Fungal diversity of root vegetables and soil rhizosphere collected from organic and conventional farms in Eastern Poland
More details
Hide details
Department of Biological Health Hazards and Parasitology, Institute of Rural Health, Lublin, Poland
Corresponding author
Teresa Kłapeć   

Department of Biological Health Hazards and Parasitology, Institute of Rural Health, Jaczewskiego 2,, 20-090 Lublin, Poland
Ann Agric Environ Med. 2018;25(2):374-381
Determination of the concentration and species composition of filamentous fungi in root vegetables (carrots and red beetroots), and the adjacent rhizosphere soil, collected on organic and conventional farms in Eastern Poland.

Material and methods:
During the period 2015–2016, a total number of 80 samples of vegetables and 40 samples of soil were examined. From each type of farm, 20 samples of vegetables and 20 samples of the adjacent soil were examined. In addition, the study included 20 samples of vegetables from organic farms and 20 samples of vegetables from conventional farms purchased on the markets in the city of Lublin in Eastern Poland. In order to determine the concentration and species composition of filamentous fungi, both in vegetables and soil, the method of plate dilutions on Malt Agar medium (Difco) with chloramphenicol was used. The study was conducted in two parallel repetitions. Inoculated media were incubated at the temperature of 30°C for 72 hours, then at room temperature for 72 hours. The species composition of fungal flora was determined using macroscopic and microscopic methods, with the help of keys and atlases.

It was found that the mean concentration of fungi was higher in vegetables and soil from conventional farms than in those from organic farms. In the case of carrots and soil from conventional farms, this concentration was 4.93 and 5.10 log10 CFU g-1, respectively, whereas from organic farms – respectively, 3.81 and 4.20 log10 CFU g-1. In the case of beetroots and soil from conventional farms, the mean concentrations were also higher compared to organic farms – 5.09 vs. 3.93 and 4.95 vs. 4.23 log10 CFU g-1. In the examined vegetables and rhizosphere soil, 61 species of filamentous fungi were found, of which 12 belonged to the genus Penicillium, 4 to the genus Fusarium, and 2 species each to the genera: Aspergillus, Cladosporium and Trichoderma. As many as 28 (45.9%) fungal species that occurred in vegetables and soil are regarded as pathogenic for humans.

Jung Y, Jang H, Matthews KR. Effect of the food production chain from farm practices to vegetable processing on outbreak incidence. Microbiol Biotechnol. 2014; 7(6): 517–527.
Maffei DF, Batalha EY, Landgraf M, Schaffner DW, Franco BD. Microbiology of organic and conventionally grown fresh produce. Brazilian J Microbiol. 2016; 47 (Suppl 1): 99–105.
Oliveira M, Usall J, Vinas I, Anguera M, Gatius F, Abadias M. Microbiological quality of fresh lettuce from organic and conventional production. Food Microbiol. 2010; 27: 679–684.
Tango CN, Choi NJ, Chung MS, Oh DH. Bacteriological quality of vegetables from organic and conventional production in different areas of Korea. J Food Protection. 2014; 77(8): 1411–1417.
Szczech M, Kowalska B. Microbiological quality of organic vegetables.Nowości Warzywnicze 2010; 51: 65–72 (in Polish).
Cabral Machado D, Marques Maia C, Dias Carvalho I, Fontoura da Silva N et al. Microbiological quality of organic vegetables produced in soil treated with different types of manure and mineral fertilizers. Braz. J. Microbiol. 2006; 37(4): 538–544.
Barkai-Golan R, Paster N. Mycotoxins in fruits and vegetables. San Diego: Academic Press. 2008.
Lugauskas A, Repečkienė J, Levinskaitė L, Mačkinaitė R, Kačergius A, Raudonienė V. Micromycetes as toxin producers detected on raw material of plant origin grown under various conditions in Lithuania. Ekologija. 2006; 3: 1–13.
Kwaśna H, Chełkowski J, Zajkowski P. Fungi. Volume XXII. Institute of Botany, PAN, Kraków 1991 (in Polish).
Samson R.A., Houbraken J, Frisvad JC, Andersen B. Food and Indoor Fungi; CBS-KNAW 2010 Fungal BiodiwerCity Centre Utrecht.
Watanabe T. Pictorial Atlas of Soil and Seed Fungi; CRC Press, Boca Raton, USA 2010.
Abadias M, Usall J, Anguera M, Solsona C, Viñas I. Microbiological quality of fresh, minimally-processed fruit and vegetables, and sprouts from retail establishments. Int J Food Microbiol. 2008; 123(1–2): 121–129.
Maffei DF, Silveria N, Catanozi M. Microbiological quality of organic and conventiolal vegetables sold in Brazil. Food Control 2013; 29(1): 226–230.
Kłapeć T, Cholewa A, Cholewa G, Dutkiewicz J, Wójcik-Fatla A. Microbiological characterization of vegetables and their rhizosphere soil in eastern Poland. Ann Agric Env Med. 2016; 23(4): 559–565.
Marin S, Ramos AJ, Cano-Sancho G, Sanchis V. Mycotoxins: Occurrence, toxicology, and exposure assessment. Food Chem Toxic. 2013; 60: 218–237.
Lillard-Roberts S. Mycotoxin list. Boletim Científico 2017; No. 46. Available at Accessed 20.01.17.
Solfrizzo M, De Girolamo A, Vitti C, Visconti A Van Den Bulk R. Liquid chromatographic determination of Alternaria toxins in carrots. JAOAC International. 2004; 87: 101–106.
Solfrizzo M, Girolamo AD, Vitti C, Tylkowska K, Grabarkiewicz-Szczęsna J, Szopińska D, et al. Toxigenic profile of Alternaria alternata and Alternaria radicina occurring on umbelliferous plants. Food Addit Contam. 2005; 22(4): 302–308.
Kuhn DM, Ghannoum MA. Indoor mold, toxigenic fungi, and Stachybotrys chartarum: infectious disease perspective. Clin Microbiol Rev. 2003; 16(1): 144–172.
Moldes-Anaya A., Rundberget T, Fæste CK, Eriksen GS, Bernhoft A. Neurotoxicity of Penicillium crustosum secondary metabolites: tremorgenic activity of orally administered penitrem A and thomitrem A and E in mice. Toxicon. 2012; 60(8): 1428–1435.
Farmakiotis D, Kontoyiannis DP. Mucormycoses. In L. Ostrosky-Zeichner, L. Sobel (Eds.), Fungal Infections, Special Issue of Infectious Disease Clinics of North America. 2016; 30: 143–163.
InspectApedia. Mold atlas of indoor clinical mold, pathogens, allergens & other indoor particles. Available at htpp:// 2017. Accessed 01.02.17.
Popescu FD. Cross-reactivity between aeroallergens and food allergens. World J Methodol. 2015; 5(2): 31–50.
Luccioli, S, Malka-Rais J, Osnuli TM, Bellanti, JA. Clinical reactivity to ingestion challenge with mixed mold extract may be enhanced in subjects sensitized to molds. Allergy Asthma Proceedings. 2009; 30(4): 433–442.
Żukiewicz-Sobczak WA., Cholewa G, Sobczak P, Silny W, Nadulski R, Wojtyła-Buciora P, et al. Enzymatic activity of fungiisolated from crops. Adv Dermatol Allergol. 2016; 33(6): 457–463.
Yike I. Fungal proteases and their pathophysiological effects. Mycopathologia. 2011; 171(5): 299–323.
Journals System - logo
Scroll to top