Gaps in DNA-Based Biomonitoring Across the Globe

McGee, Katie M.; Robinson, Chloe Victoria; Hajibabaei, Mehrdad

doi:10.3389/fevo.2019.00337

Cited by 72 publications

(61 citation statements)

References 66 publications

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“…free DNA existing in a water medium), and therefore often a wider coverage of biodiversity is detected using this sample type (Taberlet et al, 2012; Turner, Uy, & Everhart, 2015; Mehrdad Hajibabaei et al, 2019). Additionally, biomonitoring research should strive to sample taxa from a wide geographic range, including remote locations, to prevent a location bias and therefore potential under-/over-representation of taxa (McGee et al, 2019). Metabarcoding bulk-benthos single ‘mock’ and paired samples provided an opportunity to test the effectiveness of a proposed alternative preservative to ethanol for preserving macroinvertebrate DNA.…”

Section: Discussionmentioning

confidence: 99%

“…This is problematic when attempting to collect environmental samples from remote locations (i.e. air access only), which in turn directly limits the geographical extent of DNA-based biomonitoring (McGee, Robinson, & Hajibabaei, 2019). In addition, samples preserved in ethanol require a lengthy evaporation period prior to DNA extraction, due to the PCR inhibitory nature of ethanol in concentrations above 1% (Demeke & Jenkins, 2010; Schrader, Schielke, Ellerbroek, & Johne, 2012).…”

Section: Introductionmentioning

confidence: 99%

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Propylene glycol-based antifreeze as an effective preservative for DNA metabarcoding of benthic arthropods

Robinson

Porter

Wright

et al. 2020

Preprint

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Maintaining the integrity of DNA in bulk environmental samples from source to laboratory is crucial for capturing the true range of taxa present within an ecosystem. Preservation consideration of DNA is particularly important if samples are being collected in remote areas and by non-specialist ‘citizen scientists’ in nationwide programs. Traditionally, absolute ethanol is used as the preferred preservative for environmental samples collected for downstream DNA metabarcoding analyses. However, transport, shipping and DNA extraction of samples preserved in ethanol is a lengthy procedure due to safety restrictions and the requirement of full ethanol evaporation prior to extraction. We examined the efficacy of an easily accessible, non-toxic propylene glycol-based antifreeze as an alternative to absolute ethanol for preserving macroinvertebrate DNA from bulk-benthos DNA samples. We tested the differences in both cytochrome oxidase I (COI) exact sequence variants (ESVs) and COI taxonomic orders detected in both ethanol and antifreeze samples using two processing methods (no evaporation of preservative versus full evaporation). In addition, we assessed the detection of families and genera within the Arthropoda phylum for preservative type, site and processing method. Our results suggest that antifreeze is a suitable alternative to ethanol, a greater global ESV richness reported for antifreeze samples. Additionally, a higher proportion of arthropod reads in ESVs were detected in antifreeze (average 69%) compared with ethanol (average 53%). Finally, antifreeze samples produced similar results for the different processing methods, whereas ethanol samples failed to produce similar results without prior evaporation. Although ethanol is currently widely used for DNA preservation, our results demonstrate that by using antifreeze, it is possible to achieve similar taxonomic coverage and community assemblages of bulk-benthos DNA samples for macroinvertebrates, with the added simplicity and shorter laboratory processing time achieved using an easily available, unregulated preservative.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Propylene glycol-based antifreeze as an effective preservative for DNA metabarcoding of benthic arthropods

Robinson

Porter

Wright

et al. 2020

Preprint

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“…Current biomonitoring is heavily skewed toward terrestrial Europe, North America, Australia, and New Zealand (Cavallo et al, 2019;McGee et al, 2019). This is due, in part, to a lack of expertise in biomonitoring and interpretation in many countries, a global shortage of finance, as well as a limited acceptance of conventional methods.…”

Section: What Is the Appropriate Spatio-temporal Scale For Ngb?mentioning

confidence: 99%

Key Questions for Next-Generation Biomonitoring

Makiola

Compson

Baird

et al. 2020

Front. Environ. Sci.

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Classical biomonitoring techniques have focused primarily on measures linked to various biodiversity metrics and indicator species. Next-generation biomonitoring (NGB) describes a suite of tools and approaches that allow the examination of a broader spectrum of organizational levels-from genes to entire ecosystems. Here, we frame 10 key questions that we envisage will drive the field of NGB over the next decade. While Makiola et al. Questions for Next-Generation Biomonitoring not exhaustive, this list covers most of the key challenges facing NGB, and provides the basis of the next steps for research and implementation in this field. These questions have been grouped into current-and outlook-related categories, corresponding to the organization of this paper.

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“…As taxonomy-based strategy (A) depends on reference sequences for organism identification, the incompleteness of reference databases can have a major impact. Hence, completing databases, both by the "vertical" addition of more taxa and by the "horizontal" coverage of wider geographical areas, would certainly contribute to an improvement in identification (Vasselon et al, 2017;McGee et al, 2019). However, despite sustained efforts, reference databases will likely remain skewed towards some taxa while suffering from important gaps across other taxonomic groups and/or biogeographical regions (Weigand et al, 2019).…”

Section: The Environmental Genomics Revolution For Biodiversity Reseamentioning

confidence: 99%

Ecosystems Monitoring Powered by Environmental Genomics: A Review of Current Strategies with An Implementation Roadmap

Cordier¹,

Sáez²,

Apothéloz-Perret-Gentil³

et al. 2020

Preprint

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A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on biodiversity and ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental DNA and RNA to cost-efficiently and accurately monitor biodiversity, technical limitations and conceptual issues still stand in the way of its routine application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception of the methodology as being premature or “in development”, hence restraining regulators from binding these tools into legal frameworks. This review focuses on the strengths and limitations of genomics-based strategies that have emerged over the past ten years and have been classified for this purpose into three broad strategies: (A) Taxonomy-based approaches that focus on known bio-indicators or the diversity of taxonomically described taxa, (B) De novo approaches that do not require well-established taxonomy, and (C) Function-based approaches that rely on community-wide metrics, where taxa are interchangeable, or on functional profiles instead of compositional turnovers. We finally propose a roadmap for the implementation of environmental genomics into routine monitoring programs that leverage recent analytical advancements, upon which some critical limitations are alleviated.

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Gaps in DNA-Based Biomonitoring Across the Globe

Cited by 72 publications

References 66 publications

Propylene glycol-based antifreeze as an effective preservative for DNA metabarcoding of benthic arthropods

Propylene glycol-based antifreeze as an effective preservative for DNA metabarcoding of benthic arthropods

Key Questions for Next-Generation Biomonitoring

Ecosystems Monitoring Powered by Environmental Genomics: A Review of Current Strategies with An Implementation Roadmap

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