http://lod.bco-dmo.org/id/dataset/883506
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
2022-11-09
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
H2S microsensor profiling conducted alongside the destructive sampling of Chesapeake Bay sediments during incubation experiments at Horn Point Lab
2022-11-09
publication
2022-11-09
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-11-14
publication
https://doi.org/10.26008/1912/bco-dmo.883506.1
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) H2S microsensor profiling conducted alongside the destructive sampling of Chesapeake Bay sediments during incubation experiments at Horn Point Lab. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-11-09 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.883506.1 [access date]
Microsensor Profiling H2S Dataset Description: 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>Microsensor Profiling:</strong> High-resolution microsensor profiling of oxygen (O2), pH, and hydrogen sulfide (H2S) was performed on replicate sediment cores with 1 profile made per sediment core per analyte, using commercial microsensors operated with a motorized micromanipulator (Unisense A.S., Denmark). Oxygen sensor data were calibrated with a 2-point calibration using air-saturated water and anoxic zone of sediments. pH sensors were calibrated with a 3-point NBS buffer calibration. Sulfide (SumH2S) was calibrated with 5-point calibration using NaS2 (0-300 micromolar), and corrected with pH at the corresponding depth. Detailed methodology is given in Malkin et al. 2014.</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
SampleID
Treatment
CoreRep
Day
Depth_mm
SumH2S
Comment
Unisense sensors
theme
None, User defined
sample identification
treatment
replicate
time_elapsed
depth core
H2S
comments
featureType
BCO-DMO Standard Parameters
Unisense H2S microsensor
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 H2S microsensor profiling conducted alongside the destructive sampling of Chesapeake Bay sediments during incubation experiments at Horn Point Lab
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/883518.rdf
Name: SampleID
Units: unitless
Description: <p>A unique code for each sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/883519.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/883520.rdf
Name: CoreRep
Units: unitless
Description: <p>A replicate code for which sediment core was examined</p>
http://lod.bco-dmo.org/id/dataset-parameter/883521.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/883522.rdf
Name: Depth_mm
Units: millimeters (mm)
Description: <p>The depth of the measurements</p>
http://lod.bco-dmo.org/id/dataset-parameter/883523.rdf
Name: SumH2S
Units: micromolar (uM)
Description: <p>Total porewater sulfide concentration, corrected for pH</p>
http://lod.bco-dmo.org/id/dataset-parameter/883524.rdf
Name: Comment
Units: unitless
Description: <p>Additional relevant information, e.g., whether measurements were 'above' or 'below' the embedded filter</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
119261
https://darchive.mblwhoilibrary.org/bitstream/1912/29501/1/dataset-883506_microsensor-profiling-h2s__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.883506.1
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>Microsensor Profiling:</strong> High-resolution microsensor profiling of oxygen (O2), pH, and hydrogen sulfide (H2S) was performed on replicate sediment cores with 1 profile made per sediment core per analyte, using commercial microsensors operated with a motorized micromanipulator (Unisense A.S., Denmark). Oxygen sensor data were calibrated with a 2-point calibration using air-saturated water and anoxic zone of sediments. pH sensors were calibrated with a 3-point NBS buffer calibration. Sulfide (SumH2S) was calibrated with 5-point calibration using NaS2 (0-300 micromolar), and corrected with pH at the corresponding depth. Detailed methodology is given in Malkin et al. 2014.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- replaced "NA" with "nd" (no data value);<br />
- removed "Unit" column because units are provided in parameters table;<br />
- removed "Measurement" column because all measurements are H2S.</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
Unisense sensors
Unisense sensors
PI Supplied Instrument Name: Unisense sensors PI Supplied Instrument Description:Unisense sensors and micromanipulator Instrument Name: Unisense H2S microsensor Instrument Short Name:Unisense H2S Instrument Description: The Unisense H2S microsensor is a tool for studying H2S production and oxidation in a wide range of applications. The H2S microsensor is a miniaturized amperometric sensor with internal reference and a sensing anode. The anode is polarized against an internal reference. Driven by the external partial pressure, H2S from the environment penetrates through the sensor tip membrane into the electrolyte where the H2S is ultimately oxidized by the anode. This generates a current in the pA range which is measured by a picoammeter. See more on the manufacturer's website: https://www.unisense.com/H2S/