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Chapter 12 : Methods To Study Consortia and Mixed Cultures
Authors:
Boran Kartal1,
Marc Strous2
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Affiliations:
1: Department of Microbiology, Faculty of Science, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands;
2: Department of Microbiology, Faculty of Science, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
Content Type: Monograph
Publication Year:
2008
Category: Genomics and Bioinformatics; Environmental Microbiology
Book DOI:
10.1128/9781555815509
Chapter DOI:
10.1128/9781555815509.ch12
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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
Figures
Methods To Study Consortia and Mixed Cultures
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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
/content/10.1128/9781555815509.ch12.ch12fig01
FIGURE 1
Periodic system of a number of one-carbon microorganisms.
10.1128/9781555815509/f0207-01_thmb.gif
10.1128/9781555815509/f0207-01.gif
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
/content/10.1128/9781555815509.ch12.ch12fig02
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.
10.1128/9781555815509/f0209-01_thmb.gif
10.1128/9781555815509/f0209-01.gif
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
/content/10.1128/9781555815509.ch12.ch12fig03
FIGURE 3
Percoll purification of anammox bacterium K. stuttgartiensis 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 K. stuttgartiensis cells.
10.1128/9781555815509/f0213-01_thmb.gif
10.1128/9781555815509/f0213-01.gif
FIGURE 3
Percoll purification of anammox bacterium K. stuttgartiensis 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 K. stuttgartiensis 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
/content/10.1128/9781555815509.ch12.ch12fig04
FIGURE 4
Phylogenetic tree showing cultivated and uncultivated anammox bacteria. Black, described species; dark gray with a dot, marine clone; light gray, reactor clone.
10.1128/9781555815509/f0216-01_thmb.gif
10.1128/9781555815509/f0216-01.gif
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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