PS 29-175 - Unlocking the potential functions of urban soil microbial communities

Tuesday, August 8, 2017
Exhibit Hall, Oregon Convention Center
Dietrich Epp Schmidt1, Richard V. Pouyat2, David Johannes Kotze3, Katalin Szlavecz4, Miklos Dombos5, Heikki Setälä3, Ian D. Yesilonis6, Sarel Cilliers7, Elisabeth Hornung8 and Stephanie A. Yarwood9, (1)Environmental Science and Technology, University of Maryland, College Park, MD, (2)USDA Forest Service, Washington, DC, (3)Department of Environmental Sciences, University of Helsinki, Lahti, Finland, (4)Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD, (5)Institute for Soil Sciences and Agricultural Chemistry, Hungarian Academy of Sciences, Budapest, Hungary, (6)USDA Forest Service, Baltimore, MD, (7)School of Environmental Sciences and Development, North-West University - Potchefstroom Campus, Potchefstroom, South Africa, (8)Department of Ecology, Szent István University, Budapest, Hungary, (9)Department of Environmental Science and Technology, University of Maryland, College Park, MD

The Global Urban Soil Ecology Education Network (GLUSEEN) is a diffuse network of scientists using a coordinated methodology to answer basic questions about urban soil ecology. We have recently documented convergence of archaeal and fungal communities due to urban land-uses, and while the bacterial community did not converge, it was impacted by land-use. In an effort to understand the functional constraints, and to answer whether there was a convergence of functional potential under urban land-use, we conducted shotgun sequencing on the same samples, using the same DNA extract, to explore the functional profile of soil microbial communities. We explored four land-use categories that were distributed across a spectrum of management and disturbance intensities; reference (low disturbance and management outside cities); remnant (within cities, low disturbance and management); turf (high management, low disturbance within cities); and ruderal (low management, high disturbance within cities). We used Illumina’s tagmentation methodology to create the libraries, and Illumina Hiseq sequencing to generate ~360 million reads (~4 million reads per sample), for 92 samples, taken from five globally distributed cities (Baltimore, USA; Helsinki and Lahti, Finland; Budapest, Hungary; and Potchefstroom, South Africa). We used mg-RAST to annotate the sequences, generating functional gene profiles. We conducted Q-PCR to target genes that were not captured by metagenomic sequencing.


Our preliminary results suggest that we are unable to detect convergence of functional gene profiles; however we noted a number of patterns associated with both land-use and geography. For example, there was a significantly greater proportion of mercury and arsenic resistance genes under turf and ruderal land-use than in reference sites (both P<0.001). There were also some interesting patterns related to disease; a significantly higher proportion of Diphtheria pathogenicity islands in Potchefstroom turf sites (P=0.005), and significantly greater proportions of Staphylococcal pathogenicity islands in Baltimore turf sites (P=0.008); Listeria pathogenicity islands were a significant indicator of Budapest (P<0.001), and Vibrio was associated with Helsinki, Lahti and Budapest (P<0.001), though neither Listeria nor Vibrio was significantly associated with any particular land-use. We found significantly higher gene abundances of ammonia monooxygenase subunit A in turf and ruderal sites (P<0.001). Our preliminary data suggest that soil bacteria are responding to specific environmental parameters, some of which may vary at large geographic scales, and others may be impacted by urban land-use, without causing a convergence of the functional gene profile.