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Richard Bizzoco

Ph.D., IndianaUniversity
Department of Biology
Cell & Molecular Doctoral Program
Molecular Biology Masterís Program

(619) 594-5396

Discovery/isolation of new Archaea

Organisms found to thrive in extreme habitats such as the acid hot springs of Yellowstone National Park are termed extremophiles. Other than lobed spheres, culturable, aerobic high temperature low pH-adapted archaea, (pH 2-3; 70-90°C) or bacteria have so far proven difficult to isolate from their native acid hot spring environment. To date there are no successful isolations of aerobic rod shaped archaea or bacteria optimally growing as thermoacidophiles, i.e. below pH 3 and from 70° C to 90°C, although one organism, Thermofilum found deep in mud sediments in these same habitats, grows anaerobically using molecules from other nearby organisms.

Most success to date has come from the Amphitheater Springs region in Yellowstone National Park. Members of our laboratory group isolated three different organisms from the main springs in this region. We have also confirmed the presence of microbes in several other springs within Yellowstone Park, using DAPI (DNA staining) and direct examination at the electron microscopic level and X-ray microanalysis. Perhaps the advent of genome sequencing, particularly the small subunit of ribosomal RNA (16S rRNA), has been the most useful approach. This allows us to evaluate any new isolates and determine if they merit continued investigation as an undiscovered organism or if they have already been reported and described as a genus. These sequences are the blueprints for selecting representatives of the domains archaea and bacteria for further study. In association with two other laboratories (one, a federal biotechnology facility) we have begun genome sequencing of newly cultured organisms and comparison of their SSU rRNA sequences using archaea specific and bacteria specific primers with those from mesophilic, thermophilic and hyperthermophilic (>80°C) organisms. This approach helps to provide fundamental insight into the status of an isolate as a known or an undiscovered organism. Complementary physiological and structural biology studies will undoubtedly yield a large amount of new and exciting data at both the fundamental and applied level. We are seeking students for this research. 


Our first goal is to extend our sampling enrichments to include high temperature sites such as Roaring mountain 77 to 90°C at pH 2.0, Great Sulfur Spring (88°C; pH 2.0), Norris Annex (88°C; pH 2.0), and Frying Pan Spring (88°C; pH 2.2). We expect to obtain unique new organisms from these habitats. As part of this approach we are using 16S rRNA gene sequence analyses (PCR based DNA fingerprinting) with archaea and bacteria-specific primers to investigate the divesity of our mixed cultures. Analysis of a lower temperature organism (55C; pH 3) revealed a clone that matched with a high similarity (>99% over 1500 bp) to an uncultured, unknown bacterial clone.

Our second goal is to evaluate the effects of nutritional supplements on our current isolates and those obtained in the future. Here we will use various supplements such as meat, yeast and cell extracts from our thermophile cultures. Various combinations may increase our successes. We will also use this approach to isolate and grow individual organisms from our collections, both from dilutions and on solid medium. 

Our third goal is to characterize the isolates, describe their physiological and nutritional capabilities and to provide new generic descriptions of any organisms we obtain. We already know that there are many undiscovered organisms in the acid hot springs and we have obtained multiple aerobic isolations. Because this work is already underway and we have cultures presently growing, we believe these goals are realistic. We invite interested students to participate in this research.

Representative publications :

Weiss Bizzoco, R. L., N. Banish, M. Lu, and S. Saavedra. 2000. New acidophilic thermophilic microbes. Pages 117-128 in J. Seckbach, editor, Journey to diverse microbial worlds.. Kluwer Academic Publishers, Dordrecht, The Netherlands.

Lindstrom, R..F., R.F. Ramaley and R.W. Bizzoco 2002. Invisible invasion: Potential contamination of Yellowstone hot springs by human activity. Western North American Naturalist. 62:44-58.

Weiss Bizzoco, R. L., Bass, R., Vuong, T. T., Vahl, J. B., Hoang, C. L., Diaz, M. M. 2003. Selective adhesion of extremophiles for scanning electron microscopy. Journal of Microbiological Methods 55:787-790.

Ellis, D. G., Weiss Bizzoco, R. L., Maezato, Y., Baggett, J.N., Kelley, S. T. (2005) Microbiological Examination of Acidic Hot Springs of Waiotapu, North Island, New Zealand. New Zealand Journal of Marine and Freshwater Research 39:1001-1011.

Mathur, J., Bizzoco, R. W., Ellis, D. G., Lipson, D. A., Poole, A. W., Levine, R., Kelley, S.T. 2007. Effects of abiotic factors on phylogenetic diversity of bacterial communities in acidic thermal springs. Applied and Environmental Microbiology Applied and Environmental Microbiology 73:2612-2623.

Ellis, D. G., Bizzoco, R. W. and Kelley, S.T. 2008. Halophilic Archaea determined from geothermal steam vent aerosols. Environmental Microbiology 10:1582-1590.

Benson, C.A., Bizzoco, R.W., Lipson, D.A., Kelley, S.T. (2011) Microbial diversity in nonsulfur, sulfur and iron geothermal steam vents. FEMS Microbiology Ecology 76:74-88.

Tin, S., Bizzoco, R.W., Kelley, S.T. (2011) Role of the terrestrial subsurface in shaping geothermal spring microbial communities. Environmental Microbiology Reports 3:491-499.

Benson, C.A., Bizzoco, R.W., Kelley, S.T. (2012) Microbial diversity in non-sulfur and iron geothermal steam vents. Yellowstone Science 20:5-6.

Tin, S., Bizzoco, R.W., Kelley, S.T. (2012) Role of the terrestrial subsurface in shaping geothermal spring microbial communities. Environmental Microbiology Reports 4: 1.

Papers in press 

Weiss Bizzoco, R.L., Kelley, S.T. (2013) Microbial diversity in acidic high temperature steam vents. Polyextremophiles: 1-15. (in press).

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