Project Name Washington Lake Metagenomes 
Domain (1) bacteria
Investigators (1)
Institution University of Washington
Project Code CAM_PROJ_WashingtonLake
Project Type metagenome
Publications (1)


Most microbes in the biosphere remain unculturable. Whole genome shotgun (WGS) sequencing of environmental DNA (metagenomics) can be used to study the genetic and metabolic properties of natural microbial communities. However, in communities of high complexity, metagenomics fails to link specific microbes to specific ecological functions. To overcome this limitation, we developed a method to target microbial subpopulations by labeling DNA through stable isotope probing (SIP), followed by WGS sequencing. Metagenome analysis of microbes from Lake Washington in Seattle that oxidize single-carbon (C1) compounds shows specific sequence enrichments in response to different C1 substrates, revealing the ecological roles of individual phylotypes. We also demonstrate the utility of our approach by extracting a nearly complete genome of a novel methylotroph, Methylotenera mobilis, reconstructing its metabolism and conducting genome-wide analyses. This high-resolution, targeted metagenomics approach may be applicable to a wide variety of ecosystems.


Name Code Organism CDS NT Pep
WASHINGTONLAKE_SMPL_FORMALDEHYDE assembly CAM_ASM_0000501 WASHINGTONLAKE_SMPL_FORMALDEHYDE      
WASHINGTONLAKE_SMPL_FORMATE assembly CAM_ASM_0000502 WASHINGTONLAKE_SMPL_FORMATE      
WASHINGTONLAKE_SMPL_METHANE assembly CAM_ASM_0000503 WASHINGTONLAKE_SMPL_METHANE      
WASHINGTONLAKE_SMPL_METHANOL assembly CAM_ASM_0000504 WASHINGTONLAKE_SMPL_METHANOL      
WASHINGTONLAKE_SMPL_METHYLAMINE assembly CAM_ASM_0000505 WASHINGTONLAKE_SMPL_METHYLAMINE      


Sample Name PI Desc
WASHINGTONLAKE_SMPL_FORMALDEHYDE NA Formaldehyde Enrichment
WASHINGTONLAKE_SMPL_FORMATE NA Formate Enrichment
WASHINGTONLAKE_SMPL_METHANE NA Methane Enrichment
WASHINGTONLAKE_SMPL_METHANOL NA Methanol Enrichment
WASHINGTONLAKE_SMPL_METHYLAMINE NA Methylamine Enrichment