The biogeography of urban soil microbes
Urban land use is increasing faster than any other land use type globally and the World Health Organization estimates that 54% of the global population now lives within cities. Although there has been increased interest in urban ecology over the last decade, few studies have comprehensively examined urban soils and fewer still have examined microbial diversity. As part of the Global Urban Ecology and Education Network (GLUSEEN), we sampled soils from five cities: Baltimore, USA; Helsinki and Lahti, Finland; Budapest, Hungary; Potchefstroom, South Africa. Soil DNA was extracted and the genes for bacterial 16S rRNA and fungal ITS were quantified to determine fungal:bacterial ratios. The microbial community composition was determined using Illumina MiSeq. We hypothesized that treatments within the city would differ but that each city would have a unique biogeographical composition.
Q-PCR data revealed a general trend of lower 16S and ITS copy numbers in the more urbanized soil compared to those soils just outside of each city. There was however no consistent difference between the five cities. Illumina sequencing resulted in ~2 million high quality reads of the 16S with an average of 120,000 sequences per sample. Approximately 270,000 OTUs were characterized at the species level. Preliminary non-metric multidimensional scaling ordinations revealed that composition did differ between the five cities. Helsinki and Lahti were closer in composition, confirming a biogeographical pattern in urban soil bacteria.