Cities and their effects on free-living and host-associated microbes

Microbes are essential for all life on Earth and can be found in the environment or in association with host organisms, where they perform essential tasks either needed for the health of ecosystems or their hosts. Humans impact almost every habitat on our planet through various processes such as loss and degradation of habitat including urban development, pollution and climate change. As a result, microbial communities (also referred to as the microbiota, including bacteria and fungi) are expected to respond to these selective pressures by adjusting to a changing environment. In this way, human alterations of the natural landscape have the power to impact diverse microbiota (both free-living and host-associated), that in turn may affect the delivery of the services they provide to ecosystems and their hosts. Using an innovative combination of extensive cross-sectional surveys, longitudinal field experiments, DNA metabarcoding techniques and stable isotope analyses, my doctoral thesis focuses on the impacts of human activities on free-living and host-associated microbiota, with the aim to quantify the specific variation in bacterial and fungal (1) forest soil and (2) rodent (the bank vole) gut microbial communities in the context of urbanisation, and (3) the level of resistance (i.e., mechanism by which microbial communities do not change after habitat alteration) and plasticity (i.e., mechanism by which microbial communities change to match the novel environment after habitat alteration) displayed by the rodent bacterial gut microbiota in response to a change in the environment (host transfer between urban and rural forests). I found both (1) urban soil microbiota and (2) urban rodent gut microbiota to be distinct from those occurring in forests that are less impacted by urbanisation. Notably, soil pH and a dietary switch were identified as important factors in shaping the soil and bank vole gut microbiota, respectively. Additionally, I found that (3) both past (resistance) and present (plasticity) habitats influence the gut microbiota composition in a wild rodent. This thesis summarises the effects of the urban environment on microbial communities in two different systems and hereby demonstrates the far-reaching effects of urbanisation on microbial life forms.