http://lod.bco-dmo.org/id/dataset/718117
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2017-10-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Dilution batch-culture bioassay (remineralization) experiments from SBDOM11 project cruise from R/V Point Sur PS1103 in the Santa Barbara Channel, May 2011 (SBDOM project, SBC LTER project)
2017-10-30
publication
2017-10-30
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-08-28
publication
https://doi.org/10.1575/1912/bco-dmo.718117.1
Craig A. Carlson
University of California-Santa Barbara
principalInvestigator
Mark A. Brzezinski
University of California-Santa Barbara
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Carlson, C., Brzezinski, M. (2017) Dilution batch-culture bioassay (remineralization) experiments from SBDOM11 project cruise from R/V Point Sur PS1103 in the Santa Barbara Channel, May 2011 (SBDOM project, SBC LTER project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-10-30 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.718117.1 [access date]
bacterial abundance, growth rates, and DOC from SBDOM11 cruise Dataset Description: <p>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.</p> Methods and Sampling: <p>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.</p>
<p>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.</p>
<p>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.</p>
<p>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).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0850857 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0850857
completed
Craig A. Carlson
University of California-Santa Barbara
(805) 893-2541
University of California Department of Ecology, Evolution and Marine Biology
Santa Barbara
CA
93106-6150
USA
craig_carlson@ucsb.edu
pointOfContact
Mark A. Brzezinski
University of California-Santa Barbara
805-893-7061
UCSB Marine Science Institute Bldg 520 Rm 4002 Fl 4L
Santa Barbara
CA
93106
USA
mark.brzezinski@lifesci.ucsb.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample
sta_id
bottle
Initiation_date
Initiation_time
Timepoint
Date
DOC_sampling_time
DOC_Bottle_A
DOC_A_st_dev
DOC_Bottle_B
DOC_B_st_dev
Bact_abun_sampling_time
Bact_abun_A
Bact_abun_B
DNA_sampling_time
Pyrosequencing_barcode
mu_growth_A
mu_growth_B
BGE_A
BGE_B
BD LSRII flow cytometer
modified Shimadzu TOC-V
theme
None, User defined
sample identification
station
bottle
date_start
time_start
time_point
date_local
time_local
dissolved organic Carbon
cell_concentration
sequence
growth
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Flow Cytometer
Shimadzu TOC-V Analyzer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
PS1103
service
Deployment Activity
Santa Barbara Channel, 34.3 N 120.2 W
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Mechanisms controlling the production and fate of DOM during diatom blooms
https://osprey.bco-dmo.org/project/2226
Mechanisms controlling the production and fate of DOM during diatom blooms
<p>This project is also affiliated with the <a href="http://www.icess.ucsb.edu/PnB/PnB.html" target="_blank">Plumes and Blooms</a> project.</p>
<p><strong>Data:</strong><br />
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:<br />
-- SBDOM10 and SBDOM11 CTD and Niskin bottle data.</p>
<p>The following are available online (see 'Datasets' heading below):<br />
-- SBDOM10 and SBDOM11 cruise plans (available online on deployment pages: <a href="http://www.bco-dmo.org/deployment/58833">PS1009</a>, <a href="http://www.bco-dmo.org/deployment/517703">PS1103</a>)<br />
-- SBDOM10 and SBDOM11 event logs (available online; see 'Datasets' below)<br />
-- Laboratory-based Bloom in a Bottle (BIB) Experiment<br />
-- Laboratory-based Remineralization Experiments<br />
-- SBDOM10 and SBDOM11 data summaries (including CTD data, nutrients, and bacterial production)</p>
<p>
<strong>Project Description from NSF Award Proposal and Abstract:</strong><br />
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.</p>
<p>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:<br />
1) We will investigate how limitation by either N or Si impacts the quantity and chemical composition of the DOM released by diatoms.<br />
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.<br />
3) Predicted DOM dynamics based on (1) and (2) will be tested in the field during diatom blooms in the Santa Barbara Channel, California.</p>
<p>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.</p>
<p><strong>References:</strong><br />
Lancelot, C. (1983). Factors affecting phytoplankton extracellular release in the Southern Bight of the North Sea. Marine Ecology Progress Series 12: 115-121.</p>
<p>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.</p>
<p>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.</p>
<p>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.</p>
<p>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.</p>
<p>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.</p>
SBDOM
largerWorkCitation
project
eng; USA
biota
oceans
Santa Barbara Channel, 34.3 N 120.2 W
-120.2
-120.2
34.3
34.3
2011-05-11
2011-07-24
Pacific California, Santa Barbara Channel
0
BCO-DMO catalogue of parameters from Dilution batch-culture bioassay (remineralization) experiments from SBDOM11 project cruise from R/V Point Sur PS1103 in the Santa Barbara Channel, May 2011 (SBDOM project, SBC LTER project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/718487.rdf
Name: Sample
Units: unitless
Description: <p>Internal experiment ID; A/B = replicate bottles</p>
http://lod.bco-dmo.org/id/dataset-parameter/718488.rdf
Name: sta_id
Units: unitless
Description: <p>station where water for experiment was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/718489.rdf
Name: bottle
Units: unitless
Description: <p>rosette bottle from which water for experiment was drawn</p>
http://lod.bco-dmo.org/id/dataset-parameter/718490.rdf
Name: Initiation_date
Units: unitless
Description: <p>local date when experiment was begun</p>
http://lod.bco-dmo.org/id/dataset-parameter/718491.rdf
Name: Initiation_time
Units: unitless
Description: <p>local time when experiment was begun</p>
http://lod.bco-dmo.org/id/dataset-parameter/718492.rdf
Name: Timepoint
Units: unitless
Description: <p>sampling timepoint; from 0 (post-initiation) through 8</p>
http://lod.bco-dmo.org/id/dataset-parameter/718493.rdf
Name: Date
Units: unitless
Description: <p>local date on which timepoint was sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/718494.rdf
Name: DOC_sampling_time
Units: unitless
Description: <p>local time at which DOC was sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/718495.rdf
Name: DOC_Bottle_A
Units: micromol/liter
Description: <p>DOC concentration in Bottle A at specified timepoint (nd missing data = failed QC)</p>
http://lod.bco-dmo.org/id/dataset-parameter/718496.rdf
Name: DOC_A_st_dev
Units: micromol/liter
Description: <p>standard deviation between injections on Shimadzu instrument while measuring DOC in Bottle A at specified timepoint</p>
http://lod.bco-dmo.org/id/dataset-parameter/718497.rdf
Name: DOC_Bottle_B
Units: micromol/liter
Description: <p>DOC concentration in Bottle B at specified timepoint (nd missing data = failed QC)</p>
http://lod.bco-dmo.org/id/dataset-parameter/718498.rdf
Name: DOC_B_st_dev
Units: micromol/liter
Description: <p>standard deviation between injections on Shimadzu instrument while measuring DOC in Bottle B at specified timepoint</p>
http://lod.bco-dmo.org/id/dataset-parameter/718499.rdf
Name: Bact_abun_sampling_time
Units: unitless
Description: <p>local time at which bacterial abundance was sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/718500.rdf
Name: Bact_abun_A
Units: cells/liter
Description: <p>Bacterial abundance in Bottle A at specified timepoint</p>
http://lod.bco-dmo.org/id/dataset-parameter/718501.rdf
Name: Bact_abun_B
Units: cells/liter
Description: <p>Bacterial abundance in Bottle B at specified timepoint</p>
http://lod.bco-dmo.org/id/dataset-parameter/718502.rdf
Name: DNA_sampling_time
Units: unitless
Description: <p>local time at which DNA was sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/718503.rdf
Name: Pyrosequencing_barcode
Units: unitless
Description: <p>multiplexing barcode corresponding to this sample; in the combined dataset available under SRA accession number SRR1222603</p>
http://lod.bco-dmo.org/id/dataset-parameter/718504.rdf
Name: mu_growth_A
Units: cells/day
Description: <p>specific growth rate of bacterial cells in Bottle A; calculated over the exponential growth phase of the experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/718505.rdf
Name: mu_growth_B
Units: cells/day
Description: <p>specific growth rate of bacterial cells in Bottle B; calculated over the exponential growth phase of the experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/718506.rdf
Name: BGE_A
Units: unitless
Description: <p>bacterial growth efficiency (percent) in Bottle A; calculated over the exponential growth phase</p>
http://lod.bco-dmo.org/id/dataset-parameter/718507.rdf
Name: BGE_B
Units: unitless
Description: <p>bacterial growth efficiency (percent) in Bottle B; calculated over the exponential growth phase</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
24334
https://darchive.mblwhoilibrary.org/bitstream/1912/24472/1/dataset-718117_sbdom11-mini-remineralization-expt__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.718117.1
download
onLine
dataset
<p>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.</p>
<p>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.</p>
<p>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.</p>
<p>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).</p>
Specified by the Principal Investigator(s)
<p>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).</p>
<p>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).&nbsp; Linear growth was assumed.</p>
<p>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.&nbsp; BGE values &gt; 70, or those resulting from a change in DOC of &lt; 1.5 µM, were considered invalid.</p>
<p><strong>BCO-DMO Processing Notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- blank cells were replaced by 'nd' (no data)</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
PI Supplied Instrument Name: PI Supplied Instrument Description:used to conduct multiplex amplicon pyrosequencing Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
BD LSRII flow cytometer
BD LSRII flow cytometer
PI Supplied Instrument Name: BD LSRII flow cytometer PI Supplied Instrument Description:BD LSRII flow cytometer with an autosampler attachment used to obtain bacterial abundance. Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer 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) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
modified Shimadzu TOC-V
modified Shimadzu TOC-V
PI Supplied Instrument Name: modified Shimadzu TOC-V PI Supplied Instrument Description:Used to measure dissolved organic carbon concentrations Instrument Name: Shimadzu TOC-V Analyzer Instrument Short Name:Shimadzu TOC-V Instrument Description: A Shimadzu TOC-V Analyzer measures DOC by high temperature combustion method. Community Standard Description: http://onto.nerc.ac.uk/CAST/124
PI Supplied Instrument Name: PI Supplied Instrument Description:used to conduct multiplex amplicon pyrosequencing Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Cruise: PS1103
PS1103
R/V Point Sur
Community Standard Description
International Council for the Exploration of the Sea
R/V Point Sur
vessel
PS1103
Craig A. Carlson
University of California-Santa Barbara
http://dmoserv3.whoi.edu/data_docs/SBDOM/SBDOM11_cruise_plan.doc
Report describing PS1103
R/V Point Sur
Community Standard Description
International Council for the Exploration of the Sea
R/V Point Sur
vessel