Environmental DNA persistence and fish detection in captive sponges

Abstract

Large and hyper-diverse marine ecosystems pose significant challenges to biodiversity monitoring. While environmental DNA (eDNA) promises to meet many of these challenges, recent studies suggested that sponges, as ‘natural samplers’ of eDNA, could further streamline the workflow for detecting marine vertebrates. However, beyond pilot studies demonstrating the ability of sponges to capture eDNA, little is known about the journey of eDNA particles in the sponge tissues, and the effectiveness of the latter compared to water samples. Here, we present the results of a controlled aquarium experiment to examine the persistence and detectability of eDNA from three encrusting sponge species and how these compare with established water filtration techniques. Our results indicate that sponges and water samples have highly similar detectability for fish of different sizes and abundances, but different sponge species exhibit considerable variance in performance. Interestingly, one sponge appeared to mirror the eDNA degradation profile of water samples, while another sponge retained eDNA throughout the experiment. A third sponge yielded virtually no DNA sequences at all. Overall, our study suggests that some sponges will be suitable as natural samplers, while others will introduce significant problems for laboratory processing. We suggest that an initial optimization phase will be required in any future studies aiming to employ sponges for biodiversity assessment. With time, factoring in technical and natural accessibility, it is expected that specific sponge taxa may become the ‘chosen’ natural samplers in certain habitats and regions.

Optimised DNA isolation from marine sponges for natural sampler DNA (nsDNA) metabarcoding

“…However, sponge nsDNA accumulation and degradation rates still require investigation to quantify temporal variation in eDNA signals from these natural samplers (Jeunen et al, 2021) compared to aquatic eDNA accumulation and degradation rates which differ by target taxa and habitat (Harrison et al, 2019). This has been done in an artificial capacity (Cai et al, 2022), but must also be investigated in natural settings.…”

“…Different sponges may not have the same pumping and filtration efficiency or even have viable tissue for DNA extraction due to microbial loads and PCR inhibitors (Cai et al, 2022). Therefore, future research must identify the best natural samplers in both benthic and pelagic habitats from those sponges that are accessible and can withstand repeat sampling as well as understand how different sponge characteristics influence eDNA recovery (Mariani et al, 2019; Jeunen et al, 2021).…”

“…The sponge individuals were relatively young, having regrown over a few weeks after attempts to remove the sponge from the aquarium tank. This should have been enough time for eDNA to accumulate in the tissues of these sponges (Cai et al, 2022), but they may not have reached a large enough size to adequately pump and filter eDNA from the volume of water held in the tank. The BLAST identity for taxonomic assignment also had to be reduced to 80% in order to recover more species known to be present in the aquarium tank.…”

“…The sponge individuals were relatively young, having regrown over a few weeks after attempts to remove the sponge from the aquarium tank. This should have been enough time for eDNA to accumulate in the tissues of these sponges (Cai et al, 2022), but they may not have reached a large enough size to adequately pump and filter eDNA from the volume of water held in the tank. Furthermore, it is unknown whether bacterial symbionts, such as those observed in L. chondrodes (Galitz et al, 2018), influence the pumping and filtration efficiency of sponges, although results from Cai et al (2022) appear to suggest that symbiotic load may influence eDNA capture and persistence in sponge tissue.…”

“…This should have been enough time for eDNA to accumulate in the tissues of these sponges (Cai et al, 2022), but they may not have reached a large enough size to adequately pump and filter eDNA from the volume of water held in the tank. Furthermore, it is unknown whether bacterial symbionts, such as those observed in L. chondrodes (Galitz et al, 2018), influence the pumping and filtration efficiency of sponges, although results from Cai et al (2022) appear to suggest that symbiotic load may influence eDNA capture and persistence in sponge tissue. The BLAST identity for taxonomic assignment also had to be reduced to 80% in order to recover more species known to be present in the aquarium tank.…”