Environmental biotechnology

Description of the research area

The main aim of scientific projects carried out at the Faculty of Biology and Environmental Protection is to investigate the use of the metabolic potential of microorganisms for cleaning up environments that have been contaminated with toxic hydrocarbons, heavy metals, polymers and nonsteroidal anti-inflammatory drugs. Bacterial and fungal strains that are able to degrade these compounds, synthesise biosurfactants and/or are tolerant to heavy metals are screened. The sources of these valuable strains are the rhizosphere, bulk soil, plants, activated sludge, effluents and water. The strains that are selected and characterised are used in the bioaugmentation of polluted sites as well as to enhance phytostabilisation and phytoextraction. An important aspect of these studies is the implementation of monitoring that will enable the effects of contaminants and remediation techniques on functional, structural and genetic diversity of microbial communities to be established.

Scientific projects in environmental biotechnology are focused on the following topics:

  1. Microbial removal of selected aromatic compounds under co-metabolic conditions

    Research is focused on the degradation of aromatic compounds by selected bacterial strains and mixed populations of soil and sewage sludge microorganisms under co-metabolic conditions. The optimisation of the process of removing difficult degradable aromatic compounds through the selection of the type and concentration of additional carbon sources appears to be one of the crucial ways to support the processes of environmental cleanup, particularly when the tests are aimed at selecting the optimal growth substrates from the naturally occurring compounds that are derived from plants. At the same time, biodegradation processes in these conditions are accompanied by the evaluation of the activity of the key enzymes that are involved in the degradation of aromatics and the analysis of bacterial fatty acid profiles.

  2. Isolation and improvement of the enzymes that are involved in the degradation of aromatic compounds

    The studies are focused on isolating the enzymes that are involved in aromatic ring fission and the identification, sequencing and mutagenesis of the genes encoding these enzymes as well as the biochemical characterisation of mutants. The aim of the studies is to obtain enzymes that are characterised by a high degradation activity over a wide range of pH and temperature.

  3.  The effects of leachate on the functional diversity and microbial activity of activated sludge

    The study is focused on the assessment of the harmful effects of Kalina pond leachate on the functional diversity and microbial activity of activated sludge. The purpose of research is to develop an effective method of supporting the operation of activated sludge that has been exposed to toxic phenolic compounds via bioaugmentation. For this purpose, strains that have the ability to form biofilm, autoaggregate and co- aggregate are being intensively sought. Additionally, the water-repellent membrane and resistance to high concentrations of effluents will enable such bacteria to be used as potential inocula.

  4. Studies on the interactions of rhizospheric and endophytic bacteria with plants

    The aim of the project is to learn the basics of bacteria-plant interactions at the physiological and molecular levels in that are related to the assisted phytoremediation of sites that have been contaminated with aromatic compounds and heavy metals. The studies involve selecting bacterial strains that are able to degrade aromatic hydrocarbons and to promote plant growth, determining the ability of the selected strains to colonise plant tissues and identifying the genes that determine the potential ability of bacteria to colonise plants. Metal-tolerant strains are used to enhance the efficiency of the phytoextraction of heavy metals from soil. Moreover, the results will enable effective biological systems for the remediation of sites that have been contaminated with aromatic compounds and heavy metals to be developed.

  5. Functioning of microorganisms in pesticide-polluted soil

    This project focuses on the responses of non-target soil microorganisms to pesticides and changes in the structural and functional biodiversity of microbial communities. Moreover, this study deals with the effects of nanopesticides on non-target microorganisms, evaluating the toxicity of nanoproducts and assessing their environmental risk in soil conditions.

  6. Risk assessment of the spread of the genes encoding resistance to ampicillin and tetracycline

    The aim of the studies is to evaluate the impact of the effluent and sewage sludge discharge on microbial communities with special emphasis on the dissemination of plasmid-encoded antibiotic resistance among environmental strains. In this study, the diversity of microorganisms as well as the isolation and characterisation of the plasmids that are responsible for the spread of antibiotic resistance in the environment are carried out.

  7. Decomposition of plastics

    The aims of the research projects are to determine the susceptibility and/or resistance of polymer composites and compositions to degradation under laboratory and field conditions. The degradation processes of polymers are conducted in synthetic media or in soil and compost. Particular emphasis is placed on understanding the mechanisms and conditions under which plastics are decomposed by pure and mixed cultures of microorganisms such as bacteria and fungi. Our own collection of microbial strains, which have been isolated from different environments as well as reference strains from international collections, are used in the studies.

  8. Microbiological degradation of nonsteroidal anti-inflammatory drugs (NSAIDs) by selected free and immobilised bacterial strains

    The studies are focused on determining the metabolic features of the bacteria that are engaged in the degradation of NSAIDs as well as the enzymatic mechanisms and genetic regulation of these processes. The aim of this research is to obtain a formulation that is based on immobilised microorganisms that can be used in the bioremediation of environments that have been polluted with NSAIDs and in wastewater treatment plants.

  9. The use of immobilised consortia of nitrifying bacteria for the construction of a bioindicator for water contaminants

    The aim of the research is to build biosensing systems that are able to detect hazardous substances in water that are based on the control of the metabolic processes that are carried out by bacteria. Potentiometric techniques, modelling biochemical processes, μXrayCT tomography, image analysis, confocal microscopy, scanning electron microscopy SEM EDS are used to construct and test such systems.

  10. Water environment management

    These studies are based on a multi-faceted approach to the management of the aquatic environment that include using the DPSIR method to analyse the causes of the poor condition of water and mathematical modelling of ecosystems (Elcom Caedym) for the assessment and prediction of the effects of programmable/test scenarios. In this project, hydroacoustic, physical and chemical analyses of large-scale surfaces are used.

  11. Use of biomarkers for the remediation of polluted habitats.

    These researches focus on the detoxification and bio-elimination mechanisms of deleterious compounds in model invertebrate species. Reliable methods are sought for measuring the oxidative stress that is caused by deleterious compounds (including nanoparticles). Various assays (changes of the redox potential in mitochondria, caspases activity, cellular membrane asymmetry, DNA fragmentation, oxidative damage of DNA and proteins, ATP content and the level of free radicals including lipid peroxidation products) are applied for qualitative and quantitative assessments of apoptotic and/or necrotic changes in the cells of selected tissues and organs. The studies involve the immunological response and protective role of body fluids against oxidative stress, as well as the localisation of neuropeptides within the nervous system. Other research is focused on changes in the physical, chemical and biological properties of spider silk threads following short- and long-term exposure to anthropogenic and natural stressors.

    Investigations are also carried out on the use of biomarkers to evaluate the remediation effects of polluted habitats. The sensitivity of soil invertebrates to crude-oil derivatives is studied including the effects of the remediation of polluted soils.

  12. Detoxification of xenobiotics in the digestive system of selected animal species.

    These researches are aimed at the elucidation of the role of the digestive tract in the detoxification of xenobiotics. Detailed analyses of the phytophage-host plant interactions (particularly the dependence of the gut structure and function on food that is ingested) opens possibility to search for inhibitors of then natural digestive enzymes as potent agents for the control of arduous and invasive pest species such as Diabrotica virgifera, Cameraria ohridella or Spodoptera exigua. Tests are performed to identify the physiological and behavioural effects of plant secondary metabolites (e.g. methylxanthines, volatile oils, etc.) in insects. Other studies focus on the in vitro and in vivo relationship of the efficiency of the digestive system and its microflora and neuropeptide content in insects (primarily phytophages). Degenerative changes in the midgut cells of various spider species are also studied.

  13. The use of biopesticides and other methods for effective pest control.

    These researches focus on identifying the biochemical defence systems against bio-pesticides in various tissues of selected invertebrates. They involve assays of the enzymes that conduct the reactions of the first and second phase of detoxification processes including glutathione metabolism. The affinity of these enzymes to various substrates and their sensitivity to inhibitors are studied as well.

    The individual and joint effects of natural (temperature, food restriction) and anthropogenic (heavy metals, pesticides) stressors on the induction of cellular and subcellular degenerative changes (apoptosis, necrosis, autophagy) in different parts of the digestive tract is also studied during long- and short-term exposure experiments.

    Other investigations focus on the repellent and toxic properties of volatile oils and organic acids against some pests such as Tribolium confusum, Callobruchus maculatus, and Alphitobius diapterinus. Their development and survival as well as their physiological and behavioural responses are monitored during the various developmental stages of the species.

Methods and techniques used in the research

  • traditional bacteria cultivation methods
  • immobilisation of microorganisms on natural and synthetic carriers
  • liquid and gas chromatography
  • UV-VIS spectrophotometry
  • toxicity and genotoxicity tests
  • PCR and real-time PCR
  • electrophoretic methods
  • Biolog® system
  • DNA sequencing and cloning techniques
  • flame atomic absorption spectrophotometry (AAS)
  • microscopic techniques – conventional light, fluorescence confocal, transmission and scanning electron microscopy
  • µXrayCT
  • differential centrifugation
  • continuous cultivation in fermenters and biofilters
  • atomic absorption spectrometry (AAS)
  • molecular markers
  • molecular and biochemical methods for the assessment the diversity of soil microorganism communities (DGGE, BIOLOG®)
  • image cytometry
  • water pollution detecting biosensors
  • studies on the structure of enzymatic proteins
  • ELISA, Western Blotting
  • bioinformatic techniques
  • immunohistochemical techniques
  • behavioural assays (locomotor and exploratory activities)