Abstract
BackgroundGastrointestinal parasitic nematodes can impact fecundity, development, behaviour, and survival in wild vertebrate populations. Conventional monitoring of gastrointestinal parasitic nematodes in wild populations involves morphological identification of eggs, larvae, and adults from faeces or intestinal samples. Adult worms are typically required for species-level identification, meaning intestinal material from dead animals is needed to characterize the nematode community with high taxonomic resolution. DNA metabarcoding of environmental samples is increasingly used for time- and cost-effective, high-throughput biodiversity monitoring of small-bodied organisms, including parasite communities. Here, we evaluate the potential of DNA metabarcoding of faeces and soil samples for non-invasive monitoring of gastrointestinal parasitic nematode communities in a wild ruminant population.MethodsFaeces and intestines were collected from a population of wild reindeer, and soil was collected both from areas showing signs of animal congregation, as well as areas with no signs of animal activity. Gastrointestinal parasitic nematode faunas were characterized using traditional morphological methods that involve flotation and sedimentation steps to concentrate nematode biomass, as well as using DNA metabarcoding. DNA metabarcoding was conducted on bulk samples, in addition to samples having undergone sedimentation and flotation treatments.ResultsDNA metabarcoding and morphological approaches were largely congruent, recovering similar nematode faunas from all samples. However, metabarcoding provided higher-resolution taxonomic data than morphological identification in both faeces and soil samples. Although concentration of nematode biomass by sedimentation or flotation prior to DNA metabarcoding reduced non-target amplification and increased the diversity of sequence variants recovered from each sample, the pretreatments did not improve species detection rates in soil and faeces samples.ConclusionsDNA metabarcoding of bulk faeces samples is a non-invasive, time- and cost-effective method for assessing parasitic nematode populations that provides data with comparable taxonomic resolution to morphological methods that depend on parasitological investigations of dead animals. The successful detection of parasitic gastrointestinal nematodes from soils demonstrates the utility of this approach for mapping distribution and occurrences of the free-living stages of gastrointestinal parasitic nematodes.Graphical abstract
Highlights
Gastrointestinal parasitic nematodes can impact fecundity, development, behaviour, and survival in wild vertebrate populations
EPG eggs per gram, OPG oocysts per gram, LPG larvae per gram faeces –: not detected or larvae due to time of sampling or a small number of egg- or larvae-producing adult females in the gastrointestinal system and lungs
As the sampled proximal duodena had different lengths, and in one case had been nearly completely scavenged by ravens prior to sampling, parasites were identified to species but not quantified
Summary
Gastrointestinal parasitic nematodes can impact fecundity, development, behaviour, and survival in wild vertebrate populations. Conventional monitoring of GINs in wild vertebrate populations at the species level typically requires morphological identification of larval and/or adult nematodes observed during post-mortem investigations of the gastrointestinal tract from individuals that have been hunted, culled, lethal sampled, or died of natural causes [5, 15, 16]. Metabarcoding approaches allow the simultaneous identification of a wide range of GIN species, irrespective of life stage, from bulk environmental and faecal samples in a more time- and cost-effective manner than morphological surveys, making it an attractive method for identifying and monitoring occurrence of actual species of GINs in wild vertebrate populations. Concentrating nematode biomass prior to DNA extraction as is done in morphological surveys could minimize the presence of non-target organisms in the sample, increasing the probability of amplifying and sequencing target organisms, which would effectively increase sampling effort and the probability of detecting rare species
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