Abstract
Organisms continuously release DNA into their environments via shed cells, excreta, gametes and decaying material. Analysis of this 'environmental DNA' (eDNA) is revolutionizing biodiversity monitoring. eDNA outperforms many established survey methods for targeted detection of single species, but few studies have investigated how well eDNA reflects whole communities of organisms in natural environments. We investigated whether eDNA can recover accurate qualitative and quantitative information about fish communities in large lakes, by comparison to the most comprehensive long-term gill-net data set available in the UK. Seventy-eight 2L water samples were collected along depth profile transects, gill-net sites and from the shoreline in three large, deep lakes (Windermere, Bassenthwaite Lake and Derwent Water) in the English Lake District. Water samples were assayed by eDNA metabarcoding of the mitochondrial 12S and cytochrome b regions. Fourteen of the 16 species historically recorded in Windermere were detected using eDNA, compared to four species in the most recent gill-net survey, demonstrating eDNA is extremely sensitive for detecting species. A key question for biodiversity monitoring is whether eDNA can accurately estimate abundance. To test this, we used the number of sequence reads per species and the proportion of sampling sites in which a species was detected with eDNA (i.e. site occupancy) as proxies for abundance. eDNA abundance data consistently correlated with rank abundance estimates from established surveys. These results demonstrate that eDNA metabarcoding can describe fish communities in large lakes, both qualitatively and quantitatively, and has great potential as a complementary tool to established monitoring methods.
Highlights
Rapid monitoring of changes in biodiversity in response to climate change or other anthropogenic pressures is imperative, but the time and resources required to generate the necessary data are a major constraint in conservation management and ecological research
We investigated whether environmental DNA” (eDNA) can recover accurate qualitative and quantitative information about fish communities in large lakes, by comparison to the most comprehensive long-term gill-net dataset available in the UK
These results demonstrate that eDNA metabarcoding can describe fish communities in large lakes, both qualitatively and quantitatively, and has great potential as a complementary tool to established monitoring methods
Summary
Rapid monitoring of changes in biodiversity in response to climate change or other anthropogenic pressures is imperative, but the time and resources required to generate the necessary data are a major constraint in conservation management and ecological research This is relevant in large lake ecosystems, where for a number of taxa, established methods currently struggle to deliver the required data to fulfil legislative obligations such as the EC Water Framework (European_Communities 2000) and corresponding legislation elsewhere in the word. A second approach that may be more promising for estimating abundance is to carry out comprehensive spatial and temporal sampling of a given environment and calculate the proportion of sites in which a species is detected with eDNA Such “site occupancy” data is often collected in ecological studies and can be used as a proxy for abundance (MacKenzie & Nichols 2004; MacKenzie et al 2002). Recent studies indicate this approach could be very promising for analysing eDNA data from both targeted assays (Hunter et al 2015; Pilliod et al 2013; Schmidt et al 2013), and metabarcoding data (Valentini et al 2015)
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