Modeling the San Francisco Bay Ecosystem...

Modeling the San Francisco Bay Ecosystem dynamics

Qianqian Liu, Fei ChaiSchool of Marine Sciences, University of Maine

Richard Dugdale, Frances WilkersonSan Francisco State University

Yi Chao, Hongchun ZhangRemote Sensing Solutions, Inc.

November 17th, 20169th Biennial Bay-Delta Science Conference

OutlineMethod: Coupled SCHISM-CoSINE model

Ecological Model Results and Assessment

Ecological Response toHydrological ConditionsNH4 ConcentrationNH4 Inhibition ParameterBottom Grazing

Summary

Future Plan

Method: Coupled Schism-CoSiNE ModelSCHISM (Semi-Implicit Cross-scale Hydroscience Integrated System Model):

CoSiNE (Carbon, Si(OH)4, Nitrogen Ecosystem Model; Fei Chai et al. at UMaine)

Model Configuration (Courtesy of Yinglong Zhang, Virginia Institute of Marine Science)

Method: Coupled Schism-CoSiNE Model:Biogeochemical Cycle in CoSiNE (Chai et al., 2002)

Coupled with 30 Hydrodynamlcal Model

NO:r

PO~

P'WOf'/'"1"

0" Phytop ankton . .,.

Excret~n ··· ·•····~·····~··-··· ·- · . · ·· ~~·············· ....

~

Excretion

fdlcrozoootankJon

~ ~ t

Detritus Nitrogen

mm MOIOZ00¢8nkton

~ ~~ :r ;g ""

-f- Detritus Silicate

SiO("-

Method: Coupled Schism-CoSiNE Model Boundary Conditions: 3-km ROMS-CoSiNE; Rivers with discharge,

dissolved inorganic nutrients;

Sources: Nutrients from 18 WWTPS

Model Configuration (Courtesy of Yinglong Zhang, Virginia Institute of Marine Science)

Model Functioning

NH4 Conc. v.s. Chlorophyll Conc.

NH4 concentration v.s. NO3 uptake Rate

NO

3

SCHISM-CoSiNE Depth-averaged Nutrients and Chlorophyll in Control Experiment (R1)

Modelled monthly mean Chlorophyll in June, 2011 Chl-a from MERIS-NASA on 24th May, 2011

DWR-D7

Comparisons of NO3, NH4and Chlorophyllconcentrations at the station of DWRD7. Lines for model results; Stars for observations (Dugdale et al., 2015).


38.3 ~~--------~--------~----------~--------~--------~

38.1

-z «- 37 9 Q) •

'"0 :J

:t= 1U ...J

• USGS Stations

37.7

37.5

122.6 122.4 122.2 122 121.8 121.6

Longitude (0 W)

70

60

50

~ Q)

40 ..._. Q)

E -.r:. ..._. 30 c.

Q)

0

20

10

0


Comparisons of NO3, NH4 and Chlorophyll concentrations over the USGS stations in Suisun Bay. Lines for model results; Stars for observations.

Box 1: Suisun Bay -(") 30 E - 25 0 E 20 E

15 -(")

0 10 z

Jan Feb Mar Apr May Jun

- 8 (")

E ..... 0 6 E E 4 -..,. J: z 2

Jan Feb Mar Apr May Jun -(")

..E 10 0

~* ~~Gs l E 8 E 6 ->. 4 J: c. 2 0 .... 0 0 J: Jan Feb Mar Apr May Jun (.)

Model Evaluation: Scattered Plots of Nutrients

Scattered Plot of Nutrients

Nitrate: R2=0.57 Ammonium: R2=0.34

Phosphate: R2=0.28 Silicate: R2=0.70

SCHISM-CoSiNE Sensitivity Experiments

Name Design River Nutrient Source WWTPs Bottom from Rivers Grazing

Rl 1 he Base. ( ontrol ( ase 2011 l S(,S for 2011 ('onstant ~0

R2 Weaker River Dtscharge

2012 USGS for 2012 ( onstant No m 2012

R3 Double NH4 from 2011 Double NH 4 from Constant No Rivers Rivers in 2011

RIO Triple NH4 from

2011 USGS for 2011 DoubleNH4 No WWTPs

R12 No WWTPs 2011 USGS for 2011 No WWTPs No

R5 Increase Bottom

2011 USGS for 2011 Constant Yes Grazing

R6 Inhibition parameter 6.6 2011 USGS for 2011 Constant No

R7 Inhibition parameter 0.5 2011 USGS for 2011 Constant No

Constant SPM of 1 00

R8 mg/m3 in Suisun and

2011 USGS for 2011 Constant No San Pablo Bays from Apr. to Sep.

Sensitivity Experiments: Response to Different Hydrological Conditions in 2011 (R1) and 2012 (R2) for Box 1

Hydrological Conditions in 2011 and 2012

River flux at the mouth of the Sacramento and San Joaquin Rivers in 2011 and 2012 (Courtesy of USGS )

- 2011

Dec - 2012

I I I I . -.----.-.------.-.------.-.----I I I I

I I I I -.----.-.------.-.------.-.----. . . .

Sep

Aug

Jul .. ............ . ioillli ....... ...... . ...

Jun

0 1000 2000 3000 4000

the San Joaquin River

- 2011 - 2012

------

River Discharge (m3/s)

I I I I I

SCHISM-CoSiNE Simulated Nutrients Transport over the Box Regions for the Control Experiment (R1)

The red boxes partition SFB into four box regions

38.1

-z 37.9 CL.

0,) "C :::J +' +i j 37.7

37.5

123

BOX 3: Central Bay

4:SouthBay

122.5 122

Longitude {0 W}

Sensitivity Experiments: Response to Different Hydrological Conditions in 2011 (R1) and 2012 (R2) for Box 1

Volume flux at the mouth of the Sac. River in 2011 and 2012

Nutrient and Chl. concentrations within Suisun Bay Specific NH4 uptake rate

Volume of Suisun Bay

Threshold volume flux

0.25 mol/day

Dugdale (2012)

When the washout effect is significant, the strong advection suppresses the growth of phytoplankton;

When the biomass growth caused by the decrease in NH4 concentration outcompetes the washout effect, the primary production is sustained.

Washout

No Washout

Sensitivity Experiments: with 10 times mortality of phytoplankton and zooplankton at the bottom 2 layers (R5)

Annual Mean NO3 uptake rate, Chl. NO3 and NH4 concentrations in the Box Regions in R1 and R5

Comparisons of Biomass Response

Star: Box 1; Diamond: Box 2; Triangle: Box 3; Square: Box 4

(Suisun Bay)

(San Pablo Bay) (Central Bay) (South Bay)

Agree with the study by Dugdale et al. (2016) who found the invasive clams could modulate NH4 concentrations and affect the biomass by NH4inhibition.

NH

4 Inhibition

Annual Mean NO3 uptake rate, Chl. NO3 and NH4 concentrations in the Box Regions in R1 and R5

Comparisons of Biomass Response


(Suisun Bay)


Bars for Uptake RateLines for Chlorophyll

Sensitivity Experiments: with 10 times mortality of phytoplankton and zooplankton at the bottom 2 layers (R5)

Summary• Model successfully captures the spring blooms in 2011;

• In spring, river discharge regulates the nutrients uptake rate by modulating the NH4 concentration, while the washout effect can limit the biomass. There is a competition between washout effect and the dilution of NH4;

• NH4 inhibition is an important factor in regulating ecosystem response;

• At the same time, bottom grazing is important in suppressing biomass bloom.

Monthly mean Suspended Particulate Matter (SPM) concentration in 2011 and 2012 as obtained from USGS

Future Work

Sediment Model to Regulate Light

Attenuation by SPM

Acknowledgments

• This work is supported by the NASA Grant: NNX14AD79G: impacts of population growth on the San Francisco Bay and Delta ecosystem (RIO-SFE).

Thank you!

Questions?

Differences of nutrient flux across the Golden Gate and across the section between South Bay and Central Bay between the experiment R8 and the experiment R1 (R1-R8).

R8: Experiment with a constant SPM of 100 mg/m3 for Suisun Bay and San Pablo Bay between April and September.

Nutrients Flux Difference between R1 and R8 (R1 – R8)

Background: Nutrient and Biomass in spring of 2011 and 2012

USGS Stations along the deep channel of San Francisco BayBiomass and nutrient concentrations along the USGS stations in 2011 and 2012 spring

0 ~ 0 --""- 0 .... ...

!

** * * * ** * * * * -j * ~ * * * ·-· ~

-~ - .... • * * * 0:: so 50 50 . ..-... 0 z ~ 0 CD

** * * * * __. . E Q) · l!

** * * * * -g ~ \ *• :'!:: a.

** * -ro s ....I

:R 100 * . * * 100 r- ** . 100 * .

§ • * * * * * I ** * • • * c

** • * * * * * * * ** * * ~ * .i • * * 150 150 __L 150 I I

0 6 10 1& 20 40 60 80 0 5 10 1&

Chlorophyll (mg/m3) Nitrate (mmol/m3) Ammonium (mmollm3)

Observed Chlorophyll along the USGS Stations Modeled Chlorophyll along the USGS Stations

North Bay: 0-90 km Weak spring bloom; Stronger fall bloom

South Bay: 90-140 km:Strong spring bloom throughout the Bay Fall bloom stronger close to Central Bay

Ecological Model Assessment:Chlorophyll along the USGS Stations

Observed Nitrate along the USGS Stations Modeled Nitrate along the USGS Stations

Model-Observation Comparisons: Nitrate2011

North Bay: 0-90 kmLow Nitrate in springDuring fall, Nitrate increases toward Central Bay

South Bay: 90-140 kmLow Nitrate in springHigh concentration close to the southern endStronger Nitrate in Fall

Observed Phosphate along the USGS Stations Modeled Phosphate along the USGS Stations

Model-Observation Comparisons: Phosphate2011

Generally, low concentration in North Bay Higher in South Bay with relatively lower values in May

Monthly mean surface salinity for the experiments R1 (left) and R2 (right) from March to June

March

April

May

June

March

April

May

June

Monthly mean surface Chl. for R1 and R2 from March to June, and the surface Chl. from satellite MERIS on a day with good coverage from March to June

"·'

"·' '----,..-.-,--,,..~ .. ,,.---,~,.-~m.e

0 2 4 6 8 ,0 ,2 ,4 , 6 , 8 0 2 8 8 ,0 ,2 ,4 , 6 ,8 •• "

Biomass in Suisun and San Pablo Bays for the Base experiment (old one without WWTPs), and the experiments with more bottom grazing, 15 WWTPs, and constant SPM.

Simulated Surface Currents and Salinity in Every 30 Minutes

Model Results: Physical PartShorter Residence Time in North Bay than in South Bay

0 Lon9itudc (

NO3 NH4

From WWTPs 2.42 mol/s 21.3 mol/s

From Rivers 13.87 mol/s 5.73 mol/s

Model Results: Ecological PartDaily averaged NO3 Concentration

~ 3 37,8

37.7

0 Lo.--eJtude ( \1)

121.8

30

25

20

2 M

i 15

12.5

10

7.5

Model Results: Ecological PartDaily averaged NH4 Concentration

0 LO.""eltude ( 1,1)

Model Results: Ecological PartDaily averaged Phytoplankton Concentration

Nitrate and Ammonium flux for the experiment R2

Nutrients Flux for the Experiment R2: With Rivers as Obtained in 2012

I I I I - Into Coastal Ocean - From the maJor Rivers In North Bay 150

I I I I --- .,. --.-- -.·-- .. -- -.·-- .. -- -.---.----.-- . .

- From South Bay to Central Bay - From Rivers + From South Bay to Central 81 · - · - · From 18 WWPTs 100

I I I I I --- .,. --.-- -.·-- .. -- -.·-- .. -- -.---.----.-- ..

I I I I I I

so I I I I I I

-- .,. -- ·--- .,. - • ·-- ·,-- • ·-- ·,-- ·-- • · .,. - ·-- ·- r- ·--- ·- r- ·-- · ·- •

Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

-~ 0 · -· ·- · -- ·-- ·- -·- -·- -·- -·- - · - - · - - · -- ·--·--·- -·- -·- -·- -·-E ->< ::::J -L&.

E ::::J ·-c 0 E E c.(

Month in Year

Nitrate and Ammonium flux for the experiment R2 Nitrate and Ammonium flux for the experiment R1

Nutrients Flux Comparisons between R1 and R2

SCHISM-CoSiNE Simulated Nutrients Transport over the Box Regions for the Control Experiment (R1)

Nitrate and Ammonium flux for the experiment R1

From WWTPs

From the Sacramento and San Joaquin Rivers

Background

Bathymetry of the San Francisco Bay Coastal System

Populous region; High Nutrients Inputs

by Sewage Effluents;

HNLG (High Nutrient Low Growth)

Daily Averaged Surface Salinity from March to June in 2011 and 2012

2011 2012

Model Results: Physical Part In 2011, freshwater pushes salty water further into the middle bay;

In 2012, salty water moves further up into the Delta.

NH4, NO3 Concentrations and f-Ratio for the Box Regions in R1, R3, R10 and R12

Comparisons of Nutrient Concentrations

Sensitivity Experiments: Double NH4 from Rivers (R3), Triple WWTPs (R10) and Remove WWTPs (R12)






(Suisun Bay)


Ammonium Inhibition Curve

ratio

of N

O3

upt

ake

to to

tal D

IN u

ptak

e





(Suisun Bay)


Sensitivity Experiments: Inhibition Parameter 1.5 (R1), Stronger Inhibition Parameter 6.6 (R6), Weaker Inhibition Parameter 0.5 (R7)

NH4 Inhibition for S1 (The Same For S2)

NH4 Inhibition Curve (Low NH4 Corresponds to High NO3 Uptake)

R1

R7

R6

Sensitivity Experiments: Inhibition Parameter 1.5 (R1), Stronger Inhibition Parameter 6.6 (R6), Weaker Inhibition Parameter 0.5 (R7)

Annual Mean NO3 Uptake Rate, Chlorophyll and NO3 and NH4 concentrations the Box Regions in R1, R6, and R7

Comparisons of NO3 Uptake Rate

(Suisun Bay)


Bars for Uptake RateLines for Chlorophyll

NO3, NH4, and Diatom in 2011

Too High Summer Bloom

Diatom and nutrients (NO3 and NH4) concentrations at the station of DWR-D7 in 2011 and 2012

NO3, NH4, and Diatom in 2012

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Modeling the San Francisco Bay Ecosystem...

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