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.
This resource contains links to external content. Linked content is
NOT stored in HydroShare, and we can't guarantee its availability, quality, or
security.
Confirm files deletion
Consider saving a copy of the files before you delete it if it is
important to you.
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).
File larger than 1GB cannot be downloaded directly via HTTP. Please
create an iRODS account in your iRODS user zone from your profile page
if you have not done so already, and replicate the resource to your iRODS
user zone, then download the large file via iRODS clients such as
icommands and
Cyberduck.
Resource License Agreement
This resource is shared under the Creative Commons Attribution CC BY.
In downloading this resource contents you are ethically bound to respect the terms of this license.
Please confirm that you accept the terms of this license below before you can do any downloads for this resource.
Resource License Agreement
This resource is shared under the Creative Commons Attribution CC BY.
In downloading this resource contents you are ethically bound to respect the terms of this license.
Please confirm that you accept the terms of this license below before you can do any downloads for this resource.
Copy resource bag to your iRODS user zone
Are you sure you want to copy this resource bag to your iRODS user zone?
Please wait for the process to complete.
Redirecting to the referenced web URL
The content you have requested to access is not stored in HydroShare, and we can’t guarantee its availability,
quality, security, or size. If the externally linked content is large, access may take time.
Comments
Erin Jones 1 year, 8 months ago
454-pyrosequence of September samples are also available on HydroShare.
ReplyNew Comment