Find research datasets worth reusing

opencc-by-4.0May 2020View details →

SP2020_eDNA_raw_sequence_files

Raw fast5 sequence files for eDNA sequencing

F I G U R E 3 in The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches

F I G U R E 3 Comparison of trait-based metrics expressed in relative number of individuals computed from eDNA () and traditional electro-fishing (TEF;) samples in the five river stretches (RS), A, B, C, D and E. Trait categories: BEN, benthic; EUR, eurytopic; INS, insectivorous; OMN, omnivorous; PHY, phytophilic; POT, potamodromous; RHE, rheophilic; TOL, tolerant; PEL pelagic. Significance of the differences between eDNA and TEF metrics are shown: ns, not significant (P> 0.05)

F I G U R E 4 in The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches

F I G U R E 4 Boxplots (, median value;, interquartile range;, full range;, outliers) showing the variability in the eDNAadapted fish index (six metrics) computed at three sites (Brangues, Rhins and Usses) where 10 eDNA water samples were collected once. At each site, the eDNA-based six-metric fish index was computed for each of the 45 possible pairs of samples

F I G U R E 2 in The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches

F I G U R E 2 Comparison of trait-based metrics expressed in number of species computed from eDNA () and traditional electrofishing (TEF;) samples in the five river stretches (RS), A, B, C, D and E. Trait categories: BEN, benthic; EUR, eurytopic; INS, insectivorous; OMN, omnivorous; PHY, phytophilic; POT, potamodromous; RHE, rheophilic; TOL, tolerant; PEL pelagic. Significance of the differences between eDNA and TEF metrics are shown: P <0.05; P <0.01; ns, not significant (P> 0.05)

F I G U R E 1 in The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches

F I G U R E 1 Sampling locations along river stretches (RS) A to E () of the main channel of the Rhône River, France, using both traditional electro-fishing (TEF) and eDNA., Sites sampled every 2 months (September 2015– August 2016);, sites where ten eDNA water samples (filtration capsules) were collected once;, sites located on the tributaries or the Rhône River itself sampled once for eDNA. The 10 metric fish index and the adapted six-metric fish index were computed at all sites with a black filled symbol within natural water bodies

opencc-zeroApr 2024View details →

Data from: Sorting states of environmental DNA: Effects of isolation method and water matrix on recovery of membrane-bound, dissolved, and adsorbed states of eDNA

Environmental DNA (eDNA) once shed can exist in numerous states with varying behaviors including degradation rates and transport potential. In this study we consider three states of eDNA: 1) a membrane-bound state referring to DNA enveloped in a cellular or organellar membrane, 2) a dissolved state defined as the extracellular DNA molecule in the environment without any interaction with other particles, and 3) an adsorbed state defined as extracellular DNA adsorbed to a particle surface in the environment. Capturing, isolating, and analyzing a target state of eDNA provides utility for better interpretation of eDNA degradation rates and transport potential. While methods for separating different states of DNA have been developed, they remain poorly evaluated due to the lack of state-controlled experimentation. We evaluated the methods for separating states of eDNA from a single sample by spiking DNA from three different species to represent the three states of eDNA as state-specific controls. We used chicken DNA to represent the dissolved state, cultured mouse cells for the membrane-bound state, and salmon DNA adsorbed to clay particles as the adsorbed state. We performed the separation in three water matrices, two environmental and one synthetic, spiked with the three eDNA states. The membrane-bound state was the only state that was isolated with minimal contamination from non-target states. The membrane-bound state also had the highest recovery (54.11 ± 19.24 %), followed by the adsorbed state (5.08 ± 2.28 %), and the dissolved state had the lowest total recovery (2.21 ± 2.36 %). This study highlights the potential to sort the states of eDNA from a single sample and independently analyze them for more informed biodiversity assessments. However, further method development is needed to improve recovery and reduce cross-contamination.

opencc-by-4.0Nov 2024View details →

Reference Sequence Library Resources - Maine-eDNA

The following files and resources are associated with the Maine-eDNA Reference Library Research Group - aiming to create reference sequence library resources for researchers part of Maine-eDNA or otherwise interested in leveraging eDNA tools for research in the Gulf of Maine. These include: <ul> <li> RoughWorkflow.zip </li> <ul> <li> contains a NCBI scraping script to build reference databases based on an input species list, a configuration file for the script, and genbankr version - most useful for shorter species lists (time-intensive) </li> </ul> <li> 12S_REFDB.fasta </li> <ul> <li> A DADA2-compliant reference library for 12S sequences, built with the RoughWorkflow based on the GNRMaineSpecies_May2024 species list </li> </ul> <li> COI_REFDB.fasta </li> <ul> <li> A DADA2-compliant reference library for COI sequences, built with the RoughWorkflow based on the GNRMaineSpecies_May2024 species list </li> </ul> <li> GitHub Repo - referee - <a href="https://github.com/BigelowLab/referee">https://github.com/BigelowLab/referee</a> </li> <ul> <li> Scripts for building reference databases for the Maine-eDNA project through downloading GenBank - this workflow is suggested especially for large species lists </li> </ul> <li> GitHub Repo - refdbtools - <a href="https://github.com/BigelowLab/refdbtools">https://github.com/BigelowLab/refdbtools</a>  </li> <ul> <li> R language package to assist in making eDNA reference databases </li> </ul> <li> SpeciesListMeta_Shareable.xlsx </li> <ul> <li> Describes the sources from which the GNRMaineSpecies_May2024.csv and GNRMaineTaxonomiedSpecies_May2024.csv species lists were compiled - sources not associated with a link were found as separate files and are hosted elsewhere. Species list sources are courtesy of public datasets, Maine-eDNA researchers, and collaborators </li> </ul> <li> GNRMaineSpecies_May2024.csv </li> <ul> <li> A Maine (and surrounding area) species list ran through taxize’s gnr_resolve to resolve species names and fill out taxonomy (full results) </li> </ul> <li> GNRMaineTaxonomiedSpecies_May2024.csv </li> <ul> <li> A Maine (and surrounding area) species list ran through taxize’s gnr_resolve to resolve species names and fill out taxonomy (only species results that could be resolved with taxonomy) </li> </ul> </ul>   Contact Beth Y. Davis - bethy.davis4@gmail.com for questions   ### Changelog: May 16, 2023 (Version 1.0) - Initial upload July 11, 2023 (Version 1.1) - Did additional cleaning to the MaineSpeciesList_Clean file and uploaded the new version - July2023_SpeciesList May 20, 2024 (Version v3) -  Additional cleaning to correct deduplication errors and ran taxize's gnr_resolve to resolve names and fill out taxonomy. The version update adds two files, GNRMaineSpecies_May2024.csv containing the full result of gnr_resolve, and GNRMaineTaxonomiedSpecies_May2024.csv contains only those species from the original list that could be resolved with taxonomy. The SpeciesListMeta_Shareable.csv has not been updated but is still an accurate tracker of the sources from which the species names were gained from. November 27, 2024 (Version 4.0) - Updated Zenodo description and added the RoughWorkflow R files, 12S and COI files

opencc-by-4.0Mar 2022View details →

Using soil eDNA for plant diversity assessments

This data sets corresponds to a publication in Methods in Ecology and Evolution titled: Plant biodiversity assessment through soil eDNA reflects temporal and local diversity In August 2018, a single soil eDNA sample was collected from the centre of each permanent plot (1m2) in the Solhomfjell Forest Reserve stablished by the Sommerfeltia program. The soil eDNA samples were stored in individual plastic bags for transportation to the lab and stored at -20 °C prior to freeze-drying under vacuum. Each soil eDNA sample was separately homogenized with ceramic beads and one gram was used for eDNA extraction. The latter was done in five rounds of two steps: (1) CTAB/chloroform pre-treatment to increase the separation of the organic phase and (2) aqueous phase and using the E.Z.N.A. soil DNA kit following the manufacturer’s protocol (Omega Bio-tek, Norcross, Georgia, USA). The chloroplast marker trnL (UAA) intron P6 loop was chosen as its short sequence can yield amplification of old DNA material degraded in eDNA samples. This marker was amplified for each sample with the g and h primers by PCR, using three technical replicates (Taberlet et al. 2007; 5'-GGGCAATCCTGAGCCAA-3', 5'-CCATTGAGTCTCTGCACCTATC-3'). Forward and reverse primers were tagged with a unique 12 bp oligonucleotide on the 5’ end (Fadrosh et al. 2014). Unique combinations of tagged primers were set up in panels for each PCR reaction for a total of 309 samples (100 samples with 3 PCR replicates each, 5 extractions blanks and 4 PCR negatives). The PCR negatives had no DNA template and were placed on the 96th well position in each panel. Composition of PCR reactions, final volumes and number of cycles can be found in Supporting Information Data S1. The PCR products were run on a 2% agarose gel, and the amplicon concentrations were measured via band intensity using ImageLab software (Bio-Rad, California, USA). The lowest concentration (μM) available for all PCR products and its relative volume was identified and the relative concentrations of the PCR products were adjusted to this same concentration. Amplicons were pooled in one library using a Biomek 4000 automated liquid handler (Beckman Coulter Life Sciences, Indianapolis, Indiana, USA). The library was cleaned using AMPure XP reagent beads (Beckman Coulter Life Sciences, Indianapolis, Indiana, USA). The length for all amplicons in the library was determined using a Fragment Analyzer (Agilent Technologies, Santa Clara, California, USA). The library was sequenced on an Illumina MiSeq platform with 150 bp paired-end reads (Illumina Inc., San Diego, California, USA). Sequence data was analyzed and curated using OBITools 2 (Boyer et al. 2016) following the wolf tutorial with adaptations for demultiplexing dual indexes from QIIME2 (Caporaso et al. 2010). Sequences were retained with both indexes for dereplication for further analysis. Similar sequences were clustered with obiclean (Boyer et al. 2016) only when the read count of the less abundant sequence was below 5% of the most abundant sequence. To reduce multiple identifications of the same sequence, taxonomic assignment of dereplicated and denoised sequences was done by matching to three reference sequences databases containing: (i) only taxa registered in the local Solholmfjell reference library; (ii) the complete arctic boreal database for vascular plants and bryophytes (Sønstebø et al.2010; Willerslev et al. 2014; Soininen et al. 2015); and (iii) taxa available in the EMBL database (downloaded on 7/02/2020) filtered to sequences with trnL (UUA) intron g-h primers using ecoPCR tool from OBITools (Boyer et al. 2016). Resulting identifications from the three databases were merged by sequence and duplicates were eliminated giving priority to reference databases (i), (ii), and (iii) in that order. To minimize erroneous taxonomic assignments, only taxa with a 100% match to a reference sequence were retained. We observed that below this threshold, sequences remained without a taxonomic rank assigned. Further, assigned taxa names were changed to the lowest taxonomic rank possible with trnL (UUA) intron and thus are identical to those registered in vegetation surveys. When different sequences were identified with identical taxa names, a unique entry was retained and the read counts within plots and replicates were summed. Read counts were averaged across all samples and negative controls (extraction + PCR). All analyses are plot-based, and coded using R v 1.4.17 (R Core Team, 2019) and with packages listed in the code. Separate analyses are made for vascular plants and bryophytes, and/or for spruce and pine data subsets, or combinations thereof, when relevant.

opencc-zeroMay 2022View details →

Data from: eDNA metabarcoding of log hollow sediments and soils highlights the importance of substrate type, frequency of sampling and animal size, for vertebrate species detection

Fauna monitoring often relies on visual monitoring techniques such as camera trappings, which have biases leading to underestimates of vertebrate species diversity. Environmental DNA (eDNA) has emerged as a new source of biodiversity data that may improve biomonitoring; however, eDNA based assessments of species richness remain relatively untested in terrestrial environments. We investigated the suitability of fallen log hollow sediment as a source of vertebrate eDNA, across two sites in south-western Australia - one with a Mediterranean climate and the other semi-arid. We compared two different approaches (camera trapping and eDNA metabarcoding) for monitoring of vertebrate species, and investigated the effect of other factors (frequency of species, timing of visits, frequency of sampling, body size) on vertebrate species detectability. Metabarcoding of hollow sediments resulted in the detection of higher species richness in comparison Hollow sediment detected higher species richness (29 taxa: six birds, three reptiles and 20 mammals) to metabarcoding of soil at the entrance of the hollow (13 taxa: three birds, two reptiles and eight mammals). We detected 31 taxa in total with eDNA metabarcoding and 47 with camera traps, with 14 taxa detected by both (12 mammals and two birds). By comparing camera trap data with eDNA read abundance, we were able to detect vertebrates through eDNA metabarcoding that had visited the area up to two months prior to sample collection. Larger animals were more likely to be detected, and so were vertebrates that were identified multiple times in the camera traps. These findings demonstrate the importance of substrate selection, frequency of sampling, and animal size, on eDNA based monitoring. Future eDNA experimental design should consider all these factors as they affect detection of target taxa.

opencc-zeroJun 2022View details →

Environmental nucleic acids: a field-based comparison for monitoring freshwater habitats using eDNA and eRNA

Nucleic acids released by organisms and isolated from environmental substrates are increasingly being used for molecular biomonitoring. While environmental DNA (eDNA) has received attention recently, the potential of environmental RNA as a biomonitoring tool remains less explored. Several recent studies using paired DNA and RNA metabarcoding of bulk samples suggest that RNA might better reflect "metabolically active" parts of the community. However, such studies mainly capture organismal eDNA and eRNA. For larger eukaryotes, isolation of extra-organismal RNA will be important, but viability needs to be examined in a field-based setting. In this study we evaluate (a) whether extra-organismal eRNA release from macroeukaryotes can be detected given its supposedly rapid degradation, and (b) if the same field collection methods for eDNA can be applied to eRNA. We collected eDNA and eRNA from water in lakes where fish community composition is well documented, enabling a comparison between the two nucleic acids in two different seasons with monitoring using conventional methods. We found that eRNA is released from macroeukaryotes and can be filtered from water and metabarcoded in a similar manner as eDNA to reliably provide species composition information. eRNA had a small but significantly greater true positive rate than eDNA, indicating that it correctly detects more species known to exist in the lakes. Given relatively small differences between the two molecules in describing fish community composition, we conclude that if eRNA provides significant advantages in terms of lability, it is a strong candidate to add to the suite of molecular monitoring tools.

opencc-zeroSep 2022View details →

Data from: Treated like dirt: Robust forensic and ecological inferences from soil eDNA after challenging sample storage

We investigated the effect of storage duration and conditions on the assessment of the soil biota with eDNA metabarcoding. We extracted eDNA from freshly collected soil samples and again from the same samples after storage under contrasting temperature conditions and contrasting exposure (open/closed tubes). We used four different primer sets targeting bacteria, fungi, protists (cercozoans), and general eukaryotes. We quantified differences in richness, evenness, and community composition. Subsequently, we tested whether we could correctly infer habitat type and original sample identity after storage using a large reference dataset. This repository contains the un-demultiplexed fastq sequences.

opencc-by-4.0Nov 2023View details →

Biofouling sponges as natural eDNA samplers for marine vertebrate biodiversity monitoring

These are the raw sequencing data and associated analysis codes for the study of "biofouling sponges as natural eDNA samplers for marine vertebrate biodiversity monitoring".

opencc-zeroJul 2024View details →

Data from: Ecological forensic testing: Using multiple primers for eDNA detection of marine vertebrates in an estuarine lagoon subject to anthropogenic influences

Many critical aquatic habitats are in close proximity to human activity (i.e., adjacent to residences, docks, marinas, etc.), and it is vital to monitor biodiversity in these and similar areas that are subject to ongoing urbanization, pollution, and other environmental disruptions. Environmental DNA (eDNA) metabarcoding is an accessible, non-invasive genetic technique used to detect and monitor species diversity and is a particularly useful approach in areas where traditional biodiversity monitoring methods (e.g., visual surveys or video surveillance) are challenging to conduct. In this study, we implemented an eDNA approach that used a combination of three distinct PCR primer sets to detect marine vertebrates within a canal system of Biscayne Bay, Florida, an ecosystem representative of challenging sampling conditions and a myriad of impacts from urbanization. We detected fish species from aquarium, commercial, and recreational fisheries, as well as invasive, cryptobenthic, and endangered vertebrate species, including charismatic marine mammals such as the protected West Indian manatee, Trichechus manatus. Our results support the potential for eDNA analyses to supplement traditional biodiversity monitoring methods and ultimately serve as an important tool for ecosystem management. This approach minimizes stress or disturbance to organisms and removes the intrinsic risk and logical limitations of SCUBA diving, snorkeling, or deploying sensitive equipment in areas that are subject to high vessel traffic and/or low visibility. Overall, this work sets the framework to understand how biodiversity may change over different spatial and temporal scales in an aquatic ecosystem heavily influenced by urbanization and validates the use of eDNA as a complementary approach to traditional ecological monitoring methods.

opencc-zeroJul 2024View details →

Data from: A sedimentary eDNA record of the Atacama Trench reveals biodiversity changes in the most productive marine ecosystem

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.