The Decline of Pelagic Fishes in the San Francisco Estuary: An

Dr. Ted Sommer

The Decline of Pelagic Fishes in the San Francisco Estuary:

An Update

California Department of Water ResourcesIEP Pelagic Organism Decline Management Team

POD Management TeamChuck Armor DFG Randy Baxter DFG Rich Breuer DWRLarry Brown USGS

Mike Chotkowski USBRSteven Culberson CBDA

Marty Gingras DFG Bruce Herbold USEPA

Anke Mueller-Solger DWR Ted Sommer DWR Kelly Souza DFG

POD Principal Investigators•

Dept Fish and Game–

Randy Baxter, Marade

Bryant, John Budrick, Kevin Fleming, Kelly Souza, Steve Slater,Kathy Hieb, Marty Gingras

•

Dept Water Resources–

Matt Nobriga, Fred Feyrer, Ted Sommer, Bob Suits,Marc Vaysièrres,Heather Peterson,Zoltan

Matica, Peggy Lehman, Lenny Grimaldo, Mike Mierzwa, Jim Wilde, Karen Gehrts,Tanya Veldhuizen

•

US Bureau of Reclamation–

Mike Chotkowski•

US EPA–

Bruce Herbold

•

US Fish and Wildlife Service–

Gonzalo Castillo, Ken Newman•

US Geological Survey–

Joseph Simi, Cathy Ruhl,Pete Smith

•

UC Davis–

Bill Bennett, Swee Teh,Inge Werner, David Ostrach, Frank Loge

•

SF State University–

Wim Kimmerer, John Durand•

SF Estuary Institute–

Daniel Oros, Geoff Siemering, Jennifer Hayworth

•

Consultant–

Bryan Manly, BJ Miller

Figure from L. Grimaldo

Inshore Habitat Pelagic Habitat

Delta smelt

Longfin

smelt

Threadfin shadStriped bass

0 . 1

1

1 0 2

1 0 3

0 . 1

1

1 0

1 0 0

1 0 2

1 0 3

1 0 4

1 0 5

1 9 7 0 1 9 8 0 1 9 9 0 2 0 0 00 . 1

1

1 0

1 0 2

1 0 3

1 0 4

1 9 7 0 1 9 8 0 1 9 9 0 2 0 0 0

1

1 0

1 0 3

1 0 4

Abu

ndan

ce In

dex

Cat

ch p

er T

raw

l

Y e a r

D e l t a S m e l t L o n g f i n S m e l t

S t r i p e d b a s s T h r e a d f i n s h a d

Source: Kimmerer and Nobriga (2005); Sommer et al. (In Review)

Abundance Levels Are Highly Variable

1970 1980 1990 2000 1970 1980 1990 2000

Abu

ndan

ce In

dex

Striped bass

Delta Smelt

Threadfin Shad

Longfin Smelt

0 . 1

1

1 0 2

1 0 3

0 . 1

1

1 0

1 0 0

1 0 2

1 0 3

1 0 4

1 0 5

1 9 7 0 1 9 8 0 1 9 9 0 2 0 0 00 . 1

1

1 0

1 0 2

1 0 3

1 0 4

1 9 7 0 1 9 8 0 1 9 9 0 2 0 0 0

1

1 0

1 0 3

1 0 4

Abu

ndan

ce In

dex

Cat

ch p

er T

raw

l

Y e a r

D e l t a S m e l t L o n g f i n S m e l t

S t r i p e d b a s s T h r e a d f i n s h a d

Source: Kimmerer and Nobriga (2005); Sommer et al. (In Review)

The Pelagic Organism Decline

1970 1980 1990 2000 1970 1980 1990 2000

Abu

ndan

ce In

dex

Striped bass

Delta Smelt

Threadfin Shad

Longfin Smelt

54321

54321

2.0 2.5 3.0Log outflow

Log

abun

danc

e longfin smelt

striped bass

Historically Flow Has Helped Predict Fish Abundance

Adapted from Kimmerer (2002)

r2=0.765

r2=0.463

54321

54321


Log

abun

danc

e longfin smelt

striped bass

Invasive Species Shifted These Relationships


Post-Corbula

Pre-Corbula

r2=0.639

Not sig.

54321

54321


Log

abun

danc

e longfin smelt

striped bass

POD Has Further Shifted Abundance-Outflow Relationships


POD

Post-Corbula

Pre-Corbula

•

Synthesis is from POD MT, not all PIs.•

New results = unpolished story.

•

The story will change…a lot.•

We don’t plan on another big public. presentation until late February.

•

Most results have not been written up.•

Very few results have been peer-reviewed.

•

The management implications of this effort. are therefore unclear.

POD: What We Know Now Caveats

•



•

The story will change…a lot.•


•



•



•



•

The story will change…probably a lot.•


•



•



•



•


Most results have not been written up.

•

Very few results have been peer- reviewed.

•



•



•



•


•



•



•



•


•

The management implications of this effort are therefore unclear.


FISH ABUNDANCE

PHYSICAL &

CHEMICAL FISH

HABITATPrior Fish Abundance

TOP-DOWN

BOTTOM-UP

FOOD

HOME

LOSS

PARENTS

The ‘Big Three’ Questions

•

Did anything change at the same time as the Pelagic Organism Decline?

•

How and why did these factors change?

•

Did these factors affect populations of pelagic organisms?

Change with POD?

Mechanism? Population Impact?

Stock Yes ???? Yes

Habitat Yes Yes Yes

Food Some Some Yes

Mortality Yes Yes Yes

Quick Answers

PRESENT

ABUNDANCE

Prior Abundance

Stock -

Recruitment Effects

•

Extremely low stocks For all these species, environmental variables strongly affect recruitment

•

Environmental stressors probably more important at smaller population sizes

Stock -

Recruitment Effects

•

Extremely low stocks.

•

Environmental variables strongly affect recruitment

FISH ABUNDANCE

PHYSICAL &

CHEMICAL FISH

HABITAT

FISH ABUNDANCE

PHYSICAL &

CHEMICAL FISH

HABITATTemperature Turbidity SalinityContaminants

Disease

Toxic algae

00.10.20.30.40.50.60.7

1965 1975 1985 1995 2005

Year

Fall

EQ in

dex

Fall “habitat quality” has deteriorated

Striped bass

Delta smelt

Source: Feyrer et al. (CJFAS, In press)

00.10.20.30.40.50.60.7

1965 1975 1985 1995 2005

Year

Fall

EQ in

dex

Striped bass

Delta smelt

Fall EQ + Fall Abundance predicts juvenile production

Fall “habitat quality” has deteriorated

Fall habitat quality decreased as salinity intruded

0

0.1

0.2

0.3

0.4

50 70 90

mean Sep-Dec X2 (km)

Env

Qua

l Ind

ex

50

60

70

80

90

100

1960 1980 2000 2020

Year

Sep-Dec

X2 (k

m)

Kilo

met

ers

EQ

Inde

x

Source: Feyrer et al. (In press)

00.20.40.60.8

11.2

1965 1975 1985 1995 2005

Year

log

delta

sm

elt p

er to

w Suisun Confluence San Joaquin

Summer habitat changes affect regional delta smelt catches

Source: Nobriga et al. (In review)

Salinity variation also affects clams

Source: Marc Vaysierres

and others (DWR)

WetWet Dry Moderate

Other habitat stressors

•

Bioassays showed little effect (<5 %) in 2005 or 2006.

•

<15% adult

delta smelt impaired•

100 % of young

striped bass show

multiple infections

Source: Inge Werner, Swee Teh, and Dave Ostrach (UCD)

FISH ABUNDANCE

TOP-DOWN

FISH ABUNDANCE

TOP-DOWN

WaterDiversions

Predation

Winter Salvage of Delta Smelt (Nov-Mar)

80 84 88 92 96 00 040

300000

# fish

Source: IEP (2005)

Increased winter exports

Low San Joaquin River flow

Source: Simi and others (USGS)

EntrainmentIncrease in winter salvage.

Increased winter exports

Low San Joaquin River flow

y = -4E-05x + 0.7265R2 = 0.309

0

0.2

0.4

0.6

0.8

1

1.2

1.4

1.6

1.8

-10000 -5000 0 5000 10000 15000

1993-2005Mean Values for December-March

Negative Old & Middle River Flows Apparently Increase Adult Delta Smelt Entrainment

Source: Adapted from Pete Smith (USGS)

r2 = 0.31, p<0.05

Del

ta S

mel

tSW

P &

CVP

Sal

vage

(lo

g co

unt)

Combined Old & Middle River Flow (cfs)

1993-1999

2000-2005

1993-2005Mean Values for indicated periods

Negative Old & Middle River Flows Seem to Have Similar Effects on Striped Bass & Longfin

Smelt Entrainment

Source: L. Grimaldo, DWR

Strip

ed B

ass

Jan-

Apr

il Sa

lvag

e(lo

g co

unt)

Combined Old & Middle River Flow (cfs)

Long

finSm

elt

Dec

-Mar

ch S

alva

ge(lo

g co

unt)

y = -8E-05x + 2.1558R2 = 0.5398

1

1.5

2

2.5

3

3.5

-10000 -5000 0 5000 10000 15000

y = -8E-06x + 0.065R2 = 0.3483

0

0.1

0.2

0.3

-10000 -5000 0 5000 10000 15000

r2 = 0.54, p<0.01

r2 = 0.35, p<0.05

1993-1999

2000-2005

Fall delta smelt index

Summer delta smelt index

Old & Middle River flows

Source: Bryan Manly and Mike Chotkowski (USBR)

In Log-Linear Modeling Over 1981-2004, Monthly or Semi- Monthly Exports

or O&M River Flows

Individually Explain No

More Than 1.5% Of The Variation In Fall Catches

Negative Old & Middle River Flows Coincided with Low Smelt Indices in POD Years, But Not in All Previous Years

Bennett Hypothesis: Not All Smelt Are Created Equal

Larger/older females:–

Have higher fecundity.

–

Spawn early and repeatedly. –

Produce larger offspring that have higher fitness.

–

Are more subject to water project effects.

5.9 6.0 6.1 6.2 6.3 6.4

0.0

0.4

0.8

1.2

Log (striped bass abundance)

Log

(thr

eadf

in s

had

mor

talit

y)

Only POD year

Evidence of Fish Predation Effects

Larvae

Adults

There Also May Be Substantial Inshore Predation for Some Species

FISH ABUNDANCE

BOTTOM-UP

FISH ABUNDANCE

BOTTOM-UP

Food availability Food quality

Phytoplankton •

Chlorophyll levels very low compared to other estuaries

•

Long term declines, especially in Suisun Bay

•

But: No evidence of a recent decline in the Delta

Trends in the Pelagic Food Web

Zooplankton (fish food species)•

Long term declines throughout the system

•

Recent declines in Suisun Bay

•

“Waves” of species invasions

Phytoplankton Primary Production

… is related toFisheries Yields in many Marine Systems

(Nixon 1988)

Fisheries Yield =0.011 * Phytoplankton

Production1.55


… in Estuaries is typically very HIGH


… in Estuaries is typically very HIGH Narrangansett:

~310 g m-2 yr-1

Lower Hudson: ~800

Chesapeake: ~550

80

170

350

Source: S. Nixon, 1988


… in the Delta & Suisun Bay is usually very LOW

Sources: A. Jassby

(UCD), J. Cloern (USGS), IEP data


… in the Delta & Suisun Bay is usually very LOW

… and has DECLINED since the 1970s

1990s:<50 g m-2 yr-1

1970s:~100 g m-2 yr-1

Sources: A. Jassby



… CRASHED in Suisun Bay right after the 1987 Corbula invasion

0

10

20

30

40

50

Chl

a (m

g/m

3 )

0

2000

4000

6000

Cor

bula

(#/m

2 )ce1970 1975 1980 1985 1990 1995 2000 2005

0

100

200

300

400

GP

P (m

g C

/m2 -

d)

Primary Production in Suisun Bay

Corbula amurensis

Source: J. Cloern (USGS), IEP data


… CRASHED in Suisun Bay right after the Corbula

invasion

Suisun Bay 1988:~20 g m-2 yr-1

Suisun Bay 1980: ~100 g m-2 yr-1

Sources: A. Jassby


1970s

1990s

2000s:~70 g m-2 yr-1


… during the POD years

is slightly UP

in the Delta & Suisun Bay.

BUT:

Sources: A. Jassby


1970s

1990s

2000s:~70 g m-2 yr-1


… during the POD years

is slightly UP

in the Delta & Suisun Bay.

Quality???Diatom

Sources: A. Jassby


Example:ChippsIsland

Zooplankton:Waves of Invasions

and Declines

0

2000

4000

6000

8000

1972 1980 1988 1996 2004

0

6000

12000

18000

2400018??:Eurytemora

affinis

Cala

noid

Cope

pods

(CB

net

coun

t/m

3 )

Lim

noit

hona

tetr

aspi

na(P

ump

coun

t/m

3 )

Zooplankton Species Invade in “Waves”

Adult copepods at Chipps

Island, yearly averages with 5-year moving average lines

Source:A. Mueller-Solger (DWR), IEP data

0

2000

4000

6000

8000

1972 1980 1988 1996 2004

0

6000

12000

18000


affinis

1978:Sinocalanus

doerri

Cala

noid

Cope

pods

(CB

net

coun

t/m

3 )

Lim

noit

hona

tetr

aspi

na(P

ump

coun

t/m

3 )




0

2000

4000

6000

8000

1972 1980 1988 1996 2004

0

6000

12000

18000


affinis

1978:Sinocalanus

doerri 1988:

Pseudodiaptomus

forbesi

Cala

noid

Cope

pods

(CB

net

coun

t/m

3 )

Lim

noit

hona

tetr

aspi

na(P

ump

coun

t/m

3 )




0

2000

4000

6000

8000

1972 1980 1988 1996 2004

0

6000

12000

18000


affinis

1978:Sinocalanus

doerri 1988:

Pseudodiaptomus

forbesi

1993/1994:Acartiella

sinensis

Cala

noid

Cope

pods

(CB

net

coun

t/m

3 )

Lim

noit

hona

tetr

aspi

na(P

ump

coun

t/m

3 )




0

2000

4000

6000

8000

1972 1980 1988 1996 2004

0

6000

12000

18000


affinis

1978:Sinocalanus

doerri 1988:

Pseudodiaptomus

forbesi

1993/1994:Acartiella

sinensis

Limnoithona

tetraspina

Cala

noid

Cope

pods

(CB

net

coun

t/m

3 )

Lim

noit

hona

tetr

aspi

na(P

ump

coun

t/m

3 )




0

2000

4000

6000

8000

1972 1980 1988 1996 2004

0

6000

12000

18000

24000

Cala

noid

Cope

pods

(CB

net

coun

t/m

3 )

Lim

noit

hona

tetr

aspi

na(P

ump

coun

t/m

3 )



LOW!!!LOW!!!

Good Fish FoodGood Fish Food


0

2000

4000

6000

8000

1972 1980 1988 1996 2004

0

6000

12000

18000

24000

Cala

noid

Cope

pods

(CB

net

coun

t/m

3 )

Lim

noit

hona

tetr

aspi

na(P

ump

coun

t/m

3 )



High!!!High!!!


Eurytemora affinis

1974-2005

Pseudodiaptomus forbesi

1988-2005

Trends significant at p<0.05,Seasonal Kendall Test

Source: A. Mueller-Solger, DWR

Eurytemora affinis declined at almost all IEP

stations

Important Fish Food Species have Declined

Pseudodiaptomus forbesi declined in Suisun Bay &

the Confluence

P. forbesi & E. affinis Abundance in Suisun Bay is Affected by Upstream Subsidies and Clam Grazing

P. forbesi

Adapted from John Durand (SFSU)

Corbula amurensis

P. forbesi

Adapted from John Durand (SFSU)

E. affinis

Corbula amurensis

P. forbesi & E. affinis Abundance in Suisun Bay is Affected by Upstream Subsidies and Clam Grazing

1981-2005

R2= 0.77

p = <<0.001

•0

•200

•400

•600

•800

•1,000

•1,200

•0 •1,000,000 •2,000,000 •3,000,000 •4,000,000 •5,000,000 •6,000,000

Overlap of Pseudodiaptomus and Eurytemora with Delta Smelt in July

FM

WT i

nd

ex

Overlap with Food Species Helps Predict Adult Delta Smelt Recruitment

Source: BJ Miller

54321

54321


Log

abun

danc

e longfin smelt

striped bass

Reduced Food Availability Affects Abundance- Outflow Relationships


POD

Post-Corbula

Pre-Corbula

FISH ABUNDANCE

PHYSICAL &

CHEMICAL FISH

HABITATPrior Fish Abundance

TOP-DOWN

BOTTOM-UP

WaterDiversions

Predation

Food availability Food quality

Temperature Turbidity SalinityContaminants

Disease

Toxic algae

Summer

WinterSpring

Fall

Reduced Food in LSZ

Increased Predation Loss (?)

Improved Survival

Late Growth StartHigh Entrainment of Adults and Early Larvae

Decreased Number Survive to 2 Years Old

Reduced Habitat Area

Reduced Size & Egg Supply

Clams and Limnoithona

Jan-Mar ExportsVAMP

Reduced OutflowD

ELTA

S M E

L T

Summer

WinterAdults

Fall

Reduced Food in LSZ

Increased Intra-Specific Competition/Predation

Impaired Offspring

High Variability in Annual Survival

Only Largest And Healthiest Survive First Winter

Increased Entrainment

Reduced Habitat Area

Disease/ Intersex/ Lesions

Clams and Limnoithona

Maternal Contaminants

Seasonal Food

Winter Exports

Ocean Conditions

Disease

Reduced OutflowS

T R

IP

E D

B A S S

Summer

WinterSpring

Fall

Reduced Survival From Larvae To Young-Of-Year

Reduced Larval Abundance High Entrainment Loss of Adults and Larvae

Survival of Young-Of-

Year to Age-2+

Water Quantity

Food Supply

Salvage

Dec-Mar ExportsStock-recruit ?

L O N G F I N

S M E

L T

Food Supply?

Water Quality?

?Water Quantity

Salvage

Predator Abundance?

Summer

WinterSpring

Fall

Reduced Survival From Larvae To Young-Of-Year

Reduced Larval AbundanceAdult Mortality

Poor Survival of Young-

Of-Year to Age-0

Food Supply?

Water Quality?

Salvage?

Food Supply

Predator Abundance

Salvage?

Stock-recruit ?

T H R E A D F I N

S H A D

Food Supply?

Water Quality?

Salvage?

?

2006-2007 POD Studies

•

2006 Budget $3.7 + million•

60 study components

PRESENT

ABUNDANCE

Prior Abundance

-Fish and Zooplankton Surveys (DFG)-Gear Efficiency Studies (DFG)-Pelagic Fish Population and Egg Supply Estimates (DFG/USFWS)-Threadfin Shad Population Dynamics (DWR)-Statistical Analyses of Fish Abundance Trends (USBR/Manly)-Delta Smelt Growth and Survival (UCD)-Delta Smelt Stock Structure (UCD)-Trends in Apparent Growth Rates (DFG)

PHYSICAL &

CHEMICAL FISH

HABITAT

-Fall and Summer Habitat Trends (DWR)-Temporal and Spatial Changes in Habitat (EPA)-Trends in Aquatic Weeds (UCD)-Effects of Aquatic Weeds on Turbidity (USGS)-Bioassays (UCD)-Fish Pathology (UCD, USFWS)-Climate Effects (USGS)-Hydrologic Changes (USGS)-Microcystis

Studies (DWR)-Salinity Effects on Clams (SFSU)

FISH ABUNDANCE

TOP-DOWN

-Effect of Fish Behavior on Entrainment Risk (DWR)-Effects of Hydrodynamics on Fish Salvage Trends (USGS)-Particle Tracking Simulations of Entrainment (DWR)-Statistical Analyses of Salvage Data (DWR, USBR, Manly) -Power Plant Studies (Mirant, Tenera, Hanson)-Salvage History (DFG, USBR)-Modeling Striped Bass Predation in the Estuary (DWR/DFG)

FISH ABUNDANCE

BOTTOM-UP

-Phytoplankton Trends (UCD)-Zooplankton Trends (DWR)-Zooplankton Community Structure (SFSU)-Sources of Food Web Disruption (SFSU/UCD)-Changes in Benthic Biomass and Abundance (DWR)-Fish Diet and Condition (DFG)-Food Match/Mismatch (DFG)

Synthesis: Next Steps -Delta smelt life cycle and individual-based models

Bill Bennett UCD; Wim Kimmerer SFSU; Kenny Rose, LSU

-Striped bass life cycle, individual-based, and dose- response models

Frank Loge UCD; Kenny Rose, LSU-Statistical analysis of environmental effects on pelagic

fish abundanceBryan Manly, Consultant: Mike Chotkowski, USBR

-Synthesis and evaluationNational Center for Environmental Analysis and Synthesis (NCEAS), UCSB

•

Neutral location, setting, facilities, equipment, and staff to support focused synthetic work

•

>400 projects conducted by more than 3700 participants (~45% non-academic)

•

> 1200 publications in respected, peer-reviewed journals

•

In top 1% of 38,000 scientific institutions in citations in ecology

POD Work Team- Hypotheses- Needs/questions-Logistic limits

POD/”local” points of contact

Existing data New data

University Seminars Working Groups Data Infrastructure

NCEAS Parent Team

Fish Health –

Daniel Schlenk, UC Riverside

Fish Population Modeling –

Julian Dodson, Universite

Laval

Geospatial Statistics –

Dave Krolich, ECorp

Ecosystem Modeling -

George Jackson, Texas A&M

Estuarine Hydrodynamics –

Dave Jewett, US EPA

Parent Team Members

POD Timeline for Review

•

Project Work Teams (Continuous)•

Peer-Reviewed Publications (Continuous)

•

Presentations at Major Meetings–

American Fisheries Society National Meeting (Sep 2007)–

State of the Estuary Conference (Oct 2007)

•

Completion of Study Elements (Fall 2007-2008)

•

POD/NCEAS Synthesis Report I (Late 2007)•

Review by CALFED Science (Late 2007)

•

POD/NCEAS Synthesis Report II (2008)

POD InvestigationsStudies, Review, Synthesis, Presentations, PublicationsPOD InvestigationsPOD Investigations

Studies, Review, Synthesis, Presentations, Publications

PlanningPlanninge.g. Pelagic Fish

Action Plan,Delta Vision,

CALFED, BDCP, SDIP, DRMS, IEP…

Operationse.g. Delta SmeltWorking Group,

Water OperationsManagement Team,

Data Assessment Team

…

OperationsOperationse.g. Delta SmeltWorking Group,

Water OperationsManagement Team,

Data Assessment Team

…

Questions?

Documents

The Decline of Pelagic Fishes in the San Francisco Estuary: An