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J Swings

Publications and source records attributed to J Swings.

16 recordsLinked to original sources
PubMed1997

16S rRNA gene sequence analyses and inter- and intrageneric relationships of Xanthomonas species and Stenotrophomonas maltophilia.

The nearly complete, PCR-amplified, 16S rRNA gene sequences have been determined from the representative type strains of eight xanthomonad phena, including six validly described species of the genus Xanthomonas and Stenotrophomonas maltophilia. Pairwise sequence comparisons and phylogenetic analysis demonstrated that the xanthomonads comprise a monophyletic lineage-within the gamma-subclass of the Proteobacteria. Although the genus Xanthomonas was observed to comprise a cluster of very closely related species, the observed species-specific primary sequence differences were confirmed through sequencing additional strains belonging to the respective species.

Base Sequence↗
PubMed1997

Typing of the fish pathogen Listonella (Vibrio) anguillara by pyrolysis mass spectrometry.

Twenty-eight representatives of Listonella (Vibrio) anguillara serovars O1, O2 and O3 were compared by Curie-point pyrolysis mass spectrometry (PyMS). The representatives of serovars O1 and O3 formed discrete, homogeneous groups in ordination plots of the PyMS data. Strains from serovar O2 were recovered in two groups, one of which encompassed six strains including the type strain of the species and the reference strain for serovar O2, and the other included two strains which showed cross-reactions between serovars O2 and O5. The almost complete agreement found between the PyMS and the serological data suggests that pyrolysis mass spectrometry will prove to be an effective method for interstrain comparison within the species Listonella anguillara.

Animals↗
PubMed1997

Comparison of 16S ribosomal DNA sequences of all Xanthomonas species.

The phylogenetic relationships of all validly described species of the genus Xanthomonas and the type strain of Stenotrophomonas maltophilia were analyzed by sequencing and comparing 16S ribosomal DNAs (rDNAs). The two genera exhibited a mean sequence similarity value of 96.6%, corresponding to differences at 50 nucleotide positions on average. The species of the genus Xanthomonas exhibited relatively high levels of overall sequence similarity; the mean similarity value was 98.2%, which corresponds to an average of 14 mutual nucleotide differences. Within the genus Xanthomonas, a group containing Xanthomonas albilineans, Xanthomonas hyacinthi, Xanthomonas theicola, and Xanthomonas translucens clustered apart from the main Xanthomonas core, whereas Xanthomonas sacchari formed a third phylogenetic lineage. Due to the very restricted variability in 16S rDNA sequences within the genus Xanthomonas, rDNA signatures that have possible diagnostic value for differentiating the Xanthomonas species could not be determined with certainty. When sequence similarities were compared with DNA-DNA pairing data determined previously, there was only a limited correlation. This illustrates the different resolving powers of the techniques for determining phylogenetic hierarchies and for species delineation.

Base Sequence↗
PubMed1996

Isolation and identification of poly(3-hydroxyvalerate)-degrading strains of Pseudomonas lemoignei.

By using selective enrichment of polyhydroxyalkanoate-degrading bacteria and poly(3-hydroxyvalerate)-containing granules from Chromobacterium violaceum as the carbon source, 10 new Pseudomonas lemoignei strains were isolated; these strains were able to degrade poly(3-hydroxyvalerate), as well as poly(3-hydroxybutyrate), in vitro. The new isolates were characterized and identified by comparing them with P. lemoignei LMG 2207(T) (T = type strain). Like P. lemoignei LMG 2207(T) cells, the cells of the 10 new isolates contained mainly hexadecenoic, hexadecanoic, octadecenoic, and dodecanoic acids, as well as hydroxylated fatty acids, and exhibited respiration in the presence of methylpyruvate, 3-hydroxybutyrate, and 4-hydroxybutyrate, but not in the presence of the 92 other carbon sources included in Biolog GN microplates. The protein patterns of the new isolates were almost identical to each other and very similar to the protein pattern of P. lemoignei LMG 2207(T). Some of the new isolates, but not P. lemoignei LMG 2207(T), contained megaplasmids that were about 200 kbp long. The 16S ribosomal DNA genes of strain A62, a representative of the 10 new isolates, and of P. lemoignei LMG 2207(T) exhibited more than 0.99 sequence similarity. The DNA-DNA reassociation value for two representative strains was 100%, and the levels of DNA-DNA reassociation between these strains and the type strain were 60 and 61%. The taxonomy of P. lemoignei is briefly discussed.

Bacterial Proteins↗
PubMed1996

Evaluation of the DNA fingerprinting method AFLP as an new tool in bacterial taxonomy.

We investigated the usefulness of a novel DNA fingerprinting technique, AFLP, which is based on the selective amplification of genomic restriction fragments by PCR, to differentiate bacterial strains at the subgeneric level. In totals, 147 bacterial strains were subjected to AFLP fingerprinting: 36 Xanthomonas strains, including 23 pathovars of Xanthomonas axonopodis and six pathovars of Xanthomonas vasicola, one strain of Stenotrophomonas, 90 genotypically characterized strains comprising all 14 hybridization groups currently described in the genus Aeromonas, and four strains of each of the genera Clostridium, Bacillus, Acinetobacter, Pseudomonas and Vibrio. Depending on the genus, total genomic DNA of each bacterium was digested with a particular combination of two restriction endonucleases and the resulting fragments were ligated to restriction halfsite-specific adaptors. These adaptors served as primer-binding sites allowing the fragments to be amplified by selective PCR primers that extend beyond the adaptor and restriction site sequences. Following electrophoretic separation on 5% (w/v) polyacrylamide/8.3 M urea, amplified products could be visualized by autoradiography because one of the selective primers was radioactively labelled. The resulting banding patterns, containing approximately 30-50 visualized PCR products in the size range 80-550 bp, were captured by a high-resolution densitoscanner and further processed for computer-assisted analysis to determine band-based similarity coefficients. This study reveals extensive evidence for the applicability of AFLP in bacterial taxonomy through comparison of the newly obtained data with results previously obtained by well-established genotypic and chemotaxonomic methods such as DNA-DNA hybridization and cellular fatty acid analysis. In addition, this study clearly demonstrates the superior discriminative power of AFLP towards the differentiation of highly related bacterial strains that belong to the same species or even biovar (i.e. to characterize strains at the infrasubspecific level), highlighting the potential of this novel fingerprinting method in epidemiological and evolutionary studies.

Acinetobacter↗
PubMed1996

Polyphasic taxonomy, a consensus approach to bacterial systematics.

Over the last 25 years, a much broader range of taxonomic studies of bacteria has gradually replaced the former reliance upon morphological, physiological, and biochemical characterization. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them in a consensus type of classification, framed in a general phylogeny derived from 16S rRNA sequence analysis. In some cases, the consensus classification is a compromise containing a minimum of contradictions. It is thought that the more parameters that will become available in the future, the more polyphasic classification will gain stability. In this review, the practice of polyphasic taxonomy is discussed for four groups of bacteria chosen for their relevance, complexity, or both: the genera Xanthomonas and Campylobacter, the lactic acid bacteria, and the family Comamonadaceae. An evaluation of our present insights, the conclusions derived from it, and the perspectives of polyphasic taxonomy are discussed, emphasizing the keystone role of the species. Taxonomists did not succeed in standardizing species delimitation by using percent DNA hybridization values. Together with the absence of another "gold standard" for species definition, this has an enormous repercussion on bacterial taxonomy. This problem is faced in polyphasic taxonomy, which does not depend on a theory, a hypothesis, or a set of rules, presenting a pragmatic approach to a consensus type of taxonomy, integrating all available data maximally. In the future, polyphasic taxonomy will have to cope with (i) enormous amounts of data, (ii) large numbers of strains, and (iii) data fusion (data aggregation), which will demand efficient and centralized data storage. In the future, taxonomic studies will require collaborative efforts by specialized laboratories even more than now is the case. Whether these future developments will guarantee a more stable consensus classification remains an open question.

Amino Acid Sequence↗
PubMed1995

In situ biodegradation of poly(3-hydroxybutyrate) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) in natural waters.

The biodegradation of samples of poly(3-hydroxybutyrate)(P(3HB)), poly(3-hydroxybutyrate-co-10%-3-hydroxyvalerate)(P(3HB-co-10 %-3HV)), and poly 3-hydroxybutyrate-co-20%-3-hydroxyvalerate)(P(3HB-co-20%- 3HV)) was investigated in situ in natural waters. The degradation was studied by decrease in mass, molecular weight, and tensile strength. In two freshwater ponds the polymers were slowly degraded. After half a year of submersion the mass loss was less than 7%. After 358 days in a freshwater canal, 34% mass loss was recorded for the homopolymer, and 77% for the P(3HB-co-10%-3-HV) samples, while the P(3HB-co-20%-3HV) samples had completely disappeared. In seawater in the harbour of Zeebrugge, P(3HB) samples lost 31% of their initial mass, and the copolymers 49-52%, within 270 days. In all of these environments, the degradation rate was faster during the summer, when the temperature of the water was higher. No relevant changes in molecular weight could be detected, indicating that the degradation took place only at the surface of the samples. The degradation resulted in considerable loss of tensile strength of the copolymer samples. Ninety-two microorganisms, mainly bacteria, able to degrade P(3HB) in polymer overlayer plates, were isolated and identified by fatty acid analysis. The isolates from one freshwater pond belonged mainly to the bacterial genus Acidovorax, while the microorganisms from the other freshwater pond belonged to various bacterial genera, to Streptomyces, and to the mould genus Penicillium. Most of the 31 bacterial isolates from seawater were identified as Alteromonas haloplanktis. The results demonstrate that P(3HB) and P(3HB-co-3HV) samples are effectively biodegradable in natural waters under real-life conditions and reveal the biodiversity of the microflora responsible for this biodegradation.

Bacteria↗
PubMed1993

Microbial degradation of poly(3-hydroxybutyrate) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) in soils.

The microbial degradation of tensile test pieces made of poly(3-hydroxybutyrate) [P(3HB)] or a copolymer of 90% 3-hydroxybutyric acid and 10% 3-hydroxyvaleric acid was studied in soils incubated at a constant temperature of 15, 28, or 40 degrees C for up to 200 days. In addition, hydrolytic degradation in sterile buffer at temperatures ranging from 4 to 55 degrees C was monitored for 98 days. Degradation was measured through loss of weight (surface erosion), molecular weight, and mechanical strength. While no weight loss was recorded in sterile buffer, samples incubated in soils were degraded at an erosion rate of 0.03 to 0.64% weight loss per day, depending on the polymer, the soil, and the incubation temperature. The erosion rate was enhanced by incubation at higher temperatures, and in most cases the copolymer lost weight at a higher rate than the homopolymer. The molecular weights of samples incubated at 40 degrees C in soils and those incubated at 40 degrees C in sterile buffer decreased at similar rates, while the molecular weights of samples incubated at lower temperatures remained almost unaffected, indicating that molecular weight decrease is due to simple hydrolysis and not to the action of biodegrading microorganisms. The degradation resulted in loss of mechanical properties. From the samples used in the biodegradation studies, 295 dominant microbial strains capable of degrading P (3HB) and the poly(3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer in vitro were isolated and identified.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacteria↗
PubMed1992

Biodegradation of polyhydroxyalkanoates.

Degradation of poly(3-hydroxybutyrate) and copolymers with 3-hydroxyvaleric acid was investigated in natural environments, and the microorganisms involved were isolated and identified. The influence of abiotic and biotic factors on the degradation is discussed.

Bacteria↗
PubMed1990

Numerical analysis of 295 phenotypic features of 266 Xanthomonas strains and related strains and an improved taxonomy of the genus.

An extensive phenotypic description and an improved classification and nomenclature of the genus Xanthomonas are presented. A total of 266 strains obtained from different geographical areas, including representative strains of all species of the genus Xanthomonas and most pathovars of Xanthomonas campestris, as well as strains which might be genetically related to the genus Xanthomonas, were examined for 295 morphological, biochemical, and physiological features. Similarities among the strains were expressed numerically by using the coefficient of Sokal and Michener. Clustering was performed by using the unweighted average pair group method. The conclusions described below were reached. (i) The genus Xanthomonas comprises at least the following eight phena: X. campestris, Xanthomonas albilineans, Xanthomonas axonopodis, Xanthomonas fragariae, Xanthomonas populi, Xanthomonas maltophilia, Xanthomonas oryzae Swings et al. 1990, and X. campestris pv. graminis Egli and Schmidt 1982 [not X. campestris pv. graminis (Egli et al. 1975) ISPP List 1980]. (ii) X. populi (Ridé 1958) Ridé and Ridé 1978 is a separate species. (iii) X. maltophilia Swings et al. 1983 forms a separate species. (iv) X. campestris pv. oryzae ISPP List 1980 can no longer be regarded as pathovar of X. campestris, and its recent reclassification as a new species, X. oryzae (Swings et al., Int. J. Syst. Bacteriol. 40:309-311, 1990), is supported. (v) X. campestris pv. graminis Egli and Schmidt 1982 [not X. campestris pv. graminis (Egli et al. 1975) ISPP List 1980] seems to form a separate complex of highly related pathovars obtained from members of the Poaceae; the taxonomic implications of this are discussed. (vi) Strains of nearly all X. campestris pathovars cluster together in the X. campestris phenon. Within this species we were able to differentiate some entities on phenotypic grounds; these groups sometimes corresponded to named pathovars (e.g., X. campestris pv. manihotis, X. campestris pv. cassavae, X. campestris pv. phlei). In several other cases, pathovars were found to be heterogeneous. (vii) A number of dubious Pseudomonas species were identified as members of or as being close to Xanthomonas species. Both Pseudomonas betle and Pseudomonas hibiscicola are synonyms of X. maltophilia. We also confirmed that Pseudomonas mangiferaeindicae, Pseudomonas vitiswoodrowii, and Pseudomonas gardneri belong to X. campestris. (viii) Forty phenotypic features allow the differentiation of the eight Xanthomonas phena. (ix) A number of additional features of the genera Xanthomonas and Xylophilus are described.

Base Composition↗
PubMed1984

Differentiation between Xanthomonas campestris pv. oryzae, Xanthomonas campestris pv. oryzicola and the bacterial 'brown blotch' pathogen on rice by numerical analysis of phenotypic features and protein gel electrophoregrams.

Thirty-five Xanthomonas campestris pv. oryzae, fourteen X. campestris pv. oryzicola strains and six 'brown blotch' pathogens of rice, all of different geographical origin, were studied by numerical analysis of 133 phenotype features and gel electrophoregrams of soluble proteins, %G + C determinations and DNA:rRNA hybridizations. The following conclusions were drawn. (i) The Xanthomonas campestris pathovars oryzae and oryzicola display clearly distinct protein patterns on polyacrylamide gels and can be differentiated from each other by four phenotype tests. (ii) Both pathovars are indeed members of Xanthomonas which belongs to a separate rRNA branch of the second rRNA superfamily together with the rRNA branches of Pseudomonas fluorescens, Marinomonas, Azotobacter, Azomonas and Frateuria. (iii) 'Brown blotch' strains are considerably different from X. campestris pv. oryzae and oryzicola. They are not members of the genus Xanthomonas, but are more related to the generically misnamed. Flavobacterium capsulatum, Pseudomonas paucimobilis, Flavobacterium devorans and 'Pseudomonas azotocolligans' belonging in the fourth rRNA superfamily. (iv) No correlation was found between the virulence, pathogenic groups or geographical distribution of X. campestris pv. oryzae or oryzicola strains and any phenotypic or protein electrophoretic property or clustering.

Base Composition↗
PubMed1981

Gluconobacters from honey bees.

Fifty-six Gluconobacter strains and one Acetobacter strain were isolated from honey bees and their environment in three different regions in Belgium and identified phenotypically. Polyacrylamide gel electrophoresis of the soluble cell proteins showed that two different types exist within the Gluconobacter isolates: strains from type A were found in samples of the three regions, whereas strains from type B were only isolated in two of the three regions. Both types could occur in bees from the same region, from several hives of one bee keeper and from one hive. Strains from type A were almost identical with collection strain G. oxydans subsp. suboxydans NCIB 9018, whereas strains from type B constituted a new protein electrophoretic type within the genus Gluconobacter. Although Gluconobacter is apparently associated with honey bees, it is not known whether it is important or required for the bees or any hive product.

Animals↗
PubMed1981

The nitrogen requirements of Gluconobacter, Acetobacter and Frateuria.

The nitrogen requirements of 96 Gluconobacter, 55 Acetobacter and 7 Frateuria strains were examined. Only some Frateuria strains were able to grow on 0.5% yeast extract broth or 0.5% peptone broth. In the presence of D-glucose or D-mannitol as a carbon source, ammonium was used as the sole source of nitrogen by all three genera. With ethanol, only a few Acetobacter strains grew on ammonium as a sole nitrogen source. Single L-amino acids cannot serve as a sole source of carbon and nitrogen for growth of Gluconobacter, Acetobacter or Frateuria. The single L-amino acids which were used by most strains as a sole nitrogen source for growth are: asparagine, aspartic acid, glutamine, glutamic acid, proline and alanine. Some Acetobacter and Gluconobacter strains deaminated alanine, asparagine, glutamic acid, threonine, serine and proline. No Frateuria strain was able to develop on cysteine, glycine, threonine or tryptophan as a sole source of nitrogen for growth. An inhibitory effect of valine may explain the absence of growth on this amino acid. No amino acid is "essential" for Gluconobacter, Acetobacter or Frateuria.

Acetobacter↗