Phytoplankton Cellular DNA Protocol
List of appendices
A. Summary of selected equations for mussel dynamics and contributions to carbon, nitrogen and phosphorus cycles in CAEDYM (modified from Spillman et al., 2008).
B. Parameter values for the mussel model configuration used in the study.
C. Description of variables and parameters for the mussel model configuration.
D. CAEDYM data for initialization of lake conditions– data sources and remarks.
E. Parameter definitions and values for phytoplankton characteristics and processes (from Leon et al. 2011, Bocaniov et al. 2013).
F. Figure showing water density profiles for the summer 2008 observed at station K42 (a), station M66 (b) and predicted for station K42 (c), station M66 (d).
G. Figure showing wind speed during modelling period for base case and intensified storms scenario
Appendix B. Parameter values for the mussel model configuration used in the study. All literature values are measured for Dreissena bugensis (DB) or Dreissena polymorpha (DP) if the former were unavailable. For values of other biogeochemical and hydrodynamic parameters used in this ELCOM-CAEDYM configuration, see Leon et al. (2011). See Appendix C for parameter descriptions. Values for FRmax are similar to those used by Bocaniov et al. 2013 in their Lake Erie simulations for the smallest size class while kr was reduced from 0.01 to 0.0025.
Parameter and Values / Literature Values / Remarksj = 1 / j = 2 / j = 3
kBN:C / 0.25 / 0.25 / 0.25 / DP: Nitrogen 8.65-11.3% of DWa
kBP:C / 0.025 / 0.025 / 0.025 / DP: Phosphorus 0.95-1.13% of DW a
kDry:C / 0.41 / 0.41 / 0.41 / DP: Carbon to dry weightratio = 0.41 b
max / 0.002 / 0.0114 / 0.060 / DB: Based on ~10mm, ~20mm, ~35mm as max lengths of size classes c
Max size possibled
a / 0.01659 / DB: 0.01659 e
NB: Used DW=aLb in the code
b / 2.463 / DB: 2.463 e
FRmax / 480 / 480 / 480 / Values from several studiesb, c, f, g, h ;
FR = 420-1352 L g C-1day-1
ksat / 0.053 / 0.040 / 0.034 / DP: Max consumption rate 2.5-5.3% of tissue carbon per day i
DP: ~3.91-5.29% 5mm, 2.91-3.94% 20mm, 2.5-3.4% 40mm size mussels i
kfull / 0.8
/ 1.08 / Estimated
minT / 0.0 / DB: Eggs mature at 4.8Cj, p; Estimate
Tmin / 8.0 / DP: 10C k, p; Assume quaggas less than zebras
Tmax / 18.0 / DP: 22C k, p; Assume quaggas less than zebras
maxT / 25.0 / DB: 25C l, p
KSS / 20 / DP: 1mg hr-1 pseudofaeces at 20 mg L-1 sestond
maxSS / 100 / Assimilation efficiency decreases as seston mineral content increase m
kR / 0.0025 / 0.0025 / 0.0025 / DP: Base rate 1.62 ugO2 mgDW-1hr-1 at 20oC n
DB: ~40% lower rate at 20oC o
KDO / 0.25 / 0.25 / 0.25 / Estimated
KBDO / 5 / 5 / 5 / Estimated
kEx / 0.15 / 0.19 / 0.22 / DB: Assimilation efficiency (AE) ~80% at low seston d
DP: AE ~63% at low seston d
DP: AE ~40-70% (40-70% 5mm, 46-51% 20mm, 45-49% 40mm size mussel) i
Split non assimilated fraction 50:50 between excretion and egestion
kFsed / 0.2 / 0.2 / 0.2 / Estimated
kE / 0.1 / 0.1 / 0.1 / DB: Assimilation efficiency (AE) ~80% at low seston d
DP: AE ~63% at low seston d
Split non assimilated fraction 50:50 between excretion and egestion
kM / 0.001 / 0.001 / 0.001 / DB: 0-10% over 43 days under a range of food conditions though up to 35% with low food and 6oC d
a Secor, C.L. et al. 1993. Chemosphere 26: 1559-1575
b Nalepa, T.F. et al. 1993. J. Great Lakes Res. 19: 541-552
c Conroy, J.D. et al. 2005. Freshwat. Biol. 50: 1146-1162.
d Baldwin, B.S. et al. 2002. Can. J. Fish. Aquat. Sci. 59: 680-694.
ePatterson, M.W.R. 2005. J. Great Lakes Res. 31 (supp 2):223-237.
f Kryger, J. & H.U. Riisgard, 1988. Oecologia 77: 34-38.
g Horgan, M.J. & E.L. Mills, 1997. Can. J. Fish. Aquat. Sci. 54: 249-255.
h Ackerman, J.D.1999. Can. J. Fish. Aquat. Sci. 56: 1551-1561.
i McMahon, R.F. 1996. Amer. Zool. 36: 339-363.
j Roe, S.L. & H.J. MacIsaac, 1997. Can. J. Fish. Aquat. Sci. 54: 2428-2433.
k Mills, E.L. et al. 1996. Amer. Zool. 36: 271-286.
l Spidle, A.P. et al. 1995. Can. J. Fish. Aquat. Sci. 52: 2108-2119.
m Goulletquer, P. et al. 1989. J. Exp. Mar. Biol. Ecol. 132: 85-108.
n Aldridge, D.W. et al., 1995. Can. J. Fish. Aquat. Sci. 52: 1761-1767.
o Stoeckmann, A., 2003. Can. J. Fish. Aquat. Sci. 60: 126-134.
p Schneider, D.W. 1992. Can. J. Fish. Aquat. Sci. 49: 1406-1416.
Appendix C. Description of variables and parameters for the mussel model configuration.
Variable / Description / Parameter / Descriptionj
BC
BN
BP
BNum
WtLive
WtDry
L
R
η
β
Δβ
t, Δt
i
A
YC:Chl a
T
DO
SS
POM
DOM
DIM
POC
DOC
DIC
IN
PON
DON
NH4
NO3
TN
IP
POP
DOP
FRP
TP
TSi
C, N, P / Mussel size class index (j = 1, 2, 3)
Mussel internal carbon (gC)
Mussel internal nitrogen (gN)
Mussel internal phosphorus (gP)
Mussel numbers
Total mussel live weight (shell + flesh + water) (g)
Total mussel dry flesh weight (g)
Mussel length (mm)
Mussel daily ration (gC day-1)
Mussel population distribution function
Mussel carbon bin value (gC)
Mussel carbon bin size (gC)
Time (s), time step (s)
Phytoplankton group (i = 1, 2, ...)
Chlorophyll-a concentration (mgChl-a m-3)
Algal carbon to Chl a ratio (mgChl-a (mgC)-1)
Water temperature (°C)
Dissolved oxygen concentration (g m-3)
Inorganic suspended solids concentration (g m-3)
Particulate organic matter (g m-3)
Dissolved organic matter (g m-3)
Dissolved inorganic matter (g m-3)
Detrital particulate organic carbon (gC m-3)
Dissolved organic carbon (gC m-3)
Dissolved inorganic carbon (gC m-3)
Algal internal nitrogen (gN m-3)
Detrital particulate organic nitrogen (gN m-3)
Dissolved organic nitrogen (gN m-3)
Ammonium concentration (gN m-3)
Nitrate concentration (gN m-3)
Total nitrogen (gN m-3)
Algal internal phosphorus (gP m-3)
Detrital particulate organic phosphorus (gP m-3)
Dissolved organic phosphorus (gP m-3)
Filterable reactive phosphorus (g P m-3)
Total phosphorus (gP m-3)
Total silicon (gSi m-3)
Carbon, nitrogen, phosphorus / KBN:C
KBP:C
βmin
βmax
δβ
σ
a
b
p
q
KDry:C
ksat
kfull
θ
minT
maxT
Tmin
Tmax
KSS
maxSS
kR
KDO
KBDO
kE
kFsed
kFx
kM
FRmax / Bivalve internal N to C ratio
Bivalve inetrnal P to C ratio
Minimum C per bivalve (gC)
Maximum C per bivalve (gC)
Carbon distribution increment size (x10-3 gC)
Standard deviation of initial population size distribution
Multiplier: length to live weight
Exponent: length to live weight
Multiplier: live weight to dry weight
Exponent: live weight to dry weight
Multiplier: dry weight to carbon
Daily food ration for optimal growth ( gC (gC)-1 d-1)
“Fullness threshold” - fraction where mussel grazing rate slows due to satiety
Temperature multiplier for growth (°C)
Minimum temperature at which process cease (°C)
Maximum temperature at which process cease (°C)
Lower limit of optimal temperature for growth (°C)
Maximum limit of optimal temperature for growth (°C)
Upper limit of optimal SS concentrations (g m-3)
Maximum tolerable SS concentration at which filtration ceases (g m-3)
Respiration rate (day-1)
Half saturation constant for metabolic response to DO (gDO m-3)
Basal respiration rate
Fraction of grazed food to egestion
Fraction of fecal pellets entering sediments
Fraction of grazed food lost to excretion
Mortality (day-1)
Maximum filtration rate with 100% particle efficiency under optimal temperature and seston supply conditions (L (gC)-1 d-1)
Appendix D CAEDYM data for initialization of lake conditions– data sources and remarks PWQMN = Provincial Water Quality Monitoring Network, LSEMS = Lake Simcoe Conservation Authority
CAEDYM-variable / Parameter / Data sources and detailsStations: K45, K39, C6, C9, E51, S15 for May 5 and 6
WTR_TEMP / Water temperature / PWQMN
SSOL1 / Suspended solids / David Evans TSS data, filtered with GF/F filters 0.7 um pores, 47 mm diameter. Average for first 2 sampling dates late May/early June at 4 stations: 0.85 mg/L
DO / Dissolved oxygen / PWQMN
PH / pH / PWQMN
POCL / Particulate organic carbon / SSOL1 * 0.75 (based on East basin data of Lake Erie)
DOCL / Dissolved organic carbon / PWQMN
PO4 / Phosphate / PWQMN (below detection limit, set at 0.0005 mg/L
DOPL / Dissolved organic phosphate / Calculated as 29 % of TP (PWQMN data) based on data by Rebecca North, Trent University
POPL / Particulate organic phosphate / Calculated as 51 % of TP (PWQMN data) based on data by Rebecca North, Trent University
PIP / Particulate inorganic phosphate / Estimate for Lake Erie used: 1mg/L
NH4: / Ammonium / PWQMN
coded as NNHTFR(NH4 + NH3), assuming NH3 = negligible
NO3 / Nitrate / PWQMN
Calculated as NNOTFR (NO3 +NO2) - NNO2FR (NO2)
DONL / Dissolved organic nitrogen / PWQMN
Calculated as (Total Kjedahl – NH4) x 2/3
PONL / Particulate organic nitrogen / PWQMN
Calculated as (Total Kjedahl – NH4) x 1/3
PIN / Particulate inorganic nitrogen / Estimate for Lake Erie used: 1mg/L
SiO2 / Silicate / PWQMN
Silicate, averages from 1994-1996
Six Phytoplankton groups: / in parenthesis two most abundant genera for each group in Lake Simcoe: / Based on fractions of biovolumes x Chla measurements (both MOE)
MDIAT / Large and early diatoms (Fragillaria, Asterionella)
FDIAT / Small and late diatoms (Cyclotella, Dinobryon)
CRYPT / Flagellates, not included (Rhodomonas, Cryptomonas) green algae or those requiring Si
CYANO / Cyanobacteria, all the large filamentous and globular forms (Anabaena, Aphanothece)
NODUL / Large others, mostly colonial green algae (Gloeocystis , Ceratium)
CHLOR / Small others, mostly smaller chlorophytes, but also small cyanobacteria (Chlamydomonas, Carteria)
Internal P loading: / Internal P loading of phytoplankton / based on assumption C/Chl = 80; C/P = 54.3 based on Rebecca North’s measurements of Part.C and P
Formula: IP_x = P/Chl x Fractionx x Chla/1000
Internal N loading: / Internal N loading of phtyoplankton / based on assumption C/Chl = 80; C/N = 7.2 based on Rebecca North’s measurements of Part. C and N Formula: IN_x = N/Chl x Fractionx x Chla/1000
Note: Internal P and N later reduced for calibrations
Appendix EParameter definitions and values for phytoplankton characteristics and processes (from Leon et al. 2011, Bocaniov et al. 2013). Original (Bocaniov et al. 2013) value in parentheses; no parentheses implies no change. Large others (NODUL) were added as a new phytoplankton group. The asterix indicates parameters that were adjusted in accordance with the new C to Chla ratio. P0 (low external concentration at which P-uptake ceases) was corrected to 0.
Parameter / Cyanobacteria (CYANO) / Large Others (NODUL) / Small Others(CHLOR) / Flagellates
(CRYPT). / Large and early diatoms (MDIAT) / Small and late diatoms (FDIAT) / Description
YC:Chla / 80 (50) / 80 / 80 / 80 (180) / 80 (50) / 80 (50) / Ratio of C to chla (mg C (mg chla)-1)
max / 0.8 / 0.8 / 0.8 / 1.0 / 1.7 / 1.99 / Maximum growth rates of algae (d-1)
/ 1.09 / 1.06 / 1.06 / 1.06 / 1.048 / 1.075 / Temperature multiplier for growth (-)
R / 0.125 (was 0.17) / 0.1 / 0.10 ( was 0.11) / 0.11 (was 0.20) / 0.04 (was 0.13) / 0.09 (was 0.15) / Algalrespiration, mortality, and excretion (d-1)
Ri / 1.08 / 1.08 / 1.08 / 0.93 (was 1.08) / 0.90 (was 1.08) / 0.93 (was 1.035 ) / Temperature multiplier for respiration (-)
fdom / 0.7 / 0.2 / 0.2 / 0.4 / 0.4 / 0.4 / Fraction of mortality & excretion that is DOM (remainder is POM)
fresp / 0.5 / 0.2 / 0.2 / 0.2 / 0.3 / 0.3 / Fraction of algal losses that is respiration (remainder is mortality and excretion)
*UPMAX / 1.0 / 3.2 / 3.2 / 1.12 / 0.64 / 1.0 / Maximum phosphorus uptake rate (mg P (mg Chla)-1 d-1)
KP / 0.007 (was 0.09) / 0.005 / 0.005 (was 0.003) / 0.004 (was 0.003) / 0.004 (was 0.009) / 0.006 / Half saturation constant for phosphorus uptake (mg P L-1)
*IPMAX / 1.6 / 3.2 / 3.2 / 1.6 / 2.88 / 2.08 / Maximum internal phosphorus concentration (mg P (mg Chla)-1)
*IPMIN / 0.16 / 0.48 / 0.48 / 0.16 / 0.288 / 0.208 / Minimum internal phosphorus concentration (mg P (mg Chla)-1)
P0 / 0 / 0 / 0 / 0 / 0 (was 0.004) / 0 (was 0.0015) / Low concentration of phosphate at which uptake ceases (mg P L-1)
*UNMAX / 2.4 / 2.4 / 2.4 / 2.4 / 2.4 / 2.4 / Maximum nitrogen uptake rate (mg N (mg Chla)-1 d-1)
KN / 0.045 / 0.06 / 0.06 / 0.045 / 0.045 / 0.045 / Half saturation constant for nitrogen uptake (mg N L-1)
*INMAX / 6.4 / 14.4 / 14.4 / 6.4 / 6.4 / 6.4 / Maximum internal nitrogen concentration (mg N (mg Chla)-1)
*INMIN / 3.2 / 4.8 / 4.8 / 3.2 / 3.2 / 3.2 / Minimum internal nitrogen concentration (mg N (mg Chla)-1)
Ik / 130 / 130 / 100 / 40 / 60 / 60 / Onset of light saturation of photosynthesis (μE m-2 s -1)
ηA / 0.02 / 0.2 / 0.014 / 0.014 / 0.02 / .02 / Algal effect on the extinction coefficient ((g chla m-3)-1 m-1)
*Sicon / N/A / N/A / N/A / N/A / 40 (was 96) / 32 (was 62) / Constant internal silica concentration (mg Si mgChla-1)
KSi / N/A / N/A / N/A / N/A / 0.055 (was 0.150) / 0.055 / Si ½ saturation constant for algal uptake (mg Si02 L-1)
Si0 / N/A / N/A / N/A / N/A / 0.02 (was 0.1) / 0.02 / Low concentration of Si at which uptake ceases (mg Si/L)
/ 24 / 18 / 18 (was 24) / 19 / 14 (was 7) / 24 (was 19) / Standard temperature for algal growth (°C) where fT1 = 1.0
/ 30 / 25 / 25 (was 29) / 21 / 18 (was 7) / 29 (was 23) / Optimum temperature for algal growth (°C) where fT1= maximum
/ 39.0 / 31 / 31 (was 35) / 28 (was 27.5) / 27 (was 7) / 35 (was 31) / Maximum temperature for algal growth (°C) where fT1= 0
vs / 0.5 (was 0.85) / 0.5 / 0.23 / 0.23 / 1.0 (was 10) / 0.8 (was 10) / Settling velocity at 20°C (10-6m ds-1)
Appendix FFigure showing water density profiles for the summer 2008 observed at station K42 (a), station M66 (b) and predicted for station K42 (c), station M66 (d)
Appendix GFigure showing wind speed during modelling period for base case and intensified storms scenario
