Lake sediment DNA as a proxy in fish population studies: analytical challenges and opportunities (original) (raw)
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Fisheries Research
Freshwater biodiversity is under pressure from the detrimental effects of climate change, habitat degradation, biological invasion, and overfishing. Environmental DNA (eDNA) obtained directly from environmental samples can be used to evaluate the distribution of aquatic species. We developed a new set of universal PCR primers (16 S 200) for eDNA metabarcoding from mitochondrial DNA sequences. Using the new 16 S 200 primers, we detected the presence of 27 fish species distributed across four families in Lake Gehu, in southeastern China. eDNA metabarcoding and live capture methods identified 16 species in common; however, the two methods identified nine and 12 unique species, respectively. Data from eDNA metabarcoding were more consistent with results from gill net capture methods than from ground cage capture. The present study supports the effectiveness of eDNA for rapidly assessing the species composition of fish communities.This is the first attempt to designed new sets of primers for eDNA-based metabarcoding analysis of freshwater fish in China. Despite pitfalls and limitations, eDNA metabarcoding is a promising approach for assessing fish communities in freshwater lakes. Current applications of eDNA are widespread, but the new technology requires further refinement. The eDNA metabarcoding is an efficient and cost-effective method that can be used in conjunction with traditional survey methods for analyzing fish communities.
Environmental DNA for freshwater fish monitoring: insights for conservation within a protected area
PeerJ, 2018
Many fish species have been introduced in wild ecosystems around the world to provide food or leisure, deliberately or from farm escapes. Some of those introductions have had large ecological effects. The north American native rainbow trout (Walbaum, 1792) is one of the most widely farmed fish species in the world. It was first introduced in Spain in the late 19th century for sport fishing (Elvira 1995) and nowadays is used there for both fishing and aquaculture. On the other hand, the European native brown trout (L.) is catalogued as vulnerable in Spain. Detecting native and invasive fish populations in ecosystem monitoring is crucial, but it may be difficult from conventional sampling methods such as electrofishing. These techniques encompass some mortality, thus are not adequate for some ecosystems as the case of protected areas. Environmental DNA (eDNA) analysis is a sensitive and non-invasive method that can be especially useful for rare and low-density species detection and in...
ICES Journal of Marine Science, 2022
Analysing environmental DNA (eDNA) in seawater can aid in monitoring marine fish populations. However, the extent to which current methods optimize fish eDNA detection from water samples is unknown. Here, we test modifications to laboratory components of an eDNA metabarcoding protocol targeting marine finfish. As compared to baseline methods, amplifying a smaller proportion of extracted DNA yielded fewer species, and, conversely, amplifying a larger proportion identified more taxa. Higher-read species were amplified more reproducibly and with less variation in read number than were lower-read species. Among pooled samples, 20-fold deeper sequencing recovered one additional fish species out of a total of 63 species. No benefit was observed with additional PCR cycles, alternative primer concentrations, or fish-selective primers. Experiments using an exogenous DNA standard to assess absolute eDNA concentration suggested that, for a given proportion of a DNA sample, current laboratory m...
Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing
2017
Effective ecosystem conservation and resource management require quantitative monitoring of biodiversity, including accurate descriptions of species composition and temporal variations of species abundance. Therefore, quantitative monitoring of biodiversity has been performed for many ecosystems, but it is often time- and effort-consuming and costly. Recent studies have shown that environmental DNA (eDNA), which is released to the environment from macro-organisms living in a habitat, contains information about species identity and abundance. Thus, analyzing eDNA would be a promising approach for more efficient biodiversity monitoring. In the present study, we added internal standard DNAs (i.e., known amounts of short DNA fragments from fish species that have never been observed in a sampling area) to eDNA samples, which were collected weekly from a coastal marine ecosystem in Maizuru-Bay, Kyoto, Japan (from April 2015 to March 2016), and performed metabarcoding analysis using Illumi...
Metabarcoding and Metagenomics, 2020
The sampling of environmental DNA (eDNA) coupled with cost-efficient and ever-advancing sequencing technology is propelling changes in biodiversity monitoring within aquatic ecosystems. Despite the increasing number of eDNA metabarcoding approaches, the ability to quantify species biomass and abundance in natural systems is still not fully understood. Previous studies have shown positive but sometimes weak correlations between abundance estimates from eDNA metabarcoding data and from conventional capture methods. As both methods have independent biases a lack of concordance is difficult to interpret. Here we tested whether read counts from eDNA metabarcoding provide accurate quantitative estimates of the absolute abundance of fish in holding ponds with known fish biomass and number of individuals. Environmental DNA samples were collected from two fishery ponds with high fish density and broad species diversity. In one pond, two different DNA capture strategies (on-site filtration wi...
A field ecologist's guide to environmental DNA sampling in freshwater environments
Australian Zoologist
Environmental DNA, or eDNA—DNA shed from organisms and extracted from environmental samples—is an emerging survey technique that has the potential to transform biodiversity monitoring in freshwater ecosystems. We provide a brief overview of the primary methodological aspects of eDNA sampling that ecologists should consider before taking environmental samples in the field. We outline five key methodological considerations: (i) targeting single species vs multiple species; (ii) where and when to sample; (iii) how much water to collect; (iv) how many samples to take; and (v) recognising potential sources of false positives. The need to account for false negatives and false positives in eDNA surveys, and the power of species occupancy detection models in accounting for imperfect detection, is also discussed.
Optimizing environmental DNA sampling effort for fish inventories in tropical streams and rivers
Scientific Reports, 2019
environmental DNA (eDNA) metabarcoding is a promising tool to estimate aquatic biodiversity. It is based on the capture of DNA from a water sample. The sampled water volume, a crucial aspect for efficient species detection, has been empirically variable (ranging from few centiliters to tens of liters). This results in a high variability of sampling effort across studies, making comparisons difficult and raising uncertainties about the completeness of eDNA inventories. Our aim was to determine the sampling effort (filtered water volume) needed to get optimal inventories of fish assemblages in species-rich tropical streams and rivers using eDNA. Ten DNA replicates were collected in six Guianese sites (3 streams and 3 rivers), resulting in sampling efforts ranging from 17 to 340 liters of water. We show that sampling 34 liters of water detected more than 64% of the expected fish fauna and permitted to distinguish the fauna between sites and between ecosystem types (stream versus rivers). Above 68 liters, the number of detected species per site increased slightly, with a detection rate higher than 71%. Increasing sampling effort up to 340 liters provided little additional information, testifying that filtering 34 to 68 liters is sufficient to inventory most of the fauna in highly diverse tropical aquatic ecosystems. In recent years, environmental DNA (eDNA) metabarcoding has been claimed as a promising tool to estimate biodiversity and its change through time 1,2. In particular, this technique is employed to identify the free DNA released by organisms in their environment 3. In aquatic ecosystems, the use of eDNA has been widely developed during the last years and has turned from the detection of specific species of amphibians, fish, mammals, insects and crustaceans 4 to the detection of whole communities 5-10. The latter studies besides reconstructing entire aquatic communities of fishes and amphibians, compared the detection performance between eDNA metabarcoding and capture-based sampling methods used to collect specimens in streams and rivers. Through this, they showed that both methods provided similar or more complete species inventories, hence opening avenues to use this method for ecological and conservation studies. Obtaining biodiversity inventories with eDNA metabarcoding requires several subsequent steps including: DNA sampling and collection, laboratory protocols (DNA purification, marker targeting and sequencing), bioinformatics analyses and taxonomic assignment of sequences. The growing interest in this method resulted in the development of a considerable variety of protocols for each step of the eDNA procedure 11. This makes comparisons between studies challenging considering that it has been illustrated that the choice of markers 5,8 , DNA collection methods 12,13 and laboratory protocols 5,12,13 may influence the detection of aquatic species. Furthermore, the environmental conditions and the targeted taxon can also affect detection rate because eDNA release varies among taxa 12,14 and water physiochemical factors may impact eDNA degradation 15,16. Therefore, the performance of biodiversity detection in the water depends on a combination of protocols choice, as well as the environmental conditions and the targeted taxonomic group. Despite an extended literature about the optimization of eDNA sample analysis to improve detection performance, less attention has been paid to how eDNA sampling design can be optimized. Consequently, there is a