Research Projects and Publications

Despite their size, microbes are ubiquitous and seem to impact every aspect of life on Earth – from disease to climate change, biofuels to food, and the environment to our own body.

I first became interested in studying the Archaea – the lesser-studied third Domain of Life, distinct from Bacteria and Eukaryotes like us – while a graduate student. There, I focused on archaea found in the oceans, unlike the ‘extremophiles’ we are used to studying in hot springs and salt lakes. These Thaumarchaeota (now found in nearly every biome on Earth, including estuaries, lakes, soils, sediment, hot springs, etc.) are are key players in the global Nitrogen Cycle that take part in the first step of nitrification – the transformation of ammonia (a typical waste product and component of agricultural fertilizer) to nitrite. Have you ever purchased a “bioactive” rock for your fish tank at home, or seen an “activated sand” filter at an aquarium? If so, you have most certainly come in close contact with nitrification and perhaps even these ammonia-oxidizing Thaumarchaeota!

Current Research Projects:

Seasonal Dynamics of Marine Thaumarchaeota in a Coastal Upwelling System – Monterey Bay, California

  • Collected DNA and RNA, and measured a suite of physicochemical variables and nitrification rates for two years at two sites in collaboration with the Monterey Bay Aquarium Research Institute (MBARI)
  • Sequenced 16S rRNA, 18s rRNA, metagenomes, and metatranscriptomics
  • Ran quantitative PCR assays for distinct Thaumarchaeota ecotypes (“species”)
    • ‘Shallow’ water column A (WCA)
    • ‘Deep’ water column B (WCB)
    • Nitrosopumilus-like group (Nmar)
  • Generated metagenome-assembled genomes (MAGs) from datasets to gain more insight in lesser studied ecotypes (analysis in progress)
  • Resulting Publications (more info below):
    • 16. Reji, Tolar, et al., 2019a (ISME J)
    • 18. Reji, Tolar, et al., 2019b (Env Micro)
    • 21. Tolar et al., 2020 (Limnol Oceanogr)
    • 22. Reji, Tolar, et al., 2020 (Frontiers)

Funded by a grant from NSF Biological Oceanography (to C. Francis and F. Chavez)

Characterization of a low salinity ammonia-oxidizing archea: Nitrosarchaeum limnium

  • Maintained laboratory enrichment cultures (>97 % N. limnium) of two strains collected from the San Francisco Bay Delta
  • Characterized optimal growth conditions
  • Performed experiments measuring responses of N. limnium to environmental stress including temperature, salinity, & pH (analysis in progress)
  • Published chapter in Bergey’s Manual (#20, below) describing the genus Nitrosarchaeum

Funded in part through the JGI Small-Scale Sequencing Program (B. Tolar, & C. Francis)

Connections between microorganisms and geochemistry in a high-altitude floodplain along the Slate River near Crested Butte, Colorado

  • Collected microbial and geochemical samples across multiple field seasons to investigate changes as hydrological regimes shift from snowmelt to wet to dry
  • Performed inundation experiments in the field to investigate microbial responses to “wet-up” events
  • Sequenced 16S rRNA to characterize the microbial community and monitor changes from field samples and experiments (analysis in progress)

Funded through the SLAC Groundwater Quality SFA Program (PI: J. Bargar) under DOE Biological & Environmental Research

Metabolic capacity and seasonal changes in nitrogen-cycling communities within uranium-contaminated floodplain sediments near Riverton, Colorado

  • Follow-up to our 2017 investigations of microbial community dynamics during flood vs drought periods and their relationship with metals (#23: Tolar et al., 2019, Frontiers)
  • Includes metagenomic and metatranscriptomic sequencing, in addition to 16S rRNA-based community analysis, to generate MAGs and characterize mircobial metabolisms (analysis in progress)

Funded in part by a DOE grant (to C. Francis) and the SLAC Groundwater Quality SFA Program (PI: J. Bargar, DOE BER). Additional sequencing through a collaborative FICUS project through JGI and EMSL (K. Boye, C. Francis, and B. Tolar)


  1. Tolar, B.B., K. Boye, C. Bobb, K. Maher, J.R. Bargar, and C.A. Francis. Stability of floodplain subsurface microbial communities through seasonal hydrological and geochemical cycles (2020). Front Earth Sci. 8: 338.
  2. Reji, L., B.B. Tolar, F.P. Chavez, and C.A. Francis. Depth-differentiation and seasonality of planktonic microbial assemblages in the Monterey Bay upwelling system (2020). Front Aquat Microbiol. 11:1075.
  3. Tolar, B.B., L. Reji, J.M. Smith, M. Blum, J.T. Pennington, F.P. Chavez, and C.A. Francis. Time series assessment of Thaumarchaeota ecotypes in Monterey Bay reveals the importance of water column position in predicting distribution-environment relationships (2020). Limnol Oceanogr. 65: 2041-2055.
  4. Tolar, B.B., A.C. Mosier, M.B. Lund, and C.A. Francis. Nitrosarchaeum (gbm01289). In: Bergey’s Manual of Systematics of Archaea and Bacteria, Ed: W.B. Whitman, John Wiley & Sons: Hoboken, NJ (2019).
  5. Damashek, J., C.F. Edwardson, B.B. Tolar, S.M. Gifford, M.A. Moran, and J.T. Hollibaugh. Coastal ocean metagenomes and curated metagenome-assembled genomes (MAGs) from Marsh Landing, Sapelo Island (Georgia, USA) (2019). Microbiol Resour Announc 8: e00934-19.
  6. Reji, L. B.B. Tolar, J.M. Smith, F.P. Chavez, and C.A. Francis. Depth distributions of nitrite reductase (nirK) gene variants reveal spatial dynamics of thaumarchaeal ecotype populations in coastal Monterey Bay (2019). Environ Microbiol. 21: 4032-4045.
  7. Damashek, J., B.B. Tolar, Q. Liu, A.O. Okotie-Oyekan, N.J. Wallsgrove, B.N. Popp, and J.T. Hollibaugh. Microbial oxidation of nitrogen supplied as selected organic nitrogen compounds in the South Atlantic Bight (2019). Limnol Oceanogr 64: 982-995.
  8. Reji, L., B. B. Tolar,J.M. Smith, F.P. Chavez, and C.A. Francis. Differential co-occurrence relationships shaping ecotype diversification within Thaumarchaeota populations in the coastal ocean water column (2019). ISME J 13: 1144-1158.
  9. Li, P-N., J.R. Herrmann,F.P.B. Poitevin, R. Ramdasi, B.B. Tolar,J. Bargar, D. Stahl, G. Jensen, S. Wakatsuki, and H. van den Bedem. Cryo electron tomography and reaction-diffusion simulations reveal a molecular and evolutionary basis for charged archaeal surface layer proteins (2018). Biophys J 114: 495A.
  10. Li, P-N., J. Herrmann, B.B. Tolar,F. Poitevin, R. Ramdasi, J.R. Bargar, D.A. Stahl, G.J. Jensen, C.A. Francis, S. Wakatsuki, and H. van den Bedem. Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins (2018).  ISME J 12: 2389-2402.
  11. Liu, Q., B.B. Tolar, M.J. Ross, J.B. Cheek, C.M. Sweeney, N.J. Wallsgrove, B.N. Popp, and J.T. Hollibaugh. Light and temperature control the seasonal distribution thaumarchaeota in the South Atlantic Bight(2018). ISME J 12: 1473-1485.
  12. Tolar, B.B., N.J. Wallsgrove, B.N. Popp, and J.T. Hollibaugh. Oxidation of urea nitrogen in Thaumarchaeota-dominated marine nitrifying communities (2017). Environ Microbiol 19: 4838-4850.
  13. Tolar, B.B., J. Herrmann, J.R. Bargar, H. van den Bedem, S. Wakatsuki, and C.A. Francis. Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing Archaea (2017).  Environ Microbiol Reports 9: 484-491.
  14. Kremer, C.T., A.K. Williams, M. Finiguerra, A.A. Fong, A. Kellerman, S.F. Paver, B.B. Tolar, and B.J. Toscano. Realizing the potential of trait-based aquatic ecology: new tools and collaborative approaches (2017). Limnol Oceanogr 62: 253-271. *Eco-DAS
  15. Tolar, B.B., L.C. Powers, W.M. Miller, N.J. Wallsgrove, B.N. Popp, and J.T. Hollibaugh. Ammonia oxidation in the ocean is inhibited by hydrogen peroxide (2016). Front Mar Sci 3: 237.
  16. Hundey, E.J., J.H. Olker, C. Carriera, R.M. Daigle, A.K. Elgin, M. Finiguerra, N.J. Gownaris, N. Hayes, L. Heffner, N.R. Razavi, P.D. Shirey, B.B. Tolar, and E.M. Wood-Charlson. A shifting tide: Recommendations for incorporating science communication into graduate training (2016). Limnol Oceanogr Bulletin 25: 109-116. *Eco-DAS
  17. Tolar, B.B., M.J. Ross, N.J. Wallsgrove, Q. Liu, L.I. Aluwihare, B.N. Popp, and J.T. Hollibaugh. Significant rates of chemoautotrophy in Antarctic coastal waters attributed to ammonia oxidation by Thaumarchaeota (2016). ISME J 10: 2605-2619.
  18. Liu, Q., X. Lu, B.B. Tolar, X. Mou, and J.T. Hollibaugh. Concentrations, turnover rates and fluxes of polyamines in coastal waters of the South Atlantic Bight (2015). Biogeochemistry 123: 117-133.
  19. Luo, H., B.B. Tolar, B.K. Swan, C.L. Zhang, R. Stepanauskas, M.A. Moran, and J.T. Hollibaugh. Single cell genomes of marine thaumarchaeota reveal insights into population differentiation by depth (2014). ISME J 8: 732-736.
  20. Hollibaugh, J.T., S.M. Gifford, M.A. Moran, M. Ross, S. Sharma, and B.B. Tolar. Seasonal variation in the metatranscriptomes of a Thaumarchaeota population from SE USA coastal waters (2014). ISME J 8: 685-698.
  21. Smith, C.B., B.B. Tolar, J.T. Hollibaugh, and G.M. King. Alkane hydroxylase gene (alkB) phylotype composition and diversity in northern Gulf of Mexico bacterioplankton (2013). Front Aquat Microbiol 4: 370.
  22. Tolar, B.B., G.M. King, and J.T. Hollibaugh.An analysis of Thaumarchaeota populations from the northern Gulf of Mexico (2013). Front Aquat Microbiol 4: 72.
  23. King, G.M., C. Smith, B. Tolar, and J.T. Hollibaugh. Analysis of composition and structure of coastal to mesopelagic bacterioplankton communities in the northern Gulf of Mexico (2013). Front Microbiol 3: 438.
%d bloggers like this: