Accurate assessment of the impact of salmon farming on benthic sediment enrichment using foraminiferal metabarcoding

Pochon, Xavier; Wood, Susanna A.; Keeley, Nigel; Lejzerowicz, Franck; Esling, Philippe; Drew, Joshua Adam; Pawłowski, Jan

doi:10.1016/j.marpolbul.2015.08.022

Cited by 95 publications

(111 citation statements)

References 73 publications

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“…Furthermore, replicates sampled near the cages, within the same van Veen grab, will likely be very similar, while replicates within the same grab collected at distant stations will deviate more from each other. Even though the distance-tocage is no substitute for the environmental gradients that drive community changes, our data show that there is a steady trend towards increasing diversity and diversity variation among sample replicates away from the cages, a pattern which is consistent across farms and with previous studies (Pawlowski et al 2014a, Pochon et al 2015. Taken together, our results suggest that the fish farms affect their immediate surroundings, creating environmental conditions that are particularly suitable for a set of species that could then be viewed as potential bioindicators.…”

Section: Discussionsupporting

confidence: 90%

“…Correlative analyses based on common diversity metrics and exploratory analyses based on Bray-Curtis community distances showed that ecological responses could be captured better and appeared more robust when using RNA molecules. In New Zealand, we focused on the RNA signal to evidence foraminiferal responses along well-defined organic enrichment gradients and flow regimes (Pochon et al 2015). We proposed that RNA sequence abundance profiles of selected foraminiferans can be used to predict their ecological preferences and therefore their value as bioindicators.…”

Section: Introductionmentioning

confidence: 99%

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Benthic monitoring of salmon farms in Norway using foraminiferal metabarcoding

Pawłowski¹,

Esling²,

Lejzerowicz³

et al. 2016

Aquacult. Environ. Interact.

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The rapid growth of the salmon industry necessitates the development of fast and accurate tools to assess its environmental impact. Macrobenthic monitoring is commonly used to measure the impact of organic enrichment associated with salmon farm activities. However, classical benthic monitoring can hardly answer the rapidly growing demand because the morphological identification of macro-invertebrates is time-consuming, expensive and requires taxonomic expertise. Environmental DNA (eDNA) metabarcoding of meiofauna-sized organisms, such as Foraminifera, was proposed to overcome the drawbacks of macrofauna-based benthic monitoring. Here, we tested the application of foraminiferal metabarcoding to benthic monitoring of salmon farms in Norway. We analysed 140 samples of eDNA and environmental RNA (eRNA) extracted from surface sediment samples collected at 4 salmon farming sites in Norway. We sequenced the variable region 37f of the 18S rRNA gene specific to Foraminifera. We compared our data to the results of macrofaunal surveys of the same sites and tested the congruence between various diversity indices inferred from metabarcoding and morphological data. The results of our study confirm the usefulness of Foraminifera as bioindicators of organic enrichment associated with salmon farming. The foraminiferal diversity increased with the distance to fish cages, and metabarcoding provides an assessment of the ecological quality comparable to the morphological analyses. The foraminiferal metabarcoding approach appears to be a promising alternative to classical benthic monitoring, providing a solution to the morpho-taxonomic bottleneck of macrofaunal surveys.

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Section: Discussionsupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Benthic monitoring of salmon farms in Norway using foraminiferal metabarcoding

Pawłowski¹,

Esling²,

Lejzerowicz³

et al. 2016

Aquacult. Environ. Interact.

View full text Add to dashboard Cite

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“…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).…”

Section: Discussion Most Deep-sea Diversity Is Unknownmentioning

confidence: 99%

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

et al. 2016

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Deep-sea sediments represent the largest but least known ecosystem on earth. With increasing anthropogenic pressure, it is now a matter of urgency to improve our understanding of deep-sea biodiversity. Traditional morpho-taxonomic studies suggest that the ocean floor hosts extraordinarily diverse benthic communities. However, due to both its remoteness and a lack of expert taxonomists, assessing deep-sea diversity is a very challenging task. Environmental DNA (eDNA) metabarcoding offers a powerful tool to complement morpho-taxonomic studies. Here we use eDNA to assess benthic metazoan diversity in 39 deep-sea sediment samples from bathyal and abyssal depths worldwide. The eDNA dataset was dominated by meiobenthic taxa and we identified all animal phyla commonly found in the deep-sea benthos; yet, the diversity within these phyla remains largely unknown. The large numbers of taxonomically unassigned molecular operational taxonomic units (OTUs) were not equally distributed among phyla, with nematodes and platyhelminthes being the most poorly characterized from a taxonomic perspective. While the data obtained here reveal pronounced heterogeneity and vast amounts of unknown biodiversity in the deep sea, they also expose the difficulties in exploiting metabarcoding datasets resulting from the lack of taxonomic knowledge and appropriate reference databases. Overall, our study demonstrates the promising potential of eDNA metabarcoding to accelerate the assessment of deep-sea biodiversity for pure and applied deep-sea environmental research but also emphasizes the necessity to integrate such new approaches with traditional morphology-based examination of deep-sea organisms.

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“…Several studies have used metabarcoding to characterize the metazoan taxonomic composition of aquatic environments (Porazinska et al, 2009;Chariton et al, 2010;Fonseca et al, 2014;Dell'Anno et al, 2015;Leray and Knowlton, 2015;Chain et al, 2016), and an increasing number of studies have directly applied the approach for environmental biomonitoring purposes (Ji et al, 2013;Dafforn et al, 2014;Pawlowski et al, 2014;Chariton et al, 2015;Gibson et al, 2015;Pochon et al, 2015;Zaiko et al, 2015). Initial studies inferring biotic indices from molecular data show the potential of metabarcoding for evaluating aquatic ecosystem quality Visco et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment

2016

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Characterization of biodiversity has been extensively used to confidently monitor and assess environmental status. Yet, visual morphology, traditionally and widely used for species identification in coastal and marine ecosystem communities, is tedious and entails limitations. Metabarcoding coupled with high-throughput sequencing (HTS) represents an alternative to rapidly, accurately, and cost-effectively analyze thousands of environmental samples simultaneously, and this method is increasingly used to characterize the metazoan taxonomic composition of a wide variety of environments. However, a comprehensive study benchmarking visual and metabarcoding-based taxonomic inferences that validates this technique for environmental monitoring is still lacking. Here, we compare taxonomic inferences of benthic macroinvertebrate samples of known taxonomic composition obtained using alternative metabarcoding protocols based on a combination of different DNA sources, barcodes of the mitochondrial cytochrome oxidase I gene and amplification conditions. Our results highlight the influence of the metabarcoding protocol in the obtained taxonomic composition and suggest the better performance of an alternative 313 bp length barcode to the traditionally 658 bp length one used for metazoan metabarcoding. Additionally, we show that a biotic index inferred from the list of macroinvertebrate taxa obtained using DNA-based taxonomic assignments is comparable to that inferred using morphological identification. Thus, our analyses prove metabarcoding valid for environmental status assessment and will contribute to accelerating the implementation of this technique to regular monitoring programs.

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Accurate assessment of the impact of salmon farming on benthic sediment enrichment using foraminiferal metabarcoding

Cited by 95 publications

References 73 publications

Benthic monitoring of salmon farms in Norway using foraminiferal metabarcoding

Benthic monitoring of salmon farms in Norway using foraminiferal metabarcoding

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

Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment

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