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.

Balneatrix alpica gen. nov., sp. nov., a bacterium associated with pneumonia and meningitis in a spa therapy center.

In 1987, an outbreak of pneumonia and meningitis caused by an unknown bacterium occurred in a spa therapy centre. Nine isolates of this pathogen constituted a tight DNA hybridization group. rRNA-DNA hybridization and 16S rRNA sequencing showed that the studied bacteria represented a new branch in superfamily II (= gamma subclass) of the Proteobacteria, close to the genus Oceanospirillum. The new bacterium was highly polymorphic and, in young cultures, had curved Gram-negative cells, motile by polar single flagella. The new bacterium differed from the genus Oceanospirillum by its lacking the NaCl requirement and by reducing nitrate into nitrite, producing indole from tryptophan and producing acid from carbohydrates. The name Balneatrix alpica gen. nov., sp. nov. is proposed for the studied organism. The type strain is strain 4-87 (= CIP 103589).

Rapid identification of bacteria of the Comamonadaceae with amplified ribosomal DNA-restriction analysis (ARDRA).

Ribosomal rRNA gene fragments (rDNA) encompassing the 16S rDNA, the 16S-23S rDNA spacer region and part of the 23S rDNA of 95 strains belonging to 13 well-described taxa of the eubacterial family Comamonadaceae (beta subclass of the Proteobacteria or rRNA superfamily III) were enzymatically amplified using conserved primers. The fragments of approximately 2400 base pairs were subjected to restriction analysis. Restriction fragment length patterns obtained with HinfI enabled us to distinguish 9 of the 13 taxa studied. Restriction with CfoI was necessary to differentiate Acidovorax delafieldii from A. temperans and Hydrogenophaga flava from H. pseudoflava. The results indicate that amplified rDNA restriction analysis is a simple and reliable tool for the identification of bacterial species.

The catabolism of 3-ketolactose in Agrobacterium.

The existence of a novel enzyme, catalyzing the hydrolysis of 3-ketolactose, is described in the different genetic groups of the genus Agrobacterium. The enzyme differs from the other glycosidases formed by Agrobacterium during growth on lactose. The inducibility of the enzyme could be demonstrated in a strain from biotype 1, but not in a strain from biotype 2. The specific activity of the 3-ketolactose hydrolase is higher in extracts of strains belonging to biotype 2 than to biotype 1. The optimum pH of the enzyme in Tris-HCl buffer is 8.4-8.5. The K(m) value for 3-ketolactose is 2.2 × 10(-2) M. The 3-ketolactose hydrolase is stimulated by Mg(2+) and Mn(2+), and inhibited by Zn(2+). Mercaptoethanol promotes the reaction rate in extracts of strains of biotype 1 but not in extracts of strains of bio-type 2.

Numerical Analysis of Phenotypic Features and Protein Gel Electrophoregrams of a Wide Variety of Acetobacter strains. Proposal for the Improvement of the Taxonomy of the Genus Acetobacter Beijerinck 1898, 215.

Ninety-eight strains, representing all Acetobacter species and subspecies from the Approved Lists of Bacterial Names (Skerman et al., 1980), were examined in a numerical analysis of 177 phenotypic features and compared to ninety-eight Gluconobacter and seven Frateuria strains. Four phenons could be delineated, corresponding to Frateuria (phenon 1), A. aceti subsp. liquefaciens (phenon 2), Gluconobacter (phenon 3) and Acetobacter minus A. aceti subsp. liquefaciens (phenon 4). Acetobacter, Frateuria and Gluconobacter are well- could be distinguished. Comparison of the protein electrophoregrams of Acetobacter strains revealed a fairly high internal homogeneity within phenon 2, subphenons C and D. Strains of the subphenon E gave very divergent protein patterns. The following classificatory changes are proposed within the genus Acetobacter: (1) Acetobacter liquefaciens sp. nov. is proposed for the homogeneous phenon 2, containing all 12 A. aceti subsp. liquefaciens strains (% G + C range of 62.3 to 64.6; IAM 1834 as type strain); (2) for the homogeneous subphenon D containing 8 A. aceti subsp. aceti strains, the name Acetobacter aceti emend, should be retained (% G + C range of 55.9 to 59.5; NCIB 8621 as type strain); (3) for subphenon E, a heterogeneous group, containing a variety of Acetobacter subspecies (all with their type strain) the species name Acetobacter pasteurianus emend, is preserved with LMD 22.1 as type strain; this species has the broad % G + C range of 52.8 to 62.5; (4) for subphenon C, a new species, Acetobacter hansenii sp. nov. is proposed (% G + C range of 58.1 to 62.6, NCIB 8746 as type strain). Minimal descriptions and differentiating keys are provided.

A polyphasic approach towards the identification of strains belonging to Lactobacillus acidophilus and related species.

A set of 98 strains belonging to nine species of the Lactobacillus acidophilus rRNA-group have been analysed by SDS-PAGE of cellular proteins, RAPD-PCR and AFLP with fluorescently labeled primers in order to find improved methods for their identification. Strains of the following phenotypically highly similar species were examined: L. acidophilus, L. amylovorus, L. crispatus, L. johnsonii, L. gasseri, L. gallinarum, L. helveticus, L. iners and L. amylolyticus. Although the majority of the species can be differentiated by SDS-PAGE of whole-cell proteins, the latter technique showed poor discrimination between L. gasseri and L. johnsonii strains and between some strains of L. amylovorus and L. gallinarum. However, this study shows that the RAPD-PCR (using at least 3 different primers followed by numerical analysis of the combined patterns) and AFLP are most suitable genomic fingerprinting techniques for the differentiation of all the species listed above, and that databases for identification can be constructed, particularly when commercially available molecular tool-kits are used. The separate species status of the recently described L. amylolyticus and L. iners was fully confirmed.

Lactobacillus perolens sp. nov., a soft drink spoilage bacterium.

Lactic acid bacteria that are able to spoil soft drinks with low pH comprise a limited number of acidotolerant or acidophilic species of the genera Lactobacillus, Leuconostoc and Weissella. Various Gram-positive rods causing turbidity and off-flavour were isolated from orange lemonades. Physiological and biochemical studies including SDS-PAGE whole-cell protein analysis showed a homogeneous group of organisms. The 16S rRNA gene sequence analysis of two representatives revealed that they formed a phylogenetically distinct line within the genus Lactobacillus. All strains were facultatively heterofermentative, producing L-lactic acid. Based on the data presented a new species L. perolens is proposed. The name refers to the off-flavour caused by high amounts of diacetyl. The type strain of L. perolens is DSM 12744 (LMG 18936). A rRNA targeted oligonucleotide probe was designed that allows a fast and reliable identification of L. perolens.

A polyphasic taxonomic study of Chryseobacterium strains isolated from dairy sources.

A polyphasic taxonomic study, employing protein electrophoresis (SDS-PAGE), gas chromatographic analysis of cellular fatty acids (FAME), mol% G+C determination and DNA-DNA hybridizations, was undertaken on 103 dairy isolates shown to belong to Chryseobacterium. Reference strains of the Chryseobacterium species, CDC group IIb and Embedobacter brevis were included. SDS-PAGE analysis yielded good differentiation between the investigated species. About half of the strains could be clustered into nine major groups while the other half occupied a separate position. With FAME analysis no clear differentiation of the Chryseobacterium species (except C. meningosepticum) and SDS-PAGE groups could be achieved. FAME analysis, however, gave good differentiation between the Chryseobacterium and Empedobacter strains. The mol% G+C of the isolates tested, ranged between 36.4 and 39.0. The combination of SDS-PAGE and DNA-DNA hybridization identified a large group of dairy isolates as C. indologenes, one isolate as C. gleum and two new genotypic groups, comprising five and 15 dairy isolates respectively, emerged from the polyphasic study. Another large part of strains have a separate or uncertain position in Chryseobacterium and remained classified as Chryseobacterium species CDC group IIb.

Differentiation of Lactobacillus plantarum, L. pentosus and L. paraplantarum species by RAPD-PCR and AFLP.

Two high-resolution genotypic techniques (RAPD-PCR and AFLP) were evaluated for their possibility to discriminate the species Lactobacillus plantarum, Lactobacillus pentosus and Lactobacillus paraplantarum and to type these taxa at the infra-species level. In total 23 strains of L. plantarum, three strains of L. pentosus, two strains of L. paraplantarum and two related strains for which the species assignment was not clear, were studied. For RAPD-PCR, suitable oligonucleotides and amplification conditions were selected and tested. For AFLP, a double digest of total genomic DNA was used and a subset of restriction fragments was selectively amplified and visualised using different primer combinations. Both methodologies generated, species-specific electrophoretic profiles. Moreover, the presence of distinct subgroups was revealed within the species L. plantarum.

Rahnella aquatilis, a potential contaminant in lager beer breweries.

The species Rahnella aquatilis has been isolated mostly from water, soil, and, in a few cases, from human clinical specimens; little is known about its ecological role. The application of polyacrylamide gel electrophoresis of soluble proteins, DNA-DNA hybridizations and API 20 E systems has shown that Rahnella aquatilis might also be encountered as a contaminant in lager beer breweries.

Identification of Enterococcus species isolated from foods of animal origin.

Enterococci isolated from a large variety of fresh and prepared foods of animal origin during routine microbiologic control tests in a distribution firm, were identified to species level using API 20 STREP galleries supplemented with conventional tests, rapid ID32 STREP galleries and SDS-PAGE analysis. API 20 STREP tests correctly identified 77% of the strains, mainly Enterococcus faecium and E. faecalis. A simple presumptive identification scheme based on pigmentation, tetrazolium reduction and acid production from mannitol and raffinose identified 90% of the strains. More complex procedures were necessary to identify the remaining strains. Nearly all strains isolated from hard cheeses and prepared cheese-meat combinations were identified as E. faecium while E. faecalis was the most frequent species in crustaceans. In meat and in prepared meat products E. faecium, E. faecalis and less frequently E. hirae/E. durans were found. Three of four E. gallinarum strains were isolated from products containing turkey meat.

Identification and grouping of bacteria by numerical analysis of their electrophoretic protein patterns.

Improved methods for the identification and grouping of bacteria by polyacrylamide gel electrophoresis of soluble proteins are described. Electrophoretic protein patterns were obtained in rigorously standardized comditions. The results were much more reproducible than any described previously. Some of the factors affecting reproducibility were; growth conditions, time and speed of centrifugation of extracts, and conditions of gel electrophoresis. Protein patterns were compared by computing correlation coefficients from normalized densitometric tracings and clustering the strains by the unweighted average pair group method. As model systems, both Agrobacterium and Zymomonas were used because of differences in the sharpness of the peaks. The methodwas applied to 42 Agrobacterium strains. The agreement with the results of clustering by either phenotypic tests or DNA:DNA hybridization was excellent. Computerized comparisons of electrophoretic protein patterns can be a fast, easy and powerful tool for classification and identification of bacteria.

High-resolution genotypic analysis of the genus Aeromonas by AFLP fingerprinting.

We investigated the ability of a recently developed genomic fingerprinting technique, named AFLP, to differentiate the 14 currently defined DNA hybridization groups (HGs) in the genus Aeromonas. We also determined the taxonomic positions of the phenospecies Aeromonas allosaccharophila, Aeromonas encheleia, Aeromonas enteropelogenes, and Aeromonas ichthiosmia, which have not been assigned to HGs yet. A total of 98 Aeromonas type and reference strains were included in this study. For the AFLP analysis, the total genomic DNA of each strain was digested with restriction endonucleases ApaI and TaqI. Subsequently, restriction fragments were selectively amplified under high-stringency PCR conditions. The amplification products were electrophoretically separated on a polyacrylamide gel and visualized by autoradiography. Following high-resolution densitometric scanning of the resulting band patterns, AFLP data were further processed for a computer-assisted comparison. A numerical analysis of the digitized fingerprints revealed 13 AFLP clusters which, in general, clearly supported the current Aeromonas taxonomy derived from DNA homology data. In addition, our results indicated that there is significant genotypic heterogeneity in Aeromonas eucrenophila (HG6), which may lead to a further subdivision of this species. A. allosaccharophila and A. encheleia did not represent a separate AFLP cluster but were found to be genotypically related to HG8/10 and HG6, respectively. In addition, the results of the AFLP analysis also confirmed the phylogenetic findings that A. enteropelogenes and A. ichthiosmia are in fact identical to Aeromonas trota (HG13) and Aeromonas veronii (HG8/10), respectively. The results of this study clearly show that the AFLP technique is a valuable new high-resolution genotypic tool for classification of Aeromonas species and also emphasize that this powerful DNA fingerprinting method is important for bacterial taxonomy in general.

Streptococcus intestinalis Robinson et al. 1988 and Streptococcus alactolyticus Farrow et al. 1984 are phenotypically indistinguishable.

The one-dimensional whole-cell protein patterns and a variety of biochemical characteristics of the type and reference strains of Streptococcus intestinalis and Streptococcus alactolyticus were studied. All the data revealed that strains of both species were indistinguishable. Reported differences in haemolytic activity and presence of Lancefield antigens were not reproduced. All strains were alpha-haemolytic. The S. intestinalis type strain possessed the group G antigen, but a second S. intestinalis reference strain and all of the S. alactolyticus strains possessed the group D antigen. All strains produced urease activity (albeit some after prolonged incubation), a characteristic considered important for S. intestinalis. Given the congruence between whole-cell protein electrophoresis and percentage of DNA-DNA hybridization, these data suggest that Streptococcus intestinalis Robinson et al. 1988 is a junior synonym of Streptococcus alactolyticus Farrow et al. 1984.

Application of temperature-gradient gel electrophoresis in taxonomy of coryneform bacteria.

Strains belonging to the Gram-positive coryneform soil bacteria were screened genotypically by temperature-gradient gel electrophoresis (TGGE). This method allows the sequence-specific separation of amplified fragments of 16S rRNA genes. A total of 115 reference strains representing the majority of the species of the genera Aeromicrobium, Agromyces, Arthrobacter, Aureobacterium, Cellulomonas, Curtobacterium, Nocardioides and Terrabacter were characterized. Depending on the genus investigated, the resolution limit of the technique appeared to be at the species or genus level or intermediate between the two. Aberrant TGGE profiles of strains within particular taxa revealed genomic heterogeneity and generic misclassification of nine strains studied. Beyond that, indications of 16S rRNA gene heterogeneity were found within the genomes of three Curtobacterium strains. The misclassifications revealed by TGGE were confirmed using whole-cell fatty acid methyl ester analysis and subsequent comparison with a database. TGGE has been demonstrated to be a useful tool in bacterial taxonomy.

L-Sorbose metabolism in Agrobacterium tumefaciens.

The pathway of L-sorbose metabolism in Agrobacterium tumefaciens strain B6 was determined to be: L-sorbose leads to D-glucitol (sorbitol) leads to D-fructose leads to D-fructose-6-phosphate leads to D-glucose-6-phosphate. The reduction of L-sorbose and the oxidation of D-glucitol were mediated by NADPH- and NAD+-linked oxidoreductases, respectively. The intermediates, D-glucitol and D-fructose, were isolated from in vitro reaction mixtures by column chromatography on Dowex 1-borate, and identified enzymatically. D-Fructose was identified chemically by its 1H-NMR spectrum and the IR spectrum and the melting point of the fructosazone. D-Glucitol was characterized chemically by the melting point and the IR spectrum of its hexaacetate. A. tumefaciens ICPB TT111, a representative of another genetic race of Agrobacterium, lacked L-sorbose reductase and therefore failed to grow on L-sorbose; it grew normally on D-glucitol.

Numerical analysis of electrophoretic protein patterns of 'Achromobacter' group B, E and F strains from human blood.

Thirty-two clinical strains representing 'Achromobacter' groups B, E and F were characterized by one-dimensional SDS-PAGE of cellular proteins. All the strains were isolated from blood samples from hospital patients in the United Kingdom. The protein patterns, which contained 40 to 45 discrete bands, were highly reproducible and were used as the basis for a numerical analysis which included all the protein bands. The 32 'Achromobacter' strains formed two clusters at the 77% S level. The first, phenon 1, included the 28 group B and the two group E strains and the second, phenon 2, contained the two strains of group F. The strains in each phenon were characterized by a clearly distinct pattern of protein bands. Phenon 1 could be further divided at the 87% S level into three subphenons which correlated with differences in the principal bands found between 40.0 and 42.5 kD. Strains of group E clustered with group B strains from which they could not be distinguished by protein patterns. We conclude that high resolution PAGE combined with computerized analysis of protein patterns provides a useful method for the classification of this group of bacteria. Reference strains of each of the PAGE types identified are available from NCTC for inclusion in future studies.