Improved biodiversity detection using a large-volume environmental DNA sampler with in situ filtration and implications for marine eDNA sampling strategies

Govindarajan, Annette F.; McCartin, Luke; Adams, Allan; Allan, Elizabeth Andruszkiewicz; Belani, Abhimanyu; Francolini, Rene; Fujii, Justin; Gomez-Ibañez, Daniel; Kukulya, Amy; Marín, F. González; Tradd, Kaitlyn; Yoerger, D.; McDermott, J. M.; Herrera, Santiago

doi:10.1016/j.dsr.2022.103871

Cited by 21 publications

(27 citation statements)

References 53 publications

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“…Each step of the eDNA analysis process, from experimental design and sample collection to data analysis, impacts the final result (Figure 2). Of the different steps that could introduce bias (Eble et al, 2020;Shelton et al, 2022), sampling approaches and strategies are particularly underexplored (Govindarajan et al, 2022).…”

Section: Technological Needs For Otz Edna Analysesmentioning

confidence: 99%

“…Autonomous sampling with in situ filtration is an alternative approach for sample collection. In situ filtration offers numerous advantages, including reduced labor, fewer opportunities for contamination, larger sample volumes, and fewer experimental design constraints (Yamahara et al, 2019;Govindarajan et al, 2022;Truelove et al, 2022). Autonomous samplers must be mounted on platforms that access the target environment, such as…”

Section: Autonomous Edna Samplers and Sampling Platformsmentioning

confidence: 99%

“…The sampler has a high filtration rate (approximately 2 liters/minute) and uses large-area filters to accommodate large sample volumes. By sampling larger volumes, more animal taxa can be detected, making this approach well suited for environments where the eDNA signal is dilute and when it is important to detect rare species (Govindarajan et al, 2022). We took advantage of Mesobot's Lagrangian motion capabilities and our large-volume samplers to collect several time series of eDNA samples at a constant depth from the same water parcel to determine the timing of ocean twilight zone animal migrations.…”

Section: Box 1 Large-volume Edna Sampling On Mesobotmentioning

confidence: 99%

“…In a different approach, a large-volume eDNA sampler that could take 12 samples was mounted on the midwater robot Mesobot to filter seawater at a rate of about 2 liters per minute (Govindarajan et al, 2022) Frontiers in Ocean Observing -Early Online Release period of time (Figure 4). Sampling is "Lagrangian" if the sampler collects samples as it moves along with the water parcel.…”

Section: Box 1 Large-volume Edna Sampling On Mesobotmentioning

confidence: 99%

“…Current eDNA sampling strategies may not yield representative results as they may not match the appropriate temporal and spatial scales of eDNA variation. Field observations have demonstrated that eDNA concentrations decrease with depth and that there can be high variability in the types and proportions of taxa found in sampling replicates (Easson et al, 2020;Govindarajan et al, 2022).…”

Section: Filtration Time and Sample Volumementioning

confidence: 99%

See 4 more Smart Citations

Advances in Environmental DNA Sampling for Observing Ocean Twilight Zone Animal Diversity

Govindarajan¹,

Adams²,

Allan³

et al. 2023

Oceanog

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The ocean’s vast twilight, or mesopelagic, zone (200–1,000 m depth) harbors immense biomass consisting of myriad poorly known and unique animal species whose quantity and diversity are likely considerably underestimated. As they facilitate the movement of carbon from surface waters to the deep sea through feeding and migratory behaviors, ocean twilight zone (OTZ) animals are vital to regulating Earth’s climate (Ducklow et al., 2001). However, anthropogenic threats, such as climate change, ocean acidification, pollution, and overfishing pose an imminent threat to OTZ animals. Long-term spatially and temporally intensive observations are essential to our understanding of biodiversity in the OTZ, to resolving global carbon cycles, and to monitoring ocean health. Environmental DNA (eDNA) analysis, which involves studying the trace genetic signatures of organisms (Figure 1), is a promising approach to filling this urgent need. eDNA can be sampled and diagnostic genetic markers (“barcodes”) can be sequenced in order to detect the animals inhabiting a given water parcel. Other laboratory protocols (e.g., quantitative PCR, or “qPCR” and “digital droplet PCR”) can be applied to facilitate quantitative assessments of specific target species (Eble et al., 2020). In seagoing oceanographic research, eDNA assessment is transitioning from being considered an experimental approach to becoming an established routine that can be scaled up to match ocean observing needs.

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Section: Technological Needs For Otz Edna Analysesmentioning

confidence: 99%

Section: Autonomous Edna Samplers and Sampling Platformsmentioning

confidence: 99%

Section: Box 1 Large-volume Edna Sampling On Mesobotmentioning

confidence: 99%

Section: Box 1 Large-volume Edna Sampling On Mesobotmentioning

confidence: 99%

Section: Filtration Time and Sample Volumementioning

confidence: 99%

See 3 more Smart Citations

Advances in Environmental DNA Sampling for Observing Ocean Twilight Zone Animal Diversity

Govindarajan¹,

Adams²,

Allan³

et al. 2023

Oceanog

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Environmental DNA recovers fish composition turnover of the coral reefs of West Indian Ocean islands

Jaquier,

Albouy,

Bach

et al. 2024

Ecology and Evolution

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Islands have been used as model systems to study ecological and evolutionary processes, and they provide an ideal set‐up for validating new biodiversity monitoring methods. The application of environmental DNA metabarcoding for monitoring marine biodiversity requires an understanding of the spatial scale of the eDNA signal, which is best tested in island systems. Here, we investigated the variation in Actinopterygii and Elasmobranchii species composition recovered from eDNA metabarcoding along a gradient of distance‐to‐reef in four of the five French Scattered Islands in the Western Indian Ocean. We collected surface water samples at an increasing distance from reefs (0 m, 250 m, 500 m, 750 m). We used a metabarcoding protocol based on the ‘teleo’ primers to target marine reef fishes and classified taxa according to their habitat types (benthic or pelagic). We investigated the effect of distance‐to‐reef on β diversity variation using generalised linear mixed models and estimated species‐specific distance‐to‐reef effects using a model‐based approach for community data. Environmental DNA metabarcoding analyses recovered distinct fish species compositions across the four inventoried islands and variations along the distance‐to‐reef gradient. The analysis of β‐diversity variation showed significant taxa turnover between the eDNA samples on and away from the reefs. In agreement with a spatially localised signal from eDNA, benthic species were distributed closer to the reef than pelagic ones. Our findings demonstrate that the combination of eDNA inventories and spatial modelling can provide insights into species habitat preferences related to distance‐to‐reef gradients at a small scale. As such, eDNA can not only recover large compositional differences among islands but also help understand habitat selection and distribution of marine species at a finer spatial scale.

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Autonomous eDNA collection using an uncrewed surface vessel over a 4200‐km transect of the eastern Pacific Ocean

Preston,

Yamahara,

Pargett

et al. 2023

Environmental DNA

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The collection of environmental DNA (eDNA) samples is often laborious, costly, and logistically difficult to accomplish at high frequency in remote locations and over large geographic areas. Here, we addressed those challenges by combining two robotic technologies: an uncrewed surface vessel (USV) fitted with an automated eDNA sample collection device to survey surface waters in the eastern North Pacific Ocean from Alameda, CA to Honolulu, HI. USV Surveyor SD 1200 (Saildrone) carrying the Environmental Sample Processor (ESP) collected 2‐L water samples by filtration followed by RNAlater preservation at regular intervals over a 4200‐km, 29‐day transit. Sixty samples (52 field and 8 controls) were acquired and used to estimate the concentration of specific genes and assess eukaryotic diversity via targeted qPCR and metabarcoding of the cytochrome oxidase subunit I (COI) gene, respectively. Comparisons of control samples revealed important considerations for interpreting results. Samples stored at ambient temperatures onboard Surveyor over the length of the voyage had less total recoverable DNA and specific target gene concentrations compared to the same material immediately flash‐frozen after collection and stored in a laboratory. In contrast, the biodiversity of the COI genes in those samples was similar regardless of sample age and storage condition. COI genes affiliated with 40 eukaryotic phyla were found in native samples collected during the voyage. The distribution and dominance of those phyla varied across different regions, with some taxa spanning large continuous stretches >2000 km, while others were only detected in a single sample. This work highlights the utility and potential of using USVs fitted with autonomous eDNA sample collection devices to improve ocean exploration and support large, basin‐scale, systematic biodiversity surveys. Results of this study also inform future technical considerations for using automated eDNA samplers to acquire material and store it over prolonged periods under prevailing environmental conditions.

show abstract

Improved biodiversity detection using a large-volume environmental DNA sampler with in situ filtration and implications for marine eDNA sampling strategies

Cited by 21 publications

References 53 publications

Advances in Environmental DNA Sampling for Observing Ocean Twilight Zone Animal Diversity

Advances in Environmental DNA Sampling for Observing Ocean Twilight Zone Animal Diversity

Environmental DNA recovers fish composition turnover of the coral reefs of West Indian Ocean islands

Autonomous eDNA collection using an uncrewed surface vessel over a 4200‐km transect of the eastern Pacific Ocean

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