Not even a Half-baked Talk

Murray Levine

The Importance of Baseline Samples in CMOP Research:

Current Projects and Future Needs

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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 Saltgradient

What is the Baseline?

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Cruises Campaigns20

07

2008

2010

2009

July

(18

& 1

4)

Apr

il (3

)

Aug

ust

(18

& 1

4)

Nov

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r (1

8)

Apr

il (8

)

May

/Jun

e (1

0)

Sep

tem

ber

(18)

May

(18

& 1

4)

Aug

./S

ept.

(17

& 1

4)

Apr

(4)

May

/Jun

e (1

4)Ju

l/Aug

(?)

Oct

(3)

2011

Apr

(4)

Modified from original by Byron Crump

Past cruises…

3

2012

2013

2014

2015

Fa

ll (

3)

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3)

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3)

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3)

Sp

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g (

4)

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4)

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4)

Future cruises…

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What observations (samples) needed for baseline?

CTD – with DO, N, trans, Chl fluor

Water samples at several depths:

MeasurementsCoastal Lines

Plume Samples

Estuary Samples

River Samples Abbreviation description

NH4 X X X X AmmoniaSRP X X X X Inorganic Dissolved PNO3+NO2 X X X X Nitrate+Nitrite, dissolved silicaDOC X X X X Dissolved Organic CarbonTDN, TDP X X X X Dissolved Nitrogen, Dissolved PhosphorousSPM X X Suspended Particulate MatterChlA X X X X Chlorophyll aPOC, PON X X X X Carbon, Hydrogen, NitrogenHPLC pigments X X X X

BP X X X X Bacterial productionProkaryotic cell abundance X X X X Gluteraldehyde fixed samplesFlow Cytometry X X X X Paraformaldehyde fixed samplesFISH samples X X X X Formalin fixed samplesDNA (DEB) X X X X DNA on sterivex filter, fixed with DEBDNA/RNA (RNAlater) X X X X DNA/RNA on sterivex filter, fixed with RNAlater

Table 1. Biological and Chemical analyses for water samples

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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)

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One way to address the question of baseline relevance…

look at current research as measured by manuscripts in preparation

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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 estuaryLydie 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

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5. Dissolved Methane in Estuaries and the Intertidal Bellow EffectFred 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

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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

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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

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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 ZuberSubmitted to Marine Ecology Progress Series

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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

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Moving forward…

• Clarify definition of baseline stations and observations (sampling)

• In-depth discussions with interested investigators (July)

• RIG discussions

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fini

Table 1. Biological and Chemical analyses for water samples

Measurements

Coastal

Lines

Plume Sample

s

Estuary Sample

s Abbreviation descriptionNH4 X X X AmmoniaSRP X X X Inorganic Dissolved PNO3+NO2 X X X Nitrate+Nitrite, dissolved silicaDOC X X X Dissolved Organic CarbonTDN, TDP X X X Dissolved Nitrogen, Dissolved PhosphorousSPM X Suspended Particulate MatterChlA X X X Chlorophyll aPOC, PON X X X Carbon, Hydrogen, NitrogenHPLC pigments X X XBP X X X Bacterial productionRespiration X Oxygen Respiration rateProkaryotic cell abundance

X X X Gluteraldehyde fixed samples

Flow Cytometry X X X Paraformaldehyde fixed samplesFISH samples X X X Paraformaldehyde fixed samplesDNA (DEB) X X X DNA on sterivex filter, fixed with DEB*DNA-FL (DEB) X DNA of free-living bacteria (<3 um) on sterivex filter, fixed with

DEB*DNA (RNAlater) X X X DNA on sterivex filter, fixed with RNAlaterDNA-FL (RNAlater) X DNA of free-living bacteria (<3 um) on sterivex filter, fixed with

RNAlaterRNA X X X RNA on sterivex filter, fixed with RNAlaterRNA-FL X RNA of free-living bacteria (<3 um) on sterivex filter, fixed with

RNAlater

August 2007 Wecoma (CS: Crump)

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MeasurementsCoastal Lines

Plume Samples

Estuary Samples

River Samples Abbreviation description

NH4 X X X X AmmoniaSRP X X X X Inorganic Dissolved PNO3+NO2 X X X X Nitrate+Nitrite, dissolved silicaDOC X X X X Dissolved Organic CarbonTDN, TDP X X X X Dissolved Nitrogen, Dissolved PhosphorousSPM X X Suspended Particulate MatterChlA X X X X Chlorophyll aPOC, PON X X X X Carbon, Hydrogen, NitrogenHPLC pigments X X X X

BP X X X X Bacterial productionProkaryotic cell abundance X X X X Gluteraldehyde fixed samplesFlow Cytometry X X X X Paraformaldehyde fixed samplesFISH samples X X X X Formalin fixed samplesDNA (DEB) X X X X DNA on sterivex filter, fixed with DEBDNA/RNA (RNAlater) X X X X DNA/RNA on sterivex filter, fixed with RNAlater

Table 1. Biological and Chemical analyses for water samples

November 2007 Wecoma (CS: Herfort)

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Samples collected/measured

Nutrient (ammionium, nitrate, nitrite, silicate, phosphorus)Dissoved Organic CarbonDissolved Nitrogen and PhosphorusSuspended Particulate MatterChlorophyll aHPLC pigmentFlow cytometryBacterial ProductionProkaryotic AbundanceFluorescence In Situ HybridizationNucleic Acids (DNA/RNA)Primary Production (ammonium and nitrate addition)UreaPhytoplankton AbundancesYessotoxin

April 2008 Wecoma (CS: Herfort)

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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/nitrogen5.Fixed samples

1.Chlorophyll and other phytoplankton pigments (Rhode/Peterson)2.DNA and RNA samples (Selby)3.Bacterial Production measurements in radioisotope van (Malpezzi)4.Primary production (Peterson/Rohde)5.Water filtration for membrane lipid samples (Huguet)

May-June 2008 (CS: Peterson)

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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) NH4+ 1 50 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 3H 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)

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