Genomics of biological wastewater treatment

Cleaning up wastewater from domestic sewage and industrial processes is essential for safeguarding public health and the environment (for an overview of wastewater treatment processes see http://en.wikipedia.org/wiki/ Sewage_treatment). Biological wastewater treatment plants (WWTPs) employing sludge represent one of the most widely used biotechnological processes, with more than 120 billion litres treated daily in the USAalone (Fig. 1). Removal of organic carbon and other nutrients, mainly nitrogen (N) and phosphorus (P), by sludge microbes is essential in order to avoid eutrophication and deterioration of recipient surface waters (Seviour et al., 2003). The complexity of wastewater microbial communities, based on the analysis of 16S rRNA sequences, is known to be enormous (Chouari et al., 2005a,b) (Fig. 2). As we have very limited knowledge of composition, dynamics and stability of microbial communities, several processes in wastewater treatment are generally regarded as being a ‘black box’. Their improvement is often based on a trialand-error approach, which leads to inconsistent results and unexpected behaviours (Daims et al., 2006a). In recent years, with the development of several new highthroughput sequencing platforms (Hall, 2007; Marsh, 2007), metagenome sequencing strategies (Schloss and Handelsman, 2005; Tringe and Rubin, 2005; Schmeisser et al., 2007) and bioinformatics toolboxes (Chen and Pachter, 2005; Tringe et al., 2005; Foerstner et al., 2006; Raes et al., 2007), the genome analysis of complex communities has become much more accessible, albeit by no means easier. Here we give a brief update of the current status of (meta)genome sequencing and mining of wastewater-related microorganisms and communities.