknown non-spore-forming, Gram-positive, rod-shaped bacterium that was isolated from dog faeces. The bacterium grew under strictly anaerobic conditions, was asaccharolytic, and possessed a relatively high G+C content of 61 mol%. Phylogenetic analysis based on comparative 16S rRNA gene sequencing showed that the unidentified bacterium was a member of the family Coriobacteriaceae and represents a hitherto unknown subline within the genus Slackia. Based on the presented findings, a novel species, Slackia faecicanis sp. nov., is described. The type strain of Slackia faecicanis is 5WC12T (=CCUG 48399T=CIP 108281T).
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