Biological Sciences

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Trinity L Hamilton

Title: Assistant Professor

ECBR, microbial ecology and physiology, geobiology and biogeochemical cycles, photosynthesis in sulfide-rich ecosystems, environmental and ecological factors governing microbial community composition


  • Ph.D., Montana State University, Bozeman, MT, 2012 (Biochemistry).

Research Information

Research Interests

The research goals of the lab are to understand the interactions of microorganisms in natural and engineered systems and how microbial communities respond and adapt to environmental change. These research goals encompass traditional microbiology and molecular techniques as well as next generation -omics approaches in combination with high resolution geochemical and geological data. The integration of these data results in a multidisciplinary approach to examine the in situ dynamics of microbial interactions and the affect of these interactions on local and global biogeochemical cycles. For more information, please visit the lab's website.

Microbial primary productivity in the Proterozoic oceans
The delay in the rise of oxygen to present day levels at the end of the Proterozoic represents an important gap in our understanding of ancient biogeochemical cycling. One hypothesis suggests contributions to primary production by anoxygenic phototrophs, including metabolically versatile cyanobacteria, effectively limited oxygen production throughout Earth's middle age (Johnston et al., 2009). We are examining this hypothesis in Proterozoic ocean analogs with micromolar concentrations of both oxygen and sulfide in the photic zone.

Metabolically versatile Cyanobacteria
Cyanobacteria are the only bacteria that carry out oxygenic photosynthesis and therefore played a crucial role in the evolution of Earth’s atmosphere as well as diversification of microbial and higher life forms. Some Cyanobacteria can use sulfide as the electron donor to photosystem I in the absence of oxygen generation. Utilizing a model cyanobacterium isolated from an environment where low levels of oxygen and sulfide are present, we are characterizing the genetic, regulatory and biochemical underpinnings of anoxygenic photosynthetic activity.

Competitive interactions and microbial community assembly
Microbial processes that regulate availability of nutrients play key roles in shaping community composition. Our research in Yellowstone National Park reveals a strong correlation between the distribution of ammonia oxidizing archaea and nitrogen fixing aquificae in nitrogen-limited geothermal hot springs over large environmental gradients. We are employing microcosm and pure culture studies to test the hypothesis that affinity for substrate and electron donor use play key roles in structuring the biodiversity of these hydrothermal communities.

The co-occurrence of cyanobacteria and anoxygenic phototrophs is common in environments where sufficient fluxes of reduced compounds are available to support anoxygenic photosynthesis. However, the geochemical and biological factors controlling competition among co-existing phototrophs in natural environments is poorly understood. Using pure cultures and in situ studies, we are identifying the physical, geochemical, and physiological factors that affect competition among chlorophototrophs and the consequences of this competition. 

Sulfur cycling 
Euxinic conditions have been an intermittent feature of global oceans throughout Earth's history. These stratified systems have large geochemical gradients and often host phototrophic communities at the boundary between oxic and euxinic zones (chemocline). Complex biogeochemical cycles occur throughout the water column in these systems as well as within the chemocline. We are examining the carbon and sulfur cycles within chemocline communities and the underlying anoxic water column to understand the inputs (e.g., organic carbon or oxidized sulfur) necessary to maintain these stable ecosyste

Research Support

  • (PI), Hamilton, Trinity, Life on ice - The role of microbiota in glacier ice worm adaptation and biogeography, UC. (URC Faculty Awards AY2015-16), $5,950.00. 05/01/2016 to 04/30/2017. Status: Active.
  • (PI), Hamilton, Trinity, Primary Productivity in Supraglacial Ecosystems. (UC LEAF 2015‐16 SEED Award), $3,000.00. 09/01/2015 to 08/31/2016. Status: Active.
  • (Collaborator), Czaja, Andrew; Dunning, Nicholas; Hamilton, Trinity; Lentz, David; Scarborough, Vernon, Novel Molecular and Geochemical Analyses of Reservoir Sediments at the Ancient Maya City of Tikal, National Science Foundation. (BCS-1642547), $34,937.00. 09/01/2016 to 08/31/2017. Status: Active.
  • (Collaborator), Czaja, Andrew; Diefendorf, Aaron; Hamilton, Trinity; Havig, Jeff, Midwest Geobiology Conference , National Aeronautics and Space Administration. (OSGC Student-Innovative-Creative-Hands-on Project (SICHOP) grant), $2,000.00. 06/06/2016 to 12/31/2016. Status: Awarded.
  • (PI), Hamilton, Trinity, Microbe-Mineral Interactions in Glaciated Basaltic Terrains, National Aeronautics and Space Administration. (MSU G129-17-W6157 / NASA NNX16AJ64G), $49,192.00. 08/01/2016 to 07/31/2019. Status: Active.
  • (Collaborator), Buffam, Ishi; Hamilton, Trinity, Double Trouble: Effects of Algal Bloom Biomass on Methane Production in a Eutrophic Ohio Reservoir, U.S. Geological Survey. (OSU 60059469 / USGS G16AP00076), $4,967.70. 03/01/2017 to 02/28/2021. Status: Active.


Peer-reviewed Publications

  • Hamilton, T.L., Bovee R.J., Sattin S.R., Mohr, W., Gilhooly III, W.P., Lyons, Pearson, A., Macalady, J.L. (2016). Carbon and sulfur cycling below the chemocline in a meromictic lake and the identification of a novel taxonomic lineage in the FCB superphylum, Candidatus Aegiribacteria. Frontiers in Microbiology, 7, 598. [Link]
  • Harrold, Z.R., Skidmore, M., Hamilton, T.L., Desch, L., Amada, K., van Gelder, W., Roden, E., Boyd, E.S. (2016). Aerobic and anaerobic thiosulfate oxidation by a cold-adapted, subglacial chemoautotroph. Applied and Environmental Microbiology, 82, 1486. [Link]
  • Urschel, M.R., Hamilton, T.L., Roden, E.R., Boyd., E.S. (2016). (In Press). Substrate Preference, Uptake Kinetics, and Bioenergetics in a Facultatively Autotrophic, Thermoacidophilic Crenarchaeote. FEMS Microbiology Ecology. [Link]
  • Hamilton, T.L., Jones, D.S., Schaperdoth, I., Macalady, J.L. (2015). Metagenomic insights into S(0) precipitation in a terrestrial subsurface lithoautotrophic ecosystem. Frontiers in Microbiology, 5, 756. [Link]
  • Boyd, E.S., Garcia Costas, A.M., Hamilton, T.L., Mus, F., Peters, J.W. (2015). Evolution of molybdenum nitrogenase during the transition from anaerobic to aerobic metabolism. Journal of Bacteriology. [Link]
  • Havig, J.R., McCormick, M.L., Hamilton, T.L., Kump, L.R. (2015). (In Press). The behavior of biologically important trace elements across the oxic/euxinic transition of meromictic Fayetteville Green Lake, New York, USA. Geochimica Et Cosmochimica Acta. [Link]
  • Hamilton, T.L., Bryant, D.A., Macalady, J.L. (2015). The role of biology in planetary evolution: Cyanobacterial primary production in low oxygen Proterozoic oceans. Environmental Microbiology, 18, 325. [Link]
  • Mansor, M. Hamilton, T.L., Fantle, M., Macalady, J.L. (2015). Metabolic diversity and ecological niches of Achromatium populations revealed with single-cell genomic sequencing. Frontiers in Microbiology, 6, 822.
  • Telling, J., Boyd, E.S., Bone, N., Jones, E., Tranter, M., J.L., MacFarlane, Martin, P., Wadham, J., LaMarche-Gagnon, G., Skidmore, M.L., Hamilton, T.L., Hill, E., Jackson, M., Hodgson, D.A. (2015). Rock comminution as a source of hydrogen for subglacial ecosystems. Nature Geoscience, 8, 851. [Link]
  • Thiel T., Hamilton, T.L., Tomsho, L.P., Burbans, R., Gay, S.E., Ramaley, R.F., Schuster, S.C., Steinke, L.A., Bryant, D.A. (2014). Draft genome sequence of the moderately thermophilic bacterium Schleiferia thermophila strain Yellowstone (Bacteroidetes). GenomeA, 2 (4). [Link]
  • Thiel T., Hamilton, T.L., Tomsho, L.P., Burbans, R., Gay, S.E., Schuster, S.C., Ward, D.M., Bryant, D.A (2014). Draft genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus sp. strain MS-G (Chloroflexi). GenomeA, 2 (5). [Link]
  • Boyd, E.S., Hamilton, T.L., Swanson, K.D., Howells, A.E., Baxter, B.K., Meuser, J.E., Posewitz, M.C., Peters, J.W. (2014). [FeFe]-Hydrogenase Abundance and Diversity along a Vertical Redox Gradient in Great Salt Lake, USA. International Journal of Molecular Sciences, 15, 21947-21966. [Link]
  • Boyd, E.S., Hamilton, T.L., Havig, J.R., Skidmore, M., Shock, E.S. (2014). Chemolithotrophic primary production in a subglacial ecosystem. Applied and Environmental Microbiology, 80, 6146-6132. [Link]
  • Hamilton, T.L., Koonce, E., Howells, A., Havig, J.R., Jewell, T., de la Torre, J., Peters, J.W., Boyd, E.S. (2014). Competition for ammonia influences the structure of chemotrophic communities in geothermal springs. Applied and Environmental Microbiology, 80, 653-661. [Link]
  • Hamilton, T.L., Bovee R.J., Thiel, V., Sattin S.R., Mohr, W., Schaperdoth, I., Vogl K., Gilhooly III, W.P., Lyons, T.W., Tomsho, L.P., Schuster, S.C., Overmann, J., Bryant D.A., Pearson, A., Macalady, J.L. (2014). Coupled reductive and oxidative sulfur cycling in the phototrophic plate of a meromictic lake. Geobiology, 12, 451-468. [Link]
  • Macalady, J.L., Hamilton, T.L., Grettenberger, C.L., Jones, D.S., Tsao, L.E., Burgos, W.D. (2013). Energy, ecology and the distribution of microbial life. Philosophical Transactions of the Royal Society B, 368 (1622). [Link]
  • Boyd, E.S., Hamilton, T.L., Wang, J., He, L., Zhang, C.L. (2013). The role of tetraether lipid composition in the adaptation of thermophilic archaea to acidity. Frontiers in Terrestrial Microbiology, 4, 62. [Link]
  • Hamilton, T.L., Peters. J.W., Skidmore, M.L., Boyd, E.S. (2013). Molecular evidence for an active endogenous microbiome beneath glacial ice. The ISME Journal, 7, 1402-1412. [Link]
  • Duffus, B.R., Hamilton, T.L., Shepard, E., Boyd, E.S., Peters, J.W., Broderick, J.B. (2012). Radical AdoMet Enzymes in Complex Inorganic Metal Cluster Biosynthesis. Biochimica Et Biophysica Acta (BBA)-Proteins and Proteomics, 1824, 1254-1263. [Link]
  • Boyd, E.S., Hamilton, T. L., Peters. J.W. (2011). An alternative path for the evolution of biological nitrogen fixation. Frontiers in Microbiology, 2, 205. [Link]
  • Hamilton, T.L., Vogl, K., Bryant, D.A., Boyd, E.S., Peters, J.W. (2011). Environmental constraints define the distribution, composition, and evolution of chlorophototrophs in thermal features of Yellowstone National Park. Geobiology, 10, 236-249. [Link]
  • Hamilton, T.L., Jacobson, M., Ludwig, M., Boyd, E.S., Bryant, D.A., Dean, D.R., Peters, J.W. (2011). Differential accumulation of nif structural gene mRNA in Azotobacter vinelandii. Journal of Bacteriology, 193, 4534-4536. [Link]
  • Hamilton, T.L., Ludwig, M., Dixon, R., Boyd, E.S., Dos Santos, P., Setubal, J.C., Bryant, D.A., Dean, D.R., Peters, J.W. (2011). Transcriptional profiling of nitrogen fixation in Azotobacter vinelandii. Journal of Bacteriology, 193, 4477-4486. [Link]
  • Boyd, E.S., Lange, R.K., Mitchell, A.C., Havig, J.R., Hamilton, T.L., Lafrenière, M.J., Shock, E.L., Peters, J.W., Skidmore, M. (2011). Diversity, abundance, and potential activity of nitrifying and denitrifying microbial assemblages in a subglacial ecosystem., 77, 4778-4787. [Link]
  • Hamilton, T.L., Boyd, E.S., Lange, R.K., Peters, J.W. (2011). Biological nitrogen fixation in acidic high temperature geothermal springs in Yellowstone National Park, Wyoming. Environmental Microbiology, 13, 2204-2215. [Link]
  • Hamilton, T.L., Boyd, E.S., Peters, J.W. (2011). Environmental constraints underpin the phylogenetic diversity of nifH in the Yellowstone Geothermal Complex. Microbial Ecology, 10, 236-249. [Link]
  • Boyd, E.S., Anbar, A.D., Miller, S., Hamilton, T.L., Lavin, M., Peters, J.W. (2011). A late methanogen origin for molybdenum-dependent nitrogenase. Geobiology, 9, 221-232. [Link]
  • Boyd, J.M., Endrizzi, J.A., Hamilton, T.L., Downs, D.M., Peters, J.W. (2011). FAD binding by ApbE protein from Salmonella enterica: a new class of FAD binding proteins. Journal of Bacteriology, 193, 887-895. [Link]
  • Boyd, E.S., Hamilton, T.L., Spear, J.R., Lavin, M., Peters, J.W. (2010). [FeFe]-hydrogenase In Yellowstone National Park: Evidence for dispersal limitation and phylogenetic niche conservation. The ISME Journal, 4, 887-895. [Link]
  • Sarma, R, Barney, B.M., Hamilton, T.L., Jones, A., Seefeldt, L.C., Peters, J.W. (2008). Crystal structure of the L protein of Rhodobacter sphaeroides light-independent protochlorophyllide reductase with MgADP bound: a homologue of the nitrogenase Fe protein. Biochemistry, 47, 13004-13015. [Link]
  • Taylor, R.M., Maaty, W.S., Lord. C.I., Hamilton, T., Burritt, J.B., Bothner, B., Jesaitis, A.J. (2007). Cloning, sequence analysis and confirmation of derived gene sequences for three epitope-mapped monoclonal antibodies against human phagocyte flavocytochrome b. Molecular Immunology, 44, 625-637. [Link]

Book Chapters

  • Peters, J.W., Boyd, E.S., Hamilton, T.L., Rubio, L. (2011). Biochemistry of Mo-Nitrogenase. In J.W.B. Moir (Eds.), Nitrogen Cycling in Bacteria: Molecular Analysis Norfolk: Caister Academic Press.

Experience & Service

Post Graduate training and Education

  • 05/01/2013 to 12/31/2014, NASA Postdoctoral Program Fellow, The Pennsylvania State University , University Park, PA.
  • 07/01/2012 to 04/31/2013, Post-Doctoral Fellow, The Pennsylvania State University , University Park, PA.