Exploring the Use of Environmental DNA (eDNA) to Detect Animal Taxa in the Mesopelagic Zone

Govindarajan, Annette F.; Francolini, Rene; Jech, J. Michael; Lavery, Andone C.; Llopiz, Joel K.; Wiebe, Peter H.; Zhang, Weifeng

doi:10.3389/fevo.2021.574877

Cited by 37 publications

(40 citation statements)

References 102 publications

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“…Fish eDNA stratification in the ocean responds to fish vertical distribution Despite the complexity of the vertical structuring of pelagic communities (Sutton 2013) and the call for studies focusing on the deep-sea ecosystem (Mengerink et al 2014;St. John et al 2016;Martin et al 2020), to date just a few studies have used eDNA sampling to explore the deep sea (Thomsen et al 2016;Easson et al 2020;Laroche et al 2020;McClenaghan et al 2020;Govindarajan et al 2021), and none has provided insights on the deep, vertical stratification of eDNA in the ocean. Here, we observed a consistent detection of DNA of the most abundant epipelagic fish species along the water column (e.g., European anchovy is detected down to > 1000 m depth), whereas detection of DNA from deep-sea fish was restricted to the upper depth at which they were assumed to occur and below.…”

Section: Discussionmentioning

confidence: 99%

Vertical stratification of environmental DNA in the open ocean captures ecological patterns and behavior of deep‐sea fishes

Canals¹,

Mendibil²,

Santos³

et al. 2021

Limnol Oceanogr Letters

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The deep sea provides global vital functions such as sequestration of carbon from the atmosphere. The increased anthropogenic pressures and interest in expanding deep-sea fisheries make this pristine ecosystem particularly vulnerable, whose conservation largely depends on rapid knowledge acquisition. In view of the limitations of traditional methods to explore the biodiversity of this vast ecosystem, the analysis of traces of macroorganismal DNA released into the water column arises as a cost-effective, noninvasive alternative. Yet, the success of this approach requires understanding of the stratification of DNA traces in the ocean. This study provides evidence that fish DNA traces can be used to establish depth-specific fish diversity and abundance throughout the water column, opening a promising avenue for gathering knowledge about the deep-sea ecosystem.Establishing the foundations for a sustainable use of deep-sea resources relies on increasing knowledge on this inaccessible ecosystem, which is challenging with traditional methods. The analysis of environmental DNA (eDNA) emerges as an alternative, but it has been scarcely applied to deep-sea fish. Here, we have analyzed the fish eDNA contained in oceanic vertical profile samples (up to 2000 m depth) collected throughout the continental slope of the Bay of Biscay. We detected 52 different fish species, of which 25 were classified as deep-sea fish. We found an increase of deep-sea fish richness and abundance with depth, and that eDNA reflects daynight community patterns and species-specific vertical distributions that are consistent with the known diel migratory behavior of many mesopelagic fishes. These findings highlight the potential of eDNA to improve knowledge on the fish species inhabiting the dark ocean before this still pristine ecosystem is further exploited.

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Section: Discussionmentioning

confidence: 99%

Vertical stratification of environmental DNA in the open ocean captures ecological patterns and behavior of deep‐sea fishes

Canals¹,

Mendibil²,

Santos³

et al. 2021

Limnol Oceanogr Letters

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“…For the CTD samples, genomic DNA from the Sterivex filters was extracted using DNEasy Blood & Tissue extraction kits following the manufacturer’s protocol adapted to accommodate the Sterivex filter capsules (Govindarajan et al, 2021). DNA was eluted in 80 μL of molecular-grade water.…”

Section: Methodsmentioning

confidence: 99%

“…Sequencing data was received as demultiplexed fastq.gz files for each sample and was processed using Quantitative Insights Into Microbial Ecology 2 (QIIME2) version 2020.11 (Bolyen et al, 2019), following the general approach described in Govindarajan et al (2021). Raw data was deposited in Dryad.…”

Section: Methodsmentioning

confidence: 99%

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

Govindarajan

McCartin

Adams

et al. 2022

Preprint

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Metabarcoding analysis of environmental DNA samples is a promising new tool for marine biodiversity and conservation. Typically, seawater samples are obtained using Niskin bottles and filtered to collect eDNA. However, standard sample volumes are small relative to the scale of the environment, conventional collection strategies are limited, and the filtration process is time consuming. To overcome these limitations, we developed a new large-volume eDNA sampler with in situ filtration, capable of taking up to 12 samples per deployment. We conducted three deployments of our sampler on the robotic vehicle Mesobot in the Flower Garden Banks National Marine Sanctuary in the northwestern Gulf of Mexico and collected samples from 20 to 400 m depth. We compared the large volume (~40-60 liters) samples collected by Mesobot with small volume (~2 liters) samples collected using the conventional CTD-mounted Niskin bottle approach. We sequenced the V9 region of 18S rRNA, which detects a broad range of invertebrate taxa, and found that while both methods detected biodiversity changes associated with depth, our large volume samples detected approximately 66% more taxa than the CTD small volume samples. We found that the fraction of the eDNA signal originating from metazoans relative to the total eDNA signal decreased with sampling depth, indicating that larger volume samples may be especially important for detecting metazoans in mesopelagic and deep ocean environments. We also noted substantial variability in biological replicates from both the large volume Mesobot and small volume CTD sample sets. Both of the sample sets also identified taxa that the other did not; although the number of unique taxa associated with the Mesobot samples was almost four times larger than those from the CTD samples. Large volume eDNA sampling with in situ filtration, particularly when coupled with robotic platforms, has great potential for marine biodiversity surveys, and we discuss practical methodological and sampling considerations for future applications.

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“…Similarly, the addition of more targeted marker genes may have increased the number of species and taxa detected by the eDNA methodological approach. By increasing the sampling size for eDNA samples we can expect eDNA to become progressively more equivalent, or even superior, to the net trawl methodological approach in detecting taxa, as has been the case in other studies focusing on other organisms, such as fish (Thomsen et al, 2012;Boussarie et al, 2018;Govindarajan et al, 2021). However, reference specimens are required from a region to compare with obtained eDNA sequences.…”

Section: The Use Of Physical Optical and Genetic Censuses For Biodiversity Assessmentmentioning

confidence: 99%

An Integrative Assessment Combining Deep-Sea Net Sampling, in situ Observations and Environmental DNA Analysis Identifies Cabo Verde as a Cephalopod Biodiversity Hotspot in the Atlantic Ocean

et al. 2021

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The deep sea is among the largest, most biologically diverse, yet least-explored ecosystems on Earth. Baseline information on deep-sea biodiversity is crucial for understanding ecosystem functioning and for detecting community changes. Here, we established a baseline of cephalopod community composition and distribution off Cabo Verde, an archipelago in the eastern tropical Atlantic. This baseline served to test the hypothesis that Cabo Verde is biogeographically separated from other Macaronesian archipelagos and allowed the identification of cephalopod species which may play a role in the Macaronesian carbon cycle and oceanic food web. To investigate cephalopod community composition, this study used 746 individual cephalopods obtained by nets (0–1000 m) and 52 cephalopod encounters during video surveys with either towed camera (0–2500 m) or manned submersible (0–375 m). Additionally, environmental DNA (eDNA) metabarcoding on 105 seawater samples (50–2500 m), using an 18S rRNA universal cephalopod primer pair, and a species-specific primer pair for Taningia danae resulted in the detection of 32 cephalopod taxa. When combined, the three methods detected a total of 87 taxa, including 47 distinct species. Each method contributed between 7 and 54% of taxa that were not detected by the other methods, indicating that multiple methodological approaches are needed for optimal deep-sea cephalopod biodiversity assessments. This study documents the occurrences of six species and three genera for the first time in waters surrounding Cabo Verde. Video surveys and eDNA analysis detected Taningia danae recurrently (100–2500 m). eDNA metabarcoding proved to be a powerful tool for cephalopod biodiversity monitoring and complementary to traditional sampling methods. When also including literature records, Cabo Verde hosts at least 102 cephalopod taxa including 30 families and 64 benthic and pelagic species. The total number and species composition of Cabo Verde cephalopods is similar to the Canary Islands and Azores, two known cephalopod biodiversity hotspots, but the Cabo Verde octopus fauna seems to differ. Due to a range of life history characteristics, we hypothesize that the squids Taningia danae (Octopoteuthidae) and Sthenoteuthis pteropus (Ommastrephidae) are important in the carbon cycle of Macaronesia. As a cephalopod biodiversity hotspot Cabo Verde could function as a model region to investigate cephalopod biology and ecology in a rapidly changing Atlantic Ocean.

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Exploring the Use of Environmental DNA (eDNA) to Detect Animal Taxa in the Mesopelagic Zone

Cited by 37 publications

References 102 publications

Vertical stratification of environmental DNA in the open ocean captures ecological patterns and behavior of deep‐sea fishes

Vertical stratification of environmental DNA in the open ocean captures ecological patterns and behavior of deep‐sea fishes

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

An Integrative Assessment Combining Deep-Sea Net Sampling, in situ Observations and Environmental DNA Analysis Identifies Cabo Verde as a Cephalopod Biodiversity Hotspot in the Atlantic Ocean

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