Assessment of fish communities using environmental DNA: Effect of spatial sampling design in lentic systems of different sizes

Abstract

Freshwater fish biodiversity is quickly decreasing and requires effective monitoring and conservation. Environmental DNA (eDNA)‐based methods have been shown to be highly sensitive and cost‐efficient for aquatic biodiversity surveys, but few studies have systematically investigated how spatial sampling design affects eDNA‐detected fish communities across lentic systems of different sizes. We compared the spatial patterns of fish diversity determined using eDNA in three lakes of small (SL; 3 ha), medium (ML; 122 ha) and large (LL; 4,343 ha) size using a spatially explicit grid sampling method. A total of 100 water samples (including nine, 17 and 18 shoreline samples and six, 14 and 36 interior samples from SL, ML and LL, respectively) were collected, and fish communities were analysed using eDNA metabarcoding of the mitochondrial 12S region. Together, 30, 35 and 41 fish taxa were detected in samples from SL, ML, and LL, respectively. We observed that eDNA from shoreline samples effectively captured the majority of the fish diversity of entire waterbodies, and pooled samples recovered fewer species than individually processed samples. Significant spatial autocorrelations between fish communities within 250 m and 2 km of each other were detected in ML and LL, respectively. Additionally, the relative sequence abundances of many fish species exhibited spatial distribution patterns that correlated with their typical habitat occupation. Overall, our results support the validity of a shoreline sampling strategy for eDNA‐based fish community surveys in lentic systems but also suggest that a spatially comprehensive sampling design can reveal finer distribution patterns of individual species.

The utility of environmental DNA from sediment and water samples for recovery of observed plant and animal species from four Mojave Desert springs

“…For example, a single sampling event in each season represents a snapshot of diversity, whereas longitudinal eDNA studies often sample multiple times in a season (Berry et al., 2019; Milhau et al., 2019; Zhang et al., 2019), improving the detections of seasonal variation in species composition and biodiversity. Additionally, the pooling of biological replicates reduces the signal and detection of rare species (Sato et al., 2017; Zhang et al., 2020), which are often of conservation concern (Franklin et al., 2019) and a single PCR replicate captures less taxonomic diversity than duplicates or triplicates (Beentjes et al., 2019). The small sample size of springs ( n = 4) and representation of spring types (large, naturally flowing, and unmodified springs vs. small or modified springs) directly affects vegetation comparisons, as water availability may be limiting the support of a riparian plant community (Sada et al., 2005) and indirectly animal communities.…”

“…Water and sediment samples for each site were treated separately for the library preparation and although pooling replicates for each sample type reduces the detection of rare taxa, it does not substantially affect comparisons of communities (Sato et al., 2017; Zhang et al., 2020). Critically, pooled replicate samples can provide information about the presence of species that were observed by traditional methods, a major goal of our study.…”

Standards for Methods Utilizing Environmental DNA for Detection of Fish Species

“…When the number of samples is increased, to improve work efficiency and reduce analysis cost, researchers may consider pooling the water samples from multiple locations for subsequent processing. However, Sato et al [46] and Zhang et al [47] demonstrated that pooled samples decreased species detection compared to using individually processed samples, indicating that sample pooling is not useful for assessing fish assemblages. Thus, we do not recommend pooling samples for subsequent analysis.…”

“…Thus, we do not recommend pooling samples for subsequent analysis. In addition, for lentic systems such as lakes, shoreline sampling with surface water can capture most fish species eDNA [47]. We recommend that shoreline sampling can be used to briefly survey lentic systems, whereas systematic spatial sampling should be used in subtle spatial distribution pattern surveys for entire fish species in large lentic systems (e.g., a lake with a surface area of 4343 ha [47]).…”

“…When filtering water samples, the contact surface of the filters for each sample should also be treated with 10% bleach and rinsed with double-distilled H 2 O before new sample filtration [48,58] to prevent cross-contamination between samples. Furthermore, strictly setting up multiple negative controls (such as double-distilled H 2 O for blank sample) including a field blank, filtration blank, extraction blank, and PCR blank [47,92], is necessary for evaluating contamination during the entire eDNA process. In addition, considering the repeatability of eDNA results, analysis of at least some samples should be independently repeated in another laboratory as described for ancient DNA research [6,91].…”