Environmental DNA of preservative ethanol performed better than water samples in detecting macroinvertebrate diversity using metabarcoding

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.

Environmental gradients and optimal fixation time revealed with DNA metabarcoding of benthic sample fixative

Assessments of biodiversity and ecosystem status can benefit from DNA metabarcoding as a means to streamline sample processing and specimen identification. Moreover, processing the fixation medium instead of the precious material introduces straightforward protocols that allow subsequent focus on certain organisms detected among the preserved specimens. In this study, we present a proof of concept via the analysis of freshwater invertebrate samples from the Tatra Mountain lakes (Slovakia). Besides highlighting a match between the lake-specific environmental conditions and the results of our fixative DNA metabarcoding, we observed an option to fine-tune the fixation time: to prefer two weeks over a day or a month. This effect emerged from the presence/absence of individual taxa rather than from coarse per-sample records of taxonomic richness, demonstrating that metabarcoding studies-and efforts to optimize their protocols-can use the robust metrics to explore even subtle trends. We also provide evidence that fixative DNA might better capture large freshwater species than terrestrial or meiofauna.

Degree of urbanization and vegetation type shape soil biodiversity in city parks

Urbanization negatively impacts aboveground biodiversity, such as bird and insect communities. City parks can reduce these negative impacts by providing important habitat. However, it remains poorly understood how the degree of urbanization and vegetation types within city parks (e.g., lawns, woodland) impact soil biodiversity. Here we investigated the impact of the degree of urbanization (urban vs. suburban) and vegetation type (lawn, shrub-lawn, tree-lawn and tree-shrub mixtures) on soil biodiversity in parkland systems. We used eDNA metabarcoding to characterize soil biodiversity of bacteria, fungi, protists, nematodes, meso- and macrofauna across park vegetation types in urban and suburban regions in Xiamen, China. We observed a strong effect of the degree of urbanization on the richness of different soil biota groups, with higher species richness of protists and meso/macrofauna in urban compared to suburban areas, while the richness of bacteria and fungi did not differ, and the difference of nematode richness depended on vegetation type. At the functional level, increased degree of urbanization associated with greater species richness of bacterivores, plant pathogens and animal parasites. These urbanization effects were at least partly modulated by higher soil phosphorous levels in urban compared to suburban sites. Also, the vegetation type impacted soil biodiversity, particularly fungal richness, with the richness of pathogenic and saprotrophic fungi increasing from lawn to tree-shrub mixtures. Tree-shrub mixtures also had the highest connectedness between biotas and lowest variation in the soil community structure. Overall, we show that soil biodiversity is strongly linked to the degree of urbanization, with overall richness increasing with urbanization, especially in bacterivores, plant pathogens and animal parasites. Targeted management of vegetation types in urban areas should provide a useful way to help mitigate the negative effect of urbanization on soil biodiversity.

Persisting roadblocks in arthropod monitoring using non-destructive metabarcoding from collection media of passive traps

Background

Broad-scale monitoring of arthropods is often carried out with passive traps (e.g., Malaise traps) that can collect thousands of specimens per sample. The identification of individual specimens requires time and taxonomic expertise, limiting the geographical and temporal scale of research and monitoring studies. DNA metabarcoding of bulk-sample homogenates has been found to be faster, efficient and reliable, but the destruction of samples prevents a posteriori validation of species occurrences and relative abundances. Non-destructive metabarcoding of DNA extracted from collection medium has been applied in a limited number of studies, but further tests of efficiency are required with different trap types and collection media to assess the consistency of the method.

Methods

We quantified the detection rate of arthropod species when applying non-destructive DNA metabarcoding with a short (127-bp) fragment of mitochondrial COI on two combinations of passive traps and collection media: (1) water with monopropylene glycol (H2O-MPG) used in window-flight traps (WFT, 53 in total); (2) ethanol with monopropylene glycol (EtOH-MPG) used in Malaise traps (MT, 27 in total). We then compared our results with those obtained for the same samples using morphological identification (for WFTs) or destructive metabarcoding of bulk homogenate (for MTs). This comparison was applied as part of a larger study of arthropod species richness in silver fir (Abies alba Mill., 1759) stands across a range of climate-induced tree dieback levels and forest management strategies.

Results

Of the 53 H2O-MPG samples from WFTs, 16 produced no metabarcoding results, while the remaining 37 samples yielded 77 arthropod MOTUs in total, of which none matched any of the 343 beetle species morphologically identified from the same traps. Metabarcoding of 26 EtOH-MPG samples from MTs detected more arthropod MOTUs (233) than destructive metabarcoding of homogenate (146 MOTUs, 8 orders), of which 71 were shared MOTUs, though MOTU richness per trap was similar between treatments. While we acknowledge the failure of metabarcoding from WFT-derived collection medium (H2O-MPG), the treatment of EtOH-based Malaise trapping medium remains promising. We conclude however that DNA metabarcoding from collection medium still requires further methodological developments and cannot replace homogenate metabarcoding as an approach for arthropod monitoring. It can be used nonetheless as a complementary treatment when enhancing the detection of soft-bodied arthropods like spiders and Diptera.