1887

Chapter 8 : Miniaturization of Fermentations

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

Miniaturization of Fermentations, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555816827/9781555815127_Chap08-1.gif /docserver/preview/fulltext/10.1128/9781555816827/9781555815127_Chap08-2.gif

Abstract:

This chapter mainly talks about microtiter plates (MTPs) and reflects their current importance in industry and academia alike. Analysis of various culture preservation techniques and inoculum development techniques, with special attention to reproducibility of resulting cultures in terms of morphology (in MTPs and flasks), natural product yields and enzyme activity, and growth rates and nutrient utilization, is important. Variations in either inoculum or inoculation conditions may therefore lead to wide-ranging culture morphology changes. Important factors include the scheme employed for populating strains into the miniaturized format, the medium used for synchronous growth among the populations of strains in any one device, appropriate inoculation protocols, optimum strain preservation protocols, and choice of MTP format. Test tubes are used for various purposes by the microbiologist, but the chapter focuses on use of test tubes for high-throughput culturing of microbes in small volumes. Miniaturized cultivation systems are attractive not only in reducing demands for incubation space and medium but also in making the parallel handling of large numbers of strains more practicable. Provided the user is willing to invest a sufficient amount of time and effort on the optimization for their specific purpose, the presently available systems allow the cultivation at a 0.1- to 10-ml scale at a reproducibility and quality approaching those of larger-scale fermentation equipment.

Citation: Duetz W, Chase M, Bills G. 2010. Miniaturization of Fermentations, p 99-116. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch8

Key Concept Ranking

Chemicals
0.48596877
High-Performance Liquid Chromatography
0.4472137
Methyl Ethyl Ketone
0.44091493
Test Tubes
0.4302224
0.48596877
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

High-speed photograph showing the ability of a -force of 2.5 (generated by orbital shaking at 300 rpm and a shaking diameter of 50 mm) to induce a rotating movement of an aqueous solution of bromocresol blue (0.1% [wt/wt], surface tension of 72 dynes/cm) in round polyacrylate vessels with various diameters. The theoretical angle of the liquid/air surface with the horizontal plane of 68° is only reached at vessel diameters of 12 mm and higher. The angle of more than 68° at a vessel diameter of 16 mm can be explained by the situation that the shaking diameter for the bulk of the liquid is in effect approximately 60 instead of 50 mm. The practical absence of any movement of the liquid at 3 and 4 mm is due to the high surface tension.

Citation: Duetz W, Chase M, Bills G. 2010. Miniaturization of Fermentations, p 99-116. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

Schematic view of the sandwich cover ( section 8.3.1.2 ) used for (i) the prevention of (cross)-contamination of wells of a 96-square-deep-well MTP during vigorous orbital shaking and (ii) the limitation of evaporation.

Citation: Duetz W, Chase M, Bills G. 2010. Miniaturization of Fermentations, p 99-116. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3
FIGURE 3

Photographs illustrating the hydrodynamic flow pattern inside wells of various MTPs during orbital shaking at 300 rpm, at a shaking amplitude of either 50 mm (left) or 25 mm (right).

Citation: Duetz W, Chase M, Bills G. 2010. Miniaturization of Fermentations, p 99-116. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4
FIGURE 4

Synchronization of 12 isogenic cultures (0.75 ml OF LB medium) of TOP10 in wells of a 24-shallow-well MTP during orbital shaking (250 rpm, 50-mm amplitude, 30°C). The initial cultures ( = 0) were inoculated manually with toothpicks from colonies on an LB agar plate. At = 20 h, 5 μl of each of the cultures (all in stationary phase) was used as an inoculum for 12 fresh cultures: the 12 cultures now grow in a “synchronized” pattern (reach the stationary phase at the same time), which will—in most cases—result in a smaller standard deviation of the parameter under study (e.g., an enzyme activity) and in relative ease of identifying high-activity mutants.

Citation: Duetz W, Chase M, Bills G. 2010. Miniaturization of Fermentations, p 99-116. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 5
FIGURE 5

Preparation of fungal inoculum for master plate replication. Two microscope cover glasses are agitated with growing mycelium to produce a homogeneous mycelial suspension.

Citation: Duetz W, Chase M, Bills G. 2010. Miniaturization of Fermentations, p 99-116. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 6
FIGURE 6

Loading the master plate with fungal mycelium suspensions. Afterwards, the cryoreplicator tool is used to replicate each well across multiple growth conditions in the nutritional array.

Citation: Duetz W, Chase M, Bills G. 2010. Miniaturization of Fermentations, p 99-116. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 7
FIGURE 7

Static incubation of fungal growth plates for the nutritional array. The plates on the upper shelf are closed with carpenter’s clamps and supported at an 85° angle by wood tongue depressors. The plates on the lower shelf are supported by a custom-made stainless steel support.

Citation: Duetz W, Chase M, Bills G. 2010. Miniaturization of Fermentations, p 99-116. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 8
FIGURE 8

Custom-built 96-well aluminum plunger tool used to compress and separate fungal mycelium to bottom of each well while permitting solvent and culture supernatant mixture to rise to top of plate for pipetting. (A) Top view. (B) Side view. (C) Bottom view.

Citation: Duetz W, Chase M, Bills G. 2010. Miniaturization of Fermentations, p 99-116. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555816827.ch08
1. An, Z.,, G. Harris,, D. Zink,, R. Giacobbe,, P. Lu,, R. Sangari,, G. Bills,, V. Svetnik,, B. Gunter,, A. Liaw,, P. Masurekar,, J. Liesch,, S. Gould, and , W. Strohl. 2005. Expression of cosmid-size DNA of slow-growing fungi in Aspergillus nidulans for secondary metabolite screening, p. 167–187. In Z. An (ed.), Handbook of Industrial Mycology. Marcel Dekker, New York, NY.
2. Anderlei, T.,, W. Zang,, M. Papaspyrou, and , J. Buchs. 2004. Online respiration activity measurement (OTR, CTR, RQ) in shake flasks. Biochem. Eng. J. 17:187194.
3. Arain, S.,, G. T. John,, C. Krause,, J. Gerlach,, O. S. Wolfbeis, and, I. Klimant. 2006. Characterization of microtiter plates with integrated optical sensors for oxygen and pH, and their applications to enzyme activity screening, respirometry, and toxicological assays. Sensors Actuators B 113:639648.
4. Becker, R. F.,, L. P. J. Burton, and, S. E. Amos. 1996. Additives, p. 177–210. In E. P. Moore, Jr. (ed.), Polypropylene Handbook. Hanser-Gardner, Cincinnati, OH.
5. Betts, J. I., and , F. Baganz. 2006. Miniature bioreactors: current practices and future opportunities. Microb. Cell Fact. 5: 21.
6. Bills, G.,, G. Platas,, A. Fillola,, M. R. Jiménez,, J. Collado,, F. Vicente,, J. Martín,, A. González,, J. Bur-Zimmermann,, J. R. Tormo, and, F. Peláez. 2008. Enhancement of antibiotic and secondary metabolite detection from filamentous fungi by growth on nutritional arrays. J. Appl. Microbiol. 104:16441658.
7. Bills, G. F.,, J. Martín,, J. Collado,, G. Platas,, D. Overy,, J. R. Tormo,, F. Vicente,, G. Verkleij, and , P. Crous. 2009. Measuring the distribution and diversity of antibiosis and secondary metabolites in the filamentous fungi. Soc. Ind. Microbiol. News, 59:133146.
8. Bills, G. F.,, G. Platas,, D. P. Overy,, J. Collado,, A. Fillola,, M. R. Jiménez,, J. Martín,, A. González del Val,, F. Vicente,, J. R. Tormo,, F. Peláez,, K. Calati,, G. Harris,, C. Parish,, D. Xu, and , T. Roemer. 2009. Discovery of the parnafungins, antifungal metabolites that inhibit mRNA polyadenylation, from the Fusarium larvarum complex and other Hypocrealean fungi. Mycologia 101:449472.
9. Bochner, B. R. 2009. Global phenotypic characterization of bacteria. FEMS Microbiol. Rev. 33:191205.
10. Bode, H. B.,, B. Bethe,, R. Höfs, and, A. Zeeck. 2002. Big effects from small changes: possible ways to explore nature’s chemical diversity. Chembiochem 3:619627.
11. De la Cruz, T. E. E.,, B. E. Schulz,, C. P. Kubicek, and, I. S. Druzhinina. 2006. Carbon source utilization by the marine Dendryphiella species D. arenaria and D. salina. FEMS Microbiol. Ecol. 58:343353.
12. Dobson, L. F., and , D. G. O’shea. 2008. Antagonistic effect of divalent cations Ca2+ and Mg2+ on the morphological development of Streptomyces hygroscopicus var. geldanus. Appl. Microbiol. Biotechnol. 81:119126.
13. Doig, S. D.,, A. Diep, and , F. Baganz. 2005. Characterisation of a novel miniaturised bubble column bioreactor for high throughput cell cultivation. Biochem. Eng. J. 23:97105.
14. Druzhinina, I. S.,, M. Schmoll,, B. Seiboth, and, C. P. Kubicek. 2006. Global carbon utilization profiles of wild-type, mutant, and transformant strains of Hypocrea jecorina. Appl. Environ. Microbiol. 72:21262133.
15. Duetz, W. A.,, L. Rüedi,, R. Hermann,, K. O’Connor,, J. Büchs, and, B. Witholt. 2000. Methods for intense aeration, growth, storage, and replication of bacterial strains in microtiter plates. Appl. Environ. Microbiol. 66:26412646.
16. Duetz, W. A., and , B. Witholt. 2004. Oxygen transfer by orbital shaking of square vessels and deepwell microtiter plates of various dimensions. Biochem. Eng. J. 17:181185.
17. Duetz, W. A. 2007. Microtiter plates as mini-bioreactors: miniaturization of fermentation methods. Trends Microbiol. 15:470475.
18. Duetz, W. A. October, 2008. An apparatus and a method for investigation of microtiter plates subjected to orbital shaking. Netherlands Patent 86185NL00.
19. Frisvad, J. C., and , R. A. Samson. 2004. Polyphasic taxonomy of Penicillium subgenus Penicillium, a guide to identification of food and air-borne terverticillate penicillia and their mycotoxins. Stud. Mycol. 49:1173.
20. Green, H., and , J. G. Rheinwald. December, 1975. Method of controllably releasing glucose into a cell culture medium. U.S. patent 3,926,723.
21. Herath, K. B.,, G. H. Harris,, H. Jayasuriya,, D. L. Zink,, S. K. Smith,, F. Vicente,, G. F. Bills,, J. Collado,, A. González del Val,, B. Jiang,, J. N. Kahn,, S. Galuska,, R. A. Giacobbe,, G. K. Abruzzo,, E. J. Hickey,, P. A. Liberator,, T. Roemer, and, S. B. Singh. 2009. Isolation, structure and biological activity of phomafungin, a cyclic lipodepsipeptide from a widespread tropical Phoma sp. Bioorg. Med. Chem. 17:13611369.
22. Hermann, R.,, N. Walther,, U. Maier, and , J. Büchs. 2001. Optical method for the determination of the oxygen-transfer capacity of small bioreactors based on sulfite oxidation. Biotechnol. Bioeng. 74:355363.
23. Hermann, R.,, M. Lehmann, and , J. Büchs. 2003. Characterization of gas-liquid mass transfer phenomena in microtiter plates. Biotechnol. Bioeng. 81:178186.
24. Hobbs, G.,, C. M. Frazer,, D. C. J. Gardner,, J. A. Cullum, and, S. G. Oliver. 1989. Dispersed growth of Streptomyces in liquid culture. Appl. Microbiol. Biotechnol. 31:272277.
25. Isett, K.,, H. George,, W. Herber, and, A. Amanullah. 2007. Twenty-four-well plate miniature bioreactor high-throughput system: assessment for microbial cultivations. Biotechnol. Bioeng. 98:10171028.
26. Jeude, M.,, B. Dittrich,, H. Niederschulte,, T. Anderlei,, C. Knocke,, D. Klee, and, J. Buchs. 2006. Fed-batch mode in shake flasks by slow-release technique. Biotechnol. Bioeng. 95:433445.
27. Junker, B. H.,, M. Heese,, B. Burgess,, P. Masurekar,, N. Connors, and, A. Seely. 2004. Early phase process scale-up challenges for fungal and filamentous bacterial cultures. Appl. Biochem. Biotechnol. 119:241277.
28. Kensy, F.,, H. F. Zimmermann,, I. Knabben,, T. Anderlei,, H. Trauthwein,, U. Dingerdissen, and , J. Büchs. 2005. Oxygen transfer phenomena in 48-well microtiter plates: determination by optical monitoring of sulfite oxidation and verification by real-time measurement during microbial growth. Biotechnol. Bioeng. 89:698708.
29. Kubicek, C. P.,, J. Bissett,, I. Druzhinina,, C. Kullnig-Gradinger, and, G. Szakacs. 2003. Genetic and metabolic diversity of Trichoderma: a case study on South-East Asian isolates. Fungal Genet. Biol. 38:310319.
30. Minas, W.,, J. E. Bailey, and, W. Duetz. 2000. Streptomycetes in micro-cultures: growth, production of secondary metabolites, and storage and retrieval in the 96-well format. Antonie van Leeuwenhoek 78:297305.
31. Monaghan, R. L.,, M. M. Gagliardi, and , S. L. Streicher. 1999. Culture preservation and inoculum development, p. 29–48. In A. L. Demain and, J. E. Davies (ed.), Manual of Industrial Microbiology and Biotechnology, 2nd ed. ASM Press, Washington, DC.
32. O’Cleirigh, C.,, J. T. Casey,, P. K. Walsh, and , D. G. O’shea. 2005. Morphological engineering of Streptomyces hygroscopicus var. geldanus: regulation of pellet morphology through manipulation of broth viscosity. Appl. Microbiol. Biotechnol. 68:305310.
33. Ohta, K.,, H. Agematu,, T. Yamada,, K. Kaneko, and, T. Tsuchida. 2005. Production of human metabolites of cyclosporin A, AM1, AM4N and AM9, by microbial conversion. J. Biosci. Bioeng. 99:390395.
34. Ondeyka, J.,, G. Harris,, D. Zink,, A. Basilio,, F. Vicente,, G. Bills,, G. Platas,, J. Collado,, A. González,, M. de la Cruz,, J. Martín,, J. N. Kahn,, S. Galuska,, R. Giacobbe,, G. Abruzzo,, E. Hickey,, P. Liberator,, B. Jiang,, D. Xu,, T. Roemer, and, S. B. Singh. 2009. Isolation, structure elucidation and biological activity of virgineone from Lachnum virgineum using the genomewide Candida albicans fitness test. J. Nat. Prod. 72:136141.
35. Ortiz-Ochoa, K.,, S. D. Doig,, J. M. Ward, and , F. Baganz. 2005. A novel method for the measurement of oxygen mass transfer rates in small-scale vessels. Biochem. Eng. J. 25:6368.
36. Panula-Perälä, J.,, J. Šiurkus,, A. Vasala,, R. Wilmanowski,, M. G. Casteleijn, and, P. Neubauer. 2008. Enzyme controlled glucose auto-delivery for high cell density cultivations in microplates and shake flasks. Microb. Cell Fact. 7:3142.
37. Puskeiler, R.,, A. Kusterer,, G. T. John, and , D. Weuster-Botz. 2005. Miniature bioreactors for automated high-throughput bioprocess design (HTBD): reproducibility of parallel fed-batch cultivations with Escherichia coli. Biotechnol. Appl. Biochem. 42:227235.
38. Samorski, M.,, G. Muller-Newen, and, J. Buchs. 2005. Quasi-continuous combined scattered light and fluorescence measurements: a novel measurement technique for shaken microtiter plates. Biotechnol. Bioeng. 92:6168.
39. Smedsgaard, J. 1997. Micro-scale extraction procedure for standardized screening of fungal metabolite production in cultures. J. Chromatogr. A 760:264270.
40. Talbot, N. J.,, P. Vincent, and, H. G. Wildman. 1996. The influence of genotype and environment on the physiological and metabolic diversity of Fusarium compactum. Fungal Genet. Biol. 20:254267.
41. Tormo, J. R.,, J. B. Garcia,, M. DeAntonio,, J. Feliz,, A. Mira,, M. T. Diez,, P. Hernandez, and, F. Pelaez. 2003. A method for the selection of production media for actinomycete strains based on their metabolite HPLC profiles. J. Ind. Microbiol. Biotechnol. 30:582588.
42. Van Wezel, G. P.,, P. Krabben,, B. A. Traag,, B. J. F. Keijser,, R. Kerste,, E. Vijgenboom,, J. J. Heijnen, and, B. Kraal. 2006. Unlocking Streptomyces spp. for use as sustainable industrial production platforms by morphological engineering. Appl. Environ. Microbiol. 72:52835288.
43. Verdoes, J. C.,, P. J. Punt,, R. Burlingame,, J. Bartels,, R. van Dijk,, E. Slump,, M. Meens,, R. Joosten, and, M. Emalfarb. 2007. A dedicated vector for efficient library construction and high throughput screening in the hyphal fungus Chrysosporium lucknowense. Indust. Biotechnol. 3:4857.
44. Vinci, V. A., and , G. Byng. 1999. Strain improvement by nonrecombinant methods, p. 103–113. In A. L. Demain and, J. E. Davies (ed.), Manual of Industrial Microbiology and Biotechnology, 2nd ed. ASM Press, Washington, DC.
45. Whitaker, A. 1992. Actinomycetes in submerged culture. Appl. Biochem. Biotechnol. 32:2335.
46. Yang, W.,, E. A. Hartwieg,, A. Fang, and , A. L. Demain. 2003. Effects of carboxymethylcellulose and carboxypolymethylene on morphology of Aspergillus fumigatus NRRL 2346 and fumagillin production. Curr. Microbiol. 46:2427.
47. Zimmermann, H. F.,, G. T. John,, H. Trauthwein,, U. Dingerdissen, and, K. Huthmacher. 2003. Rapid evaluation of oxygen and water permeation through microplate sealing tapes. Biotechnol. Prog. 19:10611063.

Tables

Generic image for table
TABLE 1

OTRs in various types of MTPs at various volumes during orbital shaking at 300 rpm and a shaking diameter of 50 and 25 mm

Citation: Duetz W, Chase M, Bills G. 2010. Miniaturization of Fermentations, p 99-116. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch8

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