Dataset: Porites astreoides Photosynthetic Induction PAM data, St. Johh U.S. Virgin Islands

Name: Pulse Amplitude Modulation (PAM) fluorometer measurements from Porites astreoides colonies in St. John, US Virgin Islands from July to August of 2019
Published: 2023-03-21
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.892279.1

Spatial Extent: N:18.3147 E:-64.7218 S:18.3074 W:-64.7314

Temporal Extent: 2019-07-26 - 2019-08-15

Project:

Collaborative Research: Pattern and process in the abundance and recruitment of Caribbean octocorals (Octocoral Community Dynamics)

RUI: Pattern and process in four decades of change on Caribbean reefs (St John Coral Reefs)

Principal Investigator:

Peter J. Edmunds (California State University Northridge, CSUN)

Student:

John Girard (California State University Northridge, CSUN)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2023-03-21

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Pulse Amplitude Modulation (PAM) fluorometer measurements from Porites astreoides colonies in St. John, US Virgin Islands from July to August of 2019

Abstract:

These data represent the raw Diving Pulse Amplitude Modulation (PAM) fluorometer measurements from Porites astreoides colonies classified as inside or outside of octocoral canopies. These data were used to test for the potential effect of light regimes created by octocoral canopies on the photophysiology of autotrophic taxa within the understories of octocoral forests. Additionally, these datasets contain information on the octocoral community surrounding each P. astreoides colony. Data was collected between July and August of 2019 at ~ 7.0 ± 0.5-m depth at three sites (White Point, Tektite, Cabritte Horn) in Lameshur Bay St. John, U.S. Virgin Islands. These data were collected as part of an NSF Coral Reef Time Series, Virgin Islands: Long-term coral reef community dynamics in the Virgin Islands National Park and were published in Girard and Edmunds (2023).

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2023-03-21	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.892279.1	2023-05-24

Methods & Sampling

Location: Lameshur Bay St. John, U.S. Virgin Islands at ~ 7.0 ± 0.5-m depth
Research conducted from the University of the Virgin Islands Marine Station in Lameshure Bay during July – August 2019.

Methods & Sampling:

At each site (White Point, Tektite, Cabritte Horn) corals were haphazardly selected and categorized as within "dense" or "sparse" octocoral canopies. Colonies were categorized as within dense canopies if they were shaded by at least one octocoral colony ≥ 25 cm tall when it flexed in routine oscillatory water flow. Preliminary surveys showed that colonies of Porites astreoides (urn:lsid:marinespecies.org:taxname:288889) met this criterion when the distance from the nearest tall octocoral was less than half the height of the octocoral colony. The distance between P. astreoides colonies and the nearest octocoral was measured to categorize colonies of P. astreoides as within or outside the understory habitat. A single induction curve was performed on each P. astreoides on one of 16 days during July and August 2019. Sampled colonies were > 4 cm in diameter to provide space on the colony surface for the placement of the fiber-optic probe (5 mm diameter) attached to the Diving Pulse Amplitude-Modulation (PAM) fluorometer (Heinz Walz, GmbH) that was used to measure induction time. To standardize the light environment of samples all induction curves were performed between 09:00 and 11:00 hrs on clear cloudless days. In this study actinic light from the Diving PAM was set to 896 µmol photons m-2 s-1 during the induction protocol. There was a two-minute rest period between the first saturation pulse assessing Fm and the initiation of actinic light. Once turned-on, actinic light was continuously delivered for 17 minutes with a total of 13 saturating pulses being delivered one every 1.4 minutes.

Instruments:

PVC Quadrats (1 m2)
Transect tapes
Measuring ribbons with mm graduations
Underwater Fluorometer Diving-PAM (Heinz Walz GmbH)

Data Processing Description

To quantify induction time, the time to steady state photosynthesis was measured by evaluating the performance of photosystem II (PSII) using chlorophyll fluorescence (Bradbury and Baker, 1984, 1981). Calculation of the rate of production of high energy electrons by PSII (relative electron transfer rate, rETR) at a fixed Photon Flux Density is a measure of induction time (Suggett et al., 2010). rETR was calculated by the Diving PAM using the manufacturers software:

rETR = ΔF/Fm X PAR X 0.5 X 0.0001

where ΔF is the change in fluorescence (F) resulting from the saturation pulse, Fm is the maximum fluorescence, PAR is the PFD to which the sample is exposed, 0.5 is an estimate of the quanta absorbed by PSII, and 0.001 is an absorptance constant for light at the coral surface. As neither the absorptance of light by the coral surface, nor quanta by PSII, are known for P. astreoides, this equation estimates relative ETR.

BCO-DMO Data Manager Processing Notes:

* Source file "St.John_Porites Astreoides Induction_PAM data.csv" imported into the BCO-DMO data system

* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores. Can not start with a number]

* lat and lon added to the data from a site list

* Date format converted to ISO 8601 format

Data Files

File
pam.csv (Comma Separated Values (.csv), 39.18 KB) MD5:d1064679d25dc8688872f705f20b3be1 Primary data table for dataset 892279.

Supplemental Files

File

Site List
filename: site_list.csv

(Comma Separated Values (.csv), 192 bytes)
MD5:4415feb2d663fc251a671a2a7c5cac04

Site list for all dataset related to the results publication Girard and Edmunds (2023). 

Parameters (column names, descriptions, and units): 

Site, Site name used in dataset related to Girard and Edmunds (2023),unitless
lat, Site latitude,decimal degrees
lon,Site longitude,decimal degrees
Alternate_name, Alternate name for the site,unitless

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1756678
NSF Division of Ocean Sciences	OCE-2019992

Deployments

None available yet

Instruments

Fluorometer

Supplied Name: Underwater Fluorometer Diving-PAM (Heinz Walz GmbH)

Supplied Description:

Instrument Type

Generic Name: Fluorometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/113/

Generic Description:

A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Date	The date samples were collected Format: %Y-%m-%d	unitless	date
Site	Name of study site	unitless	site
lat	Site latitude	decimal degrees	lat
lon	Site longitude	decimal degrees	lon
Coral_Num	Number given, in sequence, to a Porites astreoides individual measured at a site	unitless	sample_descrip
Depth	Depth under the ocean surface of the P. astreoides individual being measured	meters (m)	depth
Elapsed_Time	Reflects the minutes since the induction protocol was started	minutes	time_elapsed
Yield	Photosynthetic yield (Y) reported directly from the PAM as a whole number, although, it is a proportion created from the F and M parameters such that Y = (M–F)/M	unitless	no_bcodmo_term
rETR	relative Electron Transport Rate reported by the PAM from Porites astreoides after each saturation pulse.	electron micromoles per square meter per secomd (umol electrons m-2 s-1)	ETR
F	Fluorescence yield reported by the PAM from Porites astreoides immediately prior to the saturation pulse at the given elapsed time.	Relative Fluorescence Units (RFU)	fluor
M	Maximum Fluorescence yield reported by the PAM from Porites astreoides during the saturation pulse at the given elapsed time.	Relative Fluorescence Units (RFU)	fluor

Database

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Dataset: Porites astreoides Photosynthetic Induction PAM data, St. Johh U.S. Virgin Islands