URLhttps://www.bco-dmo.org/dataset/628253
Download URLhttps://www.bco-dmo.org/dataset/628253/data/download
Media Typetext/tab-separated-values
CreatedDecember 4, 2015
ModifiedSeptember 16, 2016
StateFinal no updates expected
Brief DescriptionMetagenomes from Delaware estuarine riverbank sediment.

Acquisition Description

Sample collection and storage: A riverbank sediment core was extracted from the Oyster Rocks site of the Broadkill River in Milton, Delaware in July 2012, accessed on foot. Extraction was performed with a polycarbonate push core. Samples were taken in 3 cm slices along the depth of the core and frozen at -80 degrees C until DNA extractions were performed.

DNA digestion and Illumina sequencing: DNA was extracted using a MoBio Powersoil DNA kit. Extracted DNA was digested with HpaII restriction endonuclease. Illumina library preparation and 150-cycle single-read sequencing was performed on an Illumina Hi-Seq 2500 at the University of Delaware Sequencing and Genotyping Center (Delaware Biotechnology Institute).

Raw reads are publicly available through the European Nucleotide Archive at http://www.ebi.ac.uk/ena/data/view/ERP013107

Instruments

polycarbonate push core [Push Corer]
Details
Instance Description (polycarbonate push core)

A riverbank sediment core was extracted from the Oyster Rocks site of the Broadkill River in Milton, Delaware in July 2012. Extraction was performed with a polycarbonate push core.

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/

Parameters

site [site]
Details
site

Description/name of site.

Sampling site identification.
lat [latitude]
Details
lat

Latitude of sampling site.

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

lon [longitude]
Details
lon

Longitude of sampling site. (Negative = West)

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

description [brief_desc]
Details
description

Brief description of the data.

brief description, open ended, specific to the data set in which it appears

Details
ENA_ID

Project ID number in the European Nucleotide Archive.

Database identifier assigned by repository and linked to GenBank or other repository.
ENA_URL [unknown]
Details
ENA_URL

Hyperlink to European Nucleotide Archive for this project ID.

association with a community-wide standard parameter is not yet defined

Dataset Maintainers

NameAffiliationContact
Jennifer F. BiddleUniversity of Delaware
Adam MarshUniversity of Delaware
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project TitleMetagenomic analysis of microbial CpG methylation in Delaware estuarine riverbank sediment
AcronymMicrobial CpG Methylation
URLhttps://www.bco-dmo.org/project/628237
CreatedDecember 4, 2015
ModifiedDecember 4, 2015
Project Description

Marine sediments harbor a vast amount of Earth’s microbial biomass, yet little is understood regarding how cells subsist in these low-energy environments without forming endospores. DNA methylation, a reversible process that involves the addition of a methyl group to a nucleotide base via a methyltransferase, exists as a possible epigenetic mechanism for non-sporulated cells in low-energy sediment environments to regulate gene expression and potentially lower cellular activity. To investigate the presence and scope of this phenomenon in estuarine sediment microbial communities, we sequenced three metagenomic and 16S rRNA gene amplicon libraries extracted from a sediment core collected from the banks of the Oyster Rocks site of the Broadkill River, Milton, Delaware, USA. We targeted 5-methylcytosine at CpG sites by digesting metagenomic libraries with the methylation-sensitive restriction endonuclease HpaII. By quantitatively distinguishing "mixed" methylation states for populations of CpG site copies, we identified dynamic, non-binary shifts in CpG methylation for community taxa and function.

Project Maintainers
NameAffiliationRoleContact
Jennifer F. BiddleUniversity of DelawarePrincipal Investigator
Adam MarshUniversity of DelawareCo-Principal Investigator
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