The possible role of geothermal areas, such as volcanoes, in fostering biodiversity in Antarctica has received considerable recent attention. Under a geothermal refugia hypothesis, diverse life could be supported near or at geothermal sites, and we should see decreasing diversity and/or patterns of nestedness moving away from ‘hotspots’. Although there is evidence that geothermal areas have played a role in the persistence of some terrestrial species through glacial periods in Antarctica, the spatial scales at which such refugia operate is not clear. We sampled sediment from a range of locations across volcanic Deception Island in the Maritime Antarctic and used eDNA metabarcoding approaches (targeting a region of the 28S marker) to assess patterns of diversity in relation to thermal gradients. We found that although colder sites harboured significantly greater taxonomic richness than warmer sites, phylogenetic diversity was lower at colder sites (i.e. taxa at colder sites tend to be more evolutionary close to each other). We infer that increased selective processes in low-temperature environments have reduced phylogenetic diversity, supporting a hypothesis of geothermal locations acting as refugia for diverse taxa, even on fine spatial scales, in cold-climate regions such as Antarctica.

Coastal marine environments are subject to a variety of anthropogenic pressures that can negatively impact habitats and the biodiversity they harbor. Conservation actions such as marine protected areas, marine reserves, and other effective area-based conservation measures, are pivotal tools for protecting coastal biodiversity. However, to be effective, conservation area networks must be planned through a systematic conservation planning (SCP) approach. Recently, such approaches have begun to orient their goals toward the conservation of different biodiversity facets and to integrate different types of data. In this review, we illustrate how genetic data and molecular techniques can bring useful knowledge for SCP approaches that are both more comprehensive (sampling the full range of biodiversity) and more adequate (ensuring the long-term persistence of biodiversity). With an emphasis on coastal organisms and habitats, we focus on phylogenetic analysis, the estimation of neutral and adaptive intraspecific genetic diversity at different spatial levels (alpha, beta, and gamma), the study of connectivity and dispersal, and the information obtainable from environmental DNA techniques. For each of these applications, we discuss the benefits of its integration into SCP for coastal systems, its strengths and weaknesses, and the aspects yet to be developed.

Environmental DNA is a powerful tool for monitoring biodiversity. Although environmental DNA surveys have successfully been implemented in various environments, protocol choice has been shown to affect results and inferences. Thus far, few method comparison studies for soil have been undertaken. Here, we optimized the workflow for soil metabarcoding through a comparative study encompassing variation in sampling strategy (individual and combined samples), DNA extraction (PowerSoil®, NucleoSpin® Soil, PowerSoil® + phosphate buffer and NucleoSpin® Soil + phosphate buffer) and library preparation (one-step and two-step quantitative polymerase chain reaction methods). Using a partial 18S rRNA marker, a total of 309 eukaryotic taxa across 21 phyla were identified from Antarctic soil from one site in the Larsemann Hills. Our optimized workflow was effective with no notable reduction in data quality for a considerable increase in time and cost efficiency. The NucleoSpin® Soil + phosphate buffer was the best-performing extraction method. Compared to similar studies in other regions, we obtained low taxonomic coverage, perhaps because of the paucity of Antarctic terrestrial organisms in genetic reference databases. Our findings provide useful methodological insights for maximizing efficiency in soil metabarcoding studies in Antarctica and other low-biomass environments.

Cercarial dermatitis (‘swimmer's itch’; SI), characterized by small itchy bumps caused by schistosome parasites of birds and mammals, is a common problem in Michigan. Research on avian schistosomes began nearly 100 years ago in Michigan inland lakes, yet scientists are still uncovering basic biological information including the identification of local snail and parasite species that cause SI. Previous research primarily focused on lakes in the northern half of Michigan's lower peninsula, although SI occurs throughout the state. We surveyed snails and snail-borne trematodes in lakes across Michigan's lower peninsula and used quantitative polymerase chain reaction analysis of filtered water samples to identify parasites to the species level, including a recently discovered parasite species that uses the snail Planorbella (Helisoma) trivolvis as its intermediate host. Most SI mitigation efforts have focused on a parasite species hosted by the snail Lymnaea catescopium ( = Stagnicola emarginata); however, lymnaeid snails and their associated schistosome species were largely restricted to northern lakes. In contrast, P. trivolvis and its associated parasite species were common in both northern and southern Michigan lakes. A third schistosome species associated with physid snails was also present at low levels in both northern and southern lakes. These results indicate that the recently discovered parasite species and its planorbid snail intermediate host may be more important drivers of Michigan SI than previously thought, possibly due to increased definitive host abundance in recent decades. These results have potentially important implications for SI mitigation and control efforts.

Anguillicoloides crassus is an invasive nematode parasite of the critically endangered European eel, Anguilla anguilla, and possibly one of the primary drivers of eel population collapse, impacting many features of eel physiology and life history. Early detection of the parasite is vital to limit the spread of A. crassus, to assess its potential impact on spawning biomass. However accurate diagnosis of infection could only be achieved via necropsy. To support eel fisheries management we developed a rapid, non-lethal, minimally invasive and in situ DNA-based method to infer the presence of the parasite in the swim bladder. Screening of 131 wild eels was undertaken between 2017 and 2019 in Ireland and UK to validate the procedure. DNA extractions and PCR were conducted using both a Qiagen Stool kit and in situ using Whatman qualitative filter paper No1 and a miniPCR DNA Discovery-System™. Primers were specifically designed to target the cytochrome oxidase mtDNA gene region and in situ extraction and amplification takes approximately 3 h for up to 16 individuals. Our in-situ diagnostic procedure demonstrated positive predictive values at 96% and negative predictive values at 87% by comparison to necropsy data. Our method could be a valuable tool in the hands of fisheries managers to enable infection control and help protect this iconic but critically endangered species.

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 few Antarctic studies to date to have applied metabarcoding in Antarctica have primarily focused on microorganisms. In this study, for the first time, we apply high-throughput sequencing of environmental DNA to investigate the diversity of Embryophyta (Viridiplantae) DNA present in soil samples from two contrasting locations on Deception Island. The first was a relatively undisturbed site within an Antarctic Specially Protected Area at Crater Lake, and the second was a heavily human-impacted site in Whalers Bay. In samples obtained at Crater Lake, 84% of DNA reads represented fungi, 14% represented Chlorophyta and 2% represented Streptophyta, while at Whalers Bay, 79% of reads represented fungi, 20% represented Chlorophyta and < 1% represented Streptophyta, with ~1% of reads being unassigned. Among the Embryophyta we found 16 plant operational taxonomic units from three Divisions, including one Marchantiophyta, eight Bryophyta and seven Magnoliophyta. Sequences of six taxa were detected at both sampling sites, eight only at Whalers Bay and two only at Crater Lake. All of the Magnoliophyta sequences (flowering plants) represent species that are exotic to Antarctica, with most being plausibly linked to human food sources originating from local national research operator and tourism facilities.

Environmental DNA (eDNA) surveying has potential to become a powerful tool for sustainable parasite control. As trematode parasites require an intermediate snail host that is often aquatic or amphibious to fulfil their lifecycle, water-based eDNA analyses can be used to screen habitats for the presence of snail hosts and identify trematode infection risk areas. The aim of this study was to identify climatic and environmental factors associated with the detection of Galba truncatula eDNA. Fourteen potential G. truncatula habitats on two farms were surveyed over a 9-month period, with eDNA detected using a filter capture, extraction and PCR protocol with data analysed using a generalized estimation equation. The probability of detecting G. truncatula eDNA increased in habitats where snails were visually detected, as temperature increased, and as water pH decreased (P < 0.05). Rainfall was positively associated with eDNA detection in watercourse habitats on farm A, but negatively associated with eDNA detection in watercourse habitats on farm B (P < 0.001), which may be explained by differences in watercourse gradient. This study is the first to identify factors associated with trematode intermediate snail host eDNA detection. These factors should be considered in standardized protocols to evaluate the results of future eDNA surveys.

DNA barcoding is now a common tool in parasitology and epidemiology, which require good methods for identification not only of parasites and pathogens but vectors and reservoirs. This special issue presents some advances and challenges in barcoding of microbes, parasites, and their vectors and reservoirs. DNA barcoding found new applications in disease ecology, conservation parasitology, environmental parasitology and in paleoparasitology. New technologies such as next-generation sequencing and matrix-assisted laser desorption–ionization time-of-flight have made it now possible to investigate large samples of specimens. By allowing the investigation of parasites at the interface between environment, biodiversity, animal and human health, barcoding and biobanking have important policy outcomes as well as ethics and legal implications. The special issue ‘Advances and challenges in the barcoding of parasites, vectors and reservoirs’ illustrates some recent advances and proposes new avenues for research in barcoding in parasitology.