Progress 12/15/15 to 12/14/18
Outputs
Target Audience:The target audience for this work are microbial ecologists. Outreach to microbial ecologists occurred through publication of results in the scientific literature (see Products). Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?I participated in the Howard Hughes Medical Institute's Microbiology Teaching Fellows program, through which I developed and implement innovative and effective ways to teach microbiology to undergraduates. This experience culminated in teaching "Critical Analyses in Microbiology," an undergraduate seminar course which aims to develop critical thinking and problem solving skills through an exploration of seminal papers and cutting-edge research in the field of microbiology. As a result of this and other teaching experiences, I have developed and written a teaching philosophy centered around evidence based practices that: 1) foster student engagement within the classroom, 2) enable students to become critical thinkers, and 3) improve my teaching through assessment of student learning gains. I participated in the University of Wisconsin's Postdoctoral Training Course in Scientific Leadership, a course which equipped me with leadership skills necessary to succeed in a variety of career paths, including understanding interpersonal styles, managing conflict, communicating effectively, creating high-performing teams, leading successful meetings, providing feedback and motivation, and dealing with change. How have the results been disseminated to communities of interest?Results have been disseminated in the form of educational modules, public talks, conference presentations, and the scientific literature. Educational modules- In Spring 2016, I taught the undergraduate course "Critical Analyses in Microbiology." This course aims to teach undergraduate microbiology majors critical thinking and problem solving skills through an exploration of seminal papers and cutting-edge research in the field of microbiology. I developed a new module for this course focusing on systems biology, the conceptual framework underlying my research program. This module has been taught by other instructors in subsequent semesters. Public talks-Results have been presented at two public talks, including the Wisconsin Ecology Symposium and a presentation to the undergraduate microbiology club. Conference presentations- Results were disseminated through an oral presentation at the Association of Environmental Engineering and Science Professors Research and Education Conference in June 2017. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Aim 1 was 100% completed and the results were published in mSystems in 2017. We found that the freshwater Actinobacteria appear to be scavengers, subsisting preferentially on N-rich compounds but also capable of consuming sugars, and oligo- and polysaccharides These bacteria do not appear to be metabolically self-sufficient, relying on other organisms for the production of essential vitamins. We also find that these bacteria contain and strongly express a light-harvesting protein and its accessory "antenna" molecule, suggesting they are capable of photoheterotrophy. We transferred the biosynthetic machinery to synthesize this protein and its antenna molecule into E. coli and have verified the structure and function of the protein-antenna complex. These experiments demonstrated that that acI Actinobacteria have the capacity to natively synthesize a green light-dependent outward proton-pumping light-sensitive protein. This manuscript was published in Applied and Environmental Microbiology in 2018. Aim 2 is 50% complete. The scope of Aim 2 was expanded to includepersistent/abundant groups of freshwater bacteria, not just Actinobacteria, and to focus on species-species interactions, not just environmental ones. Environmental interactions- Funds from this work were used to extend existing time-series of bacterial community dynamics with data from 2012 to the present. Both time-series now contain weekly or bi-weekly measurements from 2002 to the present. Thus far, I have discovered that some freshwater bacteria have periodic behavior, suggesting they are driven by periodic environmental signals (such as temperature). Auto-regressive modeling is currently being used to link these environmental data to changes in microbial community composition. Additionally, to enable high-confidence identification of freshwater Actinobacteria within these time-series, a novel classification algorithm was developed. This algorithm was published in mSphere in 2018. Interspecies interactions-I also discovered that acI Actinobacteria have non-specific interactions with other freshwater community members. Paradoxically, this "promiscuity" persists despite their small genome size: acI Actinobacteria have a "flexible" genome, genes renderingthem functionally versatile at the population level. This flexibilty might be one of the keysto the competitiveness of streamlined "free-living" microorganisms in highly dynamic environments such as lakes. These results were published in mSphere in 2018. Aim 3 is 0% complete. Aim3 depended on successful completion of Aims 1 and 2. We discovered that our freshwater lake microbial community time-series needed to be extended for completion of Aim 2. Resources allocated for Aim 3 were re-assigned to Aim 2 and follow-up studies from insights obtained in Aim 1.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Rohwer RR, Hamilton JJ, Newton RJ, McMahon KD (2018) TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution. mSphere 3(5): e00327-18.
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Garcia SL, Buck M, Hamilton JJ, Wurzbacher C, Grossart H-P, et al. (2018) Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria. mSphere 3(3): e00202-18.
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Dwulit-Smith JR, Hamilton JJ, Stevenson DM, He S, Oyserman BO, et al. (2018) acI Actinobacteria Assemble a Functional
Actinorhodopsin with Natively Synthesized Retinal. Appl Environ Microbiol 84(24): e01678-18.
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Progress 12/15/16 to 12/14/17
Outputs
Target Audience:Proposed target audience for this work are microbial ecologists. Outreach to microbial ecologists occurred through publication of results in the journal mSystems in April 2017. Efforts also reached environmental scientists and engineers, through an oral presentation at theAssociation of Environmental Engineering and Science Professors Research and Education Conference in June 2017. Finally, these results were shared with undergraduate Microbiology students in the form of a public talk to the undergraduate microbiology club. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?I participated in the University of Wisconsin's Postdoctoral Training Course in Scientific Leadership, a course which equipped me with leadership skills necessary to succeed in a variety of career paths, including understanding interpersonal styles, managing conflict, communicating effectively, creating high-performing teams, leading successful meetings, providing feedback and motivation, and dealing with change. How have the results been disseminated to communities of interest?Results were disseminated in the form of a journal article, published in mSystems. Two additional manuscripts are under review, and pre-prints are available on bioRxiv. One applied my "reverse ecology" approach to freshwater bacteria from other environments, and the second manuscript describes how to classify 16S rRNA gene sequences used to describe microbial community composition. This work will be subsequently used in Aim 2. I also presented this work at theAssociation of Environmental Engineering and Science Professors Research and Education Conference, and in a public talk to the University of Wisconsin undergraduate Microbiology club. What do you plan to do during the next reporting period to accomplish the goals?Efforts in the next reporting period will focus on analyzing microbial community dynamics to determine environmental drivers of change in these communities.
Impacts
What was accomplished under these goals?
Aim 1 was completed and the results published in mSystems in 2017. We found that the freshwater Actinobacteria appear to be scavengers, subsisting preferentially on N-rich compounds but also capable of consuming sugars, and oligo- and poly-saccharides These bacteria do not appear to be metabolically self-sufficient, relying on other organisms for the production of essential vitamins. We also find that these bacteria contain and strongly express a light-harvesting protein and its accessory "antenna" molecule, suggesting they are capable of photoheterotrophy. We transferred the biosynthetic machinery to synthesize this protein and its antenna molecule into E. coli and have verified the structure and function of the protein-antenna complex. This manuscript is under preparation. Aim 2 is currently underway. I have acquired long-term measurements of microbial community composition from two Wisconsin lakes, Lake Mendota and Trout Bog. Funds from this project were used to extend existing time-series with data from 2012 to the present. Both time-series now contain weekly or bi-weekly measurements from 2002 to the present. Environmental data associated with these samples have also been collected. Auto-regressive modeling is currently being used to link these environmental data to changes in microbial community composition.
Publications
- Type:
Journal Articles
Status:
Under Review
Year Published:
2017
Citation:
Rohwer RR, Hamilton JJ, Newton, RJ, and KD McMahon. TaxAss: Leveraging Custom Databases Achieves Fine-Scale Taxonomic Resolution. bioRxiv. doi:10.1101/103838.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2017
Citation:
Hamilton JJ, Garcia SL, Brown BS, Oyserman BO, Moya F, Bertilsson S, Malmstrom RR, Forest KT, and KD McMahon. Microbial Ecosystems Biology: A Framework for Scaling from Genomes to Ecosystems. Association of Environmental Engineering and Science Professors Research and Education Conference. Ann Arbor, MI, June 2017.
- Type:
Other
Status:
Other
Year Published:
2017
Citation:
Hamilton, JJ. "Community Systems Biology: From Genes to Ecosystems." Public talk to undergraduate Microbiology Club.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Hamilton JJ, Garcia SL, Brown BS, Oyserman BO, Moya F, Bertilsson S, Malmstrom RR, Forest KT, and KD McMahon. Metabolic Network Analysis and Metatranscriptomics Reveals Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI. mSystems. 2:e00091-17. doi:10.1128/mSystems.00091-17.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2017
Citation:
Garcia SL, Buck M, Hamilton JJ, Wurzbacher C, Rosenblad MA, McMahon KD, Grossart HP, Warnecke F, and A Eiler. Model communities hint to promiscuous metabolic linkages between ubiquitous free-living freshwater bacteria. bioRxiv. doi:10.1101/214288.
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Progress 12/15/15 to 12/14/16
Outputs
Target Audience:Effort: In Spring 2016, I taught the undergraduate course "Critical Analyses in Microbiology." Audience: This course is taken primarily by undergraduate microbiology majors. Extended description: This course aims to develop critical thinking and problem solving skills through an exploration of seminal papers and cutting-edge research in the field of microbiology. I developed a new module for this course focusing on systems biology, the conceptual framework underlying my research program. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?I participated in the Howard Hughes Medical Institute's Microbiology Teaching Fellows program, through which I developed and implement innovative and effective ways to teach microbiology to undergraduates. This experience culminated in teaching "Critical Analyses in Microbiology," an undergraduate seminar course which aims to develop critical thinking and problem solving skills through an exploration of seminal papers and cutting-edge research in the field of microbiology. As a result of this and other teaching experiences, I have developed and written a teaching philosophy centered around evidence-based practices that 1) foster student engagement within the classroom, 2) enable students to become critical thinkers, and 3) improve my teaching through assessment of student learning gains. I am also participating in the University of Wisconsin's Postdoctoral Training Course in Scientific Leadership, a course designed to equip me with the critical leadership skills I need to succeed in a wide range of scientific career paths. How have the results been disseminated to communities of interest?Results have been disseminated via one public talk and one conference presentation-see products. A manuscript summarizing the results of Aim 1 will be submitted for publication in early 2017. A fully reproducible manuscript is also available on Github (https://github.com/joshamilton/Hamilton_acI_2016). Readers can download my raw data for themselves and rerun my exact analyses. What do you plan to do during the next reporting period to accomplish the goals?Efforts in the next reporting period will focus on Aims 2 (examine bacterial community dynamics in Lake Menodata) and 3 (Use RLQ and fourth-corner to analyze trait-environment interactions).
Impacts
What was accomplished under these goals?
Aim 1 has been completed and the results will be submitted for publication in early 2017. We found that the freshwater Actinobacteria appear to be scavengers, subsisting preferentially on N-rich compounds but also capable of consuming sugars, and oligo- and poly-saccharides These bacteria do not appear to be metabolically self-sufficient, relying on other organisms for the production of essential vitamins. We also find that these bacteria contain and strongly express a light-harvesting protein, suggesting they are capable of photoheterotrophy.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
Conference presentation - Hamilton JJ, Garcia SL, Bendall ML, Brown BS, Stevens SLR, Bertilsson S, Forest KT, Malmstrom RR, Stepanauskas R, Tringe SG, Woyke T, and KD McMahon. Metabolic Network Analysis and Metatranscriptomics of a Cosmopolitan and Streamlined Freshwater Lineage. 16th.
- Type:
Other
Status:
Published
Year Published:
2016
Citation:
Public talk - Hamilton JJ. Diving Into Freshwater Microbial Genomes to Infer Bacterial Traits. Wisconsin Ecology 22nd Annual Fall Symposium. Madison, WI, October 2016.
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