“…Where there is life, there are microbes…” (Carl Woese, 2002)
The main research interest of the laboratory is microbial diversity in extreme environments. We apply a polyphasic approach, i.e., a complementary set of microbial physiology, chemical taxonomy, and non-culture-based methods to assess and monitor microbial communities. While we use pattern recognition techniques, such as electrophoretic karyotyping and terminal restriction fragment length polymorphism (t-RFLP), signature lipid biomarker analysis, and genomic sequencing to survey and characterize selected microbial ecosystems, we also very much rely on developing new isolation and cultivation techniques. Newly isolated microorganisms are then screened in collaboration with industrial partners for novel traits and natural products.
Over the past several years, the laboratory participated in the US Department of Energy Global Initiatives for Proliferation Prevention (GIPP) program that opened new, once-in-a-lifetime opportunities for environmental sample collection. The “Search for Ancient Microorganisms in Lake Baikal” project targeted the microbial diversity present in and around Lake Baikal, the oldest and deepest continental lake in the world in south central Siberia. We collected water and soil samples from the Lake and surrounding hot springs, and participated in two expeditions of the international Baikal Drilling Project (BDRP; www.geol.sc.edu/SIL/bdp.htm). Over 2,200 strains were isolated, preserved, and identified based on biochemical tests, whole-cell fatty acid methyl ester (FAME) analysis, genomic DNA fingerprinting, and restriction enzyme profiling. Also, a larger subset of isolates underwent electron microscopic cell morphology and fine structure investigations.
The projects “Microbially Derived Agricultural Crop Protection Products” and “Screening of Botanical and Microbial Species Collected within the Territory of the Newly Independent States (NIS) of the Former Soviet Union for Pharmaceutical and Agrochemical Activities” joined our proprietary fermentation methods with high-throughput assays of the industrial partners to screen the Lake Baikal microorganisms, thousands of plant extracts, and filamentous fungi (collected in the 30-km Exclusion Zone for over a 16-year period following the 1986 nuclear power plant disaster in Chernobyl, Ukraine) for novel microbial natural products with agricultural and biomedical applications. As one of the outcomes, dozens of antifungal peptides were patented and transgenic plants of major crop plants generated that now express extremophilic microbial sequences.
The most current bioprospecting project, “Microbial Diversity for Novel Biotechnology Applications” developed a multi-year program for the systematic seasonal collection of microbial diversity in selected extreme environments on the Kamchatka peninsula, Russia (www.uga.edu/kamchatka/general.html), the Caucasus Mountain and the high salinity soils in Georgia, and the deserts of Uzbekistan.
Of the many spin-off ideas that have resulted from past and current projects, let’s only mention a few: (1) A NATO Collaborative Linkage Grant provided the seed money for a feasibility study to introduce sequences from hyperthermophilic microorganisms into major crop plants for post-harvest modification through heat activation of enzymes during storage. (2) In Tajikistan, with the support of the International Science and Technology Center (ISTC) we are investigating cattle graves, outbreaks, and clinical samples to GIS-map sites and genetically characterize the circulating Bacillus anthracis strains. (3) In a Civilian Research and Development Foundation (CRDF)-funded project, we have joined forces with institutes in Armenia, Azerbaijan, and Georgia and established a network of microbial culture collections as biotechnology resources. The web portal of the network (microbio-caucasus.lbl.gov) allows the international scientific community to access the invaluable specialized microbial cultures maintained in these countries. (5) In Azerbaijan, a collaborative investigation funded by CRDF and the National Academy of Sciences collects petroleum hydrocarbon degrading and biosurfactants expressing microorganisms to cleanup oil contaminated environments. (6) With colleagues in Japan and Georgia, we genetically engineer and screen fungi that produce high efficiency lignocellulolytic enzymes for biomass-to-biofuels applications.
Baker, S.E., Thykaer, J., Adney, W.S., Brettin, T.S., Brockman, F.J., D’Haeseleer, P., Martinez, A.D., Miller, R.M., Rokhsar, D.S., Schadt, C.W., Torok, T., Tuskan, G., Bennett, J., Berka, R.M., Briggs, S.P., heitman, J., Taylor, J., Gillian-Turgeon, B., Werner-Washburne, M., and Himmel, M.E. 2008. Fungal genome sequencing and bioenergy. Fungal Biol.Rev., 30:1-5.
Altier, D. J., Dahlbacka, G., Ellenskaya,I., Herrmann, R., Hunter-Cevera, J., McCutchen, B. F., Presnail, J. K., Rice, J. A., Schepers, E., Simmons, C. R., Torok, T., and Yalpani, N. 2007. Novel biologically active natural products by newly isolated environmental microorganisms. United States of America Patent No. 7,306,946.
Andreeva, L.S., Pechurkina, N.I., Morozova, O.V., Ryabchikova, E.I., Belikov, S.I., Puchkova, L.I., Emelyanova, E.K., Torok, T., and Repin, V.E. 2007. Roseomonas baikalica sp. nov., a new bacterial species isolated from core samples collected by deep-hole drilling at the bottom of Lake Baikal. Microbiology 76:1-8.
Andreeva, L.S., Repina, M.V., Oreshkova, S.F., Ryabchikova, E.I., Puchkova, L.I., Blinova, N.N., Repina, M.V., Pechurkina, N.I., Torok, T., and Repin, V.E. 2005. Genomic and phenotypic analysis of microorganisms isolated from the sediments of Lake Baikal. Microbiology74:709-714.
Repin, V., Torok, T., Degtyarev, S., Abdurashitov, M., Puchkova, L., Andreeva, I., Pechurkina, N., Hunter-Cevera, J. C., Geletij, V., and Kuzmin, M.I. 2001. Microbiological and biotechnological investigations of sub-bottom sediments of Lake Baikal and samples of closely located hot springs (Zmeiniy, Goryachenskij). Geology and Geophysics (Russia) 42:235-240.
Repin, V.E., Torok, T., and Kuzmin, M.I. 2001. The biodiversity of microorganisms from bottom sediments of Lake Baikal by evidence from deep boreholes. Russian Geol. Geophys., 42:231-234.
Torok, T., Mortimer, R.K., Romano, P., Suzzi, G., and Polsinelli, M. 1996. Quest for wine yeasts - An old story revisited. J. Ind. Microbiol. 17:303-313.
Past 48 months: Afrikian, E. (SMDC, Yerevan, Armenia); Andersen, G.L. (LBNL); Arkin, A. (LBNL); Auer, M. (LBNL); Biggin, M. (LBNL); Boundy-Mills, K. (UC Davis, CA); Britton, L. (UT at Austin, TX); Brodie, E. (LBNL); Cady, S. (Portland State University, OR); Campbell, N. (Jackson State University, MS); Cristoffersen, L. ((E.O. Wilson Biodiversity Foundation); Davis, A. (Jackson State University, MS); Dixon, B. (CSU East Bay.CA); Dmitrieva, V. (CERBRD, Pushchino, Russia); Drmanac, R. (Callida Genomics, Sunnyvale, CA); Green, B. (Diversa Corporation); Hazen, T. (LBNL); Herrmann, R. (DuPont); Hugenholtz, P. (LBNL); Hunter-Cevera, J. (UMBI, Baltimore, MD); Ismaylov, N. (IM, Baku, Azerbaijan); Kvesitadze, G. (Durmishidze Institute, Tbilisi, Georgia); Kuchuk, M. (ICBGE, Kiev, Ukraine); Lysov, Y. (Engelhardt Institute, Moscow, Russia); Mathur, E. (Synthetic Genomics); Peter, G. (University of Budapest, Hungary); Presnail, J. (DuPont); Repin, V. (VECTOR, Koltsovo, Russia); Robbs, F. (UMBI, BAltimor, MD); Reysenbach, A.L. (Portland State University, OR); Satorov, S. (CIFMD, Dushanbe, Tajikistan); Short, J. (E.O. Wilson Biodiversity Foundation ); Stetter, K. (University of Regensburg, Germany); Tashpulatov, J. (IM, Tashkent, Uzbekistan); Taylor, J. (UC Berkeley, CA); Tornai, J. (University of Budapest, Hungary); Venkateswaran, K. (JPL, Pasadena, CA); Wiegel, J. (University of Georgia, Athens, GA); Yalpani,. N. (Pioneer Hi-Bred); Young, M. (Montana State University, Bozeman, MT); Zhdanova, N. (IMV, Kiev, Ukraine).