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Aquatic GAMUT Bacterial Community Target Metagenomics-HiSeq

Authors: Erin Jones · Zach Aanderud
Owners: Erin Jones · iUTAH Data Manager
Resource type:Generic
Created:Jul 31, 2017 at 6:30 p.m.
Last updated: Jan 02, 2018 at 8:19 p.m. by Erin Jones

Abstract

This data was collected as part of a study to understand the connectivity and diversity of stream bacteria communities in streams flowing from high to low elevation through different types of urbanization and in different seasons. The dataset contains OTU (operational taxonomic units, the bacterial surrogate for species) abundance for bacteria at iUTAH aquatic GAMUT sites (http://data.iutahepscor.org/mdf/Data/Gamut_Network/) in three watersheds at 3 time points (November 2014, February 2015, and May 2015). Briefly, we filtered water column samples onto 0.2 um membrane filters, which were dissolved and processed with MOBIO Power Soil DNA extraction kits (alternate low protocol yield using phenol chloroform). We sequenced bacterial DNA (PCR-amplified using V4 region specific primers) using Illumina Hi-Seq. We cleaned, clustered (using 97% OTU similarity cut-off) and aligned sequences using the Kozich et al. 2013 protocol, and classified OTUs to taxonomy based on the SILVA bacteria database. Code used for processing is available at https://github.com/erinfjones/mothurcode.

There are three files; site and sample metadata (e.g. date sampled) is included in the file stream_design.txt, observed OTU counts by sample are in the .shared file, and the taxonomic classification of OTUs is in the .taxonomy file.

Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. (2013): Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology. 79(17):5112-20.

Subject Keywords

microbial ecology,target metagenomics,OTU,relative abundance,water quality,iUTAH,bacteria

How to cite

Jones, E., Z. Aanderud (2018). Aquatic GAMUT Bacterial Community Target Metagenomics-HiSeq, HydroShare, http://www.hydroshare.org/resource/c0a1bb39015444ef86ace38ae6c44e77

This resource is shared under the Creative Commons Attribution CC BY.

  http://creativecommons.org/licenses/by/4.0/
CC-BY

Sharing status:

  • Public Resource  Public
  • Sharable Resource  Shareable

Coverage

Spatial:

 Coordinate System/Geographic Projection:  WGS 84 EPSG:4326
 Coordinate Units:  Decimal degrees
Place/Area Name: Multiple Watersheds

North Latitude
41.9615°
East Longitude
-110.8809°
South Latitude
40.4010°
West Longitude
-111.9795°

Temporal:

 Start Date:
 End Date:

Content

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Authors

The people or organizations that created the intellectual content of the resource.

Name Organization Address Phone Author Identifiers
Erin Jones Brigham Young University
Zach Aanderud Brigham Young University 8014224220
Extended Metadata
Name Value
Observed Variables Rank abundance
Variable Description Relative abundance of bacterial community taxa in water column
Data Processing Method Sequences have been processed using MOTHUR (Schloss et al. 2009).
Data Collection Method Streamwater aseptically vacuum filtered in the field or lab using autoclaved Nalgene filter cups and 47 mm 0.2 um membrane filters, were stored on dry ice or liquid nitrogen until extracted with MoBIO PowerMax Soil DNA kits. PCR-amplified 16S rDNA samples were sequenced using BYU’s DNA Sequencing Center (454-Pyrosequencing or Hi-Seq).

Credits

This resource was created using funding from the following sources:
Agency Name Award Title Award Number
National Science Foundation iUTAH-innovative Urban Transitions and Aridregion Hydro-sustainability 1208732

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Comments

Erin Jones 1 year, 4 months ago

454-pyrosequence of September samples are also available on HydroShare.

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