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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