A framework for soil microbial ecology in urban ecosystems

Abstract

Nearly all ecosystems host diverse microbiomes that support vital ecosystem processes. At the same time, these ecosystems and their microbiomes are increasingly altered by human activities, particularly in highly managed urban environments. While microbial ecologists are beginning to understand the drivers of microbial assembly and the link between community structure and function in many ecosystems, few of these advances have been applied to urban ecosystems. In this synthesis, we review research on the urban soil microbiome and develop a framework to integrate soil microbial communities with urban ecosystem function. We identify disturbance, altered resources, and heterogeneity as key drivers through which human activities including urban development affect soils and their resident microorganisms. Steep environmental gradients in many urban systems present a unique opportunity to address fundamental questions in microbial ecology, such as how microbes respond to stress and how biogeochemical rates relate to microbial diversity and composition. Soil microbiomes in cities also provide ecosystem services and harms, making it crucial to understand how human activity drives those functions and the consequences for environmental and human health. We argue that much-needed integration across disturbance ecology, urban ecology, and microbial ecology will help generate practical and equitable strategies for managing ecosystem benefits in cities where most humans now live.

Urban forest soils harbour distinct and more diverse communities of bacteria and fungi compared to less disturbed forest soils

“…Future experimental studies are needed to establish directionality of the intriguing association between soil pH and the proximity to the built environment and detect the underlying mechanisms to the changes observed in bacterial and fungal communities in urban areas. One potential explanation for this interaction could be that high soil alkalinity is an inherent part of a typical built environment (Pouyat et al, 2015) due to rainwater passage through concrete materials such as pipes and street gutters (Davies et al, 2010; Nugent & Allison, 2022). Although no causal inferences could be made with the available data, our study raises important questions in relation to any attempt to implement the “Microbiome Rewilding Hypothesis,” which postulates that degradation of microbial communities in cities can simply be counteracted by restoration and rewilding of urban green spaces (Mills et al, 2017).…”

Harnessing soil biodiversity to promote human health in cities

“…Human-caused disturbance, resource changes, and loss of environmental heterogeneity in urban ecosystems are known to affect soil biodiversity, and cause the differences observed between urban and natural soil systems 19,31 . For example, urban microbial biodiversity is repeatedly being reported to become homogenized across cities 25,32 .…”

Developing systems theory in soil agroecology: Incorporating heterogeneity and dynamic instability

“…Some ideas of how social processes affect nutrient cycling have emerged as biogeo-socio-chemistry especially for urban settings (Pataki et al, 2011;Kaushal et al, 2014), and others may help address additional soil ecological dimensions of multi-functionality (Creamer et al, 2022) beyond nutrients like spatial patterns of faunal diversity and soil food web network structures. Recent studies of urban ecology already point to interesting patterns that challenge deficit narratives of societal relationships with local soils and agriculture (Bonilla-Bedoya et al, 2022;Nugent and Allison, 2022;Pindral et al, 2022;Zhang et al, 2022). Novel insights on soil socio-ecological dynamics may help guide how to tailor sustainable development initiatives by individual countries to achieve international soil governance initiatives (Farnese, 2022;García et al, 2022) like through the UN FAO Global Soil Partnership, Global Soil Biodiversity Initiative (Wall et al, 2015), and other working groups generally addressing UN sustainable development goals of combating soil and habitat degradation to enhance ecosystem services via dynamic key soil ecological indicators (Pradhan et al, 2017;Bennich et al, 2020).…”