Data Package Metadata   View Summary

Catalog of GenBank sequence read archive (SRA) entries of metagenomic DNA sequence analyses of bacterial and archaeal water column communities along the Eastern Beaufort Sea coast, North Slope, Alaska, 2012

General Information
Data Package:
Local Identifier:knb-lter-ble.19.2
Title:Catalog of GenBank sequence read archive (SRA) entries of metagenomic DNA sequence analyses of bacterial and archaeal water column communities along the Eastern Beaufort Sea coast, North Slope, Alaska, 2012
Alternate Identifier:DOI PLACE HOLDER
Abstract:

In contrast to temperate systems, Arctic lagoons that span the Alaska Beaufort Sea coast face extreme seasonality. Nine months of ice cover up to ∼1.7 m thick is followed by a spring thaw that introduces an enormous pulse of freshwater, nutrients, and organic matter into these lagoons over a relatively brief 2–3 week period. Prokaryotic communities link these subsidies to lagoon food webs through nutrient uptake, heterotrophic production, and other biogeochemical processes, but little is known about how the genomic capabilities of these communities respond to seasonal variability. This study characterizes the metabolic capabilities of microbial communities across three seasons in two lagoons and one open coastal site along the eastern Alaska Beaufort Sea coast. We used metagenomic DNA sequence data of bacterial and archaeal water column communities to identify genes of relevant biogeochemical pathways.

This data package catalogs sequence read archive (SRA) entries available through GenBank BioProject PRJNA642637 at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA642637. This data package is associated with the following publication:

Baker, Kristina D., Colleen T. E. Kellogg, James W. McClelland, Kenneth H. Dunton, and Byron C. Crump. “The Genomic Capabilities of Microbial Communities Track Seasonal Variation in Environmental Conditions of Arctic Lagoons.” Frontiers in Microbiology 12 (2021). https://doi.org/10.3389/fmicb.2021.601901.

Environmental variables (physiochemical data from YSI and HOBO data loggers, as well as organic matter analysis and stable isotope data from discrete water samples) associated with this genomic dataset are available from the Arctic Data Center:

Kenneth Dunton, Byron Crump, and James McClelland. Physical, chemical, and biological data from lagoons and open coastal waters in the nearshore environment of the eastern Alaska Beaufort Sea, 2011-2013. Arctic Data Center. doi:10.18739/A2DG13.

To join the two datasets together, please use the provided site codes (column "site_name" here) and collection dates (column "collection_date" here) in each dataset.

Instead of citing this package, which is a catalog, please cite the original GenBank data, journal article, or related Arctic Data Center dataset as appropriate. Citation guidance for the journal article and related Arctic Data Center dataset is available on the respective publishers' websites.

Short Name:baker2021
Publication Date:2021-04-02
Language:English

Time Period
Begin:
2012-04-17
End:
2012-08-15

People and Organizations
Contact:Information Manager (Beaufort Lagoon Ecosystems LTER) [  email ]
Organization:Beaufort Lagoon Ecosystems LTER
Creator:Crump, Byron C (Oregon State University)
Creator:Kellogg, Colleen TE (Hakai Institute)
Creator:Baker, Kristina (Oregon State University)
Creator:McClelland, James W (The University of Texas at Austin)
Creator:Dunton, Kenneth H (The University of Texas at Austin)

Data Entities
Data Table Name:
Catalog of genomic data archived on GenBank from Baker et al. 2021
Description:
List of SRA runs, BioSamples, and associated information
Detailed Metadata

Data Entities


Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-ble/19/2/3db1d5112a7c1173eda5b6672e93554d
Name:Catalog of genomic data archived on GenBank from Baker et al. 2021
Description:List of SRA runs, BioSamples, and associated information
Number of Records:35
Number of Columns:24

Table Structure
Object Name:BLE_LTER_Baker_2021_genomic_data.csv
Size:17707 byte
Authentication:d3880d4fbe719967a2370f4d031ed832 Calculated By MD5
Text Format:
Number of Header Lines:1
Number of Foot Lines:0
Record Delimiter:\r\n
Orientation:column
Simple Delimited:
Field Delimiter:,
Quote Character:"

Table Column Descriptions
 RunRun linkBioSampleBioSample linkBioSample modelBasesBytesEnvironment local scaleEnvironment biomeExperimentExperiment linkCollection dateGeographic location nameSite nameLatitudeLongitudeDepthDepth unitLibrary nameSample sizeSample size unitSample nameMax filter pore sizeMin filter pore size
Column Name:run  
run_link  
biosample  
biosample_link  
biosamplemodel  
bases  
bytes_b  
env_local_scale  
env_biome  
experiment  
experiment_link  
collection_date  
geo_loc_name  
site_name  
latitude  
longitude  
depth  
depth_unit  
library_name  
samp_size_L  
samp_size_unit  
sample_name  
max_filter_pore_size  
min_filter_pore_size  
Definition:RunRun linkBioSampleBioSample linkBioSample modelBasesBytesEnvironment local scale (terms from the EnvO ontology)Environment biome (terms from the EnvO ontology)ExperimentExperiment linkDate of collectionGeographic location nameSite name/codeLatitude, WGS84 datumLongitude, WGS84 datumDepth or depth range of sample collectedDepth unitLibrary nameSample sizeSample size unitSample nameMax filter pore sizeMin filter pore size
Storage Type:string  
string  
string  
string  
string  
integer  
integer  
string  
string  
string  
string  
dateTime  
string  
string  
decimal  
decimal  
string  
string  
string  
decimal  
string  
string  
string  
string  
Measurement Type:nominalnominalnominalnominalnominalratiorationominalnominalnominalnominaldateTimenominalnominalintervalintervalnominalnominalnominalrationominalnominalnominalnominal
Measurement Values Domain:
Definitionany text
Definitionany text
Definitionany text
Definitionany text
Definitionany text
Unitdimensionless
Typeinteger
Unitbyte
Typeinteger
Definitionany text
Definitionany text
Definitionany text
Definitionany text
FormatYYYY-MM-DD
Precision1
Definitionany text
Definitionany text
Unitdegree
Typereal
Unitdegree
Typereal
Definitionany text
Definitionany text
Definitionany text
Unitliter
Typereal
Definitionany text
Definitionany text
Definitionany text
Definitionany text
Missing Value Code:                                                
Accuracy Report:                                                
Accuracy Assessment:                                                
Coverage:                                                
Methods:                                                

Data Package Usage Rights

This data package is released to the public domain under Creative Commons CC0 1.0 “No Rights Reserved” (see: https://creativecommons.org/publicdomain/zero/1.0/). It may be distributed, remixed, and built upon. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. It is considered professional etiquette to provide attribution of the original work if this data package is shared or utilized in whole or by individual components. A generic citation is provided for this data package on the website of the repository where these data were obtained in the summary metadata page.

Communication (and collaboration) with the creators of this data package is recommended to prevent duplicate research or publication. The consumer of these data ("Data User" herein) is urged to contact the authors of these data if any questions about methodology or results occur. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplication or inappropriate use. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation may occur if data are used outside of the context of the original study. The Data User should be aware that periodic updates of this data package may be available from the website and it is the responsibility of the Data User to check for new versions of the data.

While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy cannot be guaranteed. This data package (with its components) is made available “as is” and with no warranty of accuracy or fitness for use. The creators of this data package and the repository where these data were obtained shall not be liable for any damages resulting from misinterpretation, use or misuse of the data package or its components. Thank you.

Keywords

By Thesaurus:
LTER Controlled Vocabulary v1bacteria, estuaries, genomics, seasonality
Geographic Names Information SystemBeaufort Sea, Jago Lagoon, Kaktovik Lagoon
BLE LTER Controlled VocabularyBeaufort Lagoon Ecosystems LTER, BLE, data inventory, LTER

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package
Description:

This study characterizes the metabolic capabilities of microbial communities across three seasons in two lagoons and one open coastal site along the eastern Alaska Beaufort Sea coast. We used metagenomic DNA sequence data of bacterial and archaeal water column communities to identify genes of relevant biogeochemical pathways. Replicate water samples from two lagoons and one coastal site near Kaktovik, AK were collected in April (full ice cover), June (ice break up), and August (open water) to represent winter, spring, and summer, respectively. Samples were size fractionated to distinguish free-living and particle-attached microbial communities.

This data package catalogs sequence read archive (SRA) entries available through GenBank BioProject PRJNA642637 at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA642637. For detailed methodology, please see original publication Baker et al. 2021.

Baker, Kristina D., Colleen T. E. Kellogg, James W. McClelland, Kenneth H. Dunton, and Byron C. Crump. “The Genomic Capabilities of Microbial Communities Track Seasonal Variation in Environmental Conditions of Arctic Lagoons.” Frontiers in Microbiology 12 (2021). https://doi.org/10.3389/fmicb.2021.601901.

Environmental variables (physiochemical data from YSI and HOBO data loggers, as well as organic matter analysis and stable isotope data from discrete water samples) associated with this genomic dataset are available from the Arctic Data Center:

Kenneth Dunton, Byron Crump, and James McClelland. Physical, chemical, and biological data from lagoons and open coastal waters in the nearshore environment of the eastern Alaska Beaufort Sea, 2011-2013. Arctic Data Center. doi:10.18739/A2DG13.

To join the two datasets together, please use the provided site codes (column "site_name" here) and collection dates (column "collection_date" here) in each dataset.

People and Organizations

Publishers:
Organization:Environmental Data Initiative
Email Address:
info@environmentaldatainitiative.org
Web Address:
https://environmentaldatainitiative.org
Creators:
Organization:Beaufort Lagoon Ecosystems LTER
Address:
750 Channel View Dr.,
Port Aransas, TX 78373 USA
Email Address:
BLE-IM@utexas.edu
Web Address:
https://ble.lternet.edu/
Individual: Byron C Crump
Organization:Oregon State University
Address:
1500 SW Jefferson Way,
Corvallis, OR 97331 USA
Email Address:
byron.crump@oregonstate.edu
Id:https://orcid.org/0000-0001-7062-1273
Individual: Colleen TE Kellogg
Organization:Hakai Institute
Address:
303-1100 Island Hwy,
Campbell River, BC Canada
Email Address:
colleen.kellogg@hakai.org
Id:https://orcid.org/0000-0003-4048-5316
Individual: Kristina Baker
Organization:Oregon State University
Address:
1500 SW Jefferson Way,
Corvallis, OR 97331 USA
Email Address:
kristina.baker63@gmail.com
Id:https://orcid.org/0000-0003-2812-5502
Individual: James W McClelland
Organization:The University of Texas at Austin
Address:
750 Channel View Dr.,
Port Aransas, TX 78383 USA
Email Address:
jimm@utexas.edu
Id:https://orcid.org/0000-0001-9619-8194
Individual: Kenneth H Dunton
Organization:The University of Texas at Austin
Address:
750 Channel View Dr.,
Port Aransas, TX 78383 USA
Email Address:
ken.dunton@utexas.edu
Id:https://orcid.org/0000-0003-3498-8021
Contacts:
Organization:Beaufort Lagoon Ecosystems LTER
Position:Information Manager
Address:
MC R8000 The University of Texas at Austin,
Austin, TX 78712 USA
Email Address:
BLE-IM@utexas.edu
Web Address:
https://ble.lternet.edu/
Metadata Providers:
Organization:Beaufort Lagoon Ecosystems LTER
Address:
750 Channel View Dr.,
Port Aransas, TX 78373 USA
Email Address:
BLE-IM@utexas.edu
Web Address:
https://ble.lternet.edu/

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period
Begin:
2012-04-17
End:
2012-08-15
Sampling Site: 
Description:Bernard Point: Sampling point at Bernard Point, North Slope, Alaska, USA
Site Coordinates:
Longitude (degree): -143.637400Latitude (degree): 70.135620
Geographic Region:
Description:Jago and Kaktovik Lagoons: Bounding box contains sampling points for the Jago and Kaktovik Lagoons, North Slope, Alaska, USA
Bounding Coordinates:
Northern:  70.109570Southern:  70.089050
Western:  -143.623300Eastern:  -143.427200

Project

Parent Project Information:

Title:LTER: Beaufort Sea Lagoons: An Arctic Coastal Ecosystem in Transition
Personnel:
Individual: Kenneth Dunton
Organization:The University of Texas at Austin, Marine Science Institute
Phone:
361-749-6744 (voice)
Email Address:
ken.dunton@utexas.edu
Id:https://orcid.org/0000-0003-3498-8021
Role:Lead Principal Investigator
Individual: James McClelland
Organization:The University of Texas at Austin, Marine Science Institute
Phone:
361-749-6756 (voice)
Email Address:
jimm@utexas.edu
Id:https://orcid.org/0000-0001-9619-8194
Role:Co-Lead Principal Investigator
Individual: Byron Crump
Organization:Oregon State University
Email Address:
byron.crump@oregonstate.edu
Id:https://orcid.org/0000-0001-7062-1273
Role:Co-Principal Investigator
Individual: Amber Hardison
Organization:Virginia Institute of Marine Science, College of William & Mary
Email Address:
akhardison@vims.edu
Id:https://orcid.org/0000-0002-0891-3731
Role:Co-Principal Investigator
Individual: Katrin Iken
Organization:University of Alaska Fairbanks
Email Address:
kbiken@alaska.edu
Id:https://orcid.org/0000-0001-7961-1012
Role:Co-Principal Investigator
Individual: Jeremy Kasper
Organization:University of Alaska Fairbanks
Email Address:
jlkasper@alaska.edu
Id:https://orcid.org/0000-0003-0975-6114
Role:Co-Principal Investigator
Individual: Vanessa Lougheed
Organization:The University of Texas at El Paso
Email Address:
vlougheed@utep.edu
Id:https://orcid.org/0000-0002-6091-1151
Role:Co-Principal Investigator
Individual: Andrew Mahoney
Organization:University of Alaska Fairbanks
Email Address:
armahoney@alaska.edu
Id:https://orcid.org/0000-0002-8699-3175
Role:Co-Principal Investigator
Individual: Bailey McMeans
Organization:University of Toronto Missisauga
Email Address:
bailey.mcmeans@utoronto.ca
Id:https://orcid.org/0000-0002-9793-6811
Role:Co-Principal Investigator
Individual: Michael Rawlins
Organization:University of Massachusetts Amherst
Email Address:
rawlins@geo.umass.edu
Id:https://orcid.org/0000-0002-3323-8256
Role:Co-Principal Investigator
Individual: Yvette Spitz
Organization:Oregon State University
Email Address:
yvette.spitz@oregonstate.edu
Id:https://orcid.org/0000-0002-6026-4900
Role:Co-Principal Investigator
Individual: Craig Tweedie
Organization:The University of Texas at El Paso
Email Address:
ctweedie@utep.edu
Id:https://orcid.org/0000-0002-3409-8881
Role:Co-Principal Investigator
Individual: Christina Bonsell
Organization:The University of Texas at Austin
Email Address:
cbonsell@utexas.edu
Id:https://orcid.org/0000-0002-8564-0618
Role:Project Manager
Individual: Nathan McTigue
Organization:The University of Texas at Austin
Email Address:
mctigue@utexas.edu
Id:https://orcid.org/0000-0002-7686-7095
Role:Project Manager
Individual: Timothy Whiteaker
Organization:The University of Texas at Austin
Email Address:
whiteaker@utexas.edu
Id:https://orcid.org/0000-0002-1940-4158
Role:Information Manager
Individual: An T. Nguyen
Organization:The University of Texas at Austin
Email Address:
enthusiast@utexas.edu
Id:https://orcid.org/0000-0001-6519-0173
Role:Information Manager
Abstract:

This project established a new Long Term Ecological Research (LTER) site along the Alaskan Arctic coastline. Research based out of Utqiagvik (formerly Barrow), Deadhorse, and Kaktovik will address how changes in shoreline erosion and freshwater inflows to the coastal ocean over seasonal, annual, and longer timeframes influence near-shore food webs. Research will be conducted in collaboration with local stakeholder groups and the U.S. Fish and Wildlife Service. This research will advance our fundamental understanding of how input of materials from land and oceanographic conditions interact to influence coastal food webs. It will also allow us to track and understand: 1) how natural climate cycles influence coastal ecosystems in the Arctic, and 2) how climate change effects such as permafrost thaw, shifting precipitation regimes, and losses of sea ice alter coastal ecosystems. Near-shore food webs along the Alaskan Arctic coastline support large populations of migratory fish and waterfowl that are essential to the culture of Iñupiat communities of northern Alaska. The research at this LTER site will create a framework for anticipating the impacts of future changes on the coastal ecosystem that are of great concern to these communities. Results from this LTER program will also be of interest to a broader science community that is working to understand potential connections between Arctic change and global carbon cycling. Finally, this LTER project includes a strong commitment to education through graduate and undergraduate student involvement, post-doctoral mentoring, continuation of a very successful Summer Science K-12 Program in Kaktovik, and establishment of a parallel K-12 program in Utqiagvik. In addition, this project will employ native high school seniors or recently graduated students living in Utqiagvik and Kaktovik as field research assistants.

Recent studies suggest that the ecological framework for understanding what controls food web structure needs to be expanded to include temporal forcing. More specifically, there is mounting evidence that differential availability of seasonally-distinct resources is critical for defining trophic linkages and maintaining stability and resilience of food webs. This new LTER program will use lagoons along the Alaskan Beaufort Sea coast as experimental units to test this concept, and broaden it to include temporal variations over longer timeframes. The Beaufort lagoons are ideal for testing this concept because they experience extreme variability in seasonal cycles, which are now subject to rapid directional shifts driven by climate change. Our overarching question is: How do variations in terrestrial inputs, local production, and exchange between lagoon and ocean waters over seasonal, inter-annual, inter-decadal, and longer timeframes interact to control food web structure through effects on carbon and nitrogen cycling, microbial and metazoan community composition, and trophic linkages? Arctic lagoons provide a unique opportunity to study these interactions in the absence of fringing wetlands that often modulate land-ocean interactions in other lagoon systems. In addition, barrier island geomorphology, which exerts a strong control on water exchange between lagoons and the open ocean, is highly dynamic in the Arctic because sea-ice effects on coastal geomorphology are superimposed on the effects of currents, sea level, and waves. Thus, connections between inputs from land and lagoon ecosystems are more direct, and water exchanges between lagoons and the open ocean are more variable than is typical of lower latitude systems. Specific study sites will be located in Elson Lagoon (western Beaufort), Simpson Lagoon and Stefansson Sound (central Beaufort), and Kaktovik and Jago lagoons (eastern Beaufort). The LTER will include seasonal field work during ice covered, ice break-up, and open water periods and also include sensor deployments for continuous measurements of key biogeochemical and hydrographic parameters.

Funding:

BLE LTER is supported by the National Science Foundation under award #1656026 (2017-08-01 to 2022-07-31).

Additional Award Information:
Funder:National Science Foundation
Funder ID:http://dx.doi.org/10.13039/100000001
Number:1656026
Title:LTER: Beaufort Sea Lagoons: An Arctic Coastal Ecosystem in Transition
URL:https://www.nsf.gov/awardsearch/showAward?AWD_ID=1656026

Maintenance

Maintenance:
Description:No regular updates anticipated.
Frequency:notPlanned
Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n    '
        |___element 'metadata'
        |     |___text '\n      '
        |     |___element 'unitList'
        |     |     |___text '\n        '
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        |     |     |     |  \___attribute 'id' = 'byte'
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        |     |     |     |  \___attribute 'id' = 'degree'
        |     |     |     |  \___attribute 'multiplierToSI' = '0.0174532924'
        |     |     |     |  \___attribute 'name' = 'degree'
        |     |     |     |  \___attribute 'parentSI' = 'radian'
        |     |     |     |  \___attribute 'unitType' = 'angle'
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        |     |     |     |  \___attribute 'abbreviation' = 'L'
        |     |     |     |  \___attribute 'id' = 'liter'
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        |     |     |     |  \___attribute 'parentSI' = 'cubicMeter'
        |     |     |     |  \___attribute 'unitType' = 'volume'
        |     |     |     |___text '\n          '
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        |     |     |     |     |___text '1000 cm^3'
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EDI is a collaboration between the University of New Mexico and the University of Wisconsin – Madison, Center for Limnology:

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