Untangling the complexity of phototroph-heterotroph interactions in the lab and in the field
EMSL Project ID
47977
Abstract
Despite the fact that ubiquitous microbial interspecies interactions form the foundation of energy flow as well as the biogeochemical cycling of carbon and other elements within natural environments, detecting these interactions at the species level and connecting them in a predictive way to genome-encoded metabolic capability remains intractable due to the both the complexity of natural systems and the lack of technologies capable of dissecting microbial populations into their subcomponent species. Furthermore, though microbial communities are known to colonize and persist in extreme environments, the environments studied to date do not typically lend themselves to the study of long-term climatic variability. Consequently, little is presently known about how such interspecies interactions are likely to shift as global climate change impacts are felt at the local level. Therefore, the overall goal of this proposal is to understand, at the species level, the dynamics of such microbial populations and their gene regulatory networks in response to environmental perturbations and to elucidate mechanisms that impart robustness and stability to microbial communities. Towards these ends, we propose to utilize EMSL's cutting-edge capabilities in cell isolation and systems analysis (flow cytometry, laser capture microdissection, RNA sequencing, and associated microscopic capabilities) coupled with genome, metagenome, and single-cell sequence data provided by JGI to generate techniques to query function and activity at the species level. We propose to first apply these techniques to tractable, simplified phototroph-heterotroph communities isolated from a benthic phototrophic microbial mat in Hot Lake, Washington. The interrogation of these simplified communities will generate insights into the modulation of gene expression in the ~20 organisms within these communities in response to variation in environmental conditions in the laboratory as well as permit the development of the requisite technologies to break a more complex microbial community into its subcomponent species and with spatial resolution. This will allow the generation of field-testable hypotheses of interspecies interactions occurring within the mat community. We finally propose to apply this approach in a spatially-resolved to the whole mat community to query interspecies interactions within defined microenvironments of the highly-laminated Hot Lake mat community. Long-term, this approach will allow the elucidation of interspecies interactions important for carbon and energy flow in the Hot Lake mat under variable environmental conditions, and, broadly applied, important to phototroph-heterotroph interactions generally.
Project Details
Project type
Large-Scale EMSL Research
Start Date
2013-10-01
End Date
2015-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Co-Investigator(s)
Team Members
Related Publications
Anderson LN, PK Koech, AE Plymale, EV Landorf , A Konopka, F Collart, MS Lipton, MF Romine, and AT Wright. 2015. "Live Cell Discovery of Microbial Vitamin Transport and Enzyme-Cofactor Interactions ." ACS Chemical Biology . doi:10.1021/acschembio.5b00918 [In Press]
Cole JK, JR Hutchison, RS Renslow, YM Kim, WB Chrisler, HE Engelmann, A Dohnalkova, D Hu, TO Metz, JK Fredrickson, and SR Lindemann. 2014. "Phototrophic Biofilm Assembly in Microbial-Mat-Derived Unicyanobacterial Consortia: Model Systems for the Study of Autotroph-Heterotroph Interactions." Frontiers in Microbiology 5:Article No. 109. doi:10.3389/fmicb.2014.00109
Jay ZJ, JP Beam, ZJ Jay, A Dohnalkova, JP Beam, R Lohmayer, B Bodle, A Dohnalkova, B Planer-Friedrich, R Lohmayer, M Romine, B Bodle, WP Inskeep, B Planer-Friedrich, M Romine, and WP Inskeep. 2015. "Pyrobaculum yellowstonensis Strain WP30 Respires on Elemental Sulfur and/or Arsenate in Circumneutral Sulfidic Geothermal Sediments of Yellowstone
Lee J., S. Haruta, S. Kato, H. Bernstein, S.R. Lindemann, D. Lee, and J.K. Fredrickson, et al. 2020. "Prediction of Neighbor-dependent Microbial Interactions from Limited Population Data." Frontiers in Microbiology 10. PNNL-SA-144026. doi:10.3389/fmicb.2019.03049
Lindemann SR, JJ Moran, JC Stegen, RS Renslow, JR Hutchison, JK Cole, A Dohnalkova, J Tremblay, K Singh, S Malfatti, F Chen, S Tringe, H Beyenal, and JK Fredrickson. 2013. "The Epsomitic Phototrophic Microbial Mat of Hot Lake, Washington: Community Structural Responses to Seasonal Cycling." Frontiers in Microbiology 4:323. doi:10.3389/fmicb.2013.00323