Genome research of extremophilic microorganisms

Extremophiles tolerate (or even need for living) extreme environmental factors, like low temperature or highly acidic pH. In several currently conducted projects we are focusing on three groups of bacteria isolated from extreme environments, i.e. (i) psychrotolerants (cold-active bacteria), (ii) metallotolerants, and (iii) bacteria capable of utilizing toxic compounds and resistant to high concentrations of such substances. The preformed analyses involve both structural and functional genomics, and are aimed to in silico reconstruct particular metabolic pathways or investigate resistance/tolerance phenotypes of the analyzed strains (e.g. arsenic resistance and biotransformation pathways). Currently, we are conducting several whole genome sequencing projects, including two arsenate-reducing bacteria of the genera Aeromonas and Shewanella and a strictly psychrophilic strain of Psychrobacter. We are particularly interested in isolation, identification and characterization of bacteria with a high application potential in various biotechnologies.

Moreover, we are performing sequencing and thorough structural and functional analyses of plasmids, phages and transposable elements of extremophilic bacteria from Arctic and Antarctic regions, and arsenic-contaminated sites in Poland. The analyses are aimed to identify the role of these mobile genetic elements (MGEs) in biology, evolution and adaptation of extremophilic bacteria. Within the sequenced MGEs maintenance and phenotypic modules are identified and then functionally characterized. We also perform complex comparative analyses of selected MGEs, which allow us to create models of similarity networks between mobile elements of bacteria inhabiting particular environments.


Metagenomics and metatranscriptomics of extreme environments

In the course of metagenomic analyses of extreme environments we analyze both taxonomic diversity (revealed by the high-throughput sequencing of the PCR amplicons of various marker genes for Bacteria, Archaea and selected Eukaryota) and functional diversity (revealed by the shotgun-sequencing of environmental samples focused on the particular metabolic process or phenomenon, e.g. heavy metals and antibiotics metabolism and resistances). Metagenomic studies are supplemented with the metatranscriptomic analyses enabling identification of “active” genetic information in extreme environments. The performed analyses are mostly of ecological value, as they allow for an insight into, e.g., seasonal changes of microbiomes within a particular environment or the overall adaptation features of complex microbial consortia inhabiting extreme environments (e.g. Arctic soils, heavy metal contaminated mines).


Genomics and biotechnology of phages

As natural parasites of bacteria, bacteriophages (phages) are the most abundant biological entities on Earth and occur in every environment inhabited by bacteria. In several ongoing projects we are focusing on isolation and identification of new phages from diverse environments, and on analyzing their biology and biotechnological potential.

One specific research aim is isolating bacteriophages that are able to effectively develop in various Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa and Klebsiella pneumoniae strains, and using them as therapeutic agents in bacterial infections in animals.

In another project we are exploring the potential of an innovative therapy against bacterial infections that is based on the combined use of nanoparticles and bacteriophages. Our integrative approach involves detailed analyses of the physico-chemical properties of phage-displayed nanoparticles as well as exploration of molecular interactions between phages and nanoparticles. In addition to advancing the field of research on new therapeutic agents, project results will expand the basic knowledge in the field of bionanomaterials. Furthermore, the results may also have an impact on the development of other economy sectors such as construction of new bionanomaterials.

In the third project we are focusing on Alphaproteobacteria and their phages. The Alphaproteobacteria are probably the most metabolically diverse class of bacteria, and are employed both in basic research and in applied research to solve biotechnological challenges. The aim of the project is to characterize a pool of lysogenic and lytic phages (and prophage sequences) of Alphaproteobacteria. The research strategy includes identification of active phages within a pool of alphaproteobacterial strains available in our collection, as well as in silico identification of prophage sequences in various genomes of Alphaproteobacteria. This is a starting point for more complex analyses in the area of structural, comparative and functional genomics, as well as phylogenetic and phylogenomic analyses, leading to the construction of evolutionary networks between particular phages. Moreover, the functional analysis of (pro)phage sequences may lead to the identification of novel enzymes useful in biotechnology and molecular biology, e.g. lytic enzymes with antibacterial properties. In the project, we also aim to create a publicly available database of Alphaproteobacteria phages, where sequences and other information on both active and cryptic prophages will be deposited.


Biodeterioration of culture heritage

Microorganisms are known for their ability to colonize various organic and inorganic materials, which may be of potential value, e.g. culture heritage objects. However, microbial colonization of such objects may enhance their deterioration,. This process is called biodeterioration, and it based on the chemical dissolution with organic or inorganic acids and ligands produced and secreted by microorganisms. The presence and activity of various bacterial and fungal groups inhabiting the culture heritage objects and causing their deterioration is influenced by various biotic and abiotic factors.

In our projects, we aim to investigate the correlation between the bacterial and fungal diversity and their activity on surfaces of historical (and archeological) objects using both classical microbiology and metagenomics approaches. We are also studying the influence of abiotic factors (e.g. the air pollution level) on the structure and functioning of microbiomes causing biodeterioration. The projects also have application significance, as they reveal the potential epidemiological risk caused by the bacteria and fungi present on the historical objects and provide instructions for culture heritage conservators on the removal of such microorganisms. Our projects are conducted in cooperation with several Polish museums, e.g. the Museum of King John’s III Palace at Wilanow.


Heavy metals resistance, transformation, biometallurgy and bioremediation

Most of the microorganisms found in the environment primarily use easily assimilable nutrients, but under extreme conditions, many of them are capable of utilizing various toxic compounds, including heavy metals or metalloids. Microorganisms can transform heavy metals (e.g. by oxidation, reduction, methylation, or complexation) and use them, e.g. as sources of energy, terminal electron acceptors and structural elements of enzymes, or they can simply remove metal ions from their cells, using various detoxification mechanisms. Due to these properties, microorganisms can be used in biometallurgy and in many bioremediation technologies.

Our group is involved in several projects that aimed to investigate the physiology, metabolism and genomics of metallotolerant microorganisms. The specific research goals include: (i) the analysis of adaptation mechanisms of microorganisms to heavy metal contaminated environments, (ii) studies on the diversity and distribution of the heavy metal resistance and metabolism genes in various environments (e.g. mines), (iii) explanation of the role of isolates and microbial consortia in bioremediation of polluted habitats (including analyses of: mobilization/immobilization of heavy metals in the context of self-purification of the contaminated environments, as well as application in bioengineering approaches), and (iv) the development of highly efficient biomining consortia for the processing of mineral deposits and selection and optimization of appropriate bioleaching systems.

In addition to basic research, our group is specializing in R&D projects, which are aimed to implement the biometallurgical and bioremediation strategies. We are working in cooperation with the Warsaw University of Technology to solve the problem of scale enlargement of various technologies developed in laboratory scale. One of our latest achievements is the construction of a pilot scale plant utilizing the potential of microbial oxidation for the removal of arsenic from contaminated waters (MicroAsOx technology).


Biodegradation of organic pollutants

Soil contamination with petroleum and other organic compounds released by industry is a worldwide environmental problem and can pose significant ecological risks. Among various technologies that have been used to purify contaminated areas, bioremediation has proven to be an economic and environmentally friendly approach. However, without professional support on how to use nutrients, terminal electron acceptors, and auxiliary substrates (e.g. vitamins) to increase the activity and stimulate the growth of indigenous microbial populations (biostimulation), and without the knowledge on how to operate with autochthonous or exogenous contaminant-degrading microorganisms (bioaugmentation) many attempts may be unsuccessful. For this reason, our group launched a scientific and commercial activity offering a whole package of services to companies involved in bioremediation. So far, the effect of our activities include development and implementation of (i) BioRem Service Pack – package of procedures for the selection of appropriate methods for biostimulation and bioaugmentation, and (ii) BioRemOil – microbial vaccines dedicated for in situ bioremediation of soil contaminated with oil. BioRem Service Pack contains guidelines for laboratory treatability and field pilot scale studies for in situ and ex situ operations. In turn, BioRemOil is a “universal” mixture of more than 120 bacterial strains capable of efficient degradation of oil and petroleum products. In addition to BioRemOil, we have developed a strategy for the selection and preparation of a dedicated bioremediation vaccine based on the indigenous microflora.

Our scientific work connected with biodegradation of organic pollutants is based on environmental screening for microorganisms suitable for various bioremediation technologies, e.g. producing various hydrolyzing enzymes, siderophores and biosurfactants. Moreover, we perform various molecular and biochemical analyses to reveal the mechanisms underlying the biodegradation of organic pollutants.


Anaerobic digestion

Our group is involved in the research concerning anaerobic digestion, a method for the treatment of organic waste aimed to reduce their amount with simultaneous production of energy in the form of methane (biogas). Our first project was established in response to the specific needs of industry and concerned the development of microbial biostarters for the initiation of the methane production process and further enhanced biogas production in plants using energy crop substrates. The end result of the project was: (i) development of a strategy for preparation of a well-balanced microbial consortium that can increase stability and the substrate degradation rate to yield a shorter start-up period for biogas production and enhanced methane formation; (ii) development of the DigestPrep mixture, which comprises a consortium of microorganisms capable of hydrolyzing lignocellulosic biomass and increasing the efficiency of biogas production in the methane fermentation process, and (iii) development of biomarkers – a set of PCR primers for the amplification of genes encoding key enzymes involved in methanogenesis, for the screening and controlling of the methane producing consortia.

Our recent scientific achievements in the area of anaerobic digestion also include a method for treatment of sewage sludge. The result of this activity was the development of the LipoPrep mixture –  a microbial hydrolytic consortium containing 33 strains with a high hydrolytic activity (mainly lipolytic, proteolytic and cellulolytic) and a wide range of tolerance to various physical and chemical conditions. Pretreatment with LipoPrep enhances the efficiency of anaerobic digestion of sewage sludge. This invention has been applied for patent protection and non-exclusive license for its use was sold to RDLS Sp. z o.o. (a spin-off company of the University of Warsaw). Based on the LipoPrep, other bioproducts and biosupplements we have launched another project, MethaPrep, which aims to the development of a novel biotechnology for enhanced utilization of raw sewage sludge and the construction of a prototype of a mobile anaerobic digester. The ongoing R&D studies include the development of the complete technological pathway starting from (i) the screening phase (analysis of biodegradability of sewage sludge and selection of a proper bioproduct), through (ii) the selection of optimum parameters of the process in a laboratory scale and (iii) experimental verification in pilot scale in wastewater treatment plants, to (iv) preparation of technical instructions necessary to initiate the industrial scale production.