- Volume 41, Issue 4, 1991

Strain PPAV, a filamentous but nonhelical mollicute, was isolated from aborted apple seeds in France in late 1979. This organism grew well in SP-4 broth, fermented glucose, and required sterol for growth, and most of its properties suggested that it belonged to the genus Mycoplasma. However, it was serologically distinct; in addition, unlike other Mycoplasma species, genome measurements consistently yielded values of about 1,000 MDa (ca. 1,500 kbp), and the organism had a growth temperature optimum of 43°C. A comparison of strain PPAV 16S rRNA sequences with those of other mollicutes revealed a high degree of sequence similarity to a strain of Mycoplasma iowae, which is commonly encountered in poultry. This relationship was confirmed by performing a restriction endonuclease pattern analysis and DNA-DNA hybridization tests. The genome size of type strain 695 of M. iowae was determined to be about 1,000 MDa (1,500 kbp) by renaturation kinetics, a value which is much higher than any other value known in the genus. Additional measurements by pulsed-field gel electrophoresis yielded values of 1,300 kbp for both strain PPAV and M. iowae. Subsequent phenotypic comparisons supported this relationship. Serologic tests with strain PPAV and other strains of M. iowae confirmed the findings of other investigators that this species is serologically heterogeneous. The high optimum temperature for growth of strain PPAV was also shared by a number of M. iowae isolates. Genome size is an inappropriate character for taxonomic assignment to the family Mycoplasmataceae because strain PPAV and other established species in this family are now known to have genomes ranging in size from 1,000 to 1,400 kbp.

The levels of DNA-DNA hybridization among members of the three major groups of Streptomyces spp. that cause potato scab did not exceed 20% for any pair. The majority of the Streptomyces scabies strains which we examined exhibited greater than 70% relatedness to the type strain, although values as low as 21% were obtained. The levels of homology between S. scabies and nonpathogenic type strains belonging to the Diastatochromogenes group ranged from 10 to 42%, while the reciprocal values obtained with labeled DNAs from Streptomyces bottropensis ATCC 25435T (T = type strain) and Streptomyces eurythermus ATCC 14975T ranged from 37 to 74% and from 2 to 24%, respectively. In contrast to S. scabies, the levels of relatedness between Streptomyces acidiscabies isolates and their type strain were high (83 to 111%). The levels of DNA relatedness within the Streptomyces albidoflavus group were uniformly low. These results are consistent with phenotypic data which indicate that pathogens in the three groups are not related. The genetic diversity of strains referred to as S. scabies exceeds the genetic diversity found at the species level, and some of these strains appear to be related to phenotypically similar nonpathogens.

The rRNA gene restriction patterns of two species of nutritionally variant streptococci, Streptococcus defectivus and Streptococcus adjacens, were determined, and the results were compared with the electrophoretic migration profiles of penicillin-binding proteins. Reference strains belonging to various streptococcal species were used as controls. Our results correlated with the results of DNA-DNA hybridization experiments and confirmed the delineation of these two species. Moreover, they demonstrated that intraspecies variations occur and suggested that there are two subspecies of S. defectivus.

The partial 16S rRNA sequences of 24 Streptococcus species were determined by reverse transcription. A comparative analysis of these sequences and the sequences of seven previously studied streptococcal species revealed the presence of several clusters within the genus. The clusters obtained from the sequence analysis agreed in general with the groups outlined on the basis of the results of nucleic acid hybridization studies, but there were some exceptions. The pyogenic group was extended to include Streptococcus agalactiae, S. parauberis, S. porcinus, and S. uberis. Four oral groups were discerned; these four groups centered on S. mutans, S. salivarius, S. anginosus, and S. oralis. Some species (e.g., S. suis and S. acidominimus) did not cluster with any particular group. Our findings are discussed in the context of data from other genetic and chemotaxonomic studies.

On the basis of three isolates (strains FC6T [T = type strain], FC4, and RG1) of extremely thermophilic chemolithoautotrophic archaebacteria obtained from solfataric fields on ão Miguel Island, Azores, the new genus Stygiolobus is described. These isolates grow obligately chemolithotrophically by reduction of S0 with H2 (H2-S0 lithotrophy) and are the first strictly anaerobic members of the order Sulfolobales. With a DNA G+C content of 38 mol%, the Stygiolobus isolates resemble Sulfolobus spp., which, however, are faculatively organotrophic and aerobic S0 oxidizers. The new isolates are also distinct from Acidianus spp., which resemble Stygiolobus by growing by H2-S0 lithotrophy. However, Acidianus spp. can also grow aerobically by S0 oxidation and have G+C contents of 31 mol%. At this time, only one species of the genus Stygiolobus is known, Stygiolobus azoricus sp. nov.; the type strain of S. azoricus is strain FC6 (= DSM 6296).

Morphological, physiological, and biochemical characteristics and the DNA base compositions of 133 thermophilic Bacillus strains were determined. A total of 54 of these strains were received as identified species (mainly Bacillus stearothermophilus, Bacillus coagulans, Bacillus brevis, and Bacillus licheniformis) from international culture collections, and 79 newly isolated strains, which were isolated mainly from sugar diffusion juices of Italian plants, were also examined. Numerical taxonomy techniques (simple matching coefficient and unweight pair grouping using the mathematical average) and DNA G+C values showed that the strains aggregated into nine clusters. Both B. licheniformis and B. brevis were well separated from the other organisms. B. stearothermophilus and B. coagulans were confirmed as separate clusters and exhibited greater heterogeneity than previously shown. The B. stearothermophilus strains clustered into four groups, three of which have been recognized previously by other authors; the members of the fourth group had distinctive characteristics, including considerable biochemical inertness, an inability to grow at temperatures greater than 60°C, and a high G+C content. Within the B. coagulans cluster the strains with characteristics very similar to those of the new species Bacillus smithii clustered together. However, the remaining strains were still clearly separated into two groups; one of these groups was considered B. coagulans sensu stricto, and the other was distinguished by morphological and biochemical criteria, such as spores which do not swell the sporangia, utilization of citrate, a higher proteolytic activity, and acidification of some carbohydrates. Our results were confirmed by comparing them with distinctive characteristics of recently described thermophilic Bacillus species.

Of 87 strains previously identified as Bacillus brevis Migula 1900, 58 had G+C contents of 47.0 to 51.9 mol%, a range that included the G+C content (48.7 mol%) of the type strain. The G+C contents for three other groups consisting of 5, 7, and 17 strains were 37.0 to 41.9, 42.0 to 46.9, and 52.0 mol% or higher, respectively. DNA reassociation studies showed that 25 of the 58 strains with G+C contents of 47.0 to 51.9 mol% were closely related genetically to the type strain and to each other. For the most part, this genetically related group was phenotypically homogeneous; variations in the fermentation of mannitol and mannose were observed. My results strongly suggest that many of the strains were misclassified as B. brevis. Consequently, much of the phenotypic heterogeneity of the species B. brevis Migula 1900 is not due to variations exhibited by genetically related organisms, but is the result of variability introduced by the presence of genetically unrelated strains.

We performed a numerical analysis of the results of biochemical and nutritional tests done with strains of nonfluorescent plant-pathogenic Pseudomonas spp. A total of 57 tests were used, and determinative tests which discriminated between taxa were identified. Pseudomonas andropogonis, P. caryophylli, P. corrugata, P. glumae, P. plantarii, and P. rubrisubalbicans were distinguished as distinct members of the genus Pseudomonas. Strains of P. ficuserectae and P. meliae formed a single cluster having affinities with P. syringae. Strains of P. cissicola were allocated to Agrobacterium spp. Strains of P. avenae, P. cattleyae, P. pseudoalcaligenes subsp. citrulli, P. pseudoalcaligenes subsp. konjaci, and P. rubrilineans formed a single relatively homogeneous cluster, within which three subclusters were discerned. Strains presently identified as P. avenae and as P. rubrilineans, including the type strain of P. cattleyae, formed a single homogeneous subcluster. Strains of P. pseudoalcaligenes subsp. citrulli and P. pseudoalcaligenes subsp. konjaci formed two subclusters. Genomic probes prepared from DNAs of the type strains of P. avenae, P. cattleyae, P. pseudoalcaligenes subsp. citrulli, P. pseudoalcaligenes subsp. konjaci, and P. rubrilineans gave positive reactions with all of the strains of these species which were tested in colony hybridization studies, but not with strains of other nonfluorescent Pseudomonas spp. The G+C ratios of these type strains were all in the range from 67 to 71 mol%, and the levels of homology determined in DNA-DNA reassociation studies were all greater than 70%. P. avenae, P. cattleyae, P. pseudoalcaligenes subsp. citrulli, P. pseudoalcaligenes subsp. konjaci, and P. rubrilineans are considered to be members of a single species, P. avenae, with P. cattleyae and P. rubrilineans as junior synonyms; P. pseudoalcaligenes subsp. citrulli and P. pseudoalcaligenes subsp. konjaci are proposed as subspecies.

The new genus Actinobispora is described. The organisms of this genus are gram positive and aerobic and produce spores in longitudinal pairs on vegetative mycelium and in longitudinal pairs or singly on aerial mycelium. The cell wall contains meso-diaminopimelic acid, and whole-cell hydrolysates contain galactose, arabinose, and xylose (an unusual type IV cell wall); the phospholipid pattern is of type PIV; the major menaquinones are MK-7(H2) and MK-9(H2). No mycolic acids are present. The guanine-plus-cytosine of the DNA is 71.0 mol%. The type species of this genus is Actinobispora yunnanensis. The type strain of this new species is strain Y-11981 (=CCTCC M 90959).

The genus Listonella, which was recently described on the basis of 5S rRNA sequence data, was found to be of dubious value on the basis of the results of a comparison of a number of taxonomic studies involving members of the Vibrionaceae. The available data suggest that 5S rRNA sequences may be of limited taxonomic use at the intra- and intergeneric levels, at least for apparently recently evolved groups, such as the Vibrionaceae. In this light, we assessed the generic assignment of the species Listonella damsela. Phenotypic characterization of 12 strains of bacteria assigned to L. damsela, including type strain ATCC 33539, revealed a strong resemblance to members of the genus Photobacterium. All of the strains conformed to major characteristics common to all known Photobacterium species. The characteristics of these organismsincluded the absence of a flagellar sheath and accumulation of poly-β-hydroxybutyrate during growth on glucose coupled with the inability to utilize dl-β-hydroxybutyrate as a sole carbon source. On the basis of the phenotypic data, we propose that L. damsela should be reassigned to the genus Photobacterium as Photobacterium damsela comb. nov.

A total of 61 strains, including members of all five currently described pathogenicity groups of Xanthomonas campestris pv. citri (groups A, B, C, D, and E) and representing a broad geographical diversity, were compared by using sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell proteins, gas chromatographic analysis of fatty acid methyl esters, and DNA-DNA hybridization. We found that all of the pathogenicity groups were related to each other at levels of DNA binding of more than 60%, indicating that they all belong to one species. Our results do not confirm a previous reclassification of X. campestris pathogens isolated from citrus in two separate species (Gabriel et al., Int. J. Syst. Bacteriol. 39:14-22, 1989). Pathogenicity groups A and E could be clearly delineated by the three methods used, and group A was the most homogeneous group. The delineation of pathogenicity groups B, C, and D was not clear on the basis of the results of sodium dodecyl sulfate-polyacrylamide gel electrophoresis of proteins and gas chromatography of fatty acid methyl esters, although these groups constituted a third subgroup on the basis of the DNA homology results.

We studied strains of an unusual streptococcus that superficially resembles Streptococcus sanguis but has fibrils that are arranged in lateral tufts. These strains were originally isolated from human throats and oral cavities and have been referred to previously as “Streptococcus sanguis I,” the “CR group,” and the “tufted-fibril group.” Until now, insufficient phenotypic data have been available to allow reliable differentiation of these strains from other viridans streptococcal species, particularly the species in the S. sanguis group. Recently, workers have proposed a scheme of phenetic tests that is based on 4-methylumbelliferyl-linked substrates and conventional biochemical tests and allows the tufted-fibril group to be differentiated; these organisms differ from other viridans species in being able to hydrolyze arginine but not esculin and in producing α-l-fucosidase but not β-glucosidase or alkaline phosphatase. These data, together with the results of our DNA-DNA hybridization experiments and the unusual ultrastructure of the tufted-fibril strains as determined by electron microscopy, demonstrate that these organisms represent a new species, for which the name Streptococcus crista is proposed. The DNA base composition is 42.6 to 43.2 mol% G+C. The type strain is strain CR311 (= NCTC 12479).

The phenotypes of 153 strains belonging or related to the genus Bifidobacterium were studied. These organisms included 38 collection strains and 115 wild strains (41 strains of human origin, 56 strains of animal origin, and 18 strains obtained from rivers or sewage). Our phenotypic analysis revealed seven main groups that were subdivided into 20 subgroups. Seven subgroups contained no type or collection strain. Among the human strains, the type strains of Bifidobacterium pseudocatenulatum and B. catenulatum fell into group I, which contained the type strains of B. adolescentis (subgroup Ib), B. dentium (subgroup Ic), and B. angulatum (ungrouped). The type strain of B. breve belonged to subgroup IIIa1, and the type strains of B. infantis and B. longum fell into subgroup IIIb1. Group VII comprised only wild strains that were isolated from human infant feces. Among the animal strains, group II consisted mainly of bifidobacteria that were isolated from pig feces and contained the type strains of B. suis (subgroup IIb), B. thermophilum (subgroup IIf), B. choerinum, and B. boum (ungrouped). Wild strains belonging to group V were isolated from pig, calf, cow, and chicken feces; this included the type strains of B. animalis (subgroup Va), B. magnum (subgroup Vb), B. pseudolongum, and B. globosum (subgroup Vc). The strains of human origin (groups I, III, and VII) were well separated from the animal strains (groups II, IV, and V). It was not surprising that the wild strains isolated from surface water or sewage were distributed in the animal groups as well as the human groups. Thus, bifidobacteria can be considered to be successful indicators of human or animal fecal pollution when they are correctly classified. The acidification patterns were not adequate to differentiate Bifidobacterium species, as determined previously by Mitsuoka (Bifidobacteria Microflora 3:11-28, 1984) and Scardovi (p. 1418-1434, in P. H. A. Sneath, N. S. Mair, M. E. Sharpe, and J. G. Holt, ed., Bergey’s Manual of Systematic Bacteriology, vol. 2, 1986). However, enzymatic tests furnished new taxonomic criteria for the genus.

Twelve strains of halophilic, methylotrophic, methanogenic bacteria, including the type strains of the validly published species Methanohalophilus mahii, Methanohalophilus zhilinae, and Methanohalobium evestigatum, as well as the type strain of Methanococcus halophilus, were compared on the basis of DNA-DNA hybridization and phenotypic characteristics. Two groups (moderately halophilic Methanohalophilus strains and extremely halophilic Methanohalobium strains) were formed on the basis of G+C contents and DNA-DNA hybridization data. Type strain SLP of Methanohalophilus mahii and type strain Z-7982 of Methanococcus halophilus exhibited 87% sequence similarity and belong to the same genus (Methanohalophilus), if not to the same species. A regulation of the International Code of Nomenclature of Bacteria implies that the specific epithet halophilus has priority by validation and should be retained. Therefore, we propose that Methanococcus halophilus should be transferred to the genus Methanohalophilus as Methanohalophilus halophilus comb. nov. (type strain, strain Z-7982 [= DSM 3094 = OCM 160]); an emended description is given. Moderately halophilic strains TR-7, Z-7404, and Z-7405, which were isolated from geographically separated sites, exhibited high levels of DNA-DNA hybridization with Methanohalophilus mahii and might be regarded as strains of the same Methanohalophilus species. The alkaliphilic organism Methanohalophilus zhilinae is a valid species in the genus Methanohalophilus. The extremely halophilic organism Methanohalobium evestigatum exhibited no significant DNA-DNA hybridization with moderately halophilic species and should be regarded as a member of an independent genus. Other extremely halophilic strains (strains Z-7408 and Z-7403) exhibited low levels of DNA-DNA hybridization with Methanohalobium evestigatum Z-7303T (= DSM 3721) (T = type strain).

A bacterial strain was previously isolated from a parasitic wasp, Nasonia vitripennis, and shown to cause the son-killer trait in wasps. The 16S rRNA sequence, DNA probes, and whole-cell fatty acid profiles suggest that it belongs to the family Enterobacteriaceae. The strain’s properties indicate a closer relationship to the genus Proteus than to the genus Escherichia, Citrobacter, or Salmonella. We propose the name Arsenophonus nasoniae gen. nov., sp. nov., for this bacterium. Strain SKI4 (ATCC 49151) is the type strain.

All aphids are thought to have an association with primary endosymbionts, which are located within specialized cells known as mycetocytes. The primary endosymbionts are gram-negative, spherical or slightly oval cells which have not been cultivated outside aphid hosts. Recently, it has been shown that the 16S rRNA sequences of the primary endosymbionts of 11 host species belonging to four aphid families are similar and thus that these organisms are related. Comparisons with the 16S rRNAs of other procaryotes indicated that the primary endosymbionts form a distinct lineage within the gamma-3 subgroup of the Proteobacteria. On the basis of these results we propose that the primary endosymbionts should be placed in Buchnera gen. nov. and Buchnera aphidicola sp. nov. The primary endosymbiont found in the mycetocytes of Schizaphis graminum (green bug) is designated the type strain of this species.

The history of the creation of the species Gordona sputi is described briefly. In addition, the mycolic acid and menaquinone compositions of this organism, which are needed to classify species in the genus Gordona, are described.

Lists of abbreviations for genus names of bacteria are expanded to accommodate 103 new entries which are names that have been validly published since the publication of an updated list by Rogosa et al. in 1986 (Int. J. Syst. Bacteriol. 36:464-472). These abbreviations are provided to serve the need for appropriate codified abbreviations for use in processing or indexing of information on computers.