Romain BARNARD
Chercheur INRA
Projet INCITE
Integrated response of plant, microbial and N Cycling InTEractions to precipitation patterns
Soil microbial communitystructure and activity
Climate change predictions in Europe: less precipitation amounts
more intense and less frequent rain events
Impacts three main aspects of plant-soil interactions, affecting productivity, C budgets and N losses
Stimulation of biogeochemical cycles
Stimulation of nutrient uptake by plants and microorganisms
N and C functions and cycling in the soil
N2OCO2
Stimulation of greenhouse gas emissions
Context
H2O
Plant water and nutrientuptake
H2O
N2OCO2
Soil microbial communitystructure and activity
N and C functions and cycling in the soil
Plant water and nutrientuptake
Impacts on biogeochemical cycles, plant-microbe competition and synchronicity2
2
2
Stability of microbial community vs. stability of biogeochemical functions3
3
Microbial activity, coupling with plant water uptake depth1
1
1
Objectives
Soil matrix↑ spatially disconnected↑ aerobic↓ osmotic potential
Soil microbes↑ spatially isolated↓ general activity↑ survival strategies
Plant↓ photosynthesis rate↓? rhizodeposition
↓ plant-microbial coupling
Drying Rewetting
Soil matrix↑ spatially connected↑ anaerobic↑ osmotic potential
Soil microbes↑ osmo-regulation↑ motility↑ burst of activity
Plant↑ photosynthesis rate ↑? rhizodeposition
↑ plant-microbial coupling
Dry - Wet
C C
Precipitation regimes: Equal total volume but different frequency
Frequent Small volume
0-5 cm
10-15 cm
30-35 cm
Infrequent Large volume
1 Depth
Engelhardt et al. (2018) The ISME Journal
1 Depth
100 200 300 400 500
−26
−25
−24
−23
−22
Root biomass (g m-2
)
d1
3C
in
mic
rob
ial b
iom
ass (‰
)
●
●
Freq. Infreq.
● ●
topmiddlebottom
Frequent treatment:
↑ live root biomass
↑ available C
↑ 13C immobilization
Infrequent treatment:Loss of plant-microbial coupling in top soil layer
Precipitation regime legacy effect on C flux from plant to microbes
100 200 300 400 500
−26
−25
−24
−23
−22
Root biomass (g m-2
)
d1
3C
in
mic
rob
ial b
iom
ass (‰
)
●
●
Freq. Infreq.
● ●
topmiddlebottom
1 Depth
Active Inactive
Depth 12 20
Precipitation legacy ns ns
Depth x Precip. leg. ns ns
% variance explained
Freq InfreqRewetting response shaped bacterial communities
Analysing active and inactive community independently: large amount of variation due to depth
but no effect of precipitation legacy
BACTERIA
FUNGI1400
1450
1500
1550
1600
avg_all[avg_all$activity == "active", ]$SimRec
obs index
●
●
act. inact.
● ●
top
middle
bottom
600
800
1000
1200
1400
fung_avg_all[fung_avg_all$activity == "active", ]$SimRec
fung_avg_a
ll[fu
ng_avg_all$
activity =
= "
active",
]$ob
s
●
●
40 60 80 100 120 140
Spe
cie
s r
ich
ne
ss
Evenness (Simpson reciprocal index)
1 Depth
Across different environmental conditions of the soil profile, the diversity of active
bacteria is unchanged and they are phylogenetically clustered
Overall: No significant effect of precipitation history on bacterial or fungal
diversity, but depth response
Across precipitation treatments:
1400
1450
1500
1550
1600
avg_all[avg_all$activity == "active", ]$SimRec
obs index
●
●
act. inact.
● ●
top
middle
bottom
600
800
1000
1200
1400
fung_avg_all[fung_avg_all$activity == "active", ]$SimRec
fung_avg_a
ll[fu
ng_avg_all$
activity =
= "
active",
]$ob
s
●
●
40 60 80 100 120 140
Spe
cie
s r
ich
ne
ss
Evenness (Simpson reciprocal index)
1400
1450
1500
1550
1600
avg_all[avg_all$activity == "active", ]$SimRec
obs index
●
●
act. inact.
● ●
top
middle
bottom
600
800
1000
1200
1400
fung_avg_all[fung_avg_all$activity == "active", ]$SimRec
fung_avg_a
ll[fu
ng_avg_all$
activity =
= "
active",
]$ob
s
●
●
40 60 80 100 120 140
Spe
cie
s r
ich
ne
ss
Evenness (Simpson reciprocal index)
1400
1450
1500
1550
1600
avg_all[avg_all$activity == "active", ]$SimRec
obs index
●
●
act. inact.
● ●
top
middle
bottom
600
800
1000
1200
1400
fung_avg_all[fung_avg_all$activity == "active", ]$SimRec
fung_avg_a
ll[fu
ng_avg_all$
activity =
= "
active",
]$ob
s
●
●
40 60 80 100 120 140
Spe
cie
s r
ich
ne
ss
Evenness (Simpson reciprocal index)
1 Depth
Frequent Infrequent
Top 0-5cm depth: significant precipitation regime effects on microbial diversity
Precipitation pattern affected not only fungal:bacterial ratio but also their relative activity
1400
1450
1500
1550
1600
avg_all[avg_all$activity == "active", ]$SimRec
obs index
act. inact.
freq.
infreq.
600
800
1000
1200
1400
fung_avg_all[fung_avg_all$activity == "active", ]$SimRec
fung_avg_a
ll[fu
ng_avg_all$
activity =
= "
active",
]$ob
s
20 40 60 80 100 120 140
Spe
cie
s r
ich
ne
ss
Evenness (Simpson reciprocal index)
BACTERIA
FUNGI
In top soil:
At 0-5 cm depth: bacterial seed bank reflects legacy more than active players.
1 Depth
top bottom
Top orders
Bottom orders
FUNGIdominated by phylum Ascomycota
top bottom
Depth groups are dominated by different classes of Proteobacteria
Top and bottom group contain completely different orders of fungi
BACTERIA
Nutrients and time2
NH4+
Microbial biomass N
N2O
nitrification denitrification
Under less frequent precipitationUnder high N inputs
amoA (archaea)potential nitrification
nirK, nirS, nosZ1, nosZ2potential denitrification
biomassphotosynthesis rate
N uptake
Alternating wetter and drier conditions stimulated nitrification-denitrification sequences
N input increased plant N uptake through increased microbial turnover
(underfreq water)
Engelhardt et al. unpubl. data
NO3-
Nutrients and time2
Infrequent precipitation decreased fungal:bacterial ratio
Potential consequences on soil food web stability, as well as soil C sequestration,
and N retention
Nutrients and time
Frequent water, high NFrequent water, low NInfrequent water, high NInfrequent water, low NBACTERIA
During 29 hours after rewetting:
FUNGI
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−0.08 −0.06 −0.04 −0.02 0.00 0.02 0.04
−0.03
−0.02
−0.01
0.00
0.01
0.02
0.03
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F_10N
F_5N
I_10N
I_5N
Bacteria Fungi
Precipitation legacy 18 36
N legacy 35 10
Time after rewetting ns ns
Precip. leg. x Time ns ns
Stability of the microbial community structure over time, after the large immediate response to rewetting
% variance explained
2
Nutrients and time
Soil greenhouse gas emissions upon rewetting
2
Frequent precipitation pattern enhances soil CO2 emissions
upon rewetting
Contrasts with soil-only studies: contribution of root respiration
CO2
N2O
Nutrients and time
Plant-microbial competition for soil inorganic N
2
Frequent precipitation pattern enhances plant competitiveness for N
after rewetting
Soilfood web stability
• Depth shapes structure of soil microbial community more than precipitation legacy
• Top soil is where precipitation history matters:> shift in fungal vs bacterial dominance > loss of plant microbial coupling under infrequent precipitation
• N cycling is stimulated by dry-wet amplitude
• Soil CO2 emissions upon rewetting are related to both root respiration and soil microbial activity
Impact
Soil C sequestration
Soil N losses
Soil CO2
emissionsNext challenge: predictability
Ecosystem property at stake:
INRA Dijon
Ilonka EngelhardtAmy Welty
WSL (Switzerland)
Arthur GesslerLucía GalianoJosé Carlos Miranda
Lawrence LivermoreNational Lab (USA)
Steve Blazewicz
Uni Zurich (Switzerland)
Pascal Niklaus
Lund University(Sweden)
Annelein Meisner
Thanks