Framework for Urban Soil Microbial Ecology
Many ecosystem processes depend on soil microbiomes that contain a diverse and abundant array of bacteria, fungi, and archaea (Reeseet al. , 2016; Ramirez et al. , 2014; Wang et al. , 2018). Soil microbial communities drive the cycling of key nutrients including carbon, nitrogen, and phosphorus within ecosystems (Aislabie & Deslippe, 2013). Soil microbes also support primary producer growth and diversity, promote soil health by removing heavy metals and other contaminants, and regulate soil carbon storage. Microbiologists and microbial ecologists have therefore made an effort to understand how the environment drives microbial community activity in order to predict the direction and magnitude of microbial consequences for ecosystem function.
Our proposed framework (Figure 1) draws on previously published ideas but fills a knowledge gap by emphasizing the intersection between humans and microbial function in urban ecosystems. Humans create and intensively manage urban environments and are thus a key component of our framework. Human society, including economies, cultures/values, policies, technologies, and resources determine how the urban environment is structured and how it functions (Alberti, 1999; Byrne, 2007). However, these factors are difficult to capture quantitatively and are generally outside the wheelhouse of microbial ecologists. To address this challenge, we draw from Pickett and Cadenasso’s (2009) analysis of altered resources, disturbance, and heterogeneity as the key mechanisms through which humans shape urban soils (Arrow A). Altered resources, disturbance, and heterogeneity are factors ecologists are already well-equipped to study and can be used to understand how complex societal dynamics ultimately change environmental drivers. These changes, particularly in soils, have consequences for microbial community composition and function (Arrow B), which will in turn cause shifts in environmental resource pools and fluxes (Arrow C) (Hallet al. , 2018). Finally, the environmental changes driven by microbial activity feed back to human society through the creation of environmental services or harms (Arrow D). Humans may adjust policy and behavior accordingly, which starts the cycle over again.
Our framework is useful because it synthesizes existing knowledge on urban ecology, microbial ecology, and urban soil science. Moreover, we elaborate on how disturbance, altered resources, and heterogeneity (Arrow A) influence urban ecosystem functioning through impacts on microbial communities (Arrows B and C). We then develop and discuss key questions to address knowledge gaps in our framework that limit fundamental understanding of urban microbial ecology and microbial ecology more broadly. Finally, we offer suggestions to facilitate collaboration needed among ecologists, biogeochemists, and social scientists to understand how the human-environment-microbe feedback loop plays out in cities around the world. Such collaboration will improve our decision-making and management strategies in urban spaces with the ultimate goals of sustainability and environmental justice.