- Volume 50, Issue 5, 2000

A group of strains with potent extracellular enzymic activity were isolated from the surfaces of the chain-forming sea-ice diatom Melosira and from an unidentified macrophyte collected from the Eastern Antarctic coastal zone. 16S rDNA sequence analysis indicated that the strains belonged to the genus Cellulophaga and showed greatest similarity to the species Cellulophaga baltica (sequence similarity 97%). Phenotypic characteristics, DNA base composition and DNA-DNA hybridization values clearly separate the Antarctic strains from Cellulophaga baltica and other Cellulophaga species. Thus, the strains form a distinct and novel species and have the proposed name Cellulophaga algicola sp. nov. (type strain IC166T = ACAM 630T). In addition, it was recognized that the species Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989, a species phylogenetically remote from the type species of the genus Cytophaga, possessed 16S rDNA sequences and phenotypic and chemotaxonomic traits similar to those of other Cellulophaga species. Thus, it was proposed that the species Cytophaga uliginosa be renamed as Cellulophaga uliginosa comb. nov.

Strains traditionally identified as Proteus vulgaris formed three biogroups. Biogroup 1, characterized by negative reactions for indole production, salicin fermentation and aesculin hydrolysis, is now known as Proteus penneri. Biogroup 2, characterized by positive reactions for indole, salicin and aesculin, was shown by DNA hybridization (hydroxyapatite method) to be a genetic species separate from biogroup 1 and from biogroup 3 which is positive for indole production and negative for salicin and aesculin. In this study, 52 strains were examined, of which 36 strains were Proteus vulgaris biogroup 3, which included the current type strain of the species P. vulgaris (ATCC 29905T), and compared to seven strains of Proteus vulgaris biogroup 2 and nine type strains of other species in the genera Proteus, Providencia and Morganella. By DNA hybridization, these 36 strains were separated into four distinct groups, designated as Proteus genomospecies 3, 4, 5 and 6. DNAs within each separate Proteus genomospecies were 74-99% related to each other in 60 degrees C hybridization reactions with < or = 4.5% divergence between related sequences. Proteus genomospecies 3 contained the former P. vulgaris type strain and one other strain and was negative in reactions for salicin fermentation, aesculin hydrolysis and deoxyribonuclease, unlike the reactions associated with strains considered as typical P. vulgaris which are positive in reactions for salicin, aesculin and DNase. Genomospecies 3 can be distinguished from Proteus genomospecies 4, 5 and 6 because it is negative for Jordan's tartrate. Proteus genomospecies 4, containing five strains, was differentiated from Proteus penneri, genomospecies 3 and 6 and most, but not all, strains of genomospecies 5, by its ability to ferment L-rhamnose. Proteus genomospecies 5 and 6, containing 18 and 11 strains, respectively, could not be separated from each other by traditional biochemical tests, by carbon source utilization tests or SDS-PAGE of whole-cell proteins. In an earlier publication, a request was made to the Judicial Commission that the former type strain of P. vulgaris (ATCC 13315) be replaced by P. vulgaris biogroup 2 strain ATCC 29905T, a strain considered more biochemically typical of P. vulgaris strains. This would have the effect of assigning the name P. vulgaris to P. vulgaris biogroup 2. Since this request has been acceded to, the name Proteus hauseri is herein proposed for Proteus vulgaris genomospecies 3. Its type strain is ATCC 700826T. Proteus genomospecies 4, 5 and 6 will remain unnamed until better phenotypic differentiation can be accomplished. All Proteus genomospecies were similar in their antimicrobial susceptibility patterns. Nineteen strains were isolated from urine, four from faeces, two from wounds, nine from other human sources and two from animals.

The systematic relationships of intracellular bacteria of 13 Camponotus species (carpenter ants) from America and Europe were compared to those of their hosts. Phylogenetic trees of the bacteria and the ants were based on 16S rDNA (rrs) gene sequences and mitochondrial cytochrome oxidase subunit I (COI) gene sequences, respectively. The bacterial endosymbionts of Camponotus spp. form a distinct lineage in the y-subclass of the Proteobacteria. The taxa most closely related to these bacteria are endosymbionts of aphids and the tsetse fly. The bacterial and host phylogenies deduced from the sequence data show a high degree of congruence, providing significant evidence for cospeciation of the bacteria and the ants and a maternal transmission route of the symbionts. The cloned rrs genes of the endosymbionts contain putative intervening sequences (IVSs) with a much lower G+C content than the mean of the respective rrs genes. By in situ hybridization specific 16S rDNA oligonucleotide probes verified the presence of the bacteria within tissues of three of the eukaryotic hosts. It is proposed that the endosymbionts of these three carpenter ants be assigned to a new taxon 'Candidatus Blochmannia gen. nov.' with the symbionts of the individual ants being species named according to their host, 'Candidatus Blochmannia floridanus sp. nov.', 'Candidatus Blochmannia herculeanus sp. nov.' and 'Candidatus Blochmannia rufipes sp. nov.'.

Of 42 rhizobial isolates from Medicago sativa and Melilotus spp. growing in arid saline fields in Xinjiang, China, 40 were identified as Sinorhizobium meliloti by a polyphasic approach. However, diverse groups were obtained from these isolates in numerical taxonomy and SDS-PAGE of proteins. They could grow at pH 10.5 and were tolerant to 2.5-4.0% (w/v) NaCl.

A high-resolution phylogenetic analysis of Nitrobacter strains and their neighbours was made using the rrs-rrl intergenic spacer sequence and the hypervariable part of the rrl gene. The phylogenetic tree obtained was consistent with that which was obtained previously but was much more discriminating, permitting the design of genus-specific primers.

Two strains that were strongly able to degrade trichloroethylene were isolated from contaminated environmental samples. The isolates are non-motile, aerobic, non-spore-forming, gram-positive coccoid to short rods with cell-wall peptidoglycan containing meso-diaminopimelic acid. The major type of menaquinone is MK-8(H4). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. Mycolic acids were absent. The G+C content of the DNA was 72 mol%. Furthermore, comparison of 16S rDNA sequences shows that the isolates clearly belong to the genus Janibacter. The isolates differ from Janibacter limosus at the species level, as shown by the value for DNA-DNA hybridization. It is therefore proposed that the strains be assigned to the genus Janibacter as Janibacter brevis sp. nov.

DNA-DNA relatedness of all validly described Thermoactinomyces species was determined to infer the genetic relationships between them. The levels of DNA-DNA relatedness among the type strains of Thermoactinomyces species ranged from 2-5 to 92.8%. Based on DNA relatedness data, the type strains of Thermoactinomyces intermedius, Thermoactinomyces putidus, Thermoactinomyces dichotomicus and Thermoactinomyces peptonophilus were considered to be distinct species of the genus Thermoactinomyces. However, the relationship between the type strains of Thermoactinomyces vulgaris and Thermoactinomyces candidus and the relationship between the type strains of Thermoactinomyces sacchari and Thermoactinomyces thalpophilus were reevaluated from levels of DNA-DNA relatedness. The independent DNA relatedness values between Thermoactinomyces vulgaris KCTC 9076T and Thermoactinomyces candidus KCTC 9557T were 90.8 and 92.8%. Thermoactinomyces thalpophilus KCTC 9789T and Thermoactinomyces sacchari KCTC 9790T exhibited independent values of 85.6 and 87.3%. Accordingly, on the basis of DNA-DNA relatedness data together with 16S rDNA sequence data determined recently, it is proposed that Thermoactinomyces candidus should be considered as a synonym of Thermoactinomyces vulgaris and Thermoactinomyces thalpophilus be considered as a synonym of Thermoactinomyces sacchari.

A moderately halophilic actinomycete, designated HA-9T, was isolated from a saltern in Kunsan, Republic of Korea, and was the subject of polyphasic identification. Analysis of 16S rDNA indicated that the isolate belonged to the genus Nocardiopsis, but differed genetically from other Nocardiopsis species. Strain HA-9T contained meso-diaminopimelic acid, no diagnostic sugars, hexa- or octa-hydrogenated menaquinones with 10 isoprene units, straight-chain saturated or monounsaturated, iso-, anteiso-, 10-methyl branched fatty acids with 13-18 carbons and type III phospholipids. All of these characters consistently assign the isolate to the genus Nocardiopsis. All of the validly described Nocardiopsis species, including moderately halophilic Nocardiopsis halophila, can be differentiated from the saltern isolate using morphological and physiological traits. On the basis of polyphasic evidence, the name Nocardiopsis kunsanensis sp. nov. is proposed for strain HA-9T (= KCTC 9831T), which is designated the type strain.

A Gram-positive, catalase-negative, facultatively anaerobic, coccus-shaped bacterium, designated IH25T, was isolated from kimchi, a traditional Korean vegetable product. Phylogenetic analysis based on almost complete 16S rDNA sequences placed the isolate in a monophyletic clade corresponding to the genus Leuconostoc. All validly described species in the genus Leuconostoc, with the exception of Leuconostoc fallax, showed high sequence identity of over 97%. The 16S rDNA sequence of strain IH25T showed the highest homology to those of Leuconostoc gelidum DSM 5578T (98.9%) and Leuconostoc citreum KCTC 3526T (98.3 %). However, DNA-DNA hybridization experiments indicated that the organism represents a novel genomic species in the genus, since the previously known leuconostocs share DNA homology with strain IH25T of less than 70%. In this work, it is proposed that isolate IH25T be classified in the genus Leuconostoc as Leuconostoc kimchii sp. nov. The type strain of Leuconostoc kimchii is IH25T (= KCTC 2386T = IMSNU 11154T).

Ureaplasma urealyticum has been divided into 14 serovars. Recently, subdivision of U. urealyticum into two species has been proposed: U. parvum (previously U. urealyticum parvo biovar), comprising four serovars (1, 3, 6, 14) and U. urealyticum (previously U. urealyticum T-960 biovar), 10 serovars (2, 4, 5, 7-13). The multiple-banded antigen (MBA) genes of these species contain both species and serovar/subtype specific sequences. Based on whole sequences of the 5'-ends of MBA genes of U. parvum serovars and partial sequences of the 5'-ends of MBA genes of U. urealyticum serovars, we previously divided each of these species into three MBA genotypes. To further elucidate the relationships between serovars, we sequenced the whole 5'-ends of MBA genes of all 10 U. urealyticum serovars and partial repetitive regions of these genes from all serovars of U. parvum and U. urealyticum. For the first time, all four serovars of U. parvum were clearly differentiated from each other. In addition, the 10 serovars of U. urealyticum were divided into five MBA genotypes, as follows: MBA genotype A comprises serovars 2, 5, 8; MBA genotype B, serovar 10 only; MBA genotype C, serovars 4, 12, 13; MBA genotype D, serovar 9 only; and MBA genotype E comprises serovars 7 and 11. There were no sequence differences between members within each MBA genotype. Further work is required to identify other genes or other regions of the MBA genes that may be used to differentiate U. urealyticum serovars within MBA genotypes A, C and E. A better understanding of the molecular basis of serotype differentiation will help to improve subtyping methods for use in studies of the pathogenesis and epidemiology of these organisms.

On the basis of genetic analysis, molecular karyotyping and sequence analyses of the 18S rRNA and internal transcribed spacer (ITS) region, three new Saccharomyces species are described, Saccharomyces cariocanus (with type strain NCYC 2890T), Saccharomyces kudriavzevii (with type strain NCYC 2889T) and Saccharomyces mikatae (with type strain NCYC 2888T). Genetic and molecular analyses did not confirm the previously observed conspecificity of Saccharomyces paradoxus and S. cariocanus. The latter species exhibits postzygotic isolation from representative strains from all known geographical populations of S. paradoxus: European, Far-East Asian, North American and Hawaiian.

The phylogeny of kinetoplastid flagellates was investigated by determining the sequences of the small-subunit (18S) rRNA from Bodo designis, Bodo saltans K, Bodo saltans P, Bodo sorokini, Bodo sp. (cf. uncinatus), Cruzella marina, Cryptobia helicis, Dimastigella mimosa and Parabodo nitrophilus and analysing these data together with several previously obtained sequences. The root of the kinetoplastid tree was tentatively determined to be attached to the branch of B. designis and/or Cruzella marina. Within this topology, the suborder Trypanosomatina appears as a late-emerging monophyletic group, while the suborder Bodonina is paraphyletic. Within the bodonid subtree, the branches of parasitic organisms were intermingled with free-living ones, implying multiple transitions to parasitism. The tree indicates that the genera Cryptobia and Bodo are artificial taxa. In addition, the separation of the fish cryptobias and Trypanoplasma borreli as different genera was not supported.