Habitat Quality, Toxics, and Salmon in the Lower … 1, O. Paul Olson , Sean Sol1, David Teel , Gina Ylitalo1, Jina Sagar 2, and Catherine Corbett 1NOAA Fisheries Northwest Fisheries

Habitat Quality, Toxics, and Salmon in the Lower Columbia Estuary: Multi-Year Coordinated Fish, Fish Prey, Habitat and Water Quality Data Collection under the Ecosystem Monitoring Project

Lyndal Johnson1, Paul Chittaro1, Dan Lomax1, Kate Macneale1, O. Paul Olson1, Sean Sol1, David Teel1, Gina

Ylitalo1, Jina Sagar2, and Catherine Corbett2

1NOAA Fisheries Northwest Fisheries Science Center, Seattle, WA, USA

4Lower Columbia River Estuary Partnership, Portland, OR, USA

Lower Columbia Estuary Partnership Science Workgroup Meeting

October 23, 2012

Portland

Portland

Ilwaco

Deer Island

Goat Island Burke Island

Secret River

Welch Island

Washougal Lemon Island

Reed Island

Estuary Partnership’s Ecosystem Monitoring Program

Major Program components:

Water Quality (USGS) Vegetation Monitoring (PNNL)

Invertebrate prey (NOAA Fisheries)

Fish (NOAA Fisheries)

emergent

vegetation

tows

open water tows

beach seining

Ecosystem Monitoring Results

• Distinctive fish communities by reach

Fish Community Composition

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%weatherfish, oriental

sucker, largescale

surf smelt

sturgeon, Whites

stickleback

starry flounder

shiner perch

shad

sculpin sp.

sandlance

pumpkinseed

pike, walleye

yellow perch

peamouth

pikeminnow

mosquitofish

killifish

goby

crappie

chub sp.

chiselmouth

catfish sp.

carp sp.

yellow bullhead

brown bullhead

bluegill

smallmouth bass

largemouth bass

salmonids

Species diversity and richness

0

0.5

1

1.5

2

2.5

Shann

on-W

einer

index

0

5

10

15

20

25

30

number

of s

pecies

Fish Community Composition over the Sampling Season

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100% other

sucker, largescale

surf smelt

stickleback

starry flounder

shiner perch

shad

sculpin sp.

sandlance

pumpkinseed

yellow perch

peamouth

pikeminnow

killifish

crappie

chub sp.

chiselmouth

carp sp.

bullhead sp.

bluegill

smallmouth bass

salmonids



• Multiple salmon species and stocks with distinctive patterns of occurrence by reach

Salmonid Catch Composition

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

steelhead

chum

coho

chinook

Unmarked Chinook density by site and month

0

50

100

150

200

250

300

350

400

450

fis

h p

er

10

00

m2

April

May

June

July

August

Lower Columbia/Willamette Stocks:

• West Cascade Range Falls

• West Cascade Range Springs

• Spring Creek Group Falls

• Upper Willamette Springs

Interior Columbia Stocks:

• Upper and Middle Columbia Springs

• Snake River Spring/Summers

• Snake River Falls

• Deschutes River Summer/Falls

Chinook Salmon Genetic Groups

Genetic Stocks

0%

20%

40%

60%

80%

100%

unmarked chinook

Rogue River

West Cascades Spr

Willamette River Spr

Deschutes fall

Snake Fall

Upper Columbia SuF

Spring Creek Fall

West Cascades Fall

0%

20%

40%

60%

80%

100%

marked chinook

West Cascades Spr

Upper Willamette Spr

Snake Fall

Upper Columbia SuF

Spring Creek Fall

West Cascades Fall

Campbell Slough PIT tag array results from 2011

Detection Date

Range

No of

fish

detected

Range of days

between first

and last

detections

Species Tag site Tag Date

Range

6/3/11 1 5 Northern pike

minnow

Mouth of Lewis

River

4/3/10

7/12/11-7/20/11 7 1-12 Chinook

salmon

Little White Salmon

Hatchery (Columbia

Gorge, WA)

6/6/11-6/7/11

7/12/11

5 1-3 Chinook

salmon

Lyons Ferry

Hatchery (Snake

River, WA)

4/13/11-4/16/11

7/12/11 3 1-8 Chinook

salmon

Dworshak Hatchery

(Clearwater River,

ID)

5/26/11-6/6/11

7/12/11 1 9 Chinook

salmon

Irrigon Hatchery

(Middle Columbia,

OR)

4/20/11

7/13/11 4 10 sockeye

salmon

Sawtooth Hatchery

(Salmon River, ID)

4/6/11




• Measures of fish condition

Fish condition factor by site for unmarked chinook

0

0.2

0.4

0.6

0.8

1

1.2

1.4

1.6

Con

dition

Fact

or (± S

D)

Fish condition factor by month unmarked chinook

0

0.2

0.4

0.6

0.8

1

1.2

1.4

unmarked

marked

Lipid Content in unmarked Chinook salmon from EMP Sites

ab ab

ab b

a

ab

ab

0.0

0.5

1.0

1.5

2.0

2.5

Phopholipids

Cholesterol

Free Fatty Acids

Triglycerides

Wax esters

Lipid content typically 1-1.5%; no significant differences among sites

Salmon Growth rates (estimated from otoliths)

a a

a a a

b

b

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

grow

th r

ate

(mm/d

ay) fo

r past

7 d

ays

Lower growth rates in fish from Reach C sites

Salmon Growth rates by origin and stock

abc

b c abc

abc abc a

00.10.20.30.40.50.60.70.8

Desc

hut

es

Fal

l (n

=6)

Spr

ing

Cre

ek

Gro

up f

all

(n=9

4)

West

Cas

cades

Fal

l

(n=9

2)

West

Cas

cades

Spr

ing

(n=4

)

Sna

ke F

all

(n=7

)

Upp

er

Col

umbia

Sum

mer/

Fal

l…

Upp

er

Willa

mett

e

Riv

er

Spr

ing…

grow

th r

ate

(mm/d

ay)

b a

0

0.2

0.4

0.6

0.8

unmarked (n=183) marked (n=78)

grow

th r

ate

(mm/d

ay)

Growth rates lower in unmarked fish and in West Cascades fall chinook Most Reach C fish from these groups




• Variety of prey but consistent preference by Chinook for Dipteran prey; found at highest densities in nearshore emergent vegetation

Composition of available prey

Consumed prey: Diptera 65% of prey were Diptera

emergent

vegetation open water

Source of preferred prey items?

Emergent vegetation





• Evidence of human activity even at relatively undisturbed sites

− Non-native species, especially in Reaches E-H

Non-native species

0

10

20

30

40

50

60

% o

f to

tal se

cies

that

are

non

-

native

0

10

20

30

40

50

60

70

% n

on-na

tive

spe

cies

in c

atc

h






–Non-native species, especially in Reaches E-H

–Dominance of hatchery fish, especially in Reaches E-H

Marked vs. Unmarked Chinook and Coho Salmon

0%

20%

40%

60%

80%

100%

% o

f co

ho

salm

on c

atc

h

Coho salmon

unmarked

marked

0%

20%

40%

60%

80%

100%

% o

f ch

inoo

k s

alm

on c

atc

h

Chinook salmon

undetermined

unmarked

marked








–High summer water temperatures at most sites

Water Temperature The typical water

temperature range

from 5-10°C in

February-April,

rising to 20-25°C in

August, then

declining to 5-10°C

by Nov/Dec .

Lower

temperatures at

Hardy Slough,

Pierce Island,

Bradwood Slough

Water

temperatures

above preferred

range for salmon

in July and August

0

5

10

15

20

25

30

wate

r te

mp

era

ture

0C

A-Ilwaco Slough

B-Secret River

B-Welch Island

C-Ryan Island

C-Bradwood Slough

C-Jackson Island

C-Whites Island

C-Wallace Island

C-Lord/Walker Island

E-Sandy Island

E-Deer Island

E-Goat Island

E-Burke Island

F-Campbell Slough

G-Lemon Island

G-Washougal

G-Reed Island

H-Sand Island

H-Franz Lake

H-Pierce Island

H-Hardy Slough






–Non-native species, especially in Reaches F-H

–Dominance of hatchery fish, especially in Reaches F-H


–Chemical contaminants, especially below Portland/Vancouver

Persistent organic pollutants in Chinook salmon

0

1000

2000

3000

4000

5000

6000

7000

8000n

g/g

lip

id

PBDEs

PCBs

DDTs

PCBs: 21% of samples at or above estimated toxic effects threshold

PBDEs: 30% of samples at or above estimated toxic effects threshold

Persistent organic pollutants in Chinook salmon

0

1000

2000

3000

4000

5000

6000

7000

8000n

g/g

lip

id

PBDEs

PCBs

DDTs

PCBs: 21% of samples at or above estimated toxic effects threshold

PBDEs: 30% of samples at or above estimated toxic effects threshold

Summary of Findings








–Chemical contaminants, especially below Portland/Vancouver

Management Implications

• Tidal freshwater emergent marsh habitats are important to multiple salmon stocks

• Quality of these habitats would be maintained and improved by activities that will

–Preserve nearshore emergent vegetation

–Moderate summer temperatures

–Reduce the spread of non-native species

–Reduce chemical contamination

Documents

Habitat Quality, Toxics, and Salmon in the Lower … 1, O. Paul Olson , Sean Sol1, David Teel , Gina Ylitalo1, Jina Sagar 2, and Catherine Corbett 1NOAA Fisheries Northwest Fisheries