Viral and bacterial counts from filtered water, stained with SYBR Green and counted using epifluorescent microscopy, from samples collected on R/V Knorr cruise KN210-04 in the Western Atlantic Ocean in 2013 (Deep Atlantic DOM project)

Data Type: Cruise Results
Version: 12 Aug 2014
Version Date: 2014-08-12

» Dissolved Organic Matter Composition in the Deep Atlantic Ocean (Deep Atlantic DOM)

» Ocean Carbon and Biogeochemistry (OCB)
Hewson, IanCornell University (Cornell)Principal Investigator, Contact
Eggleston, ErinCornell University (Cornell)Contact
Rauch, ShannonWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager


Spatial Extent: N:9.703869 E:-23.999036 S:-38.0026 W:-55.304343
Temporal Extent: 2013-03-26 - 2013-05-06

Dataset Description

Viral and bacterial counts from filtered water, stained with SYBR Green and counted using epifluorescent microscopy. Duplicates were collected at each depth during the KN210-04 cruise.

Acquisition Description

Samples for viral and bacterial counts were collected in 50 mL Falcon tubes, held at 4 degrees C until processing, and processed within two hours. SYBR slides were prepared according to Noble and Fuhruman (Noble and Fuhrman, 1998). Briefly, samples were fixed in v/v 2% formalin and then filtered over a 25 mm 0.02 um anodisc filter (Whatman). Varying volumes were fixed depending on the depth of sample collection (surface and DCM: 3 ml; mesopelagic: 10 ml; AAIW, NADW and AABW: 20 ml). The filter was stained with 2.5x10-3 SYBR Green 1 dilution in nuclease free water, and mounted on a slide with antifade solution (0.1% p-phenylenediamine in 1:1 PBS:Glycerol) and stored at -20 degrees C until enumeration. Under epifluorescence microscopy 10 fields of view were selected at random and >200 viruses and >200 bacteria were counted. Calculations for total number or viruses and bacteria in a sample account for volume filtered, magnification and size of the grid included while counting.

Samples from station 1 and 2 were fixed with the wrong concentration of antifade and therefore faded before accurate counts could be made.

Noble, R. T., and Fuhrman, J. A. (1998). Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat Microb Ecol 14, 113-118. doi:10.3354/ame014113

Processing Description

Any missing values and/or depths indicate that the slide was not countable, either due to fading or cracked filters in transit.

BCO-DMO Processing Notes:
- Parameter names were modified to conform with BCO-DMO naming conventions.
- lat_start and lon_start were added by joining the data to the event log and matching on the unique event number.
- Replaced missing values with 'nd' to indicate 'no data'.
- 22 Nov 2017: made dataset public (was previously restricted).

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castConsecutive cast number for the instrument. dimensionless
stationIdentification number of the sampling station. dimensionless
date_start_utcDate (UTC) given as 4-digit year - 2-digit month - 2-digit day. YYYYmmdd
time_start_utcTime (UTC) given as hour - minute. HHMM
event_startThe event number from the ELOG maintained during the cruise. dimensionless
lat_startLatitude at the time the event started (from the cruise event log). decimal degrees
lon_startLongitude at the time the event started (from the cruise event log). decimal degrees
niskinNiskin bottle number. dimensionless
depthDepth. meters (m)
pressPressure. decibars (db)
lab_stickerLab identification number. dimensionless
vir_abundViral abundance. viral abundance per milliliter (per mL)
vir_abund_SEStandard error associated with viral abundance. viral abundance per milliliter (per mL)
bact_abundBacterial abundance. bacterial abundance per milliliter (per mL)
bact_abund_SEStandard error associated with bacterial abundance. bacterial abundance per milliliter (per mL)
VBRVirus to bacteria ratio (virus:bacteria). dimensionless

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Dataset-specific Instrument Name
Epifluorescent microscope
Generic Instrument Name
Fluorescence Microscope
Generic Instrument Description
Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.

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R/V Knorr
Start Date
End Date
Western Atlantic cruise started at Montevideo, Uruguay and ended at Bridgetown, Barbados. Science Objectives: 1. Characterize deep ocean dissolved organic matter in water masses of western Atlantic Ocean. 2. Characterize microbial community at selected stations and at selected depths. 3. Characterize metabolic capabilities of surface, mesopelagic and bathypelagic microbial consortia vis-a-vis the degradation of organic matter from each zone. 4. Examine metabolic and phylogenetic links between microbes in different marine zones (surface, meso-pelagic and bathypelagic depths). Science Activities: 1. Collection of discrete water samples by Niskin-bottles. 2. Collection of microbial communities from these water samples, by in-situ pumping, or by net-traps and net-tows. 3. Incubation experiments in lab and on deck. 4. Underway mass spectrometry and flow cytometry, from seawater intake. More information is available from the WHOI Cruise Planning Synopsis. Additional cruise information and original data are available from the NSF R2R Data Catalog.

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Project Information

Dissolved Organic Matter Composition in the Deep Atlantic Ocean (Deep Atlantic DOM)

Coverage: Western Atlantic Ocean

Transformations of dissolved organic matter (DOM) in the deep ocean have profound impacts on the global carbon cycle due to the sequestration of carbon dioxide (CO2) away from the atmosphere. Although research has been conducted on the high molecular weight component of this material, the same cannot be said for low molecular weight DOM because the needed analytical techniques have not been available to determine its composition and reactivity.

In recent years, a research team at Woods Hole Oceanographic Institution has acquired the necessary analytical capability. As such, in this project, they will carry out the first systematic survey of deep ocean DOM in the western Atlantic Ocean to characterize the low molecular weight fraction of DOM in southward flowing North Atlantic Deep Water (NADW), northward flowing Antarctic Bottom Water (AABW), and Antarctic Intermediate Water (AAIW). Using ultrahigh resolution mass spectrometry and multi-stage fragmentation coupled to liquid chromatography, the scientists will determine the spatial variability in the composition of DOM along the flow path of the water masses, as well as assess the source water, transport, and surface processes that contribute to temporal changes in DOM composition. These results will be augmented with structural elucidation and quantitative assays of unique marker compounds for each water mass. Results will provide important insights into the biogeochemical reactions that govern DOM dynamics in the deep ocean.

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Program Information

Ocean Carbon and Biogeochemistry (OCB)

Coverage: Global

The Ocean Carbon and Biogeochemistry (OCB) program focuses on the ocean's role as a component of the global Earth system, bringing together research in geochemistry, ocean physics, and ecology that inform on and advance our understanding of ocean biogeochemistry. The overall program goals are to promote, plan, and coordinate collaborative, multidisciplinary research opportunities within the U.S. research community and with international partners. Important OCB-related activities currently include: the Ocean Carbon and Climate Change (OCCC) and the North American Carbon Program (NACP); U.S. contributions to IMBER, SOLAS, CARBOOCEAN; and numerous U.S. single-investigator and medium-size research projects funded by U.S. federal agencies including NASA, NOAA, and NSF.

The scientific mission of OCB is to study the evolving role of the ocean in the global carbon cycle, in the face of environmental variability and change through studies of marine biogeochemical cycles and associated ecosystems.

The overarching OCB science themes include improved understanding and prediction of: 1) oceanic uptake and release of atmospheric CO2 and other greenhouse gases and 2) environmental sensitivities of biogeochemical cycles, marine ecosystems, and interactions between the two.

The OCB Research Priorities (updated January 2012) include: ocean acidification; terrestrial/coastal carbon fluxes and exchanges; climate sensitivities of and change in ecosystem structure and associated impacts on biogeochemical cycles; mesopelagic ecological and biogeochemical interactions; benthic-pelagic feedbacks on biogeochemical cycles; ocean carbon uptake and storage; and expanding low-oxygen conditions in the coastal and open oceans.

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Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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