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Not even a Half-baked Talk. Murray Levine. The Importance of Baseline Samples in CMOP Research: Current Projects and Future Needs. What is the Baseline?. Baseline sample set (53 samples) Coastal lines NH, CR, LP (36 samples) Plume (12 samples) - PowerPoint PPT Presentation
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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 Saltgradient
What is the Baseline?
2
Cruises Campaigns20
07
2008
2010
2009
July
(18
& 1
4)
Apr
il (3
)
Aug
ust
(18
& 1
4)
Nov
embe
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)
Fa
ll (
3)
Fa
ll (
3)
Fa
ll (
3)
Sp
rin
g (
4)
Sp
rin
g (
4)
Sp
rin
g (
4)
Future cruises…
?4
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
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 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
8
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
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 ZuberSubmitted 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
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)
16
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)
17
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)
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/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)
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) 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)
20