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

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

doi:10.1371/journal.pone.0093893

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.

Highlights

Plant-microbe-soil interactions play a vital role in maintaining plant health and productivity in agricultural and horticultural crops
The genera most associated with the suppressive fields identified through the similarity percentage (SIMPER) analysis largely contained putative endophytes, saprophytes and fungi that may play a role in disease suppression (Figure 5)
While we found that the fungal component of soil communities was different in suppressive versus their paired non-suppressive soil, bacteria and their interactions with fungi and plants could be important to biological disease suppression [13], [30], [91], and is the subject of continuing work for these soils

Summary

Introduction

Plant-microbe-soil interactions play a vital role in maintaining plant health and productivity in agricultural and horticultural crops. Roots of cereals, pasture plants and oil seed crops are prone to attack by soilborne necrotrophic pathogens such as Rhizoctonia solani, Fusarium pseudograminearum, Gaeumannomyces graminis var tritici and Pythium spp These are among the most difficult groups of plant pathogens to control due to their ability to persist in crop residues [1]–[4]. Long-term adoption of crop management practices that supply higher levels of biologically-available carbon inputs either through crop residues or addition of composts and organic manures can support higher levels of suppression This occurs through changes to the composition and activity of the soil microbial community [7], [21]–[23]

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Conclusion