Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA

Ruppert, Krista M.; Kline, Richard J.; Rahman, Saydur

doi:10.1016/j.gecco.2019.e00547

Cited by 693 publications

(642 citation statements)

References 198 publications

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“…Plant community measurements also represent an exciting new possibility for metagenomic terrestrial plant community surveying. Whereas PCR, classically used in eDNA studies, focuses on amplifying the DNA from a single species, a metagenomic study analyzes all DNA present in a sample without the need for a priori identification of single species targets (Ruppert, Kline, & Rahman, 2019). The implementation of this kind of metagenomic study could be used to help further and test theoretical and experimental ecological questions and assist in management practices.…”

Section: Discussionmentioning

confidence: 99%

Analyzing airborne environmental DNA: A comparison of extraction methods, primer type, and trap type on the ability to detect airborne eDNA from terrestrial plant communities

2019

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Airborne environmental DNA (eDNA) research has typically focused on the detection of pollen from anemophilous terrestrial plant species; however, recent findings have expanded the definition of airborne eDNA to include a variety of eDNA sources, such as leaf and flower fragments. While methods for capturing pollen are well studied, there is less known about how to best analyze and capture more broadly defined bulk airborne eDNA samples. Therefore, this study aimed to identify efficient techniques for the extraction and amplification of airborne eDNA and how best to capture these samples. First, we collected samples using Big Spring Number Eight dust traps and quantified the influence of three different extraction methods (cetrimonium bromide‐chloroform, DNeasy Plant Maxi Kit, and DNeasy PowerPlant Pro DNA Isolation Kit) and two global plant primer sets (targeting the trnL and ITS2 genes) on quantitative polymerase chain reaction (qPCR)‐based terrestrial plant detection. Additionally, we examined how best to capture airborne eDNA by comparing the performance of three difference passive dust collectors (Big Spring Number Eight, Modified Wilson and Cooke, and Marble dust collectors). We found that the detection of airborne eDNA was significantly influenced by both the extraction methods employed and choice of qPCR primer. Additionally, we found that all three traps preformed similarly but the Big Spring Number Eight dust traps trended as consistently one of the most effective, shedding light on the nonhomogeneous nature of airborne eDNA. This study represents the first methodology paper focusing on airborne eDNA as a bulk environmental sample containing more than just pollen. In the future, additional research should examine more about the ecology of airborne eDNA (origin, state, transport, fate), explore active dust collectors compared to the passive traps used here, and develop the application of metabarcoding for airborne eDNA analysis.

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Section: Discussionmentioning

confidence: 99%

Analyzing airborne environmental DNA: A comparison of extraction methods, primer type, and trap type on the ability to detect airborne eDNA from terrestrial plant communities

2019

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“…This analysis highlights the potential of LDA as a method to reveal small subsets of OTUs that are characteristic of specific environmental conditions from large environmental DNA data sets. As such, LDA could help define "indicator species" for biomonitoring (Ruppert, Kline, & Rahman, 2019).…”

Section: F I G U R Ementioning

confidence: 99%

Latent Dirichlet Allocation reveals spatial and taxonomic structure in a DNA‐based census of soil biodiversity from a tropical forest

Sommeria‐Klein

Zinger

Coissac

et al. 2019

Molecular Ecology Resources

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High‐throughput sequencing of amplicons from environmental DNA samples permits rapid, standardized and comprehensive biodiversity assessments. However, retrieving and interpreting the structure of such data sets requires efficient methods for dimensionality reduction. Latent Dirichlet Allocation (LDA) can be used to decompose environmental DNA samples into overlapping assemblages of co‐occurring taxa. It is a flexible model‐based method adapted to uneven sample sizes and to large and sparse data sets. Here, we compare LDA performance on abundance and occurrence data, and we quantify the robustness of the LDA decomposition by measuring its stability with respect to the algorithm's initialization. We then apply LDA to a survey of 1,131 soil DNA samples that were collected in a 12‐ha plot of primary tropical forest and amplified using standard primers for bacteria, protists, fungi and metazoans. The analysis reveals that bacteria, protists and fungi exhibit a strong spatial structure, which matches the topographical features of the plot, while metazoans do not, confirming that microbial diversity is primarily controlled by environmental variation at the studied scale. We conclude that LDA is a sensitive, robust and computationally efficient method to detect and interpret the structure of large DNA‐based biodiversity data sets. We finally discuss the possible future applications of this approach for the study of biodiversity.

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“…The addition of more data will be necessary to distinguish rare from misidentified species, as will integration of different kinds of biodiversity inventories in community platforms such as GBIF. Because of the accessibility of various data sources on the GBIF platform, we were able to show 11 fish species found with eDNA are first reports at the beach, as were 76 phyla that had no record in GBIF, which showcases eDNA as a feasible method to both fill inventory gaps and to include the more challenging branches of the tree of life (Ruppert et al, 2019).…”

Section: Discussionmentioning

confidence: 97%

Beach environmental DNA fills gaps in photographic biomonitoring to track spatiotemporal community turnover across 82 phyla

Meyer

Schweizer

Kwan

et al. 2019

Preprint

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Abstract:Environmental DNA (eDNA) metabarcoding is emerging as a biomonitoring tool available to the citizen science community that promises to augment or replace photographic observation. However, eDNA results and photographic observations have rarely been compared to document their individual or combined power. Here, we use eDNA multilocus metabarcoding, a method deployed by the CALeDNA Program, to inventory and evaluate biodiversity variation along the Pillar Point headland near Half Moon Bay, California. We describe variation in presence of 13,000 taxa spanning 82 phyla, analyzed spatiotemporal patterns of beta diversity, and identified metacommunities. Inventory and measures of turnover across space and time from eDNA analysis were compared to the same measures based on in the Global Biodiversity Information Facility (GBIF), which contains information largely contributed by iNaturalist. We find eDNA depicted local signals with high seasonal turnover, especially in prokaryotes. We find a diverse community dense with pathogens and parasites in the embayment, and a State Marine Conservation Area (SMCA) with lower species richness than the rest of the beach peninsula, but with beta diversity signals showing resemblance to adjacent unprotected tidepools. The SMCA differs in observation density, with higher density of protozoans, and animals in Ascidiacea, Echinoidea, and Polycladida. Local contributions to beta diversity are elevated in a section of East-facing beach. GBIF observations were mostly from outside the SMCA, limiting some spatial comparisons. However, our findings suggest eDNA samples can link the SMCA sites to sites with better GBIF inventory, which may provide hypotheses for whether observations can be imputed for one site given observations from another. Results additionally supported >3800 largely novel biological interactions that no GBIF data had shown. This research, and accompanying interactive website supports eDNA as a gap-filling tool to measure biodiversity that is available to community and citizen scientists.

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Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA

Cited by 693 publications

References 198 publications

Analyzing airborne environmental DNA: A comparison of extraction methods, primer type, and trap type on the ability to detect airborne eDNA from terrestrial plant communities

Analyzing airborne environmental DNA: A comparison of extraction methods, primer type, and trap type on the ability to detect airborne eDNA from terrestrial plant communities

Latent Dirichlet Allocation reveals spatial and taxonomic structure in a DNA‐based census of soil biodiversity from a tropical forest

Beach environmental DNA fills gaps in photographic biomonitoring to track spatiotemporal community turnover across 82 phyla

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