Color Plates
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Editors:
J. Colin Murrell1,
Andrew S. Whiteley2
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Affiliations:
1: School of Life Sciences, The University of Warwick, Coventry, United Kingdom;
2: Centre for Ecology and Hydrology, Walling ford, United Kingdom
Content Type: Monograph
Publication Year:
2011
Category: Environmental Microbiology; Applied and Industrial Microbiology
e-ISBN
:
9781555816896
Book DOI:
10.1128/9781555816896
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Color Plates
Citation:
Murrell J, Whiteley A.
2011.
Color Plates,
In
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
/content/10.1128/9781555816896.ch10back01.ch10cp01
COLOR PLATE 1 (CHAPTER 10)
Conceptual view of carbon flow (I) through anaerobic methane-oxidizing communities based on compound-specific SIP of lipids (Blumenberg et al., 2005; Wegener et al., 2008, Jagersma et al., 2009), and of nitrogen assimilation capabilities (II) (Orphan et al., 2009; Dekas et al., 2009). (I) Label incorporation from 13CH4: (a) predominantly into lipids of sulfate-reducing bacteria, and archaeal lipids of ANME to some extent (Blumenberg et al., 2005; Jagersma et al., 2009); (b) predominantly into archaeal lipids (Wegener et al., 2008). (c) Label incorporation from 13CO2 occurred into archaeal and bacterial lipids; however, sulfate reducers were only labeled when methane was available as energy substrate (d) (Wegener et al., 2009). (II) (e) N2 is fixed by ANME cells only and (f) eventually transferred to sulfate-reducing bacteria, whereas (g) other nitrogen compounds are assimilated by both ANME and sulfate-reducing bacteria (Orphan et al., 2009; Dekas et al., 2009).
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COLOR PLATE 1 (CHAPTER 10)
Conceptual view of carbon flow (I) through anaerobic methane-oxidizing communities based on compound-specific SIP of lipids (Blumenberg et al., 2005; Wegener et al., 2008, Jagersma et al., 2009), and of nitrogen assimilation capabilities (II) (Orphan et al., 2009; Dekas et al., 2009). (I) Label incorporation from 13CH4: (a) predominantly into lipids of sulfate-reducing bacteria, and archaeal lipids of ANME to some extent (Blumenberg et al., 2005; Jagersma et al., 2009); (b) predominantly into archaeal lipids (Wegener et al., 2008). (c) Label incorporation from 13CO2 occurred into archaeal and bacterial lipids; however, sulfate reducers were only labeled when methane was available as energy substrate (d) (Wegener et al., 2009). (II) (e) N2 is fixed by ANME cells only and (f) eventually transferred to sulfate-reducing bacteria, whereas (g) other nitrogen compounds are assimilated by both ANME and sulfate-reducing bacteria (Orphan et al., 2009; Dekas et al., 2009).
Citation:
Murrell J, Whiteley A.
2011.
Color Plates,
In
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
/content/10.1128/9781555816896.ch10back01.ch10cp02
COLOR PLATE 2 (CHAPTER 10)
Patterns of carbon flow through microbial communities identified by SIP. (A) Primary assimilation of a 13C-labeled substrate and cross-feeding on 13C-labeled products and intermediates involving different levels of labeling in secondary carbon feeders (red, highly labeled; hatched, partially labeled). (B) Carbon flow in syntrophic coupling (e.g., interspecies hydrogen and/or acetate transfer) involving simultaneous labeling of spatial associated syntrophic partners. (C) Predation and higher-level trophic cascades involving predatory (or detrivorous) bacteria, Bdellovibrio-like bacteria, and higher trophic level predators and detrivores such as grazing protozoa (flagellates, amoeba, ciliates) and fungi.
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10.1128/9781555816896/f0348-01.gif
Click to view
COLOR PLATE 2 (CHAPTER 10)
Patterns of carbon flow through microbial communities identified by SIP. (A) Primary assimilation of a 13C-labeled substrate and cross-feeding on 13C-labeled products and intermediates involving different levels of labeling in secondary carbon feeders (red, highly labeled; hatched, partially labeled). (B) Carbon flow in syntrophic coupling (e.g., interspecies hydrogen and/or acetate transfer) involving simultaneous labeling of spatial associated syntrophic partners. (C) Predation and higher-level trophic cascades involving predatory (or detrivorous) bacteria, Bdellovibrio-like bacteria, and higher trophic level predators and detrivores such as grazing protozoa (flagellates, amoeba, ciliates) and fungi.
Citation:
Murrell J, Whiteley A.
2011.
Color Plates,
In
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
/content/10.1128/9781555816896.ch10back01.ch14cp03
COLOR PLATE 3 (CHAPTER 14)
Diagram of the major steps employed in single-cell analysis by HISH-SIMS. Samples are collected from the environment and incubated with labeled substrates under in situ or near in situ conditions (pulse-chase experiments). Subsequently, subsamples are fixed as in FISH, added to Au-Pd-coated filters, and hybridized with specific, HRP-labeled oligonucleotide probes. Following the deposition of F-containing tyramides, the samples are first analyzed by epifluorescence microscopy to verify the success of the hybridization, and afterwards by nanoSIMS. Up to seven masses can be collected simultaneously, allowing the detection, in a single scan, of the total biomass (12C14N-;), the specific label uptake (e.g., 13C, 15N), and the cell identity (19F or other halogens). Element ratios (e.g., 13C/12C, 15N/14N) allow quantification of the amount of label incorporated by individual cells.
10.1128/9781555816896/f0349-01_thmb.gif
10.1128/9781555816896/f0349-01.gif
Click to view
COLOR PLATE 3 (CHAPTER 14)
Diagram of the major steps employed in single-cell analysis by HISH-SIMS. Samples are collected from the environment and incubated with labeled substrates under in situ or near in situ conditions (pulse-chase experiments). Subsequently, subsamples are fixed as in FISH, added to Au-Pd-coated filters, and hybridized with specific, HRP-labeled oligonucleotide probes. Following the deposition of F-containing tyramides, the samples are first analyzed by epifluorescence microscopy to verify the success of the hybridization, and afterwards by nanoSIMS. Up to seven masses can be collected simultaneously, allowing the detection, in a single scan, of the total biomass (12C14N-;), the specific label uptake (e.g., 13C, 15N), and the cell identity (19F or other halogens). Element ratios (e.g., 13C/12C, 15N/14N) allow quantification of the amount of label incorporated by individual cells.
Citation:
Murrell J, Whiteley A.
2011.
Color Plates,
In
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
/content/10.1128/9781555816896.ch10back01.ch14cp04
COLOR PLATE 4 (CHAPTER 14)
NanoSIMS images of mixed E. coli-Azoarcus sp. cultures showing the uptake of [13C]glucose by individual E. coli cells. A, D, total biomass as 12C14N-; B, E, Identification based on detection of 19F-; C, F, ratio images of 13C/12C. The E. coli cells were identified by hybridization with the HRP-labeled GAM42a probe, followed by deposition of fluorine-containing tyramides. The section highlighted in panel A was chosen for more detailed analysis by nanoSIMS (panels D, E, and F).
10.1128/9781555816896/f0350-01_thmb.gif
10.1128/9781555816896/f0350-01.gif
Click to view
COLOR PLATE 4 (CHAPTER 14)
NanoSIMS images of mixed E. coli-Azoarcus sp. cultures showing the uptake of [13C]glucose by individual E. coli cells. A, D, total biomass as 12C14N-; B, E, Identification based on detection of 19F-; C, F, ratio images of 13C/12C. The E. coli cells were identified by hybridization with the HRP-labeled GAM42a probe, followed by deposition of fluorine-containing tyramides. The section highlighted in panel A was chosen for more detailed analysis by nanoSIMS (panels D, E, and F).
Citation:
Murrell J, Whiteley A.
2011.
Color Plates,
In
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
/content/10.1128/9781555816896.ch10back01.ch14cp05
COLOR PLATE 5 (CHAPTER 14)
NanoSIMS images showing [15N]ammonia (panel B) and 13C-inorganic carbon (panel D) incorporation by single cells of the purple sulfur bacterium Lamprocystis purpurea from Lake Cadagno, Switzerland. L. purpurea was identified by hybridization with the specific probe Apur453 (Tonolla et al., 1999), followed by deposition of fluorine-containing tyramides (panel C). (A) Total biomass, 12C14N-.
10.1128/9781555816896/f0350-02_thmb.gif
10.1128/9781555816896/f0350-02.gif
Click to view
COLOR PLATE 5 (CHAPTER 14)
NanoSIMS images showing [15N]ammonia (panel B) and 13C-inorganic carbon (panel D) incorporation by single cells of the purple sulfur bacterium Lamprocystis purpurea from Lake Cadagno, Switzerland. L. purpurea was identified by hybridization with the specific probe Apur453 (Tonolla et al., 1999), followed by deposition of fluorine-containing tyramides (panel C). (A) Total biomass, 12C14N-.
Citation:
Murrell J, Whiteley A.
2011.
Color Plates,
In
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
/content/book/10.1128/9781555816896.ch10back01
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