Analysis of rice microbial communities under different storage conditions using culture-dependent and -independent techniques
Main Article Content
Keywords
mold community, PCR-DGGE, rice, traditional culture
Abstract
Rice is a staple food for over half of the world’s population, and fungal spoilage in stored rice may occur when the moisture content and temperature are conducive. Aspergillus sp. and Penicillium sp. are the most harmful toxigenic species that produce harmful mycotoxins. Molds pose a potential threat to public health and cause a huge economic loss. Therefore, it is of great importance to find out how molds multiply in rice. This study focused on the isolation and identification of fungi presented in rice and their evolution in rice with different moisture contents stored for varying periods of time and under different temperatures. Mold community was detected every month using the culture-dependent and -independent method of polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Significant differences were detected by the traditional culture method under different storage conditions. For potato dextrose agar (PDA) media, high temperature and moisture were suitable for the dominant strains including Penicillium aurantiogriseum and Penicillium oxalicum. In particular, P. oxalicum competitively inhibited the other fungi. For Rose Bengal medium, no difference was observed under different storage conditions, and only typical strains such as Aspergillus candidus and Alternaria were detected. PCR-DGGE identified some uncultured strains such as Trichoderma sp. and Cladosporium sp., the dominant strains and the flora diversity such as Aspergillus restrictus and Eurotium athecium. These results indicated that storage conditions greatly shape fungal growth. This study provides a foundation for the evolution of fungal flora in rice during storage in China and may help in developing biological control methods to prevent mold contamination in rice.
References
Sheikha, AFE, Bouvet, JM, & Montet, D, 2011. Biological bar code for determining the geographical origin of fruits using 28s rDNA fingerprinting of fungal communities by PCR-DGGE: An application to shea tree fruits. Qual Assur Saf Crop., 3(1):40–7. 10.1111/j.1757-837X.2010.00090.x
Bennett JW, Klich M, 2003. Mycotoxins. Clin Microbiol Rev., 16:497–516. 10.1128/CMR.16.3.497-516.2003
Brjesson T, Stllman U, Schnürer J, 1990. Volatile metabolites and other indicators of Penicillium aurantiogriseum growth on different substrates. Appl Environ Microbiol., 56(12):3705–10. 10.1128/aem.56.12.3705-3710.1990
Cal AD, Melgarejo P., 2001. Repeated applications of Penicillium oxalicum prolongs biocontrol of fusarium wilt of tomato plants. Eur J Plant Pathol., 107(8):805–11. 10.1023/A:1012432404886
Cal AD, Pascual S, Larena I, Melgarejo P, 2010. Biological control of Fusarium oxysporum f. sp. lycopersici. Plant Pathol ., 44(5):909–17. 10.1111/j.1365-3059.1995.tb02750.x
Cal AD, Redondo C, Sztejnberg A, Melgarejo P, 2008. Biocontrol of powdery mildew by Penicillium oxalicum in open-field nurseries of strawberries. Biol Control., 47(1):103–7. 10.1016/j.biocontrol.2008.07.010
Chattopadhyay SK, Nandi B, Ghosh P, Thakur S, 1987. A new mycotoxin from Aspergillus candidus link isolated from rough rice. Mycopathologia., 98(1):21–6. 10.1007/BF00431013
Cocolin L, Alessandria V, Dolci P, Gorra R, Rantsiou K, 2013. Culture independent methods to assess the diversity and dynamics of microbiota during food fermentation. Int J Food Microbiol., 167(1):29–43. 10.1016/j.ijfoodmicro.2013.05.008
Cortés-Rojas D, Beltrán-Acosta C, Zapata-Narvaez Y, Chaparro M, Cruz-Barrera M, 2021. Seed coating as a delivery system for the endophyte trichoderma koningiopsis th003 in rice (Oryza sativa). Appl Microbiol Biotechnol., 105(1889–1904). 10.1007/s00253-021-11146-9
Delgado S, Rachid CT, Fernández E, Rychlik T, Alegría Á, Peixoto RS, et al., 2013. Diversity of thermophilic bacteria in raw, pasteurized and selectively-cultured milk, as assessed by culturing, PCR-DGGE and pyrosequencing. Food Microbiol., 36(1):103–11. 10.1016/j.fm.2013.04.015
Demirci T, Akin N, Atik DS, Zkan ER, Akyol S, 2021. Lactic acid bacteria diversity and dynamics during ripening of traditional Turkish goatskin tulum cheese produced in Mut region assessed by culturing and PCR-DGGE. LWT–Food Sci Technol., 138(5):110701. 10.1016/j.lwt.2020.110701
Dong H, Chen Q, Wang W, Peng S, Huang J, Cui K, et al., 2017. The growth and yield of a wet-seeded rice-ratoon rice system in central China. Field Crops Res., 208:55–9. 10.1016/j.fcr.2017.04.003
Duong LM, Jeewon R, Lumyong S, Hyde KD, 2006. DGGE coupled with ribosomal DNA gene phylogenies reveal uncharacterized fungal phylotypes. Fungal Diversity., 23(6):121–138. http://hdl.handle.net/10722/223170
El Sheikha A, 2019. Molecular detection of mycotoxigenic fungi in foods: The case for using PCR-DGGE. Food Biotechnol., 33(1):54–108. 10.1080/08905436.2018.1547644
Fleurat-Lessard F, 2017. Integrated management of the risks of stored grain spoilage by seedborne fungi and contamination by storage mould mycotoxins–An update. J Stored Prod Res., 71:22–40. 10.1016/j.jspr.2016.10.002
Gock MA, Hocking AD, Pitt JI, Poulos PG, 2003. Influence of temperature, water activity and pH on growth of some xerophilic fungi. Int J Food Microbiol., 81(1):11–19. 10.1016/S0168-1605(02)00166-6
Iheanacho HE, Njobeh PB, Dutton FM, Steenkamp PA, Steenkamp L, Mthombeni JQ, et al., 2014. Morphological and molecular identification of filamentous Aspergillus flavus and Aspergillus parasiticus isolated from compound feeds in South Africa. Food Microbiol., 44:180–4. 10.1111/jfpp.14178
Iqbal A, Khalil IA, Shah H, 2006. Aflatoxin contents of stored and artificially inoculated cereals and nuts. Food Chem., 98(4):699–703. 10.1016/j.foodchem.2005.06.034
Jiang Y, Gao F, Xu XL, Su Y, Ye KP, Zhou GH, 2010. Changes in the bacterial communities of vacuum-packaged pork during chilled storage analyzed by PCR–DGGE. Meat Sci., 86(4):889–95. 10.1016/j.meatsci.2010.05.021
Lahouar A, Marin S, Crespo-Sempere A, Saïd S, Sanchis V, 2016. Effects of temperature, water activity and incubation time on fungal growth and aflatoxin B1 production by toxinogenic Aspergillus flavus isolates on sorghum seeds. Rev. Argent. Microbiol., 48(1):78–85. 10.1016/j.ram.2015.10.001
Larena I, Sabuquillo P, Melgarejo P, Cal AD, 2010. Biocontrol of fusarium and verticillium wilt of tomato by Penicillium oxalicum under greenhouse and field conditions. J Phytopathol., 151(9):507–12. 10.1046/j.1439-0434.2003.00762.x
Leite AM, Mayo B, Rachid CT, Peixoto RS, Silva JT, Paschoalin VMF, et al., 2012. Assessment of the microbial diversity of Brazilian kefir grains by PCR-DGGE and pyrosequencing analysis. Food Microbiol., 31(2):215–21. 10.1016/j.fm.2012.03.011
Louis Feinstein, 1969. Grain Storage—the Role of Fungi in Quality Loss, Bulletin of the Entomological Society of America, 15(3):259. 10.1093/besa/15.3.259
Li QQ, Dang L Z, Zhang YP, Jiang J X, Zhang CM, Xiang NJ, et al., 2015. Isocoumarins from the fermentation products of a plant entophytic fungus Penicillium oxalicum. Nat Prod Res., 17(9):876–81. 10.1080/10286020.2015.1039997
Mannaa M, Kim KD, 2017. Influence of temperature and water activity on deleterious fungi and mycotoxin production during grain storage. Mycobiology., 45(4):240–54. 10.5941/MYCO.2017.45.4.240
Mathan, S, Smith, AA, Kumaran, J, & Prakash, S, 2011. Anticancer and antimicrobial activity of Aspergillus protuberus sp1 isolated from marine sediments of south Indian coast. Chinese J Nat Med., 4: 286–292. http://www.cqvip.com/QK/86968X/201104/38511487.html
Maturano YP, Mestre MV, Combina M, Toro ME, Vazquez F, Esteve-Zarzoso B, 2016. Culture-dependent and independent techniques to monitor yeast species during cold soak carried out at different temperatures in winemaking. Int J Food Microbiol., 237:142–9. 10.1016/j.ijfoodmicro.2016.08.013
Mohapatra D, Kumar S, Kotwaliwale N, Singh KK, 2017. Critical factors responsible for fungi growth in stored food grains and non-chemical approaches for their control. Ind Crops Prod., 108:162–82. 10.1016/j.indcrop.2017.06.039
Naseer R, Sultana B, Khan MZ, Naseer D, Nigam P, 2014. Utilization of waste fruit-peels to inhibit aflatoxins synthesis by Aspergillus flavus: A biotreatment of rice for safer storage. Bioresource Technol., 172:423–8. 10.1016/j.biortech.2014.09.017
Oh JY, Kim EN, Ryoo MI, Kim KD, 2008. Morphological and molecular identification of Penicillium islandicum isolate KU101 from stored rice. Plant Pathol J., 24(4):469–73. 10.5423/PPJ.2008.24.4.469
Oh JY, Sang MK, Oh JE, Lee HJ, Ryoo MI, Kim KD, 2010. Microbial population, aflatoxin contamination, and predominant Aspergillus species in Korean stored rice. Plant Pathol J., 26(2):121–9. 10.5423/PPJ.2010.26.2.121
Paola M, Victoria M, Mariana C, Maria ET, 2016. Culture-dependent and independent techniques to monitor yeast species during cold soak carried out at different temperatures in winemaking — ScienceDirect. Int J Food Microbiol., 237:142–9. 10.1016/j.ijfoodmicro.2016.08.013
Park JW, Choi SY, Hwang HJ, Kim YB, 2005. Fungal mycoflora and mycotoxins in Korean polished rice destined for humans. IntJ Food Microbiol., 103(3):305–14. 10.1016/j.ijfoodmicro.2005.02.001
Paterson RRM, Lima N, 2010. How will climate change affect mycotoxins in food? Food Res Int., 43(7):1902–14. 10.1016/j.foodres.2009.07.010
Sabuquillo P, Cal AD, Melgarejo P, 2005. Dispersal improvement of a powder formulation of Penicillium oxalicum, a biocontrol agent of tomato wilt. Plant Dis., 89(12):1317–23. 10.1094/PD-89-1317
Sabuquillo P, Cal, AD, Melgarejo P, 2006. Biocontrol of tomato wilt by Penicillium oxalicum formulations in different crop conditions. Biol Control., 37(3):256–65. 10.1016/j.biocontrol.2006.02.009
Sempere F, Santamarina MP, 2010. Study of the interactions between Penicillium oxalicum Currie & Thom and Alternaria alternata (Fr.) Keissler. Brazilian J Microbiol., 41(3):700–6. 10.1590/S1517-83822010005000003
Somjaipeng S, Ta-uea P, 2016. Evaluation of the effect of water activity and temperature on lag phase and growth rate of aflatoxigenic aspergillus section flavi strains isolated from stored rice grain. Agric Agric Sci Proc., 11:38–45. 10.1016/j.aaspro.2016.12.007
Sultana B, Naseer R, Nigam P, 2015. Utilization of agro-wastes to inhibit aflatoxins synthesis by Aspergillus parasiticus: A biotreatment of three cereals for safe long-term storage. Biores Technol., 197:443–50. 10.1016/j.biortech.2015.08.113
Wang C, Esteve-Zarzoso B, Cocolin L, Mos A, Rantsiou K, 2015. Viable and culturable populations of Saccharomyces cerevisiae, Hanseniaspora uvarum and Starmerella bacillaris (synonym Candida zemplinina) during barbera must fermentation. Food Res Int., 78(12):195–200. 10.1016/j.foodres.2015.10.014
Windels CE, Kommedahl T, 1982. Pea cultivar effect on seed treatment with Penicillium oxalicum in the field. Phytopathology., 72(5):541–3. 10.1094/Phyto-77-541