Bacterial cell counts during CDOM monoculture experiment

Website: https://www.bco-dmo.org/dataset/748415
Data Type: experimental
Version: 1
Version Date: 2018-10-17

Project
» Collaborative Research: Planktonic Sources of Chromophoric Dissolved Organic Matter in Seawater (PlankDOM)
ContributorsAffiliationRole
Ziervogel, KaiUniversity of New Hampshire (UNH)Principal Investigator
Copley, NancyWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Abstract
This dataset is from a laboratory experiment. Four phytoplankton cultures and their associated bacterial communities were incubated in replicate roller bottles (1.9 L) over 3-6 weeks under laboratory conditions. Bacterial dynamics in the culture bottles were measured and correlated with geochemical parameters to determine the role of bacterial activities on the formation of CDOM in the cultures (Kinsey et al., 2018, see below). The data include bacterial cell counts during CDOM monoculture experiment. The phytoplankton cultures were Skeletonema sp., Leptocylindrus sp., Phaeocystis sp. and Coscinodiscus sp. Growth stages were initial, exponential, stationary, and degradation.


Coverage

Temporal Extent: 2016-08 - 2017-03

Dataset Description

This dataset is from a laboratory experiment. Four phytoplankton cultures and their associated bacterial communities were incubated in replicate roller bottles (1.9 L) over 3-6 weeks under laboratory conditions. Bacterial dynamics in the culture bottles were measured and correlated with geochemical parameters to determine the role of bacterial activities on the formation of CDOM in the cultures (Kinsey et al., 2018, see below).

The data include bacterial cell counts during CDOM monoculture experiment. The phytoplankton cultures were Skeletonema sp., Leptocylindrus sp., Phaeocystis sp. and Coscinodiscus sp. Growth stages were initial, exponential, stationary, and degradation.


Acquisition Description

Bacterial cells were enumerated by flow cytometry. At each sampling point 1 mL of experimental or control water was fixed with 0.1% glutaraldehyde (final concentration) for 10 min at room temperature in the dark, and stored frozen at -80 °C. Prior to analysis, thawed samples were pipetted through a cell strainer (Flowmi, 70 µm porosity) and stained with SYBR Green I for 15 min on ice in the dark. Counts were performed with a FACSCalibur flow cytometer (Becton-Dickson) using fluorescent microspheres (Molecular Probes) of 1 µm in diameter as internal size standard. Cells were enumerated according to their right angle scatter and green fluorescence using the FloJo 7.6.1 software.


Processing Description

BCO-DMO Processing Notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- repeated data in 'taxa' and 'time_point_day' columns to create a flat file


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Related Publications

Kinsey, J. D., Corradino, G., Ziervogel, K., Schnetzer, A., & Osburn, C. L. (2018). Formation of Chromophoric Dissolved Organic Matter by Bacterial Degradation of Phytoplankton-Derived Aggregates. Frontiers in Marine Science, 4. doi:10.3389/fmars.2017.00430. Table 3.
Results

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Parameters

ParameterDescriptionUnits
taxonphytoplankton unitless
time_point_daygrowth phase (initial/exponential/stationary/degradation) and the number of days since the start of the experiment days
time_starttime at start of experiment unitless
time_endtime at end of experiment unitless
cell_countbacterial cell count as determined by flow cytometry cells
flow_rateflow rate of the sample microliters/minute
time_elapsed_minflow count duration minutes
volumevolume of sample microliters
concentration_uLbacterial cell concentration cells/microliter
concentration_mLbacterial cell concentration cells/milliliter


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Instruments

Dataset-specific Instrument Name
FACSCalibur flow cytometer (Becton-Dickson)
Generic Instrument Name
Flow Cytometer
Dataset-specific Description
Used to make cell counts.
Generic Instrument Description
Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells. (from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)


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Project Information

Collaborative Research: Planktonic Sources of Chromophoric Dissolved Organic Matter in Seawater (PlankDOM)

Coverage: Northern Atlantic Ocean, 34.65 N, 69.63 W


NSF abstract:

Chromophoric dissolved organic matter (CDOM) is a small but important fraction of the marine carbon pool that interacts with solar radiation and thus affects many photochemical and biological processes in the ocean. Despite its importance, the chemical basis for the formation of oceanic CDOM remains unclear. CDOM may be formed from two possible sources: 1) heterotrophic bacterial transformations of primary productivity (plankton-derived), or 2) terrestrially-derived. This project will examine the role of phytoplankton as a source of CDOM in the ocean by utilizing a powerful, new technique to measure particulate organic matter absorbance and fluorescence, discrete chemical measurements of probable precursors to planktonic CDOM, and enzymatic assays. Results of this research will provide new insights into the origin and production of planktonic CDOM and its transformation by heterotrophic bacteria. This research on CDOM will be shared broadly through a module at a North Carolina Aquarium, and streaming live feeds of shipboard activities to elementary school classrooms.

Terrestrial and oceanic dissolved organic matter (DOM) differ in their chemical composition. Laboratory and open-ocean observations suggest that bacterial transformation of phytoplankton DOM produces humic-like CDOM signals that are visually similar to those in terrestrial CDOM. However, prior studies of oceanic CDOM using absorbance and fluorescence fit an electronic interaction (EI) model of intramolecular charge transfer (CT) reactions between donor and acceptor molecules common to partially-oxidized terrestrial molecules found in humic substances. This project will test the hypothesis that phytoplankton and bacteria provide a source of donors and acceptors that are microbially-transformed and linked, enabling CT contacts between them and creating oceanic CDOM. To address this, researchers will systematically study phytoplankton growth, including marine snow formation. A new technique for measuring base-extracted POM (BEPOM) absorbance and fluorescence will be used to incorporate planktonic CDOM results into the EI model, and supplemented with measurements of its probable chemical precursors. These experiments will improve understanding of how the production of CDOM in the ocean is linked to the optics and chemistry of planktonic CDOM formation. Determining the time course and extent of phytoplankton POM and DOM transformation by heterotrophic bacteria during the same phytoplankton growth experiments will provide an in-depth understanding as to how bacterial transformation of marine snow-associated planktonic organic matter drives CDOM production throughout the ocean.



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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