- Volume 44, Issue 4, 1994

Methanolobus bombayensis B-1T (= OCM 438T) (T = type strain) was isolated from Arabian Sea sediments obtained near Bombay, India. This strain grew on methylamines, methanol, and dimethyl sulfide, but it did not catabolize H2-CO2, acetate, or formate. The cells were nonmotile, irregular coccoids (diameter, 1.0 to 1.5 µm) and occurred singly. Electron micrographs revealed that a cell membrane and a protein cell wall were present. The cells grew fastest at mesophilic temperatures, at a neutral pH, and at salinity levels near the salinity level of the ocean, and they required about 30 mM divalent cations (Mg2+ and Ca2+). The cells grew in mineral medium, but growth was greatly stimulated by yeast extract and peptones. The guanine-plus-cytosine content of the DNA was 39.2 ± 0.1 mol%. A comparison of 16S rRNA sequences showed that strain B-1T was phylogenetically related to Methanolobus vulcani, but the sequences of these organisms differed by 2%.

The 16S rRNA sequences of aerobic LL-diaminopimelic acid-containing coryneform bacteria were compared, and the sequence of Nocardioides fastidiosa exhibited a high level of similarity to the sequence of Aeromicrobium erythreum but not to the sequences of the other species of the genus Nocardioides. Furthermore, analyses of menaquinone systems and cellular fatty acids revealed that N. fastidiosa was similar to A. erythreum but differed from the other Nocardioides species. On the basis of chemotaxonomic data and DNA-DNA hybridization and comparative 16S rRNA results, we propose that N. fastidiosa should be transferred to the genus Aeromicrobium as Aeromicrobium fastidiosum comb. nov. (type strain, IFO 14897).

An organism that is able to reductively ortho-dechlorinate 2,4-dichlorophenol and 3-chloro-4-hydroxyphenylacetate (3-C1-4-OHPA) was isolated from a methanogenic lake sediment. This organism, an anaerobic, motile, Gram-type-positive, rod-shaped bacterium, grew in the presence of 0.1% yeast extract when pyruvate, lactate, formate, or hydrogen was used as the electron donor for reductive dehalogenation of 3-C1-4-OHPA. Sulfite, thiosulfate, and sulfur were reduced to sulfide, nitrate was reduced to nitrite, and fumarate was reduced to succinate. Dissimilatory reduction of sulfate could not be demonstrated, and no adenylylsulfate reductase was detected with an immunoassay. The organism fermented two pyruvate molecules to one lactate molecule, one acetate molecule, and one carbon dioxide molecule. The pH and temperature optima for both growth and dechlorination of 3-C1-4-OHPA were 7.5 and 38°C, respectively. The doubling time under these conditions was approximately 3.5 h. On the basis of the results of a 16S rRNA analysis and the inability of the organism to use sulfate as an electron acceptor, strain JW/IU-DC1 is described as the type strain of the new taxon Desulfitobacterium dehalogenans gen. nov., sp. nov.

The genus Hydrogenobacter consists of extremely thermophilic, obligately chemolithotrophic organisms that exhibit anaerobic anabolism but aerobic catabolism. Preliminary studies of the phylogenetic position of these organisms based on limited 16S ribosomal DNA sequence data suggested that they belong to one of the earliest branching orders of the Bacteria. In this study, the complete 16S ribosomal DNA sequences of two type strains, Hydrogenobacter thermophilus TK-6 and Calderobacterium hydrogenophilum Z-829, and another isolate, Hydrogenobacter sp. strain T3, were determined, and the phylogenetic positions of these organisms were examined. Our results revealed that the two type strains are members of a single genus, the genus Hydrogenobacter. Our results also verified the previous conclusion that the Aquifex-Hydrogenobacter complex belongs to a very early branching order, the “ “Aquificales.” “ Within this order, the relationships among the various organisms are such that only a single family, the “ “Aquificaceae,” can be recognized at this time. Given the early branching point of the “ “Aquificales,” “the characteristics of these organisms support the view that the last common ancestor of existing life was thermophilic and suggest that this ancestor may have fixed carbon chemoautotrophically.

The results of DNA-DNA hybridization studies and 16S ribosomal DNA sequence comparisons and chemotaxonomic data clearly indicated that Rhodococcus luteus Nesterenko et al. 1982 (O. A. Nesterenko, T. M. Nogina, S. A. Kasumova, E. I. Kvasnikow, and S. G. Batrakov, Int. J. Syst. Bacteriol. 32:1–14, 1982) and Rhodococcus fascians (Tilford) Goodfellow 1984 (M. Goodfellow, Syst. Appl. Microbiol. 5:225–229, 1984) represent a single species. On the basis of priority R. luteus must be considered a later subjective synonym of R. fascians.

A total of 23 strains of halophilic histamine-producing bacteria previously isolated from marine fish and seawater were studied phenotypically, genotypically, and phylogenetically. These organisms are facultatively anaerobic, gram-negative, short rods that are motile by means of one to three unsheathed polar flagella. They are mesophilic and nonluminescent, produce oxidase, utilize D-glucose but not D-mannitol as a carbon and energy source, and accumulate poly-β-hydroxybutyrate. The guanine-plus-cytosine contents of the DNAs are ca. 41 mol%. Genomic DNA hybridization experiments revealed that some of the isolates exhibited low levels of reassociation (less than 40%) with previously described Photobacterium species. 16S rRNA gene sequence information confirmed the phylogenetic position of one of the isolates, strain C-8T (T = type strain), as a member of the genus Photobacterium. Therefore, we concluded that these organisms are members of a new species of the genus Photobacterium and propose the name Photobacterium histaminum sp. nov. for them. The type strain is strain C-8 (= JCM 8968).

Two new species, Porphyromonas gingivicanis and Porphyromonas crevioricanis, are proposed for black-pigmented, asaccharolytic, anaerobic, nonmotile, non-spore-forming, gram-negative, rod-shaped organisms. These organisms were isolated from the gingival crevicular fluids of beagles. P. gingivicanis and P. crevioricanis do not grow in the presence of 20% bile. They exhibit less than 5% DNA-DNA homology with the type strains of Porphyromonas gingivalis (strain ATCC 33277), Porphyromonas endodontalis (strain ATCC 35406), and Porphyromonas asaccharolytica (strain ATCC 25260), which were isolated from humans, or with the type strains of Porphyromonas salivosa (strain NCTC 11632) and Porphyromonas circumdentaria (strain NCTC 12469), which were isolated from cats. The major cellular fatty acid of P. gingivicanis and P. crevioricanis is 13-methyltetradecanoic acid (iso-C15:0 acid). Glutamate and malate dehydrogenases are present in both species, and 6-phosphogluconate and glucose-6-phosphate dehydrogenases are absent; neither organism exhibits trypsin activity. P. gingivicanis and P. crevioricanis produce large amounts of acetic and isovaleric acids and minor amounts of isobutyric and succinic acids as end products of metabolism in GAM medium. P. gingivicanis also produces large amounts of butyric acid and small amounts of propionic acid, while P. crevioricanis produces large amounts of propionic acid and minor amounts of butyric and phenylacetic acids. The G+C contents of the DNA of P. gingivicanis is 41 to 42 mol%; the G+C content of the DNA of P. crevioricanis is 44 to 45 mol%. Catalase is produced by P. gingivicanis but not by P. crevioricanis; strains of P. crevioricanis agglutinate sheep erythrocytes, but strains of P. gingivicanis do not. The type strain of P. gingivicanis is NUM 301 (= ATCC 55562), and the type strain of P. crevioricanis is NUM 402 (= ATCC 55563).

A new beta-hemolytic streptococcal species, Streptococcus phocae, was isolated from organ specimens obtained from seals. This taxon is described on the basis of the results of a study of 22 strains. S. phocae was serologically somewhat heterogeneous (group antigen -/F/C). Strains belonging to this species exhibited high levels of DNA-DNA homology to each other, as determined by DNA-DNA hybridization, but low levels of DNA-DNA homology to the type strains of other streptococcal species. A simple scheme for the differentiation of S. phocae from other beta-hemolytic streptococci is presented. Strain 8399 H1 (= NCTC 12719) is the type strain of S. phocae.

Ninety genotypically characterized Aeromonas strains, including members of all 14 currently established genospecies, were studied by performing gas-liquid chromatographic analysis of their cellular fatty acid methyl esters (FAMEs). A total of 44 fatty acids and two alcohols were found in members of the genus Aeromonas. All 90 strains contained 12:0, 13:0 iso, 14:0, 15:0 iso 30H, 16:0, 16:1 ω7c, 17:0 iso, iso 17:1 ω9c, summed feature 3 (16:1 iso I and/or 14:0 30H), and summed feature 7 (18:1 ω7c, 18:1 ω9t, and/or 18:1 ω12t), whereas all but one strain (99%) also contained 15:0 iso. Although the FAME profiles were very similar, minor quantitative variations could be used to differentiate phenospecies and/or hybridization groups. A cluster analysis of the mean data revealed five FAME clusters, which were compared with phenotypic and genotypic groups identified in the genus Aeromonas. Hybridization groups that constituted the Aeromonas hydrophila complex, the Aeromonas caviae complex, and the Aeromonas sobria complex were basically grouped into distinct FAME clusters. The taxonomic positions of hybridization groups 7 and 11 in these clusters, however, remained unclear. All of our results were highly reproducible. A new database of Aeromonas FAME fingerprints was generated, and this database can be used for rapid identification of unknown aeromonads. Using a large set of well-characterized aeromonads, we demonstrated for the first time that gas-liquid chromatographic FAME analysis can be used to differentiate the majority of the phenospecies and/or hybridization groups in the genus Aeromonas.

The name “Bacillus laevolacticus” Nakayama and Yanoshi 1967 was not included on the Approved Lists of Bacterial Names and therefore has no standing in bacteriological nomenclature. In this study 22 catalase-positive, acid-tolerant, facultatively anaerobic, lactic acid-producing Bacillus strains were examined taxonomically and compared with a number of strains belonging to phenetically similar Bacillus species (Bacillus coagulans, Bacillus smithii, ““Bacillus vesiculiferous”) and with Sporolactobacillus. The G+C contents (43 to 45 mol%), DNA-DNA homology values (72 to 98%), and results of phenetic similarity analyses revealed that the members of the “B. laevolacticus” group were very homogeneous in their phenotypic and genotypic characteristics and clearly distinguishable from other Bacillus and Sporolactobacillus species. On the basis of these findings, revival of the name Bacillus laevolacticus is proposed.

Two new strains (AS130 and AS140) of phototrophic purple nonsulfur bacteria isolated from activated sludge were characterized and compared with Rhodopseudomonas rosea and some other species of the genus Rhodopseudomonas. The new isolates produced pink photosynthetic cultures, had rod-shaped cells that divided by budding, and formed intracytoplasmic membranes of the lamellar type together with bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series. They were also characterized by their capacity for complete denitrification and their production of both ubiquinone-10 and rhodoquinone-10 as major quinones. The isolates were phenotypically most similar to R. rosea but exhibited low levels of genomic DNA hybridization to this species and to all other Rhodopseudomonas species compared. Phylogenetic analyses on the basis of PCR-amplified 16S rRNA gene sequences showed that our isolates and R. rosea formed a cluster distinct from other members of the genus Rhodopseudomonas. The phenotypic, genotypic, and phylogenetic data show that the new isolates and R. rosea should be placed in a new single genus rather than included in the genus Rhodopseudomonas. Thus, we propose to transfer R. rosea to a new genus, Rhodoplanes, as Rhodoplanes roseus gen. nov., comb. nov. (type species) and to designate strains AS130 and AS140 a new species, Rhodoplanes elegans sp. nov.

The partial 16S rRNA gene sequences of representative strains of two groups of anaerobic, gram-negative, pigmented, asaccharolytic, rod-shaped bacteria isolated from subgingival plaque of dogs with naturally occurring periodontal disease were determined. A comparative analysis of the rRNA sequence data revealed that the two groups of organisms represent previously unknown lines of descent within the genus Porphyromonas. On the basis of our phylogenetic findings and the phenotypic distinctiveness of the organisms, two new species, Porphyromonas cangingivalis and Porphyromonas cansulci, are proposed.

Two mollicutes (strains 0502T [T = type strain] and J233T), which were isolated from the surfaces of broccoli (Brassica oleracea var. italica) plants or the crown tissues of the coconut palm (Cocos nucifera), were capable of sustained growth in serum-free (or cholesterol-free) mycoplasma broth media. Examination by electron and dark-field microscopic techniques revealed that the cells of each strain were small, nonhelical, nonmotile, pleomorphic, and coccoid and that each cell was surrounded by a single cytoplasmic membrane. No evidence of a cell wall was found. The organisms were filterable and grew rapidly in most conventional mycoplasma culture medium formulations containing horse or fetal bovine sera under either aerobic or anaerobic conditions. The optimum temperature for growth of both organisms was 30°C, but multiplication occurred over a temperature range from 18 to 37°C. Both strains catabolized glucose, but did not hydrolyze arbutin, arginine, or urea. The genome size of strain 0502T was 1,215 kbp, and the DNA base composition (guanine-plus-cytosine content) was 35.5 mol%. The genome size of strain J233T was 1,610 kbp, and the DNA base composition was 30.0 mol%. The two isolates were not serologically related to each other or to the type strains of 11 previously described Acholeplasma species. Strain 0502 (= ATCC 49388) is the type strain of Acholeplasma brassicae sp. nov., and strain J233 (= ATCC 49389) is the type strain of Acholeplasma palmae sp. nov.

Twenty mollicute strains isolated primarily from insect hosts were characterized and arranged into eight new species in the genus Mesoplasma. Morphological examination of the organisms by electron and dark-field microscopic techniques revealed that the cells of each strain were small, nonhelical, nonmotile, pleomorphic, and coccoid and that each cell was surrounded by a single cytoplasmic membrane with no evidence of a cell wall. Although the new mollicutes grew well in media containing horse or fetal bovine serum, growth in serum-free or cholesterol-free medium occurred only when the medium contained 0.04% polyoxyethylene sorbitan (Tween 80). The optimum temperature for growth was usually 30°C, but multiplication generally occurred over a temperature range of 10 to 32°C. All strains catabolized glucose. Most strains did not hydrolyze arginine or urea, although three related strains isolated from fireflies (the strain PUPA-2T [T = type strain] group) did hydrolyze arginine. The genome sizes ranged from 825 to 930 kbp, and the DNA base compositions (guanine-plus-cytosine contents) ranged from 26.5 to 31.6 mol%. The proposed type strains of the eight new species were not serologically related to the type strains of four other Mesoplasma species, five Entomoplasma species, 11 Acholeplasma species, and 100 Mycoplasma species and subspecies. Strain PS-1 (= ATCC 49582) is the type strain of Mesoplasma pleciae sp. nov., strain PUPA-2 (= ATCC 49581) is the type strain of Mesoplasma photuris sp. nov., strain YJS (= ATCC 43706) is the type strain of Mesoplasma syrphidae sp. nov., strain CHPA-2 (= ATCC 49578) is the type strain of Mesoplasma chauliocola sp. nov., strain ELCA-2 (= ATCC 49579) is the type strain of Mesoplasma corruscae sp. nov., strain GRUA-1 (= ATCC 49580) is the type strain of Mesoplasma grammopterae sp. nov., strain BARC 779 (= ATCC 49583) is the type strain of Mesoplasma coleopterae sp. nov., and strain BARC 857 (= ATCC 49584) is the type strain of Mesoplasma tabanidae sp. nov.

The results of our experiments showed that the 5’-terminal sequences of 23S rRNAs can be used to distinguish different genera of actinomycetes, including the genera Streptomyces, Micromonospora, Amycolatopsis, and Saccharomonospora. There are small differences (<1%) among the sequences of some strains belonging to the genera Streptomyces (two strains) and Saccharomonospora (seven strains). On the basis of the results of morphological and biochemical analyses, strain 9022 belongs in the genus Saccharomonospora; however, there are distinct differences in the cell wall compositions and the 5’ termini of the 23S rRNA sequences of this strain and members of the genus Saccharomonospora. Hence, strain 9022 cannot be classified in the genus Saccharomonospora.

A total of 80 bacterial strains isolated from different Sesbania and Acacia species growing in various sites in Senegal (West Africa) were compared with 35 reference strains of Rhizobium, Bradyrhizobium, Azorhizobium, and Agrobacterium species and with 33 representative strains of the different groups of Brazilian isolates described on the basis of the results of a numerical analysis of the whole-cell protein patterns obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Fifty-two strains could be placed in three protein electrophoretic clusters, two of which were different from the clusters containing various reference or representative strains, while 30 other strains could not be placed in any group. The strains belonging to the three clusters were studied by determining their nodulation host ranges and their morphological, physiological, and auxanographic characteristics. Representative strains of the three clusters were also genotypically characterized by determining their DNA base compositions, by performing DNA-DNA and DNA-rRNA hybridization experiments, and by determining their 16S rRNA gene sequences. Our results showed that two of the clusters identified on the basis of SDS-PAGE data are genotypically and phenotypically distinct groups that belong on the Rhizobium meliloti-Rhizobium fredii rRNA branch. The third cluster is localized on the Rhizobium loti rRNA branch in the vicinity of Rhizobium huakuii and contains strains isolated in Africa, in Brazil, and in New Zealand from different leguminous species. On the basis of the results of the present study, we propose to emend the genus Sinorhizobium and to reclassify R. meliloti as Sinorhizobium meliloti comb. nov. In addition, two new species, Sinorhizobium saheli and Sinorhizobium teranga, are proposed for isolates from Senegal.

Phenotypic properties (growth characteristics, utilization of carbon and nitrogen sources, and intrinsic antibiotic resistance) of 53 Rhizobium strains isolated from root nodules of the temperate-zone legumes Astragalus spp. (29 strains), Oxytropis campanulata (7 strains), Hedysarum alpinum (7 strains), Ononis arvensis (3 strains), Glycyrrhiza spp. (4 strains), and Coronilla varia (3 strains) were compared with those of other Rhizobium, Brady rhizobium, and Agrobacterium strains. The final matrix, containing 83 strains and 56 nonsymbiotic features, was used for computer cluster analysis. The dendrogram showed that the new strains of temperate-zone rhizobia formed a cluster separate from both Rhizobium and Bradyrhizobium spp. Two large groups of temperate-zone rhizobia were revealed. Group 1 included rhizobial strains originating from different geographical regions with a temperate climate, while group 2 included strains from the same geographical origin, South Siberia. The strains of recognized Rhizobium species were clustered, in general, with each other as expected from phylogenetic relatedness.

The organization of the ribosomal genes is unique in Borrelia burgdorferi in that the rrl (23S) and rrf (5S) genes are tandemly duplicated. We took advantage of this uniqueness to assess the restriction polymorphism of PCR products obtained with primers at the 3′ end of the first rrf gene and at the 5′ end of the second rrl gene. An amplicon that was 226 to 266 bp long was generated from 99 of 100 B. burgdorferi sensu lato strains. The nuclease MseI restriction polymorphism of the amplicons provided a useful tool for identifying B. burgdorferi sensu stricto, Borrelia garinii, Borrelia afzelii (formerly group VS461), and Borrelia japonica (formerly group F63B). Furthermore, it allowed us to recognize four new genomic groups, which were confirmed by DNA-DNA hybridization data. Two of these genomic groups comprised European strains, and the other two groups contained American strains. The American genomic groups involved vectors with enzootic cycles quite different from those of B. burgdorferi sensu stricto, which previously was the only Lyme disease Borrelia species known to occur in the United States. Our method could be used for rapid screening of strain collections and for epidemiological and medical purposes.

Gram-negative, mesophilic, obligately anaerobic strains Kysw2T (T = type strain), Kyval, and Kyprop isolated from an anoxic mud sample obtained from the Kysing Fjord south of Århus (Denmark) and strains GypropT and GylacT isolated from the Guayamas Basin (Gulf of California) all exhibit complete oxidation of a wide range of electron donors (e. g., dicarboxylic acids and amino acids) linked to stoichiometric reduction of elemental sulfur to hydrogen sulfide. A comparative 16S ribosomal DNA sequence analysis revealed that these five strains, together with a previously described isolate (strain Gö11), constitute a coherent cluster of descent. This cluster belongs phylogenetically to a branch of the delta subclass of the Proteobacteria and is characterized by members of the genera Pelobacter and Desulfuromonas. Within the cluster strains Kysw2T and Kyval, strains Gyprop1 and Kyprop, and strains GylacT and Gö11 have identical 16S ribosomal DNA sequences. The levels of DNA-DNA relatedness were 89% between strains Kysw2T and Kyval, 98% between strains GypropT and Kyprop, and 73% between strains GylacT and Gö11. The levels of DNA-DNA relatedness between members of the three DNA relatedness groups were less than 30%. On the basis of genomic data and phenotypic characteristics, a new genus, Desulfuromusa, is described; this new genus includes three new species, for which the names Desulfuromusa kysingii, Desulfuromusa bakii, and Desulfuromusa succinoxidans are proposed. The type species of the genus Desulfuromusa is D. kysingii. Strains Kysw2 (= DSM 7343), Gyprop (= DSM 7345), and Gylac (= DSM 8270) are the type strains of D. kysingii, D. bakii, and D. succinoxidans, respectively.