1
|
Scotta C, Mulet M, Sánchez D, Gomila M, Ramírez A, Bennasar A, García-Valdés E, Holmes B, Lalucat J. Identification and genomovar assignation of clinical strains of Pseudomonas stutzeri. Eur J Clin Microbiol Infect Dis 2012; 31:2133-9. [PMID: 22282021 DOI: 10.1007/s10096-012-1547-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 01/03/2012] [Indexed: 11/25/2022]
Abstract
The identification of Pseudomonas stutzeri clinical isolates through conventional phenotypic methods was compared with identification through partial rpoD gene sequencing. We observed that commercial phenotypic systems easily confuse P. stutzeri with other Pseudomonas species. We also demonstrated that most of the clinical strains of P. stutzeri herein studied (79%) belonged to genomovar 1 of the species. We propose the use of partial rpoD gene sequence analysis as a complementary molecular tool for the precise routine identification and genomovar assignation of P. stutzeri clinical isolates, as well as for typing and epidemiological studies.
Collapse
Affiliation(s)
- C Scotta
- Microbiología, Departamento de Biología, Universidad de las Islas Baleares, 07122, Palma de Mallorca, Islas Baleares, España.
| | | | | | | | | | | | | | | | | |
Collapse
|
2
|
Aguilera M, Monteoliva-Sánchez M, Suárez A, Guerra V, Lizama C, Bennasar A, Ramos-Cormenzana A. Paenibacillus jamilae sp. nov., an exopolysaccharide-producing bacterium able to grow in olive-mill wastewater. Int J Syst Evol Microbiol 2001; 51:1687-1692. [PMID: 11594596 DOI: 10.1099/00207713-51-5-1687] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Endospore-forming strains were isolated from corn-compost treated with olive-mill wastewater ('alpechin'). The strains were taxonomically studied and proposed as a novel Paenibacillus species. These organisms (strains B.3T, B.7 and B.9) were particularly distinguishable from other aerobic spore-forming species by their ability to grow optimally in 100% (v/v) olive-mill wastewater at 30 degrees C and pH 7.0 and concomitant production of an interesting exopolysaccharide. Chemotaxonomic analysis revealed that MK-7 was the predominant menaquinone, the major fatty acid was anteiso C15:0 and the cell wall contained meso-diaminopimelic acid. The DNA G+C content was 40.7 mol%. Comparative sequence analysis of 16S rDNA with different reference species from the genera Bacillus, Paenibacillus, Brevibacillus, Aneurinibacillus, Alicyclobacillus, Halobacillus, Virgibacillus, Amphibacillus, Coprobacillus and Gracilibacillus indicated that the isolated strains were highly related to the genus Paenibacillus. Strain B.3T formed an evolutionary lineage distinct from other species within the evolutionary radiation encompassing the genus Paenibacillus. Strain B.3T was a close relative of Paenibacillus polymyxa, but DNA-DNA relatedness data with this species was very low (relative binding ratio < 16%). Based on the morphological and physiological characteristics, as well as on the phylogenetic position determined by 16S rDNA analysis and DNA-DNA relatedness data, it is concluded that these strains should be designated a novel species, for which the name Paenibacillus jamilae sp. nov. is proposed. The type strain is B.3T (= CECT 5266T = DSM 13815T).
Collapse
|
3
|
Lünsdorf H, Strömpl C, Osborn AM, Bennasar A, Moore ER, Abraham WR, Timmis KN. Approach to analyze interactions of microorganisms, hydrophobic substrates, and soil colloids leading to formation of composite biofilms, and to study initial events in microbiogeological processes. Methods Enzymol 2001; 336:317-31. [PMID: 11398409 DOI: 10.1016/s0076-6879(01)36598-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
MESH Headings
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacterial Physiological Phenomena
- Base Sequence
- Biofilms/growth & development
- Chromatography, Gas
- Colloids
- DNA Fingerprinting
- DNA Primers/genetics
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- Microscopy, Electron
- Microscopy, Electron, Scanning
- Polymorphism, Restriction Fragment Length
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Soil Microbiology
- Spectrum Analysis
Collapse
Affiliation(s)
- H Lünsdorf
- Division of Microbiology, GBF, German Research Centre for Biotechnology, D-38124 Braunschweig, Germany
| | | | | | | | | | | | | |
Collapse
|
4
|
Guasp C, Moore ER, Lalucat J, Bennasar A. Utility of internally transcribed 16S-23S rDNA spacer regions for the definition of Pseudomonas stutzeri genomovars and other Pseudomonas species. Int J Syst Evol Microbiol 2000; 50 Pt 4:1629-1639. [PMID: 10939670 DOI: 10.1099/00207713-50-4-1629] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteria identified and classified as Pseudomonas stutzeri, on the basis of traditional criteria, are recognized to be markedly heterogeneous, such that a systematic phenotypic characterization has not been correlated with genotypic groupings (i.e. genomovars) based upon DNA-DNA similarities. The internally transcribed 16S-23S rDNA spacer (ITS1) regions of P. stutzeri were analysed with respect to the ability of these nucleic acid regions to differentiate and identify the genomic groups (i.e. genomovars) of P. stutzeri. The ITS1s of 34 strains of P. stutzeri were amplified by PCR and the PCR product was subjected to RFLP analysis, which allowed the differentiation and identification of the strains to their respective genomovars. Sequence determination and analysis of ITS1s supported further the results obtained by RFLP, i.e. nucleotide signatures were identified in strains belonging to different genomovars. The ITS1s of all strains of P. stutzeri contained the tandem tRNA(Ile)/tRNA(Ala) genes and did not exhibit distinct sequence heterogeneity between different operons of a strain. Phylogenetically informative variable sites were located, exclusively, in non-coding regions. The results of the RFLP and sequence analysis of ITS1s supported and correlated with the phylogenetic relationships estimated from 16S rRNA gene sequence comparisons and DNA-DNA hybridizations, offering an alternative tool for genomovar and species differentiation.
Collapse
|
5
|
Bennasar A, de Luna G, Cabrer B, Lalucat J. Rapid identification of Salmonella typhimurium, S. enteritidis and S. virchow isolates by polymerase chain reaction based fingerprinting methods. Int Microbiol 2000; 3:31-8. [PMID: 10963331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
In this study we used and evaluated three rapid molecular typing methods for the identification of three frequent, clinically significant Salmonella serovars on the basis of the ease, simplicity and reproducibility of the chosen methods. We determined the genetic diversity among several isolates of Salmonella enteritidis, S. typhimiurium and S. virchow, and compared them with other enterobacteria by using the repetitive extragenic palindromic (REP) sequences, the enterobacterial repetitive intergenic consensus (ERIC) sequences, and the 16S-23S rDNA intergenic spacer region (ITS 1). The objective was to evaluate their potential application to discriminate among members of the species Salmonella enterica subspecies enterica using the genetic diversity of the group found by genomic fingerprinting. The three different serovars of Salmonella studied gave reproducible and distinguishable profiles using whichever of the above mentioned polymerase chain reaction (PCR) methods assayed. The conserved patterns in each serovar allowed for easy differentiation from other serovars of Salmonella.
Collapse
MESH Headings
- Bacterial Typing Techniques
- Consensus Sequence
- DNA Fingerprinting/methods
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/genetics
- DNA, Ribosomal/isolation & purification
- Genetic Variation
- Genome, Bacterial
- Polymerase Chain Reaction
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- Reproducibility of Results
- Salmonella/classification
- Salmonella/genetics
- Salmonella/isolation & purification
- Salmonella enteritidis/genetics
- Salmonella enteritidis/isolation & purification
- Salmonella typhimurium/genetics
- Salmonella typhimurium/isolation & purification
- Species Specificity
Collapse
Affiliation(s)
- A Bennasar
- Department of Biology, Microbiology, University of the Balearic Islands, and Mediterranean Institute of Advanced Studies (CSIC-UIB), Spain.
| | | | | | | |
Collapse
|
6
|
Abraham WR, Strömpl C, Meyer H, Lindholst S, Moore ER, Christ R, Vancanneyt M, Tindall BJ, Bennasar A, Smit J, Tesar M. Phylogeny and polyphasic taxonomy of Caulobacter species. Proposal of Maricaulis gen. nov. with Maricaulis maris (Poindexter) comb. nov. as the type species, and emended description of the genera Brevundimonas and Caulobacter. Int J Syst Bacteriol 1999; 49 Pt 3:1053-73. [PMID: 10425763 DOI: 10.1099/00207713-49-3-1053] [Citation(s) in RCA: 159] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The genus Caulobacter is composed of prosthecate bacteria often specialized for oligotrophic environments. The taxonomy of Caulobacter has relied primarily upon morphological criteria: a strain that visually appeared to be a member of the Caulobacter has generally been called one without challenge. A polyphasic approach, comprising 16S rDNA sequencing, profiling restriction fragments of 16S-23S rDNA interspacer regions, lipid analysis, immunological profiling and salt tolerance characterizations, was used to clarify the taxonomy of 76 strains of the genera Caulobacter. Brevundimonas, Hyphomonas and Mycoplana. The described species of the genus Caulobacter formed a paraphyletic group with Caulobacter henricii, Caulobacter fusiformis, Caulobacter vibrioides and Mycoplana segnis (Caulobacter segnis comb. nov.) belonging to Caulobacter sensu stricto. Caulobacter bacteroides (Brevundimonas bacteroides comb. nov.), C. henricii subsp. aurantiacus (Brevundimonas aurantiaca comb. nov.), Caulobacter intermedius (Brevundimonas intermedia comb. nov.), Caulobacter subvibrioides (Brevundimonas subvibrioides comb. nov.), C. subvibrioides subsp. albus (Brevundimonas alba comb. nov.), Caulobacter variabilis (Brevundimonas variabilis comb. nov.) and Mycoplana bullata belong to the genus Brevundimonas. The halophilic species Caulobacter maris and Caulobacter halobacteroides are different from these two genera and form the genus Maricaulis gen. nov. with Maricaulis maris as the type species. Caulobacter leidyia was observed to cluster with species of the genus Sphingomonas. Caulobacter crescentus is synonymous with C. vibrioides and C. halobacteroides is synonymous with Maricaulis maris as determined by these analyses and DNA-DNA hybridization. Biomarkers discerning these different genera were determined. The necessary recombinations have been proposed and a description of Maricaulis is presented.
Collapse
MESH Headings
- Antigens, Bacterial/analysis
- Bacteria/chemistry
- Bacteria/classification
- Bacteria/genetics
- Bacterial Typing Techniques
- Blotting, Western
- Caulobacter/chemistry
- Caulobacter/classification
- Caulobacter/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- Fresh Water/microbiology
- Genes, rRNA
- Humans
- Lipids/analysis
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- Seawater/microbiology
- Sequence Analysis, DNA
- Water Microbiology
Collapse
Affiliation(s)
- W R Abraham
- Gesellschaft für Biotechnologische Forschung mbH, Braunschweig, Germany.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Abstract
Detailed characterization of the genetic variability among strains belonging to Pseudomonas stutzeri was achieved using different rapid molecular typing methods based on polymerase chain reaction (PCR), Southern blot and Western blot. Consensus motifs complementary to fragments of repetitive elements dispersed throughout the genomes of bacteria were used as primers and allowed differentiation at subspecies levels. Further and simple differentiation was also achieved based on the direct amplification of spacer regions between 16S and 23S rRNA, combined with single-strand conformation polymorphism (SSCP) analysis of the generated fragments. These methods are fast, sensitive, reliable for determining relationships, and have demonstrated a great genetic diversity among the strains of Ps. stutzeri studied in agreement with the heterogeneous phenotypic traits of the species.
Collapse
Affiliation(s)
- A Bennasar
- Departament de Biologia Ambiental, Microbiologia, Universitat de les Illes Balears, Palma de Mallorca, Spain.
| | | | | | | |
Collapse
|
8
|
Wagner-Döbler I, Bennasar A, Vancanneyt M, Strömpl C, Brümmer I, Eichner C, Grammel I, Moore ER. Microcosm enrichment of biphenyl-degrading microbial communities from soils and sediments. Appl Environ Microbiol 1998; 64:3014-22. [PMID: 9687466 PMCID: PMC106808 DOI: 10.1128/aem.64.8.3014-3022.1998] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
A microcosm enrichment approach was employed to isolate bacteria which are representative of long-term biphenyl-adapted microbial communities. Growth of microorganisms was stimulated by incubating soil and sediment samples from polluted and nonpolluted sites with biphenyl crystals. After 6 months, stable population densities between 8 x 10(9) and 2 x 10(11) CFU/ml were established in the microcosms, and a large percentage of the organisms were able to grow on biphenyl-containing minimal medium plates. A total of 177 biphenyl-degrading strains were subsequently isolated and characterized by their ability to grow on biphenyl in liquid culture and to accumulate a yellow meta cleavage product when they were sprayed with dihydroxybiphenyl. Isolates were identified by using a polyphasic approach, including fatty acid methyl ester (FAME) analysis, 16S rRNA gene sequence comparison, sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell proteins, and genomic fingerprinting based on sequence variability in the 16S-23S ribosomal DNA intergenic spacer region. In all of the microcosms, isolates identified as Rhodococcus opacus dominated the cultivable microbial community, comprising a cluster of 137 isolates with very similar FAME profiles (Euclidean distances, <10) and identical 16S rRNA gene sequences. The R. opacus isolates from the different microcosms studied could not be distinguished from each other by any of the fingerprint methods used. In addition, three other FAME clusters were found in one or two of the microcosms analyzed; these clusters could be assigned to Alcaligenes sp., Terrabacter sp., and Bacillus thuringiensis on the basis of their FAME profiles and/or comparisons of the 16S rRNA gene sequences of representatives. Thus, the microcosm enrichments were strongly dominated by gram-positive bacteria, especially the species R. opacus, independent of the pollution history of the original sample. R. opacus, therefore, is a promising candidate for development of effective long-term inocula for polychlorinated biphenyl bioremediation.
Collapse
Affiliation(s)
- I Wagner-Döbler
- Department of Microbiology, GBF National Research Institute for Biotechnology, D-38124 Braunschweig, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Abstract
The microbial content of printing paper machines, running at a temperature of 45-50 degrees C and at pH 4.5-5, was studied. Bacteria were prevalent colonizers of the machine wet end and the raw materials. A total of 390 strains of aerobic bacteria were isolated and 86% of these were identified to genus and species by biochemical, chemotaxonomic and phylogenetic methods. The most common bacteria found at the machine wet end were Bacillus coagulans and other Bacillus species, Burkholderia cepacia, Ralstonia pickettii, and in pink slimes, accumulating in the wire area and press section, species of Deinococcus, aureobacterium and Brevibacterium. Paper-making chemicals also contained species of Aureobacterium, B. cereus, B. licheniformis, B. sphaericus, Bordetella, Hydrogenophaga, Klebsiella pneumoniae, Pantoea agglomerans, Pseudomonas stutzeri, Staphylococcus and sometimes other enteric bacteria, but these did not colonize the process water. Yeasts and moulds were not present in significant numbers. A total of 131 strains were tested for their potential to degrade paper-making raw materials; 91 strains were found to have degradative activity, mainly species of Burkholderia and Ralstonia, Sphingomonas and Bacillus, and enterobacteria produced enzymes which degraded paper-making chemicals. Stainless steel adhering strains occurred in slimes and wire water and were identified as Burkholderia cepacia, B. coagulans and Deinococcus geothermalis. Coloured slimes were formed on the machine by species of Deinococcus, Acinetobacter and Methylobacterium (pink), Aureobacterium, Pantoea and Ralstonia (yellowish) and Microbulbifer-related strains (brown). The impact of the strains and species found in the printing paper machine community on the technical quality of paper, machine operation, and as a potential biohazard (Hazard Group 2 bacteria), is discussed.
Collapse
Affiliation(s)
- O M Väisänen
- Department of Applied Chemistry and Microbiology, University of Helsinki, Finland
| | | | | | | | | | | |
Collapse
|
10
|
Bennasar A, Guasp C, Lalucat J. Molecular Methods for the Detection and Identification of Pseudomonas stutzeri in Pure Culture and Environmental Samples. Microb Ecol 1998; 35:22-33. [PMID: 9459656 DOI: 10.1007/s002489900057] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- A Bennasar
- Departament de Biologia Ambiental, Microbiologia, Universitat de les Illes Balears, and Institut Mediterrani d'Estudis Avancats (CSIC-UIB), 07071 Palma de Mallorca, Spain
| | | | | |
Collapse
|
11
|
Bennasar A, Rosselló-Mora R, Lalucat J, Moore ER. 16S rRNA gene sequence analysis relative to genomovars of Pseudomonas stutzeri and proposal of Pseudomonas balearica sp. nov. Int J Syst Bacteriol 1996; 46:200-5. [PMID: 8573496 DOI: 10.1099/00207713-46-1-200] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We compared the 16S rRNA gene sequences of 14 strains of Pseudomonas stutzeri, including type strain CCUG 11256 and strain ZoBell (= ATCC 14405), which represented the seven P. stutzeri genomovars (DNA-DNA similarity groups) that have been described. Our sequence analysis revealed clusters which were highly correlated with genomovar clusters derived from DNA-DNA hybridization data. In addition, we identified signature nucleotide positions for each genomovar. We found that the 16S rRNA gene sequences of genomovar 6 strains SP1402T (T = type strain) and LS401 were different enough from the sequence of the type strain of P. stutzeri that these organisms should be placed in a new species, Pseudomonas balearica. The type strain of P. balearica is strain SP1402 (= DSM 6083).
Collapse
Affiliation(s)
- A Bennasar
- Departamento de Biología Ambiental, Universitat de les Illes Baleares, Palma de Mallorca, Spain
| | | | | | | |
Collapse
|