May 15, 2019

Urban Microbiome

Interest in the microbial element of ecosystems has recently led to significant efforts to understand how the microbial components of the human gut influence health outcomes for individuals. This work is now known as being focused on the Human Micriobiome. The growing interest in the linkages between human well-being and microbial systems has also led to the beginning of investigations into the character of the Urban Microbiome; all the microbial elements of urbanized systems, be they in soil, air, water, or on surfaces.

The first step in our efforts to characterize the Urban Microbiome in Seattle is an investigation of the bacterial microbiome of a subset of Seattle parks. Building on previous work conducted in New York’s Central Park, we are attempting to determine if the community of microscopic soil biota in Seattle’s urban parks differs from global biodiversity in a meaningful manner. While of course we would not expect to find evidence of organisms that specialize at the extremes of the pH or temperature scales, or those that form relationships with organisms that are not present in Seattle, urban conditions may shape soil communities. Through this work we are also attempting to lay the groundwork for investigating if/how the microbiome of Seattle’s urban parks vary from non-urban parks(and other areas) around the greater Puget Sound, and contribute to characterizing the Urban Microbiome generally.

Due to the fact that no park in Seattle is truly equivalent to Central Park, we have sampled from a set of smaller, varied parks with different uses, cover types, and surrounding characteristics. These parks are Cowen Park, the I-5 Colonnade, and Jefferson Park. This also allows us to extend the work somewhat through finding parks in varied urban contexts, as well as across an age and usage gradient, though our statistical power in attributing causative relationships between urban context, park characteristics, and community structure and diversity is likely to be moderate.

The collection of soil samples from the parks has been completed, and work to characterize them physically and from a genomics perspective is on-going. Soil characteristics like pH, carbon and nitrogen content, and (in a sub-sample) metal content will be determined. Sequencing work will be focused on bacteria, on ribosomal RNA in regions that allow for identification of bacterial organisms into ‘phylotypes’ and the construction of rough community structure. Once this work is complete, we will assess how the relative abundances and diversity of soil bacteria compare to the global soil community, Central Park in NYC, between the selected Seattle Parks, and possibly how they vary with internal structure of the parks themselves.