Meta-analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment

Abstract

DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated the consistency of this technique with traditional morpho-taxonomic approaches. These individual studies have used DNA metabarcoding to assess diversity and community structure of aquatic organisms both in marine and freshwater systems globally over the last decade. However, a systematic analysis of the comparability and effectiveness of DNA-based community assessment across all of these studies has hitherto been lacking. Here, we performed the first meta-analysis of available studies comparing traditional methods and DNA metabarcoding to measure and assess biological diversity of key aquatic groups, including plankton, microphytobentos, macroinvertebrates, and fish. Across 215 data sets, we found that DNA metabarcoding provides richness estimates that are globally consistent to those obtained using traditional methods, both at local and regional scale. DNA metabarcoding also generates species inventories that are highly congruent with traditional methods for fish. Contrastingly, species inventories of plankton, microphytobenthos and macroinvertebrates obtained by DNA metabarcoding showed pronounced differences to traditional methods, missing some taxa but at the same time detecting otherwise overseen diversity. The method is generally sufficiently advanced to study the composition of fish communities and replace more invasive traditional methods. For smaller organisms, like macroinvertebrates, plankton and microphytobenthos, DNA metabarcoding may continue to give complementary rather than identical estimates compared to traditional approaches. Systematic and comparable data collection will increase the understanding of different aspects of this complementarity, and increase the effectiveness of the method and adequate interpretation of the results.

Keywords: DNA; diversity assessment; fish; invertebrates; meta-analysis; metabarcoding; microorganisms.

FIGURE 1

Study workflow. Gamma diversity (i.e., regional richness) and alpha diversity (i.e., local richness) values were extracted for different taxonomic groups from 99 studies. For each type of diversity, the relative fraction of taxa detected by the traditional method only (green), by DNA metabarcoding only (red) and by both methods (yellow) were compared. The log‐ratio between the total diversity detected by DNA metabarcoding and the total diversity detected by the traditional method was also assessed [Color figure can be viewed at wileyonlinelibrary.com]

FIGURE 2

Overview of the different comparisons extracted from the studies included in the meta‐analysis. (a) Geographic location of the comparisons. Colours indicate the group of organisms used (plankton and microphytobenthos in green, macroinvertebrates in blue, fish in orange and other types in light grey). (b) Number of comparisons (n) across the different groups of organisms. (c–g) Number of comparisons (n) across biomes (marine includes brackish waters), taxonomic levels of identification, genetic markers, origins of DNA and sequencing technologies. The “multi” category includes comparisons combining several other categories

FIGURE 3

Histograms of the log‐ratio between the total diversity detected by DNA metabarcoding and the total diversity detected by the traditional method. The left panel shows gamma diversity (i.e., regional richness) and the right panel alpha diversity (i.e. mean local richness). Density estimates (kernel bandwidth = 0.25) for each group of organisms are represented as coloured overlays [Color figure can be viewed at wileyonlinelibrary.com]

FIGURE 4

Relative fraction of diversity detected by the traditional method only, by DNA metabarcoding only and by both methods. Data are presented for different groups of organisms identified at species level only. Boxplots show medians, first and third quartiles, and full ranges (limited to 1.5 × interquartile range). Grey lines connect values from the same comparison. Framed numbers below each panel indicate the number of comparisons represented. (a–c) Gamma diversity for plankton and microphytobenthos, macroinvertebrates and fish. (d–f) Alpha diversity for plankton and microphytobenthos, macroinvertebrates and fish [Color figure can be viewed at wileyonlinelibrary.com]