1996 Columbia River Estuary Turbidity Maximum Microbiology Data Sets ---------------------------------------------------------------------- 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 ---------------------------------------------------------------------------------------------------------------------------------- 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 96S1101,07/09/1996,13:10,,,,19.94,3.03,0.92,4.63,19.02,7.66,,,,,, 96S1105,07/09/1996,14:59,,,,8.46,2.31,0.77,1.28,7.69,3.58,,,,,, 96S1109,07/09/1996,17:00,,,,81.51,12.34,10.40,16.48,71.12,28.83,,,,,, 96S1113,07/09/1996,19:04,,,,99.20,31.08,4.86,7.85,94.33,38.94,,,,,, 96S1117,07/09/1996,21:00,,,,48.22,5.82,2.75,12.36,45.47,18.18,,,,,, 96S1121,07/09/1996,23:08,,,,49.95,7.38,1.76,2.63,48.19,10.01,,,,,, 96S1125,07/10/1996,1:01,,,,30.22,16.54,0.15,0.35,30.06,16.89,,,,,, 96S1129,07/10/1996,3:01,,,,13.04,1.68,0.26,0.54,12.78,2.22,,,,,, 96S1133,07/10/1996,5:04,,,,12.55,2.75,0.50,0.45,12.04,3.20,,,,,, 96S1137,07/10/1996,7:04,,,,15.87,1.48,0.36,0.51,15.51,1.99,,,,,, 96S1141,07/10/1996,9:01,,,,71.80,15.59,2.22,0.96,69.58,16.55,,,,,, 96S1145,07/10/1996,10:59,,,,84.74,16.45,1.36,0.42,83.38,16.87,,,,,, 96S1149,07/10/1996,13:02,,,,65.03,9.41,0.43,0.33,64.60,9.74,,,,,, 96S1153,07/10/1996,15:03,,,,18.74,5.07,0.93,0.63,17.81,5.70,,,,,, 96S1157,07/10/1996,17:03,,,,35.96,11.25,10.01,7.70,25.95,18.95,,,,,, 96S1158,07/10/1996,18:03,,,,65.44,22.25,7.23,5.18,58.22,27.44,,,,,, 96S1161,07/10/1996,18:54,,,,,,,,,,,,,,, 96U1117,07/18/1996,7:04,,,,16.60,3.59,0.79,4.09,15.82,7.68,,,,,, 96N1101,07/19/1996,5:01,,,,113.04,3.48,86.92,15.04,26.12,18.52,,,,,, 96N1105,07/19/1996,7:01,,,,75.40,2.18,0.12,1.72,75.28,3.90,,,,,, 96N1109,07/19/1996,9:09,,,,15.05,3.73,1.57,3.98,13.47,7.71,,,,,, 96N1113,07/19/1996,11:07,,,,12.58,1.52,0.78,0.93,11.80,2.46,,,,,, 96N1117,07/19/1996,13:00,,,,30.24,5.58,1.35,1.02,28.89,6.60,,,,,, 96N1121,07/19/1996,15:09,,,,53.19,17.23,4.45,1.81,48.74,19.04,,,,,, 96N1125,07/19/1996,17:05,,,,110.73,20.44,9.44,5.13,101.29,25.57,,,,,, 96N1129,07/19/1996,19:04,,,,90.75,19.40,13.17,19.34,77.58,38.74,,,,,, 96N1133,07/19/1996,21:07,,,,16.10,3.14,0.39,0.83,15.71,3.97,,,,,, 96N1137,07/19/1996,23:07,,,,12.41,2.16,1.85,1.07,10.56,3.23,,,,,, 96N1141,07/20/1996,1:01,,,,119.25,26.37,37.29,30.60,81.97,56.97,,,,,, 96N1145,07/20/1996,3:04,,,,92.01,5.46,25.52,13.44,66.48,18.91,,,,,, 96N1149,07/20/1996,5:09,,,,90.19,32.31,21.44,8.69,68.75,41.00,,,,,, 96N1153,07/20/1996,7:04,,,,89.04,11.57,23.93,8.46,65.11,20.03,,,,,, 96N1157,07/20/1996,9:03,,,,21.92,6.16,3.48,0.83,18.45,6.99,,,,,, 96N1161,07/20/1996,11:01,,,,14.75,2.71,1.07,0.46,13.69,3.17,,,,,, 96V1101,07/25/1996,17:32,183,,,73.16,15.93,,,,,,,,,, 96V1103,07/25/1996,17:39,88,,,48.91,26.30,,,,,,,,,, 96V1105,07/25/1996,17:41,108,,,74.69,28.24,,,,,,,,,, 96V1107,07/25/1996,17:45,60,,,57.93,9.71,,,,,,,,,, 96V1109,07/25/1996,17:47,15,,,46.80,6.80,,,,,,,,,, 96V1201,07/25/1996,17:55,138,,,83.41,17.31,,,,,,,,,, 96V1203,07/25/1996,17:57,110,,,90.43,18.81,,,,,,,,,, 96V1205,07/25/1996,18:04,164,,,110.72,28.04,,,,,,,,,, 96V1207,07/25/1996,18:07,71,,,60.80,25.56,,,,,,,,,, 96V1209,07/25/1996,18:10,34,,,49.53,14.73,,,,,,,,,, 96V1301,07/25/1996,18:17,92,,,39.12,10.99,,,,,,,,,, 96V1303,07/25/1996,18:20,84,,,26.48,5.23,,,,,,,,,, 96V1305,07/25/1996,18:23,71,,,30.10,7.93,,,,,,,,,, 96V1307,07/25/1996,18:26,54,,,31.01,11.93,,,,,,,,,, 96V1309,07/25/1996,18:29,42,,,32.27,7.68,,,,,,,,,, 96V1401,07/25/1996,18:34,65,,,29.66,2.24,,,,,,,,,, 96V1403,07/25/1996,18:36,46,,,23.35,4.69,,,,,,,,,, 96V1405,07/25/1996,18:39,40,,,24.66,3.17,,,,,,,,,, 96V1407,07/25/1996,18:41,29,,,19.95,5.44,,,,,,,,,, 96V1409,07/25/1996,18:44,24,,,17.77,3.50,,,,,,,,,, 96V1501,07/25/1996,18:51,32,,,21.36,7.36,,,,,,,,,, 96V1503,07/25/1996,18:54,29,,,14.57,7.41,,,,,,,,,, 96V1505,07/25/1996,18:56,24,,,17.44,7.65,,,,,,,,,, 96V1507,07/25/1996,18:59,28,,,19.46,10.55,,,,,,,,,, 96V1509,07/25/1996,19:02,24,,,20.22,6.75,,,,,,,,,,