Molecular diet analysis in mussels and other metazoan filter feeders and an assessment of their utility as natural eDNA samplers

Active or passive? A multi-marker approach to compare active and passive eDNA sampling in riverine environments

Environmental DNA (eDNA) is increasingly used in biodiversity monitoring with several collection techniques proposed. Those applied to aquatic eDNA can now be divided into two categories: active and passive sampling. Active sampling involves the deliberate and controlled collection of environmental samples, and the most common method is water filtration. Passive sampling is a more recent technique that involves capturing eDNA by relying on its adsorption to samplers, which can be fabricated from various materials, and submerged for minutes, hours or weeks. In this study, we compared the performance of water filtration and Passive eDNA Sampling (PEDS) with granular active carbon in terms of detected taxa collected from four different sites of the same river system. eDNA samples were amplified for three molecular markers for 18S rRNA, 12S rRNA and COI genes, with primers according to the literature that target invertebrates and vertebrates. The study revealed that PEDS detected on average more species in 18S rRNA and 12S rRNA assays, with 18S rRNA results presenting a significantly higher homogeneity of read variances between samples. Biological communities captured differed between PEDS and filters. The former method retrieved a significant number of microinvertebrates and chironomids (Chironomidae, Diptera), detecting a similar number of vertebrates to filters, but with lower performance in the detection of fish. Notably, both methods performed well with amphibians, successfully identifying all species linked to lotic environments in the studied area. Compared to PEDS, the eDNA capture protocol using filters yielded more sequences identified as ephemeropterans, trichopterans, and acarines. In addition, PEDS was more cost-effective and environmentally sustainable. These findings imply that there is no definitive superior eDNA sampling method. Consequently, in conjunction with studies proposing new methods of eDNA sampling, studies comparing their performance with a broad taxonomic representation will be pivotal.

Insights into trophic interactions: DNA metabarcoding reveals species composition in black-tailed gull fecal samples in coastal environments of South Korea

This study explored the algae, zooplankton, macroinvertebrate, fish, and parasitic single-celled organism communities in Larus crassirostris (black-tailed gull) fecal samples from Baengnyeongdo, Hongdo, and Ulleungdo in South Korea. The fecal samples can identify key species consumed by black-tailed gull, providing insights into their, trophic interactions, and habitat dependencies. Using DNA metabarcoding, we identified algae, zooplankton, macroinvertebrate, fish, and intestinal and single-celled parasite species in the fecal samples. Parasitic single-celled organisms, such as Rhogostoma sp., Rhogostoma schuessleri, Eimeria furonis, and Aggregata eberthi, showed differing relative abundances at each sampling location, indicating variability in parasite diversity in the fecal DNA analysis of birds at each site. Intestinal parasites showed similar site-specific variability, though Clistobothrium sp. and Tetrabothrius sp. were common at all locations. Algae species, including Heterocapsa steinii, Heterocapsa niei, and Sargassum cristaefolium, also displayed habitat-specific patterns, as did zooplankton, with Calanus sp., Corycaeus speciosus, and Caprella californica being dominant on Baengnyeongdo, Hongdo, and Ulleungdo, respectively. In the macroinvertebrate communities, Octopus sinensis was prevalent at all locations but at varying abundances. Site-specific dominant fish species were also identified, with Ammodytes personatus, Decapterus maruadsi, and Arctoscopus japonicus highly predominant on Baengnyeongdo, Hongdo, and Ulleungdo, respectively. Other fish species, such as Ammodytes hexapterus, were detected in lower frequencies, suggesting a diverse diet for the seabirds. These results offer insights into the species composition and ecological dynamics in black-tailed gull populations across disparate Korean islands.

Passive eDNA sampling facilitates biodiversity monitoring and rare species detection

Environmental DNA (eDNA) technology has revolutionized biomonitoring, but challenges remain regarding water sample processing. The passive eDNA sampler (PEDS) represents a viable alternative to active, water filtration-based eDNA enrichment methods, but the effectiveness of PEDS for surveying biodiverse and complex natural water bodies is unknown. Here, we collected eDNA using filtration and glass fiber filter-based PEDS (submerged in water for 1 d) from 27 sites along the final reach of the Yangtze River and the coast of the Yellow Sea, followed by eDNA metabarcoding analysis of fish biodiversity and quantitative PCR (qPCR) for a critically endangered aquatic mammal, the Yangtze finless porpoise. We ultimately detected 98 fish species via eDNA metabarcoding. Both eDNA sampling methods captured comparable local species richness and revealed largely similar spatial variation in fish assemblages and community partitions between the river and sea sites. Notably, the Yangtze finless porpoise was detected only in the metabarcoding of eDNA collected by PEDS at five sites. Also, species-specific qPCR revealed that the PEDS captured porpoise eDNA at more sites (7 vs. 2), in greater quantities, and with a higher detection probability (0.803 vs. 0.407) than did filtration. Our results demonstrate the capacity of PEDS for surveying fish biodiversity, and support that continuous eDNA collection by PEDS can be more effective than instantaneous water sampling at capturing low abundance and ephemeral species in natural waters. Thus, the PEDS approach can facilitate more efficient and convenient eDNA-based biodiversity surveillance and rare species detection.

Tracking climate-change-induced biological invasions by metabarcoding archived natural eDNA samplers

In a time of unprecedented environmental change, understanding the response of organisms and ecosystems to change is paramount1. However, our knowledge of anthropogenic impacts on ecosystems is limited by a lack of standardized retrospective biomonitoring data2. Here, we use a four-decade time series of archived blue mussels to trace spatiotemporal biodiversity change in coastal ecosystems. The filter-feeding mussels, which were initially collected for pollution monitoring, can serve as natural eDNA samplers, carrying an imprint of the surrounding aquatic community at the time of sampling3. By sequencing the preserved DNA, we characterize highly diverse mussel-associated communities and reconstruct the invasion trajectory of an invasive species, the barnacle Austrominius modestus. We quantitatively trace population growth of the invader to the detriment of native taxa and uncover repeated population collapses and reinvasions after cold winters. By providing highly resolved temporal data on community assembly and global warming-driven invasion processes, natural eDNA sampler time series overcome a critical shortfall in our understanding of biodiversity change in the Anthropocene.

Molecular Diet Analysis of Asian Clams for Supplementary Biodiversity Monitoring: A Case Study of Nakdong River Estuary

Environmental DNA (eDNA) extracted from the gut contents of filter feeders can be used to identify biodiversity in aquatic ecosystems. In this study, we used eDNA from the gut contents of the Asian clam Corbicula fluminea to examine biodiversity within estuarine ecosystem. Field sampling was conducted at three points in the Nakdong River Estuary, which is characterised by closed estuarine features resulting from the presence of an estuarine barrage. The collected C. fluminea samples were dissected to separate the gut contents, and the extracted eDNA was amplified using 18S V9 primer targeting all eukaryote-derived DNA. The amplified DNA was sequenced using a next-generation sequencing (NGS) technique, and a BLASTn search was performed based on the National Centre for Biotechnology Information (NCBI) database for taxa identification. We obtained 23 unique operational taxonomic units (OTUs), including fish (approximately 8.70%), copepods (approximately 17.39%), and green algae (approximately 21.74%), representing a wide range of habitats. Furthermore, 8 out of the 20 families were identified through comparisons with reference data from conventional field surveys, and the OTUs of elusive migratory fish were detected. The results support the application of C. fluminea as an eDNA sampler for supplementary biodiversity monitoring.