Phytoplankton classification using
ocean color data : theoretical concepts
requires
study of Physics and Biology that is implicit
within these reflectance spectra
[email protected]
Short course on ‘Ocean color remote sensing – data processing and application’
at INCOIS Hyderabad (12 November 2014)
Major Phytoplankton Groups in the Indian Ocean
i. Diatoms (non-motile, fast growing)
ii. Dinoflagellates
can perform vertical migration
species N. sci. (green and red)
iii. Cyanobacteria / blue-green algae
can perform photosynthesis
genus Trichodesmium
species erythraeum, thiebautii
iv. Green flagellates
Green Noctiluca scintillans / Green tide
Noctiluca is a large (200 - 2000 µm) dinoflagellate.
It is heterotrophic (non-photosynthetic) and phagotrophic (engulfs its food)
It appears pink, red or green
due to presence of symbionts and ingested food
18-25 Feb 2009
Phytoplankton –
Class image /
MODIS
NAS: Two species; N. sci (green tide) and diatoms co-exist
FEEDING
Green Noctiluca
diatom
NS feeds on diatom, also contains green endosymbiont “Pedinomonas noctilucae”,
FAVORABLE CONDITIONS FOR Noctiluca
# Nutrient abundance i.e. availability of food
# Temperature: prefer low temperatures ( < 24o C),
# high salinity
 convection
In situ measurements
Optical properties
Lu, Ed  Lw , Lwn , Rrs
Hyper spectral radiometer
Biogeochemical properties
Chlorophyll
Phytoplankton taxonomy
Species Count
Fluorometer
Microscope
Microscope
Hydrographic properties
Temperature and conductivity
Current
CTD
ADCP
Physico-chemical properties
Nutrient (NO3, PO4, Si)
DO
Auto analyzer
Dosimat
Meteorological parameters
Wind speed and direction
Anemometer
Process study
Primary Production
New Production
Secondary Production
Scintillation counter
Mass spectrometer
Bongo net
Rrs spectra of Non-bloom oceanic waters

Rrs= Lu(0+)/Ed(0+)
Blue: 450-480 nm
Rrs
Chl: 0.27 (mg.m-3)
0.21
0.36
0.26
0.16
0.37
0.4
0.88
0.16
0.12
0.12
wavelength (nm) 
Rrs spectra of diatom dominating waters

Rrs
Blue: 450-480 nm
Green: 495-570 nm
i. high reflectance due to low chl,
ii. spectra looks shrunk because when chl is low,
peak shifts towards blue
chlorophyll, diatoms, NS
1.09 , 3600, 240
1.02, 3200, 80
0.37, 2600, 1520
0.72, 5226, 677
0.39, 5675, 262
0.76, 4400, 460
1.2, 6100, 0
0.19, 10500, 1850
wavelength (nm) 
1.4, 31000, 1600
Rrs spectra of non-bloom, diatom and green Noctiluca dominating waters

Rrs
diatom
17 February 2009, oc bl
ns(9600) dia(864) (27.7)
16 March 2011, oc bl
ns(1352) dia(10000) (27.7)
10 February 2009, nb
ns(nil) dia(nil) (0.27)
nb
Trend of increasing
reflectance is unique for NS
NS
wavelength (nm) 

Rrs
i. Noct. is a luminescent organism.
noct. emission 
max at 470 (blue)
Relative energy
Rrs spectra of Noctiluca dominating waters
Light is released when
the water is disturbed
420
Further, increase in refl. Peak
at 530 (green) due to symbiont
Precino. (peko plank), of green colour
580
 (nm) 
same station revisited
after 2 weeks
amino acid and DOM absorb in
uv (350-400), hence low refl.
min at 440 due to phyto abs
17 February 2009, oc bl ns(9600)
dia(864) (chl=27.7)
3 March 2009, oc bl ns(24000)
dia(30000) (chl=0.987)
wavelength (nm) 
Rrs
Blue: 450-480 nm
Coastal water spectra added
Green: 495-570 nm
Red: 620-740 nm
Noctiluca scintillans
diatoms
non-bloom oceanic
non-bloom coastal
The clue for phytoplankton
species identification is to
exploit
difference in spectral shapes
wavelength (nm) 
Noctiluca Rrs spectra
Magnitude of Rrs and
shape of the spectra depend on
0.003
Rrs
- Chlorophyll concentration
0.987
0.002
- Change in physiological state of phytoplankton
(chl:c ratio is an indicator)
27.7
Spectral shapes change because IOP changes
0.001
300
- a* decreases and bb increases with
(i) increasing cell size / pigment composition
i.e. species
(ii) cell density (packaging effect)
400
500
600
700 nm
wavelength (nm) 
bb(470)
bb(700)
3 March 2009, ss263,NS+dia
1 March 2009, ss263,non-bloom-oc
Rrs
Peak shifts from blue to green
With increase in chl. / change in phyto species
Peak extended to 530 nm (dark green)
due to presence of symbiont Peko plankton
within Noctiluca
17 February 2009, oc bl
ns(9600) dia(864) (27.7)
14 February 2009, oc bl
ns(24)
dia(1224)
(1.09)
Non-bloom
oceanic
13 Diatoms
February 2009, oc bl
ns(8) dia(460) (1.02)
Noctiluca scintillans
10 February 2009, nb
ns(nil) dia(nil) (0.27)
wavelength (nm) 
Shape of the spectra can be quantified using derivative or band ratio
0.00006
This spectral region no good for class discr.
All classes are mixed
dR/d
0.00004
1st derivative
0.00002
NSMODIS, oc bl ns
17F
10F
MODIS, oc nb
Non-bloom
9M
NSMODIS, oc bl ns
0
300
350
400
450
500
550
600
650
wavelength (nm) 
MODIS bands
10M
MODIS, oc dia
diatoms
diatoms
11M
MODIS, oc dia
-0.00002
-0.00004
1st derivative at 488, 3 classes are separate
Exploit for species discrimination
-0.00006
700

Rrs(488)-Rrs(443)
Rrs(488)-Rrs(531)

Initial validation (qualitative)
60o 30’ E
63o 15’ E
66o E
68o 45’ E
24o 45’ N
2
MODIS, 2 March 2013
1
22o N
Noctiluca Millaris
Oman
Diatoms
Non-bloom oceanic
19o 15’ N
Non-bloom coastal
CLOUD
Land / cloud
16o 30’ N
60o 30’ E
63o 15’ E
66o E
68o 45’ E
60o E
64o E
68o E
72o E
76o E
7 March 2013
240 N
240 N
non-bloom coastal
Gujarat
NW coast of India
Oman
2
non-bloom oceanic
200 N
200 N
1
SUNGLINT/
diatoms
CLOUD
land / cloud
160 N
ns
60o E
64o E
68o E
72o E
1
2
7-3-2013
ship location: 190- 00’, 670- 49’
water sample: ns - 2200 cells.l-1,
diatoms - 9700
8-3-2013
ship location: 210- 00’, 680- 00’
water sample: ns - 10000 cells.l-1,
diatoms - 2400 cells.l-1
160 N
76o E
Rrs
Rrs
Reference spectra
7 March 2013
Non-bloom
NS - 2200 cells.l-1,
diatom – 9700 cells.l-1
diatom
NS
Wavelength (nm)
Wavelength (nm)
7 March 2013
Rrs
8 March 2013
NS - 10000
diatom - 2400
Reference spectra and spectra from mixed species
look identical in shape.
dominating species dictates the optical response,
Wavelength (nm)
The product reveals anticipated temporal variability
60oE
64oE
68oE
72oE
60oE
64oE
72oE
01 Jan – 08 Jan, 2013
24 Nov – 01 Dec, 2012
A
24oN
68oE
B 24oN
20oN
16oN
20oN
Initial bloom
Pre-bloom
16oN
06 Mar – 13 Mar, 2013
C
24oN
30 Mar – 06 Apr, 2013
D 24oN
20oN
20oN
16oN
Active bloom
60oE
64oE
68oE
72oE
60oE
Phytoplankton species identification from Aqua/MODIS
non-bloom
coastal
16oN
Post-bloom
non-bloom
oceanic
diatoms
noctiluca
scintillans
Land/
Cloud
64oE
68oE
72oE
Rrs
Sources of Errors
547
spectral region where
difference in shape exists
NS
diatoms
non-bloom
wavelength (nm) 
412
443 469 488
531 555
645 667 678
0.004Rrs
0.0035
inputs from satellite
are discrete point values
and not a spectrum
0.003
0.0025
av.NS
noct. for MODIS bands
0.002
avdiatoms
diatoms for MODIS bands
non-bloom
non-bloom
oceanic
0.0015
from MODIS
0.001
0.0005
1.1E-17
300
350
400
450
500
550
-0.0005
wavelength (nm) 
600
650
700
R
0.0045 rs
Error in Rrs retrieval
Rrs
0.004
0.0035
0.003
0.0025
0.002
0.0015
0.001
0.0005
0
0.004
0.0035
10 February 2009
(MODIS)
10 Februay 2009
(ship)
300 350 400 450 500 550 600 650 700
nm
0.003
MODIS derived Rrs(443) < Rrs(490)
0.0025
Accuracy requirement for retrieval of Rrs from
10 Feb. 2009, off shore nb. (0.27)
satellite data is stringent for species identification
0.002
10 Feb 2009
0.0015
0.001
17o N / 72o E (90 m)
coastal station
0.0005
0
300
350
400
450
500
550
wavelength (nm) 
600
650
700
Bottom Lines
Spectral shape of reflectance spectra helps species discrimination
The approach discriminates between Noctiluca and diatoms
Dominating species (cell density) dictates the optical response,
Error source: Retrieval of Rrs in coastal waters leads to erroneous species det.
Bottom Lines
Red Noctiluca scintillans / Red Tide
Heterotrophic - feed on diatoms and other phytoplankton ,
red color is due to ingested food (diatom)
Major Limiting Factors :
Positively correlated with phosphate, silicates and nitrogen
Favorable temperature (18-25°C)
Toxicity :
Non-toxic, sometimes cause fish mortality by oxygen depletion
High ammonia content of vacuole irritates fish and avoid bloom areas
Prey for copepods
68o E
72o E
76o E
Red Noctiluca
+ ship station at
12o 51’ N, 74o 29’ E
20o N
29 September 2014
16o N
20o N
16o N
Threshold of R developed
to detect green Noctiluca
holds good for red
Noctiluca also
+
12o N
12o N
nm MODIS bands
Diatom is the food for red Noctiluca
and can be seen in vicinity
Blue: 450-480 nm
8o N
68o E
coastal Non-bl
72 oE
76o E
Green: 495-570 nm
diatom N. Sci Land
Red: 620-740 nm
21
22
23
24
25
density
26
27
0
Trichodesmium
100
-
a colonial,filamentous cyanobacterium
200
Occurs when waters are warm, calm and stratified  low nutrient levels
tricho
NS
nb2
It 300
is a diazotroph; that is, it fixes atmospheric nitrogen into biologically usable form
ammonium
400
and
contribute to surrounding ecosystems by its fixation of carbon and nitrogen
500
Tricho 24 March 2013
@ 9-59 N, 75-27 E
1000 m
depth (m)
Trichodesmium erythrium
Non-bloom
bb(650)
SS314
24 March 2013

Rrs(Sr-1)
Phytoplankton–cyanobacteria (bg algae)–trichodesmium erythraeum
Issues
495
• Tricho occurs in small patches
1 km resolution is not sufficient
• Operational at corr model for coastal waters
• Disperse
while operating radiometer
545 565
(nm)
Continuous derivative spectra from radiometer data
Tricho discriminated from
normal waters
dRrs/d
Non-bloom
Tricho erythraeum
dRrs/d
350
400
450
500
To perform tricho detection from available
satellite data (MODIS) where bands are
limited, use discrete spectra like this
550
600
650
(nm) Satlantic radioeter
Use such spectra to suggest new bands future sensors.
ex. Two narrow bands as shown are good for tricho discrimination
3 abs bands of phyco ery: 495, 547, 562
Discrete derivative spectra from MODIS data
412
443 469 488
531 547 555 645 667
(nm) MODIS bands
68o E
72o E
76o E
Rrs
2-9 June 2009
20o N
20o N
16o N
16o N
12o N
12o N
412
8o N
8o N
68o E
72o E
Tricho
Non-bl
76o E
Land / cl
Trichodesmium erythraeum
in SEAS, off Kollam, Kochi and Kannur
observed during 29 May – 11 June 2009
443 469 488 531 547 555 645 667 678
(nm) MODIS bands
MODIS: 14-21 March 2010
Cruise: SS273
Ship Station: 14 March 2010
13 43.03 N, 73 – 26.44 E
Tricho: 3.28x106 cells/l
?
+
Upper patch should be dia
Rrs
Rrs spectra similar for dia and tricho from 488 to 531
Therefore, dia and tricho can not be distinguished
443
469
488
531
547
555
645
667
678
(nm) MODIS bands
68oE
72oE
76oE
MODIS: 14-21 March 2010
dRrs/d
20oN
dia , tricho and nb separable
16oN
+
12oN
8oN
68oE
No discrimination between
diatom and tricho
443
469
diatom and tricho separable
488
531
547
555
645
667
(nm) MODIS bands
72oE
76oE
24-31 Oct 13
24-31 Oct 13
1-8Nov 13
1. Signature of green Noctiluca can be seen early in October
2. Besides convection, eddy is another Noctiluca-triggering mechanism
3. Signature of green Noctiluca disappears when eddy turns week (9-16 November, 2013)
Chlorophyll / MODIS
diatoms N. Sci
9-16Nov 13
coastal Non-bl
9-16 Nov 13
HIGH
Land/cloud
1-8 Nov 13
Phytoplankton class / MODIS
Utilization of value-added product
Early detection of green Noctiluca from MODIS
LOW
chlorphyll
16-18 March 2012
Phytoplankton species image and
chlorophyll images are matching
Phytoplankton group
16-18 March 2012
24o N
24o N
LOW
20o N
HIGH
20oAqua/MODIS
N
Phytoplankton species identification from
non-bloom
coastal
non-bloom
oceanic
diatoms
noctiluca
scintillans
Pattern of ns & dia are matching with chl. (NS  v. high chl, diatoms  moderate chl)
Reason: NS requires
large quantity
of phytoplanktono prey to support optimal
growth
o
o
o
60
64
68
72 E
Land/
Cloud
Chlorophyll/ MODIS
17 February 2009
18-25 February 2009
24o N
24o N
20o N
22o N
Cyclonic eddies are the most
probable locations of N. sci.
16o N
60o E
64o E
coastal
68o E
Non-bloom Diatoms
72o E
N. Sci
66o E
70o E
Land
0.01
Phytoplankton Class
Ship cruise (17F 09)
Bloom station at
21o 05’ N, 66o 45’ E
68o E
20o N
Phyto species image reveals N. sci. (dark
green)
(N.sci. : 19600 cells.L-1, dia : 860 cells.L-1)
chlorophyll (mg.m-3 )
12
Chl / MODIS reveals cyclonic eddy
(chl at the center = 27.7 mg.m-3)
N = 85
chl (min) mg.m-3
chl (max) mg.m-3
Diatoms
0.4
2.9
N. Scintillans
2.4
27.7
non-bloom oceanic
0.15
0.9
Ship data from NEAS,
off shore waters within
the Indian EEZ
for Jan – March period
Chlorophyll image can be used as a proxy to phytoplankton class image as first-cut information
Log10 (cells.L-1) 
8
y = 0.909x2 + 1.7159x + 3.0091
R² = 0.7583
6
y = 1.5936x + 3.2166
R² = 0.5859
4
 Diatoms

N. scintillans
2
Log10(chl) 
0
-1.5
-1
-0.5
0
0.5
1
1.5
8 – 15 Nov 12
1A
1 – 8 Jan 13
9 – 16 Jan 2013
17 – 24 Nov 13

25 Nov – 2 Dec 13
appearance of diatoms in patches can be seen (in green colour)
3-10 Dec 13
2B
18 – 25 Dec 12
emergence of Noctiluca scintillans can be seen in traces of dark green on the right
9 – 16 Nov 13
1B
10 – 17 Dec 12
diatoms in patches can be seen (in green colour),
26 Dec – 31 Dec 12
3A
24 Nov – 1 Dec 12
non-bloom water over all (in cyan colour)
2 - 9 Dec 12
2A
16 – 23 Nov 12
11-18 Dec 13
19-26 Dec 13
spatial extent of diatoms is seen increased (green colour)
27-31 Dec 13
1-8 Jan 14
3B
diatoms shrinking, no signature of of Noctiluca
coastal Non-bl
diatoms N. Sci Land

9-16 Jan 14
31 Oct – 7 Nov 2012
8 Nov – 15 Nov 2012
N1
16 Nov – 23 Nov 2012
N3
Study of evolution and decay of the blooms
using time-series phytoplankton class images
24 Nov – 1 Dec 2012
18 Dec – 25 Dec 2012
coastal Non-bl
diatoms N. Sci
Land
2 Dec – 9 Dec 2012
D1
26 Dec – 31 Dec 2012
10 Dec – 17 Dec 2012
1 Jan – 8 Jan 2013
+
9 Jan – 16 Jan 2013
J2
17 Jan – 24 Jan 2013
25 Jan – 1 Feb 2013
1W
2 Feb – 9 Feb 2013
2W
10 Feb – 17 Feb 2013
F2
18 Feb – 25 Feb 2013
F3
1E
diatoms increased, NS also reappeared
26 Feb – 5 Mar 2013
6 Mar – 13 Mar 2013
M2
14
–
21
2230
Mar
–––
29
Mar
2013
7Mar
Apr
Mar
14
6 Mar
Apr 2013
3W, 2E
Evolution and dist. of NS can be monitored using time-series phytoplankton class images
diatoms shrunk,
NS disappeared
coastal Non-bl
diatoms N. Sci
Land
spread of diatoms increasing,
NS also picked up
This period and beyond
both species on decline
5
Log10 (Number of pixels)
Temporal variability
At any stage, diatoms dominate over Noctiluca
4
diatoms
3
2
1
As NS peak develops,
spatial extent of diatoms decreases sharply
– the pattern indicates that NS feeds on diatom
31O-7N
2012
2D-9D
1J-8J
2013
2F-9F
6M-13M
7A-14A Time
N. Sci
Diatoms – Noctiluca coupling
4 Feb – 6 Feb 2013
coastal Non-bl
diatoms N. Sci
7 Feb – 9 Feb 2013
10 Feb – 12 Feb 2013
Land
Matching pattern of diatoms and NS observed with time delay (3 days)
It means, NS aggregates for feeding purpose where diatoms are there .
Diatoms emerge first, NS develops afterwards  demonstrated from rs data
At any stage diatoms dominate over Noctiluca
As nutrient increases; diatoms appears first,
N. sci. follows with a time lag of 1 week or less
Noctiluca-daitoms are coupled due to feeding mechanism
Besides convection, eddy is another bloom-forming mechanism
Signature of (green) Noctiluca can be seen early in late October
Bottom Lines