Understanding disease ecology is vital in preventing future outbreaks of established infections and to predict the emergence of new pathogens. In recent decades there have been a number of high profile infectious diseases which have swept across countries and in some cases the world. Many of these begin as generalist emerging infections; such microbes are difficult to study in the wild due to their inherently ambiguous life histories and complex associations with numerous hosts and the environment. In this PhD a number of techniques are used to pinpoint and further understand the life history of one such pathogen Mycobacterium ulcerans, the causative agent of Buruli ulcer, in the hope that this data can be used to predict and prevent future outbreaks and can be applied to other emerging infections. The results of this study include the first identification of the pathogen in the environment for a whole new continent, South America. Further to this it has led to the discovery of the likely ecological niche of the bacilli by linking its presence to specific functional groups of organisms. In turn the occurrences of these groups have been related to anthropogenic conditions such as deforestation and human mediated land use. Finally complex links between climatic fluctuations and outbreaks of the disease in Southern America and Cameroon, central Africa help complete our understanding of this mysterious disease.