Dr. Eric Daniel Becraft

Assistant Professor, University of North Alabama

Department of Biology UNA Box 5048

Florence, AL 35632

ebecraft@una.edu

General Research Interests:

      I study microbial diversity, ecology, and evolution in the context of microbial community structure and function. My main focus areas are: 1) the identification and genomics of uncultured bacterial and archaeal phyla and their contributions environmental systems; 2) microbial evolution, speciation and genetic modes of adaptation; 3) microbiology in extreme environments. I am also interested in co-evolved symbiotic interactions and the contribution of microorganisms to global geochemical cycling.  

Education:

• Ph.D. Ecology and Environmental Sciences (2006-2013) Montana State University (Dr. David Ward).

• B.S. Microbiology (2002-2005) University of Texas at Austin.

• A.S. Biology (2000-2002) Del Mar College.

 Professional Experiences

• Assistant Professor, University of North Alabama, Florence, AL. Department of Biology (August 2018-present).

• Postdoctoral scholar, Bigelow Laboratory for Ocean Sciences, East Boothbay, ME. (2015-2018, P.I. Dr. Ramunas Stepanauskas). Untangling the genealogy of uncultivated microorganisms.

• Postdoctoral scholar, Department of Biological Sciences, Northern Illinois University, DeKalb, IL. (2013-2015, P.I. Dr. Wesley Swingley). Analyses of uncultivated microorganisms in extreme environments.

• Ph.D. candidate, Land Resources and Environmental Sciences, Montana State University, Bozeman, MT. (2006-2013, mentor Dr. David Ward). The ecology and evolution of thermophilic Synechococcus species.

• Laboratory technician, Department of Integrative Biology, University of Texas at Austin, Austin, TX. (2004-2005, employer Dr. Lauren Ancel-Meyers). Co-evolution of complex bacterial communities.

• Laboratory technician, Department of Integrative Biology, University of Texas at Austin, Austin, TX. (2004-2005, employer Dr. Ulrich Muller). Co-evolution of bacterial-fungus-ant mutualisms.

• Undergraduate assistant, Department of Integrative Biology, University of Texas at Austin, Austin, TX. (2003-2004, mentor Dr. Robert Goldman). Experimental microbial evolution to extreme environments.

Publications in Alphabetical order († indicates co-first author)

• Beam, J. P., Becraft, E. D., Brown, J. M., Schulz, F., Jarett, J. K., Bezuidt, O., Poulton, N. J., Clark, K., Dunfield, P. F., Ravin, N. V., Spear, J. R., Hedlund, B. P., Kormas, K. A., Sievert, S. M., Elshahed, M. S., Barton, H. A., Stott, M. B., Eisen, J. A., Moser, D. P., . . . Stepanauskas, R. (2020). Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN. Front Microbiol, 11, 1848. https://doi.org/10.3389/fmicb.2020.01848.

• Becraft, E. D., Cohan, F. M., Kuhl, M., Jensen, S. I., & Ward, D. M. (2011). Fine-scale distribution patterns of Synechococcus ecological diversity in microbial mats of Mushroom Spring, Yellowstone National Park. Appl Environ Microbiol, 77(21), 7689-7697. https://doi.org/10.1128/AEM.05927-11.

• Becraft, E. D., Dodsworth, J. A., Murugapiran, S. K., Ohlsson, J. I., Briggs, B. R., Kanbar, J., De Vlaminck, I., Quake, S. R., Dong, H., Hedlund, B. P., & Swingley, W. D. (2016). Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes. Appl Environ Microbiol, 82(4), 992-1003. https://doi.org/10.1128/AEM.03140-15.

• Becraft, E. D., Dodsworth, J. A., Murugapiran, S. K., Thomas, S. C., Ohlsson, J. I., Stepanauskas, R., Hedlund, B. P., & Swingley, W. D. (2017). Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs. Front Microbiol, 8, 2082. https://doi.org/10.3389/fmicb.2017.02082.

• †Becraft, E. D., †Jackson, B. D., †Nowack, S., Klapper, I., & Ward, D. M. (2020). Relationship between Microorganisms Inhabiting Alkaline Siliceous Hot Spring Mat Communities and Overflowing Water. Appl Environ Microbiol, 86(23). https://doi.org/10.1128/AEM.00194-20.

• Becraft, E. D., Lau Vetter, M. C. Y., Bezuidt, O. K. I., Brown, J. M., Labonte, J. M., Kauneckaite-Griguole, K., Salkauskaite, R., Alzbutas, G., Sackett, J. D., Kruger, B. R., Kadnikov, V., van Heerden, E., Moser, D., Ravin, N., Onstott, T., & Stepanauskas, R. (2021). Evolutionary stasis of a deep subsurface microbial lineage. ISME J. https://doi.org/10.1038/s41396-021-00965-3.

• Becraft E. D. and Moya A. (2021) Editorial: Searching for the Boundaries of Microbial Speciation in a Rapidly Evolving World. Front. Microbiol. 12:808595. doi: 10.3389/fmicb.2021.808595.

• †Becraft, E. D., †Wood, J. M., Cohan, F. M., & Ward, D. M. (2020). Biogeography of American Northwest Hot Spring A/B'-Lineage Synechococcus Populations. Front Microbiol, 11, 77. https://doi.org/10.3389/fmicb.2020.00077.

• Becraft, E. D., Wood, J. M., Rusch, D. B., Kuhl, M., Jensen, S. I., Bryant, D. A., Roberts, D. W., Cohan, F. M., & Ward, D. M. (2015). The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park. Front Microbiol, 6, 590. https://doi.org/10.3389/fmicb.2015.00590.

• Becraft, E. D., Woyke, T., Jarett, J., Ivanova, N., Godoy-Vitorino, F., Poulton, N., Brown, J. M., Brown, J., Lau, M. C. Y., Onstott, T., Eisen, J. A., Moser, D., & Stepanauskas, R. (2017). Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla. Front Microbiol, 8, 2264. https://doi.org/10.3389/fmicb.2017.02264.

• Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., Eloe-Fadrosh, E. A., Tringe, S. G., Ivanova, N. N., Copeland, A., Clum, A., Becraft, E. D., Malmstrom, R. R., Birren, B., Podar, M., Bork, P., . . . Woyke, T. (2017). Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol, 35(8), 725-731. https://doi.org/10.1038/nbt.3893.

• Chen, M. L., Becraft, E. D., Pachiadaki, M., Brown, J. M., Jarett, J. K., Gasol, J. M., Ravin, N. V., Moser, D. P., Nunoura, T., Herndl, G. J., Woyke, T., & Stepanauskas, R. (2020). Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f. Front Microbiol, 11, 376. https://doi.org/10.3389/fmicb.2020.00376.

• Jarett, J. K., Dzunkova, M., Schulz, F., Roux, S., Paez-Espino, D., Eloe-Fadrosh, E., Jungbluth, S. P., Ivanova, N., Spear, J. R., Carr, S. A., Trivedi, C. B., Corsetti, F. A., Johnson, H. A., Becraft, E. D., Kyrpides, N., Stepanauskas, R., & Woyke, T. (2020). Insights into the dynamics between viruses and their hosts in a hot spring microbial mat. ISME J, 14(10), 2527-2541. https://doi.org/10.1038/s41396-020-0705-4.

• †Kim, W. E., †Charov, K., †Dzunkova, M., †Becraft, E. D., †Brown, J., Schulz, F., Woyke, T., La Clair, J. J., Stepanauskas, R., & Burkart, M. D. (2021). Synthase-Selective Exploration of a Tunicate Microbiome by Activity-Guided Single-Cell Genomics. ACS Chem Biol, 16(5), 813-819. https://doi.org/10.1021/acschembio.1c00157.

• Kim, Y. M., Nowack, S., Olsen, M. T., Becraft, E. D., Wood, J. M., Thiel, V., Klapper, I., Kuhl, M., Fredrickson, J. K., Bryant, D. A., Ward, D. M., & Metz, T. O. (2015). Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms. Front Microbiol, 6, 209. https://doi.org/10.3389/fmicb.2015.00209.

• Matheus Carnevali, P. B., Schulz, F., Castelle, C. J., Kantor, R. S., Shih, P. M., Sharon, I., Santini, J. M., Olm, M. R., Amano, Y., Thomas, B. C., Anantharaman, K., Burstein, D., Becraft, E. D., Stepanauskas, R., Woyke, T., & Banfield, J. F. (2019). Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. Nat Commun, 10(1), 463. https://doi.org/10.1038/s41467-018-08246-y.

• Melendrez, M. C., Becraft, E. D., Wood, J. M., Olsen, M. T., Bryant, D. A., Heidelberg, J. F., Rusch, D. B., Cohan, F. M., & Ward, D. M. (2015). Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat. Front Microbiol, 6, 1540. https://doi.org/10.3389/fmicb.2015.01540.

• Nowack, S., Olsen, M. T., Schaible, G. A., Becraft, E. D., Shen, G., Klapper, I., Bryant, D. A., & Ward, D. M. (2015). The molecular dimension of microbial species: 2. Synechococcus strains representative of putative ecotypes inhabiting different depths in the Mushroom Spring microbial mat exhibit different adaptive and acclimative responses to light. Front Microbiol, 6, 626. https://doi.org/10.3389/fmicb.2015.00626.

• Olsen, M. T., Nowack, S., Wood, J. M., Becraft, E. D., LaButti, K., Lipzen, A., Martin, J., Schackwitz, W. S., Rusch, D. B., Cohan, F. M., Bryant, D. A., & Ward, D. M. (2015). The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat. Front Microbiol, 6, 604. https://doi.org/10.3389/fmicb.2015.00604.

• Ohlsson, J. I., Osvatic, J. T.; Becraft E. D., Swingley W. D. Microbial Community in Hyperalkaline Steel Slag-Fill Emulates Serpentinizing Springs. Diversity. 2019;11(7):103.

• Sackett, J. D., Kruger, B. R., Becraft, E. D., Jarett, J. K., Stepanauskas, R., Woyke, T., & Moser, D. P. (2019). Four Draft Single-Cell Genome Sequences of Novel, Nearly Identical Kiritimatiellaeota Strains Isolated from the Continental Deep Subsurface. Microbiol Resour Announc, 8(11). https://doi.org/10.1128/MRA.01249-18.

• Stepanauskas, R., Fergusson, E. A., Brown, J., Poulton, N. J., Tupper, B., Labonte, J. M., Becraft, E. D., Brown, J. M., Pachiadaki, M. G., Povilaitis, T., Thompson, B. P., Mascena, C. J., Bellows, W. K., & Lubys, A. (2017). Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles. Nat Commun, 8(1), 84. https://doi.org/10.1038/s41467-017-00128-z.

• Steunou, A. S., Jensen, S. I., Brecht, E., Becraft, E. D., Bateson, M. M., Kilian, O., Bhaya, D., Ward, D. M., Peters, J. W., Grossman, A. R., & Kuhl, M. (2008). Regulation of nif gene expression and the energetics of N2 fixation over the diel cycle in a hot spring microbial mat. ISME J, 2(4), 364-378. https://doi.org/10.1038/ismej.2007.117.

• Youssef, N. H., Farag, I. F., Hahn, C. R., Jarett, J., Becraft, E. D., Eloe-Fadrosh, E., Lightfoot, J., Bourgeois, A., Cole, T., Ferrante, S., Truelock, M., Marsh, W., Jamaleddine, M., Ricketts, S., Simpson, R., McFadden, A., Hoff, W., Ravin, N. V., Sievert, S., . . . Elshahed, M. (2019). Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities. Appl Environ Microbiol, 85(10). https://doi.org/10.1128/AEM.00110-19.

Invited Talks

• Yellowstone Club seminar series, Montana State University, Bozeman, MT (2009). The ecology and evolution of thermophilic Synechococcus species.

• NSF Frontiers in Integrative Biology Research (FIBR) workshop entitled “Do species matter in microbial communities?” (2010). Do microbial ecotypes predicted from theory-based analyses of molecular data exhibit unique patterns of distribution and gene expression?

• Bigelow Laboratory for Ocean Sciences, East Boothbay, ME (2016). Untangling the genealogy of microbial dark matter.

• Northern Illinois University, Biological Sciences Departmental seminar series, DeKalb, IL (2015). Genomic analyses of “dark matter” populations in geothermal springs using a novel read-first binning method. (2017) Untangling the genealogy of microbial dark matter.

• Montana State University, Thermal Biology Institute, Bozeman, MT (2017). Untangling the genealogy of microbial dark matter.

• Sanford Underground Research Institute (SURF), Lead, SD (2017). The deep subsurface as a reservoir for microbial dark matter.

• Joint Genome Institute (JGI), New Lineages of Life (Nelli) workshop, Walnut Creek, CA (2017). Rokubacteria: genomic giants among the uncultured bacterial phyla.

• International Society of Subsurface Microbiology (ISSM) conference, Rotorua, New Zealand (2017). The subsurface as a reservoir for microbial dark matter and refuge for early-Earth cataclysmic events.  

• South Eastern Branch of the American Society for Microbiology conference, Georgia Tech, Atlanta, GA (2018). Bacterial relics of the Pangaea super-continent?

• Association of Southeastern Biologists conference, Memphis, TN (2019). Bacterial relics of the Pangaea super-continent?

• Student researcher (Cayman Gardner) gave talk at South Eastern Branch of the American Society for Microbiology conference (virtual) (2020). Dendrolitic cone formation investigation: Profile from anoxic layer of geothermal hot spring in California.

• International Metagenomics Forum (http://egg.umh.es/metforum.html) (2021). Evolutionary stasis of a deep subsurface microbial lineage.

• University of Tennessee, Biological Sciences Department, Knoxville, TN (2021). Evolutionary stasis of a deep subsurface microbial lineage.

• San Diego State University, Biology Department, San Diego, CA (2021). Evolutionary stasis of a deep subsurface microbial lineage. Presentation on November 8th, 2021.

Affiliated Grants

• National Science Foundation Frontiers in Integrative Biology Research Program (EF-0328698, PI: David Ward). FIBR: Do Species Matter in Microbial Communities? $4,999,690. August 2003-2011. Graduate student.

• National Science Foundation Office of International Science &Engineering (OISE 0968421, PI: Brian Hedlund). PIRE: Toward a holistic and global understanding of hot spring ecosystems: A US-China based international collaboration. $3,879,301. August 2010-2018. Postdoctoral researcher.

• National Science Foundation Division of Environmental Biology (OCE-1335810, PI: Ramunas Stepanauskas). $1,836,781. September 2014-2018. Untangling the Deep Genealogy of Microbial Dark Matter. Lead Postdoctoral researcher.

• National Science Foundation Division of Environmental Biology (1441771, PI: Duane Moser). $204,995. September 2014-2018. Untangling the Deep Genealogy of Microbial Dark Matter. Lead Postdoctoral researcher.

• University of North Alabama Undergraduate Research Grants. (UNA 40227, PI: Eric Becraft). Understanding the contributions of microbial metabolisms to geological structures. $8,817. February 2019-2021.

• NSF proposal for Research Coordination Networks in Undergraduate Biology Education (RCN-UBE). Computational education consortium: Big data analysis techniques for reproducibility and transparency in life sciences. $5,000,000. In review. Collaborator and committee member.

Professional Development and Posters Presented

• Prokaryotic annotation and analysis training, TIGR (2005).

• IGERT, Genomics of Closely Related Organisms conference, University of Arizona, Tuson, AZ (2006).

• Yellowstone National Park Research Coordination Network Workshop, Bozeman, MT (2006 and 2007).

• NSF Frontiers in Integrative Biology Research (FIBR) workshop entitled “Do species matter in microbial communities?” Montana State University, Bozeman, MT (2006, 2008 and 2010).

• ASM general meeting: Toronto, Canada (2007); Boston, MA (2016).

• Gordon Conference: Applied & Environmental Microbiology, South Hadley, MA (2009).

• Thermophiles conference, Big Sky, MT (2011).

• Midwest Geomicrobiology conference, Chicago, IL (2014).

• Single Cell Genomics workshop, Bigelow Laboratory of Ocean Sciences, East Boothbay Harbor, ME (2015).

• ISME (International Society of Microbial Ecology): Seattle, WA (2010); Copenhagen, Denmark (2012); Seoul, South Korea (2014); Montreal, Canada (2016).

• Nelli (New Lineages of Life) Conference, Joint Genome Institute, Walnut Creek, CA (2017).

• Frontiers in Microbiology Journal, Review Editor (2019).

• Student Researchers (Cayman Gardner and Larissa Hussein). South Eastern Branch of the American Society for Microbiology conference, Huntsville, AL. (2020). Cone WOR3: Return of the Reductase.

Scientific contributions and awards

• Ward, DM, Melendrez, MM, Becraft, ED, Klatt, CG, Wood, JM, Cohan, FM. Metagenomic approaches for the identification of microbial species. Handbook of Molecular Microbial Ecology, Volume 1; Metagenomics and Complementary Approaches, First Edition. Edited by Franis J. de Bruijn, Wiley-Blackwell. 2011; Chapter 13:105-109.

• Vishnivetskaya TA, Perler F, Ramaley R, Spear J, Swingley W, Becraft ED, Ziolkowski L, Polosukhina D. The International Workshop on Biology and Biotechnology of Thermophilic Microorganisms. NSF Technical Report, October 2016. DOI: 10.13140/RG.2.2.18519.88484.

• NASA Exobiology grant panel, San Diego, CA (2018).

• Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N., Schulz, F., Wu, D., Paez-Espino, D., Chen, I. M., Huntemann, M., Palaniappan, K., Ladau, J., Mukherjee, S., Reddy, T. B. K., Nielsen, T., Kirton, E., Faria, J. P., Edirisinghe, J. N., Henry, C. S., . . . Eloe-Fadrosh, E. A. (2021). A genomic catalog of Earth's microbiomes. Nat Biotechnol, 39(4), 499-509. https://doi.org/10.1038/s41587-020-0718-6. Member of IMG consortium.

• Guest Editor: Frontiers of Microbiology special topic. Searching for the boundaries of Microbial Speciation in a Rapidly Evolving World. https://www.frontiersin.org/research-topics/14864/searching-for-the-boundaries-of-microbial-speciation-in-a-rapidly-evolving-world.

• ISME J. 2021 paper of the year award. Evolutionary stasis of a deep subsurface microbial lineage. https://www.nature.com/collections/aedhjihhgh.

Press

·QCD news. UNA Professor Publishes Paper on Early Evolution in Photosynthesis. (2018) http://quadcitiesdaily.com/?p=509466.

·Phys Org. Study reveals two major microbial groups can't breathe (2020). https://phys.org/news/2020-08-reveals-major-microbial-groups.html.

·EurekAlert! Living Fossils: Microbe Discovered in evolutionary Stasis for Millions of Years (2021) https://www.eurekalert.org/news-releases/666574.  

·ZME Science. Fossil Friday: Microbes discovered deep underground remain virtually unchanged Since 175 million years ago (2021). https://www.zmescience.com/science/fossil-friday-microbes-underground-living-fossil-426587.

·Science Alert. These Bizarre Underground Microbes Haven't Evolved For 175 Million Years (2021). https://www.sciencealert.com/these-weird-chthonic-microbes-haven-t-evolved-for-millions-of-years.

University Teaching and Mentoring

Assistant professor teaching experience

• BI101 Introductory Biology, University of North Alabama, Fall 2018. Primary instructor.

• BI306 Genetics, University of North Alabama, Spring 2019. Primary instructor.

• BI307 Microbiology, University of North Alabama, Fall 2018 and Spring 2019. Primary instructor.

• BI407 Microbial Ecology and Evolution, University of North Alabama, Spring 2020. Primary instructor.

Previous teaching experience

• MB 420 Microbial Physiology, Montana State University, Fall 2006 and 2007. Phototrophic metabolisms.

• MB 415 Microbial Diversity, Ecology, and Evolution, Montana State University, Spring 2006. Bacterial motility and chemotaxis.

• MB 415 Microbial Diversity, Ecology, and Evolution, Montana State University, Spring 2008. Co-instructor and teaching assistant.

• Thermal Biology Institute outreach program, Master of Science in Science Education (MSSE) (phototrophic metabolisms and microscope utilization), Spring 2010.

  • MB 513 Microbial Ecology, Montana State University, Spring 2012. Teaching assistant. 

  • BIO 468/568 Geomicrobiology, Northern Illinois University, Spring 2014 and 2015. Microorganisms in extreme environments.

Undergraduate and graduate student mentoring experience

• Served on masters graduate committee for Daniel Nuccio, Northern Illinois University (2020).

• Graduate students mentored at NIU:

  • J. Ingemar Ohlsson

  • Daniel Nuccio

  • Mentor for undergraduate students selected for participation in the Research Education for Undergraduates (REU) program:

• Lori List, Katherine Olson and Marie Kroeger Machalinski. Northern Illinois University, 2014

• Allen Rene Fonteyn and Jared Sherwood, Northern Illinois University, 2015

• Johanna Holman, Bigelow Laboratory for Ocean Sciences, 2016.

• Michael Chen, Bigelow Laboratory for Ocean Sciences, 2017.

  • Undergraduates mentored at Northern Illinois University:

• Tori Hardy, Amy Daly, Karley Davidson.

  • Undergraduates mentored at University of Northern Alabama:

• 2018-2019 – Andrea Engelthaler

• 2019-2020 – Larissa Hussein, Cayman Gardner, Nhi Nguyen, Jennifer Ahlbrand. Michael Agee

• 2020-2021 – Larissa Hussein, Cayman Gardner, Mackenzie Abts

• 2021-2022 – Mackenzie Abts, Breylee Linder, Tersa D’Ablaing, Gregory Gilmore