Comparative genomic analysis of two putative novel Idiomarina species from hypersaline miocene deposits.

Background: Hypersaline habitats, as extreme environments, are a great source of well-adapted organisms with unique properties as they have evolved various strategies to cope with these extreme conditions. Bioinformatics and genomic mining may shed light on evolutionary relationships among them. Therefore, the aim of this study was to assess the biodiversity and especially the strategies evolved within the Idiomarina genus, with the primary focus on the taxonomy and genomic adaptations of two novel strains affiliated with Idiomarina genus isolated from unique environment - brines of two Early Miocene salt deposits.

Gene and domain shuffling in lytic cassettes of spp. bacteriophages.

Unlabelled: The genomes of and bacteriophages were analysed for gene shuffling in the lytic cassettes of bacteriophages infecting. It was found that enterococcal bacteriophages could be classified into well-defined groups based on the size of their genomes and each size group had its own conserved gene composition of lytic cassettes. Enterococcal bacteriophages use a relatively broad spectrum of holins and endolysins with variable cell-wall binding (CWB) and catalytic domains, and most of them utilise a lytic cassette with more than two genes.

Cold Sulfur Springs-Neglected Niche for Autotrophic Sulfur-Oxidizing Bacteria.

Since the beginning of unicellular life, dissimilation reactions of autotrophic sulfur bacteria have been a crucial part of the biogeochemical sulfur cycle on Earth. A wide range of sulfur oxidation states is reflected in the diversity of metabolic pathways used by sulfur-oxidizing bacteria. This metabolically and phylogenetically diverse group of microorganisms inhabits a variety of environments, including extreme environments.

Antibiotic Resistance and Genetic Variability of spp. from Wastewater Treatment Plant in Kokšov-Bakša (Košice, Slovakia).

This study investigated the genetic variability and antibiotic resistance of community depending on the stage of wastewater treatment in Kokšov-Bakša for the city of Košice (Slovakia). After cultivation, bacterial isolates were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and their sensitivity to ampicillin, kanamycin, tetracycline, chloramphenicol and ciprofloxacin was examined. spp.

Bacterial Community Structure of Two Cold Sulfur Springs in Slovakia (Central Europe).

Sulfur-oxidizing bacteria, especially those from hot springs, have attracted the attention of microbiologists for more than 150 years. In contrast, the microbial diversity of cold sulfur springs remains largely unrecognized. Culture-dependent and culture-independent approaches were used to study the diversity of sulfur-oxidizing bacterial communities in two cold sulfur springs in Slovakia.

Diversity, heavy metals, and antibiotic resistance in culturable heterotrophic bacteria isolated from former lead-silver-zinc mine heap in Tarnowskie Gory (Silesia, Poland).

Mine tailings represent a great environmental concern due to their high contents of heavy metals. Cultivation analysis of microbiota of Tarnowskie Góry (Poland) mine tailing showed the occurrence of bacteria with colony-forming units as low as 5.7 × 10 per one gram of dried substrate.

The Application of MALDI-TOF MS for a Variability Study of .

In recent decades, the significant deterioration of the health status of honey bees has been observed throughout the world. One of the most severe factors affecting the health of bee colonies worldwide is American foulbrood disease. This devastating disease, with no known cure, is caused by the Gram-positive spore-forming bacteria of species.

Intragenomic Variability of ITS Sequences in .

is a species of common white rot polyporoid fungi found worldwide. Despite playing an important role in deadwood decay, the species strains are used in bioremediation due to its ability to degrade polycyclic hydrocarbons and some of them are important etiological agents of chronic coughs and are associated with lung inflammations. In our experiments, diversity within the species was investigated using molecular approaches and we found that sequence diversity seen at ITS sequence level is not due to cryptic speciation but to intragenomic variability of ITS sequences in this species.

Deep Subsurface Hypersaline Environment as a Source of Novel Species of Halophilic Sulfur-Oxidizing Bacteria.

The sulfur cycle participates significantly in life evolution. Some facultatively autotrophic microorganisms are able to thrive in extreme environments with limited nutrient availability where they specialize in obtaining energy by oxidation of reduced sulfur compounds. In our experiments focused on the characterization of halophilic bacteria from a former salt mine in Solivar (Presov, Slovakia), a high diversity of cultivable bacteria was observed.

Biodiversity of Actinomycetes from Heavy Metal Contaminated Technosols.

Technosols are artificial soils generated by diverse human activities and frequently contain toxic substances resulting from industrial processes. Due to lack of nutrients and extreme physico-chemical properties, they represent environments with limited bacterial colonization. Bacterial populations of technosols are dominated usually by Actinobacteria, including streptomycetes, known as a tremendous source of biotechnologically important molecules.

New Endophytic Fusarium spp. from Fraxinus excelsior Leaves in Slovakia.

is currently suffering from ash dieback disease caused by the fungus . Co-occurrence of large numbers of other fungi with endophytic as well as pathogenic lifestyles has been observed on . In this study, new endophytic spp.

Peptidoglycan hydrolase enterolysin a recognizes lipoteichoic acid chains in the cell walls of sensitive bacteria.

C-terminal domain of peptidoglycan hydrolase enterolysin A (EnlA) is involved in specific recognition and binding to the target cell envelopes and represents true cell wall binding (CWB) domain. Sensitivity/resistance to EnlA is dependent on binding ability/disability of its CWB domain. We assume that main mechanism of resistance against EnlA is absence of the specific receptor on the cell surface, which is necessary for binding of the enzyme molecule.

Effects of high- and low-fiber diets on fecal fermentation and fecal microbial populations of captive chimpanzees.

We examined fiber fermentation capacity of captive chimpanzee fecal microflora from animals (n = 2) eating low-fiber diets (LFDs; 14% neutral detergent fiber (NDF) and 5% of cellulose) and high-fiber diets (HFDs; 26% NDF and 15% of cellulose), using barley grain, meadow hay, wheat straw, and amorphous cellulose as substrates for in vitro gas production of feces. We also examined the effects of LFD or HFD on populations of eubacteria and archaea in chimpanzee feces. Fecal inoculum fermentation from the LFD animals resulted in a higher in vitro dry matter digestibility (IVDMD) and gas production than from the HFD animals.

Treponema zioleckii sp. nov., a novel fructan-utilizing species of rumen treponemes.

During studies on fructan degradation in the rumen, a Treponema-like bacterium able to utilize Timothy grass fructan, commercial inulin and sucrose as the sole carbon source was recovered from sheep rumen. At least two different fructanolytic enzymes were identified in cell-free extracts of the isolated bacterium. Characterization of the strain by a polyphasic approach indicated that it can be regarded as a representative of a new bacterial species within the genus Treponema.

Heterologous expression of functionally active enterolysin A, class III bacteriocin from Enterococcus faecalis, in Escherichia coli.

The heterologous expression of enterolysin A (EnlA), heat-labile class III bacteriocin from Enterococcus faecalis II/1 with anti-listerial activity, was studied in Escherichia coli. The PCR amplified products of enterolysin A structural gene, N-terminal part of EnlA with endopeptidase-like activity and C-terminal part of EnlA similar to a lysis gene of bacteriophage, were cloned in prelinearized pQE-30UA expression vector. The expression of EnlA structural gene led to the synthesis and secretion of functional-active His-tagged enterolysin A protein, which was purified to homogeneity using His-Select Cartridge and was shown to be fully active against the indicator strain.

A unique pair of GATC specific DNA methyltransferases in Mitsuokella multiacida.

Two GATC specific methylases together with Sau3AI isoschizomeric restriction endonuclease were partially characterized in Mitsuokella multiacida 46/5. This is the first report on the presence of solitary Dam methyltransferase alongside GATC specific restriction-modification system resulting in the unusual two-fold methylation of the GATC motifs.

Multiple restriction-modification systems are present in rumen treponemes.

Type II restriction endonucleases were purified by heparin-sepharose followed by ion chromatography from Treponema strains. The results indicate that in addition to frequently cutting GATC-specific restriction enzymes, the tested strains also possess rarely cutting endonucleases. The purified restriction endonucleases represent four different sequence specificities, comprising isoschizomers of DrdI, AflII, Tth111I and NdeI.

Underrepresentation of short palindromes in Selenomonas ruminantium DNA: evidence for horizontal gene transfer of restriction and modification systems?

Molecular analysis of isolates of the rumen bacterium Selenomonas ruminantium revealed a high variety and frequency of site-specific (restriction) endonucleases. While all known S. ruminantium restriction and modification systems recognize hexanucleotide sequences only, consistently low counts of both 6-bp and 4-bp palindromes were found in DNA sequences of S.

Different restriction and modification phenotypes in ruminal lactate-utilizing bacteria.

Analysis of restriction and modification activities in lactate-utilizing bacteria belonging to the Megasphaera elsdenii and Mitsuokella multiacida species revealed the presence of GATC-specific, MboI isospecific, restriction-modification (R-M) systems in all strains tested. While restriction endonucleases isolated from M. elsdenii strains were found to be sensitive to Dam methylation, enzymes from M.