Methodology from Smyth, A. R., Piehler, M. F. and Grabowski, J. H. (2015), Habitat context influences nitrogen removal by restored oyster reefs. J Appl Ecol, 52: 716–725. doi:10.1111/1365-2664.12435

Sediment cores (contained in 6·4-cm-diameter by 17-cm-long polycarbonate tubes, 10 cm depth) were collected adjacent to each reef habitat (n = 3) and control habitat (without reefs, n = 3) in each context at low tide on 28 June 2010. Cores collected from oyster reefs did not contain live oysters. Additionally, ~100 L of water was collected for use in the laboratory incubations. Following collection, sediment cores and water were transported to an environmental chamber (Bally, Inc., Morehead City, NC, USA) at The University of North Carolina Institute of Marine Sciences in Morehead City, NC. Surface water measurements of dissolved O2, salinity and water temperature (YSI 600 Series Sonde and Model 650 data logger; Yellow Springs Instruments, Yellow Springs, OH, USA) were also collected. Oyster density in the reef was determined by placing a 0·25-m2 quadrat on each reef (one quadrat per reef) and counting all the oysters present with a shell length >25 mm (Powers et al. 2009).

Data Processing Description

Statistical analyses were performed using r 2.13.1 (R Foundation for Statistical Computing 2011). Linear mixed-effects models (lme in R nlme package), where habitat nested in sampling location was included as a random effect for the intercept, were used to investigate the effects of oyster reef presence, habitat context, nitrate concentration (ambient vs. elevated) and the interaction between these factors on response variables. Fluxes of N2, NOx ( [math formula] + [math formula] ) [math formula] , denitrification efficiency and SOD were analysed using all three fixed effects. For sediment organic matter, only habitat context and reef presence were included as fixed effects. The effects of ambient vs. elevated nitrate concentration and habitat context on oyster reef-mediated changes in denitrification were also analysed with a mixed-effects model (fixed effects: nitrate concentration × habitat context; random effects: habitat nested in location). Relationships between oyster density and habitat context were made using a mixed-effects model (fixed effects: habitat context; random effects: habitat nested in location). Comparisons were conducted using linear contrasts and judged against an alpha level of 0·05. Interactions were assessed using Tukey's HSD (lsmeans in R lsmeans package). Assumptions of homogeneity were tested using Levene's tests. Regression analyses were used to investigate the effect of oyster density on denitrification. Models with the lowest Akaike's information criterion corrected for small sample sizes (AICc) were chosen.

BCO-DMO Processing Notes:

- column names reformatted to comply with BCO-DMO naming standards.
- lat and lon columns added to correspond with locations.

Data Files

File
oysters.csv (Comma Separated Values (.csv), 809 bytes) MD5:aabf5010bc3674327ce46a3704b725f3 Primary data file for dataset ID 704333

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1233372

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Cheerystone_Inlet		2013-05-01	shoreside Virginia	Bongkeun Song (Principal Investigator) Mark J. Brush (Co-Principal Investigator) Michael F. Piehler (Co-Principal Investigator) Craig Tobias (Co-Principal Investigator)	data info

Instruments

Multi Corer

Supplied Name: Core

Supplied Description:

Used to collect core samples

Instrument Type

Generic Name: Multi Corer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/51/

Generic Description:

The Multi Corer is a benthic coring device used to collect multiple, simultaneous, undisturbed sediment/water samples from the seafloor. Multiple coring tubes with varying sampling capacity depending on tube dimensions are mounted in a frame designed to sample the deep ocean seafloor. For more information, see Barnett et al. (1984) in Oceanologica Acta, 7, pp. 399-408.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
reef_ID	PI issued site ID	unitless	site
habitat	Type of substrate where oysters were measured	unitless	site
location	PI issued location IDs that correspond to specific coordinates and experimental treatments	unitless	site
lat	Latitude	decimal degrees	lat
lon	Longitude	decimal degrees	lon
bucket	PI issued ID of oyster collection measured	unitless	sample
weight_ttl	Total weight of oysters	kilograms	weight
weight_liveOyster	Weight of live oysters	kilograms	weight
weight_shell	Weight of oyster shells	kilograms	weight
count	Oyster count in each bucket sample	count	count
density	Density of oysters in each sample	count per meter	density
length_avg	Average length of each oyster in the sample	centimeters	length
length_stDev	Standard deviation from the mean of oyster lengths	unitless	length
length_median	Median oyster length from the sample	centimeters	length