http://lod.bco-dmo.org/id/dataset/883171
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
2022-11-02
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Geochemistry and microscopy from incubation experiments of Chesapeake Bay sediments conducted at Horn Point Laboratory
2022-11-02
publication
2022-11-02
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-11-14
publication
https://doi.org/10.26008/1912/bco-dmo.883171.1
Sairah Malkin
University of Maryland Center for Environmental Science
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: Malkin, S. (2022) Geochemistry and microscopy from incubation experiments of Chesapeake Bay sediments conducted at Horn Point Laboratory. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-11-02 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.883171.1 [access date]
Geochemistry and Microscopy from Incubation Experiments Dataset Description: <p>This is the first of 4 datasets associated with "Incubation Experiment (Liau) CB Sediments".&nbsp;There is additionally an amplicon dataset (16S rRNA gene, RNA and DNA) associated with this experiment: NCBI Sequence Read Archive, under BioProject PRJNA833464, accession numbers SAMN27993143 to SAMN27993196. The NCBI data will not be publicly available in May 2023.</p> Methods and Sampling: <p>The source material was collected from Chesapeake Bay (38.55505 N, 76.42794 W) (mesohaline), water column depth 26 meters, sediment horizon 0-10 centimeter below sea floor.</p>
<p>Incubation conditions: 16 degrees Celsius, S=15.5, dark, aerated.</p>
<p><strong>Incubation Set-up:</strong> Sediments were homogenized and packed into polycarbonate core liners, sealed with a stopper at the bottom, and open to aerated aquarium water at the top. In a subset of cores, a polycarbonate filter (pore size 0.2 microns) was secured at 0.5 cm depth, to prevent downward growth of cable bacteria in these treatments. Sediments were incubated for up to 46 days. At 6 time points, microsensor profiles were measured, followed by destructive sampling.</p>
<p><strong>Porewater extraction</strong>: Sediments were sectioned at 0.5 cm depth increments in an anaerobic glove bag under nitrogen atmosphere. Porewaters were separated by centrifugation (3500 rpm for 10 minutes), and filtered (0.2 micron) and aliquoted in the anaerobic glove bag. Samples for ferrous iron measurements were preserved with trace-metal grade nitric acid (final pH &lt; 2).</p>
<p><strong>Geochemical Measurements</strong>: Porewater sulfate and chloride were analyzed by suppressed ion chromatography following 100-fold dilutions (Dionex Integrion IC). Porewater ferrous iron (Fe2+) was measured colorimetrically using the Ferrozine assay. Ammonium was measured colorimetrically using the phenol hypochlorite method.</p>
<p><strong>Cell Enumeration: </strong>Samples for microbial cell enumeration were preserved in 96% molecular grade ethanol (1:1 v/v), gently mixed with sterile autoclaved toothpicks, and stored at -20°C. Sediment-associated cells were separated from sediment grains using an acetate buffer to dissolve carbonates, followed by washing with NaCl solution, and then gentle vortexing with a detergent mixed with methanol (Lunau et al. 2005, Kallmeyer et al. 2008). Cells were recovered using density centrifugation with Nycodenz (50% w/v). Cable bacteria filaments were enumerated using fluorescence in situ hybridization (FISH) with the DSB706 oligoprobe (Malkin et al. 2022), and total cell counts were enumerated following staining with SyBR Green I.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756877 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756877
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756851 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756851
completed
Sairah Malkin
University of Maryland Center for Environmental Science
410-221-8418
2020 Horns Point Rd.
Cambridge
MD
21613
USA
smalkin@umces.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_ID
Treatment
Day
TopDepth_cm
BottomDepth_cm
NH4_uM
Fe2_uM
Cl_mM
SO4_mM
Microscopy_DSB706_cell_cm3
Microscopy_AllSingleCells_cells_cm3
Zeiss AxioCam MR camera
Zeiss Axiophot fluorescent microscope
Dionex Integrion IC with IonPac AS-19 analytical column
ThermoScientific Genesis UV/Vis
theme
None, User defined
sample identification
treatment
time_elapsed
depth core
Ammonium
Iron
chloride
sulfate
abundance
featureType
BCO-DMO Standard Parameters
Aquarium
Camera
Centrifuge
Fluorescence Microscope
Ion Chromatograph
Spectrophotometer
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.
Collaborative Research: Probing the Metabolic and Electrical Interactions of Cable Bacteria in Anoxic Sediments
https://osprey.bco-dmo.org/project/773452
Collaborative Research: Probing the Metabolic and Electrical Interactions of Cable Bacteria in Anoxic Sediments
<p><em>NSF Award Abstract:</em><br />
Marine sediments represent the world's largest repository of stored organic carbon, and understanding how microorganisms break down this carbon is an imperative for understanding global carbon cycling. Yet long-standing questions remain regarding how networks of microorganisms work together to accomplish the complete breakdown of organic carbon in marine sediments. Sediment microbes interact in a myriad of ways that couple their metabolism to the break down of organic carbon, including by sharing products of metabolism. Accumulating evidence further suggests that some microorganisms can interact by transferring electrons directly to other unrelated microorganisms. This ability occurs across diverse microorganisms and appears to be widespread in the biosphere, particularly in anaerobic environments such as marine sediments. This project addresses emerging questions about the identity and metabolic linkages between microorganisms that work together in natural anaerobic marine and estuarine sediments to break down organic carbon. The investigators approach these questions by focusing on the influence of a keystone bacterium on its surrounding microbial community. "Cable bacteria" are a recently discovered group of long filamentous bacteria that act as electrical conductors in aquatic sediments providing a conduit for electrons to commute from deeper sulfidic sediments up to the surface oxygen layer by the process of centimeter-scale electron transport. Since their discovery about 6 years ago, these bacteria have been observed in a wide range of depositional sedimentary environments, often at extremely high cell densities. Where these bacteria are abundant, such as in coastal marine muds, they drive intense localized changes in pH and strongly influence the mineral cycling. This research explores the direct and indirect influence of cable bacteria on the metabolic activity of associated microorganisms. This project also advance the education and training of two early-career investigators, two PhD students, and undergraduate students. The skills and expertise gained from these PhD research projects will enable the students to be competitive in academic pursuits and in bioinformatics and technology applications relevant to private industry. The scientific discoveries emerging from this work is being incorporated into undergraduate and graduate level courses in marine microbial ecology. The research team will reach out to the broader community by hosting public lectures promoting a better understanding of environmental microbial ecology.</p>
<p>The proposed work is to investigate the role of cable bacteria in structuring sediment microbial communities. Due to their growth strategy and morphology, cable bacteria are particularly amenable to experimental manipulation, providing an outstanding opportunity to better understand community interactions among microorganisms in a natural and complex anaerobic environment. The investigators will explore the interactions and relationships between cable bacteria and their associated microbial community by manipulating the growth and activity of cable bacteria and quantifying the resultant microbial community response. Specifically, this project aims to (1) identify microorganisms whose growth is enhanced by cable bacteria, (2) identify metabolic processes linked with cable bacteria activity using metatranscriptomics, (3) test specific metabolic links between sediment microorganisms and cable bacteria activity using a DNA-stable isotope probing (SIP) approach, and (4) visually confirm the identity and quantify key microorganisms associated with cable bacteria using microscopy. As more is learned about the identity and the mechanisms by which microorganisms are metabolically linked in anoxic sediments, we will be better able to understand and make predictions about how microorganisms function in their environment and how they can be utilized in bioengineered systems.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Anoxic Sediment Bacteria Interactions
largerWorkCitation
project
eng; USA
oceans
-76.42794
-76.42794
38.55505
38.55505
2018-12-01
2019-01-31
Chesapeake Bay sediments; Mid-Atlantic Coastal sediments
0
BCO-DMO catalogue of parameters from Geochemistry and microscopy from incubation experiments of Chesapeake Bay sediments conducted at Horn Point Laboratory
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/883267.rdf
Name: Sample_ID
Units: unitless
Description: <p>A unique code for each sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/883268.rdf
Name: Treatment
Units: unitless
Description: <p>The treatment of the sediments; values are “NoFilter” or “Filter”, as described in methods</p>
http://lod.bco-dmo.org/id/dataset-parameter/883269.rdf
Name: Day
Units: days
Description: <p>Time of sampling after cores were homogenized and incubated in days</p>
http://lod.bco-dmo.org/id/dataset-parameter/883270.rdf
Name: TopDepth_cm
Units: centimeters below surface
Description: <p>The upper depth of the sediment sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/883271.rdf
Name: BottomDepth_cm
Units: centimeters below surface
Description: <p>The lower depth of the sediment sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/883272.rdf
Name: NH4_uM
Units: micromolar (uM)
Description: <p>Porewater ammonium concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/883273.rdf
Name: Fe2_uM
Units: micromolar (uM)
Description: <p>Porewater ferrous iron concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/883274.rdf
Name: Cl_mM
Units: millimolar (mM)
Description: <p>Porewater chloride concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/883275.rdf
Name: SO4_mM
Units: millimolar (mM)
Description: <p>Porewater sulfate concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/883276.rdf
Name: Microscopy_DSB706_cell_cm3
Units: cells per cubic centimeter
Description: <p>Microscopy counts using DSB706 oligo probe (i.e., cable bacteria)</p>
http://lod.bco-dmo.org/id/dataset-parameter/883277.rdf
Name: Microscopy_AllSingleCells_cells_cm3
Units: cells per cubic centimeter
Description: <p>Microscopy counts of all single cells (SYBR Green)</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
3594
https://darchive.mblwhoilibrary.org/bitstream/1912/29498/1/dataset-883171_geochemistry-and-microscopy-incubation-experiments__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.883171.1
download
onLine
dataset
<p>The source material was collected from Chesapeake Bay (38.55505 N, 76.42794 W) (mesohaline), water column depth 26 meters, sediment horizon 0-10 centimeter below sea floor.</p>
<p>Incubation conditions: 16 degrees Celsius, S=15.5, dark, aerated.</p>
<p><strong>Incubation Set-up:</strong> Sediments were homogenized and packed into polycarbonate core liners, sealed with a stopper at the bottom, and open to aerated aquarium water at the top. In a subset of cores, a polycarbonate filter (pore size 0.2 microns) was secured at 0.5 cm depth, to prevent downward growth of cable bacteria in these treatments. Sediments were incubated for up to 46 days. At 6 time points, microsensor profiles were measured, followed by destructive sampling.</p>
<p><strong>Porewater extraction</strong>: Sediments were sectioned at 0.5 cm depth increments in an anaerobic glove bag under nitrogen atmosphere. Porewaters were separated by centrifugation (3500 rpm for 10 minutes), and filtered (0.2 micron) and aliquoted in the anaerobic glove bag. Samples for ferrous iron measurements were preserved with trace-metal grade nitric acid (final pH &lt; 2).</p>
<p><strong>Geochemical Measurements</strong>: Porewater sulfate and chloride were analyzed by suppressed ion chromatography following 100-fold dilutions (Dionex Integrion IC). Porewater ferrous iron (Fe2+) was measured colorimetrically using the Ferrozine assay. Ammonium was measured colorimetrically using the phenol hypochlorite method.</p>
<p><strong>Cell Enumeration: </strong>Samples for microbial cell enumeration were preserved in 96% molecular grade ethanol (1:1 v/v), gently mixed with sterile autoclaved toothpicks, and stored at -20°C. Sediment-associated cells were separated from sediment grains using an acetate buffer to dissolve carbonates, followed by washing with NaCl solution, and then gentle vortexing with a detergent mixed with methanol (Lunau et al. 2005, Kallmeyer et al. 2008). Cells were recovered using density centrifugation with Nycodenz (50% w/v). Cable bacteria filaments were enumerated using fluorescence in situ hybridization (FISH) with the DSB706 oligoprobe (Malkin et al. 2022), and total cell counts were enumerated following staining with SyBR Green I.</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing:</strong><br />
Standard curves with a minimum of 5 concentrations were analyzed to calibrate the geochemistry data. Microscopy counts were computed based on minimum cell counts. For cable bacteria, a minimum of 200 fields or 30 filaments were counted (whichever came first). For single total cell counts, a minimum of 400 cells were counted, appropriately diluted to be captured in 10-20 fields. The proportion of the slide examined was computed based on the field size, confirmed with a stage micrometer.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- replaced "NA" with "nd" (no data value);<br />
- renamed fields to comply with BCO-DMO naming conventions.</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: Instrument Name: Aquarium Instrument Short Name:Aquarium Instrument Description: Aquarium - a vivarium consisting of at least one transparent side in which water-dwelling plants or animals are kept
Zeiss AxioCam MR camera
Zeiss AxioCam MR camera
PI Supplied Instrument Name: Zeiss AxioCam MR camera PI Supplied Instrument Description:Zeiss Axiophot fluorescent microscope equipped with a digital Zeiss AxioCam MR camera, and Zen Pro software Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/
PI Supplied Instrument Name: Instrument Name: Centrifuge Instrument Short Name: Instrument Description: A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.
Zeiss Axiophot fluorescent microscope
Zeiss Axiophot fluorescent microscope
PI Supplied Instrument Name: Zeiss Axiophot fluorescent microscope PI Supplied Instrument Description:Zeiss Axiophot fluorescent microscope equipped with a digital Zeiss AxioCam MR camera, and Zen Pro software 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/
Dionex Integrion IC with IonPac AS-19 analytical column
Dionex Integrion IC with IonPac AS-19 analytical column
PI Supplied Instrument Name: Dionex Integrion IC with IonPac AS-19 analytical column PI Supplied Instrument Description:Porewater sulfate and chloride were analyzed by suppressed ion chromatography. Instrument Name: Ion Chromatograph Instrument Short Name:Ion Chromatograph Instrument Description: Ion chromatography is a form of liquid chromatography that measures concentrations of ionic species by separating them based on their interaction with a resin. Ionic species separate differently depending on species type and size. Ion chromatographs are able to measure concentrations of major anions, such as fluoride, chloride, nitrate, nitrite, and sulfate, as well as major cations such as lithium, sodium, ammonium, potassium, calcium, and magnesium in the parts-per-billion (ppb) range. (from http://serc.carleton.edu/microbelife/research_methods/biogeochemical/ic.html)
ThermoScientific Genesis UV/Vis
ThermoScientific Genesis UV/Vis
PI Supplied Instrument Name: ThermoScientific Genesis UV/Vis PI Supplied Instrument Description:Used to determine NH4 and Fe Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/