Christian Steinberg INRA Dijon- France

Physical  proper.es  

Chemical  proper.es  

O2,  CO2  H20  

structure  

Soil: a complex environment, A reservoir of biodiversity

The seat of multitrophic interactions responsible for its functioning and crop production  

algae    102-­‐104/g  soil  

mesofauna  macrofauna  

protozoa  +60  species  103-­‐1011/m2  

nematodes  +60  species  106-­‐108/m2  

Physical  proper.es  

Chemical  proper.es  

O2,  CO2  H20  

structure  

More  than  104    genotypes/  g  soil  

bacteria    106-­‐109/g  soil  

fungi  103-­‐106/g  soil  

algae    102-­‐104/g  soil  

mesofauna  macrofauna  

protozoa  +60  species  103-­‐1011/m2  

nematodes  +60  species  106-­‐108/m2  

Physical  proper.es  

Chemical  proper.es  

O2,  CO2  H20  

structure  

an.biosis  parasi.sm  

More  than  104    genotypes/  g  soil  

bacteria    106-­‐109/g  soil  

fungi  103-­‐106/g  soil  

algae    102-­‐104/g  soil  

mesofauna  macrofauna  

protozoa  +60  species  103-­‐1011/m2  

nematodes  +60  species  106-­‐108/m2  

symbioses  disease  

C  &  N  cycles  

Physical  proper.es  

Chemical  proper.es  

O2,  CO2  H20  

structure  

compe..on  

Why are management strategies of short duration efficiency?

Binary interactions : crop target population

Methods :

• pesticides • resistant varieties • GM plants • healthy seeds • physic therapy • biocontrol agents

Risks }  To create partial or total ecological

voids according to the action spectrum of chemical molecules.

}  To create partial ecological voids (eradication of major pests)

}  To circumvent the effect of the methods by bioaggressors or other pathotypes (adaptation).

}  To stimulate other pest invasion and multiplication (no competition).

Why are management strategies of short duration efficiency?

Binary interactions : crop target population

http://www.ecofinders.eu/

Spatial scale ? Integration level? Representativity?

}  Ecofinders }  Soil quality assesment

Extraction d'ADN total du sol

et purification

PCR spécifique avec une amorce

marquée par un fluorochrome

Purification des produits de PCR

Digestion des produits de PCR

Séparation des fragments par

électrophorèse sur gel de polyacrylamide

(séquenceur à capillaires)

Détection des fragments marqués

Traitement des données et analyse en composantes principales

x x

x

x

x

x

x

10000 20000 30000 40000 50000 60000 70000 80000

100 200 300 400 500 600 700

Fluorescence

Taille estimée (pb)

3' 5'

3' 5'

3' 5'

3' 5'

5'

3'

3'

5'

par une enzyme de restriction

Relation structure / diversité (T-RFLP sur souches)

Comparaison des structures

3' 5'

5' 3' 3' 5'

5' 3' 3' 5'

5' 3'

Terminal restriction fragment length polymorphism (T-RFLP) analysis

Land use,

increasing anthropogenic activities and biotic reactions

100m transect

Années 57 56 55 54 53 52 51 50 49 48 47 46 45 44 43 42 41 40 39 38 37 36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1pin > maïs

Sauturges 1 an maïs

Chanterelle 2 ans maîs

Lagassey 4 ans maïs

Sauturges 7 ans maïs

Belle Viste 13 ans maïs

Belle Viste 20 ans maïs

Belle Viste 32 ans maïs

Bourrideys 43 ans maîs

Bel Air 56 ans maïs

maïs > pinSolférino 1 an forêt

Bourrideys 11 ans forêt

Bourdieu 40 ans forêt

forêt maïs

}  Chronosequence of land use -  forest = every 40 years -  corn monocropped = 1, 2, 4, 7, … 56 years -  carrot rotation (every 4 years) = 2 cycles

Edel-Hermann et al 2011

Axe

2 :

13.9

%

M1A M1B M1C M1D

M1E

M7A M7B

M7C

M7D M7E

M17A M17B

M17C

M17D

M17E

M24A M24B

M24C

M24D

M24E

M36A

M36B

M36C

M36D

M36E

M47A M47B M47C M47D M47E

M60A

M60B

M60C

M60D

M60E

F1A

F1B F1C F1D

F1E

F7A

F7B

F7C

F7D

F7E

F17A

F17B

F17C F17D F17E

F24A F24B

F24C

F24D

F24E F47A

F47B

F47C

F47D

F47E

F60A F60B

F60C F60D

F60E

M4A

M4B M4C

M4D M4E

F4A F4B F4C

F4D F4E

Axe 1 : 31.3 %

1 year

4 years

}  Structure of fungal communities, from forest to maize (same for the bacteria)

Forest

Maize

7 years

CP Rh 1 CP Rh 2

CP Rh 3

CP Rh 4

CP Rh 5

CP Rh 6 CP Rh 7

CP Rh 8

CP Rh 9 CP Rh 10

CP Rh 11

CP Rh 12

CP 0 1

CP 0 2 CP 0 3

CP 0 4

CP 0 5

CP 0 6

CP 0 7

CP 0 8 CP 0 9

CP 0 10

CP 0 11

CP 0 12

CS 0 1 CS 0 2

CS 0 3 CS 0 4

CS 0 5 CS 0 6

CS 0 7 CS 0 8 CS 0 9

CS 0 10 CS 0 11 CS 0 12

CS Rh 1

CS Rh 2

CS Rh 3

CS Rh 4

CS Rh 5

CS Rh 6

CS Rh 7

CS Rh 8

CS Rh 9 CS Rh 10

CS Rh 11

CS Rh 12

M RH 1

M RH 2

M RH 3

M RH 4

M RH 5 M RH 6

M RH 7

M RH 8 M RH 9

M RH 10 M RH 11

M RH 12 M 0 1

M 0 2 M 0 3 M 0 4 M 0 5

M 0 6

M 0 7

M 0 8 M 0 9

M 0 10 M 0 11

M 0 12

bio 13

bio 14

bio 15 bio 16 bio 17

bio 18

bio 19 bio 20 bio 21

bio 22

bio 23

bio 24 bio 25 bio 26 bio 27

12.09%

24.9%

Organic carrots

Early carrots

Full season carrots Conventionnal maize

1 year

Edel-Hermann et al 2011

}  Structure of fungal communities, from maize to carrots

Landes Forêt Maïs Carotte Phytoparasites Criconema Criconema stricts Helicotylenchus Helicotylenchus Helicotylenchus

Helicotylenchus Hemicriconemoides Hemicriconemoides Hemicriconemoides Hemicycliophora Hemicycliophora Hemicycliophora Heterodera Heterodera Heterodera Paratylenchus Paratylenchus Pratylenchus Pratylenchus Pratylenchus Rotylenchus Rotylenchus Rotylenchus Trichodorus Trichodorus Trichodorus Trichodorus Tylenchorhynchus Tylenchorhynchus Tylenchorhynchus Tylenchorhynchus

Généralistes Aphelenchoides Aphelenchoides

Aphelenchoides Ditylenchus Filenchus Filenchus Filenchus Tylenchidae Psilenchus Psilenchus Rotylenchus Tylencholaimus Tylencholaimus Tylencholaimus Tylenchus Tylenchus Tylenchus Dorylaimida Dorylaimida Dorylaimida Dorylaimida

Carrot significantly reduces both richness and diversity

Mateille 2011

Agricultural practices : Biofumigation,

Tillage,

Preceeding crops,

Organic amendments,

…,

-Raddish Sowing Crushing and burying radish

4 weeks

Carrot sowing Harvest

April June July

T0 T1 T2

October

}  Bio-disinfection by introduction of a Brassicaceae (fodder radish)

Intermediate crop in maize-carrot rotation

Fungi

T0

T1

T2

T0 T1 T2

T1

T2

T0

41,3%

26,6%

Bacteria

T0

T1

T2

T1

T2

T0 T1

T2

T0 57,4%

22%

C OM Bd

Fungi

T0

T1

T2

T0 T1 T2

T1

T2

T0

41,3%

26,6%

Bacteria

T0

T1

T2

T1

T2

T0 T1

T2

T0 57,4%

22%

C OM Bd

Janvier 2007

0

20

40

60

0 2 4 6 8 10 12

% dead plants

a

b

Control Organic Matter

Biodisinfection

Soil Inoculum Potential

Days

Conclusion: Bio-disinfection by Brassicaceae: - allows to control damping-off and root necrosis for the coming culture (fungi, nematodes) - does not decrease or can sometime increase the risk of attacks for the following crops. - Need for combining several strategies (bio-disinfection + BCA)

Friberg et al 2009

Conclusion: Bio-disinfection by Brassicaceae: - allows to control damping-off and root necrosis for the coming culture (fungi, nematodes) - does not decrease or can sometime increase the risk of attacks for the following crops. - Need for combining several strategies (bio-disinfection + BCA)

V. dahliae R. solani - cauliflowe

P.nicot- tomato

P. cinnamomi-

lupin

Cylindrocl -adium spatiphylli

R. solani- pine

F. oxysporum

flax

GR 6 14,52 -87,29 0,00 23,81 24,14 83,51 2,08 dec01 -21,37 57,80 52,17 -24,26 -27,90 0,87 64,17 GR5 31,73 0,00 -3,20 -11,54 15,35 58,23

dec02 -15,36 49,74 17,39 -3,47 -28,00 20,97 70,52 Ut 0303 1,28 68,03 28,99 -17,33 -18,53 -11,33 67,21 CO 7 34,76 32,10 14,49 48,53 -48,84 8,44 65,18 CO 16 31,47 35,29 58,82 -28,57 1,55 1,77 63,81 GR3a 38,05 11,90 61,30 -11,54 1,09 63,07 CO2 87,23 28,57 9,70 -23,08 -7,05 71,94

BOM 0303 -24,46 66,37 23,19 -20,80 63,54 29,92 65,81 GR3b 59,41 -4,24 2,94 71,43 23,81 4,48 47,89

1.02Ba 86,46 47,62 3,20 19,23 -0,88 45,66 CO 4 32,88 2,35 2,94 38,10 32,41 92,65 56,07 1.02S 74,03 50,00 3,20 34,62 -1,70 66,71 IS BS -2,11 67,77 5,80 58,93 22,46 57,04 68,13 8.1S 86,25 38,10 3,20 53,85 -1,36 63,33

CO 17 52,96 8,47 91,18 57,14 47,38 4,92 32,85 CO 14 49,88 -10,12 67,65 47,62 100,00 27,24 65,86

--

-- --

composts

Organic amendments

Termorshuizen et al 2006

V. dahliae R. solani - cauliflowe

P.nicot- tomato

P. cinnamomi-

lupin

Cylindrocl -adium spatiphylli

R. solani- pine

F. oxysporum

flax

GR 6 14,52 -87,29 0,00 23,81 24,14 83,51 2,08 dec01 -21,37 57,80 52,17 -24,26 -27,90 0,87 64,17 GR5 31,73 0,00 -3,20 -11,54 15,35 58,23

dec02 -15,36 49,74 17,39 -3,47 -28,00 20,97 70,52 Ut 0303 1,28 68,03 28,99 -17,33 -18,53 -11,33 67,21 CO 7 34,76 32,10 14,49 48,53 -48,84 8,44 65,18 CO 16 31,47 35,29 58,82 -28,57 1,55 1,77 63,81 GR3a 38,05 11,90 61,30 -11,54 1,09 63,07 CO2 87,23 28,57 9,70 -23,08 -7,05 71,94

BOM 0303 -24,46 66,37 23,19 -20,80 63,54 29,92 65,81 GR3b 59,41 -4,24 2,94 71,43 23,81 4,48 47,89

1.02Ba 86,46 47,62 3,20 19,23 -0,88 45,66 CO 4 32,88 2,35 2,94 38,10 32,41 92,65 56,07 1.02S 74,03 50,00 3,20 34,62 -1,70 66,71 IS BS -2,11 67,77 5,80 58,93 22,46 57,04 68,13 8.1S 86,25 38,10 3,20 53,85 -1,36 63,33

CO 17 52,96 8,47 91,18 57,14 47,38 4,92 32,85 CO 14 49,88 -10,12 67,65 47,62 100,00 27,24 65,86

--

-- --

composts

Organic amendments

Termorshuizen et al 2006

V. dahliae R. solani - cauliflowe

P.nicot- tomato

P. cinnamomi-

lupin

Cylindrocl -adium spatiphylli

R. solani- pine

F. oxysporum

flax

GR 6 14,52 -87,29 0,00 23,81 24,14 83,51 2,08 dec01 -21,37 57,80 52,17 -24,26 -27,90 0,87 64,17 GR5 31,73 0,00 -3,20 -11,54 15,35 58,23

dec02 -15,36 49,74 17,39 -3,47 -28,00 20,97 70,52 Ut 0303 1,28 68,03 28,99 -17,33 -18,53 -11,33 67,21 CO 7 34,76 32,10 14,49 48,53 -48,84 8,44 65,18 CO 16 31,47 35,29 58,82 -28,57 1,55 1,77 63,81 GR3a 38,05 11,90 61,30 -11,54 1,09 63,07 CO2 87,23 28,57 9,70 -23,08 -7,05 71,94

BOM 0303 -24,46 66,37 23,19 -20,80 63,54 29,92 65,81 GR3b 59,41 -4,24 2,94 71,43 23,81 4,48 47,89

1.02Ba 86,46 47,62 3,20 19,23 -0,88 45,66 CO 4 32,88 2,35 2,94 38,10 32,41 92,65 56,07 1.02S 74,03 50,00 3,20 34,62 -1,70 66,71 IS BS -2,11 67,77 5,80 58,93 22,46 57,04 68,13 8.1S 86,25 38,10 3,20 53,85 -1,36 63,33

CO 17 52,96 8,47 91,18 57,14 47,38 4,92 32,85 CO 14 49,88 -10,12 67,65 47,62 100,00 27,24 65,86

--

-- --

composts

Organic amendments

Termorshuizen et al 2006

Tillage,

and crop residues,

and preceding crop,

and rotation scheme,

and,…

1 2 3 4 5

6 7 8

9 10

11 12

13

14 15

16

PC1 20.1%

PC2 11.2% Bacteria

Tillage No Tillage

1 2 3 4 5

6 7 8

9 10

11 12

13

14 15

16

PC1 20.1%

PC2 11.2% Bacteria

Tillage No Tillage

1

2

3 4

5

6 7

8

9

10 11 12

13 14 15

16 Fungi

PC1 41.%

PC2 15.6%

Tillage

No tillage

1 2 3 4 5

6 7 8

9 10

11 12

13

14 15

16

PC1 20.1%

PC2 11.2% Bacteria

Tillage No Tillage

1

2

3 4

5

6 7

8

9

10 11 12

13 14 15

16 Fungi

PC1 41.%

PC2 15.6%

Tillage

No tillage

1

2

3

4 5

6

7

8

9 10 11 12 13

14 15 16

Nematodes

PC1 53%

PC2 14.6%

Tillage No Tillage Abid et al 2012

1 2 3 4 5

6 7 8

9 10

11 12

13

14 15

16

PC1 20.1%

PC2 11.2% Bacteria

Tillage No Tillage

1

2

3 4

5

6 7

8

9

10 11 12

13 14 15

16 Fungi

PC1 41.%

PC2 15.6%

Tillage

No tillage

1

2

3

4 5

6

7

8

9 10 11 12 13

14 15 16

Nematodes

PC1 53%

PC2 14.6%

Tillage No Tillage

Shallow vs Mouldboard tillage

No Til +Til FHB/Spikelets 19.8% 13% * FHB/ears 9.4% 5.6% * Yield (Kg/ha) 7666 8473 **

Protozoa : DON > tillage

Abid et al 2012

http://www.grainsessential.ca/francais/pdf/kids/ soil

seeds

Aerial infestation

Crop residues

Tillage system

Fusarium head blight

Diseases on -stem bases -crown -roots

Preceding crop

A   B  

Population dynamics of F. graminearum in crop residues

}  ð Presence of putative direct or/and indirect antagonistic (micro)organismes

}  ð Qualitative and quantitative role of crop residues: preceding crop, intermediate crop, …

Leplat et al 2012

Fusarium graminearum Produces mycotoxins (such as DON

Deoxynivalenol )

Causes Fusarium head blight and seedling blight

Do mycotoxins have an impact on soil microflora and fauna during the decomposition of crop residues in the soil ?

Fusarium graminearum Produces mycotoxins (such as DON

Deoxynivalenol )

Causes Fusarium head blight and seedling blight

F. graminearum overwinters in the soil, on crop residues and serve as

primary inoculum

(antagonists, decomposers)

Soil microflora and fauna

Crop residue + mycotoxins

Produces disease to the next crop

Survival

F.  graminearum

Competition and  antagonism

Crop residues

Plant  of  origin

Quantity

Preceding crop

Substrate

+/-­‐

O2 availability

+/-­‐

ð Risk assessment

ð Mathematical models

Week 8 Week 24

No earthworm

Plus earthworms

week 0

- Contribution of earthworms to the incorporation of wheat straw (and other plant residues) in the soil - Decomposition ö mineralization and C sequestration

Suppressive soil of Chateaurenard - empirical approach è Fo47 - functional genomics è functional groups

% Healthy plants

Châteaurenard

0%

20%

40%

60%

80%

100%

0 10 20 30 40 50 60

Comparative Metagenomics and Metatranscriptomics of various suppressive soils :

- Fusarium wilt

- R. solani diseases

- Take-all decline

0 104 p/g soil

⇒  To analyze the response to anthropogenic activities

1 - Understanding the process of assemblage of the species (or similar) => response traits

⇒  To analyze the response to anthropogenic activities

Pool local d’espèces

espèces ab

onda

nce communauté 1

Ecosystème état & fonctionnement

Traits d’effet végétaux

espèces ab

onda

nce communauté 2 bioagresseurs

espèces

abon

danc

e communauté 3 auxiliaires

Traits de réponse

filtres environnementaux

filtres historiques

santé des sols

=> Multitrophic interactions (IOBC)

2 - Managing the pathogenic activity through biodiversity (effect traits)

1 - Understanding the process of assemblage of the species (or similar) => response traits

Ecology of soil-borne plant pathogens

Sébastien Aimé

Cécile Heraud

Véronique Edel-Hermann

Christian Steinberg

Chantal Olivain

Léon Fayolle

Nadine Gautheron Elodie Gautheron

Rémi Chaussod

Julie Laurent Katia Siegel

Muhammad Abid