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Consequences of environmental DNA pooling
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  • Ralph Wainer,
  • Hayley Ridgway,
  • Eirian Jones,
  • Duane Peltzer,
  • Ian Dickie
Ralph Wainer
Bio-Protection Research Centre
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Hayley Ridgway
Bio-Protection Research Centre
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Eirian Jones
Lincoln University
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Duane Peltzer
Landcare Research New Zealand
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Ian Dickie
Bio-Protection Research Centre
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Abstract

DNA-based techniques are increasingly used to assess biodiversity both above- and belowground. Most effort has focussed on bioinformatics and sample collection, whereas less is known about the consequences of mixing collected environmental DNA (eDNA), post-extraction and pre-PCR. We applied varying degrees of pooling to stand-alone eDNA samples collected across a non-native plant invasion density gradient, and compared the fungal communities of pooled and unpooled samples. Pooling soil eDNA decreased observable fungal rarefied richness in our samples, led to phylum-specific shifts in proportional abundance, and increased the sensitivity of detection for the invasive plant’s overall impact on fungal diversity. We demonstrate that pooling fungal eDNA could change the outcome of similar eDNA studies where the aim is to: 1) identify the rare biosphere within a soil community, 2) estimate species richness and proportional abundance, or 3) assess the impact of an invasive plant on soil fungi. Sample pooling might be appropriate when determining larger-scale overarching responses of soil communities, as pooling increased the sensitivity of measurable effects of an invasive plant on soil fungal diversity.

Peer review status:UNDER REVIEW

30 Sep 2020Submitted to Molecular Ecology Resources
20 Oct 2020Assigned to Editor
20 Oct 2020Submission Checks Completed
21 Oct 2020Reviewer(s) Assigned
16 Nov 2020Review(s) Completed, Editorial Evaluation Pending