Freshwater diatom biomonitoring through benthic kick-net metabarcoding

PloS One
V. C. MaitlandMehrdad Hajibabaei

Abstract

Biomonitoring is an essential tool for assessing ecological conditions and informing management strategies. The application of DNA metabarcoding and high throughput sequencing has improved data quantity and resolution for biomonitoring of taxa such as macroinvertebrates, yet, there remains the need to optimise these methods for other taxonomic groups. Diatoms have a longstanding history in freshwater biomonitoring as bioindicators of water quality status. However, multi-substrate periphyton collection, a common diatom sampling practice, is time-consuming and thus costly in terms of labour. This study examined whether the benthic kick-net technique used for macroinvertebrate biomonitoring could be applied to bulk-sample diatoms for metabarcoding. To test this approach, we collected samples using both conventional multi-substrate microhabitat periphyton collections and bulk-tissue kick-net methodologies in parallel from replicated sites with different habitat status (good/fair). We found there was no significant difference in community assemblages between conventional periphyton collection and kick-net methodologies or site status, but there was significant difference between diatom communities depending on site (P = 0.042). Thes...Continue Reading

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Citations

Jul 31, 2021·The Science of the Total Environment·Stéfano Zorzal-Almeida, Valéria de Oliveira Fernandes

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Methods Mentioned

BETA
scraping
scrapings
PCR
PCRs
electrophoresis

Software Mentioned

vegan
R package
VSEARCH
goeveg
geom
R
SCVURL
conda
CUTADAPT
SeqPrep

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