Lurking in the water: testing eDNA metabarcoding as a tool for ecosystem-wide parasite detection.

In the light of global biodiversity change and emerging disease, there is an urgent need to establish efficient monitoring programmes of parasites in aquatic ecosystems. However, parasite identification is time-consuming, requires a high degree of taxonomic expertize and in general requires lethal sampling. The use of environmental DNA methodology to identify parasites has the potential to circumvent these limitations. This study evaluates the use of eDNA metabarcoding to detect the presence of all species of nematode and platyhelminth parasites in two New Zealand lakes. We developed two novel metabarcoding primer pairs targeting a region of cytochrome oxidase I gene (COI) specific to platyhelminths and nematodes. We successfully detected parasite DNA in both lakes. Platyhelminth DNA yield was in general greater than nematode DNA yield. This most likely results from the larger biomass of the former quantified using traditional methods, or the presence of free-swimming life stages in the life cycle of many platyhelminths. By using eDNA, we did not detect all expected parasite families revealed through traditional methods, likely due to a lack of sequencing data available from public databases such as GenBank. As such, genetic resources need to include full reference sequences if parasitology is to truly harness eDNA to characterize and monitor parasite biodiversity in natural systems.

The people vs science: can passively crowdsourced internet data shed light on host-parasite interactions?

Every internet search query made out of curiosity by anyone who observed something in nature, as well as every photo uploaded to the internet, constitutes a data point of potential use to scientists. Researchers have now begun to exploit the vast online data accumulated through passive crowdsourcing for studies in ecology and epidemiology. Here, we demonstrate the usefulness of iParasitology, i.e. the use of internet data for tests of parasitological hypotheses, using hairworms (phylum Nematomorpha) as examples. These large worms are easily noticeable by people in general, and thus likely to generate interest on the internet. First, we show that internet search queries (collated with Google Trends) and photos uploaded to the internet (specifically, to the iNaturalist platform) point to parts of North America with many sightings of hairworms by the public, but few to no records in the scientific literature. Second, we demonstrate that internet searches predict seasonal peaks in hairworm abundance that accurately match scientific data. Finally, photos uploaded to the internet by non-scientists can provide reliable data on the host taxa that hairworms most frequently parasitize, and also identify hosts that appear to have been neglected by scientific studies. Our findings suggest that for any parasite group likely to be noticeable by non-scientists, information accumulating through internet search activity, photo uploads, social media or any other format available online, represents a valuable source of data that can complement traditional scientific data sources in parasitology.

Synchronised monitoring of plant and insect diversity: a case study using automated Malaise traps and DNA-based methods.

The occurrence and distribution of insects and their possible associations with plant species are largely unknown in Germany and baseline data to monitor future trends are urgently needed. Using newly-designed automated Malaise trap multi-samplers, the occurrence of insect species and their potential associations with plants was monitored synchronously at two contrasting field sites in Germany: an urban botanical garden and a forest research station. Taxa were identified by metabarcoding of the insects and the plant traces present in the preservative ethanol of the Malaise trap samples. For comparison, a botanical survey was conducted in the vicinity of the traps. Across both sites, we identified a total of 1290 exact sequence variants (ESVs) assigned to Insecta, of which 205 are known to be pollinators. In the botanical garden, we detected the occurrence of 128 plant taxa, of which 41 also had one of their known insect pollinator species detected. Insect species richness was highest in May, mainly attributed to an increase in Diptera. These results present a case study of the applicability of automated sampling and DNA-based methods to monitor the timings of flowering and corresponding activity of plant-visiting insects.

Antarctic cushion star Odontaster validus larval performance is negatively impacted by long-term parental acclimation to elevated temperature.

Cross-generational responses, when the parents' environment influences offspring performance, may contribute to species resilience to climate change in rapidly warming regions such as coastal Antarctica. Adult Antarctic sea stars Odontaster validus were conditioned in the laboratory to two temperature treatments (ambient, 0 °C and warming, +3 °C) for two years, and their gametes were used to generate larval offspring. The response of their larvae to five temperatures (0 °C, 1 °C, 2 °C, 3 °C, and 4 °C) was examined over 145 days. Adults conditioned to 3 °C produced significantly smaller eggs compared with those from 0 °C conditioned adults. After fertilisation, larval size, development, and survival were comparable in offspring from 0 °C and 3 °C conditioned parents. After 34 days of development, while survival was greater in offspring from 3 °C adults, offspring size was reduced during the transition from the gastrula to the bipinnaria larva. After ~50 days, survival in larvae from 3 °C conditioned adults decreased, and larval development was arrested at the bipinnaria stage (the exception being for larva reared at 4 °C which reached the early-brachiolaria). By the end of the experiment (145 days), offspring of the 0 °C conditioned adults had greater survival (17.6-34.3 %) and growth (final size = 697 to 773 µm) and had reached the early-brachiolaria larval stage, compared to those from the 3 °C conditioned adults (survival 7.0-19.3 %; growth final size = 380 to 624 µm) with early-brachiolaria larval stages mostly absent. Long-term acclimation of adults in elevated temperatures projected for the end of the century did not result in positive carryover outcomes for offspring, and did not lead to offspring being better suited to elevated temperatures. While O. validus adults may survive exposure to projected warming and produce viable gametes, their larval offspring may have lower developmental success. The downstream effects of poor recruitment of a key species such as O. validus would have important outcomes for coastal Antarctic ecosystems.

iParasitology: Mining the Internet to Test Parasitological Hypotheses.

Digital data (internet queries, page views, social media posts, images) are accumulating online at increasing rates. Tools for compiling these data and extracting their metadata are now readily available. We highlight the possibilities and limitations of internet data to reveal patterns in host-parasite interactions and encourage parasitologists to embrace iParasitology.

The complete mitochondrial genome of the deep-sea sponge Poecillastra laminaris (Astrophorida, Vulcanellidae).

The complete mitochondrial genome of a New Zealand specimen of the deep-sea sponge Poecillastra laminaris (Sollas, 1886) (Astrophorida, Vulcanellidae), from the Colville Ridge, New Zealand, was sequenced using the 454 Life Science pyrosequencing system. To identify homologous mitochondrial sequences, the 454 reads were mapped to the complete mitochondrial genome sequence of Geodia neptuni (GeneBank No. NC_006990). The P. laminaris genome is 18,413 bp in length and includes 14 protein-coding genes, 24 transfer RNA genes and 2 ribosomal RNA genes. Gene order resembled that of other demosponges. The base composition of the genome is A (29.1%), T (35.2%), C (14.0%) and G (21.7%). This is the second published mitogenome for a sponge of the order Astrophorida and will be useful in future phylogenetic analysis of deep-sea sponges.

The complete mitochondrial genome of the deep-sea stony coral Solenosmilia variabilis (Scleractinia, Caryophylliidae) and its inter-individual variation.

Three individual-specific DNA libraries of the deep-sea scleractinian coral Solenosmilia variabilis (Duncan, 1873) were constructed to obtain complete mitochondrial genomes using the 454 Life Science pyrosequencing system. Two mitogenomes were successfully assembled: both were 15,968 bp in length, with base composition of A (24.2%), T (41.1%), C (13.7%) and G (21.0%). The genome contains 13 protein-coding genes, 2 ribosomal RNA genes, 2 transfer RNA genes and a D-loop region. The two mitogenomes were almost identical, with only 5 nucleotide differences (0.03%), including a synonymous substitution within the nad1, nad2 and nad4L genes, and two transversions in the D-loop region. This inter-individual variation indicates that these genes and/or region are potential candidates as molecular markers for population genetic research. The mitogenome of S. variabilis will be useful for future phylogenetic and phylogeographic studies of deep-sea corals.