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Image of COLOR PLATE 1 (PREFACE) Periodic table of the elements highlighting the currently known major, minor, trace, and biologically active elements. Updated from Wackett et al. (2004).. 10.1128/9781555817190.cp1

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COLOR PLATE 1 (PREFACE) Periodic table of the elements highlighting the currently known major, minor, trace, and biologically active elements. Updated from Wackett et al. (2004).. 10.1128/9781555817190.cp1

Periodic table of the elements highlighting the currently known major, minor, trace, and biologically active elements. Updated from Wackett et al. (2004).. 10.1128/9781555817190.cp1

Citation: Stolz J, Oremland R. 2011. COLOR PLATES, In Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC.
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Image of COLOR PLATE 2 (CHAPTER 2) Culture-independent approaches to understand community structure. (A) Strategy for construction of clone libraries. Samples are collected from a given environment such as Lake Matano. The total DNA is isolated from the sample with use of commercial kits. This DNA is used for PCR amplification using degenerate 16S rDNA primers. The PCR products are then cloned into appropriate cloning vectors that are also commercially available. The inserts of each plasmid are then sequenced using primers that are specific for regions of the plasmid. The sequence obtained is then compared with comprehensive databases that have 16S rDNA sequence data to determine the organism with the closest 16S rDNA sequence. (B) General strategy for performing FISH. A collected sample is fixed to preserve the natural structure and physiological state of the cells and to permeabilize the cells. The samples are then hybridized to a fluorescently labeled probe that targets a desired group of organisms. The excess probe is washed, and cells that are now fluorescently labeled can be visualized and quantified using epifluorescence microscopy or sorted and quantified using flow cytometry. 10.1128/9781555817190.cp2

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COLOR PLATE 2 (CHAPTER 2) Culture-independent approaches to understand community structure. (A) Strategy for construction of clone libraries. Samples are collected from a given environment such as Lake Matano. The total DNA is isolated from the sample with use of commercial kits. This DNA is used for PCR amplification using degenerate 16S rDNA primers. The PCR products are then cloned into appropriate cloning vectors that are also commercially available. The inserts of each plasmid are then sequenced using primers that are specific for regions of the plasmid. The sequence obtained is then compared with comprehensive databases that have 16S rDNA sequence data to determine the organism with the closest 16S rDNA sequence. (B) General strategy for performing FISH. A collected sample is fixed to preserve the natural structure and physiological state of the cells and to permeabilize the cells. The samples are then hybridized to a fluorescently labeled probe that targets a desired group of organisms. The excess probe is washed, and cells that are now fluorescently labeled can be visualized and quantified using epifluorescence microscopy or sorted and quantified using flow cytometry. 10.1128/9781555817190.cp2

Culture-independent approaches to understand community structure. (A) Strategy for construction of clone libraries. Samples are collected from a given environment such as Lake Matano. The total DNA is isolated from the sample with use of commercial kits. This DNA is used for PCR amplification using degenerate 16S rDNA primers. The PCR products are then cloned into appropriate cloning vectors that are also commercially available. The inserts of each plasmid are then sequenced using primers that are specific for regions of the plasmid. The sequence obtained is then compared with comprehensive databases that have 16S rDNA sequence data to determine the organism with the closest 16S rDNA sequence. (B) General strategy for performing FISH. A collected sample is fixed to preserve the natural structure and physiological state of the cells and to permeabilize the cells. The samples are then hybridized to a fluorescently labeled probe that targets a desired group of organisms. The excess probe is washed, and cells that are now fluorescently labeled can be visualized and quantified using epifluorescence microscopy or sorted and quantified using flow cytometry. 10.1128/9781555817190.cp2

Citation: Stolz J, Oremland R. 2011. COLOR PLATES, In Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC.
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Image of COLOR PLATE 3 (CHAPTER 2) FISH-MAR and isotope arrays as methods for understanding the function of specific organisms in a community. (A) FISH-MAR involves collecting a sample and incubating the sample with a desired radiolabeled substrate. The sample is then used to perform FISH as described in Color Plate 2. The same sample is then treated with a photographic emulsion and the cells are then visualized by inverse confocal microscopy. Comparison of the FISH image and the photographic image reveals organisms that incorporated the radiolabel into cell material using the substrate provided. (B) Isotope array is a modification of the DNA microarray approach that involves the incubation of the sample with a radiolabeled substrate. The RNA from the sample is then isolated and fluorescently labeled. This labeled RNA sample is then hybridized to a DNA microarray that has 16S rDNA oligos for a number of predetermined microbial species spotted onto a glass slide. The fluorescence indicates the organisms that are present in a given sample and comparison with the radiographic image confirms which of these organisms incorporated the label into their RNA. 10.1128/9781555817190.cp3

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COLOR PLATE 3 (CHAPTER 2) FISH-MAR and isotope arrays as methods for understanding the function of specific organisms in a community. (A) FISH-MAR involves collecting a sample and incubating the sample with a desired radiolabeled substrate. The sample is then used to perform FISH as described in Color Plate 2. The same sample is then treated with a photographic emulsion and the cells are then visualized by inverse confocal microscopy. Comparison of the FISH image and the photographic image reveals organisms that incorporated the radiolabel into cell material using the substrate provided. (B) Isotope array is a modification of the DNA microarray approach that involves the incubation of the sample with a radiolabeled substrate. The RNA from the sample is then isolated and fluorescently labeled. This labeled RNA sample is then hybridized to a DNA microarray that has 16S rDNA oligos for a number of predetermined microbial species spotted onto a glass slide. The fluorescence indicates the organisms that are present in a given sample and comparison with the radiographic image confirms which of these organisms incorporated the label into their RNA. 10.1128/9781555817190.cp3

FISH-MAR and isotope arrays as methods for understanding the function of specific organisms in a community. (A) FISH-MAR involves collecting a sample and incubating the sample with a desired radiolabeled substrate. The sample is then used to perform FISH as described in Color Plate 2 . The same sample is then treated with a photographic emulsion and the cells are then visualized by inverse confocal microscopy. Comparison of the FISH image and the photographic image reveals organisms that incorporated the radiolabel into cell material using the substrate provided. (B) Isotope array is a modification of the DNA microarray approach that involves the incubation of the sample with a radiolabeled substrate. The RNA from the sample is then isolated and fluorescently labeled. This labeled RNA sample is then hybridized to a DNA microarray that has 16S rDNA oligos for a number of predetermined microbial species spotted onto a glass slide. The fluorescence indicates the organisms that are present in a given sample and comparison with the radiographic image confirms which of these organisms incorporated the label into their RNA. 10.1128/9781555817190.cp3

Citation: Stolz J, Oremland R. 2011. COLOR PLATES, In Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC.
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Image of COLOR PLATE 4 (CHAPTER 2) “Loss-of-function” genetic strategies to determine what genes are responsible for a particular phenotype in an environmental isolate. (A) Random transposon mutagenesis. This approach involves the use of randomly inserting transposons to find a desired genetic locus. A plasmid carrying a transposon and a selectable marker usually for antibiotic resistance is introduced into an environmental isolate either via conjugation or other means. The plasmid carrying the transposon cannot replicate in the environmental isolate. However, once the plasmid is transferred to the isolate, a transposition event occurs randomly into the chromosome of the isolate, conferring a selectable phenotype. Subsequent selection and search for the loss of the desired phenotype results in identification of a genetic locus likely responsible for the phenotype. Later complementation experiments confirm that the genetic locus predicted to confer the phenotype is indeed due to the identified locus. (B) Targeted gene deletion via homologous recombination. Bioinformatic or other means allow the prediction of a genetic locus that likely confers a desired phenotype. The upstream and downstream region of the desired locus is cloned into a plasmid vector that carries both a selectable marker (usually resistance to an antibiotic) and a counterselectable marker (a gene whose presence causes the cell to die when a certain selection is applied). This vector is then transferred to the isolate and selection is applied. The inability of the carrier plasmid to replicate in the isolate forces the plasmid to integrate into the chromosome via homologous recombination when selected for antibiotic resistance. Subsequent segregation and counterselection lead to deletion of the desired gene. 10.1128/9781555817190.cp4

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COLOR PLATE 4 (CHAPTER 2) “Loss-of-function” genetic strategies to determine what genes are responsible for a particular phenotype in an environmental isolate. (A) Random transposon mutagenesis. This approach involves the use of randomly inserting transposons to find a desired genetic locus. A plasmid carrying a transposon and a selectable marker usually for antibiotic resistance is introduced into an environmental isolate either via conjugation or other means. The plasmid carrying the transposon cannot replicate in the environmental isolate. However, once the plasmid is transferred to the isolate, a transposition event occurs randomly into the chromosome of the isolate, conferring a selectable phenotype. Subsequent selection and search for the loss of the desired phenotype results in identification of a genetic locus likely responsible for the phenotype. Later complementation experiments confirm that the genetic locus predicted to confer the phenotype is indeed due to the identified locus. (B) Targeted gene deletion via homologous recombination. Bioinformatic or other means allow the prediction of a genetic locus that likely confers a desired phenotype. The upstream and downstream region of the desired locus is cloned into a plasmid vector that carries both a selectable marker (usually resistance to an antibiotic) and a counterselectable marker (a gene whose presence causes the cell to die when a certain selection is applied). This vector is then transferred to the isolate and selection is applied. The inability of the carrier plasmid to replicate in the isolate forces the plasmid to integrate into the chromosome via homologous recombination when selected for antibiotic resistance. Subsequent segregation and counterselection lead to deletion of the desired gene. 10.1128/9781555817190.cp4

“Loss-of-function” genetic strategies to determine what genes are responsible for a particular phenotype in an environmental isolate. (A) Random transposon mutagenesis. This approach involves the use of randomly inserting transposons to find a desired genetic locus. A plasmid carrying a transposon and a selectable marker usually for antibiotic resistance is introduced into an environmental isolate either via conjugation or other means. The plasmid carrying the transposon cannot replicate in the environmental isolate. However, once the plasmid is transferred to the isolate, a transposition event occurs randomly into the chromosome of the isolate, conferring a selectable phenotype. Subsequent selection and search for the loss of the desired phenotype results in identification of a genetic locus likely responsible for the phenotype. Later complementation experiments confirm that the genetic locus predicted to confer the phenotype is indeed due to the identified locus. (B) Targeted gene deletion via homologous recombination. Bioinformatic or other means allow the prediction of a genetic locus that likely confers a desired phenotype. The upstream and downstream region of the desired locus is cloned into a plasmid vector that carries both a selectable marker (usually resistance to an antibiotic) and a counterselectable marker (a gene whose presence causes the cell to die when a certain selection is applied). This vector is then transferred to the isolate and selection is applied. The inability of the carrier plasmid to replicate in the isolate forces the plasmid to integrate into the chromosome via homologous recombination when selected for antibiotic resistance. Subsequent segregation and counterselection lead to deletion of the desired gene. 10.1128/9781555817190.cp4

Citation: Stolz J, Oremland R. 2011. COLOR PLATES, In Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC.
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Image of COLOR PLATE 5 (CHAPTER 2) Gain-of-function genetic strategy to determine the genes responsible for a particular phenotype. Heterologous complementation involves isolation of genomic DNA from an environmental isolate. This DNA is then cloned into a plasmid that can replicate in an organism that is closely related to the environmental isolate being studied that lacks the phenotype specific to the environmental isolate (a heterologous host). The plasmid is then transferred to the heterologous host using conjugation. If a genetic locus can confer the phenotype being sought, then we determine the sequence of the inserted DNA. The identity of the genetic locus can then be revealed by homology searches in publicly available sequence databases. 10.1128/9781555817190.cp5

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COLOR PLATE 5 (CHAPTER 2) Gain-of-function genetic strategy to determine the genes responsible for a particular phenotype. Heterologous complementation involves isolation of genomic DNA from an environmental isolate. This DNA is then cloned into a plasmid that can replicate in an organism that is closely related to the environmental isolate being studied that lacks the phenotype specific to the environmental isolate (a heterologous host). The plasmid is then transferred to the heterologous host using conjugation. If a genetic locus can confer the phenotype being sought, then we determine the sequence of the inserted DNA. The identity of the genetic locus can then be revealed by homology searches in publicly available sequence databases. 10.1128/9781555817190.cp5

Gain-of-function genetic strategy to determine the genes responsible for a particular phenotype. Heterologous complementation involves isolation of genomic DNA from an environmental isolate. This DNA is then cloned into a plasmid that can replicate in an organism that is closely related to the environmental isolate being studied that lacks the phenotype specific to the environmental isolate (a heterologous host). The plasmid is then transferred to the heterologous host using conjugation. If a genetic locus can confer the phenotype being sought, then we determine the sequence of the inserted DNA. The identity of the genetic locus can then be revealed by homology searches in publicly available sequence databases. 10.1128/9781555817190.cp5

Citation: Stolz J, Oremland R. 2011. COLOR PLATES, In Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC.
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Image of COLOR PLATE 6 (CHAPTER 3) Black smokers venting 296°C fluid on the Inferno metal sulfide deposit (top) and 25°C diffuse fluid venting in the Marker 113/62 hydrothermal field (bottom), both within the Axial Volcano caldera in the northeastern Pacific Ocean. Photos courtesy of NOAA Vents Program, NeMO Project. 10.1128/9781555817190.cp6

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COLOR PLATE 6 (CHAPTER 3) Black smokers venting 296°C fluid on the Inferno metal sulfide deposit (top) and 25°C diffuse fluid venting in the Marker 113/62 hydrothermal field (bottom), both within the Axial Volcano caldera in the northeastern Pacific Ocean. Photos courtesy of NOAA Vents Program, NeMO Project. 10.1128/9781555817190.cp6

Black smokers venting 296°C fluid on the Inferno metal sulfide deposit (top) and 25°C diffuse fluid venting in the Marker 113/62 hydrothermal field (bottom), both within the Axial Volcano caldera in the northeastern Pacific Ocean. Photos courtesy of NOAA Vents Program, NeMO Project. 10.1128/9781555817190.cp6

Citation: Stolz J, Oremland R. 2011. COLOR PLATES, In Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC.
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Image of COLOR PLATE 7 (CHAPTER 4) (A) Seafloor pillow basalt from the Loihi Seamount immediately after collection by ROV Jason. (B) Seafloor pillow basalt being sampled later on board the ship. (C and D) Paired petrographic thin section and synchrotronbased μX-ray fluorescence images. These show the transition through basalt glass (left; green), the palagonite weathering rind (blue/purple, infilling cracks), and the precipitation rind that formed on the exterior of the rock during interaction with hydrothermal fluids (red). 10.1128/9781555817190.cp7

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COLOR PLATE 7 (CHAPTER 4) (A) Seafloor pillow basalt from the Loihi Seamount immediately after collection by ROV Jason. (B) Seafloor pillow basalt being sampled later on board the ship. (C and D) Paired petrographic thin section and synchrotronbased μX-ray fluorescence images. These show the transition through basalt glass (left; green), the palagonite weathering rind (blue/purple, infilling cracks), and the precipitation rind that formed on the exterior of the rock during interaction with hydrothermal fluids (red). 10.1128/9781555817190.cp7

(A) Seafloor pillow basalt from the Loihi Seamount immediately after collection by ROV (B) Seafloor pillow basalt being sampled later on board the ship. (C and D) Paired petrographic thin section and synchrotronbased μX-ray fluorescence images. These show the transition through basalt glass (left; green), the palagonite weathering rind (blue/purple, infilling cracks), and the precipitation rind that formed on the exterior of the rock during interaction with hydrothermal fluids (red). 10.1128/9781555817190.cp7

Citation: Stolz J, Oremland R. 2011. COLOR PLATES, In Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC.
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Image of COLOR PLATE 8 (CHAPTER 4) Flow chart of typical seafloor exposure experiment, including preparation of the experiment (top row) and different downstream analyses carried out after recovery of experiment, weeks to years after initial deployment. Note that the initial thick sections may be derived from rocks collected from the seafloor (as in this case- “seafloor reacted” indicates rocks that were collected from the seafloor and later deployed in exposure experiments), or standard rocks purchased from suppliers. Different colored arrows and boxes indicate different analysis pipelines. EXAFS, extended X-ray absorption fine structure. 10.1128/9781555817190.cp8

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COLOR PLATE 8 (CHAPTER 4) Flow chart of typical seafloor exposure experiment, including preparation of the experiment (top row) and different downstream analyses carried out after recovery of experiment, weeks to years after initial deployment. Note that the initial thick sections may be derived from rocks collected from the seafloor (as in this case- “seafloor reacted” indicates rocks that were collected from the seafloor and later deployed in exposure experiments), or standard rocks purchased from suppliers. Different colored arrows and boxes indicate different analysis pipelines. EXAFS, extended X-ray absorption fine structure. 10.1128/9781555817190.cp8

Flow chart of typical seafloor exposure experiment, including preparation of the experiment (top row) and different downstream analyses carried out after recovery of experiment, weeks to years after initial deployment. Note that the initial thick sections may be derived from rocks collected from the seafloor (as in this case- “seafloor reacted” indicates rocks that were collected from the seafloor and later deployed in exposure experiments), or standard rocks purchased from suppliers. Different colored arrows and boxes indicate different analysis pipelines. EXAFS, extended X-ray absorption fine structure. 10.1128/9781555817190.cp8

Citation: Stolz J, Oremland R. 2011. COLOR PLATES, In Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC.
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Image of COLOR PLATE 9 (CHAPTER 4) Confocal imaging of catalyzed reported deposition-fluorescence in situ hybridization on polished basalt chip incubated at the seafloor on the EPR. The top panel is a composite of multiple layers (slices). The middle and bottom panels are two individual slices, with three-dimensional renderings of the slice surface on the side and above each panel. Stained cells appear in green in the top panel and in red in the middle and bottom panels. Yellow arrows in the middle panel indicate polishing scratches that are preferably colonized by microbes. Note that these features are not naturally occurring; rather, they are an artifact of the sample preparation. The side panels of the three-dimensional structure illustrate colonization of pits and pores. 10.1128/9781555817190.cp9

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COLOR PLATE 9 (CHAPTER 4) Confocal imaging of catalyzed reported deposition-fluorescence in situ hybridization on polished basalt chip incubated at the seafloor on the EPR. The top panel is a composite of multiple layers (slices). The middle and bottom panels are two individual slices, with three-dimensional renderings of the slice surface on the side and above each panel. Stained cells appear in green in the top panel and in red in the middle and bottom panels. Yellow arrows in the middle panel indicate polishing scratches that are preferably colonized by microbes. Note that these features are not naturally occurring; rather, they are an artifact of the sample preparation. The side panels of the three-dimensional structure illustrate colonization of pits and pores. 10.1128/9781555817190.cp9

Confocal imaging of catalyzed reported deposition-fluorescence in situ hybridization on polished basalt chip incubated at the seafloor on the EPR. The top panel is a composite of multiple layers (slices). The middle and bottom panels are two individual slices, with three-dimensional renderings of the slice surface on the side and above each panel. Stained cells appear in green in the top panel and in red in the middle and bottom panels. Yellow arrows in the middle panel indicate polishing scratches that are preferably colonized by microbes. Note that these features are not naturally occurring; rather, they are an artifact of the sample preparation. The side panels of the three-dimensional structure illustrate colonization of pits and pores. 10.1128/9781555817190.cp9

Citation: Stolz J, Oremland R. 2011. COLOR PLATES, In Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC.
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Image of COLOR PLATE 10 (CHAPTER 4) CORK observatory colonization chambers (FLOCS) with a schematic diagram of their deployment within a sealed hole in the subseafloor. The left panel depicts FLOC chambers, which are designed to be used in conjunction with passive geochemical sampling systems and pumps (OSMO pump; Wheat et al. [2000]) and other sensors. Center panel depicts how they can be deployed in sealed hydrological and geological horizons (sealed by packers) at different depths for conducting discrete experiments under different basement conditions. Right panel shows the modular modern FLOC (Orcutt et al., 2010) chamber design, which can also be a variety of colonization materials, for example, rock chips, polished sections, glass wool, and so on. Figure adapted with permission from Orcutt et al. (2010). 10.1128/9781555817190.cp10

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COLOR PLATE 10 (CHAPTER 4) CORK observatory colonization chambers (FLOCS) with a schematic diagram of their deployment within a sealed hole in the subseafloor. The left panel depicts FLOC chambers, which are designed to be used in conjunction with passive geochemical sampling systems and pumps (OSMO pump; Wheat et al. [2000]) and other sensors. Center panel depicts how they can be deployed in sealed hydrological and geological horizons (sealed by packers) at different depths for conducting discrete experiments under different basement conditions. Right panel shows the modular modern FLOC (Orcutt et al., 2010) chamber design, which can also be a variety of colonization materials, for example, rock chips, polished sections, glass wool, and so on. Figure adapted with permission from Orcutt et al. (2010). 10.1128/9781555817190.cp10

CORK observatory colonization chambers (FLOCS) with a schematic diagram of their deployment within a sealed hole in the subseafloor. The left panel depicts FLOC chambers, which are designed to be used in conjunction with passive geochemical sampling systems and pumps (OSMO pump; Wheat et al. [2000]) and other sensors. Center panel depicts how they can be deployed in sealed hydrological and geological horizons (sealed by packers) at different depths for conducting discrete experiments under different basement conditions. Right panel shows the modular modern FLOC (Orcutt et al., 2010) chamber design, which can also be a variety of colonization materials, for example, rock chips, polished sections, glass wool, and so on. Figure adapted with permission from Orcutt et al. (2010). 10.1128/9781555817190.cp10

Citation: Stolz J, Oremland R. 2011. COLOR PLATES, In Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC.
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Image of COLOR PLATE 11 (CHAPTER 10) Illustration of the four models for direct electron transfer by a gram-positive bacterium. Biofilm contained redox mediator (a), “nanowires” (b), conductive cell walls (c), or cytochrome chain linking the inner membrane to cell surface (d). Ferric iron is shown as a representative exogenous electron acceptor. Image courtesy of Dr. H. K. Carlson. 10.1128/9781555817190.cp11

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COLOR PLATE 11 (CHAPTER 10) Illustration of the four models for direct electron transfer by a gram-positive bacterium. Biofilm contained redox mediator (a), “nanowires” (b), conductive cell walls (c), or cytochrome chain linking the inner membrane to cell surface (d). Ferric iron is shown as a representative exogenous electron acceptor. Image courtesy of Dr. H. K. Carlson. 10.1128/9781555817190.cp11

Illustration of the four models for direct electron transfer by a gram-positive bacterium. Biofilm contained redox mediator (a), “nanowires” (b), conductive cell walls (c), or cytochrome chain linking the inner membrane to cell surface (d). Ferric iron is shown as a representative exogenous electron acceptor. Image courtesy of Dr. H. K. Carlson. 10.1128/9781555817190.cp11

Citation: Stolz J, Oremland R. 2011. COLOR PLATES, In Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC.
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Image of COLOR PLATE 12 (CHAPTER 12) Hierarchical cluster analysis of whole-genome, temporal gene expression for D. vulgaris cells exposed to nitrate (He et al., in review), nitrite (He et al., 2006), or Cr(VI) (Klonowska et al., 2006). The gene expression data from exponential-and stationary-growth phases (Clark et al., 2006) were also compared with the different stress conditions. The analysis was done with Multiple Experiment Viewer v4.4 (Saeed et al., 2003) with a Pearson correlation as the distance metric and a complete linkage clustering. 10.1128/9781555817190.cp12

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COLOR PLATE 12 (CHAPTER 12) Hierarchical cluster analysis of whole-genome, temporal gene expression for D. vulgaris cells exposed to nitrate (He et al., in review), nitrite (He et al., 2006), or Cr(VI) (Klonowska et al., 2006). The gene expression data from exponential-and stationary-growth phases (Clark et al., 2006) were also compared with the different stress conditions. The analysis was done with Multiple Experiment Viewer v4.4 (Saeed et al., 2003) with a Pearson correlation as the distance metric and a complete linkage clustering. 10.1128/9781555817190.cp12

Hierarchical cluster analysis of whole-genome, temporal gene expression for cells exposed to nitrate (He et al., in review), nitrite (He et al., 2006), or Cr(VI) (Klonowska et al., 2006). The gene expression data from exponential-and stationary-growth phases (Clark et al., 2006) were also compared with the different stress conditions. The analysis was done with Multiple Experiment Viewer v4.4 (Saeed et al., 2003) with a Pearson correlation as the distance metric and a complete linkage clustering. 10.1128/9781555817190.cp12

Citation: Stolz J, Oremland R. 2011. COLOR PLATES, In Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC.
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Image of COLOR PLATE 13 (CHAPTER 13) Differential in gel expression analysis (DIGE) of proteins from A. ehrlichii grown aerobically with acetate (labeled with Cy3, red fluorescence) and anaerobically with NO3-, AsO3-, and CO2 (labeled with Cy5, green fluorescence). Protein spots with equal protein abundance expressed under both conditions appear yellow. The numbered spots on the gel correspond to the list of numbered proteins identified by MALDI-TOF/MS. 1, porin; 2, nitrous-oxide reductase; 3, citrate synthase; 4, nitrate transporter; 5, putative nitrate transporter; 6, phosphoribulokinase; 7, fructose-1,6-bisphosphate aldolase; 8, branched-chain amino acid ABC transporter; 9, triosephosphate isomerase; 10, superoxide dismutase; 11, 2-oxoglutarate dehydrogenase. 10.1128/9781555817190.cp13

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COLOR PLATE 13 (CHAPTER 13) Differential in gel expression analysis (DIGE) of proteins from A. ehrlichii grown aerobically with acetate (labeled with Cy3, red fluorescence) and anaerobically with NO3-, AsO3-, and CO2 (labeled with Cy5, green fluorescence). Protein spots with equal protein abundance expressed under both conditions appear yellow. The numbered spots on the gel correspond to the list of numbered proteins identified by MALDI-TOF/MS. 1, porin; 2, nitrous-oxide reductase; 3, citrate synthase; 4, nitrate transporter; 5, putative nitrate transporter; 6, phosphoribulokinase; 7, fructose-1,6-bisphosphate aldolase; 8, branched-chain amino acid ABC transporter; 9, triosephosphate isomerase; 10, superoxide dismutase; 11, 2-oxoglutarate dehydrogenase. 10.1128/9781555817190.cp13

Differential in gel expression analysis (DIGE) of proteins from grown aerobically with acetate (labeled with Cy3, red fluorescence) and anaerobically with NO , AsO , and CO (labeled with Cy5, green fluorescence). Protein spots with equal protein abundance expressed under both conditions appear yellow. The numbered spots on the gel correspond to the list of numbered proteins identified by MALDI-TOF/MS. 1, porin; 2, nitrous-oxide reductase; 3, citrate synthase; 4, nitrate transporter; 5, putative nitrate transporter; 6, phosphoribulokinase; 7, fructose-1,6-bisphosphate aldolase; 8, branched-chain amino acid ABC transporter; 9, triosephosphate isomerase; 10, superoxide dismutase; 11, 2-oxoglutarate dehydrogenase. 10.1128/9781555817190.cp13

Citation: Stolz J, Oremland R. 2011. COLOR PLATES, In Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC.
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Image of COLOR PLATE 14 (CHAPTER 13) Heat map visualization of the relative differences in protein abundances obtained by LC-MS/MS of D. desulfuricans cells exposed to chromium (average of n = 3). Control, growth on nitrate alone; Treatment 1, growth on nitrate with chromate (100 μM); Treatment 2, two-hour exposure to chromate (100 μM). Scale runs from yellow (high abundance) to black (low abundance). Hierarchical clustering was done using the PermutMatrix program (Caraux and Pinloche, 2005). 10.1128/9781555817190.cp14

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COLOR PLATE 14 (CHAPTER 13) Heat map visualization of the relative differences in protein abundances obtained by LC-MS/MS of D. desulfuricans cells exposed to chromium (average of n = 3). Control, growth on nitrate alone; Treatment 1, growth on nitrate with chromate (100 μM); Treatment 2, two-hour exposure to chromate (100 μM). Scale runs from yellow (high abundance) to black (low abundance). Hierarchical clustering was done using the PermutMatrix program (Caraux and Pinloche, 2005). 10.1128/9781555817190.cp14

Heat map visualization of the relative differences in protein abundances obtained by LC-MS/MS of cells exposed to chromium (average of = 3). Control, growth on nitrate alone; Treatment 1, growth on nitrate with chromate (100 μM); Treatment 2, two-hour exposure to chromate (100 μM). Scale runs from yellow (high abundance) to black (low abundance). Hierarchical clustering was done using the PermutMatrix program (Caraux and Pinloche, 2005). 10.1128/9781555817190.cp14

Citation: Stolz J, Oremland R. 2011. COLOR PLATES, In Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC.
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Image of COLOR PLATE 15 (CHAPTER 14) GeoChip 3.0. Microbial community DNA was labeled with Cy5 fluorescent dye and hybridized to the array. Brighter colors represent higher signal intensities. 10.1128/9781555817190.cp15

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COLOR PLATE 15 (CHAPTER 14) GeoChip 3.0. Microbial community DNA was labeled with Cy5 fluorescent dye and hybridized to the array. Brighter colors represent higher signal intensities. 10.1128/9781555817190.cp15

GeoChip 3.0. Microbial community DNA was labeled with Cy5 fluorescent dye and hybridized to the array. Brighter colors represent higher signal intensities. 10.1128/9781555817190.cp15

Citation: Stolz J, Oremland R. 2011. COLOR PLATES, In Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC.
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Image of COLOR PLATE 16 (CHAPTER 15) Medium matrix of Ohio River sediment enrichment cultures after 7 days of incubation. Electron donor, from top row to bottom row: no donor, acetate, hydrogen plus acetate, formate, lactate, pyruvate. Concentrations of As(V), from left to right, are 0, 1, 5, 10, and 20 mM. Copious quantities of arsenic trisulfide were produced in the 5 mM cultures where electron donor was provided. 10.1128/9781555817190.cp16

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COLOR PLATE 16 (CHAPTER 15) Medium matrix of Ohio River sediment enrichment cultures after 7 days of incubation. Electron donor, from top row to bottom row: no donor, acetate, hydrogen plus acetate, formate, lactate, pyruvate. Concentrations of As(V), from left to right, are 0, 1, 5, 10, and 20 mM. Copious quantities of arsenic trisulfide were produced in the 5 mM cultures where electron donor was provided. 10.1128/9781555817190.cp16

Medium matrix of Ohio River sediment enrichment cultures after 7 days of incubation. Electron donor, from top row to bottom row: no donor, acetate, hydrogen plus acetate, formate, lactate, pyruvate. Concentrations of As(V), from left to right, are 0, 1, 5, 10, and 20 mM. Copious quantities of arsenic trisulfide were produced in the 5 mM cultures where electron donor was provided. 10.1128/9781555817190.cp16

Citation: Stolz J, Oremland R. 2011. COLOR PLATES, In Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC.
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Image of COLOR PLATE 17 (CHAPTER 16) (A) Fluorescence spectra of size-fractionated glutathione-stabilized CdSe produced by Veillonella atypica (inset shows fractions 1 and 2 under UV light). (B) High-resolution TEM of glutathione-stabilized CdSe and accompanying EDX spectrum of fraction 1. 10.1128/9781555817190.cp17

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COLOR PLATE 17 (CHAPTER 16) (A) Fluorescence spectra of size-fractionated glutathione-stabilized CdSe produced by Veillonella atypica (inset shows fractions 1 and 2 under UV light). (B) High-resolution TEM of glutathione-stabilized CdSe and accompanying EDX spectrum of fraction 1. 10.1128/9781555817190.cp17

(A) Fluorescence spectra of size-fractionated glutathione-stabilized CdSe produced by (inset shows fractions 1 and 2 under UV light). (B) High-resolution TEM of glutathione-stabilized CdSe and accompanying EDX spectrum of fraction 1. 10.1128/9781555817190.cp17

Citation: Stolz J, Oremland R. 2011. COLOR PLATES, In Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC.
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Image of COLOR PLATE 18 (CHAPTER 16) Electron micrographs of As-S precipitate formed by Citrobacter strain TSA-1 grown in the presence of arsenate in media with cysteine sulfide as a reducing agent and trace levels of sulfate (inset shows yellow precipitate). (A) SEM image. (B) High-resolution TEM image. (C and D) Scanning transmission electron microscope-EDX mapping images and spectrum (inset shows SEM image of strain TSA-1). 10.1128/9781555817190.cp18

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COLOR PLATE 18 (CHAPTER 16) Electron micrographs of As-S precipitate formed by Citrobacter strain TSA-1 grown in the presence of arsenate in media with cysteine sulfide as a reducing agent and trace levels of sulfate (inset shows yellow precipitate). (A) SEM image. (B) High-resolution TEM image. (C and D) Scanning transmission electron microscope-EDX mapping images and spectrum (inset shows SEM image of strain TSA-1). 10.1128/9781555817190.cp18

Electron micrographs of As-S precipitate formed by strain TSA-1 grown in the presence of arsenate in media with cysteine sulfide as a reducing agent and trace levels of sulfate (inset shows yellow precipitate). (A) SEM image. (B) High-resolution TEM image. (C and D) Scanning transmission electron microscope-EDX mapping images and spectrum (inset shows SEM image of strain TSA-1). 10.1128/9781555817190.cp18

Citation: Stolz J, Oremland R. 2011. COLOR PLATES, In Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC.
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