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Biological suppression of Rhizoctonia disease in Wheat – Effect of carbon and Nitrogen levels in soil
Gupta V.V.S.R. and D. K. RogetJohn Coppi & Stasia Kroker
Disease suppression Pathogen Diseaseseverity
INTRODUCTION Examples and hypothesisInvestigations Incubation assay, Field observations and analysesCONCLUSIONS
0
1
2
3
4
1979 1984 1989 1994 1999 2004
Year
Rhiz
octo
nia
root
dam
age
ratin
g
Cultivated Pasture/Wheat
Direct Drill Pasture/Wheat
Direct Drill Wheat/WheatAnthesis spraying
Disease suppression is the ‘ability of a soil to suppress disease incidence or severity even in the presence of the pathogen, host plant and favourable environmental conditions’
Disease suppression is an inherent property of all biologically active soils through the microbial (biological) activity and plant-microbe (biota)-pathogen interactions but the level of suppression ability varies with edaphic and environmental variables.
Examples of enhanced disease suppression against Rhizoctonia bare patch in long-term field experiments in South Australia
Roget 1995; Gupta et al. 2009
P-C IC-DD
Waikerie (MSF)
Avon
• Higher levels of disease suppression resulting in very low levels of disease incidence after 5-7 years
• Management practices with higher levels of biologically available carbon inputs and C turnover.
• Suppression is a function of the population, activity and composition of the microbiota community.
>7 years
Avon:Calcic Xerosol, pH 8.4 (water), Clay 12%Organic C - 1.6%, Total N – 0.15%
Waikerie:Alfisol, pH 8.6 (water), Clay 6%Organic C – 0.68%, Total N – 0.05%
Measurements and Methods
• Long-term monitoring of disease incidence Avon: 1979-2004Waikerie: 1998-2009
• R. solani AG8 inoculum DNA level• Suppression potential Incubation
tests• Catabolic diversity of microbial
communities• C and N turnover
0
1
2
3
4
1979 1984 1989 1994 1999
Year
Rhi
zoct
onia
root
dam
age
ratin
g
Cultivated Pasture/Wheat
Direct Drill Pasture/Wheat
Direct Drill Wheat/Wheat
Anthe
Altered population & diversity Stable community
-------- Rs. DNA level = 60 pg/g ---------
Incidence of Rhizoctonia root damage measured at tillering in Direct Drilled Wheat plots at Avon, South Australia during 1982-2004 Roget 1995; Gupta and Roget 2007
Increased C inputs & No-Till
Changes in decomposition Rates and temporal dynamics
Wide C:N ratio crop residues
High immobilization duringLate autumn & Summer minLow min N levels
MB = 500µgC/gMQ = 3.5% (<2%)Eassim = 15%-26%
• A number of microflora and micro- and meso-fauna have been suggested to play a role in Disease Suppression
• Disease suppression potential in 2007 and disease incidence in 2009:Intensive crop (DD) > Intensive crop (CC) > Pasture-crop
• Intensive cropping systems supported higher levels of microbial activity compared to traditional pasture/crop rotations
–C inputs: ~1.0 t C/ha/y compared to <0.35 t C/ha/y
Another example for the development of disease suppression after 7-10 years, MSF cropping system trial (AB) - Waikerie
3P-C
10IC-DD11
IC-DD
MSF coresite - Rs patchscoring (Sept 1, 2009)
0.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
4.0
4.5
1 2 3 4 5 6 7 8 9 10 11
Treatment number
# ro
ws
lsd (P<0.05)
P-C IC(L)-Cult IC - DD
-0.1
-0.05
0
0.05
0.1
0.15
-0.2 -0.15 -0.1 -0.05 0 0.05 0.1 0.15 0.2
pc1 (65%)
pc2
(20%
)
Wheat-Wheat (DD)
Wheat-Legume (CC)
Wheat-Pasture (Hi)
Wheat-Pasture (DP)
Wheat-Legume (DD)
Wheat-Canola (DD)
LSD (P<0.05)
Catabolic diversity of Microbial communities in a Mallee soil after 8 years of new farming systems
DSP=0.94
DSP=0.65
DSP=0.85
0
0.5
1
1.5
2
2.5
3
3.5
Nil 0.05gms 0.1gms 0.25gms 0.5gms
Carbon substrate (Sucrose) Amendment
Rhi
zoct
onia
root
dam
age
ratin
g LSD P=0.05
Effect of addition of carbon substrate on the incidence of Rhizoctonia root rot on wheat (Disease suppression potential)
• 300 g soil / pot• 2 wk pre-incubation with
inoculum & amendments• 6 wk old plants assessed
for disease incidence
Effect of addition of different carbon substrates on the incidence of Rhizoctonia root rot on wheat (Disease suppression potential)
0.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
1gm 3gms 5gms
Aver
age
Rhi
zoct
onia
Amount of Substrate
Sucrose
Cellulose
Wheat Straw
C-substrates that didn’t reduce disease incidence: Starch, Gelatin, Chitin
0
1
2
3
4
1979 1984 1989 1994 1999 2004
Year
Rhi
zoct
onia
root
dam
age
ratin
g
Cultivated Pasture/Wheat
Direct Drill Pasture/Wheat
Direct Drill Wheat/Wheat
Anthesis spraying
Altered population & diversity Stable community Altered expression
------------------ Rs. DNA level = 60 pg/g --------------
Incidence of Rhizoctonia root damage measured at tillering in Direct Drilled Wheat plots at Avon, South Australia during 1982-2004 Roget 1995; Gupta and Roget 2007
0
1
2
3
4
1979 1984 1989 1994 1999 2004
Year
Rhi
zoct
onia
root
dam
age
ratin
g
Cultivated Pasture/Wheat
Direct Drill Pasture/Wheat
Direct Drill Wheat/Wheat
Anthesis spraying
Altered population & diversity Stable community Altered expression
------------------ Rs. DNA level = 60 pg/g --------------
Incidence of Rhizoctonia root damage measured at tillering in Direct Drilled Wheat plots at Avon, South Australia during 1982-2004 Roget 1995; Gupta and Roget 2007
Supp. micro
Increased C inputs & No-Till
Changes in decomposition Rates and temporal dynamics
Green crop residuesLow C:N ratio
Late autumn &Summer mineralizationHigh min N levels
Wide C:N ratio crop residues
High immobilization duringLate autumn & Summer minLow min N levels
DSP
0
1
2
3
4
1979 1984 1989 1994 1999 2004
Year
Rhi
zoct
onia
root
dam
age
ratin
g
Cultivated Pasture/Wheat
Direct Drill Pasture/Wheat
Direct Drill Wheat/Wheat
Anthesis spraying
Green crop residuesLow C:N ratio
Late autumn &Summer mineralizationHigh min N levels
Altered population & diversity Stable community Altered expression
------------------ Rs. DNA level = 60 pg/g --------------
Incidence of Rhizoctonia root damage measured at tillering in Direct Drilled Wheat plots at Avon, South Australia during 1982-2004 Roget 1995; Gupta and Roget 2007
0
10
20
30
40
50
60
70
80
Sept Oct Nov Jan March May
Mineral N (m
g N /kg
in su
rface
20 cm
dep
th) 2003
1999
0
0.5
1
1.5
2
2.5
3
Nil Sucrose 1g Sucrose 3g Sucrose 5g
Carbon substrate (Sucrose) Amendment
Rhi
zoct
onia
root
dam
age
ratin
g Nil NN (10% C)
LSD P=0.05
Addition of N resulted in:• a change in the composition of bacterial and fungi• modified Cellulase to Chitinase ratio• No change in the Rs DNA level
Effect of addition of carbon substrate and mineral N on the incidence of rhizoctonia root rot on wheat
• The level of disease suppressive activity against soilborne fungal disease Rhizoctonia bare patch is a function of the population, activity and composition of the microbial community.
- Phylogenetically diverse group of microbiota community
• Management practices that add higher levels of biologically available C over longer periods (>7 y) could support higher levels of suppression
• C and N turnover i.e. Timing of mineral N accumulation in the surface soil seem to influence the expression of disease suppression
• Catabolic profiles obtained with c-substrate utilization assay showed significant differences between suppressive and non-suppressive soils
Conclusions Pathogen Diseaseseverity
0
1
2
3
4
1979 1984 1989 1994 1999 2004
Year
Rhiz
octo
nia
root
dam
age
ratin
g
Cultivated Pasture/Wheat
Direct Drill Pasture/Wheat
Direct Drill Wheat/WheatAnthesis spraying
Functional Microbial Ecology for Farming Systems
DisclaimerThe information, advice and/or procedures contained in this publication are provided for the sole purpose of disseminating information relating to scientific and technical matters in accordance with the functions of CSIRO under the Science and Industry Act 1949. To the extent permitted by law CSIRO shall not be held liable in relation to any loss or damage incurred by the use/or reliance upon any information and/or procedure contained in this publication.
Mention of any product in this publication is for information purposes only and does not constitute a recommendation of any such product either express or implied by CSIRO.
This publication contains information that is unpublished and can not be reproduced in any form without the written consent from the authors.
Inoculum survival & growth during off-season
Infection &Disease incidence
DiseaseSuppression
Grow
th of inoculum
from source to root
Plant responseto infection
Habitat
Components of soilborne diseases in Australian agroecosystem
Driving variables• Environmental
regulators• Pathogen diversity• Farming systems
in Australia
Off-
seas
onC
rop
seas
on
Rhizoctonia bare patch
Avon
Waikerie
Waikerie+St
SBay
SBay+St
-2.0 -1.0 0.0-1.5
1.0
-1.0
2.0
-0.5
0.0
0.5
1.0
1.5
-0.5 1.50.5-1.5
Can
onic
al v
aria
te 2
(23%
)
Canonical variate 1 (54%)
Catabolic diversity of microbial communities (based on C-substrate utilization profiles)
31 types of carbon substratesMonosaccharides (6)Oligosaccharides (3)Amino acids (16)Carboxylic acids (6)
PCA of bacterial communities in South Australian cropping soils in relation to their disease suppression potential
-2
-1.5
-1
-0.5
0
0.5
1
1.5
2
2.5
-4 -3 -2 -1 0 1 2 3
pc 1 (48.1%)
pc 2
(23.
9%)
Avon - Suppressive
Avon - (Non-Suppressive)
Kuchel-C (Non-Suppressive)
Kuchel-W (Suppressive)
Gupta, Neate & Roget (2007)
Ave. Catabolic potential:Avon > Waikerie ~ Streaky BayDisease supp. potential:Avon > Waikerie > Streaky Bay
Survey - Rhizoctonia disease suppression potential in soils from farmer fields
Pathogen Diseaseseverity
Rhizoctonia Disease suppression potential in Mallee focus farms in SA, Vic and NSW (2001)
0.0
0.5
1.0
1.5
2.0
2.5
3.0
Ackl
and
Berg
er
Gor
man
MR
S
Has
tings
Min
ney
Buf
fon
Cro
ok
May
nard
Wai
kerie
Duf
field
Pedl
er
Obs
t
Latta
Vivi
en
Ham
pel
Doy
le 1
Wor
mal
d
Hul
l
Gra
nt
Gre
iger
Sta
rick
Stoe
ckel
Aikm
an
Kaes
ler
Kuch
el
Schi
rmer
Doy
le 2
Rob
bins
1
DSm
ith
Elfo
rd
Sch
aeffe
r
Wur
st
Rob
bins
2
Rhi
zoct
onia
root
dam
age
rati
ng
lsd (P<0.05)
Decreasing potential for suppression
Avon
Improved disease suppression included systems with higher levels of C inputs e.g. intensive cropping, stubble retention, limited grazing and limited or no cultivation
Level of Rs inoculum usingSpecies specific PCR probing
Disease suppression is not an absolute characteristic but a continuum from highly suppressive soils to poorly suppressive (ie. conducive) soils (Roget et al. 1999)
• A number of microflora and micro- and meso-fauna have been suggested to play a role
• Biocontrol organismsBacteria – Microbacteria sp., Bacillus sp.,
Pseudomonas brassiacearum, Streptomces sp.Fungi – Trichoderma sp., Streptoverticillium sp.,
Penicillium griseofulvum• PGPR – Exiguobacterium acetylicum, Pantoea
agglomerans
• Protozoa – Ripidomyxa perforans, Valhkampfia sp., Thecamoeba granifera, Arachnula impatiens
• Nematodes – Aphelenchus avenae, Tylenchus spp.
Pathogen Diseaseseverity
Unr
avel
ling
the
‘pla
nt p
robi
otic
-bla
ck b
ox’ …
.
Bird et al. 1995; Gupta et al. 1999; Ross et al. 2000; Yang et al. 2005; Barnett et al., 2006
Diversity of microbiota potentially involved in disease suppression at Avon, SA
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