Optimized <scp>DNA</scp> isolation from marine sponges for natural sampler <scp>DNA</scp> metabarcoding

Harper, Lynsey R.; Neave, Erika F.; Sellers, Graham S.; V., Cunnington, Alice; Arias, María Belén; Craggs, Jamie; MacDonald, Barry; Riesgo, Ana; Mariani, Stefano

doi:10.1002/edn3.392

Cited by 4 publications

(5 citation statements)

References 103 publications

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“…The need for increased replication likely stems from a lack of understanding about the process of eDNA accumulation in the sponge tissue matrix. Further research into laboratory protocol development to efficiently extract eDNA from sponge tissues (Harper et al 2023), as well as gaining a better understanding of eDNA accumulation by sponges (Cai et al 2022), are essential to progress the applicability of sponges as natural eDNA samplers. Our results show significant differences in estimated replication between treatments, with frozen samples requiring increased tissue biopsies to reliably detect 90% of the fish diversity within a specimen compared to dried and ethanol-submerged specimens.…”

Section: Discussionmentioning

confidence: 99%

Unlocking Antarctic molecular time-capsules – recovering historical environmental DNA from museum-preserved sponges

Jeunen,

Mills,

Lamare

et al. 2024

Preprint

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Marine sponges have recently emerged as efficient natural environmental DNA (eDNA) samplers. The ability of sponges to accumulate eDNA provides an exciting opportunity to reconstruct contemporary communities and ecosystems with high temporal and spatial precision. However, the use of historical eDNA (heDNA), trapped within the vast number of specimens stored in scientific collections, opens up the opportunity to begin to reconstruct the communities and ecosystems of the past. Here, using a variety of Antarctic sponge specimens stored in an extensive marine invertebrate collection, we were able to recover information on Antarctic fish biodiversity from specimens up to 20 years old. We successfully recovered 64 fish heDNA signals from 27 sponge specimens. Alpha diversity measures did not differ among preservation methods, but sponges stored frozen had a significantly different fish community composition compared to those stored dry or in ethanol. Our results show that we were consistently and reliably able to extract the heDNA trapped within marine sponge specimens, thereby enabling the reconstruction and investigation of communities and ecosystems of the recent past with a spatial and temporal resolution previously unattainable. Future research into heDNA extraction from other preservation methods, as well as the impact of specimen age and collection method will strengthen and expand the opportunities for this novel resource to access new knowledge on ecological change during the last century.

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Section: Discussionmentioning

confidence: 99%

Unlocking Antarctic molecular time-capsules – recovering historical environmental DNA from museum-preserved sponges

Jeunen,

Mills,

Lamare

et al. 2024

Preprint

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“…The efficiency of sponge eDNA metabarcoding surveys could be further enhanced by gaining a better understanding of how sponges accumulate eDNA and how to optimally obtain eDNA from sponge tissue biopsies (Harper et al., 2023; Mariani et al., 2019). The increased variability observed in eDNA composition between Haliclona scotti samples within a site compared to water eDNA signals demonstrates the need for protocol optimization (Figure 5d–f).…”

Section: Discussionmentioning

confidence: 99%

“…The increased variability observed in eDNA composition between Haliclona scotti samples within a site compared to water eDNA signals demonstrates the need for protocol optimization (Figure 5d–f). Unlike the myriad of studies on protocol optimization for water eDNA (Sanches & Schreier, 2020; Spens et al., 2016), only a single study has investigated the impact of various DNA extraction protocols on eDNA signal recovery from sponge tissues thus far (Harper et al., 2023). Since the use of optimized protocols is linked to increased DNA concentration, diversity detection consistency, and probability of rare taxa (Spens et al., 2016), additional research into protocol optimization for sponge eDNA surveys is required.…”

Section: Discussionmentioning

confidence: 99%

“…Further exacerbating the time commitment for water filtration is the increased water volume required to be processed in marine eDNA studies compared to freshwater ecosystems (Bowers et al., 2021). To circumvent the need for water filtration, multiple alternative methods have been successfully trialed, including passive filtration (Bessey et al., 2021; Jeunen, von Ammon, et al., 2022; Kirtane et al., 2020; Verdier et al., 2021), autonomous sampling (Hansen et al., 2020; Yamahara et al., 2019), and direct sampling of filter‐feeding organisms such as marine sponges (Brodnicke et al., 2023; Cai et al., 2022; Harper et al., 2023; Jeunen, Cane, et al., 2023; Jeunen, Lamare, et al., 2023; Mariani et al., 2019; Neave et al., 2023; Turon et al., 2020).…”

Section: Introductionmentioning

confidence: 99%

“…The use of marine sponges to investigate eDNA signals commenced after the observation of natural eDNA accumulation through their filter‐feeding strategy (Mariani et al., 2019). Thus far, optimal DNA extraction protocols have been investigated (Harper et al., 2023), as well as eDNA retention time in sponges through a mesocosm experiment to gain insight into temporal detection (Cai et al., 2022). Furthermore, high spatial resolutions have been observed, with different eDNA signals on small spatial scales representing the local biological community (i.e., fish and vertebrates; Jeunen, Cane, et al., 2023; Turon et al., 2020).…”

Section: Introductionmentioning

confidence: 99%

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Unveiling the hidden diversity of marine eukaryotes in the Ross Sea: A comparative analysis of seawater and sponge eDNA surveys

Jeunen,

Lamare,

Cummings

et al. 2023

Environmental DNA

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The Ross Sea, Antarctica, while largely pristine, is experiencing increased anthropogenic pressures, necessitating enhanced biomonitoring efforts for conservation purposes. Environmental DNA (eDNA) extracted from marine sponges provides a promising approach for biodiversity monitoring in remote areas by circumventing the need for time‐consuming water filtration. Investigations into the efficacy of eDNA signal detection across the tree of life from marine sponges have yet to be fully explored. Here, we conducted a seawater and sponge eDNA metabarcoding survey at seven coastal locations in the Ross Sea to assess spatial eukaryote biodiversity patterns and investigate eDNA signal differences between both substrates. In total, we detected 1450 operational taxonomic units (OTUs) across 30 phyla. Significant differences in water and sponge eDNA signal richness and composition were observed, with a partial overlap in OTU detection between both substrates and, thereby, underscoring the crucial role of substrate selection in eDNA metabarcoding surveys. Furthermore, alpha and beta diversity analyses revealed distinct eDNA signals among sampling locations, which were corroborated by known species distributions. However, only 135 OTUs (9%) could be successfully assigned to species level, and 574 OTUs (40%) were unable to be taxonomically classified, due to limitations in the reference database. Our results provide evidence for the potential of eDNA monitoring in remote areas, demonstrate the need to consider more sophisticated sampling strategies whereby multiple eDNA substrates are incorporated, and highlight the importance of complete reference databases for robust taxonomy assignment of eDNA signals.

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Characterizing Antarctic fish assemblages using eDNA obtained from marine sponge bycatch specimens

Jeunen,

Lamare,

Devine

et al. 2023

Rev Fish Biol Fisheries

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International conservation goals have been set to mitigate Southern Ocean ecosystem deterioration, with multiple monitoring programs evaluating progress towards those goals. The scale of continuous monitoring through visual observations, however, is challenged by the remoteness of the area and logistical constraints. Given the ecological and economic importance of the Southern Ocean, it is imperative that additional biological monitoring approaches are explored. Recently, marine sponges, which are frequently caught and discarded in Southern Ocean fisheries, have been shown to naturally accumulate environmental DNA (eDNA). Here, we compare fish eDNA signals from marine sponge bycatch specimens to fish catch records for nine locations on the continental shelf (523.5–709 m) and 17 from the continental slope (887.5–1611.5 m) within the Ross Sea, Antarctica. We recorded a total of 20 fishes, with 12 fishes reported as catch, 18 observed by eDNA, and ten detected by both methods. While sampling location was the largest contributor to the variation observed in the dataset, eDNA obtained significantly higher species richness and displayed a significantly different species composition compared to fish catch records. Overall, eDNA read count correlated more strongly with fish abundance over biomass. Species composition correlated on a regional scale between methods, however eDNA signal strength was a low predictor of catch numbers at the species level. Our results highlight the potential of sponge eDNA monitoring in the Southern Ocean by detecting a larger fraction of the fish community compared to catch recordings, thereby increasing our knowledge of this understudied ecosystem and, ultimately, aiding conservation efforts.

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Optimized DNA isolation from marine sponges for natural sampler DNA metabarcoding

Cited by 4 publications

References 103 publications

Unlocking Antarctic molecular time-capsules – recovering historical environmental DNA from museum-preserved sponges

Unlocking Antarctic molecular time-capsules – recovering historical environmental DNA from museum-preserved sponges

Unveiling the hidden diversity of marine eukaryotes in the Ross Sea: A comparative analysis of seawater and sponge eDNA surveys

Characterizing Antarctic fish assemblages using eDNA obtained from marine sponge bycatch specimens

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