keeping an eye on the carbon...
TRANSCRIPT
Ph
oto
co
urt
esy
of
Ja
ke
Bry
an
t@e
nvir
ofo
to.c
om
Keeping an eye on the
carbon balance
Alice Holt, UK
Team Effort
Toshie
Mizunuma
Edoardo
Cremonese
Jérôme
Ogée
Lisa
Wingate
Mirco Migliavacca
Acknowledgements
Kenlo Nasahara & Shin Nagai
Timo Vesala, Pasi Kolari & Janne Levula
Andrew Richardson
Matthew Wilkinson & James Morison
Jim Gray Seed Trust, Microsoft Research
Specnet-FLUXNET committee for invitation
and all the FLUXNET PIs for their help
Barbara Köstner, Thomas Grünwald
Olaf Kolle, Alexander Knohl, Werner Kutsch & Markus Reichstein
Catherine Van Ingen
Ph
oto
co
urt
esy
of
Ja
ke
Bry
an
t@e
nvir
ofo
to.c
om
Dario Papale and the IMECC support team
Picea abies L.
Prunus ssp.
Tharandt
International Phenological Garden Niemand et al., 2005
Köstner et al., 2005
Classical approach to recording start of growing season
Date
of
May s
ho
ot
Phenological monitoring since 1962
Grünwald & Bernhofer, 2007
Tharandt CarboEurope Tower, Dresden, Germany
Picea abies L.
Net Ecosystem Exchange
[ mol CO2 m-2 s-1]
Alternative approach to investigate forest ‘growth’ variability
Picea abies L. Prunus ssp.
Tharandt
International Phenological Garden
Net Ecosystem Exchange
[ mol CO2 m-2 s-1]
Together new possibilities to study ‘functional phenology’
Niemand et al., 2005
Köstner et al., 2005
FLUXNET sites encouraged to mount webcams on towers
hmmm, we need
more cameras
like this on
flux towers...
Dennis Baldocchi et al., 2005
Year Webcam Installed
2000 2002 2004 2006 2008 2010 2012
Nu
mb
er
of
flu
x s
ites
wit
h w
eb
cam
s
0
10
20
30
40
50
60
Europe
Asia
North America
Central and South America
Growing webcam network at European FLUXNET sites
‘digital number-DN’
Extracting a colour signal from digital images
Richardson et al., 2007, 2009
Bartlett Deciduous Forest Ameriflux Tower, New Hampshire, USA
Strong seasonality in colour signal
0.40
0.35
120 180 240 300
DOY
0.45
0.40
0.35
Relative Channel Brightness ‘digital number-DN’
Green Dn
Total Dn
Red Dn
Total Dn
% G
reen
% R
ed
Richardson et al., 2007, 2009
Bartlett Deciduous Forest Ameriflux Tower, New Hampshire, USA
Strong seasonality in colour signal
0.40
0.35
120 180 240 300
DOY
0.45
0.40
0.35
Relative Channel Brightness ‘digital number-DN’
Green Dn
Total Dn
Red Dn
Total Dn
50
25
0
120 180 240 300
DOY
% G
reen
% R
ed
Green Excess Index
2G
ree
n D
N -
(Re
d D
N +
Blu
e D
N)
Richardson et al., 2007, 2009
Bartlett Deciduous Forest Ameriflux Tower, New Hampshire, USA
Latitudinal distribution of webcams in deciduous flux sites C
olo
ur
Fra
cti
on
in R
ed
, G
reen
& B
lue C
han
nels
DOY100 200 300
0
0.3
0
0.3
0
0.3
0
0.3
0
0.3
0
0.3
00
0.3
Italy
Larch
45°50’ N
07°34’ E
Switzerland
Beech & Ash
47°28’ N
08°21’ E
Italy
Oak
42°39’ N
08°21’ E
Germany
Beech & Ash
51°04’ N
10°28’ E
England
English Oak
51°07’ N
00°51’ W
Belgium
Beech
50°18’ N
05°59’ E
Denmark
Beech
55°29’ N
11°38’ E
Torgnon
Str
en
gth
of
sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Lägeren
Str
en
gth
of
sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Hainich
Str
en
gth
of
sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Sorø
Str
en
gth
of
sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Alice Holt
Str
en
gth
of
sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Vielsalm
Str
en
gth
of
sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Roccarespampani
DOY
0 100 200 300
Str
en
gth
of
sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5Blue 2009
Red 2009
Green 2009
Red 2010
Green 2010
Blue 2010
DOY
0 100 200 300
Str
en
gth
of
sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Red 2008
Green 2008
Blue 2008
Red 2011
Green 2011
Blue 2011
Green2005
Red 2005
Blue 2005
Green2007
Red 2007
Blue 2007
Green2003
Red 2003
Blue 2003
Green2006
Red 2006
Blue 2006
Green2004
Red 2004
Blue 2004
Latitudinal distribution of webcams in evergreen flux sites
DOY100 200 300
0
0.3
0
0.3
0
0.3
0
0.3
0
0.3
0
0.3
00
0.3
Germany
Norway Spruce
50°58’ N
13°34’ E
Germany
Norway Spruce
50°27’ N
11°27’ E
Belgium
Scots Pine
50°18’ N
05°59’ E
Scotland
Sitka Spruce
56°36’ N
3°47’ E
Sweden
Scots Pine & Spruce
60°05’ N
17°28’ E
Belgium
Scots Pine
51°18’ N
04°31’ E
Finland
Scots Pine
61°50’ N
24°17’ E
Vielsalm
DOY
0 100 200 300
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Las Majadas del Tietar
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Tharandt
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Aberfeldy
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Norunda
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
HyytiäläS
tren
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Wetzstein
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
0.1
0.2
0.3
0.4
0.5
0.1
0.2
0.3
0.4
0.5
Brasschaat
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Vielsalm
DOY
0 100 200 300
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Las Majadas del Tietar
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Tharandt
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Aberfeldy
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
NorundaS
tren
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Hyytiälä
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Wetzstein
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
0.1
0.2
0.3
0.4
0.5
0.1
0.2
0.3
0.4
0.5
Brasschaat
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Co
lou
r F
racti
on
in R
ed
, G
reen
& B
lue C
han
nels
Webcams in grass and cropland flux sites
DOY100 200 300
0.31
0.33
0.31
0.33
0
0.3
0
0.3
0
0.3
0
0.3
00
0.3
Italy
Grassland
45°50’ N
07°34’ E
Switzerland
Grassland
47°07’ N
08°32’ E
France
Grassland
45°38’ N
02°44’ E
Germany
Crops
50°54’ N
13°31’ E
Germany
Grassland
50°54’ N
13°31’ E
Belgium
Grassland
50°55’ N
04°44’ E
Germany
Crops
51°06’ N
10°54’ E
Torgnon
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.300
0.325
0.350
0.375
Früebüel
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.31
0.32
0.33
0.34
0.35
Klingenberg
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Lonzee
Str
en
gh
t o
f s
ign
al
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Grillenburg
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Laqueuille
DOY
0 100 200 300
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
Gebesee
Str
en
gh
t o
f sig
nal
in R
GB
ch
an
nel
0.1
0.2
0.3
0.4
0.5
0.6
Co
lou
r F
racti
on
in R
ed
, G
reen
& B
lue C
han
nels
Filtering and extracting phenological metrics
Filtering Cremonese, Migliavacca & Richardson
Data courtesy of Knohl, Kolle & Werner
Median of Absolute Deviation for the median (Papale et al., 2006)
MAX value filter over 5-day window (Sonnentag et al., AGU, 2006)
Remove unrealistic data Green Fraction <0.2 and Excess <-40
Hainich, Germany
DOY 2008
Filtering and extracting phenological metrics
Filtering Cremonese & Migliavacca
Data courtesy of Knohl, Kolle & Werner
Gapfill by fitting
a spline to
MAD MAX
filtered data (d.f. = length (data)/8)
Hainich forest
Hainich, Germany
Bayesian change point analysis for extraction of phenometrics
DOY 2008
Po
ste
rio
r M
ea
n o
f th
e
Gre
en
Ex
ce
ss
In
de
x
Bayesian fitting Cremonese & MigliavaccaData courtesy of Knohl, Kolle & Werner
Bayesian model for a change point problem
(Barry & Hartigan, 1993)
Script adapted from a genome analysis study
(Erdmann & Emerson, 2011)
Hainich, Germany
Bayesian extraction of phenological metrics
DOY 2008
Po
ste
rio
r M
ea
n o
f th
e
Gre
en
Ex
ce
ss
In
de
x
Po
ste
rio
r P
rob
ab
ilit
y
of
a c
ha
ng
e
0
1
0.4
0.8
0.6
0.2
Bayesian fitting Cremonese & Migliavacca
budburst leaf fall
other significant
changes
Data courtesy of Knohl, Kolle & Werner
174 days
Growing season length often retrieved from NDVI products
Jeong et al., GCB 2011
Gre
en E
xcess
[-]
0
50
100
150
200
DOY 2003
0 100 200 300
Cum
ula
tive N
EE
[gC
m-2
]
-15
-10
-5
0
5
Daily
Tem
pera
ture
[oC
]
-20
-10
0
10
20
30
So
il h
um
idit
y[%
]
0
20
40
60
Carbon uptake period and green signal consistent
Ne
t E
co
syste
m C
O2
Exc
ha
ng
e
[gC
m-2
d-1
]
CO2 uptake period
Hainich Forest, Germany
Data courtesy of Knohl, Kolle & Werner
Gre
en
Exce
ss
[-]
0
50
100
150
200
DOY 2003
0 100 200 300
Cu
mu
lative
NE
E
[gC
m-2
]
-200
0
200
400
600D
aily
Te
mp
era
ture
[oC
]
-20
-10
0
10
20
30
So
il h
um
idit
y[%
]
0
20
40
60
CO2 uptake period
Carbon uptake period and green signal consistent
Hainich Forest, Germany
Data courtesy of Knohl, Kolle & Werner
Interannual variability in growing season length
Hainich Forest, Germany
Data courtesy of Knohl, Kolle & Werner
Sta
rt D
ate
100
110
120
130
140
Carbon Uptake Period
Green Excess Index
En
d D
ate
270
280
290
300
310
Year
2002 2003 2004 2005 2006 2007 2008 2009
Len
gth
of
'gro
win
g' s
eas
on
150
160
170
180
190
Gro
win
g s
ea
so
n
len
gth
En
d d
ay
Sta
rt d
ay
Is the green signal a good indicator of growing season length?
Pelkonen & Hari, 1980
Bergh & Linder, 1999
Mäkelä et al., 2004
Ensminger et al., 2004
Spring recovery of
photosynthetic CO2 uptake
inhibited by
low air temperatures
in evergreen conifer forests
Air
Te
mp
era
ture
[oC
]
-24
-16
-8
0
8
16
24
Air Temperature
Date
1/1/2008 1/7/2008 1/1/2009 1/7/2009 1/1/2010 1/7/2010 1/1/2011
Net
Eco
syste
m E
xch
an
ge
[g C
m-2
d-1
]
-12
-8
-4
0
4
8
12
Obs
Hyytiälä Forest, Finland
Coniferous evergreen forests strongly regulated by temperature
Spring CO2 uptake
regulated by air temperature
Data courtesy of Vesala, Kolari, Levula
Tower observations
Air temperature 3-day mean
Date
1/1/2008 1/7/2008 1/1/2009 1/7/2009 1/1/2010 1/7/2010 1/1/2011
Net
Eco
syste
m E
xch
an
ge
[g C
m-2
d-1
]
-12
-8
-4
0
4
8
12
Obs Date
1/1/2008 1/7/2008 1/1/2009 1/7/2009 1/1/2010 1/7/2010 1/1/2011
Net
Eco
syste
m E
xch
an
ge
[g C
m-2
d-1
]
-12
-8
-4
0
4
8
12
Obs
Hyytiälä Forest, Finland
Need to account for photosynthetic acclimation in conifer forests
Without temperature acclimation
photosynthesis models
don’t work well
Data courtesy of Vesala, Kolari, Levula
Modelling by Ogée
MuSICA model without acclimationTower observations
Date
1/1/2008 1/7/2008 1/1/2009 1/7/2009 1/1/2010 1/7/2010 1/1/2011
Net
Eco
syste
m E
xch
an
ge
[g C
m-2
d-1
]
-12
-8
-4
0
4
8
12
Obs Date
1/1/2008 1/7/2008 1/1/2009 1/7/2009 1/1/2010 1/7/2010 1/1/2011
Net
Eco
syste
m E
xch
an
ge
[g C
m-2
d-1
]
-12
-8
-4
0
4
8
12
Obs
1/1/2008 1/7/2008 1/1/2009 1/7/2009 1/1/2010 1/7/2010 1/1/2011
-12
-8
-4
0
4
8
12
MuSICA Acclimation
Hyytiälä Forest, Finland
Need to account for photosynthetic acclimation in conifer forests
Data courtesy of Vesala, Kolari, Levula
Modelling by Ogée
MuSICA model without acclimationTower observations
MuSICA model WITH acclimation
Adding a temperature acclimation
(Mäkelä et al., 2004) function
improves the model
Air
Te
mp
era
ture
[oC
]
-24
-16
-8
0
8
16
24
Air Temperature
Date
1/1/2008 1/7/2008 1/1/2009 1/7/2009 1/1/2010 1/7/2010 1/1/2011
Net
Eco
syste
m E
xch
an
ge
[g C
m-2
d-1
]
-12
-8
-4
0
4
8
12
Obs
Hyytiälä Forest, Finland
Spring green signal does not indicate start of ‘growing’ season
Webcam indicates a change in
canopy colour before there
is a net CO2 uptake
Data courtesy of Vesala, Kolari, Levula
Modelling by Ogée
Tower observations
Air temperature 3-day mean
Green Excess Index
Date
1/1/2008 1/7/2008 1/1/2009 1/7/2009 1/1/2010 1/7/2010 1/1/2011
Net
Eco
syste
m E
xch
an
ge
[g C
m-2
d-1
]
-12
-8
-4
0
4
8
12
Obs Date
1/1/2008 1/7/2008 1/1/2009 1/7/2009 1/1/2010 1/7/2010 1/1/2011
Net
Eco
syste
m E
xch
an
ge
[g C
m-2
d-1
]
-12
-8
-4
0
4
8
12
Obs
Hyytiälä Forest, Finland
Photometabolic activity in spring stimulated by incoming radiation
Data courtesy of Vesala, Kolari, Levula
Modelling by Ogée
MuSICA model without acclimation
Webcam change matches the
timing and rate of change
predicted by model
with no acclimation
Tower observations
Green Excess Index
Air
Te
mp
era
ture
[oC
]
-24
-16
-8
0
8
16
24
Air Temperature
Air
Te
mp
era
ture
[oC
]
-24
-16
-8
0
8
16
24
Air Temperature
Gre
en
Excess
[-]
-75
-50
-25
0
25
50
75
Green Excess Index
Hyytiälä Forest, Finland
Need to account for photosynthetic acclimation in boreal forests
Subtle phenology signals
can be detected
in Scots Pine canopies
Green down signal
Air temperature 3-day mean
Green Excess Index
Date
1/1/2008 1/7/2008 1/1/2009 1/7/2009 1/1/2010 1/7/2010 1/1/2011
Net
Eco
syste
m E
xch
an
ge
[g C
m-2
d-1
]
-12
-8
-4
0
4
8
12
Obs
Date
1/1/2008 1/7/2008 1/1/2009 1/7/2009 1/1/2010 1/7/2010 1/1/2011
Net
Eco
syste
m E
xch
an
ge
[g C
m-2
d-1
]
-12
-8
-4
0
4
8
12
Obs
Air
Te
mp
era
ture
[oC
]
-24
-16
-8
0
8
16
24
Air Temperature
Air
Te
mp
era
ture
[oC
]
-24
-16
-8
0
8
16
24
Air Temperature
Gre
en
Excess
[-]
-75
-50
-25
0
25
50
75
Green Excess Index
Need to account for photosynthetic acclimation in boreal forests
Subtle phenology signals
can be detected
in Scots Pine canopies
Green down signal
Elongation of brown shoots
Air temperature 3-day mean
Green Excess Index
Hyytiälä Forest, Finland
Frost events impact green signal and CO2 uptake
Alice Holt, England
Courtesy of Mizinuma, Wilkinson & PEN
Gre
en
Exce
ss
[-]
0
50
100
DOY 2010
0 100 200 300
Gro
ss P
rim
ary
Pro
du
ctivity
(3-d
ay r
un
nin
g m
ea
n)
[mo
l C
O2 m
-2d
-1]
0.0
0.5
1.0
Daily
Min
imum
Te
mp
era
ture
(3-d
ay r
un
nin
g m
ea
n)
[oC
]
-10
0
10
20
Frost events impact green signal and CO2 uptake
Alice Holt, England
Courtesy of Mizinuma, Wilkinson & PEN
Gre
en
Exce
ss
[-]
0
50
100
DOY 2010
0 100 200 300
Gro
ss P
rim
ary
Pro
du
ctivity
(3-d
ay r
un
nin
g m
ea
n)
[mo
l C
O2 m
-2d
-1]
0.0
0.5
1.0
Daily
Min
imum
Te
mp
era
ture
(3-d
ay r
un
nin
g m
ea
n)
[oC
]
-10
0
10
20
Frost damaged
Ash leaves
Frost events impact green signal and CO2 uptake
Alice Holt, England
Courtesy of Mizinuma, Wilkinson & PEN
Gre
en
Exce
ss
[-]
0
50
100
DOY 2010
0 100 200 300
Gro
ss P
rim
ary
Pro
du
ctivity
(3-d
ay r
un
nin
g m
ea
n)
[mo
l C
O2 m
-2d
-1]
0.0
0.5
1.0
Daily
Min
imum
Te
mp
era
ture
(3-d
ay r
un
nin
g m
ea
n)
[oC
]
-10
0
10
20
Frost damaged
Ash leaves
Po
ste
rio
r
pro
bab
ilit
y 1
0
Frost
event
Gre
en E
xcess
[-]
0
50
100
150
200
DOY 2003
0 100 200 300
Cum
ula
tive N
EE
[gC
m-2
]
-15
-10
-5
0
5
Daily
Tem
pera
ture
[oC
]
-20
-10
0
10
20
30
So
il h
um
idit
y[%
]
0
20
40
60
Colour signals affected by extreme events?
Ne
t E
co
syste
m C
O2
Exc
ha
ng
e
[gC
m-2
d-1
]
2003 heatwave
Hainich Forest, Germany
Data courtesy of Knohl, Werner & Kolle
Conclusions
Carbon uptake does not always coincide with
the green up signal
The webcam network at flux sites can
help us monitor and probe large scale
vegetation responses to climatic shifts
Webcams are a cheap and simple way to
obtain dynamic information on canopy state
Rich detail in the image signal that can be
linked to weather events affecting growing
season length
Thank you to all the flux site PIs and staff
Hella Ahrends, Marc Aubinet, Manuela Balzarolo, Gielen Bert, Nina Buchmann, Faye Carroll,
Robert Clement, Edoardo Cremonese, Lars Eklundh, Werner Eugster, Cristina Gimeno
John Grace, Thomas Grünwald, Bernard Heinesch, Margareta.Hellstrom, Andreas Ibrom
Ivan Janssens, Mike Jones, Sabina Keller, Katja Klump, Olaf Kolle, Alexander Knohl
Werner Kutsch, Quentin Laffineur, Janne Levula, Anders Lindroth, Bernard Longdoz
Maurizio Mencuccini, Mirco Migliavacca, Toshie Mizunuma, Eddy Moors, Dario Papale
Joao Periera, Filipe Costa e Silva, Jean-Francois Soussana, Catherine Van Ingen, Timo Vesala
Matthew Wilkinson, Jans Wilma