Ideating iDNA: Lessons and limitations from leeches in legacy collections

Abstract

Indirect methods for conducting faunal inventories present great promise, and genomic inventories derived from environmental sources (eDNA) are improving. Invertebrate ingested DNA (iDNA) from terrestrial leeches in the family Haemadipsidae has shown potential for surveying vertebrates and biodiversity monitoring in protected areas. Here we present an initial, and critical, evaluation of the limitations and biases of current iDNA protocols for biodiversity monitoring using both standard and NGS barcoding approaches. Key findings include the need for taxon relevant multi-locus markers and reference databases. In particular, the limitations of available reference databases have profound potential to mislead and bias eDNA and iDNA results if not critically interpreted. Nevertheless, there is great potential for recovery of amplifiable DNA from gut contents of invertebrate museum specimens which may reveal both temporal patterns and cryptic diversity in protected areas with increased efficiency. Our analyses of ingested DNA (iDNA) from both freshly stored and previously collected (legacy) samples of terrestrial leeches successfully identified vertebrates from Myanmar, Australia and Madagascar and indicate the potential to characterize microbial communities, pathogen diversity and interactions at low cost.

Macrobdella decora: Old World Leech Gut Microbial Community Structure Conserved in a New World Leech

“…In both leech species, the gut microbial communities are dominated by Aeromonas, Bacteroidales, and Clostridiales species. This is consistent with previous findings that Bacteroidetes and Aeromonas are common but not obligate in the gut of animals and insects fed on blood (46-51). Siddall et al have shown that many sanguivorous leeches maintain a gut symbiosis with Aeromonas and Bacteroidetes species (8).…”

Macrobdella decora : Old World Leech Gut Microbial Community Structure Conserved in a New World Leech

“…with previous findings that Bacteroidetes and Aeromonas are commonly (but not universally) found in the gut of animals and insects fed on blood (43)(44)(45)(46)(47)(48). Siddall et al showed that many sanguivorous leeches maintain a gut symbiosis with Aeromonas and Bacteroidetes species (10), and we therefore hypothesize that the conserved taxonomic orders have been evolutionarily maintained in hirudinid leeches despite host species diversification and geographic separation.…”

The potential of aquatic bloodfeeding and nonbloodfeeding leeches as a tool for iDNA characterisation

“…In this study, a universal primer set targeting a partial fragment of the COI barcode region (mlCOIintF/jgHCO2198) (Leray et al, 2013 ; Geller et al, 2013 ) was chosen to allow detection of diet across a broad taxonomic range of metazoans (Leray et al, 2013 ). In addition, this primer set can also provide information about possible metazoan endoparasites (Bohmann et al, 2018 ) and can simultaneously coamplify leech DNA, thereby providing DNA barcode‐based host identification; another study using multiple primer sets have also detected vertebrate, parasite and bacterial DNA (Siddall et al, 2019 ). Nevertheless, this coamplification can cause lower detection rates of the diet, as the leech DNA can overpower the diet DNA in the leech gut contents.…”

“…For terrestrial leeches (including members of the families Xerobdellidae, Cylicobdellidae, Americobdellidae and Haemopidae), detailed information is also lacking; for example, the diet of the Mexican terrestrial leech Diestecostoma mexicana (Baird, 1869) is still completely unknown. The major exception to this is the family Haemadipsidae, for which the diet is relatively well understood through studies on invertebrate‐derived DNA, or iDNA, which aim to monitor vertebrates through DNA detection in leech bloodmeals (Drinkwater et al, 2020 ; Fahmy et al, 2019 , 2020 ; Schnell et al, 2012 , 2018 ; Nguyen et al, 2021 ; Siddall et al, 2019 ; Tessler et al, 2018 ; Weiskopf et al, 2018 ). As such, the dearth of data extends across the leech phylogeny, rather than being explicit to certain taxa.…”