Multi-marker DNA metabarcoding reflects tardigrade diversity in different habitats

Abstract

Like meiofauna in general, tardigrades are often neglected in ecological and environmental surveys. Tardigrades occur in all parts of the world, from deep marine sediments to alpine environments, and are present in most ecosystems. They are therefore potentially good candidates for biomonitoring programs. However, sampling of these minute animals is both tedious and time-consuming, impeding their inclusion in large-scale ecological surveys. In this study we argue that using a multi-marker metabarcoding approach on environmental DNA partly can overcome this barrier. Samples of moss, lichens and leaf litter were investigated both by morphology-based methods and DNA metabarcoding, and the results were compared in terms of tardigrade diversity and community composition of the sampled microhabitats. DNA metabarcoding using three markers detected more species of tardigrades than identification by morphology in most samples. Also, metabarcoding detected the same community differences and microhabitat distribution patterns as morphology-based methods. In general, metabarcoding of litter samples was unreliable, with only one out of three markers consistently amplifying and detecting tardigrades. The low availability of tardigrade reference sequences in public databases restricts the taxonomic resolution in eDNA surveys, but this impediment is partly circumvented by utilizing multiple markers

Desiccation risk favours prevalence and diversity of tardigrade communities and influences their trophic structure in alpine ephemeral rock pools

“…The small size of these habitats makes them amenable to experimental manipulation, or even in situ creation of new pools (see for example Evans et al, 2016;Sommers et al, 2019). In addition, their relative simplicity makes the application of metabarcoding (Arakawa, 2020;Topstad et al, 2021) possible, which would provide a complete and unbiased inventory of the meiofauna hosted in this unique and understudied ecosystem.…”

A novel metabarcoding primer pair for environmental DNA analysis of Cephalopoda (Mollusca) targeting the nuclear 18S rRNA region

“…Therefore, we recommend appreciating the complementary nature of primers sets and assigning a confidence value to a species detection rather than fully discarding single marker detections. Secondly, employing multiple markers is useful with limited availability of reference sequences [ 72 ]. By searching for multiple markers, the reference database can include species that might have a reference sequence for one region, but not the other.…”

Soil environmental DNA metabarcoding in low-biomass regions requires protocol optimization: a case study in Antarctica

“…massive parallel sequencing technologies) to identify organisms through traces of DNA left in the environment such as in soil, water, faeces or adhered to actual organisms (Pietramellara et al 2009, Kircher & Kelso 2010, Bohmann et al 2014, Tanaka et al 2014, Boyer et al 2015, Lynggaard et al 2019, Ruppert et al 2019, Thomsen & Sigsgaard 2019). eDNA metabarcoding can be used to detect single or multiple taxa (Bakker et al 2017, Alexander et al 2020, Rota et al 2020, Schütz et al 2020, Zhang et al 2020, Topstad et al 2021), for environmental samples originating from varied ecosystems (Edwards et al 2018, Mariani et al 2019, Clark et al 2020, Fraija-Fernández et al 2020, Webster et al 2020, Carrasco-Puga et al 2021), using fresh or old eDNA samples (Barnes & Turner 2016, Williams et al 2016, Collins et al 2018, Foucher et al 2020) and to study ancient ecosystems (Jørgensen et al 2012, Gugerli et al 2013, Alsos et al 2016, Ruppert et al 2019).…”