DOI: 10.5061/dryad.66t1g1k92
title: Data from: A sedimentary eDNA record of the Atacama Trench reveals biodiversity changes in the most productive marine ecosystem

description: The hadopelagic environment remains highly understudied due to the
 inherent difficulties in sampling at these depths. The use of sediment
 eDNA can overcome some of these restrictions as settled and preserved DNA
 represent an archive of the biological communities. We use sediment eDNA
 to assess changes in the community within one of the world’s most
 productive open ocean ecosystems: the Atacama Trench. The ecosystems
 around the Atacama Trench have been intensively fished and are affected by
 climate oscillations, but the understanding of potential impacts on the
 marine community is limited. We sampled five sites using sediment cores at
 water depths from 2400 to ~8000m. The chronologies of the sedimentary
 record were determined using 210Pbex. Environmental DNA was extracted from
 core slices and metabarcoding was used to identify the eukaryote community
 using two separate primer pairs for different sections of the 18S rDNA
 gene (V9 and V7) effectively targeting pelagic taxa.  The
 reconstructed communities were similar among markers and mainly composed
 of chordates and members of the Chromista kingdom. Alpha-diversity was
 estimated for all sites in intervals of 15 years (from 1842 to 2018),
 showing a severe drop in biodiversity from 1970 to 1985 that aligns with
 one of the strongest known El Niño events. We argue that the harsh adverse
 ENSO events potentially combined with extensive fishing efforts during
 this period of time resulted in a distinct reduction of marine
 biodiversity. Fish and cnidarian read abundance was examined separately to
 determine if fishing had a direct impact, but no direct relation was
 found. These results demonstrate that sediment eDNA can be a valuable
 emerging tool providing insight in historical perspectives on ecosystem
 developments. This study constitutes one of the first steps toward an
 improved understanding of the importance of environmental and
 anthropogenic drivers in affecting open and deep ocean communities.
description: # Atacama Trench sedDNA community dataset
 [https://doi.org/10.5061/dryad.66t1g1k92](https://doi.org/10.5061/dryad.66t1g1k92) Data obtained from sedDNA collection in the Atacama Trench. Two different kinds of datasets are presented.  1.- Sample data (Atacama18sMiniFinalSampledataCorrected and AtacamaEuka02FinalSampleDataCorrected) from each of the different layers of the sediment cores utilized for analyses. Each layer is interpreted as a unique eDNA sample.  2.- Taxonomic tables (18SAtacama_TaxaFinal and AtacamaTaxaEuka02Final) according to the v7 and v9 primers respectively, from Kingdom to Species. Contains information about whether the individual is primarily pelagic or benthic in its adult stage and the reference consulted for said information.  ## Description of the data and file structure Taxonomic data tables include the different taxa identified by sedDNA sequencing, down to the species level if possible, as well as the sequence from where this taxonomic data was obtained. The habitat in which the adult stage individual typically lives is included in order to separate the pelagic individuals.  Sample data contains all the information obtained for each of the layers of the Atacama cores. Abbreviations are as follows: NPP-Net Primary Productivity SST-Sea Surface Temperature PDO-Pacific Decadal Oscillation TOC-Total Organic Carbon FAO-Food and Agriculture Organization of the United Nations **Descriptions for sample data table:** * sample_ID: Full name the sample is identified with. * Core: Sediment core in which the sample was collected in. * type: Used to separate between samples and controls. * HasAge: Identifier to separate samples that were able to be assigned to a specific year utilizing Pb210 chronologies. * Waste: Identifier to separate samples that were noted to have come from a mass wasting event and therefore not used for analyses due to skewed chronologies. * New_TimePeriod15: Time Periods in which the samples were assigned into. * core_slice: The slice of the core the sample pertains to in centimeters.  * Core_Depth: The depth of the core submerged into the sediment. * Water_Depth: The depth at which the core was collected. * NPP_10ymean: The mean net primary production of the area in 10 year intervals. * NPP_20ymean: The mean net primary production of the area in 20 year intervals. * New_SST: The Sea Surface Temperature of the closest available grid square where the sample was obtained from at the specific year determined by geochronologies. Obtained from the ICOADS gridded dataset by NOAA. Measured in degrees centigrade.  * Organic_Carbon: Organic Carbon found in the sample. * Nitrogen: Nitrogen found in the sample.  * Oceanic_*Nino*_Index: Running 3-month average sea surface temperatures in the east-central tropical Pacific between 120°-170°W, near the International Dateline, and whether they are warmer or cooler than average. Obtained from NOAA. * Nino 1+2: Oceanic Nino Index specifically for the 1+2 region, where Chile, the study region is found. * Nino 1+2_Average: Oceanic Nino Index specifically for the 1+2 region, averaged for the 15 year time periods. * Reported_Catch: Tons of fish catches reported by the Chilean goverment according to their official sources. * New_*Catch*_FAO: Tons of fish catches reported by the FAO for Chile. * New_*Aquaculture_*FAO: Tons of fish produced by aquaculture for Chile according to FAO. * Interdecadal_*Pacific_*Oscillation_Index: Index based on the difference between the SSTA averaged over the central equatorial Pacific and the average of the SSTA in the Northwest and Southwest Pacific. It is a measure of interdecadal variability in the Pacific. Obtained from NOAA. * PDO_Average: Average of the Pacific Oscillation Index over the 15 year time periods. * Chlorophyll_*a*_Concentration: Chlorophyll a concentration yearly mean at the ocean surface measured in mg per cubic meter. * Distance_*to_*coast_km: Distance to the nearest land point from the collection point of sample. In the sample data datasets, unavailable information is marked as "NA", while "null" is marked for control samples which do not have any of the above information. **Descriptions for taxonomic data table:** * Kingdom: The taxonomic kingdom the identified sequence has been assigned to. * Phylum: The taxonomic phylum the identified sequence has been assigned to. * Class: The taxonomic class the identified sequence has been assigned to. * Order: The taxonomic order the identified sequence has been assigned to. * Family: The taxonomic family the identified sequence has been assigned to. * Genus: The taxonomic genus the identified sequence has been assigned to. * Species: The taxonomic species the identified sequence has been assigned to. * Sequence: The full unique sequence which has been assigned a taxonomy. * Lineage: Full taxonomy of the identified sequence, from kingdom to species separated by ";". * species_*clean_*ncbi: Confirmation of the species' name according to the NCBI official database. * AphiaID_ncbi: Assigned identification number for the taxon using the Aphia system. * isMarine: Identification if the individual is marine or terrestrial. 1 for marine, 0 for not marine.  * Notes.on.habitat: Notes made on the habitat of the identified taxa. * overall_habitat: Identified habitat the adult life stage of the taxa typically lives in according to references. Separates different pelagic layers, identifies parasites and free-living organisms. * simplified_habitat: Simplified habitat the adult life stage of the taxa typically lives in according to references, only benthic, pelagic or terrestrial. * depth.notes: Notes made about the depth at which the individual is typically found in. * Coastal/Open.Habitat: Identified habitat the adult life stage of the taxa typically lives in according to references, in either a coastal or open ocean zone.  * Notes.on.Coastal/Open.Habitat: Notes made about the habitat the adult life stage of the taxa typically lives in according to references, in either a coastal or open ocean zone.  * References_used: Contains the reference or references utilized to assign the identified taxa's habitat, in APA format. In the taxa datasets, unavailable information is marked as "NA". ## Sharing/Access information Sequencing data for this project may be found in NCBI's sequence read archive (SRA) under the BioProject **PRJNA1001897.**