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Chapter 59 : Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology

Authors: Frank B. Dazzo, Michael Schmid, Anton Hartmann
Content Type: Reference
Publication Year: 2007

Category: Environmental Microbiology

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Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , Page 1 of 2

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Abstract:

This chapter describes the application of fluorescent molecular probes used with immunofluorescence microscopy (IFM) and fluorescence in situ hybridization (FISH) techniques for studies of microbial autecology, with an emphasis on soil and root-associated microbes. Proper filter sets must be used to match the specific optical requirements for excitation and emission of fluorescent light by different fluorochromes. Fluorescein isothiocyanate (FITC), and to a lesser extent tetramethyl rhodamine isothiocyanate (TRITC), are common fluorochromes for single labeling experiments of IFM. There are two general approaches in immunofluorescence staining: direct and indirect. Both approaches involve the production, in an immunologically competent animal (e.g., rabbit), of a primary specific antibody against the antigen of interest. The exciting innovations in image analysis technology featured in Center for Microbial Ecology Image Analysis System (CMEIAS) v. 3.0 software will undoubtedly enhance the ecological analysis of in situ bacterial colonization using immunofluorescence and other discriminating microscopy techniques operating at single cell resolution. A large online probeBase database provides an overview of more than 700 published oligonucleotide probes and their characteristics for prokaryotic rRNAs suitable for FISH. The potential ability of FISH-MAR techniques to target the ecological niche for physiological groups of microorganisms in environmental samples may help to close the gap to the general enzymatic measurements, which are also very much increased in sensitivity. CMEIAS can extract an abundance of quantitative information on microbial community structure from the multiprobe FISH image.

Citation: Dazzo F, Schmid M, Hartmann A. 2007. Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , p 712-733. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch59
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Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology*
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Citation: Dazzo F, Schmid M, Hartmann A. 2007. Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , p 712-733. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch59
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Citation: Dazzo F, Schmid M, Hartmann A. 2007. Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , p 712-733. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch59
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Citation: Dazzo F, Schmid M, Hartmann A. 2007. Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , p 712-733. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch59
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FIGURE 1
Differences in mean cell luminosity between typical 4+ and 3+ immunofluorescence reactions. Cells of bv. trifolii E11 are reacted with different dilutions of a strain-specific, polyvalent rabbit antiserum. (Left) Typical 4+ and 3+ reactions; (right) ascending sort of mean cell luminosity for 4+ and 3+ immunofluorescent reactions measured by CMEIAS image analysis. Note the higher, more uniform mean luminosity for the population of cells producing the 4+ reaction.
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FIGURE 1

Differences in mean cell luminosity between typical 4+ and 3+ immunofluorescence reactions. Cells of bv. trifolii E11 are reacted with different dilutions of a strain-specific, polyvalent rabbit antiserum. (Left) Typical 4+ and 3+ reactions; (right) ascending sort of mean cell luminosity for 4+ and 3+ immunofluorescent reactions measured by CMEIAS image analysis. Note the higher, more uniform mean luminosity for the population of cells producing the 4+ reaction.

Citation: Dazzo F, Schmid M, Hartmann A. 2007. Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , p 712-733. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch59
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FIGURE 2
In situ detection of bv. trifolii on the root surface of its host, white clover (), using indirect IFM with a monoclonal antibody specific for its lipopolysaccharide O-antigen. (A) Conventional epifluorescence. Immunofluorescent cells have aggregated at the tip of a root hair, where the host lectin, trifoliin A, accumulates. (B) Confocal laser scanning epifluorescence. Immunofluorescent cells have developed a microcolony on the rhizoplane.
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FIGURE 2

In situ detection of bv. trifolii on the root surface of its host, white clover (), using indirect IFM with a monoclonal antibody specific for its lipopolysaccharide O-antigen. (A) Conventional epifluorescence. Immunofluorescent cells have aggregated at the tip of a root hair, where the host lectin, trifoliin A, accumulates. (B) Confocal laser scanning epifluorescence. Immunofluorescent cells have developed a microcolony on the rhizoplane.

Citation: Dazzo F, Schmid M, Hartmann A. 2007. Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , p 712-733. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch59
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FIGURE 3
Use of optical sectioning with the laser scanning confocal microscope to detect bv. trifolii cells within the overlap of a markedly curled root hair of white clover. This step precedes primary host infection in the -legume symbiosis. Bacteria are stained by immunofluorescence using a monoclonal antibody against their somatic O-antigen. Bar, 10 µm.
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FIGURE 3

Use of optical sectioning with the laser scanning confocal microscope to detect bv. trifolii cells within the overlap of a markedly curled root hair of white clover. This step precedes primary host infection in the -legume symbiosis. Bacteria are stained by immunofluorescence using a monoclonal antibody against their somatic O-antigen. Bar, 10 µm.

Citation: Dazzo F, Schmid M, Hartmann A. 2007. Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , p 712-733. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch59
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FIGURE 4
Epifluorescence micrograph of immunofluorescent cells of bv. trifolii 0403 colonized on the root surface (especially at junctions between epidermal cells) below the root hair region of a white clover seedling. Bar scale, 20.0 µm.
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FIGURE 4

Epifluorescence micrograph of immunofluorescent cells of bv. trifolii 0403 colonized on the root surface (especially at junctions between epidermal cells) below the root hair region of a white clover seedling. Bar scale, 20.0 µm.

Citation: Dazzo F, Schmid M, Hartmann A. 2007. Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , p 712-733. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch59
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FIGURE 5
Frequency (left) and 2-D scatterplots (right) of the CMEIAS plotless spatial distribution analyses of the first and second nearest neighbor distances (NND) separating each individual bacterium shown in Fig. 4 .
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Image of FIGURE 5
FIGURE 5

Frequency (left) and 2-D scatterplots (right) of the CMEIAS plotless spatial distribution analyses of the first and second nearest neighbor distances (NND) separating each individual bacterium shown in Fig. 4 .

Citation: Dazzo F, Schmid M, Hartmann A. 2007. Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , p 712-733. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch59
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FIGURE 6
Geostatistical analysis of the bacterial colonization of the root surface shown in Fig. 4 . (Left) Semivariogram autocorrelation plot and best-fit spherical model of the local spatial density; (right) 2-D kriging map derived from the autocorrelation model depicting the local density of bacteria interpolated over the entire spatial domain.
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FIGURE 6

Geostatistical analysis of the bacterial colonization of the root surface shown in Fig. 4 . (Left) Semivariogram autocorrelation plot and best-fit spherical model of the local spatial density; (right) 2-D kriging map derived from the autocorrelation model depicting the local density of bacteria interpolated over the entire spatial domain.

Citation: Dazzo F, Schmid M, Hartmann A. 2007. Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , p 712-733. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch59
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FIGURE 7
(Top) 2-D projection of a 3-D confocal image stack showing microcolonies of two different ribotypes of nitrite-oxidizing bacteria, genus , in a biofilm from a wastewater treatment plant. The image was rendered by the program DAIME and provided courtesy of Frank Maixner and Holger Daims (University of Vienna, Vienna, Austria). (Bottom) Formamide concentration series for the determination of optimal hybridization conditions for a newly designed 16S rRNA-targeted oligonucleotide probe using the program DAIME. Data courtesy of Sebastian Lücker and Holger Daims (University of Vienna, Vienna, Austria).
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Image of FIGURE 7
FIGURE 7

(Top) 2-D projection of a 3-D confocal image stack showing microcolonies of two different ribotypes of nitrite-oxidizing bacteria, genus , in a biofilm from a wastewater treatment plant. The image was rendered by the program DAIME and provided courtesy of Frank Maixner and Holger Daims (University of Vienna, Vienna, Austria). (Bottom) Formamide concentration series for the determination of optimal hybridization conditions for a newly designed 16S rRNA-targeted oligonucleotide probe using the program DAIME. Data courtesy of Sebastian Lücker and Holger Daims (University of Vienna, Vienna, Austria).

Citation: Dazzo F, Schmid M, Hartmann A. 2007. Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , p 712-733. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch59
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FIGURE 8
(Left) Bacteria with ectomycorrhizal hyphae. The ectomycorrhizal fungus was retrieved from roots of beech trees in the Kranzberg forest near Freising, Germany. For FISH analysis, the following probes were applied: EUB338Mix Cy3, Bet42a Fluos, and Gam42a Cy5. Due to concomitant binding of probes, beta-proteobacteria are stained yellow (Beta42a Fluos plus EUB338Mix Cy3) and other (non-beta- or -gamma proteobacteria) are labeled red (EUB338Mix Cy3). Another unidentified organism that hybridized with none of the three fluorescent probes is included in the image because of its blue autofluorescence. (Right) on wheat roots. Wheat seedlings were inoculated with Sp245, and their colonization was visualized by FISH analysis. The following oligonucleotide probes were applied: EUB-338Mix Cy3 and Abras-1420-Cy5. Due to concomitant binding of both probes, the bacterial cells display magenta fluorescence. The computer-rendered orthogonal view displays the third dimension in the 3-D--stack of -optisections.
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Image of FIGURE 8
FIGURE 8

(Left) Bacteria with ectomycorrhizal hyphae. The ectomycorrhizal fungus was retrieved from roots of beech trees in the Kranzberg forest near Freising, Germany. For FISH analysis, the following probes were applied: EUB338Mix Cy3, Bet42a Fluos, and Gam42a Cy5. Due to concomitant binding of probes, beta-proteobacteria are stained yellow (Beta42a Fluos plus EUB338Mix Cy3) and other (non-beta- or -gamma proteobacteria) are labeled red (EUB338Mix Cy3). Another unidentified organism that hybridized with none of the three fluorescent probes is included in the image because of its blue autofluorescence. (Right) on wheat roots. Wheat seedlings were inoculated with Sp245, and their colonization was visualized by FISH analysis. The following oligonucleotide probes were applied: EUB-338Mix Cy3 and Abras-1420-Cy5. Due to concomitant binding of both probes, the bacterial cells display magenta fluorescence. The computer-rendered orthogonal view displays the third dimension in the 3-D--stack of -optisections.

Citation: Dazzo F, Schmid M, Hartmann A. 2007. Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , p 712-733. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch59
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FIGURE 9
Distribution of microbial abundance in the community represented by the FISH image of Fig. 8 , left panel. CMEIAS was used to segment the microbes in the image according to their foreground color ranges and then measure the cumulative cell bio-volume for each microbial ribotype.
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Image of FIGURE 9
FIGURE 9

Distribution of microbial abundance in the community represented by the FISH image of Fig. 8 , left panel. CMEIAS was used to segment the microbes in the image according to their foreground color ranges and then measure the cumulative cell bio-volume for each microbial ribotype.

Citation: Dazzo F, Schmid M, Hartmann A. 2007. Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , p 712-733. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch59
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Tables

Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology*
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Citation: Dazzo F, Schmid M, Hartmann A. 2007. Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , p 712-733. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch59
/content/10.1128/9781555815882.ch59.ch56nt01
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Citation: Dazzo F, Schmid M, Hartmann A. 2007. Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , p 712-733. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch59
/content/10.1128/9781555815882.ch59.ch59tab01
TABLE 1
CMEIAS image analysis of the in situ abundance and spatial distribution of the immunofluorescent bacteria shown in Fig. 5
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TABLE 1

CMEIAS image analysis of the in situ abundance and spatial distribution of the immunofluorescent bacteria shown in Fig. 5

Citation: Dazzo F, Schmid M, Hartmann A. 2007. Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , p 712-733. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch59
/content/10.1128/9781555815882.ch59.ch59tab02
TABLE 2
CMEIAS image analysis of the spatial abundance and distribution of individual ribotype populations distinguished by multiprobe FISH in the community image shown in Fig. 8 , left panel
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TABLE 2

CMEIAS image analysis of the spatial abundance and distribution of individual ribotype populations distinguished by multiprobe FISH in the community image shown in Fig. 8 , left panel

Citation: Dazzo F, Schmid M, Hartmann A. 2007. Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , p 712-733. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch59
/content/10.1128/9781555815882.ch59.ch59tab03
TABLE 3
CMEIAS image analysis of the ribotype diversity distinguished by multiprobe FISH and weighted by biovolume abundance in the community image shown in Fig. 8 , left panel
Generic image for table
TABLE 3

CMEIAS image analysis of the ribotype diversity distinguished by multiprobe FISH and weighted by biovolume abundance in the community image shown in Fig. 8 , left panel

Citation: Dazzo F, Schmid M, Hartmann A. 2007. Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools for Soil- and Plant-Associated Microbial Autecology , p 712-733. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch59

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