From a single-cell as a microcosm to complex microbial consortia that inhabit extreme environments, our research probes how microorganisms adapt and respond to environmental stresses. Our research spans the fields of molecular biology, metagenomics, microbial ecology, and planetary science. We use archaeal model systems in the lab and do fieldwork in extreme deserts around the world.

Archaea are abundant in extreme environments, presenting an opportunity to gain insights into molecular adaptations to hostile habitats. Archaea are evolutionarily closer to Eukarya as emphasized by the recent discovery of the Asgard archaeal superphylum. This close evolutionary relationship between the archaeal and eukaryal domains is expressed by similarities of central dogma processes (replication, transcription, and translation) and an expected complexity in the Archaea. We thus stand to discover novel mechanisms and processes by studying the molecular biology of Archaea. We use the haloarchaeon Haloferax volcanii as a model to investigate regulatory mechanisms, at the post-transcriptional and translational level, in response to environmental stressors

Deserts and hypersaline environments represent the dry limits for life on Earth. These are fragile ecosystems and, as such, are unique model systems to study the effect of climate change on communities and ecosystems. Under the harsh conditions of hyper-arid deserts, microorganisms find refuge inside rocks as a survival strategy. We use these endolithic microbial communities from the Atacama, Namib, Negev, and Mojave Deserts and the Dry Valleys of Antarctica to address fundamental questions in microbial ecology.

Our research is directly related to Astrobiology. Visit the Institute for Planets and Life web site

Atacama Desert, Chile

Molecular Biology of Archaea

Gelsinger D.R., R. Reddy, K. Whittington, S. Debic and J. DiRuggiero. 2021. Post-transcriptional regulation of redox homeostasis by the small RNA SHOxi in haloarchaea. RNA Biol. 31:1-15 PubMed PMID: 33522404.

Gelsinger D.R., E. Dallon, R. Reddy, F. Mohammad, A.R. Buskirk, and J. DiRuggiero. 2020. Ribosome profiling in archaea reveals leaderless translation, novel translational initiation sites, and ribosome pausing at single codon resolution. Nucleic Acids Res. 48:5201-516 PubMed PMID: 32382758; selected as a Breakthrough Article by the Editors of Nucleic Acids Res.

Schmid A.K., Allers T., and J DiRuggiero. 2020. SnapShot: Biogeography and molecular adaptations of microbial extremophiles. Cell 180:818-818.e1 PubMed PMID:32084345.

Gelsinger, D. and J. DiRuggiero. 2018. Transcriptional landscape and regulatory roles of small non-coding RNAs in the oxidative stress response of the haloarchaeon Haloferax volcanii. J Bacteriol 200:e00779-17 PubMed PMID:29463600.

Gelsinger D. and J. DiRuggiero. 2018. The non-coding regulatory RNA revolution in Archaea. Genes 9:E141 PubMed PMID:29510582.

Microbial Ecology

Ertekin E., V. Meslier, A. Browning, J. Treadgold, and J. DiRuggiero. 2021. Functional and taxonomic diversity is driven by substrate architecture in endolithic communities from extreme environments. Env. Microbiol. 23: 3937–3956 PubMed PMID: 33078515.

Uritskiy G., A. Munn, M. Dailey, D.R. Gelsinger, S. Getsin, A. Davila, P. McCullough, J. Taylor and J. DiRuggiero. 2020. Environmental factors driving spatial heterogeneity in desert halophile microbial communities. Front. Microbiol. 11:578660 PubMed PMID: 33193201

Huang W., E. Ertekin, T. Wang, L. Cruz, M. Dailey, J. DiRuggiero and D. Kisailus. 2020. Life on the rocks: gypsum as a water source for microorganisms in the Atacama Desert. Proc Natl Acad U.S.A. 202001613 PubMed PMID: 32382758.

Uritskiy G., M. Tisza, D. Gelsinger, A. Munn, J. Taylor and J. DiRuggiero. 2020. Cellular life from the three domains and viruses are transcriptionally active in a hypersaline desert community. Env. Microbiol. doi:10.1111/1462-2920.15023 PubMed PMID: 32307861.

Gelsinger D., G. Uritskiy, R. Reddy, A. Munn, K. Farney, and J. DiRuggiero. 2020. Regulatory non-coding small RNAs are diverse and abundant in an extremophilic microbial community. mSystems 5:e00584-19. PubMed PMID: 32019831.

Qu E., Omelon C., Oren O., Meslier V., Cowan D.A., Maggs-Kölling G., and J. DiRuggiero. 2020. Trophic selective pressures organize the composition of endolithic microbial communities from global deserts. Front. Microbiol. 10:2952 PubMed PMID: 31969867.

Uritskiy G., S. Getsin, A. Munn, B. Gomez-Silva, A. Davila, B. Glass, J. Taylor and J. DiRuggiero. 2019. Halophilic microbial community compositional shift after a rare rainfall in the Atacama Desert. ISMEJ 13:2737–2749 PubMed PMID:31273300.

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Graduate Students

Sadhana Chidambaran

Frank Liu

Lorna Mitchison-Field (rotation)

Kevin Catalan

Emma Dallon

Postdoctoral fellow

Cesar Perez-Fernandez

Undergraduate Students

Betty Huang

Leo Busse

Assistant Research Scientist

Bayleigh Murray