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Giant Kelp Microbiome Altered in the Presence of Epiphytes

General Information
Data Package:
Local Identifier:knb-lter-sbc.132.1
Title:Giant Kelp Microbiome Altered in the Presence of Epiphytes
Alternate Identifier:DOI PLACE HOLDER
Abstract:

This data package includes data tables documenting microbial community on kelp blades as well as surrounding water column, and R script that analyzes diversity of the microbiomes in kelp forests.

Samples were collected using stand up paddle boards at two kelp beds in the Santa Barbara Channel: Arroyo Quemado (AQ: 34° 28.127′ N, 120° 07.285′ W) and Mohawk Reef (MR; 34° 23.660′ N, 119° 43.800′ W) from May to August, 2018. Seawater samples were also collected as part of this project and to compare kelp microbiomes to microbial communities in the surrounding water column.

This work was conducted by AK James, CJ English, N Nidzieko, CA Carlson, and EG Wilbanks.

This data package is a mirror of a GitHub project: https://github.com/ajamesk10/KELP_SBC_16S_2018

Short Name:Microbiome diversity in Epiphytes
Publication Date:2020-03-29
Language:English

Time Period
Begin:
2018-05-01
End:
2018-08-31

People and Organizations
Contact:Information Manager, Santa Barbara Coastal LTER [  email ]
Organization:Santa Barbara Coastal LTER
Creator:James, Anna 
Creator:Nidzieko, Nick 
Creator:Carlson, Craig A 
Creator:Wilbanks, Lizzy 

Data Entities
Other Name:
KELP_SBC_16S_2018_master
Description:
A zip file that includes R code and data tables for microbiomes diversity analysis
Detailed Metadata

Data Entities

Non-Categorized Data Resource

Name:KELP_SBC_16S_2018_master
Entity Type:otherEntity
Description:A zip file that includes R code and data tables for microbiomes diversity analysis
Physical Structure Description:
Object Name:KELP_SBC_16S_2018_master.zip
Size:1268372 byte
Authentication:a512d26bba54b5bdaf90b71b678ffa81 Calculated By MD5
Externally Defined Format:
Format Name:ZIP
Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-sbc/132/1/064ad60c69b8c30733f920185140a04b

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:
LTER Controlled Vocabulary v1genetics, LTER, macroalgae, Santa Barbara Coastal
SBC-LTER Controlled VocabularyCommunity Structure, Kelp Forest, Reef
Ecological Archivesgiant kelp
nonegenetic diversity, giant kelp, LTER, macroalgae, Macrocystis pyrifera

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:

The Giant kelp microbiomes community diversity analysis is scripted in R. The R script processes raw sequencing reads archived in the Sequence Read Archive data repository through NCBI (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA612503). The data-products, including species percent cover (four csv files), taxa information, sample information, were outputted from the code and kept in this package. The community diversity analysis were conducted in the latter half of the R script, and the result can be visualized at the end.

Regarding the genetic analysis, gene amplicons of the V4 region of the bacterial 16S rRNA gene were generated using 515F and 806R-B primers as described by Wear et al. (2018). Sequencing was conducted at the University of California, Davis DNA Technologies Core on an Illumina MiSeq using PE250.

Reference

Wear, E. K., Wilbanks, E. G., Nelson, C. E., Carlson, C. A. (2018). Primer Selection Impacts Specific Population Abundances But Not Community Dynamics in a Monthly Time-Series 16S rRNA Gene Amplicon Analysis of Coastal Marine Bacterioplankton. Environmental Microbiology. 20:2709--2726. DOI: 10.1111/1462-2920.14091

People and Organizations

Publishers:
Organization:Santa Barbara Coastal Long Term Ecological Research Project
Creators:
Organization:Santa Barbara Coastal LTER
Address:
Marine Science Institute University of California,
Santa Barbara, CA 93106 USA
Email Address:
sbclter@msi.ucsb.edu
Individual: Anna James
Address:
Marine Science Institute University of California,
Santa Barbara, CA 93106 US
Email Address:
ajames@ucsb.edu
Individual: Nick Nidzieko
Address:
Department of Geography University of California,
Santa Barbara, CA 93106-4060 US
Email Address:
nidzieko@ucsb.edu
Individual: Craig A Carlson
Address:
Department of Ecology, Evolution and Marine Biology University of California,
Santa Barbara, CA 93106-9620 US
Phone:
805-893-2541
Email Address:
craig.carlson@lifesci.ucsb.edu
Id:https://orcid.org/0000-0003-2591-5293
Individual: Lizzy Wilbanks
Address:
Department of Ecology, Evolution and Marine Biology University of California,
Santa Barbara, CA 93106-9620 US
Phone:
805-893-2601
Email Address:
elizabeth.wilbanks@lifesci.ucsb.edu
Contacts:
Position:Information Manager, Santa Barbara Coastal LTER
Address:
Marine Science Institute,
University of California,
Santa Barbara, California 93106-6150 United States
Phone:
805 893 2071 (voice)
Email Address:
sbclter@msi.ucsb.edu
Web Address:
https://sbclter.msi.ucsb.edu/

Temporal, Geographic and Taxonomic Coverage

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

Time Period
Begin:
2018-05-01
End:
2018-08-31
Sampling Site: 
Description:AQUE: Arroyo Quemado Reef: Arroyo Quemado Reef depth range from 5.4 m to 10.7 m. Reference on Land is close to US101/Arroyo Quemada Ln.
Site Coordinates:
Longitude (degree): -120.11905Latitude (degree): 34.46774988
Sampling Site: 
Description:MOHK: Mohawk Reef: Mohawk Reef depth ranges from 4.5m to 6.0 m. Reference on land is Mohawk Rd / Edgewater Way.
Site Coordinates:
Longitude (degree): -119.72957Latitude (degree): 34.3940708

Project

Parent Project Information:

Title:Santa Barbara Coastal Long Term Ecological Research Project
Personnel:
Individual:Dr. Robert 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. Dan Reed
Address:
Marine Science Institute,
University of California,
Santa Barbara, California 93106-6150 United States
Phone:
805 893 8363 (voice)
Email Address:
dan.reed@lifesci.ucsb.edu
Role:Co-principal Investigator
Individual:Dr. Adrian Stier
Address:
Department of Ecology, Evolution and Marine Biology,
University of California,
Santa Barbara, California 93106-9260 United States
Phone:
805 893 5467 (voice)
Email Address:
adrian.stier@lifesci.ucsb.edu
Role:Co-principal Investigator
Individual:Dr. Gretchen Hoffman
Address:
Department of Ecology, Evolution and Marine Biology,
University of California,
Santa Barbara, California 93106-9620 United States
Phone:
805 893 6175 (voice)
Email Address:
hofmann@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
Abstract:

The primary research objective of the Santa Barbara Coastal LTER is to investigate the importance of land and ocean processes in structuring giant kelp (Macrocystis pyrifera ) forest ecosystems. As in many temperate regions, the shallow rocky reefs in the Santa Barbara Channel, California, are dominated by giant kelp forests. Because of their close proximity to shore, kelp forests are influenced by physical and biological processes occurring on land as well as in the open ocean. SBC LTER research focuses on measuring and modeling the patterns, transport, and processing of material constituents (e.g., nutrients, carbon, sediment, organisms, and pollutants) from terrestrial watersheds and the coastal ocean to these reefs. Specifically, we are examining the effects of these material inputs on the primary production of kelp, and the population dynamics, community structure, and trophic interactions of kelp forest ecosystems.

Funding:

NSF Award OCE-9982105, OCE-0620276, OCE-1232779, OCE-1831937

Other Metadata

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.

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