Showing papers in "International Journal of Systematic and Evolutionary Microbiology in 2003"
TL;DR: Environmental sequence data indicate that this phylum is widespread in nature and has a phylogenetic breadth (19% 16S rDNA sequence divergence) that is greater than well-known phyla such as the Actinobacteria (18% divergence).
Abstract: A phylogenetically novel aerobic bacterium was isolated from an anaerobic-aerobic sequential batch reactor operated under enhanced biological phosphorus removal conditions for wastewater treatment. The isolation strategy used targeted slowly growing polyphosphate-accumulating bacteria by combining low-speed centrifugations and prolonged incubation on a low-nutrient medium. The isolate, designated strain T-27T, was a gram-negative, rod-shaped aerobe. Cells often appeared to divide by budding replication. Strain T-27T grew at 25-35 degrees C with an optimum growth temperature of 30 degrees C, whilst no growth was observed below 20 degrees C or above 37 degrees C within 20 days incubation. The pH range for growth was 6.5-9.5, with an optimum at pH 7.0. Strain T-27T was able to utilize a limited range of substrates, such as yeast extract, polypepton, succinate, acetate, gelatin and benzoate. Neisser staining was positive and 4,6-diamidino-2-phenylindole-stained cells displayed a yellow fluorescence, indicative of polyphosphate inclusions. Menaquinone 9 was the major respiratory quinone. The cellular fatty acids of the strain were mainly composed of iso-C15:0, C16:1 and C14:0. The G + C content of the genomic DNA was 66 mol%. Comparative analyses of 16S rRNA gene sequences indicated that strain T-27T belongs to candidate division BD (also called KS-B), a phylum-level lineage in the bacterial domain, to date comprised exclusively of environmental 16S rDNA clone sequences. Here, a new genus and species are proposed, Gemmatimonas aurantiaca (type strain T-27T=JCM 11422T=DSM 14586T) gen. nov., sp. nov., the first cultivated representative of the Gemmatimonadetes phyl. nov. Environmental sequence data indicate that this phylum is widespread in nature and has a phylogenetic breadth (19% 16S rDNA sequence divergence) that is greater than well-known phyla such as the Actinobacteria (18% divergence).
407 citations
TL;DR: The YB1T strain, the aetiological agent of tissue lysis of the coral Pocillopora damicornis, was characterized as a novel Vibrio species on the basis of 16S rDNA sequence, DNA-DNA hybridization data, AFLP and GTG5-PCR genomic fingerprinting patterns and phenotypic properties, including the cellular fatty acid profile.
Abstract: Vibrio sp. YB1T (=ATCC BAA-450T =LMG 20984T), the aetiological agent of tissue lysis of the coral Pocillopora damicornis, was characterized as a novel Vibrio species on the basis of 16S rDNA sequence, DNA–DNA hybridization data (G+C content is 45·6 mol%), AFLP and GTG5-PCR genomic fingerprinting patterns and phenotypic properties, including the cellular fatty acid profile. The predominant fatty acids were 16 : 0 and 18 : 1ω7c. The name Vibrio coralliilyticus sp. nov. is proposed for the novel coral-pathogenic species. In addition to strain YB1T, which was isolated from the Indian Ocean, five additional strains of V. coralliilyticus have been isolated, three from diseased P. damicornis in the Red Sea, one from diseased oyster larvae (Kent, UK) and one from bivalve larvae (Brazil). The six V. coralliilyticus strains showed high genotypic and phenotypic similarities and all were pathogenic to P. damicornis. The closest phylogenetic neighbours to V. coralliilyticus are Vibrio tubiashii, Vibrio nereis and Vibrio shilonii.
399 citations
TL;DR: Phylogenetic analysis demonstrated that strain T1 18(T) is most closely related to the genus Rhodoferax, which is not a phototroph and does not ferment fructose, and physiological and phylogenetic differences are proposed as a novel species, RhodoferAX ferrireducens sp.
Abstract: To further investigate the diversity of micro-organisms capable of conserving energy to support growth from dissimilatory Fe(III) reduction, Fe(III)-reducing micro-organisms were enriched and isolated from subsurface sediments collected in Oyster Bay, VA, USA. A novel isolate, designated T118T, was recovered in a medium with lactate as the sole electron donor and Fe(III) as the sole electron acceptor. Cells of T118T were Gram-negative, motile, short rods with a single polar flagellum. Strain T118T grew between pH 6·7 and 7·1, with a temperature range of 4–30 °C. The optimal growth temperature was 25 °C. Electron donors utilized by strain T118T with Fe(III) as the sole electron acceptor included acetate, lactate, malate, propionate, pyruvate, succinate and benzoate. None of the compounds tested was fermented. Electron acceptors utilized with either acetate or lactate as the electron donor included Fe(III)–NTA (nitrilotriacetic acid), Mn(IV) oxide, nitrate, fumarate and oxygen. Phylogenetic analysis demonstrated that strain T118T is most closely related to the genus Rhodoferax. Unlike other species in this genus, strain T118T is not a phototroph and does not ferment fructose. However, phototrophic genes may be present but not expressed under the experimental conditions tested. No Rhodoferax species have been reported to grow via dissimilatory Fe(III) reduction. Based on these physiological and phylogenetic differences, strain T118T (=ATCC BAA-621T=DSM 15236T) is proposed as a novel species, Rhodoferax ferrireducens sp. nov.
357 citations
TL;DR: The proposal that sequence analysis of a small set of protein-encoding genes could reliably assign novel strains or isolates to bacterial species is strongly supported.
Abstract: Thirty-two protein-encoding genes that are distributed widely among bacterial genomes were tested for the potential usefulness of their DNA sequences in assigning bacterial strains to species. From publicly available data, it was possible to make 49 pairwise comparisons of whole bacterial genomes that were related at the genus or subgenus level. DNA sequence identity scores for eight of the genes correlated strongly with overall sequence identity scores for the genome pairs. Even single-gene alignments could predict overall genome relatedness with a high degree of precision and accuracy. Predictions could be refined further by including two or three genes in the analysis. The proposal that sequence analysis of a small set of protein-encoding genes could reliably assign novel strains or isolates to bacterial species is strongly supported.
328 citations
TL;DR: Pinnipeds appear to be the natural host for this 'seal bacillus', although the organism is also pathogenic in guinea pigs, rabbits, humans, Brazilian tapir and, possibly, cattle.
Abstract: A comparison of Mycobacterium tuberculosis complex isolates from seals (pinnipeds) in Australia, Argentina, Uruguay, Great Britain and New Zealand was undertaken to determine their relationships to each other and their taxonomic position within the complex. Isolates from 30 cases of tuberculosis in six species of pinniped and seven related isolates were compared to representative and standard strains of the M. tuberculosis complex. The seal isolates could be distinguished from other members of the M. tuberculosis complex, including the recently defined 'Mycobacterium canettii' and 'Mycobacterium caprae', on the basis of host preference and phenotypic and genetic tests. Pinnipeds appear to be the natural host for this 'seal bacillus', although the organism is also pathogenic in guinea pigs, rabbits, humans, Brazilian tapir (Tapirus terrestris) and, possibly, cattle. Infection caused by the seal bacillus is predominantly associated with granulomatous lesions in the peripheral lymph nodes, lungs, pleura, spleen and peritoneum. Cases of disseminated disease have been found. As with other members of the M. tuberculosis complex, aerosols are the most likely route of transmission. The name Mycobacterium pinnipedii sp. nov. is proposed for this novel member of the M. tuberculosis complex (the type strain is 6482(T)=ATCC BAA-688(T)=NCTC 13288(T)).
323 citations
TL;DR: The phylogenetic relationship of 12 ammonia-oxidizing isolates (eight nitrosospiras and four nitrosomonads) was investigated and the estuarine isolate Nitrosomonas sp.
Abstract: The phylogenetic relationship of 12 ammonia-oxidizing isolates (eight nitrosospiras and four nitrosomonads), for which no gene sequence information was available previously, was investigated based on their genes encoding 16S rRNA and the active site subunit of ammonia monooxygenase (AmoA). Almost full-length 16S rRNA gene sequences were determined for the 12 isolates. In addition, 16S rRNA gene sequences of 15 ammonia-oxidizing bacteria (AOB) published previously were completed to allow for a more reliable phylogeny inference of members of this guild. Moreover, sequences of 453 bp fragments of the amoA gene were determined from 15 AOB, including the 12 isolates, and completed for 10 additional AOB. 16S rRNA gene and amoA-based analyses, including all available sequences of AOB pure cultures, were performed to determine the position of the newly retrieved sequences within the established phylogenetic framework. The resulting 16S rRNA gene and amoA tree topologies were similar but not identical and demonstrated a superior resolution of 16S rRNA versus amoA analysis. While 11 of the 12 isolates could be assigned to different phylogenetic groups recognized within the betaproteobacterial AOB, the estuarine isolate Nitrosomonas sp. Nm143 formed a separate lineage together with three other marine isolates whose 16S rRNA sequences have not been published but have been deposited in public databases. In addition, 17 environmentally retrieved 16S rRNA gene sequences not assigned previously and all originating exclusively from marine or estuarine sites clearly belong to this lineage.
314 citations
TL;DR: In this paper, the diversity of strains of S. bovis biotype II was analyzed, and it was confirmed that they belong to different species, either S. equinus or S. infantarius.
Abstract: ‘Streptococcus bovis/Streptococcus equinus’ is a large bacterial complex including different species frequently isolated from infections of humans (Streptococcus gallolyticus, Streptococcus infantarius) or animals (S. bovis, S. equinus, Streptococcus alactolyticus). The separation of S. bovis into three different biotypes has been partially correlated with genetic differentiation. In addition, recent advances in bacterial phylogeny have led to the inclusion of Streptococcus macedonicus and Streptococcus waius in this complex. The aim of this study was to improve physiological differentiation between species related to the complex and to clarify their respective phylogenetic positions. In this study, physiological, genetic and phylogenetic analyses of a set of 88 streptococcal strains were performed. The diversity of strains of S. bovis biotype II was analysed, and it was confirmed that they belong to different species, either S. equinus or S. infantarius. It was demonstrated that S. gallolyticus, S. bovis biotype II.2, S. macedonicus and S. waius form a single DNA cluster separated into three different subspecies. They are delineated by different biochemical traits, limited DNA–DNA relatedness and noticeable divergence in 16S rDNA sequences. According to the current definition of species, the names S. gallolyticus subsp. gallolyticus subsp. nov., S. gallolyticus subsp. pasteurianus subsp. nov. and S. gallolyticus subsp. macedonicus subsp. nov. are proposed for these three subspecies.
314 citations
TL;DR: Phylogenetic analyses based on 16S rDNA sequences revealed that both strains belong to an uncultured, previously recognized clone lineage of the phylum Chloroflexi (formerly known as green non-sulfur bacteria) and suggested that each strain should be classified into a new independent genus.
Abstract: Two thermophilic, Gram-negative, non-spore-forming, multicellular filamentous micro-organisms were isolated from thermophilic granular sludge in an upflow anaerobic sludge blanket reactor treating fried soybean-curd manufacturing waste water (strain UNI-1T) and from a hot spring sulfur-turf in Japan (strain STL-6-O1T). The filaments were longer than 100 μm and of 0·2–0·3 μm (strain UNI-1T) or 0·7–0·8 μm (strain STL-6-O1T) in width. Strain UNI-1T was a strictly anaerobic organism. The optimum temperature for growth was around 55 °C; growth occurred in the range 50–60 °C. The optimum pH for growth was around 7·0; growth occurred in the range pH 6·0–8·0. Strain STL-6-O1T was a facultatively aerobic bacterium. The optimum temperature for growth was around 55 °C; growth occurred in the range 37–65 °C. The optimum pH for growth was around 7·5–8·0; growth occurred in the range pH 7·0–9·0. The two organisms grew chemo-organotrophically on a number of carbohydrates and amino acids in the presence of yeast extract. The G+C content of the DNA of strains UNI-1T and STL-6-O1T was 54·5 and 59·0 mol%, respectively. Major cellular fatty acids for strain UNI-1T were C16 : 0, C15 : 0, C14 : 0 and C18 : 0, whereas those for strain STL-6-O1T were C18 : 0, C16 : 0, C17 : 0 and iso-C17 : 0. MK-10 was the major quinone from aerobically grown STL-6-O1T cells. Phylogenetic analyses based on 16S rDNA sequences revealed that both strains belong to an uncultured, previously recognized clone lineage of the phylum Chloroflexi (formerly known as green non-sulfur bacteria). These phenotypic and genetic properties suggested that each strain should be classified into a new independent genus; hence, the names Anaerolinea thermophila and Caldilinea aerophila are proposed for strains UNI-1T (=JCM 11387T=DSM 14523T) and STL-6-O1T(=JCM 11388T=DSM 14525T), respectively. These strains represent the type and sole species of the genera Anaerolinea and Caldilinea, respectively.
309 citations
TL;DR: Biochemical criteria, deduced from a numerical taxonomy study of phenotypic characteristics and serological reactions, allowed discrimination of strains belonging to the four genomospecies and it is proposed to retain the P. carotovorum subspecies in the genus Pectobacterium.
Abstract: A collection of 42 strains belonging to the five subspecies of Pectobacterium carotovorum (subspecies atrosepticum, betavasculorum, carotovorum, odoriferum and wasabiae) and 11 reference and type strains of biovars of Pectobacterium chrysanthemi, Pectobacterium cacticidum and Brenneria paradisiaca were studied by DNA–DNA hybridization, numerical taxonomy of 120 phenotypic characteristics, serology and new phylogenetic analysis of previously reported sequences from a database of aligned 16S rDNA sequences. The P. carotovorum subspecies formed a clade according to neighbour-joining methods, but they formed two paraphyletic clusters according to maximum-likelihood and maximum-parsimony. However, phylogenetic analysis of 16S rDNA sequences alone is not sufficient to justify generic differentiation and therefore, it is proposed to retain the P. carotovorum subspecies in the genus Pectobacterium. The strains of P. carotovorum were distributed in four genomospecies: genomospecies 1, harbouring all strains of subsp. atrosepticum, genomospecies 2, including the strains of subsp. betavasculorum isolated from sugar beet, sunflower, potato, hyacinth and artichoke, genomospecies 3, clustering all strains of subsp. wasabiae isolated from wasabi in Japan, and genomospecies 4, gathering together strains of subsp. carotovorum and strains of subsp. odoriferum. Four strains of P. carotovorum subsp. carotovorum remained unclustered. Biochemical criteria, deduced from a numerical taxonomy study of phenotypic characteristics and serological reactions, allowed discrimination of strains belonging to the four genomospecies. Thus, it is proposed that three genomospecies be elevated to species level as Pectobacterium atrosepticum sp. nov. (type strain CFBP 1526T=LMG 2386T =NCPPB 549T =ICMP 1526T), Pectobacterium betavasculorum sp. nov. (type strain CFBP 2122T=LMG 2464T =NCPPB 2795T =ICMP 4226T) and Pectobacterium wasabiae sp. nov. (type strain CFBP 3304T=LMG 8404T =NCPPB 3701T =ICMP 9121T). Only two subspecies are maintained within P. carotovorum, subsp. carotovorum (type strain CFBP 2046T=LMG 2404T =NCPPB 312T =ICMP 5702T) and subsp. odoriferum (type strain CFBP 1878T=LMG 5863T =NCPPB 3839T =ICMP 11553T), for which discriminating tests are available.
305 citations
TL;DR: The phylogenetic relationships of all known species of the genus Aeromonas were investigated by using the sequence of gyrB, a gene that encodes the B-subunit of DNA gyrase, which proved to be an excellent molecular chronometer for phylogenetic studies.
Abstract: The phylogenetic relationships of all known species of the genus Aeromonas were investigated by using the sequence of gyrB, a gene that encodes the B-subunit of DNA gyrase. Nucleotide sequences of gyrB were determined from 53 Aeromonas strains, including some new isolates, which were also characterized by analysis of the 16S rDNA variable regions. The results support the recognition of the family Aeromonadaceae, as distinct from Plesiomonas shigelloides and other enteric bacteria. This phylogenetic marker revealed strain groupings that are consistent with the taxonomic organization of all Aeromonas species described to date. In particular, gyrB results agreed with 16S rDNA analysis; moreover, the former showed a higher capacity to differentiate between species. The present analysis was useful for the elucidation of reported discrepancies between different DNA-DNA hybridization sets. Additionally, due to the sequence diversity found at the intraspecies level, gyrB is proposed as a useful target for simultaneous identification of species and strains. In conclusion, the gyrB gene has proved to be an excellent molecular chronometer for phylogenetic studies of the genus Aeromonas.
285 citations
TL;DR: On the basis of phenotypic properties, phylogenetic and genomic data, strains YkJ-103T and YKJ-105 should be placed in the genus Psychrobacter as members of a new species, for which the name Psych Robacter jeotgali sp.
Abstract: Two Gram-negative, non-motile, non-spore-forming and moderately halophilic cocci (strains YKJ-103T and YKJ-105) were isolated from the traditional Korean fermented seafood, jeotgal. The two strains grew optimally at 25-30 degrees C and grew at 4 and 36 degrees C, but not above 37 degrees C. They grew in the presence of 0-10% (w/v) NaCl with an optimum of 2-3% (w/v) NaCl. Strains YKJ-103T and YKJ-105 were chemotaxonomically characterized by having ubiquinone-8 (0-8) as the predominant isoprenoid quinone and C18:1omega9c as the major fatty acid. The polar lipid analysis indicated the presence of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G + C contents of strains YKJ-103T and YKJ-105 were 44 and 43 mol%, respectively. Strains YKJ-103T and YKJ-105 showed no difference in their 16S rDNA sequences, and their mean level of DNA-DNA relatedness was 92.3%. Phylogenetic analysis based on 16S rDNA sequences showed that the two strains form a distinct phylogenetic lineage within the cluster comprising Psychrobacter species. Strains YKJ-103T and YKJ-105 exhibited 16S rDNA similarities of 96.6% with the type strain of Psychrobacter proteolyticus, the closest Psychrobacter species, and of 94.5-95.9% with type strains of other Psychrobacter species. On the basis of phenotypic properties, phylogenetic and genomic data, strains YKJ-103T and YKJ-105 should be placed in the genus Psychrobacter as members of a new species, for which the name Psychrobacter jeotgali sp. nov. is proposed. The type strain of the new species is strain YKJ-103T (=KCCM 41559T = JCM 11463T).
TL;DR: A novel mesophilic, sulfur- and thiosulfate-oxidizing bacterium, strain OK10(T), was isolated from deep-sea sediments at the Hatoma Knoll in the Mid-Okinawa Trough hydrothermal field and represents the sole species of a new genus, Sulfurimonas autotrophica, proposed.
Abstract: A novel mesophilic, sulfur- and thiosulfate-oxidizing bacterium, strain OK10T, was isolated from deep-sea sediments at the Hatoma Knoll in the Mid-Okinawa Trough hydrothermal field. Cells of strain OK10T were short rods, each being motile by means of a single polar flagellum. The isolate grew at 10–40 °C (optimum 25 °C) and pH 4·5–9·0 (optimum pH 6·5). It grew chemolithoautotrophically with elemental sulfur, sulfide and thiosulfate as sole electron donors and oxygen as electron acceptor. Molecular hydrogen did not support growth. The G+C content of the genomic DNA of strain OK10T was 35·2 mol%. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that the isolate belonged to the e-Proteobacteria. On the basis of its physiological and molecular characteristics, strain OK10T (=ATCC BAA-671T=JCM 11897T) represents the sole species of a new genus, Sulfurimonas, for which the name Sulfurimonas autotrophica is proposed.
TL;DR: A novel genus and species within the gamma-Proteobacteria are proposed, Oleispira antarctica gen. nov., sp.
Abstract: The taxonomic characteristics of two bacterial strains, RB-8(T) and RB-9, isolated from hydrocarbon-degrading enrichment cultures obtained from Antarctic coastal marine environments (Rod Bay, Ross Sea), were determined. These bacteria were psychrophilic, aerobic and Gram-negative with polar flagella. Growth was not observed in the absence of NaCl, occurred only at concentrations of Na+ above 20 mM and was optimal at an NaCl concentration of 3-5% (w/v). The major cellular fatty acids were monounsaturated straight-chain fatty acids. The strains were able to synthesize the polyunsaturated fatty acid eicosapentaenoic acid (20: 5omega3) at low temperatures. The DNA G + C contents were 41-42 mol%. The strains formed a distinct phyletic line within the gamma-Proteobacteria, with less than 89.6% sequence identity to their closest relatives within the Bacteria with validly published names. Both isolates exhibited a restricted substrate profile, with a preference for aliphatic hydrocarbons, that is typical of marine hydrocarbonoclastic micro-organisms such as Alcanivorax, Marinobacter and Oleiphilus. On the basis of ecophysiological properties, G + C content, 16S rRNA gene sequences and fatty acid composition, a novel genus and species within the gamma-Proteobacteria are proposed, Oleispira antarctica gen. nov., sp. nov.; strain RB-8(T) (= DSM 14852(T) = LMG 21398(T)) is the type strain.
TL;DR: Genotypic and phenotypic analyses support the creation of two novel species: Silicibacter pomeroyi sp.nov.
Abstract: Three Gram-negative, rod-shaped, aerobic bacteria that were capable of degrading dimethylsulfoniopropionate (DMSP) were isolated from marine waters. These isolates (DSS-3T, DSS-10 and ISMT) exhibited the ability to demethylate and cleave DMSP, as well as to degrade other sulfur compounds related to DMSP that are cycled in marine environments. Intracellular poly-β-hydroxybutyrate inclusions, surface blebs and one polar, complex flagellum that rotated exclusively in the clockwise direction were observed for DSS-3T. The outer membrane of ISMT was separated from the cytoplasm at the poles in a toga-like morphology. The primary fatty acid in both strains was C18 : 1 ω7c. DNA G+C contents for the isolates were 68·0±0·1, 68·1±0·1 and 66·0±0·2 mol% for DSS-3T, DSS-10 and ISMT, respectively. 16S rRNA gene sequence analyses placed these organisms within the Roseobacter lineage of the α-Proteobacteria. Closely related species were Silicibacter lacuscaerulensis and Ruegeria atlantica (DSS-3T and DSS-10) and Roseovarius tolerans (ISMT). Neither DSS-3T nor ISMT exhibited 16S rRNA similarity >97 % or DNA–DNA hybridization values >45 % to their nearest described relatives. Genotypic and phenotypic analyses support the creation of two novel species: Silicibacter pomeroyi sp. nov. with strain DSS-3T (=ATCC 700808T=DSM 15171T) as the type strain, and Roseovarius nubinhibens sp. nov. with strain ISMT (=ATCC BAA-591T=DSM 15170T) as the type strain.
TL;DR: The data suggest that strains BL2(T) and A1 represent a novel species of Methylocella; the name Methyla silvestris sp.
Abstract: Two strains of Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped, methane-oxidizing bacteria were isolated from an acidic forest cambisol near Marburg, Germany, and were designated as strains BL2(T) and A1. These bacteria were morphologically and phenotypically similar to Methylocella palustris K(T). The cells possess a highly specific bipolar appearance. They lack the intracytoplasmic membranes common to all methane-oxidizing bacteria except Methylocella, but contain a vesicular membrane system connected to the cytoplasmic membrane. A soluble methane monooxygenase was present, but no particulate methane monooxygenase could be detected. These bacteria utilize the serine pathway for carbon assimilation. Strains BL2(T) and A1 are moderately acidophilic, mesophilic organisms capable of growth at pH values between 4.5 and 7 (with an optimum at pH 5.5) and at temperatures between 4 and 30 degrees C. Compared with Methylocella palustris K(T), these strains have greater tolerance of cold temperatures, dissolved salts and methanol. On the basis of 16S rRNA gene sequence identity, of species with validly published names, strain BL2(T) is most closely related to Methylocella palustris K(T) (97.3 % identity), Beijerinckia indica subsp. indica ATCC 9039(T) (97.1 %) and Methylocapsa acidiphila B2(T) (96.2 %). The DNA G+C content is 60 mol% and the major phospholipid fatty acid is 18 : 1omega7. Strain BL2(T) showed only 21-22 % DNA-DNA hybridization with Methylocella palustris K(T). The data therefore suggest that strains BL2(T) and A1 represent a novel species of Methylocella; the name Methylocella silvestris sp. nov. is proposed, with strain BL2(T) (=DSM 15510(T)=NCIMB 13906(T)) as the type strain.
TL;DR: To accommodate this emerging coral pathogen, the creation of a new genus and species is proposed, Aurantimonas coralicida gen. nov., sp.
Abstract: A bacterium previously isolated from a diseased colony of the scleractinian coral Dichocoenia stokesi (common name elliptical star coral) was subjected to a detailed polyphasic taxonomic characterization. The isolate, designated WP1T, was halophilic and strictly aerobic and formed golden-orange-pigmented colonies after prolonged incubation. Cells of WP1T were Gram-negative, rod-shaped and showed a characteristic branching rod morphology. Chemotaxonomically, WP1T was characterized by having Q-10 as the major respiratory lipoquinone and sym-homospermidine as the main component of the cellular polyamine content. The predominant constituent in the cellular fatty acid profile was C18 : 1
ω7c, along with C19 : 0 cyclo ω8c and C16 : 0. Other fatty acids present in smaller amounts were C17 : 0, C18 : 0, C16 : 1
ω7c, C20 : 1
ω7c and C18 : 1 2-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. Minor amounts of diphosphatidylglycerol, phosphatidylmonomethylethanolamine and phosphatidyldimethylethanolamine were present. The G+C content of the genomic DNA was 66·3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence showed that WP1T represents a separate subline of descent within the order ‘Rhizobiales’ of the ‘Alphaproteobacteria’. The new line of descent falls within the group of families that includes the Rhizobiaceae, Bartonellaceae, Brucellaceae and ‘Phyllobacteriaceae’, with no particular relative within this group. The 16S rRNA gene sequence similarity to all established taxa within this group was not higher than 92·0 % (to Mesorhizobium mediterraneum). To accommodate this emerging coral pathogen, the creation of a new genus and species is proposed, Aurantimonas coralicida gen. nov., sp. nov. (type strain WP1T=CIP 107386T =DSM 14790T).
TL;DR: A significant number of chimeric 16S rDNA sequences of diverse origin were identified in the public databases by partial treeing analysis, suggesting that chimeric sequences, representing phylogenetically novel non-existent organisms, are routinely being overlooked in molecular phylogenetic surveys despite a general awareness of PCR-generated artefacts amongst researchers.
Abstract: A significant number of chimeric 16S rDNA sequences of diverse origin were identified in the public databases by partial treeing analysis. This suggests that chimeric sequences, representing phylogenetically novel non-existent organisms, are routinely being overlooked in molecular phylogenetic surveys despite a general awareness of PCR-generated artefacts amongst researchers.
TL;DR: Two studies on the evolution of the M. tuberculosis complex based on the presence/absence of regions of difference have shown that the group of caprine isolates (or its ancestor) is older than M. bovis, reinforcing the original suggestion that the caprine mycobacterial strains are a taxon of theM.
Abstract: Mycobacterium tuberculosis complex isolates recovered from goats were originally classified as Mycobacterium tuberculosis subsp. caprae; however, this subspecies was recently reclassified as Mycobacterium bovis subsp. caprae. Besides biochemical (sensitivity to pyrazinamide) and epidemiological features, strains of this unusual member of the M. tuberculosis complex show a special combination of pncA, oxyR, katG and gyrA gene polymorphisms. Sequence analysis of the gyrB gene in these strains reveals special nucleotide substitutions not found in other members of the M. tuberculosis complex that can be used to differentiate caprine mycobacterial strains from M. bovis and other members of the M. tuberculosis complex. M. tuberculosis subsp. caprae now appears not to be restricted to Spanish goats, as strains of this organism have been isolated from cattle, wild boar and pigs. Its occurrence has also been reported in France, Austria and Germany. Two studies on the evolution of the M. tuberculosis complex based on the presence/absence of regions of difference have shown that the group of caprine isolates (or its ancestor) is older than M. bovis (or its ancestor). These findings reinforce the original suggestion that the caprine mycobacterial strains are a taxon of the M. tuberculosis complex, independent of M. bovis. Within the current context of the existing nomenclature of the M. tuberculosis complex, it is proposed that M. tuberculosis subsp. caprae be elevated to species status, as Mycobacterium caprae comb. nov., sp. nov.
TL;DR: An overview of the controversial proposal for the major eukaryote taxon "Excavata" is presented, with phylogenetic diagnoses for Excavata and for two novel taxon names, Fornicata (Carpediemonas, retortamonads, diplomonads) and Preaxostyla (Trimastix, oxymonads).
Abstract: An overview of the controversial proposal for the major eukaryote taxon ‘Excavata’ is presented. Excavata is predicted to include at least ten distinct groups: jakobids, Malawimonas, Trimastix, Carpediemonas, retortamonads, diplomonads, Heterolobosea, oxymonads, parabasalids and Euglenozoa. These ‘excavates' have broadly similar flagellar apparatus organizations, for which a ‘universal’ terminology is provided. Most, but not all, of these organisms share a distinctive suspension-feeding groove, as well as some or all of a set of seven other proposed cytoskeletal apomorphies. Cladistic analyses of morphological data do not resolve high-level relationships within Excavata. Excavate-rich molecular phylogenies recover some robust clades, but do not support or strongly refute the monophyly of Excavata. A partial classification for excavates is presented, with phylogenetic diagnoses for Excavata and for two novel taxon names, Fornicata (Carpediemonas, retortamonads, diplomonads) and Preaxostyla (Trimastix, oxymonads).
TL;DR: The phylogenetic classification presented here is in general in agreement with current classifications based on phenotypic and molecular data, but the findings suggest, however, that in some cases, further divisions or, conversely, further groupings might be warranted.
Abstract: The nucleotide sequences of the 3' end of the 16S rDNA and the 16S-23S internal transcribed spacer (ITS) of 40 Bacillaceae species were determined. These included 21 Bacillus, 9 Paenibacillus, 6 Brevibacillus, 2 Geobacillus, 1 Marinibacillus and 1 Virgibacillus species. Comparative sequence analysis of a 220 bp region covering a highly conserved 150 bp sequence located at the 3' end of the 16S rRNA coding region and a conserved 70 bp sequence located at the 5' end of the 16S-23S ITS of the 40 species and six sequences available in GenBank were used to infer the phylogenetic relationships between all 46 taxa. When a maximal distance (D(max), where D refers to the number of nucleotide substitutions per site) of 0.31 was introduced as a threshold to determine groupings, 10 phylogenetically distinct clusters were revealed. Twenty-six Bacillus species were separated in seven groups (I, II, III, IV, V, VI and X), but Bacillus circulans remained ungrouped. All six Brevibacillus species under study were in Group VII. The nine Paenibacillus species fell into two distinct groups (VIII and IX). Species with D(max) values within 0.05 were considered to be very closely related. These were Bacillus psychrophilus and Bacillus psychrosaccharolyticus in Group II; 'Bacillus maroccanus' and Bacillus simplex in Group II; Bacillus amyloliquefaciens, Bacillus atrophaeus, Bacillus mojavensis and Bacillus subtilis in Group VI; Bacillus fusiformis and Bacillus sphaericus in Group VI; Brevibacillus brevis and Brevibacillus formosus in Group VII; Paenibacillus gordonae and Paenibacillus validus in Group VIII; and Bacillus anthracis, Bacillus cereus, Bacillus mycoides and Bacillus thuringiensis in Group X. The phylogenetic classification presented here is, in general, in agreement with current classifications based on phenotypic and molecular data. Our findings suggest, however, that in some cases, further divisions or, conversely, further groupings might be warranted. Should current classifications be re-examined in the light of our results, D(max) values of 0.31 and 0.05, as exemplified here, may prove useful threshold values for the grouping of Bacillaceae into taxa akin to genera and species, respectively. These D(max) thresholds may also reveal, in a different way, bacterial species for which further characterization might be warranted for proper classification and/or reassignment.
TL;DR: An anaerobic, halorespiring bacterium able to reduce tetrachloroethene to cis-dichloroethne was isolated from an an aerobic soil polluted with chlorinated aliphatic compounds.
Abstract: An anaerobic, halorespiring bacterium (strain PCE-M2(T) = DSM 13726(T) = ATCC BAA-583(T)) able to reduce tetrachloroethene to cis-dichloroethene was isolated from an anaerobic soil polluted with chlorinated aliphatic compounds. The isolate is assigned to the genus Sulfurospirillum as a novel species, Sulfurospirillum halorespirans sp. nov. Furthermore, on the basis of all available data, a related organism, Dehalospirillum multivorans DSM 12446(T), is reclassified to the genus Sulfurospirillum as Sulfurospirillum multivorans comb. nov.
TL;DR: Results from DNA-DNA hybridizations and comparison of protein patterns indicated that the seven strains are members of three distinct species, and three novel species of the genus Sphingomonas are proposed.
Abstract: Seven psychrotolerant, Gram-negative bacterial strains, five dust- and airborne isolates (MA101bT, MA306a, MA405/90, MA-olkiT and NW12T) and two from the Antarctic (Ant 20 and M3C203B-B), were subjected to a polyphasic characterization to determine their taxonomic position. High 16S rDNA sequences similarities (99·3–100·0 %) demonstrated that they were closely related to each other. Phylogenetic evaluation of their 16S rDNA sequences revealed that they are members of the genus Sphingomonas sensu stricto, encompassing a separate branch within this genus. They shared 94·4–96·6 % 16S rDNA sequence similarity with species of this genus. All Sphingomonas-specific signature nucleotides were also detected. The presence of the major ubiquinone Q-10, sym-homospermidine as the predominant polyamine, Sphingomonadaceae-specific sphingoglycolipid in the polar lipid patterns and a fatty acid profile containing C14 : 0 2-OH and lacking 3-OH fatty acids were in agreement with identification of these strains as members of the genus Sphingomonas sensu stricto. Results from DNA–DNA hybridizations and comparison of protein patterns indicated that the seven strains are members of three distinct species. One species is represented by strains MA101bT, MA306a and MA405/90, the second by strains NW12T, Ant 20 and M3C203B-B and the third by one strain, MA-olkiT. Their distinction at the species level was also supported by results of biochemical characterization and partly supported by riboprints and genomic fingerprints. On the basis of these results, three novel species of the genus Sphingomonas are proposed: Sphingomonas aurantiaca sp. nov., consisting of strains MA101bT (=DSM 14748T=LMG 21377T), MA306a and MA405/90 (=DSM 14749=LMG 21378), Sphingomonas faeni sp. nov. MA-olkiT (=DSM 14747T=LMG 21379T) and Sphingomonas aerolata sp. nov., represented by strains NW12T (=DSM 14746T=LMG 21376T), Ant 20 (=ICMP 13599) and M3C203B-B (=SMCC M3C203B-B).
TL;DR: Together, these two organisms can be instrumental in reconstructing the early evolution of dinoflagellates and apicomplexans by helping to reveal aspects of the ancestors of both groups.
Abstract: Oxyrrhis marina and Perkinsus marinus are two alveolate species of key taxonomic position with respect to the divergence of apicomplexans and dinoflagellates. New sequences from Oxyrrhis, Perkinsus and a number of dinoflagellates were added to datasets of small-subunit (SSU) rRNA, actin, α-tubulin and β-tubulin sequences, as well as to a combined dataset of all three protein-coding genes, and phylogenetic trees were inferred. The parasitic Perkinsus marinus branches at the base of the dinoflagellate clade with high support in most of the individual gene trees and in the combined analysis, strongly confirming the position originally suggested in previous SSU rRNA and actin phylogenies. The SSU rRNA from Oxyrrhis marina is extremely divergent, and it typically branches with members of the Gonyaulacales, a dinoflagellate order where SSU rRNA sequences are also divergent. Conversely, none of the three protein-coding genes of Oxyrrhis is noticeably divergent and, in trees based on all three proteins individually and in combination, Oxyrrhis branches at the base of the dinoflagellate clade, typically with high bootstrap support. In some trees, Oxyrrhis and Perkinsus are sisters, but most analyses indicate that Perkinsus diverged prior to Oxyrrhis. Morphological characters have previously pointed to Oxyrrhis as an early branch in the dinoflagellate lineage; our data support this suggestion and significantly bolster the molecular data that support a relationship between Perkinsus and dinoflagellates. Together, these two organisms can be instrumental in reconstructing the early evolution of dinoflagellates and apicomplexans by helping to reveal aspects of the ancestors of both groups.
TL;DR: It is proposed that the three genera Brumimicrobium, Cryomorpha and Crocinitomix belong to a new family, Cryomorphaceae fam.
Abstract: Several cold-adapted strains isolated from a variety of algal-rich Antarctic and Southern Ocean samples formed three distinct groups within the class Flavobacteria, phylogenetically distant from other cultivated species The first taxon, designated Algoriphagus ratkowskyi gen nov, sp nov, was isolated from sea ice and from saline lake cyanobacterial mats and includes non-motile, strictly aerobic, saccharolytic rod-like or serpentine strains that were most closely related to the genus Cyclobacterium according to 16S rDNA sequence analysis (sequence similarity 0·85) The second taxon, designated Brumimicrobium glaciale gen nov, sp nov, isolated from sea ice and from continental shelf sediment, formed gliding, rod-like cells that were facultatively anaerobic with a fermentative metabolism The third taxon, designated Cryomorpha ignava gen nov, sp nov, isolated from Southern Ocean particulates and from quartz stone subliths, included strictly aerobic, pleomorphic rod-like cells Brumimicrobium glaciale and Cryomorpha ignava were most closely allied with ‘Microscilla aggregans var catalatica’, which, on the basis of its distinctive taxonomic traits, is also proposed as a new genus and species, Crocinitomix catalasitica gen nov, sp nov It is proposed that the three genera Brumimicrobium, Cryomorpha and Crocinitomix belong to a new family, Cryomorphaceae fam nov (type genus Cryomorpha), as they possess generally similar morphological and ecophysiological characteristics and form a common and distinct clade within class Flavobacteria
TL;DR: On the basis of phenotypic and genotypic analyses, three novel species of the genus Pseudomonas are proposed: pseudomonas koreensis sp.
Abstract: Among Pseudomonas strains isolated from Korean agricultural soils, four strains (Ps 9-14 group: Ps 1-2, Ps 1-10, Ps 5-5 and Ps 9-14T) from the Suwon, Goesan and Samchok regions, three strains (Ps 3-10 group: Ps 2-22, Ps 3-1 and Ps 3-10T) from Umsong Region and four strains (Pss 26 group: Pss 14, Pss 25, Pss 26T and Pss 27) from Jinju Region were identified as three independent groups on the basis of 16S rDNA sequence analysis. While, on the basis of 16S rDNA sequence analysis, Ps 9-14T and Ps 3-10T form a phyletic line with Pseudomonas jessenii CIP 105274T, 'Pseudomonas pavonaceae' IAM 1155 and Pseudomonas graminis DSM 11363T, Pss 26T is grouped with Pseudomonas citronellolis ATCC 13674T and Pseudomonas nitroreducens IAM 1439T. According to DNA-DNA hybridization studies, strain Ps 9-14T shows high DNA relatedness to strain Ps 3-10T (52%) and Pseudomonas migulae CIP 105470T (49%) and strain Ps 3-10T reveals high relatedness to strain Ps 9-14T (48%) and P. jessenii CIP 105274T (45%). Strain Pss 26T shows high relatedness to P. citronellolis LMG 18378T (54%), P. nitroreducens ATCC 33634T (48%) and Pseudomonas aeruginosa LMG 1242T (48%). On the basis of phenotypic and genotypic analyses, three novel species of the genus Pseudomonas are proposed: Pseudomonas koreensis sp. nov. (type strain Ps 9-14T =LMG 21318T =KACC 10848T) for the Ps 9-14 group, Pseudomonas umsongensis sp. nov. (type strain Ps 3-10T =LMG 21317T =KACC 10847T) for the Ps 3-10 group and Pseudomonas jinjuensis sp. nov. (type strain Pss 26T =LMG 21316T =KACC 10760T) for the Pss 26 group.
TL;DR: The phylogenetic distance from any validly described species within the genus Chryseobacterium, as indicated from 16S rRNA gene sequence similarities, and its phenotypic properties demonstrate that strain B2T represents a novel species, for which the name ChrySEobacterius defluvii sp.
Abstract: A Gram-negative, rod-shaped, non-spore-forming, yellow-pigmented bacterium (strain B2T) isolated from wastewater of a sequence batch reactor showing enhanced phosphorus removal was investigated to determine its taxonomic status. Complete 16S rRNA gene sequence analysis indicated that the organism should be placed in the genus Chryseobacterium. The strain contained a polyamine pattern with sym-homospermidine as the major compound, menaquinone MK-6 as the predominant menaquinone and ai-C15 : 0, i-C15 : 0 and C16 : 1 as the major fatty acids. Phosphatidylethanolamine and several unidentified lipids were detected in the polar lipid profile. Phylogenetically, strain B2T was most closely related to Chryseobacterium indoltheticum and Chryseobacterium gleum (96·2 and 95·9 % 16S rRNA gene sequence similarity, respectively). The phylogenetic distance from any validly described species within the genus Chryseobacterium, as indicated from 16S rRNA gene sequence similarities, and its phenotypic properties demonstrate that strain B2T represents a novel species, for which the name Chryseobacterium defluvii sp. nov. is proposed; the type strain is B2T (=DSM 14219T =CIP 107207T).
TL;DR: The taxonomic position of a group of five D-sorbitol- and lactose-negative enterobacterial isolates recovered from diarrhoeal stools of children at the International Centre for Diarrhoeal Disease Research, Bangladesh was investigated by DNA-DNA hybridization, phenotypic characterization and 16S rDNA sequencing.
Abstract: The taxonomic position of a group of five D-sorbitol- and lactose-negative enterobacterial isolates recovered from diarrhoeal stools of children at the International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B), was investigated by DNA-DNA hybridization, phenotypic characterization and 16S rDNA sequencing. These strains were originally identified as 'Hafnia alvei-like' with the API 20E system but, in fact, show more phenotypic and genotypic resemblance to members of the genus Escherichia. By 16S rDNA sequencing, one representative strain of the ICDDR,B group was shown to be closely affiliated to the genera Escherichia and Shigella. Using the fluorimetric microplate hybridization method, the diarrhoeagenic ICDDR,B isolates were found to constitute a homogeneous taxon (> or = 82% internal DNA relatedness), with the closest affiliation to the type strains of Escherichia coli (55-64%) and Shigella flexneri (54-60%). The DNA-DNA hybridization levels were much lower with members of other described Escherichia species (16-45%) and with the type strain of H. alvei (9-17%). The G + C content of the ICDDR,B strains ranged from 50.5 to 50.7 mol%. Together with the diagnostic characteristics reported previously, including the presence of the eaeA gene of enteropathogenic E. coli and of the E. coli and Shigella-specific phoE gene, it is concluded that the ICDDR,B strains represent a novel taxon in the genus Escherichia, for which the name Escherichia albertii sp. nov. is proposed. Its type strain is Albert 19982(T) (= LMG 20976(T) = CCUG 46494(T)).
TL;DR: A polyphasic taxonomic approach involving phenotypic characterization, near-complete 16S rDNA sequence data and DNA-DNA hybridization analyses support the view that seven novel genomic species can be differentiated in this group of isolates.
Abstract: Thirteen isolates of Acinetobacter were obtained from activated sludge plants in Victoria, Australia. Earlier 16S–23S rDNA genomic fingerprinting and partial 16S rDNA sequence data had suggested that these isolates might contain previously undescribed species. This view was confirmed here. A polyphasic taxonomic approach involving phenotypic characterization, near-complete 16S rDNA sequence data and DNA–DNA hybridization analyses support the view that seven novel genomic species can be differentiated in this group of isolates. However, when fluorescence in situ hybridization (FISH) studies were performed with a 16S-rRNA-targeted probe specific for the genus Acinetobacter, used to identify Acinetobacter in activated sludge plants, all these strains responded positively. This suggests that these isolates would not have been missed in earlier FISH studies where their role as polyphosphate-accumulating bacteria has been questioned. This report describes these isolates and proposes that they be named Acinetobacter baylyi (type strain B2T=DSM 14961T =CIP 107474T), Acinetobacter bouvetii (type strain 4B02T=DSM 14964T =CIP 107468T), Acinetobacter grimontii (type strain 17A04T=DSM 14968T =CIP 107470T), Acinetobacter tjernbergiae (type strain 7N16T=DSM 14971T =CIP 107465T), Acinetobacter towneri (type strain AB1110T=DSM 14962T =CIP 107472T), Acinetobacter tandoii (type strain 4N13T=DSM 14670T =CIP 107469T) and Acinetobacter gerneri (type strain 9A01T=DSM 14967T =CIP 107464T).
TL;DR: It is concluded that there is little scientific support for the proposal to group the agrobacteria into the genus Rhizobium and consequently recommend retention of the genus AGROBACTERIUM.
Abstract: Members of the genus Agrobacterium constitute a diverse group of organisms, all of which, when harbouring the appropriate plasmids, are capable of causing neoplastic growths on susceptible host plants. The agrobacteria, which are members of the family Rhizobiaceae, can be differentiated into at least three biovars, corresponding to species divisions based on differential biochemical and physiological tests. Recently, Young et al. [Int J Syst Evol Microbiol 51 (2003), 89–103] proposed to incorporate all members of the genus Agrobacterium into the genus Rhizobium. We present evidence from classical and molecular comparisons that supports the conclusion that the biovar 1 and biovar 3 agrobacteria are sufficiently different from members of the genus Rhizobium to warrant retention of the genus Agrobacterium. The biovar 2 agrobacteria cluster more closely to the genus Rhizobium, but some studies suggest that these isolates differ from species of Rhizobium with respect to their capacity to interact with plants. We conclude that there is little scientific support for the proposal to group the agrobacteria into the genus Rhizobium and consequently recommend retention of the genus Agrobacterium.
TL;DR: The congruence of SSU rDNA and beta-tubulin trees with one another and with morphological data does suggest that further sampling of molecular data will eventually put gregarine diversity into a phylogenetic context.
Abstract: Gregarines are thought to be deep-branching apicomplexans. Accordingly, a robust inference of gregarine phylogeny is crucial to any interpretation of apicomplexan evolution, but molecular sequences from gregarines are restricted to a small number of small-subunit (SSU) rDNA sequences from derived taxa. This work examines the usefulness of SSU rDNA and β-tubulin sequences for inferring gregarine phylogeny. SSU rRNA genes from Lecudina (Mingazzini) sp., Monocystis agilis Stein, Leidyana migrator Clopton and Gregarina polymorpha Dufour, as well as the β-tubulin gene from Leidyana migrator, were sequenced. The results of phylogenetic analyses of alveolate taxa using both genes were consistent with an early origin of gregarines and the putative ‘sister’ relationship between gregarines and Cryptosporidium, but neither phylogeny was strongly supported. In addition, two SSU rDNA sequences from unidentified marine eukaryotes were found to branch among the gregarines: one was a sequence derived from the haemolymph parasite of the giant clam, Tridacna crocea, and the other was a sequence misattributed to the foraminiferan Ammonium beccarii. In all of our analyses, the SSU rDNA sequence from Colpodella sp. clustered weakly with the apicomplexans, which is consistent with ultrastructural data. Altogether, the exact position of gregarines with respect to Cryptosporidium and other apicomplexans remains to be confirmed, but the congruence of SSU rDNA and β-tubulin trees with one another and with morphological data does suggest that further sampling of molecular data will eventually put gregarine diversity into a phylogenetic context.