Environmental Data Initiative logo
EDI Staging Environment

Data Package Metadata   View Summary

SBC LTER and MBON: Sea urchin microbiomes in Southern California

General Information
Data Package:
Local Identifier:edi.702.2
Title:SBC LTER and MBON: Sea urchin microbiomes in Southern California
Alternate Identifier:DOI PLACE HOLDER
Abstract:

Sea urchins are key grazers in coastal seas, where they can survive a variety of conditions and diets, enhancing their ecological impact on coral reefs, kelp forests, and other ecosystems. These data describe a comparative study of the microbiomes of the two dominant sea urchin species in southern California, the red urchin Mesocentrotus franciscanus, and the purple urchin Strongylocentrotus purpuratus across three rocky reef habitats that differed in the types and availability of food resources: kelp forests, urchin barrens and a hydrocarbon seep.

Short Name:Sea urchin microbiomes
Publication Date:2021-01-22
Language:English

Time Period
Begin:
2016-01-01
End:
2016-09-21

People and Organizations
Contact:Information Manager, Southern California Bight Marine Biodiversity Observation Network (SCB MBON) [  email ]
Creator:Miller, Paige (UCSB)
Creator:Lamy, Thomas (UCSB)
Creator:Page, Henry M (UCSB)
Creator:Miller, Robert J (UCSB)

Data Entities
Data Table Name:
Sea urchins microbiome OTU table
Description:
An OTU by samples data table
Data Table Name:
OTU taxonomy table
Description:
An OTU by taxonomic rank
Data Table Name:
Sample description table
Description:
Descrition of the samples by species of sea urchins and habitat types
Detailed Metadata

Data Entities

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/702/2/a326ea997759b01adbab16df392ff0cc
Name:Sea urchins microbiome OTU table
Description:An OTU by samples data table
Number of Records:33864
Number of Columns:3

Table Structure
Object Name:OTU_table_microbiome_sea_urchins_long.csv
Size:665858 byte
Authentication:d7bb168bd089a538cf7f8224982f54d1 Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\n
Orientation:column
Simple Delimited: no
Field Delimiter:,

Table Column Descriptions
 OTU_nameSampleIDnum_read
Column Name:OTU_name  
SampleID  
num_read  
Definition:OTU taxon nameSample IDNumber of reads
Storage Type:string  
string  
short  
Measurement Type:nominalnominalratio
Measurement Values Domain:
Definitionany text
Definitionany text
Unitnumber
Precision1
Typeinteger
Missing Value Code:      
Accuracy Report:      
Accuracy Assessment:      
Coverage:      
Methods:      

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/702/2/9329c17239446579717cd28af27c4ad4
Name:OTU taxonomy table
Description:An OTU by taxonomic rank
Number of Records:408
Number of Columns:8

Table Structure
Object Name:Tax_table_microbiome_sea_urchins.csv
Size:42442 byte
Authentication:e9f2c75cd5a8357a79187f506522d299 Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited: no
Field Delimiter:,

Table Column Descriptions
 OTU_nameKingdomPhylumClassOrderFamilyGenusSpecies
Column Name:OTU_name  
Kingdom  
Phylum  
Class  
Order  
Family  
Genus  
Species  
Definition:OTU taxon nameSpecies ranking kingdomSpecies ranking phylumSpecies ranking classSpecies ranking orderSpecies ranking familySpecies ranking genusSpecies ranking species
Storage Type:string  
string  
string  
string  
string  
string  
string  
string  
Measurement Type:nominalnominalnominalnominalnominalnominalnominalnominal
Measurement Values Domain:
Definitionany text
Definitionany text
Definitionany text
Definitionany text
Definitionany text
Definitionany text
Definitionany text
Definitionany text
Missing Value Code:  
CodeNA
Explvalue not recorded or not available
CodeNA
Explvalue not recorded or not available
CodeNA
Explvalue not recorded or not available
CodeNA
Explvalue not recorded or not available
CodeNA
Explvalue not recorded or not available
CodeNA
Explvalue not recorded or not available
CodeNA
Explvalue not recorded or not available
Accuracy Report:                
Accuracy Assessment:                
Coverage:                
Methods:                

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/702/2/d42c9ad1a4d889e3aaedad6bb2978381
Name:Sample description table
Description:Descrition of the samples by species of sea urchins and habitat types
Number of Records:83
Number of Columns:3

Table Structure
Object Name:Sample_table_microbiome_sea_urchins.csv
Size:1309 byte
Authentication:3b65c6582e008b87cb9c8f1c60887e07 Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited: no
Field Delimiter:,

Table Column Descriptions
 SampleIDTreatmentGroupsppID
Column Name:SampleID  
TreatmentGroup  
sppID  
Definition:Sample IDTreatment of the sampling: hydrocarbon Seep, urchin barrens, or kelp forestsSpecies ID: Mesocentrotus franciscanus (MF) and Strongylocentrotus purpuratus (SF)
Storage Type:string  
string  
string  
Measurement Type:nominalnominalnominal
Measurement Values Domain:
Definitionany text
Definitionany text
Definitionany text
Missing Value Code:      
Accuracy Report:      
Accuracy Assessment:      
Coverage:      
Methods:      

Data Package Usage Rights

This data package is released under the Creative Commons License Attribution 4.0 International (CC BY 4.0, see https://creativecommons.org/licenses/by/4.0/). This license states that consumers ("Data Users" herein) may distribute, adapt, reuse, remix, and build upon this work, as long as they give appropriate credit, provide a link to the license, and indicate if changes were made. If redistributed, a Data User may not apply additional restrictions or technological measures that prevent access.

The Data User has an ethical obligation to cite the data source appropriately in any publication or product that results from its use, and notify the data contact or creator. Communication, collaboration, or co-authorship (as appropriate) with the creators of this data package is encouraged to prevent duplicate research or publication. The Data User 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. 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 data are updated periodically 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 of data sets 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.

Keywords

By Thesaurus:
nonegenomics study, invertebrate, mobile invertebrate, Santa Barbara Channel, Southern California

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:

We sampled sea urchins from both urchin barrens and kelp forests at two reefs, Naples Reef (34° 25’ N, 119° 57’ W) and Arroyo Quemado (34° 28’ N, 120° 07′ W), from the kelp forest at Mohawk Reef (34° 23’ N, 119° 43’ W), where there was no significant barren area, and from Jackpot Seep (34° 24’ N, 119° 52’ W), a rocky reef with active hydrocarbon seeps, at depths of 10-14 meters from February to April 2016. Urchin barrens were characterized by a lack of giant kelp, sparse macroalgae in general, and high densities of sea urchins. Jackpot Seep is a rocky reef with active hydrocarbon seeps and little algae, where we observed urchins grazing on microbial mats that characterize seeps in the region.

Twelve adult sea urchins of each species were collected in each of the three habitats, totaling 36 per species. To characterize the microbial communities of potential food items for the urchins, we also collected six samples of giant kelp (Macrocystic pyrifera) blades, three from Mohawk Reef and three from Arroyo Quemado, and 15 samples of bacterial mats from Jackpot Seep. DNA from urchin gut, kelp, and microbial mat samples was extracted and The V3-V4 region of the 16S ribosomal gene was amplified.The raw sequence data can be found on NCBI: https://www.ncbi.nlm.nih.gov/sra/PRJNA643824

For detail method, please see the method section in article: Miller PM, Lamy T, Page HM, Miller RJ. Sea urchin microbiomes vary with habitat and resource availability. Accepted in Limnology and Oceanography Letters.

People and Organizations

Publishers:
Organization:Environmental Data Initiative
Email Address:
info@environmentaldatainitiative.org
Web Address:
https://environmentaldatainitiative.org
Creators:
Individual: Paige Miller
Organization:UCSB
Address:
Marine Science Institute University of California,
Santa Barbara, CA 93106-6150 US
Email Address:
paigemiller@ucsb.edu
Individual: Thomas Lamy
Organization:UCSB
Address:
Marine Science Institute University of California,
Santa Barbara, CA 93106-6150 US
Email Address:
thomas.lamy27@gmail.com
Id:https://orcid.org/0000-0002-7881-0578
Individual: Henry M Page
Organization:UCSB
Address:
Marine Science Institute University of California,
Santa Barbara, CA 93106-6150 US
Email Address:
page1@ucsb.edu
Individual: Robert J Miller
Organization:UCSB
Address:
Marine Science Institute University of California,
Santa Barbara, CA 93106-6150 US
Phone:
805-893-6174
Email Address:
miller@msi.ucsb.edu
Id:https://orcid.org/0000-0002-8350-3759
Contacts:
Organization:SCB MBON
Position:Information Manager, Southern California Bight Marine Biodiversity Observation Network
Address:
Marine Science Institute,
University of California,
Santa Barbara, California 93106-6150 United States
Email Address:
sbcbon@msi.ucsb.edu
Web Address:
http://sbc.marinebon.org

Temporal, Geographic and Taxonomic Coverage

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

Time Period
Begin:
2016-01-01
End:
2016-09-21
Sampling Site: 
Description:California, USA: Naples Reef
Site Coordinates:
Longitude (degree): -119.95Latitude (degree):  34.416667
Sampling Site: 
Description:California, USA: Arroyo Quemado
Site Coordinates:
Longitude (degree): -120.116667Latitude (degree):  34.466667
Sampling Site: 
Description:California, USA: Mohawk Reef
Site Coordinates:
Longitude (degree): -119.716667Latitude (degree): 34.383333
Sampling Site: 
Description:California, USA: Jackpot Seep
Site Coordinates:
Longitude (degree): -119.866667Latitude (degree):  34.40

Project

Parent Project Information:

Title:Southern California Bight Marine Biodiversity Observation Network
Personnel:
Individual:Dr. Robert J Miller
Address:
Marine Science Institute,
University of California,
Santa Barbara, California 93106-6150 United States
Phone:
805 893 6174 (voice)
Email Address:
miller@msi.ucsb.edu
Role:Principal Investigator
Individual:Dr. Daniel Reed
Address:
Marine Science Institute,
University of California,
Santa Barbara, California 93106-6150 United States
Phone:
805 893 8363 (voice)
Email Address:
reed@lifesci.ucsb.edu
Role:Co-Principal Investigator
Individual:Dr. David Siegel
Address:
Institute for Computational Earth System Science,
University of California,
Santa Barbara, California 93106-3060 United States
Phone:
805 893 4547 (voice)
Email Address:
davey@icess.ucsb.edu
Role:Co-Principal Investigator
Individual:Dr. Craig Carlson
Address:
Department of Ecology, Evolution and Marine Biology,
University of California,
Santa Barbara, California 93106-9620 United States
Phone:
805 893 2541 (voice)
Email Address:
craig.carlson@lifesci.ucsb.edu
Role:Co-Principal Investigator
Individual:Dr. Kevin D Lafferty
Address:
US Geological Survey Western Ecological Research Center,
University of California,
Santa Barbara, California 93106 United States
Email Address:
Klafferty@usgs.gov
Role:Co-Principal Investigator
Individual:Dr. B.S. Manjunath
Address:
Department of Electrical and Computer Engineering,
University of California,
Santa Barbara, California 93106-9560 United States
Phone:
805 893 7112 (voice)
Email Address:
manj@ece.ucsb.edu
Role:Co-Principal Investigator
Individual:Dr. Andrew Rassweiler
Address:
Department of Biological Science,
Florida State University,
Tallahassee, Florida 32306-4295 United States
Phone:
850 644 1555 (voice)
Email Address:
rassweiler@bio.fsu.edu
Role:Co-Principal Investigator
Abstract:

The Southern California Bight Marine Biodiversity Observation Network (SCB MBON) is designed to provide a complete picture of marine biodiversity in the region. SCB MBON is developing a widely applicable research model that integrates new information with existing data to improve current research and monitoring programs and provide greater insight into marine biodiversity.

Funding:

MBON is funded by National Aeronautics and Space Administration (NASA), Bureau of Ocean Energy Management (BOEM), and National Oceanic and Atmospheric Administration (NOAA).

Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n    '
        |___element 'metadata'
        |     |___text '\n      '
        |     |___element 'unitList'
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'number'
        |     |     |     |  \___attribute 'name' = 'number'
        |     |     |     |  \___attribute 'unitType' = 'dimensionless'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'a number'
        |     |     |     |___text '\n        '
        |     |     |___text '\n      '
        |     |___text '\n    '
        |___text '\n  '

Copyright 2024 Environmental Data Initiative. This material is based upon work supported by the National Science Foundation under grants #2223103 and #2223104. Any opinions, findings, conclusions, or recommendations expressed in the material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. Please contact us with questions, comments, or for technical assistance regarding this web site or the Environmental Data Initiative. Please read our privacy policy to know what information we collect about you and to understand your privacy rights.

EDI is a collaboration between the University of New Mexico and the University of Wisconsin – Madison, Center for Limnology:

UNM logo UW-M logo