The use of environmental DNA (eDNA) methods for community analysis has recently been developed. High-throughput parallel DNA sequencing (HTS), called eDNA metabarcoding, has been increasingly used in eDNA studies to examine multiple species. However, eDNA metabarcoding methodology requires validation based on traditional methods in all natural ecosystems before a reliable method can be established. To date, relatively few studies have performed eDNA metabarcoding of fishes in aquatic environments where fish communities were intensively surveyed using multiple traditional methods. Here, we have compared fish communities’ data from eDNA metabarcoding with seven conventional multiple capture methods in 31 backwater lakes in Hokkaido, Japan. We found that capture and field surveys of fishes were often interrupted by macrophytes and muddy sediments in the 31 lakes. We sampled 1 L of the surface water and analyzed eDNA using HTS. We also surveyed the fish communities using seven different capture methods, including various types of nets and electrofishing. At some sites, we could not detect any eDNA, presumably because of the polymerase chain reaction (PCR) inhibition. We also detected the marine fish species as sewage-derived eDNA. Comparisons of eDNA metabarcoding and capture methods showed that the detected fish communities were similar between the two methods, with an overlap of 70%. Thus, our study suggests that to detect fish communities in backwater lakes, the performance of eDNA metabarcoding with the use of 1 L surface water sampling is similar to that of capturing methods. Therefore, eDNA metabarcoding can be used for fish community analysis but environmental factors that can cause PCR inhibition, should be considered in eDNA applications.

The use of environmental DNA (eDNA) has recently been employed to evaluate the distribution of various aquatic macroorganisms. Although this technique has been applied to a broad range of taxa, from vertebrates to invertebrates, its application is limited for aquatic insects such as aquatic heteropterans. Nepa hoffmanni (Heteroptera: Nepidae) is a small (approx. 23 mm) aquatic heteropteran that inhabits wetlands, can be difficult to capture and is endangered in Japan. The molecular tool eDNA was used to evaluate the species distribution of N. hoffmanni in comparison to that determined using hand-capturing methods in two regions of Japan. The eDNA of N. hoffmanni was detected at nearly all sites (10 eDNA-detected sites out of 14 sites), including sites where N. hoffmanni was not captured by hand (five eDNA-detected sites out of six captured sites). Thus, this species-specific eDNA technique can be applied to detect small, sparsely distributed heteropterans in wetland ecosystems. In conclusion, eDNA could be a valuable technique for the detection of aquatic insects inhabiting wetland habitats, and could make a significant contribution to providing distribution data necessary to species conservation.

Environmental DNA (eDNA) techniques utilizing DNA fragments from water have recently been developed to investigate the distribution and abundance/biomass of aquatic organisms. The eDNA technique is based on the analysis of DNA fragments in sampled water; thus, an unmanned aerial vehicle (UAV; drone) would be a useful way of collecting water for eDNA sampling, and may consequently allow us to extend eDNA surveys both spatially and temporally. Here, we developed a new method of water collection by using UAV with bleachable equipment, to avoid DNA contamination. To test the performance and contamination risk of UAV water sampling in eDNA surveys, we sampled water from a dam reservoir, detected eDNA from two fish species, and compared the water samples obtained by UAV with those obtained by boat. Additionally, we investigated contamination using blank samples. The results revealed that our UAV water sampling method performed similar to the boat sampling method. No positive signals were detected in the blank samples, including those used for UAV sampling, transportation, filtering, and PCR blanks. Our UAV method can be used to investigate species distributions using eDNA. Combinations of UAV technologies, including remote and thermal sensing, will enable efficient environmental monitoring in various waterbodies.

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Environmental DNA (eDNA) is a powerful tool for monitoring the distribution of aquatic macro-organisms. However, environmental factors, including the water temperature and water quality, can affect the inhibition and/or degradation of eDNA, which complicates accurate estimations of eDNA concentrations and the detection of the presence/absence of species in natural habitats. Further very few eDNA studies have been conducted for reptiles, especially with respect to estimating their biomass and/or abundances. Here we examined the relationship between the visually-observed number of red-eared sliders (Trachemys scripta elegans) and eDNA concentrations across 100 ponds. Additionally, we evaluated the effect of water quality on red-eared slider eDNA concentration in these ponds. We found that there was a significant positive correlation between the observed number of red-eared sliders and the eDNA concentration in the ponds. On comparing various water quality indicators, including dissolved nitrogen, dissolved phosphorous, organic matter, and chlorophyll a (Chl. a), we found that only Chl. a had a negative correlation with the red-eared slider eDNA concentration, while we did not find any inhibition in the quantitative PCR. We conclude that concentrations of eDNA can potentially be used for estimating the abundance of the red-eared slider. Additionally, Chl. a might indirectly influence the degradation of eDNA through the microorganisms bonded to the phytoplankton in the ponds, as microbial activity is thought to decrease eDNA persistence.

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Although environmental DNA (eDNA) metabarcoding is acknowledged to be an exceptionally useful and powerful tool for monitoring surveys, it has limited applicability, particularly for nationwide surveys. To evaluate the performance of eDNA metabarcoding in broad-scale monitoring, we examined the effects of species ecological/biological traits and ecosystem characteristics on species detection rates and the consequences for community analysis. We conducted eDNA metabarcoding on fish communities in 18 Japanese lakes on a country-wide scale. By comparing species records, we found that certain species traits, including body size, body shape, saltwater tolerance, and habitat preferences, influenced eDNA detection. We also found that the proportion of species detected decreased significantly with an increase in lake surface area, owing to an ecosystem-size effect on species detection. We conclude that species traits, including habitat preferences and body size, and ecosystem size should be taken into consideration when assessing the performance of eDNA metabarcoding in broad-scale monitoring.

Diel vertical migration (DVM), which is a wellknown behavior of planktonic organisms, is influenced by several factors, including predation, ultraviolet radiation, temperature, and food. The larvae of Chaoborus (Diptera) exhibit DVM in lakes and ponds. However, it is unclear whether the DVM of Chaoborus larvae changes seasonally and whether induction cues influence the seasonal pattern of DVM. In this study, we report that Chaoborus larvae showed DVM throughout the year in a eutrophic lake (Lake Fukami-ike, Japan). Our laboratory experiment demonstrated that the larvae showed DVM in response to light change even when they were not exposed to fish kairomone at water temperatures typical of winter and summer in the studied lake. These results differed from those of previous studies on other Chaoborus populations showing that both fish kairomone and light change were necessary to induce DVM, which suggests variation in the induction cues among local populations. We suggest that for Chaoborus larvae in Lake Fukami-ike, a seasonally continuous DVM induced solely by light change is adaptive to their particular habitat where the population is exposed to fish predation throughout the year.