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1.  Gene sequences of the pil operon reveal relationships between symbiotic strains of Vibrio fischeri 
Symbiosis between the bobtail squid Euprymna scolopes (Mollusca: Cephalopoda) and Vibrio fischeri bacteria has been a well-studied model for understanding the molecular mechanisms of colonization and adherence to host cells. For example, pilin expression has been observed to cause subtle variation in colonization for a number of Gram-negative bacteria with eukaryotic hosts. To investigate variation amongst pil genes of closely related strains of vibrios, we amplified pil genes A, B, C and D to determine orientation and sequence similarity to other symbiotic vibrios. The pilA gene was found to be upstream from all other pil genes, and not contiguous with the rest of the operon. The pilB, pilC and pilD loci were flanked at the 3′ end by yacE, followed by a conserved hypothetical gene. DNA sequences of each pil gene were aligned and analysed phylogenetically using parsimony for both individual and combined gene trees. Results demonstrate that certain pil loci (pilB and pilD) are conserved among strains of V. fischeri, but pilC differs in sequence between symbiotic and free-living strains. Phylogenetic analysis of all pil genes gives better resolution of Indo-west Pacific V. fischeri symbionts compared with analysis of the 16S rRNA gene. Hawaiian and Australian symbiotic strains form one monophyletic tree, supporting the hypothesis that V. fischeri strain specificity is selected by the geographical location of their hosts and is not related to specific squid species.
doi:10.1099/ijs.0.65370-0
PMCID: PMC3374725  PMID: 18523167
2.  Polynucleobacter rarus sp. nov., a free-living planktonic bacterium isolated from an acidic lake 
The heterotrophic, aerobic, facultatively anaerobic under denitrifying conditions, catalase- and oxidase-positive, non-motile strain MT-CBb6A5T, which was isolated from an acidic lake located in Wisconsin (USA), was characterized. The strain grew on NSY medium over a temperature range of 15–30 °C and a NaCl range of 0.0–0.3 % (w/v). The predominant fatty acids were C16 : 0,C18 : 1ω7c, 11-methyl C18 : 1ω7c, feature 3 (including C16 : 1ω7c), and feature 2 (including C14 : 0 3-OH). The DNA G+C content of the strain was 40.3 mol%. Phylogenetic analysis as well as strong similarities in phenotypic and chemotaxonomic traits indicated the affiliation with the genus Polynucleobacter. 16S rRNA gene sequence similarity values with the two described species of the genus Polynucleobacter ranged from 95.6 to 96.0 %. The strain differs from the two described species of the genus Polynucleobacter in the ability to assimilate oxalic and glycolic acids, and in the presence of the fatty acids C15 : 1ω8c and C16 : 0 3-OH as well as in quantitative differences in fatty acid composition. It has to be assumed that the strain shares with other free-living bacteria of the genus Polynucleobacter a planktonic lifestyle in the water column of freshwater habitats. Based on the phylogeny revealed and the chemotaxonomic and phenotypic differences from Polynucleobacter necessarius and Polynucleobacter cosmopolitanus, we propose to establish the novel species Polynucleobacter rarus sp. nov. with the type strain MT-CBb6A5T (=DSM 21648T =CIP 109928T).
doi:10.1099/ijs.0.017350-0
PMCID: PMC3280894  PMID: 20435748
3.  Halococcus qingdaonensis sp. nov., a halophilic archaeon isolated from a crude sea-salt sample 
A Gram-negative, extremely halophilic, coccoid archaeal strain, CM5T, was isolated from a crude sea-salt sample collected near Qingdao, China. The organism grew optimally at 35–40 °C and pH 6.0 in the presence of 20 % (w/v) NaCl. Its colonies were red in colour and it could use glucose as a sole carbon source for growth. The 16S rRNA gene sequence of CM5T was most closely related to those of Halococcus species. Its pattern of antibiotic susceptibility was similar to those of other described Halococcus species. Biochemical tests revealed no sign of H2S production or gelatin liquefaction. The main polar lipids of strain CM5T were phosphatidylglycerol, phosphatidylglycerol methylphosphate and sulfated diglycosyl diether. No phosphatidylglycerol sulfate was present. The DNA G+C content of strain CM5T was 61.2 mol% and it gave DNA–DNA reassociation values of 33.7, 57.1 and 29.6 %, respectively, with Halococcus salifodinae DSM 8989T, Halococcus dombrowskii DSM 14522T and Halococcus morrhuae ATCC 17082T. Based on its morphological and chemotaxonomic properties and phylogenetic analysis of 16S rRNA gene sequence data, we propose that CM5T should be classified within a novel species, Halococcus qingdaonensis sp. nov., with strain CM5T (=CGMCC 1.4243T=JCM 13587T) as the type strain.
doi:10.1099/ijs.0.64673-0
PMCID: PMC3182530  PMID: 17329792
4.  Halorubrum chaoviator sp. nov., a haloarchaeon isolated from sea salt in Baja California, Mexico, Western Australia and Naxos, Greece 
Three halophilic isolates, strains Halo-G*T, AUS-1 and Naxos II, were compared. Halo-G* was isolated from an evaporitic salt crystal from Baja California, Mexico, whereas AUS-1 and Naxos II were isolated from salt pools in Western Australia and the Greek island of Naxos, respectively. Halo-G*T had been exposed previously to conditions of outer space and survived 2 weeks on the Biopan facility. Chemotaxonomic and molecular comparisons suggested high similarity between the three strains. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the strains clustered with Halorubrum species, showing sequence similarities of 99.2–97.1 %. The DNA–DNA hybridization values of strain Halo-G*T and strains AUS-1 and Naxos II are 73 and 75 %, respectively, indicating that they constitute a single species. The DNA relatedness between strain Halo-G*T and the type strains of 13 closely related species of the genus Halorubrum ranged from 39 to 2 %, suggesting that the three isolates constitute a different genospecies. The G+C content of the DNA of the three strains was 65.5–66.5 mol%. All three strains contained C20C20 derivatives of diethers of phosphatidylglycerol, phosphatidylglyceromethylphosphate and phosphatidylglycerolsulfate, together with a sulfated glycolipid. On the basis of these results, a novel species that includes the three strains is proposed, with the name Halorubrum chaoviator sp. nov. The type strain is strain Halo-G*T (=DSM 19316T =NCIMB 14426T =ATCC BAA-1602T).
doi:10.1099/ijs.0.000463-0
PMCID: PMC3182535  PMID: 19567575
6.  Limnohabitans curvus gen. nov., sp. nov., a planktonic bacterium isolated from a freshwater lake 
The chemoorganotrophic, aerobic, facultatively anaerobic, non-motile strain MWH-C5T isolated from the water column of oligo-mesotrophic Lake Mondsee (Austria) was phenotypically, phylogenetically, and chemotaxonomically characterized. The predominant fatty acids of the strain were C16:1ω7c/ω6c, C16:0, C12:1, and C8:0-3OH, the major quinone was ubiquinone Q-8, and the G+C content of the DNA of the strain was 55.5 mol%. The 16S rRNA gene similarity to the closest related type species were 96.6% (Curvibacter delicatus) and 95.7% (Rhodoferax fermentans). The phylogenetic analysis of the 16S rRNA gene sequences revealed the affiliation of the strain with the family Comamonadaceae (Betaproteobacteria), however, the revealed phylogenetic position of the strain did not indicate the affiliation to any previously described genus within this family. A family-wide comparison of traits revealed that the strain possesses a unique combination of G+C value, major fatty acids, and major 3-hydroxy fatty acid. Furthermore, the strain differs in several traits from the closest related genera. Based on the phylogeny of the strain and the differences to the closest related genera, we propose to establish the genus Limnohabitans gen. nov. to accommodate this strain, and to place the strain in the new species Limnohabitans curvus sp. nov., with the type strain MWH-C5T (DSM 21645T, = CCUG 56720 T). The type strain is closely related to a large number of uncultured bacteria detected by cultivation-independent methods in various freshwater systems.
doi:10.1099/ijs.0.013292-0
PMCID: PMC3091418  PMID: 19671731
7.  Limnohabitans planktonicus sp. nov., and Limnohabitans parvus sp. nov., two novel planktonic Betaproteobacteria isolated from a freshwater reservoir 
Two strains II-B4T and II-D5T, isolated from the meso-eutrophic freshwater Římov Reservoir (Czech Republic) were phenotypic ally, phylogenetically and chemotaxonomically characterized. Both strains are chemoorganotrophic, facultatively anaerobic, rod-shaped, non-motiles with identical G+C contents of their DNA of 59.9 mol%. Their major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and their major fatty acids were C16:1ω7c/C16:1ω6c, C16:0, C18:1ω7c/C18:1ω6c and C12:0. Both strains contained Q-8 as the only respiratory quinone component. The 16S rRNA sequences of the two strains posses a similarity of 99.0%, however the DNA-DNA reassociation value was only 26.7%, and the strains can be discriminated from each other by several chemotaxonomic and biochemical traits. The phylogenetic analysis of the 16S rRNA gene sequences revealed the affiliation of both strains with the genus Limnohabitans within the family Comamonadaceae. The two investigated strains represent a narrow phylogenetic cluster (so-called R-BT065 cluster) formed by a large number of environmental sequences obtained from the pelagic zones of various freshwater habitats. We propose to place the two strains in separate new species within the genus Limnohabitans. The two proposed species are Limnohabitans planktonicus sp. nov. with the type strain II-D5T (= DSM 21594T = CIP 109844T), and Limnohabitans parvus sp. nov. with the type strain II-B4T (= DSM 21592T = CIP 109845T).
doi:10.1099/ijs.0.018952-0
PMCID: PMC3091486  PMID: 20061501
8.  Limnohabitans australis sp. nov., isolated from a freshwater pond, and emended description of the genus Limnohabitans 
A chemo-organotrophic, aerobic, non-motile strain, MWH-BRAZ-DAM2DT, isolated from a freshwater pond in Brazil, was characterized phenotypically, phylogenetically and chemotaxonomically. Phylogenetic analysis of 16S rRNA gene sequences indicated affiliation of the strain with the genus Limnohabitans (Comamonadaceae, Betaproteobacteria). 16S rRNA gene sequence similarities between the isolate and Limnohabitans curvus MWH-C5T, representing the type species of the genus, and the type strains of Limnohabitans parvus and Limnohabitans planktonicus were 98.2, 96.5 and 97.0%, respectively. DNA–DNA reassociation analyses with DNA of the type strains of all three previously described Limnohabitans species revealed similarity values in the range 26.2–44.6%. The predominant fatty acids of the isolate were C16 : 1ω7c/ω6c, C16 : 0, C12 : 0 and C8 : 0 3-OH, the major quinone was ubiquinone Q-8 and the DNA G+C content was 55.8 mol%. The isolate could be discriminated from the type strains of the three Limnohabitans species by several phenotypic traits including differences in the utilization of several carbon sources. Based on the phylogeny of the isolate and its differences from the three most closely related species, the isolate represents a novel species for which the name Limnohabitans australis sp. nov. is proposed. The type strain is MWH-BRAZ-DAM2DT (=DSM 21646T=CCUG 56719T).
doi:10.1099/ijs.0.022384-0
PMCID: PMC3031073  PMID: 20118294
9.  Limnohabitans australis sp. nov., isolated from a freshwater pond, and emended description of the genus Limnohabitans 
A chemo-organotrophic, aerobic, non-motile strain, MWH-BRAZ-DAM2DT, isolated from a freshwater pond in Brazil, was characterized phenotypically, phylogenetically and chemotaxonomically. Phylogenetic analysis of 16S rRNA gene sequences indicated affiliation of the strain with the genus Limnohabitans (Comamonadaceae, Betaproteobacteria). 16S rRNA gene sequence similarities between the isolate and Limnohabitans curvus MWH-C5T, representing the type species of the genus, and the type strains of Limnohabitans parvus and Limnohabitans planktonicus were 98.2, 96.5 and 97.0 %, respectively. DNA–DNA reassociation analyses with DNA of the type strains of all three previously described Limnohabitans species revealed similarity values in the range 26.2–44.6 %. The predominant fatty acids of the isolate were C16 : 1ω7c/ω6c, C16 : 0, C12 : 0 and C8 : 0 3-OH, the major quinone was ubiquinone Q-8 and the DNA G+C content was 55.8 mol%. The isolate could be discriminated from the type strains of the three Limnohabitans species by several phenotypic traits including differences in the utilization of several carbon sources. Based on the phylogeny of the isolate and its differences from the three most closely related species, the isolate represents a novel species for which the name Limnohabitans australis sp. nov. is proposed. The type strain is MWH-BRAZ-DAM2DT (=DSM 21646T=CCUG 56719T).
doi:10.1099/ijs.0.022384-0
PMCID: PMC3031073  PMID: 20118294
12.  Nocardia iowensis sp. nov. 
Summary
Nocardia sp. NRRL 5646, originally isolated from a garden soil sample in Osceola, Iowa, USA was initially of interest as an antibiotic producer, contains biocatalytically important enzymes, and the first described nitric oxide synthase enzyme system in bacteria. A polyphasic taxonomic study was done to phenotypically and genotypically differentiate strain NRRL 5646 from other related species. Chemotaxonomic analyses included fatty acid methyl ester profile [major components: C16:1 ω6c, C16:1 ω7c, C16:0, C18:1 ω9c and C18:0 10-methyl]; quinone [major component: cyclo MK-8 (H4)]; polar lipid [major components: diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside] and mycolic acid determinations, and the results supported placement within the genus Nocardia. Biochemical testing and evaluation of 16S rRNA, 65 kDa heat shock protein (hsp65) and preprotein translocase (secA1) gene sequences demonstrated the differences between NRRL 5646 and other described Nocardia spp. Previous studies have demonstrated that other genetic sequences (carboxylic acid reductase, Nocardia phosphopantytheinyl transferase and GTP cyclohydrolase I) from NRRL 5646 also help to substantiate its uniqueness. 16S rRNA gene sequence similarity values of 98.8 % were observed between NRRL 5646 and Nocardia tenerifensis or Nocardia brasiliensis. However, NRRL 5646 could be clearly distinguished from these and many other validly described Nocardia spp. by DNA-DNA hybridization. Consequently, we propose that strain NRRL 5646 represents a new species and suggest the name Nocardia iowensis sp. nov. The type strain is NRRL 5646 (= UI 122540T = NRRL B-24671T = DSM 45197T).
doi:10.1099/ijs.0.007427-0
PMCID: PMC2759412  PMID: 19622667
13.  Nocardia iowensis sp. nov., an organism rich in biocatalytically important enzymes and nitric oxide synthase 
Nocardia strain NRRL 5646, isolated from a garden soil sample in Osceola, Iowa, USA, was initially of interest as an antibiotic producer. It contained biocatalytically important enzymes and represented the first described nitric oxide synthase enzyme system in bacteria. The present polyphasic taxonomic study was undertaken to differentiate strain NRRL 5646T from related species of the genus Nocardia. Chemotaxonomic analyses included determinations of the fatty acid methyl ester profile (C16 : 1ω6c/C16 : 1ω7c, C16 : 0, C18 : 1ω9c and C18 : 0 10-methyl as major components), quinone [cyclo MK-8(H4) as the major component], polar lipid (diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside as major components) and mycolic acid. These results supported its placement within the genus Nocardia. Biochemical testing and 16S rRNA, 65-kDa heat-shock protein (hsp65) and preprotein translocase (secA1) gene sequence analyses differentiated strain NRRL 5646T from recognized Nocardia species. Previous studies have demonstrated that other genetic sequences (carboxylic acid reductase, Nocardia phosphopantetheinyl transferase and GTP cyclohydrolase I) from strain NRRL 5646T can also be used to substantiate its uniqueness. The level of 16S rRNA gene sequence similarity between strain NRRL 5646T and the type strains of Nocardia tenerifensis and Nocardia brasiliensis was 98.8 %. However, strain NRRL 5646T could be clearly distinguished from these Nocardia species based on DNA–DNA hybridization data. Consequently, strain NRRL 5646T is considered to represent a novel species of the genus Nocardia, for which the name Nocardia iowensis sp. nov. is proposed. The type strain is NRRL 5646T (=UI 122540T=NRRL B-24671T=DSM 45197T).
doi:10.1099/ijs.0.007427-0
PMCID: PMC2759412  PMID: 19622667
14.  Pyramidobacter piscolens gen. nov., sp. nov., a member of the phylum “Synergistetes” isolated from the human oral cavity 
Four strains of anaerobic Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group distinct from any validly published species. 16S rRNA and 23S rRNA gene sequence analyses and DNA:DNA reassociation data revealed the strains to constitute a novel group within the phylum “Synergistetes” and most closely related to Jonquetella anthropi. Two libraries of randomly cloned DNA were prepared from strain W5455 and sequenced to provide a genome survey as a resource for metagenomic studies. A new genus and species, Pyramidobacter piscolens gen. nov., sp. nov. is proposed to accommodate these strains. The genus Pyramidobacter comprises strains that are anaerobic non-motile, asaccharolytic bacilli that produce acetic and isovaleric acids and minor to trace amounts of propionic, isobutyric, succinic and phenyl-acetic acids as end products of metabolism. P. piscolens produces hydrogen sulphide but is otherwise largely biochemically unreactive. Growth is stimulated by the addition of glycine to broth media. The G + C content of the DNA of the type strain is 59 mol %. The type strain of Pyramidobacter piscolens sp. nov. is W5455T (=DSM 21147T =CCUG 55836).
doi:10.1099/ijs.0.000364-0
PMCID: PMC2868594  PMID: 19406777
15.  Pyramidobacter piscolens gen. nov., sp. nov., a member of the phylum ‘Synergistetes’ isolated from the human oral cavity 
Four strains of anaerobic, Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group distinct from any species with validly published names. 16S rRNA and 23S rRNA gene sequence analyses and DNA–DNA reassociation data revealed that the strains constituted a novel group within the phylum ‘Synergistetes’ and were most closely related to Jonquetella anthropi. Two libraries of randomly cloned DNA were prepared from strain W5455T and were sequenced to provide a genome survey as a resource for metagenomic studies. A new genus and novel species, Pyramidobacter piscolens gen. nov., sp. nov., is proposed to accommodate these strains. The genus Pyramidobacter comprises strains that are anaerobic, non-motile, asaccharolytic bacilli that produce acetic and isovaleric acids and minor to trace amounts of propionic, isobutyric, succinic and phenylacetic acids as end products of metabolism. P. piscolens gen. nov., sp. nov. produced hydrogen sulphide but was otherwise largely biochemically unreactive. Growth was stimulated by the addition of glycine to broth media. The G+C content of the DNA of the type strain was 59 mol%. The type strain of Pyramidobacter piscolens sp. nov. is W5455T (=DSM 21147T=CCUG 55836T).
doi:10.1099/ijs.0.000364-0
PMCID: PMC2868594  PMID: 19406777
16.  Revised minimal standards for description of new species of the class Mollicutes (division Tenericutes) 
Minimal standards for novel species of the class Mollicutes (trivial term, mollicutes), last published in 1995, require revision. The International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Mollicutes proposes herein revised standards that reflect recent advances in molecular systematics and the species concept for prokaryotes. The mandatory requirements are: (i) deposition of the type strain into two recognized culture collections, preferably located in different countries; (ii) deposition of the 16S rRNA gene sequence into a public database, and a phylogenetic analysis of the relationships among the 16S rRNA gene sequences of the novel species and its neighbours; (iii) deposition of antiserum against the type strain into a recognized collection; (iv) demonstration, by using the combination of 16S rRNA gene sequence analyses, serological analyses and supplementary phenotypic data, that the type strain differs significantly from all previously named species; and (v) assignment to an order, a family and a genus in the class, with an appropriate specific epithet. The 16S rRNA gene sequence provides the primary basis for assignment to hierarchical rank, and may also constitute evidence of species novelty, but serological and supplementary phenotypic data must be presented to substantiate this. Serological methods have been documented to be congruent with DNA–DNA hybridization data and with 16S rRNA gene placements. The novel species must be tested serologically to the greatest extent that the investigators deem feasible against all neighbouring species whose 16S rRNA gene sequences show >0.94 similarity. The investigator is responsible for justifying which characters are most meaningful for assignment to the part of the mollicute phylogenetic tree in which a novel species is located, and for providing the means by which novel species can be identified by other investigators. The publication of the description should appear in a journal having wide circulation. If the journal is not the International Journal of Systematic and Evolutionary Microbiology, copies of the publication must be submitted to that journal so that the name may be considered for inclusion in a Validation List as required by the International Code of Bacteriological Nomenclature (the Bacteriological Code). Updated informal descriptions of the class Mollicutes and some of its constituent higher taxa are available as supplementary material in IJSEM Online.
doi:10.1099/ijs.0.64722-0
PMCID: PMC2220054  PMID: 17978244

Results 1-16 (16)