microbial communities and n cycling in diverse soils · 2018-06-13 · david d. myrold department...
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David D. Myrold Department of Crop and Soil Science
Oregon State University
Microbial Communities and N Cycling in Diverse Soils
Pierre Lecture 2017
N Cycle—A Historical Perspective
Alexander (1961) Introduction to Soil Microbiology p.246
Schimel & Bennett (2004) Ecology 85:591
Shift in Emphasis in N Mineralization
Daims et al. (2016) Trends Microbiol 9:699
New Processes and Organisms
N assimilation
N mineralization
N2 fixation
Denitrification
Nitrification
Anammox
Broad phylogenetic representation
Narrow phylogenetic representation
Structure-Function Connections in the N Cycle
Nitrification—A Focus of the Last Decade
• 1890—Ammonia-oxidizing bacteria (AOB) and nitrate-oxidizing bacteria (NOB) (Frankland & Frankland (1890) Phil
Trans Royal Soc B 181:107; Winogradsky (1891) Ann Inst Pasteur 5:577)
• 2005—Ammonia-oxidizing archaea (AOA) (Könneke et al.
(2005) Nature 437:543)
• 2016—Comammox, an organism (Nitrospira spp.)
capable of complete nitrification (NH4+ NO3
-) (Daims
et al. (2016) Nature 528:504; van Kessel et al. (2016) Nature 528:555)
Nitrification
Wrage et al. (2001) Soil Biol Biochem 33:1723
(amo) (hao) (nxr)
H+
Acidification Impacts of Nitrification
(1928) J Am Soc Agron 20:254
(1970) Agron J 62:106
(1977) Soil Sci Soc Am J 41:368
Nitrification Niche
The set of physical and chemical properties, as well as biological interactions, that allow the activity, growth, or survival of a particular nitrifying taxon.
Physical • Temperature
• Water
• Structure
• Porosity
• Texture
• Bulk density
Chemical • NH4
+/NH3
• pH
• C:N ratio
• Inhibitors/toxicities
• O2, CO2
• Salinity
• Micronutrients
• CEC
• Mineralogy
Niche Determining Factors
Biological • AOA and AOB
characteristics • Cell size, µmax, KS, Topt,
alternate substrates, etc.
• Ammonification rate
• Nitrate-oxidation rate
• Plant activities
Approaches for Niche Identification
• Genome analysis
• Isolate physiology
• Taxa abundance and composition (DNA)
• Activity • Transcripts (RNA)
• SIP (growth)
• Selective inhibitors
Microbial Communities of Oregon—Selection Scheme
Sampling Sites
Ammonia-oxidizer (AOA) Distribution
Burgess (unpublished data)
Ammonia-oxidizer (AOB) Distribution
Burgess (unpublished data)
AOA/AOB Ratio
Burgess (unpublished data)
Nitrite-oxidizer (NOB) Distribution
Burgess (unpublished data)
NOB:(AOA+AOB) Ratio
Burgess (unpublished data)
Taylor et al. (2013) Appl Environ Microbiol 79:6544
Differentiating AOA vs. AOB Activity
1-octyne (C8)
Acetylene (C2)
(1986) Soil Sci Soc Am J 50:1998
Lu et al. (2015) Soil Biol Biochem 85:54
Nitrification Niches Along a Forest Nitrogen Gradient
Douglas-fir Red alder
Soil Factors Related to AOA and AOB Abundance
Lu et al. (2015) Soil Biol Biochem 85:54
Soil Factors Related to AOA and AOB Abundance
Lu et al. (2015) Soil Biol Biochem 85:54
Lu et al. (2015) Soil Biol Biochem 85:54
Soil Factors Related to AOA Activity
Soil Factors Related to AOA Activity
Lu et al. (2015) Soil Biol Biochem 85:54
Nitrification Niches in Managed Soils
Response of AOA and AOB to Ammonia Addition
Giguere et al. (2015) Soil Sci Soc Am J 79:1366
Klamath Cropped (Summer)
0 20 40 60 80 100
NO
3
- + N
O2
- Accu
mu
latio
n
(mg
-N k
g-1
so
il d
-1)
0
2
4
6
8
10
12
KCl extractable NH4
+ (mg-N kg
-1 soil)
0 20 40 60 80 100 120 140 160 180
Total
AOA
AOB
Klamath non-cropped (Summer)
Ma
xim
um
Nitri
fica
tio
n R
ate
(mg
NO
3
- + N
O2
- -N
kg
-1 s
oil d
-1)
0
2
4
6
8
10
12
14
16
18
20
AOA
AOB
Non-cropped Cropped
Summer
Non-cropped Cropped
Winter
Management and Seasonal Effects on AOA and AOB
Giguere et al. (2015) Soil Sci Soc Am J 79:1366
Temperature Optima for AOA and AOB
Taylor et al. (2017) ISME J 11:896
0 10 20 30 40
Temperature (°C)
0 10 20 30 40
Nitrifica
tio
n P
ote
ntia
l
(m
ol g
-1 s
oil
d-1
)
0.0
0.1
0.2
0.3
0.4
0.5
AOA
AOB
Cropped Non-cropped
Temperature Optima for AOA and AOB
Taylor et al. (2017) ISME J 11:896
Macromolecular Rate Theory (MMRT)
Parameter Unit AOA AOB ΔHTo
‡ kJ mol-1 K-1 4.1 ± 0.7 7.2 ± 1.9 ΔCP
‡ kJ mol-1 K-1 -5.6 ± 0.6 -9.3 ± 0.9 ΔSTo
‡ kJ mol-1 K-1 -0.25 ± 0.00 -0.24 ± 0.01 Topt C 33.1 ± 1.4 20.0 ± 1.1
Ts_max C 20.9 ± 1.1 11.1 ± 0.9
Giguere et al. (2017) Soil Biol Biochem 104:30
Uncoupling of Ammonia and Nitrite Oxidation
Giguere et al. (2017) Soil Biol Biochem 104:30
Uncoupling of Ammonia and Nitrite Oxidation
Uncoupling of Ammonia and Nitrite Oxidation
Giguere et al. (2017) Soil Biol Biochem 104:30
Uncoupling of Ammonia and Nitrite Oxidation
Giguere et al. (2017) Soil Biol Biochem 104:30
Potential Mechanisms of Uncoupling/Recoupling
• Unbalanced populations—growth required
• Insufficient enzymatic capacity—protein synthesis required
• Unmatched kinetics—taxon switching
• Spatial separation
Nitrobacter nxrA
Pendleton Madras Klamath
nxr
A c
op
ies
g-1
so
il
1e+6
1e+7
1e+8
1e+9
1e+10
0 h
24 h
48 h
AOB amoA
Pendleton Madras Klamath
AO
B a
mo
A c
op
ies
g-1
so
il
1e+6
1e+7
1e+8
1e+9
1e+10
0 h
24 h
48 h
AOA amoA
Pendleton Madras Klamath
AO
A a
mo
A c
op
ies
g-1
so
il
1e+6
1e+7
1e+8
1e+9
1e+10
0 h
24 h
48 h
Nitrospira nxrB
Pendleton Madras Klamath
nxr
B c
op
ies
g-1
so
il
1e+6
1e+7
1e+8
1e+9
1e+100 h
24 h
48 h
A B
C D
AAAA
AA
AAA
AAAAA
A AAA
AA
A
AAAAA
A
AAA
AAA
AAA
Giguere et al. (submitted) Environ Microbiol
Mechanisms of Uncoupling/Recoupling
Giguere et al. (submitted) Environ Microbiol
Klamath
Time (h)9 24 48
Madras
NO3
- (-AB)
NO3
- (+AB)
Pendleton NO
2
- (-AB)
NO2
- (+AB)
*
*
*
*
*
a
b
c
A
B
C
aA
bB
cC
aAaA
bB
bB
*cC
cC
aAaA
bA
bAB
cB cC
†
†
†
†
A
B
C
0
100
200
300
400
NO
2
- or
NO
3
- (
M)
0
20
40
60
80
100
120
140
160
0
20
40
60
80
100
120
140
160
Klamath
Time (h)9 24 48
Madras
NO3
- (-AB)
NO3
- (+AB)
Pendleton NO
2
- (-AB)
NO2
- (+AB)
*
*
*
*
*
a
b
c
A
B
C
aA
bB
cC
aAaA
bB
bB
*cC
cC
aAaA
bA
bAB
cB cC
†
†
†
†
A
B
C
0
100
200
300
400
NO
2
- or
NO
3
- (
M)
0
20
40
60
80
100
120
140
160
0
20
40
60
80
100
120
140
160
Klamath
Time (h)9 24 48
Madras
NO3
- (-AB)
NO3
- (+AB)
Pendleton NO
2
- (-AB)
NO2
- (+AB)
*
*
*
*
*
a
b
c
A
B
C
aA
bB
cC
aAaA
bB
bB
*cC
cC
aAaA
bA
bAB
cB cC
†
†
†
†
A
B
C
0
100
200
300
400
NO
2
- or
NO
3
- (
M)
0
20
40
60
80
100
120
140
160
0
20
40
60
80
100
120
140
160
Klamath
Time (h)9 24 48
Madras
NO3
- (-AB)
NO3
- (+AB)
Pendleton NO
2
- (-AB)
NO2
- (+AB)
*
*
*
*
*
a
b
c
A
B
C
aA
bB
cC
aAaA
bB
bB
*cC
cC
aAaA
bA
bAB
cB cC
†
†
†
†
A
B
C
0
100
200
300
400
NO
2
- or
NO
3
- (
M)
0
20
40
60
80
100
120
140
160
0
20
40
60
80
100
120
140
160
Klamath
Time (h)9 24 48
Madras
NO3
- (-AB)
NO3
- (+AB)
Pendleton NO
2
- (-AB)
NO2
- (+AB)
*
*
*
*
*
a
b
c
A
B
C
aA
bB
cC
aAaA
bB
bB
*cC
cC
aAaA
bA
bAB
cB cC
†
†
†
†
A
B
C
0
100
200
300
400
NO
2
- or
NO
3
- (
M)
0
20
40
60
80
100
120
140
160
0
20
40
60
80
100
120
140
160
Mechanisms of Uncoupling/Recoupling
Giguere et al. (submitted) Environ Microbiol
NO2
- (M)
0 100 200 300 400 500N
O2
- con
sum
ption
rate
(
mol g
-1 d
-1)
0.0
0.5
1.0
1.5
2.0
2.5
3.0+AB: R
2=0.65
Km=173 M NO2
-
Vmax=1.0 mol g-1
d-1
-AB: R2=0.70
Km=138 M NO2
-
Vmax=1.8 mol g-1
d-1
0 100 200 300 400 500
NO
2
- con
sum
ption
rate
(
mol g
-1 d
-1)
0
1
2
3
4
5+AB: R
2=0.75
Km=48 M NO2
-
Vmax=1.5 mol g-1
d-1
-AB: R2=0.85
Km=96 M NO2
-
Vmax=2.9 mol g-1
d-1
A
B
NO2
- (M)
0 100 200 300 400 500
NO
2
- con
sum
ption
rate
(
mol g
-1 d
-1)
0.0
0.5
1.0
1.5
2.0
2.5
3.0+AB: R
2=0.65
Km=173 M NO2
-
Vmax=1.0 mol g-1
d-1
-AB: R2=0.70
Km=138 M NO2
-
Vmax=1.8 mol g-1
d-1
0 100 200 300 400 500
NO
2
- con
sum
ption
rate
(
mol g
-1 d
-1)
0
1
2
3
4
5+AB: R
2=0.75
Km=48 M NO2
-
Vmax=1.5 mol g-1
d-1
-AB: R2=0.85
Km=96 M NO2
-
Vmax=2.9 mol g-1
d-1
A
BNO2
- (M)
0 100 200 300 400 500
NO
2
- co
nsu
mp
tio
n r
ate
(
mo
l g
-1 d
-1)
0.0
0.5
1.0
1.5
2.0
2.5
3.0+AB: R
2=0.65
Km=173 M NO2
-
Vmax=1.0 mol g-1
d-1
-AB: R2=0.70
Km=138 M NO2
-
Vmax=1.8 mol g-1
d-1
0 100 200 300 400 500
NO
2
- co
nsu
mp
tio
n r
ate
(
mo
l g
-1 d
-1)
0
1
2
3
4
5+AB: R
2=0.75
Km=48 M NO2
-
Vmax=1.5 mol g-1
d-1
-AB: R2=0.85
Km=96 M NO2
-
Vmax=2.9 mol g-1
d-1
A
B
Spatial Scale: Nearest Neighbors and Niche Space
Raynaud & Nunan (2014) PLoS ONE 9:e87217
Conclusions about Nitrifier Niche Space
• It’s really more complicated than a single, explanatory variable, but generalities about drivers have been found • Numbers and activities of AOA do tend to dominate as:
• NH3 availability decreases
• pH decreases
• T increases
• Complexity of AOA and AOB responses to environmental drivers are a function of: • Genotypic and phenotypic variation among taxa
• Temporal variation in drivers
• Spatial heterogeneity
Acknowledgements
• Peter Bottomley
• Anne Taylor
• Xinda Lu
• Andrew Giguere
• Chris Burgess