Ludmila Tvrzová

Achromobacter marplatensis sp. nov., isolated from a pentachlorophenol-contaminated soil

A polyphasic taxonomic approach was applied to the study of a Gram-negative bacterium (B2(T)) isolated from soil by selective enrichment with pentachlorophenol. 16S rRNA gene sequence analysis of strain B2(T) showed that the strain belongs to the genus Achromobacter within the Betaproteobacteria. The 16S rRNA gene sequence displayed more than 99 % similarity to the sequences of the type strains of all species of Achromobacter, with the highest sequence similarity to those of Achromobacter spanius CCM 7183(T) and A. piechaudii CCM 2986(T) (99.8 %). On the basis of phylogenetic analysis, genomic DNA-DNA relatedness and phenotypic characteristics, including chemotaxonomic (cellular fatty acid profile) analysis, a novel species is proposed, Achromobacter marplatensis sp. nov., with the type strain B2(T) ( = CCM 7608(T)  = CCUG 56371(T)  = CECT 7342(T)).

The influence of growth conditions on strain differentiation within the Lactobacillus acidophilus group using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling.

RATIONALE Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling of bacteria is often used to distinguish isolates beyond the species level, even to the level of individual strains. However, the influence of bacterial growth conditions on the discriminatory power of the method to the strain level has not yet been properly evaluated. METHODS For the purpose of this study, we used an extraction protocol recommended for clinical laboratories for MALDI-TOF MS profiling of bacteria. Seventeen closely related strains of the Lactobacillus acidophilus group were cultivated under various growth conditions (growth medium, time, and temperature) and analyzed. RESULTS Out of a total of 327 samples, 80 % were correctly assigned to the species level and 13 % only to the genus level. When using data obtained from strains cultured for lengthy periods (7 days), the identification success rate was reduced due to poor signal quality, whereas with shorter cultivation times there was no influence of growth conditions on the assignment of particular strains to their corresponding species. However, variations in certain cultivation parameters were found to influence identification and differentiation of most of the examined strains. Strain discrimination was frequently found to be dependent on the selection of culture conditions. MALDI-TOF MS data treatment (strain-specific peak detection, BioTyper scoring, subtyping, or cluster analysis) also contributed to the discriminatory power of the method. CONCLUSIONS When MALDI-TOF MS profiling of bacteria is used for strain discrimination, the cultivation conditions should be properly optimized and controlled as they significantly contribute to the discriminatory power of the method.

Characterization of Rhodococcus wratislaviensis strain J3 that degrades 4-nitrocatechol and other nitroaromatic compounds

The bacterial strain J3 was isolated from soil by selective enrichment on mineral medium containing 4-nitrocatechol as the sole carbon and energy source. This strain was identified as Rhodococcus wratislaviensis on the basis of morphology, biochemical, physiological and chemotaxonomic characterization and complete sequencing of the 16S rDNA gene. The isolated bacterium could utilize 4-nitrocatechol, 3-nitrophenol and 5-nitroguaiacol as sole carbon and energy sources. Stoichiometric release of nitrites was measured during degradation of 4-nitrocatechol both in growing cultures and for stationary phase cells. The J3 strain was unable to degrade 4-nitroguaiacol, 2-nitrophenol, 4-nitrophenol, 2,4-dinitrobenzoic acid, 4,5-dimethoxy-2-nitrobenzoic acid and 2,3-difluoro-6-nitrophenol. The J3 strain is deposited in the Czech Collection of Microorganisms as CCM 4930.

Evaluation of the MALDI-TOF MS profiling for identification of newly described Aeromonas spp.

The genus Aeromonas comprises primarily aquatic bacteria and also serious human and animal pathogens with the occurrence in clinical material, drinking water, and food. Aeromonads are typical for their complex taxonomy and nomenclature and for limited possibilities of identification to the species level. According to studies describing the use of MALDI-TOF MS in diagnostics of aeromonads, this modern chemotaxonomical approach reveals quite high percentage of correctly identified isolates. We analyzed 64 Aeromonas reference strains from the set of 27 species. After extending the range of analyzed Aeromonas species by newly described ones, we proved that MALDI-TOF MS procedure accompanied by Biotyper tool is not a reliable diagnostic technique for aeromonads. We obtained quite high percentage of false-positive, incorrect, and uncertain results. The identification of newly described species is accompanied with misidentifications that were observed also in the case of pathogenic aeromonads.

Degradation of 5-nitroguaiacol by soil bacteria of the genusRhodococcus

Two bacterial strains were isolated from forest soil by selective enrichment of the mineral medium containing 4-nitropyrocatechol as the sole carbon and energy source. Both strains could utilize 4-nitropyrocatechol and 5-nitroguaiacol. Degradation of 5-nitroguaiacol and stoichiometric release of nitrites was measured during its degradation both in growing culture and for resting cells. Both strains were unable to degrade other nitroaromatic compounds such as 4-nitroguaiacol, 2-nitrophenol, 3-nitrophenol, 4-nitrophenol, 2,4-dinitrobenzoic acid, 4,5-dimethyoxy-2-nitrobenzoic acid and 2,3-difluoro-6-nitrophenol. One strain was identified asRhodococcus opacus and the second one asRhodococcus sp.