Simple Matching Coefficient Research Articles

Taxonomic Utility of Restriction Endonuclease Fingerprinting of Large DNA Fragments from Streptomyces Strains

Using a method known as low-frequency restriction fragment analysis (LFRFA) (M. L. Beyazova and M. P. Lechevalier, Int. J. Syst. Bacteriol. 42:422-433, 1992), we determined the molecular weights of Ase I restriction fragments of Streptomyces DNAs by pulsed-field gel electrophoresis. The levels of similarity of fragment patterns among strains were determined by using the simple matching coefficient, and clustering was performed by using the unweighted pair group with mathematical average algorithm. A total of 59 strains representing eight species and the numerically classified taxon Streptomyces cyaneus group A18 (S. T. Williams, M. Goodfellow, G. Alderson, E. M. H. Wellington, P. H. A. Sneath, and M. J. Sackin, J. Gen. Microbiol. 129:1743-1813, 1983) were studied. Forty-two strains (six species) formed eight clusters at levels of similarity of more than 80%; 17 strains (including the entire S. cyaneus group) were unclustered. Cluster 1 contained all of the Streptomyces albus strains studied plus two strains of Streptomyces somaliensis and two strains of Streptomyces lavendulae. Cluster 2 contained 8 of the 12 Streptomyces fradiae strains examined plus one strain each of S. somaliensis and S. lavendulae. Cluster 3 was heterogeneous in terms of species. Cluster 4 contained two S. somaliensis strains; cluster 5 contained three S. fradiae strains; cluster 6 contained three Streptomyces rimosus strains; and clusters 7 and 8 contained seven and three Streptomyces ipomoea strains, respectively. The S. cyaneus group strains exhibited no clustering among themselves or with the other species examined. Some Streptomyces species which exhibited high levels of similarity (85 to 95%) in physiological tests (e.g., S. albus and the S. fradiae strains in cluster 2) exhibited high levels of similarity in the LFRFA (84 and 81%, respectively). Other taxa (S. cyaneus group) which exhibited equally high levels of physiological similarity (90%) appeared to be unrelated as determined by the LFRFA. Species with lower levels of physiological similarity (e.g., S. somaliensis[75%], S. lavendulae[63%], and S. rimosus[68%]) exhibited low levels of LFRFA similarity (75, 64, and 54%, respectively). High levels of DNA-DNA relatedness (≫90%) (S. ipomoea) were reflected in high levels of similarity as determined by the LFRFA (75 to 100%); lower levels of DNA-DNA relatedness (ca. 70%) (S. cyaneus group) were reflected in low levels of LFRFA similarity (strains not clustered). We concluded that the presently used physiological tests reflect too small a portion of the genome to be universally useful in streptomycete species characterization. In contrast, high levels of DNA-DNA relatedness (≫90%) and high LFRFA similarity values will probably both be valuable in species delineation in actinomycetes.

Classification of the spoilage flora of raw and pasteurized bovine milk, with special reference to Pseudomonas and Bacillus

Eighty-one bacterial strains isolated from refrigerated raw milk, 124 from pasteurized milk and cream stored at 5 degrees C and 7 degrees C, and 19 type and reference strains of Pseudomonas spp. and Bacillus spp. were characterized by numerical phenotypic analysis. Data were processed with simple matching (SSM) and Jaccard (SJ) coefficients, and UPGMA clustering. Fourteen clusters of Gram-negative bacteria were formed at SJ = 79% (SSM = 90%). Raw milk was exclusively spoilt by Gram-negative bacteria, the majority of which were Pseudomonas fluorescens biovar I, Ps. fragi, Ps. lundensis and Ps. fluorescens biovar III. Minor groups in raw milk included Enterobacteriaceae spp. and Acinetobacter spp. Pasteurized milk was spoilt by essentially the same Gram-negative organisms in 65% (5 degrees C) and 50% (7 degrees C) of the cases. The phenotypic characteristics of Gram-negative bacteria are given. Bacillus polymyxa (both temperatures) and B. cereus (only at 7 degrees C) were responsible for 77% of samples spoiled by the Gram-positive organisms. Minor milk spoilage groups included other Bacillus spp. and lactic acid bacteria. All Bacillus spp. grew fermentatively in milk, and most strains denitrified. It is suggested that: (i) industrial recontamination tests of pasteurized milk are directed against Pseudomonas; (ii) milk is stored at 5 degrees C or lower to avoid growth of B. cereus; and (iii) the significance of gas-producing and nitrate/nitrite-reducing Bacillus strains is recognized in cheese production.

Comparison of strains of Pseudomonas syringae pv. savastanoi from olive leaves and knots

A collection of strains of Pseudomonas syringae pv. savastanoi was subjected to numeric phenetic analysis of 60 characters using unweighted average linkage on the simple matching coefficient. Most strains recovered by washing random leaves in April and October shared lower similarity values between themselves than with the majority of those isolated from 6-month-old knots in October and April, respectively.

Systematic Assessment of Geographically and Clinically Diverse Aeromonads

Numerical taxonomy was used to analyze data obtained on 167 Aeromonas strains collected from the USA, N.E. Africa, Bangladesh, India, Indonesia, and Puerto Rico. The strains included clinical, environmental, and veterinary isolates. Each strain was tested at 36°C ± 1°C for 80 unit characters that included morphological, biochemical, antimicrobial resistance, and virulence-associated markers. The data for 50 of these characters were analyzed by the SAS/TAXAN® program using Simple Matching and Jaccard coefficients. At a similarity coefficient of 85%, the 167 strains clustered into 12 phenons plus 13 single unclustered strains. All clusters but one contained only one DNA group definition strain. The major clusters resembled the three clinical species Aeromonas hydrophila, Aeromonas veronii biovar sobria, and Aeromonas caviae , with smaller clusters for the species Aeromonas veronii biovar veronii and Aeromonas schubertii . Additional clusters delineated were: an “arabinose-negative” biovar of A. hydrophila and clusters for two newly validated species, A. jandaei and A. trota . This systematic assessment provides a comprehensive taxonomic study of a geographically and clinically diverse group of aeromonads and delineates, for the first time, essentially all of the currently recognized genospecies using phenotypic clustering.

Numerical taxonomy of Lactobacillus spp. associated with healthy and diseased mucosa of the human intestines

Two-hundred and fifty Lactobacillus strains isolated from healthy and diseased mucosa of human intestines of 75 individuals and 49 reference strains were phenotypically classified using 49 unit characters. Data were processed by the Jaccard (SJ) and Simple Matching (SSM) coefficients, and unweighted pair group algorithm with arithmetic averages. Seventeen major clusters were defined at the 76% SJ-similarity level which approximately correspond to the SSM-level of 91%. Seven clusters could be identified: Lactobacillus plantarum (isolates recovered from 5% of the patients), Lact. casei subsp. rhamnosus (17% of the patients), Lact. casei subsp. pseudoplantarum (5% of the patients), Leuconostoc mesenteroides subsp. mesenteroides (3% of the patients), Lact. buchneri (4% of patients), Lact. reuteri (4% of the patients) and Lact. salivarius subsp. salivarius (9% of the patients). Unassigned clusters 1 and 3 both contained homofermentative Lactobacillus strains. Cluster 1 included the type strains of Lact. crispatus, Lact. acidophilus, Lact. jensenii and Lact. gasseri, and cluster 3, the type strains of Lact. delbrueckii subsp. lactis, Lact. agilis and Lact. casei subsp. tolerans. Clusters 1 and 3 were found in 15% and 25% of the patients, respectively. Unassigned clusters 2, 6, 7, 8 and 10 contained homofermentative Lactobacillus strains but no reference strains. Clusters 11, 12, 15 and 17 were made up of heterofermentative Lactobacillus strains but no reference strains. Phenotypical characteristics of the clusters are given. No obvious trends in species (cluster) composition between different intestinal locations could be noted. Most clusters contained isolates from both diseased and healthy mucosa. Exceptions were cluster 15 and cluster 17 which only included isolates from healthy mucosa, and cluster 11 which only included isolates from diseased mucosa. Cluster 15 was isolated in 12% of the patients, and cluster 11 in 8%.

Using randomly amplified polymorphic DNA for evaluating genetic relationships among papaya cultivars

We have applied the recently developed technique of random amplification of polymorphic DNA (RAPD) to the analysis of the relationships among ten cultivars of papaya (Carica papaya L.). Eleven ten-base synthetic oligonucleotides were chosen that gave multiple PCR amplification products using papaya DNA as template. These 11 primers amplified a total of 102 distinct fragments. Cultivars were scored for presence or absence of RAPD fragments and grouped by cluster analysis using simple matching coefficients of similarity. A dendrogram of the ten cultivars was constructed. Of the ten cultivars seven were of the Hawaiian type, and all of these grouped to one branch of the tree. Divisions within the Hawaiian, branch were mostly consistent with the known genetic background of these cultivars. Three non-Hawaiian, cultivars were also analyzed. The minimum similarity detected was 0.7 suggesting that the domesticated papaya germ plasm is quite narrow. Our results show that RAPD technology is a rapid, precise and sensitive technique for genomic analysis.

Rathayibacter gen. nov., Including the Species Rathayibacter rathayi comb. nov., Rathayibacter tritici comb. nov., Rathayibacter iranicus comb. nov., and Six Strains from Annual Grasses

A new genus, Rathayibacter, is proposed to accommodate three species of gram-positive, aerobic, coryneform bacteria previously placed in the genus Clavibacter (Rathayibacter rathayi comb. nov., Rathayibacter tritici comb. nov., and Rathayibacter iranicus comb. nov.), as well as six strains that were isolated from annual cereal grasses, may be responsible for ryegrass toxicity, and are very similar to the recently described organism Clavibacter toxicus sp. nov. (I. T. Riley and K. M. Ophel, Int. J. Syst. Bacteriol. 42:64-68, 1992). The properties of members of the genus Rathayibacter include coryneform morphology, peptidoglycan based on 2,4-diaminobutyric acid (type B2γ), predominant menaquinones of the MK-10 type, and phosphatidylglycerol and diphosphatidylglycerol as basic polar lipids. The DNA base compositions range from 63 to 72 mol% G+C. The members of the new genus form a phenetic cluster distinct from Clavibacter spp. at a level of 71% (simple matching coefficient) and exhibit 7 to 9% DNA-DNA reassociation with strains of Clavibacter spp. In contrast to Clavibacter spp., most Rathayibacter strains are associated with nematodes belonging to the genus Anguina. The Rathayibacter species differ from species belonging to related genera (e.g., Clavibacter and Agromyces species) in the following characteristics: Menaquinone and whole-cell sugar compositions, results of lysozyme-sodium dodecyl sulfate test (which indicates differences in cell wall composition), ability to utilize a number carbon sources, resistance to bacteriocins of some Clavibacter spp., and other characteristics. The Rathayibacter species can be differentiated from each other by following characteristics: Presence or absence of xylose and galactose in the cell walls, fatty acid composition, ability to assimilate various sources of carbon and nitrogen, hydrolytic activity, tolerance to 5% NaCI and 0.03% potassium tellurite, susceptibility to iranicin, and absence or presence of plasmids of certain sizes. The type species of the genus Rathayibacter is R. rathayi. The type strains of the species are R. rathayi VKM Ac-1601 (= ICMP 2574), R. iranicus VKM Ac-1602 (= ICMP 3496), and R. tritici VKM Ac-1603 (= ICMP 2626).

Numerical Taxonomy of Gram-Negative, Oxidase-Positive Rods from Carcharhinid Sharks

Clustering and ordination were used to analyze the results of a study involving phenotypic characterization (61 tests) of 197 strains of gram-negative, oxidase-positive, rod-shaped bacteria isolated from carcharhinid sharks. Also included in the data set were data for 39 reference strains representing the genera Aeromonas, Plesiomonas, and Vibrio. Unweighted pair group mathematical averaging cluster analysis resolved nine major groups of operational taxonomic units (OTUs) at simple matching coefficient (SSM) values of ≥66.5%. In turn, each group contained one or more OTU clusters (phena) at SSM values of ≥72.6%. A total of 27 phena were resolved; 14 phena were identified as Vibrio species and contained 182 of the 236 OTUs in the study. Additional phena were identified as members of the genus Aeromonas (two phena), the genus Photobacterium (three phena), the genus Alteromonas (two phena), and Plesiomonas shigelloides (one phenon). One phenon resembled descriptions of the genera Moraxella and Neisseria and Pasturella piscicida. The remaining four phena were not identified. The largest phena were identified as Vibrio damsela (52 OTUs) and Vibrio alginolyticus (48 OTUs). Vibrio carchariae and Vibrio harveyi formed subclusters (SSM values, ≥82%) within the third largest phenon (24 OTUs), which was resolved at an SSM value of ≥72.6%. Human pathogens (e.g., Vibrio cholerae) and fish pathogens (e.g., Aeromonas salmonicida, Pasteurella piscicida, and V. damsela were isolated from the sharks. Approximately 58% of all of the strains isolated and tested in this study were urease positive.

Numerical classification of coryneform bacteria and related taxa.

A numerical taxonomy of 604 strains of the genera Arthrobacter, Aureobacterium, Brevibacterium, Cellulomonas, Clavibacter, Corynebacterium, Curtobacterium, Microbacterium, Nocardia, Nocardioides, Rhodococcus, Terrabacter and Tsukamurella was undertaken based on 280 physiological characters with the aid of miniaturized tests. Clustering was by the unweighted pair group method (UPGMA) with 12 different measures of similarity. Test error, overlap between the phena and cophenetic correlation coefficients for the classifications obtained with the Jaccard coefficient (SJ), the Pearson coefficient (SP), the simple-matching coefficient (SSM), and the Dice coefficient (SD) as measures of similarity were within acceptable limits. Clusters were defined at the 55.0 to 70.5% levels (SJ). The compositions of clusters corresponded largely the delineations of 81.1 to 93.5% (SSM), 29.1 to 55.0% (SP), and 55.3 to 81.1% (SD). A total of 31 major clusters (containing five or more strains), 41 minor clusters and subclusters (containing less than five strains), and 54 single-member clusters were obtained in the UPGMA/SJ study. The following conclusions were reached: (i) A high degree of similarity between the genera Aureobacterium, Cellulomonas, Clavibacter, Curtobacterium and Microbacterium found in phylogenetic-based studies could be shown also phenetically. Strains belonging to these genera were found in SJ clusters 1 to 45, often representing closely related, or single species. (ii) Several strains of the plant pathogenic coryneform bacteria assigned to the genus Clavibacter and Curtobacterium flaccumfaciens were found to be within one SJ cluster, indicating the high similarity between these genera. The current classification of species within the genera Curtobacterium and Clavibacter is unsatisfactory; a close relationship to Microbacterium suggests a reclassification into a redefined genus. Subspecies of Clavibacter and pathovars of Curtobacterium flaccumfaciens should only be retained for practical purposes. (iii) Bacteria belonging to the genus Corynebacterium, including Corynebacterium glutamicum, C. ammoniagenes, C. minutissimum, C. striatum, C. variabilis, C. kutscheri, C. diphtheriae, C. pseudotuberculosis, and ‘C. ulcerans’ formed a separate complex of the distinct, adjacent clusters 47 to 63. The physiologically inactive species C. mycetoides, C. pseudodiphtheriticum, C. xerosis, C. renale and C. pilosum were found in clusters 116 to 126. (iv) Differences between the Arthrobacter globiformis group and the Arthrobacter nicotianae group were reflected in the structure of the phenogram, species differentiation being based on only a few characters. (v) Strains assigned to the four species of the genus Brevibacterium were grouped into two clusters; the taxonomic implications are discussed. (vi) The results of the study are largely in line with a previously published numerical survey and with chemotaxonomic and genetic data. Suggestions for an improved classification for some species is given in addition to an extensive data-base on physiological reactions for differentiation purposes.

Diversity among Streptomyces Strains Causing Potato Scab

Eighty Streptomyces isolates, including 35 potato scab-inducing strains and 12 reference strains of Streptomyces scabies, were physiologically characterized by a total of 329 miniaturized tests. Overall similarities of all strains were determined by numerical taxonomy, with the unweighted average linkage (UPGMA) algorithm and simple matching (S(sm)) and Jaccard (S(j)) coefficients used as measures for similarity. Three cluster groups (A to C) were defined at a similarity level of 80.1% (S(sm)); these groups contained 14 clusters and 24 unclustered strains defined at a similarity level of 86.5% (S(sm)). Cluster group A contained strains phenotypically related to S. griseus or S. exfoliatus, whereas cluster group B contained strains which were phenotypically related to S. violaceus or S. rochei. The majority of the pathogenic isolates and reference strains were assigned to S. violaceus (57%) and S. griseus (22%). A DNA probe derived from the rRNA operon of S. coelicolor IMET 40271 was used to detect restriction fragment length polymorphisms (RELPs) among 40 pathogenic and nonpathogenic Streptomyces isolates. Southern blots revealed a high degree of diversity among the pathogenic strains tested. No significant correlation between numerical classification and RFLP grouping of Streptomyces strains could be revealed. The results obtained suggest that RFLP data are of minor importance in classification of Streptomyces species and that genes for pathogenicity determinants are spread among different Streptomyces species by mobilizable elements.

Isozyme analysis of Kenyan phlebotomine sandflies (Diptera: Ppsychodidae) by isoelectric focusing (IEF) on pharmacia phast system™

The isoenzyme profiles of nine sandfly species ( Phlebotomus duboscqi, P. elegonensi, P. martini, P. pedifer, Sergentomiya antennatus, S. bedfordi, S. garnhami, S. graingeri and S. schwetzi) from Kenya collected from the field and reared in the Medical Vectors Research Programme of the ICIPE were determined by isoelectric focusing (IEF) on mini ultra-thin polyacrylamide gels supplied by Pharmacia. Three of the nine isoenzymes screened (MDH, G-6-PD, PGM, ME, ICD, GAPDH, 6-PDG, HK and GPI), namely GPI, PGM and ME, gave banding patterns of taxonomic value. Cluster analysis of the simple matching coefficients gave two distinct groupings corresponding to previously described Sergentomyia and Phlebotomus respectively. However, S. garnhami, previously grouped in the genus Sergentomyia, was found to be associated with the genus Phlebotomus.

Phenotypic Characteristics of the Genus Agrobacterium.

One hundred and eight strains of Agrobacterium isolated from soil and from affected plants of 13 species, together with type and representative strains, were subjected to cluster analysis using 28 phenotypic characters out of the 36 examined. Data were analyzed by applying the unweighted average pair-group method (UPGMA) on the simple matching coefficient (SSM). At 80% SSM, 5 clusters were recognized, 3 of which corresponded to biovars 1, 2 and 3. These biovars were each grouped into a tight cluster, indicating that each of them is phenotypically homogeneous. Two additional clusters comprised (a) 3 overseas strains (IFO 13261 and 13260 of A. rubi, and NCPPB 1650 of A. tumefaciens), and (b) 6 Japanese strains of A. tumefaciens isolated from cherry and kiwifruit. The former cluster neighbored biovar 3 and the latter biovar 2, respectively. All strains in each biovar gave uniform reactions for the following 15 characters, which are therefore considered to be useful for the differentiation and the identification of the biovars: production of 3-ketolactose; esculin hydrolysis in Sneath's medium; arbutin hydrolysis; arginine dihydrolase in Thornley's medium; growth factor requirement; litmus milk reaction; pellicle in ferric ammonium citrate solution; growth at 35°C, and on New and Kerr medium; utilization of citrate, and L-tyrosine; oxidase by growth on PPGA; acid from dulcitol, and α-methyl-D-glucoside; and alkali from L-tartrate.

Distribution of epiphytic bacteria on olive leaves and the influence of leaf age and sampling time

Mesophilic heterotrophic, aerobic or facultatively anaerobic bacteria that grow on yeast tryptone glucose extract agar were isolated from the surface of olive leaves of 3 or 4 different ages in January, April, July, and October from 1984 to 1989. Unweighted average linkage cluster analysis on either the Jaccard coefficient or the simple matching coefficient recovered 1,701 representative strains in 32 phena defined at the 70% and 80% similarity level, respectively. Of these, 25 were identified to genus or lower level. From the identity of the representative strains, the frequency of occurrence among the phylloplane bacteria over the 6-year period was estimated at 51% forPseudomonas syringae, followed byXanthomonas campestris (6.7%),Erwinia herbicola (6%),Acetobacter aceti (4.7%),Gluconobacter oxydans (4.3%),Pseudomonas fluorescens (3.9%),Bacillus megaterium (3.8%),Leuconostoc mesenteroides subsp.dextranicum (3.1%),Lactobacillus plantarum (2.8%),Curtobacterium plantarum (2.2%),Micrococcus luteus (2.2%),Arthrobacter globiformis (1.4%),Klebsiella planticola (1.2%),Streptococcus faecium (1.2%),Clavibacter sp. (0.98%),Micrococcus sp. (0.82%),Serratia marcescens (0.81%),Bacillus subtilis (0.57%),Cellulomonas flavigena (0.4%),Erwinia sp. (0.37%),Zymomonas mobilis (0.3%),Bacillus sp. (0.29%),Alcaligenes faecalis (0.27%),Erwinia carotovora (0.08%), andPseudomonas aeruginosa (0.04%). Bacterial communities on leaves of a given age at a given time during any one year displayed a very similar structure but differed significantly from those on the leaves of the same age at a different time or on the leaves of a different age at any time during any one year. Communities on the leaves of a given age at a given time of the year were invariably dominated by one or another of only 9 taxa, which accounted for 22 to 98.5% of the isolates from those leaves. The communities on 10- and 13-month-old leaves were invariably made up of fewer taxa than those on younger leaves at the same time of the year.

A numerical taxonomic study of Propionibacterium strains from dairy sources

T.J. BRITZ AND K‐H.J. RIEDEL. 1991. Phenotypic results from 81 tests conducted on 73 propionibacteria, including five type strains, 22 reference strains, unidentified propionibacteria and strains isolated from dairy sources, were analysed by numerical taxonomy. Characters giving uniform results were excluded. With the simple matching coefficient and the single linkage cluster analysis, 61 cultures were recovered in five major clusters. Final linkage of all the Propionibacterium cultures examined was at the 77% S‐level. The results clearly showed that it was possible to distinguish between the ‘classical’ and ‘cutaneous’Propionibacterium spp., corresponding with the type habitat of each group. The major ‘classical’ clusters were equated with the P. freudenreichii, P. thoenii, P. jensenii and P. acidipropionici species, while the only major ‘cutaneous’ cluster was equated with the P. acnes species. The major clusters were identified by relating them to specific type strains and by comparing phenotypic characteristics. The differentiating characteristics of each cluster were determined. The largest cluster, representing 37% of the strains, was equated with P. jensenii but contained cultures that produced an atypical brown/red pigment. These strains, although positively identified as P. jensenii, could also be identified as the ‘old’‘P. rubrum’ species. Thus if pigmentation is used as differential characteristic two distinct groups of propionibacteria could be identified within the P. jensenii species.

Characterization of halotolerant Thermus isolates from shallow marine hot springs on S. Miguel, Azores

Summary: Fifteen yellow-pigmented halotolerant Thermus strains from shallow marine hot springs on a beach on S. Miguel, Azores, several isolates from terrestrial hot springs on S. Miguel and mainland Portugal, and four reference strains were subjected to a numerical taxonomy study based on 61 characters by unweighted average linkage analysis (UPGMA) using the simple matching (S SM) coefficient. This analysis produced four clusters at the 75% similarity level. Two clusters, A and B, were composed of halotolerant strains from the beach hot springs and one strain isolated inland, all of which also grew at 80°C; cluster C was composed of strains from one hot spring in mainland Portugal, while cluster D was composed of terrestrial strains from the Furnas area of S. Miguel. ‘T. thermophilus’ HB-8 and Thermus B were also halotolerant, also grew at 80 °C, and formed a large group at the 61% similarity level with the strains of clusters A and B.

Numerical Analysis and DNA Base Compositions of Some Thermophilic Bacillus Species

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 degrees 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.

Deleya salina sp. nov., a Moderately Halophilic Gram-Negative Bacterium

Deleya salina sp. nov., which was isolated from hypersaline habitats, is described. Our description is based on 26 strains that exhibit high levels of phenotypic similarity (simple matching coefficient, >74%) and DNA-DNA homology (<71%). The organisms are moderately halophilic gram-negative rods; growth occurs at salt concentrations between 2.5 and 20% (wt/vol) (optimal growth occurs at a salt concentration of 5% [wt/vol]). D. salina is aerobic, nonmotile, and catalase and oxidase positive. The cells accumulate poly-β-hydroxybutyrate, and the G+C contents of the DNAs range from 60.4 to 64.2 mol%. The type strain is strain F8-11 (= ATCC 49509).

Numerical Taxonomy of Moderately Halophilic Gram-negative Rods Isolated from the Salar de Atacama, Chile

Summary A total of 161 moderately halophilic Gram-negative rods isolated from The Salar de Atacama, Northern Chile, were examined for 119 phenotypic characters including morphological, physiological, biochemical, nutritional and antimicrobial susceptibility tests. The results together with those from reference strains, were subjected to numerical analysis, using both, the Simple Matching (S SM ) and Jaccard (S J ) coefficients and clustered by the unweighted pair group method of association (UPGMA). Using the S SM coefficient and UPGMA clustering, five phenons were obtained at a 70% similarity level. Representative strains from each phenon were chosen to determine DNA base composition and cellular morphology by electron microscopy. Strains in phenon A were assigned to the genus Vibrio . Strains in the other four phenons could not be assigned to any recognised taxon but their similarities to the genera Acinetobacter (phenon B), Marinomonas (phenon C) and Alteromonas (phenons D and E) are discussed.

Polyphasic Taxonomic Study of the Genera Gordona and Tsukamurella Including the Description of Tsukamurella wratislaviensis sp. nov.

Representatives of the genera Gordona and Tsukamurella together with related actinomycetes were the subject of chemotaxonomic, numerical taxonomic and DNA homology studies. In the numerical analysis the organisms were examined for 116 unit characters and the data sorted using the simple matching, Jaccard and pattern coefficients; clustering was achieved using the unweighted pair group method with arithmetic averages algorithm. The numerical groupings were not affected by the statistics used or by test error, estimated at 1.9%. The numerical taxonomic data supported the integrity of the four validly described species of Gordona but indicated that the genus Tsukamurella might encompass a species in addition to Tsukamurella paurometabola. The putative new strains had chemical, enzymic, nutritional and tolerance properties consistent with their assignment to the genus Tsukamurella and formed a DNA homology group corresponding to the one formed by the Tsukamurella paurometabola strains. It is proposed that the new taxon be assigned to the genus Tsukamurella as Tsukamurella wratislaviensis.

Aeromonas hydrophila: Variability in biochemical characteristics of environmental isolates

A total of 161 strains, including 144 aeromonads, of which 100 had been isolated from water and sediment samples from the Chesapeake Bay, five clinical and 33 Anacostia River isolates of Aeromonas hydrophila, six Aeromonas sobria, and ten reference cultures were examined in a numerical taxonomy study in which each of the strains were examined for 56 unit characters. Similarity between strains was computed using the simple matching (SSM) and Jaccard (SJ) coefficients. The strains were clustered by unweighted average linkage and single linkage algorithms. Results of all analyses yielded similar clusterings of strains. Of the 161 strains included in the study, 148 were recovered in seven major clusters. A large cluster of Aeromonas hydrophila yielded two sub-clusters. From the results of the taxonomic analysis it is concluded that several biovars of Aeromonas hydrophila can be isolated from the aquatic environment, but geographical or site specific distribution of the biovars could not be detected.