Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Related Publications
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

This dataset includes results from dilution batch-culture bioassay experiments reporting bacterial abundance, growth rates, barcode sequences and DOC were from the SBDOM 11 cruise in May 2011.

Dilution batch-culture bioassay experiments were established 11 May 2011 - 15 May 2011 on the SBDOM 11 cruise using water samples collected from the upper 8m of the water column. Water was gravity-filtered from the sampling Niskin bottle through two mixed cellulose ester filters (1.2 µm and 0.2 µm). Duplicate 500 mL polycarbonate bottles were filled with 375 mL 0.2 µm filtrate (filter sterilized media) and 125 mL 1.2 µm filtrate (bacterial inoculum) collected from the same cast. Bottles were incubated in the dark at 11degrees C for 10 weeks. Samples for bacterial abundance, DOM, and community composition by DNA were collected by decanting from the bottle at specified intervals.

DOC was quantified by high-temperature combustion on a modified Shimadzu TOC-V. We used 1.5 µM DOC as a detection limit for these experiments.

Bacterial abundance was measured using a BD LSRII flow cytometer with an autosampler attachment. Samples were preserved in sterile cryovials with 0.2% final concentration paraformaldehyde, then stored frozen until analysis. Samples were stained with SYBR Green I for enumeration.

DNA was collected from duplicate bottles combined (to conserve volume); 125 mL from each bottle was vacuum-filtered onto a 0.2 µm polyethersulfone filter and frozen. Samples were lysed in sucrose lysis buffer with 1% w/v sodium dodecyl sulfate and 0.2 mg mL-1 proteinase-K, and genomic DNA was extracted using a Qiagen DNEasy silica centrifugation kit. DNA was used to conduct multiplex amplicon pyrosequencing using primers 8F and 338R, following the protocol of Nelson et al. (2014; doi: 10.1111/1462-2920.12241). Sequence analysis was conducted in mothur (Schloss et al. 2009; doi: 10.1128/AEM.01541-09) using a non-redundant subset of the SILVA SSU Ref 16S alignment database (v111) curated as in Nelson et al. (2014).

DOC concentrations at timepoints 0, 3, and 7 were corrected for bacterial biomass by subtracting bacterial abundance multiplied by a standard conversion factor of 10 fg C cell-1 (Fukuda et al. 1998).

µ: µ was calculated as the rate of change of the natural log of bacterial cell abundance during exponential growth, defined here as extending from the end of lag phase to the start of stationary phase and/or to the maximum biomass observed (with additional abundance measurements from the lag and stationary phases averaged when available to increase robustness of estimates).  Linear growth was assumed.

BGE: BGE was calculated as the rate of change in bacterial cell biomass [bacterial abundance multiplied by a standard conversion factor of 10 fg C cell-1 (Fukuda et al. 1998)] divided by the slope of the DOC drawdown from experiment initiation to one week, then multiplied by 100 to format as a percent.  BGE values > 70, or those resulting from a change in DOC of < 1.5 µM, were considered invalid.

BCO-DMO Processing Notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- blank cells were replaced by 'nd' (no data)

This project is also affiliated with the Plumes and Blooms project.

Data:
The following data files have been submitted to BCO-DMO but are not yet available online. Data are restricted until June 2016. Please contact the PI for access prior to public availability:
-- SBDOM10 and SBDOM11 CTD and Niskin bottle data.

The following are available online (see 'Datasets' heading below):
-- SBDOM10 and SBDOM11 cruise plans (available online on deployment pages: PS1009, PS1103)
-- SBDOM10 and SBDOM11 event logs (available online; see 'Datasets' below)
-- Laboratory-based Bloom in a Bottle (BIB) Experiment
-- Laboratory-based Remineralization Experiments
-- SBDOM10 and SBDOM11 data summaries (including CTD data, nutrients, and bacterial production)

Project Description from NSF Award Proposal and Abstract:
Diatom blooms are known to produce prodigious quantities of DOM upon entering nutrient stress with a chemical composition that varies with the type of nutrient limitation (Si or N). This variable composition likely influences the nutritional value of DOM to microbes driving species successions towards functional groups of heterotrophic prokaryotes that are best able to metabolize particular forms of DOM. To date each side of this coupled system of production/consumption has been examined independently. A few studies have examined how limitation by different limiting nutrients affects the chemical character of the DOM produced by phytoplankton, while others have focused on the fate of DOM without detailed understanding of the mechanisms influencing its initial chemical composition.

We propose to investigate the mechanisms determining the character and fate of DOM produced during temperate diatom blooms. Specifically we will investigate how physiological stress on diatoms induced by different limiting nutrients influences the production, chemical composition of DOM and the microbial community structure that respond to it to better understand the mechanisms driving the accumulation and persistence of DOM in marine systems. The research will involve both laboratory and field experiments. The novel aspects of this work are:
1) We will investigate how limitation by either N or Si impacts the quantity and chemical composition of the DOM released by diatoms.
2) Assess how the differences in the chemical composition of the DOM produced under N or Si limitation affect its lability by examining the productivity, growth efficiency and community structure of heterotrophic bacterioplankton responding to the release of substrates.
3) Predicted DOM dynamics based on (1) and (2) will be tested in the field during diatom blooms in the Santa Barbara Channel, California.

While experiments investigating aspects of either 1 or 2 have been conducted successfully in the past (Lancelot, 1983; Billen and Fontigny, 1987; Goldman et al., 1992; Carlson et al.,1999; Cherrier and Bauer, 2004; Conan et al., 2007) ours will be the first study to combine these approaches in an integrated assessment of the mechanisms governing both the production and fate of DOM produced by diatom blooms experiencing limitation by different nutrients.

References:
Lancelot, C. (1983). Factors affecting phytoplankton extracellular release in the Southern Bight of the North Sea. Marine Ecology Progress Series 12: 115-121.

Billen, G. and A. Fontigny (1987). Dynamics of a Phaeocystis -dominated spring bloom in Belgian coastal waters. II. Bacterioplankton dynamics. Mar. Ecol. Prog. Ser. 37: 249-257.

Goldman, J.C., D.A. Hansell and M.R. Dennett (1992). Chemical characterization of three large oceanic diatoms: potential impact on water column chemistry. Marine Ecology Progress Series 88: 257-270.

Carlson, C.A., N.R. Bates, H.W. Ducklow and D.A. Hansell (1999). Estimation of bacterial respiration and growth efficiency in the Ross Sea, Antarctica. Aquatic Microbial Ecology 19: 229-244.

Cherrier, J. and J.E. Bauer (2004). Bacterial utilization of transient plankton-derived dissolved organic carbon and nitrogen inputs in surface ocean waters. Aquatic Microbial Ecology 35(3): 229-241.

Conan, P., M. Sondegaard, T. Kragh, F. Thingstad, M. Pujo-Pay, P.J.l.B. Williams, S. Markager, G. Cauwet, N.H. Borch, D. Evans and B. Rieman (2007). Partitioning of organic production in marine plankton communities: The effects of inorganic nutrient ratios and community composition on new dissolved organic matter. Limnology and Oceanography 52(2): 753-765.