U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2019-1042

Prepared in cooperation with U.S. Fish and Wildlife Service

Monitoring Annual Trends in the Abundance of Eelgrass 

(Zostera marina) at Izembek National Wildlife 

Refuge in 2018
Cover: U.S. Fish and Wildlife Service personnel surveying eelgrass (Zostera 

marina) in Izembek Lagoon, Alaska, 2015. Photograph by David Ward, U.S. 

Geological Survey (public domain).
Monitoring Annual Trends in Abundance of Eelgrass

(Zostera marina) at Izembek National Wildlife Refuge, 

Alaska, 2018

By David H. Ward and Courtney L. Amundson

Prepared in cooperation with the U.S. Fish and Wildlife Service

Open-File Report 2019–1042

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

DAVID BERNHARDT, Secretary

U.S. Geological Survey

James F. Reilly II, Director

U.S. Geological Survey, Reston, Virginia: 2019 

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Suggested citation:

Ward, D.H., and Amundson, C.L., 2019, Monitoring annual trends in abundance of eelgrass (Zostera 

marina) at Izembek National Wildlife Refuge, Alaska, 2018: U.S. Geological Survey Open-File Report 

2019-1042, 8 p., https://doi.org/10.3133/ofr20191042. 

ISSN 2331-1258 (online)
iii

Contents

Abstract ......................................................................................................................................................... 1

Introduction.................................................................................................................................................... 1

Methods......................................................................................................................................................... 2

Lagoon-Wide Survey.................................................................................................................................. 2

Site-Specific Eelgrass Survey at Grant Point ............................................................................................. 4

Calibration Plots ......................................................................................................................................... 4

Trend Analysis ........................................................................................................................................... 4

Results and Discussion ................................................................................................................................. 4

Grant Point Survey..................................................................................................................................... 5

Trends in Eelgrass Abundance .................................................................................................................. 7

Acknowledgements........................................................................................................................................ 8

References Cited........................................................................................................................................... 8

Figures

Figure 1. Satellite image with overlay showing distribution of sampling points used to monitor trends in the 

abundance of eelgrass (Zostera marina) in Izembek Lagoon, Izembek National Wildlife Refuge, Alaska, 

2018 (A) and all years (B; 9 years: 2007–11 and 2015–18) of the lagoon-wide point surveys. ..................... 3

Figure 2. Graphs showing mean shoot length and width of eelgrass sampled along two transects in 

Izembek Lagoon, Alaska, during April–May and July–August at the Old Boat Launch.................................. 5

Figure 3. Graphs showing annual deviation in mean air temperature over 12 years (2007–18) during 

winter (A) and growing season (B) as recorded at the Cold Bay Airport, Alaska. Cold Bay airport is located 

about 12 km south of Izembek Lagoon.......................................................................................................... 6

Figure 4. Graph showing predicted aboveground biomass of eelgrass at Izembek Lagoon, Alaska, based 

on the lagoon-wide (points and 95 percent confidence interval bars) and Old Boat Launch (OBL) surveys 

during the peak of the growing season.......................................................................................................... 7
iv

Conversion Factors

U.S. customary units to International System of Units

Multiply By To obtain

Length

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

square mile (mi2) 2.590 square kilometer (km2) 

Flow rate

cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s)

International System of Units to U.S. customary units

Multiply By To obtain

Length

meter (m) 3.281 foot (ft) 

meter (m) 1.094 yard (yd) 

kilometer (km) 0.6214 mile (mi)

kilometer (km) 0.5400 mile, nautical (nmi) 

Area

square kilometer (km2) 0.3861 square mile (mi2)

Flow rate

meter per year (m/yr) 3.281 foot per year (ft/yr) 

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

°F = (1.8 × °C) + 32 
1 

Monitoring Annual Trends in Abundance of Eelgrass

(Zostera marina) at Izembek National Wildlife Refuge, 

Alaska, 2018

By David H. Ward and Courtney L. Amundson

Abstract 

A lagoon-wide, point-sampling survey of eelgrass (Zostera marina) abundance was 

conducted in Izembek Lagoon, Alaska, August 7–16, 2018, the ninth year of annual surveys 

(2007–11, 2015–18). Mean predicted aboveground biomass of eelgrass across 116 sampled 

points was 238 grams per square meter (g m-2) (95 percent confidence interval: 203–278 g m-2) 

in 2018, an increase of 240 percent from the previous year’s low estimate of 97 g m-2 (95 percent

confidence interval: 78–120 g m-2). The increase marked the third year since 2015 where 

eelgrass biomass was above the long-term mean (158 g m-2). Eelgrass biomass was stable over 

the 9 years of this survey. A separate (transect) survey for eelgrass abundance at Grant Point-Old 

Boat Launch showed annual trends in eelgrass biomass similar to the lagoon-wide survey, but 

over a slightly longer time (2007–18). The estimates of above-average eelgrass biomass in 

Izembek Lagoon were likely influenced by relatively warm air temperatures and little or no ice 

in winter (air temperatures 2.7 degrees Celsius greater than the 12-year mean) and average (cool) 

air temperatures during the growing season (April–August) in 2018. 

Introduction 

Eelgrass (Zostera marina) is the predominant macrophyte of protected embayments of 

southwestern Alaska, providing a wide range of ecosystem services to the coastal marine 

environment. Along the coast of the Izembek National Wildlife Refuge (INWR) in southwestern

Alaska (fig. 1), eelgrass forms extensive meadows and some of the largest eelgrass meadows in 

the world (Ward and others, 1997; Hogrefe and others, 2014). These seagrass meadows support a 

rich diversity of marine organisms, virtually the entire Pacific flyway population of black brant 

(Branta bernicla nigricans), and significant numbers of emperor geese (Anser canagicus), 

cackling geese (Branta hutchinsii), dunlin (Calidris alpina), rock sandpipers (Calidris 

ptilocnemis), and Steller’s eiders (Polysticta stelleri; King and Dau, 1981; Petersen and others, 

1994; Fredrickson, 2001; Lewis and others, 2013). 

The U.S. Fish and Wildlife Service and the Alaska Department of Fish Game, through 

the Izembek State Game Refuge, are stewards of the 34,200 hectares of aquatic lands in Izembek 

Lagoon (Alaska Department of Fish and Game, 2010). As part of this stewardship, INWR 

initiated a long-term monitoring program to assess the health and trends in the eelgrass 

population in Izembek Lagoon. A key component of this monitoring program is a lagoon-wide, 

point-sampling survey, which was initially developed and tested between 2007 and 2011. The

primary objective of the lagoon-wide survey was to provide an annual estimate of above-ground 
2 

biomass of eelgrass in Izembek Lagoon. This information may have important implications for 

management of the Pacific black brant population because eelgrass abundance in the lagoon is 

positively associated with the number of overwintering (r = 0.631) brant at INWR. Here, we 

present preliminary results on eelgrass abundance in Izembek Lagoon in 2018. 

Methods 

Lagoon-Wide Survey

To estimate eelgrass abundance in Izembek Lagoon in the study’s early years (2007–09), 

we distributed sample points systematically across the entire lagoon. Later, we used a stratified 

random design (2010–11, 2015–18). The stratification was based on a July 2006 Landsat image 

of the distribution of eelgrass and non-vegetated (channels and mud/sand flats) areas in the 

lagoon (Hogrefe and others, 2014). Since the inception of the lagoon-wide survey in 2007, we 

have sampled 74–282 points per year. In 2018, we sampled 116 points (fig. 1). 

Sample points were located by boat using a Global Positioning System (GPS) unit and 

sampled by snorkeling in dry suits during high tide. At each point, we measured water 

temperature, salinity, and depth, estimated cover of eelgrass and seaweeds, and determined the 

presence or absence of sessile invertebrates: mussels (Mytilus edulis), sponges, sea stars

(Pisaster/Evasterias spp.), gastropods, Caprellid shrimp, and Telmessus crabs within four, 0.25 

square meter (m2

) quadrats. The quadrats were positioned 1–4 meters (m) from the GPS point in 

the four cardinal directions, thereby defining a sampling area of less than 50 m2 centered on the 

GPS point. Cover was defined as the part of the quadrat area obscured by eelgrass or seaweeds 

while viewed from above. Eelgrass was assessed to an approximate depth of 2.5 m below

MLLW (mean lower low water), the approximate maximum depth of eelgrass in Izembek 

Lagoon (Ward and others, 1997). If eelgrass was present in a quadrat, 10 representative 

vegetative shoots were collected and measured for shoot length (meristem to tip of longest leaf) 

and width. If seaweeds were present, we estimated percent cover of all seaweed species 

combined and identified the most abundant species in the quadrat. 
3 

Figure 1. Satellite image with overlay showing distribution of sampling points used to monitor trends in the 

abundance of eelgrass (Zostera marina) in Izembek Lagoon, Izembek National Wildlife Refuge, Alaska,

2018 (A) and all years (B; 9 years: 2007–11 and 2015–18) of the lagoon-wide point surveys. Green, 

eelgrass; brown, non-vegetative; blue, water.
4 

Site-Specific Eelgrass Survey at Grant Point

Supplemental to the lagoon-wide survey, we sampled seasonal changes in eelgrass cover, 

shoot length and width of eelgrass within randomly placed quadrats along two permanently 

established 100-m-long transects at Grant Point (that is, Old Boat Launch [OBL]; fig. 1A) in 

April and August. The transects were aligned parallel to the shoreline, with one situated in the 

high (0.5 m mean lower low water [MLLW]) intertidal about 30 m from the proximal edge of the 

eelgrass meadow and the other placed in the lower (-0.2 MLLW) intertidal, about 65 m from the 

distal edge of the meadow. We estimated the percent cover of eelgrass and picked representative 

shoots within 10 0.25 m2 quadrats. Following collections (less than 2 days), 10 vegetative shoots 

were measured for length (meristem to tip of longest leaf) and width. 

Calibration Plots 

To convert percent cover estimates to above-ground biomass of eelgrass, we harvested 

shoots from 15 to 30 quadrats taken at Grant Point (that is, New Boat Launch [NBL] and OBL; 

fig. 1 inset). We estimated percent cover and collected all eelgrass shoots within the quadrat, 

removed dead leaves and belowground parts of the plant, and selected 10 representative shoots 

that were later measured for shoot length (meristem to tip of longest leaf) and shoot width. We 

then dried entire samples to constant mass at 50 degrees Celsius and weighed (g) them to 

determine biomass per quadrat, which was scaled to g m2

. Calibration points represented the 

lagoon-wide range of sampling date, percent eelgrass cover and water depth. 

Trend Analysis

Using calibration data, we estimated the functional relationship between eelgrass shoot 

length and percent cover and dried biomass per quadrat, using a log-Gamma generalized linear 

model. We then used this functional relationship to predict eelgrass biomass for lagoon-wide 

sampling. We assumed areas without eelgrass had biomass of zero without error and used a logithurdle log-Gamma model to separate zero and non-zero counts. Predicted biomass with error 

was used as the response variable in a generalized linear mixed model that included effects of 

substrate type (mud, sand, mud and sand mixture, cobble/rock), day of year of the survey, tideadjusted water depth, water temperature, and year on eelgrass biomass given it was present at a 

point. We implemented models using a Bayesian analysis framework in Jags (Plummer, 2003) 

run through the jagsUI package (Kellner, 2018) in R (R Core Team, 2018). We combined OBL 

transect and Grant Point calibration data collected 2007–18 and analyzed them separately using 

the same model structure. We then compared results to Lagoon-wide biomass estimates. 

Results and Discussion

A total of 464 quadrat-points (116 points) were sampled in Izembek Lagoon on 6 days 

between August 6 and 17 2018 (fig. 1A). Strong winds prevented boat surveys on a third (4 days) 

of the 10-day sampling period. Eelgrass was present on 93 percent of the quadrat-points, and 

when present, occurred at a mean cover of 69 + 34 percent [SD]. Mean length and width of 

eelgrass shoots were 42.2 + 47.8 centimeters (range = 5–284 centimeters) and 2.0 + 0.60 

millimeters (range = 1–5 millimeters), respectively. 

In contrast to eelgrass, seaweeds were present on slightly over half of the points (57 

percent), and when present, occurred at relatively low mean cover of 17 + 18 percent. Four 

genera of seaweeds were identified, and the predominant genera were 
5 

Cladophora/Chaetomorpha (72 percent of quadrat-points) and Chordaria (25 percent of quadratpoints). The presence of the five macro-invertebrates was highly variable across quadrat-points. 

Gastropods (66 percent of quadrat-points) were the most commonly encountered invertebrate 

followed by Caprillid shrimp (24 percent), mussels (11 percent), sponges (10 percent), sea stars 

(3 percent), and Telmessus crabs (2 percent). 

Grant Point Survey

The Grant Point survey occurred on April 20 and August 10. At the start of the growing 

season in April, overall mean shoot length and width of eelgrass were similar in 2018 and 2017 

and were of average size compared to mean shoot lengths and widths in other years (fig. 2). By

the peak of the growing season in August, the shoots tripled in length and were about 15 percent

wider than in April. Mean shoot size in August increased in 2018 from the decade low in 2017 

but was similar in mean shoot size to the rest of the study period (fig. 2). 

Figure 2. Graphs showing mean shoot length and width of eelgrass sampled along two transects in 

Izembek Lagoon, Alaska, during April–May and July–August at the Old Boat Launch. ND, no data 

collected. 
6 

Winter (January–April) 2018 was the second warmest since 2007, the year lagoon-wide 

surveys were started in Izembek Lagoon, with mean air temperature 2.7 degrees Celsius greater 

than the 12-year mean (fig. 3A). This was also the sixth winter in the last eight with little or no 

ice in Izembek Lagoon. Mean air temperatures moderated during the growing season (May–

August), with the mean air temperature during this season only slightly greater in 2018 than over 

the 12-year period (fig. 3B). 

Figure 3. Graphs showing annual deviation in mean air temperature over 12 years (2007–18) during

winter (A) and growing season (B) as recorded at the Cold Bay Airport, Alaska. Cold Bay airport is located 

about 12 km south of Izembek Lagoon. Data obtained online from National Centers for Environmental 

Information at National Oceanic and Atmospheric Adminstration, https://www.ncdc.noaa.gov/cdo-web/. 
7 

Trends in Eelgrass Abundance

Mean predicted biomass of eelgrass based on the lagoon-wide survey was 238 g m-2 (95 

percent confident interval [CI]: 203–278 g m-2) in 2018, a 2.4 × increase in eelgrass biomass

from 2017 (fig. 4). Despite wide variability in mean annual estimates (minimum of 45 g m-2 in 

2008 to maximum of 330 g m-2 in 2015), no trend was detected over the 9-year study period, 

2007–11 and 2015–18 (fig. 4). 

Mean predicted biomass of eelgrass in August at OBL was 190 g m-2 (95 percent CI: 

113–307 g m-2) in 2018 and was higher in the low intertidal zone (mean = 245 g m-2, 95 percent

CI: 144–404 g m-2) than high intertidal zone (mean = 148 g m-2, 95 percent CI: 86–243 g m-2). 

Overall, mean predicted biomass across years was similar between the two surveys (that is, 

confidence intervals overlapped), except in 2007 and 2008, suggesting that OBL estimates can 

provide insight into trends for the entire lagoon between 2011 and 2015 (spanning data missing

in the lagoon-wide survey). 

Figure 4. Graph showing predicted aboveground biomass of eelgrass at Izembek Lagoon, Alaska, based 

on the lagoon-wide (points and 95 percent confidence interval bars) and Old Boat Launch (OBL) surveys 

during the peak of the growing season. Predictions are for mean day of year, tide-adjusted water depth, 

water temperature and mud substrate type. Means, solid lines; shaded area, 95 percent confidence 

interval. 
8

Acknowledgements

We are especially thankful to Thomas Riecke (University of Nevada-Reno) and Damian 

Menning (U.S. Geological Survey, Alaska Science Center) for their assistance with the surveys 

in 2018. We also thank Greg Risdahl and Leticia Melendez (U.S. Fish and Wildlife Service

[USFWS] Izembek National Wildlife Refuge) for their support of the eelgrass monitoring 

program. This study was funded by the USFWS under an Interagency Agreement to the U.S. 

Geological Survey (#FF07RIZM00000-4500121400).

References Cited

Alaska Department of Fish and Game, 2010, Izembek State Game Refuge management plan:

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North America: Ithaca, New York, Cornell Lab of Ornithology, accessed February 9, 2019, at

https://doi.org/10.2173/bna.571.

Hogrefe, K.R., Ward, D.H., Donnelly, T.F., and Dau, N., 2014, Establishing a baseline for 

regional scale monitoring of eelgrass (Zostera marina) habitat on the lower Alaska Peninsula: 

Remote Sensing, v. 6, p. 12447–12477.

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bernicla), in Poole, A.F., ed., The birds of North America: Ithaca, New York, Cornell Lab of

Ornithology, accessed February 9, 2019, at https://doi.org/10.2173/bna.337.

Petersen, M.R., Schmutz, J.A., and Rockwell, R.F., 1994, Emperor Goose (Chen canagica), in

Poole, A.F., ed., The birds of North America: Ithaca, New York, Cornell Lab or Ornithology, 

accessed February 9, 2019, at https://doi.org/10.2173/bna.97.

Plummer, M., 2003, JAGS—A program for analysis of Bayesian graphical models using Gibbs 

sampling: Proceedings of the 3rd international workshop on distributed statistical computing,

accessed February 9, 2019, at http://citeseer.ist.psu.edu/plummer03jags.html.

R Core Team, 2018, R—A language and environment for statistical computing: Vienna, Austria, 

R Foundation for Statistical Computing, accessed February 9, 2019, at https://www.Rproject.org/.

Ward, D.H., Markon, C.J., and Douglas, D.C., 1997, Distribution and stability of eelgrass beds at 

Izembek Lagoon, Alaska: Aquatic Botany, v. 58, p. 229–240.
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For more information concerning the research in this report, contact the

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ISSN 2331-1258 (online)

https://doi.org/10.3133/series20191042

Ward and Amudnson—Monitoring Annual Trends in the Abundance of Eelgrass at Izembek National Wildlife Refuge in 2018—Open-File Report 2019-1042