Peer-reviewed publications and book chapters

member of the Hatzenpichler lab       shared first authorship       * corresponding author

​​​​16. ​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, accepted (2017) PDF

15. 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) PDF coming soon


14. Tavormina PL, Hatzenpicher R, McGlynn SE, Chadwick G, Dawson K, Connon S, and Orphan VJ. Methyloprofundus. Book chapter in Bergey’s Manual of Systematics of Archaea and Bacteria. John Wiley & Sons, Inc. doi: 10.1002/9781118960608.gbm01414 (2016)   PDF
Description of genus Methyloprofundus and its type species M. sediment from deep-sea sediment.

13. Miranda PJ, McLain N, Hatzenpichler R, Orphan VJ, Dillon JG. Characterization of chemosynthetic microbial mats associated with intertidal hydrothermal sulfur vents in White Point, San Pedro, CA. Front Microbiol, 7: 1163 (2016)   PDF

Diversity, micron-scale spatial associations, and metabolic activity of sulfate-reducers and sulfur-oxidizers in a microbial mat community.

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

>Covered by a 'News & Views' article in Nature Microbiol     >Press release by the DOE Joint Genome Institute

Discovery of Verrucomicrobial-Archaeal consortia in methane seep sediments via BONCAT-directed activity-based cell-sorting. Demonstrates, for the first time, that all major sub-clades of ANME are physiologically active under controlled conditions.

11. Hatzenpichler R* and Orphan VJ. Detection of protein-synthesizing microorganisms in the environment via bioorthogonal non-canonical amino acid tagging (BONCAT). Book chapter for Hydrocarbon and Lipid Microbiology Protocols, Vol. 7: Single-cell and single-molecule methods. Springer Protocols Handbooks, DOI 10.1007/8623_2015_61 (2015)   PDF

Provides a description of how to design and perform BONCAT experiments using the two bioorthogonal amino acids AHA and HPG.

10. 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, accepted (2014)   PDF

​Reports the isolation and growth characteristics of the gammaproteobacterial methane-oxidizer Methylococcaceae strain WF1.

9. 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)   PDF

Describes a microfluidics-based workflow for genetically targeted isolation and cultivation of microbes from clinical samples.

8. 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)     PDF

>Cover article   >Covered by a 'Research Highlight' in Environ Microbiol

Describes the first application of bioorthogonal labeling and click chemistry for fluorescent tracking of protein synthesis in individual, FISH-identified cells within environmental samples.

7. 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]   PDF

Reports on the enrichment and draft genome of a novel, moderately thermophilic group I.1a ammonia-oxidizing archaeon. 

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

A review of our current knowledge of the diversity and physiology of ammonia-oxidizing archaea, the factors controlling their ecology, and their role in the biogeochemical cycling of carbon and nitrogen.

5. Spang A, Poehlein A, Offre P, Zumbrägel S, Haider S, Rychlik N, Nowka B, Schmeisser C, Lebedeva E, Rattei T, Bӧhm C, Schmid M, Galushko A, Hatzenpichler R, Weinmaier T, Daniel R, Schleper C, Spieck E, Streit W, and Wagner M. The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: Insights into metabolic versatility and environmental adaptations. Environ Microbiol, 14: 3122–3145 (2012)   PDF

Reports the complete genome sequence of group I.1b AOA Ca. Nitrososphaera gargensis from a geothermal spring..

4. Mußmann M, Brito I, Pitcher A, Damsté JS, Hatzenpichler R, Richter A, Nielsen JL, Nielsen P H, Müller A, Daims H, Wagner M, and Head IM. Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers. Proc Natl Acad Sci U.S.A., 108: 16771-16776 (2011)   PDF

Demonstrates that some amoA gene-carrying and expressing group I.1b thaumarchaeotes are not obligate chemolithoautotrophs.

3. Shapiro OH, Hatzenpichler R*, Buckley DH, Zinder SH, and Orphan VJ. Multicellular photo-magnetotactic bacteria. Environ Microbiol Rep, 3: 233–238 (2011)   >Chief Editor’s Choice Article 2011   [equal contribution]   PDF

Reports a newly discovered phototactic behavior of multicellular magnetotactic bacteria from salt marsh sediment.

2. 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)   >Cover article   >Most cited TiM-paper of the past 5 years   PDF

Confirms the assignment of three novel archaea to the proposed phylum Thaumarchaeota and reveals a lineage-specific set of core informational processing genes.

1. 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 U.S.A., 105: 2134-2139 (2008)   PDF

Reports enrichment and physiological characterization of the ammonia-oxidizing archaeon Ca. Nitrososphaera gargensis, and provides first evidence that the concentration of ammonia is a niche-differentiating factor between archaeal and bacterial ammonia oxidizers.