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

Penton, C. Ryan and Gupta, V. V. S. R. and Tiedje, James M. and Neate, Stephen M. and Ophel-Keller, Kathy and Gillings, Michael and Harvey, Paul and Pham, Amanda and Roget, David K. (2014) Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing. PLoS One, 9 (4). pp. 1-12.

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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 nonsuppressive 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.


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Item Type: Article (Commonwealth Reporting Category C)
Refereed: Yes
Item Status: Live Archive
Additional Information: Copyright: 2014 Penton et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Faculty / Department / School: Current - Faculty of Health, Engineering and Sciences - School of Agricultural, Computational and Environmental Sciences
Date Deposited: 12 Jun 2014 04:25
Last Modified: 26 Aug 2015 02:54
Uncontrolled Keywords: DNA extraction; endophyte; fungal community; fungal plant disease; fungus identification; Fusarium; gene sequence; geographic distribution; LSU gene; microbial diversity; mycoparasite; Penicillium; plant fungus interaction; pyrosequencing; Rhizoctonia solani; rhizosphere fungus; RNA gene; soil analysis; Xylariales
Fields of Research : 06 Biological Sciences > 0607 Plant Biology > 060704 Plant Pathology
05 Environmental Sciences > 0503 Soil Sciences > 050303 Soil Biology
06 Biological Sciences > 0605 Microbiology > 060504 Microbial Ecology
Socio-Economic Objective: D Environment > 96 Environment > 9604 Control of Pests, Diseases and Exotic Species > 960413 Control of Plant Pests, Diseases and Exotic Species in Farmland, Arable Cropland and Permanent Cropland Environments
Identification Number or DOI: 10.1371/journal.pone.0093893
URI: http://eprints.usq.edu.au/id/eprint/25187

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