During the microbiological research performed within the scope of activities of Czech expeditions based at the Johann Gregor Mendel Station at James Ross Island, Antarctica, two psychrotrophic gram-stain negative non-fluorescent strains CCM 8506T and CCM 8507 from soil were extensively characterized using genotypic and phenotypic methods. Initial characterization using ribotyping with HindIII restriction endonuclease and phenotyping implies that both isolates belong to a single Pseudomonas species. Sequencing of rrs, rpoB, rpoD and glnA genes of strain CCM 8506(T) confirmed affiliation of investigated strains within the genus Pseudomonas. Further investigation using automated ribotyping with EcoRI (RiboPrinter(®) Microbial Characterisation System), whole-cell protein profiling using the Agilent 2100 Bioanalyzer system, extensive biochemical testing and DNA-DNA hybridization experiments confirmed that both investigated strains are members of a single taxon which is clearly separated from all hitherto described Pseudomonas spp. Based on all findings, we describe a novel species Pseudomonas gregormendelii sp. nov. with the type strain CCM 8506(T) (=LMG 28632T).

• MeSH
• Bacterial Proteins genetics   metabolism   MeSH
• DNA, Bacterial genetics   MeSH
• Phylogeny MeSH
• Pseudomonas classification   genetics   isolation & purification   metabolism   MeSH
• Soil Microbiology * MeSH
• DNA, Ribosomal genetics   MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Publication type
• Journal Article MeSH
• Geographicals
• Antarctic Regions MeSH
• Names of Substances
• Bacterial Proteins MeSH
• DNA, Bacterial MeSH
• DNA, Ribosomal MeSH
• RNA, Ribosomal, 16S MeSH

Pseudomonas monteilii CCM 3423 bacterial strain, deposited at the Czech Collection of Microorganisms, was originally isolated by Haľama and Augustín (1980) as a bacterium degrading aromatic hydrocarbons and derivates. A detailed study supported by a molecular genetics method of sequence analyses of rrs and rpoD genes was used to reclassify the strain, originally stored as 'Pseudomonas putida'. The physiological characteristics of the strain are complemented with research in the capacity to utilize selected organic pollutants (anthracene, benz[a]anthracene, benzo[b]fluoranthene, benzo[k]fluoranthene, benzo[a]pyrene, fluorene, naphthalene, phenanthrene). The obtained results point at very good biodegradation properties of the strain. Already after 7 days of the bacterial strain's action, there was a decrease in all the organic contaminants to 79.8 ± 2.6 %. In 14 days, the amount of organic contaminants dropped to 59.3 ± 2.8 %. After 21 days of biodegradation experiments, the overall quantity of the observed organic substances fell below the half limit to 45.7 ± 2.5 % of residuals. Finally, after 28 days, the residue was 35.4 ± 2.2 %, and after 35 days of the action of P. monteilii, the tested samples contained mere 27.8 ± 2.8 % of organic pollutants. The results imply that Pseudomonas monteilii CCM 3423 is a prospective strain in terms of further biotechnological application in contaminated environment.

• MeSH
• Biodegradation, Environmental MeSH
• Bronchi microbiology   MeSH
• Phylogeny MeSH
• Environmental Pollutants metabolism   MeSH
• Humans MeSH
• Molecular Sequence Data MeSH
• Polycyclic Aromatic Hydrocarbons metabolism   MeSH
• Pseudomonas classification   genetics   isolation & purification   metabolism   MeSH
• Environmental Restoration and Remediation instrumentation   methods   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Evaluation Study MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Environmental Pollutants MeSH
• Polycyclic Aromatic Hydrocarbons MeSH

During Czech expeditions at James Ross Island, Antarctica, in the years 2007-2009, the bacterial diversity of the genus Pseudomonas was studied. Twelve fluorescent Pseudomonas strains were isolated from various samples and were subjected to a detailed taxonomic study. A polyphasic approach included genotypic and phenotypic analyses. The genotypic analysis involved sequencing of rrs, rpoB and rpoD genes, DNA-DNA hybridization (DDH) studies as well as manual ribotyping using HindIII endonuclease. The phenotypic characterization included conventional tests as well as biotyping using the Biolog system, protein profiling by SDS-PAGE, and MALDI-TOF MS analysis. Our taxonomic study revealed that all isolates belonged to the same Pseudomonas species with psychrotrophic growth not exceeding 37 °C. The cultures showed a unique position among the phylogenetically related pseudomonads. DDH experiment between the proposed type strain of the antarctic isolates and the closest neighbour P. arsenicoxydans CCM 8423(T) showed only 40.9-50.1 % similarity, thus confirming that the characterized strains do not belong to the P. arsenicoxydans species. According to the results obtained we propose the name P. prosekii sp. nov. for this novel Pseudomonas taxon with type strain AN/28/1(T) (=CCM 7990(T) and LMG 26867(T)).

• MeSH
• DNA, Bacterial chemistry   genetics   MeSH
• DNA-Directed RNA Polymerases genetics   MeSH
• Phylogeny MeSH
• Nucleic Acid Hybridization MeSH
• Environmental Microbiology * MeSH
• Molecular Sequence Data MeSH
• Pseudomonas classification   genetics   isolation & purification   physiology   MeSH
• Ribotyping MeSH
• DNA, Ribosomal chemistry   genetics   MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Sequence Analysis, DNA MeSH
• Cluster Analysis MeSH
• Sigma Factor genetics   MeSH
• Bacterial Typing Techniques MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Antarctic Regions MeSH
• Names of Substances
• DNA, Bacterial MeSH
• DNA-Directed RNA Polymerases MeSH
• DNA, Ribosomal MeSH
• RNA polymerase beta subunit MeSH Browser
• RNA polymerase sigma 70 MeSH Browser
• RNA, Ribosomal, 16S MeSH
• Sigma Factor MeSH

Fluorescent Pseudomonas putida CCM 3656 (ATCC 11250) was analysed according to the methods of polyphasic approach which were based on sequence analyses involving the rpoB and rrs genes, manual ribotyping using endonuclease HindIII, DNA base composition determination and DNA-DNA hybridization. The results obtained by these genotyping methods showed that the strain CCM 3656 is distant from P. putida taxon, which was supported with phenotype characterization represented by whole-cell protein profile analysis, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry profiling and extended biotyping. The DNA-DNA hybridization experiments performed between the strain CCM 3656 and the closest relatives revealed 77 % similarity with Pseudomonas jessenii. However, the outcomes of sequencing, ribotyping and phenotype characterization allow distinguishing the studied strain from P. jessenii. On the basis of the obtained taxonomic data, we suggest reclassifying strain CCM 3656 to a novel subspecies of P. jessenii and propose naming P. jessenii subsp. pseudoputida subsp. nov. with CCM 3656(T) as type strain. Furthermore, we present an amended description of P. jessenii and proposal of P. jessenii subsp. jessenii subsp. nov.

• MeSH
• DNA-Directed RNA Polymerases genetics   MeSH
• Phylogeny MeSH
• Nucleic Acid Hybridization MeSH
• Molecular Sequence Data MeSH
• Proteome analysis   MeSH
• Pseudomonas chemistry   classification   genetics   MeSH
• Ribotyping MeSH
• DNA, Ribosomal chemistry   genetics   MeSH
• Sequence Analysis, DNA MeSH
• Cluster Analysis MeSH
• Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MeSH
• Bacterial Typing Techniques MeSH
• Base Composition MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• DNA-Directed RNA Polymerases MeSH
• Proteome MeSH
• DNA, Ribosomal MeSH
• RNA polymerase beta subunit MeSH Browser

• MeSH
• Bacterial Proteins genetics   metabolism   MeSH
• Enterococcus classification   enzymology   genetics   isolation & purification   MeSH
• Phylogeny MeSH
• Gram-Positive Bacterial Infections diagnosis   microbiology   MeSH
• Humans MeSH
• Molecular Sequence Data MeSH
• Superoxide Dismutase genetics   MeSH
• Bacterial Typing Techniques methods   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Evaluation Study MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Bacterial Proteins MeSH
• Superoxide Dismutase MeSH

Nine Aeromonas strains having a brown exopigment were isolated during the microbiological examination of river water. These brown-pigmented aeromonads were characterized by the phenotyping, fatty-acid methyl-ester analysis and ribotyping. All methods identically confirmed that the group of brown-pigmented aeromonads is quite heterogeneous. Apart from the Aeromonas media taxon, the brown-pigmented aeromonads in river water were represented also by strains of A. allosaccharophila and A. salmonicida subsp. pectinolytica.

• MeSH
• Aeromonas classification   genetics   isolation & purification   metabolism   MeSH
• Pigments, Biological metabolism   MeSH
• Phylogeny MeSH
• Molecular Sequence Data MeSH
• Fresh Water microbiology   MeSH
• Bacterial Typing Techniques MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Pigments, Biological MeSH

Antibiotic susceptibility or resistance, urease activity, detection of the structural genes for bacteriocin production, bacteriocin activity as well as sensitivity of the isolates to enterocins (Ent) A and M were determined in 23 isolates of new species Enterococcus haemoperoxidus and E. moraviensis. The majority of the strains were antibiotic sensitive and exhibited low urease activity (< 10 nkat/mL). The most frequently detected genes for Ent were entA and entP. However, only the strain 466 of E. haemoperoxidus produced an antibacterial substance with inhibitory activity against 21 G+ indicators. It was partially purified reaching an activity of up to 12 800 AU/mL. This bacteriocin active strain also possessed the genes for EntA and EntP. The other strains did not inhibit the indicator strains. The substance produced by the 466 strain was active even after a 5-months storage at +4 and -20 degrees C. This substance has proteolytic and hydrophilic character, pH optimum of bacteriocin production by this strain being between 4 and 7. While E. moraviensis strains showed sensitivity to EntA (produced by E. faecium EK13) and to EntM (produced by E. faecium AL41), E. haemoperoxidus strains were sensitive to EntA (except strain 382) but less sensitive to the treatment by EntM.

• MeSH
• Drug Resistance, Bacterial * MeSH
• Bacteriocins genetics   metabolism   MeSH
• Enterococcus drug effects   genetics   metabolism   MeSH
• Microbial Sensitivity Tests MeSH
• Water Microbiology MeSH
• Fresh Water microbiology   MeSH
• Urease metabolism   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Bacteriocins MeSH
• Urease MeSH

A series of lactobacilli isolated from dairy products were characterized using biotyping and ribotyping with EcoRI and HindIII restriction enzymes. Biotyping assigned 14 strains as Lactobacillus casei, 6 strains as Lactobacillus paracasei subsp. paracasei and 12 as Lactobacillus rhamnosus. The obtained ribotype patterns separated all analyzed strains into two clearly distinguished groups corresponding to L. rhamnosus and L. casei/L. paracasei subsp. paracasei. The HindIII ribotypes of individual strains representing these two groups were visually very similar. In contrast, EcoRI ribotyping revealed high intraspecies variability. All ribotypes of L. casei and L. paracasei subsp. paracasei dairy strains were very close and some strains even shared identical ribotype profiles. The type strains L. casei CCM 7088T (= ATCC 393T) and Lactobacillus zeae CCM 7069T revealing similar ribopatterns formed a separate subcluster using both restriction enzymes. In contrast, the ribotype profile of L. casei CCM 7089 (= ATCC 334) was very close to ribopatterns obtained from the dairy strains. These results support synonymy of L. casei and L. paracasei species revealed by other studies as well as reclassification of the type strain L. casei CCM 7088T as L. zeae and designation of L. casei CCM 7089 as the neotype strain.

• MeSH
• Species Specificity MeSH
• Phenotype MeSH
• Lacticaseibacillus rhamnosus classification   isolation & purification   MeSH
• Lacticaseibacillus casei classification   isolation & purification   MeSH
• Dairy Products microbiology   MeSH
• Ribotyping MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Comparative Study MeSH

A group of sixteen esculin-positive fluorescent pseudomonads isolated from an underground brook flowing through a cave complex was characterized by biotyping, multiple enzyme restriction fragment length polymorphism analysis of 16S rDNA (MERFLP), ribotyping and whole-cell fatty-acid methyl-esters analysis (FAME). All strains were phenotypically close to Pseudomonas fluorescens, but they revealed high biochemical variability as well as some reactions atypical for P. fluorescens species. Because identification of pseudomonads by of biochemical testing is often unclear, further techniques were employed. Fingerprints obtained by MERFLP clearly showed that all strains represent P. fluorescens species. Ribotyping separated the strains analyzed into four groups corresponding almost completely (with the exception of one strain) to the clustering based on biochemical profiles. FAME analysis grouped all the strains into one cluster together with the P. putida (biotype A, B), P. chlororaphis and P. fluorescens biotype F representatives, but differentiated them from other FAME profiles of all pseudomonads included in the standard library TSBA 40 provided by MIDI, Inc.

• MeSH
• DNA, Bacterial analysis   MeSH
• Esculin metabolism   MeSH
• Fatty Acids analysis   MeSH
• Polymorphism, Restriction Fragment Length MeSH
• Pseudomonas fluorescens chemistry   classification   genetics   metabolism   MeSH
• DNA Restriction Enzymes metabolism   MeSH
• Ribotyping MeSH
• DNA, Ribosomal analysis   MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Fresh Water microbiology   MeSH
• Bacterial Typing Techniques * MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• DNA, Bacterial MeSH
• Esculin MeSH
• Fatty Acids MeSH
• DNA Restriction Enzymes MeSH
• DNA, Ribosomal MeSH
• RNA, Ribosomal, 16S MeSH

Two DNA-based techniques were used for species identification of enterococci. PvuII digestion of the genus-specific PCR product yielded four different restriction profiles among 20 enterococcal species; one of them was species-specific for E. faecium. In the second case, 32 reference strains belonging to 20 enterococcal species were divided to 12 groups by amplification of internal transcribed spacer of rRNA operon. Interspecies and some intraspecies profile variability was determined. Both methods gave similar results.

• MeSH
• Species Specificity MeSH
• Enterococcus classification   genetics   metabolism   MeSH
• DNA, Intergenic chemistry   genetics   MeSH
• Polymerase Chain Reaction methods   MeSH
• DNA, Protozoan chemistry   genetics   MeSH
• Deoxyribonucleases, Type II Site-Specific metabolism   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• CAGCTG-specific type II deoxyribonucleases MeSH Browser
• DNA, Intergenic MeSH
• DNA, Protozoan MeSH
• Deoxyribonucleases, Type II Site-Specific MeSH