1992 Columbia River Estuary Turbidity Maximum Microbiology Data Sets

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1) Associated Metadata and Format of Data Files


Title:    METADATA FOR MICROBIOLOGY DATA SETS FROM PUMP CASTS
     COLUMBIA RIVER LMER PROJECT

Contact: John A. Baross
     School of Oceanography
     University of Washington
     Box 357940
     Seattle, WA  98195-7940  USA
     email: jbaross@u.washington.edu

Principle Investigators (Institution) and research area: 
     John Baross (Univ. of Washington School of Oceanography)
microbiology
     Byron Crump (Univ. of Washington School of Oceanography)
microbiology

Data Description:  Organic matter of terrestrial, riverine, and
marine origins are trapped by physical processes in estuarine
turbidity maxima (ETM).  It has been hypothesized that these
concentrations of organic material fuel an active microbial loop. 
Free-living bacteria and those associated with particles are
responsible for remineralization of organic matter and serve as
carbon sources for protozoa and zooplankton (Baross et al. 1994).

Spatial and Temporal Resolution: Pump cast sampling, and
associated CTD casts took place from a fixed vessel during one
28-35 day cruise per year in 1990, 1991, 1992, 1995, and 1996.
During 1997 and early 1998, samples were collected during 2-week
"seasonal" cruises in May, July, and October (1997) and February
to March (1998).  During 1999, sampling was conducted for 2 weeks
in June on the Columbia River and for 2 weeks in July on the
Fraser River in British Columbia, Canada.

Explanation of Code:
Format of code is: YYBSENN         
YY   first two digits indicate year
B    letter(s) indicates boundary location or tidal series as
follows: U=upstream (beyond salt wedge), D=downstream (below
estuarine turbidity maximum),N=neap tide, S=spring tide,
SN=spring-neap transition, E= ebb, F=flood, L=long time series,
YB=Young's Bay, CB=Cathlamet Bay
S    number of sample series at that location/tidal stage
E    event number (sequence) within that series (an 'E' or 'F'
may follow this number indicating and ebb or flood tide sampling
NN   two (or three) digits indicate CTD cast number that
corresponds to the pump cast
*    An asterisk after the code indicates CTD data taken from the
downcast immediately prior to the pump cast

Chemical measurements.
Suspended particulate mass (SPM) was determined by filtering the
material in a known volume of sample onto pre-weighed 0.45 ?m, 47
mm diameter polycarbonate filters.  Particulate organic carbon
(POC) and particulate nitrogen (PN) were determined on samples
filtered through precombusted GF/F filters, dried, and processed
with a Leeman Labs CE440 CHN analyzer calibrated with an
acetanilide standard.
SPM_BC    Suspended particulate mass                   mg l-1
POC_BC    Particulate organic carbon                   ug l-1
PN_BC     Particulate nitrogen                         ug l-1

Particle fractionation
Measurements on free-living microorganisms were made with water
samples filtered gently by floating a plastic 100-ml filter tower
(Millipore) fitted with a 3-um polycarbonate filter (Poretics) on
1 L of sample water in a 2 L beaker.  Large particles settled to
the bottom of the beaker and therefore did not clog the filter. 
Water flowed up through the filter into the filter tower as the
tower sank, and was drawn out of the tower with a pipette. 
Particle-attached prokaryotic cell concentrations and thymidine
incorporation rates were calculated by subtracting filtered water
measurements from unfiltered (whole) water measurements (Crump &
Baross 1996).
Thymidine incorporation rates
Thymidine incorporation rates were determined by measuring the
incorporation of methyl-tritiated thymidine (TdR., Fuhrman & Azam
1982) (20 nM final conc. at 64 Ci mmol-1) into the cold
trichloroacetic acid (TCA) insoluble fraction of macromolecules
in four 10 ml (1991 to 1995) or six 5 ml (1996 to 1999)
subsamples incubated with constant agitation at in situ
temperature.  Duplicate (or triplicate) incubations were
terminated at 0 and 60 minutes with 0.25 M NaOH (final conc.,
Zweifel et. al 1995).  TCA precipitated macromolecules were
washed twice with ice cold 5% TCA and twice with ice cold 80%
ethanol (Crump & Baross 1996, Crump et al. 1998).
W.TdR          Whole water thymidine incorporation rate     
          pmol l-1 h-1
ciW.TdR   95% confidence interval for W.TdR                 pmol
l-1 h-1
F.TdR          Free-living bacteria thymidine incorporation rate
          pmol l-1 h-1
ciF.TdR   95% confidence interval for F.TdR                 pmol
l-1 h-1
A.TdR          Particle-attached bacteria thymidine incorporation
rate pmol l-1 h-1
ciA.TdR   95% confidence interval for A.TdR                 pmol
l-1 h-1

Cell enumeration
Bacteria concentrations were determined from glutaraldehyde-
(1991 to 1992) or formaldehyde-fixed (1995 to 1999) (2% final
conc.) with direct counts using a Zeiss UEM epifluorescent
microscope (Hobbie et. al 1977) and DAPI stain (Porter & Feig
1980).  Cells were enumerated in 30 fields per filter.
W.cells   Whole water prokaryotic cell concentration        
     cells x 109 l-1
CiW.cells 95% confidence interval for W. cells              
     cells x 109 l-1
F.cells        Free-living bacteria prokaryotic cell
concentration       cells x 109 l-1
CiF.cells 95% confidence interval for F. cells              
     cells x 109 l-1
A.cells        Particle-attached prokaryotic cell concentration
          cells x 109 l-1
CiA.cells 95% confidence interval for A. cells              
     cells x 109 l-1


Bibliography

Baross JA, Crump B, and Simenstad CA (1994) Elevated 'microbial
loop' activities in the Columbia River estuarine turbidity
maximum. In: KR Dyer and RJ Orth, eds., Changes in fluxes in
estuaries: Implications from science to management (ECSA22/ERF,
Plymouth, September 1992). pp 459-464.  Olsen and Olsen,
Fredensborg, Denmark

Crump BC, Baross JA (1996) Particle-attached bacteria and
heterotrophic plankton in the Columbia River Estuary.  Mar Ecol
Prog Ser 138:265-273

Crump BC, Simenstad CA, Baross JA (1998) Dominance of
particle-attached bacteria in the Columbia River Estuary. Aquat
Microb Ecol 14:7-18

Fuhrman J, Azam F (1982) Thymidine incorporation as a measure of
heterotrophic bacterioplankton production in marine surface
waters: evaluation and field results.  Mar Biol 66:109

Hobbie JE, Daley RJ, Jasper S (1977) Use of nuclepore filters for
counting bacteria by fluorescence microscopy.  Appl Environ
Microbiol 33:1225

Porter KG, Feig YS (1980) The use of DAPI for identifying and
counting aquatic microflora. Limnol Oceanogr 25: 943-948

Zweifel UL, Wikner J, Hagstrom A, Lundberg E, Norrman B (1995)
Dynamics of dissolved carbon in a coastal ecosystem.  Limnol
Oceanogr 40:299-305


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2) Data Files
==================================================================================================================================

Code,Date,Time,SPM_BC,POC_BC,PN_BC,W.TdR,ciW.TdR,F.TdR,ciF.TdR,A.TdR,ciA.TdR,W.cells,ciW.cells,F.cells,ciF.cells,A.cells,ciA.cells
92SN1181,05/21/92,15:05,,,,55.50,13.86,,,,,,,,,,
92SN1185,05/21/92,17:00,,,,80.97,31.49,,,,,,,,,,
92SN1189,05/21/92,19:04,,,,54.14,96.55,,,,,,,,,,
92SN1193,05/21/92,21:03,,,,65.48,113.95,,,,,,,,,,
92SN1197,05/21/92,23:00,,,,,,,,,,,,,,,
92SN11101,05/22/92,1:03,,,,62.71,25.79,,,,,,,,,,
92SN11105,05/22/92,3:05,,,,53.15,14.16,,,,,,,,,,
92SN11109,05/22/92,5:03,,,,64.53,42.54,,,,,,,,,,
92SN11113,05/22/92,7:04,,,,68.61,47.41,,,,,,,,,,
92SN11117,05/22/92,9:07,,,,14.05,20.75,,,,,,,,,,
92SN11121,05/22/92,11:01,,,,13.35,6.66,,,,,,,,,,
92SN11125,05/22/92,13:01,,,,87.14,28.81,,,,,,,,,,
92SN11129,05/22/92,15:02,,,,99.69,65.68,,,,,,,,,,
92SN11133,05/22/92,17:02,,,,113.65,4.67,,,,,,,,,,
92SN11137,05/22/92,19:02,,,,97.40,59.16,,,,,,,,,,
92SN11141,05/22/92,21:03,,,,101.09,58.71,,,,,,,,,,
92SN11141,05/22/92,21:07,,,,72.02,17.23,,,,,,,,,,
92SN11141,05/22/92,21:10,,,,28.93,12.88,,,,,,,,,,
92SN11145,05/22/92,23:06,,,,73.58,51.13,,,,,,,,,,
92SN11149,05/23/92,1:03,,,,54.06,23.34,,,,,,,,,,
92SN11153,05/23/92,3:03,,,,76.57,7.84,,,,,,,,,,
92SN11157,05/23/92,5:03,,,,47.45,12.34,,,,,,,,,,
92SN11161,05/23/92,7:04,,,,36.26,29.62,,,,,,,,,,
92SN11165,05/23/92,9:03,,,,67.15,146.73,,,,,,,,,,
92SN11165,05/23/92,9:07,,,,18.21,35.20,,,,,,,,,,
92SN11165,05/23/92,0:09,,,,11.35,42.69,,,,,,,,,,
92SN11169,05/23/92,11:00,,,,49.77,24.03,,,,,,,,,,
92SN11169,05/23/92,11:04,,,,6.16,4.52,,,,,,,,,,
92SN11169,05/23/92,11:08,,,,9.86,8.75,,,,,,,,,,
92SN11173,05/23/92,13:03,,,,46.08,11.43,,,,,,,,,,
92SN11177,05/23/92,15:01,,,,15.87,32.14,,,,,,,,,,
92SN11181,05/23/92,17:02,,,,44.72,14.54,,,,,,,,,,
92SN11185,05/23/92,19:02,,,,24.47,6.87,,,,,,,,,,
92SN11189,05/23/92,21:02,,,,12.77,19.90,,,,,,,,,,
92SN11193,05/23/92,23:04,,,,80.60,44.65,,,,,,,,,,
92SN11197,05/24/92,1:03,,,,73.38,19.27,,,,,,,,,,
92SN11201,05/24/92,3:04,,,,65.12,18.17,,,,,,,,,,
92SN11205,05/24/92,5:03,,,,37.28,75.41,,,,,,,,,,
92SN11209,05/24/92,7:03,,,,40.24,287.98,,,,,,,,,,
92SN11213,05/24/92,9:05,,,,46.47,46.36,,,,,,,,,,
92SN11217,05/24/92,11:04,,,,88.55,20.25,,,,,,,,,,
92SN11221,05/24/92,12:59,,,,91.56,28.83,,,,,,,,,,
92SN11225,05/24/92,15:01,,,,85.50,31.83,,,,,,,,,,
92D1125,05/25/92,19:02,,,,9.42,21.34,,,,,,,,,,
92D1125,05/25/92,19:05,,,,9.85,8.71,,,,,,,,,,
92D1125,05/25/92,19:08,,,,12.22,6.14,,,,,,,,,,
92D1145,05/26/92,5:06,,,,70.19,55.28,,,,,,,,,,
92D1149,05/26/92,7:05,,,,1.92,3.28,,,,,,,,,,
92S13F09,05/30/92,10:42,,,,,,,,,,,,,,,
92S13F09,05/30/92,10:46,,,,,,,,,,,,,,,
92S13F09,05/30/92,10:46,,,,,,,,,,,,,,,
92S1401A,05/31/92,5:15,,,,,,,,,,,,,,,
92S1401B,05/31/92,5:20,,,,,,,,,,,,,,,
92S1405,05/31/92,6:04,,,,,,,,,,,,,,,
92S1409,05/31/92,7:02,,,,,,,,,,,,,,,
92S1413,05/31/92,7:13,,,,,,,,,,,,,,,
92S1417,05/31/92,9:02,,,,,,,,,,,,,,,
92S1421,05/31/92,10:01,,,,,,,,,,,,,,,
92S1425,05/31/92,11:02,,,,,,,,,,,,,,,
92S1429,05/31/92,12:02,,,,,,,,,,,,,,,
92S1433,05/31/92,13:01,,,,,,,,,,,,,,,
92S1437,05/31/92,14:01,,,,,,,,,,,,,,,
92S1441,05/31/92,15:02,,,,,,,,,,,,,,,
92S1445,05/31/92,16:02,,,,,,,,,,,,,,,
92S1449,05/31/92,17:02,,,,,,,,,,,,,,,
92S1453,05/31/92,18:03,,,,,,,,,,,,,,,
92S1457,05/31/92,19:02,,,,,,,,,,,,,,,
92S15F04,06/01/92,10:17,,,,,,,,,,,,,,,
92S15F04,06/01/92,10:17,,,,,,,,,,,,,,,
92S15F04,06/01/92,10:17,,,,,,,,,,,,,,,
92S15E05,06/01/92,16:44,,,,,,,,,,,,,,,
92S15E05,06/01/92,16:48,,,,,,,,,,,,,,,
92S15E05,06/01/92,16:46,,,,,,,,,,,,,,,
92N2119,06/05/92,9:31,,,,49.92,6.81,,,,,,,,,,
92N2119,06/05/92,9:33,,,,42.49,19.15,,,,,,,,,,
92N2119,06/05/92,9:34,,,,27.79,29.79,,,,,,,,,,
92N2121,06/05/92,10:01,,,,46.59,3.36,,,,,,,,,,
92N2121,06/05/92,10:03,,,,27.02,10.88,,,,,,,,,,
92N2121,06/05/92,10:04,,,,36.16,4.12,,,,,,,,,,
92N2229,06/06/92,12:01,,,,68.24,12.59,,,,,,,,,,
92N2229,06/06/92,12:03,,,,36.41,24.60,,,,,,,,,,
92N2229,06/06/92,12:04,,,,24.86,15.08,,,,,,,,,,
92N2231,06/06/92,12:32,,,,63.67,19.76,,,,,,,,,,
92N2231,06/06/92,12:38,,,,31.08,0.91,,,,,,,,,,
92N2231,06/06/92,12:39,,,,26.98,5.57,,,,,,,,,,
92N2306,06/07/92,14:00,,,,,,,,,,,,,,,
92N2306,06/07/92,14:04,,,,,,,,,,,,,,,
92N2306,06/07/92,14:06,,,,,,,,,,,,,,,
92N2308,06/07/92,15:02,,,,,,,,,,,,,,,
92N2308,06/07/92,15:04,,,,,,,,,,,,,,,
92N2308,06/07/92,15:08,,,,,,,,,,,,,,,
92N2312,06/07/92,16:13,,,,,,,,,,,,,,,
92N2312,06/07/92,16:16,,,,,,,,,,,,,,,
92N2312,06/07/92,16:19,,,,,,,,,,,,,,,
92N2529,06/09/92,19:03,,,,36.17,2.07,,,,,,,,,,
92N2529,06/09/92,19:06,,,,46.74,3.61,,,,,,,,,,
92N2529,06/09/92,19:08,,,,32.77,8.79,,,,,,,,,,
92N2533,06/09/92,21:02,,,,47.88,11.33,,,,,,,,,,
92N2533,06/09/92,21:05,,,,32.40,8.48,,,,,,,,,,
92N2533,06/09/92,21:07,,,,31.57,7.32,,,,,,,,,,
92U2113,06/12/92,8:03,,,,12.08,10.44,,,,,,,,,,
92U2113,06/12/92,8:06,,,,10.52,4.60,,,,,,,,,,
92U2113,06/12/92,8:08,,,,9.83,6.69,,,,,,,,,,
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