Plants and fungal diversity analysed by DNA Metabarcoding on canadian pollen sample of honeybees (Apis Mellifera L.) along an urban-rural gradient and across seasons

Abstract

The expansion of urbanised areas plays a major role in the sharp loss of biodiversity and threatens the balance of ecosystems and the production of their services to human society. Over the years, cities have become the place where vital issues are at stake for the maintenance of nature in a hostile environment. It is therefore essential to rethink the management of these environments in order to make them more attractive both for city dwellers and for the fauna and flora. These new green spaces will provide pollinators with floral resources and a place to find refuge in cities. This thesis is part of a continuum of studies carried out in recent years, the primary aim of which is to highlight the influence that the urban-rural gradient and seasonality (variation in months) may have on the richness and composition of plant species. A complementary study aimed at revealing the role that pollinators, and more specifically honeybees Apis mellifera L., 1758, play in the vectoring of microorganisms such as fungi during foraging activities. To this end, 44 pollen samples were collected from 13 sites in and around the city of Toronto between May and September 2020. These will be subjected to DNA analysis by metabarcoding, using the ITS marker gene, in order to perform taxonomic classification and biodiversity analyses. This classification was carried out using the naïve-bayes workbook and various reference databases and will make it possible to determine the most suitable database for the following analyses. The taxonomic results allowed the identification of plants and fungi and their characteristics (vegetation structure - herbaceous or woody and status - exotic or native) which were linked to the 2 spatial and temporal factors. Diversity α, or species richness was measured in 3 ways, the number of species per sample, the Shannon index and the Simpson index. It was then evaluated by applying a generalized linear model (GLM). Diversity β, or species composition was measured by the Jaccard index to calculate the Jaccard distance matrix for constrained ordination (NMDS) followed by multivariate analysis of variance (PERMANOVA) and a post-hoc test to pairwise compare compositional dissimilarities. Species richness and composition are strongly influenced by season and month, whereas the urban-rural gradient has little influence on plants. However, fungi are slightly more dependent on this gradient. The plant and fungus species identified in the samples have characteristics that can have both harmful and beneficial impacts on their environment. This master thesis aims to provide decision support for future (re)development of green spaces or greening of streets and buildings in urban and peri-urban environments. It will also shed light on the role of honeybees in the spread of micro-organisms, such as fungi, and its consequences on flowers, pollinator colonies and humans.