ECI Genomics Group Receives Award from the Department of Energy's Joint Genome Institute

Author: Heather DeWitt

Stuart Jones

Biology Assistant Professor Stuart Jones, along with collaborators Maureen Coleman (University of Chicago) and Ryan Newton (University of Wisconsin, Milwaukee School of Freshwater Science), received an award for a large amount (400 gigabase pairs) of genomic and metagenomic sequencing from the Department of Energy's Joint Genome Institute. The project will focus on microbial communities of the Great Lakes.  Below is the project description included with their proposal.

More information on the Community Sequencing Program from which they received the sequencing can be found at:



Abstract: Freshwater has been called the oil of the 21st century. Increasing global demand, coupled with threats ranging from climate change to industrial contamination, are straining earth’s limited freshwater resources. Not only are these freshwaters vital for human activities, they are also key players in global biogeochemical cycling. Their contributions have long been overlooked because of their small areal extent, but it is increasingly clear that freshwaters are disproportionately active sites of carbon and greenhouse gas cycling, driven in large part by microbial communities. Linking microbial taxonomic and functional diversity with biogeochemical fluxes of carbon and other nutrients, and with the maintenance of clean water, is a major challenge for microbial ecologists. Among global freshwater systems, the Laurentian Great Lakes are of primary importance, holding nearly 20% of earth’s surface freshwater, yet only a handful of studies have sought to characterize their microbial communities. To this end, we propose the first comprehensive characterization of the microbial diversity and activity of the Great Lakes, integrating deep 16S rRNA tag sequencing, metagenomics, metatranscriptomics, and single-cell amplified genomes (SAGs).

Scope of Work: We request a combination of sequence datasets that together will provide an unprecedented view of freshwater microbial diversity and metabolism. To span seasonality and environmental gradients, we will provide samples from two cruises, in April and August 2012, across all five Great Lakes and along a water column depth profile. We propose the following:

1. Ultra-high-throughput amplicon (tag) sequencing of 16S rRNA genes from two pools – community genomic DNA and community RNA – to capture community-wide taxonomic diversity and taxon-specific relative activity, at relatively deep coverage (~100,000 sequences per sample, 150 samples, rDNA & rRNA, ~10Gbp total).

2. Metagenomic sequencing of whole-community genomic DNA, to characterize genome- wide functional diversity along environmental gradients (2Gbp/sample, ~160Gbp total).

3. Coupled metatranscriptomic sequencing (RNA-Seq) of whole-community mRNA, to assess taxonomic and gene-level activity at the level of transcriptional expression (2Gbp/sample, ~160Gbp total).

4. Single-cell amplified genomes (SAGs) to link single-locus-based taxonomic identity with genome-wide functional diversity from shotgun metagenomics (~60Gbp total). We request collaboration with JGI to produce SAG libraries and for preliminary assembly and annotation via IMG.

Together, this strategy amounts to ~390 Gbp of sequencing. Details regarding sample selection are provided in the Project Description. Our team has experience in analyses of all four types of data, hence we will conduct most analyses, though we also welcome collaboration with JGI scientists.