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-ChemTax.03
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:Georgia Sea Grant College Program
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:John
Last Name:Hobbie
Address line 1:Ecosystems Center
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
Keywords:LTER, PIE, Plum Island Ecosystems, Massachusetts, Parker River, Plum Island Sound, population dynamics, chlorophyll, phytoplankton, estuary, CHEMTAX, pigments
Abstract:Water column samples are collected along an estuarine salinity gradient, filtered, and stored for later pigment analyses by HPLC. Pigment data are then used by CHEMTAX, calibrated with an appropriate matrix of pigment ratios, to determine phytoplankton groupings .Data are presented in terms of chlorophyll a concentrations partitioned among the major phytoplankton groups as determined by CHEMTAX.
This file contains chlorophyll and phytoplankton classification data from samples that are collected as part of our monitoring surveys of the Parker River estuary each spring and late summer (typically high vs low freshwater input).

PLEASE NOTE THAT THIS IS AN EVOLVING DATASET because ongoing microscopic analysis of phytoplankton samples leads to continued refinement of CHEMTAX. Because of such refinements and because of some sampling changes, this record has two parts: one covering 2003-2006, the other 2008-2010.

For 2003-2006, sampling station along the Plum Island Sound-Parker River were at fixed geographic locations. Phytoplankton groupings were determined using a basic set of pigment ratios in CHEMTAX, resulting in 5 groupings: Diatoms, Dinoflagellates, Cyanobacteria, Chlorophytes,and Cryptophytes.

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), 0 to 9.5 km which encompasses approximately the first 9.5 km of the transect, with 0 km at the mouth of Plum Island Sound; the Lower Parker River (EST-PR-LowerParkerBND), ~9.5 to 14.5 km; the Middle Parker River (EST-PRMiddleParkerBND), ~14.5 to 18.75 km, and the Upper Parker River (EST-PR-UpperParker BND)., ~18.75 to 24.25 km (just below the Parker River Dam).

In addition, the 2008-2010 data have been analyzed by CHEMTAX using a more refined set of pigment ratios (see Lewitus et al., 2005), resutling in some changes and additions to the phytoplankton groupings: Dinophyceae are now in four categories, A , B ,C ,D with Dino- A grouping with Diatoms, Dino-B its own group, Dino-C grouping with Haptophyceae-A and Chrysophyceae-A ( an additonal group) and Dino-D grouping with Haptophyceae-B, another additional group; also added were Prasinophyceae-A, Prasinophyte-b, Chrysophyceae-B, Raphidophyceae-A, and Euglenophyceae.
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-ChemTax.csv
Data File Name EST-PR-ChemTax
Beginning Date 4/16/2003
End Date 8/31/2010
Number of Data Records 285
Other Files to Reference
Availability Status Type 1
Quality Control Information
Maintenance Description On going collections
Log of Changes: Version 01, 24Sep2007, Initial data publication on the web using Excel to EML metadata
Version 02, 28Jan2010, data and keyword update
Version 03, 12Mar2012, major data and metadata update due to Chem Tax algorithm changes and new scheme for identifying sample locations. See metadata for explanations. Used MarcrosExportEML_HTML (working)pie_excel2007.xlsm 2/28/2012 8:18 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 Parker River, ~24 km upstream from ocean endpoint Parker River, ~23 km upstream from ocean endpoint Parker River, ~22 km upstream from ocean endpoint Parker River, ~21 km upstream from ocean endpoint Parker River, ~19.5 km upstream from ocean endpoint Parker River, ~17.25 km upstream from ocean endpoint Parker River, ~15.75 km upstream from ocean endpoint Parker River, ~14.5 km upstream from ocean endpoint, just downstream of branchpoint with Mill River Parker River, ~12.5 km upstream from ocean endpoint Parker River, ~11 km upstream from ocean endpoint Plum Island Sound, ~8.5 km upstream from ocean endpoint, at Nelson Island Plum Island Sound, ~2.7 km upstream from ocean endpoint, at the Ipswich Bay Yacht Club Plum Island Sound, ocean enpoint defined as "0" km 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 42.75085508 42.75174265 42.748294 42.75219747 42.75697423 42.75708039 42.76247293 42.75472052 42.76258164 42.76177168 42.74716149 42.70978014 42.69437          
Longitude -70.92796269 -70.91691665 -70.914959 -70.91020899 -70.90897971 -70.89690988 -70.88417006 -70.87582063 -70.85821174 -70.83675555 -70.82008701 -70.79483658 -70.751674          
Elevation                                    
                                     
                                     
 
TAXONOMIC COVERAGE:
Taxonomic Protocols CHEMTAX
Organisms studied Bacillariophyceae; Dinphyceae; Chlorophyceae; Chrysophyceae; Haptophyceae; Cryptophyceae; Prasinophyceae; Euglenaphyceae; Cyanobacteria; Rhaphidophyceae
 
Methods:EXPERIMENTAL DESIGN AND METHODS:
Samples are collected and processed by PIE researchers. 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 (1 gallon for each of 11 stations (IBYC, Nelson, Stations 24, 22, 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.Beginning in 2008 station names do not correspond to previous 2003 - 2006 fixed static locations, samples were collected in salinity space. Check latitude, longitude and distance data for specific sampling location.

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
Data through 2006 were run with CHEMTAX algorithms assuming pigment ratios typical of estuarine populations. Data from 2008-2010 were run with a more sopisticated set of pigment ratios to more closely reflect Parker River/Plum Island Sound estuary after consideration of direct counts by light microscopy of a subset of duplicate samples (David Borkman, URI) . As a result, some groups were added and existing groups were refined. We are continuing the comparisons between CHEMTAX and microscopy, which may lead to further refinements to the calibration, and we plan to rerun the entire dataset with the improved algorithm. Currently, group names are designated as CT1 (CHEMTAX run 1) for 2003-2006, and CT2(CHEMTAX run 2) for 2008-2010. Results for groups that kept the same name in both runs may not be directly comparable (eg. Chlorophytes _CT1 and Chlorophytes _CT2).

Taxa identified by microscopy (2008-2009) include a (*) in the metadata variable description:

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-mmm-yyyy)   datetime     dd-mmm-yyyy   blank cell
Site location sampled, either specific station or bounding box   nominal         blank cell
Latitude Latitude of sample location in NAD 83 geographic coordinates (decimal degrees) degree ratio   real     blank cell
Longitude Longitude of sample location in NAD 83 geographic coordinates (decimal degrees) degree ratio   real     blank cell
Distance distance upstream from the mouth of the estuary kilometer interval   real     blank cell
Sample Name Water sample name for correspondence to other water chemistry   nominal         blank cell
Subsample Name Chem tax specific subsample name   nominal         blank cell
Fraction either whole water or < 20 um (size fraction 0.7 to 20 um)   nominal         blank cell
Volume total volume of water filtered for analysis milliliter ratio   real     blank cell
Temp temperature (oC) celsius interval   real     blank cell
Salinity salinity (ppt) partPerThousand interval   real     blank cell
Total Chla Total chlorophyll a microgramPerLiter ratio   real     blank cell
Diatoms_CT1 Chlorophyll a concentration associated with diatoms microgramPerLiter ratio   real     blank cell
Dinoflagellates_CT1 Chlorophyll a concentration associated with dinoflagellates microgramPerLiter ratio   real     blank cell
DiatomandDinoA _CT2 Chlorophyll a concentration associated with diatoms and Dinoflagellate Group A (Lewitus et al, 2005; Dino Group A represented by diatom species of Thalassiosira*, Cylindrotheca*, and Nitzchia, and Dino_A species of Kryptoperidinium) microgramPerLiter ratio   real     blank cell
DinoflagellatesB_CT2 Chlorophyll a concentration associated with dinoflagellate Group B (Lewitus et al, 2005; Dino Group B represented by Prorocentrum* and Amphidinium microgramPerLiter ratio   real     blank cell
Cyanobacteria_CT1 Chlorophyll a concentration associated with cyanobacteria microgramPerLiter ratio   real     blank cell
Cyanobacteria_CT2 Chlorophyll a concentration associated with cyanobacteria (Lewitus et al, 2005; represented by Anabaenopsis, Synechococcus, Limnothrix, and an undescribed filamentous strain) microgramPerLiter ratio   real     blank cell
Chlorophytes_CT1 Chlorophyll a concentration associated with chlorophytes microgramPerLiter ratio   real     blank cell
Chlorophytes_CT2 Chlorophyll a concentration associated with chlorophytes (Lewitus et al, 2005; represented by Chlorella, Ankistrodesmus) microgramPerLiter ratio   real     blank cell
PrasinophytesA_CT2 Chlorophyll a concentration associated with Prasinophyte Group A (Lewitus et al, 2005; represented by Pyramimonas* and Nephroselmis) microgramPerLiter ratio   real     blank cell
PrasinophytesB_CT2 Chlorophyll a concentration associated with Prasinophyte Group B (Lewitus et al, 2005; represented by Mackey et al 1996 Prasinophyceae Type 2: ) microgramPerLiter ratio   real     blank cell
Cryptophytes_CT1 Chlorophyll a concentration associated with cryptophytes microgramPerLiter ratio   real     blank cell
Cryptophytes_CT2 Chlorophyll a concentration associated with cryptophytes (Lewitus et al, 2005; represented by Cryptomonas*, Hemiselmis, Chroomonas, and Storeatula) microgramPerLiter ratio   real     blank cell
HaptophytesA_ChryosphytesA_DinoflagellatesC_CT2 Chlorophyll a concentration associated with Haptophytes GroupA, Chrysophytes Group A and Dinoflagellates Group C (Lewitus et al, 2005; HaptoA represented by Isochrysis, Pavlova, and Chryso-A by Ochromonas) microgramPerLiter ratio   real     blank cell
HaptophytesB_DinoflagellatesD_CT2 Chlorophyll a concentration associated with Haptophytes GroupB and Dinoflagellates Group D (Lewitus et al, 2005; HaptoA represented by Mackey et al 1996 Haptophyte type 4 which could include Phaeocystis*) microgramPerLiter ratio   real     blank cell
ChrysophytesB_CT2 Chlorophyll a concentration associated with Chrysophytes Group B (Lewitus et al, 2005; represented by Mackey et al 1996 Chrysophyceae Type 2: an example of this group is Pelagococcus subviridis (Pinckney pers. com.)) microgramPerLiter ratio   real     blank cell
RaphidophytesA_CT2 Chlorophyll a concentration associated with Raphidophytes Group A (Lewitus et al, 2005; represented by Heterosigma akashiwo) microgramPerLiter ratio   real     blank cell
Euglenophytes_CT2 Chlorophyll a concentration associated with Euglenophytes (Lewitus et al, 2005; represented by Euglena* sp.) microgramPerLiter ratio   real     blank cell