Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing.
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.
Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America.
C Ryan
CR
Penton
CSIRO Ecosystem Sciences, Glen Osmond, South Australia, Australia.
V V S R
VV
Gupta
Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America.
James M
JM
Tiedje
Department of Agriculture, Fisheries and Forestry, Queensland, Leslie Research Centre, Towoomba, Queensland, Australia.
Stephen M
SM
Neate
SARDI, Glen Osmond, South Australia, Australia.
Kathy
K
Ophel-Keller
Department of Biological Sciences, Macquarie University, North Ryde, New South Wales, Australia.
Michael
M
Gillings
CSIRO Ecosystem Sciences, Glen Osmond, South Australia, Australia.
Paul
P
Harvey
Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America.
Amanda
A
Pham
CSIRO Ecosystem Sciences, Glen Osmond, South Australia, Australia.
David K
DK
Roget
D001419:Bacteria / Q000235:genetics*; D004271:DNA, Fungal / Q000235:genetics; D005658:Fungi / Q000235:genetics*; D010802:Phylogeny; D058441:Rhizosphere; D012987:Soil; D012988:Soil Microbiology; D013021:South Australia
D004271:DNA, Fungal; D012987:Soil