Environmental DNA reflects spatial and temporal jellyfish distribution

Abstract

Recent development of environmental DNA (eDNA) analysis allows us to survey underwater macro-organisms easily and cost effectively; however, there have been no reports on eDNA detection or quantification for jellyfish. Here we present the first report on an eDNA analysis of marine jellyfish using Japanese sea nettle (Chrysaora pacifica) as a model species by combining a tank experiment with spatial and temporal distribution surveys. We performed a tank experiment monitoring eDNA concentrations over a range of time intervals after the introduction of jellyfish, and quantified the eDNA concentrations by quantitative real-time PCR. The eDNA concentrations peaked twice, at 1 and 8 h after the beginning of the experiment, and became stable within 48 h. The estimated release rates of the eDNA in jellyfish were higher than the rates previously reported in fishes. A spatial survey was conducted in June 2014 in Maizuru Bay, Kyoto, in which eDNA was collected from surface water and sea floor water samples at 47 sites while jellyfish near surface water were counted on board by eye. The distribution of eDNA in the bay corresponded with the distribution of jellyfish inferred by visual observation, and the eDNA concentration in the bay was ~13 times higher on the sea floor than on the surface. The temporal survey was conducted from March to November 2014, in which jellyfish were counted by eye every morning while eDNA was collected from surface and sea floor water at three sampling points along a pier once a month. The temporal fluctuation pattern of the eDNA concentrations and the numbers of observed individuals were well correlated. We conclude that an eDNA approach is applicable for jellyfish species in the ocean.

Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement

“…However, we discovered that several aspects of eDNA metabarcoding require further optimization prior to implementation in established monitoring programs. The impact of vertical zonation on eDNA patterns (Minamoto et al, ), temporal stability (Bista et al, ), abiotic influences on eDNA persistence (Stoeckle et al, ), and the correlation between eDNA signal strength and true abundance (Jo et al, ), have received little attention to date and require more investigation. In agreement with the growing body of eDNA studies in the literature, the data from the Aramoana site indicate that eDNA metabarcoding surveys, when appropriately executed, will be a powerful tool in the management and conservation of marine environments.…”

The sceptical optimist: challenges and perspectives for the application of environmental DNA in marine fisheries

“…This finding coincides with the fact that the gastrointestinal tract is the largest external body surface facing the environment and its epithelial cells have the fastest renewal rate of all tissues in the vertebrate body (Crosnier, Stamataki, & Lewis, ; Helander & Fändriks, ). The eDNA particle production rate from individual macro‐organisms are also affected by a variety of factors such as the size of the individual (Maruyama et al., ), biomass/density (Doi et al., ; Maruyama et al., ), diet (Klymus et al., ), health status (Pilliod, Goldberg, Arkle, Waits, & Richardson, ), species (Minamoto et al., ; Sassoubre et al., ; Tréguier et al., ), season (Spear, Groves, Williams, & Waits, ), and potentially sex. Further, changes in biotic and abiotic factors can potentially, directly or indirectly, through complex interactions, affect shedding rates due to changes in stress, metabolism, behaviour or health of the source organism.…”

“…Abiotic environmental factors, such as temperature, solar radiation and pH, cause large variation in the persistence of eDNA particles (Strickler, Fremier, & Goldberg, ). Temperature is generally one of the most influential factors, where a reduction in temperature can extend the preservation of eDNA particles from a couple of days in temperate aquatic ecosystems to hundreds of thousands of years under permafrost (Corinaldesi, Beolchini, & Dell'Anno, ; Minamoto et al., ). An illustrative study by Strickler et al.…”

“…In brackish and marine environments persistence time have been found to be relatively shorter than in freshwater, with eDNA falling below limit of detection after 0.9 days ( Platichthys flesus , Pleuronectidae) (Thomsen et al., ), 6.9 days ( Gasterosteus aculeatus , Gasterosteidae) (Thomsen et al., ), 4 and 7.8 days ( Rhincodon typus , Rhincodontidae) (Sigsgaard et al., ), 3–4 days ( Engraulis mordax, Engraulidae; Sardinops sagax , Clupeidae and Scomber japonicas , Scombridae) (Sassoubre et al., ) and <1–2.5 days ( Zearaja maugeana , Rajidae) (Weltz et al., ). Decay rates show that there is a 1.5%–10.1% reduction in numbers of eDNA particles per hour in brackish and marine environments across several species of fish and one jellyfish (3% per hour) (Minamoto et al., ; Sassoubre et al., ; Thomsen et al., ). In comparison, freshwater studies have generally found longer persistence times for a range of organisms, for example 21–44 days (Goldberg, Sepulveda, Ray, Baumgardt, & Waits, ), 8–11 days (Pilliod et al., ), 14 days (Dejean et al., ) and 25 days (Dejean et al., ), but at a similar pace, at 5.1%–15% reduction of eDNA particles per hour (Eichmiller, Best, & Sorensen, ; Maruyama et al., ).…”

“…Thus, obtaining knowledge of the size and age structure of the target species in the sampling area is still essential. Even without taking body geometrics or environmental factors into account, studies have found large interspecific variation in eDNA shedding among tank replicates of equally sized individuals (Minamoto et al., ; Pilliod et al., ). Klymus et al.…”