Soil microbial community composition and tolerance to contaminants in an urban brownfield site

Abstract

Brownfields are unused sites that likely contain hazardous substances due to previous commercial or industrial use. These sites are a priority for remediation and redevelopment because of the risk to humans, flora, and fauna. Bioremediation of brownfield sites can be facilitated by in situ microbial communities, but little research exists that characterizes microbial communities at these sites or understands which microbial taxa may play a role in successful bioremediation at Brownfields. We sequence three gene markers (16S ribosomal RNA, 18S ribosomal RNA and Fungal Internal Transcribed Spacer) in 36 soil samples collected at five depths from a defunct urban rail yard in Los Angeles to: (1) profile the composition of the soil microbiome across depths; (2) determine the extent to which hazardous chemicals predict microbiome variation; and (3) identify microbial taxonomic groups that may metabolize these contaminants. Detected contaminants in the samples include heavy metals, petroleum hydrocarbons, and polycyclic aromatic hydrocarbons. Bacterial, eukaryotic, and fungal communities all varied with depth and with concentrations of arsenic, chromium, cobalt, and lead. 18S rRNA microbiome richness was positively correlated with cobalt and lead concentrations. Furthermore, bacterial Paenibacillus and Iamia, eukaryotic Actinochloris, and fungal Alternaria were enriched in contaminated soils compared to uncontaminated soils and were identified as taxa of interest for future bioremediation trials. Based on our results, we recommend the use of test plots that combine in situ native microorganisms and plant-associated mycorrhizae to determine bioremediation potential. We also recommend incorporating DNA-based microbial community profiling in brownfield site assessment and cleanup monitoring.