The complete genomes of Enterococcus faecalis bacteriophages were analyzed for tetranucleotide words avoidance. Very similar tetranucleotide composition was found in all tested genomes with strong underrepresentation of palindromic GATC and GGCC words. This avoidance could be explained as a protection mechanism against host restriction-modification systems as a clear correlation was found between avoidance of palindromic words and the specificity of E. faecalis restriction and modification systems. No similar avoidance of tetranucleotide words was observed for non-palindromic words. A weak correlation was observed between avoidance of tetranucleotide palindromes in bacteriophage genomes and the possession of phage encoded DNA methyltransferases confirming the interrelation between bacteriophage genomes composition and restriction and modification systems in enterococci
Lenka Maliničová, Peter Pristaš and Peter Javorský
Bioinformatic Analysis of Prophage Endolysins and Endolysin-Like Genes from the Order Lactobacillales
Endolysins belonging to the group of peptigoglycan hydrolases, which are able to cleave peptidoglycan in bacterial cell walls, become an extensively studied group of enzymes. Thanks to their narrow target specificity and low probability of resistance they are considered to be an appropriate alternative to conventional antibiotics. The present paper concerns the occurrence of endolysin and endolysin-like genes in genomes of bacteria belonging to the order Lactobacillales. Using bioinformatic programmes we compared and analysed protein sequences of catalytic and cell wall binding (CWB) domains of these enzymes, their preferred combinations, their phylogenetic relationship and potential occurence of natural "domain shuffling". The existence of this phenomenon in selected group of enzymes was confirmed only in limited range, so we assume that the natural trend is the distribution of "well-tried" combinations of catalytic and CWB domains of endolysin genes as a whole.
Simona Kvasnová, Ľudmila Hamarová and Peter Pristaš
Heavy metal pollution is one of the most important environmental issues of today. Bioremediation by microorganisms is one of technologies extensively used for pollution treatment. In this study, we investigated the heavy metal resistance and zinc bioaccumulation by microbial consortium isolated from nickel sludge disposal site near Sereď (Slovakia). The composition of consortium was analyzed based on MALDI-TOF MS of cultivable bacteria and we have shown that the consortium was dominated by bacteria of genus Arthrobacter. While consortium showed very good growth in the zinc presence, it was able to remove only 15 % of zinc from liquid media. Selected members of consortia have shown lower growth rates in the zinc presence but selected isolates have shown much higher bioaccumulation abilities compared to whole consortium (up to 90 % of zinc removal for NH1 strain). Bioremediation is frequently accelerated through injection of native microbiota into a contaminated area. Based on data obtained in this study, we can conclude that careful selection of native microbiota could lead to the identification of bacteria with increased bioaccumulation abilities.
Peter Pristas, Jana Kiskova, Ivana Timkova, Lenka Malinicova, Alena Luptakova, Maria Kusnierova and Jana Sedlakova-Kadukova
The genus Acidithiobacillus comprises 7 species of Gram-negative obligatory acidophilic chemolithotrophic bacteria that derive energy mainly from the oxidation of reduced sulphur compounds. Four of the species also catalyse the dissimilatory oxidation of ferrous iron while three (A. thiooxidans, A. albertensis, and A. caldus) do not. Bacteria from the genus Acidithiobacillus are often associated with mineral biotechnologies (biomining) and acid mine drainage. While acceleration of mineral solubilisation is a positive aspect in environmental biotechnologies, it is undesirable in acid mine drainage with strong negative ecological impact and there is profound interest in genetics and genomics of these bacteria. Representatives of Acidithiobacillus genus occur world-wide, however there are limited data on Acidithiobacillus spp. variability from Slovakia. In our work the variability of Acidithiobacillus spp., from Slovakia was analysed and the presence of A ferrooxidans was detected. In addition, for the first time we report here on the occurrence of A. albertensis as well. Comparative analyses confirmed pronounced genetic and genomic diversity within the genus, especially within A. ferrooxidans and A. thioxidans complexes. Based on data presented, several Acidithiobacillus species could be considered as a complex species and the description of several new species is very probable in the near future.
Peter Pristas, Zuzana Stramova, Simona Kvasnova, Jana Judova, Zuzana Perhacova, Barbora Vidova, Zuzana Sramkova and Andrej Godany
Waste disposal sites from non-ferrous metal industry constitute environments very hostile for life due to the presence of very specialized abiotic factors (pH, salt concentration, heavy metals content). In our experiments microflora of two waste disposal sites in Slovakia – brown mud disposal site from aluminium production near Ziar nad Hronom and nickel sludge disposal site near Sered - was analyzed for cultivable bacteria. Isolated bacteria were characterized by a combination of classical microbiological approaches and molecular methods and the most of isolated bacteria shown a poly-extremotolerant phenotype. The most frequently halotolerant (resistant to the high level of salt concentrations) and alkalitolerant (resistant to the high pH level) bacteria belonging to the Actinobacteria class were detected. The most of bacteria shown very high level of heavy metal resistance e.g. more than 500 μg/ml for Zn2+ or Cu2+. Based on our data, waste disposal sites thus on one side represents an important environmental burden but on other side they are a source of new poly-extremotolerant bacterial strains and species possibly used in many biotechnology and bioremediation applications.
Anna Vandžurová, Gabriel Bódy, Peter Javorský and Peter Pristaš
Gradual increasing of glycerol concentration up to 10% using sheep ruminal fluid as an inoculum for in vitro cultivation was accompanied by significant changes in bacterial population as documented by DGGE analysis. The resulting bacterial consortium was composed of three dominant bacteria with Actinomyces related bacterium to be predominant. Upon cultivation on media with glycerol as a sole carbon source a single bacterium was cultivated from this consortium. Isolate G10 was found to be anaerobic, Gram-positive rod-shaped bacterium. Phylogenetic analysis based on 16S rRNA gene sequences showed that G10 isolate is related to the Actinomyces ruminicola species (97.7% of similarity). The role of rumen actinobacteria is largely unknown and their participation in glycerol utilization (tolerance) has not been described yet. The G10 bacterium and related consortium could be possibly used to improve glycerol tolerance and uptake by ruminants
Nikola Š Šipošová, Veronika Liptáková, Simona Kvasnová, Petra Kosorínová and Peter Pristaš
Multiple metallotolerant bacterial strains were isolated from soil and drainage water samples collected from three industrially heavy metals polluted areas in Slovakia. Obtained bacterial isolates were identified using MALDI-TOF mass spectrometry and bacterial isolates that belonged to the Acinetobacter genus were subjected for the further study. A. calcoaceticus was found to be prevalent species among analyzed Acinetobacter spp. strains, followed by A. lwoffii and A. johnsonii. A. calcoaceticus strains exhibited higher minimum inhibitory concentration to Mn, Zn, and Cu cations compared to A. lwoffii and A. johnsonii. On the other hand minimum inhibitory concentration to Co and Ni were identical in all Acinetobacter spp. isolates. Genetic analyses demonstrated multiple plasmids presence in A. lwoffii and A. johnsonii but not in A. calcoaceticus. Using ERIC-PCR the presence of two different genotypes of A. calcoaceticus was detected in heavy metal polluted environments in Slovakia.
Jana Sedláková-Kaduková, Jana Kisková, Lenka Maliničová, Ivana Timková, Stanislav Jeleň and Peter Pristaš
Sulphur-oxidising autotrophic bacterial communities in deep biosphere from weathered ore samples from active gold mine Hodruša-Hámre, Slovakia were analysed using cultivation approach followed by DNA extraction, PCR amplification and 16S rRNA gene analyses. Indirect measurement of pH changes in cultivation media evidenced the presence of acidophilic bacteria with active production of acids. The decrease of pH was observed at the beginning of isolation and later pH in range of 1.5 – 2 was maintained in both, sulphuric acid and thiosulphate, media. The presence of homogenous population of gram-negative rods was proved by Gram staining. Molecular analyses have revealed that the population of sulphur-oxidising bacteria in gold mine is dominated by a single species of Aciditiobacillus genus, identified as A. albertensis, suggesting the low level of autotrophic bacteria diversity in deep deposits. For the first time this species was isolated from weathered rocks of a gold mine subsurface environment.