Molecular diet analysis in zebra and quagga mussels (Dreissenaspp.) and an assessment of the utility of aquatic filter feeders as biological eDNA filters

Abstract

Molecular gut content analysis is a popular tool to study food web interactions and was recently also suggested as an alternative source for DNA based biomonitoring. However, the overabundant consumer’s DNA often outcompetes that of its diet during PCR. Blocking approaches are an efficient means to reduce consumer amplification while retaining broad specificity for dietary taxa. We here designed an assay to monitor the eukaryotic diet of mussels and test their utility as biological eDNA filters to monitor planktonic communities. We designed several rDNA primer sets with a broad taxonomic suitability for eukaryotes, which suppress the amplification of mussels. The primers were tested using mussel DNA extracts and the results were compared to eDNA water samples collected next to the mussel colonies. Taxonomic recovery, as well as patterns of alpha and beta diversity, were compared between mussels and water samples. In addition, we analyzed time series samples of mussel samples from different German rivers. Our primer sets efficiently block the amplification of various mussel genera. The recovered DNA reflects a broad dietary preference across the eukaryotic tree of life and considerable taxonomic overlap with filtered water samples. We also recover various taxa of possible commensals and parasites, associated with the mussels. Our protocol will enable large scale dietary analysis in mussels, facilitate aquatic food web analysis, elucidate the ecological impact of invasive bivalves and the rapid survey of mussel aquacultures for pathogens. Moreover, we show that mussels could serve as an interesting complementary DNA source for biomonitoring.

The bug in a teacup—monitoring arthropod–plant associations with environmental DNA from dried plant material

“…Leaf material can be easily collected in paper bags and dried in the field using silica gel, or in the laboratory by freeze-drying or using drying ovens at moderate temperature. The subsequent grinding in a mortar or blender is also straightforward [27]. Arthropod DNA in dry plant material appears to be very temporally stable: indeed, we found DNA from true plant-associated arthropods to be dominant over that of storage pests, which would have entered the sample later.…”

Towards exhaustive community ecology via DNA metabarcoding

“…We excluded strictly methodological studies (e.g., testing the performance of primers), reviews and meta-analyses, and studies focusing on intraspecific evolutionary patterns. After a detailed screening, we also excluded diet studies, and studies on symbionts or parasites (overall, 72 studies evaluated; see Table S1a) because none of them attempted exhaustive reconstruction of communities, and they used primers focusing on the taxa assumed to be the diet or the symbionts of target organisms (see Weber et al, 2023).…”

“…Nonetheless, just obtaining the list of taxa living in a specific environment provides little insight on how they interact, and analyses of biotic interactions involving a large number of taxa remain extremely challenging. In addition to species occurrences, metabarcoding studies can provide direct information on species interactions, for instance through the analysis of diet, parasites and the host-associated microbiota (Alberdi et al, 2019;Bass et al, 2015;Ravindran, 2019;Roslin & Majaneva, 2016;Taberlet et al, 2018;Weber et al, 2023), but direct observations of interaction can only focus on a few taxa, and are not enough to reconstruct what happens across all the trophic levels. In the last years, novel frameworks have been proposed for the multitrophic and multitaxa analysis of communities in absence of direct observation of interactions, on the basis of species traits, phylogenetic information and machine learning algorithms (Fricke et al, 2022;Gravel et al, 2019), even though a lot of work remains to be done to assess their power, strengths and limitations (Burian et al, 2021;D'Amen et al, 2018;Fricke et al, 2022;Gravel et al, 2019).…”

Framing Cutting-Edge Integrative Deep-Sea Biodiversity Monitoring via Environmental DNA and Optoacoustic Augmented Infrastructures

“…For this purpose, eDNA water sampling should also be provided in real-time by autonomous and independent samplers (e.g., Yamahara et al, 2019;Hansen et al, 2020;Jacobsen, 2021;Moore et al, 2021), with prototypes presently under construction (e.g., the Adjustable Volume eDNA Sampler 1 , and the Robotic Cartridge Sampling Instrument-RoCSI 2 ) or that can be adjusted for this purpose, as the SALSA system (Kersten et al, 2019;Brandt et al, 2021) 3 . An alternative to water samplers, would be an opportunistic use of filter feeding organisms such as sponges or bivalves, that act as natural "DNA traps, " concentrating eDNA from water that can be retrieved at different time points (Mariani et al, 2019;Turon et al, 2020;Weber et al, 2021). The advantage of adding eDNA to ecological monitoring protocols is its ability to cross-validate data from other methodologies (e.g., imaging) (e.g., Aguzzi et al, 2019).…”