Assessing the microbial ecology of sewer biofilms for pathogens, antibiotic resistance, and SARS-COV-2 and drinking water biofilters for manganese removal
Creators: name: Morales Medina, William
Publisher: name: No Publisher Supplied
Year: 2021

description: Microbes play a major role in engineered water and wastewater systems. Sewer systems including their biofilms can harbor human pathogens and antibiotic resistant bacteria that can threaten public heath during sewer overflow events. Sewers can also be used to track community infections during outbreaks or pandemics. In contrast to sewer biofilm harboring pathogens, drinking water biofilters use the metabolism of microbes to remove contaminants from drinking water. The research presented here focused on studying the microbiome of sewer biofilms and the potential of this matrix to accumulate pathogens, corrosion causing prokaryotes, bacteria carrying antibiotic resistance genes (ARG), and SARS-CoV-2 viral particles. To do this, field and simulated biofilm samples were collected and analyzed through 16S rRNA gene sequencing to study the microbial community and qPCR targeting selected ARGs. In the simulated biofilm samples, the microbiome, ARG profile and 16S rRNA gene abundance was analyzed as a factor of pipe material (PVC vs concrete), and source of microbes and operation (sewer sediment and batch feed vs wastewater and continuous feed). The same factors were then evaluated before and after a standardized bleach disinfection treatment. Results showed some ARGs concentrations near the number of 16S rRNA gene copies (~108 gene copies/cm2). Taxa containing potential human pathogens and corrosion causing prokaryotes accumulated in the biofilms. Pipe material did not affect ARG accumulation nor the microbial community structure. Field sewer biofilm samples showed no differences between the community and ARG profile between combined and separate sanitary sewers. Viability PCR (propidium monoazide PCR) allowed for the detection of viable cells in the simulated system biofilms after the disinfection treatment. Dislodging of cells from the biofilm appeared to be the main mechanism of action for PVC surfaces while cell dislodging, and membrane disruption were similar for concrete surfaces. The same simulated sewer system was used to evaluate the potential for SARS-CoV-2 genome to accumulate in sewer biofilms. Results showed that after 28 days, up to ~700 genome copies/cm2 were detected in the biofilm, suggesting that biofilm may retard flux and potentially serve as source of SARS-CoV-2 to the wastewater, thus potentially affecting wastewater-based epidemiology data and community infection tracking. In a separate field study, the physiological state of the sewer sediment and wastewater microbiome and the occurrence of ARGs transcripts was evaluated using RNA- based or 16S rRNA sequencing and reverse transcription qPCR. Field sewer sediment and wastewater samples were collected and compared as a factor of sewer type. Results showed that actively transcribed ARGs were more common in sediment samples than in wastewater. The microbiome analysis showed the presence of metabolically active taxa containing potential human pathogens and corrosion causing prokaryotes in both matrices. No differences in the active microbiome were detected as a factor of sewer type (i.e., combined vs separate sanitary sewers during baseflow). The results highlighted the hazard posed by sewer overflows, due to the presence of active pathogens. The use of biofilters for drinking water treatment has been increasing in recent years in the US. Biofilters are effective at removing aesthetic contaminants such as manganese (Mn) from drinking water while also reducing the concentration of organic matter, which is the precursor of carcinogenic disinfection by-products. However, an acclimation period of bacterial adaptation is needed to achieve optimal Mn removal. As part of this research, the abiotic factors affecting the microbial community was evaluated during the acclimation period in full scale biofilters. To do this, monthly biofilter influent and media samples were collected to analyze cellular abundance in the biofilm and study the changes in the microbial community throughout time. Filter core samples were also collected to study the effect of backwashing on the microbial community. Results showed that acclimation for Mn removal was achieved after nine months despite the fact that bacterial taxa involved in Mn oxidation were present in all the biofilter media samples all along. Water temperature changes due to season, along with the filter start-up appeared to affect the microbial community structure. Biofilter backwash affected the bacterial diversity causing homogenization of cells throughout the filter core. These results can provide insight to the temporal changes in the microbial community that take place during biofilter acclimation for Mn removal.