Project description:Camera traps are valuable sampling tools commonly used to inventory and monitor wildlife communities but are challenged to reliably sample small animals. We introduce a novel active camera trap system enabling the reliable and efficient use of wildlife cameras for sampling small animals, particularly reptiles, amphibians, small mammals and large invertebrates. It surpasses the detection ability of commonly used passive infrared (PIR) cameras for this application and eliminates problems such as high rates of false triggers and high variability in detection rates among cameras and study locations. Our system, which employs a HALT trigger, is capable of coupling to digital PIR cameras and is designed for detecting small animals traversing small tunnels, narrow trails, small clearings and along walls or drift fencing.
Project description:Environmental DNA (eDNA) metabarcoding is a promising tool for monitoring marine biodiversity, but remains underutilised in Africa. In this study, we evaluated the ability of aquatic eDNA metabarcoding as a tool for detecting biodiversity associated with a South African kelp forest, an ecosystem that harbours high diversity of species, many of which are endemic, but are also sensitive to changing environmental conditions and anthropogenic pressures. Using fine-scale spatial (1 m and 8 m) and temporal (every four hours for 24 h) sampling of aquatic environmental DNA and targeting two gene regions (mtDNA COI and 12S rRNA), metabarcoding detected 880 OTUs representing 75 families in the broader metazoan community with 44 OTUs representing 24 fish families. We show extensive variability in the eDNA signal across space and time and did not recover significant spatio-temporal structure in OTU richness and community assemblages. Metabarcoding detected a broad range of taxonomic groups, including arthropods, ascidians, cnidarians, echinoderms, ctenophores, molluscs, polychaetes, ichthyofauna and sponges, as well as Placozoa, previously not reported from South Africa. Fewer than 3% of OTUs could be identified to species level using available databases (COI = 19 OTUs, 12S = 11 OTUs). Our study emphasizes that kelp-forest associated biodiversity in South Africa is understudied, but that with careful consideration for sampling design in combination with increased barcoding efforts and the construction of regional databases, eDNA metabarcoding will become a powerful biomonitoring tool of kelp-forest associated biodiversity.
Project description:Environmental DNA is increasingly being used for assessing the presence and relative abundance of fish in freshwater, but existing protocols typically rely on filtering large volumes of water which is not always practical. We compared the effects of water volume, filtration type and eDNA extraction procedures in the detection of fish in three freshwater bodies (pond, lake and river) using a short fragment of the 12s rRNA mtDNA gene. Quantification of eDNA capture efficiency after DNA extraction, as well as amplification efficiency, were evaluated by conventional PCR and quantitative PCR. No significant differences on eDNA capture yield were found among freshwater bodies, but increasing water volume had a positive effect on eDNA capture and amplification efficiency. Although highest eDNA capture rates were obtained using 2 L of filtered water, 100 mL syringe filtration in combination with ethanol- sodium acetate precipitation proved to be more practical and increased quantitative PCR amplification efficiency by 6.4%. Our results indicate that such method may be optimal to detect fish species effectively across both lotic and lentic freshwater environments.
Project description:Subterranean ecosystems are understudied and challenging to conventionally survey given the inaccessibility of underground voids and networks. In this study, we conducted a eukaryotic environmental DNA (eDNA) metabarcoding survey across the karst landscape of Christmas Island, (Indian Ocean, Australia) to evaluate the utility of this non-invasive technique to detect subterranean aquatic 'stygofauna' assemblages. Three metabarcoding assays targeting the mitochondrial 16S rRNA and nuclear 18S genes were applied to 159 water and sediment samples collected from 23 caves and springs across the island. Taken together, our assays detected a wide diversity of chordates, cnidarians, porifera, arthropods, molluscs, annelids and bryozoans from 71 families across 60 orders. We report a high level of variation between cave and spring subterranean community compositions which are significantly influenced by varying levels of salinity. Additionally, we show that dissolved oxygen and longitudinal gradients significantly affect biotic assemblages within cave communities. Lastly, we combined eDNA-derived community composition and environmental (water quality) data to predict potential underground interconnectivity across Christmas Island. We identified three cave and spring groups that showed a high degree of biotic and abiotic similarity indicating likely local connectivity. This study demonstrates the applicability of eDNA metabarcoding to detect subterranean eukaryotic communities and explore underground interconnectivity.