Dataset: ZEN 2014 Site Survey Data
Deployment: ZEN2_2014

Eelgrass 2014 Site Survey Data

Principal Investigator:

J. Emmett Duffy (Smithsonian Institution, TMON)

Co-Principal Investigator:

Kevin Alexander Hovel (San Diego State University, SDSU)

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

Scientist:

Dr Pamela L Reynolds (University of California-Davis, UC Davis)

Contact:

Dr Pamela L Reynolds (University of California-Davis, UC Davis)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Global biodiversity and functioning of eelgrass ecosystems (Zostera Experimental Network 2) (ZEN 2)

Data URL:

https://www.bco-dmo.org/dataset-deployment/712086/data

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Description

Methods & Sampling

Dataset acquisition description

Twenty meter square plots (2 meters apart) were sampled at 50 eelgrass meadows ("sites") in summer 2014. Abiotic parameters were quantified in situ and/or using local monitoring station data. The epifaunal community was quantified as in Duffy et al. 2015. Seagrass density was quantified in 20cm diameter rings, and dry mass from 20 cm diameter cores which captured all above ground mass, and below ground to a depth of 20 cm. A three centimeter section from each of 5 shoots per plot was quantified for leaf carbon and nitrogen (processed at the Virginia Institute of Marine Science), while another 3 cm section was utilized for plant genetic analyses (processed by J. Olsen at the University of Groningen). Additional details are included in the Zostera Experimental Network 2014 survey handbook protocol, available upon request.

Methodology is available from: J. Emmett Duffy, et al. Biodiversity mediates top-down control in eelgrass ecosystems: A global comparative-experimental approach. 2015. Ecology Letters 18:7 (696–705). DOI: 10.1111/ele.12448.

Data Processing Description

Dataset Processing Description

Data were aggregated and quality checked manually and through use of analysis scripts. Biotic values are site means.

BCO-DMO Processing:
- added conventional header with dataset name, PI name, version date
- renamed some parameters to BCO-DMO standard
- replaced . with _
- replaced special characters with ascii characters
- reformatted date from m/d/y to yyyy-mm-dd
- reduced digits to right of decimal
- sorted data by Latitude

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1336206	NSF Division of Ocean Sciences
OCE-1336741	NSF Division of Ocean Sciences
OCE-1336905	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

CHN Elemental Analyzer

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: CHN Elemental Analyzer

Acronym: CHN_EA

Generic Description:

A CHN Elemental Analyzer is used for the determination of carbon, hydrogen, and nitrogen content in organic and other types of materials, including solids, liquids, volatile, and viscous samples.

Refractometer

Supplied Name:

Supplied Description:

Used to measure salinity

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.

Temperature Logger

Supplied Name:

Supplied Description:

HOBO Pendant temperature loggers

Instrument Type

Generic Name: Temperature Logger

Generic Description:

Records temperature data over a period of time.

Thermal Cycler

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Thermal Cycler

Generic Description:

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
Site_Code	Two letter code for the specific ZEN partner (25 total).	unitless	site
Site	The 2 letter ZEN Site.Code followed by the subsite A or B (50 total)	unitless	site
Subsite	Designation of the ZEN sub-site (A or B; except for LI where it is 1 or 2).	unitless	site
Subsite_Name	The partner-provided name for their subsite (50 total).	unitless	site
Ocean	Two choices: Atlantic or Pacific	unitless	site_descrip
Coast	Combination of Basin and Ocean. Four choices: East.Atlantic; West.Atlantic; East.Pacific; West.Pacific	unitless	site_descrip
Basin	Location along the ocean basin margin. Two choices: East or West.	unitless	site_descrip
Latitude	Latitude of the site of deployment in decimal degrees	decimal degrees	lat
Longitude	Longitude of the site of deployment in decimal degrees	decimal degrees	lon
Sampling_Time	Two choices 1 or 2. Internal coding to differentiate for sites which conducted two separate sampling efforts.	unitless	sample_descrip
Month	Calendar month in which the sampling occurred.	unitless	month
Date_Collected	Specific date the specific measurement was collected for a given variable. Format: yyyy-mm-dd	unitless	date
Temperature_C	Seawater temperature in degrees Celsius taken in the middle of the seagrass canopy height at low tide during sampling. Appropriate local monitoring station data substituted if in situ data not available.	degrees Celsius	temp
Salinity_ppt	Salinity (in ppt) taken in the middle of the seagrass canopy height at low tide during sampling. Appropriate local monitoring station data substituted if in situ data not available.	parts per thousand	sal
Day_length_hours	Length (in hours) of daylight for the day on which the sampling was conducted using date-calendar.	hours	length_day
GenotypicRichness	Genotypic richness (G-1/N-1) of Zostera marina from one shoot per plot. Provided by J.Olsen. Genotypic richness ranges from 0 (all individuals the same) to 1 (all individuals different) and is a measure of the number of distinct genotypes. (Genotype = a clone.) Genotypes are multilocus with 8 16 or 24 loci involved.	unitless	no_bcodmo_term
AllelicRichness	Allelic richness (Â) of Zostera marina from one shoot per plot. Provided by J.Olsen. Interpretation: the average number of alleles per locus; normalized to 7 genets.	unitless	no_bcodmo_term
Inbreeding	Inbreeding coefficient (FIS) of Zostera marina from one shoot per plot. Provided by J.Olsen.	unitless	no_bcodmo_term
Mean_Shoots_Zmarina_per_m2	Mean density of Zostera marina shoots per square meter (from sampling hoops or other methods)	shoots per square meter	abundance
SD_Shoots_Zmarina_per_m2	Standard deviation of the number of Zostera marina shoots per square meter	shoots per square meter	abundance
SE_Shoots_Zmarina_per_m2	Standard error of the number of Zostera marina shoots per square meter	shoots per square meter	abundance
Mean_Site_Std_Periphyton	Mean standardized loading of periphyton (g dried periphyton/dry g Zostera)	unitless	no_bcodmo_term
SD_Site_Std_Periphyton	Standard deviation of Mean.Site.Std.Periphyton	unitless	no_bcodmo_term
SE_Site_Std_Periphyton	Standard error of Mean.Site.Std.Periphyton	unitless	no_bcodmo_term
Mean_Site_Std_SessileInvertebrate	Mean standardized loading of sessile invertebrates	grams dry sessile invertebrates/dry grams Zostera	no_bcodmo_term
SD_Site_Std_SessileInvertebrate	Standard deviation of Mean.Site.Std.SessileInvertebrate	grams dry sessile invertebrates/dry grams Zostera	no_bcodmo_term
SE_Site_Std_SessileInvertebrate	Standard error of Mean.Site.Std.SessileInvertebrate	grams dry sessile invertebrates/dry grams Zostera	no_bcodmo_term
Mean_Site_Std_TotalEpibiota	Mean standardized loading of total epibiota (periphyton + sessile invertebrates) on Zostera marina	grams total dried epibiota/dry grams Zostera	no_bcodmo_term
SD_Site_Std_TotalEpibiota	Standard deviation of Mean.Site.Std.TotalEpibiota	grams total dried epibiota/dry grams Zostera	no_bcodmo_term
SE_Site_Std_TotalEpibiota	Standard error of Mean.Site.Std.TotalEpibiota	grams total dried epibiota/dry grams Zostera	no_bcodmo_term
Sheath_Width_cm	Mean widest measurement of the leaf sheath	centimeters	width
Shealth_Length_cm	Mean length of the longest intact sheath; from the meristem to the top of the sheath	centimeters	length
Longest_Leaf_Length_cm	Mean length from the meristem to the tip of the longest leaf	centimeters	length
SD_Sheath_Width_cm	Standard deviation of Sheath.Width.cm	centimeters	width
SD_Shealth_Length_cm	Standard deviation of Sheath.Length.cm	centimeters	length
SD_Longest_Leaf_Length_cm	Standard deviation of Longest.Leaf.Length	centimeters	length
SE_Sheath_Width_cm	Standard error of Sheath.Width.cm	centimeters	width
SE_Shealth_Length_cm	Standard error of Sheath.Length.cm	centimeters	length
SE_Longest_Leaf_Length_cm	Standard error of Longest.Leaf.Length	centimeters	length
Below_Zmarina_g	Mean dry belowground mass (g) of Zostera marina per square meter	grams/meter^2	mass
Below_OtherSeagrass_g	Mean dry belowground mass (g) of seagrass species excluding Zostera marina per square meter	grams/meter^2	mass
Above_Zmarina_g	Mean dry aboveground mass (g) of Zostera marina per square meter	grams/meter^2	mass
Above_OtherSeagrass_g	Mean dry aboveground mass (g) of seagrass species excluding Zostera marina per square meter	grams/meter^2	mass
Macroalgae_g	Mean dry mass (g) of macroalgae per square meter (based on seagrass core collections)	grams/meter^2	mass
TOTAL_Seagrass_Biomass	Mean dry mass (g) of all seagrass (below + above)	grams	mass
Total_Seagrass_Biomass_Above	Mean dry mass (g) of all aboveground seagrass mass	grams	mass
Total_Seagrass_Biomass_Below	Mean dry mass (g) of all belowground seagrass mass	grams	mass
SD_Below_Zmarina_g	Standard deviation of Below.Zmarina.g	grams	mass
SD_Below_OtherSeagrass_g	Standard deviation of Below.OtherSeagrass.g	grams	mass
SD_Mean_Above_Zmarina_g	Standard deviation of Above.Zmarina.g	grams	mass
SD_Above_OtherSeagrass_g	Standard deviation of OtherSeagrass.g	grams	mass
SD_Macroalgae_g	Standard deviation of Macroalgae.g	grams	mass
SD_Mean_Total_Seagrass_Biomass_Above	Standard deviation of Mean.Total.Seagrass.Biomass.Above	grams	mass
SD_Mean_Total_Seagrass_Biomass_Below	Standard deviation of Mean.Total.Seagrass.Biomass.Below	grams	mass
SE_Below_Zmarina_g	Standard error of Below.Zmarina.g	grams	mass
SE_Below_OtherSeagrass_g	Standard error of Below.OtherSeagrass.g	grams	mass
SE_Mean_Above_Zmarina_g	Standard error of Above.Zmarina.g	grams	mass
SE_Above_OtherSeagrass_g	Standard error of OtherSeagrass.g	grams	mass
SE_Macroalgae_g	Standard error of Macroalgae.g	grams	mass
SE_Mean_Total_Seagrass_Biomass_Above	Standard error of Mean.Total.Seagrass.Biomass.Above	grams	mass
SE_Mean_Total_Seagrass_Biomass_Below	Standard error of Mean.Total.Seagrass.Biomass.Below	grams	mass
Mean_Leaf_PercN	Mean leaf percent nitrogen in the young growth Zostera marina tissue	percent	N
Mean_Leaf_PercC	Mean leaf percent carbon in the young growth Zostera marina tissue	percent	C
SD_Mean_Leaf_PercN	Standard deviation of Mean.Leaf.PercN	percent	N
SD_Mean_Leaf_PercC	Standard deviation of Mean.Leaf.PercC	percent	C
SE_Mean_Leaf_PercN	Standard error of Mean.Leaf.PercN	percent	N
SE_Mean_Leaf_PercC	Standard error of Mean.Leaf.PercC	percent	C
Mean_Epifaunal_Richness	Mean richness of epifanua per plot. Richness counts based on lowest taxonomic resolution identified per specimen (primarily species level)	unitless	no_bcodmo_term
SE_Epifaunal_Richness	Standard error of Mean.Epifaunal.Richness	unitless	no_bcodmo_term
SD_Epifaunal_Richness	Standard deviation of Mean.Epifaunal.Richness	unitless	no_bcodmo_term
Mean_Mesograzer_Richness	Mean richness of epifauna per plot identified as mesograzer taxa. Richness counts based on lowest taxonomic resolution identified per specimen (priarily species level)	unitless	no_bcodmo_term
SE_Mesograzer_Richness	Standard error of Mean.Mesograzer.Richness	unitless	no_bcodmo_term
SD_Mesograzer_Richness	Standard deviation of Mean.Mesograzer.Richness	unitless	no_bcodmo_term
Mean_Total_Abund	Mean total abundance of epifauna per plot sample: counts of animals per dry mass of the plants they were collected from	# animals/grams plant	abundance
SE_Total_Abund	Standard error of Mean.Total.Abund	# animals/grams plant	abundance
SD_Total_Abund	Standard deviation of Mean.Total.Abund	# animals/grams plant	abundance
Mean_Total_Abund_Mesograzers	Mean total abundance of epifauna per plot sample identified as mesograzer taxa	# animals/grams plant	abundance
SE_Total_Abund_Mesograzers	Standard error of Mean.Total.Abund.Mesograzers	# animals/grams plant	abundance
SD_Total_Abund_Mesograzers	Standard deviation of Mean.Total.Abund.Mesograzers	# animals/grams plant	abundance
Mean_Std_Total_Abund	Mean total abundance of epifauna per plot sample standardized by the total dry mass (g) of macrophytes from which the sample was collected	# animals/grams plant	abundance
SE_Std_Total_Abund	Standard error of Mean.Std.Total.Abund	# animals/grams plant	abundance
SD_Std_Total_Abund	Standard deviation of Mean.Std.Total.Abund	# animals/grams plant	abundance
Mean_Std_Total_Abund_Mesograzers	Mean total abundance of epifauna per plot sample identified as mesograzer taxa; standardized by the total dry mass (g) of macrophytes from which the sample was collected	# animals/grams plant	abundance
SE_Std_Total_Abund_Mesograzers	Standard error of Mean.Std.Total.Abund.Mesograzers	# animals/grams plant	abundance
SD_Std_Total_Abund_Mesograzers	Standard deviation of Mean.Std.Total.Abund.Mesograzers	# animals/grams plant	abundance
Site_Epifaunal_Richness	Total richness of epifauna at the site. Richness counts based on lowest taxonomic resolution identified per specimen (primarily species level)	unitless	no_bcodmo_term
Site_Mesograzer_Richness	Total richness of epifauna identified as mesograzer taxa at the site. Richness counts based on lowest taxonomic resolution identified per specimen (primarily species level)	unitless	no_bcodmo_term
epifauna_max_size	Maximum sieve size (mm) of epifauna collected at the site	millimeters	no_bcodmo_term
epifauna_med_size	Median sieve size (mm) of epifauna collected at the site	millimeters	no_bcodmo_term
mesograzers_max_size	Maximum sieve size (mm) of epifauna identified to be mesograzer taxa colected at the site	millimeters	no_bcodmo_term
mesograzers_med_size	Median sieve size (mm) of epifauna identified to be mesograzer taxa collected at the site	millimeters	no_bcodmo_term

Database

Contribute Data

Dataset: ZEN 2014 Site Survey Data
Deployment: ZEN2_2014

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: ZEN 2014 Site Survey DataDeployment: ZEN2_2014

Dataset acquisition description

Dataset Processing Description

Dataset: ZEN 2014 Site Survey Data
Deployment: ZEN2_2014