Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing

C. Ryan Penton, V. V.S.R. Gupta, James M. Tiedje, Stephen M. Neate, Kathy Ophel-Keller, Michael Gillings, Paul Harvey, Amanda Pham, David K. Roget

Research output: Contribution to journalArticle

61 Scopus citations

Abstract

Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils 'suppressive' or 'non-suppressive' for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria , Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression.

Original languageEnglish (US)
Article numbere93893
JournalPloS one
Volume9
Issue number4
DOIs
StatePublished - Apr 3 2014

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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    Penton, C. R., Gupta, V. V. S. R., Tiedje, J. M., Neate, S. M., Ophel-Keller, K., Gillings, M., Harvey, P., Pham, A., & Roget, D. K. (2014). Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing. PloS one, 9(4), [e93893]. https://doi.org/10.1371/journal.pone.0093893