Using Short-Term Enrichments and Metagenomics to Obtain Genomes from uncultured Activated Sludge Microorganisms

The dominant mode of microbial life is in complex communities, often consisting of hundreds to thousands of species. With the novel high throughput ‘-omics’ approaches studies of such complex ecosystems have become within reach (Jansson et al., 2012). Common for the -omics approaches is that they depend on system-specific reference genomes in order to analyze the vast amounts of data (Albertsen et al., 2012). This limits the application of -omics to environments for which a comprehensive catalogue of reference genomes exists e.g. the human gut.
Several strategies for obtaining microbial genomes exist today, but their ability to obtain complete genomes from complex microbial communities on a large scale is still inadequate (Lasken, 2012). In theory, conventional metagenomics should be able to recover genomes from complex communities, but in practice the approach is hampered by the presence of microdiversity. This leads to fragmented and chimeric de novo assemblies, which prevent the extraction of complete genomes. The new approach presented here involves reducing the impact of microdiversity and increasing genome extraction efficiency by what we term “metagenome triangulation”. The microdiversity was reduced by short-term enrichment under defined conditions favoring certain functional groups of organisms. Bioinformatic genome extraction was greatly improved by utilizing multiple metagenomes where the microorganisms were in different abundances. In this study we retrieved 15 complete genomes and numerous near complete genomes from an activated sludge plant carrying out N and P removal.