-
Volume 51,
Issue 2,
2001
Volume 51, Issue 2, 2001
- Articles
-
-
-
Methylosarcina fibrata gen. nov., sp. nov. and Methylosarcina quisquiliarum sp.nov., novel type 1 methanotrophs.
More LessTwo novel species of obligate methane-oxidizing bacteria, isolated from landfill soil, were characterized. Both strains were unusual in that some members of the population grew in irregularly shaped, refractile cell packets that resembled sarcina-like clusters. Electron microscopy revealed that the cell packets were covered with a slime layer and the cells contained many large granular inclusion bodies. The individual cells of each strain were sometimes motile and had differing morphologies. Isolate AML-C10T was always coccoidal in shape, and the cells were covered with extracellular fibrils. Isolate AML-D4T was pleomorphic, changing from rod to coccal form, sometimes exhibiting an unusual fusiform morphology. AML-D4T lacked the extensive fibrillar matrix observed with AML-C10T. Both strains utilized only methane and methanol as carbon sources. In stationary phase, the cells of each strain swelled in size and formed cysts. Aside from morphological differences, strains could also be distinguished from each other by cellular protein patterns, as well as by temperature and pH tolerances. 16S rDNA phylogenetic analysis showed that these are type I methanotrophs (family: Methylococcaceae) most closely related to the Methylobacter/Methylomicrobium clade, although they form a monophyletic grouping supported by moderately high bootstrap values. By 16S rDNA database searches, the most similar species to both isolates were Methylobacter spp. However, partial particulate methane monooxygenase sequence analysis suggested that these bacteria might be more closely related to Methylomicrobium than Methylobacter. Furthermore, cellular fatty acid profiles of the strains more closely resemble those of Methylomicrobium, although the absence of significant levels of 16:1omega5c argues for the uniqueness of these two strains. On the basis of the results described here, it is proposed that a new genus should be created, Methylosarcina gen. nov., harbouring two species, Methylosarcina fibrata sp. nov. (type species) and Methylosarcina quisquiliarum sp. nov. The type strains are AML-C10T (= ATCC 700909T = DSM 13736T) and AML-D4T (= ATCC 700908T = DSM 13737T), respectively.
-
-
-
-
Comparison of sequence analysis of 16S-23S rDNA spacer regions, AFLP analysis and DNA-DNA hybridizations in Bradyrhizobium.
More LessThe sequences of the 16S-23S rDNA intergenic spacer region of 62 strains of Bradyrhizobium, including representatives of the three valid species, were determined. The majority of strains had a single rRNA operon type and all contained a tRNA(Ala) and a tRNA(Ile) gene. Analysis of the sequence data produced groupings in line with previously obtained AFLP data. DNA-DNA hybridizations were performed to determine to what extent spacer sequences and AFLP profiles reflected the overall genomic similarities. Strains belonging to the same AFLP group, and strains with spacer sequences diverging less than 4%, were found to belong to the same genospecies. More remote relationships (DNA homology levels of 40-60%) between species were reflected in the spacer sequence analysis, but not in the AFLP analysis. For the genus Bradyrhizobium, 16S-23S rDNA spacer sequence analysis provides taxonomic information similar, but not always identical to that obtained by DNA-DNA hybridizations. Our results indicate that this genus consists of a group of four highly related genospecies (Bradyrhizobium japonicum, Bradyrhizobium liaoningense and two other genospecies) and at least three other genospecies, one of which is Bradyrhizobium elkanii.
-
-
-
Re-evaluation of the classical Mycoplasma lipophilum cluster (Weisburg et al. 1989) and description of two new clusters in the hominis group based on 16S rDNA sequences.
More LessThe Mycoplasma lipophilum cluster (Weisburg et al. 1989) in the hominis group of the mollicutes is re-evaluated in this work to update the phylogenetic framework for classification of species within the genus Mycoplasma. Therefore, sequences of the 16S rRNA gene were determined from previously described species, and 11 were found to be closely related to the M. lipophilum cluster. A selection of members of the other hitherto defined clusters of the hominis group was included for phylogenetic analysis, revealing that the classical M. lipophilum cluster could be re-organized into two clusters, namely the M. lipophilum cluster and the Mycoplasma bovis cluster. The former was found to contain two species, while the latter contained 20 species. The two clusters were closely related, sharing an ancestral branch with the Mycoplasma synoviae cluster. Furthermore, the M. bovis cluster could be divided into subclusters. Interestingly, two species, Mycoplasma equigenitalium and Mycoplasma elephantis, formed a distinct and early branch of the M. lipophilum, M. bovis and M. synoviae clusters. This entity was termed the M. equigenitalium cluster. The clusters and subclusters could be verified by using neighbour-joining and maximum-likelihood analyses on a variety of data sets, bootstrap calculations, secondary structure analysis and signature nucleotides. Therefore, the new 16S rDNA data presented in this work were used to re-evaluate the M. lipophilum cluster, leading to the definition of two additional clusters. At present, the mollicutes belonging to the hominis group can be classified into ten evolutionary lineages.
-
-
-
Amycolatopsis albidoflavus sp. nov.
More LessThe generic position of an actinomycete strain, 'Pseudonocardia sp.' IMSNU 22139, was investigated by the phylogenetic analysis of 16S rDNA sequence. Comparative studies of 16S rDNA sequences indicated that this organism consistently formed a distinct clade within the radiation of the genus Amycolatopsis of the family Pseudonocardiaceae. This organism was also found to have chemotaxonomic properties consistent with those of the genus Amycolatopsis, which were represented by a type IV cell wall (meso-diaminopimelic acid, arabinose and galactose), a major menaquinone of MK-9(H4), a predominant fatty acid of 14-methylpentadecanoic acid, phosphatidylmethylethanolamine as a diagnostic phospholipid (a phospholipid type PII pattern) and DNA base composition of 68.5 mol% G+C. On the basis of physiological properties, cellular fatty acid profiles and its unique phylogenetic position, this organism is readily differentiated from all of the validly described species of the genus Amycolatopsis, and the name Amycolatopsis albidoflavus sp. nov. is proposed for it. The type strain is IMSNU 22139T (= KCTC 9471T = ATCC 53205T).
-
-
-
Campylobacter hominis sp. nov., from the human gastrointestinal tract.
A J Lawson, S L On, J M Logan and J StanleySequences of 16S rDNA of a novel campylobacter from faeces of healthy humans were previously shown to originate from a new taxon, 'Candidatus Campylobacter hominis', which could not be cultured. Since phylogenetic analysis suggested that anaerobic conditions might be required for growth, an isolation strategy was developed employing initial non-selective membrane filtration onto fastidious anaerobe agar. Campylobacters were then isolated from the resulting mixed microbial flora by a dilution strategy and/or by immunomagnetic separation with genus-specific polyclonal antibody. Isolates were identified by a genus and taxon-specific PCR assay, and 16S rDNA nucleotide sequence analysis was carried out. All isolates exhibited the typical Campylobacter characteristics of being non-fermentative, oxidase-positive, catalase-negative and Gram-negative. Unusually, however, they were straight rods lacking flagella. The 16S rDNA nucleotide sequence analysis, DNA and mol% G+C were consistent with a new Campylobacter species whose nearest phylogenetic neighbours were Campylobacter gracilis and Campylobacter sputorum. The unique species status of the isolates was further confirmed by taxonomic analysis of 47 phenotypic characteristics. The name Campylobacter hominis sp. nov. is proposed for the new species, the type strain of which is NCTC 13146T (= LMG 19568T).
-
-
-
Hahella chejuensis gen. nov., sp. nov., an extracellular-polysaccharide-producing marine bacterium.
More LessA bacterial strain, designated 96CJ10356T, which produced abundant extracellular polysaccharides and red pigment was isolated from marine sediment collected from Marado, Cheju Island, Republic of Korea. The organism is Gram-negative, aerobic, rod-shaped and motile. Growth was not observed in the absence of NaCl, and was optimal at an NaCl concentration of 2%. The strain contained oxidase and catalase, and was able to hydrolyse aesculin and gelatin. The major cellular fatty acids were saturated or monounsaturated straight-chain fatty acids. An almost complete 16S rDNA sequence of the test strain was determined. Phylogenetic analysis based on the neighbour-joining and Fitch-Margoliash methods indicated that the organism formed a distinct phyletic line within the gamma Proteobacteria. This relationship was also supported by sequence comparison, as no valid bacterial species showed more than 90% sequence homology with the isolate. It is clear from polyphasic evidence that the isolate merits the status of genus in the gamma subclass of the Proteobacteria, and the name Hahella chejuensis gen. nov., sp. nov. is proposed for the marine isolate 96CJ10356T (= KCTC 2396T = IMSNU 11157T).
-
-
-
Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes.
J Keswani and W B WhitmanThe relationship between 16S rRNA sequence similarity (S) and the extent of DNA hybridization (D) was well described by the equation In(-InD) = 0.53 [In(-InS)]+2.201 when D was determined by either the S1 nuclease or membrane filter methods. When the presence of nonultrametric rRNA sequences and differences between genera or families were controlled, this relationship accounted for 78% of the variability of D given S, and it was possible to estimate the distribution of D from S with a known precision. Thus, D<0.70 was expected to occur 50, 95 and 99% of the time when S was 0.998, 0.992 and 0.986, respectively. The relationship between D and S varied between prokaryotic taxa even within the same subphylum, and more precise estimates of D could be made when the relationship for a particular taxon was known. The relationship between D and S was not significantly different between the prokaryotic domains, and S appeared to be a quasi-molecular clock of approximately constant rate when averaging effects and stochastic factors were taken into account. The relationship between logD and logS was nonlinear, and D provided a very poor measure of relatedness for distantly related organisms. For instance, within the range 1.0 >S> 0.95, D decreased from 1.0 to 0.15; and within the range 0.95 >S> 0.90, D decreased from 0.15 to 0.06. Lastly, at least some of the rRNA sequences from about one-third of the taxa examined had nonultrametric properties where S was much lower than expected from the value of D. For these taxa, S was a poor indicator of relatedness for closely related strains. Thus, the ultrametric properties of rRNA sequences should be tested before making taxonomic or phylogenetic conclusions based upon S.
-
-
-
Actinomyces catuli sp. nov., from dogs.
More LessAn Actinomyces-like bacterium was recovered from two dogs. Based on cellular morphology and biochemical criteria, the unknown bacterium resembled the genus Actinomyces but it did not appear to correspond to any of the currently recognized species of this genus. PAGE analysis of whole-cell proteins confirmed that the strain was phenotypically distinct from all other Actinomyces species and comparative 16S rRNA gene sequencing showed that the bacterium represents an unknown sub-line within the genus. Based on phenotypic and phylogenetic evidence, it is proposed that the bacterium from dogs be classified as a new species of the genus Actinomyces, Actinomyces catuli. The type strain of Actinomyces catuli is CCUG 41709T (= CIP 106507T).
-
-
-
Aerococcus urinaehominis sp. nov., isolated from human urine.
P A Lawson, E Falsen, M Ohlén and M D CollinsPhenotypic and phylogenetic studies were performed on an unknown Gram-positive catalase-negative coccus isolated from human urine. Comparative 16S rRNA gene sequencing demonstrated that the organism represents a new subline within the genus Aerococcus. The unknown bacterium was readily distinguished from the three currently recognized Aerococcus species, Aerococcus christensenii, Aerococcus urinae and Aerococcus viridans, by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from urine be classified as Aerococcus urinaehominis sp. nov. The type strain of Aerococcus urinaehominis is CCUG 42038bT (= CIP 106675T).
-
-
-
Polyphasic taxonomy of the basidiomycetous yeast genus Rhodosporidium: Rhodosporidium kratochvilovae and related anamorphic species.
More LessThe phenotypic and genetic heterogeneity of the basidiomycetous yeast species Rhodosporidium kratochvilovae was investigated in a group of recent isolates and collection strains. A polyphasic taxonomic approach was followed which included micromorphological studies, nuclear staining, determination of sexual compatibility, physiological characterization, comparison of electrophoretic isoenzyme patterns, PCR fingerprinting, determination of mol% G+C, DNA-DNA reassociation experiments and 26S and ITS rDNA sequence analysis. The results allowed a more natural circumscription of the species, both from the genetic and phenotypic perspectives. The relationships with anamorphic species of the genus Rhodotorula were studied and isolates previously identified as Rhodotorula glutinis were found to belong to Rhodosporidium kratochvilovae. Other isolates included in the study were found to represent members of Rhodotorula glutinis var. dairenensis. Rhodosporidium kratochvilovae was found to include heterothallic strains, besides those already known to be self-sporulating. A total of 17 isolates, which were found to belong to this species, were heterothallic, self-sporulating and anamorphic strains. It is anticipated that integrated polyphasic studies of basidiomycetous yeasts will provide a more coherent classification system and the basis for accurate identification schemes, which in turn are essential for detailed ecological studies.
-
-
-
Candida orba sp. nov., a new cactus-specific yeast species from Queensland, Australia.
More LessA new species of yeast from decaying cladodes of Opuntia cactus, Candida orba, is described. This species is a member of a four-species clade of cactophilic yeasts. The new species has only been found in one region of Queensland, Australia, where it was presumably introduced during attempts to eradicate prickly pear cactus. DNA-DNA relatedness, phylogenetic analysis, physiological differences, killer-sensitivity profiles and mating reactions establish the distinctness of the taxon as a new species. C. orba is most closely related to Phaffomyces thermotolerans, a species found associated with columnar cacti in the North American Sonoran Desert. The type strain of C. orba, isolated from rotting cladodes of Opuntia stricta in the State of Queensland, Australia, is strain UCD-FST 84-833.1T (= CBS 8782T = NRRL Y-27336T = ATCC MYA-341). Only the h- mating type of the species has been recovered. The lack of the opposite mating type could be the result of a bottleneck during its introduction to Australia. The original geographic/host distribution of this species in the Americas is unknown.
-
-
-
Recommendations of the subcommittee on the taxonomy of Campylobacter and related bacteria.
P Vandamme and S L OnThe ICSB Subcommittee on the taxonomy of Campylobacter and related bacteria has discussed several contemporaneous issues and makes the following recommendations. (i) The reported synonymy between Campylobacter coli and Campylobacter hyoilei was based on valid taxonomic arguments. The subcommittee therefore discourages the use of the name C. hyoilei. (ii) The revised infrasubspecific nomenclature of Campylobacter sputorum is endorsed. C sputorum is subdivided into C. sputorum biovar sputorum (characterized by the absence of catalase and urease activity); C. sputorum biovar faecalis (characterized by catalase but not urease activity); and C. sputorum biovar paraureolyticus (characterized by urease, but not catalase activity). (iii) The subcommittee points out that 'Flexispira rappini' is a taxon that is circumscribed by means of morphological criteria. It encompasses multiple Helicobacter species, including Helicobacter billis and Helicobacter trogontum. (iv) Finally, the subcommittee wishes to point out that the etymology of several specific or subspecific epithets of Campylobacter taxa has been corrected and that the spelling of the epithet 'fecalis' was corrected to 'faecalis'.
-
-
-
Recommended conservation of the names Streptococcus sanguis, Streptococcus rattus, Streptococcus cricetus, and seven other names included in the Approved Lists of Bacterial Names. Request for an opinion.
More LessWith reference to the first Principle of the International Code of Nomenclature of Bacteria, which emphasizes stability of names, it is proposed that the original names Streptococcus sanguis, Streptococcus rattus, Streptococcus cricetus, Erwinia ananas, Eubacterium tarantellus, Lactobacillus sake, Nitrosococcus oceanus, Pseudomonas betle, Rickettsia canada and Streptomyces rangoon, all included in the Approved Lists of Bacterial Names, be conserved. Request for an Opinion.
-
-
-
Nomenclatural type of orders: corrections necessary according to Rules 15 and 21a of the Bacteriological Code (1990 Revision), and designation of appropriate nomenclatural types of classes and subclasses. Request for an opinion.
More LessAn important aspect of the Bacteriological Code (1990 Revision) is the designation of nomenclatural types to the various taxonomic ranks to provide a suitable reference point for the unambiguous identification of the taxon. Although the nomenclatural type of the species is the designated strain, and the nomenclatural type of the genus is the type species, the nomenclatural type of both the family and the order is the 'genus on whose name the name of the relevant taxon is based'. However, in some cases a genus has not been designated as the nomenclatural type of an order. Twelve cases that are contrary to the Rules listed and appropriate corrections are proposed. In addition, several classes have been named for which no nomenclatural type has been designated; this brings into question whether they can be considered to have been validly published, as well as highlighting the fact that they would be/are illegitimate.
-
Volumes and issues
-
Volume 75 (2025)
-
Volume 74 (2024)
-
Volume 73 (2023)
-
Volume 72 (2022 - 2023)
-
Volume 71 (2020 - 2021)
-
Volume 70 (2020)
-
Volume 69 (2019)
-
Volume 68 (2018)
-
Volume 67 (2017)
-
Volume 66 (2016)
-
Volume 65 (2015)
-
Volume 64 (2014)
-
Volume 63 (2013)
-
Volume 62 (2012)
-
Volume 61 (2011)
-
Volume 60 (2010)
-
Volume 59 (2009)
-
Volume 58 (2008)
-
Volume 57 (2007)
-
Volume 56 (2006)
-
Volume 55 (2005)
-
Volume 54 (2004)
-
Volume 53 (2003)
-
Volume 52 (2002)
-
Volume 51 (2001)
-
Volume 50 (2000)
-
Volume 49 (1999)
-
Volume 48 (1998)
-
Volume 47 (1997)
-
Volume 46 (1996)
-
Volume 45 (1995)
-
Volume 44 (1994)
-
Volume 43 (1993)
-
Volume 42 (1992)
-
Volume 41 (1991)
-
Volume 40 (1990)
-
Volume 39 (1989)
-
Volume 38 (1988)
-
Volume 37 (1987)
-
Volume 36 (1986)
-
Volume 35 (1985)
-
Volume 34 (1984)
-
Volume 33 (1983)
-
Volume 32 (1982)
-
Volume 31 (1981)
-
Volume 30 (1980)
-
Volume 29 (1979)
-
Volume 28 (1978)
-
Volume 27 (1977)
-
Volume 26 (1976)
-
Volume 25 (1975)
-
Volume 24 (1974)
-
Volume 23 (1973)
-
Volume 22 (1972)
-
Volume 21 (1971)
-
Volume 20 (1970)
-
Volume 19 (1969)
-
Volume 18 (1968)
-
Volume 17 (1967)
-
Volume 16 (1966)
-
Volume 15 (1965)
-
Volume 14 (1964)
-
Volume 13 (1963)
-
Volume 12 (1962)
-
Volume 11 (1961)
-
Volume 10 (1960)
-
Volume 9 (1959)
-
Volume 8 (1958)
-
Volume 7 (1957)
-
Volume 6 (1956)
-
Volume 5 (1955)
-
Volume 4 (1954)
-
Volume 3 (1953)
-
Volume 2 (1952)
-
Volume 1 (1951)
Most Read This Month
