Skip to main content

FECB: A Functional Encyclopedia of Cyanobacteria - Building the knowledge framework for an enhanced understanding of carbon and nitrogen cycling


EMSL Project ID
48099

Abstract

There has been a great interest by the Department of Energy (DOE) to increase the phylogenetic coverage of genome sequences from across the phyla archaea and bacteria – including cyanobacteria. The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project, which is an ongoing project at DOE’s Joint Genome Institute (JGI), has been filling the genomic gaps in the prokaryotic tree of life. The recently launched GEBA-cyano project, led by Dr. Cheryl Kerfeld at the JGI, was designed to improve the understanding of the genetic basis of cyanobacterial ecophysiology by sequencing the genomes of 54 phylogenetically diverse strains of cyanobacteria that could be grown under axenic conditions. Cyanobacteria are eminently DOE mission relevant organisms, playing key roles in global carbon and nitrogen cycling, as platforms for green biotechnology, and as biofuel feedstock. Here we propose to extend and complement the GEBA and GEBA-cyano projects by performing phylogenetic and functional analyses of mixed populations of cyanobacteria and heterotrophic prokaryotes collected from extreme environments. Extremophilic communities that possess a relatively low complexity will be used to establish a workflow designed to isolate and cultivate individual microorganisms that have been recalcitrant to prior attempts to grow them in axenic culture. To achieve our goals, we will utilize specimens from the Culture Collection of Microorganisms from Extreme Environments (CCMEE), which consists of over 1,200 samples of cyanobacteria-dominated communities, collected over the period of four decades by senior members of our team. The CCMEE provides a unique resource for the scientific community by providing samples of cyanobacteria isolates and consortia composed of photoautotrophic cyanobacteria and heterotrophic prokaryotes.
In this project, we propose to determine whether results obtained by in silico analysis can be used successfully to infer physiological requirements for axenic growth of organisms. The project will provide new insights for photosynthetic systems across different scales (from molecular, to single cell, to population, to ecosystem scales). The results obtained during this project will enable us to determine whether such isolation efforts can lead to the isolation of viable specimens of microorganism with eminent DOE relevance and of value to the scientific community, including strains that have to date not been cultivated in pure culture.

Project Details

Project type
FICUS Research
Start Date
2013-10-01
End Date
2015-12-31
Status
Closed

Team

Principal Investigator

Matthias Hess
Institution
University of California, Davis

Team Members

Bernard Henrissat
Institution
Architecture et Fonction des Macromolécules Biologiques Laboratory

Vincent Lombard
Institution
Architecture et Fonction des Macromolécules Biologiques Laboratory

Richard Castenholz
Institution
University of Oregon

Kevin Keegan
Institution
Argonne National Laboratory

Peter Larsen
Institution
Argonne National Laboratory

Trent Northen
Institution
Lawrence Berkeley National Laboratory

Stephen Lindemann
Institution
Purdue University

Anantharaman Kalyanaraman
Institution
Washington State University

Related Publications

Renslow RS, SR Lindemann, JK Cole, Z Zhu, and CR Anderton. 2016. "Quantifying element incorporation in multispecies biofilms using nanoscale secondary ion mass spectrometry image analysis." Biointerphases 11(2):02A322. doi:10.1116/1.4941764