uid=PIE,o=lter,dc=ecoinformatics,dc=org all public read EST-PR-ChemTax.03 Plum Island Ecosystems LTER Program Charles Hopkinson

Georgia Sea Grant College Program University of Georgia 229 Marine Sciences Athens GA 30602 USA

Plum Island Ecosystems LTER Program John Hobbie

Ecosystems Center MBL 7 MBLSt Woods Hole MA 02543 USA

Plum Island Ecosystems LTER Program

The Ecosystems Center Marine Biological Lab 7 MBL St Woods Hole MA 02543 USA

(508) 289 7485 pie_im@mbl.edu http://ecosystems.mbl.edu/PIE/ Hap Garritt additional investigator Jane Tucker additional investigator Emily Gaines additional investigator William Lee additional investigator Christina Maki additional investigator Aaron Strong additional investigator Rebecca Prosser additional investigator Colin Millar additional investigator 2007 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. LTER PIE Plum Island Ecosystems Massachusetts Parker River Plum Island Sound population dynamics chlorophyll phytoplankton estuary CHEMTAX pigments Acceptance and utilization of PIE-LTER data requires that: The Principal Investigator be sent a notice stating reasons for acquiring any data and a description of the publication intentions. 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 A copy of any resultant publications should be sent to: Principal Investigator Ecosystems Center Marine Biological Laboratory Woods Hole, MA 02543 http://ecosystems.mbl.edu/PIE/data/EST/EST-PR-ChemTax.html Parker River, ~24 km upstream from ocean endpoint -70.92796269 -70.92796269 42.75085508 42.75085508 Parker River, ~23 km upstream from ocean endpoint -70.91691665 -70.91691665 42.75174265 42.75174265 Parker River, ~22 km upstream from ocean endpoint -70.914959 -70.914959 42.748294 42.748294 Parker River, ~21 km upstream from ocean endpoint -70.91020899 -70.91020899 42.75219747 42.75219747 Parker River, ~19.5 km upstream from ocean endpoint -70.90897971 -70.90897971 42.75697423 42.75697423 Parker River, ~17.25 km upstream from ocean endpoint -70.89690988 -70.89690988 42.75708039 42.75708039 Parker River, ~15.75 km upstream from ocean endpoint -70.88417006 -70.88417006 42.76247293 42.76247293 Parker River, ~14.5 km upstream from ocean endpoint, just downstream of branchpoint with Mill River -70.87582063 -70.87582063 42.75472052 42.75472052 Parker River, ~12.5 km upstream from ocean endpoint -70.85821174 -70.85821174 42.76258164 42.76258164 Parker River, ~11 km upstream from ocean endpoint -70.83675555 -70.83675555 42.76177168 42.76177168 Plum Island Sound, ~8.5 km upstream from ocean endpoint, at Nelson Island -70.82008701 -70.82008701 42.74716149 42.74716149 Plum Island Sound, ~2.7 km upstream from ocean endpoint, at the Ipswich Bay Yacht Club -70.79483658 -70.79483658 42.70978014 42.70978014 Plum Island Sound, ocean enpoint defined as "0" km -70.751674 -70.751674 42.69437 42.69437 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. -70.823195 -70.75 42.755688 42.690641 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. -70.875749 -70.823195 42.763809 42.753232 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. -70.90153 -70.875749 42.763953 42.754172 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. -70.929061 -70.90153 42.759027 42.748102 2003-04-16 2010-08-31 CHEMTAX Genus Bacillariophyceae Genus Dinphyceae Genus Chlorophyceae Genus Chrysophyceae Genus Haptophyceae Genus Cryptophyceae Genus Prasinophyceae Genus Euglenaphyceae Genus Cyanobacteria Genus Rhaphidophyceae On going collections 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 Data Manager

The Ecosystems Center Marine Biological Lab 7 MBL St Woods Hole MA 02543 USA

(508) 289 7485 pie_im@mbl.edu http://ecosystems.mbl.edu/PIE/ Plum Island Ecosystems LTER

The Ecosystems Center Marine Biological Lab 7 MBL St Woods Hole MA 02543 USA

(508) 289 7485 pie_im@mbl.edu http://ecosystems.mbl.edu/PIE/ 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) pers-1 http://www.biol.sc.edu/~jpinckney/Protocols.html Pigment analysis was performed as described by the online protocol. CHEMTAX classification of phytoplankton groups was performed using pigment ratios for estuarine taxa as given in: Lewitus, AJ, DL White, RG Tymowski, ME Geesey, SN Hymel, and PA Noble . 2005. Adapting the CHEMTAX method for assessing phytoplankton taxonomic compostion in southeastern U.S. estuaries. Estuaries 28: 160-172. For some groups, Lewitus et al. refer to: Mackey, MD, DJ Mackey, HW Higgins, and SW Wright. 19996. CHEMTAX-A program for estimating class abundances from chemical markers: Application to HPLC measurements of phytoplankton. Mar. Ecol. Prog. Ser 144: 265-283. Anne Giblin

The Ecosystems Center Marine Biological Lab 7 MBL St Woods Hole MA 02543 USA

(508) 289 7488 agiblin@mbl.edu Lead PI Hap Garritt

The Ecosystems Center Marine Biological Lab 7 MBL St Woods Hole MA 02543 USA

(508) 289 7485 pie_im@mbl.edu Information Manager The Plum Island Ecosystems (PIE) LTER is an integrated research, education and outreach program whose goal is to develop a predictive understanding of the long-term response of watershed and estuarine ecosystems at the land-sea interface to changes in climate, land use and sea level. The principal study site is the Plum Island Sound estuary, its coupled Parker, Rowley and Ipswich River watersheds and the adjacent coastal ocean, the Gulf of Maine. The PIE LTER focuses on how several aspects of global change influence organic matter and inorganic nutrient biogeochemistry and estuarine foodwebs. The inputs of organic matter and nutrients from land, ocean and marshes interact with the external drivers (climate, land use, river discharge, sea level) to dictate the extent and degree of nutrient and organic matter processing and determine the spatial patterns of estuarine productivity and trophic structure. This material is based upon work supported by the National Science Foundation under Grants OCE-9726921, OCE-0423565. Any opinions, findings, conclusions, or recommendations expressed in the material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. The Plum Island Ecosystems (PIE) LTER site, is located in northeastern Massachusetts, 42.72 N, 70.85 W. The PIE LTER lies at the interface of a thinly soiled, formerly glaciated New England land mass and the highly productive Gulf of Maine. Three watersheds comprise the estuarine drainage basin: Parker (155 km2), Rowley (26 km2) and Ipswich (404 km2). The Ipswich River watershed is highly urbanized with Boston "bedroom" communities encroaching in the headwater region while the Parker is less urbanized and retains a higher proportion of forest. -71.2198 -70.7568 42.8276 42.4965 0 100 meter EST-PR-ChemTax.csv Phytoplankton identification using HPLC and Chem Taxonomy along transects in the Plum Island Sound estuary EST-PR-ChemTax.csv 1 \r\n column , http://ecosystems.mbl.edu/PIE/data/EST/data/EST-PR-ChemTax.csv Date Date date of sampling (dd-mmm-yyyy) dd-mmm-yyyy Site Site location sampled, either specific station or bounding box location sampled, either specific station or bounding box Latitude Latitude Latitude of sample location in NAD 83 geographic coordinates (decimal degrees) degree real Longitude Longitude Longitude of sample location in NAD 83 geographic coordinates (decimal degrees) degree real Distance Distance distance upstream from the mouth of the estuary kilometer real Sample Name Sample Name Water sample name for correspondence to other water chemistry Water sample name for correspondence to other water chemistry Subsample Name Subsample Name Chem tax specific subsample name Chem tax specific subsample name Fraction Fraction either whole water or < 20 um (size fraction 0.7 to 20 um) either whole water or < 20 um (size fraction 0.7 to 20 um) Volume Volume total volume of water filtered for analysis milliliter real Temp Temp temperature (oC) celsius real Salinity Salinity salinity (ppt) partPerThousand real Total Chla Total Chla Total chlorophyll a microgramPerLiter real Diatoms_CT1 Diatoms_CT1 Chlorophyll a concentration associated with diatoms microgramPerLiter real Dinoflagellates_CT1 Dinoflagellates_CT1 Chlorophyll a concentration associated with dinoflagellates microgramPerLiter real DiatomandDinoA _CT2 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 real DinoflagellatesB_CT2 DinoflagellatesB_CT2 Chlorophyll a concentration associated with dinoflagellate Group B (Lewitus et al, 2005; Dino Group B represented by Prorocentrum* and Amphidinium microgramPerLiter real Cyanobacteria_CT1 Cyanobacteria_CT1 Chlorophyll a concentration associated with cyanobacteria microgramPerLiter real Cyanobacteria_CT2 Cyanobacteria_CT2 Chlorophyll a concentration associated with cyanobacteria (Lewitus et al, 2005; represented by Anabaenopsis, Synechococcus, Limnothrix, and an undescribed filamentous strain) microgramPerLiter real Chlorophytes_CT1 Chlorophytes_CT1 Chlorophyll a concentration associated with chlorophytes microgramPerLiter real Chlorophytes_CT2 Chlorophytes_CT2 Chlorophyll a concentration associated with chlorophytes (Lewitus et al, 2005; represented by Chlorella, Ankistrodesmus) microgramPerLiter real PrasinophytesA_CT2 PrasinophytesA_CT2 Chlorophyll a concentration associated with Prasinophyte Group A (Lewitus et al, 2005; represented by Pyramimonas* and Nephroselmis) microgramPerLiter real PrasinophytesB_CT2 PrasinophytesB_CT2 Chlorophyll a concentration associated with Prasinophyte Group B (Lewitus et al, 2005; represented by Mackey et al 1996 Prasinophyceae Type 2: ) microgramPerLiter real Cryptophytes_CT1 Cryptophytes_CT1 Chlorophyll a concentration associated with cryptophytes microgramPerLiter real Cryptophytes_CT2 Cryptophytes_CT2 Chlorophyll a concentration associated with cryptophytes (Lewitus et al, 2005; represented by Cryptomonas*, Hemiselmis, Chroomonas, and Storeatula) microgramPerLiter real HaptophytesA_ChryosphytesA_DinoflagellatesC_CT2 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 real HaptophytesB_DinoflagellatesD_CT2 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 real ChrysophytesB_CT2 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 real RaphidophytesA_CT2 RaphidophytesA_CT2 Chlorophyll a concentration associated with Raphidophytes Group A (Lewitus et al, 2005; represented by Heterosigma akashiwo) microgramPerLiter real Euglenophytes_CT2 Euglenophytes_CT2 Chlorophyll a concentration associated with Euglenophytes (Lewitus et al, 2005; represented by Euglena* sp.) microgramPerLiter real ratio of two quantities as parts per thousand (1:1000) micrograms per liter