http://lod.bco-dmo.org/id/dataset/847974
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)
Microscopy counts (Beggiatoa-like filaments, Cable bacteria), together with in situ temperature and salinity and surface sediment chlorophyll concentrations, of ex situ sediment cores collected in the Chesapeake Bay 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.847974.1
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) Microscopy counts (Beggiatoa-like filaments, Cable bacteria), together with in situ temperature and salinity and surface sediment chlorophyll concentrations, of ex situ sediment cores collected in the Chesapeake Bay 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.847974.1 [access date]
Microscopy Counts Dataset Description: Methods and Sampling: <p><strong>Methodology:</strong><br />
Immediately after sediment core retrieval, temperature and salinity of the water overlying sediments were measured with hand-held sensors (Orion Star A329 portable multimeter).</p>
<p>In the lab, surficial sediments were sectioned at 0.5 cm depth increments from which aliquots were collected for microscope enumeration of <em>Beggiatoa</em>-like filaments and cable bacteria filaments. <em>Beggiatoa</em>-like filament enumeration proceeded by methods adapted from Jorgensen et al. 2010 (doi: 10.1111/j.1574-6941.2010.00918), using inverted light microscopy (Zeiss AxioVert A1) with Utermöhl well slides. Filaments were identified as living <em>Beggiatoa</em>-like filaments if they were motile, unpigmented, and contained refractive sulfur granules. The length and diameter of each<em> Beggiatoa</em>-like filament encountered was recorded. Data are reported as volumetric density of<em> Beggiatoa</em>-like filaments (computed assuming a cylindrical shape), integrated to 5.0 cm depth.</p>
<p>To enumerate cable bacteria, cells were first detached from sediment particles using methods adapted from Kallmeyer et al. 2008, using density centrifugation with Nycodenz (50% wt/vol), and finally captured on filters (0.2 µm cellulose acetate). The identity of cable bacteria was first confirmed using fluorescent <em>in situ</em> hybridization (FISH) with the DSB706 oligoprobe (Schauer et al. 2014) on a subset of samples, and then enumerated following staining by Sybr Green I. A minimum of 200 randomly selected fields were viewed at 630X (Zeiss Axio Imager 2). Data are reported as cumulative length of cable bacteria filaments per volume of sediment, and as cumulative volume of cable bacteria computed assuming a cylindrical shape and cell diameter of 1 micron, each integrated to 4.0 cm depth.</p>
<p>For analysis of chlorophyll <em>a</em> (Chl<em>a</em>) concentration in surface sediments (0-0.5 cm), pigments were extracted into 90% acetone, applying agitation by gentle sonication, and pooling 2-3 successive extractions. Pigment concentration was determined colorimetrically (ThermoScientific Evolution 60S), applying the empirical formula of (Jeffrey et al. 1975).</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). Immediately after sediment core retrieval, temperature and salinity of the water overlying sediments were measured with hand-held sensors (Orion Star A329 portable multimeter). Cores were then 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. Core sectioning was conducted within 1 day of core retrieval.</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
T_degC_BW
Salinity_BW
Begg_Density
DSB_Density_len
DSB_Density_vol
SurfaceChla
Zeiss Axio Imager 2
gravity corer (Uwitec)
Zeiss AxioVert A1
Orion Star A329 portable multimeter
ThermoScientific Evolution 60S
theme
None, User defined
date
year
month of year
day of month
site
latitude
longitude
depth_w
water temperature at measurement depth
salinity
density
chlorophyll a
featureType
BCO-DMO Standard Parameters
Fluorescence Microscope
Gravity Corer
Inverted Microscope
Multi Parameter Portable Meter
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
-76.49402
-76.42794
38.55505
38.55728
2017-03-27
2018-08-24
Chesapeake Bay sediments; Mid-Atlantic Coastal sediments
0
BCO-DMO catalogue of parameters from Microscopy counts (Beggiatoa-like filaments, Cable bacteria), together with in situ temperature and salinity and surface sediment chlorophyll concentrations, of ex situ sediment cores collected in the Chesapeake Bay 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/847990.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/847991.rdf
Name: Year
Units: unitless
Description: <p>year of field sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/847992.rdf
Name: Month
Units: unitless
Description: <p>month of field sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/847993.rdf
Name: Day
Units: unitless
Description: <p>day of month of field sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/847994.rdf
Name: site
Units: site
Description: <p>site of sediment collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/847995.rdf
Name: lat
Units: degrees North
Description: <p>latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/847996.rdf
Name: lon
Units: degrees East
Description: <p>longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/847997.rdf
Name: site_depth
Units: meters (m)
Description: <p>depth of sampling site</p>
http://lod.bco-dmo.org/id/dataset-parameter/847998.rdf
Name: T_degC_BW
Units: degrees Celsius
Description: <p>Temperature, in situ, of bottom water</p>
http://lod.bco-dmo.org/id/dataset-parameter/847999.rdf
Name: Salinity_BW
Units: unitless
Description: <p>Salinity, in situ, of bottom water</p>
http://lod.bco-dmo.org/id/dataset-parameter/848000.rdf
Name: Begg_Density
Units: cubic millimeters per square centimeter (mm^3 cm^-2)
Description: <p>Density of Beggiatoa-like filaments, integrated to 5 cm depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/848001.rdf
Name: DSB_Density_len
Units: meters per square centimeter (m cm-2)
Description: <p>Density of cable bacteria filaments, integrated to 4 cm depth, expressed as sum length of filaments</p>
http://lod.bco-dmo.org/id/dataset-parameter/848002.rdf
Name: DSB_Density_vol
Units: cubic millimeters per square centimeter (mm^3 cm^-2)
Description: <p>Density of cable bacteria filaments, integrated to 4 cm depth, expressed as sum volume of filaments</p>
http://lod.bco-dmo.org/id/dataset-parameter/848003.rdf
Name: SurfaceChla
Units: micrograms Chla per gram DW sediment
Description: <p>Extracted Chla concentration in surface (0-0.5cm depth) sediment</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
2934
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/75ae6669-d844-57d6-a134-0aaa4b22ff58/content
download
https://doi.org/10.26008/1912/bco-dmo.847974.1
download
onLine
dataset
<p><strong>Methodology:</strong><br />
Immediately after sediment core retrieval, temperature and salinity of the water overlying sediments were measured with hand-held sensors (Orion Star A329 portable multimeter).</p>
<p>In the lab, surficial sediments were sectioned at 0.5 cm depth increments from which aliquots were collected for microscope enumeration of <em>Beggiatoa</em>-like filaments and cable bacteria filaments. <em>Beggiatoa</em>-like filament enumeration proceeded by methods adapted from Jorgensen et al. 2010 (doi: 10.1111/j.1574-6941.2010.00918), using inverted light microscopy (Zeiss AxioVert A1) with Utermöhl well slides. Filaments were identified as living <em>Beggiatoa</em>-like filaments if they were motile, unpigmented, and contained refractive sulfur granules. The length and diameter of each<em> Beggiatoa</em>-like filament encountered was recorded. Data are reported as volumetric density of<em> Beggiatoa</em>-like filaments (computed assuming a cylindrical shape), integrated to 5.0 cm depth.</p>
<p>To enumerate cable bacteria, cells were first detached from sediment particles using methods adapted from Kallmeyer et al. 2008, using density centrifugation with Nycodenz (50% wt/vol), and finally captured on filters (0.2 µm cellulose acetate). The identity of cable bacteria was first confirmed using fluorescent <em>in situ</em> hybridization (FISH) with the DSB706 oligoprobe (Schauer et al. 2014) on a subset of samples, and then enumerated following staining by Sybr Green I. A minimum of 200 randomly selected fields were viewed at 630X (Zeiss Axio Imager 2). Data are reported as cumulative length of cable bacteria filaments per volume of sediment, and as cumulative volume of cable bacteria computed assuming a cylindrical shape and cell diameter of 1 micron, each integrated to 4.0 cm depth.</p>
<p>For analysis of chlorophyll <em>a</em> (Chl<em>a</em>) concentration in surface sediments (0-0.5 cm), pigments were extracted into 90% acetone, applying agitation by gentle sonication, and pooling 2-3 successive extractions. Pigment concentration was determined colorimetrically (ThermoScientific Evolution 60S), applying the empirical formula of (Jeffrey et al. 1975).</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). Immediately after sediment core retrieval, temperature and salinity of the water overlying sediments were measured with hand-held sensors (Orion Star A329 portable multimeter). Cores were then 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. Core sectioning was conducted within 1 day of core retrieval.</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
Zeiss Axio Imager 2
Zeiss Axio Imager 2
PI Supplied Instrument Name: Zeiss Axio Imager 2 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/
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/
Zeiss AxioVert A1
Zeiss AxioVert A1
PI Supplied Instrument Name: Zeiss AxioVert A1 Instrument Name: Inverted Microscope Instrument Short Name: Instrument Description: An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana).
Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives.
The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Orion Star A329 portable multimeter
Orion Star A329 portable multimeter
PI Supplied Instrument Name: Orion Star A329 portable multimeter Instrument Name: Multi Parameter Portable Meter Instrument Short Name: Instrument Description: An analytical instrument that can measure multiple parameters, such as pH, EC, TDS, DO and temperature with one device and is portable or hand-held.
ThermoScientific Evolution 60S
ThermoScientific Evolution 60S
PI Supplied Instrument Name: ThermoScientific Evolution 60S 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/