title: The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat.
abstract: Genomes were obtained for three closely related strains of Synechococcus that are representative of putative ecotypes (PEs) that predominate at different depths in the 1 mm-thick, upper-green layer in the 60°C mat of Mushroom Spring, Yellowstone National Park, and exhibit different light adaptation and acclimation responses. The genomes were compared to the published genome of a previously obtained, closely related strain from a neighboring spring, and differences in both gene content and orthologous gene alleles between high-light-adapted and low-light-adapted strains were identified. Evidence of genetic differences that relate to adaptation to light intensity and/or quality, CO2uptake, nitrogen metabolism, organic carbon metabolism, and uptake of other nutrients were found between strains of the different putative ecotypes. In situ diel transcription patterns of genes, including genes unique to either low-light-adapted or high-light-adapted strains and different alleles of an orthologous photosystem gene, revealed that expression is fine-tuned to the different light environments experienced by ecotypes prevalent at various depths in the mat. This study suggests that strains of closely related PEs have different genomic adaptations that enable them to inhabit distinct ecological niches while living in close proximity within a microbial community.
authors.affiliation: Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA.
authors.forename: Millie T
authors.initials: MT
authors.lastname: Olsen
authors.affiliation: Department of Mathematical Sciences, Montana State University Bozeman, MT, USA.
authors.forename: Shane
authors.initials: S
authors.lastname: Nowack
authors.affiliation: Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA.
authors.forename: Jason M
authors.initials: JM
authors.lastname: Wood
authors.affiliation: Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA.
authors.forename: Eric D
authors.initials: ED
authors.lastname: Becraft
authors.affiliation: Department of Energy, Joint Genome Institute Walnut Creek, CA, USA.
authors.forename: Kurt
authors.initials: K
authors.lastname: LaButti
authors.affiliation: Department of Energy, Joint Genome Institute Walnut Creek, CA, USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Lipzen
authors.affiliation: Department of Energy, Joint Genome Institute Walnut Creek, CA, USA.
authors.forename: Joel
authors.initials: J
authors.lastname: Martin
authors.affiliation: Department of Energy, Joint Genome Institute Walnut Creek, CA, USA.
authors.forename: Wendy S
authors.initials: WS
authors.lastname: Schackwitz
authors.affiliation: J. Craig Venter Institute Rockville, MD, USA.
authors.forename: Douglas B
authors.initials: DB
authors.lastname: Rusch
authors.affiliation: Department of Biology, Wesleyan University Middletown, CT, USA.
authors.forename: Frederick M
authors.initials: FM
authors.lastname: Cohan
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA ; Department of Chemistry and Biochemistry, Montana State University Bozeman, MT, USA.
authors.forename: Donald A
authors.initials: DA
authors.lastname: Bryant
authors.affiliation: Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: Ward
keywords: adaptation; comparative genomics; microbial mats; microbial species; thermophilic Synechococcus