SRA accession and collection metadata for sediments samples collected at two Chesapeake Bay stations from Mar 2017 to Aug 2018

Website: https://www.bco-dmo.org/dataset/963428
Data Type: Other Field Results
Version: 1
Version Date: 2025-06-02

Project
» Collaborative Research: Probing the Metabolic and Electrical Interactions of Cable Bacteria in Anoxic Sediments (Anoxic Sediment Bacteria Interactions)
ContributorsAffiliationRole
Malkin, SairahUniversity of Maryland Center for Environmental Science (UMCES/HPL)Principal Investigator
Mickle, AudreyWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Abstract
To examine the seasonality of sulfur oxidizers in surface sediments in seasonality oxygen stressed sediments of the Chesapeake Bay, surface sediments (0-0.5 cm depth) were collected on 10 occasions spanning all seasons over the course of two years by gravity coring at a pair of stations with differing summer bottom water oxygen concentrations. Samples were collected from March of 2017 to August of 2018. One station was located in the central channel which experiences severe summer hypoxia (CB4.3C) and one station was located on an adjacent shoal where bottom waters are better ventilated (CB4.3W; station names associated with Chesapeake Bay Water Quality Monitoring Program). At both stations, the waters are mesohaline and the sediments are fine grained. The study was designed to enable a description of the seasonality of benthic microbial communities at paired locations with contrasting degrees of bioturbation. This dataset includes collection metadata, Sequence Read Archive (SRA) and BioSample accessions under BioProject PRJNA613483 at The National Center for Biotechnology Information and are associated with BCO-DMO datasets, all listed under related datasets. The SRA project title is “Chesapeake Bay Surface Sediment Seasonal Study”.


Coverage

Location: Chesapeake Bay sediments, at two stations, CB4.3C (38.55505 N -76.42794 W; 26 m depth) and CB4.3W (38.55728 N -76.49402 W; 9m depth).
Spatial Extent: N:38.55728 E:-76.42794 S:38.55505 W:-76.49402
Temporal Extent: 2017-03-27 - 2018-08-16

Methods & Sampling

From March of 2017 to August of 2018, sediments samples were collected at two Chesapeake Bay stations: CB4.3C (38.55505 N -76.42794 W; 26 m depth) and CB4.3W (38.55728 N -76.49402 W; 9m depth). 

Replicate sediment cores were collected using a gravity corer (Uwitec; clear PVC liners, Ø = 8.6 cm), 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. From each station, one sediment core was subsampled for nucleic acids, microscopy, and chlorophyll a (Chl a) analyses, two cores were used for microsensor profiling. Sampling was undertaken from small vessels (Parker or Wetsig boats). Surface sediments (0–0.5 cm) were transferred to 5-mL cryovials, rapidly frozen in a liquid nitrogen-charged dry shipper, and stored at -80 degC. 

This data set refers to the DNA samples. DNA was extracted from a thawed sediment aliquot. Prior to cell lysis, carbonates were dissolved in an acetate buffer–PBS solution with gentle mixing, and soluble (extracellular) DNA was removed by washing in Tris- EDTA buffer with gentle mixing. Cell lysis was achieved using a combination of bead-beating, repeated heat-thaw cycling, and chemical lysis. Extracted DNA was purified by two washes with a chloroform–isoamyl alcohol solution and then precipitated with a PEG 8000-NaCl solution in the presence of linear polyacrylamide at room temperature. A final wash was made in 70% ethanol, and the resultant DNA pellet was allowed to air dry and then dissolved in water. Extracted DNA quality was checked by agarose gel electrophoresis, and its concentration was measured by fluorometry (Qubit 2.0 fluorometer; Invitrogen) using Qubit dsDNA assay kits. Further purification was found to be unnecessary. The hypervariable region V4-V5 of the 16S rRNA gene was targeted for amplification, using the modified primer pair515F-Y/926R (GTG YCA GCM GCC GCG GTA A)/(CCG YCA ATT YMT TTR AGT TT) (Parada et al. 2015). Amplification,  barcoding, and sequencing were performed at the Bioanalytical Services Laboratory (BASLAB, IMET). Amplification proceeded via two steps, first for gene amplification and the second for adding indexes, and clean-up was accomplished using AMPure XP beads (Beckman Coulter). Amplicons were sequenced using an Illumina MiSeq platform (2 x 300 nt paired-end reads).


BCO-DMO Processing Description

- Imported "SRA_samples_ChesapeakeBay_sediments_2017-2018.xlsx" into BCO-DMO system
- Added "Latitude" and "Longitude" for stations as described in the metadata
- Exported file as "963428_v1_sra_samples_cb_sediments.csv"


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Data Files

File
963428_v1_sra_samples_cb_sediments.csv
(Comma Separated Values (.csv), 1.08 KB)
MD5:33cd516438010f043e9c933cb7770327
Primary data file for dataset ID 963428, version 1

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Related Publications

Malkin, S. Y., Liau, P., Kim, C., Hantsoo, K. G., Gomes, M. L., & Song, B. (2022). Contrasting controls on seasonal and spatial distribution of marine cable bacteria (Candidatus Electrothrix) and Beggiatoaceae in seasonally hypoxic Chesapeake Bay. Limnology and Oceanography, 67(6), 1357–1373. Portico. https://doi.org/10.1002/lno.12087
Methods
,
Results
Parada, A. E., Needham, D. M., & Fuhrman, J. A. (2016). Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environmental Microbiology, 18(5), 1403–1414. doi:10.1111/1462-2920.13023
Methods

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Related Datasets

IsRelatedTo
Malkin, S. (2021) H2S 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 doi:10.26008/1912/bco-dmo.847949.1 [view at BCO-DMO]
Relationship Description: This dataset includes measurements collected from the same set of field sampling campaigns using the same sediment cores.
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 doi:10.26008/1912/bco-dmo.847974.1 [view at BCO-DMO]
Relationship Description: This dataset includes measurements collected from the same set of field sampling campaigns.
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 doi:10.26008/1912/bco-dmo.847923.1 [view at BCO-DMO]
Relationship Description: This dataset includes measurements collected from the same set of field sampling campaigns using the same sediment cores.
Malkin, S. (2022) O2 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 2022-11-08 doi:10.26008/1912/bco-dmo.883412.1 [view at BCO-DMO]
Relationship Description: This dataset includes measurements collected from the same set of field sampling campaigns using the same sediment cores.
References
University of Maryland Center for Environmental Sciences. Chesapeake Bay Surface Sediment Seasonal Study. 2020/05. In: BioProject [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; 2011-. Available from: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA613483.

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Parameters

ParameterDescriptionUnits
sample_name

Unique Sample Name

unitless
bioproject_accession

Accession number in NCBI

unitless
collection_date

Date of sample collection

unitless
Station_Name

Name of station (CB4.3C or CB4.3W)

unitless
Latitude

Latitude of sample collection, postive is North

decimal degrees
Longitude

Longitude of sample collection, negative is West

decimal degrees


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Instruments

Dataset-specific Instrument Name
MiSeq platform
Generic Instrument Name
Automated DNA Sequencer
Dataset-specific Description
 Amplification,  barcoding, and sequencing were performed at the Bioanalytical Services Laboratory (BASLAB, IMET), where amplicons were sequenced using an Illumina MiSeq platform. 
Generic Instrument Description
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.

Dataset-specific Instrument Name
water bath
Generic Instrument Name
circulating water bath
Dataset-specific Description
Replicate sediment cores were collected using a gravity corer (Uwitec; clear PVC liners, Ø = 8.6 cm), 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. 
Generic Instrument Description
A device designed to regulate the temperature of a vessel by bathing it in water held at the desired temperature. [Definition Source: NCI] 

Dataset-specific Instrument Name
Qubit 2.0 fluorometer
Generic Instrument Name
Fluorometer
Dataset-specific Description
Extracted DNA was quantified using a Qubit 2.0 fluorometer (Invitrogen).
Generic Instrument Description
A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.

Dataset-specific Instrument Name
Uwitec gravity corer
Generic Instrument Name
Gravity Corer
Dataset-specific Description
Coring was undertaken using a Uwitec gravity corer. 
Generic 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).


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Project Information

Collaborative Research: Probing the Metabolic and Electrical Interactions of Cable Bacteria in Anoxic Sediments (Anoxic Sediment Bacteria Interactions)

Coverage: Chesapeake Bay sediments; Mid-Atlantic Coastal sediments


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.



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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