Publication Database

The use of fly iDNA to monitor wildlife and study sylvatic anthrax ecology at human-wildlife interfaces (2023)

Art

Hochschulschrift

Autor

Mueena, Jahan (WE 7)

Quelle

Berlin: Mensch und Buch Verlag, 2023 — iv, 116 Seiten

Sprache

Englisch

Verweise

URL (Volltext): https://refubium.fu-berlin.de/handle/fub188/41922

Kontakt

Institut für Mikrobiologie und Tierseuchen

Robert-von-Ostertag-Str. 7-13
14163 Berlin
+49 30 838 51843 / 66949
mikrobiologie@vetmed.fu-berlin.de

Abstract / Zusammenfassung

Wildlife and disease monitoring plays a vital role in preparing and understanding our changing world; not only for gaining insights into ecological dynamics and pandemic preparedness, but also for formulating effective strategies to combat the global decline in biodiversity, particularly in resource poor tropical biodiversity hotspots. Invertebrate sources of eDNA, such as fly iDNA have demonstrated their value as a cost and resource efficient biomonitoring tool. They are not only effective in tracking wildlife diversity and identifying wild pathogens, but also hold promise for in-depth exploration of various aspects of wildlife and pathogen ecology. Considering the successful implementation of fly iDNA in previous studies for both of these aspects animal and pathogen detection in isolation, here I examined if fly iDNA can provide insights into disease ecology along different habitat types. I also explored the potential for flies to serve as a mechanical vector along these different habitats, in particular looking at primate associated flies, and their potential to move pathogens from the pristine forest to human use areas. Lastly, I explored potential ways to optimize existing fly iDNA analysis schemes, so that they can maximizing the sampling throughput and reduce costs, in an effort to enable broader-scale biodiversity assessments. For the first study, fly iDNA were molecularly analysed to investigate the geographic distribution of a sylvatic anthrax causing pathogen, Bacillus cereus biovar anthracis (Bcbva) and revealed significant variation in the detection of Bcbva across the habitats spanning from Taï rainforest to the nearby villages. In addition, whole genome sequencing of Bcbva from positive fly pools revealed considerable overlap with the genomic diversity of Bcbva described with decades of surveillance efforts. Metabarcoding of fly iDNA was also conducted to analyse the composition of both fly and mammal communities along this ecological gradient, with the goal of exploring potential associations with the detection of Bcbva. The highest detection of Bcbva was found in the area where the most diverse mammal community was detected, in the forest. No Bcbva was detected in the village habitat, where the least diverse mammal community was detected, suggesting a strong reliance of Bcbva on the rainforest ecosystem. However, the study also demonstrated the highest fly community at the edge of the forest, with flies from both anthropogenic and the forest areas found at this interface, which highlighted the potential risk of flies to act as disease transmitting vector between rainforest wildlife and the human habitants in surrounding villages. Therefore, in our second study, I conducted a mark-recapture experiment to study the movement patterns of flies associated with non-human primates in the vicinity of Kibale National Park, Uganda. Flies Marked within non-human primate groups were subsequently recaptured in areas used by humans, with 19 marked flies were captured with a recapture effort of 28,615 recapture effort flies. The application of metabarcoding on the flies collected within non-human primate groups unveiled the presence of DNA from various eukaryotic parasites associated with primates. In summary, these findings underscore the potential role of flies as potential vectors facilitating interactions between non-human primates, livestock, and humans in this ecologically diverse region. In the third and final study of this thesis, I explored the potential of bulk fly pooling based destructive and non-destructive extraction schemes. I did this using flies captured across eight different sites in five African countries representing three different habitats and subsequently compared the findings with a previous study by Gogarten et al. (2020), which used the same flies but extracted destructively in smaller pools. While both of the bulk fly pool based extraction methods resulted in a significant reduction of cost and resources, the bulk non-destructive extraction method provided similarly effective to the more labour intensive smaller pool extraction methods used previously. This suggest that in some cases, particularly where pooling does not lose valuable information, as would be the case for some disease ecology investigations, the non-destructive bulk pooling method may be the most effective strategy. In conclusion, the use of fly iDNA for biomonitoring represents a promising avenue for investigating disease ecology across various habitat types. Simultaneously, flies at human-wildlife interfaces may move between these habitats, thus highlighting their potential to serve as potential vectors for emerging infectious pathogens in the wild. And finally, it appears that the approach of bulk pooling fly bodies and subsequently employing a non-digestion buffer for DNA extraction has the potential to streamline the conventional fly extraction process, and has the potential to help bring these methods into more resource poor research laboratories. These innovations bring with them the potential to facilitate the widespread use of fly iDNA for terrestrial biomonitoring.