Moving eDNA surveys onto land: Strategies for active eDNA aggregation to detect invasive forest insects

Valentin, Rafael; Fonseca, Dina M.; Gable, Sydney; Kyle, Kathleen; Hamilton, George C.; Nielsen, Anne L.; Lockwood, Julie L.

doi:10.1111/1755-0998.13151

Cited by 107 publications

(160 citation statements)

References 62 publications

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“…Surveys targeting eDNA involve the collection of environmental samples from a location which usually comprises water, soil or sediments (Turner et al, 2015;Buxton et al, 2018;Spitzen-van der Sluijs et al, 2020;Valentin et al, 2020). These samples are then processed following forensic protocols for the extraction of DNA that has been released by organisms into the environment.…”

Section: Introductionmentioning

confidence: 99%

Comparison of eDNA and visual surveys for rare and cryptic bromeliad-dwelling frogs

Barata¹

2021

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Surveys of rare or cryptic species may miss individuals or populations that are actually present. Despite the increasing use of environmental DNA (eDNA) analysis to survey species in ponds, rivers, and lakes, very few studies have attempted to use eDNA for the detection of species using very small water bodies such as those accumulated within plants. Our aim was to investigate the feasibility of an eDNA sampling method for detecting Crossodactylodes itambe, an endemic bromeliad-dwelling frog from a remote location in Brazil. We collected water samples from 19 bromeliads for which we had observational data from direct visual surveys. We compared occupancy estimated from direct observations with the results from quantitative real-time PCR based eDNA assays. For observational surveys, we used a single season occupancy model. We applied a novel Bayesian occupancy model to estimate occupancy from eDNA samples, as well as false positives and false negatives at different stages of the workflow. eDNA from bromeliad tanks provided reliable estimates, with very low error levels and improved detection when compared to detectability from direct observation. Estimated occupancies using eDNA and visual survey methods were similar. The method is feasible for species restricted to small water bodies and exposed to direct UV radiation, and particularly useful to survey remote locations and confirm species presence. eDNA analysis provides a viable alternative to destructive sampling of bromeliads or direct observation methods that require logistically challenging repeated observations. Therefore, eDNA methods may be widely applicable to sampling programmes of other amphibians that live in plants.

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Section: Introductionmentioning

confidence: 99%

Comparison of eDNA and visual surveys for rare and cryptic bromeliad-dwelling frogs

Barata¹

2021

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“…Both species‐specific and metabarcoding studies have highlighted the importance of sampling strategy for eDNA detection in aquatic and terrestrial systems (Gasparini et al., 2020; Goldberg et al., 2018; Harper, Handley, et al, 2019; Lawson Handley et al., 2019; Leempoel et al., 2020; Valentin et al., 2020). Concerning crayfish burrow commensals, such as the Eastern Massasauga and Kirtland's Snake, crayfish burrows are often complex (Hasiotis & Mitchell, 1993), and snake movements within them are poorly understood.…”

Section: Discussionmentioning

confidence: 99%

“…These elements individually or combined may explain the low eDNA detection rates observed for semi‐fossorial and/or semi‐aquatic snakes in previous investigations (Baker et al., 2018; Halstead et al., 2017; Merkling, 2018; Ratsch et al., 2020; Rose et al., 2019). As such, snake eDNA detection may be improved through sampling strategies that consider species’ ecology and behavior, enable greater and continuous soil coverage at higher replication (Leempoel et al., 2020; Zinger et al., 2020) or aggregate eDNA on various terrestrial substrata (Valentin et al., 2020), and account for abiotic and biotic factors.…”

Section: Discussionmentioning

confidence: 99%

“…Over the past decade, the utility of eDNA analysis has grown rapidly, and its efficacy has been demonstrated from freshwater, marine, subterranean, terrestrial, and airborne samples (e.g., Franklin et al., 2019; Harper et al., 2020; Johnson, Cox, & Barnes, 2019; Niemiller et al., 2018; Thomsen et al., 2012). Since eDNA analysis was first applied to macrobiota (Ficetola et al., 2008), it has become an important conservation and management tool that is capable of detecting both invasive and imperiled species at low abundances in numerous contexts (e.g., Gasparini, Crookes, Prosser, & Hanner, 2020; Goldberg, Strickler, & Fremier, 2018; Kessler, Ash, Barratt, Larson, & Davis, 2020; de Souza, Godwin, Renshaw, & Larson, 2016; Tréguier et al., 2014; Valentin et al., 2020; Wacker et al., 2019).…”

Section: Introductionmentioning

confidence: 99%

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Environmental DNA is effective in detecting the federally threatened Louisiana Pinesnake (Pituophis ruthveni)

et al. 2020

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Successful conservation of rare, threatened, or endangered (RTE) species is dependent upon rapid and accurate assessment of their distribution and abundance. However, assessments are challenging as RTE species typically exist as numerically small populations in often fragmented habitats and can possess complex natural histories. Environmental DNA (eDNA) analysis may provide a rapid, cost‐effective means of assessing RTE species presence/absence in viable habitat patches. We evaluated the efficacy of eDNA surveillance for the Louisiana Pinesnake (Pituophis ruthveni), an elusive, semi‐fossorial, nonvenomous colubroid snake endemic to Louisiana and Texas, USA, that has dramatically declined in both distribution and abundance. We developed two quantitative polymerase chain reaction (qPCR) assays that target the mitochondrial cytochrome c oxidase subunit I (COI) and mitochondrially encoded ATP synthase membrane subunit 6 (ATP6) genes. We validated each assay in silico, in vitro, and in situ, and investigated the influence of eDNA extraction method and genetic marker on assay performance. Both assays were highly sensitive and successfully detected the Louisiana Pinesnake under artificial and field conditions, including bedding samples collected from captive snake enclosures (100%), soil samples from Louisiana Pinesnake release sites (100%), and soil samples from sites where Louisiana Pinesnakes were documented via radio telemetry (45%). Although differences between genetic markers were negligible, assay performance was strongly influenced by eDNA extraction method. Informed by our results, we discuss methodological and environmental factors influencing Louisiana Pinesnake eDNA detection and quantification, broader implications for management and conservation of the Louisiana Pinesnake and other terrestrial reptiles and provide recommendations for future research. We suggest that eDNA surveys can more effectively assess Louisiana Pinesnake occupancy than conventional sampling, highlighting the need for comprehensive eDNA monitoring initiatives to better identify suitable habitat that will promote persistence of this imperiled species going forward.

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“…As the use of eDNA metabarcoding has extended to the study of soils in more remote locations (Tedersoo et al 2014;Detheridge et al 2020) and to more applied deployment in nature conservation site monitoring by statutory organisations (Geml et al 2014;Detheridge et al 2018;Latch 2020;Valentin et al 2020), the issue of soil storage between sampling and subsequent analysis has become an important consideration. Such concerns have interested soil scientists for many decades, but usually in relation to the metabolic status of soil organisms, assessed via community level physiological profiles (CLPP), soil respiration etc.…”

Section: Introductionmentioning

confidence: 99%

Soil stabilisation for DNA metabarcoding of plants and fungi. Implications for sampling at remote locations or via third-parties

Clasen¹,

Detheridge²,

Scullion³

et al. 2020

MBMG

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Storage of soil samples prior to metagenomic analysis presents a problem. If field sites are remote or if samples are collected by third parties, transport to analytical laboratories may take several days or even weeks. The bulk of such samples and requirement for later homogenisation precludes the convenient use of a stabilisation buffer, so samples are usually cooled or frozen during transit. There has been limited testing of the most appropriate storage methods for later study of soil organisms by eDNA approaches. Here we tested a range of storage methods on two contrasting soils, comparing these methods to the control of freezing at -80 °C, followed by freeze-drying. To our knowledge, this is the first study to examine the effect of storage conditions on eukaryote DNA in soil, including both viable organisms (fungi) and DNA contained within dying/dead tissues (plants). For fungi, the best storage regimes (closest to the control) were storage at 4 °C (for up to 14 d) or active air-drying at room temperature. The worst treatments involved initial freezing, followed by thawing which led to significant later spoilage. The key spoilage organisms were identified as Metarhizium carneum and Mortierella spp., with a general increase in saprotrophic fungi and reduced abundances of mycorrhizal/biotrophic fungi. Plant data showed a similar pattern, but with greater variability in community structure, especially in the freeze-thaw treatments, probably due to stochastic variation in substrates for fungal decomposition, algal proliferation and some seed germination. In the absence of freeze drying facilities, samples should be shipped refrigerated, but not frozen if there is any risk of thawing.

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Moving eDNA surveys onto land: Strategies for active eDNA aggregation to detect invasive forest insects

Cited by 107 publications

References 62 publications

Comparison of eDNA and visual surveys for rare and cryptic bromeliad-dwelling frogs

Comparison of eDNA and visual surveys for rare and cryptic bromeliad-dwelling frogs

Environmental DNA is effective in detecting the federally threatened Louisiana Pinesnake (Pituophis ruthveni)

Soil stabilisation for DNA metabarcoding of plants and fungi. Implications for sampling at remote locations or via third-parties

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