Dataset: Gene Abundance

Name: Microbial gene abundance of coastal wetland soil cores collected in June 2018 from Barataria Bay, Louisiana
Published: 2021-02-10
Keywords: gene abudance, microbial activity, Barataria Bay, wetland submergence, coastal wetlands, soil organic matter, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.840278.1

Spatial Extent: N:29.443547 E:-89.8998 S:29.443547 W:-89.8998

Temporal Extent: 2018-06 - 2018-06

Project:

Fate of Coastal Wetland Carbon Under Increasing Sea Level Rise: Using the Subsiding Louisiana Coast as a Proxy for Future World-Wide Sea Level Projections (Submerged Wetland Carbon)

Principal Investigator:

Lisa G. Chambers (University of Central Florida, UCF)

Co-Principal Investigator:

Robert L. Cook (Louisiana State University, LSU)

John R. White (Louisiana State University Dept. of Oceanography and Coastal Science, LSU-DOCS)

Zuo Xue (Louisiana State University Dept. of Oceanography and Coastal Science, LSU-DOCS)

Student:

Havalend E. Steinmuller

Contact:

Lisa G. Chambers (University of Central Florida, UCF)

BCO-DMO Data Manager:

Dana Stuart Gerlach (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Taylor Heyl (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2021-02-10

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Microbial gene abundance of coastal wetland soil cores collected in June 2018 from Barataria Bay, Louisiana

Abstract:

Nine coastal wetland soil cores (150cm) collected in June 2018 from Barataria Bay, Louisiana were analyzed for microbial gene abundance

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2021-02-10	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.840278.1	2021-05-21

Methods & Sampling

Nine coastal wetland soil cores were collected in June 2018 from Barataria Bay, Louisiana, a shallow open water basin located west of the Mississippi River Delta. Soil cores were collected along three transects, roughly 1 meter apart, that consisted of three points: the coastal fringe (0 m inland), 1 meter inland, and 2 meters inland. Soil cores were collected in polycarbonate tubes via the push core method to a depth of 150 cm, and field-extruded into 15 separate 10-cm intervals. Soils were stored in polyethylene bags on ice and immediately transported back to the laboratory, where they were kept at 4 °C until sample analysis was complete.

This dataset includes analyses of microbial gene abundance. Quantitative PCR analysis on a CFX96 Touch Real-Time PCR Detection system was used to measure the number of gene copies of bacteria (16S), sulfate reduction (dsRa), and archaea (Arch) genes.

Soil samples were sieved through a 2mm seive, then centrifuged at 4000 rpm at 25°C for 1 minute, and excess water decanted. DNA was extracted from soil subsamples (0.25 grams each) following DNAeasy PowerSoil Extraction Kit (QIAGEN, Hilden, Germany). Primers were selected to amplify specific taxonomic and functional genes of interest within the samples -- sulfate reduction (dsrA), all bacteria (16S), and all archaea (Arch). Genomic DNA from Desulfobacterium autotrophicum (Strain DSM 3382) was used to establish standard curves for both amplification of the 16S gene and the dsrA gene, while Methanococcus voltae (Strain A3) was used to establish standard curves for amplification of the Arch gene. Each 25 microliter reaction contained 5 microliters DNA, 1.25 microliters of each 0.1uM primer (forward and reverse), 12.5 microliters of SYBR green MasterMix, and 12.5 microliters of PCR-grade water. Each reaction initially proceeded through steps at 50°C and 95°C, then through 50 cycles of denaturing at 95°C, annealing, and extending at 72°C.

[For details on primers and primer annealing temperatures, see Steinmuller and Chambers (2019)].

Data Processing Description

Data processing:
All statistical analysis was performed in R (R Institute for Statistical Computing, Vienna, Austria) using RStudio (RStudio Inc., Boston, MA, USA). The Shapiro-Wilk test was used to verify assumptions of normality, and a logarithmic transformation was performed on all datasets. Levene’s test was used to determine homogeneity of variance. A linear mixed-effect model (package ‘lmer’) was used to test the following predictor variables: depth, distance inland, and the interaction of depth and distance inland on the samples collected from the marsh. Isotopic determinations and quantitative PCR analysis was performed exclusively on the three replicate cores taken 1 meter inland, and thus depth was the only predictor variable tested for those parameters. Following determination of significance within one of the predictor variables, the package ‘lsmeans’ was used for post-hoc pairwise comparisons using the Tukey method.

BCO-DMO processing:
- Added a conventional header with dataset name, PI names, version date
- Adjusted parameter names to comply with database requirements.
- Units removed and added to Parameter Description metadata section.
- Added Latitude and Longitude columns, converted DMS to DD
- Added column for Date of sample collection
- Missing data entries replaced with 'nd'

Data Files

File
gene_abundance.csv (Comma Separated Values (.csv), 9.69 KB) MD5:4ccfa86d7add837d4546dff3b4dca144 Primary data file for dataset ID 840278

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1635837

Deployments

None available yet

Instruments

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.

Push Corer

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Push Corer

Generic Description:

Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.

Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/

Thermal Cycler

Supplied Name: CFX96 Touch Real-Time PCR Detection System

Supplied Description:

The number of gene copies for each sample was determined through qPCR analysis on a CFX96 Touch Real-Time PCR Detection System

Instrument Type

Generic Name: Thermal Cycler

Generic Description:

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Field_Replicate	Denotation of whether core was the 1st (A), 2nd (B), or 3rd (C) core pulled from the site	unitless	replicate
Depth	Soil depth below the surface	centimeters (cm)	depth
Plate_Replicate	Denotation of whether the plate was the 1st, 2nd, or 3rd plate run as analytical replicates	unitless	replicate
Bacteria	Abundance of 16S gene within a given subsample of soil	gene copies	genetic_conc
dsrA	Abundance of dsrA gene within a given subsample of soil	gene copies	genetic_conc
Archaea	Abundance of Arch gene within a given subsample of soil	gene copies	genetic_conc
Latitude	Latitude	decimal degrees	lat
Longitude	Longitude (west is negative)	decimal degrees	lon
Date_collected	Date of sample collection Format: yyyy-mm-dd	unitless	date

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Dataset: Gene Abundance