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.