Bacterial assemblages of urban microbiomes mobilized by runoff waters match land use typologies and harbor core species involved in pollutant degradation and opportunistic human infections

Abstract

Cities are patchworks of urban catchments divided into functional units according to their commercial, residential and industrial activities, and socio-urbanistic patterns. The hypothesis of city surface microbiomes being structured by socio-urbanistic variables leading to an emergence of synurbic taxa was tested. According to the r/K microbial ecology theory, a gradient of well-adapted synurbic K-strategists and of opportunistic -r-strategists should occur over city surfaces. K-strategists would be core components while r-ones would be transiently detected. To resolve these patterns, sub-catchments (n = 21) of an area of high commercial and industrial activities were investigated over three time periods covering one year. The sub-catchments' land use patterns and associated human behaviors were converted into socio-urbanistic variables and groupings. Bacterial cells mobilized by runoffs per sub-catchment were recovered, and analyzed by classical approaches, microbial source tracking DNA assays and DNA meta-barcoding approaches. Relationships between these datasets, the runoff physico-chemical properties, and descriptors of the socio-urbanistic groupings were investigated. 16S rRNA meta-barcoding analyses showed evidence of the occurrence of K- and r-like strategists. Twenty-eight core genera were identified, and correlation networks revealed large bacterial modules organized around actinobacterial taxa involved in hydrocarbon degradation processes. Other bacterial networks were related to the occurrences of hygienic wastes, and involved bacteria originating from fecal contaminations. Several r-strategists like Sulfurospirillum were recorded and found associated to point source pollutions. The tpm-metabarcoding approach deciphered these r / K strategists at the species level among more than ten genera. Nine core K-like Pseudomomas species were identified. The P. aeruginosa human opportunistic pathogen and P. syringae phytopathogens were part of these K-strategists. Other tpm-harboring bacterial pathogens showed r-like opportunistic distribution patterns. Correlation network analyses indicated a strong incidence of hygienic wastes and hydrocarbon-pollutions on tpm-harboring bacteria. These analyses demonstrated the occurrence of core synurbic bacterial K-strategists over city surfaces.

Keywords: Core microbiome; DNA metabarcoding; Petrol engines; Runoff; Urban microbiology.