Environmental DNA effectively captures functional diversity of coastal fish communities

Abstract

Robust assessments of taxonomic and functional diversity are essential components of research programmes aimed at understanding current biodiversity patterns and forecasting trajectories of ecological changes. Yet, evaluating marine biodiversity along its dimensions is challenging and dependent on the power and accuracy of the available data collection methods. Here we combine three traditional survey methodologies (underwater visual census strip transects [UVCt], baited underwater videos [BUV] and small-scale fishery catches [SSFc]), and one novel molecular technique (environmental DNA metabarcoding [eDNA]-12S rRNA and cytochrome oxidase subunit 1 [COI]) to investigate their efficiency and complementarity in assessing fish diversity. We analysed 1,716 multimethod replicates at a basin scale to measure the taxonomic and functional diversity of Mediterranean fish assemblages. Taxonomic identities were investigated at species, genus and family levels. Functional identities were assessed using combinations of morphological, behavioural and trophic traits.We show that: (a) SSFc provided the higher taxonomic diversity estimates followed by eDNA, and then UVCt and BUV; (b) eDNA was the only method able to gather the whole spectrum of considered functional traits, showing the most functionally diversified and least redundant fish assemblages; and (c) the effectiveness of eDNA in describing functional structure reflected its lack of selectivity towards any considered functional trait. Our findings suggest that the reach of eDNA analysis stretches beyond taxon detection efficiency and provides new insights into the potential of metabarcoding in ecological studies.

Estuarine molecular bycatch as a landscape-wide biomonitoring tool

“…Since the inception of eDNA-based biodiversity assessment, there has been an emphasis on comparing detection performance with well-established biomonitoring approaches that use capture, visual or acoustic identification (Jerde et al 2011; Foote et al 2012; Thomsen et al 2012; Yamamoto et al 2016). The popularity of eDNA-based analysis today owes much to the realisation that, in many important contexts, the new tool offered significant advantages over conventional sampling methods, either through sheer improvement of detection efficacy (Boussarie et al 2018; McElroy et al 2020), through the discovery of its unique complementarity (Aglieri et al 2020; Harper et al 2020), or by simply being less resource-intensive (Bálint et al 2018; Aglieri et al 2020). On the other hand, little effort has gone into evaluating the intrinsically serendipitous nature of high-throughput sequencing, which, irrespective of the metabarcoding markers chosen, consistently yields substantial amounts of non-target sequences.…”

“…Aquatic environments have been the main beneficiaries of this ‘eDNA revolution’, largely owing to the utility of eDNA-based methods for exploring inherently poorly accessible realms, and the relative ease of collecting water, within which DNA naturally disperses, thus facilitating species detection. The utility of the methods ranges from the relatively straightforward recovery of rare (Boussarie et al 2018) and invasive (Imamura et al 2020) species, to more sophisticated inference on habitat gradients (Sigsgaard et al 2019), productivity dynamics (Kelly et al 2016; Djurhuus et al 2020) and ecosystem structure (Aglieri et al 2020; Harper et al 2020). It is now possible consider aquatic eDNA as a useful tool for tackling some of the most pressing biodiversity conservation challenges in a swift, affordable and standardised way, particularly given growing interest in the generation and curation of reference DNA sequence databases.…”

“….R.,Handley, L.L., Carpenter, A.I., Ghazali, M., Di Muri, C., Macgregor, C.J.,3 Logan, T.W., Law, A., Breithaupt, T.,Read, D.S., McDevitt, A.D. & Hänfling, B. (2019b) 3 Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey (Carassius carassius) on pond invertebrate diversity -a comparison of conventional and molecular tools.…”

The Case of Lionfish (Pterois miles) in the Mediterranean Sea Demonstrates Limitations in EU Legislation to Address Marine Biological Invasions

“…The emergence of participatory initiatives [15,89] and citizen science have been found effective mostly in monitoring the distribution of NIS and for early detection, particularly for conspicuous taxa such as the lionfish [90][91][92][93][94][95]. Other survey methods have been found able to capture different and complementary views of an ecosystem [96,97]. To understand mechanisms underlying ecological patterns and impacts by NIS, a targeted and hypothesisdriven research strategy is needed [98].…”

Sifting environmental DNA metabarcoding data sets for rapid reconstruction of marine food webs

“…In the last decade, the rapid expansion of eDNA metabarcoding in a marine biomonitoring context has generated countless examples of its effectiveness in assessing marine biodiversity (e.g. Aglieri et al., 2020; Boussarie et al., 2018; Sigsgaard et al., 2020). Despite a growing body of literature in freshwater habitats (e.g.…”