Vertebrate diversity revealed by metabarcoding of bulk arthropod samples from tropical forests

Abstract

Background: Thousands of bulk arthropod samples are collected globally every year for monitoring programs, conservation efforts, and ecosystem assessments. The taxonomic contents of these samples can be assessed either morphologically or molecularly using DNA metabarcoding coupled with high-throughput sequencing, the latter of which has gained popularity in recent years. In a related field, only vertebrateingesting invertebrates, such as carrion flies and blood-feeding leeches, are targeted for collection, and metabarcoding is carried out on the vertebrate DNA in their gut contents to provide information on vertebrate diversity (invertebrate-derived DNA, iDNA). Aims:Here, we show that the two approaches can be combined, that is, that vertebrate DNA can be detected through metabarcoding of bulk arthropod samples.Materials and Methods: Two metabarcoding primer sets were used to PCR amplify mammal and vertebrate DNA in DNA extracted from bulk arthropod samples collected with pitfall and Malaise traps in tropical forests in Brazil and Tanzania. Results:In total, 32 vertebrate taxa were detected representing mammals, amphibians, and birds. Detected taxa were within, or close to, their known geographical distributions. Conclusion:This study demonstrates that with a relatively small additional investment, information on vertebrate diversity can be obtained from bulk arthropod samples. This is of particular interest in projects where bulk arthropod samples are collected and extracted with the aim to use metabarcoding to assess arthropod taxa.In such studies, the additional information on vertebrates can further inform ecological assessments and monitoring programs and function as a supplement to traditional survey methods of vertebrates.

Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring

“…After manual inspection, 192 papers were removed from this list because they clearly were outside a biodiversity context. The full list of all papers considered is available upon request [Colour figure can be viewed at wileyonlinelibrary.com] 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020Microbial Macrobial Both the DNA extracted from bulk samples (see, for example , Lynggaard et al, 2019;Nielsen et al, 2019, both studies working on bulk samples but published in a journal dedicated to eDNA). Hence, the same term is used in slightly different ways for different types of studies, which can lead to misunderstandings or confusion.…”

“…On the other hand, the definition of eDNA sensu stricto only referring to (mostly or even exclusively extracellular) DNA of macrobial organisms is especially used in conservation biology to monitor invasive and/or endangered species (Borrell et al., 2018; Lacoursière‐Roussel & Deiner, 2019; O'Sullivan et al, 2020), as well as in ecology to survey animal and plants communities and to study biodiversity patterns in aquatic ecosystems (see Deiner et al., 2016; Nguyen et al., 2020). Sometimes, the eDNA concept also includes the DNA extracted from bulk samples (see, for example, Lynggaard et al., 2019; Nielsen et al., 2019, both studies working on bulk samples but published in a journal dedicated to eDNA). Hence, the same term is used in slightly different ways for different types of studies, which can lead to misunderstandings or confusion.…”

Advances and prospects of environmental DNA in neotropical rainforests

“…For example, DNA extracted from owl pellets in central Brazil provided meaningful information regarding the diversity of small mammals (Rocha et al 2015). Likewise, vertebrate communities are better described by the DNA contained in blood feeding arthropods collected with Malaise traps and pitfall traps than with classical or camera trap-based inventories, as shown for forests in Panama and Brazil (Rodgers et al 2017;Lynggaard et al 2019). This approach further revealed variation in vertebrate community composition, consistent with a gradient of anthropogenic pressures in French Guiana, with a decline of diversity in the areas experiencing the highest pressures (Kocher, de Thoisy, François Catzeflis, et al 2017).…”

A new method of metabarcoding Microsporidia and their hosts reveals high levels of microsporidian infections in mosquitoes (Culicidae)

“…DNA metabarcoding, which allows for rapid and cost‐effective identification of the biodiversity of the entire sample across a wide range of taxa and habitats, has proved its usefulness for prokaryotic and eukaryotic species identification. Many examples of this approach have been provided in biodiversity assessment of bacteria (e.g., Adamczyk et al., 2019; Cordier, 2019; Thapa, Zhang, & Allen, 2019), fungi (e.g., Hu et al., 2019; Luis et al., 2019; Xiao et al., 2019), plants (e.g., Bell et al., 2019; Tnah et al., 2019; Veldman et al., 2020) and animals from micro‐ to megafauna (e.g., Dopheide et al., 2019; Head et al., 2018; Lynggaard et al., 2019). However, there are still groups of organisms for which metabarcoding could offer new perspectives, especially with regard to high‐throughput identification and diagnostics of pathogens and pests (Tedersoo, Drenkhan, Anslan, Morales‐Rodriguez, & Cleary, 2018).…”