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1 - Introduction to bacterial physiology and metabolism

Published online by Cambridge University Press:  05 September 2012

Byung Hong Kim  and
Geoffrey Michael Gadd
Byung Hong Kim
Affiliation:
Korea Institute of Science and Technology, Seoul
Geoffrey Michael Gadd
Affiliation:
University of Dundee
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Summary

The biosphere has been shaped both by physical events and by interactions with the organisms that occupy it. Among living organisms, prokaryotes are much more metabolically diverse than eukaryotes and can also thrive under a variety of extreme conditions where eukaryotes cannot. This is possible because of the wealth of genes, metabolic pathways and molecular processes that are unique to prokaryotic cells. For this reason, prokaryotes are very important in the cycling of elements, including carbon, nitrogen, sulfur and phosphorus, as well as metals and metalloids such as copper, mercury, selenium, arsenic and chromium. A full understanding of the complex biological phenomena that occur in the biosphere therefore requires a deep knowledge of the unique biological processes that occur in this vast prokaryotic world.

After publication in 1995 of the first full DNA sequence of a free-living bacterium, Haemophilus influenzae, whole genome sequences of hundreds of prokaryotes have now been determined and many others are currently being sequenced (www.genomesonline.org/). Our knowledge of the whole genome profoundly influences all aspects of microbiology. Determination of entire genome sequences, however, is only a first step in fully understanding the properties of an organism and the environment in which the organism lives. The functions encoded by these sequences need to be elucidated to give biochemical, physiological and ecological meaning to the information. Furthermore, sequence analysis indicates that the biological functions of substantial portions of complete genomes are so far unknown.

Type
Chapter
Information
Bacterial Physiology and Metabolism , pp. 1 - 6
Publisher: Cambridge University Press
Print publication year: 2008

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Trevors, J. T. (2003). Origin of the first cells on Earth: a possible scenario. Geomicrobiology Journal 20, 175–183.CrossRefGoogle Scholar
Meer, J. R. & Sentchilo, V. (2003). Genomic islands and the evolution of catabolic pathways in bacteria. Current Opinion in Biotechnology 14, 248–254.CrossRefGoogle ScholarPubMed
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Boucher, Y., Nesbo, C. L. & Doolittle, W. F. (2001). Microbial genomes: dealing with diversity. Current Opinion in Microbiology 4, 285–289.CrossRefGoogle ScholarPubMed
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Groisman, E. A. & Ehrlich, S. D. (2003). Genomics: a global view of gene gain, loss, regulation and function. Current Opinion in Microbiology 6, 479–481.CrossRefGoogle ScholarPubMed
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Ward, N. & Fraser, C. M. (2005). How genomics has affected the concept of microbiology. Current Opinion in Microbiology 8, 564–571.CrossRefGoogle ScholarPubMed
Cowan, D. A. (2004). The upper temperature for life – where do we draw the line?Trends in Microbiology 12, 58–60.CrossRefGoogle Scholar
Deming, J. (2002). Psychrophiles and polar regions. Current Opinion in Microbiology 5, 301–309.CrossRefGoogle ScholarPubMed
Javaux, E. J. (2006). Extreme life on Earth: past, present and possibly beyond. Research in Microbiology 157, 37–48.CrossRefGoogle ScholarPubMed
Mock, T. & Thomas, D. N. (2005). Recent advances in sea-ice microbiology. Environmental Microbiology 7, 605–619.CrossRefGoogle ScholarPubMed
Simonato, F., Campanaro, S., Lauro, F. M., Vezzi, A., D'Angelo, M., Vitulo, N., Valle, G. & Bartlett, D. H. (2006). Piezophilic adaptation: a genomic point of view. Journal of Biotechnology 126, 11–25.CrossRefGoogle ScholarPubMed
Steven, B., Leveille, R., Pollard, W. H. & Whyte, L. G. (2006). Microbial ecology and biodiversity in permafrost. Extremophiles 10, 259–267.CrossRefGoogle ScholarPubMed
Anderson, N. L., Matheson, A. D. & Steiner, S. (2000). Proteomics: applications in basic and applied biology. Current Opinion in Biotechnology 11, 408–412.CrossRefGoogle ScholarPubMed
Chen, L. & Vitkup, D. (2007). Distribution of orphan metabolic activities. Trends in Biotechnology 25, 343–348.CrossRefGoogle ScholarPubMed
Dufrene, Y. F. (2002). Atomic force microscopy, a powerful tool in microbiology. Journal of Bacteriology 184, 5205–5213.CrossRefGoogle ScholarPubMed
Whitfield, E. J., Pruess, M. & Apweiler, R. (2006). Bioinformatics database infrastructure for biotechnology research. Journal of Biotechnology 124, 629–639.CrossRefGoogle ScholarPubMed
Downs, D. M. (2006). Understanding microbial metabolism. Annual Review of Microbiology 60, 533–559.CrossRefGoogle ScholarPubMed
Galperin, M. Y. (2004). All bugs, big and small. Environmental Microbiology 6, 435–437.CrossRefGoogle ScholarPubMed
Klamt, S. & Stelling, J. (2003). Two approaches for metabolic pathway analysis?Trends in Biotechnology 21, 64–69.CrossRefGoogle ScholarPubMed
Papin, J. A., Price, N. D., Wiback, S. J., Fell, D. A. & Palsson, B. O. (2003). Metabolic pathways in the post-genome era. Trends in Biochemical Sciences 28, 250–258.CrossRefGoogle ScholarPubMed
Park, S., Lee, S., Cho, J., Kim, T., Lee, J., Park, J. & Han, M. J. (2005). Global physiological understanding and metabolic engineering of microorganisms based on omics studies. Applied Microbiology and Biotechnology 68, 567–579.CrossRefGoogle ScholarPubMed
Postgate, J. R. (1992). Microbes and Man, 3rd edn. Cambridge: Cambridge University Press.Google Scholar
Crawford, R. L. (2005). Microbial diversity and its relationship to planetary protection. Applied and Environmental Microbiology 71, 4163–4168.CrossRefGoogle ScholarPubMed
DeLong, E. F. (2001). Microbial seascapes revisited. Current Opinion in Microbiology 4, 290–295.CrossRefGoogle ScholarPubMed
Fernandez, L. A. (2005). Exploring prokaryotic diversity: there are other molecular worlds. Molecular Microbiology 55, 5–15.CrossRefGoogle ScholarPubMed
Fredrickson, J. & Balkwill, D. (2006). Geomicrobial processes and biodiversity in the deep terrestrial subsurface. Geomicrobiology Journal 23, 345–356.CrossRefGoogle Scholar
Pedros-Alio, C. (2006). Marine microbial diversity: can it be determined?Trends in Microbiology 14, 257–263.CrossRefGoogle ScholarPubMed
Rappe, M. S. & Giovannoni, S. J. (2003). The uncultured microbial majority. Annual Review of Microbiology 57, 369–394.CrossRefGoogle ScholarPubMed
Gadd, G. M., Semple, K. T. & Lappin-Scott, H. M. (2005). Micro-organisms and Earth Systems: Advances in Geomicrobiology. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Galperin, M. Y. (2004). Metagenomics: from acid mine to shining sea. Environmental Microbiology 6, 543–545.CrossRefGoogle ScholarPubMed
Geesey, G. G. (2001). Bacterial behavior at surfaces. Current Opinion in Microbiology 4, 296–300.CrossRefGoogle ScholarPubMed
Ivanov, M. V. & Karavaiko, G. I. (2004). Geological microbiology. Microbiology-Moscow 73, 493–508.CrossRefGoogle ScholarPubMed
Johnston, A. W. B., Li, Y. & Ogilvie, L. (2005). Metagenomic marine nitrogen fixation – feast or famine?Trends in Microbiology 13, 416–420.CrossRefGoogle ScholarPubMed
Karl, D. (2002). Nutrient dynamics in the deep blue sea. Trends in Microbiology 10, 410–418.CrossRefGoogle ScholarPubMed
Riesenfeld, C. S., Schloss, P. D. & Handelsman, J. (2004). Metagenomics: genomic analysis of microbial communities. Annual Review of Genetics 38, 525–552.CrossRefGoogle ScholarPubMed
Shively, J. M., English, R. S., Baker, S. H. & Cannon, G. C. (2001). Carbon cycling: the prokaryotic contribution. Current Opinion in Microbiology 4, 301–306.CrossRefGoogle ScholarPubMed
Tyson, G. W. & Banfield, J. F. (2005). Cultivating the uncultivated: a community genomics perspective. Trends in Microbiology 13, 411–415.CrossRefGoogle ScholarPubMed
Altermann, W. & Kazmierczak, J. (2003). Archean microfossils: a reappraisal of early life on Earth. Research in Microbiology 154, 611–617.CrossRefGoogle ScholarPubMed
Arber, W. (2000). Genetic variation: molecular mechanisms and impact on microbial evolution. FEMS Microbiology Reviews 24, 1–7.CrossRefGoogle ScholarPubMed
Boucher, Y., Douady, C. J., Papke, R. T., Walsh, D. A., Boudreau, M. E., Nesbo, C. L., Case, R. J. & Doolittle, W. F. (2003). Lateral gene transfer and the origins of prokaryotic groups. Annual Review of Genetics 37, 283–328.CrossRefGoogle ScholarPubMed
Groisman, E. A. & Casadesus, J. (2005). The origin and evolution of human pathogens. Molecular Microbiology 56, 1–7.CrossRefGoogle ScholarPubMed
Koch, A. L. (2003). Were Gram-positive rods the first bacteria?Trends in Microbiology 11, 166–170.CrossRefGoogle ScholarPubMed
Koch, A. L. & Silver, S. (2005). The first cell. Advances in Microbial Physiology 50, 227–259.CrossRefGoogle ScholarPubMed
Moran, N. (2003). Tracing the evolution of gene loss in obligate bacterial symbionts. Current Opinion in Microbiology 6, 512–518.CrossRefGoogle ScholarPubMed
Orgel, L. E. (1998). The origin of life – a review of facts and speculations. Trends in Biochemical Sciences 23, 491–495.CrossRefGoogle ScholarPubMed
Ouzounis, C. A., Kunin, V., Darzentas, N. & Goldovsky, L. (2006). A minimal estimate for the gene content of the last universal common ancestor – exobiology from a terrestrial perspective. Research in Microbiology 157, 57–68.CrossRefGoogle ScholarPubMed
Rainey, P. B. & Cooper, T. F. (2004). Evolution of bacterial diversity and the origins of modularity. Research in Microbiology 155, 370–375.CrossRefGoogle ScholarPubMed
Sallstrom, B. & Andersson, S. G. E. (2005). Genome reduction in the α-proteobacteria. Current Opinion in Microbiology 8, 579–585.CrossRefGoogle ScholarPubMed
Trevors, J. T. (1997). Bacterial evolution and metabolism. Antonie van Leeuwenhoek 71, 257–263.CrossRefGoogle ScholarPubMed
Trevors, J. T. (2003). Origin of the first cells on Earth: a possible scenario. Geomicrobiology Journal 20, 175–183.CrossRefGoogle Scholar
Meer, J. R. & Sentchilo, V. (2003). Genomic islands and the evolution of catabolic pathways in bacteria. Current Opinion in Biotechnology 14, 248–254.CrossRefGoogle ScholarPubMed
Weinbauer, M. G. & Rassoulzadegan, F. (2004). Are viruses driving microbial diversification and diversity?Environmental Microbiology 6, 1–11.CrossRefGoogle ScholarPubMed
Boucher, Y., Nesbo, C. L. & Doolittle, W. F. (2001). Microbial genomes: dealing with diversity. Current Opinion in Microbiology 4, 285–289.CrossRefGoogle ScholarPubMed
Clayton, R. A., White, O. & Fraser, C. M. (1998). Findings emerging from complete microbial genome sequences. Current Opinion in Microbiology 1, 562–566.CrossRefGoogle ScholarPubMed
Conway, T. & Schoolnik, G. K. (2003). Microarray expression profiling: capturing a genome-wide portrait of the transcriptome. Molecular Microbiology 47, 879–889.CrossRefGoogle ScholarPubMed
Doolittle, R. F. (2005). Evolutionary aspects of whole-genome biology. Current Opinion in Structural Biology 15, 248–253.CrossRefGoogle ScholarPubMed
Francke, C., Siezen, R. J. & Teusink, B. (2005). Reconstructing the metabolic network of a bacterium from its genome. Trends in Microbiology 13, 550–558.CrossRefGoogle ScholarPubMed
Glaser, P. & Boone, C. (2004). Beyond the genome: from genomics to systems biology. Current Opinion in Microbiology 7, 489–491.CrossRefGoogle ScholarPubMed
Groisman, E. A. & Ehrlich, S. D. (2003). Genomics: a global view of gene gain, loss, regulation and function. Current Opinion in Microbiology 6, 479–481.CrossRefGoogle ScholarPubMed
Koonin, E. V. (2004). Comparative genomics, minimal gene-sets and the last universal common ancestor. Nature Reviews Microbiology 1, 127–136.CrossRefGoogle Scholar
Nelson, K. E. (2003). The future of microbial genomics. Environmental Microbiology 5, 1223–1225.CrossRefGoogle ScholarPubMed
Puhler, A. & Selbitschka, W. (2003). Genome research on bacteria relevant for agriculture, environment and biotechnology. Journal of Biotechnology 106, 119–120.CrossRefGoogle Scholar
Ward, N. & Fraser, C. M. (2005). How genomics has affected the concept of microbiology. Current Opinion in Microbiology 8, 564–571.CrossRefGoogle ScholarPubMed
Cowan, D. A. (2004). The upper temperature for life – where do we draw the line?Trends in Microbiology 12, 58–60.CrossRefGoogle Scholar
Deming, J. (2002). Psychrophiles and polar regions. Current Opinion in Microbiology 5, 301–309.CrossRefGoogle ScholarPubMed
Javaux, E. J. (2006). Extreme life on Earth: past, present and possibly beyond. Research in Microbiology 157, 37–48.CrossRefGoogle ScholarPubMed
Mock, T. & Thomas, D. N. (2005). Recent advances in sea-ice microbiology. Environmental Microbiology 7, 605–619.CrossRefGoogle ScholarPubMed
Simonato, F., Campanaro, S., Lauro, F. M., Vezzi, A., D'Angelo, M., Vitulo, N., Valle, G. & Bartlett, D. H. (2006). Piezophilic adaptation: a genomic point of view. Journal of Biotechnology 126, 11–25.CrossRefGoogle ScholarPubMed
Steven, B., Leveille, R., Pollard, W. H. & Whyte, L. G. (2006). Microbial ecology and biodiversity in permafrost. Extremophiles 10, 259–267.CrossRefGoogle ScholarPubMed
Anderson, N. L., Matheson, A. D. & Steiner, S. (2000). Proteomics: applications in basic and applied biology. Current Opinion in Biotechnology 11, 408–412.CrossRefGoogle ScholarPubMed
Chen, L. & Vitkup, D. (2007). Distribution of orphan metabolic activities. Trends in Biotechnology 25, 343–348.CrossRefGoogle ScholarPubMed
Dufrene, Y. F. (2002). Atomic force microscopy, a powerful tool in microbiology. Journal of Bacteriology 184, 5205–5213.CrossRefGoogle ScholarPubMed
Whitfield, E. J., Pruess, M. & Apweiler, R. (2006). Bioinformatics database infrastructure for biotechnology research. Journal of Biotechnology 124, 629–639.CrossRefGoogle ScholarPubMed

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