1887

Chapter 11 : Enrichment and Isolation

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

Preview this chapter:
Zoom in
Zoomout

Enrichment and Isolation, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817497/9781555812232_Chap11-1.gif /docserver/preview/fulltext/10.1128/9781555817497/9781555812232_Chap11-2.gif

Abstract:

A section of this chapter focuses on the use of enrichment and cultivation procedures with molecular methods, such as wholecell fluorescent in situ hybridization (FISH) or denaturing gradient gel electrophoresis (DGGE), to monitor the progress of an enrichment, to evaluate the presence of contaminants, and to identify new isolates. Biophysical enrichments make use of such conditions as growth temperature, heat treatment, sonic oscillation, or UV irradiation to kill or inhibit the rest of the population. Biological enrichments may make use of specific hosts for selective growth of a particular organism, or they may take advantage of some pathogenic property, such as invasiveness, which the rest of the population does not possess. Bacteria are usually isolated from enrichment cultures by spatially separating the organisms in or on a solid medium and subsequently allowing them to grow into colonies. The chapter is designed to demonstrate the multiplicity and in many instances the considerable ingenuity of enrichment and isolation methods for bacteria by presenting specific selected examples. The buoyant density of bacteria in pure culture and in samples from natural aquatic environments has been studied by density gradient centrifugation in Percoll gradients, and the average density of a representative bacterium is 1.080 pg µm . Isolation of species, particularly those from the environment, can sometimes be facilitated by acidification of samples to pH 2.2, which kills contaminants more quickly than it does the species.

Citation: Teske A, Cypionka H, Holt J, Krieg N. 2007. Enrichment and Isolation, p 215-269. 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.ch11

Key Concept Ranking

Microbial Ecology
0.6236902
Bacteria and Archaea
0.614384
Denaturing Gradient Gel Electrophoresis
0.41157982
0.6236902
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

Isoelectric focusing. Schematic (A) and photograph (B) of apparatus for isoelectric focusing of whole bacterial cells. The cathode (–) and anode (+) consist of platinum wires which are connected to a power supply ( ).

Citation: Teske A, Cypionka H, Holt J, Krieg N. 2007. Enrichment and Isolation, p 215-269. 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.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

Capillary enrichment method, based on chemotactic attraction of motile bacteria to different carbon and sulfur sources in glass microcapillaries ( ).

Citation: Teske A, Cypionka H, Holt J, Krieg N. 2007. Enrichment and Isolation, p 215-269. 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.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3
FIGURE 3

FeS-based growth of Fe-oxidizing bacteria in gradient tubes. The four tubes on the left contain cultures of Fe-oxidizing bacteria, and the single tube on the far right represents an abiotic control. In culture tubes, a distinct band of cells develops at ca. 1 cm from the air-medium interface at the tops of the tubes. The milky region that can be seen clearly at the tops of the tubes is comprised principally of Fe oxide particles, which directly overlie the band of cell growth. In the control tube, Fe oxides develop from ca. 1 cm from the top of the tube to ca. 3 cm from the FeS-medium interface at the bottom ( ).

Citation: Teske A, Cypionka H, Holt J, Krieg N. 2007. Enrichment and Isolation, p 215-269. 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.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4
FIGURE 4

Useful streak plate method for obtaining wellisolated colonies. (A) With a glass marker pencil, draw a “T” on the bottom of the petri dish to divide the plate into three sections. (B) Streak a loopful of culture lightly back and forth on the surface of the agar over section 1 as shown. Raise the lid of the dish just enough to allow the streaking to be done, and then replace it. Flame sterilize the loop, and allow it to cool (15s). (C) Draw the loop over section 1 as shown, and immediately streak back and forth over section 2. Flame the needle, and allow it to cool. (D) Draw the loop over section 2 as shown, and then streak back and forth over section 3. (E) Incubate the dish in an inverted position as shown, to prevent drops of condensed water on the lid from falling onto the agar surface. Section 1 will develop the heaviest amount of growth, and section 2 or 3 will usually have well-isolated colonies.

Citation: Teske A, Cypionka H, Holt J, Krieg N. 2007. Enrichment and Isolation, p 215-269. 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.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 5
FIGURE 5

Streaking an anaerobic roll tube ( ). (A) Loop needle (platinum or stainless steel; nichrome will cause oxidation of the medium). (B) Gassing cannula for continuous purging of the tube with oxygen-free gas. (C) Prereduced agar medium coating the inner wall of the tube. (D) Motor-driven tube holder for rotating the roll tube during streaking. Insert the needle with a loopful of inoculum to the bottom of the tube, press the loop flat against the agar, and draw it upward. After streaking in this manner for one-fourth of the way up the tube, turn the loop so that it is perpendicular to the agar (as shown), and continue to streak upward to the top. Remove the gas cannula, replace the rubber stopper in the tube, and incubate the culture in a vertical position.

Citation: Teske A, Cypionka H, Holt J, Krieg N. 2007. Enrichment and Isolation, p 215-269. 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.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 6
FIGURE 6

Membrane filter design and setups for aerobic and anaerobic incubation. Bacterial cells from precultures are filtered onto 0.2-μm-pore-size polycarbonate membrane filters and placed in PBS solution to avoid desiccation. Coverslips are covered with a thin layer of silicone oil. The membrane filters are mounted on the coverslip with the bacteria towards the silicone oil. The filter sandwich can be incubated either floating on a liquid surface or submerged within a liquid growth medium. For aerobic incubation, the filters can also be placed directly on a growth medium without being mounted on the coverslips ( ).

Citation: Teske A, Cypionka H, Holt J, Krieg N. 2007. Enrichment and Isolation, p 215-269. 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.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 7
FIGURE 7

Colonies of oxygen-sensitive anaerobes using the agar shake technique. A dilution series was established from right to left, eventually yielding well-isolated colonies. The tubes are sealed with a sterile mixture of paraffin and mineral oil to maintain anaerobic conditions (photo courtesy of Norbert Pfennig [ ]).

Citation: Teske A, Cypionka H, Holt J, Krieg N. 2007. Enrichment and Isolation, p 215-269. 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.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 8
FIGURE 8

(A) MPN dilution series, here shown with Hungate tubes in three parallel dilution series. The inoculum is transferred anaerobically using N2-flushed syringes (H. Cypionka).

Citation: Teske A, Cypionka H, Holt J, Krieg N. 2007. Enrichment and Isolation, p 215-269. 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.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 9
FIGURE 9

MPN counts for anaerobes with a microtiter plate. Inside an anaerobic glove box, four different samples are diluted down to 1:106 on a deep-well microtiter plate. For each sample, a row remains uninoculated as a control. The wells are sealed with a capmat, and the plate is stored in an anoxic bag with an oxygen-consuming catalyst such as Merck Anaerocult A and an oxygen indicator such as phenol red (H. Cypionka).

Citation: Teske A, Cypionka H, Holt J, Krieg N. 2007. Enrichment and Isolation, p 215-269. 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.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 10
FIGURE 10

Schematic illustration of the Microdrop® device for automated inoculation of 170-μl aliquots of a bacterial suspension into a 96-well microtiter plate ( ).

Citation: Teske A, Cypionka H, Holt J, Krieg N. 2007. Enrichment and Isolation, p 215-269. 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.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 11
FIGURE 11

Apparatus for washing of filamentous bacteria ( ).

Citation: Teske A, Cypionka H, Holt J, Krieg N. 2007. Enrichment and Isolation, p 215-269. 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.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 12
FIGURE 12

Isolation of a single bacterial cell of (arrow, larger cells) with the Bactotip method. The smaller cells are sp. (Left) Schematic drawing; (right) corresponding phase-contrast micrographs. Bar, 10 μm ( ).

Citation: Teske A, Cypionka H, Holt J, Krieg N. 2007. Enrichment and Isolation, p 215-269. 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.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 13
FIGURE 13

Optical tweezers for the isolation of bacteria. (a) Principle of the optical tweezers. A strongly focused laser beam on an object as small as a prokaryotic cell creates downward forces (Fa and Fb) on the cell, which allow the cell to be dragged in any direction as long as the beam force remains on it. (b) Isolation. The laser beam can lock onto a single cell present in a mixture in a capillary tube and drag the optically trapped cell away from the other cells. In the example used here, the desired cell is dragged from right to left. Once the desired cell is far enough from the other cells, the capillary is severed, the laser is turned off, and the cell is flushed into a tube of sterile medium ( ).

Citation: Teske A, Cypionka H, Holt J, Krieg N. 2007. Enrichment and Isolation, p 215-269. 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.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 14
FIGURE 14

Use of DGGE in the analysis of mixed cultures and enrichments. After DNA isolation from the sample or mixed culture, PCR, and DGGE, the sequences of the DGGE bands are determined and compared to the sequence information available from databases, to identify the components of the microbial mixture, and subsequently to select culture conditions to separate and isolate the bacterial species in pure culture. For verification, the DGGE bands of the pure culture are compared to the DGGE pattern of the original sample (A. Teske).

Citation: Teske A, Cypionka H, Holt J, Krieg N. 2007. Enrichment and Isolation, p 215-269. 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.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555817497.chap11
1. Aaronson, S. 1970. Experimental Microbial Ecology. Academic Press, Inc., New York, NY. Contains a wealth of detailed methods for enrichment and isolation of a great variety of bacteria..
2. Balows, A.,, H. G. Trüper,, M. Dworkin,, W. Harder,, and K.-H. Schleifer (ed.). 1992. The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, vol. 1-4, 2nd ed. Springer- Verlag, New York, NY. A comprehensive treatment of the prokaryotic world including isolation and enrichments of all types. Some chapters are classics on methodology and techniques, such as “Gram-negative mesophilic sulfate-reducing bacteria” by F. Widdel and F. Bak, vol. IV, p. 3352-3378..
3. Collins, V. G., 1969. Isolation, cultivation and maintenance of autotrophs, p. 1 52. In J. R. Norris, and D. W. Ribbons (ed.), Methods in Microbiology, vol. 3B. Academic Press, Inc., New York, NY. A comprehensive treatment of the principles and techniques for enrichment and isolation of photo- and chemoautotrophs..
4. Knudsen, G. R.,, M. J. McInerney,, L. D. Stetzenbach,, and R. L. Crawford (ed.). 2001. Manual of Environmental Microbiology, 2nd ed. ASM Press, Washington, DC. With a general methodology section on microbial cultivation, identification, and community analysis, and chapters on specialized methodology for microbiological sampling, activity measurements, and specific microorganisms of environmental interest..
5. Krieg, N. R.,, and J. G. Holt (ed.). 1984. Bergey’s Manual of Systematic Bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore, MD.
6. Lebeda, D. P. 1990. Isolation of Biotechnological Organisms from Nature. McGraw-Hill Publishing Co., New York, NY. Covers both prokaryotic and eukaryotic microorganisms and presents selected techniques for isolation of organisms of potential biotechnological importance.
7. Murray, P. (ed.). 1999. Manual of Clinical Microbiology, 7th ed. ASM Press, Washington, DC. Principles and methods for enrichment, isolation, and identification of pathogenic bacteria, rickettsias, viruses, and fungi.
8. Sneath, P. H. A.,, N. S. Mair,, M. E. Sharpe,, and J. G. Holt (ed.). 1986. Bergey’s Manual of Systematic Bacteriology, vol. 2. The Williams & Wilkins Co., Baltimore, MD.
9. Staley, J. T.,, M. P. Bryant,, N. Pfenning,, and J. G. Holt (ed.). 1989. Bergey’s Manual of Systematic Bacteriology, vol. 3. The Williams & Wilkins Co., Baltimore, MD.
10. Veldkamp, H., 1970. Enrichment cultures of prokaryotic organisms, p. 305 361. In J. R. Norris, and D. W. Ribbons (ed.), Methods in Microbiology, vol. 3A. Academic Press, Inc., New York, NY. Emphasizes the theoretical aspects of enrichment cultures and presents methods for the enrichment of specific organisms..
11. Williams, S. T.,, M. E. Sharpe,, and J. G. Holt (ed.). 1989. Bergey’s Manual of Systematic Bacteriology, vol. 4. The Williams & Wilkins Co., Baltimore, MD. References 5, 8, 9, and 11 contain descriptions of all the genera of prokaryotes with discussions of their enrichment and isolation..
12. Allen, O. N. 1957. Experiments in Soil Bacteriology, 3rd ed. Burgess Publishing Co., Minneapolis, MN.
13. Amann, R. I.,, W. Ludwig,, and K.-H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143 169.
14.American Public Health Association. 1960. Standard Methods for the Examination of Dairy Products, 11th ed. American Public Health Association, New York, NY.
15. Ammerman, J. W.,, and F. Azam. 1981. Dissolved cyclic adenosine monophosphate (cAMP) in the sea and uptake of cAMP by marine bacteria. Mar. Ecol. Prog. Ser. 5: 85 89.
16. Aragno, M.,, and H. G. Schlegel. 1978. Aquaspirillum autotrophicum, a new species of hydrogen-oxidizing, facultatively autotrophic bacteria. Int. J. Syst. Bacteriol. 28: 112 116.
17. Armbruster, E. H. 1969. Improved technique for isolation and identification of Sphaerotilus. Appl. Microbiol. 17: 320 321.
18. Ashkin, A.,, and J. M. Dziedzic. 1987. Optical trapping and manipulation of viruses and bacteria. Science 235: 1517 1520.
19. Ashkin, A.,, J. M. Dziedzic,, and Y. Yamane. 1987. Optical trapping and manipulation of single cells using infrared laser beams. Nature (London) 330: 769 771.
20. Attwood, M. M.,, and W. Harder. 1962. A rapid and specific enrichment procedure for Hyphomicrobium spp. Antonie Leeuwenhoek J. Microbiol. Serol. 38: 369 378.
21. Bak, F.,, and H. Cypionka. 1987. A novel type of energy metabolism involving fermentation of inorganic sulphur compounds. Nature 326: 891 892.
22. Balch, W. E.,, G. E. Fox,, L. J. Magrum,, C. R. Woese,, and R. S. Wolfe. 1979. Methanogens: reevaluation of a unique biological group. Microbiol. Rev. 43: 260 296.
23. Barnes, E. M. 1956. Methods for the isolation of faecal streptococci (Lancefield Group D) from bacon factories. J. Appl. Bacteriol. 18: 193 203.
24. Baron, E. J.,, and S. M. Finegold. 1990. Bailey & Scott’s Diagnostic Microbiology, 8th ed. C. V. Mosby Co., St. Louis, MO.
25. Batchelor, S. E.,, M. Cooper,, S. R. Chhabra,, L. A. Glover,, G. S. A. B. Stewart,, P. Williams,, and J. I. Prosser. 1997. Cell density-regulated recovery of starved biofilm populations of ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 63: 2281 2286.
26. Bazylinski, D. A.,, R. B. Frankel,, and H. W. Jannasch. 1988. Anaerobic magnetite production by a marine, magnetotactic bacterium. Nature (London) 334: 518 519.
27. Becking, J.-H., 1984. Genus Beijerinckia Derx 1950, p. 315. In N. R. Krieg, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore, MD.
28. Belly, R. T.,, B. B. Bohlool,, and T. D. Brock. 1973. The genus Thermoplasma. Ann. N. Y. Acad. Sci. 225: 94 107.
29. Biebl, H.,, and N. Pfennig,. 1981. Isolation of members of the family Rhodospirillaceae, p. 267 273. In M. P. Starr,, H. Stolp,, H. G. Trüper,, A. Balows,, and H. G. Schlegel (ed.), The Prokaryotes. A Handbook on Habitats, Isolation, and Identification of Bacteria. Springer-Verlag, New York, NY.
30. Blakemore, R. P.,, D. Maratea,, and R. S. Wolfe. 1979. Isolation and pure culture of a freshwater magnetic spirillum in chemically defined medium. J. Bacteriol. 140: 720 729.
31. Blaser, M. J.,, I. D. Berkowitz,, R. M. LaForce,, J. Cravens,, L. B. Reller,, and W.-L. L. Wang. 1979. Campylobacter enteritis: clinical and epidemiologic features. Ann. Intern. Med. 91: 179 184.
32. Brock, T. D., 1984. Genus Thermus Brock and Freeze 1969, p. 333 339. In N. R. Krieg, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore, MD.
33. Brock, T. D.,, and H. Freeze. 1969. Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophile. J. Bacteriol. 98: 289 297.
34. Bruns, A.,, H. Cypionka,, and J. Overmann. 2002. Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea. Appl. Environ. Microbiol. 68: 3978 3987.
35. Bruns, A.,, H. Hoffelner,, and J. Overmann. 2003. A novel approach for high throughput cultivation assays and the isolation of planktonic bacteria. FEMS Microbiol. Ecol. 45: 161 171.
36. Bruns, A.,, U. Nübel,, H. Cypionka,, and J. Overmann. 2003. Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton. Appl. Environ. Microbiol. 69: 1980 1989.
37. Buchholz-Cleven, B. E. E.,, B. Rattunde,, and K. L. Straub. 1997. Screening for genetic diversity of isolates of anaerobic Fe(II)-oxidizing bacteria using DGGE and whole-cell hybridization. Syst. Appl. Microbiol. 20: 301 309.
38. Buchner, P. 1965. Endosymbiosis of Animals with Plant Microorganisms. Interscience Publishers, New York, NY.
39. Bukatsch, F. 1968. Anreicherung und Isolierung mariner Leuchtbakterien. Zentbl. Bakteriol. 1. Abt. Suppl. Heft 1: 399 406.
40. Burggraf, S.,, P. Heyder,, and N. Eis. 1997. A pivotal Archaea group. Nature 385: 780.
41. Button, D. K.,, F. Schut,, P. Quang,, R. Martin,, and B. R. Robertson. 1993. Viability and isolation of marine bacteria by dilution culture: theory, procedures, and initial results. Appl. Environ. Microbiol. 59: 881 891.
42. Calcott, P. H.,, and J. R. Postgate. 1972. On substrateaccelerated death in Klebsiella aerogenes. J. Gen. Microbiol. 70: 115 122.
43. Canale-Parola, E., 1984. Genus I. Spirochaeta Ehrenberg 1835, p. 41. In N. R. Krieg, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore, MD.
44. Canale-Parola, E.,, S. L. Rosenthal,, and D. G. Kupfer. 1966. Morphological and physiological characteristics of Spirillum gracile sp. n. Antonie Leeuwenhoek J. Microbiol. Serol. 32: 113 124.
45. Cataldi, M. S. 1940. Aislamiento de Beggiatoa alba en cultivo puro. Rev. Inst. Bacteriol. Dept. Nac. Hig. (Buenos Aires) 9: 393 423.
46. Chapman, G. H. 1944. The isolation of streptococci from mixed cultures. J. Bacteriol. 48: 113 114.
47. Christensen, B.,, T. Torsvik,, and T. Lien. 1992. Immunomagnetically captured thermophilic sulfate-reducing bacteria from North Sea oil waters. Appl. Environ. Microbiol. 58: 1244 1248.
48. Claus, D.,, and R. C. W. Berkeley,. 1986. Genus Bacillus Cohn 1872, p. 1114 1120. In P. H. A. Sneath,, N. S. Mair,, M. E. Sharpe,, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vo1. 2. The Williams & Wilkins Co., Baltimore, MD.
49. Claus, D.,, and F. Fahmy,. 1984. Genus Sporosarcina Kluyver and Van Niel 1936, p. 1204. In P. H. A. Sneath,, N. S. Mair,, M. E. Sharpe,, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 2. The Williams & Wilkins Co., Baltimore, MD.
50. Claus, D.,, and N. Walker. 1964. The decomposition of toluene by soil bacteria. J. Gen. Microbiol. 36: 107 122.
51. Coates, J. D.,, D. J. Ellis,, E. Roden,, K. Gaw,, E. L. Blunt- Harris,, and D. R. Lovley. 1998. Recovery of humicsreducing bacteria from a diversity of sedimentary environments. Appl. Environ. Microbiol. 64: 1504 1509.
52. Connon, S. A.,, and S. J. Giovannoni. 2002. Highthroughput methods for culturing micro-organisms in very-low-nutrient media yield diverse new marine isolates. Appl. Environ. Microbiol. 68: 3878 3885.
53. Corbel, M. J.,, and W. J. Brinley-Morgan,. 1984. Genus Brucella Meyer and Shaw 1920, p. 377 382. In N. R. Krieg, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore, MD.
54. Cottrell, M. T.,, and D. L. Kirchman. 2000. Natural assemblages of marine Proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high- molecular-weight dissolved organic matter. Appl. Environ. Microbiol. 66: 1692 1697.
55. Couch, J. N. 1949. A new group of organisms related to Actinomyces. J. Elisha Mitchell Sci. Soc. 65: 315 318.
56. Curry, J. C.,, and G. E. Borovian. 1976. Selective medium for distinguishing micrococci from staphylococci in the clinical laboratory. J. Clin. Microbiol. 4: 455 457.
57. Daims, H.,, A. Brühl,, R. Amann,, K.-H. Schleifer,, and M. Wagner. 1999. The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set. Syst. Appl. Microbiol. 22: 434 444.
58. Darland, G.,, T. D. Brock,, W. Samsonoff,, and S. F Conti. 1970. A thermophilic, acidophilic mycoplasma isolated from a coal refuse pile. Science 170: 1416 1418.
59. Davis, B. D.,, R. Dulbecco,, H. N. Eisen,, H. S. Ginsberg,, W. B. Wood,, and M. McCarty. 1973. Microbiology, 2nd ed. Harper & Row, Hagerstown, MD.
60. Dawes, E. A.,, and P. J. Senior. 1973. The role and regulation of energy reserve polymers in microorganisms. Adv. Microb. Physiol. 10: 135 266.
61. Döbereiner, J.,, and V. L. D. Baldani. 1979. Selective infection of maize roots by streptomycin-resistant Azospirillum lipoferum and other bacteria. Can. J. Microbiol. 25: 1264 1268.
62. Döbereiner, J.,, I. E. Marriel,, and M. Nery. 1976. Ecological distribution of Spirillum lipoferum Beijerinck. Can. J. Microbiol. 22: 1461 1473.
63. Edwards, K. J.,, D. R. Rogers,, C. O. Wirsen,, and T. M. McCollom. 2003. Isolation and characterization of novel psychrophilic, neutrophilic, Fe-oxidizing, chemolithoautotrophic alpha- and gamma-proteobacteria from the deep sea. Appl. Environ. Microbiol. 69: 2906 2913.
64. Emerson, D.,, and C. Moyer. 1997. Isolation and characterization of novel iron-oxidizing bacteria that grow at circumneutral pH. Appl. Environ. Microbiol. 63: 4784 4792.
65. Farrell, I. D. 1974. The development of a new selective medium for the isolation of Brucella abortus from contaminated sources. Res. Vet. Sci. 16: 280 286.
66. Faust, L.,, and R. S. Wolfe. 1961. Enrichment and cultivation of Beggiatoa alba. J. Bacteriol. 81: 88 106.
67. Ferenci, T. 1996. Adaptation to life at micromolar nutrient levels: the regulation of Escherichia coli glucose transport by endoinduction and cAMP. FEMS Microbiol. Rev. 18: 301 317.
68. Ferris, M. J.,, A. L. Ruff-Roberts,, E. D. Kopcynski,, M. M. Bateson,, and D. M. Ward. 1996. Enrichment culture and microscopy conceal diverse thermophilic Synechococcus populations in a single hot spring microbial mat habitat. Appl. Environ. Microbiol. 62: 1045 1050.
69. Ferris, M. J.,, and D. M. Ward. 1997. Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 63: 1375 1381.
70. Finegold, S. M.,, W. J. Martin,, and E. G. Scott. 1978. Bailey and Scott’s Diagnostic Microbiology, 5th ed. The C. V. Mosby Co., St. Louis, MO.
71. Finster, K.,, W. Liesack,, and B. J. Tindall. 1997. Desulfospira joergensii, gen. nov., sp. nov., a new sulfatereducing bacterium isolated from marine surface sediment. Syst. Appl. Microbiol. 20: 201 208.
72. Freeman, B. A. 1977. Burrows’ Textbook of Microbiology, 21st ed. The W. B. Saunders Co., Philadelphia, PA.
73. Fröhlich, J.,, and H. König. 1999. Rapid isolation of single microbial cells from mixed natural and laboratory populations with the aid of a micromanipulator. Syst. Appl. Microbiol. 22: 249 257.
74. Fröstl, J. M.,, and J. Overmann. 1998. Physiology and tactic response of the phototrophic consortium “ Chlorochromatium aggregatum.” Arch. Microbiol. 169: 129 135.
75. Gerloff, G. C.,, G. P. Fitzgerald,, and F. Skoog. 1950. The isolation, purification and culture of blue-green algae. Am. J. Bot. 37: 216 218.
76. Gibbons, N. E., 1969. Isolation, growth and requirements of halophilic bacteria, p. 169 183. In J. R. Norris, and D. W. Ribbons (ed.), Methods in Microbiology, vol. 3B. Academic Press, Inc., New York, NY.
77. Grant, M. A.,, and J. G. Holt. 1977. Medium for the selective isolation of members of the genus Pseudomonas from natural habitats. Appl. Environ. Microbiol. 33: 1222 1224.
78. Guerrero, R.,, S. Pedrós-Alió,, T. N. Schmidt,, and J. Mas. 1985. A survey of buoyant density of microorganisms in pure cultures and natural samples. Microbiologia 1: 53 65.
79. Hagedorn, C.,, and J. G. Holt. 1975. A nutritional and taxonomic survey of Arthrobacter soil isolates. Can. J. Microbiol. 21: 353 361.
80. Hampp, E. G. 1957. Isolation and identification of spirochaetes obtained from unexposed canals of pulpinvolved teeth. Oral Surg. Oral Med. Oral Pathol. 101: 1100 1104.
81. Han, S. O.,, and P. B. New. 1998. Isolation of Azospirillum spp. from natural soils by immunomagnetic separation. Soil Biol. Biochem. 30: 975 980.
82. Hanert, H. H., 1992. The genus Gallionella. p. 4082 4088. In A. Balows,, H. G. Trüper,, M. Dworkin,, W. Harder,, and K.-H. Schleifer (ed.), The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications. 2nd ed. Springer-Verlag, New York, NY.
83. Hanson, A. W. 1970. Isolation of spirochaetes from primates and other mammalian species. Br. J. Vener. Dis. 46: 303 306.
84. Hanson, A. W.,, and G. R. Cannefax. 1964. Isolation of Borrelia refringens in pure culture from patients with condylomata acuminata. J. Bacteriol. 88: 111 113.
85. Hespell, R. B., 1984. Genus Serpens Hespell 1977, p. 373. In N. R. Krieg, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore, MD.
85.a. Højberg, O.,, S. J. Binnerup,, and J. Sørensen. 1997. Growth of silicone-immobilized bacteria on polycarbonate membrane filters, a technique to study microcolony formation under anaerobic conditions. Appl. Environ. Microbiol. 63: 2920 2924.
86. Holdeman, L. V.,, E. P. Cato,, and W. E. C. Moore (ed.). 1977. Anaerobe Laboratory Manual, 4th ed. Virginia Polytechnic Institute and State University, Blacksburg.
87. Huber, R.,, S. Burggraf,, T. Mayer,, S. M. Barns,, P. Rossnagel,, and K. O. Stetter. 1995. Isolation of a hyperthermophilic archaeum predicted by in-situ RNA analysis. Nature 376: 57 58.
88. Hugenholtz, P.,, B. M. Goebel,, and N. R. Pace. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180: 4765 4774.
89. Hungate, R. E. 1950. The anaerobic cellulolytic bacteria. Bacteriol. Rev. 14: 1 49.
90. Hungate, R. E., 1969. A roll tube method for cultivation of strict anaerobes, p. 117 132. In J. R. Norris, and D. W. Ribbons (ed.), Methods in Microbiology, vol. 3B. Academic Press, Inc., New York, NY.
91. Hylemon, P. B.,, J. S. Wells, Jr.,, J. H. Bowdre,, T. O. MacAdoo,, and N. R. Krieg. 1973. Designation of Spirillum volutans Ehrenberg 1832 as type species of the genus Spirillum Ehrenberg 1832 and designation of the neotype strain of S. volutans. Int. J. Syst. Bacteriol. 23: 20 27.
92. Inoue, K. 1976. Quantitative ecology of microorganisms of Syowa Station in Antarctica and isolation of psychrophiles. J. Gen. Appl. Microbiol. 22: 143 150.
93. Inoue, K.,, and K. Komagata. 1976. Taxonomy study on obligately psychrophilic bacteria isolated from Antarctica. J. Gen. Appl. Microbiol. 22: 165 176.
94. Iverson, W. P. 1966. Growth of Desulfovibrio on the surface of agar media. Appl. Microbiol. 14: 529 534.
95. Jannasch, H. 1967. Enrichments of aquatic spirilla in continuous culture. Arch. Mikrobiol. 69: 165 173.
96. Jannasch, H. 1968. Competitive elimination of Enterobacteriaceae from seawater. Appl. Microbiol. 16: 1616 1618.
97. Jaspers, E.,, and J. Overmann. 1997. Separation of bacterial cells by isoelectric focusing, a new method for analysis of complex microbial communities. Appl. Environ. Microbiol. 63: 3176 3181.
98. Johnson, R. C.,, and S. Faine,. 1984. Genus I. Leptospira Noguchi 1917, p. 64. In N. R. Krieg, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore, MD.
99. Johnstone, K. I., 1969. The isolation and cultivation of single organisms, p. 455 471. In J. R. Norris, and D. W. Ribbons (ed.), Methods in Microbiology, vol. 1. Academic Press, Inc., New York, NY.
100. Jones, J. G. 1979. A Guide to Methods for Estimating Microbial Numbers and Biomass in Fresh Water. Scientific publication no. 39. Freshwater Biological Association, Ambleside, United Kingdom.
101. Kaeberlein, T.,, K. Lewis,, and S. S. Epstein. 2002. Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296: 1127 1129.
102. Kane, M. D.,, L. K. Poulsen,, and D. A. Stahl. 1993. Monitoring the enrichment and isolation of sulfatereducing bacteria by using oligonucleotide hybridization probes designed from environmentally derived 16S rRNA sequences. Appl. Environ. Microbiol. 59: 682 686.
103. Kaplan, H.,, and E. Greenberg. 1985. Diffusion of autoinducer is involved in regulation of the Vibrio fischeri luminescence system. J. Bacteriol. 163: 1210 1214.
104. Kelly, R. T., 1984. Genus IV Borrelia Swellengrebel 1907, p. 58. In N. R. Krieg, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore, MD.
105. Kenny, G. E., 1974. Mycoplasma, p. 333 337. In E. H. Lennette,, E. H. Spaulding,, and J. P. Truant (ed.), Manual of Clinical Microbiology, 2nd ed. American Society for Microbiology, Washington, DC.
106. Kersters, K.,, and J. De Ley,. 1984. Genus III. Agrobacterium Conn, p. 247. In N. R. Krieg, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore, MD.
107. Klee, A. J. 1993. A computer program for the determination of most probable number and its confidence limits. J. Microbiol. Methods 18: 91 98.
108. Kocur, M., 1986. Genus I. Micrococcus Cohn 1872, p. 1005. In P. H. A. Sneath,, N. S. Mair,, M. E. Sharpe,, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 2. The Williams & Wilkins Co., Baltimore, MD.
109. Kramer, P. A.,, and D. Jones. 1969. Media selective for Listeria monocytogenes. J. Appl. Bacteriol. 32: 381 394.
110. Kucera, S.,, and R. S. Wolfe. 1957. A selective enrichment method for Gallionella ferruginea. J. Bacteriol. 74: 344 349.
111. la Rivière, J. W. M., , and K. Schmidt,. 1989. Genus Achromatium 1893, p. 2132. In J. T. Staley,, M. P. Bryant,, N. Pfennig,, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 3. The Williams & Wilkins Co., Baltimore, MD.
112. Leadbetter, E. R. 1963. Growth and morphogenesis of Sporocytophaga myxococcoides. Bacteriol. Proc. 1963: 42.
113. Lederberg, J. 1954. A simple method for isolating individual microbes. J. Bacteriol. 88: 258 259.
114. 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 microautoradiography—a new tool for structure function analyses in microbial ecology. Appl. Environ. Microbiol. 65: 1289 1297.
115. Leifson, E. 1936. New selenite enrichment media for the isolation of typhoid and paratyphoid ( Salmonella) bacilli. Am. J. Hyg. 24: 423 432.
116. Lennette, E. H.,, A. Balows,, W. J. Hausler, Jr.,, and J. P. Truant (ed.). 1980. Manual of Clinical Microbiology, 3rd ed. American Society for Microbiology, Washington, DC.
117. Lichstein, H. C.,, and E. L. Oginsky. 1965. Experimental Microbial Physiology. W. H. Freeman and Co., San Francisco, CA.
118. Linn, D. M.,, and N. R. Krieg. 1971. Occurrence of two organisms in the type strain of Spirillum lunatum: rejection of the name Spirillum lunatum and characterization of Oceanospirillum maris subsp. williamsiae and an unclassified vibrioid bacterium. Int. J. Syst. Bacteriol. 28: 131 138.
119. Loewen, P. C.,, B. Hu,, J. Strutinsky,, and R. Sparling. 1998. Regulation in the rpoS region of Escherichia coli. Can. J. Microbiol. 44: 707 717.
120. Lovley, D. R.,, and E. J. P. Phillips. 1987. Rapid assay for microbially reducible ferric iron in aquatic sediments. Appl. Environ. Microbiol. 53: 1536 1540.
121. Lovley, D. R.,, and E. J. P. Phillips. 1988. Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese. Appl. Environ. Microbiol. 54: 1472 1480.
122. Lovley, D. R.,, J. F. Stolz,, G. L. Nord,, and E. J. P. Phillips. 1987. Anaerobic production of magnetite by a dissimilatory iron-reducing microorganism. Nature 330: 252 254.
123. Lovley, D. R.,, J. D. Coates,, E. L. Blunt-Harris,, E. J. P. Phillips,, and J. C. Woodward. 1996. Humic substances as electron acceptors for microbial respiration. Nature 382: 445 448.
124. Lovley, D. R.,, J. L. Fraga,, E. L. Blunt-Harris,, L. A. Hayes,, E. J. P. Phillips,, and J. D. Coates. 1998. Humic substances as a mediator for microbially catalyzed metal reduction. Acta Hydrochim. Hydrobiol. 26: 152 157.
125. Lovley, D. R.,, K. Kashefi,, M. Vargas,, J. M. Tor,, and E. L. Blunt-Harris. 2000. Reduction of humic substances and Fe(III) by hyperthermophilic microorganisms. Chem. Geol. 169: 289 298.
126. Mabbitt, L. A.,, and M. Zielinika. 1956. The use of a selective medium for the enumeration of lactobacilli in cheddar cheese. J. Appl. Bacteriol. 18: 95 101.
126.a. Madigan, M. E.,, J. M. Martinko,, and J. Parker. 2000. Brock Biology of Microorganisms, 9th ed. Prentice-Hall, Upper Saddle River, NJ.
127. Madonna, A. J.,, F. Basile,, E. Furlong,, and K. J. Vorhees. 2001. Detection of bacteria from biological mixtures using immunomagnetic separation combined with matrix-assisted laser desorption/ionization time-offlight mass spectrocopy. Rapid Commun. Mass Spectrom. 15: 1068 1074.
128. Matin, A.,, C. Veldhuis,, V. Stegeman,, and M. Veenhuis. 1979. Selective advantage of a Spirillum sp. in a carbonlimited environment. Accumulation of poly-8-hydroxybutyric acid and its role in starvation. J. Gen. Microbiol. 112: 349 355.
129. Matin, A.,, and H. Veldkamp. 1978. Physiological basis of the selective advantage of a Spirillum sp. in a carbonlimited environment. J. Gen. Microbiol. 106: 187 197.
130. Matsunaga, T.,, T. Sakaguchi,, and R. Tadokoro. 1991. Magnetite formation by a magnetic bacterium capable of growing aerobically. Appl. Microbiol. Biotechnol. 35: 651 655.
131. Maymó-Gatell, X.,, T. Anguish,, and S. H. Zinder. 1999. Reductive dechlorination of chlorinated ethenes and 1,2- dichlorethane by “ Dehalococcoides ethenogenes” 195. Appl. Environ. Microbiol. 65: 3108 3113.
132. Maymó-Gatell, X.,, Y.-T. Chien,, J. M. Gossett,, and S. H. Zinder. 1997. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276: 1568 1571.
133. Maymó-Gatell, X.,, V. Tandoi,, J. M. Gossett,, and S. H. Zinder. 1995. Characterization of an H2-utilizing enrichment culture that reductively dechlorinates tetrachloroethene to vinyl chloride and ethene in the absence of methanogenesis and acetogenesis. Appl. Environ. Microbiol. 61: 3928 3933.
134. McCurdy, H. D. 1963. A method for the isolation of myxobacteria in pure culture. Can. J. Microbiol. 8: 282 285.
135. McCurdy, H. D., 1989. Order Myxococcales Tchan, Pochon, and Prevot 1948, p. 2142. In J. T. Staley,, M. P. Bryant,, N. Pfenning,, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 3. The Williams & Wilkins Co., Baltimore, MD.
136. Meiklejohn, J. 1950. The isolation of Nitrosomonas europaea in pure culture. J. Gen. Microbiol. 4: 185 191.
137. Miller, T. L.,, and M. J. Wolin. 1974. A serum bottle modification of the Hungate technique for cultivating obligate anaerobes. Appl. Microbiol. 27: 985 987.
138. Moench, T. T., Genus “ Bilophococcus,” p. 1889. In J. T. Staley,, M. P. Bryant,, N. Pfenning,, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 3. The Williams & Wilkins Co., Baltimore, MD.
138.a. Mohn, W. W.,, and J. M. Tiedje. 1990. Strain DCB-1 conserves energy for growth from reductive dechlorination coupled to formate oxidation. Arch. Microbiol. 153: 267 271.
139. Morita, R. Y. 1975. Psychrophilic bacteria. Bacteriol. Rev. 39: 144 167.
140. Murray, R. G. E., 1984. Genus Lampropedia Schroeter 1886, p. 405. In N. R. Krieg, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore, MD.
141. Murray, R. G. E., 1986. Genus I. Deinococcus Brooks and Murray 1981, p. 1039. In P. H. A. Sneath,, N. S. Mair,, M. E. Sharpe,, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 2. The Williams & Wilkins Co., Baltimore, MD.
142. Murray, R. G. E., 1992. The family Deinococcaceae, p. 3733 3744. In A. Balows,, H. G. Trüper,, M. Dworkin,, W. Harder,, and K.-H. Schleifer (ed.), The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, 2nd ed. Springer-Verlag, New York, NY.
143. Muyzer, G.,, T. Brinkhoff,, U. Nübel,, C. Santegoeds,, H. Schäfer,, and C. Wawer,. 1998. Denaturing gradient gel electrophoresis (DGGE) in microbial ecology, vol. 3.4.4, p. 1 27. In A. D. L. Akkermans,, J. D. van Elsas,, and F. J. de Bruijn (ed.), Molecular Ecology Manual. Kluwer Academic Publishers, Dordrecht, The Netherlands.
144. Muyzer, G.,, E. C. De Waal,, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59: 695 700.
145. Muyzer, G.,, and K. Smalla. 1998. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Leeuwenhoek 173: 127 141.
146. Myrivk, Q. N.,, N. N. Pearsall,, and R. S. Weiser. 1974. Fundamentals of Medical Bacteriology and Mycology. Lea & Febiger, Philadelphia, PA.
147. Nelson, D. C., 1992. The genus Beggiatoa, p. 3171 3180. In A. Balows,, H. G. Trüper,, M. Dworkin,, W. Harder,, and K.-H. Schleifer (ed.), The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, 2nd ed. Springer-Verlag, New York, NY.
148. Nelson, D. C.,, B. B. Jørgensen,, and N. P. Revsbech. 1986. Growth pattern and yield of a chemoautotrophic Beggiatoa sp. in oxygen-sulfide microgradients. Appl. Environ. Microbiol. 52: 225 233.
149. New, P. B.,, and A. Keer. 1972. Biological control of crown gall: field measurements and glass-house experiments. J. Appl. Bacteriol. 35: 279 287.
150. Orchard, V. A.,, M. Goodfellow,, and S. T. Williams. 1977. Selective isolation and occurrence of nocardiae in soil. Soil Biol. Biochem. 9: 233 238.
151. Ouverney, 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.
152. Palleroni, N. J. 1980. A chemotactic method for the isolation of Actinoplanaceae. Arch. Microbiol. 128: 53 55.
153. Pernthaler, J.,, F.-O. Glöckner,, W. Schönhuber,, and R. Amann,. 2001. Fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes, p. 207 226. In J. Paul (ed.), Methods in Microbiology, Academic Press, New York, NY.
154. Peterson, J. E., 1969. Isolation, cultivation and maintenance of the myxobacteria, p. 185 210. In J. R. Norris, and D. W. Ribbons (ed.), Methods in Microbiology, vol. 3B. Academic Press, Inc., New York, NY.
155. Pfennig, N.,, and H. Biebl. 1976. Desulfuromonas acetoxidans gen. nov. and sp. nov., a new anaerobic, sulfurreducing, acetate-oxidizing bacterium. Arch. Microbiol. 110: 3 12.
156. Pfennig, N.,, and H. Biebl,. 1981. The dissimilatory sulfur- reducing bacteria, p. 941 947. In M. P. Starr,, H. Stolp,, H. G. Trüper,, A. Balows,, and H. G. Schlegel (ed.), The Prokaryotes, vol 1. Springer, Berlin, Germany.
157. Phillips, E. J. P.,, and D. R. Lovley. 1987. Determination of Fe(III) and Fe(II) in oxalate extracts of sediment. Soil Sci. Soc. Am. J. 51: 938 941.
158. Poindexter, J. S. 1964. Biological properties and classification of the Caulobacter group. Bacteriol. Rev. 28: 231 295.
159. Porter, J.,, and R. W. Pickup. 1998. Separation of natural populations of coliform bacteria from freshwater and sewage by magnetic-bead cell sorting. J. Microbiol. Methods 33: 221 226.
160. Pramer, D. A.,, and E. L. Schmidt. 1964. Experimental Soil Microbiology. Burgess Publishing Co., Minneapolis, MN.
161. Preston, C.,, Y. W. Ke,, T. F. Molinski,, and D. F. DeLong. 1996. A psychrophilic crenarcheon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov. Proc. Natl. Acad. Sci. USA 93: 6241 6246.
162. Pringsheim, E. G. 1964. Heterotrophism and species concepts in Beggiatoa. Am. J. Bot. 51: 898 913.
163. Reichenbach, H., 1989. Genus 1. CytophagaWinogradsky 1929, p. 2015 2050. In J. T. Staley,, M. P. Bryant,, N. Pfennig,, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 3. The Williams & Wilkins Co., Baltimore, MD.
164. Richardson, J. H.,, and W. E. Barkley. 1988. Biosafety in Microbiological and Biomedical Laboratories, 2nd ed. U.S. Department of Health and Human Services, HHS publication no. (NIH) 88-8395, U.S. Government Printing Office, Washington, DC.
165. Rippka, R.,, J. Derueiles,, J. B. Waterbury,, M. Herdman,, and R. Y. Stanier. 1979. Generic assignments, strain histories and properties of pure cultures of cyanobacteria. J. Gen. Microbiol. 111: 1 61.
166. Rittenberg, B. T.,, and S. C. Rittenberg. 1962. The growth of Spirillum volutans in mixed and pure cultures. Arch. Mikrobiol. 42: 138 153.
167. Rosebury, T. 1962. Microorganisms Indigenous to Man. McGraw-Hill Book Co., New York, NY.
168. Rosebury, T.,, and G. Foley. 1942. Isolation and pure cultivation of the smaller mouth spirochaetes by an improved method. Proc. Soc. Exp. Biol. Med. 47: 368 374.
169. Rosebury, T.,, J. B. McDonald,, S. A. Ellison,, and S. G. Engel. 1951. Media and methods for separation and cultivation of oral spirochaetes. Oral Surg. Oral Med. Oral Pathol. 4: 68 85.
170. Sampalo, M.-J. A. M.,, E. M. R. da Silva,, J. Döbereiner,, M. G. Yates,, and F. O. Pedrosa,. 1981. Autography and methylotrophy in Derxia gummosa, p. 447. In A. H. Gibson, and W. E. Newton (ed.), Current Perspectives in Nitrogen Fixation, Canberra, Australia, Dec. 1-5, 1980. Elsevier/North Holland Biomedical Press, Amsterdam, The Netherlands.
171. Schleifer, K.-H.,, D. Schüler,, S. Spring,, N. Weizenegger,, R. Amann,, W. Ludwig,, and M. Köhler. 1991. The genus Magnetospirillum gen. nov.: description of Magnetospirillum gryphiswaldense sp. nov. and transfer of Aquaspirillum magnetotacticum to Magnetospirillum magnetotacticum comb. nov. Syst. Appl. Microbiol. 14: 379 385.
172. Schroth, M. N.,, J. P. Thompson,, and D. C. Hildebrand. 1965. Isolation of Agrobacterium tumefaciens-A. radiobacter group from soil. Phytopathology 55: 645 647.
173. Schultz, J. E.,, G. I. Latter,, and A. Matin. Differential regulation by cyclic AMP of starvation protein synthesis in Escherichia coli. J. Bacteriol. 170: 3903 3909.
174. Seeliger, H. P. R.,, and D. Jones,. 1986. Genus Listeria Pirie 1940, p. 1235 1245. In P. H. A. Sneath,, N. S. Mair,, M. E. Sharpe,, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 2. The Williams & Wilkins Co., Baltimore, MD.
175. Segerer, A. H.,, and K. O. Stetter,. 1992. The genus Thermoplasma, p. 712 718. In A. Balows,, H. G. Trüper,, M. Dworkin,, W. Harder,, and K.-H. Schleifer (ed.), The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, 2nd ed. Springer-Verlag, New York, NY.
176. Sehgal, S. N.,, and N. E. Gibbons. 1960. Effect of some metal ions on the growth of Halobacterium cutirubrum. Can. J. Microbiol. 6: 165 169.
177. Shelton, D. R.,, and J. M. Tiedje. 1984. Isolation and partial characterization of bacteria in an anaerobic consortium that mineralizes 3-chlorobenzoic acid. Appl. Environ. Microbiol. 48: 840 848.
178. Singh, B. 1947. Myxobacteria in soils and composts: their distribution, number and lytic action on bacteria. J. Gen. Microbiol. 1: 1 10.
179. Slack, J. M.,, and I. S. Snyder. 1978. Bacteria and Human Disease. Year Book Medical Publishers, Chicago, IL.
180. Smibert, R. M.,, and R. L. Claterbaugh. 1972. A chemically- defined medium for Treponema strain PH-7 isolated from the intestine of a pig with swine dysentery. Can. J. Microbiol. 18: 1073 1078.
181. Smith, L. D.,, and V. R. Dowell,. 1974. Clostridium, p. 376 380. In E. H. Lennette,, E. H. Spaulding,, and J. P. Truant (ed.), Manual of Clinical Microbiology, 2nd ed. American Society for Microbiology, Washington, DC.
182. Sorokin, D. Y.,, A. Teske,, L. A. Robertson,, and J. G. Kuehnen. 1999. Anaerobic oxidation of thiosulfate to tetrathionate by obligately heterotrophic bacteria, belonging to the Pseudomonas stutzeri group. FEMS Microbiol. Ecol. 30: 113 123.
183. Stanier, R. Y.,, R. Kunisawa,, M. Mandel,, and G. Cohen- Bazire. 1971. Purification and properties of unicellular blue-green algae (order Chroococcales). J. Bacteriol. Rev. 35: 171 205.
184. Stanier, R. Y.,, N. J. Palleroni,, and M. Doudoroff. 1966. The aerobic pseudomonads: a taxonomic study. J. Gen. Microbiol. 43: 159 271.
185. Stolp, H.,, and M. P. Starr. 1963. Bdellovibrio bacteriovorus gen. et sp. n., a predatory, ectoparasitic, and bacteriolytic microorganism. Antonie Leeuwenhoek J. Microbiol. Serol. 29: 217 248.
186. Strohl, W. R., 1989. Genus I. Beggiatoa Trevisan 1842, p. 2095 2096. In J. T. Staley,, M. P. Bryant,, N. Pfennig,, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 3. The Williams & Wilkins Co., Baltimore, MD.
187. Strohl, W. R.,, and J. M. Larkin. 1978. Enumeration, isolation, and characterization of Beggiatoa from freshwater sediments. Appl. Environ. Microbiol. 36: 755 770.
188. Stürmeyer, H.,, J. Overmann,, H.-D. Babenzien,, and H. Cypionka. 1998. Ecophysiological and phylogenetic studies of Nevskia ramosa in pure culture. Appl. Environ. Microbiol. 64: 1890 1894.
189. Swift, S.,, M. J. Lynch,, L. Fish,, D. F. Kirke,, J. M. Tomas,, G. S. A. B. Steward,, and P. Williams. 1999. Quorum sensing-dependent regulation and blockade of exoprotease production in Aeromonas hydrophila. Infect. Immun. 67: 5192 5199.
190. Swings, J.,, J. De Ley,, and M. Gillis,. 1984. Genus 111. Frateuria Swings et al. 1980, p. 211. In N. R. Krieg, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore, MD.
191. Tamir, H.,, and C. Gilvarg. 1966. Density gradient centrifugation for the separation of sporulating forms of bacteria. J. Biol. Chem. 241: 1085 1090.
192. Tchan, Y.-T.,, and P. B. New,. 1984. Genus 1. Azotobacter Beijerinck 1901, p. 220. In N. R. Krieg, and J. G. Holt (ed.), Bergey’s Manual of Systematic Bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore, MD.
193. Teske, A.,, N. B. Ramsing,, K. Habicht,, M. Fukui,, J. Küver,, B. B. Jørgensen,, and Y. Cohen. 1998. Sulfatereducing bacteria and their activities in cyanobacterial mats of Solar Lake, Sinai (Egypt). Appl. Environ. Microbiol. 64: 2943 2951.
194. Teske, A.,, P. Sigalevich,, Y. Cohen,, and G. Muyzer. 1996. Molecular identification of bacteria from a coculture by denaturing gradient gel electrophoresis of 16S ribosomal DNA fragments as a tool for isolation in pure cultures. Appl. Environ. Microbiol. 62: 4210 4215.
195. Thamdrup, B.,, K. Finster,, J. W. Hansen,, and F. Bak. 1993. Bacterial disproportionation of elemental sulfur coupled to chemical reduction of iron or manganese. Appl. Environ. Microbiol. 59: 101 108.
196. Thompson, J. P.,, and V. B. D. Skerman. 1979. Azotobacteraceae: The Taxonomy and Ecology of the Aerobic Nitrogen-Fixing Bacteria. Academic Press Ltd., London, United Kingdom.
197. Torsvik, V.,, J. Goksoyr,, and F. L. Daae. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56: 782 787.
198. Turley, C. M., 1993. Direct estimates of bacterial numbers in seawater samples without incurring cell loss due to sample storage, p. 143 147. 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..
199. Van Niel, C. B. 1971. Techniques for the enrichment, isolation, and maintenance of the photosynthetic bacteria. Methods Enzymol. 23: 3 28.
200. Veldkamp, H. 1961. A study of two marine agar-decomposing, facultatively anaerobic myxobacteria. J. Gen. Microbiol. 26: 331 342.
201. Verma, U. K.,, D. J. Brenner,, W. L. Thacker,, R. F. Benson,, G. Vesey,, J. B. Kurtz,, P. J. L. Dennis,, A. G. Steigerwalt,, J. S. Robinson,, and C. W. Moss. 1992. Legionella shakespearei sp. nov., isolated from cooling tower water. Int. J. Syst. Bacteriol. 42: 404 407.
202. Vester, F.,, and K. Ingvorsen. 1998. Improved most-probable- number method to detect sulfate-reducing bacteria with natural media and a radiotracer. Appl. Environ. Microbiol. 64: 1700 1707.
203. Vishniac, W.,, and M. Santer. 1957. The thiobacilli. Bacteriol. Rev. 21: 195 213.
204. Von Rheinbaben, K. E.,, and R. M. Hodlak. 1981. Rapid distinction between micrococci and staphylococci with furazolidone agars. Antonie Leeuwenhoek J. Microbiol. Serol. 47: 41 51.
205. Vreeland, R. H., 1992. The family Halomonadaceae, p. 3181 3188. In A. Balows,, H. G. Trüper,, M. Dworkin,, W. Harder,, and K.-H. Schleifer (ed.), The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, 2nd ed. Springer- Verlag, New York, NY.
206. Warke, G. M.,, and S. A. Dhala. 1968. Use of inhibitors for selective isolation and enumeration of cytophagas from natural substrates. J. Gen. Microbiol. 51: 43 48.
207. Waterbury, J. B.,, and R. Y. Stanier. 1978. Patterns of growth and development in pleurocapsalean cyanobacteria. Microbiol. Rev. 42: 2 44.
208. Watkins, J.,, and K. P. Sleath. 1981. Isolation and enumeration of Listeria monocytogenes from sewage, sewage sludge and river water. J. Appl. Bacteriol. 50: 1 9.
209. Whitman, W. B.,, D. C. Coleman,, and W. J. Wiebe. 1998. Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. USA 95: 6578 6583.
210. Widdel, E.,, and N. Pfennig. 1977. A new anaerobic, sporing, acetate-oxidizing sulfate-reducing bacterium, Desulfotomaculum (emend.) acetoxidans. Arch. Microbiol. 112: 119 122.
211. Widdel, F. 1983. Methods for enrichment and pure culture isolation of filamentous gliding sulfate-reducing bacteria. Arch. Microbiol. 134: 282 285.
212. Wiley, W. R.,, and J. L. Stokes. 1962. Requirement of an alkaline pH and ammonia for substrate oxidation by Bacillus pasteurii. J. Bacteriol. 84: 730 734.
213. Williams, M. A.,, and S. C. Rittenberg. 1957. A taxonomic study of the genus Spirillum Ehrenberg. Int. Bull. Bacteriol. Nomencl. Taxon. 7: 49 111.
214. Williams, R. A. D.,, and M. S. Da Costa,. 1992. The genus Thermus and related microorganisms, p. 3745 3753. In A. Balows,, H. G. Trüper,, M. Dworkin,, W. Harder,, and K.-H. Schleifer (ed.), The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, 2nd ed. Springer- Verlag, New York, NY..
215. Wilson, G. S.,, and A. A. Miles. 1964. Topley and Wilson’s Principles of Bacteriology and Immunity, 5th ed. The Williams & Wilkins Co., Baltimore, MD.
216. Wolfe, R. A.,, R. K. Thauer,, and N. Pfennig. 1987. A ‘capillary racetrack’ for isolation of magnetotactic bacteria. FEMS Microbiol. Ecol. 45: 31 35.
217. Zeikus, J. G. 1977. The biology of methanogenic bacteria. Bacteriol. Rev. 41: 514 541.
218. Zengler, K.,, G. Toledo,, M. Rappe,, J. Elkins,, E. J. Mathur,, J. M. Short,, and M. Keller. 2002. Cultivating the uncultured. Proc. Natl. Acad. Sci. USA 99: 15681 15686.

Tables

Generic image for table
TABLE 1

Examples of the use of antibiotics in selective media

Citation: Teske A, Cypionka H, Holt J, Krieg N. 2007. Enrichment and Isolation, p 215-269. 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.ch11
Generic image for table
TABLE 2

Some unusual carbon sources for free-living nitrogen fixers

See references , and .

Citation: Teske A, Cypionka H, Holt J, Krieg N. 2007. Enrichment and Isolation, p 215-269. 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.ch11

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