Data from: Persistence of marine fish environmental DNA and the influence of sunlight
| Main Authors: | Andruszkiewicz, Elizabeth A., Sassoubre, Lauren M., Boehm, Alexandria B. |
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| Format: | info dataset |
| Terbitan: |
, 2018
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/5015491 |
Daftar Isi:
- Harnessing information encoded in environmental DNA (eDNA) in marine waters has the potential to revolutionize marine biomonitoring. Whether using organism-specific quantitative PCR assays or metabarcoding in conjunction with amplicon sequencing, scientists have illustrated that realistic organism censuses can be inferred from eDNA. The next step is establishing ways to link information obtained from eDNA analyses to actual organism abundance. This is only possible by understanding the processes that control eDNA concentrations. The present study uses mesocosm experiments to study the persistence of eDNA in marine waters and explore the role of sunlight in modulating eDNA persistence. We seeded solute-permeable dialysis bags with water containing indigenous eDNA and suspended them in a large tank containing seawater. Bags were subjected to two treatments: half the bags were suspended near the water surface where they received high doses of sunlight, and half at depth where they received lower doses of sunlight. Bags were destructively sampled over the course of 87 hours. eDNA was extracted from water samples and used as template for a Scomber japonicus qPCR assay and a marine fish-specific 12S rRNA PCR assay. The latter was subsequently sequenced using a metabarcoding approach. S. japonicus eDNA, as measured by qPCR, exhibited first order decay with a rate constant ~0.01 hr -1 with no difference in decay rate constants between the two experimental treatments. eDNA metabarcoding identified 190 organizational taxonomic units (OTUs) assigned to varying taxonomic ranks. There was no difference in marine fish communities as measured by eDNA metabarcoding between the two experimental treatments, but there was an effect of time. Given the differences in UVA and UVB fluence received by the two experimental treatments, we conclude that sunlight is not the main driver of fish eDNA decay in the experiments. However, there are clearly temporal effects that need to be considered when interpreting information obtained using eDNA approaches.
- OTU table after bioinformatics pipelineTable of OTUs (rows) by sample (columns) after bioinformatics pipeline. See "OTUs fasta file" for representative sequences of each OTU. See "metadata file" to match library and tag number of samples to sample names.OTU_table.csvOTUs fasta fileList of representative sequences for each OTU; to be paired with OTU tableOTUs.fastametadata fileList of samples sequenced with library and tag combinations; to be paired to OTU tabledecay_meta.csvOTU table for blanksBlanks were run on separate sequencing run. This file is the OTU table for the blanks including their annotation based on the same criteria outlined in the manuscript.OTU_table_for_blanks.xlsxLibrary 1 fastq file read 1eaa-decay1_S1_L001_R1_001.fastq.gzLibrary 1 fastq file read 2eaa-decay1_S1_L001_R2_001.fastq.gzLibrary 2 fastq file read 1eaa-decay2_S2_L001_R1_001.fastq.gzLibrary 2 fastq file read 2eaa-decay2_S2_L001_R2_001.fastq.gzLibrary 3 fastq file read 1eaa-decay3_S3_L001_R1_001.fastq.gzLibrary 3 fastq file read 2eaa-decay3_S3_L001_R2_001.fastq.gz