The abundant core community of activated sludge

Understanding the microbial ecology of a system requires that the observed population dynamics can be linked to their metabolic functions. However, functional characterization is laborious and the choice of organisms should be prioritized with those that are frequently abundant (core) or transiently abundant are thus putatively making the greatest contribution to carbon turnover in the system. We analysed the microbial communities in 13 Danish wastewater treatment plants with nutrient removal in consecutive years and a single plant periodically over 6 years, using Illumina sequencing of 16S rRNA amplicons of the V4 region. The plants contained a core community of 63 abundant genus-level OTUs that made up 68% of the total reads. A core community consisting of abundant OTUs was also observed within the incoming wastewater to 3 plants. The net growth rate for individual OTUs was quantified using mass balance, and it was found that 10% of the total reads in the activated sludge were from slow or non-growing OTUs, and that their measured abundance was primarily due to immigration with the wastewater. Transiently-abundant organisms were also identified. Among them the genus Nitrotoga (class Betaproteobacteria) was the most abundant putative nitrite oxidizer in a number of activated sludge plants which challenges previous assumptions that Nitrospira (phylum Nitrospirae) are the primary nitrite-oxidizers in activated sludge systems with nutrient removal.