Volumen 56 (2017): Heft 3 (January 2017)

More and more attention has been paid to environmental chlamydiae in recent years. They were classified as pathogenic bacteria for both humans and animals. Thanks to molecular biology techniques, the following nine families of environmental chlamydiae were assigned to the order of Chlamydiales: Candidatus Clavichlamydiaceae, Criblamydiaceae, Parachlamydiaceae, Candidatus Piscichlamy- diaceae, Rhabdochlamydiaceae, Simkaniaceae, Waddliaceae, Candidatus Actinochlamydiacae and Candidatus Parilichlamydiaceae. These bacteria are considered the infectious factors of zoonoses due to the fact that they can be found among pets and livestock such as cats, guinea pigs, sheep, cattle, and even fish. Many of these animals also suffer from diseases caused by these bacteria. In this study, while characterizing environmental chlamydiae, special attention has been paid to illnesses of the respiratory tract caused by Simkania negevensis, and to the abortions among people and ruminants caused by Waddlia chondrophila. Furthermore, the species of the Rhabdochlamydiaceaefamily , as well as the bacteria from the Parachlamydiaceae family responsible for eye illnesses in humans and animals, are also characterized in this work. Lastly, newly discovered fish chlamydiae, which are potential factors of illnesses in humans and terrestial animals, are also presented in this paper.

1. Introduction. 2. Pathogenicity of environmental chlamydiae for humans and animals. 2.1. Pathogenicity of the Parachlamydiaceaefamily. 2.2. Pathogenicity of the Simkaniaceae family. 2.3. Pathogenicity of the Rhabdochlamydiaceae family. 2.4. Pathogenicity of the Waddliaceae family. 2.5. Pathogenicity of other chlamydia. 3. Diagnostics of environmental chlamydiae. 4. Conclusions

Mycorrhiza is a symbiotic relationship between living cells of the roots of higher plants and non-pathogenic fungi which inhabit soil and belong to Glomeromycota (endomycorrhizae) and Basidiomycota, Ascomycota (ectomycorrhizae). Although the phenomenon of mycorrhiza was discovered by a Polish botanist F.D. Kamieński already in 1881, various stages of establishing the symbiotic relationship between the partners are still not fully understood and explained. According to the current knowledge, the roots of host plants release strigolactones, which stimulate germination and branching of spores of arbuscular fungi. As a result, the fungi synthesize molecular signals, i.e. chitooligosaccharides (COs) and lipochitooligosaccharides (LCOS), called MycF factors. Thanks to the development of molecular biology techniques the probable cascade of events during the recognition of fungal MycF factor by the host-plant has been outlined. The enzyme 3-hydroxy-3-methylglutaryl coenzyme A reductase 1 (HMGR1) and also its product, mevalonic acid (MVA), play an essential role in the biosynthesis of sterols and isoprenoids in a plant cell. The recent studies indicate that these compounds may also play a very important role during establishing of the symbiotic mycorrhizal relationship. It is believed that MVA detects and transmits MycF factor to a cell nucleus of a host-plant triggering numerous necessary mechanisms in the plant cell to activate next steps of the mycorrhizal symbiosis. The discovery of HMGR1 and MVA sheds new light on symbiotic nature of mycorrhiza. This paper is a review of the current knowledge on the signal exchange during symbiotic interactions between mycorrhizal fungi and host plants.

1. Introduction. 2. Symbiotic nature of arbuscular fungi. 3. Arbuscular mycorrhiza in early stages. 4. Exchange of signaling molecules during arbuscular mycorrhiza formation. 5. Mevalonic acid – secondary signaling molecule messengers in the arbuscular mycorrhiza. 6. Protein kinase CCaMK as a key element in the establishment of arbuscular mycorrhiza. 7. Summary

In recent years, the incoming information about the emergence of new superbacteria and superviruses has been causing growing anxiety. However, also fungi are with increasing frequency reported as the sources of intercontinental microbiological hazards. According to the latest reports, quickly spreading, multidrug-resistant and difficult to identify yeast Candida auris may soon become the center of attention for clinicians, laboratory diagnosticians and the groups of advisers on the hospital-acquired infections, also in Poland. Unfortunately, the methods employed in routine microbiological diagnostics in the Polish medical laboratories cannot reliably identify this dangerous species. It is, therefore, necessary to implement measures to develop this field.

1. Introduction. 2. Candida spp. infections. 3. New fungal pathogen–Candida auris. 3.1. Epidemiology and pathogenicity. 3.2. Difficulties with identification. 3.3. Virulence factors. 3.4. Drug resistance of C. auris. 4. Preventive actions. 5. Summary

Nitroaromatic compounds are present in the environment mainly as industry products. They pose a serious risk to our health (often exhibiting strong mutagenic and carcinogenic effect) as well as to the environment. Most of the nitroaromatic compounds are stable due to considerable resistance to degradation and they persist in the environment for a long time. In this review, we present the current state of knowledge concerning biodegradation of nitroaromatic compounds. In the first part, general information regarding their proprieties, synthesis and sources as well as pathways of microbial aerobic or anaerobic degradation are described. In some cases microorganisms have evolved several pathways of degradation specific nitrocompound, for instance nitrobenzene, which we describe in detail. The second part of the publication focuses on environmental bioremediation of nitrocompounds.

1. Introduction. 2.2. Characteristics of aromatic nitrocompounds. 2.1. Chemical properties and synthesis nitroarenes. 2.2. Synthetic aromatic nitrocompounds. 3. The aromatic nitrocompounds in the environment. 4. Risks related to aromatic nitrocompounds. 5. Biodegradation of aromatic nitrocompounds. 5.1. Microbial degradation of aromatic compounds. 5.1.1. Aerobic degradation. 5.1.2. Reductive degradation nitroarenes. 5.1.2.1. Anaerobic digestion. 5.1.3 Degradation of nitrobenzene – an example of alternative distribution pathway. 6. Bioremediation. 6.1. Bioremediation of aromatic nitro compounds – examples of implementation. 6.1.1. Bioremediation engineering in situ. 6.1.2. Bioremediation engineering ex situ. 6.2. Limitations of the bioremediation process and strategies to overcome them. 7. Summary

Chitin, an insoluble linear β-1,4-linked polymer of N-acetylglucosamine, is the second most abundant polysaccharide in nature after cellulose. It is present in cell walls of several fungi, exoskeletons of insects and crustacean shells. Enzymatic hydrolysis of this polysaccharide is carried out in the presence of glycoside hydrolases-chitinases. They are produced by microorganisms, insects, plants, and animal, but it is the bacterial chitinases which play a fundamental role in degradation of the chitin. Chitinases and their products, chito-oligomers, have been of interest in recent years due to their wide range of applications in agriculture, medicine and industry. This review focuses on the enzymatic properties of the bacterial chitinases and their potential applications in various kinds of biotechnology.

1. Introduction. 2. Sources of chitin and its structure. 3. Chitinases – structure and function. 4. Chitinase – producing bacteria. 5. The role of bacterial chitinases in green biotechnology. 6. Application of chitinases in white biotechnology. 7. Application of chitinases in red biotechnology. 8. Summary

Helicobacter pylori commonly colonizes the human gastric mucosa. Infections with this microorganism can contribute to serious health consequences, such as peptic ulceration, gastric adenocarcinoma and gastric mucosa-associated lymphoid tissue lymphoma. Chronic persistence of this bacteria in the host organism is probably strongly dependent on the secretion of outer membrane vesicles (OMV). These organelles are small, electron-dense, extracellular structures which are secreted in large amounts during stressful conditions, among others. H. pylori OMV mediate transfer of virulence factors such as toxins and immunomodulatory compounds. They contribute to avoiding a response from the host immune system and inducing chronic gastritis. OMV secretion also affects the formation of cell aggregates, microcolonies and biofilm matrix. Enhanced OMV production is connected to maintenance of direct contact through cell-cell and cell-surface interactions. A key component of OMV, which determines their structural function, is extracellular DNA (eDNA) anchored to the surface of these organelles. eDNA associated with OMV additionally determines the genetic recombination in the process of horizontal gene transfer. H. pylori is naturally competent for genetic transformation and is constantly capable of DNA uptake from the environment. The natural competence state promotes the assimilation of eDNA anchored to the OMV surface. This is probably dependent on ComB and ComEC components, which are involved in the transformation process. For this reason, the OMV secretion mediates intensive exchange of genetic material, promotes adaptation to changing environmental conditions and enables persistent infecting of the gastric mucosa by H. pylori.

1. Introduction. 2. Secretion of outer membrane vesicles by H. pylori. 3. Proteome of H. pylori outer membrane vesicles. 4. Transport of virulence factors through OMV. 4.1. Toxin VacA. 4.2. Oncoprotein CagA. 4.3. Other substances. 5. OMV involvement in biofilm formation. 5.1. Functions of biofilm. 5.2. OMV influence on bacterial biofilm formation. 5.3. OMV influence on biofilm formation by H. pylori. 5.4. Structural function of H. pylori extracellular DNA. 6. Extracellular DNA as an information carrier. 6.1. Influence on virulence. 6.2. Transformation. 6.3. Natural competence of H. pylori. 7. Conclusions

Bacterial Dsb (disulfide bond) enzymes are involved in the oxidative folding of many proteins, through the formation of disulfide bonds between thiol groups of cysteine residues. This process is critical for the correct folding and structural stability of many secreted and membrane proteins. The rapidly expanding number of sequenced bacterial genomes has revealed the enormous diversity among bacterial Dsb systems. While the Escherichia coli oxidative protein folding has been studied in great details, the mechanism of the Dsb systems functioning in other bacteria are rather poorly understood. Herein, we present the current methodology, both in vivo and in vitroexperimental techniques, which allow us to understand the functioning of the Dsb proteins and has broaden our knowledge in the field of biochemistry and microbiology of this posttranslational protein modification. Many bacterial virulence factors are extracytoplasmic Dsb-dependent proteins. Thus, this system plays an important role in bacterial pathogenesis and the proteins of the Dsb network represent possible targets for new drugs.

1. Introduction. 2. Analysis of the Dsb functioning in vivo. 2.1. Determination of the in vivo redox state. 2.2. Phenotypic assay of the mutated strains. 3. Analysis of the Dsb functioning in vitro. 3.1. Insulin reduction assay. 3.2. Determination of the redox potential. 3.3. Assay of the oxidative and isomerase activity. 3.4. Determination of the pKa value of the cysteine residue 3.5. Determination of the interaction between DsbA and DsbB. 3.6. Protein structures. 3.7. Searching for Dsb protein substrates. 4. Conclusions

Empiric therapy has been applied in the treatment of Lyme disease. This therapy is selected following the sensitivity analysis of the proposed drug in all species of bacteria which can cause a similar type of infection and on the basis of the clinical efficacy of antibiotic treatment. Established schemes based on data collected from many centers in the world, including type of antibiotic, dose and duration of his administration, and the stage and form of Lyme disease have been created. Number of in vitromethods of spirochetes susceptibility to antibiotics has been also developed. Unfortunately, the lack of standardization often makes it impossible to compare the results of MIC and MBC. Furthermore, little is known about the interactions of the various antimicrobial substances and spirochetes. There is a need for testing of clinical strains isolated from patients after treatment, which would explain the problems associated with “refractory” cases of Lyme disease. The paper presents the research on the antibiotic-spirochete interactions observed in vitro.

1. Introduction. 2. In vitro culture and growth of Borreliaburgdorferisensulato. 3. In vitro susceptibility of Borreliaburgdorferisensustricto strains to antimicrobial agents. 4. Summary

Biodiversity is a key concept in finding important features of new microorganisms. Microorganisms play an important role in the soil ecosystem and participate, among others, in such processes as the maintenance of soil structure, humification, release of organic compounds, disposal of pollutants and transformation of organic matter. The maintenance of competent state of soil microbial communities, i.e. the appropriate microorganism count, activity and diversity, is a necessary condition for the functioning of a highly complex system such as the soil. Phyllosphere bacteria have the potential to influence plant biogeography and ecosystem function through their influence on plant performance under different environmental conditions, but the drivers of variation in leaf-associated bacterial biodiversity among host plants are not well understood. Hence, undoubtedly, an important research aspect is the selection and development of indicators to evaluate microbial biodiversity of the soil and plant phyllosphere. In this publication, selected molecular methods used for the diversity assessment of microorganisms have been presented.

1. Introduction. 2. Denaturing Gradient Gel Electrophoresis DGGE, Temperature Gradient Gel Electrophoresis TGGE, 3. SSCP – single strand conformation polymorphism. 4. Real-Time Quantitative PCR. 5. Summary

The research on similarity between bacteria in outbreak investigations enables the identification of bacterial strain responsible for infections, their source and modes of transmission. These investigations are also necessary for the analysis of spreading of bacteria, not only locally, e.g. in a hospital in a specific country, but also internationally and globally. Therefore, it is of great importance to have the most up to date knowledge regarding different methods used in bacterial typing. This review discusses and compares methods facilitating bacterial typing at a strain level. Phenotyping methods analysed in this article are: Biotyping, Antimicrobial Susceptibility Typing, Phage Typing and protein-based methods. Genotyping techniques reviewed in this article are based on digestion of genomic DNA, methods using amplification of DNA, and based on sequencing DNA. This would include Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS). Methods used in identification of bacterial strains are being constantly improved, and gaining more in depth knowledge and familiarising with their effectiveness enables better analysis and control of epidemiological situation e.g. in hospitals.1. Introduction. 2. Phenotyping methods. 2.1. Biotyping. 2.2. Phage typing. 2.3. Antimicrobial susceptibility typing. 2.4. Protein-based methods. 2.5. Mass spectrometry. 3. Genotyping methods. 3.1. Genotyping without DNA sequencing. 3.1.1. REA-PFGE. 3.1.2. RFLP and PCR-RFLP. 3.1.3. AFLP. 3.1.4. RAPD. 3.1.5. Microarrays. 3.1.6. MLVA. 3.2. Genotyping using DNA sequencing 3.2.1. Sequencing technologies. 3.2.2. MLST and SLST. 3.2.3. WGS – wgSNP, cgMLST, wgMLST. 3.2.4. Advantages and disadvantages of WGS. 4. Popularity of typing methods in biomedical research – PubMed database analysis. 5. Conclusions