People | Jennifer F Biddle

• B.S., With Honors, Biotechnology, Rutgers University, 1999.
• Ph.D., Biochemistry and Molecular Biology, Pennsylvania State University, 2006.

Microbial populations and processes in subseafloor marine environments

1. Genomics and metagenomics of uncultured groups of Archaea
   (http://www.jgi.doe.gov/sequencing/why/phylotypes.html)
   Our first glimpse at the marine subsurface showed that many unique groups of Archaea are present there. Working with the Joint Genome Institute, we will continue to sequence interesting Archaea from sediments and aim to develop a good genomic architecture with which to explore new subsurface environments.

    

2. Exploring new subsurface habitats
   (http://teskelab.wordpress.com/, http://northpondexpedition.usc.edu)
   Recent coring and drilling expeditions have retrieved sediments from new areas of the mid-Atlantic, Guaymas Basin and Gulf of Mexico. In continued collaboration with Andreas Teske, we will explore what microbial phylotypes are present in these environments and examine how certain microbes are related to environmental factors. Cruise participation with the Integrated Ocean Drilling Program will be available to students interested in exploring new environments.

    

3. Finding a deep biosphere analog in Delaware
   The local environment in Delaware is rich in environments that may house relatives of deep biosphere microbes. Since a long term goal is to cultivate these microbes and explore their biochemical pathways, we will embark on a mission to use genetic signatures to find a deep biosphere analog that we can repeatedly sample.

    

4. Pavilion Lake research project
   (http://www.pavilionlake.com)
   Pavilion Lake hosts some amazing microbial structures which are thought to be modern analogs of ancient stromatolites. These microbialites host diverse microbial communities, yet at different depths in the lake, they form different structures. We will use molecular techniques to explore the microbialites and determine who or what is responsible for morphology changes in the superstructure. Dr. Art Trembanis from the University of Delaware is also involved in the project. This ongoing collaboration includes summer field work in British Columbia.

   Funded by NASA's Delaware Space Grant Consortium

Joseph Russell, PhD student (BS, University of Arizona, Microbiology, 2008)

Bingran Cheng, MS student (BS, Xiamen University, 2010)

Glenn Christman, Bioinformaticist (MS, Johns Hopkins University, 2012; MS University of Delaware, 2010)

William Orsi, Postdoctoral Fellow (joint with Virginia Edgcomb at Woods Hole Oceanographic Institution)

Methods in Molecular Biology, MAST 616 (lecture) and 617 (lab), Spring 2010,2011,2012

Marine Molecular Sciences, MAST643 Fall 2011,2012,2013

Environmental Bioinformatics, MAST698 (joint with Dr. Marsh), Spring 2013

Summer workshops: EU-US Bioinformatics Training 2012, 2013

Interested undergraduates, graduates and postdocs should contact Dr. Biddle directly

Luke J. McKay, Barbara J. MacGregor, Jennifer F. Biddle, Daniel B. Albert, Howard P. Mendlovitz, Daniel R. Hoer, Julius S. Lipp, Karen G. Lloyd, Andreas P. Teske (2012) Spatial heterogeneity and underlying geochemistry of phylogenetically diverse orange and white Beggiatoa mats in Guaymas Basin hydrothermal sediments. Deep Sea Res. 67:21-31.

Kyoko Kubo, Karen G. Lloyd, Jennifer F. Biddle, Rudolf Amann, Andreas Teske, Katrin Knittel (2012) Archaea of the Miscellaneous Crrenarchaeotal Group (MCG) are abundant, diverse, and widespread in marine sediments.  ISME J. 2012 1-17.  doi:10.1038/ismej.2012.37

Amanda Martino, Matthew E. Rhodes, Jennifer F. Biddle, Leah D. Brandt, Lynn P. Tomsho, Christopher H. House (2012) Novel degenerate PCR method for whole genome amplification applied to Peru Margin (ODP leg 201) subsurface samples. Frontiers in Extreme Microbiology 3:17.  doi:10.3389/fmicb.2012.00017.

Virginia P. Edgcomb, Jennifer F. Biddle (2012) Microbial eukaryotes in the marine subsurface?  In: Cellular Origin, Life in Extreme Habitats and Astrobiology, Volume 21, edited by A.V. Altenbach, J.M. Bernhard and J. Seckback, Springer Science Business Media B.V.

Jennifer F. Biddle, Jason B. Sylvan, William J. Brazelton, Benjamin J. Tully, Katrina J. Edwards, Craig L. Moyer, John F. Heidelberg, William C. Nelson (2012) Prospects for the study of evolution in the deep biosphere.  Frontiers in Extreme Microbiology 2:285. doi: 10.3389/fmicb.2011.00285.

Jennifer F. Biddle (2011) Metagenomics of the marine subsurface: The first glimpse from the Peru Margin, ODP Site 1229.  In: Handbook of Molecular Microbial Ecology II.  Edited by F.J. de Bruijn, Wiley Blackwell, New Jersey.

Jennifer F. Biddle, Zena Cardman, Howard Mendlovitz, Daniel B. Albert, Karen G. Lloyd, Antjue Boetius, Andreas Teske (2011) Anaerobic oxidation of methane at different temperature regimes in Guaymas Basin hydrothermal sediments. ISME J. 2011 1-14.

Jennifer F. Biddle, James Robert White, Andreas P. Teske, Christopher H. House (2011) Metagenomics of the subsurface Brazos-Trinity Basin (IODP Site 1320): comparison with other sediment and pyrosequenced metagenomes. ISME J. 5:1038-1047.

Karen G. Lloyd, Daniel B. Albert, Jennifer F. Biddle, Jeffrey P. Chanton, Oscar Pizarro, Andreas Teske (2010) Spatial structure and activity of sedimentary microbial communities underlying a Beggiatoa spp. mat in a Gulf of Mexico hydrocarbon seep. PLoS One 5(1):e8738. 

Yu-Shih Lin, Jennifer F. Biddle, Julius S. Lipp, Beth N. Orcutt, Thomas Holler, Andreas Teske, Kai-Uwe Hinrichs (2010) Effect of storage conditions on archael and bacterial communities in subsurface marine sediments. Geomicrobiology Journal, 27(3):261-272. 

Jennifer F. Biddle, Sorel Fitz-Gibbon, Stephan C. Schuster, Jean E. Brenchley, Christopher H. House (2008) Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. PNAS, 105(30):10583-10588. 

Andreas Teske, Jennifer F. Biddle (2007) Analysis of deep subsurface microbial communities by functional genes and genomics. In: Links Between Geological Processes, Microbial Activities and Evolution of Life, edited by Y. Dilek, H. Furnes & K. Muehlenbachs, Springer Science B.V., Dordrecht, The Netherlands.

Jennifer F. Biddle, Julius S. Lipp, Mark A. Lever, Karen G. Lloyd, Ketil B. Sørensen, Rika Anderson, Helen F. Fredricks, Marcus Elvert, Timothy J. Kelly, Daniel P. Schrag, Mitchell L. Sogin, Jean E. Brenchley, Andreas Teske, Christopher H. House, Kai-Uwe Hinrichs (2006) Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru.

My research is focused around the deep biosphere.  Microorganisms have been found deep within the Earth and the majority of these microbes are in the marine subsurface.  Research has shown many of these deeply buried microbes to be unlike the microbes in surface environments.  Much more needs to be known about these organisms, including what they do and how they survive in such extreme conditions.