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Underwater Videographic Survey of Submerged Aquatic Vegetation in Sequim Bay, WA August 2011 by James G. Norris, Ian E. Fraser, and Hannah Julich Submitted To: Hansi Hals Environmental Planning Manager Jamestown S’Klallam Tribe 1033 Old Blyn Highway Sequim, WA 98382 March 31, 2012
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  • Underwater Videographic Survey of Submerged Aquatic Vegetation in Sequim Bay, WA

    August 2011

    by

    James G. Norris, Ian E. Fraser, and Hannah Julich

    Submitted To:

    Hansi Hals Environmental Planning Manager

    Jamestown S’Klallam Tribe 1033 Old Blyn Highway

    Sequim, WA 98382

    March 31, 2012

  • Marine Resources Consultants PO Box 816

    Port Townsend, WA 98368 (360) 385-4486

    [email protected] [email protected]

    Underwater Videographic Survey of Submerged Aquatic Vegetation in Sequim Bay, WA

    August 2011

    by

    James G. Norris, Ian E. Fraser, and Hannah Julich

    Submitted To:

    Hansi Hals Environmental Planning Manager

    Jamestown S’Klallam Tribe 1033 Old Blyn Highway

    Sequim, WA 98382

    March 31, 2012

    March 31, 2012 Date Signature (James G. Norris)

  • 2011 Sequim Bay Submerged Aquatic Vegetation Survey Final Report

    ii

    Table of Contents Table of Contents .................................................................................................................. ii List of Tables ........................................................................................................................ ii List of Figures ...................................................................................................................... iii Introduction............................................................................................................................1 Methods .................................................................................................................................2

    Overview ............................................................................................................................2 Study Sites ..........................................................................................................................3 Sampling Plan .....................................................................................................................5 Survey Equipment and Methods..........................................................................................5 Field Sampling Procedures..................................................................................................7 Tide Heights........................................................................................................................8 Underwater Video Data Post-Processing .............................................................................8 Parameter Estimation ........................................................................................................11 Personnel ..........................................................................................................................12

    Results..................................................................................................................................13 Eelgrass.............................................................................................................................13 Macroalgae .......................................................................................................................16 Other Observations............................................................................................................23

    Discussion ............................................................................................................................26 Methodology Evaluation ...................................................................................................26 Eelgrass.............................................................................................................................27 Macroalgae .......................................................................................................................30 Other Observations............................................................................................................31

    Recommendations ................................................................................................................32 Acknowledgments ................................................................................................................32 References............................................................................................................................33 Appendix A........................................................................................................................A-1

    List of Tables Table 1. Site and sample polygon areas for all sites and vegetation categories. ..................... 5 Table 2. Survey equipment used onboard the R/V Brendan D II during the 2011

    Sequim Bay submerged aquatic vegetation survey................................................. 6 Table 3. Sample processing notes from site sjs0995. ............................................................ 9 Table 4. Examples of common macroalgae species in the “Big Blades,”

    “Fuzzy/Bushy,” and “Ulvoids” categories seen on this survey. ............................ 10 Table 5. Notation and formulae for estimating vegetation fraction and areal extent at

    a single site. ........................................................................................................ 11 Table 6. Notation and formulae for estimating vegetation fraction within a given

    depth zone........................................................................................................... 12 Table 7. Summary statistics for eelgrass. ............................................................................ 13 Table 8. Summary statistics for Big Blades. ....................................................................... 17 Table 9. Summary statistics for Fuzzy/Bushy. .................................................................... 19 Table 10. Summary statistics for Ulvoids. ............................................................................ 21

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    Table 11. Animals observed during video post-processing. .................................................. 23 Table 12. Depths of sand dollar observations by site. ........................................................... 24

    List of Figures

    Figure 1. Illustration of eelgrass area coverage, eelgrass fraction, and patchiness................... 2 Figure 2. Illustration of mean minimum and maximum eelgrass depths. ................................ 2 Figure 3. Illustration of the line intercept sampling and estimation method. ........................... 3 Figure 4. Sequim Bay study sites. .......................................................................................... 4 Figure 5. The R/V Brendan D II............................................................................................. 6 Figure 6. Launching the camera towfish and “flying” the towfish during a transect. .............. 8 Figure 7. Underwater video transects (yellow) and eelgrass observations (red) during

    the August 2011 survey. ...................................................................................... 14 Figure 8. Eelgrass mean minimum (left) and maximum (right) depths (ft below

    MLLW)............................................................................................................... 15 Figure 9. North vs south eelgrass depth profile comparisons for the west and east

    shores.................................................................................................................. 15 Figure 10. Coefficient of variation as a function of estimated vegetation fractions for

    three macroalgae categories................................................................................. 16 Figure 11. Underwater video transects (yellow) and Big Blades observations (red)

    during the August 2011 survey. ........................................................................... 18 Figure 12. Underwater video transects (yellow) and Fuzzy/Bushy observations (red)

    during the August 2011 survey. ........................................................................... 20 Figure 13. Underwater video transects (yellow) and Ulvoids observations (red) during

    the August 2011 survey. ...................................................................................... 22 Figure 14. Sand dollar (Dendraster excentricus) observations (red)...................................... 24 Figure 15. Spot prawn observations (red) during the August 2011 Sequim Bay survey......... 25 Figure 16. Sample echograph from the BioSonics echosounder showing two large

    schools of fish. .................................................................................................... 25 Figure 17. Tracks for which we observed significant wood waste (cyan) and eelgrass

    observations (red)................................................................................................ 26 Figure 18. DNR ShoreZone data showing continuous (green), patchy (purple), and

    absent (black) eelgrass......................................................................................... 27 Figure 19. Eelgrass observations (red) from the 2000 and 2001 DNR SVMP survey

    and the 2011 survey (yellow transects). ............................................................... 28 Figure 20. Estimated mean minimum and maximum eelgrass depths (with confidence

    intervals) for flats47. ........................................................................................... 29 Figure 21. Estimated mean minimum and maximum eelgrass depths at the Jamestown

    DNR SVMP core site from 2001 to 2009. ........................................................... 29 Figure 22. Vegetation depth profiles from the north and south ends of Sequim Bay. ............ 30 Figure 23. Two branches of flood tide (black arrows) as described in Marmorino and

    Smith (2007). ...................................................................................................... 31 Figure 24. Eelgrass distribution near the mouth of Chimacum Creek in Port Townsend

    Bay (from Norris and Fraser, 2005). .................................................................... 32

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    Introduction Submerged aquatic vegetation, especially eelgrass (Zostera marina), is critical habitat for

    many fish species, including Pacific salmon. In March 1999 the National Marine Fisheries Service listed Hood Canal and Strait of Juan de Fuca summer chum salmon (Oncorhynchus keta) as threatened under the US Endangered Species Act. That same year only seven summer chum returned to Jimmycomelately (JCL) Creek, a tributary at the head of Sequim Bay. At about the same time the Jamestown S’Klallam Tribe in partnership with Clallam County, the Washington Department of Fish and Wildlife, Clallam Conservation District, US Environmental Protection Agency, and numerous private and non-government organizations began implementing the JCL Creek Restoration Project. One goal of this project is to restore summer chum salmon to JCL Creek.

    In August 2011 the Jamestown S’Klallam Tribe contracted with Marine Resources Consultants to survey the submerged aquatic vegetation (SAV) in Sequim Bay, WA. The purpose of the survey was to gather baseline data that can be used to detect SAV changes over time. These data will complement other long-term environmental monitoring data being collected throughout the bay.

    Change analysis requires a rigorous statistical survey framework. We used methods consistent with the Washington State Department of Natural Resources (DNR) Submerged Vegetation Monitoring Project (SVMP) (Dowty 2005). Vegetation was divided into four categories—eelgrass and three macroalgae categories based on easily identifiable morphological traits (described in detail in the Methods section): Big Blades, Fuzzy/Bushy, and Ulvoids. For each category the following parameters were estimated: (1) vegetation fraction; (2) areal extent; (3) mean minimum depth of occurrence; (4) mean maximum depth of occurrence; and (5) patchiness index. These parameters describe in statistical terms the characteristics of each vegetation bed and provide a means of comparing a single bed over time or different beds at the same time (see Dowty 2005 for a complete description and discussion of these parameters).

    Fig. 1 illustrates the concepts of areal extent, vegetation fraction, and patchiness index using eelgrass as an example (the concepts are identical for macroalgae). In this figure all three eelgrass beds have the same eelgrass areal extent (i.e., number of square meters of seabed with at least some eelgrass, shown in green) within the bed boundary (shown in red). Although eelgrass bed “a” is smaller than beds “b” and “c,” the fraction is 100% and the eelgrass area is the same. Beds “b” and “c” have the same eelgrass fraction (about 65%), but bed “c” has a much higher patchiness index.

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    Figure 1. Illustration of eelgrass area coverage, eelgrass fraction, and patchiness.

    Fig. 2 illustrates the concepts of mean minimum and maximum vegetation depths (again

    using eelgrass as an example). Each transect running perpendicular to the isobaths has a minimum and maximum eelgrass depth associated with it. If transects within a site are selected randomly, averaging the collection of minimum (or maximum) depth observations provides an unbiased estimate of mean minimum (or maximum) eelgrass depth for a site. Note that for depth estimates to be valid the transects must pass through depths that are shallower and deeper than the vegetated area. Figure 2. Illustration of mean minimum and maximum eelgrass depths.

    Methods

    Overview The DNR SVMP methods divide large study areas (e.g., Puget Sound, Sequim Bay) into

    smaller “fringe” and/or “flats” sites. Fringe sites are 1000 m sections of shoreline as measured by the -20 ft isobath. (Note: All depths in this report are given in feet below mean lower low water—MLLW). Flats sites are generally larger with irregular shorelines (e.g., Travis Spit) or broad shallow embayments (e.g., south end of Sequim Bay). All DNR SVMP sites have unique identification codes. The shallow boundary of a site is usually near the MLLW isobath (shallower than any eelgrass grows) and the deep boundary extends to the vegetation limit (e.g., -15 to -40 ft for eelgrass surveys).

    To estimate vegetation parameters within individual sites the DNR SVMP uses a modified version of line intercept sampling (Norris et al. 1997; Fig. 3). First, a reconnaissance survey is conducted to delineate a “sample polygon” around the vegetation of interest and its area

    Mean min eelgrass depth

    Mean max eelgrass depth

    Mean Lower Low Water

    a b c

    Mean min eelgrass depth

    Mean max eelgrass depth

    Mean Lower Low Water

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    calculated analytically (e.g., using a Computer Aided Design or Graphical Information System computer program). Note that a sample polygon may be the entire site or a much smaller area within the site. The goal is to concentrate the transects in the area where the target vegetation is located. Second, randomly selected linear transects (for parameter estimation) are placed completely through the sample polygon and their lengths within the polygon computed. Third, the lengths of each transect that are touching the vegetation of interest are computed. Fourth, the sum of the vegetated transect portions is divided by the sum of the transect lengths within the polygon to get an unbiased estimate of the fraction of the polygon that has the vegetation of interest. This fraction estimate comes with variance estimates so confidence intervals can be computed and statistical tests conducted. Finally, the area within the sample polygon with the target vegetation is estimated by multiplying the known area of the polygon by the estimated vegetation fraction.

    Figure 3. Illustration of the line intercept sampling and estimation method.

    Study Sites We used the DNR SVMP “fringe” and “flats” sites to divide Sequim Bay into individual

    study sites. Sequim Bay includes 12 DNR SVMP “fringe” sites (sjs0994 – sjs0999 along the west shore; sjs1002 - sjs1007 along the east shore) and two SVMP “flats sites. Flats47 includes Travis Spit and Middle Ground at the north end and flats48 covers the southern end of the bay including the mouth of JCL Creek (Fig. 4). The depth limits within DNR SVMP sites are not explicitly specified because they depend on the vegetation type. We conducted a brief pilot survey on August 4, 2011 to determine the likely maximum depth of vegetation growth. The pilot survey consisted of four transects, all of which suggested that maximum eelgrass and macroalgae depths were about -20 ft and -50 ft, respectively.

    Based on the Pilot Study we decided to extend the northern DNR SVMP sites (flats47, sjs0994 – sjs0997, and sjs1004 – sjs1007) to the -60 ft isobath and the southern DNR SVMP sites (flats48, sjs0998-sjs0999, sjs1002-sjs1003) to the -30 ft isobaths. We defined two large regions in the center of the bay. The NorthCenter region included depths greater than -60 ft, but excluded a deepwater region (greater than -90 ft) just east of the John Wayne Marina. The SouthCenter region included depths greater than -30 ft and less than -60 ft (Fig. 4).

    For the shallow edge we used the shallow ends of our transects and the NOAA chart shoreline as our guides in drawing the sample polygons. The vertices of the polygons defining study sites and sample polygons are included in the electronic deliverables for this project. Table 1 gives the areas within each site and sample polygon. Note that for each site the eelgrass sample polygon is much smaller than the site area. Most macroalgae sample

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    polygons were the entire site. The only two exceptions were sjs0998 and sjs1003 where Big Blades were observed only in the northern portion of each site.

    Figure 4. Sequim Bay study sites.

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    Table 1. Site and sample polygon areas for all sites and vegetation categories.

    Sample Polygon Areas (m2)

    Site Site Area (m2) Eelgrass Big Blades Fuzzy/Bushy Ulvoids

    flats47 1,207,536 352,575 1,207,536 1,207,536 1,207,536flats48 478,112 93,999 na 478,112 478,112sjs0994 258,355 52,261 258,355 258,355 258,355sjs0995 293,010 104,811 293,010 293,010 293,010sjs0996 142,174 47,075 142,174 142,174 142,174sjs0997 177,826 20,053 177,826 177,826 177,826sjs0998 80,687 32,443 58,139 80,687 80,687sjs0999 130,550 51,629 na 130,550 nasjs1002 115,033 36,691 na 115,033 115,033sjs1003 77,480 28,487 11,597 77,480 77,480sjs1004 117,984 34,872 117,984 117,984 117,984sjs1005 103,365 35,836 103,365 103,365 103,365sjs1006 143,226 53,874 143,226 143,226 143,226sjs1007 114,651 49,999 114,651 114,651 114,651

    NorthCenter 5,793,254 na 5,793,254 5,793,254 5,793,254SouthCenter 2,346,298 na na 2,346,298 na

    Total 11,579,541 994,605 8,421,117 11,579,541 9,102,693

    Sampling Plan Within each flats and fringe site we conducted at least 11 randomly selected underwater

    videographic transects perpendicular to the shoreline beginning as shallow as possible (to ensure that we capture the nearshore edge of any vegetation) and continuing to the -60 ft (northern sites) or -30 ft (southern sites) isobaths. In flats48 we conducted a meandering transect to help delineate the margins of the eelgrass bed (this transect was not used for estimating parameters). For the NorthCenter and SouthCenter sites we conducted five randomly selected transects in an east-west orientation across the bay.

    Survey Equipment and Methods Vessel

    We conducted sampling aboard the 36-ft R/V Brendan D II (Fig. 5). We acquired position data using a sub-meter differential global positioning system (DGPS) with the antenna located at the tip of the A-frame used to deploy the camera towfish. Differential corrections were received from the United States Coast Guard public DGPS network using the NAD 83 datum. A laptop computer running Hypack Max hydrographic survey software stored position data, depth data from one echosounder (Garmin), and user-supplied transect information onto its hard drive. Position data were stored in both latitude/longitude and State Plane coordinates (Washington North, US Survey Feet). All data were updated at 1 s intervals. Table 2 lists all the equipment used during this survey.

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    Figure 5. The R/V Brendan D II.

    Table 2. Survey equipment used onboard the R/V Brendan D II during the 2011 Sequim Bay

    submerged aquatic vegetation survey. Item Manufacturer/Model Differential GPS Trimble AgGPS 132 (sub-meter accuracy) Depth Sounders BioSonics DE4000 system (including Dell laptop computer

    with Submerged Aquatic Vegetation software) Garmin FishFinder 250

    Underwater Cameras (2) SplashCam Deep Blue Pro Color (Ocean Systems, Inc.) Lasers Deep Sea Power & Light Underwater Light Deep Sea Power & Light RiteLite (500 watt) Navigation Software Hypack Max Video Overlay Controller Intuitive Circuits TimeFrame DVD Recorder Sony VRD-MC6 Digital Video Tape Recorder Sony digital tape deck GVD800

    Video Data We obtained underwater video images using an underwater camera mounted in a

    down-looking orientation on a weighted towfish. Two parallel red lasers mounted 10 cm apart created two red dots in the video images as a scaling reference. We mounted a second forward-looking underwater camera on the towfish to give the winch operator a better view of the seabed. We deployed the towfish directly off the stern of the vessel using the A-frame and winch. Video monitors located in both the pilothouse and the work deck assisted the helmsman and winch operator control the speed and vertical position of the towfish. The weight of the towfish kept the camera positioned directly beneath the DGPS antenna, thus ensuring that the position data accurately reflected the geographic location of the camera. A video overlay controller integrated DGPS data (date, time) and user supplied transect

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    information (transect number and site code) into the video signal. We stored video images directly onto a Sony Digital8 videotape and onto a DVD-R disk.

    Depth Data Our primary depth sounder was a BioSonics DE4000 system. The advantage of this

    system is its ability to accurately measure distance between the transducer and the seabed, even when the seabed is covered with dense vegetation (e.g., eelgrass and/or macroalgae). Other depth sounders often measure distance only to the top of the vegetation canopy. The BioSonics system does not produce depth readings in real time. Instead, it records on a laptop computer all of the returning raw signals in separate files for individual transects. During post-processing, individual transect files are combined into larger files and processed through EcoSAV software (part of the BioSonics system). The output is a single text file with time, depth, and position data. These data are then smoothed to remove white noise (if necessary) and merged with the tide correction data to give corrected depths.

    Our backup depth sounder was a Garmin FishFinder 250. Although this echosounder provided real-time estimates of depth (which were recorded by the Hypack Max program), it often estimated depth only to the top of the vegetation canopy rather than to the seabed.

    For both echosounders, we mounted the portable transducers on poles attached to the starboard (Garmin) and port (BioSonics) corners of the transom. Since the DGPS antenna was mounted along the centerline of the vessel, each transducer was offset 1.5 m from the DGPS antenna. During analysis, we ignored this slight offset and assumed that depth readings from both depth sounders were taken at the location of the DGPS antenna.

    Field Sampling Procedures At the start of each transect the winch operator lowered the camera to just above the

    seabed. Visual references were noted and all video recorders and data loggers were started. As the vessel moved along the transect the winch operator viewed live video on a monitor and raised and lowered the camera towfish to follow the seabed contour (Fig. 6). The field of view changed with the height above the bottom. The vessel speed was held as constant as possible (average speed for this survey was 0.59 m/sec). At the end of the transect, we stopped the recorders, retrieved the camera towfish, and moved the vessel to the next sampling position. On three occasions (sjs1007 tracks 1 - 3) we used a van Veen grab sampler to collect live specimens for species verification (Z. marina vs Z. japonica). We maintained field notes for each transect (Appendix A).

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    Figure 6. Launching the camera towfish and “flying” the towfish during a transect.

    Tide Heights We used the BioSonics echosounder to gather bathymetry data. Raw depths collected

    from the echosounder measure the distance between the seabed and the transducer. We applied three factors to correct these depths to the MLLW vertical datum:

    • transducer offset (i.e., distance between the transducer and the water surface);

    • predicted tidal height (i.e., predicted distance between the surface and MLLW);

    • tide prediction error (i.e., predicted tidal height minus the observed tidal height at a reference station).

    Corrected depth equals depth below the transducer plus the transducer offset minus the predicted tidal height plus the tide prediction error. We measured the transducer offsets directly each day. We used the computer program Tides and Currents Pro 3.0 (Nobletec Corporation) to get predicted tide heights at Sequim Bay entrance (station ID 0985; 48.03 N, 123.05 W). We computed tide prediction errors by comparing the computer program predicted tide heights for the Port Townsend reference station (station ID 0995; 48.90 N, 122 45.00 W) with actual observed tide heights published by the National Oceanic and Atmospheric Administration on their web site (http://tidesandcurrents.noaa.gov).

    Underwater Video Data Post-Processing Data stored on the laptop computer were downloaded and organized into spreadsheet files

    including blank columns for video code (0 = cannot view the seabed; 1 = seabed in view) and vegetation codes for each category (0 = absent; 1 = present). Note that although the vegetation categories are mutually exclusive (i.e., no species are included in more than one category; see next subsection), it is possible for a single second of video footage (about 0.35 m2 of the seabed) to contain all categories of vegetation.

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    Each underwater video transect required two or three review passes through the footage to assign codes (only one or two vegetation categories can be processed during a single pass). Processing notes were too extensive to include in this report. Instead, they are included in the electronic deliverables. Table 3 shows a sample from the processing notes for site sjs0995.

    Table 3. Sample processing notes from site sjs0995. Run Track Comment

    2 7 Narrow but dense band of Zm. Boundaries of bed sharply defined. Deep ulvoids present. Color is very clear, even at depth. Nearby browns/reds aid in

    identification. Most ulvoids small, but some larger than 20 cm. They do not appear to be moving.

    Video from 17:56:59 - 17:58:08 illustrates deep ulvoids well. 9 Murky water in the Zm zone makes distinguishing f/b hard. Quality better by 18:29:45. F/b larger and denser after the Zm zone, extending about 1 minute. Some deepwater ulvoids, but not at many as track 7. 10 Very similar to previous track, but video quality much better. 11 Narrow band of Zm. Sparser than previous tracks. Otherwise, similar to Tr. 7 -10. 12 A few straggly Zm at the beginning of the track. Large, dense brown and red f/b in mid-depths, grading to low, sparse, but largely

    continuous alga at depth. 3 1 Numerous deep ulvoids. 16:16:49 - Pisaster 17:10 - Pisaster 16:19:01 - Pycnopodia :29 - Pycnopodia :20:01 - Pycnopodia :43 - Pycnopodia :53 - Very small Pycnopodia (~10cm across) 20:03 - Anemone 22:56 - Anemone 23:15 - Anemone 20:22 - Cucumber 20:26 - Red rock crab 22:17 - Red rock crab 20:55 - Solaster 21:01 - Unknown small deep red/orange star 23:03 - C. magister 23:14 - C. magister 2 16:33:02 - Northern sculpin 34:54 - School of small fish 37:20 - A few small bottom fish 38:46 - 3 red rock crabs 38:56 - Anemone 39:00 - Small Pycnopodia 39:30 - Large Pycnopodia 40:51 - C. magister 41:02 - Unknown large star (~30cm across) 42:00 - Sm star Patchy blades throughout. Mostly Laminarians, some Chondracanthus, other reds.

    Each data record represents 1 s of video footage, or approximately a 0.59 m long segment

    of a transect. A vegetation category was recorded as present if it was observed in the canopy.

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    Drift vegetation was excluded from classification whenever it was observed. Note that this classification of vegetation as present in the canopy differs from the DNR Submerged Vegetation Monitoring Project (SVMP) protocol which requires an eelgrass plant to be rooted within the field of view to be counted as “present.” This difference between protocols reflects the fact that it is often impossible to see whether algae are attached because the seabed is obscured by the multi-layered vegetation canopy.

    Vegetation Categories We used the same macroalgae categories that we used in a previous survey for Clallam

    County (Norris et al. 2011). These categories were defined after consultation with DNR staff and included “Big Blades,” “Fuzzy/Bushy,” and Ulvoids. These categories can be identified from underwater video footage and represent different morphological types.

    Table 4 lists some examples of common taxa found in the three macroalgae categories based on the taxonomy of Gabrielson et al. (2006). In general, the Big Blades category included only algae with blades over 30 cm long. However, smaller specimens of a species clearly recognized as a “Big Blade” type were included also. Red epiphytes on seagrasses or kelp (e.g., Smithora naiadum) are included in the “Fuzzy/Bushy” category. Small (less than 10 in high) “Fuzzy/Bushy” algae in deep water are sometimes referred to as “turf algae.” The Ulvoids category includes all green blades and tubes, including species that are commonly referred to by many as within the genera Ulva and Enteromorpha. These genera have changed substantially based on recent taxonomic work, and Enteromorpha no longer appears in the algal key for this region. Molecular analysis is generally required to differentiate genera and species.

    Table 4. Examples of common macroalgae species in the “Big Blades,” “Fuzzy/Bushy,” and

    “Ulvoids” categories seen on this survey. Big Blades (Brown and Red)

    Fuzzy/Bushy (Brown and Red)

    Ulvoids

    Brown Agarum fimbriatum Alaria spp Cymathere triplicata Desmarestia (ligulate species

    such as ligulata, munda, foliecea)

    Laminaria spp Saccharina spp. Red Chondracanthus exasperatus Mazzaella splendens

    Brown Desmarestia spp. (cylindrical

    species such as viridis) Sargassum muticum Red Callophyllis spp Euthora cristata Odonthalia spp. Plocamium spp. Sarcodiotheca gaudichaudii Smithora naiadum

    Ulva spp.

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    Parameter Estimation Vegetation Fraction and Areal Extent

    For each study region we estimated macroalgae fraction and areal extent for the four vegetation categories using methods described in Norris et al. (1997) and Dowty (2005). We calculated the area (A) of each sample polygon using AutoCAD tools. For each straight-line transect, we computed (using proprietary software) the length of the transect passing through the study region polygon and the lengths associated with vegetation presence. Table 5 lists the notation and formulae for estimating fraction and areal extent within a single study region.

    Table 5. Notation and formulae for estimating vegetation fraction and areal extent at a single

    site. Parameter Estimation formula Definition

    n Number of transects passing through the sample polygon.

    A

    Area within the sample polygon. This value is determined after the sample polygon is drawn using AutoCAD or ArcGIS or some other analytical means.

    il Length of transect i that has vegetation of interest (e.g., Big Blades).

    iL Length of transect i within the sample polygon.

    ρ̂ ∑∑

    ii

    ii

    L

    l

    Estimated vegetation fraction (i.e., fraction of sample area A that has Big Blades).

    )ˆ(ρVar 1

    ˆˆ21

    222

    2 −

    +−

    ⋅− ∑∑ ∑

    n

    LlLl

    Lnf i

    ii i

    iii ρρ Estimated variance of ρ̂ .

    Ê Aρ̂ Estimated area of vegetation within sample polygon. )ˆ(EVar )ˆ(2 ρVarA Estimated variance of Ê .

    CI )ˆ(28.1ˆ EVarECI ±=

    Approximate 80% confidence interval around Ê assuming a normal distribution.

    Since each video observation also has an associated depth observation, it is possible to

    estimate the vegetation fraction within any given depth zone (Table 6). For our depth zone estimates we used 1 ft wide depth zones centered around whole numbers (e.g., the -2 ft depth zone ranged from -1.50 ft to -2.49 ft). We smoothed the resulting array of vegetation fractions by averaging each fraction estimate with the two previous and two subsequent estimates.

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    Table 6. Notation and formulae for estimating vegetation fraction within a given depth zone. Parameter Estimation formula Definition

    dn Number of transects passing through both the sample polygon and depth zone d.

    dil , Length of transect i that has vegetation within depth zone d.

    diL , Length of transect i within the sample polygon and within depth zone d.

    dρ̂ ∑∑

    idi

    idi

    L

    l

    ,

    ,

    Estimated vegetation fraction (i.e., fraction of area within depth zone d that has vegetation of interest).

    )ˆ( dVar ρ 1

    ˆˆ21

    2,

    2,,

    2,

    2 −

    +−

    ⋅− ∑∑ ∑

    d

    idid

    i idididdi

    dd n

    LlLl

    Lnf

    ρρ Estimated variance of dρ̂ .

    Mean Minimum and Maximum Vegetation Depths Minimum and maximum vegetation depths refer to the shallow- and deepwater boundaries

    of vegetation growth. Consider a straight-line transect oriented perpendicular to the isobaths (i.e., running shallow to deep) and passing through an eelgrass bed. If one records the depths at which eelgrass is observed at regular intervals along the transect, there will be both a minimum and a maximum depth observation. If measurements are taken along many such transects, one will have a collection of minimum and maximum depth measurements. Our parameters of interest are the averages of these collections of minimum and maximum depth measurements. We used depths from BioSonics echosounder to estimate these parameters for each vegetation category.

    Patchiness Index Patchiness index was computed as the number of patch/gap transitions per 100 m of

    straight-line transect length. A gap was defined to be a transect section at least 1 m long with no target vegetation.

    Personnel Field personnel consisted of Ian Fraser (skipper and chief scientist) and Ryan Charrier

    (deckhand) on all survey days. Hannah Julich did all of the video post-processing. James Norris performed the data analysis and primary report writing.

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    Results

    Eelgrass Eelgrass (Z. marina) was observed along nearly the entire shoreline (Table 7; Fig. 7). We

    did not observe any Z. japonica. We estimated a total of 52.1 hectares (129 acres) of seabed with at least some eelgrass. Eelgrass fraction estimates ranged from 0.21 to 0.66 with coefficients of variation ranging from 0.03 to 0.30. Patchiness indices were relatively low, ranging from 0.0 to 3.5. Mean minimum eelgrass depths were similar throughout the bay, ranging from -0.2 ft to -2.6 ft (Fig. 8a). However, mean maximum eelgrass depths were greatest in the northern sites (e.g., -13.0 ft at sjs0994) and were lowest in the southern sites (e.g., -4.1 ft at flats48) (Fig. 8b). Fig. 9 plots selected eelgrass depth profiles and clearly illustrates the differences between the northern and southern sections of the bay.

    Table 7. Summary statistics for eelgrass.

    Site Areal

    Extent (m2)

    cv Frac Patch Index

    Min Depth

    (ft)

    Max Depth

    (ft)

    DepthRange

    (ft)flats47 225,310 0.09 0.64 2.0 -0.6 -12.1 11.5flats48 33,835 0.30 0.36 0.9 -1.2 -4.1 2.9sjs0994 24,656 0.18 0.47 3.5 -1.7 -13.0 11.3sjs0995 22,102 0.24 0.21 2.7 -2.6 -10.3 7.7sjs0996 22,176 0.08 0.47 2.2 -0.2 -6.9 6.7sjs0997 13,166 0.09 0.66 0.8 -0.2 -5.2 5.0sjs0998 16,432 0.11 0.51 0.5 -0.9 -4.9 4.0sjs0999 24,151 0.18 0.47 0.8 -1.8 -5.7 3.9sjs1002 18,178 0.04 0.47 0.5 -1.6 -6.1 4.5sjs1003 17,900 0.10 0.63 0.0 -0.7 -7.3 6.6sjs1004 21,547 0.06 0.62 1.4 -0.6 -8.8 8.2sjs1005 23,374 0.05 0.65 0.5 -0.7 -11.2 10.5sjs1006 28,388 0.03 0.53 0.4 -1.6 -10.2 8.6sjs1007 29,939 0.05 0.60 2.1 -1.1 -12.1 11.0

    NorthCenter 0 na na na na na naSouthCenter 0 na na na na na na

    Sum or average 521,154 0.52 1.3 -1.1

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    Figure 7. Underwater video transects (yellow) and eelgrass observations (red) during the

    August 2011 survey.

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    Figure 8. Eelgrass mean minimum (left) and maximum (right) depths (ft below MLLW).

    Figure 9. North vs south eelgrass depth profile comparisons for the west and east shores.

    Eelgrass Depth ProfilesEast Shore

    0.0

    0.2

    0.4

    0.6

    0.8

    1.0

    -20-15-10-505

    Depth (ft below MLLW)

    Vege

    tatio

    n Fr

    actio

    n

    sjs1002

    sjs1007

    Eelgrass Depth ProfilesWest Shore

    0.0

    0.2

    0.4

    0.6

    0.8

    1.0

    -20-15-10-505

    Depth (ft below MLLW)

    Vege

    tatio

    n Fr

    actio

    n

    sjs0994

    sjs0999

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    Macroalgae Before discussing the results for each macroalgae category, a few general comments

    applicable to all categories are in order. First, we emphasize that each “vegetation fraction” estimate must be interpreted carefully so as not to confuse it with the more common concept of “percent cover” typically used in quadrat sampling. For example, a fraction of 0.50 does not mean that 50% of the seabed is covered with the target vegetation. Instead, it means that 50% of the 1 s time intervals along a transect (about 0.59 m long) has at least some target vegetation growing on it.

    Second, the quality of the macroalgae fraction estimates (as measured by the coefficients of variation) is influenced not only by variability between transects, but also by the vegetation fraction itself. In general, the higher the fraction the lower the coefficient of variation (Fig. 10).

    Big Blades

    0.00

    0.10

    0.20

    0.30

    0.40

    0.50

    0.60

    0.00 0.20 0.40 0.60 0.80

    Vegetation Fraction

    Coe

    ffic

    ent o

    f Var

    iatio

    n

    Fuzzy and Bushy

    0.00

    0.10

    0.20

    0.30

    0.40

    0.50

    0.60

    0.00 0.20 0.40 0.60 0.80

    Vegetation Fraction

    Coe

    ffic

    ent o

    f Var

    iatio

    n

    Ulvoids

    0.00

    0.10

    0.20

    0.30

    0.40

    0.50

    0.60

    0.00 0.20 0.40 0.60 0.80

    Vegetation Fraction

    Coe

    ffic

    ent o

    f Var

    iatio

    n

    Figure 10. Coefficient of variation as a function of estimated vegetation fractions for three

    macroalgae categories.

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    Big Blades Big Blades was the least abundant category; we estimated a total of 73 ha (181 acres) of

    Big Blade macroalgae in the bay, with 57% of the total (42 ha) located in a single site—flats47 (Table 8; Fig. 11). The southern portion of the bay (flats48, sjs0999, sjs1002, and SouthCenter) had no measurable Big Blades. Among the sites that had some Big Blades the vegetation fraction ranged from 0.02 in the NorthCenter region to 0.35 in flats47. Patchiness indices varied from 1.7 to 11.3 with an average of 4.4. Mean minimum depths for Big Blades ranged from -2.5 ft to -13.5 ft with an average of -8.0 ft.

    Table 8. Summary statistics for Big Blades.

    Site Areal

    Extent (m2)

    cv Frac Patchiness Index

    MinDepth

    (ft)flats47 418,175 0.14 0.35 10.1 -2.5flats48 0 na na na nasjs0994 49,556 0.07 0.19 11.3 -6.5sjs0995 27,477 0.30 0.09 3.2 -5.5sjs0996 29,695 0.12 0.21 5.0 -3.3sjs0997 12,552 0.36 0.07 3.8 -7.5sjs0998 1,117 0.33 0.06 2.3 -13.5sjs0999 0 na na na nasjs1002 0 na na na nasjs1003 628 0.50 0.05 2.8 -11.1sjs1004 7,777 0.36 0.07 2.9 -9.1sjs1005 14,737 0.29 0.14 2.8 -9.2sjs1006 8,179 0.10 0.06 3.0 -13.5sjs1007 20,218 0.11 0.18 3.5 -6.6

    NorthCenter 143,914 0.45 0.02 1.7 SouthCenter 0 na na na na

    Sum or average 734,025 0.12 4.4 -8.0

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    Figure 11. Underwater video transects (yellow) and Big Blades observations (red) during the

    August 2011 survey.

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    Fuzzy/Bushy The Fuzzy/Bushy category was the most abundant vegetation in the bay. We estimated a

    total of 274 ha (677 acres). Although it was present at every site, two sites (flats47 and NorthCenter) accounted for two thirds of the area (Table 9; Fig.12). In contrast the two southern most sites (flats48 and SouthCenter) accounted for less than 1%. Note that track 2 in the NorthCenter site had relatively little macroalgae compared to adjacent tracks 1 and 3 (Fig. 12). Vegetation fractions ranged from 0.01 to 0.82 and patchiness indices ranged from 0.2 to 9.0 with an average of 5.0. Mean minimum depths ranged from -0.3 to -11.8 with an average of -2.8.

    Table 9. Summary statistics for Fuzzy/Bushy.

    Site Areal

    Extent (m2)

    cv Frac Patchiness Index

    MinDepth

    (ft)flats47 936,394 0.07 0.78 6.3 -0.3flats48 3,283 0.50 0.01 0.2 -9.6sjs0994 212,978 0.04 0.82 3.7 -2.5sjs0995 111,764 0.15 0.38 6.0 -1.6sjs0996 75,211 0.05 0.53 4.7 -2.0sjs0997 83,493 0.12 0.47 6.4 -2.6sjs0998 52,960 0.06 0.66 5.2 -1.1sjs0999 7,946 0.19 0.06 2.6 -4.8sjs1002 8,415 0.43 0.07 2.6 -11.8sjs1003 41,522 0.08 0.54 6.4 -1.9sjs1004 68,419 0.10 0.58 6.7 -0.7sjs1005 52,195 0.09 0.51 4.6 -1.3sjs1006 106,402 0.03 0.74 6.4 1.6sjs1007 72,333 0.06 0.63 8.3 -0.7

    NorthCenter 885,323 0.38 0.15 9.0 naSouthCenter 22,411 0.51 0.01 0.2 na

    Sum or average 2,741,049 0.43 5.0 -2.8

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    Figure 12. Underwater video transects (yellow) and Fuzzy/Bushy observations (red) during

    the August 2011 survey.

    N1

    N2

    N3

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    Ulvoids We estimated a total of 128 ha (316 acres) of Ulvoids with 73% located in flats47 and

    NorthCenter (Table 10; Fig. 13). Two sites had no Ulvoids (sjs0999 and SouthCenter). Vegetation fractions ranged form 0.04 to 0.54 and patchiness indices ranged form 0.0 to 6.0 with an average of 3.0. Mean minimum depths ranged form +1.3 ft to -2.4 ft (average -0.2 ft).

    Table 10. Summary statistics for Ulvoids.

    Site Areal

    Extent (m2)

    cv Frac Patchiness Index

    Min Depth

    (ft) flats47 654,825 0.11 0.54 6.0 0.3 flats48 26,345 0.46 0.06 2.1 -0.4 sjs0994 87,504 0.14 0.34 6.0 -2.4 sjs0995 54,185 0.34 0.18 1.2 -0.1 sjs0996 4,581 0.44 0.03 1.1 -0.3 sjs0997 18,961 0.27 0.10 0.0 -0.6 sjs0998 25,112 0.07 0.31 3.7 -0.7 sjs0999 0 na na na na sjs1002 4,726 0.59 0.04 0.7 -1.9 sjs1003 16,814 0.22 0.22 2.8 0.4 sjs1004 17,987 0.30 0.15 5.3 0.7 sjs1005 19,853 0.23 0.19 1.6 1.3 sjs1006 32,021 0.09 0.22 3.9 0.1 sjs1007 39,723 0.08 0.35 5.1 0.5

    NorthCenter 275,759 0.51 0.05 2.5 na SouthCenter 0 na na na na

    Sum or average 1,278,396 0.2 3.0 -0.2

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    Figure 13. Underwater video transects (yellow) and Ulvoids observations (red) during the

    August 2011 survey.

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    23

    Other Observations Table 11 lists the most common animal observations mentioned in the processing notes.

    Note that these observations are not direct counts of individual animals; they are the number of 1 s video segments in which one or more animals were observed. While these observations cannot be used to estimate abundances, they provide a subjective overview of the species occupying Sequim Bay. Eel-like fish, mostly Snake pricklebacks (Lumpenus sagitta), were the most numerous (heaviest concentrations in the center of the bay), followed by Dungeness crabs (Cancer magister) and sand dollars (Dendraster excentricus). Sand dollar beds were found only along the east shore of the bay (Fig. 14) between -2.4 ft and +1.6 ft (Table 12).

    We observed a dense concentration of large bivalve siphons, probably geoducks (Panopea generosa) and/or horse clams (Tresus spp) in the navigation channel west of Middle Ground (flats47 tracks 8 and 9). We also observed a few groups of spot prawns (Pandalus platycerus) just south of John Wayne Marina resting on clumps of vegetation in depths of about -70 ft (Fig. 15). The BioSonics echosounder frequently recorded large schools of fish (most likely forage fish) (Fig. 16). We also saw birds feeding on bait balls throughout the survey. The field and processing notes mention significant wood waste or logs at site sjs0999 (tracks 7-11) and flats48 (tracks 9-11), near the old log boom area (Fig. 17). The mean maximum eelgrass depth for the log boom tracks was significantly shallower than the adjacent tracks to the north (-4.8 ft vs -6.5 ft; two-sample t-test, unequal variances, p = 0.5). Table 11. Animals observed during video post-processing.

    Animal Number of 1 s Video

    Segment ObservationsEel-like fishes (mostly Snake pricklebacks, Lumpenus sagitta) 1,797 Dungeness crab (Cancer magister) 438 Sand dollars (Dendraster excentricus) 379 Unidentified fish 336 Unidentified anemone 321 Unidentified sea star 223 Sunflower star (Pycnopodia helianthodes) 128 Unidentified crab 124 California sea cucumber (Parastichopus californicus) 53 Unidentified flatfish 45 Red rock crab (Cancer productus) 27 Short-spined sea star (Pisaster brevispinus) 27

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    Figure 14. Sand dollar (Dendraster excentricus) observations (red). Table 12. Depths of sand dollar observations by site.

    Depth (ft) Site n Minimum Maximum Mean

    sjs1003 78 0.6 -0.3 0.1 sjs1004 149 1.0 -0.9 0.3 sjs1005 61 1.6 -1.2 0.4 sjs1006 3 -1.2 -1.4 -1.3 sjs1007 88 0.6 -2.4 -0.7 All Sites 379 1.6 -2.4 0.0

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    Figure 15. Spot prawn observations (red) during the August 2011 Sequim Bay survey.

    Figure 16. Sample echograph from the BioSonics echosounder showing two large schools of

    fish.

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    Figure 17. Tracks for which we observed significant wood waste (cyan) and eelgrass

    observations (red).

    Discussion

    Methodology Evaluation Our coefficients of variation (cv) for vegetation fraction and areal extent estimates were

    quite good for eelgrass. Nine of 14 sites had cvs less than 10%, three were between 10% and 20%, and two were between 20% and 30%. For macroalgae estimates our cvs were very good for the Fuzzy/Bushy category (nine were less than 10%) and poor for the Ulvoids (only two sites were less than 10% and six were over 30%). Better macroalgae estimates will require higher sampling intensity.

    Underwater videography has several limitations. With some exceptions it is impossible to identify individual species. This limitation could be improved by better lighting, adding high resolution still photographs (e.g., taken periodically along each transect), and/or collecting voucher specimens. Also, underwater videography only records the top of the vegetation canopy. Layering of vegetation is common within vegetation canopies. Vegetation below the top layer is generally missed by underwater videography. This limitation is most pronounced in complex, multi-layered algal beds.

    Our methodology for assigning vegetation “present” codes fails to distinguish between high and low plant densities. This may make it difficult to detect change, even within the broad macroalgae categories. The problem stems from the fact that we collect position data only once per second and the vessel covers approximately 0.5 to1.0 m/s. Each 1 m segment is assigned a “present” code if one or many individual plants are seen on the video during that segment. Thus, a change from many to one individual per segment will not be detected. The heart of the change detection issue is how the vegetated community changes. If it changes by increasing or decreasing density uniformly within the same bed margins, this methodology

  • 2011 Sequim Bay Submerged Aquatic Vegetation Survey Final Report

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    will not detect it. However, if changes occur at the bed margins or in large patches, this methodology has high likelihood of detecting it.

    Eelgrass Our eelgrass results were consistent with the DNR ShoreZone survey (Berry et al. 2001),

    which also showed a nearly continuous band of eelgrass around the bay (Fig. 18). Since eelgrass is critical habitat for juvenile salmon, this is good news for the salmon recovery efforts on JCL Creek. However, we also found that eelgrass beds at the southern end of the bay occupy a fairly narrow depth range (e.g., -1.2 ft to -4.1 ft at flats48) while those at the north end of the bay occupy a broader range (e.g., -0.6 ft to -12.1 ft at flats47). During our survey, visibility was lowest in the south bay and was caused by abundant plankton in the water column. The seabed was mostly mud and sand and did not appear to be a limiting factor for eelgrass growth. This suggests that low light availability may be limiting eelgrass growth in the south bay. Since algae blooms can be enhanced by human-induced factors, such as nutrient loading, it will be important to monitor both nutrients and eelgrass depths as part of the JCL Creek Restoration Program.

    Figure 18. DNR ShoreZone data showing continuous (green), patchy (purple), and absent

    (black) eelgrass.

    The only other previous eelgrass surveys in Sequim Bay are for flats47 which was surveyed by the DNR SVMP in both 2000 and 2001 (Berry et al. 2003). The DNR SVMP will sample this site again in 2012. Our results for flats47 were consistent with the general eelgrass distribution found during the SVMP surveys (Fig. 19). Unfortunately, our areal extent

  • 2011 Sequim Bay Submerged Aquatic Vegetation Survey Final Report

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    estimates are not directly comparable to the DNR SVMP 2000 and 2001 estimates because our survey did not include the north side of Travis Spit.

    Our estimated flats47 mean minimum and maximum eelgrass depths were nearly identical to those of the 2000 and 2001 DNR SVMP surveys (Fig. 20). The nearest other depth data are from the Jamestown DNR SVMP core site (i.e., sampled every year). This site encompasses a large portion of the area between Travis Spit and Dungeness Bay. Between 2001 and 2009 mean minimum and maximum eelgrass depths at the Jamestown site were -0.5 ft and -19.3 ft, respectively. This mean minimum depth is nearly identical to our flats47 estimate (-0.6 ft), but the mean maximum depth is significantly deeper than our flats47 estimate (-12.1 ft).

    Figure 19. Eelgrass observations from the 2000 and 2001 DNR SVMP surveys (gray

    transects, light red eelgrass) and the 2011 survey (yellow transects, dark red eelgrass).

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    Flats47Mean Minimum Eelgrass Depths

    -16.0-14.0-12.0-10.0-8.0-6.0-4.0-2.00.02.0

    Yr 2000 Yr 2001 Yr 2011

    Feet

    Flats47Mean Maximum Eelgrass Depths

    -16.0-14.0-12.0-10.0-8.0-6.0-4.0-2.00.02.0

    Yr 2000 Yr 2001 Yr 2011

    Feet

    Figure 20. Estimated mean minimum and maximum eelgrass depths (with confidence

    intervals) for flats47.

    Jamestown (core003)Mean Minimum Eelgrass Depths

    -30.0

    -25.0

    -20.0

    -15.0

    -10.0

    -5.0

    0.0

    2001 2002 2003 2004 2005 2006 2007 2008 2009

    Feet

    Jamestown (core003)Mean Maximum Eelgrass Depths

    -30.0

    -25.0

    -20.0

    -15.0

    -10.0

    -5.0

    0.0

    2001 2002 2003 2004 2005 2006 2007 2008 2009

    Feet

    Figure 21. Estimated mean minimum and maximum eelgrass depths at the Jamestown DNR

    SVMP core site from 2001 to 2009.

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    Macroalgae Macroalgae exhibited even more dramatic differences between the north and south

    portions of the bay (Fig. 22). At the south end (flats48) there was virtually no vegetation of any kind deeper than -10 ft, there were no Big Blades at all and very few Fuzzy/Bushy observations, and the highest macroalgae fraction was for Ulvoids at just over 20%. In contrast, the north end (flats47) had macroalgae fractions greater than 50% for all three categories from MLLW to -25 ft. As with eelgrass, we speculate that lower light availability in the south bay is the primary cause of these dramatic differences.

    flats47 Depth Profiles

    0.00.10.20.30.40.50.60.70.80.91.0

    -60-50-40-30-20-10010

    Depth (ft below MLLW)

    Vege

    tatio

    n Fr

    actio

    n

    Eelgrass

    Blades

    FAB

    Ulvoids

    flats48 Depth Profiles

    0.00.10.20.30.40.50.60.70.80.91.0

    -60-50-40-30-20-10010

    Depth (ft below MLLW)

    Vege

    tatio

    n Fr

    actio

    n

    Eelgrass

    FAB

    Ulvoids

    Figure 22. Vegetation depth profiles from the north and south ends of Sequim Bay.

    The fact that track 2 in the NorthCenter site had much less macroalgae than adjacent

    tracks 1 and 3 (e.g., Fig. 12) is difficult to explain. We reviewed the video footage a second time to confirm the differences. We can only speculate on the cause. Perhaps the seabed characteristics are different, but given the generally poor visibility during these transects it is impossible to tell. Current patterns may also contribute to the differences. Marmorino and Smith (2007) used infrared imagery to track flood currents into Sequim Bay. They found the flow is split by Middle Ground into two branches (Fig. 23). The dominant branch flows almost due south along the shore past John Wayne Marina and forms a mushroom shaped

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    plum that advances to about 1 nm south of the marina. This plum passes over track N3. The secondary branch flows in a southeasterly direction north of Middle Ground and passes over track N1. Track N2 appears to pass through a relatively stagnant section of the NorthCenter site between the two branches. It is tempting to speculate that lower current velocity may result in more fine grained sediment leaving fewer attachments for macroalgae along track N2. An animation of the current patterns described in Marmorina and Smith (2007) can be viewed at http://rsd-www.nrl.navy.mil/7230/sequim_bay.htm.

    Figure 23. Two branches of flood tide (black arrows) as described in Marmorino and Smith

    (2007).

    Other Observations We observed no eelgrass directly over the old log boom area at the southwest corner of

    the bay (Fig. 17). We found a similar result in an eelgrass study near the mouth of Chimacum Creek in Port Townsend Bay (Norris and Fraser 2005)—no eelgrass in the area of the old log boom operations (Fig. 24). Our conclusions from that report are equally applicable to Sequim Bay:

    It seems possible that previous logging operations inhibited eelgrass growth. Log rafts tied to the pilings … may have shaded the seabed, contributed significant wood waste (e.g., bark) to the seabed; or directly uprooted eelgrass by resting on the seabed during low tides. Also, propeller wash from tugs working around the log rafts may have scoured the seabed and removed eelgrass. Cessation of logging operations eliminated shading, uprooting, and propeller wash as factors inhibiting eelgrass growth, leaving only wood waste as a continuing possible limiting factor. If further restoration actions are considered for this area, removing wood waste from potential eelgrass habitat should be included.

    N1

    N2

    N3

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    Figure 24. Eelgrass distribution near the mouth of Chimacum Creek in Port Townsend Bay

    (from Norris and Fraser, 2005).

    Recommendations

    We have the following recommendations. 1. Continue monitoring eelgrass as funding permits, especially in the south end of the

    bay. Given the effort level to restore summer chum salmon in JCL Creek, it seems prudent to also monitor the subtidal critical habitat.

    2. For any further vegetation surveys increase the sampling intensity for macroalgae species. Also, in the deep central regions include tracks in a north-south orientation.

    3. Consider removing wood waste from the old log boom area in the south bay to encourage eelgrass growth near the mouth of JCL Creek. This area has the largest gap in the otherwise continuous fringing eelgrass bed around the bay.

    4. Consider fish abundance surveys (otter trawl, beam trawl) to track changes in the benthic fish community.

    5. Consider hydroacoustic/midwater trawl surveys to track changes in forage fish abundance and distribution.

    6. Consider identifying the large bivalves west of Middle Ground and conducting an abundance survey.

    Acknowledgments

    Funding for this project was provided by the Environmental Protection Agency Puget Sound Tribal Capacity (EPA Contract No: 10EPA PSP402). We thank Lohna O’Rourke for her helpful administrative and scientific assistance and Tiffany Royal for her excellent press coverage.

    Log boom area

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    References Berry, H.D., Harper, J.R., Mumford, Jr., T.F., Bookheim, B.E., Sewell, A.T., and Tamayo,

    L.J. 2001. The Washington State ShoreZone Inventory User’s Manual. Olympia, WA: DNR Nearshore Habitat Program.

    Berry, H.D., Sewell, A.T., Wyllie-Echeverria, S., Reeves, B.R., Mumford, Jr., T.F., Skalski,

    J.R., Zimmerman, R.C., and Archer, J. 2003. Puget Sound Submerged Vegetation Monitoring Project: 2000-2002 Monitoring Report. Olympia, WA: DNR Nearshore Habitat Program.

    Dowty, P. 2005. A study of sampling and analysis methods: Submerged Vegetation

    Monitoring Project at year 4. Nearshore Habitat Program, Aquatic Resources Division, Washington State Department of Natural Resources, 1111 Washington St SE, 1st Floor, PO Box 47027, Olympia, WA.

    Gabrielson, P.W., T.B. Widdowson, and S.C. Lindstrom. 2006. Keys to the Seaweeds and

    Seagrasses of Southeast Alaska, British Columbia, Washington and Oregon. Phycological Contribution No. 7, University of British Columbia, Department of Botany. 209 pp.

    Marmorino, G.O., and G.B. Smith. 2007. Infrared imagery of a turbulent intrusion in a

    stratified environment. Estuaries and Coasts. Vol. 30. No. 4, p 671-678. Norris, J.G., S. Wyllie-Echeverria, T. Mumford, A. Bailey, and T. Turner. 1997. Estimating

    basal area coverage of subtidal seagrass beds using underwater videography. Aquatic Botany 58:269-287.

    Norris, J.G., and I.E. Fraser. 2005. Underwater videographic and hydroacoustic eelgrass

    survey of the Chimacum/Irondale beach restoration site. Report submitted to the North Olympic Salmon Coalition, Chimacum, WA.

    Norris, J.G., I.E. Fraser, and H. Julich. 2011. Defining Fish Use of Subtidal Vegetated

    Habitats of the Elwha and Comparative Shorelines. Report submitted to Clallam County, 223 E. 4th Street, Suite 5, Port Angeles, WA 98362.

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    A-1

    Appendix A

    Field Notes

    Site Date Time Track Comment

    sjs0994 8/7/2011 1611 1 Greens, then a little eelgrass, then mixed alga on shell and gravel.

    1630 2 Same 1645 3 Had to halt in middle to avoid collision with sailboat. 1706 4 More eelgrass. 1723 5 Broader eelgrass area. Mostly algae-free hump in deeper area. 1739 6 Start at marina mouth. Some Zm just there. 1752 7 Off breakwater. Some Zm, greens, then steeply down with

    much shell hash. 8 Abort. Inverter breaker tripped. 1826 9 Off SE edge of breakwater. A fair bit of Zm and algae until it

    drops down to 100 ft. 1836 10 Less Zm. Doesn't go as deep. 1847 11 Lots of greens and Zm leaves in the deep—detritus

    collection? 1859 12 Only a few Zm plants near breakwater. Otherwise a fair bit of

    algae.

    sjs0995 8/5/2011 0815 1 Greens at start, then Zm, then mixed algae for a while. Algae on deep slope may be detritus?

    0829 2 Big jumble of algae at very end (ie bottom of slope). Zm more sparse in this area.

    0843 3 Similar. Pile at bottom of slope has big shrimp all over it. 0856 4 Didn't hit pile at the end of this one. Zm more sparse, but over

    a larger range. 0913 5 Zm over broader range. 0930 6 South shore of cove. Much less algae. Sparse Zm. Very little

    greens and no big browns. 0917 7 Maybe 1 Zm plant. Dominated by tufty brown scrub. 1000 8 Similar, but with more (some) Zm near shore. 1011 9 More variety in browns? 1023 10 A bit more Zm. Barely got to inside edge. 1036 11 Back to middle of site. Lots of green on first half of track.

    Maybe 1 Zm plant. Maybe 2-3 others seen on BS.

    sjs0996 8/5/2011 1103 1 Zm shallow, then some browns. Mostly of the tufty sort. 1114 2 Just at the inside edge of Zm at start. 1124 3 Zm more mixed with algae. Maybe more variety of algae. 1134 4 Just at the inside edge of Zm at start. Ending survey here now

    until higher tide. 8/6/2011 0936 5 Start just at shallow edge of Zm, then some algae to about 30

    ft. Mostly the tufty brown one that looks like a dish scrubber. 0947 6 Started inside Zm. Some rocks with algae here. 0957 7 Similar. Maybe a bit less algae on the deep end. 1006 8 Pebbles with green algae, then Zm, then browns. Some scraps

    on the slope down. 1017 9 More sand at shallow end. Lots of shrimp toward deep end. 1027 10 Similar.

  • 2011 Sequim Bay Submerged Aquatic Vegetation Survey Final Report

    A-2

    Site Date Time Track Comment

    1037 11 Just starts at inside edge of Zm. sjs0997 8/6/2011 1053 1 Start at shallow edge of Zm, mixed with greens. Then

    browns, mostly the tufty one. 1104 2 No Zm. Cobbles with algae at start. 1116 3 Just south of Park launch ramp. Some greens and Zm for a

    bit, then steep slope to 50 ft. 1125 4 Same. Moving south. 1136 5 Maybe more small browns on slope. 1148 6 Gentler slope with more algae. Good visibility. 1200 7 Similar, but less Zm and more algae. 1210 8 Similar to previous. More algae near deep end. Is this a

    collection point? 1222 9 No Zm. Still algae filled. 1234 10 Pretty much the same as 9. 1247 11 No Zm, but it looked like we passed over a patch while

    backing in.

    sjs0998 8/6/2011 1306 1 Start just at start of eelgrass. Mixed algae after, then mud/silt down slope.

    1315 2 Same. South of private dock. 1325 3 Didn't start BioSonics. Sand shoal comes out further here.

    Some time of bare sand before Zm. Change tapes after this track.

    1334 4 More Zm. Sand shoal out even further. 1345 5 No comments. 8/13/2011 1821 6 Greens with Zm. Then tufty browns (red?) to the end. Better

    visibility. Track labeled Track01 on video. 1829 7 Same as above. 1837 8 North of schoolhouse point a bit of eelgrass, then lots of

    greens, then the tufty brown (red?). 1846 9 South of point. Some greens, then Zm. Less algae. 1854 10 Not much algae after eelgrass. 1903 11 No BioSonics. More algae, but relatively sparse.

    sjs0999 8/5/2011 1707 1 Decent eelgrass, but almost no algae (except thick plankton bloom at start). Visibility good in middle.

    1717 2 Less Zm. Better visibility. Lots of fish on BS. 1727 3 One bit of brown algae. Some wood. 1735 4 About 40 ft of Zm on this one. Good visibility once outside of

    Zm and before -30 ft depth. 1742 5 More Zm. Some fuzz on downslope. Tire at deep end. 1751 6 Similar. Note: All of the following tracks are over the old log boom

    area and had significant amounts of wood waste. 1801 7 More Zm on shallow plateau. More algae of some sort in

    deeper log dump area. Some reds out deep. 1816 8 Similar. 1829 9 More algae in shallows. Less Zm. 1844 10 Maybe a little Zm, maybe not. 1900 11 No Zm. A little algae. Heavy plankton until near the deep

    end.

    sjs1002 8/4/2011 1706 1 Small Zm fringe with a little algae, then steep drop. 1713 2 Similar. 1720 3 Very bad visibility after about 25 ft.

  • 2011 Sequim Bay Submerged Aquatic Vegetation Survey Final Report

    A-3

    Site Date Time Track Comment

    1729 4 Visibility absolute zero after 30 ft. No bottom visible; no lasers visible.

    1740 5 Stopped to offer assistance to capsized canoe … refused. 1749 6 Not much algae. 1757 7 Canoe made it to shore. 1808 8 Some strip of eelgrass and mixed algae with terrible visibility

    after 25 ft. 1819 9 Visibility a bit better at the deep end on this one. 1827 10 Same, almost no algae. 1836 11 Same. Stalled at deep end to look at bare mud better.

    sjs1003 8/13/2011 1650 1 Dendraster, the Zm, then algae (browns, reds?). Down slope to silty zone.

    1657 2 Same. 1704 3 Greens (Enteromorpha) just before Dendraster. 1711 4 No Dendraster on this one. 1718 5 Enteromorpha then Zm and algae, then just algae (browns,

    reds?). 1726 6 Same. 1735 7 Less Zm. 1749 8 No Zm. Heavy greens in shallow areas. 1753 9 Tip of Goose Point. Greens, then some small browns. Very

    steep. 1758 10 As above. 1803 11 South of Goose Point. Greens less heavy. Spots of Zm.

    sjs1004 8/13/2011 1447 1 Just shy of shallow edge of Zm (a couple of feet). Dense plankton still. Zm, some algae, but not a lot. Steep slope. Pretty much just sand.

    1458 2 Plankton bloom dense only in upper layer of water. Pretty clear deeper.

    1505 3 Sparse greens before a bit of Zm, then tufty browns and STEEP slope.

    1514 4 Gentler top slope. Wider Zm area. More generous mix of algae.

    1527 5 Less Zm. Gentle constant slope. 1539 6 Same. 1552 7 Slope steeper, less algae. Visibility goes bad after 70 ft. 1604 8 Dendraster at start the last few tracks. 1616 9 Steeper slope down to about 70 ft, then levels out. 1626 10 Same. 1636 11 Same.

    sjs1005 8/7/2011 1919 1 Greens and Zm, then just greens, then steep slope down. Visibility degrades after about 70 ft.

    1927 2 Same. 1935 3 Adjusted track south a bit to avoid a float. 1941 4 Steeper. 1948 5 Left eelgrass clicks on too long (on the real-time field map). 1955 6 Pretty continuous features so far. 2003 7 Left algae clicker on too long. 2010 8 No comment. 2018 9 Lots of brown/red scrubby algae down slope. 2025 10 No comment. 2032 11 Less algae at this end of the site.

  • 2011 Sequim Bay Submerged Aquatic Vegetation Survey Final Report

    A-4

    Site Date Time Track Comment

    sjs1006 8/6/2011 1853 1 Left the clickers on a bit long. Same stuff as previous site

    (sjs1007). 1901 2 More eelgrass. More algae. More variety. 1911 3 Less and less. Track goes deeper this time. 1920 4 Sun really getting in my eyes on the last half of these tracks;

    can't see much detail here. 1928 5 Left Zm clicker on too long. 1939 6 A lot of the brown, tufty algae in the deeper depths here. 1950 7 Left algae clicker on too long. 2001 8 No comment. 2011 9 No comment. 2019 10 No comment. 2027 11 Lots of crab pots about.

    sjs1007 8/6/2011 1713 1 Green algae and eelgrass mixed for some time. Very clear water … great visibility. Z. japonica? Grab samples produced only small Zm … no japonica.

    1723 2 Greens with eelgrass then with browns and reds down slope. Grab samples produced only small Zm, no Zj.

    1731 3 Same. Left clicker on too long. Labeled Track02 on video overlay. Grab samples produced only small Zm, no Zj.

    1744 4 Similar. Labeled Track03 on ppv file. Labeled Track02 on video tape.

    1753 5 More shell and gravel on downslope. 1800 6 Water gets kind of cloudy past about 75 ft. 1808 7 Pretty much the same. 1816 8 Did not start BS on this one. 1824 9 Zm seemed to end a bit earlier on this one. 1832 10 Less eelgrass again. 1840 11 Less eelgrass, more algae.

    flats47 8/7/2011 1025 1 Started about 2 ft shy of min Zm. Very little algae. Steep slope to about 60 ft.

    1052 2 Had to wait a few minutes to get shallow edge of Zm. More algae on this one. Wind at our tail made us go faster than desired, but not too bad. Pretty good visibility.

    1108 3 Left Dig8 tape on between tracks. Longer high plateau with Zm. More algae down slope.

    1126 4 Longer plateau and steeper downslope. 1144 5 Greens with Zm, then mixing with browns. Slope less steep. 1211 6 Muck like 5. 1235 7 Wider variety of algae on first half. Zm near spit, then algae

    on down. 1307 8 Up and over north end of middle ground. Lots of algae.

    Pacific sand lance on video. Lots of active bird feeding. Last 2 minutes missing from Dig8 tape.

    1348 9 Up and over south end of middle ground. Some Zm here. Lots of algae.

    1422 10 Across entrance. Lots of algae and a spot of Zm. 1433 11 Across entrance to lagoon. Algae and a bit of grass. 1451 12 South of middle ground. Algae and eelgrass in two different

    areas. 1514 13 Dig8 tape runs out last 2 minutes.

  • 2011 Sequim Bay Submerged Aquatic Vegetation Survey Final Report

    A-5

    Site Date Time Track Comment

    flats48 8/4/2011 1853 1 A bit of eelgrass near shore, then nothing much. Stalled for a while to look at mud and pricklebacks.

    1900 2 Pretty much the same. 1916 3 Similar again, but maybe some algae in the -20 ft range. 1925 4 More algae in the mid-depths, but terrible visibility there. 1944 5 Same. 2002 6 More algae in the -8 to -12 ft range. Greens. 2020 7 Deep to shallow. No eelgrass. 2042 8 Shallow to deep. More eelgrass--right after geoduck tubes. 8/5/2011 1923 9 Maybe a Zm plant or two, but could have been enteromorpha

    ropes. Heavy plankton in the shallows. Wood waste and old logs right at deep end.

    1942 10 No Zm. Green algae ropes in the shallows. Wood waste. 2000 11 Similar. 8/13/2011 1920 12 Meander to define Zm area and edge of geoduck aquaculture

    area.

    NorthCenter 8/4/2011 1411 1 BS set to 30 m, so lost bottom on that sounder for a while. Cable also only good to about - 95 ft. Depth down to about -120 ft. Bits of decaying algae throughout … mostly in 70 - 75 ft range. Some growing?

    1506 2 Change BS to 40 m range. Tape change at about 1522. Really nothing growing. Slow down to look closely at 1528. Visibility improves markedly above 70 ft. A few scraps on the west half. Deep trench to 130 ft near marina.

    1601 3 More algae pieces scattered along -90 ft plain. Still not convinced its growing there. Tape change at 1630. Worse visibility toward east end.

    8/5/2011 1149 4 Did not start Dig8 until track almost done. Better visibility on west side. More algae scraps on the west side.

    1238 5 Terrible visibility on west side. Not as deep. Flocculent sea floor.

    SouthCenter 8/5/2011 1340 1 Good track for seeing detail of the central basin plain. East

    half less clear. 1424 2 East part quite turbid. Tape change at 1450. No algae to speak

    of until right near the end. 1503 3 Visibility somewhere between last two tracks. Not much to

    see. 1547 4 Tape change at 1607. 1623 5 Very turbid. Lots of fish on sounders here (head of bay). No

    algae to speak of. Abbreviations:

    Zm Eelgrass (Zostera marina) Zj Zostera japonica

    BS BioSonics echosounder Dig8 Sony digital8 tape