10.5061/DRYAD.104KG
Andujar, Carmelo
Institute of Zoology
Arribas, Paula
Natural History Museum
Gray, Clare
Imperial College London
Bruce, Katherine
Natural History Museum
Woodward, Guy
Imperial College London
Yu, Douglas W.
University of East Anglia
Kunming Institute of Zoology
Vogler, Alfried P.
Natural History Museum
Data from: Metabarcoding of freshwater invertebrates to detect the effects
of a pesticide spill
Dryad
dataset
2017
biomonitoring
Freshwater ecosystems
2017-10-17T18:47:10Z
2017-10-17T18:47:10Z
en
https://doi.org/10.1111/mec.14410
1617386769 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Biomonitoring underpins the environmental assessment of freshwater
ecosystems and guides management and conservation. Current methodology for
surveys of (macro)invertebrates uses coarse taxonomic identification where
species-level resolution is difficult to obtain. Next-generation
sequencing of entire assemblages (metabarcoding) provides a new approach
for species detection, but requires further validation. We used
metabarcoding of invertebrate assemblages with two fragments of the cox1
"barcode" and partial nuclear ribosomal (SSU) genes, to assess
the effects of a pesticide spill in the River Kennet (Southern England).
Operational Taxonomic Unit (OTU) recovery was tested under72 parameters
(read denoising, filtering, pair merging and clustering). Similar
taxonomic profiles were obtained under a broad range of parameters. The
SSU marker recovered Platyhelminthes and Nematoda, missed by cox1,while
Rotifera were only amplified with cox1. A reference set was created from
all available barcode entries for Arthropoda in the BOLD database and
clustered into OTUs. The River Kennet metabarcoding produced matches to
207 of these reference OTUs, five times the number of species recognised
with morphological monitoring. The increase was due to: greater taxonomic
resolution (e.g. splitting a single morphotaxon ‘Chironomidae’ into 55
named OTUs); splitting of binomial species names into multiple molecular
OTUs in species complexes; and the use of a filtration-flotation protocol
for extraction of minute specimens (meiofauna). Community analyses
revealed strong differences between "impacted" vs.
"control" samples, detectable with each gene marker, for each
major taxonomic group, and for meio- and macro-faunal samples separately.
Thus, highly resolved taxonomic data can be extracted at a fraction of the
time and cost of traditional non-molecular methods, opening new avenues
for freshwater invertebrate biodiversity monitoring and molecular ecology.
Raw metabarcode data Slot 1 (12 libraries)Raw metabarcode data Slot 1 (12
libraries). Inlcudes R1 and R2 files for macrofauna samples from the 3
impacted and 3 control sites, each sampled at two times after pesticide
spill. More info on
paper.Raw_metabarcode_data_Slot_1_(12_libraries).rarRaw_metabarcode_data_Slot_2_(12_libraries)Raw metabarcode data Slot 2 (12 libraries). Inlcudes R1 and R2 files for meiofauna samples from the 3 impacted and 3 control sites, each sampled at two times after pesticide spill. More info on paper.