Plum Island Ecosystems LTER Database

Acceptance and utilization of LTER data requires that:

(1) The Principal Investigator be sent a notice stating reasons for acquiring any data and a description of the publication intentions.
(2) The Principal Investigator of the data set be sent a copy of the report or manuscript prior to submission and be adequately cited in any resultant publications.
(3) A copy of any resultant publications should be sent to:

Principal Investigator
Ecosystems Center
Marine Biological Laboratory
7 MBL St.
Woods Hole, MA 02543

Dataset URLs:METADATA: HTML, Rich Text, XML(EML compliant)
DATA: Comma Delimited, Excel file with Metadata and data
Dataset ID:EST-PR-PlanktonChemTax.01
Dataset Title:Phytoplankton identification using HPLC and Chem Taxonomy along transects in the Plum Island Sound estuary
Investigator 1: 
First Name:Charles
Last Name:Hopkinson
Address line 1:
Address line 2:University of Georgia
Address line 3:229 Marine Sciences
City:Athens
State:GA
Zip Code:30602
Country:USA
Investigator 2: 
First Name:Anne
Last Name:Giblin
Address line 2:MBL
Address line 3:7 MBLSt
City:Woods Hole
State:MA
Zip Code:02543
Country:USA
Associate Investigators:Hap Garritt, Jane Tucker, Emily Gaines, William Lee, Christina Maki, Aaron Strong, Rebecca Prosser, Colin Millar, Catherine Caruso, Samuel Kelsey, Samantha Bond
Keywords:LTER, PIE, Plum Island Ecosystems, Massachusetts, Parker River, population dynamics, chlorophyll, phytoplankton, estuary, CHEMTAX, pigments
Abstract:Water column samples are collected along an estuarine salinity gradient as part of our monitoring surveys of the Parker River estuary each spring and late summer (typically high vs low freshwater input). Samples are filtered, and stored frozen for later pigment analyses by HPLC. Pigment data are then analyzed by CHEMTAX, calibrated to a matrix of pigment ratios based on taxonomy and enumeration of selected subsamples by microspcopy. Data are presented in terms of chlorophyll a concentrations partitionaed among the major phytoplankton groups as determined by CHEMTAX.

For 2003-2006, sampling stations along the Plum Island Sound-Parker River were at fixed geographic locations at specific "Bends" in the river. In 2008, we began sampling the water column in salinity space rather than at specific geographic locations along the river. This sampling approach was adopted in order to follow particular water masses in this macrotidal estuary. In practical terms, it means that sampling locations, or stations, are not static. Therefore, we have mapped the 11 sampling locations (latitude and longitude are logged at each station) from each transect along the mainstem of the estuary, so each station may be placed along the river (to the nearest 0.5km) as well as in salinity space. We have also used the km marker to assign the sampling locations from each survey to one of four bounding boxes : the Sound (Plum Island Sound; EST-PR-SoundBND) which encompasses approximatly the first 9.5 km or the transect, with Okm at the mouth of the sound; the Lower Parker River (EST-PR-LowerParkerBND) , ~9.5 - 14.5 km; the Middle Parker River (EST-PRMiddleParkerBND), ~14.5 - 18.75 km, and the Upper Parker River (EST-PR-UpperParker BND)., ~18.75 to 24.25 km (the Parker R. Dam).
Contact: Plum Island Ecosystems LTER Information Manager
The Ecosystems Center
Marine Biological Lab
7 MBL St
Woods Hole, MA 02543
Phone (508) 289 7485
Email: pie_im@mbl.edu
Online URL: http://ecosystems.mbl.edu/PIE/
DATA FILE INFORMATION:
Data File URL http://ecosystems.mbl.edu/PIE/data/EST/data/EST-PR-PlanktonChemTax.csv
Data File Name EST-PR-PlanktonChemTax
Beginning Date 4/16/2003
End Date 8/28/2012
Number of Data Records 373
Other Files to Reference
Availability Status Type 1
Quality Control Information
Maintenance Description On going collections
Log of Changes: Version 01: 17Sep2013, metadata and data created to comply with importation to Drupal and LTER PASTA. Used MarcrosExportEML_HTML (working)pie_excel2007_Sep2013.xlsm 9/10/13 12:02 PM for QA/QC to EML 2.1.0
 
RESEARCH LOCATION: EST-PR-Bend-0 EST-PR-Bend-4 EST-PR-Bend-6 EST-PR-Bend-8 EST-PR-Bend-12 EST-PR-Bend-16 EST-PR-Bend-18 EST-PR-Bend-20 Mill EST-PR-Bend-22 EST-PR-Bend-24 EST-SO-Bend-Nelson EST-SO-Bend-IBYC EST-SO-Bend-Ocean EST-PR-SoundBND EST-PR-LowerParkerBND EST-PR-MiddleParkerBND EST-PR-UpperParkerBND  
Geographic Description Plum Island estuarine water column transect station, Parker River pond below Central St Dam in Byfield, MA, 24 km from Plum Island Sound mouth reference Plum Island estuarine water column transect station, Parker River, 22.7 km from Plum Island Sound mouth reference Plum Island estuarine water column transect station, Parker River, 22 km from Plum Island Sound mouth reference Plum Island estuarine water column transect station, Parker River, 21 km from Plum Island Sound mouth reference Plum Island estuarine water column transect station, Parker River, 19.5 km from Plum Island Sound mouth reference Plum Island estuarine water column transect station, Parker River, 17.3 km from Plum Island Sound mouth reference Plum Island estuarine water column transect station, Parker River, 15.9 km from Plum Island Sound mouth reference Plum Island estuarine water column transect station, Parker River, 14.3 km from Plum Island Sound mouth reference Plum Island estuarine water column transect station, Parker River, 12.4 km from Plum Island Sound mouth reference Plum Island estuarine water column transect station, Parker River, 10.7 km from Plum Island Sound mouth reference Plum Island estuarine water column transect station, Plum Island Sound near Nelson Island, 8.3 km from Plum Island Sound mouth reference Plum Island estuarine water column transect station, Plum Island Sound, near Ipswich Bay Yacht Club pier, 3.1 km from Plum Island Sound mouth reference Plum Island estuarine water column transect station, Plum Island Sound 0 km, Plum Island Sound mouth reference station Plum Island Sound; the most downstream section (bounding box)of the Parker River Estuary transect, as defined in the context of the PIE nutrient and phytoplankton long-term monitoring program, encompassing the first 9.5 km along the transect. The Lower Parker River; the nutrient and phytoplankton transect section (bounding box), from where the Parker R. empties into Plum Island Sound (at river km 9.5) to just downstream of the entrance to the Mill River, 14.5 km. The Middle Parker River; the nutrient and phytoplankton transect section (bounding box), from just downstream of the entrance to the Mill River, 14.5 km, to just west (upstream) of the Middle Road Bridge, river km 18.75. The Upper Parker River; the nutrient and phytoplankton transect section (bounding box), from just west (upstream) of the Middle Road Bridge, river km 18.75 to the Parker River Dam, river km 24.25.  
Location Bounding Box                                    
West Bounding Coordinate                           -70.823195 -70.875749 -70.90153 -70.929061  
East Bounding Coordinate                           -70.75 -70.823195 -70.875749 -70.90153  
North Bounding Coordinate                           42.755688 42.763809 42.763953 42.759027  
South Bounding Coordinate                           42.690641 42.753232 42.754172 42.748102  
OR if single point location                                    
Latitude 42.750855 42.751743 42.748294 42.752197 42.756974 42.75938 42.762473 42.754721 42.762582 42.761772 42.747161 42.70978 42.69437          
Longitude -70.927963 -70.916917 -70.914959 -70.910209 -70.90898 -70.896245 -70.88417 -70.875821 -70.858212 -70.836756 -70.820087 -70.794837 -70.751674          
Elevation                                    
                                     
                                     
 
TAXONOMIC COVERAGE:
Taxonomic Protocols CHEMTAX
Organisms studied Bacillariophyceae; Dinophyceae; Chlorophyceae; Chrysophyceae; Haptophyceae; Cryptophyceae; Prasinophyceae; Euglenaphyceae; Cyanobacteria
 
Methods:EXPERIMENTAL DESIGN AND METHODS:

Samples are collected and processed by PIE researchers. For 2003-2006, sampling stations along the Plum Island Sound-Parker River were at fixed geographic locations at specific "Bends" in the river, reflected in the site name. In 2008, we began sampling the water column in salinity space rather than at specific geographic locations along the river. This sampling approach was adopted in order to follow particular water masses in this macrotidal estuary. In practical terms, it means that sampling locations, or stations, are not static. Therefore, we have mapped the 11 sampling locations (latitude and longitude are logged at each station) from each transect along the mainstem of the estuary, so each station may be placed along the river (to the nearest 0.5km) as well as in salinity space. We have also used the km marker to assign the sampling locations from each survey to one of four bounding boxes : the Sound (Plum Island Sound; EST-PR-SoundBND) which encompasses approximatly the first 9.5 km or the transect, with Okm at the mouth of the sound; the Lower Parker River (EST-PR-LowerParkerBND) , ~9.5 - 14.5 km; the Middle Parker River (EST-PRMiddleParkerBND), ~14.5 - 18.75 km, and the Upper Parker River (EST-PR-UpperParker BND)., ~18.75 to 24.25 km (the Parker R. Dam).

HPLC and Chem Tax analyses are performed by the HPLC Photopigment Analysis Facility at the University of South Carolina, under the direction of Dr. James Pinckney.

The procedure is similar to the standard method for filtering water samples for Chl a analysis
by fluorometry or spectrophotometry. For HPLC analysis, the approach is to collect as much
material as possible to provide high resolution of all the algal groups present and facilitate
the confirmation of pigment identities by comparisons with absorption spectra for authentic
standards. The basic filtration steps are as follows:

1. Collect water (2 gallons for IBYC, Nelson, Station 24, Station 22 and 1 gallon for Stations 20, 18, 16, 12, 8, 4, 0) in a clean container. Keep the water cool and in the dark during transport and short-term storage (an insulated cooler with a little ice works well). The time from collection to filtration should be less than 3 hours.

There will be a whole water sample filtered as described below, need 2 replicates or 2 filters per station.

There will also be a < 20 um sample which is whole water prescreened through 20 um nitex where the filtrate will then be filtered as described below, need 2 replicates or 2 filters per station.

2. Using square-ended forceps (to prevent poking a hole in the filter), place a single Whatman GF/F filter (2.5cm) onto a Gelman filter funnel. Make sure the funnel forms a tight seal with the base.
3. The filter funnel should be attached to a vacuum system. We use a home-made PVC manifold that holds several funnels, and each funnel has a valve to open/close the vacuum. The manifold is attached to heavy-walled tygon tubing and a large vacuum flask (5 gallon glass water bottle). A second hose runs from the carboy to the vacuum pump. Use a moderate vacuum for the filtrations (ca. 100 to 200 mm Hg, or <7 in. Hg vac).
4. Open the vacuum and pour in a pre-measured amount (using a clean graduated cylinder) of sample water. This is the tricky part. You may have to use trial and error to determine how much water you can filter before the filter clogs. Samples closer to the mouth of Plum Island Sound will require larger volumes (500-1000ml) than samples up the Parker River (150-700ml) depending upon season and discharge. Filter water samples in duplicate, then pool the two filters for HPLC analyses. Be sure to record the total volume of water filtered for each duplicate sample.
5. Using square-tipped forceps, gently fold the filter in half, with the side containing the sample on the inside of the fold. Remove the filter, keeping it folded, and place the filter between two sheets of tissue paper (we use paper towels). Gently press the filter with your thumb to remove excess water from the filter. (Excess water in the filter reduces the extraction efficiency of the acetone solvent).
6. Label the outside of a small piece of aluminum foil (a square piece with dimensions of 5 x 5 cm) with the sample identification number. Use a black sharpie pen and make sure the ink dries (sharpie ink will destroy the pigment analysis….and the filters are magnets for sharpie ink!)
7. Place the duplicate filters together (keeping them folded in half) onto the foil and fold the foil so that the label appears on the outside. Make sure the filter is completely covered by the foil wrapper. Bend the edges of the foil to make sure the filter is sealed within the foil. Place the foil in a freezer (the colder the better). Transport to MBL in small ChemTax cooler box with ice pack. Keep the sample completely frozen and in the dark until you are ready to conduct the HPLC analysis. Samples can be stored for as long as 1 year at -80 C.
8. Fill out ChemTax Transect data sheet with information about samples.
9. For shipping t othe USC lab, the samples should be sent Express Overnight in a styrofoam cooler filled with dry ice. Fill any empty space with newspaper. Please let the lab know when you are shipping so that thety can be on the lookout for the shipment. Plan shipments to avoid weekend delays.

NOTES and COMMENTS
The initial pigment ratios used by ChemTax were based on published values for estuarine populations (Roy et al. 2011; Schlüter et al., 2000) selected to fit results of microscopy of a subset of duplicate samples (David Borkman, URI) from the Parker River estuary.  Microscopy was important in both defining the groups and for qualitative evaluation of ChemTax. At PIE, the chlorophyll a apportioned to the combined category "Diatoms & Chrysophytes" is largely diatom chlorophyll. We are continuing the comparisons between CHEMTAX and microscopy, which may lead to further refinements to the calibration.


Taxa identified by microscopy (2008-2009):

Bacillariophyceae:
Diatoms, centric: Chaetoceros debilis , Chaetoceros spp. <10 um dia, Chaetoceros spp. 10-30 um dia, Chaetoceros spp. 10-30 um dia , Coscinodiscus spp. (30 - 60 um diameter) , Dactyliosolen
fragilissima , Odontella spp. , Skeletonema spp. , Stephanodiscus spp. , Thalassiosira rotula , Thalassiosira spp. <10 um dia, Thalassiosira spp. 10-30 um dia, unidentified Centric diatom <10 um dia
Diatoms, pennate: Amphora spp. ,Cocconeis scutellum , Cylindrotheca closterium , Gyrosigma spp., Licmophora abreviata, naviculoid diatom <10um, Pennate diatom <10 um L, Pennate diatom 10-30 um L,
Pennate diatom 30-60 um L , Pleurosigma aestuarii , Pleurosigma spp. , Pseudo-nitzschia pseudodelicatissima , Pseudo-nitzschia spp., Surirella spp., Synedra spp., Thalassionema nitzschioides

Dinophyceae: Ceratium lineatum , Gymnodinium spp. <20 um long , Gymnodinium spp. 20 - 40 um long, Heterocapsa rotundata , Heterocapsa triquetra, Prorocentrum minimum, Gyrodinium spp (20-40 um L),
Protoperidinium spp. (30-60 um diameter) , Protoperidinium spp. (30-60 um diameter), Scrippsiella trochoidea

Prasinophyceae: Pyramimonas spp. (Prasino A; could be clone PRD18DOI, AY948021; Prasino B may be reassigned to Chlorophytes, pending further refinement of the pigment matrix)
Chrysophyceae: Dinobryon spp., Calycomonas wulfii (both ChrysoA; ChrysoB types have not been identified at PIE, but an example would be Pelagococcus subviridi)
Euglenophyceae: Eutreptia / Eutreptiella spp.
Cryptophyceaes: Cryptomonads <20 um L
microflagellates: unidentified phytoflagellates<10 um diameter (likely includes Prasinophytes identified by CHEMTAX)
Dictychophyceae (silicoflagellate): Dictyocha speculum (has pigment composition similar to HaptophyteB)
Raphidophyceae: not yet identified at PIE; but could include Heterosigma, Fibrocapsa
Cyanobacteria: unidentified Nostoc-like species.
Prymnesiophyceae: Phaeocysitis (Hapto-B) (Phylum Haptophyta)

Data Table

Variable Name Variable Description Units Measurement Scale Code Information Number Type DateTime Format Missing Value Code Missing Value Code Explanation
Date date of sampling (dd-mon-yyyy)   datetime     dd-mon-yyyy NA NA = sample or value missing or lost
Site name of site sampled   nominal       NA NA = sample or value missing or lost
Latitude latitude of the sampling site (decimal degrees) degree ratio   real   NA NA = sample or value missing or lost
Longitude longitude of the sampling site (decimal degrees) degree ratio   real   NA NA = sample or value missing or lost
Distance distance upstream from the mouth of the estuary kilometer interval   real   NA NA = sample or value missing or lost
SampleName water sample identification name   nominal       NA NA = sample or value missing or lost
SubsampleName ChemTax associated subsample of water sample   nominal       NA NA = sample or value missing or lost
BottleName Sampling bottle name   nominal       NA NA = sample or value missing or lost
SampleType either whole water or < 20 um size fraction   nominal       NA NA = sample or value missing or lost
Volume total volume of water filtered for analysis milliliter ratio   real   NA NA = sample or value missing or lost
Temp temperature (oC) celsius interval   real   NA NA = sample or value missing or lost
Salinity salinity (ppt) partPerThousand interval   real   NA NA = sample or value missing or lost
TotalChlA Total chlorophyll a microgramPerLiter ratio   real   NA NA = sample or value missing or lost
DiatomsandChrysophytes Chlorophyll a concentration associated with diatoms and chrysophytes; for PIE, largely diatoms microgramPerLiter ratio   real   NA NA = sample or value missing or lost
Cryptophytes Chlorophyll a concentration associated with cryptophytes microgramPerLiter ratio   real   NA NA = sample or value missing or lost
Chlorophytes Chlorophyll a concentration associated with chlorophytes microgramPerLiter ratio   real   NA NA = sample or value missing or lost
Dinoflagellates Chlorophyll a concentration associated with dinoflagellates microgramPerLiter ratio   real   NA NA = sample or value missing or lost
Euglenophytes Chlorophyll a concentration associated with euglenophytes microgramPerLiter ratio   real   NA NA = sample or value missing or lost
Prasinophytes Chlorophyll a concentration associated with prasinophytes microgramPerLiter ratio   real   NA NA = sample or value missing or lost
Haptophytes Chlorophyll a concentration associated with haptophytes microgramPerLiter ratio   real   NA NA = sample or value missing or lost
Prymnesiophytes Chlorophyll a concentration associated with prymnesiophytes microgramPerLiter ratio   real   NA NA = sample or value missing or lost
Cyanobacteria Chlorophyll a concentration associated with cyanobacteria microgramPerLiter ratio   real   NA NA = sample or value missing or lost
Comments Comments or notes about specific samples or values   nominal       NA NA = sample or value missing or lost