http://lod.bco-dmo.org/id/dataset/847923
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
2021-04-07
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
pH from microsensor profiles of ex situ sediment cores collected in the Chesapeake Bay and measured during 2017-2018
2021-04-07
publication
2021-04-07
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-04-26
publication
https://doi.org/10.26008/1912/bco-dmo.847923.1
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. (2021) pH from microsensor profiles of ex situ sediment cores collected in the Chesapeake Bay and measured during 2017-2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-04-07 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.847923.1 [access date]
Microsensor profiles - pH Dataset Description: Methods and Sampling: <p><strong>Methodology:</strong><br />
High-resolution microsensor profiling of O₂, pH, and H₂S was performed on replicate sediment cores retrieved from the sampling sites, with 1 or 2 replicate profiles made per sediment core per analyte, using commercial microsensors operated with a motorized micromanipulator (Unisense A.S., Denmark). pH sensors were calibrated with a 3-point NBS buffer calibration. Detailed methodology is given in Malkin et al., 2014.</p>
<p><strong>Sampling and Analytical Procedures:</strong><br />
Replicate sediment cores were collected using a gravity corer (Uwitec; clear PVC liners, Ø = 8.6 cm), capped, kept in the dark at bottom water temperature in a water bath, and transported back to the laboratory, where they were held in a climate-controlled room. Microsensor profiling was conducted within 1 day of core retrieval.</p>
<p><strong>Instruments:</strong><br />
Unisense A.S. microsensors (Denmark) and motorized micromanipulator system were used for data collection. The 4 channel microsensor multimeter was used, with the following microsensors: Ox-50, pH-200, and H2S-100. Each sensor was used consecutively and so resultant data is provided separately as individual datasets. SensorTrace Suite software was used for data collection.</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
date_local
Year
Month
Day
site
lat
lon
site_depth
CoreRep
ProfileRep
sensor_depth_mm
value_pHNBS
Flag
gravity corer (Uwitec)
Unisense A.S. microsensors (Denmark)
theme
None, User defined
date
year
month of year
day of month
site
latitude
longitude
depth_w
replicate
depth core
pH
quality flag
featureType
BCO-DMO Standard Parameters
Gravity Corer
Unisense pH microelectrode
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
-76.49402
-76.42794
38.55505
38.55728
2017-03-28
2018-08-24
Chesapeake Bay sediments; Mid-Atlantic Coastal sediments
0
BCO-DMO catalogue of parameters from pH from microsensor profiles of ex situ sediment cores collected in the Chesapeake Bay and measured during 2017-2018
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/847936.rdf
Name: date_local
Units: unitless
Description: <p>date of field sampling (local time zone; EST); format: YYYY-MM-DD</p>
http://lod.bco-dmo.org/id/dataset-parameter/847937.rdf
Name: Year
Units: unitless
Description: <p>year of field sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/847938.rdf
Name: Month
Units: unitless
Description: <p>month of field sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/847939.rdf
Name: Day
Units: unitless
Description: <p>day of month of field sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/847940.rdf
Name: site
Units: site
Description: <p>site of sediment collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/847941.rdf
Name: lat
Units: degrees North
Description: <p>latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/847942.rdf
Name: lon
Units: degrees East
Description: <p>longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/847943.rdf
Name: site_depth
Units: meters (m)
Description: <p>depth of sampling site</p>
http://lod.bco-dmo.org/id/dataset-parameter/847944.rdf
Name: CoreRep
Units: unitless
Description: <p>core replicate (A or B)</p>
http://lod.bco-dmo.org/id/dataset-parameter/847945.rdf
Name: ProfileRep
Units: unitless
Description: <p>replicate profiles within a core (A or B)</p>
http://lod.bco-dmo.org/id/dataset-parameter/847946.rdf
Name: sensor_depth_mm
Units: millimeters (mm)
Description: <p>depth of microsensor</p>
http://lod.bco-dmo.org/id/dataset-parameter/847947.rdf
Name: value_pHNBS
Units: calibrated NBS standard
Description: <p>calibrated value of pH microsensor</p>
http://lod.bco-dmo.org/id/dataset-parameter/847948.rdf
Name: Flag
Units: unitless
Description: <p>indication of measurement problem or caution</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
1671165
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/030c676b-7a3d-530a-ace4-5093a5869d62/content
download
https://doi.org/10.26008/1912/bco-dmo.847923.1
download
onLine
dataset
<p><strong>Methodology:</strong><br />
High-resolution microsensor profiling of O₂, pH, and H₂S was performed on replicate sediment cores retrieved from the sampling sites, with 1 or 2 replicate profiles made per sediment core per analyte, using commercial microsensors operated with a motorized micromanipulator (Unisense A.S., Denmark). pH sensors were calibrated with a 3-point NBS buffer calibration. Detailed methodology is given in Malkin et al., 2014.</p>
<p><strong>Sampling and Analytical Procedures:</strong><br />
Replicate sediment cores were collected using a gravity corer (Uwitec; clear PVC liners, Ø = 8.6 cm), capped, kept in the dark at bottom water temperature in a water bath, and transported back to the laboratory, where they were held in a climate-controlled room. Microsensor profiling was conducted within 1 day of core retrieval.</p>
<p><strong>Instruments:</strong><br />
Unisense A.S. microsensors (Denmark) and motorized micromanipulator system were used for data collection. The 4 channel microsensor multimeter was used, with the following microsensors: Ox-50, pH-200, and H2S-100. Each sensor was used consecutively and so resultant data is provided separately as individual datasets. SensorTrace Suite software was used for data collection.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- changed date format to YYYY-MM-DD;<br />
- converted longitude from positive degrees West to negative degrees East.</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
gravity corer (Uwitec)
gravity corer (Uwitec)
PI Supplied Instrument Name: gravity corer (Uwitec) Instrument Name: Gravity Corer Instrument Short Name:Gravity Corer Instrument Description: The gravity corer allows researchers to sample sediment layers at the bottom of lakes or oceans. The coring device is deployed from the ship and gravity carries it to the seafloor. (http://www.whoi.edu/instruments/viewInstrument.do?id=1079). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/51/
Unisense A.S. microsensors (Denmark)
Unisense A.S. microsensors (Denmark)
PI Supplied Instrument Name: Unisense A.S. microsensors (Denmark) PI Supplied Instrument Description:Unisense A.S. microsensors (Denmark) and motorized micromanipulator system were used for data collection. The 4 channel microsensor multimeter was used, with the following microsensors: Ox-50, pH-200, and H2S-100. Each sensor was used consecutively. Instrument Name: Unisense pH microelectrode Instrument Short Name:Unisense pH Instrument Description: The Unisense pH microelectrode is a miniaturized conventional pH electrode. The instrument is designed for research applications. It is based on selective diffusion of protons through pH glass, and the determination of potentials between the internal electrolyte and an internal or external reference electrode. It has a range of tip sizes (10 um-1.1 mm), a measurement range of pH 2-10 (linear 4-9) and detection limit of 0.1 pH unit. See more on the manufacturer's website: https://www.unisense.com/