Urban microbiomes and urban agriculture: What are the connections and why should we care?

Abstract

A large percentage (~50 %) of the global human population lives in urban systems. The transition from largely rural to urban lifestyles began gradually, but has accelerated. Given the magnitude of anthropogenic changes in the Earth system as a whole and concerns about resource availability and continued population growth, questions about the sustainability of urban systems have become a focal point for a variety of research and civic efforts, including programs promoting urban agriculture as a means to provide local food sources and to better manage critical nutrients such as nitrogen and phosphorus. The last decade or so has also witnessed a remarkable transformation in our understanding of the centrality of microbes for virtually all aspects of human life and wellbeing. However, this transformation has not yet been incorporated into a fuller understanding of the biology and ecology of urban life. Research on microbial assemblages (or microbiomes) in the built environment, particularly building interiors, has provided compelling examples of the importance of microbes, but these results provide at most an incomplete picture of microbial distribution and activity in urban systems. For example, though very little is known about microbial interactions with urban agriculture, the success of urban agriculture and its potential to contribute to urban sustainability will depend in part of incorporating new knowledge about soil and plant microbiomes to optimize production and to minimize some of the adverse effects of agriculture in traditional settings (e.g., greenhouse gas emission, nitrogen and phosphorus eutrophication). To that end, this review defines and provides examples of the microbiome concept and the significance of microbiomes in urban systems; it also identifies large knowledge gaps and unanswered questions that must be addressed to develop a robust and predictive understanding of urban biology and ecology.