Abstract
Long-term non-irrigation (N-IRR) and irrigation (IRR) might affect pathogen communities causing seed-rot, root-rot, and damping-off of soybean. Characterization and quantification of Pythium, Fusarium, and Rhizoctonia spp. are critical for understanding the ecology of these microorganisms and management of root diseases. The populations and communities of Pythium, Fusarium, and Rhizoctonia were assessed in soils with long-term N-IRR and IRR using soil dilution plating, denaturing gradient gel electrophoresis (DGGE), and DNA sequence analysis. Disease incidences of seed-rot, root-rot, and damping-off of soybean were also evaluated with the soils from N-IRR and IRR in a growth chamber. Results showed that the population densities of Pythium and Rhizoctonia based on dilution plating and richness based on DGGE were significantly lower in soils with N-IRR than IRR, whereas the population densities of Fusarium and richness of Fusarium were significantly higher in soils with N-IRR than IRR. Cluster analysis based on DGGE band patterns demonstrated that the communities of Pythium, Fusarium, and Rhizoctonia were separated based on N-IRR and IRR. Species diversities of some Pythium, Fusarium, or Rhizoctonia were impacted differently in soils with N-IRR and IRR. Moreover, canonical correspondence analysis (CCA) showed that the disease incidences were positively correlated with levels of soil moisture, pH, the populations of Pythium and Rhizoctonia, richness of Pythium and Rhizoctonia, and negatively correlated with soil porosity, humic matter, and potassium. Long-term N-IRR and IRR could impact pathogen populations and communities and disease incidences differently, and the disease complex might be caused by different species under different systems.
Similar content being viewed by others
References
Ajayi-Oyetunde, O. O., & Bradley, C. A. (2017). Identification and characterization of Rhizoctonia species associated with soybean seedling disease. Plant Disease, 101, 520–533.
Allen, T. W., Bradley, C. A., Sisson, A. J., Byamukama, E., Chilvers, M. I., Coker, C. M., Collins, A. A., Damicone, J. P., Dorrance, A. E., Dafault, N. S., et al. (2017). Soybean yield loss estimates due to diseases in the United States and Ontario, Canada, from 2010 to 2014. Plant Health Progress, 18, 19–27.
Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25, 3389–3402.
Broders, K. D., Lipps, P. E., Paul, P. A., & Dorrance, A. E. (2007). Characterization of Pythium spp. associated with corn and soybean seed and seedling disease in Ohio. Plant Disease, 91, 727–735.
Broders, K. D., Wallhead, M. W., Austin, G. D., Lipps, P. E., Paul, P. A., Mullen, R. W., & Dorrance, A. E. (2009). Association of soil chemical and physical properties with Pythium species diversity, community composition, and disease incidence. Phytopathology, 99, 957–967.
Burgess, L. W. (1981). General ecology of the Fusaria. In P. E. Nelson, T. A. Toussoun, & R. J. Cook (Eds.), Fusarium: Disease, biology, and taxonomy (pp. 225–235). University Park: Pennsovinia University Press.
Condron, L. M., Hopkins, D. W., Gregorich, E. G., Black, A., & Waklin, S. A. (2014). Long-term irrigation effects on soil organic matter under temperate grazed pasture. European Journal of Soil Science, 65, 741–750.
Cook, R. J., & Papendick, R. I. (1970). Soil water potential as a factor in the ecology of Fusarium roseum f. sp. cerealis culmorum. Plant and Soil, 32, 131–145.
Díaz Arias, M. M., Leandro, L. F., & Munkvold, G. P. (2013). Aggressiveness of Fusarium species and impact of root infection on growth and yield of soybeans. Phytopathology, 103, 822–832.
Dick, M. W. (1990). Keys to Pythium (p. 64). Reading: Department of Botany, University of Reading Published by Dick M.W.
Dorrance, A. E., Berry, S. A., Bowen, P., & Lipps, P. E. (2004). Characterization of Pythium spp. from three Ohio fields for pathogenicity on corn and soybean and metalaxyl sensitivity. Online. Plant Health Progress https://doi.org/10.1094/PHP-2004-0202-01-RS.
Dorrance, A. E., Kleinhenz, M. D., McClure, S. A., & Tuttle, N. T. (2003). Temperature, moisture, and seed treatment effects on Rhizoctonia solani root rot of soybean. Plant Disease, 87, 533–538.
Entry, J. A., Mills, D., Mathee, K., Jayachandran, K., Sojka, R. E., & Narasimhan, G. (2008). Influence of irrigated agriculture on soil microbial diversity. Applied Soil Ecology, 40, 146–154.
Fernández, M. R., Huber, D., Basnyat, P., & Zentner, R. P. (2008). Impact of agronomic practices on populations of Fusarium and other fungi in cereal and noncereal crop residues on the Canadian prairies. Soil and Tillage Research, 100, 60–71.
Fierer, N., Leff, J. W., Adams, B. J., Nielsen, U. N., Bates, S. T., Lauber, C. L., Owens, S., Gilbert, J. A., Wall, D. H., & Caporaso, J. G. (2012). Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proceedings of the National Academy of Sciences of the United States of America, 109, 21390–21395.
Garbeva, P., Postma, J., van Veen, J. A., & van Elsas, J. D. (2006). Effect of above-ground plant species on soil microbial community structure and its impact on suppression of Rhizoctonia solani AG 3. Environmental Microbiology, 8, 233–246.
Geiser, D. M., Jimenez-Gascol, M. D. M., Kang, S., Makalowska, I., Veeraraghavan, N., Ward, T. J., Zhang, N., Kuldau, G. A., & O’Donnell, K. (2004). FUSARIUM-ID v. 1.0: A DNA sequence database for identifying Fusarium. European Journal of Plant Pathology, 110, 473–479.
Griffith, D. R., Mannering, J. V., & Moldenhauer, W. C. (1977). Conservation tillage in the eastern corn belt. Journal of Soil and Water Conservation, 32, 20–28.
Franzluebbers, A., Steiner, J. L., Karlen, D., Griffin, T., & Jeremy, S. 2011. Rainfed farming systems in the USA in: Rainfed farming systems. pp. 511–560.
French, E. R., & Kennedy, B. W. (1963). The role of Fusarium in the root rot complex of soybean in Minnesota. Plant Disease Reporter, 47, 672–676.
Kirkpatrick, M. T., Rupe, J. C., & Rothrock, C. S. (2006). Soybean response to flooded soil conditions and the association with soilborne plant pathogenic genera. Plant Disease, 90, 592–596.
Koohafkan, P., & Stewart, B. A. (2008). Water and cereals in drylands (The Food and Agriculture Organization of the United Nations and Earthscan).
Kranz, W. L., Martin, D. L., Irmak, S., van Donk, S. J., & Yonts, C. D. (2008). Minimum center pivot design capacities in Nebraska. http://extensionpublications.unl.edu/assets/pdf/g1851.pdf
Leslie, J. F., & Summerell, B. A. (2006). The Fusarium laboratory manual (p. 388). Ames: Blackwell Publishing Ltd..
Lewis, J. A., & Papavizas, G. C. (1977). Factors affecting Rhizoctonia solani infection of soybeans in the greenhouse. Plant Disease Reporter, 61, 196–200.
Liu, B., Shen, W. S., Wei, H. H., & Correll, J. C. (2018). Microbial communities in soils with different population densities of soybean cyst nematodes. Canadian Journal of Plant Pathology, 40, 48–60.
Liu, B., Shen, W. S., Wei, H. H., Smith, H., Louws, F., Steadman, J. R., & Correll, J. C. (2016). Rhizoctonia communities in soybean fields and their relation with other soil microbial and nematode communities. European Journal of Plant Pathology, 144, 671–686.
Liu, B., Wei, H. H., Shen, W. S., Smith, H., & Correll, J. C. (2019). Long-term effect of dryland and irrigation on soil Fusarium communities in wheat. Canadian Journal of Plant Pathology, 41, 1–11.
Martin, F. N., & Loper, J. E. (1999). Soilborne plant diseases caused by Pythium spp.: Ecology, epidemiology, and prospects for biological control. Critical Reviews in Plant Sciences, 18, 111–181. https://doi.org/10.1080/07352689991309216.
Muyzer, G., De Waal, E. C., & Uitterlinden, A. G. (1993). Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes for 16S rRNA. Applied and Environmental Microbiology, 59, 695–700.
Nash, S. M., & Snyder, W. C. (1962). Quantitative estimations by plate counts of propagules of the bean root rot Fusarium in field soils. Phytopathology, 52, 567–572.
Nelson, B. D., Hansen, J. M., Windels, C. E., & Helms, T. C. (1997). Reaction of soybean cultivars to isolates of Fusarium solani from the Red River Valley. Plant Disease, 81, 664–668.
Ogoshi, A. (1996). Introduction - the genus Rhizoctonia. In B. Sneh, S. Jabaji-Hare, S. Neate, & G. Dijst (Eds.), Rhizoctonia species: Taxonomy, molecular biology, ecology, pathology and disease control (pp. 1–9). Dordrecht: Kluwer Academic Publishers.
Okello, P. N., & Mathew, F. M. (2019). Cross pathogenicity studies show South Dakota isolates of Fusarium acuminatum, F. equiseti, F. graminearum, F. oxysporum, F. proliferatum, F. solani, and F. subglutinans from either soybean or corn are pathogenic to both crops. Plant Health Progress, 20, 44–49.
Pankhurst, C. E., McDonald, H. J., & Hawke, B. G. (1995). Influence of tillage and crop rotation on the epidemiology of Pythium infections of wheat in a red-brown earth of South Australia. Soil Biology and Biochemistry, 27, 1065–1073.
Ploetz, R. C., Mitchell, D. J., & Gallaher, R. N. (1985). Characterization and pathogenicity of Rhizoctonia species from a reduced-tillage experiment multicropped to rye and soybean in Florida. Phytopathology, 75, 833–839.
Ramette, A. (2007). Multivariate analyses in microbial ecology. FEMS Microbiological Ecology, 62, 142–160.
Rojas, J. A., Jacobs, J. L., Napieralski, S., Karaj, B., Bradley, C. A., Chase, T., Esker, P. D., Giesler, L. J., Jardine, D. J., Malvick, D. K., Markell, S. G., Nelson, B. D., Robertson, A. E., Rupe, J. C., Smith, D. L., Sweets, L. E., Tenuta, A. U., Wise, K. A., & Chilvers, M. I. (2017). Oomycete species associated with soybean seedlings in North America-part II: Diversity and ecology in relation to environmental and edaphic factors. Phytopathology, 107, 293–304.
Rupe, J. C., Robbins, R. T., & Gubur, E. E., Jr. (1997). Effect of crop rotation on soil population densities of Fusarium solani and Heterodera glycines and on the development of sudden death syndrome of soybean. Crop Protection, 16, 575–580.
Sharon, M., Kuninaga, S., Hyakumachi, M., & Sneh, B. (2006). The advancing identification and classification of Rhizoctonia spp. using molecular and biotechnological methods compared with the classical anastomosis grouping. Mycoscience, 47, 299–316.
Schroeder, K. L., Martin, F. N., de Cock, A. W. A. M., Lévesque, A., Spies, C. F. J., Okubara, P. A., & Paulitz, T. C. (2013). Molecular detection and quantification of Pythium species: Evolving taxonomy, new tools, and challenges. Plant Disease, 97, 4–20.
Shannon, C. E., & Weaver, W. (1963). The mathematical theory of communication (5th ed.). Chicago: Urbana University of Illinois Press.
Sneh, B., Burpee, L., & Ogoshi, A. (1991). Identification of Rhizoctonia species. St. Paul: American Phytopathological Society.
Stubbs, M. (2016). Irrigation in U.S. agriculture: On-farm technologies and best management practices. https://fas.org/sgp/crs/misc/R44158.pdf
Tachibana, H. (1968). Rhizoctonia solani root rot epidemic of soybeans in Central Iowa 1967. Plant Disease Reporter, 52, 613–614.
Waterhouse, G. M. (1967). Key to Pythium Pringsheim. Mycological Papers no. 109. Kew: Commonwealth Mycological Institute.
Zhang, B. Q., & Yang, X. B. (2000). Pathogenicity of Pythium populations from corn-soybean rotation fields. Plant Disease, 84, 94–99.
Acknowledgements
This research was supported by a grant from the Nebraska Soybean Board. The authors thank the anonymous grower for allowing sampling his farm, associate editor Dr. Deanna Lillian Funnell-Harris and an anonymous reviewer for carefully editing the manuscript.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Human and animal rights
This research did not involve human participants and/or animals.
Rights and permissions
About this article
Cite this article
Liu, B., Wei, H., Shen, W. et al. Long-term effect of non-irrigation and irrigation on soil Pythium, Fusarium, and Rhizoctonia communities and their relation with seed-rot, root-rot, and damping-off of soybean. Eur J Plant Pathol 158, 297–314 (2020). https://doi.org/10.1007/s10658-020-02059-w
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10658-020-02059-w