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Aquatic GAMUT Bacterial Community Target Metagenomics-454 Pyro


Authors: Erin Jones · Zach Aanderud
Owners: iUTAH Data Manager · Erin Jones
Resource type:Generic
Created:Jul 27, 2016 at 12:36 a.m.
Last updated: Jan 02, 2018 at 8:20 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 in September 2014. Briefly, water column samples were filtered onto 0.2 um membrane filters, which were dissolved and processed with MOBIO Power Soil DNA extraction kits. We sequenced bacterial DNA (PCR-amplified using V4-region specific primers) using 454-pyrosequencing (an older sequencing method with more limitations). We cleaned, clustered (using 97% OTU similarity cut-off) and aligned sequences using the Schloss 2011 protocol, and classified OTUs to taxonomy based on the SILVA bacteria database. Code used for analysis 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.

Schloss PD, Gevers D, Westcott SL. (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PloS ONE. 6:e27310.

Subject Keywords

metagenomics,microbial ecology,water quality,Rank abundance,iUTAH

How to cite

Jones, E., Z. Aanderud (2018). Aquatic GAMUT Bacterial Community Target Metagenomics-454 Pyro, HydroShare, http://www.hydroshare.org/resource/48fc6871c51d436b83000a8d29ddb702

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

Illumina Hi-Seq samples from September 2014-October 2015 are also available on HydroShare.

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