Office: 111 Chemistry Biochemistry Building
Labs: 152 and 157
Phone: 406-994 5469



Research Group Website:


University of Vienna, Austria, Ph.D. (2006-2011)
University of Vienna, Austria, Master of Science (2001-2006)

Awards and honors:

NASA Early Career Award, 2016
Postdoctoral Fellowship by the NSF Center for Dark Energy Biosphere Investigations, 2014
Marie Curie Fellow via an Erwin Schrӧdinger Postdoctoral Scholarship of the Austrian Science Fund, 2011
O.K. Earl Postdoctoral Fellowship in Geobiology by the Division of Geological and Planetary Sciences, Caltech, 2011
Doc.Award for outstanding PhD thesis by the City of Vienna, 2011
Pre-doctoral fellowship of the Austrian Academy of Sciences, 2007


Our research activities focus on microbial ecophysiology: the study of the physiology of microorganisms with respect to their habitat. We are interested in how the activity of the “uncultured majority” – the large number of microbes that evades cultivation under laboratory conditions – impacts humans and the environment on a micron to global scale. We believe that only by gaining an understanding of microbes directly in their habitats researchers will be able to elucidate the mechanisms of microbial interactions with the biotic and abiotic world. To accomplish these goals, we apply an integrative approach that bridges the two extremes of the microbial scale bar: the individual cell and the whole community.

Very broadly, the research questions the Hatzenpichler lab addresses are:
(1) who is doing what (linking phylogenetic identity and physiological function),
(2) what are the abiotic and biotic factors controlling microbial in situ activity,
(3) how does this activity affect the environment and us humans,
(4) what are the limits to microbial metabolism in terms of energy, space, and time, and
(5) how can we discover novel structures and functions within uncharted branches of the tree of life?

We currently work with three main sample types: sediments from the Guaymas deep-sea basin, geothermal springs in Yellowstone National Park, and a New England salt marsh. We are particularly interested in revealing the physiology, biogeochemical impact, and ecology of only very recently discovered archaea and bacteria.

Research projects in our group are suitable for students with interests in biochemistry, bioorthogonal chemistry, cell physiology, biogeochemistry, and/or environmental microbiology. Students can expect to learn techniques that may include: in field experimentation, genome sequencing, genome annotation, fluorescence in situ hybridization, bioorthogonal compound labeling, stable isotope labeling, single cell resolved Raman spectroscopy, fluorescence activated cell sorting, and proteomics.

We collaborate with many research groups not only across campus but the entire U.S. to achieve our ultimate goal of a system-wide understanding of microbes directly in their environment.

Our research is generously supported by the National Science Foundation (NSF), the Gordon and Betty Moore Foundation, and the National Aeronautics and Space Administration (NASA).











Retrieving hydrothermal sediment samples by submersible Alvin.


Some of Yellowstone National Park geothermal features we sampled in 2017.  All research in Yellowstone was performed under research permit YELL-2017-SCI-8010.


Protein synthesis active cells in a 74ºC hot spring are visualized after incubated hot spring material in the presence of non-canonical amino acids directly in the field. Later in the lab, protein-making cells are then stained (red). DNA in cells is stained in blue. 

Learn more about our research at

Recent Publications:

Marlow JJ and Hatzenpichler R. Assessing metabolic activity at methane seeps: a testing ground for slow-growing environmental systems. Book chapter in Microbial life in the deep biosphere. Accepted (2017)

McKay LJ, Hatzenpichler R, Inskeep WP, and Fields MW. Occurrence and expression of novel methyl-coenzyme M reductase gene (mcrA) variants in hot spring sediments. Nat Sci Rep, 7:7252 (2017)

Miranda PJ, McLain NK, Hatzenpichler R, Orphan VJ, and Dillon J. Characterization of chemosynthetic microbial mats associated with intertidal hydrothermal sulfur vents in White Point, San Pedro, CA, USA. Front Microbiol, accepted (2016)

Hatzenpichler R, Connon SA, Goudeau D, Malmstrom R, Woyke T, Orphan VJ. Visualizing in situ translational activity for identifying and sorting slow-growing archaeal-bacterial consortia.  Proc Natl Acad Sci USA, 113: E4069-E4078 (2016)

Tavormina PL, Hatzenpichler R, McGlynn S, Chadwick G, Dawson K, Connon S, and Orphan VJ. Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the Deep Sea 1 clade of marine methanotrophs.Int J Syst Evo Microbiol,65: 251–259 (2015)

Hatzenpichler R, Scheller S, Tavormina PL, Babin B, Tirrell D, and Orphan VJ. In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry. Environ Microbiol, 16: 2568-2590 (2014)

Ma L, Kim J, Hatzenpichler R, Karymov MA, Hubert N, Hanan IM, Chang EB, and Ismagilov RF. Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project’s Most Wanted taxa. Proc Natl Acad Sci USA, 111: 9768–9773 (2014)

Lebedeva EV, Hatzenpichler R, Pelletier E, Schuster N, Hauzmayer S, Bulaev A, Grigorjeva NV, Galushko A, Schmid M, Palatinsky M, Le Paslier D, Daims H, and Wagner M. Enrichment and genome sequence of the group I.1a ammonia-oxidizing archaeon “Ca. Nitrosotenuis uzonensis” representing a clade globally distributed in thermal habitats. PLoS One, 8: e80835 (2013)           (equal contribution)

Hatzenpichler R. Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea. Appl Environ Microbiol, 78: 7501-7510 (2012)

Shapiro OH, Hatzenpichler R, Buckley DH, Zinder SH, and Orphan VJ. Multicellular photo-magnetotactic bacteria. Environ Microbiol Rep, 3: 233-238 (2011) (equal contribution)

Spang A, Hatzenpichler R, Brochier-Armanet C, Rattei T, Tischler P, Spieck E, Streit W, Stahl DA, Wagner M, and Schleper C. Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol 18:331-40 (2010)

Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A, Daims H, and Wagner M. A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc Natl Acad Sci USA, 105: 2134-2139 (2008)