Dataset: Geochemistry and Microscopy from Incubation Experiments

Name: Geochemistry and microscopy from incubation experiments of Chesapeake Bay sediments conducted at Horn Point Laboratory
Published: 2022-11-02
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.883171.1

Spatial Extent: N:38.55505 E:-76.42794 S:38.55505 W:-76.42794

Temporal Extent: 2018-12 - 2019-01

Project:

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

Principal Investigator:

Sairah Malkin (University of Maryland Center for Environmental Science, UMCES/HPL)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-11-02

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Geochemistry and microscopy from incubation experiments of Chesapeake Bay sediments conducted at Horn Point Laboratory

Abstract:

These data were collected as part of a sediment incubation experiment, to investigate potential interactions between estuarine cable bacteria and their associated microbial community. Sediments were collected from the main channel of Chesapeake Bay at a mesohaline station that experiences seasonal oxygen depletion. The upper 10 centimeters (cm) of sediment was homogenized under anaerobic conditions, packed into polycarbonate core liners, and incubated in a dark climate-controlled room in aerated aquaria with artificial seawater (S=15.5; T=16 degrees Celsius). In a sub-set of core tubes, a 0.2 micron polycarbonate filter was held embedded at 0.5 cm depth, to block the downward growth of cable bacteria while allowing for porewater diffusion. The sediments (with and without embedded filters) were destructively sampled on 6 dates over 46 days, at which time nucleic acids, samples for microscopy, and samples for porewater geochemistry were collected. Microsensor profiling (oxygen (O2), pH, hydrogen sulfide (H2S)) was conducted alongside the destructive sampling. Associated nucleic acid data are available through NCBI Sequence Read Archive, under Bioproject PRJNA833464. Sediment porewaters were handled anaerobically, and were extracted by centrifugation followed by filtration (0.2 micron in-line filters). Geochemical data include porewater anions (sulfate and chloride) measured by ion chromatography, and ammonium and ferrous iron concentrations measured by standard colorimetric methods. Microscopy data include both counts of cable bacteria measured with FISH oligoprobe DSB706, and total single cell bacteria. The dataset was generated by Pinky Liau under the supervision of Dr. Sairah Malkin, Horn Point Laboratory, U. Maryland Center for Environmental Sciences.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2022-11-02	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.883171.1	2022-11-14

Description

This is the first of 4 datasets associated with "Incubation Experiment (Liau) CB Sediments". There is additionally an amplicon dataset (16S rRNA gene, RNA and DNA) associated with this experiment: NCBI Sequence Read Archive, under BioProject PRJNA833464, accession numbers SAMN27993143 to SAMN27993196. The NCBI data will not be publicly available in May 2023.

Methods & Sampling

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.

Incubation conditions: 16 degrees Celsius, S=15.5, dark, aerated.

Incubation Set-up: 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.

Porewater extraction: 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 < 2).

Geochemical Measurements: Porewater sulfate and chloride were analyzed by suppressed ion chromatography following 100-fold dilutions (Dionex Integrion IC). Porewater ferrous iron (Fe2+) was measured colorimetrically using the Ferrozine assay. Ammonium was measured colorimetrically using the phenol hypochlorite method.

Cell Enumeration: Samples for microbial cell enumeration were preserved in 96% molecular grade ethanol (1:1 v/v), gently mixed with sterile autoclaved toothpicks, and stored at -20°C. Sediment-associated cells were separated from sediment grains using an acetate buffer to dissolve carbonates, followed by washing with NaCl solution, and then gentle vortexing with a detergent mixed with methanol (Lunau et al. 2005, Kallmeyer et al. 2008). Cells were recovered using density centrifugation with Nycodenz (50% w/v). Cable bacteria filaments were enumerated using fluorescence in situ hybridization (FISH) with the DSB706 oligoprobe (Malkin et al. 2022), and total cell counts were enumerated following staining with SyBR Green I.

Data Processing Description

Data Processing:
Standard curves with a minimum of 5 concentrations were analyzed to calibrate the geochemistry data. Microscopy counts were computed based on minimum cell counts. For cable bacteria, a minimum of 200 fields or 30 filaments were counted (whichever came first). For single total cell counts, a minimum of 400 cells were counted, appropriately diluted to be captured in 10-20 fields. The proportion of the slide examined was computed based on the field size, confirmed with a stage micrometer.

BCO-DMO Processing:
- replaced "NA" with "nd" (no data value);
- renamed fields to comply with BCO-DMO naming conventions.

Data Files

File
geochem.csv (Comma Separated Values (.csv), 3.51 KB) MD5:792d3f827a6a9580d7cc1cae63a8775b Primary data file for dataset ID 883171

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1756877
NSF Division of Ocean Sciences	OCE-1756851

Deployments

None available yet

Instruments

Aquarium

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Aquarium

Generic Description:

Aquarium - a vivarium consisting of at least one transparent side in which water-dwelling plants or animals are kept

Camera

Supplied Name: Zeiss AxioCam MR camera

Supplied Description:

Zeiss Axiophot fluorescent microscope equipped with a digital Zeiss AxioCam MR camera, and Zen Pro software

Instrument Type

Generic Name: Camera

Acronym: camera

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/311/

Generic Description:

All types of photographic equipment including stills, video, film and digital systems.

Centrifuge

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Centrifuge

Generic Description:

A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.

Fluorescence Microscope

Supplied Name: Zeiss Axiophot fluorescent microscope

Supplied Description:

Zeiss Axiophot fluorescent microscope equipped with a digital Zeiss AxioCam MR camera, and Zen Pro software

Instrument Type

Generic Name: Fluorescence Microscope

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/

Generic 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.

Ion Chromatograph

Supplied Name: Dionex Integrion IC with IonPac AS-19 analytical column

Supplied Description:

Porewater sulfate and chloride were analyzed by suppressed ion chromatography.

Instrument Type

Generic Name: Ion Chromatograph

Generic Description:

Ion chromatography is a form of liquid chromatography that measures concentrations of ionic species by separating them based on their interaction with a resin. Ionic species separate differently depending on species type and size. Ion chromatographs are able to measure concentrations of major anions, such as fluoride, chloride, nitrate, nitrite, and sulfate, as well as major cations such as lithium, sodium, ammonium, potassium, calcium, and magnesium in the parts-per-billion (ppb) range. (from http://serc.carleton.edu/microbelife/research_methods/biogeochemical/ic.html)

Spectrophotometer

Supplied Name: ThermoScientific Genesis UV/Vis

Supplied Description:

Used to determine NH4 and Fe

Instrument Type

Generic Name: Spectrophotometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/

Generic 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.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Sample_ID	A unique code for each sample	unitless	sample
Treatment	The treatment of the sediments; values are “NoFilter” or “Filter”, as described in methods	unitless	treatment
Day	Time of sampling after cores were homogenized and incubated in days	days	time_elapsed
TopDepth_cm	The upper depth of the sediment sample	centimeters below surface	depth_core
BottomDepth_cm	The lower depth of the sediment sample	centimeters below surface	depth_core
NH4_uM	Porewater ammonium concentration	micromolar (uM)	NH4
Fe2_uM	Porewater ferrous iron concentration	micromolar (uM)	Fe
Cl_mM	Porewater chloride concentration	millimolar (mM)	chloride
SO4_mM	Porewater sulfate concentration	millimolar (mM)	SO4
Microscopy_DSB706_cell_cm3	Microscopy counts using DSB706 oligo probe (i.e., cable bacteria)	cells per cubic centimeter	abundance
Microscopy_AllSingleCells_cells_cm3	Microscopy counts of all single cells (SYBR Green)	cells per cubic centimeter	abundance

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Database

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Dataset: Geochemistry and Microscopy from Incubation Experiments