We developed environmental DNA (eDNA) detection protocols to assist in habitat identification for conservation for the US federally endangered Hine’s emerald dragonfly (Somatochlora hineana). Larval S. hineana have been observed in groundwater-fed calcareous fen habitats in Illinois, Wisconsin, Michigan, and Missouri in the USA, and Ontario, Canada. Habitat destruction and fragmentation have been the primary cause of S. hineana population decline1. Therefore, a key part of conservation efforts to benefit S. hineana is the identification and protection of any remaining habitat areas. Conventional sampling for the presence of S. hineana often includes both adult and larval sampling.
Larval S. hineana surveys include benthic-sampling and the pumping of crayfish burrows. Larval S. hineana are most often found in the burrows of Cambarus (= Lacunicambarus) diogenes throughout the year and are almost exclusively found in C. diogenes burrows during their overwintering period2. Comprehensive larval surveys can take months to complete, require intensive training of field personnel, are reliant on favorable weather conditions, and are only effective if late instar larvae can be collected for identification. Adult S. hineana surveys are difficult due to short flight season, habitat segregation by sex, large potential flight range (adults can range for many kilometers from larval habitat), risk of harm when netting adult dragonflies, and difficulty observing genitalia characteristics necessary for accurate species identification when in flight1.
Given the restrictions of conventional sampling techniques, there has been a great need to develop a method to expedite field site identification. Environmental DNA can be used to guide and prioritize locations for conventional surveying methods, increasing the speed at which habitats can be identified for protection and restoration.
Environmental DNA (eDNA) is a relatively new surveillance method used to detect the presence of a species within a habitat by collecting environmental samples (e.g., soil and water) that contain cell fragments and exogenous DNA3. Mitochondrial genes, which are more plentiful and have a higher resistance to degradation than nuclear genes, are targeted and amplified to determine species presence or absence4,5,6,7.
Currently, there is a taxonomic skew toward fish, amphibian, and mollusk eDNA studies7,8 suggesting the need to determine if eDNA methods can be useful for detecting aquatic insects. Environmental DNA analysis from 27 taxa of freshwater arthropods had been published as of 2019; some of these taxa include Procambarus clarkii, Pacifastacus leniusculus, and Gammarus pulex8. Additionally, the critically endangered plecopteran Isogenus nubecula was detected using eDNA methods9.
The potential advantages of using eDNA rather than traditional surveying methods include the reduction of field labor hours10, reduced impact to sensitive habitats7, and a lower threshold of detection11,12. Additionally, eDNA has proven to be an effective tool when traditional methods require timely/costly surveying efforts6 and for detecting cryptic invasive species10.
Although there is always some risk of damaging the habitat when studying a system, environmental DNA sampling (i.e., water, soil, ice) is much less invasive and has far less potential for harming native and endangered species than many traditional surveying methods7. For example, electrofishing can cause damage in the form of removing/killing fish from the sample site13. Traditional sampling methods for larval populations of S. hineana include benthic sampling (monitoring populations in stream beds) and burrow-pumping (a novel technique used to locate larvae within crayfish burrows)2. These techniques can disrupt flow patterns within shallow streams, collapse burrows, and harm/kill sampled individuals.
While there has been some speculation that eDNA sampling may have high false-positive rates due to ancient DNA contamination from extirpated populations, studies show that eDNA typically becomes undetectable in water within 1–44 days after source removal10,14,15,16,17,18,19,20,21 and approximately 144 days in soil22. This suggests that eDNA surveys are contemporaneous and can be used to inform conservation efforts.
Environmental DNA degradation is likely more complex in a field setting, and the persistence (defined here as the length of time eDNA remains detectable within a habitat or mesocosm) and net-accumulation (defined here as the difference between the amount of eDNA produced and the amount of eDNA degraded over time) are likely to vary depending on numerous factors that alter source/sink dynamics3. Spatiotemporal dynamics are especially important in affecting the persistence and accumulation of eDNA in the field and need to be accounted for when developing eDNA methodologies23. Concentrations of eDNA may fluctuate spatially and/or temporally as a result of fluctuations in biomass18,24,25, transport through a flowing system17,26,27,28, age structuring of target populations7,16, feeding activity29, life-history events5, seasonal habitat preference13,30, water temperature24,31,32,33, hydrology13,27, inhibition13,27, and microbial activity34. Some studies show that water pH affects eDNA degradation rates19, while others do not35. Similarly, some studies show that UV light exposure affects eDNA degradation rates17, while others show no such effect36.
In this study, we focused on the effects that seasonal shifts in temperature have on the persistence and net-accumulation of larval S. hineana eDNA. Since temperature drives the production of eDNA through metabolic processes31 and directly alters the rate of microbial degradation of eDNA32, it may be the most important variable driving seasonal shifts in eDNA detection.
Somatochlora hineana larval molting activity varies with seasonal changes, the net-accumulation of S. hineana eDNA within a habitat. Adult S. hineana females lay eggs within streams and streamlets during their flight period (July–early August). Eggs typically mature over winter. In the following year, hatching of pro-larva from eggs occurs between April and June. All S. hineana larvae go through approximately 12 larval instars (F-11 to F-0). The first 6 larval instars (F-11 through F-6) occur rapidly within the first year, and the final 6 (F-5 through F-0) occur more slowly over a period of 2–4 years1. Since S. hineana larvae take several years to fully mature, they survive overwintering in shallow, partially frozen streams within Cambarus (= Lacunicambarus) diogenes crayfish burrows. While S. hineana larvae overwinter within burrows, they rarely consume food or molt, thus reducing the amount of eDNA shed2.
The net-accumulation of larval S. hineana eDNA was likely to increase with increasing temperatures2,31,37, while the persistence of larval S. hineana eDNA was likely to decrease with increasing temperatures32. Therefore, we assessed the seasonal shift in persistence and net-accumulation of larval S. hineana eDNA in temperature-controlled mesocosms that reflect the larval overwintering period (5.0 °C) and the larval active period (16.0 °C). This study provided preliminary information regarding the seasonal shift in eDNA production for larval S. hineana. Understanding the seasonal dynamics of larval S. hineana eDNA is vital for efficient detection of this rare aquatic species using eDNA protocols. Our mesocosm results have informed subsequent field sampling of S. hineana eDNA.
Source: Ecology - nature.com
