Data from: Multi-tool marine metabarcoding bioassessment for baselining and monitoring species and communities in kelp habitats
Data files
Jul 25, 2025 version files 5.06 GB
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CHNMS_12S_FinalDataset_Lib1.xlsx
14.71 KB
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CHNMS_12S_FinalDataset_Lib2.xlsx
12.26 KB
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CHNMS_12S_rawMOTUsTab_Lib1.csv
157.08 KB
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CHNMS_12S_rawMOTUsTab_Lib2.csv
69.44 KB
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CHNMS_MOTUsDataset-COICobbles.csv
3.01 MB
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CHNMS_MOTUsDataset-COIeDNA.csv
619.69 KB
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CHNMS_rawMOTUtab-COICobbles.csv
7.81 MB
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CHNMS_rawMOTUtab-COIeDNA.csv
1.74 MB
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CHNMS_taxoDataset-COICobbles.csv
112.72 KB
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CHNMS_taxoDataset-COIeDNA.csv
65.78 KB
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Lib1_Tele02_R1.fastq.gz
150.58 MB
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Lib1_Tele02_R2.fastq.gz
166.70 MB
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Lib2_Tele02_R1.fastq.gz
140.50 MB
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Lib2_Tele02_R2.fastq.gz
140.99 MB
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LibCobbles_COI_R1.fastq.gz
835.49 MB
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LibCobbles_COI_R2.fastq.gz
855.08 MB
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LibeDNA_COI_R1.fastq.gz
1.35 GB
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LibeDNA_COI_R2.fastq.gz
1.40 GB
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ngsfilter_Lib1Tele02.txt
4.36 KB
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ngsfilter_Lib2Tele02.txt
4.58 KB
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NGSfilterCOI_cobbles.txt
7.53 KB
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NGSfilterCOI_eDNA.txt
7.16 KB
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README.md
4.86 KB
Abstract
The astonishing biological diversity found in Californian kelp forests requires efficient and robust monitoring tools to better understand ecological trends and mitigate against loss or disruption of ecosystem services due to human pressure and climate changes. With environmental DNA (eDNA) metabarcoding becoming a popular biodiversity assessment approach, we set out to evaluate a combination of powerful, rapid and sustainable eDNA solutions for characterizing marine community composition in kelp-dominated habitats along the central California coast, in the newly proposed Chumash Heritage National Marine Sanctuary. We employed and compared the efficiency of several eDNA collection approaches, including ‘traditional’ surface water filtration, the collection of organisms encrusting cobble rocks and various deployments of an artificial passive sampler, the metaprobe (i.e., attached to divers, dangled from a boat, and cast from the shore using a fishing rod). By combining the information from fish specific (Tele02 12S) and universal metazoan (COI) markers, we ‘captured’ 501 unique marine taxa, belonging to at least 36 phyla, over 400 of which were identified to genus/species level, and including 52 vertebrate species typical of Californian kelp forest ecosystems. Despite differences in the type of biodiversity returned by the tested sampling methods, the overall community structure of the surveyed area was highly spatially structured and strongly influenced by the biogeographic break around Point Conception (Humqaq). We discuss the benefits of integrating eDNA metabarcoding in existing monitoring programs and devising a reproducible approach to monitor faunal changes in kelp forest habitats and beyond.
Dataset DOI: 10.5061/dryad.02v6wwqfv
Description of the data and file structure
This project contains raw reads data, metadata, MOTU tables and final datasets from samples collected using several eDNA collection approaches, including ‘traditional’ surface water filtration, the collection of organisms encrusting cobble rocks and various deployments of an artificial passive sampler, the metaprobe. Raw reads files and ngsfilter files with sample barcodes are from four different libraries, two sequenced with Tele02 12S barcode and two with COI.In all MOTU tables and final datasets, molecular operational taxonomic units (MOTUs) or species are represented in rows, while the columns correspond to their taxonomy and the different sampling sites.
Files and variables
File: Lib1_Tele02_R1.fastq.gz
Description: Tele02 forward FastQ file from the first library sequenced with an Illumina iSeq 2x150 bp run
File: Lib1_Tele02_R2.fastq.gz
Description: Tele02 reverse FastQ file from the first library sequenced with an Illumina iSeq 2x150 bp run
File: ngsfilter_Lib1Tele02.txt
Description: Primers and unique dual-tag combinations (forward and reverse) associated with each of the samples of the first Tele02 12S library. The columns of the file correspond to: name of the project, samples, dual oligo-tags, forward primer and reverse primer.
File: Lib2_Tele02_R1.fastq.gz
Description: Tele02 forward FastQ file from the second library sequenced with an Illumina iSeq 2x150 bp run
File: Lib2_Tele02_R2.fastq.gz
Description: Tele02 reverse FastQ file from the second library sequenced with an Illumina iSeq 2x150 bp run
File: ngsfilter_Lib2Tele02.txt
Description: Primers and unique dual-tag combinations (forward and reverse) associated with each of the samples of the second Tele02 12S library. The columns of the file correspond to: name of the project, samples, dual oligo-tags, forward primer and reverse primer.
File: LibCobbles_COI_R1.fastq.gz
Description: COI forward FastQ file from the cobble library sequenced with an Illumina MiSeq 2x250 bp run
File: LibCobbles_COI_R2.fastq.gz
Description: COI reverse FastQ file from the cobble library sequenced with an Illumina MiSeq 2x250 bp run
File: NGSfilterCOI_cobbles.txt
Description: Primers and unique dual-tag combinations (forward and reverse) associated with each of the samples of the cobble COI library. The columns of the file correspond to: name of the project, samples, dual oligo-tags, forward primer and reverse primer.
File: LibeDNA_COI_R1.fastq.gz
Description: COI forward FastQ file from the aqueous eDNA library sequenced with an Illumina MiSeq 2x250 bp run
File: LibeDNA_COI_R2.fastq.gz
Description: COI reverse FastQ file from the aqueous eDNA library sequenced with an Illumina MiSeq 2x250 bp run
File: NGSfilterCOI_eDNA.txt
Description: Primers and unique dual-tag combinations (forward and reverse) associated with each of the samples of the aqueous eDNA COI library. The columns of the file correspond to: name of the project, samples, dual oligo-tags, forward primer and reverse primer.
File: CHNMS_12S_rawMOTUsTab_Lib1.csv
Description: Raw MOTU table with taxonomic assignment of the first Tele02 12S library
File: CHNMS_12S_FinalDataset_Lib1.xlsx
Description: Final filtered dataset of the first Tele02 12S library where only taxonomic assignments above 95% identity are kept
File: CHNMS_12S_rawMOTUsTab_Lib2.csv
Description: Raw MOTU table with taxonomic assignment of the second Tele02 12S library
File: CHNMS_12S_FinalDataset_Lib2.xlsx
Description: Final filtered dataset of the second Tele02 12S library where only taxonomic assignments above 95% identity are kept
File: CHNMS_rawMOTUtab-COIeDNA.csv
Description: Raw MOTU table with taxonomic assignment of the aqueous eDNA library
File: CHNMS_rawMOTUtab-COICobbles.csv
Description: Raw MOTU table with taxonomic assignment of the cobble library
File: CHNMS_MOTUsDataset-COIeDNA.csv
Description: Aqueous eDNA library dataset where unassigned and poorly assigned MOTUs are kept
File: CHNMS_MOTUsDataset-COICobbles.csv
Description: Cobble library dataset where unassigned and poorly assigned MOTUs are kept
File: CHNMS_taxoDataset-COICobbles.csv
Description: Aqueous eDNA library dataset where all the unclassified and < 80% identity MOTUs were removed
File: CHNMS_taxoDataset-COIeDNA.csv
Description: Cobble library dataset where all the unclassified and < 80% identity MOTUs were removed