1b:I[42426,["/_next/static/immutable/chunks/1xctgzqre-wsy.js","/_next/static/immutable/chunks/06_-wz6pdtp2b.js","/_next/static/immutable/chunks/30e52g49hg40p.js","/_next/static/immutable/chunks/02yq6tul2z-oh.js","/_next/static/immutable/chunks/10bx_ec2vj7n_.js","/_next/static/immutable/chunks/33bfn03fo8xnt.js","/_next/static/immutable/chunks/0tfjf78scu61b.js","/_next/static/immutable/chunks/31xnvej4n1bi9.js"],"default"] 1c:Taf6,

Methodology:
Immediately after sediment core retrieval, temperature and salinity of the water overlying sediments were measured with hand-held sensors (Orion Star A329 portable multimeter).

In the lab, surficial sediments were sectioned at 0.5 cm depth increments from which aliquots were collected for microscope enumeration of Beggiatoa-like filaments and cable bacteria filaments. Beggiatoa-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 Beggiatoa-like filaments if they were motile, unpigmented, and contained refractive sulfur granules. The length and diameter of each Beggiatoa-like filament encountered was recorded. Data are reported as volumetric density of Beggiatoa-like filaments (computed assuming a cylindrical shape), integrated to 5.0 cm depth.

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 in situ 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.

For analysis of chlorophyll a (Chla) 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).

Sampling and Analytical Procedures:
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.

1d:T5b4,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.1e:T1042,NSF Award Abstract: 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. 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. 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.6:["$","$L1b",null,{"dataset":{"_id":"847974","description":"","problem":"","acquisition":"$1c","processing":"

BCO-DMO Processing:
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date of field sampling (local time zone; EST); format: YYYY-MM-DD

","units":{"_id":"","name":"unitless"},"type":{"_id":"1070","name":"date","description":"

date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)

"}},{"_id":"847991","name":"Year","format":"","frictionlessType":"integer","description":"

year of field sampling

","units":{"_id":"","name":"unitless"},"type":{"_id":"1062","name":"year","description":"

year, reported as YYYY, e.g. 1995

"}},{"_id":"847992","name":"Month","format":"","frictionlessType":"integer","description":"

month of field sampling

","units":{"_id":"","name":"unitless"},"type":{"_id":"1115","name":"month","description":"

Month of year; numeric 1 to 12.

"}},{"_id":"847993","name":"Day","format":"","frictionlessType":"integer","description":"

day of month of field sampling

","units":{"_id":"","name":"unitless"},"type":{"_id":"1113","name":"day","description":"

day of month; numeric 1 to 31

"}},{"_id":"847994","name":"site","format":"","frictionlessType":"string","description":"

site of sediment collection

","units":{"_id":"","name":"site"},"type":{"_id":"1124","name":"site","description":"

Sampling site identification.

"}},{"_id":"847995","name":"lat","format":"","frictionlessType":"number","description":"

latitude

","units":{"_id":"","name":"degrees North"},"type":{"_id":"730","name":"latitude","description":"

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

"}},{"_id":"847996","name":"lon","format":"","frictionlessType":"number","description":"

longitude

","units":{"_id":"","name":"degrees East"},"type":{"_id":"731","name":"longitude","description":"

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datasets as degrees, minutes

"}},{"_id":"847997","name":"site_depth","format":"","frictionlessType":"integer","description":"

depth of sampling site

","units":{"_id":"","name":"meters (m)"},"type":{"_id":"818","name":"depth_w","description":"

water depth, in meters

"}},{"_id":"847998","name":"T_degC_BW","format":"","frictionlessType":"number","description":"

Temperature, in situ, of bottom water

","units":{"_id":"","name":"degrees Celsius"},"type":{"_id":"733","name":"temperature","description":"

water temperature at measurement depth

"}},{"_id":"847999","name":"Salinity_BW","format":"","frictionlessType":"number","description":"

Salinity, in situ, of bottom water

","units":{"_id":"","name":"unitless"},"type":{"_id":"955","name":"sal","description":"

Salinity: The amount (mass or quantity of matter) of salt per amount (volume or mass) of a body of water.

"}},{"_id":"848000","name":"Begg_Density","format":"","frictionlessType":"number","description":"

Density of Beggiatoa-like filaments, integrated to 5 cm depth

","units":{"_id":"","name":"cubic millimeters per square centimeter (mm^3 cm^-2)"},"type":{"_id":"806","name":"density","description":"

density, in mass per unit volume

"}},{"_id":"848001","name":"DSB_Density_len","format":"","frictionlessType":"integer","description":"

Density of cable bacteria filaments, integrated to 4 cm depth, expressed as sum length of filaments

","units":{"_id":"","name":"meters per square centimeter (m cm-2)"},"type":{"_id":"806","name":"density","description":"

density, in mass per unit volume

"}},{"_id":"848002","name":"DSB_Density_vol","format":"","frictionlessType":"number","description":"

Density of cable bacteria filaments, integrated to 4 cm depth, expressed as sum volume of filaments

","units":{"_id":"","name":"cubic millimeters per square centimeter (mm^3 cm^-2)"},"type":{"_id":"806","name":"density","description":"

density, in mass per unit volume

"}},{"_id":"848003","name":"SurfaceChla","format":"","frictionlessType":"number","description":"

Extracted Chla concentration in surface (0-0.5cm depth) sediment

","units":{"_id":"","name":"micrograms Chla per gram DW sediment"},"type":{"_id":"766","name":"chlorophyll a","description":"

Total chlorophyll a pigment. See dataset for units of measurement; often reported in: milligrams per cubic meter (mg/m3); micrograms/liter (ug/L); nanograms/liter (ng/L).

CAUTION Within JGOFS MERGED water column products: this parameter is derived from HPLC methodology and the units are nanograms/liter; however; this parameter name is also used for a variety of water and nonwater column sampling; derived via the fluorometric method; units will also vary.

"}}],"related_publications":[{"id":"737009","citation":"Jeffrey, S. W., & Humphrey, G. F. (1975). New spectrophotometric equations for determining chlorophylls a, b, c1 and c2 in higher plants, algae and natural phytoplankton. Biochemie Und Physiologie Der Pflanzen, 167(2), 191–194. doi:10.1016/s0015-3796(17)30778-3\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"850278","citation":"Jørgensen, B. B., Dunker, R., Grünke, S., & Røy, H. (2010). Filamentous sulfur bacteria, Beggiatoa spp., in arctic marine sediments (Svalbard, 79°N). FEMS Microbiology Ecology, no–no. doi:10.1111/j.1574-6941.2010.00918.x\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"847983","citation":"Kallmeyer, J., Smith, D. C., Spivack, A. J., & D’Hondt, S. (2008). New cell extraction procedure applied to deep subsurface sediments. Limnology and Oceanography: Methods, 6(6), 236–245. doi:10.4319/lom.2008.6.236\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"847984","citation":"Schauer, R., Risgaard-Petersen, N., Kjeldsen, K. U., Tataru Bjerg, J. J., B Jørgensen, B., Schramm, A., & Nielsen, L. P. (2014). Succession of cable bacteria and electric currents in marine sediment. The ISME Journal, 8(6), 1314–1322. doi:10.1038/ismej.2013.239\r\n","relation_type":["Methods"],"relation_desc":""}],"related_datasets":[{"_id":"963428","name":"SRA accessions from Chesapeake Bay sediment samples 2017-2018","url":"","relation_type":"IsRelatedTo","type_desc":"

The dataset is related to another dataset.

\n","relation_desc":"This dataset includes measurements collected from the same set of field sampling campaigns.","citation":"Malkin, S. (2025) SRA accession and collection metadata for sediments samples collected at two Chesapeake Bay stations from Mar 2017 to Aug 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-06-02 doi:10.26008/1912/bco-dmo.963428.1"}],"services":[{"grouping":"","items":[{"name":"View Data","description":"An in-browser view of the primary tabular data file","url":"https://www.bco-dmo.org/dataset/847974/data/view","contentType":"text/html","actionType":"view"}]},{"grouping":"Metadata","items":[{"name":"HTML","description":"A simple HTML page of the dataset metadata","url":"https://www.bco-dmo.org/dataset/847974/description","contentType":"text/html","actionType":"view"},{"name":"PDF","description":"A PDF of the HTML dataset metadata","url":"https://www.bco-dmo.org/dataset/847974/Dataset_description.pdf","contentType":"application/pdf","actionType":"download"},{"name":"ISO 19115-2 (NOAA Profile)","description":"","url":"https://www.bco-dmo.org/dataset/847974/iso","contentType":"application/xml","actionType":"download"}]}],"programs":[],"projects":[{"_id":"773452","name":"Collaborative Research: Probing the Metabolic and Electrical Interactions of Cable Bacteria in Anoxic Sediments","acronym":"Anoxic Sediment Bacteria Interactions","description":"$1e"}],"archives":[{"id_value":"10.26008/1912/bco-dmo.847974.1","url":"https://doi.org/10.26008/1912/bco-dmo.847974.1","date_assigned":"2021-04-26","version_date":"2021-04-07","archiver":"Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)","archiver_id":"272"}],"license":{"name":"Creative Commons Attribution 4.0","id":"CC-BY-4.0","uri":"https://creativecommons.org/licenses/by/4.0/","spdxUri":"https://spdx.org/licenses/CC-BY-4.0"},"metrics":{"views":{"count":150},"downloads":{"count":309}}},"fileId":"903330"}]