Characterization of bacterial communities in wastewater with enhanced taxonomic resolution by full-length 16S rRNA sequencing

Abstract

Wastewater treatment is crucial to environmental hygiene in urban environments. However, wastewater treatment plants (WWTPs) collect chemicals, organic matter, and microorganisms including pathogens and multi-resistant bacteria from various sources which may be potentially released into the environment via WWTP effluent. To better understand microbial dynamics in WWTPs, we characterized and compared the bacterial community of the inflow and effluent of a WWTP in Berlin, Germany using full-length 16S rRNA gene sequences, which allowed for species level determination in many cases and generally resolved bacterial taxa. Significantly distinct bacterial communities were identified in the wastewater inflow and effluent samples. Dominant operational taxonomic units (OTUs) varied both temporally and spatially. Disease associated bacterial groups were efficiently reduced in their relative abundance from the effluent by the WWTP treatment process, except for Legionella and Leptospira species which demonstrated an increase in relative proportion from inflow to effluent. This indicates that WWTPs, while effective against enteric bacteria, may enrich and release other potentially pathogenic bacteria into the environment. The taxonomic resolution of full-length 16S rRNA genes allows for improved characterization of potential pathogenic taxa and other harmful bacteria which is required to reliably assess health risk.

Figure 1

Relative abundance of dominant bacterial phyla (contributing more than 1% to the total bacterial community) in inflow and effluent samples after data rarefaction. (A) Bar charts show the percentage bacterial taxonomic composition for each sample. (B) Boxplots showing the average relative abundance of the dominant bacterial phyla between inflow and effluent. The p-value (p) indicates the significance of the differences based on a PERMANOVA with p < 0.05 being significant.

Figure 2

Average relative abundance of families contributing more than 1.0% to the total bacterial community in inflow and/or effluent. Only families of the three most abundant phyla Proteobacteria, Bacteroidetes and Firmicutes are shown.

Figure 3

Principal coordinate analysis (PCoA) of the bacterial community based on Bray-Curtis similarity. Inflow and effluent samples are defined as circles and squares, respectively. Different sampling time points are indicated by blue colour for February, green colour for April, red colour for July and brown colour for October.

Figure 4

Relative abundance (after rarefaction) of genera with known potential pathogens. They were grouped in environmental, waterborne and enteric, and are shown for each sample of inflow and effluent.