Department of Soil and Plant System


Preparation and storage of samples

  • Preparation and dispensing of microbiological culture media
  • Sterilization of microbiological media, small glass and laboratory equipment
  • Environmental samples homogenization
  • Preparation of inoculating fluids and diluter used in microbiological analyses
  • Preparation of microscope slides and automatically stain using Gram method
  • Preparation and culturing of fungi in microcultures
  • Storage of bacterial and fungal strains in microbanks in low temperature freezer (to -85 ° C)

Analyses based on molecular biology techniques

  • Selection and optimization of the DNA isolation methods from environmental samples, mycelium and bacteria and yeast cells
  • Identification of bacteria based on 16S rRNA sequencing analysis
  • Identification of fungi based on D2 fragment sequencing, located within the gene encoding the large subunit of the ribosome (LSU)
  • Analysis of genetic profile of microorganisms by amplified fragment length polymorphism (AFLP)
  • Phylogenetic analysis of bacterial and fungal strains isolated from environmental samples
  • Genetic diversity of bacterial and fungal communities using polymerase chain reaction and denaturing  gradient gel electrophoresis (PCR-DGGE) and terminal restriction fragment length polymorphism (t-RFLP)
  • Detection of microorganisms, especially heat resistant fungi by the moloecular biology methods (PCR, qPCR, LAMP)
  • Detection and expression analysis of genes encoding cellulose degradation enzymes (PCR, qPCR, qRT-PCR)

Analyses based on BIOLOG System

  • Identification and characterization of metabolic profile of fungi (FF plates)
  • Identification and characterization of metabolic profile of bacteria(GEN III plates)
  • Identification and characterization of metabolic profile of yeast (YT plates)
  • Identification and characterization of metabolic profile of anaerobic microorganisms(AN plates)
  • Functional microbial diversity evaluation based on characterization of soil metabolic profile (ECO plates)
  • Microorganisms analysis by phenotype microarrays method (PM plates)
  • Evaluation of microorganisms sensitivity to chemical compounds, plant extracts and fungicides (MT2 plates)
  • Assessment of various compounds, waste and products degradation by microorganisms (MT2 plates)

Classical microbiological methods

  • Total number of bacteria and fungi evaluation in environmental samples
  • Evaluation number of heat resistant fungi and their isolation from environmental samples
  • Qualitative and quantitative evaluation of proteolytic, pectinolytic, cellulolytic and amylolytic, microorganisms, ammonifying and nitrifying bacteria in environmental samples
  • Identification of fungi based on macro- and microscopic observations
  • Soil respiratory activity evaluation
  • Assess the sensitivity of fungi to fungicides
  • Evaluation of the microbiological air contamination using air sampler
  • Evaluation of water microbial quality using membrane filter method

Classical biochemical analyses

  • Enzymatic activity evaluation of bacterial and fungal strains (cellulase, pectinesterase, polygalacturonase, protease, lipase)
  • Soil enzymatic evaluation using spectrophotometric methods (dehydrogenases, protease, urease, acid and alkaline phosphatase, β-glucosidase)
  • Evaluation of ammonification and nitrification rate in soil environment
  • Evaluation of soil enzymatic activity using fluorimetric methods (leucine aminopeptidase, esterase, acid and alkaline phosphatase, arylosulphatase, β-glucosidase)