DOI: 10.5061/dryad.02v6wwqfv
title: Data from: Multi-tool marine metabarcoding bioassessment for baselining and monitoring species and communities in kelp habitats

description: 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.
description: # Data from: Multi-tool marine metabarcoding bioassessment for baselining
 and monitoring species and communities in kelp habitats Dataset DOI:
 [10.5061/dryad.02v6wwqfv](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 &lt; 80% identity MOTUs were
 removed #### File: CHNMS_taxoDataset-COIeDNA.csv **Description:** Cobble
 library dataset where all the unclassified and &lt; 80% identity MOTUs
 were removed