Chinook & Steelhead Habitat Requirements

John McMillan photo

Phil Roni, George Pess & Tim Beechie Tracy Hillman Watershed Program BioAnalysts, Inc.

Northwest Fisheries Science Center Biose, Idaho

Salmon life cycle

Chinook Life history diversity

Chinook salmon life history types

Freshwater Estuary Ocean

1-4 wks

1-4 mos

days

1-2 mos

3-6 mos

days

wks

1 yr 2 yr 3 yr 4 yrs 5 yrs 6 yrs

1-2 yrs days

After C. Greene (unpublished) & Wissmar and Simenstad 1998

Steelhead Life history diversity

Freshwater Estuary ? Ocean

days

0 yr weeks

months

days

wks

1 yr 1 yr 2 yr 2 yr 3 yr 3 yr 4 yrs 4 yrs

days

Landscape Scale Habitat Requirements

II. Micro and Meso-Habitat Requirements

Roger Peters photo T. Hillman photo

Adult Holding – Chinook • Adequate

– Depth – Cover – Temperature

• Cool H20 refuge areas – Proximity of pools to spawning areas

Torgersen et al. 1999

Adult holding habitat requirements

Bottom Temp.

Depth

Substrate

Shadow

- Not used- Used

- Not used - Used

--44 --33 --22 --11 00 11 22 33 44

WWaarmrm Bottom Temp. CCooldld

SShhalalllowow Depth DDeepeep

SSmamallll Substrate CCoaoarrssee

SSccaarrcece Shadow AAbundbundanan

Baigun, C.R.M. 2003, Nakamoto et al. 1994

Summer steelhead

– Colder water – Deeper pools – More cover – Larger substrate

tt

•

Step poolS: 0.03-0.08 Pool riffle Cascade Plane bed

S > 0.08 S: 0.01-0.03 S: < 0.01

http:0.01-0.03http:0.03-0.08

Forced pool riffle Plane bed S: 0.01-0.03 S: 0.01-0.03

http:0.01-0.03http:0.01-0.03

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I · .· .·. · / / f ,'. \ , . .. ~ ' ~ J ,

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Adult holding habitat & what it means to restoration

Increased pool density = increased redd density

Chin

ook

salm

on re

dds/

km

Montgomery et al. 1999 Channel widths per pool

~30 times as Chinook salmon redds in Forced Pool-Riffle Channels

Forced-Pool Riffle Channel Plane Bed Channel

Adult Spawning Habitat

Chinook Spawning Habitat

• Depth > 24 cm

• Velocity 30-91 (cm/s)

• Substrate 1.3-10.2cm – Fines < 20%

• Temp ~ 5 to 14oC

1.0

0.5

0 0

Water depth (m)

Chinook salmon

0.5 0.25

Steelhead trout

Data from Bjornn and Reiser (1991)

Velo

city

(m/s

)

Steelhead Spawning Habitat

• Depth > 24 cm 1.0 Steelhead

Chinook trout salmon

s) (m

/yt 0.5

cioleV

Data from Bjornn a nd Reiser ( 1991) 0

0

0.25 0.5

Water depth (m)

• Velocity 40-91 (cm/s)

• Substrate 0.6-10.2cm – Fines < 20%

• Temp ~ 4 to 10oC

Adult Spawning • Considerations for restoration project

selection – Pools, cover and holding areas close to spawning

areas (increase LWD, Riparian cover)

– Adequate cool water refuges (deep pools) • Increase LWD, riparian cover, • Reduce excess sediment filling pools

J. McMillan photos

Incubation Habitat

•

•

•

•

Chinook

Temperature 5 to 13 (but as low as 0.6) (Bell 1990; Bjornn & Riser 1991)

Fines/infiltration < 20% – Jensen et al. 2009

Limited scour/high flows

DO – saturation (> 7mg/l) – Low DO groundwater? – % Organics?

Steelhead

• Temperature ~4 to 13 • (Bell 1990)

• Fines/Infiltration < 20% – Jensen et al. 2009

• Limited scour/high flows

• DO – saturation (> 7 mg/l) – Low DO groundwater? – % Organics?

Estimates of Salmonid Egg-to-Fry Bradford 1995

n = 18 n = 18 n = 11

n = 4 n = populations

?

100 • • e ChiMok 1 • • • (b) {;. {;. l:l Stul.t\ud • e • 0 0 O Cotlo 4 • 80

0 0 0 Chu.m

"· 8 .... 0 ·" 0 " ~ D rn 60 0 0 ~ .. D ~ .... .2 0 II "' • D o ., • w

40 D D 0 c • • ., • !! • • ., 0 0 0. •• 0 Q 0 0 •

20 o D D • • o 'h •

D oO D

0 • 0 10 20 30 40 so

Perr.ent 5ediment

Adult Fitness Important

Yakima River Chinook Survival by Male-Female Cross

Johnson, Roni & Pess In press.

Incubation Habitat

• Possible considerations for project selection – Reduce road, grazing, upland impacts, bank

erosion (fines, temp, DO, scour)

– Restore riparian areas (fines, scour, temp)

– Remove channel confinement (scour)

Fry Habitat Requirements

Chinook fry • Low velocities

• Shallow water

Steelhead fry • Low velocities

• Shallow water

John McMillan photo

Note About Habitat Suitability Curves • General based on literature – varies based on ecoregion,

watershed or even tributary

• Figure on atlantic salmon

Top graphs fish.< 9 cm, Bottom graphs > 9cm

Source Maki-Petays et al. 2012

Chinook and Steelhead Fry Habitat

Daytime Habitat • Post-emergent Chinook and

steelhead cluster at stream margins in slow (0-10 cm/s) and shallow water (

0.25

0.2.

N 0.15

E :c-~ LL

0 .1

0.05

0 -'--

dOllY from BJorrn ;md &:k cr i1.'9:91

Runs

Chinook parr 1+ Steelhead

Pocketwat@r

1Ha1b itat iliype

Summer rearing

Seasonal habitat preferences for Yakima River Chinook - Allen 2000

Summer rearing

• Chinook – Temp ~ 12-14C – Vel 0-25 cm/s – 15-60 cm

• Steelhead – 10-13 C – 4 – 40 cm/s – 15 to 70 cm

• Changes with – Fish size – Season

Seasonal use of cover for Yakima River

Chinook - Allen 2000

Summer rearing – Seasonal Change in Cover

• Chinook – Temp ~ 12-14C – Vel 0-25 cm/s – 15-60 cm

• Steelhead – 10-13 C – 4 – 40 cm/s – 15 to 70 cm

• Changes with – Fish size – Season

Chinook and Steelhead Summer Parr Habitat Selection

Daytime Habitat

• As Chinook grow, they use

faster (2-44 cm/s) and deeper (25-300 cm) water, and select brush, woody debris, or cobble/boulder cover.

• As steelhead grow, they use faster (2-34 cm/s) and deeper (19-190 cm) water, and use cobbles and boulders for cover.

Nighttime Habitat • At night, both Chinook and

steelhead move into shallow, quite (

Summer rearing

• Day and Night Habitat Requirements – High temps fish hide/seek cover during day – Concealment, cover, substrate become even more

important

• Changes in habitat requirements with growth.

Winter Rearing

• Chinook – slower water – side channels/off-channel

areas

– Cobble/concealment habitat

• Steelhead – Cover/ concealment

habitat

– Day vs night habitat use Mean juvenile spring Chinook densities in pools with high (blue diamonds) and low (open diamonds) winter concealment habitat scores. Source Van Dyke et al. 2009 (Grande Ronde River)

-1

-0.5

0

0.5

1

1.5

2

2.5

3

3.5

4

Hab

itat U

tiliz

atio

n In

dex

Winter

Summer

Dam Backwater Plunge Scour Glide LG-Riffle HG-Riffle Cascade Pools Riffles Increasing Gradient

Source Roni 2003 – data from 28 streams in Washington and Oregon

Winter Rearing – Steelhead 1+ preferences change with season

Chinook and Steelhead Winter Parr Habitat Selection

Daytime Habitat

• During periods when temperatures are less than 10°C, both Chinook and steelhead parr remain concealed in cover (woody debris or coarse substrate).

Nighttime Habitat

•

•

Both species emerge from cover at night and reside near the stream bed over sand, bedrock, or boulders in depths that range from 50-200 cm.

Both species use velocities less than 2 cm/s at night.

Summer & Winter Rearing

• What it means to restoration – Restoration that improves/maintains

• Temperature • Pools • Cover • Substrate size/embeddedness • Cool water refuge areas (off-channel or ground water)

10m

100

m 1

km 1

0km

10

0km

Spa

tial s

cale

Annual migration

Seasonal Migration

Short-term movement

Diel movement

Day Months Year

Frequency

Movement & Migration

• Important to consider movement and migration

• Within reach • Often limited in

summer and winter

• Among reaches and habitat

• Often large seasonal movements fall and spring

Micro-habitat scale North Fork Stillaguamish

50 feet

ngineered log jam

Sl ide courtesy of Roger Peters

used Flow

• Juvenile steelhead {172mm)

movement in the Elwha River

N • one fish fo r 10 hrs.

the entire reach

60 3) 0 60 120 180 240

~~~liiiiiiiiiiii~l~~lliiiiiiiiiiiil--1 Feet

Fish #: 1990

Day 2 : 68

Time of day: night

Count: 3990Slide cou rt esy of Roger Peters

I

~120m

Elwha tracks Hour

0 19

• 20

• 21

Reach scale Winter

0

10

20

30

40

50

60

70

Perc

ent o

f tag

ged

Chin

ook

Seasonal Chinook parr emigrating from Valley Creek to Salmon River

Aug-Oct Nov-Feb Mar-June Season detected outmigrating

Source: Achord et al. 2012

Watershed Scale Movement

Smolt Migration

• Adequate Flow

• Suitable Temperature

• No barriers/diversions

• Predators

Limiting Factors

Photo by John McMillan

Spawning Summer Winter habitat rearing rearing Smolt

What is limiting factors analysis?

• Compares the relative carrying capacity of different habitat types in a freshwater system.

• Identifies “possible factors limiting production” in freshwater

• Valid across specific spatial scales such as the sub-basin and watershed.

What is limiting factors analysis? Analysis steps

1. Classify habitat types

2. Identify fish use by habitat type

3. Devise methods of estimating change for each habitat type

- Disconnected, lost, degraded, or restored habitats

4. Assess habitat change – historic v. current, current v. restored

5. Estimate relative effects of each loss on production

Habitats or habitat quality associated with a specific life stage or season may limit potential

Photo by John McMillan

Spawning Summer Winter habitat rearing rearing Smolt

Juve

nile

Chi

nook

45,000

40,000

35,000

30,000

25,000

20,000

15,000

10,000

5,000

0 Spawning Summer rearing Winter rearing

What Habitat is Limiting?

Adult trout

Photo by John McMillan Juvenile trout

White et al. 2011

Target the right life stage & focus on limiting factors

• Trout populations 20 years after

wood placement – Adult trout abundance

• increased rapidly after structures

were installed

• remained 53% higher in treatment sections 21 years later.

– Juvenile trout abundance

• No change detected • Fry recruitment is strongly

influenced by effects of annual

snowmelt runoff.

Photo by John McMillan

Target the right life stage & focus on limiting factors

• Trout populations 20 years after wood placement – The increase in pool volume

& wetted area has maintained over time.

White et al. 2011, Roni et al. 2002

Photo by John McMillan

Discuss the longevity of restoration over time, what does it mean to the resource?

• Structures & fish abundance meta-analysis

– Salmonid densities decrease after two years.

– However, most studies do not go beyond 1 year monitoring.

Whiteway et al. 2010

Estimating Habitat Benefits

Salmon Habitat Restoration type Streams/Rivers

small – accessible Wood placement

small - inaccessible Barrier removal

medium Boulder weir placements

large Logjam construction

Floodplain habitat

lost side channels Develop groundwater channels

lost sloughs Floodplain reconnection

Develop scenarios to compare current v. restored

*Small =

Mean Increase in SmoltsMean increase in smolts due to restoration actions

LWD Boulder weirs Logjams Floodplain Groundwater channels

Barrier removal

Coho

Steelhead

n = 30 n = 18

n = 1 n = 30 n = 11

n = 6

Smol

ts p

er m

or m

2

0.90

0.70

0.50

0.30

0.10

-0.10

-0.30

Roni et al. 2010

Increase in Steelhead Smolts

479

948

417

114

646

177

708

239

770

301

832

-37,

-24,

-12,

12,

25,

37,

50,

62,

75,

87,

Freq

uenc

y

800

Mean = 33,308

700

600

500

400

300 c

200

100

0

Increase in steelhead smolts

Compare virtual “increase by restoration action” to assess relative change in habitat capacity & fish use

0% 10% 20% 30% 40% 50% 60% 70% 80% 90%

100%

Coho - All Steelhead - All

LWD Bldr. Weir ELJ Floodplain CGW Barrier Removal

In-channel

Floodplain

Barrier

In-channel

Floodplain

Barrier

Roni et al. 2010

Compare virtual “before v. after” to assess relative change in habitat capacity & fish use by

a one or several restoration actions

2%

12%

Esti

mat

ed ju

veni

le C

hino

ok s

alm

on le

ss

than

50m

m c

apac

ity

250,000

200,000

150,000

100,000

50,000

0 0.0 10.0 20.0 30.0 40.0 50.0 60.0 70.0

Current

Cover increase due to wood placement

Distance downstream of Lewiston Dam (km)

Beechie et al. in press

Conclusions & Key Points • Important to understand habitat requirements when

planning restoration

• Different restoration actions will address different habitat requirements

• Target the right life stage and focus on limiting factors

• However, fish use whole watershed and restoration/improvement needs to address this and restore watershed

Conclusions & Key Points (cont.)

• Document approach for identifying current conditions and improvements due to restoration

• Acknowledge limitations of approach(es) used

• For long-term recovery need to couple – short-term habitat improvement with – long-term restoration

References • Achord, S, B.P. Sanford, S.G. Smith, W.R. Wassard, and E.F. Prentice. 2012. In-Stream Monitoring of PIT-tagged Wild Spring/Summer Chinook Salmon

Juveniles in Valley Creek, Idaho. AFS Symposium 76

• Allen, M.A. 2000. Seasonal Microhabitat Use by Juvenile Spring Chinook Salmon in the Yakima River Basin, Washington. Rivers 7:314-342.

• Allen, M. A. and T. J. Hassler. 1986. Species profile: life histories and environmental requirements of coastal fishes and invertebrates (Pacific Southwest) -- Chinook Salmon, Fish and Wildlife Service, U. S. Army Corps of Engineers: 26.

• Barnhart, R. A. (1986). Species profile: life histories and environmental requirements of coastal fishes and invertebrates (Pacific Southwest) -steelhead, Fish and Wildlife Service,U. S. Army Corps of Engineers: 21.

• Baigu´n, C. R. 2003. Characteristics of deep pools used by adult summer steelhead in Steamboat Creek, Oregon. North American Journal of Fisheries Management 23:1167–1174.

• Bell, M.O. 1990. 1991 Fisheries Handbook of engineering requirements and biological criteria. USACE, Portland, OR

• Beechie, T.J., G.R. Pess, and H. Imaki. 2012. Estimated changes to Chinook salmon (Oncorhynchus tshawytscha) and steelhead (Oncorhynchus mykiss) habitat carrying capacity from rehabilitation actions for the Trinity River, North Fork Trinity to Lewiston Dam. Report to USFWS, Arcata, CA.

• Beechie, T. J., M. Liermann, E. M. Beamer, R. Henderson. 2005. A classification of habitat types in a large river and their use by juvenile salmonids. Transactions of the American Fisheries Society, 134:717-729.

• Beechie, T.J., H. Moir, and G. Pess. 2008. Hierarchical physical controls on salmonid spawning location and timing. Pages 83-102 in D.A. Sear and P. DeVries, editors. Salmonid spawning habitat in rivers: physical controls, biological responses, and approaches to remediation. American Fisheries Society, Symposium 65, Bethsda, Maryland.

• Bjornn, T.C., and D.W. Reiser. 1991. Habitat requirements of salmonids in streams. In Influences of Forest and Rangeland Management on Salmonid Fishes and Their Habitats. Edited by William R. Meehan. American Fisheries Society Special Publication 19:83-138

• Bradford, M. J. 1995. Comparative review of Pacific salmon survival rates. Canadian Journal of Fisheries and Aquatic Sciences 52(6): 1327-1338.

• Greig, S. M., D. A. Sear, et al. 2005. "The impact of fine sediment accumulation on the survival of incubating salmon progeny: Implications for sediment management." Science of the Total Environment 344(1-3): 241-258.

References • Hayes, S. A., M. H. Bond. C. V. Hanson, E. V. Freund, J. J. Smith, E. C. Anderson, A. J. Ammann, and R. B.

MacFarlane. 2008. Steelhead growth in a small central California watershed: upstream and estuarine rearing patterns. Transactions of the American Fisheries Society 137(1):114-128.

• High B, Perry CA, Bennett DH 2006. Temporary staging of Columbia River summer steelhead in cool-water areas and its effect on migration rates. Trans Am Fish Soc 135:519–528

• Jensen, D. W., E. A. Steel, E. A. Fullerton and G. Pess. 2009.. Impact of fine sediment on egg-to-fry survival of Pacific salmon: a meta-analysis of published studies. Reviews in Fisheries Science 17(3):348–359

• Johnson, C. P. Roni and G. Pess. In press. Parental effect as a Primary Factor Limiting Egg-to-Fry Survival of Spring Chinook Salmon Oncorhynchus tshawytscha in the Upper Yakima River Basin. Transactions of American Fisheries Society. (accepted with minor revision)

• Keefer, M. L., C. A. Peery, T. C. Bjornn, M. A. Jepson, and L. C. Stuehrenberg. 2004a. Hydrosystem, dam, and reservoir passage rates of adult Chinook salmon and steelhead in the Columbia and Snake rivers. Transactions of the American Fisheries Society 133:1413–1439.

• Montgomery, D.R., Buffington, J.M., Smith, R.D., Schmidt, K.M., and Pess, G. 1995. Pool spacing in forest channels. Water Resour. Res. 31: 1097-1105.

• Montgomery, D.R., Beamer, E.M., Pess, G.R., and Quinn, T.P. 1999. Channel type and salmonid spawning distribution and abundance. Can. J. Fish. Aquat. Sci. 56: 377–387.

• Nakamoto, R. J. 1994. Characteristics of pools used by adult summer steelhead oversummering in the New River, California. Transactions of the American Fisheries Society 123: 757-765.

References

• Pess, G. R., D. R. Montgomery, T. J. Beechie, L. Holsinger. 2002. Anthropogenic alterations to the biogeography of salmon in Puget Sound. Pages 129 154 in Montgomery, D. R., S. Bolton, D. B. Booth. (Eds.) Restoration of Puget Sound Rivers. University of Washington Press, Seattle, WA.

• Peters, R., C. Cook-Tabor, T. Levy, D. Lantz, and M. Liermann. In prep. Habitat selection by juvenile Chinook salmon: Multi-scale assessment. Report for Seattle Public Utilities, Seattle, WA.

• Raleigh, R.F. W.J. Miller, and P. C. Nelson. 1986 Habitat suitability index modesl and instream flow suitability curves: chinook salmon. USFWS Biological Report 82(10.122).

• Raleigh, R.F. , T. Hickman, R.J. Solomon, P.C. Nelson. 1984. Habitat suitability information: rainbow trout. USFWS Biological ReportOBS82/10.60

• Roni, P., G. R. Pess, T. J. Beechie, S. A. Morley. 2010. Estimating salmon and steelhead response to watershed restoration: How much restoration is enough? North American Journal of Fisheries Management, 30:1469-1484.

• Roni, P., T. J. Beechie, R. E. Bilby, F. E. Leonetti, M. M. Pollock, G. R. Pess. 2002. A review of stream restoration techniques and a hierarchical strategy for prioritizing restoration in Pacific Northwest watersheds. North American Journal of Fisheries Management, 22(1):1-20.

• White, S. C. Gowan, K. Fausch, J. Harris, and C. Saunders. 2011. Response of trout populations in five Colorado streams two decades after habitat manipulation. CJFAS 68: 2057-2063

• Whiteway, S.L., Biron, P.M., Zimmerman, A., Venter, O., and Grant, J.W.A. 2010. Do in-stream restoration structures enhance salmonid abundance? a meta-analysis. CJFAS 67: 831– 841. doi:10.1139/F10-021.

• Wissmar and Simenstad 1998

http:ReportOBS82/10.60

Chinook & Steelhead Habitat RequirementsSalmon life cycleChinook Life history diversitySteelhead Life history diversityLandscape Scale Habitat RequirementsII. Micro and Meso-Habitat RequirementsAdult Holding – ChinookAdult holding habitat requirementsSlide Number 9Slide Number 10Adult holding & what it means to restoration Adult holding habitat & �what it means to restorationSlide Number 13Adult Spawning HabitatChinook Spawning Habitat�Steelhead Spawning Habitat�Adult SpawningIncubation HabitatEstimates of Salmonid Egg-to-Fry�Bradford 1995 Egg to Fry SurvivalAdult Fitness Important�Yakima River Chinook Survival by Male-Female CrossIncubation HabitatFry Habitat RequirementsChinook frySteelhead fryNote About Habitat Suitability CurvesChinook and Steelhead Fry HabitatSummer rearingSummer rearingSummer rearing – Seasonal Change in CoverChinook and Steelhead Summer Parr Habitat SelectionSummer rearingWinter RearingWinter Rearing – Steelhead 1+�preferences change with seasonChinook and Steelhead Winter Parr Habitat SelectionSummer & Winter RearingMovement & MigrationSlide Number 38Slide Number 39Watershed Scale MovementSmolt MigrationLimiting FactorsWhat is limiting factors analysis?Slide Number 44Habitats or habitat quality associated with a specific life stage or season may limit potentialWhat Habitat is Limiting?Target the right life stage & focus on limiting factorsTarget the right life stage & focus on limiting factorsDiscuss the longevity of restoration over time, what does it mean to the resource?Estimating Habitat BenefitsDevelop scenarios to compare current v. restoredSlide Number 52Increase in Steelhead SmoltsCompare virtual “increase by restoration action” to assess relative change in habitat capacity & fish useCompare virtual “before v. after” to assess relative change in habitat capacity & fish use by a one or several restoration actionsConclusions & Key PointsConclusions & Key Points (cont.)ReferencesReferencesReferences