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

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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