Environmental DNA filtration techniques affect recovered biodiversity

Markus Majaneva,Ola H Diserud,Mehrdad Hajibabaei,Erik Boström,Torbjørn Ekrem,Shannon H C Eagle

doi:10.1038/s41598-018-23052-8

Abstract

Freshwater metazoan biodiversity assessment using environmental DNA (eDNA) captured on filters offers new opportunities for water quality management. Filtering of water in the field is a logistical advantage compared to transport of water to the nearest lab, and thus, appropriate filter preservation becomes crucial for maximum DNA recovery. Here, the effect of four different filter preservation strategies, two filter types, and pre-filtration were evaluated by measuring metazoan diversity and community composition, using eDNA collected from a river and a lake ecosystem. The filters were preserved cold on ice, in ethanol, in lysis buffer and dry in silica gel. Our results show that filters preserved either dry or in lysis buffer give the most consistent community composition. In addition, mixed cellulose ester filters yield more consistent community composition than polyethersulfone filters, while the effect of pre-filtration remained ambiguous. Our study facilitates development of guidelines for aquatic community-level eDNA biomonitoring, and we advocate filtering in the field, using mixed cellulose ester filters and preserving the filters either dry or in lysis buffer.

Highlights

Freshwater ecosystem assessments based on morphologically identified macroinvertebrate communities are an essential part of water quality management[1,2]
Filters were stored in 99% ethanol (EtOH), silica gel (Dry), Qiagen lysis buffer ATL (Buffer) or kept cold (Ice) until DNA was extracted in the laboratory. 500 mL of molecular grade H2O was filtered and the filters stored with the respective methods as negative controls (B)
In addition to membrane type, the filter construction itself can influence DNA capture efficiency: Sterivex-GP capsule filters were recently compared with standard filters and found to outperform polycarbonate track-etch (PCTE) and glass microfiber (GMF), but not Cellulose nitrate (CN) filters as long as DNA was extracted from the filter within the capsule[25]

Summary

Introduction

Freshwater ecosystem assessments based on morphologically identified macroinvertebrate communities are an essential part of water quality management[1,2]. The use of short, standardized DNA sequences to identify species, i.e. DNA barcoding[8], can overcome many of the aforementioned problems given well-populated reference libraries[9,10], and high-throughput parallel sequencing of DNA from bulk samples (i.e. DNA metabarcoding) can further increase efficiency and reduce cost of identification, potentially revolutionizing macroinvertebrate-based assessments[11,12]. In addition to bulk samples, the DNA metabarcoding approach may be applied to genetic material that is obtained directly from the environment, referred to as environmental DNA (eDNA)[13]. Cellulose nitrate (CN) filters have resulted in the highest DNA yield when compared with polyethene sulfone (PES), polyvinylidene fluoride (PVDF) and polycarbonate (PC) filters[26] and glass microfiber (GMF) filters were shown to outperform PC filters[23] In another study, both CN and PES filters yielded higher numbers of DNA copies than polycarbonate track-etch (PCTE) and GMF membrane filters[27]. In addition to membrane type, the filter construction itself can influence DNA capture efficiency: Sterivex-GP capsule filters were recently compared with standard filters and found to outperform PCTE and GMF, but not CN filters as long as DNA was extracted from the filter within the capsule[25]

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Conclusion