Dataset: Eelgrass Shoot Metrics

Name: Eelgrass shoot metrics from ecological field surveys in six regions along the eastern Pacific coast in June through August of 2019, 2020, and 2021.
Published: 2022-10-13
Keywords: seagrass wasting disease, Zostera marina, artificial intelligence, temperature anomaly, intertidal, biota, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.878857.1

Spatial Extent: N:55.739078 E:-117.10621 S:32.62535 W:-133.342896

Temporal Extent: 2019-07-02 - 2021-07-28

Project:

Collaborative Research: The role of a keystone pathogen in the geographic and local-scale ecology of eelgrass decline in the eastern Pacific (Eelgrass disease)

Principal Investigator:

Drew Harvell (Cornell University, Cornell)

Co-Principal Investigator:

J. Emmett Duffy (Smithsonian Environmental Research Center, SERC)

Carla P. Gomes (Cornell University, Cornell)

Timothy Hawthorne (University of Central Florida, UCF)

John J. Stachowicz (University of California-Davis, UC Davis)

Scientist:

Lillian Aoki (Cornell University, Cornell)

Data Manager:

Lillian Aoki (University of Oregon)

BCO-DMO Data Manager:

Dana Stuart Gerlach (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-10-13

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Eelgrass shoot metrics from ecological field surveys in six regions along the eastern Pacific coast in June through August of 2019, 2020, and 2021.

Abstract:

These data were collected during ecological field surveys of eelgrass (Zostera marina) meadows along the eastern Pacific from southeastern Alaska to southern California. Parameters measured include seagrass morphology, meadow condition (e.g. shoot densities), and incidence and severity of eelgrass wasting disease. Data were collected within the intertidal area of 32 eelgrass meadows distributed in six regions (five-six meadows sampled in the regions of Alaska, British Columbia, Washington, Oregon, California - Bodega Bay, and California - San Diego). Surveys were conducted in between late June and early August in 2019, 2020, and 2021 by teams from six institutions. The influence of disease on seagrass dynamics is not well understood, and these data can further understanding of the environmental drivers of disease by connecting wasting disease with eelgrass condition across a broad geographic gradient.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2022-10-13	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.878857.1	2022-10-21

Methods & Sampling

Field transect surveys

Field surveys of eelgrass meadow sites were conducted at mid-summer low tides at field sites along the west coast of North America in the U.S. and Canada. Samples and data were collected within the intertidal area of 32 eelgrass meadows distributed in six regions (Alaska, British Columbia, Washington, Oregon, California -Bodega Bay, and California -San Diego). Surveys were conducted between late June and early August in 2019, 2020, and 2021 by teams from six institutions.

For each site, three 20 meter transects were laid parallel to the shore at the shoreward (upper edge) of continuous eelgrass, and three lower (intertidal) 20 meter transects were laid at least 4 meters closer to the water. Along each transect, individual eelgrass shoots (blades/leaves) were collected for analysis at 4, 8, 12, 16, and 20 meters). Leaf and shoot samples were transported in individual containers on ice to the laboratory for immediate processing.

Transect locations were recorded using a hand-held GPS (exact model varied between field locations). Salinity was measured at the time of sampling using a refractometer. Temperature loggers (HOBO MX 2201 and UA-001-64, Onset, Bourne, MA) were deployed at each eelgrass meadow site to provide a continuous record of in situ temperature. For HOBO data, see https://www.bco-dmo.org/dataset/877355 and Related Datasets section below.

Laboratory (Morphology and Imaging)

In the lab, eelgrass blades were cleaned and prepared for morphology and imaging to capture disease metrics (see https://www.bco-dmo.org/dataset/879780). Shoot morphology measurements (sheath length, number of leaves, canopy height) were taken by hand in the laboratory. The third-rank leaf from each shoot was analyzed for epiphyte load and grazing scars. Epiphytes were gently scraped from the third-rank leaf onto a pre-weighed foil tin using a flexible plastic ruler. Tins were dried at 60 degrees Celsius until the mass was constant. Epiphyte mass was calculated using the values for the dry weight of the tin with and without the epiphyte sample. The balances used to measure the epiphyte mass had precision of 0.001 grams. Epiphyte load was standardized as the mass of epiphytes per unit of leaf area.

Third-rank leaves were further analyzed for disease metrics through imaging. Cleaned leaves were placed between sheets of acetate and imaged at high resolution (600 dpi) using an Epson Perfection V550 scanner. The high-resolution images were saved in TIFF format and then processed using a program developed by the authors. The Eelgrass Lesion Image Segmentation Application (EeLISA) uses machine learning to identify healthy and diseased eelgrass tissue and outputs the following metrics:

disease prevalence (presence or absence of disease on a given leaf)
disease lesion area (absolute size of wasting disease lesions), and
disease severity (proportion of leaf area damaged by disease).

~ For details on the development, testing, and training of EeLISA, see Rappazzo et al. (2021).
~ For methodology details, see Aoki et al. (2022)
~ Additional details for the field surveys are available in the Eelgrass Disease Project Handbook.
~ For 16S rRNA amplicon sequencing of eelgrass associated bacteria, refer to NCBI BioProject PRJNA802566 in the Related Datasets section below.

Data Processing Description

BCO-DMO Processing:
- Imported data from source file "meter_level_shoot_metrics.csv" into the BCO-DMO data system. Data file imported using missing data identifier "NA".
- Converted date to year-month-day format
- Joined this data with the file "eelgrass_study_revised_site_metadata.csv" which had coordinates converted to decimal degrees and consistent LocationNames.
- converted Grazing Scars to have consistent presence/absence instead of mixed (Y/N and numerical)
- Added conventional header with dataset name, PI name, version date.
- Modified parameter (column) names to conform with BCO-DMO naming conventions.

Parameters/Fields for Supplemental Files
(The following parameter descriptions are for the Supplemental File titled "Eelgrass study site metadata". For this dataset's fields, please see the heading "Parameters" below).

SampleCollectionDate: Date when samples were collected in the field
Region: Two-letter identifier for the geographic region where the sample was collected (AK=Alaska, BC=British Columbia, WA=Washington, OR=Oregon, BB=Bodega Bay in California, SD=San Diego in California)
SiteCode: One-letter identifier for site within a geographic region where the sample was collected (A, B, C, D, E, F)
LocationName: Full name of each sampling site (eelgrass meadow) where samples were taken
TidalHeight: Single letter indicating the tidal height at which samples were collected. U = upper tidal height; L = lower tidal height
Transect: Integer indicating the transect at which samples were collected. Upper transects = 1, 2, 3; Lower transects = 4, 5, 6.
SampleProcessingDate: Date when samples were processed in the lab
Depth: Depth relative to MLLW (mean lower low water)
Salinity: Salinity of surface water at the time of sampling (point measurement made with refractometer or probe)
LocationComments: Comments describing location including changes between sampling year
TransectBeginDecimalLatitude: Latitudinal coordinate for the beginning (meter 0) of the transect
TransectBeginDecimalLongitude: Longitudinal coordinate for the beginning (meter 0) of the transect
TransectEndDecimalLatitude: Latitudinal coordinate for the end (meter 20) of the transect
TransectEndDecimalLongitude: Longitudinal coordinate for the end (meter 20) of the transect
Year: Year in which samples were collected

Data Files

File
shoot_metrics.csv (Comma Separated Values (.csv), 399.51 KB) MD5:f1f86cdb31601499e14e0c018cd665e4 Primary data file for dataset ID 878857

Supplemental Files

File

Eelgrass study site metadata
filename: eelgrass_study_revised_site_metadata.csv

(Comma Separated Values (.csv), 50.38 KB)
MD5:e17548ddde013aa9a344b97a16e3dfaf

Combined site metadata for eelgrass wasting disease study sites on the western coast of the U.S. and Canada

SampleCollectionDate:  Date when samples were collected in the field

Region: Two-letter identifier for the geographic region where the sample was collected (AK=Alaska, BC=British Columbia, WA=Washington, OR=Oregon, BB=Bodega Bay in California, SD=San Diego in California)

SiteCode: One-letter identifier for site within a geographic region where the sample was collected (A, B, C, D, E, F)

LocationName: Full name of each sampling site (eelgrass meadow) where samples were taken

TidalHeight: Single letter indicating the tidal height at which samples were collected.  U = upper tidal height; L = lower tidal height

Transect: Integer indicating the transect at which samples were collected.  Upper transects = 1, 2, 3; Lower transects = 4, 5, 6.

SampleProcessingDate: Date when samples were processed in the lab

Depth: Depth relative to MLLW (mean lower low water)

Salinity: Salinity of surface water at the time of sampling (point measurement made with refractometer or probe)

LocationComments: Comments describing location including changes between sampling year

TransectBeginDecimalLatitude: Latitudinal coordinate for the beginning (meter 0) of the transect

TransectBeginDecimalLongitude: Longitudinal coordinate for the beginning (meter 0) of the transect

TransectEndDecimalLatitude: Latitudinal coordinate for the end (meter 20) of the transect

TransectEndDecimalLongitude: Longitudinal coordinate for the end (meter 20) of the transect

Year: Year in which samples were collected

NSF Eelgrass Disease Project 2019 Handbook
filename: eelgrass_disease_project_handbook_v1.2.pdf

(Portable Document Format (.pdf), 1.38 MB)
MD5:f8f77aaf781cc5170a168012c938be31

NSF Eelgrass Disease Project 2019 Handbook v1.2 from MarineGEO

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1829890
NSF Division of Ocean Sciences	OCE-1829921
NSF Division of Ocean Sciences	OCE-1829922
NSF Division of Ocean Sciences	OCE-1829992

Deployments

None available yet

Instruments

Global Positioning System Receiver

Supplied Name: hand-held GPS

Supplied Description:

Transect locations were recorded using a hand-held GPS (exact model varied between field locations).

Instrument Type

Generic Name: Global Positioning System Receiver

Acronym: GPS

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/POS03/

Generic Description:

The Global Positioning System (GPS) is a U.S. space-based radionavigation system that provides reliable positioning, navigation, and timing services to civilian users on a continuous worldwide basis. The U.S. Air Force develops, maintains, and operates the space and control segments of the NAVSTAR GPS transmitter system. Ships use a variety of receivers (e.g. Trimble and Ashtech) to interpret the GPS signal and determine accurate latitude and longitude.

Image scanner

Supplied Name: Epson Perfection V550 scanner

Supplied Description:

Cleaned eelgrass blades were imaged at high resolution (600 dpi) using an Epson Perfection V550 scanner.

Instrument Type

Generic Name: Image scanner

Acronym: scanner

Generic Description:

An electronic device that generates a digital representation of an image for data input to a computer.
OR a receiver designed to search for a signal within a specified frequency range. [Definition Source: NCI]

Onset HOBO Pendant MX2201 temperature logger

Supplied Name: HOBO MX2201 temperature logger

Supplied Description:

Instrument Type

Generic Name: Onset HOBO Pendant MX2201 temperature logger

Acronym: Onset HOBO Pendant MX2201

Generic Description:

The Onset HOBO MX2201 is an in-situ instrument for wet or underwater applications. It supports soil temperature, temperature, and water temperature. A one-channel logger that records up to approximately 96,000 measurements or internal logger events with 8K bytes memory. It has a polypropylene housing case. Uses Bluetooth to transmit data. Can be used with a solar radiation shield. Measurement range: -20 deg C to 70 deg C. Accuracy: +/- 0.50 deg C from 0 deg C to 50 deg C. Water depth rating: 30.5 m

Onset HOBO Pendant Temperature/Light Data Logger

Supplied Name: HOBO UA-001-064 temperature logger

Supplied Description:

Instrument Type

Generic Name: Onset HOBO Pendant Temperature/Light Data Logger

Acronym: Onset HOBO Pendant Temp/Light

Generic Description:

The Onset HOBO (model numbers UA-002-64 or UA-001-64) is an in-situ instrument for wet or underwater applications. It supports light intensity, soil temperature, temperature, and water temperature. A two-channel logger with 10-bit resolution can record up to approximately 28,000 combined temperature and light measurements with 64K bytes memory. It has a polypropylene housing case. Uses an optical USB to transmit data. A solar radiation shield is used for measurement in sunlight. Temperature measurement range: -20 deg C to 70 deg C (temperature). Light measurement range: 0 to 320,000 lux. Temperature accuracy: +/- 0.53 deg C from 0 deg C to 50 deg C. Light accuracy: Designed for measurement of relative light levels. Water depth rating: 30 m.

Refractometer

Supplied Name: refractometer (?? need info on make/model from PIs)

Supplied Description:

Salinity was measured at the time of sampling using a refractometer.

Instrument Type

Generic Name: Refractometer

Generic Description:

A refractometer is a laboratory or field device for the measurement of an index of refraction (refractometry). The index of refraction is calculated from Snell's law and can be calculated from the composition of the material using the Gladstone-Dale relation.

In optics the refractive index (or index of refraction) n of a substance (optical medium) is a dimensionless number that describes how light, or any other radiation, propagates through that medium.

scale

Supplied Name: Balance

Supplied Description:

Balances used to measure epiphyte mass had precision of 0.001 g

Instrument Type

Generic Name: scale

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB13/

Generic Description:

An instrument used to measure weight or mass.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Sample_Date	Date when samples were collected in the field Format: %Y-%m-%d	unitless	date
Sample_Id	Unique code identifying field samples based on the region, site, transect, tidal height, and sample replicate	unitless	sample
Region	Two-letter identifier for the geographic region where the sample was collected (AK=Alaska, BC=British Columbia, WA=Washington, OR=Oregon, BB=Bodega Bay in California, SD=San Diego in California)	unitless	region
Site_Code	One-letter identifier for the site within a geographic region where the sample was collected (A, B, C, D, E, F)	unitless	site
Location	Full name of each sampling site (eelgrass meadow) where samples were taken	unitless	site_descrip
Tidal_Height	Single letter indicating the tidal height at which samples were collected. U = upper tidal height; L = lower tidal height	unitless	tide
Depth	Depth relative to MLLW (mean lower low water)	meters (m)	depth
Salinity	Salinity of surface water at the time of sampling (point measurement made with refractometer or probe)	ppt	sal
Transect	Integer indicating the transect at which samples were collected. Upper transects = 1, 2, 3; Lower transects = 4, 5, 6.	unitless	transect
Meter	Exact meter along the transect where an individual sample was collected (m4, m8, m12, m16, m20)	unitless	transect_station
Blade	Integer indicating the replicate number for the disease and epiphyte blades collected along each transect. Values are 1-25	unitless	sample
Longest_Blade_Length	Length of the longest blade in a shoot measured by hand in the lab	millimeters (mm)	length
Longest_Blade_Width	Width of the longest blade in a shoot measured by hand in the lab	millimeters (mm)	width
Sheath_Length	Length of the sheath, measured by hand in the lab	millimeters (mm)	length
Scanned_Blade_Length	length of individual blades, from the top of the sheath to the tip, measured by hand in the lab; scanned blades are 3rd rank at all sites expect 2nd rank at OR	millimeters (mm)	length
Scanned_Blade_Width	Width of individual blade measured by hand in the lab; scanned blades are 3rd rank at all sites except 2nd rank at OR	millimeters (mm)	width
Prevalence_Hand	Presence or absence of disease based on a rapid manual assessment during processing; this value is NOT used for further analysis but is a quick confirmation that disease absence was verified for any totally healthy shoots that were not scanned during processingFactor indicating the presence or absence of wasting disease on a blade based on a rapid manual assessment during processing. Values are 0 = healthy or disease is absent; 1 = disease is present. (This value is NOT used for further analysis but is a quick confirmation that disease absence was verified for any totally healthy shoots that were not scanned during processing)	unitless	flag
Grazing_Scars	Integer indicating the presence or absence of grazing scars on the third rank blade. 0= no grazing scar; 1= grazing scars are present	unitless	flag
Broken_Tip	Code indicating presence of a broken leaf tip on an individual blade, Y = yes, tip is broken, N = no, tip is intact	unitless	flag
Epiphyte_Dry_Mass	Dry mass of epiphytes scraped from the scanned blade	grams (g)	mass_dry
Blade_Area_Hand	Blade area of scanned blade calculated from measurements of length and width made by hand in the lab	centimeters squared (cm2)	area_measured
Number_Leaves	Count of leaves on the shoot (not collected in 2019)	unitless	count
TransectBeginDecimalLatitude	Latitudinal coordinate for the beginning (meter 0) of the transect	decimal degrees	lat
TransectBeginDecimalLongitude	Longitudinal coordinate for the beginning (meter 0) of the transect	decimal degrees	lon
TransectEndDecimalLatitude	Latitudinal coordinate for the end (meter 20) of the transect	decimal degrees	lat
TransectEndDecimalLongitude	Longitudinal coordinate for the end (meter 20) of the transect	decimal degrees	lon
Notes	Comments from field and lab	unitless	comment

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Dataset: Eelgrass Shoot Metrics