High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities

Abstract

Large-scale studies on community ecology are highly desirable but often difficult to accomplish due to the considerable investment of time, labor and, money required to characterize richness, abundance, relatedness, and interactions. Nonetheless, such large-scale perspectives are necessary for understanding the composition, dynamics, and resilience of biological communities. Small invertebrates play a central role in ecosystems, occupying critical positions in the food web and performing a broad variety of ecological functions. However, it has been particularly difficult to adequately characterize communities of these animals because of their exceptionally high diversity and abundance. Spiders in particular fulfill key roles as both predator and prey in terrestrial food webs and are hence an important focus of ecological studies. In recent years, large-scale community analyses have benefitted tremendously from advances in DNA barcoding technology. High-throughput sequencing (HTS), particularly DNA metabarcoding, enables community-wide analyses of diversity and interactions at unprecedented scales and at a fraction of the cost that was previously possible. Here, we review the current state of the application of these technologies to the analysis of spider communities. We discuss amplicon-based DNA barcoding and metabarcoding for the analysis of community diversity and molecular gut content analysis for assessing predator-prey relationships. We also highlight applications of the third generation sequencing technology for long read and portable DNA barcoding. We then address the development of theoretical frameworks for community-level studies, and finally highlight critical gaps and future directions for DNA analysis of spider communities.

ASAP: assemble species by automatic partitioning

“…This is for example useful in groups for which there is no pre‐existing hypotheses to test, or for which unknown/incorrectly delimited species represent the majority of the diversity (e.g., microbial communities or hyperdiverse groups of eukaryotes, such as insects, spiders, nematodes, molluscs). Furthermore, DNA barcodes are now routinely produced using NGS approaches, providing large numbers of sequences often not assignable to known and sequenced species (Kennedy et al., 2020), and for which methods such as ASAP are welcome to e.g., compare species diversity among sites.…”

A powerful long metabarcoding method for the determination of complex diets from faecal analysis of the European pond turtle (Emys orbicularis, L. 1758)

“…Indeed, even by successfully coupling the identification of the genus Carex with several different amplified genes (i.e., rbcL , trnL‐trnF , matK and 28S), and long amplicons (>800–1,200 bp), taxonomic assignment at the species level was not possible and the final identification remained at the genus level, “ Carex sp.” This may be caused by the difficultly associated with discriminating between closely related species or, more probably, by the incomplete nature of the NCBI database. Indeed, many species have not yet been added to this database (Kennedy et al., 2020). To identify the aforementioned plants to a higher taxonomic level, we recommend the elaboration of a local DNA sequence database, containing the plant species representing the known botanical diversity of the studied areas.…”

“…HTS has been used to assess the diet composition of a wide taxonomic range of animals. Animals whose diets have been successfully investigated have included mammals (Buglione et al., 2018; De Barba et al., 2014; Esnaola et al., 2018; Robeson et al., 2017), birds (Crisol‐Martinìez et al., 2016; Han & Oh, 2018), reptiles (Caut et al., 2019; Kartzinel & Pringle, 2015; Koizumi et al., 2017), fish (Barbato et al., 2019; Harms‐Tuohy et al., 2016; Riccioni et al., 2018) and arthropods (Kamenova et al., 2018; Kennedy et al., 2020; Krehenwinkel et al., 2016). For most species, faecal samples, in contrast to stomach contents, can easily be obtained, with a minimal level of interaction and harm inflicted on the studied animal.…”

Challenges and opportunities of species distribution modelling of terrestrial arthropod predators

“…Despite the many technical challenges, environmental DNA and metabarcoding face becoming standard survey tools (Deiner et al, 2017), including in our focal groups (Toju and Baba 2018, Piper et al 2019, Kennedy et al 2020. Their ability to provide reliable absence data and to produce a massive amount of presence data is predicted to improve the efficiency of SDMs in the near future (Muha et al 2017).…”