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

Christopher 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

53 Citations (Scopus)

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
Externally publishedYes

Fingerprint

Fungal Structures
suppressive soils
fungal communities
community structure
Soil
Genes
plant pathogens
Soils
soil-borne diseases
microbial communities
soil
rhizosphere
disease control
genes
sowing
Xylaria
mycoparasites
fungi
Rhizoctonia
Alternaria

ASJC Scopus subject areas

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

Cite this

Penton, C., Gupta, V. V. S. R., Tiedje, J. M., Neate, S. M., Ophel-Keller, K., Gillings, M., ... 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

Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing. / Penton, Christopher; Gupta, V. V S R; Tiedje, James M.; Neate, Stephen M.; Ophel-Keller, Kathy; Gillings, Michael; Harvey, Paul; Pham, Amanda; Roget, David K.

In: PLoS One, Vol. 9, No. 4, e93893, 03.04.2014.

Research output: Contribution to journalArticle

Penton, C, Gupta, VVSR, Tiedje, JM, Neate, SM, Ophel-Keller, K, Gillings, M, Harvey, P, Pham, A & Roget, DK 2014, 'Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing', PLoS One, vol. 9, no. 4, e93893. https://doi.org/10.1371/journal.pone.0093893
Penton, Christopher ; Gupta, V. V S R ; Tiedje, James M. ; Neate, Stephen M. ; Ophel-Keller, Kathy ; Gillings, Michael ; Harvey, Paul ; Pham, Amanda ; Roget, David K. / Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing. In: PLoS One. 2014 ; Vol. 9, No. 4.
@article{fdb69b0773114e5eb6e39db0d00d0c86,
title = "Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing",
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.",
author = "Christopher Penton and Gupta, {V. V S R} and Tiedje, {James M.} and Neate, {Stephen M.} and Kathy Ophel-Keller and Michael Gillings and Paul Harvey and Amanda Pham and Roget, {David K.}",
year = "2014",
month = "4",
day = "3",
doi = "10.1371/journal.pone.0093893",
language = "English (US)",
volume = "9",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "4",

}

TY - JOUR

T1 - Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing

AU - Penton, Christopher

AU - Gupta, V. V S R

AU - Tiedje, James M.

AU - Neate, Stephen M.

AU - Ophel-Keller, Kathy

AU - Gillings, Michael

AU - Harvey, Paul

AU - Pham, Amanda

AU - Roget, David K.

PY - 2014/4/3

Y1 - 2014/4/3

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84899082948&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84899082948&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0093893

DO - 10.1371/journal.pone.0093893

M3 - Article

C2 - 24699870

AN - SCOPUS:84899082948

VL - 9

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 4

M1 - e93893

ER -