Highlighted Text:
Show |
Hide
Full text loading...
Chapter 57 : Quantifying the Metabolic Activity of Soil- and Plant-Associated Microbes
Author:
Guy R. Knudsen
Content Type: Reference
Publication Year:
2007
Category: Environmental Microbiology
Book DOI:
10.1128/9781555815882
Chapter DOI:
10.1128/9781555815882.ch57
MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
Preview this chapter:
Quantifying the Metabolic Activity of Soil- and Plant-Associated Microbes, Page 1 of 2
< Previous page | Next page > /docserver/preview/fulltext/10.1128/9781555815882/9781555813796_Chap57-1.gif /docserver/preview/fulltext/10.1128/9781555815882/9781555813796_Chap57-2.gif
Abstract:
The seemingly infinite variety of metabolic processes and products suggests potential for a correspondingly vast array of detection methodologies, and the scope of available technology for monitoring microbial metabolic activity is increasing so rapidly that it is difficult to catalog the available methods. Soil, the rhizosphere, and the phyllosphere are populated by complex communities of organisms, including microbes (bacteria, archaea, fungi, and protists) but also typically including plant and animal components. The rhizosphere and phyllosphere are defined by the presence of a plant, so it is inherently impossible to characterize microbial activity in these habitats through the study of genetically uniform microbial strains in isolation. Respirometry is increasingly being used for determination of biodegradation kinetics, and microcosm screening studies often are performed under controlled conditions to evaluate biodegradability potential and options for bioremediation. Several methods for estimating the metabolic activity levels of microbial populations involve quantification of cellular pools and rates of synthesis of specific biochemical components including RNA, DNA, ATP, and total adenine nucleotide. A number of methods for the quantification of metabolic activity and/or biomass of individuals, populations, or microbial communities involve direct microscopic observation of cells. This chapter has attempted to provide an overview of a number of these new methodologies, but it only presents a snapshot in time, as the number of new techniques and the opportunities they present for environmental microbiology continue to rapidly expand.
Citation:
Knudsen G.
2007.
Quantifying the Metabolic Activity of Soil- and Plant-Associated Microbes,
p 697-703.
In
Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed),
Manual of Environmental Microbiology, Third Edition.
ASM Press, Washington, DC.
doi: 10.1128/9781555815882.ch57
Key Concept Ranking
- Environmental Microbiology
- 0.5868771
- Microbial Ecology
- 0.57613385
- Confocal Laser Scanning Microscopy
- 0.41324556
0.5868771
References
/content/book/10.1128/9781555815882.ch57
1.
Anderson, J. P. E. 1982. Soil respiration, p. 831–871. In A. L. Page,, R. H. Miller, and, D. R. Keeney (ed.), Methods of Soil Analysis, part 2. American Society of Agronomy, Madison, Wis.
2.
Back, J. P.,, and R. G. Kroll. 1991. The differential fluorescence of bacteria stained with acridine orange and the effects of heat. J. Appl. Bacteriol. 71: 51– 58.
3.
Bae, Y. S.,, and G. R. Knudsen. 2000. Cotransformation of Trichoderma harzianum with β-glucuronidase and green fluorescent protein genes provides a useful tool for monitoring fungal growth and activity in natural soils. Appl. Environ. Microbiol. 66: 810– 815.
4.
Bae, Y. S.,, and G. R. Knudsen. 2005. Soil microbial bio-mass influence on growth and biocontrol efficacy of Trichoderma harzianum. Biol. Control 32: 236– 242.
5.
Betts, R. P.,, P. Bankes, and, J. G. Banks. 1989. Rapid enumerations of viable micro-organisms by staining and direct microscopy. Lett. Appl. Microbiol. 9: 199– 202.
6.
Bottomley, P. J.,, and S. P. Maggard. 1990. Determination of viability within serotypes of a soil population of Rhizobium leguminosarum bv. Trifolii. Appl. Environ. Microbiol. 56: 533– 540.
7.
Burlage, R. S. 1997. Emerging technologies: bioreporters, biosensors, and microprobes, p. 115–123. 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, D.C.
8.
Button, D. K.,, and B. R. Robertson. 1989. Kinetics of bacterial processes in natural aquatic systems based on bio-mass as determined by high-resolution flow cytometry. Cytometry 10: 558– 563.
9.
Carman, K. R. 1993. Microautoradiographic detection of microbial activity, p. 397–404. 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, Fla.
10.
Coleman, D. C.,, and B. Fry. 1991. Carbon Isotope Techniques. Academic Press, Inc., New York, N.Y.
11.
Dandurand, L. M.,, D. J. Schotzko, and, G. R. Knudsen. 1997. Spatial patterns of rhizoplane populations of Pseudomonas fluorescens. Appl. Environ. Microbiol. 63: 3211– 3217.
12.
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. 347–358. 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, Fla.
13.
Dumas, B.,, S. Centis,, N. Sarrazin, and, M.-T. EsquerréTugayé. 1999. Use of green fluorescent protein to detect expression of an endopolygalacturonase gene of Colletotrichum lindemuthianum during bean infection. Appl. Environ. Microbiol. 65: 1769– 1771.
14.
Findlay, R. H.,, P. C. Pollard,, D. J. W. Moriarty, and, D. C. White. 1985. Quantitative determination of microbial activity and community nutritional status in estuarine sediments: evidence for a disturbance artifact. Can. J. Microbiol. 31: 493– 498.
15.
Findlay, R. H.,, M. B. Trexler,, J. B. Guckert, and, D. C. White. 1990. Laboratory study of disturbance in marine sediments: response of a microbial community. Mar. Ecol. Prog. Ser. 61: 121– 133.
16.
Findlay, R. H.,, and D. White. 1987. A simplified method for bacterial nutritional status based on the simultaneous determination of phospholipid and endogenous storage lipid poly beta-hydroxy alkanoate. J. Microbiol. Methods 6: 113– 120.
17.
Garland, J. L.,, and A. L. Mills. 1991. Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Appl. Environ. Microbiol. 57: 2351– 2359.
18.
Gilbert, P. M.,, and D. G. Capone. 1993. Mineralization and assimilation in aquatic, sediment and wetland systems, p. 243–272. In R. Knowles and, T. H. Blackburn (ed.), Nitrogen Isotope Techniques. Academic Press, Inc., New York, N.Y.
19.
Hinchee, R. E.,, and M. Arthur. 1991. Bench scale studies of the soil aeration process for bioremediation of petroleum hydrocarbons. J. Appl. Biochem. Biotechnol. 28: 901– 906.
20.
Hobbie, J. E. 1990. Measuring heterotrophic activity in plankton. Methods Microbiol. 22: 235– 250.
21.
Hobbie, J. E.,, R. J. Daley, and, S. Jasper. 1977. Use of Nuclepore filters for counting bacteria by fluorescence microscopy. Appl. Environ. Microbiol. 33: 1225– 1228.
22.
Huang, C.-T.,, G. A. McFeters, and, P. S. Stewart. 1996. Evaluation of physiological staining, cryoembedding and autofluorescence quenching techniques on fouling bio-films. Biofouling 9: 269– 277.
23.
Huang, C.-T.,, F. P. Yu,, G. A. McFeters, and, P. S. Stewart. 1995. Nonuniform spatial patterns of respiratory activity within biofilms during disinfection. Appl. Environ. Microbiol. 61: 2252– 2256.
24.
James, G. A.,, D. R. Korber,, D. E. Caldwell, and, W. J. Costerton. 1995. Digital image analysis of growth and starvation responses of a surface-colonizing Acinetobacter sp. J. Bacteriol. 177: 907– 915.
25.
Karl, D. M. 1979. Measurement of microbial activity and growth in the ocean by rates of stable ribonucleic acid synthesis. Appl. Environ. Microbiol. 38: 850– 860.
26.
Karl, D. M. 1981. Simultaneous rates of ribonucleic acid and deoxyribonucleic acid syntheses for estimating growth and cell division of aquatic microbial communities. Appl. Environ. Microbiol. 42: 802– 810.
27.
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. 483–494. 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, Fla.
28.
Karl, D. M. 1983. Total microbial biomass estimation derived from the measurement of particulate adenosine-5′-triphosphate, p. 359–368. 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, Fla.
29.
Kemp, P. F.,, S. Lee, and, J. LaRoche. 1993. Evaluating bacterial activity from cell-specific ribosomal RNA content measured with oligonucleotide probes, p. 415–422. 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, Fla.
30.
Kepner, R. L.,, Jr., and J. R. Pratt. 1994. Use of fluorochromes for direct enumeration of total bacteria in environmental samples. Microbiol. Rev. 58: 603– 615.
31.
Knowles, R.,, and T. H. Blackburn. 1991. Nitrogen Isotope Techniques. Academic Press, Inc., New York, N.Y.
32.
Knudsen, G. R. 2005. Bacteriology of soil and plants, p. 195–210. In P. Borriello,, P. R. Murray, and, G. Funke (ed.), Topley & Wilson’s Microbiology and Microbial Infections, 10th ed., Bacteriology. Hodder Arnold, London, England.
33.
Lawrence, J. R.,, D. R. Korber,, G. M. Wolfaardt, and, D. E. Caldwell. 1997. Analytical imaging and microscopy techniques, p. 29–51. 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, D.C.
34.
Lee, N.,, P. H. Nielsen,, K. H. Andreasen,, S. Juretschko,, J. L. Nielsen,, K.-H. Schleifer, and, M. Wagner. 1999. Combination of fluorescent in situ hybridization and micro-autoradiography—a new tool for structure-function analyses in microbial ecology. Appl. Environ. Microbiol. 65: 1289– 1297.
35.
Li, Y.,, W. A. Dick, and, O. H. Tuovinen. 2004. Fluorescence microscopy for visualization of soil microorganisms—a review. Biol. Fertil. Soils 39: 301– 311.
36.
Lübeck, M.,, I. M. B. Knudsen,, B. Jensen,, U. Thrane,, C. Janvier, and, D. F. Jensen. 2002. GUS and GFP transformation of the biocontrol strain Clonostachys rosea IK726 and the use of these marker genes in ecological studies. Mycol. Res. 106: 815– 826.
37.
McFeters, G. A.,, A. Singh,, S. Byun,, P. R. Callis, and, S. Williams. 1991. Acridine orange staining reaction as an index of physiological activity in E. coli. J. Microbiol. Methods 13: 87– 97.
38.
McFeters, G. A.,, F. P. Yu,, B. H. Pyle, and, P. S. Stewart. 1995. Physiological methods to study biofilm disinfection. J. Ind. Microbiol. 15: 333– 338.
39.
Mikkelsen, L.,, N. Roulund,, M. Lübeck, and, D. F. Jensen. 2001. The perennial ryegrass endophyte Neotyphodium lolii genetically transformed with the green fluorescent protein gene ( gfp) and visualization in the host plant. Mycol. Res. 105: 644– 650.
40.
Moriarty, D. J. W.,, D. C. White, and, T. J. Wassenberg. 1985. A convenient method for measuring rate of phospholipid synthesis in seawater and sediments: its relevance to the determination of bacterial productivity and the disturbance artifacts introduced by measurements. J. Microbiol. Methods 3: 321– 330.
41.
Nordgren, A. 1988. Apparatus for the continuous long term monitoring of soil respiration rate in large numbers of samples. Soil Biol. Biochem. 20: 955– 958.
42.
Nordgren, A.,, E. Baath, and, B. Soderstrom. 1988. Evaluation of soil respiration characteristics to assess heavy metal effects on soil microorganisms using glutamic acid as a substrate. Soil Biol. Biochem. 20: 949– 954.
43.
Norton, J. M.,, and M. K. Firestone. 1991. Metabolic status of bacteria and fungi in the rhizosphere of ponderosa pine seedlings. Appl. Environ. Microbiol. 57: 1161– 1167.
44.
Ong, S. K.,, R. E. Hinchee,, R. Hoeppel, and, R. Schultz. 1991. In situ respirometry for determining aerobic degradation rates, p. 541–545. In R. E. Hinchee and, R. F. O’Fenbuttel (ed.), In Situ Bioremediation. Butterworth-Heinemann, Boston, Mass.
45.
Oren, A.,, and T. H. Blackburn. 1979. Estimation of sediment denitrification rates at in situ nitrate concentrations. Appl. Environ. Microbiol. 37: 174– 176.
46.
Orr, K. A.,, and G. R. Knudsen. 2004. Use of GFP and image analysis to quantify proliferation of Trichoderma harzianum in nonsterile soil. Phytopathology 94: 1383– 1389.
47.
Ouverney, C. C.,, and J. A. Fuhrman. 1999. Combined microautoradiography-16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ. Appl. Environ. Microbiol. 65: 1746– 1752.
48.
Padgett, D. E. 1993. Distinguishing bacterial from non-bacterial decomposition of Spartina alterniflora by respirometry, p. 465–469. 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, Fla.
49.
Palmborg, C.,, and A. Nordgren. 1993. Modelling microbial activity and biomass in forest soil with substrate quality measured using near infrared reflectance spectroscopy. Soil Biol. Biochem. 25: 1713– 1718.
50.
Parkinson, K. J. 1981. An improved method for measuring soil respiration in the field. J. Appl. Ecol. 18: 221– 228.
51.
Paul, E. A.,, and F. E. Clark. 1989. Soil Microbiology and Biochemistry. Academic Press, Inc., New York, N.Y.
52.
Pyle, B. H.,, S. C. Broadaway, and, G. A. McFeters. 1995. A rapid, direct method for enumerating respiring entero-hemorrhagic Escherichia coli O157:H7 in water. Appl. Environ. Microbiol. 61: 2614– 2619.
53.
Pyle, B. H.,, S. C. Broadaway, and, G. A. McFeters. 1995. Factors affecting the determination of respiratory activity on the basis of cyanoditolyl tetrazolium chloride reduction with membrane filtration. Appl. Environ. Microbiol. 61: 4304– 4309.
54.
Rodriguez, G. G.,, D. Phipps,, K. Ishiguro, and, H. F. Ridgway. 1992. Use of a fluorescent redox probe for direct visualization of actively respiring bacteria. Appl. Environ. Microbiol. 58: 1801– 1808.
55.
Rogers, A. W. 1977. Techniques of Autoradiography. Elsevier/North-Holland Biomedical, New York, N.Y.
56.
Rogers, K. R. 1995. Biosensors for environmental applications. Biosens. Bioelectron. 10: 533– 541.
57.
Rohel, E. A.,, A. C. Payne,, B. A. Fraaije, and, D. W. Hollomon. 2001. Exploring infection of wheat and carbohydrate metabolism in Mycosphaerella graminicola transformants with differentially regulated green fluorescent protein expression. Mol. Plant-Microbe Interact. 14: 156– 163.
58.
Smalla, K., U. Wachtendorf,, H. Heuer,, W. Liu, and, L. Forney. 1998. Analysis of BIOLOG GN substrate utilization patterns by microbial communities. Appl. Environ. Microbiol. 64: 1220– 1225.
59.
Smith, J. J.,, and G. A. McFeters. 1997. Mechanisms of INT (2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl tetrazolium chloride), and CTC (5-cyano-2,3-ditolyl tetrazolium chloride) reduction in Escherichia coli K-12. J. Microbiol. Methods. 29: 161– 175.
60.
Stenström, J.,, B. Stenberg, and, M. Johansson. 1998. Kinetics of substrate-induced respiration (SIR): theory. Ambio 27: 35– 39.
61.
Stotzky, G. 1965. Microbial respiration, p. 1550–1570. In C. A. Black et al. (ed.), Methods of Soil Analysis. American Society of Agronomy, Madison, Wis.
62.
Stotzky, G. 1997. Quantifying the metabolic activity of microbes in soil, p. 453–458. 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, D.C.
63.
Tabor, P. S.,, and R. A. Neihof. 1982. Improved microautoradiographic method to determine individual microorganisms active in substrate uptake in natural waters. Appl. Environ. Microbiol. 44: 945– 950.
64.
Ward, D. M.,, M. M. Bateson,, R. Weller, and, A. L. Ruff-Roberts. 1992. Ribosomal RNA analysis of microorganisms as they occur in nature. Adv. Microb. Ecol. 12: 219– 286.
65.
White, D. C.,, H. C. Pinkart, and, D. B. Ringelberg. 1997. Biomass measurements: biochemical approaches, p. 91–101. 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, D.C.
66.
White, D. C.,, G. A. Smith, and, G. R. Stanton. 1984. Biomass, community structure, and metabolic activity of the microbiota in benthic marine sediments and sponge spicule mats. Antarct. J. US 29: 125– 126.
67.
White, D. C.,, and A. T. Tucker. 1969. Phospholipid metabolism during bacterial growth. J. Lipid Res. 10: 220– 223.
68.
Winding, A.,, S. J. Binnerup, and, J. Sorenson. 1994. Viability of indigenous soil bacteria assayed by respiratory activity and growth. Appl. Environ. Microbiol. 60: 2869– 2875.
69.
Xu, H.-S.,, N. Roberts,, F. L. Singleton,, R. W. Atwell,, D. J. Grimes, and, R. R. Colwell. 1982. Survival and viability of nonculturable Escherichia coli and Vibrio cholerae in the estuarine and marine environment. Microb. Ecol. 8: 313– 323.
70.
Xu, K. D.,, P. S. Stewart,, F. Xia,, C-T. Huang, and, G. A. McFeters. 1998. Spatial physiological heterogeneity in Pseudomonas aeruginosa biofilm is determined by oxygen availability. Appl. Environ. Microbiol. 64: 4035– 4039.
71.
Yu, F. P.,, and G. A. McFeters. 1994. Rapid in situ assessment of physiological activities in bacterial biofilms using fluorescent probes. J. Microbiol. Methods 20: 1– 10.
72.
Zeilinger, S.,, C. Galhaup,, K. Payer,, S. L. Woo,, R. L. Mach,, C. Fekete,, M. Lorito, and, C. P. Kubicek. 1999. Chitinase gene expression during mycoparasitic interaction of Trichoderma harzianum with its host. Fungal Genet. Biol. 26: 131– 140.