Faeces of generalist predators as ‘biodiversity capsules’: A new tool for biodiversity assessment in remote and inaccessible habitats

Boyer, Stéphane; Cruickshank, Robert; Wratten, Stephen D.

doi:10.1016/j.fooweb.2015.02.001

Cited by 37 publications

(53 citation statements)

References 67 publications

(55 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…One of the issues complicating the interpretation of molecular information derived from food web studies is the source of DNA: whether it originates directly from the prey of focal predators or does it derive from lower steps in the food chain, a phenomenon commonly referred to as secondary predation (Boyer, Cruickshank, & Wratten, ; Sheppard et al., ). As the odonates are among the top predators of the insect world, they might consume many other predatory species, resulting in secondary predation.…”

Section: Discussionmentioning

confidence: 99%

Pellets of proof: First glimpse of the dietary composition of adult odonates as revealed by metabarcoding of feces

Kaunisto

Roslin

Sääksjärvi

et al. 2017

Ecology and Evolution

View full text Add to dashboard Cite

Recent advances in molecular techniques allow us to resolve the diet of unstudied taxa. Odonates are potentially important top‐down regulators of many insects. Yet, to date, our knowledge of odonate prey use is based mainly on limited observations of odonates catching or eating their prey. In this study, we examine the potential use of metabarcoding in establishing the diet of three adult odonate species (Lestes sponsa, Enallagma cyathigerum, and Sympetrum danae) at a site in southwestern Finland. To this purpose, we compared three different methods for extracting DNA from fecal samples: the Macherey‐Nagel Nucleospin XS kit, a traditional salt extraction, and the Zymo Research Fecal Microprep kit. From these extracts, we amplified group‐specific mitochondrial markers (COI and 16S rRNA) from altogether 72 odonate individuals, and compared them to comprehensive reference libraries. The three odonate species show major overlap in diet, with no significant differences between individuals of different size and/or gender, reflecting opportunistic foraging of adult odonates. Of a total of 41 different prey species detected, the most frequently consumed ones were Diptera, with additional records of six other orders. Based on our data, the best DNA extraction method is the traditional salt extraction, as it provides the most information on prey content while also being the most economical. To our knowledge, this is the first study to resolve the species‐level diet of adult odonates. Armed with the appropriate methodological caveats, we are ready to examine the ecological role of odonates in both terrestrial and aquatic food webs, and in transferring subsidies between these two realms.

show abstract

Section: Discussionmentioning

confidence: 99%

Pellets of proof: First glimpse of the dietary composition of adult odonates as revealed by metabarcoding of feces

Kaunisto

Roslin

Sääksjärvi

et al. 2017

Ecology and Evolution

View full text Add to dashboard Cite

show abstract

“…Spider webs represent a potential noninvasive source of DNA for conservation, ecology, and management studies (Blake, McKeown, Bushell, & Shaw, 2016;Xu, Yen, Bowman, & Turner, 2015). They are able to trap a part of the local arthropod biodiversity present in natural (even pristine), agricultural, or urban habitats and may serve as "biodiversity capsules" (sensu Boyer, Cruickshank, & Wratten, 2015), especially for flying insects. To date, DNA extracted from spider webs enabled the detection of both the predator and its prey using diagnostic PCR under controlled conditions (Blake et al, 2016;Xu et al, 2015).…”

Section: The Capture Of Biodiversity By Spider Websmentioning

confidence: 99%

One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies

Corse

Tougard

Archambaud‐Suard

et al. 2019

Ecology and Evolution

View full text Add to dashboard Cite

In diet metabarcoding analyses, insufficient taxonomic coverage of PCR primer sets generates false negatives that may dramatically distort biodiversity estimates. In this paper, we investigated the taxonomic coverage and complementarity of three cytochrome c oxidase subunit I gene (COI) primer sets based on in silico analyses and we conducted an in vivo evaluation using fecal and spider web samples from different invertivores, environments, and geographic locations. Our results underline the lack of predictability of both the coverage and complementarity of individual primer sets: (a) sharp discrepancies exist observed between in silico and in vivo analyses (to the detriment of in silico analyses); (b) both coverage and complementarity depend greatly on the predator and on the taxonomic level at which preys are considered; (c) primer sets’ complementarity is the greatest at fine taxonomic levels (molecular operational taxonomic units [MOTUs] and variants). We then formalized the “one‐locus‐several‐primer‐sets” (OLSP) strategy, that is, the use of several primer sets that target the same locus (here the first part of the COI gene) and the same group of taxa (here invertebrates). The proximal aim of the OLSP strategy is to minimize false negatives by increasing total coverage through multiple primer sets. We illustrate that the OLSP strategy is especially relevant from this perspective since distinct variants within the same MOTUs were not equally detected across all primer sets. Furthermore, the OLSP strategy produces largely overlapping and comparable sequences, which cannot be achieved when targeting different loci. This facilitates the use of haplotypic diversity information contained within metabarcoding datasets, for example, for phylogeography and finer analyses of prey–predator interactions.

show abstract

“…Water, soil, and even air samples have been discussed to be suitable for eDNA studies (Brennan et al, ; George et al, ; Taberlet, Coissac, Hajibabaei, et al, ). Similarly, gut contents and scats have been highlighted as useful in describing regional biodiversity and used in eDNA‐like surveys (Boyer et al, ; Siegenthaler et al, ; Taberlet, Coissac, Pompanon, Brochmann, & Willerslev, ). Boyer et al () first suggested this approach, considering that feces from generalist predators could be regarded as “biodiversity capsules,” used to infer on species occurrence, distribution, and abundance.…”

Section: Important New Research Avenues From Diet Studies Using Dna Mmentioning

confidence: 99%

“…In their study, these authors further suggested the potential value of such approach for detecting small and “cryptic” species in remote environments, and in their closing arguments, they suggest that the efficiency of such an approach should be empirically compared to traditional biodiversity surveys. The guidelines established by Boyer et al () differed according to the proposed study goals. For instance, the authors recommended the use of universal primers for species inventory and estimates of local species abundances, whereas more specific primers should be preferred for dietary and food web assessments (Boyer et al, ).…”

Section: Important New Research Avenues From Diet Studies Using Dna Mmentioning

confidence: 99%

“…The guidelines established by Boyer et al () differed according to the proposed study goals. For instance, the authors recommended the use of universal primers for species inventory and estimates of local species abundances, whereas more specific primers should be preferred for dietary and food web assessments (Boyer et al, ). Although this approach has still limited empirical application and has been mostly viewed as a promising tool (Berry et al, ), a similar methodology has been applied to determine whether fecal samples from the generalist Bryde's whale Balaenoptera edeni brydai could be used as proxies for zooplankton diversity across seasons (Carroll et al, ).…”

Section: Important New Research Avenues From Diet Studies Using Dna Mmentioning

confidence: 99%

See 1 more Smart Citation

DNA metabarcoding in diet studies: Unveiling ecological aspects in aquatic and terrestrial ecosystems

2019

View full text Add to dashboard Cite

Effective conservation of species and ecosystems requires the understanding of important ecological traits, such as dietary habits, food webs, and trophic niches. In diet studies, the visual identification of partially digested prey has been enhanced with the recent more powerful and accurate technique, DNA barcoding. Here, we summarize the contribution of this recent methodology to the investigation of both terrestrial and aquatic taxa diet, and compare the level of novelty uncovered through the use of this technique regarding species' ecology. From a total of 150 studies analyzed, focusing on more than 250 vertebrate wild species, seven domesticated taxa, and humans, we suggest that barcoding has led to more significant findings for aquatic taxa and ecosystems, where direct observations of feeding events and consequent trophic niche understanding are typically limited. Finally, we introduce the term dietary DNA (dDNA) to describe environmental approaches that use DNA extracted from gut, stomach, or fecal contents, aiming to assess both species dietary habits and describe local biodiversity. Particularly, we highlight the complementarity of environmental DNA (eDNA) and dDNA as a new tool for biodiversity assessments in remote areas, including most of the aquatic realm.

show abstract

Faeces of generalist predators as ‘biodiversity capsules’: A new tool for biodiversity assessment in remote and inaccessible habitats

Cited by 37 publications

References 67 publications

Pellets of proof: First glimpse of the dietary composition of adult odonates as revealed by metabarcoding of feces

Pellets of proof: First glimpse of the dietary composition of adult odonates as revealed by metabarcoding of feces

One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies

DNA metabarcoding in diet studies: Unveiling ecological aspects in aquatic and terrestrial ecosystems

Contact Info

Product

Resources

About