Microbiology in Earth's Most Crucial and Vulnerable Environments
The Mackelprang Environmental Microbiology Lab seeks to understand microbial communities in a changing world and their effects on global biogeochemical cycles. We also investigate the boundaries at which life can exist to inform the search for life in extraterrestrial environments. We have a strong focus on microbial life in permafrost (permanently frozen soil), but also study other systems including desert biological soil crusts, prairie soils, and honeybees.
Research
Our research is organized around two main foci.
Climate Change: Environmental microbes are the engines driving crucial biogeochemical cycles. Climate change is altering microbe-environment interactions with globally significant consequences. In permafrost, thaw is exposing enormous amounts of undecomposed carbon to the metabolism of microbial communities, who are "breathing" it out as methane and carbon dioxide. We use multiple strategies including field manipulation experiments, laboratory incubations, and long-term observational surveys to understand the the factors controlling community membership, function, and turnover during permafrost thaw. Combining cutting-edge technologies including metagenomics, metatranscriptomics, metaproteomics and FT-ICR MS with culture-based work and statistical analyses enables us gain understanding at the systems level.
Exobiology: A primary goal of exobiology is to understand the origin, evolution, and distribution of life in the universe. Put more simply, if life exists elsewhere what might it look like? One way this is accomplished is through the study of environments on Earth that are analogous to extraterrestrial environments. We investigate life strategies of microbes in extreme environments such as ancient permafrost and desert biocrusts to determine how life survives through geologic time in extraterrestrial analogues.
Meet the Team
Rachel Mackelprang, Ph.D.
PI
Mike Snyder
Research Associate
Suzi Arzoumanyan
Graduate Student
Jonathan Corpeno
Graduate Student
Serena Hernandez
Graduate Student
Carolina Gonzalez
Graduate Student
Shannon Arias Ortega
Undergrad Student
Jessica Sandoval
Undergrad Student
Elenora Sarkisyan
Undergrad Student
Publications
Waldrop MP, Chabot CL, Liebner S, Holm S, Snyder MW, Dillon M, Dudgeon SR, Douglas TA, Leewis MC, Walter Anthony KM, McFarland JW, Arp CD, Bondurant AC, Tas N, Mackelprang R. 2023. Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients. ISME J. https://doi.org/10.1038/s41396-023-01429-6
Jessica G. Ernakovich, Robyn A. Barbato, Virginia I. Rich, Christina Schädel, Rebecca E. Hewitt, Stacey J. Doherty, Emily D. Whalen, Benjamin W. Abbott, Jiri Barta, Christina Biasi, Chris L. Chabot, Jenni Hultman, Christian Knoblauch, Maggie C. Y. Lau Vetter, Mary-Cathrine Leewis, Susanne Liebner, Rachel Mackelprang, Tullis C. Onstott, Andreas Richter, Ursel M. E. Schütte, Henri M. P. Siljanen, Neslihan Taş, Ina Timling, Tatiana A. Vishnivetskaya, Mark P. Waldrop, Matthias Winkel. (2022). Microbiome assembly in thawing permafrost and its feedbacks to climate. Global Change Biology, 28, 5007-5026. https://doi.org/10.1111/gcb.16231
Mary-Cathrine Leewis, Corey R. Lawrence, Marjorie S. Schulz, Malak M. Tfaily, Christian Orlando Ayala-Ortiz, Gilberto E. Flores, Rachel Mackelprang, Jack W. McFarland. (2022). The influence of soil development on the depth distribution and structure of soil microbial communities. Soil Biol Biogeochem., 208808. https://doi.org/10.1016/j.soilbio.2022.108808.
Rachel Mackelprang, Parag Vaishampayan, Kirsten Fisher. (2022). Adaptation to environmental extremes structures functional traits in biological soil crust and hypolithic microbial communities. (2022). mSystems. e01419-21. https://doi.org/10.1128/msystems.01419-21
Miner, K.R., D’Andrilli, J., Mackelprang, R. et al. (2021). Emergent biogeochemical risks from Arctic permafrost degradation. Nat. Clim. Change. 11, 809-818.
https://doi.org/10.1038/s41558-021-01162-y
Lalla SJ, Kaneshige KR, Miller DR, Mackelprang R, Mogul R. 2020. Quantification of endospores in ancient permafrost using time-resolved terbium luminescence. Analytical Biochemistry. 612:113957.
Akopyan M, Gompert Z, Klonoski K, Vega A, Kaiser K, Mackelprang R, Rosenblum EB, Robertson JM. 2020. Genetic and phenotypic evidence of a contact zone between divergent colour morphs of the iconic red-eyed treefrog. Molecular Ecology. 29:4442-4456.
Leewis MC, Berlemont R, Podgorski D, Srinivas A, Zito P, Spencer RGM, Mcfarland J, Douglas TA, Conaway C, Waldrop M, Mackelprang R. 2020 Life at the frozen limit: Microbial Carbon Metabolism Across a Late Pleistocene Permafrost Chronosequence. Frontiers in Microbiology. 11:1753
Burkert A, Douglas TA, Waldrop MP, Mackelprang R. 2019. Changes in the active, dead, and dormant microbial community structure across a Pleistocene permafrost chronosequence. Applied and Environmental Microbiology 85:e02646-18
Mackelprang R, Grube AM, Lamendella R, et al. 2018. Microbial community structure and functional potential in cultivated and native tallgrass prairie soils of the Midwestern United States. 2018. Front. Microbiol. 9:1775. doi: 10.3389/fmicb.2018.01775
Wright J, Kirchner V, Bernard W, Ulrich N, McLimans C, Campa MF, Hazen T, Macbeth T, Marabello D, McDermott J, Mackelprang R, Roth K, Lamendella R. 2017. Bacterial community dynamics in dichloromethane-contaminated groundwater undergoing natural attenuation. Front. Microbiol. 98:2300.
Mackelprang R, Burkert A, Haw M, Mahendrarajah T, Conaway CH, Douglas TA, Waldrop MP. 2017. Microbial survival strategies in ancient permafrost: insights from microbial metagenomics. ISME J. 11:2305-2318.
Mackelprang R, Jacobsen CS, Jansson JK, Tas N. Permafrost meta-omics and climate change. Annual Reviews of Earth and Planetary Sciences. 2016. DOI: 10/1146/annurev-earth-060614-105126
Mackelprang R, Mason OU. Marine microbiology: community clean up. Nature Microbiology 2016; 1:16102.
Hultman J, Waldrop MP, Mackelprang R, et al. Multi-omics of permafrost, active layer, and thermokarst bog soil microbiomes. Nature 2015; 521:208-212
Prestat E, David MM, Hultman J, Tas N, Lamendella R, Dvornik J, Mackelprang R, et al. FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus. Nucleic Acids Research 2014: doi: 10.1093/nar/gku702
Juarez M, Reyes M, Coleman T, Rotenstein L, Sao S, Martinez D, Jones M, Mackelprang R, De Bellard ME. Characterization of the trunk neural crest in the bamboo shark, Chiloscyllium punctatum. J Comp Neurol 2013; 521: 3303-20
Graham DE, Wallenstein MD, Vishnivetskaya TA, Waldrop MP, Phelps TJ, Pfiffner SM, Onstott TC, Whyte LG, Rivkina E, Gilichinsky DA, Elias DA, Mackelprang R, VerBerkmoes NC, Hettich RL, Wagner DW, Wullschleger SD, Jansson JK. Microbes in the thawing permafrost: The unknown variable in the climate change equation. ISME J 2012; 6:709-712
Mason OU, Hazen TC, Borglin S, Chain P, Dubinsky EA, Fortney J, Han J, Holman H-YN, Hultman J, Lamendella R, Mackelprang R, Tom LM, Tringe SG, Woyke T, Zhou J, Rubin EM, Jansson JK. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J 2012; 6:1715-1727
Mackelprang R, Waldrop MP, DeAngelis KM, Chavarria K, Blazewicz SJ, Rubin EM, Jansson JK. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 2011; 480:368-371
Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Field D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Konstantindis K, Kostka J, Kyrpides N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R. Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci. 2010; 3:243-248
Mackelprang R, Rubin E. New tricks with old bones. Science 2008; 321:211-212.
Mackelprang R, Livingston RJ, Eberle MA, Carlson CS, Yi Q, Akay JM, Nickerson DA. Sequence diversity, natural selection and linkage disequilibrium in the human T cell receptor alpha/delta locus. Human Genetics 2006; 119:255-266.
Yvert G, Brem RB, Whittle JW, Akey JM, Foss E, Smith EN, Mackelprang R, Kruglyak L. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nature Genetics 2003; 35:57-64.
Mackelprang R, Carlson CS, Subrahmanyan L, Livingston RJ, Eberle MA, Nickerson DA. Sequence variation in the human T-cell receptor loci. Immunol Rev 2002; 190:26-39.
Mackelprang R, Dearing MD, St Jeor S. High prevalence of Sin Nombre virus in rodent populations, central Utah: a consequence of human disturbance? Emerg Infect Dis 2001; 7:480-482
Scientific Reports, white papers, and book chapters
Mackelprang R, Tas N, Waldrop M. In press. Functional response of microbial communities to permafrost thaw. In Liebner S, Iganzert L (eds.) Microbial life in the cryosphere and its feedback on global change. De Gruyter.
BL Carrier, DW Beaty, MA Meyer, JG Blank, L Chou, S DasSarma, DJ Des Marais, JL Eigenbrode, N Grefenstette, NL Lanza, AC Schuerger, P Schwendner, HD Smith, CR Stoker, JD Tarnas, KD Webster, C Bakermans, BK Baxter, MS Bell, SA Benner, HH Bolivar Torres, PJ Boston, R Bruner, BC Clark, P DasSarma, AE Engelhart, ZE Gallegos, ZK Garvin, PJ Gasda, JH Green, RL Harris, ME Hoffman, T Kieft, AHD Koeppel, PA Lee, X Li, KL Lynch, R Mackelprang, PR Mahaffy, LH Matthies, MA Nellessen, HE Newsom, DE Northup, BRW O'Connor, SM Perl, RC Quinn, LA Rowe, B Sauterey, MA Schneegurt, Dirk Schulze-Makuch, LA Scuderi, MN Spilde, V Stamenković, JA Torres Celis, D Viola, BD Wade, CJ Walker, RC Wiens, AJ Williams, JM Williams, J Xu. 2020. Mars Extant Life: What’s Next? Astrobiology. 6:785-814.
MSPG (MSR Science Planning Group: co-chairs M. Meyer and E. Sefton-Nash; facilitation D. W. Beaty and B. L. Carrier; and D. Bass, F. Gaubert, M. M. Grady, T. Haltigin, A. D. Harrington, Y. Liu, D. Martin, B. Marty, R. Mattingly, S. Siljeström, E. Stansbery, K. Tait, M. Wadhwa, L. White), & A. M. B. Anesio, L. Bonal, A. Bouvier, J. C. Bridges, J. R. Brucato, K. L. French, U. Gommel, H. V. Graham, J. M. C. Holt, G. Kreck, R. Mackelprang, F. M. McCubbin, K. Olsson-Francis, A. B. Regberg, A. Saverino, M. A. Sephton, & C. K. Sio (2019) Science-Driven Contamination Control Issues Associated with the Receiving and Initial Processing of the MSR Samples. Unpublished workshop report, posted 09/20/19 at https://mepag.jpl.nasa.gov/reports.cfm.
David W Beaty, Monica M Grady, Harry Y McSween, Elliot Sefton‐Nash, Brandi L Carrier, Francesca Altieri, Yuri Amelin, Eleonora Ammannito, Mahesh Anand, Liane G Benning, Janice L Bishop, Lars E Borg, Dale Boucher, John R Brucato, Henner Busemann, Kathleen A Campbell, Andrew D Czaja, Vinciane Debaille, David J Des Marais, Michael Dixon, Bethany L Ehlmann, Jack D Farmer, David C Fernandez‐Remolar, Justin Filiberto, Jennifer Fogarty, DP Glavin, YS Goreva, Lydia J Hallis, Andrea Dawn Harrington, Elisabeth M Hausrath, Chris DK Herd, B Horgan, M Humayun, Thorsten Kleine, J Kleinhenz, R Mackelprang, N Mangold, LE Mayhew, JT McCoy, FM McCubbin, SM McLennan, DE Moser, F Moynier, JF Mustard, PB Niles, GG Ori, F Raulin, Petra Rettberg, MA Rucker, N Schmitz, SP Schwenzer, MA Sephton, R Shaheen, ZD Sharp, DL Shuster, S Siljeström, CL Smith, JA Spry, A Steele, TD Swindle, IL Ten Kate, NJ Tosca, T Usui, MJ Van Kranendonk, M Wadhwa, BP Weiss, SC Werner, F Westall, RM Wheeler, J Zipfel, MP Zorzano. 2019. The potential science and engineering value of samples delivered to Earth by Mars sample return. Meteoritics and Planetary Science. 54:S3-S512
Funding/Support
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