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.
Results/Conclusions
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.