Mitigating N2O emissions - an ES delivered by soil microbes

Mitigating N2O emissions - an ES delivered by soil microbes

Sara Hallin

Dept. Forest Mycology & Plant PathologySwedish University of Agricultural Sciences, Uppsala

ClimBEco Annual MeetingAug 24-25, 2017

Höllviken

« the microbial zoo »

Biomass in soil: 10 ton/ha• Bacteria 1-2 ton

Bacteria occupy <0.3% of pore space

Fungi: 10 – 100 m/gBacterial cells: 107 – 1010/g

”Species”: 103 – 104/g

N

“Leaky pipe” – N losses from soil

N2ON2O

Leaching

NH4+ NH2OH

NitrificationNO3

- NO2- NO N2O

N2

DenitrificationNO2

-

N2O

(Philippot & Hallin 2011, Trends Plant Sci.)

N2O

(Redrawn from Hallin et al. 2017 Trends Microbiol.)

NirS

NosZNORNirK

NO3- NO2

- NO N2O N2

N

OO

O

N

OO

O

N

OO

O

N

OO

O

N

OO

O

N

OO

O

NONON2

NON2ONONONO3- NO2- Denitrification

N

OO

O

N

OO

O

N

OO

O

N

OO

O

N

OO

O

N

OO

O

N N

N NN N

NONON2

NON2ONONONO3- NO2- Denitrification

ON N

ON NON N

NONON2

NON2ONONONO3- NO2- Denitrification

ON NON N

N N

N N

NONON2

NON2ONONONO3- NO2- Denitrification

nirKnirSnornosZ

652 genomes with denitrification genes:

SSU tree

(Graf et al, 2014 PLOS ONE)

• 30% have nosZwithout nir genes

• 24% have only nosZ –true N2O sinks

nirK+nosZ

70% of nosZ genomes have a complete denitrification pathway

(Graf et al, 2014 PLOS ONE)

Nearly 46% of 652 genomes potential N2O reducers

(Jones et al. 2013 ISME J)

Clade I

Clade II

Denitrification pathway

(Graf et al, 2014 PLOS ONE)

A new clade of the N2O reductase - N2O sink?

nosZ Clade I and II abundance in soils and other systems

Soil

WWTPWetland

Rice paddies Sediments

% o

f tot

al b

acte

rial c

omm

unity

(Jones et al. 2013 ISME J)

Clade IClade II

Clade I Clade II

(Orellana et al. 2014 mBio)

Reduction of N2O produced by inherent soil microbes by inocculating Dyadobacter fermentans into arable soils:

(Domeignoz-Horta et al, 2016 Soil Biol Biochem)

• nosZ II• not capable of denitrification• not capable of N2O production• N2O reduction coupled to growth

N2O

N2O reducing strain

No strain addedLOW inocculation levelHIGH inocculation level

First evidence that non-denitrifying N2O-reducers contribute to soil N2O reduction

Deni

trifi

catio

nen

d-pr

oduc

trat

io(N

2O/[

N2O

+ N

2])

Agricultural soils

(Domeignoz-Horta et al, 2016 Soil Biol Biochem)

In the soil

rN2O/r[N2+ N2O]Non-inoculated

rN2O/r[N2+ N2O]108 cells g-1 soil DW

rN2O/r[N2+ N2O]109 cells g -1 soil DW

Source

Sink

N2O s i n k i n d e

0.00.2

0.40.6

0.81.0

0.0

0.2

0.40.6

0.81.0

0.0

0.2

0.4

0.6

0.8

1.0

-0.15

-0.10

-0.05

0.00

0.05

0.10

0.15

0.20

Capacity to consume N2O:

(Jones et al, 2014 Nature Climate Change)

Range of potential soil N2O sink capacity across 47 soils

Factors underlying N2O source or sink

Variable importanceStructural equation modeling

Factors underlying soil N2O source or sink

(Jones et al, 2014 Nature Climate Change)

Associated with plants

Treatments:• Sunflower• Barley• Control

• Soil A• Soil B

nosZ I

Soil A

nosZ II

Soil B

(Graf et al, manuscript)

(Graf et al, 2016 Soil Biol Biochem)

Soil A Soil B

nosZ

II:no

sZI r

atio

Niche differentiation between clade I and clade II

(Graf et al, manuscript)

Net

Rel

ated

ness

Inde

x (N

RI)

nosZ I nosZ I

nosZ II nosZ II

Soil A Soil B

Farming system & practices

14 long-term trials, +/-N

(Putz et al, manuscript)

Deni

trifi

catio

n en

d pr

oduc

t rat

io(N

2O/(

N2O

+N2)

)

nosZ/nir gene abundance

r2 = 0.49p < 0.0001

Long-term effects of N-fertilization on N2O reducers

***

Rela

tive

Abun

canc

e [%

]

*** **

Effect of site on the nosZ clade I community structure

Effect of site and fertilization on the nosZ clade II community structure**

* * **

% c

hang

efr

om u

nfer

tlize

d

nirS

nosZ InirK

NO3- NO2

- NO N2O N2

nosZ II

(Putz et al, manuscript)

Specific taxa change and abundance of denitrifiers increase

Community structure of N2O reducers:

N kg ha-1 y-1 0 150 0 120Soil C:NO3

- 0.64 0.70 0.55 0.50

NO3- NO2

- nir nosZNO2-NH4

+ nrfA NO N2O N2

(Schleusner et al, manuscript)

Long-term effects of cropping system on fate of nitrate

Denitrification

Dissimilatorty nitrate reduction to ammonium

(DNRA)

Nitrogen lossNitrogen retention

Cropping system overrule fertilization

C to nitrate ratio drives differences

Ley more DNRA activity and less N2O emissions, confirms gene data

DNRA bacteria : DenitrifiersN2O reducers : Denitrifiers

(Schleusner et al, manuscript)

Ecosystem scale

(Juhanson et al, 2017 SBB; Enwall et al, 2010 AEM)

• α diversity, abundance, comunity structure, assemblymechansims show nichedifferentiation

• Suggest biotic interactions drive nosZ clade II microbes

Spatial study of clade I and II nosZ communities across 44 ha

nirK abundancenosZI/nosZII

ON NON N

N N

N N

NONON2

NON2ONONONO3- NO2- Denitrification

Agricultural Diversification – Digging Deeper

Oscar and Lili LammFoundation

INRA, France:Laurent PhilippotDavid BruLuiz Domeignoz-HortaAymé Spor

Univ. Gothenburg:Philipp SchleusnerTobias Rütting

Microbial Ecology:Chris JonesDaniel GrafMartina PutzMaren EmmerichMing ZhaoMaria HellmanJaanis Juhansson

Awesome team Collaborators Funding

PhD position on fungal denitrification openingContact me: Sara.Hallin@slu.se

HI: Agricultural Diversification enhances Soil Biodiversity and EcosystemSustainability

(Bender et al. 2017. Trends Ecol Evol)