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Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: do DNA extraction methods matter?

Vasselon, Valentin and Domaizon, Isabelle and Rimet, Frederic and Kahlert, Maria and Bouchez, Agnes (2017). Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: do DNA extraction methods matter? Freshwater Science. 36:1, 162-177
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Official URL: http://dx.doi.org/10.1086/690649

Abstract

Current freshwater biomonitoring with diatoms is based on microscopic examination of the morphology of their silica skeleton. This standardized approach is time consuming and requires a high degree of taxonomic expertise. Metabarcoding combined with high-throughput sequencing (HTS) has great potential for next-generation biomonitoring applications but requires standardization. Molecular inventories are strongly influenced by the DNA extraction method used, but the effect of extraction protocols has not been tested to enable selection of the best DNA extraction method for HTS metabarcoding. We used 5 DNA extraction methods combining various types of cell lysis and DNA purification to extract DNA from 8 pure diatom cultures and 8 samples from streams and lakes with differing water quality. We compared the methods based on: 1) quality and purity of the extracted DNA, 2) community inventories obtained from HTS targeting the ribulose-1, 5-bisphosphate carboxylase (rbcL) barcode, and 3) similarity between molecular and microscopy-based inventories of community composition and the Specific Pollutionsensitivity Index [SPI]. A method based on GenElute™-LPA had higher extraction efficiency than the 4 commercial kits but had the highest polymerase chain reaction inhibition level. All 5 methods were efficient for HTS, and method did not affect operational taxonomic unit richness. We observed variations in the relative abundance of some taxa within Nitzschia, Amphora, Encyonema, Gomphonema, and Navicula between 2 of the 5 methods, but method did not affect global diatom community composition or SPI values. SPI values calculated from microscopy-based inventories and molecular inventories based on all 5 extraction methods were strongly correlated. For convenience purposes (high DNA quantity and low cost), we encourage standardization of HTS diatom biomonitoring based on the SA-Gen method.

Authors/Creators:Vasselon, Valentin and Domaizon, Isabelle and Rimet, Frederic and Kahlert, Maria and Bouchez, Agnes
Title:Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: do DNA extraction methods matter?
Series/Journal:Freshwater Science (2161-9565)
Year of publishing :2017
Volume:36
Number:1
Page range:162-177
Number of Pages:16
Publisher:University of Chicago Press, The Society for Freshwater Science
ISSN:2161-9565
Language:English
Publication Type:Journal article
Refereed:Yes
Article category:Scientific peer reviewed
Version:Published version
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Ecology
(A) Swedish standard research categories 2011 > 1 Natural sciences > 105 Earth and Related Environmental Sciences > Environmental Sciences (social aspects to be 507)
Agrovoc terms:Bacillariophyceae, DNA sequence
Keywords:next-generation biomonitoring, DNA extraction methods, metabarcoding, high-throughput sequencing, diatom communities
URN:NBN:urn:nbn:se:slu:epsilon-e-4091
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-4091
Additional ID:
Type of IDID
DOI10.1086/690649
ID Code:14206
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Dept. of Aquatic Sciences and Assessment
Deposited By: SLUpub Connector
Deposited On:15 May 2017 08:42
Metadata Last Modified:26 Jun 2017 06:59

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