1887

Chapter 37 : Nucleotide Fingerprints in Nature

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $30.00

Preview this chapter:
Zoom in
Zoomout

Nucleotide Fingerprints in Nature, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817497/9781555812232_Chap37-1.gif /docserver/preview/fulltext/10.1128/9781555817497/9781555812232_Chap37-2.gif

Abstract:

Microorganisms are the key to Earth’s habitability. They harvest light energy, produce organic matter, and facilitate the turnover of key bioelements like nitrogen (N), phosphorus (P), and sulfur (S). Furthermore, it now appears that certain ubiquitous marine microorganisms, e.g., , and , may have reduced cell quotas of membrane phospholipids, so they would not be accurately represented in the environmental microbial biomass assessment. The correlations between nucleic acid synthesis, protein synthesis, and cell growth are so universally accepted that they lend themselves well to the study of complex microbial assemblages in nature. This chapter focuses on the most basic and most widely used aspect of the environmental microbial nucleotide fingerprint, namely, the measurement of cellular ATP as a biomass indicator. The preferred method of ATP quantification is the firefly bioluminescence reaction, but a variety of analytical techniques are available for either discrete sample or continuous flow analyses. A review of analytical issues concerned with ATP extraction efficiency from soils has recently appeared. ADP and AMP are both quantitatively coextracted with ATP. Despite recent and significant progress, the field of microbial ecology is still "methods-limited" with regard to the most fundamental properties of natural microbial assemblages, namely, biomass and metabolic activity estimation of the total population.

Citation: Karl D. 2007. Nucleotide Fingerprints in Nature, p 869-878. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch37

Key Concept Ranking

Microbial Ecology
1.3875698
Environmental Microbiology
1.3652616
Chemicals
0.6523289
DNA Synthesis
0.48462537
High-Performance Liquid Chromatography
0.45508718
Natural Environment
0.4495669
1.3875698
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

References

/content/book/10.1128/9781555817497.chap37
1. Atkinson, D. E. 1969. Regulation of enzyme function. Annu. Rev. Microbiol. 23;4768.
2. Azam, F.,, and R. E. Hodson. 1977. Dissolved ATP in the sea and its utilization by marine bacteria. Nature 267:696698.
3. Bertilsson, S.,, O. Berglund,, D. M. Karl,, and S. W. Chisholm. 2003. Elemental composition of marine Prochlorococcus and Synechococcus: implications for the ecological stoichiometry of the sea. Limnol. Oceanogr. 48:17211731.
4. Björkman, K.,, and D. M. Karl. 2001. A novel method for the measurement of dissolved adenosine and guanosine triphosphate in aquatic habitats: applications to marine microbial ecology. J. Microbiol. Meth. 47:159167.
5. Bossard, P.,, and D. M. Karl. 1986. The direct measurement of ATP and adenine nucleotide pool turnover in microorganisms: a new method for environmental assessment of metabolism, energy flux and phosphorus dynamics. J. Plankton Res. 8:113.
6. Chapman, A. G.,, and D. E. Atkinson. 1977. Adenine nucleotide concentrations and turnover rates. Their correlation with biological activity in bacteria and yeast. Adv. Microb. Physiol. 15:253306.
7. Costerton, J. W.,, R. T. Irvin,, and K. J. Cheng. 1981. The bacterial glycocalyx in nature and disease. Annu. Rev. Microbiol. 35:299324.
8. Craven, D. B.,, R. A. Jahnke,, and A. F. Carlucci. 1986. Fine-scale vertical distributions of microbial biomass and activity in California Borderland sediments. Mar. Biol. 83: 129139.
9. Cuhel, R. L.,, and J. B. Waterbury. 1984. Biochemical composition and short term nutrient incorporation patterns in a unicellular marine cyanobacterium, Synechococcus (WH7803). Limnol. Oceanogr. 29:370374.
10. DeLuca, M.,, and W. D. McElroy. 1978. Purification and properties of firefly luciferase. Methods Enzymol. 57:315.
11. Dobbs, F. C.,, and R. H. Findlay,. 1993. Analysis of microbial lipids to determine biomass and detect the response of sedimentary microorganisms to disturbance, p. 347358. In P. F. Kemp,, B. F. Sherr,, E. B. Sherr,, and J. J. Cole (ed.), Handbook of Methods in Aquatic Microbial Ecology. Lewis Publishers, Boca Raton, FL.
12. Franzen, J. S.,, and S. B. Binkley. 1961. Comparison of the acid-soluble nucleotides in Escherichia coli at different growth rates. J. Biol. Chem. 236:515519.
13. Guckert, J. B.,, C. P. Antworth,, P. D. Nichols,, and D. C. White. 1985. Phospholipid, ester-linked fatty acid profiles as reproducible assays for changes in prokaryotic community structure of estuarine sediments. FEMS Microbiol. Ecol. 31:147158.
14. Hodson, R. E.,, O. Holm-Hansen,, and F. Azam. 1976. Improved methodology for ATP determination in marine environments. Mar. Biol. 34:143149.
15. Holm-Hansen, O.,, and C. R. Booth. 1966. The measurement of adenosine triphosphate in the ocean and its ecological significance. Limnol. Oceanogr. 11:510519.
16. Holm-Hansen, O.,, and D. M. Karl. 1978. Biomass and adenylate energy charge determination in microbial cell extracts and environmental samples. Methods Enzymol. 57: 7385.
17. Jones, J. G.,, and B. M. Simon. 1977. Increased sensitivity in the measurement of ATP in freshwater samples with a comment on the adverse effect of membrane filtration. Freshwater Biol. 7:253260.
18. Karl, D. M. 1978. A rapid sensitive method for the measurement of guanine ribonucleotides in bacterial and environmental extracts. Anal. Biochem. 89:581595.
19. Karl, D. M. 1978. Determination of GTP, GDP and GMP in cell and tissue extracts. Methods Enzymol. 57:8594.
20. Karl, D. M. 1978. Occurrence and ecological significance of GTP in the ocean and in microbial cells. Appl. Environ. Microbiol. 36:349355.
21. Karl, D. M. 1980. Cellular nucleotide measurements and applications in microbial ecology. Microbiol. Rev. 44:739796.
22. Karl, D. M., 1986. Determination of in situ microbial biomass, viability, metabolism and growth, p. 85176. In J. S. Poindexter, and E. R. Leadbetter (ed.), Bacteria in Nature, vol. 2. Methods and Special Applications in Bacterial Ecology. Plenum Press, New York, NY.
23. Karl, D. M., 1993. Adenosine triphosphate (ATP) and total adenine nucleotide (TAN) pool turnover rates as measures of energy flux and specific growth rate in natural populations of microorganisms, p. 483494. In P. F. Kemp,, B. F. Sherr,, E. B. Sherr,, and J. J. Cole (ed.), Current Methods in Aquatic Microbial Ecology. Lewis Publishers, Boca Raton, FL.
24. Karl, D. M., 1993. Microbial RNA and DNA synthesis derived from the assimilation of [2-3H] adenine, p. 471481. In P. F. Kemp,, B. F. Sherr,, E. B. Sherr,, and J. J. Cole (ed.), Current Methods in Aquatic Microbial Ecology. Lewis Publishers, Boca Raton, FL.
25. Karl, D. M., 1993. Total microbial biomass estimation derived from the measurement of particulate adenosine-5'- triphosphate, p. 359368. In P. F. Kemp,, B. F. Sherr,, E. B. Sherr,, and J. J. Cole (ed.), Current Methods in Aquatic Microbial Ecology. Lewis Publishers, Boca Raton, FL.
26. Karl, D. M.,, and P. Bossard. 1985. Measurement and significance of ATP and adenine nucleotide pool turnover in microbial cells and environmental samples. J. Microbiol. Meth. 3:125139.
27. Karl, D. M.,, and P. Bossard. 1985. Measurement of microbial nucleic acid synthesis and specific growth rate by 32PO4 and [3H]adenine: field comparison. Appl. Environ. Microbiol. 50:706709.
28. Karl, D. M.,, and D. B. Craven. 1980. Effects of alkaline phosphatase activity on nucleotide measurements in aquatic microbial communities. Appl. Environ. Microbiol. 40:549561.
29. Karl, D. M.,, and F. C. Dobbs,. 1998. Molecular approaches to microbial biomass estimation in the sea, p. 2989. In K. E. Cooksey (ed.), Molecular Approaches to the Study of the Ocean. Chapman & Hall, London, United Kingdom.
30. Karl, D. M.,, and O. Holm-Hansen. 1976. Effects of luciferin concentration on the quantitative assay of ATP using crude luciferase preparations. Anal. Biochem. 75: 100112.
31. Karl, D. M.,, and O. Holm-Hansen,. 1978. ATP, ADP and AMP determinations in water samples and algal cultures, p. 197206. In J. A. Hellebust, and J. S. Craigie (ed.), Handbook of Phycological Methods, Vol. III. Physiological and Biochemical Methods. Cambridge University Press, New York, NY.
32. Karl, D. M.,, and O. Holm-Hansen. 1978. Methodology and measurement of adenylate energy charge ratios in environmental samples. Mar. Biol. 48:185197.
33. Karl, D. M.,, D. R. Jones,, J. A. Novitsky,, C. D. Winn,, and P. Bossard. 1987. Specific growth rates of natural microbial communities measured by adenine nucleotide pool turnover. J. Microbiol. Meth. 6:221235.
34. Karl, D. M.,, and G. Tien. 1992. MAGIC: a sensitive and precise method for measuring dissolved phosphorus in aquatic environments. Limnol. Oceanogr. 37:105116.
35. Kirchman, D.,, J. Sigda,, R. Kapuscinski,, and R. Mitchell. 1982. Statistical analysis of the direct count method for enumerating bacteria. Appl. Environ. Microbiol. 44:376382.
36. Koch, A., 1994. Growth measurement, p. 248277. In P. Gerhardt,, R. G. E. Murray,, W. A. Wood,, and N. R. Krieg (ed.), Methods for General and Molecular Bacteriology. ASM Press, Washington, DC.
37. Laws, E. A.,, D. Jones,, and D. M. Karl. 1986. Method for assessing heterogeneity in turnover rates within microbial communities. Appl. Environ. Microbiol. 52:866874.
38. Levin, G. V.,, J. R. Clendenning,, E. W. Chappelle,, A. H. Heim,, and E. Rocek. 1964. A rapid method for detection of microorganisms of ATP assay. BioScience 14:3738.
39. Lipmann, F. 1941. Metabolic generation and utilization of phosphate bond energy. Adv. Enzymol. Relat. Areas Mol. Biol. 1:99162.
40. Madsen, E. L. 1998. Epistemology of environmental microbiology. Environ. Sci. Tech. 32:429439.
41. Maki, J. S.,, M. E. Sierszen,, and C. C. Remsen. 1983. Measurements of dissolved adenosine triphosphate in Lake Michigan. Can. J. Fish. Aquat. Sci. 40:542547.
42. Martens, R. 2001. Estimation of ATP in soil: extraction methods and calculation of extraction efficiency. Soil Biol. Biochem. 33:973982.
43. Moriarty, D. J. W. 1986. Measurement of bacterial growth rates in aquatic systems using rates of nucleic acid synthesis. Adv. Microbiol. Ecol. 9:245264.
44. Nawrocki, M. P.,, and D. M. Karl. 1989. Dissolved ATP turnover in the Bransfield Strait, Antarctica, during a spring bloom. Mar. Ecol. Prog. Ser. 57:3544.
45. Novitsky, J. A. 1983. Heterotrophic activity throughout a vertical profile of seawater and sediment in Halifax Harbor, Canada. Appl. Environ. Microbiol. 45:17611766.
46. Pinkart, H. C.,, D. B. Ringelberg,, Y. M. Piceno,, S. J. Macnaughton,, and D. C. White,. 2002. Biochemical approaches to biomass measurements and community structure analysis, p. 101113. In C. J. Hurst,, R. L. Crawford,, G. R. Knudsen,, M. J. McInerney,, and L. D. Stetzenbach (ed.), Manual of Environmental Microbiology, 2nd ed. ASM Press, Washington, DC.
47. Smith, R. J. 1979. Increasing guanosine 3'-diphosphate 5'-diphosphate concentration with decreasing growth rate in Anacystis nidulans. J. Gen. Microbiol. 113:403405.
48. Strehler, B. L. 1968. Bioluminescence assay: principles and practice. Meth. Biochem. Anal. 16:99181.
49. Sutcliffe, W. H., Jr.,, E. A. Orr,, and O. Holm-Hansen. 1976. Difficulties with ATP measurements in inshore waters. Limnol. Oceanogr. 21:145149.
50. White, D. C.,, R. J. Bobbie,, S. J. Morrison,, D. K. Oosterhof,, C. W. Taylor,, and D. A. Meeter. 1977. Determination of microbial activity of estuarine detritus by relative rates of lipid biosynehtsis. Limnol. Oceanogr. 22:10891099.
51. White, D. C.,, W. M. Davis,, J. S. Nickels,, J. D. King,, and R. J. Bobbie. 1979. Determination of sedimentary microbial biomass by extractible lipid phosphate. Oecologia (Berlin) 40:5162.
52. White, D. C.,, H. C. Pinkart,, and D. B. Ringelberg,. 1997. Biomass measurements: Biochemical approaches, p. 91101. In C. J. Hurst,, G. R. Knudsen,, M. J. McInerney,, L. D. Stetzenbach,, and M. V. Walter (ed.), Manual of Environmental Microbiology. ASM Press, Washington, DC.
53. Wiebe, W. J.,, and K. Bancroft. 1975. Use of adenylate energy charge ratio to measure growth rate of natural microbial communities. Proc. Natl. Acad. Sci. USA 72:21122115.
54. Wilson, D. F.,, M. Stubbs,, R. L. Veech,, M. Erecinska,, and H. A. Krebs. 1974. Equilibrium relations between the oxidation-reduction reactions and the adenosine triphosphate synthesis in suspensions of isolated liver cells. Biochem. J. 140:5764.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error