Discovering Species-level Functions in Complex Microbial Communities

Source: Kalyuzhnaya et al. (2008). High-resolution metagenomics targets specific functional types in complex microbial communities. Nature Biotrech 26 (9): 1029-1034.

Environmental genomics (metagenomics) has become a hot topic in molecular biology; however, it is costly and highly dependent on the number of reference genomes available. Thus, studying highly complex communities like those of soil or lake sediments are not currently feasible. In this study, the authors use a labeling method to target the species that are specific for a given function. In this case, they have studied methylotrophy and through the usage of labled methane, methanol, methylamine, formaldehyde and formate, they have focused on the species directly assimilating these substrates through extracting the labeled fraction of the genomic DNA extracted from the community (using isopycnic centrifugation).

The 16S rRNA analysis shows that the samples enriched for methylotrophy are way less complex than the initial sample largely including the bona fide methylotrophs: Methylobacter tundripaludum, Methylomonas sp., Methylotenera mobilis, Methyloversatilis universalis, Ralstonia eutropha. It should be noted that some of the enriched species may not be methylotrophs but rather secondary links in the food chain (e.g. using 13C-CO2 produced by methylotrophs).

The authors demonstrate the utility of their approach through identifying a novel methylotroph and reconstructiong its genome and metabolic network.