ADANSONIAN ANALYSIS AND DEOXYRIBONUCLEIC ACID BASE COMPOSITION OF SOME GRAM-NEGATIVE BACTERIA

The current status on the taxonomy of Pseudomonas revisited: An update

The genus Pseudomonas described in 1894 is one of the most diverse and ubiquitous bacterial genera which encompass species isolated worldwide. In the last years more than 70 new species have been described, which were isolated from different environments, including soil, water, sediments, air, animals, plants, fungi, algae, compost, human and animal related sources. Some of these species have been isolated in extreme environments, such as Antarctica or Atacama desert, and from contaminated water or soil. Also, some species recently described are plant or animal pathogens. In this review, we revised the current status of the taxonomy of genus Pseudomonas and the methodologies currently used for the description of novel species which includes, in addition to the classic ones, new methodologies such as MALDI-TOF MS, MLSA and genome analyses. The novel Pseudomonas species described in the last years are listed, together with the available genome sequences of the type strains of Pseudomonas species present in different databases.

Correlation of taxonomic criteria for a collection of marine bacteria

Numerical taxonomy was done on 208 strains of marine bacteria. The collection was segregated into eight groups, seven of which contained Vibrio sp. Nucleic acid base ratio studies on a typical Vibrio sp. from each group and other genera were done. The phenotypically different Vibrio sp. had a narrow range of base ratios. The other genera had base ratios more similar to the base ratios reported for their genus than to each other as marine bacteria. The taxonomic groups are compared with generic classification and the strains' sources of isolations.

TAXONOMY OF PSEUDOMONAS PISCICIDA (BEIN) BUCK, MEYERS, AND LEIFSON

Hansen, A. J. (University of Idaho, Moscow), O. B. Weeks, and R. R. Colwell. Taxonomy of Pseudomonas piscicida (Bein) Buck, Meyers, and Leifson. J. Bacteriol. 89:752-761. 1965.-Twenty strains of marine bacteria showing the properties of pigmentation and icthyotoxicity were studied for selected physiological features. A quantitative taxonomic analysis with an electronic computer was performed. Eighteen species of Pseudomonas were included in the computer analysis as reference strains. The marine collection formed a homogeneous cluster, 80% similarity, and showed a 67 to 70% similarity to certain of the Pseudomonas species: P. atlantica, P. geniculata, P. synxantha, and P. taetrolens. The marine strains are treated as a phenon describing the species P. piscicida. The species was characterized by the hypothetical Median Organism concept; P. piscicida 14 corresponded most closely to the Median Organism.

SIMILARITY OF XANTHOMONAS AND PSEUDOMONAS DEOXYRIBONUCLEIC ACID

De Ley, J. (State University, Ghent, Belgium), and S. Friedman. Similarity of Xanthomonas and Pseudomonas deoxyribonucleic acid. J. Bacteriol. 89:1306-1309. 1965.-Pronounced deoxyribonucleic acid (DNA) hybridization was detected with the DNA-agar method within the group of Xanthomonas and between Xanthomonas and Pseudomonas. Sheared, denatured C(14)-DNA from X. pelargonii hybridized 80 to 100% with high molecular weight, denatured agar-bound DNA from eight different Xanthomonas nomenspecies. The near identity of the DNA in these nine strains favors their inclusion in one genetic species, for which the name Xanthomonas campestris is proposed. In addition, 60 to 80% of the Xanthomonas DNA hybridized with DNA from several Pseudomonas strains. These results are evidence of the close genetic relationship between the two genera.

Identification of Proteus penneri sp. nov., formerly known as Proteus vulgaris indole negative or as Proteus vulgaris biogroup 1

The name Proteus penneri sp. nov. is proposed for a group of organisms previously called Proteus vulgaris indole negative or P. vulgaris biogroup 1. All of these strains were salicin negative, esculin negative, and chloramphenicol resistant (zone size, less than 14 mm). DNA relatedness studies indicated that when DNA from P. penneri strain 1808-73 was labeled and tested against unlabeled DNA from 13 other P penneri strains, a highly related group was formed (88 to 99% relatedness at 60 degrees C and 67 to 99% relatedness at 75 degrees C). Strain 1808-73 (ATCC 33519) is proposed as the type strain of P. penneri. In this study, two distinct groups of indole-positive P. vulgaris strains were also apparent. The first group (defined as P. vulgaris biogroup 2) was indole positive, salicin positive, and esculin positive, and the second group (defined as P. vulgaris biogroup 3) was indole positive, salicin negative, and esculin negative. The current type strain of P. vulgaris (ATCC 13315) belongs to biogroup 3. The DNA from P. penneri strains was not highly related to labeled DNA from the type strain of P. vulgaris (14 to 30% relatedness at 75 degrees C) or from P. vulgaris strain PR 1 (ATCC 29905), which belongs to biogroup 2 (27 to 33% relatedness at 75 degrees C). Strains of biogroup 2 were sensitive to chloramphenicol (zone size, greater than 19mm), and 10 of these strains formed a highly related group by DNA hybridization when DNA from PR 1 was labeled (64 to 100% relatedness at 60 degrees C and 70 to 100% relatedness at 75 degrees C), but they were not highly relatedness to the type strain of P. vulgaris (51 to 68% relatedness at 60 degrees C and 14 to 44% relatedness at 75 degrees C). Further DNA relatedness studies are needed on strains of biogroup 3 before a definitive taxonomic proposal can be made for these two indole-positive biogroups.

Identification of Vibrio hollisae sp. nov. from patients with diarrhea

The name Vibrio hollisae (synonym = Special Bacteriology group EF-13) is proposed for a new group of 16 strains that occurred in stool cultures of patients with diarrhea. V. hollisae is a small gram-negative rod, which is motile with a single polar flagellum. No lateral or peritrichous flagella were observed, even when it was grown on a solid medium. Sodium chloride is required for growth, so V. hollisae is a halophilic vibrio. Strains were positive (36 degrees C, 24 or 48 h) for oxidase (Kovacs), indole production, nitrate reduction to nitrite, and fermentation of D-glucose (acid, no gas), L-arabinose, D-galactose, and D-mannose. Strains were negative for the following tests often used in enteric bacteriology: lipase (corn oil); deoxyribonuclease; gelatinase; methyl red; Voges-Proskauer; utilization of citrate, acetate, and malonate; L-lysine decarboxylase (Møllers); L-ornithine decarboxylase (Møllers); L-arginine dihydrolase (Møllers); growth in KCN medium; and acid production from D-adonitol, D-arabitol, cellobiose, dulcitol, erythritol, glycerol (25% delayed positive at 7 days), i-(myo)-inositol, lactose, maltose, D-mannitol, melibiose, alpha-methyl-D-glucoside, mucate, raffinose, L-rhamnose, salicin, D-sorbitol, sucrose, trehalose, and D-xylose. None of the strains was motile (semisolid medium) at 36 degrees C at 48 h, but by 7 days 88% were motile. The strains did not grow within 2 days when plated on thiosulfate-citrate-bile salts-sucrose (TCBS) agar or MacConkey agar, but they grew on sheep blood agar and marine agar. By DNA-DNA hybridization (75 degrees C, hydroxyapatite with (32)P), V. hollisae was only 0 to 4% related to 21 named species in Vibrio and Photobacterium. The type strain is designated ATCC 33564, which has a mean guanineplus-cytosine content in DNA of 50 mol%. With the disk diffusion method V. hollisae had relatively large zones of inhibition around penicillin, ampicillin, carbenicillin, cephalothin, colistin, polymyxin B, streptomycin, kanamycin, gentamicin, tetracycline, chloramphenicol, and sulfadiazine. Future studies should focus on the isolation of this new vibrio and its ecology and relationship to human diseases.

Host factor for coliphage Qbeta RNA replication is present in Pseudomonas putida

Host Factor (HF)1, is a 12000 molecular weight polypeptide that is found in uninfected Escherichia coli and is required as a hexamer along with Qbeta replicase for in vitro replication of Qbeta phage RNA. It has recently been found to be associated with ribosomes and to bind tightly to poly(A). We report here the identification and purification of HF from Pseudomonas putida. HF can be detected in crude extracts by both functional activity in the Qbeta RNA replication assay and by immunodiffusion with antibody made against E. coli HF. HF from E. coli and P. putida chromatograph similarly on DEAE-cellulose and phosphocellulose. They have similar but not identical molecular weights as judged by SES-polyacrylamide gel electrophoresis. Like E. coli HF, P. putida HF was found to be associated with ribosomes and to bind tightly to poly(A). Furthermore, the pure protein from P. putida has full funcitonal activity in the in vitro Qbeta RNA replication assay. The findings that HF has been conserved during evolution, is associated with ribosomes, and binds poly(A), suggest that HF may be an important translational element in uninfected cells and that its role involves an interaction with RNA.

Vibrio psychroerythrus sp. n.: classification of the psychrophilic marine bacterium, NRC 1004

A red-pigmented organism, formerly known as marine psychrophile NRC 1004, has been classified as Vibrio psychroerythrus sp. n. Classification was mainly based on morphology, the ability of the organism to oxidize and ferment glucose, its sensitivity to vibriostat 0/129, and its deoxyribonucleic acid base composition of 40.0 moles% guanine plus cytosine, determined by thermal denaturation. The organism gave positive reactions for catalase, oxidase, and starch hydrolysis and produced acid from maltose and dextrin but not from arabinose. It was indole- and citrate-negative and reduced nitrate to nitrite without producing gas.

Taxonomy of aerobic marine eubacteria

Two hundred and eighteen strains of nonfermentative marine bacteria were submitted to an extensive morphological, physiological, and nutritional characterization. All the strains were gram-negative, straight or curved rods which were motile by means of polar or peritrichous flagella. A wide variety of organic substrates served as sole sources of carbon and energy. The strains differed extensively in their nutritional versatility, being able to utilize from 11 to 85 carbon compounds. Some strains had an extracellular amylase, gelatinase, lipase, or chitinase and were able to utilize n-hexadecane and to denitrify. None of the strains had a yellow, cell-associated pigment or a constitutive arginine dihydrolase system, nor were they able to hydrolyze cellulose or agar. The results of the physiological and nutritional characterization were submitted to a numerical analysis which clustered the strains into 22 groups on the basis of phenotypic similarities. The majority of these groups were separable by a large number of unrelated phenotypic traits. Analysis of the moles per cent guanine plus cytosine (GC) content in the deoxyribonucleic acid of representative strains indicated that the peritrichously flagellated groups had a GC content of 53.7 to 67.8 moles%; polarly flagellated strains had a GC content of 30.5 to 64.7 moles%. The peritrichously flagellated groups were assigned to the genus Alcaligenes. The polarly flagellated groups, which had a GC content of 43.2 to 48.0 moles%, were placed into a newly created genus, Alteromonas; groups which had a GC content of 57.8 to 64.7 moles% were placed into the genus Pseudomonas; and the remaining groups were left unassigned. Twelve groups were given the following designations: Alteromonas communis, A. vaga, A. macleodii, A. marinopraesens, Pseudomonas doudoroffi, P. marina, P. nautica, Alcaligenes pacificus, A. cupidus, A. venustus, and A. aestus. The problems of assigning species of aerobic marine bacteria to genera are discussed.

Polyphasic taxonomy of the genus vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species

A set of 86 bacterial cultures, including 30 strains of Vibrio cholerae, 35 strains of V. parahaemolyticus, and 21 representative strains of Pseudomonas, Spirillum, Achromobacter, Arthrobacter, and marine Vibrio species were tested for a total of 200 characteristics. Morphological, physiological, and biochemical characteristics were included in the analysis. Overall deoxyribonucleic acid (DNA) base compositions and ultrastructure, under the electron microscope, were also examined. The taxonomic data were analyzed by computer by using numerical taxonomy programs designed to sort and cluster strains related phenetically. The V. cholerae strains formed an homogeneous cluster, sharing overall S values of >/=75%. Two strains, V. cholerae NCTC 30 and NCTC 8042, did not fall into the V. cholerae species group when tested by the hypothetical median organism calculation. No separation of "classic" V. cholerae, El Tor vibrios, and nonagglutinable vibrios was observed. These all fell into a single, relatively homogeneous, V. cholerae species cluster. V. parahaemolyticus strains, excepting 5144, 5146, and 5162, designated members of the species V. alginolyticus, clustered at S >/=80%. Characteristics uniformly present in all the Vibrio species examined are given, as are also characteristics and frequency of occurrence for V. cholerae and V. parahaemolyticus. The clusters formed in the numerical taxonomy analyses revealed similar overall DNA base compositions, with the range for the Vibrio species of 40 to 48% guanine plus cytosine. Generic level of relationship of V. cholerae and V. parahaemolyticus is considered dubious. Intra- and intergroup relationships obtained from the numerical taxonomy studies showed highly significant correlation with DNA/DNA reassociation data.

Polyphasic taxonomy of the genus Vibrio: polynucleotide sequence relationships among selected Vibrio species

Polynucleotide relationships among selected Vibrio species were examined by means of deoxyribonucleic acid (DNA) reassociation reactions and chromatography on hydroxyapatite. Relative levels of intraspecific DNA duplex formation (V. cholerae-V. cholerae and V. parahaemolyticus-V. parahaemolyticus) were found to be high at 60 C (>80%), and only minimally reduced at 75 C. Interspecific DNA duplexes between V. cholerae DNA and that of the non-cholera vibrios also exhibited high relative levels of formation at 60 C (>80%) and, with one exception, were only slightly reduced at 75 C. The thermal stability of these duplexes formed at 60 or 75 C was virtually identical to that of homologous V. cholerae DNA duplexes. The degree of reassociation and the thermal stability of V. cholerae-non-cholera vibrio DNA duplexes suggests relatively little evolutionary divergence in these organisms. In all other interspecific DNA reassociation reactions, only low levels of DNA duplex formation were noted at 60 C (<25%), and these were drastically reduced (>50%) at 75 C. The degree of nucleotide sequence divergence indicated by these reactions suggests that these Vibrio species are not significantly related to V. cholerae or V. parahaemolyticus. Reassociation reactions between V. cholerae DNA and the DNA of V. parahaemolyticus indicated these species were not significantly related to each other.

Reexamination of the association between melting point, buoyant density, and chemical base composition of deoxyribonucleic acid

The equations currently used for the calculation of the chemical base composition of deoxyribonucleic acid (DNA), expressed as moles per cent guanine plus cytosine (% GC), from either buoyant density (rho) or midpoint of thermal denaturation (T(m)) were recalculated by using only sets of data on DNA determined with the same strains. All available information from the literature was screened and supplemented by unpublished data. The results were calculated by regression and correlation analysis and treated statistically. From the data on 96 strains of bacteria, it was calculated that% GC = 2.44 (T(m) - 69.4). T(m) appears to be unaffected by the substitution of cytosine by hydroxymethylcytosine. This equation is also valid for nonbacterial DNA. From the data on 84 strains of bacteria, the relation% GC = 1038.47 (-1.6616) was calculated. The constants in this equation are slightly modified when data on nonbacterial DNA are included. Both correlations differ only slightly from those currently used, but now they lean on a statistically sound basis. As a control, the relation between rho and T(m) was calculated from data of 197 strains; it agrees excellently with the above two equations.

Electrically heated cuvette chamber for deoxyribonucleic acid melting point determinations

An electrically heated cuvette chamber has been constructed and found to yield a deoxyribonucleic acid melting point of 91.5 C for Escherichia coli B, as previously reported.

Vibrio parahaemolyticus from the blue crab Callinectes sapidus in Chesapeake Bay

Strains of Vibrio parahaemolyticus, the etiologic agent of "Shirasu" food poisoning in Japan, were isolated from moribund blue crabs Callinectes sapidus and identified by biochemical and serological techniques.

Mutant of Bacterium paracoli 5099 with an altered DNA: identification as a Flavobacterium

A difference in the base composition of the DNA of Bacterium paracoli 5099 and of a "mutant" (No. 1975) derived from it was found. This is in accordance with the finding of others. However, biochemical tests revealed that the "mutant" was a Flavobacterium, whereas the parent strain belonged to a species of Escherichia. The base composition of the DNA of the "mutant" is similar to that reported for the DNA of Flavobacterium.

Properties of bacteria isolated from deep-sea sediments

Thirty-eight isolates were subjected to taxonomic analysis by computer. Of the 38 isolates, 31 were from sediment samples collected at depths from 9,400 to 10,400 meters in the Philippine and Marianas Trenches of the Pacific Ocean, and 7 cultures were from seawater samples collected at various depths from surface to 4,000 meters and from several locations in the Pacific Ocean. A total of 116 characteristics were determined for each isolate, coded, and transferred to punch cards. Similarity values were obtained by computer analysis, with the use of two recently developed computer programs. Five distinct phenetic clusters were observed from the numerical analyses. Four of the clusters were identified as species of the genus Pseudomonas, and one, as an aerogenic species of Aeromonas. Group IV was identified as pigmented Pseudomonas fluorescens, and the major cluster, consisting of groups I and II, which merged at a species level of similarity, was treated as a new species of Pseudomonas. The 38 strain data were compared with data for 132 marine and nonmarine strains previously subjected to computer taxonomic analysis. The barotolerant deep-sea strains, with the exception of the deep-sea P. fluorescens isolates, clustered separately from all other marine strains.

Numerical taxonomy of some named bacterial cultures

Forty-two cultures, representing 22 genera of bacteria, were tested for 123 properties. The data obtained were coded and subjected to Adansonian analysis by electronic computer. At 80% or greater similarity levels, six distinct groups were present: group 1, which contained the enterobacteria and Aeromonas; group 2 contained Pseudomonas, Vibrio cuneatus, Achromobacter, and Acinetobacter; group 3 contained Agrobacterium; group 4, the largest cluster, had two subgroups, 4a, containing the Gram-positive cocci, Nocardia, Mycobacterium, and Arthrobacter spp., and 4b, containing the streptomycetes; group 5 contained Cytophaga and group 6, containing Bacillus spp., Bacillus pantothenticus, and Protaminobacter alboflavus, did not share a high phenetic similarity with any of the above cultures and the clusters were regarded as isolated and single-item. The results confirmed earlier indications that the evaluation of taxonomic relationships by numerical methods can indicate areas in need of closer examination.

Purification and characterization of the beta-galactosidase of Aeromonas formicans

Rohlfing, S. R. (Western Reserve University, Cleveland, Ohio), and I. P. Crawford. Purification and characterization of the beta-galactosidase of Aeromonas formicans. J. Bacteriol. 91:1085-1097. 1966.-The beta-galactosidase of Aeromonas formicans was purified by diethylaminoethyl cellulose chromatography and gel filtration on Sephadex G-200. The properties of the enzyme molecule were compared with purified beta-galactosidase from Escherichia coli. The sedimentation coefficients and electrophoretic mobilities of the two enzymes were not significantly different; the electrophoretic mobility of urea-produced subunits of the two enzymes was also similar. The stabilities of the two enzymes to denaturing agents provided measurable differences; E. coli beta-galactosidase is relatively more heat-stable and more resistant to the action of urea. The amino acid compositions of the two proteins revealed significant differences in several amino acids, particularly alanine, arginine, glycine, and leucine. The comparisons cited suggest that A. formicans and E. coli are not completely unrelated, for their beta-galactosidases show considerable structural similarity.

Numerical survey of some bacterial taxa

Focht, D. D. (Iowa State University, Ames), and W. R. Lockhart. Numerical survey of some bacterial taxa. J. Bacteriol. 90:1314-1319. 1965.-A numerical analysis was made of 77 properties of each of 43 bacterial strains, representing 25 genera from 8 families in the orders Eubacteriales and Pseudomonadales. Four major groups were found, related to one another at approximately the same level of similarity: (1) a large cluster containing the subgroups (1a) Athiorhodaceae-Spirillaceae, (1b) Xanthomonas, and (1c) "inactive" Micrococcaceae-Achromobacteraceae; (2) a cluster containing the "active" Micrococcaceae and Lactobacillaceae; (3) the enterobacteria; and (4) Aeromonas. There was a sharp distinction between the branches of groups 1a, 1c, and 2. The composition of groups was essentially the same whether or not fermentation of carbohydrates (28 characters) was included in the analysis. Several individual strains, notably, Bacillus subtilis, Leuconostoc mesenteroides, Pseudomonas aeruginosa, and Erwinia amylovora, were related to none of the groups, and others (two species of Proteus, Flavobacterium devorans, and Lactobacillus casei) showed only minimal quantitative relationships with their groups. These results suggest that there may be significant variation in levels of similarity within microbial groups presently accorded equivalent taxonomic rank, and that some present distinctions among taxa, particularly at the generic level, cannot be confirmed on the basis of overall similarity.

Application of replica plating and computer analysis for rapid identification of bacteria in some foods. I. Identification scheme

A method was devised and tested for a quantitative identification of microbial flora in foods. The colonies developing on the initial isolation plates were picked with sterile toothpicks and inoculated on a master plate in prearranged spacing and order. The growth on the master plates was then replicated on a series of solid-agar plates containing differential or selective agents. The characteristic growth and physiological responses of microbial isolates to penicillin, tylosin, vancomycin, streptomycin, chloramphenicol, neomycin, colistin, and to S S Agar, Staphylococcus Medium No. 110, and Potato Dextrose Agar were recorded, together with Gram reaction and cell morphology. This information was then fed into an IBM 1410 digital computer which grouped and analyzed each isolate into 10 microbial genera, or groups, according to the identification key. The identification scheme was established by use of reference culture studies and from the literature. This system was used to analyze the microbial flora in dover sole (Microstomus pacificus) and ground beef. The method described in this article enables one to examine large numbers of microbial isolates with simplicity.

ADANSONIAN ANALYSIS AND DEOXYRIBONUCLEIC ACID BASE COMPOSITION OF SERRATIA MARCESCENS

Colwell, R. R. (Georgetown University, Washington, D.C.), and M. Mandel. Adansonian analysis and deoxyribonucleic acid base composition of Serratia marcescens. J. Bacteriol. 89:454-461. 1965.-A total of 33 strains of Serratia marcescens were subjected to Adansonian analysis for which more than 200 coded features for each of the organisms were included. In addition, the base composition [expressed as moles per cent guanine + cytosine (G + C)] of the deoxyribonucleic acid (DNA) prepared from each of the strains was determined. Except for four strains which were intermediate between Serratia and the Hafnia and Aerobacter group C of Edwards and Ewing, the S. marcescens species group proved to be extremely homogeneous, and the different strains showed high affinities for each other (mean similarity, S = 77%). The G + C ratio of the DNA from the Serratia strains ranged from 56.2 to 58.4% G + C. Many species names have been listed for the genus, but only a single clustering of the strains was obtained at the species level, for which the species name S. marcescens was retained. S. kiliensis, S. indica, S. plymuthica, and S. marinorubra could not be distinguished from S. marcescens; it was concluded, therefore, that there is only a single species in the genus. The variety designation kiliensis does not appear to be valid, since no subspecies clustering of strains with negative Voges-Proskauer reactions could be detected. The characteristics of the species are listed, and a description of S. marcescens is presented.

Characteristics of non-cholera Vibrios isolated from cases of human diarrhoea

Eighty-two organisms tentatively identified as non-cholera vibrios were isolated from cases of diarrhoea occurring in East Pakistan. In 19 well-studied cases they were the predominant organism recovered, and a rise in agglutinating-antibody titre was found in six of these cases.Because of this additional evidence that non-cholera vibrios cause diarrhoeal disease, it was necessary to evaluate simple screening tests as a means of recognizing them. It was found that all organisms that produced a gelatinase "zone", had typical vibrio morphology on microscopic examination, produced colonies showing a characteristic picture when examined by oblique light microscopy, and gave a positive "string" test were vibrios. Agglutination tests with vibrio O group I antiserum and with antirough vibrio serum distinguished the organisms from Vibrio cholerae. Since these organisms may be discarded by enteric diagnostic procedures directed mainly towards the isolation and identification of Salmonella and Shigella, it is recommended that the screening tests for these organisms be carried out in cases of diarrhoea of unknown etiology.