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Variations in terrestrial arthropod DNA metabarcoding methods recovers robust beta diversity but variable richness
Teresita M Porter1,2, Dave M Morris3, Nathan Basiliko4
1Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, ON, P6A 2E5, Canada. terrimporter@gmail.com.
Scientific Reports
|December 5, 2019
Summary
DNA metabarcoding of forest soil arthropods offers a scalable biomonitoring solution. Individual soil sample processing yields higher biodiversity estimates than pooled samples, improving ecological integrity assessments.
Area of Science:
- Ecology
- Molecular Biology
- Environmental Science
Background:
- Terrestrial arthropods are crucial indicators of forest ecological integrity.
- Traditional phenotypic identification is limited by expertise, hindering widespread biomonitoring.
- DNA metabarcoding offers a scalable alternative for arthropod biodiversity assessment.
Purpose of the Study:
- To determine optimal field sampling and DNA extraction replication for soil arthropod biodiversity assessments.
- To evaluate the impact of sample pooling on biodiversity metrics.
- To assess the utility of DNA metabarcoding for forest biomonitoring.
Main Methods:
- DNA metabarcoding of the COI gene from forest soil arthropods.
- Comparison of biodiversity metrics (richness, beta diversity) between individually processed and pooled samples.
- Analysis of DNA extraction replication effects on richness estimates.
Main Results:
- Individually processed soil samples yielded significantly higher richness (488-614 variants) compared to pooled samples (165-191 variants).
- No significant difference in richness was observed between 1 or 3 pooled DNA extractions.
- Beta diversity remained robust across different methodological approaches.
- Taxonomic identification to species level was limited, but unnamed exact sequence variants were useful for site discrimination and indicator identification.
Conclusions:
- Individual processing of soil samples is recommended for maximizing arthropod richness detection in metabarcoding studies.
- DNA metabarcoding of soil arthropods, particularly using COI markers, is a scalable and effective method for biomonitoring forest ecological integrity.
- Continued DNA barcoding of local taxa is essential for building comprehensive reference databases to support metabarcoding efforts.
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