Not even a Half-baked Talk Murray Levine The Importance of Baseline Samples in CMOP Research: Current Projects and Future Needs 1

Baseline sample set (53 samples) Coastal lines NH, CR, LP (36 samples) Plume (12 samples) Estuary salinity gradient (5 samples) La Push line Newport Hydroline Columbia River line Plume Salt gradient What is the Baseline? 2

Cruises Campaigns July (18 & 14) April (3) August (18 & 14) November (18) April (8)May/June (10) September (18) May (18 & 14) Aug./Sept. (17 & 14) Apr (4) May/June (14) Jul/Aug (?)Oct (3) 2011 Apr (4) Modified from original by Byron Crump Past cruises… 3

Fall (3) Spring (4) Future cruises… ? 4

What observations (samples) needed for baseline? CTD – with DO, N, trans, Chl fluor Water samples at several depths: 5

Issues for discussion: Interrupt time series after 3 years? Minimal sampling to keep series going? Useful? Given our experience… new ideas, constraints, opportunities (e.g., Joint Genome Institute proposal) 6

One way to address the question of baseline relevance… look at current research as measured by manuscripts in preparation 7

1.Seasonal variation in protist assemblages of the Columbia River coastal margin assessed using morphology and 18S rRNA gene sequences Peter Kahn, Lydie Herfort, Tawnya D. Peterson, Lee Ann McCue, Peter Zuber 2. Oxygen Depletion: Two-Way Shelf-Estuary Linkages In The Coastal Margin Of A Large River Antonio Baptista, Charles Seaton 3. Myrionecta rubra bloom initiation in the Columbia River estuary Lydie Herfort, Tawnya Peterson, Victoria Campbell, Sheedra Futrell and Peter Zuber Submitted to Estuarine Coastal and Shelf Science 4. Study of bloom formation and retention of Myrionecta rubra in the Columbia River estuary using a Lagrangian modeling approach Scott Durski, Yvette Spitz, Antonio Baptista, Joe Cho 8

5. Dissolved Methane in Estuaries and the Intertidal Bellow Effect Fred Prahl, Tawnya Peterson, Joe Needoba 6. River nitrogen loading to the Oregon coastal zone Joseph Needoba, Andrew Barnard 7. Myrionecta rubra bloom vertical and horizontal dynamics in the Columbia River estuary Lydie Herfort, Curtis Roegner, Tawnya Peterson, P Zuber, A Baptista 8. Myrionecta rubra red tides relationship to the Columbia River estuary biogeochemistry Lydie Herfort, Tawnya Peterson, Fred Prahl, Peter Zuber 9

9. Remote Sensing of Salinity Intrusions in a Marine Estuary Thomas B. Sanford 10. Lagrangian observations in CR Plume: Dye and Drifter studies Murray Levine, Yun Jung, Mike Kosro 11. Biogeochemical Exchange between the Columbia River Estuary and its Adjacent Continental Shelf Fred Prahl, Burke Hales 12. Seasonal Variation in the Dynamics of Willamette River Dissolved Methane Concentrations Sara E. Anthony, Fredrick G. Prahl 10

13. Ubiquitous dissolved inorganic carbon assimilation by marine heterotrophic bacteria in the Pacific Northwest coastal ocean as determined by DNA-based stable isotope probing Suzanne DeLorenzo, Bradley Tebo, S Brauer, Chelsea Edgmont, Lydie Herfort, P Zuber 14. AUV based observations of the Columbia River ETM Craig McNeil, Andrey Shcherbina, Trina Litchendorf 15. Development of a microarray-based, high resolution fingerprinting analysis of the diatom genus Pseudo-nitzschia (Bacillariophyceae) for mapping of species/strain distribution in Oregon and Washington coastal waters Mariya Smit, Holly Simon 16. Distribution of the diatom genus Pseudo-nitzschia (Bacillariophyceae) ribotypes in the northeastern Pacific Ocean using DNA microarray analysis Michelle Maier, Tawnya Peterson 11

17. Three regions within the northern California Current system Stephen Pierce, Murray Levine 18. Short-term variability in bacterioplankton community composition and gene expression in the Columbia River plume and coastal ocean Byron Crump 19. A classification scheme for the Columbia River plume with relevance for biological production Tawnya Peterson, Murray Levine, Caroline Fortunato, Byron Crump 20. Protist 18S rRNA gene sequence analysis reveals multiple sources of organic matter contributing to turbidity maxima of the Columbia River estuary Lydie Herfort, Tawnya D. Peterson, Lee Ann McCue, and Peter Zuber Submitted to Marine Ecology Progress Series 12

21. Spatial variability of bacterioplankton communities overwhelms seasonal patterns across a river to ocean gradient. Fortunato CS, Herfort L, Zuber P, Baptista A, and Crump BC 13

Moving forward… Clarify definition of baseline stations and observations (sampling) In-depth discussions with interested investigators (July) RIG discussions 14

15 fini

Table 1. Biological and Chemical analyses for water samples Measurements Coast al Lines Plume Sample s Estuary Sample s Abbreviation description NH4XXXAmmonia SRPXXXInorganic Dissolved P NO3+NO2XXXNitrate+Nitrite, dissolved silica DOCXXXDissolved Organic Carbon TDN, TDPXXXDissolved Nitrogen, Dissolved Phosphorous SPMXSuspended Particulate Matter ChlAXXXChlorophyll a POC, PONXXXCarbon, Hydrogen, Nitrogen HPLC pigmentsXXX BPXXXBacterial production RespirationXOxygen Respiration rate Prokaryotic cell abundance XXXGluteraldehyde fixed samples Flow CytometryXXXParaformaldehyde fixed samples FISH samplesXXXParaformaldehyde fixed samples DNA (DEB)XXXDNA on sterivex filter, fixed with DEB* DNA-FL (DEB)XDNA of free-living bacteria (<3 um) on sterivex filter, fixed with DEB* DNA (RNAlater)XXXDNA on sterivex filter, fixed with RNAlater DNA-FL (RNAlater)XDNA of free-living bacteria (<3 um) on sterivex filter, fixed with RNAlater RNAXXXRNA on sterivex filter, fixed with RNAlater RNA-FLXRNA of free-living bacteria (<3 um) on sterivex filter, fixed with RNAlater August 2007 Wecoma (CS: Crump) 16

November 2007 Wecoma (CS: Herfort) 17

April 2008 Wecoma (CS: Herfort) 18

II. Water sample processing Filling up bottles from CTD for biology team (Rohde, Peterson) Dissolved and particulate chemistry (nutrients and organic matter) (Smit, Malpezzi) 1.Nitrate plus nitrite, nitrite, ammonium, phosphate, silicic acid 2.Dissolved organic carbon/nitrogen 3.Total suspended solids 4.Particulate organic carbon/nitrogen 5.Fixed samples Chlorophyll and other phytoplankton pigments (Rhode/Peterson) DNA and RNA samples (Selby) Bacterial Production measurements in radioisotope van (Malpezzi) Primary production (Peterson/Rohde) Water filtration for membrane lipid samples (Huguet) May-June 2008 (CS: Peterson) 19

2. Water sampling Most water samples will be subsampled for: DNA (OHSU) 1 sterivex, 4 ml RNAlater, Cha‐seal, male luer plug (Zuber) RNA (OHSU) 1 sterivex, 4 ml RNAlater, Cha‐seal, male luer plug (Zuber) DNA (UMCES) 2 sterivex, 2 ml DNA Extraction Buffer, Cha‐seal, male luer plug (Crump) POC/N 2 ashed 25mm GF/F filters (Crump) SPM 2 pre‐weighed GF/F filters, labeled petri plate (Crump) Nutrients 1 nutrient bottle; Fill to shoulder (Needoba) NH ml plastic centrifuge tube, measured on board if possible (Needoba) TDN/TDP 1 pre‐extracted 30 ml bottle; add EXACTLY 20 ml of sample (provided by UMCES Horn Point Laboratory analytical services; Crump) DOC 1 polypropylene 20ml scintillation vial; fill to shoulder (Crump) CDOM 60 mL combusted amber glass bottle; fill to shoulder and refrigerate (Needoba) Flow cytometry 1 5ml cryo tube, 0.1ml paraformaldehyde (provided by ?) ChlA/phaeo 1 25mm GF/F filter, 2ml cryovial (Needoba) Cell counts 1 glass 7ml scint vial, 0.25ml 25% pre‐filtered glutaraldehyde (Crump) Phyto counts 100 mL French squares preserved with Lugols iodine (Peterson) FlowCAM 50 mL corning centrifuge tubes (Peterson) BP Bacterial production rate measured as 3 H‐leucine incorporation rate Select water samples will be subsampled for: PP Primary Production rate (Kahn) CH4 Methane concentration (Prahl) CH4 uptake Methane uptake rate (Peterson, Prahl) Nutrient expts. Water incubated with nitrate, silicate, or nitrate+silicate amendments (Bender & Durkin) DNA/RNA (UW) DNA/RNA (Bender & Durkin) FC flow cytometry samples (Bender & Durkin) Lugols Lugol’s fixed seawater (Bender & Durkin; Maier & Peterson) PDMPO silica staining (Bender & Durkin) Fv/Fm Photosynthetic parameters using a PhytoPAM fluorometer (Bender & Durkin; Blakely) BioSi Biogenic Silica (Bender & Durkin) Urea Urea concentration (Bender & Durkin) Alkaline phosphatase Blakely Domoic acid McKibben, Maier August 2009 New Horizon (CS: Peterson) 20