Global database of microbes in wastewater treatment systems

Activated sludge is the most commonly applied bioprocess throughout the world for wastewater treatment, and have been used for more than 100 years. Microorganisms are key to the process, but still our knowledge of the microbial identity and function is limited. Microbes can be identified by sequencing the 16S rRNA gene, and large-scale surveys can take place by amplicon sequencing. However, most of the microbes remains unidentified, since the current full-length 16S rRNA gene databases are underpopulated, ecosystem skewed, and biased by primers.
In this study, we aim to establish a wastewater treatment-specific reference database, comprised of full-length microbial 16S rRNA gene sequences from wastewater treatment systems across the world (the Global Database of Microbes in Wastewater Treatment Systems), by applying a novel high-throughput, primer-free sequencing method. More than 500 treatment plants from more than 35 countries are already included, making it the largest of its kind to date. The included plants cover most process designs (e.g. carbon-, nitrogen-, and phosphorus removal, and both activated sludge, granules and biofilters). Here we present an overview of procedures for sampling, sample handling, sequencing, bioinformatic pipeline, and examples of the improved reference database and taxonomy.
The prospects of the database are exciting, promising to provide a unique identification tag for all future analyses of wastewater treatment systems, and with time to link function to specific species, e.g. via updated versions of the MiDAS field guide. Furthermore, the long sequences will allow for better evaluation and design of primers for future studies.