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Study

Study Name: Freshwater sediment microbial communities from Lake Washington, Seattle, USA, for methane and nitrogen cycles

Projects

Biosamples

Organisms

Biosamples: 11 Seq. Projects: 11
STUDY NAME
GOLD Study ID Gs0060820
Study Name Freshwater sediment microbial communities from Lake Washington, Seattle, USA, for methane and nitrogen cycles
Other Names Lake Washington Sediment Methane and Nitrogen Cycles
NCBI Umbrella Bioproject Name
NCBI Umbrella Bioproject ID
Legacy ER Study ID 15820
Legacy GOLD ID Gm00201
Added By Nikos Kyrpides on 2009-09-12 00:00:00.0
Last Modified By Michelle Isbandi on 2014-09-03 00:00:00.0
STUDY DESCRIPTION
PI Lumila Chistoserdova
Description 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.
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GOLD CLASSIFICATION
Ecosystem Environmental
Ecosystem Category Aquatic
Ecosystem Type Freshwater
Ecosystem Subtype Lentic
Specific Ecosystem Sediment
Metagenomic Study Yes
STUDY COMPOSITION
Number of Biosamples 11
Number of Organisms 0
Number of Seq Projects 11
Number of Analysis Projects 13
Number of Related Studies 0

 

 

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