http://lod.bco-dmo.org/id/dataset/882570
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
2022-10-15
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Laboratory data on cell abundance of Minutocellus polymorphus in experiments measuring TEP and production of microaggregates
2022-11-04
publication
2022-11-04
revision
BCO-DMO Linked Data URI
2022-11-04
creation
http://lod.bco-dmo.org/id/dataset/882570
Susanne Neuer
Arizona State University
principalInvestigator
Hinsby Cadillo-Quiroz
Arizona State University
principalInvestigator
Bianca N. Cruz
Arizona State University
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: Neuer, S., Cruz, B. N., Cadillo-Quiroz, H. (2022) Laboratory data on cell abundance of Minutocellus polymorphus in experiments measuring TEP and production of microaggregates. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-11-04 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/882570 [access date]
Methods and Sampling: <p>In this study, one diatom and three bacteria species were grown and measured.&nbsp; <em>Minutocellus polymorphus</em> were incubated with or without the addition of bacteria in flasks and sampled throughout their growth (representative of bloom conditions), to determine the production of transparent exopolymeric particles (TEP) and the formation of micro-aggregates, and in roller tanks to investigate the formation of sinking aggregates (representative of end of bloom conditions).&nbsp; Additional details are in Cruz &amp; Neuer, 2022.&nbsp;&nbsp;</p>
<p>Two growth experiments were carried out independently:<br />
1. Growth experiment 1 with the addition of <em>Marinobacter adhaerens</em><br />
2.&nbsp;Growth experiment 2 with the addition of <em>Pseudoalteromonas carrageenovora</em> and <em>Vibrio thalassae&nbsp;</em></p>
<p>Stock cultures of marine Minutocellus polymorphus (CCMP497, National Center for Marine Algae and Microbiota, NCMA) were maintained in L1 medium prepared in artificial seawater and incubated in an environmental growth chamber (Conviron) at 23 ± 1 °C.&nbsp; &nbsp;Stock cultures of <em>Vibrio thalassae </em>(DSM102810, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH), <em>Pseudoalteromonas carrageenovora</em> (DSM6820, DSMZ), and <em>Marinobacter adhaerens</em> HP15 were maintained on Marine Agar (BD Difco 2216, Becton Dickinson, NJ; ZoBell, 1941) plates at 23 ± 1 °C.&nbsp;</p>
<p>Triplicate cultures of <em>Minutocellus polymorphus </em>(CCMP497) with and without the addition of known particle-associated marine bacteria (<em>M. adhaerens</em>, <em>P. carrageenovora, </em>and <em>V. thalassae</em>) were sampled every other day for 19-23 days for the quantification of:</p>
<ul>
<li>single cells [this dataset]</li>
<li>suspended microaggregates (aggregates ca. 5-60 μm) [Suspended Microaggregates dataset]</li>
<li>TEP (Transparent Exopolymeric Particles) [TEP Concentration dataset]</li>
</ul>
<p>This dataset contains single cell abundances&nbsp;of diatoms and bacteria determined using epifluorescence microscopy.&nbsp;The other measurements can be found in the Related Datasets section below.&nbsp;&nbsp;</p>
<p>Cell abundances in the cultures were determined with the use of epifluorescence microscopy (Carl Zeiss AxioScope.A1). Glutaraldehyde-fixed samples were stained with the nucleic acid dye DAPI (4′,6-diamidino-2-phenylindole, 0.03 M, Sigma-Aldrich), and filtered onto gray 0.2 µm pore-size polycarbonate membranes (GVS Life Technologies, ME). Chlorophyll-a emission by M. polymorphus cells and DAPI-stained bacteria were visualized under 450–490 nm excitation and 380–400 nm, respectively.</p>
<p>Suspended microaggregates (i.e., non-sinking particles with an equivalent spherical diameter of&nbsp;5-60 microns) were quantified using a Multisizer 3 Particle Counter.&nbsp;&nbsp;TEP concentrations were determined as in Bittar et al. (2018). The stocks of Alcian-Blue dye used for TEP quantification had calibration factors (or f-factors) of 81.70 for experiments with <em>M. adhaerens</em> and 83.83 for experiments with <em>P. carrageenovora </em>and <em>V. thalassae</em>.</p>
<p>For additional Methods details, see Cruz &amp; Neuer, 2022.&nbsp;&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1658527 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1658527
onGoing
Susanne Neuer
Arizona State University
480-727-7254
College of Liberal Arts and Sciences School of Life Sciences 427 East Tyler Mall
Tempe
AZ
85287-4501
USA
susanne.neuer@asu.edu
pointOfContact
Hinsby Cadillo-Quiroz
Arizona State University
School of Life Sciences University of Arizona
Tempe
85287
AZ
hinsby@asu.edu
pointOfContact
Bianca N. Cruz
Arizona State University
bncruz1@mainex1.asu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Experiment_ID
Culture
Culture_type
Organism_counted
Days
Cell_Abundance_rep1
Cell_Abundance_rep2
Cell_Abundance_rep3
Conviron growth chamber
Multisizer 3 Particle Counter
AxioScope.A1 (Carl Zeiss, Germany)
theme
None, User defined
experiment id
experiment type
species scientific name (binomial)
days
cell_concentration
featureType
BCO-DMO Standard Parameters
Algal Growth Chamber
Coulter Counter
Fluorescence Microscope
instrument
BCO-DMO Standard Instruments
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.
Aggregation of Marine Picoplankton
https://osprey.bco-dmo.org/project/710239
Aggregation of Marine Picoplankton
<p>NSF abstract:</p>
<p>Marine phytoplankton are microscopic algae that live in the sunlit zone of the ocean. They play an important role in the uptake of carbon dioxide from the atmosphere through photosynthesis, similar to what plants do on land, and are the basis of the marine food web. However, instead of storing this organic carbon in leaf tissue and roots, marine phytoplankton are grazed by planktonic animals, or die and subsequently sink out of the sunlit zone in the form of aggregates, also called "Marine Snow". These particles not only export the organic carbon contained in their cells to the deep ocean, but also serve as food for animals and bacteria that live in the deep. A considerable portion of these phytoplankton are extremely small, among the tiniest of all organisms known. These extremely small cells have not been thought to play an important role in the formation and sinking of marine snow; however, recent findings challenge this view. This project will investigate how the smallest of these phytoplankton contribute to the rain of sinking particles from the sunlit surface to the deep ocean. This research is important because, in some of the largest expanses of the open oceans, these minute cells dominate the phytoplankton community, and larger plankton organisms are very sparse. The project, through a combination of work in the laboratory and at a field station, will shed light on how these tiny phytoplankton cells make aggregates, which ultimately enable them to sink as "Marine Snow". The project also provides unique opportunities for undergraduate students at Arizona State University, a land-locked public university, to gain experience in working with marine research. The project will serve to educate one PhD student, one MS student in an accelerated BS-MS program, and 8-10 undergraduate students/semester in a unique, inquiry based learning effort termed Microbial EducatioN Training and OutReach (MENTOR). The undergraduate students will also participate in Arizona State University (ASU)'s School of Life Sciences, Undergraduate Research Program (SOLUR), which seeks to increase the participation of minorities in science. They will also contribute towards developing web and classroom materials, based on this project, which will then be distributed through a partnership with the award-winning ASU-sponsored Ask A Biologist K-12 web site.</p>
<p>The oceanic "biological carbon pump", the photosynthetically mediated transformation of dissolved inorganic carbon into particulate and dissolved organic carbon and its subsequent export to deep water, functions as a significant driver of atmospheric carbon uptake by the oceans. The traditional view of the biological carbon pump in the ocean is that of sinking of large aggregates (marine snow) or fecal pellets, which are made up of large, mineral ballasted cells of phytoplankton. However, recent evidence, stemming from in situ investigations of particulate matter, trap studies and modelling studies, have shown that micron-sized phytoplankton such as picocyanobacteria as well as picoeukaryotes can contribute significantly to the sinking of particulate matter. The specific mechanisms behind the sinking of these micrometer sized cells remain elusive as the cells are too small to sink on their own, and mesozooplankton is likely unable to ingest single cells. Intriguingly, recent research by the investigators has shown that the ubiquitous picocyanobacteria Synechococcus are able to form aggregates and sink at velocities comparable to those of marine snow. They found that the matrix of the Synechococcus aggregates was made of Transparent Exopolymeric Particles (TEP), and that TEP production was enhanced under nutrient limited culture conditions. Interaction with clays and presence of heterotrophic bacteria also enhanced aggregation and sinking velocity. This study aims to further investigate aggregation of other common picoplankton in the laboratory and aggregation occurring in natural settings at an oligotrophic open ocean site, the Bermuda Atlantic Time-series Site (BATS). Ultimately, this project will increase and refine our understanding of the role of the smallest phytoplankton in aggregation and sinking - information vital to understanding carbon cycling processes in the oceans.</p>
Marine Plankton Aggregation
largerWorkCitation
project
eng; USA
biota
oceans
-111.92828937936
-111.92828937936
33.419410120974
33.419410120974
2021-12-01
2022-08-01
Bermuda Atlantic Time-Series station
0
BCO-DMO catalogue of parameters from Laboratory data on cell abundance of Minutocellus polymorphus in experiments measuring TEP and production of microaggregates
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/882596.rdf
Name: Experiment_ID
Units: unitless
Description: <p>Experiment ID describing the experiment in which the organism grew</p>
http://lod.bco-dmo.org/id/dataset-parameter/882597.rdf
Name: Culture
Units: unitless
Description: <p>Experimental culture, listing the organisms grown</p>
http://lod.bco-dmo.org/id/dataset-parameter/882598.rdf
Name: Culture_type
Units: unitless
Description: <p>Culture type, either co-culture or axenic (diatom-only control)</p>
http://lod.bco-dmo.org/id/dataset-parameter/882599.rdf
Name: Organism_counted
Units: unitless
Description: <p>Organism that was measured for cell abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/882600.rdf
Name: Days
Units: days
Description: <p>Days since start of experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/882601.rdf
Name: Cell_Abundance_rep1
Units: cells per milliliter (cells/mL)
Description: <p>Cell abundance of first replicate as determined using epifluorescence microscopy</p>
http://lod.bco-dmo.org/id/dataset-parameter/882602.rdf
Name: Cell_Abundance_rep2
Units: cells per milliliter (cells/mL)
Description: <p>Cell abundance of second replicate as determined using epifluorescence microscopy</p>
http://lod.bco-dmo.org/id/dataset-parameter/882603.rdf
Name: Cell_Abundance_rep3
Units: cells per milliliter (cells/mL)
Description: <p>Cell abundance of third replicate as determined using epifluorescence microscopy</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
https://osprey.bco-dmo.org/dataset/882570/data/download
download
onLine
dataset
<p>In this study, one diatom and three bacteria species were grown and measured.&nbsp; <em>Minutocellus polymorphus</em> were incubated with or without the addition of bacteria in flasks and sampled throughout their growth (representative of bloom conditions), to determine the production of transparent exopolymeric particles (TEP) and the formation of micro-aggregates, and in roller tanks to investigate the formation of sinking aggregates (representative of end of bloom conditions).&nbsp; Additional details are in Cruz &amp; Neuer, 2022.&nbsp;&nbsp;</p>
<p>Two growth experiments were carried out independently:<br />
1. Growth experiment 1 with the addition of <em>Marinobacter adhaerens</em><br />
2.&nbsp;Growth experiment 2 with the addition of <em>Pseudoalteromonas carrageenovora</em> and <em>Vibrio thalassae&nbsp;</em></p>
<p>Stock cultures of marine Minutocellus polymorphus (CCMP497, National Center for Marine Algae and Microbiota, NCMA) were maintained in L1 medium prepared in artificial seawater and incubated in an environmental growth chamber (Conviron) at 23 ± 1 °C.&nbsp; &nbsp;Stock cultures of <em>Vibrio thalassae </em>(DSM102810, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH), <em>Pseudoalteromonas carrageenovora</em> (DSM6820, DSMZ), and <em>Marinobacter adhaerens</em> HP15 were maintained on Marine Agar (BD Difco 2216, Becton Dickinson, NJ; ZoBell, 1941) plates at 23 ± 1 °C.&nbsp;</p>
<p>Triplicate cultures of <em>Minutocellus polymorphus </em>(CCMP497) with and without the addition of known particle-associated marine bacteria (<em>M. adhaerens</em>, <em>P. carrageenovora, </em>and <em>V. thalassae</em>) were sampled every other day for 19-23 days for the quantification of:</p>
<ul>
<li>single cells [this dataset]</li>
<li>suspended microaggregates (aggregates ca. 5-60 μm) [Suspended Microaggregates dataset]</li>
<li>TEP (Transparent Exopolymeric Particles) [TEP Concentration dataset]</li>
</ul>
<p>This dataset contains single cell abundances&nbsp;of diatoms and bacteria determined using epifluorescence microscopy.&nbsp;The other measurements can be found in the Related Datasets section below.&nbsp;&nbsp;</p>
<p>Cell abundances in the cultures were determined with the use of epifluorescence microscopy (Carl Zeiss AxioScope.A1). Glutaraldehyde-fixed samples were stained with the nucleic acid dye DAPI (4′,6-diamidino-2-phenylindole, 0.03 M, Sigma-Aldrich), and filtered onto gray 0.2 µm pore-size polycarbonate membranes (GVS Life Technologies, ME). Chlorophyll-a emission by M. polymorphus cells and DAPI-stained bacteria were visualized under 450–490 nm excitation and 380–400 nm, respectively.</p>
<p>Suspended microaggregates (i.e., non-sinking particles with an equivalent spherical diameter of&nbsp;5-60 microns) were quantified using a Multisizer 3 Particle Counter.&nbsp;&nbsp;TEP concentrations were determined as in Bittar et al. (2018). The stocks of Alcian-Blue dye used for TEP quantification had calibration factors (or f-factors) of 81.70 for experiments with <em>M. adhaerens</em> and 83.83 for experiments with <em>P. carrageenovora </em>and <em>V. thalassae</em>.</p>
<p>For additional Methods details, see Cruz &amp; Neuer, 2022.&nbsp;&nbsp;</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO&nbsp;Processing Notes:&nbsp;<br />
- Excel sheet "M.polymorphus_Microaggregates_and_TEP- Cell Abundance.xlsx" was processed and saved as CSV file<br />
- Added a conventional header with dataset name, PI name, version date<br />
- Modified parameter names to conform with BCO-DMO naming conventions<br />
- Rounded cell abundances to 3 decimal places<br />
- Blank values in this dataset are displayed as "nd" for "no data."&nbsp; nd is the default missing data identifier in the BCO-DMO system.</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
Conviron growth chamber
Conviron growth chamber
PI Supplied Instrument Name: Conviron growth chamber PI Supplied Instrument Description:Stock cultures of marine Minutocellus polymorphus were incubated in an environmental growth chamber (Conviron) at 23 ± 1 °C Instrument Name: Algal Growth Chamber Instrument Short Name: Instrument Description: A chamber specifically designed for the growth of algae in flasks. The chamber typically provides controlled temperature, humidity, and light conditions.
Multisizer 3 Particle Counter
Multisizer 3 Particle Counter
PI Supplied Instrument Name: Multisizer 3 Particle Counter PI Supplied Instrument Description:Suspended microaggregates were quantified using a Multisizer 3 Particle Counter Instrument Name: Coulter Counter Instrument Short Name: Instrument Description: An apparatus for counting and sizing particles suspended in electrolytes. It is used for cells, bacteria, prokaryotic cells and virus particles. A typical Coulter counter has one or more microchannels that separate two chambers containing electrolyte solutions.
from https://en.wikipedia.org/wiki/Coulter_counter
AxioScope.A1 (Carl Zeiss, Germany)
AxioScope.A1 (Carl Zeiss, Germany)
PI Supplied Instrument Name: AxioScope.A1 (Carl Zeiss, Germany) PI Supplied Instrument Description:Single cell abundance of diatoms and bacteria were determined using epifluorescence microscopy Instrument Name: Fluorescence Microscope Instrument Short Name: 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/