Institute of Plant Genetics
Polish Academy of Sciences

Plant Microbiomics

Plant Microbiomcs Team


dr hab. Lidia Błaszczyk, Prof. IPG PAS


dr Sylwia Salamon

mgr Polina Havrysh




Research profile

The aim of the research is: i) to assess the diversity of microorganisms inhabiting underground and above-ground parts as well as internal tissues of plants; ii) to determine the method of transmission of endogenous microorganisms and to evaluate the impact of the host genotype, individual plant organs and plant growth conditions on the composition and distribution of rhizospheric, phyllospheric and endospheric microorganisms; iii) to understand the morphological, anatomical, physiological and molecular response of plants to changes in their microbiome; iv) to determine the role of epigenetic mechanisms (DNA methylation, lncRNA, microRNA and post-transcriptional histone modifications) in multidirectional interactions of plants with pathogenic and symbiotic fungi, including the assessment of the impact of DNA methylation on long-term epigenetics and intergenerational memory of the plant to stress caused by fungal colonization and, ultimately, v) the selection of endogenous microorganisms for use as plant growth biostimulants and biological agents to reduce fungal diseases and for bioaugmentation of metallophytes.

We use microbiological methods, both classical and based on high-throughput techniques (microscopy, Sanger sequencing, DNA barcoding, metabarcoding), biochemical (spectrometric and mass spectroscopy), physiological (non-invasive methods of measuring the photosynthetic efficiency of plants), morpho-anatomical (light, confocal and scanning electron microscopy, immunolabeling methods), high-throughput sequencing, high-throughput degradome sequencing, DNA bisulfite conversion and sequencing, CpG methylation quantification, pirosequencing, Real time-PCR, digital PCR, high resolution melting analysis, basic bioinformatic and statistical analyses.

Our main achievements are:

-       determining the structure and dynamics of the mycobiome associated with the endosphere of various cultivars and forms of wheat;

-       preview of the interactions of endophytic fungi with the host plant;

-       documenting that growing conditions and the plant organ influence the structure and species diversity of endophytic fungi inhabiting the wheat endosphere;

-       disclosure of fungi from the genera Alternaria and Penicillium and the species Fusarium proliferatum as the so-called core microbiome of Polish wheat varieties.

-       documenting that F. proliferatum, Trichoderma koningii, Trichoderma hamatum, Penicillium crustosum, Penicillium olsonii, Lecanicillium lecanii and Cladosporium sp. are capable of vertical transmission between plant generations, and F. proliferatum, P. olsonii, P. expansum and T. hamatum are capable of horizontal transmission and colonization of wheat plant tissues;

-       creating and maintaining a collection of over 1,000 strains of wheat endophytic fungi.


Key words

Crops, microbiome, endophyte transmission, wheat-fungi interactions, epigenetics, biocontrol, remodeling plant microbiome


Selected recent publications (see all in Scopus)

1. Hoppe K., Chełkowski J., Błaszczyk L., Bocianowski J. (2023) Observation of changes in Fusarium mycotoxin profiles in maize grain over the last decade in Poland. Food Control 110248: DOI: 10.1016/j.foodcont.2023.110248

3. Salamon S., Mikołajczak K., Błaszczyk L. (2023) Constellation of the endophytic mycobiome in spring and winter wheat cultivars grown under various conditions. Scientific Reports 13: 8277. DOI 10.1038/s41598-023-35261-x

4. Błaszczyk L., Ćwiek-Kupczyńska H., Hoppe Gromadzka K., Basińska-Barczak A., Stępień Ł., Kaczmarek J., Lenc L. (2023) Containment of Fusarium culmorum and its mycotoxins in various biological systems by antagonistic Trichoderma and Clonostachys strains. Journal of Fungi 9: 289. DOI: 10.3390/jof9030289

5. Salamon S., Żok J., Gromadzka K., Błaszczyk L. (2021) Expression patterns of miR398, miR167, and miR159 in the interaction between bread wheat (Triticum aestivum L.) and pathogenic Fusarium culmorum and beneficial Trichoderma fungi. Pathogens 10: 1461. DOI: 10.3390/pathogens10111461

6. Błaszczyk L., Salamon S., Mikołajczak K. (2021) Fungi inhabiting the wheat endosphere. Pathogens 10: 1288. DOI:10.3390/pathogens10101288

7. Błaszczyk L., Waśkiewicz A., Gromadzka K., Mikołajczak K., Chełkowski J. (2021) Sarocladium and Lecanicillium associated with maize seeds and their potential to form selected secondary metabolites. Biomolecules 11: 98. DOI:10.3390/biom11010098

8. Basińska-Barczak A., Błaszczyk L., Szentner K. (2020) Plant cell wall changes in common wheat roots as a result of their interaction with beneficial fungi of Trichoderma. Cells 9: 2319. DOI:10.3390/cells9102319

9. Salamon S., Mikołajczak K., Błaszczyk L., Ratajczak K., Sulewska H. (2020) Changes in root-associated fungal communities in Triticum aestivum ssp. spelta L. and Triticum aestivum ssp. vulgare L. under drought stress and in various soil processing. PLOS ONE 15:e0240037. DOI:10.1371/journal.pone.0240037

10. Cłapa T., Mikołajczak K., Błaszczyk L., Narożna D. (2020) Development of high-resolution melting PCR (HRM-PCR) assay to identify native fungal species associated with the wheat endosphere. Journal of Applied Genetics 61:629-635. DOI:10.1007/s13353-020-00578-0


Projects (finished recently or current)


National Science Center

Type Project number (link to NCN) Project title in Polish Project title in English Project leader / partners Financing (PLN) Start date End date
Miniatura 023/07/X/NZ9/00844 Ocena efektywności wchłaniania i procesowania syntetycznych dwuniciowych RNA
przez grzyby endofityczne pszenicy - staż naukowy na Uniwersytecie Bolońskim.
Assessment of the efficiency of absorption and processing of synthetic double-stranded RNAs
by endophytic fungi of wheat - research internship at the University of Bologna.
Sylwia Salamon 49 992 zł 20-09-2023  
Opus 24 2022/47/B/NZ9/01282 RNACTiON: microRNA i siRNA- mediatorzy w komunikacji pomiędzy pszenicą zwyczajną, a patogenicznymi i symbiotycznymi grzybami RNACTiON: microRNAs and siRNA- mediators in communication between common wheat and pathogenic and symbiotic fungi Lidia Błaszczyk 2 145 800 27-06-2023 26-06-2027
OPUS 14 2017/27/B/NZ9/01591 Dynamika mykobiomu endosfery pszenicy zwyczajnej (Triticum aestivum L.) i jej wpływ na wzrost i kondycję rośliny The common wheat (Triticum aestivum L.) endosphere mycobiome dynamics and its impact on the growth and fitness of plant Lidia Błaszczyk 1 374 700 29-06-2018 28-03-2022
OPUS 10 2015/19/B/NZ9/03083 Molekularne podstawy reakcji pszenicy (Triticum aestivum L.) na kolonizację korzeni przez gatunki Trichoderma The molecular basis of wheat responses (Triticum aestivum L.) to Trichoderma spp. root colonization Lidia Błaszczyk 608 400 23-06-2016 6/22/2020







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