- Volume 59, Issue 10, 2009
Volume 59, Issue 10, 2009
- New Taxa
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- Firmicutes And Related Organisms
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Phylogeny and molecular taxonomy of the Bacillus subtilis species complex and description of Bacillus subtilis subsp. inaquosorum subsp. nov.
More LessThe Bacillus subtilis species complex is a tight assemblage of closely related species. For many years, it has been recognized that these species cannot be differentiated on the basis of phenotypic characteristics. Recently, it has been shown that phylogenetic analysis of the 16S rRNA gene also fails to differentiate species within the complex due to the highly conserved nature of the gene, yet DNA–DNA hybridization values fall well below 70 % for the same species comparisons. As a complementary approach, we propose that phylogenetic analysis of multiple protein-coding loci can be used as a means to detect and differentiate novel Bacillus taxa. Indeed, our phylogenetic analyses revealed the existence of a previously unknown group of strains closely related to, but distinct from, Bacillus subtilis subsp. spizizenii. Results of matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses revealed that the group produces a novel surfactin-like lipopeptide with mass m/z 1120.8 that is not produced by the other currently recognized subspecies. In addition, the group displayed differences in the total cellular content of the fatty acids C16 : 0 and iso-C17 : 1 ω10c that distinguish it from the closely related B. subtilis subsp. spizizenii. Consequently, the correlation of these novel phenotypic traits with the phylogenetic distinctiveness of this previously unknown subspecies group showed that phylogenetic analysis of multiple protein-coding loci can be used as a means to detect and differentiate novel Bacillus taxa. Therefore, we propose that this new group should be recognized as representing a novel taxon, Bacillus subtilis subsp. inaquosorum subsp. nov., with the type strain NRRL B-23052T (=KCTC 13429T=BGSC 3A28T).
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Bavariicoccus seileri gen. nov., sp. nov., isolated from the surface and smear water of German red smear soft cheese
The phylogenetic position and physiological characters of six hitherto-unknown lactic acid bacterial isolates, which form part of the surface microbiota of German red smear soft cheese, are reported. The coccoid cells are aerotolerant, Gram-positive, catalase-negative and non-motile. The cell-wall peptidoglycan contains alanine, glutamic acid, lysine and aspartic acid and is of the A4α type (l-Lys–d-Asp). The sequences of the 16S rRNA, groEL and rpoB genes of the six isolates are identical and reveal that these isolates represent an independent lineage within the radiation of the family Enterococcaceae in the phylum Firmicutes. Their closest phylogenetic neighbour is the lactic acid bacterium Atopobacter phocae M1590/94/2T, with which they share 94.9 % 16S rRNA gene sequence similarity; representatives of other genera such as Granulicatella, Carnobacterium and Trichococcus are more distantly related. DNA–DNA hybridization studies reveal that the six isolates are members of a single species, and this is confirmed by similarities in biochemical characteristics. The six isolates were assigned four different groups by Fourier-transform infrared and randomly amplified polymorphic DNA typing. Therefore, it is formally proposed that these isolates should be classified in a single novel species of a novel genus and be named Bavariicoccus seileri gen. nov., sp. nov. The type strain of Bavariicoccus seileri is WCC 4188T (=DSM 19936T =CCUG 55508T).
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‘Candidatus Phytoplasma tamaricis’, a novel taxon discovered in witches'-broom-diseased salt cedar (Tamarix chinensis Lour.)
More LessSalt cedar trees with pronounced witches'-broom symptoms were observed in their natural habitat in China. 16S rRNA gene sequences unique to phytoplasmas were detected in every DNA sample extracted from stem and leaf tissues of the symptomatic trees, revealing a direct association between phytoplasma infection and the salt cedar witches'-broom (SCWB) disease. Phylogenetic analysis of the SCWB phytoplasma 16S rRNA gene sequence indicated that the SCWB phytoplasma belonged to a subclade consisting of several mutually distinct ‘Candidatus Phytoplasma’ taxa including ‘Ca. Phytoplasma prunorum’, ‘Ca. Phytoplasma mali’, ‘Ca. Phytoplasma pyri’ and ‘Ca. Phytoplasma spartii’. Pairwise sequence similarity scores calculated from an alignment of near full-length 16S rRNA genes revealed that SCWB phytoplasma shared 96.6 % or less sequence similarity with each previously described or proposed ‘Ca. Phytoplasma’ taxon, justifying the recognition of SCWB phytoplasma as a novel taxon, ‘Candidatus Phytoplasma tamaricis’. The distinct virtual RFLP pattern derived from the SCWB phytoplasma 16S rRNA gene sequence, together with its lower-than-threshold similarity coefficient values with RFLP patterns of any of the 29 previously established groups, supported the recognition of a new 16Sr group, designated 16SrXXX, salt cedar witches'-broom phytoplasma group.
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Halobacillus salsuginis sp. nov., a moderately halophilic bacterium from a subterranean brine
A moderately halophilic, endospore-forming, Gram-positive, catalase- and oxidase-positive, motile, rod-shaped, aerobic bacterium, designated strain JSM 078133T, was isolated from a subterranean brine sample collected from a salt mine in Hunan Province, China. Strain JSM 078133T was able to grow with 1–23 % (w/v) total salts (optimum, 5–10 %) and at pH 6.0–10.0 (optimum, pH 7.5) and 10–45 °C (optimum, 30 °C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The predominant respiratory quinone was menaquinone 7 (MK-7) and the major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. The genomic DNA G+C content of strain JSM 078133T was 42.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 078133T belongs to the genus Halobacillus, and was related most closely to the type strains of Halobacillus campisalis (97.1 % sequence similarity), Halobacillus alkaliphilus (97.0 %) and Halobacillus yeomjeoni (96.8 %). The combination of phylogenetic analysis, DNA–DNA relatedness data, phenotypic characteristics and chemotaxonomic data supported the view that strain JSM 078133T represents a novel species of the genus Halobacillus, for which the name Halobacillus salsuginis sp. nov. is proposed. The type strain is JSM 078133T (=DSM 21185T=KCTC 13236T).
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Thalassobacillus cyri sp. nov., a moderately halophilic Gram-positive bacterium from a hypersaline lake
More LessA Gram-positive, moderately halophilic bacterium, designated strain HS286T, was isolated from water of the hypersaline Lake Howz-Soltan in Iran. Cells were strictly aerobic, rod-shaped, motile and able to produce ellipsoidal endospores at a central-subterminal position in swollen sporangia. Isolate HS286T grew in a complex medium supplemented with 1–15 % (w/v) NaCl, with optimum growth at 8.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain HS286T was closely related to Thalassobacillus devorans G-19.1T (99.4 % gene sequence similarity). The other closest species were Halobacillus yeomjeoni MSS-402T (96.9 %) and other species of the genus Halobacillus (with 96.7–93.5 % similarity). Strain HS286T had cell-wall peptidoglycan based on meso-diaminopimelic acid and MK-7 as the respiratory isoprenoid quinone. The major fatty acids were anteiso-C15 : 0 (43.8 %), iso-C16 : 0 (21.4 %), iso-C14 : 0 (9.4 %), anteiso-C17 : 0 (8.7 %) and iso-C15 : 0 (7.0 %) and the polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, two phospholipids and a glycolipid. The DNA G+C content was 43.0 mol%. All of these features confirmed the placement of isolate HS286T within the genus Thalassobacillus. However DNA–DNA hybridization between strain HS286T and the only recognized species of the genus Thalassobacillus, T. devorans G-19.1T, was 27.3 %, showing unequivocally that the novel isolate constituted a new genospecies. Strain HS286T could be clearly differentiated from T. devorans and other phylogenetic neighbours on the basis of several phenotypic, genotypic and chemotaxonomic features. Therefore, strain HS286T constitutes a novel species, for which the name Thalassobacillus cyri sp. nov. is proposed. The type strain is HS286T (=CCM 7597T=JCM 15722T).
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Bhargavaea cecembensis gen. nov., sp. nov., isolated from the Chagos–Laccadive ridge system in the Indian Ocean
More LessA novel Gram-positive, rod-shaped, non-motile, non-spore-forming bacterium, strain DSE10T, was isolated from a deep-sea sediment sample collected at a depth of 5904 m from the Chagos–Laccadive ridge system in the Indian Ocean. Cells of strain DSE10T were positive for catalase, oxidase, urease and lipase activities and contained iso-C14 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0 as the major fatty acids. The major respiratory quinones were MK-6 and MK-8 and the major lipids were phosphatidylglycerol and diphosphatidylglycerol. The cell-wall peptidoglycan contained diaminopimelic acid as the diagnostic diamino acid. A blast sequence similarity search based on 16S rRNA gene sequences indicated that the genera Planococcus, Planomicrobium, Bacillus and Geobacillus were the nearest phylogenetic neighbours to the novel isolate with gene sequence similarities ranging from 94.9 to 95.2 %. Phylogenetic analyses using neighbour-joining, minimum-evolution and maximum-parsimony methods indicated that strain DSE10T formed a deeply rooted lineage distinct from the clades represented by the genera Planococcus, Planomicrobium, Bacillus and Geobacillus. Further, strain DSE10T could be distinguished from the above-mentioned genera based on the presence of signature nucleotides G, A, C, T, C, A, G, C and T at positions 182, 444, 480, 492, 563, 931, 1253, 1300 and 1391, respectively, in the 16S rRNA gene sequence. Based on the phenotypic and phylogenetic characteristics determined in this study, strain DSE10T was assigned as the type species of a new genus, Bhargavaea gen. nov., as Bhargavaea cecembensis sp. nov. The type strain of Bhargavaea cecembensis gen. nov., sp. nov. is DSE10T (=LMG 24411T=JCM 14375T). The genomic DNA G+C content of strain DSE10T is 59.5±2.5 mol%.
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- Proteobacteria
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Pseudochrobactrum lubricantis sp. nov., isolated from a metal-working fluid
A Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (KSS 7.8T) was isolated from a water-mixed metal-working fluid. On the basis of 16S rRNA gene and recA sequence similarities, the isolate was clearly grouped in the genus Pseudochrobactrum. This allocation was confirmed by fatty acid data (major fatty acids: C18 : 2 ω7c and C19 : 0 cyclo ω8c), polar lipid profile (major components: phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine, plus moderate amounts of phosphatidylmonomethylethanolamine and unknown aminolipid AL1), quinone system (ubiquinone Q-10) and polyamine pattern (spermidine and putrescine predominant). DNA–DNA pairing with the most closely related Pseudochrobactrum species showed values ranging from 24.2 to 45.7 %, and physiological and biochemical data clearly differentiated this isolate from described Pseudochrobactrum species. This organism represents a novel species of the genus Pseudochrobactrum, for which the name Pseudochrobactrum lubricantis sp. nov. is proposed, with the type strain KSS 7.8T (=CCUG 56963T=CCM 7581T).
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Transfer of Defluvibacter lusatiensis to the genus Aquamicrobium as Aquamicrobium lusatiense comb. nov. and description of Aquamicrobium aerolatum sp. nov.
More LessAnalysis of the 16S rRNA gene sequences of the type strains of Aquamicrobium defluvii and Defluvibacter lusatiensis shows a similarity of 98.3 %. There is no evidence for clear phenotypic differences between these organisms that justifies assignment to different genera. Both have ubiquinone Q-10 as the dominant quinone type and very similar fatty acid profiles, with 18 : 1ω7c and 19 : 0 cyclo ω8c predominating. A proposal is made to transfer Defluvibacter lusatiensis to the genus Aquamicrobium as Aquamicrobium lusatiense comb. nov. (type strain S1T =CIP 106844T =DSM 11099T). Furthermore, a novel species within this genus, Aquamicrobium aerolatum sp. nov., is described, with strain Sa14T (=CCUG 57044T =DSM 21857T), isolated from air in a duck shed, as the type strain.
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Pseudomonas brassicacearum subsp. neoaurantiaca subsp. nov., orange-pigmented bacteria isolated from soil and the rhizosphere of agricultural plants
A large group of 38 strains of saprophytic bacteria was isolated from soil and the rhizosphere of agricultural plants. The novel organisms were Gram-negative, aerobic, rod-shaped bacteria that produced a green fluorescent pigment, a red–orange diffusible pigment and a complex mixture of phloroglucinol derivates with antimicrobial activity. The latter have not been found in other bacteria, but are peculiar to ferns. The bacteria were vigorous denitrifiers that synthesized levan from sucrose and liquefied gelatin, but were found not to degrade aesculin, starch, agar, Tween 80 or DNA. Bacterial growth was found to occur at 4 °C but not at 40 °C. The predominant cellular fatty acids were 16 : 0, 16 : 1(n-7), 18 : 1(n-7) and 17 : 0 cyclo. The G+C content of the novel bacteria was 61.0–62.9 mol%. 16S rRNA gene sequence analysis indicated that the representative strain CIP 109457T had a clear affiliation with Pseudomonas sensu stricto groups, with the nearest relatives being Pseudomonas brassicacearum, P. thivervalensis, P. corrugata, P. mediterranea and P. kilonensis. DNA–DNA hybridization experiments showed that the group of isolated strains exhibited high levels of genetic relatedness (81–100 %), confirming that they are representatives of the same species. At the same time, they bound at low levels (4−46 %) with DNA of the type strains of their nearest relatives with the exception of P. brassicacearum; DNA binding of 90 % with the DNA of P. brassicacearum CIP 107059T suggested that the bacteria studied belong to this species. Analysis of taxonomic data indicated that the group of novel bacteria maintain a distinct phenotypic profile, allowing the description of novel subspecies within P. brassicacearum, for which the following names are proposed: Pseudomonas brassicacearum subsp. brassicacearum subsp. nov. (type strain DBK11T =CFBP 11706T =CIP 107059T =DSM 13227T =JCM 11938T) and Pseudomonas brassicacearum subsp. neoaurantiaca subsp. nov., with the type strain CIP 109457T (=ATCC 49054T =IMV 387T =VKM B-1524T).
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Andreprevotia lacus sp. nov., isolated from a fish-culture pond
A bacterial strain designated GFC-1T was isolated from a fish-culture pond in Taiwan and was characterized by using the polyphasic taxonomic approach. Strain GFC-1T was Gram-negative, aerobic, rod-shaped, motile and non-spore-forming. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belonged to the genus Andreprevotia of the family Neisseriaceae and its closest neighbour was Andreprevotia chitinilytica JS11-7T (97.0 % sequence similarity). The results of physiological and biochemical tests allowed clear phenotypic differentiation of isolate GFC-1T from A. chitinilytica JS11-7T. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1 ω7c. The DNA G+C content was 63.0 mol%. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and physiological data, strain GFC-1T should be classified as representing a novel species and a second member of the genus Andreprevotia, for which the name Andreprevotia lacus sp. nov. is proposed. The type strain is GFC-1T (=BCRC 17832T=LMG 24502T).
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Chromobacterium piscinae sp. nov. and Chromobacterium pseudoviolaceum sp. nov., from environmental samples
More LessTwo strains (LMG 3947 and LMG 3953) of motile, Gram-negative, violet-pigmented bacteria, respectively isolated in 1972 and before 1953 from environmental samples and previously assigned to Chromobacterium violaceum, were studied again in detail for their taxonomic position. 16S rRNA gene sequence analysis showed that both strains clustered together with the type strain of Chromobacterium violaceum (99.8 % sequence similarity for strain LMG 3953T and 98.9 % sequence similarity for LMG 3947T). recA sequence similarities were significantly lower (95–96 %), and fatty acid profiles were also different from those reported for C. violaceum and other Chromobacterium species. Both strains exhibit polar-lipid profiles consisting of the major compound phosphatidylethanolamine and moderate amounts of phosphatidylglycerol in addition to some minor lipids. The quinone systems consist of the major compound ubiquinone Q-8 and moderate amounts of Q-7. Polyamine patterns are composed of the major compounds putrescine and 2-hydroxyputrescine, moderate amounts of 1,3-diaminopropane and variable amounts of cadaverine and spermidine. The results of DNA–DNA hybridizations and physiological as well as biochemical tests allowed both genotypic and phenotypic differentiation of the two strains from described Chromobacterium species. It is evident from the genotypic and phenotypic data that both strains represent novel species in the genus Chromobacterium, for which we propose the names Chromobacterium piscinae sp. nov. (type strain LMG 3947T =CCM 3329T) and Chromobacterium pseudoviolaceum sp. nov. (type strain LMG 3953T =CCM 2076T =NCTC 8182T).
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Methylovirgula ligni gen. nov., sp. nov., an obligately acidophilic, facultatively methylotrophic bacterium with a highly divergent mxaF gene
Two strains of Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped bacteria were isolated from beechwood blocks during decay by the white-rot fungus Hypholoma fasciculare and were designated strains BW863T and BW872. They are capable of methylotrophic growth and assimilate carbon via the ribulose-bisphosphate pathway. In addition to methanol, the novel isolates utilized ethanol, pyruvate and malate. Strains BW863T and BW872 are obligately acidophilic, mesophilic organisms capable of growth at pH 3.1–6.5 (with an optimum at pH 4.5–5.0) and at 4–30 °C. Phospholipid fatty acid profiles of these bacteria contain unusually large amounts (about 90 %) of C18 : 1 ω7c, thereby resembling the profiles of Methylobacterium strains. The predominant quinone is Q-10. The DNA G+C content of the novel isolates is 61.8–62.8 mol%. On the basis of 16S rRNA gene sequence similarity, strains BW863T and BW872 are most closely related to the acidophilic methanotroph Methylocapsa acidiphila B2T (96.5–97 %). Comparative sequence analysis of mxaF, the gene encoding the large subunit of methanol dehydrogenase, placed the MxaF sequences of the two novel strains in a cluster that is distinct from all previously described MxaF sequences of cultivated methylotrophs. The identity between the MxaF sequences of the acidophilic isolates and those from known alpha-, beta- and gammaproteobacterial methylotrophs was respectively 69–75, 61–63 and 64–67 %. The data therefore suggest that strains BW863T and BW872 represent a novel genus and species of methylotrophic bacteria, for which the name Methylovirgula ligni gen. nov., sp. nov. is proposed. Strain BW863T (=DSM 19998T =NCIMB 14408T) is the type strain of Methylovirgula ligni.
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Dissection of the genus Methylibium: reclassification of Methylibium fulvum as Rhizobacter fulvus comb. nov., Methylibium aquaticum as Piscinibacter aquaticus gen. nov., comb. nov. and Methylibium subsaxonicum as Rivibacter subsaxonicus gen. nov., comb. nov. and emended descriptions of the genera Rhizobacter and Methylibium
More Less16S rRNA gene sequenced-based phylogeny indicates that Rhizobacter dauci ATCC 43778T branches within the radiation of Methylibium type strains. A comparative chemotaxonomic study including fatty acid methyl esters, polar lipids and polyamines reveals significant differences that, in combination with the topology of phylogenetic trees, support a dissection of the genus Methylibium. The proposals of this study include the transfer of Methylibium fulvum to the genus Rhizobacter as Rhizobacter fulvus comb. nov. (type strain Gsoil 322T =KCTC 12591T =DSM 19916T) and the reclassification of Methylibium aquaticum as Piscinibacter aquaticus gen. nov., comb. nov. (the type strain of Piscinibacter aquaticus is IMCC1728T =KCCM 42364T =NBRC 102349T =DSM 19915T) and of Methylibium subsaxonicum as Rivibacter subsaxonicus gen. nov., comb. nov. (the type strain of Rivibacter subsaxonicus is BF49T =DSM 19570T =CIP 109700T). As a consequence of these reclassifications, emended descriptions of the genera Methylibium and Rhizobacter are provided.
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Salinihabitans flavidus gen. nov., sp. nov., isolated from a marine solar saltern
More LessA Gram-negative, non-motile and rod-shaped bacterial strain, ISL-46T, belonging to the Alphaproteobacteria, was isolated from a marine solar saltern in Korea, and subjected to a polyphasic taxonomic study. Strain ISL-46T grew optimally at pH 7.0–8.0 and 30 °C and in the presence of 7 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone and C19 : 0 cyclo ω8c, C18 : 1 ω7c and 11-methyl C18 : 1 ω7c as the major fatty acids. The DNA G+C content was 63.5 mol%. Strain ISL-46T exhibited 16S rRNA gene sequence similarity values of 94.1–95.3 % to members of the phylogenetically related genera Roseivivax, Salipiger, Citreicella, Yangia and Citreimonas. Strain ISL-46T could be differentiated from the above-mentioned genera by differences in compositions of the major fatty acids and in some phenotypic properties. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain ISL-46T is considered to represent a novel genus and species, for which the name Salinihabitans flavidus gen. nov., sp. nov. is proposed. The type strain is ISL-46T (=KCTC 22485T=CCUG 56758T).
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Fodinicurvata sediminis gen. nov., sp. nov. and Fodinicurvata fenggangensis sp. nov., poly-β-hydroxybutyrate-producing bacteria in the family Rhodospirillaceae
Two Gram-negatively stained, facultatively anaerobic, non-motile, vibrioid and rod-shaped, chemoheterotrophic bacterial strains, designated YIM D82T and YIM D812T, were isolated from a salt mine in Yunnan, south-west China. DNA–DNA hybridization, genomic DNA G+C content and phylogenetic analyses based on 16S rRNA gene sequences divided the two isolates into two distinct genospecies that were also clearly differentiated by fatty acid profiles, carbon source utilization patterns, antibiotic susceptibility and biochemical characteristics. The two isolates grew in the presence of 1.5–20 % NaCl, and optimally at 28 °C and pH 7.5. The genomic DNA G+C contents of strains YIM D82T and YIM D812T were 61.5 and 62.3 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains YIM D82T and YIM D812T were members of the family Rhodospirillaceae and showed 90.5–90.6 % and 90.1–90.2 % similarities with their closest relatives, Rhodovibrio sodomensis and Rhodovibrio salinarum, respectively. Differential phenotypic and genotypic characteristics of the two isolates from recognized genera showed that the two strains should be classified as representing a new genus and two novel species for which the names Fodinicurvata sediminis gen. nov., sp. nov. (type strain YIM D82T=DSM 21159T=KCTC 22351T) and Fodinicurvata fenggangensis sp. nov. (type strain YIM D812T=CCTCC AA 208037T=DSM 21160T) are proposed.
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Pseudomonas caeni sp. nov., a denitrifying bacterium isolated from the sludge of an anaerobic ammonium-oxidizing bioreactor
More LessTwo Gram-negative, rod-shaped, motile, aerobic bacterial strains designated HY-14T and HY-24 were isolated from the sludge of an anaerobic ammonium-oxidizing bioreactor. The strains could not grow with 5 % (w/v) NaCl, did not produce acid from d-glucose or utilize d-glucose, gluconate or citrate as a sole carbon source. Summed feature 3 and C16 : 0 were the most abundant fatty acids; hydroxyl fatty acids C12 : 0 3-OH and C10 : 0 3-OH were also present. Fatty acid C12 : 0 2-OH was absent. The DNA G+C contents of strains HY-14T and HY-24 were 50.6±0.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains HY-14T and HY-24 formed a monophyletic clade within the genus Pseudomonas. The highest sequence similarities were to Pseudomonas pseudoalcaligenes DSM 50188T (95.9 %). On the basis of phenotypic and phylogenetic properties, strains HY-14T and HY-24 are proposed as a novel species of the genus Pseudomonas, for which the name Pseudomonas caeni sp. nov. is proposed. The type strain is HY-14T (=KCTC 22292T=CCTCC AB208156T).
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Arcobacter thereius sp. nov., isolated from pigs and ducks
More LessDuring a Danish study on the prevalence of campylobacteria in pig abortions and food of animal origin, eight Gram-negative, slightly curved, rod-shaped, non-spore-forming bacteria were clustered by using amplified fragment length polymorphism analysis in a distinct phenon within the genus Arcobacter. In the present study, numerical analysis of whole-cell protein profiles also showed that all isolates clustered in a single group distinct from other recognized Arcobacter species. DNA–DNA hybridization among two representative strains exhibited a mean DNA–DNA relatedness value of 79 %. DNA–DNA hybridization with the type strains of recognized Arcobacter species revealed levels of DNA–DNA relatedness of 41 % or less. The DNA G+C content of the type strain was 28.5 mol%. Pairwise comparison of the 16S rRNA gene sequences with those of the type strains of established species identified Arcobacter cryaerophilus (97.9 %), Arcobacter cibarius (97.5 %) and Arcobacter skirrowii (97.2 %) as the nearest phylogenetic neighbours. The isolates could be distinguished from other Arcobacter species by means of the following biochemical tests: activities of catalase and urease, reduction of nitrate and growth on minimal medium, lack of growth at 37 °C under standardized aerobic and microaerobic conditions, in 4 % NaCl and 1 % glycine media. Finally, DNA fingerprints obtained by using enterobacterial repetitive intergenic consenus-PCR showed that the eight isolates represent eight strains of a single novel Arcobacter species, for which the name Arcobacter thereius sp. nov. is proposed. The type strain is LMG 24486T (=CCUG 56902T).
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Marinobacter szutsaonensis sp. nov., isolated from a solar saltern
More LessA Gram-negative, aerobic, non-spore-forming, halophilic bacterial strain, NTU-104T, was isolated from the Szutsao saltern in southern Taiwan, which was previously used as salt production field. The novel isolate grew optimally at 35–40 °C, at pH 7.5–8.0 and in the presence of 5 % (w/v) NaCl. The major fatty acids were C16 : 0, C18 : 1 ω9c, C16 : 1 ω9c, C12 : 0 3-OH and C12 : 0. The predominant quinone was Q-9. Phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine were the predominant polar lipids. The DNA G+C content was 56.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed the affiliation of the novel isolate to the genus Marinobacter. DNA–DNA hybridization results between strain NTU-104T and the type strains of the most closely related species, Marinobacter pelagius and Marinobacter koreensis, were 36.4 % and 33.2 %, respectively. On the basis of phenotypic, phylogenetic and genetic analyses, strain NTU-104T is considered to represent a novel species of the genus Marinobacter. The name Marinobacter szutsaonensis sp. nov. is proposed, with strain NTU-104T (=BCRC 17809T=CGMCC 1.7011T=JCM 15751T) as the type strain.
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Vogesella lacus sp. nov., isolated from a soft-shell turtle culture pond
A non-pigmented, Gram-negative, aerobic, rod-shaped bacterium, strain GR13T, was isolated using nutrient agar from a water sample from a pond used for the culture of soft-shell turtles (Trionyx sinensis), Pingtung County, Taiwan. 16S rRNA gene sequence studies indicated that the novel strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Vogesella. Its closest neighbours were Vogesella indigofera ATCC 19706T and Vogesella perlucida DS-28T (both with 97.4 % gene sequence similarity). The novel isolate could be distinguished from these species by several phenotypic characteristics. The predominant fatty acids were summed feature 3 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH; 60 %), C16 : 0 (13.6 %) and C18 : 1 ω7c (12.5 %). The DNA G+C content of strain GR13T was 63 mol%. The DNA–DNA hybridization values for the novel strain with V. indigofera and V. perlucida were <25 %. On the basis of the 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, it is concluded that strain GR13T represents a novel species in the genus Vogesella, for which the name Vogesella lacus sp. nov. is proposed. The type strain is GR13T (=BCRC 17836T=LMG 24504T).
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- Evolution, Phylogeny And Biodiversity
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Dickeya species relatedness and clade structure determined by comparison of recA sequences
More LessUsing sequences from the recA locus, we have produced a phylogeny of 188 Dickeya strains from culture collections and identified species relatedness and subspecies clade structure within the genus. Of the six recognized species, Dickeya paradisiaca, D. chrysanthemi and D. zeae were discriminated with long branch lengths. The clade containing the D. paradisiaca type strain included just one additional strain, isolated from banana in Colombia. Strains isolated from Chrysanthemum and Parthenium species made up most of the clade containing the D. chrysanthemi type strain, and the host range of this species was extended to include potato. The D. zeae clade had the largest number of sequevars and branched into two major sister clades that contained all of the Zea mays isolates, and were identified as phylotypes PI and PII. The host range was increased from six to 13 species, including potato. The recA sequence of an Australian sugar-cane strain was sufficiently distinct to rank as a new species-level branch. In contrast to these species, Dickeya dadantii, D. dianthicola and D. dieffenbachiae were distinguished with shorter branch lengths, indicating relatively closer relatedness. The recA sequence for the type strain of D. dadantii clustered separately from other strains of the species. However, sequence comparison of three additional loci revealed that the D. dadantii type strain grouped together with the six other D. dadantii strains that were sequenced. Analysis of all four loci indicated that the D. dadantii strains were most closely related to D. dieffenbachiae. Three further branches (DUC-1, -2 and -3) were associated with these three species, which all diverged from a common origin and can be considered as a species complex. The large clade containing the D. dianthicola type strain comprised 58 strains and had little sequence diversity. One sequevar accounted for the majority of these strains, which were isolated nearly exclusively from eight hosts from Europe. Isolation of this sequevar on multiple occasions from Dianthus and (more recently) potato demonstrates that this lineage has become established in these species. The D. dadantii clade comprised 11 sequevars, and the known host range of the species was extended from eight to 19 species. New hosts included several ornamental species and potato. The clade DUC-1 was made up exclusively of potato strains originating from Europe, which had identical sequences, whilst DUC-2 strains were isolated mostly from a variety of monocotyledonous species. A single strain from Aglaonema sp. made up DUC-3. A single sequevar constituted the D. dieffenbachiae clade. The phylogenetic method described will provide a simple means for identification to the species and intraspecies level, which will support efforts to control these pathogens based on monitoring and surveillance.
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 54 (2004)
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Volume 53 (2003)
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Volume 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)