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Chapter 12 : Methods To Study Consortia and Mixed Cultures

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Abstract:

Nowadays many experimental approaches exist that one could not even imagine in Koch’s days. An alternative approach that focuses on dealing with undefined populations of microbes in the laboratory is the scope of this chapter. The approach consists of four steps. The first step is the definition of an ecological niche. In the second step, the complement of the niche is engineered in a laboratory bioreactor, which is to become an enrichment culture. In the third step, the culture is characterized in molecular detail. Finally, the detailed information is used to investigate the importance of the described processes and microbes in nature. In this approach, the target organism remains in continuous culture under chemo-spatio-temporal conditions that define its natural niche, in an open system that allows competition. With this approach and appropriate primers it is possible to specifically quantify a single organism or a clade of microorganisms. For example, the abundance of Crenarchaeota in soils can be shown by real-time PCR of ammonium monooxygenase genes from archaea and bacteria. Epifluorescence microscopy is of great value to visualize relative abundances determined with cloning or denaturing gradient gel electrophoresis (DGGE). The study of microorganisms in undefined mixed cultures could be applied more generally and has great potential for environmental microbiology.

Citation: Kartal B, Strous M. 2008. Methods To Study Consortia and Mixed Cultures, p 205-219. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch12

Key Concept Ranking

Environmental Microbiology
0.8232507
Microbial Ecology
0.81370574
Bacteria and Archaea
0.7541235
Denaturing Gradient Gel Electrophoresis
0.4968302
Viruses
0.408046
0.8232507
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Figures

Image of FIGURE 1
FIGURE 1

Periodic system of a number of one-carbon microorganisms.

Citation: Kartal B, Strous M. 2008. Methods To Study Consortia and Mixed Cultures, p 205-219. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch12
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Image of FIGURE 2
FIGURE 2

Experimental setups for enrichment in continuous culture. (A) Chemostat, (B) chemostat with an internal settler, (C) chemostat with a membrane unit, and (D) sequencing batch reactor.

Citation: Kartal B, Strous M. 2008. Methods To Study Consortia and Mixed Cultures, p 205-219. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch12
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Image of FIGURE 3
FIGURE 3

Percoll purification of anammox bacterium from an enrichment culture. (A) FISH micrograph of an anammox cluster (light gray) from an enrichment culture with other microorganisms. (B) Anammox cell suspension on Percoll gradient before centrifugation. (C) “Anammox band” that forms after centrifugation. (D) FISH micrograph of Percoll-separated cells.

Citation: Kartal B, Strous M. 2008. Methods To Study Consortia and Mixed Cultures, p 205-219. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch12
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Image of FIGURE 4
FIGURE 4

Phylogenetic tree showing cultivated and uncultivated anammox bacteria. Black, described species; dark gray with a dot, marine clone; light gray, reactor clone.

Citation: Kartal B, Strous M. 2008. Methods To Study Consortia and Mixed Cultures, p 205-219. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch12
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References

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1. Amann, R. I.,, B. J. Binder,, R. J. Olson,, S. W. Chisholm,, R. Devereux, and, D. A. Stahl. 1990. Combination of 16S ribosomal-RNA-targeted oligonucleotide probes with flow-cytometry for analyzing mixed microbial-populations. Appl. Environ. Microbiol. 56:19191925.
2. Bartosch, S.,, I. Wolgast,, E. Spieck, and, E. Bock. 1999. Identification of nitrite oxidizing bacteria with monoclonal antibodies recognizing the nitrite oxidoreductase. Appl. Environ. Microbiol. 65:41264133.
3. Beja, O.,, L. Aravind,, E. V. Koonin,, M. T. Suzuki,, A. Hadd,, L. P. Nguyen,, S. Jovanovich,, C. M. Gates,, R. A. Feldman,, J. L. Spudich,, E. N. Spudich, and, E. F. DeLong. 2000. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289:19021906.
4. Broda, E. 1977. 2 Kinds of lithotrophs missing in nature. Z. Allg. Mikrobiol. 17:491493.
5. Canto-Nogues, C.,, D. Hockley,, C. Grief,, S. Ranjbar,, J. Bootman,, N. Almond, and, I. Herrera. 2001. Ultrastructural localization of the RNA of immunodeficiency viruses using electron microscopy in situ hybridization and in vitro infected lymphocytes. Micron 32:579589.
6. Elias, D. A.,, M. E. Monroe,, R. D. Smith,, J. K. Fredrickson, and, M. S. Lipton. 2006. Confirmation of the expression of a large set of conserved hypothetical proteins in Shewanella oneidensis MR-1. J. Microbiol. Methods 66:223233.
7. Hinrichs, K. U.,, J. M. Hayes,, S. P. Sylva,, P. G. Brewer, and, E. F. DeLong. 1999. Methane consuming archaebacteria in marine sediments. Nature 398:802805.
8. Huston, W. M.,, H. R. Harhangi,, A. P. Leech,, C. S. Butler,, M. S. M. Jetten,, H. den Camp, and, J. W. B. Moir. 2007. Expression and characterisation of a major c-type cytochrome encoded by gene kustc0563 from Kuenenia stuttgartiensis as a recombinant protein in Escherichia coli. Protein Expr. Purif. 51:2833.
9. Jansen, M. L. A.,, J. A. Diderich,, M. Mashego,, A. Hassane,, J. H. de Winde,, P. Daran-Lapujade, and, J. T. Pronk. 2005. Prolonged selection in aerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae causes a partial loss of glycolytic capacity. Microbiology-Sgm 151:16571669.
10. Kartal, B.,, M. M. M. Kuypers,, G. Lavik,, J. Schalk,, H. J. M. Op den Camp,, M. S. M. Jetten, and, M. Strous. 2007a. Anammox bacteria disguised as denitrifiers: nitrate reduction to dinitrogen gas via nitrite and ammonium. Environ. Microbiol. 9:635642.
11. Kartal, B.,, J. Rattray,, L. van Niftrik,, J. van de Vossenberg,, M. Schmid,, R. I. Webb,, S. Schouten,, J. A. Fuerst,, J. S. Sinninghe Damsté,, M. S. M. Jetten, and, M. Strous. 2007b. Candidatus “Anammoxoglobus propionicus” gen. nov., sp. nov., a new propionate oxidizing species of anaerobic ammonium oxidizing bacteria. Syst. Appl. Microbiol. 30:3949.
12. Könneke, M.,, A. E. Bernhard,, J. R. de la Torre,, C. B. Walker,, J. B. Waterbury, and, D. A. Stahl. 2005. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543546.
13. Kowalchuk, G. A.,, J. R. Stephen,, W. De Boer,, J. I. Prosser,, T. M. Embley, and, J. W. Woldendorp. 1997. Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl. Environ. Microbiol. 63:14891497.
14. Kuenen, J. G.,, and H. Veldkamp. 1973. Effects of organic compounds on growth of chemostat cultures of Thiomicrospira pelophila, Thiobacillus thioparus and Thiobacillus neapolitanus. Arch. Mikrobiol. 94:173190.
15. Kuypers, M. M. M.,, A. O. Sliekers,, G. Lavik,, M. Schmid,, B. B. Jørgensen,, J. G. Kuenen,, J. S. Sinninghe Damsté,, M. Strous, and, M. S. M. Jetten. 2003. Anaerobic ammonium oxidation by anammox bacteria in the Black Sea. Nature 422:608611.
16. Lechene, C.,, F. Hillion,, G. McMahon,, D. Benson,, A. M. Kleinfeld,, J. P. Kampf,, D. Distel,, Y. Luyten,, J. Bonventre,, D. Hentschel,, K. M. Park,, S. Ito,, M. Schwartz,, G. Benichou, and, G. Slodzian. 2006. High-resolution quantitative imaging of mammalian and bacterial cells using stable isotope mass spectrometry. J. Biol. 5:30.
17. 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. 65:12891297.
18. Leininger, S.,, T. Urich,, M. Schloter,, L. Schwark,, J. Qi,, G. W. Nicol,, J. I. Prosser,, S. C. Schuster, and, C. Schleper. 2006. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806809.
19. Lindsay, M. R.,, R. I. Webb,, M. Strous,, M. S. Jetten,, M. K. Butler,, R. J. Forde, and, J. A. Fuerst. 2001. Cell compartmentalisation in planctomycetes:novel types of structural organisation for the bacterial cell. Arch. Microbiol. 175:413429.
20. Mashego, M. R.,, M. L. A. Jansen,, J. L. Vinke,, W. M. van Gulik, and, J. J. Heijnen. 2005. Changes in the metabolome of Saccharomyces cerevisiae associated with evolution in aerobic glucose-limited chemostats. FEMS Yeast Res. 5:419430.
21. Muyzer, G.,, E. C. Dewaal, 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 ribosomal-RNA. Appl. Environ. Microbiol. 59:695700.
22. Myers, R. M.,, S. G. Fischer,, L. S. Lerman, and, T. Maniatis. 1985. Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Res. 13:31313145.
23. Nogueira, R.,, and L. F. Melo. 2006. Competition between Nitrospira spp. and Nitrobacter spp. in nitrite oxidizing bioreactors. Biotechnol. Bioeng. 95:169175.
24. Novick, A.,, and L. Szilard. 1950. Description of the chemostat. Science 112:715716.
25. Okabe, S.,, T. Kindaichi,, Y. Nakamura, and, T. Ito. 2005. Ecophysiology of autotrophic nitrifying biofilms. Water Sci. Technol. 52:225232.
26. Orphan, V. J.,, C. H. House,, K. U. Hinrichs,, K. D. McKeegan, and, E. F. DeLong. 2002. Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. Proc. Natl. Acad. Sci. USA 99:76637668.
27. 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. 65:17461752.
28. Radajewski, S.,, P. Ineson,, N. R. Parekh, and, J. C. Murrell. 2000. Stable isotope probing as a tool in microbial ecology. Nature 403:646649.
29. Raghoebarsing, A. A.,, A. Pol,, K. T. van de Pas-Schoonen,, A. J. P. Smolders,, K. F. Ettwig,, W. I. C. Rijpstra,, S. Schouten,, J. S. Sinninghe Damsté,, H. J. M. Op den Camp,, M. S. M. Jetten, and, M. Strous. 2006. A microbial consortium couples anaerobic methane oxidation to denitrification. Nature 440:918921.
30. Schleper, C.,, E. F. DeLong,, C. M. Preston,, R. A. Feldman,, K. Y. Wu, and, R. V. Swanson. 1998. Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum. J. Bacteriol. 180:50035009.
31. Schmid, M.,, K. Walsh,, R. Webb,, W. I. C. Rijpstra,, K. van de Pas-Schoonen,, M. J. Verbruggen,, T. Hill,, B. Moffett,, J. Fuerst,, S. Schouten,, J. S. Sinninghe Damsté,, J. Harris,, P. Shaw,, M. Jetten, and, M. Strous. 2003. Candidatus “Scalindua brodae”, sp nov., Candidatus “Scalindua wagneri”, sp nov., two new species of anaerobic ammonium oxidizing bacteria. Syst. Appl. Microbiol. 26:529538.
32. Schouten, S.,, M. Strous,, M. M. M. Kuypers,, W. I. C. Rijpstra,, M. Baas,, C. J. Schubert,, M. S. M. Jetten, and, J. S. Sinninghe Damsté. 2004. Stable carbon isotopic fractionations associated with inorganic carbon fixation by anaerobic ammonium-oxidizing bacteria. Appl. Environ. Microbiol. 70:37853788.
33. Sinninghe Damsté, J. S.,, S. Schouten,, E. C. Hopmans,, A. C. T. van Duin, and, J. A. J. Geenevasen. 2002a. Crenarchaeol:the characteristic core glycerol dibiphytanyl glycerol tetraether membrane lipid of cosmopolitan pelagic crenarchaeota. J. Lipid Res. 43:16411651.
34. Sinninghe Damsté, J. S.,, M. Strous,, W. I. C. Rijpstra,, E. C. Hopmans,, J. A. J. Geenevasen,, A. C. T. van Duin,, L. A. van Niftrik, and, M. S. M. Jetten. 2002b. Linearly concatenated cyclobutane lipids form a dense bacterial membrane. Nature 419:708712.
35. Strous, M.,, J. A. Fuerst,, E. H. M. Kramer,, S. Logemann,, G. Muyzer,, K. T. van de Pas-Schoonen,, R. Webb,, J. G. Kuenen, and, M. S. M. Jetten. 1999a. Missing lithotroph identified as new planctomycete. Nature 400:446449.
36. Strous, M.,, J. G. Kuenen, and, M. S. M. Jetten. 1999b. Key physiology of anaerobic ammonium oxidation. Appl. Environ. Microbiol. 65:32483250.
37. Strous, M.,, E. Pelletier,, S. Mangenot,, T. Rattei,, A. Lehner,, M. W. Taylor,, M. Horn,, H. Daims,, D. Bartol-Mavel,, P. Wincker,, V. Barbe,, N. Fonknechten,, D. Vallenet,, B. Segurens,, C. Schenowitz-Truong,, C. Medigue,, A. Collingro,, B. Snel,, B. E. Dutilh,, H. J. M. Op den Camp,, C. van der Drift,, I. Cirpus,, K. T. van de Pas-Schoonen,, H. R. Harhangi,, L. van Niftrik,, M. Schmid,, J. Keltjens,, J. van de Vossenberg,, B. Kartal,, H. Meier,, D. Frishman,, M. A. Huynen,, H. W. Mewes,, J. Weissenbach,, M. S. M. Jetten,, M. Wagner, and, D. Le Paslier. 2006. Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440:790794.
38. Tappe, W.,, A. Laverman,, M. Bohland,, M. Braster,, S. Rittershaus,, J. Groeneweg, and, H. W. van Verseveld. 1999. Maintenance energy demand and starvation recovery dynamics of Nitrosomonas europaea and Nitrobacter winogradskyi cultivated in a retentostat with complete biomass retention. Appl. Environ. Microbiol. 65:24712477.
39. Teske, A. P. 2005. The deep subsurface biosphere is alive and well. Trends Microbiol. 13:402404.
40. Tyson, G. W.,, J. Chapman,, P. Hugenholtz,, E. E. Allen,, R. J. Ram,, P. M. Richardson,, V. V. Solovyev,, E. M. Rubin,, D. S. Rokhsar, and, J. F. Banfield. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:3743.
41. Tyson, G. W.,, I. Lo,, B. J. Baker,, E. E. Allen,, P. Hugenholtz, and, J. F. Banfield. 2005. Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp nov from an acidophilic microbial community. Appl. Environ. Microbiol. 71:63196324.
42. Van de Graaf, A. A.,, A. Mulder,, P. Debruijn,, M. S. M. Jetten,, L. A. Robertson, and, J. G. Kuenen. 1995. Anaerobic oxidation of ammonium is a biologically mediated process. Appl. Environ. Microbiol. 61:12461251.
43. Wuchter, C.,, B. Abbas,, M. J. L. Coolen,, L. Herfort,, J. van Bleijswijk,, P. Timmers,, M. Strous,, E. Teira,, G. J. Herndl,, J. J. Middelburg,, S. Schouten, and, J. S. Sinninghe Damsté. 2006. Archaeal nitrification in the ocean. Proc. Natl. Acad. Sci. USA 103:1231712322.

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