Genomics, metagenomics and metatranscriptomics of extreme environments

We are focusing on three groups of bacteria isolated from extreme environments, i.e. (i) psychrotolerants (cold-active bacteria, mainly from Arctic and Antarctica), (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 the metabolic pathways or investigate resistance/tolerance phenotypes of the analyzed strains. Currently, we are conducting several whole-genome sequencing projects. 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 mobile genetic elements (MGEs) of extremophilic bacteria to identify their role in host biology, evolution and adaptation. We also perform complex computational analyses, which allow us to create similarity networks reflecting relationships between analyzed MGEs e.g. in the light of their biogeography.

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). 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 the particular environment or the overall adaptation features of complex microbial consortia inhabiting extreme environments (e.g. Arctic soils).


Genomics and molecular biology of phages

In our projects we are combining two complementary approaches, i.e. metagenomic analysis of the global metavirome of the particular ecological niche and small-scale classical analyses of culturable phage isolates. We are focusing on studying viromes of various extreme environments (e.g. heavy metal contaminated mine). By combining high-throughput sequencing, complex bioinformatic analyses and molecular biology techniques, we try to expand our understanding of the relationships between phages and bacteria (and thus to identify the novel host-phage systems) in extreme environments as well as reveal the role of phages in biology and adaptation of their bacterial hosts to harsh environmental conditions. Our analyses involve also thorough functional characterization of various genetic modules of phages, e.g. methyltransferase genes, which may shed light onto the co-evolution of phages and their bacterial hosts. We are also performing in silico identification of prophage sequences in bacterial genomes and we are applying their structural, comparative and functional characterization, as well as phylogenetic and phylogenomic analyses, leading to the construction of the evolutionary networks for particular groups of viruses.


Biodeterioration of cultural heritage

Microbial colonization of the cultural heritage objects may enhance their deterioration. This process is called biodeterioration, and it is based on the chemical dissolution with the usage of metabolites (mainly acids) produced 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 metagenomic 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

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 aim 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 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. 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). Currently, we are working on the development of the novel systems combining fly-ash-derived functionalized materials with microorganisms for the enhanced bioremediation of soils, waters and industrial gases contaminated with toxic metals and organic pollutants.


Antibiotic resistance

We conduct complex analyses of antibiotic resistance in pristine (e.g. Arctic soils) and anthropogenically-shaped (e.g. wastewater treatment plants) environments, applying combined culture-dependent and culture-independent methods. We are mainly (but not exclusively) focusing on resistances to critically important antimicrobials, e.g. colistin. We study the occurrence, diversity, prevalence and phylogeography of antibiotic resistance genes in various environments by integrating quantitative and qualitative approaches. Moreover, we developed novel bioinformatic tools for tracking antibiotic resistance in various environments. Amongst our latest achievements is a literature-based, manually-curated database of PCR primers for the detection of antibiotic resistance genes (LCPDb-ARG; and Currently, this database is comprised of over 600 PCR primer pairs designed for the amplification of genes conferring resistance to antibiotics representing 10 classes of antimicrobial agents. Four parameters were assigned for each primer pair, namely: specificity, efficacy, taxonomic efficacy and model success metric. These parameters were evaluated using a novel (developed by us) bioinformatic tool, UniPriVal, which can be used to validate every primer pair against various sequence databases. Calculating these parameters for each primer pair enabled obtaining rankings of primers specific to the particular gene, which facilitate further selection of the most suitable ones for the planned analyses.


Biodegradation of organic pollutants and anaerobic digestion

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. 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. 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 linked 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. Currently, we are working on the development of the novel systems combining fly-ash-derived functionalized materials with microorganisms for the enhanced bioremediation of soils, waters and industrial gases contaminated with heavy metals and organic pollutants.

Our group is also involved in researches 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 projects were 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 results of the project are: (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 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 studies was the development of the LipoPrep mixture – a microbial hydrolytic consortium containing 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. In another project, MethaPrep, we developed a novel biotechnology for enhanced utilization of raw sewage sludge and constructed a prototype of a mobile anaerobic digester.


Plant growth promotion

We investigate the influence of soil bioaugmentation with various bacteria and fungi on the growth rate, morphology of plants, their metal tolerance and metals bioaccumulation efficiency. Currently, we are working on the development of the novel biofertilizers combining fly-ash-derived functionalized materials with immobilized microorganisms and their metabolites. Moreover, we are extending our studies of microbial-driven plant growth promotion by analyzing (with the application of the metagenomic approach) the impact of supplemented microorganisms on the structure and activity of autochthonous microbial communities in soil.


Microfluidics for ultrahigh-throughput screening

We develop and implement ultrahigh-throughput technologies that will allow us to select the most efficient microbial consortia from thousands or even millions of combinations of environmental strains or microbial sub-populations. Droplet microfluidics offers an unprecedented increase in the number of reactions (up to 100 million), that can be measured within a single day using optical readouts, such as fluorescence or absorbance. The detection and sorting of droplets can be based on the bacterial growth or presence of detectable products of bioconversion. The most active strains selected using microfluidic ultrahigh throughput methods are then characterized using genomic and phenotypic analysis.


Single-cell genomics

Organisms are built of a large number of diverse and highly specialized cells. To better understand the roles of each cell, we should study them at the single-cell level. One of the most significant achievements of analytical sciences in the last ten years was implementing a droplet microfluidic technology for analyzing single cells using RNA sequencing (RNA-seq). Droplet-based profiling of single-cell transcriptomes allowed for a very detailed description of the physiological state of thousands of single cells and led to an efficient determination of cell types, trajectories, and interactions. These methods are especially indispensable in research fields dealing with highly heterogeneous tissues – such as oncology, immunology, embryology, and other areas of biomedical research. In our research projects, we are applying already established unique techniques, as well as developing novel multi-step microdroplet assays to study transcriptomes and genomes of single cells.


RNA metabolism

The Laboratory of Epitranscriptomics focuses on studying the effects of chemically modified nucleotide presence in RNA on cellular RNA-dependent processes. The areas of group’s interests include modifications of ribonucleic acids in eukaryotic cells and viruses. Viruses use chemically modified nucleotides to hide their genetic material from receptors of host cell immune response pathways. Using biochemical, molecular and cellular biology methods, our team is trying to understand how chemical modifications of viral RNA affect its immunogenic potential and stability in infected cells. Furthermore, we are investigating how epitranscriptomic modifications occurring in eukaryotic mRNA alter its biological properties. We are interested in how protein biosynthesis or the stability of the transcript itself is affected by modifications present especially at mRNA 5′ end.