A molecular‐based approach for examining responses of eukaryotes in microcosms to contaminant‐spiked estuarine sediments

Abstract

Ecotoxicological information for most contaminants is limited to a small number of taxa, and these are generally restricted to comparatively hardy organisms that are readily extractable from test media and easily identifiable. Advances in DNA sequencing can now provide a comprehensive view of benthic invertebrate diversity. The authors applied 454 pyrosequencing to examine the responses of benthic communities in microcosms exposed to sediments with elevated concentrations of triclosan, the endpoint being eukaryl communities that have successfully vertically migrated through the manipulated sediments. The biological communities associated with the 3 treatments (control triclosan, low triclosan [14 mg/kg], and high triclosan [180 mg/kg]) clustered into 3 groups: control/low (n = 6 controls and 4 low), moderate (n = 2 low), and high (n = 5 high). One sample was discarded as an outlier. The most pronounced change as a response to triclosan was the loss of number of metazoan operational taxonomic units (OTUs), indicative of the control/low and moderate groups, with this being most evident in the range of taxa associated with the classes Chromadorea and Bivalvia and the phylum Kinorhyncha. The authors also describe a range of other taxa that aided discrimination between the groups; compare findings with traditionally obtained meio- and macrofaunal communities obtained from the same experiment; and illustrate some of the advantages and limitations associated with both the molecular and traditional approaches. The described approach illustrates the capacity for amplicon sequencing to provide ecologically relevant information that can be used to strengthen an understanding of how sedimentary communities respond to a range of environmental stressors.

Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries

“…As there is a weak statistical relationship between the number of sequence reads and organism biomass or abundance (Egge et al, 2013), all MOTU data were converted to presence or absence prior to computation (Chariton et al, 2014). Ordination of MOTU data was performed by non-metric multidimensional scaling (nMDS) using the Jaccard similarity coefficient in the Primer 6 þ statistical package (Plymouth Marine Laboratory, UK).…”

“…Previously, we have cautioned against the use of MOTU richness in DNA-derived ecological studies, as bioinformatic pipelines generally overly inflate true sequence richness (Chariton et al, 2014). As shown in the present study, and that by Morgan et al (2013), an accurate measure of sequence richness (i.e.…”

Worldwide Analysis of Sedimentary DNA Reveals Major Gaps in Taxonomic Knowledge of Deep-Sea Benthos

“…These uncertainties should not undermine the potential of metabarcoding to better understand the diversity of poorly known communities. Indeed, the total information obtained from a large number of taxa in parallel provides a good estimator of environmental community diversity that has many practical applications for ecosystem assessment and monitoring (Chariton et al, 2010(Chariton et al, , 2014Czernik et al, 2013;Stephenson et al, 2013;Lallias et al, 2014;Pawlowski et al, 2014;Willerslev et al, 2014;Guardiola et al, 2015;Lejzerowicz et al, 2015;Pochon et al, 2015;Boschen et al, 2016).…”

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

“…2012; Chariton et al. 2014). However, data processing for a metabarcoding study can be a daunting task for ecologists who wish to identify the species present in a sample, and even for bioinformaticians trying to validate their methods (McPherson 2009).…”