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?

Our approach to these problems is inherently multi-disciplinary and multi-scaled. In order to address previously unrecognized physiologies and cellular interactions of uncultured microbes, we employ a unique combination of (meta)genomics (as hypotheses generator), high-through-put bioorthogonal labeling-based metabolic screening (to identify geochemical and biotic parameters driving microbial ecology), and targeted stable isotope probing (to identify specific growth-sustaining substrates). Because these approaches target the whole microbiome as well as the individual cell, we do not depend on the existence of samples enriched in a target population, as is often necessitated in ecological studies.

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)