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Chapter 2.1.3 : New Devices for Cultivation

Authors: Yoshiteru Aoi1, Slava Epstein3
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Affiliations: 1: Institute of Sustainable Sciences and Development, Hiroshima University, Hiroshima, Japan; 2: Department of Biology, Northeastern University, Boston, MA, USA; 3: Department of Biology, Northeastern University, Boston, MA, USA
Content Type: Reference
Publication Year: 2016

Category: Environmental Microbiology

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Abstract:

One of the most important observations in microbiology is that the vast majority of microorganisms from most environments on the planet do not grow on artificial media. This is a significant impediment for both academic and applied microbiology, necessitating innovations in cultivation technologies. Several recently advanced methodologies offer a promise to close the gap between the high richness of environmental species and low number of their cultivable representatives. This chapter will describe the state of the art in microbial cultivation methods, their principles and application. These methods are categorized into two types: “in situ cultivation” whereby microbes are cultivated in situ, and “high throughput cultivation”, mostly in vitro. In the first group, the following methods are described in detail, 1) Diffusion chamber, 2) i-chip, 3) Microbial trap, and 4) Hollow Fiber Membrane Chamber. In the second group, we focus on Gel miro-droplets (GMDs) based cultivation and micro-fabrication based technologies. The chapter will also discuss their relative merits and respective biases.

Citation: Aoi Y, Epstein S. 2016. New Devices for Cultivation, p 2.1.3-1-2.1.3-8. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.1.3
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New Devices for Cultivation
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Citation: Aoi Y, Epstein S. 2016. New Devices for Cultivation, p 2.1.3-1-2.1.3-8. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.1.3
/content/10.1128/9781555818821.ch2.1.3.ch2.1.3F1
FIGURE 1

Photographic (a) and schematic (b) image of the diffusion chamber. A polycarbonate membrane is attached to the bottom of the metal disc, the other membrane is glued to the upper surface of disc. The inner space is filled with microbial cells mixed with agar. After the inoculation and assembly the diffusion chamber is placed in the natural environment for incubation. (A part of the figure is reprinted from ). doi:10.1128/9781555818821.ch2.1.3.f1

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10.1128/9781555818821/2934ch67f01.gif
Image of FIGURE 1
FIGURE 1

Photographic (a) and schematic (b) image of the diffusion chamber. A polycarbonate membrane is attached to the bottom of the metal disc, the other membrane is glued to the upper surface of disc. The inner space is filled with microbial cells mixed with agar. After the inoculation and assembly the diffusion chamber is placed in the natural environment for incubation. (A part of the figure is reprinted from ). doi:10.1128/9781555818821.ch2.1.3.f1

Citation: Aoi Y, Epstein S. 2016. New Devices for Cultivation, p 2.1.3-1-2.1.3-8. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.1.3
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FIGURE 2

Isolation chip, or i-chip, for high-throughput microbial cultivation : (a) dipping a plate with multiple through-holes into a suspension of cells leads to capturing (on average) single cell (b); (c) i-chip assembly; membranes cover arrays of through-holes from each side: Upper and bottom plates with matching holes press the membranes against the central (loaded) plate. Screws provide sufficient pressure to seal the content of individual through-holes, each becoming a miniature diffusion chamber containing (on average) a single cell. (Reprinted from [2010], ed. R. H. Baltz, J. E. Davies, and A. Demain, Washington, DC, ASM Press.). doi:10.1128/9781555818821.ch2.1.3.f2

10.1128/9781555818821/2934ch67f02_thmb.gif
10.1128/9781555818821/2934ch67f02.gif
Image of FIGURE 2
FIGURE 2

Isolation chip, or i-chip, for high-throughput microbial cultivation : (a) dipping a plate with multiple through-holes into a suspension of cells leads to capturing (on average) single cell (b); (c) i-chip assembly; membranes cover arrays of through-holes from each side: Upper and bottom plates with matching holes press the membranes against the central (loaded) plate. Screws provide sufficient pressure to seal the content of individual through-holes, each becoming a miniature diffusion chamber containing (on average) a single cell. (Reprinted from [2010], ed. R. H. Baltz, J. E. Davies, and A. Demain, Washington, DC, ASM Press.). doi:10.1128/9781555818821.ch2.1.3.f2

Citation: Aoi Y, Epstein S. 2016. New Devices for Cultivation, p 2.1.3-1-2.1.3-8. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.1.3
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FIGURE 3

Photographs of a 48-chamber HFMC showing (a) overall system, (b) membrane part, (c) injection part, and (d) cross-sectional SEM image of a hollow fiber membrane. Bar represents 200 µm. (Reprinted from ). doi:10.1128/9781555818821.ch2.1.3.f3

10.1128/9781555818821/2934ch67f03_thmb.gif
10.1128/9781555818821/2934ch67f03.gif
Image of FIGURE 3
FIGURE 3

Photographs of a 48-chamber HFMC showing (a) overall system, (b) membrane part, (c) injection part, and (d) cross-sectional SEM image of a hollow fiber membrane. Bar represents 200 µm. (Reprinted from ). doi:10.1128/9781555818821.ch2.1.3.f3

Citation: Aoi Y, Epstein S. 2016. New Devices for Cultivation, p 2.1.3-1-2.1.3-8. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.1.3
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FIGURE 4

Microscopic image of GMDs before the incubation (a) and containing microcolony after the incubation (b); the bright area in the droplet shown in (b) is a microbial colony. The microcolony containing GMDs was sorted by using cell sorter FACS Aria II (Becton Dickinson) after the incubation. Bars represent 20 µm. doi:10.1128/9781555818821.ch2.1.3.f4

10.1128/9781555818821/2934ch67f04_thmb.gif
10.1128/9781555818821/2934ch67f04.gif
Image of FIGURE 4
FIGURE 4

Microscopic image of GMDs before the incubation (a) and containing microcolony after the incubation (b); the bright area in the droplet shown in (b) is a microbial colony. The microcolony containing GMDs was sorted by using cell sorter FACS Aria II (Becton Dickinson) after the incubation. Bars represent 20 µm. doi:10.1128/9781555818821.ch2.1.3.f4

Citation: Aoi Y, Epstein S. 2016. New Devices for Cultivation, p 2.1.3-1-2.1.3-8. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.1.3
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