Structured Review

Eppendorf AG biofilm
Clustering pattern of pioneer <t>biofilm-forming</t> eukaryotic communities formed on the C0, P 0 and P F surfaces. ( a–c ) the clustering patterns of pioneer biofilm-forming the eukaryotic communities adhering to the C 0 , P 0 and P F surfaces (EC 0 , EP 0 and EP F ) based on the Unweighted Pair-Group Method with Arithmetic means (UPGMA) method. ( d ) the multidimensional scale (MDS) analysis of the clustering patterns of the early pioneer eukaryotic communities (EC 0 , EP 0 and EP F ) on the C 0 , P 0 and P F surfaces.
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Images

1) Product Images from "Differential Colonization Dynamics of Marine Biofilm-Forming Eukaryotic Microbes on Different Protective Coating Materials"

Article Title: Differential Colonization Dynamics of Marine Biofilm-Forming Eukaryotic Microbes on Different Protective Coating Materials

Journal: Polymers

doi: 10.3390/polym11010161

Clustering pattern of pioneer biofilm-forming eukaryotic communities formed on the C0, P 0 and P F surfaces. ( a–c ) the clustering patterns of pioneer biofilm-forming the eukaryotic communities adhering to the C 0 , P 0 and P F surfaces (EC 0 , EP 0 and EP F ) based on the Unweighted Pair-Group Method with Arithmetic means (UPGMA) method. ( d ) the multidimensional scale (MDS) analysis of the clustering patterns of the early pioneer eukaryotic communities (EC 0 , EP 0 and EP F ) on the C 0 , P 0 and P F surfaces.
Figure Legend Snippet: Clustering pattern of pioneer biofilm-forming eukaryotic communities formed on the C0, P 0 and P F surfaces. ( a–c ) the clustering patterns of pioneer biofilm-forming the eukaryotic communities adhering to the C 0 , P 0 and P F surfaces (EC 0 , EP 0 and EP F ) based on the Unweighted Pair-Group Method with Arithmetic means (UPGMA) method. ( d ) the multidimensional scale (MDS) analysis of the clustering patterns of the early pioneer eukaryotic communities (EC 0 , EP 0 and EP F ) on the C 0 , P 0 and P F surfaces.

Techniques Used:

The Single-stranded Conformation Polymorphism (SSCP) patterns of the early biofilm-forming eukaryotic microbial communities developed on the C 0 , P 0 and P F surfaces.
Figure Legend Snippet: The Single-stranded Conformation Polymorphism (SSCP) patterns of the early biofilm-forming eukaryotic microbial communities developed on the C 0 , P 0 and P F surfaces.

Techniques Used:

2) Product Images from "Evaluation of Phototrophic Stream Biofilms Under Stress: Comparing Traditional and Novel Ecotoxicological Endpoints After Exposure to Diuron"

Article Title: Evaluation of Phototrophic Stream Biofilms Under Stress: Comparing Traditional and Novel Ecotoxicological Endpoints After Exposure to Diuron

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2018.02974

FC-CS in diuron-treated stream biofilms. (A) Biofilms were assessed by flow cytometry after sampling on d 0 , d 7 , d 14 , and d 21 , and altogether mapped by viSNE. viSNE maps are shown in single color, with each point in the viSNE map representing a single cell or particle from the biofilms or (B) colored according to fluorescence intensity at 695 nm and according to the forward scatter (full set of scattering and fluorescence intensities displayed in Supplementary Figure S4 ). (C) Subpopulations (SP 1–20) categorized based on the viSNE map and optical scatter and fluorescence intensities. Some cells (4.7%) were not assigned due to lack of distinct properties. Comparison of subpopulation properties with data acquired from reference species and pigment-bleached reference samples (Supplementary Figure S5 ) allowed for assigning subpopulations to types of organisms and potentially decaying cells.
Figure Legend Snippet: FC-CS in diuron-treated stream biofilms. (A) Biofilms were assessed by flow cytometry after sampling on d 0 , d 7 , d 14 , and d 21 , and altogether mapped by viSNE. viSNE maps are shown in single color, with each point in the viSNE map representing a single cell or particle from the biofilms or (B) colored according to fluorescence intensity at 695 nm and according to the forward scatter (full set of scattering and fluorescence intensities displayed in Supplementary Figure S4 ). (C) Subpopulations (SP 1–20) categorized based on the viSNE map and optical scatter and fluorescence intensities. Some cells (4.7%) were not assigned due to lack of distinct properties. Comparison of subpopulation properties with data acquired from reference species and pigment-bleached reference samples (Supplementary Figure S5 ) allowed for assigning subpopulations to types of organisms and potentially decaying cells.

Techniques Used: Flow Cytometry, Cytometry, Sampling, Fluorescence

Extracellular polymeric substances (EPS) extraction of stream biofilm samples after diuron exposure. (A) EPS composition as % of total DOC after 3 weeks. BP, biopolymers; BB, building blocks of humic substances; LMW acids, low molecular weight acids; N/A, neutral/amphiphilic compounds. (B) Protein concentration per extracted DOC (μg/mg) over time. Data is presented as box plots according to Tukey. ∗ , ∗∗ , and ∗∗∗ represent the significant difference between the control and diuron-treated community at d21 ( ∗ P ≤ 0.05, ∗∗ P ≤ 0.01, ∗∗∗ P ≤ 0.001), n = 5.
Figure Legend Snippet: Extracellular polymeric substances (EPS) extraction of stream biofilm samples after diuron exposure. (A) EPS composition as % of total DOC after 3 weeks. BP, biopolymers; BB, building blocks of humic substances; LMW acids, low molecular weight acids; N/A, neutral/amphiphilic compounds. (B) Protein concentration per extracted DOC (μg/mg) over time. Data is presented as box plots according to Tukey. ∗ , ∗∗ , and ∗∗∗ represent the significant difference between the control and diuron-treated community at d21 ( ∗ P ≤ 0.05, ∗∗ P ≤ 0.01, ∗∗∗ P ≤ 0.001), n = 5.

Techniques Used: Molecular Weight, Protein Concentration

3) Product Images from "New Methods for Analysis of Spatial Distribution and Coaggregation of Microbial Populations in Complex Biofilms"

Article Title: New Methods for Analysis of Spatial Distribution and Coaggregation of Microbial Populations in Complex Biofilms

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.01727-13

Effects of different algorithm parameters on the automatic slicing of biofilm images. (A to C) The same biofilm image sliced with 5, 10, or 20% smoothing of the surface line. The slicing direction is from top to bottom. The slices are colorized for illustrational
Figure Legend Snippet: Effects of different algorithm parameters on the automatic slicing of biofilm images. (A to C) The same biofilm image sliced with 5, 10, or 20% smoothing of the surface line. The slicing direction is from top to bottom. The slices are colorized for illustrational

Techniques Used:

Sequential FISH on cryosectioned biofilms.
Figure Legend Snippet: Sequential FISH on cryosectioned biofilms.

Techniques Used: Fluorescence In Situ Hybridization

Coaggregation analysis of Nitrospira and AOB in biofilms from three systems. The mean abundance of Nitrospira relative to the abundance that would be expected if the nitrifiers were randomly distributed is plotted against the distance from the biomass
Figure Legend Snippet: Coaggregation analysis of Nitrospira and AOB in biofilms from three systems. The mean abundance of Nitrospira relative to the abundance that would be expected if the nitrifiers were randomly distributed is plotted against the distance from the biomass

Techniques Used:

Automated slicing of biofilm images. (A) Greyscale image of cryosectioned biofilm labeled by FISH with the EUB338 probe mixture. (B) The same image as in panel A after binarization and the removal of noise and small particles. (C) The same image as in
Figure Legend Snippet: Automated slicing of biofilm images. (A) Greyscale image of cryosectioned biofilm labeled by FISH with the EUB338 probe mixture. (B) The same image as in panel A after binarization and the removal of noise and small particles. (C) The same image as in

Techniques Used: Labeling, Fluorescence In Situ Hybridization

The sequential-FISH procedure. The first FISH was performed with multiple partly overlapping probes targeting NOB, AOB, or Betaproteobacteria . In a second iteration, the same biofilm was subjected to FISH with the EUB338 probe mixture. After each round
Figure Legend Snippet: The sequential-FISH procedure. The first FISH was performed with multiple partly overlapping probes targeting NOB, AOB, or Betaproteobacteria . In a second iteration, the same biofilm was subjected to FISH with the EUB338 probe mixture. After each round

Techniques Used: Fluorescence In Situ Hybridization

Images exemplifying biofilm structure and stratification. Cryosectioned biofilms from the pilot plant NTF2 (A) and MBBR T1 (B) show cells hybridized with the AOB probe mixture and the EUB338 probe mixtures (yellow), Nitrospira cells hybridized with probe
Figure Legend Snippet: Images exemplifying biofilm structure and stratification. Cryosectioned biofilms from the pilot plant NTF2 (A) and MBBR T1 (B) show cells hybridized with the AOB probe mixture and the EUB338 probe mixtures (yellow), Nitrospira cells hybridized with probe

Techniques Used:

4) Product Images from "Reduced ability to detect surface-related biofilm bacteria after antibiotic exposure under in vitro conditions"

Article Title: Reduced ability to detect surface-related biofilm bacteria after antibiotic exposure under in vitro conditions

Journal: Acta Orthopaedica

doi: 10.1080/17453674.2016.1246795

Heat flow (y-axis, μW) development over time (x-axis, hours) of S. aureus (panels A–D), S. epidermidis (E–G), E. coli (H), and P. acnes (I–K) exposed to different antibiotics. The numbers above each curve indicate the respective antibiotic concentrations. The range for x-axis is different in the case of P. acnes (72 h). Furthermore, y-axis range was changed for non-staphylococci that showed markedly different heat flow levels. The positive controls were biofilms on beads not previously exposed to antibiotics (0 μg/mL). The experiments were performed in triplicate, and a representative experiment is shown.
Figure Legend Snippet: Heat flow (y-axis, μW) development over time (x-axis, hours) of S. aureus (panels A–D), S. epidermidis (E–G), E. coli (H), and P. acnes (I–K) exposed to different antibiotics. The numbers above each curve indicate the respective antibiotic concentrations. The range for x-axis is different in the case of P. acnes (72 h). Furthermore, y-axis range was changed for non-staphylococci that showed markedly different heat flow levels. The positive controls were biofilms on beads not previously exposed to antibiotics (0 μg/mL). The experiments were performed in triplicate, and a representative experiment is shown.

Techniques Used: Flow Cytometry

5) Product Images from "Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms"

Article Title: Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.02146-14

Profiles of measured total dissolved sulfide, oxygen, pH, and calculated sulfide production rate in the biofilm. Negative depths in the profile represent the distance from the biofilm surface into the wastewater.
Figure Legend Snippet: Profiles of measured total dissolved sulfide, oxygen, pH, and calculated sulfide production rate in the biofilm. Negative depths in the profile represent the distance from the biofilm surface into the wastewater.

Techniques Used:

Model-predicted sulfate and soluble biodegradable COD profiles in the biofilm.
Figure Legend Snippet: Model-predicted sulfate and soluble biodegradable COD profiles in the biofilm.

Techniques Used:

The SRB (A) and MA (B) proportions of total microorganisms (bacteria and archaea) detected by FISH within the sewer biofilms. C. Methanomethylophilus , “ Candidatus Methanomethylophilus.”
Figure Legend Snippet: The SRB (A) and MA (B) proportions of total microorganisms (bacteria and archaea) detected by FISH within the sewer biofilms. C. Methanomethylophilus , “ Candidatus Methanomethylophilus.”

Techniques Used: Sulforhodamine B Assay, Fluorescence In Situ Hybridization

FISH images of different sections of the sewer reactor biofilm. (A and B) Images of the biofilm sections cut perpendicularly to the substratum, with SRB in white (A) and MA in purple (B). Arrows indicate the biofilm surface. (C and D) Images of biofilm sections cut parallel to the substratum at depths of 100 μm and 700 μm, respectively, with SRB in white, archaea in red, and other bacteria in green, blue, and yellow. (E and F) Images of biofilm sections cut parallel to the substratum at depths of 100 μm and 700 μm, respectively, with MA in purple, other archaea in red, and bacteria in green. Scale bars, 50 μm.
Figure Legend Snippet: FISH images of different sections of the sewer reactor biofilm. (A and B) Images of the biofilm sections cut perpendicularly to the substratum, with SRB in white (A) and MA in purple (B). Arrows indicate the biofilm surface. (C and D) Images of biofilm sections cut parallel to the substratum at depths of 100 μm and 700 μm, respectively, with SRB in white, archaea in red, and other bacteria in green, blue, and yellow. (E and F) Images of biofilm sections cut parallel to the substratum at depths of 100 μm and 700 μm, respectively, with MA in purple, other archaea in red, and bacteria in green. Scale bars, 50 μm.

Techniques Used: Fluorescence In Situ Hybridization, Sulforhodamine B Assay

Schematic of the laboratory-scale anaerobic, annular biofilm reactor.
Figure Legend Snippet: Schematic of the laboratory-scale anaerobic, annular biofilm reactor.

Techniques Used:

Comparison of model-predicted results with the experimentally measured data. (A) Relative abundances of SRB and MA. (B) Sulfide concentration profiles in the biofilm.
Figure Legend Snippet: Comparison of model-predicted results with the experimentally measured data. (A) Relative abundances of SRB and MA. (B) Sulfide concentration profiles in the biofilm.

Techniques Used: Sulforhodamine B Assay, Concentration Assay

Heat map displaying the distribution of the predominant SRB (A) and MA (B) in different biofilm layers from the biofilm surface to the bottom (Layer 1 to Layer 5).
Figure Legend Snippet: Heat map displaying the distribution of the predominant SRB (A) and MA (B) in different biofilm layers from the biofilm surface to the bottom (Layer 1 to Layer 5).

Techniques Used: Sulforhodamine B Assay

6) Product Images from "New Derivatives of Pyridoxine Exhibit High Antibacterial Activity against Biofilm-Embedded Staphylococcus Cells"

Article Title: New Derivatives of Pyridoxine Exhibit High Antibacterial Activity against Biofilm-Embedded Staphylococcus Cells

Journal: BioMed Research International

doi: 10.1155/2015/890968

The amount of viable S. aureus (a, c) and S. epidermidis (b, d) biofilm-detached (a, b) and biofilm-embedded (c, d) cells after 24 h exposition to antimicrobials, CFUs/mL.
Figure Legend Snippet: The amount of viable S. aureus (a, c) and S. epidermidis (b, d) biofilm-detached (a, b) and biofilm-embedded (c, d) cells after 24 h exposition to antimicrobials, CFUs/mL.

Techniques Used:

The antibacterial effect of ciprofloxacin and miramistin against biofilm-embedded S. aureus and S. epidermidis cells. Bacteria were grown for 72 h to form a rigid biofilm. Next the medium was replaced by the fresh one after double washing to remove nonadherent cells; antibiotics were added as indicated followed by 24 h incubation. Afterwards the number of viable cells was evaluated by staining the cells with propidium iodide and acridine orange. The estimated percentage of nonviable cells is given in the lower right corner of each panel. Magnification ×63.
Figure Legend Snippet: The antibacterial effect of ciprofloxacin and miramistin against biofilm-embedded S. aureus and S. epidermidis cells. Bacteria were grown for 72 h to form a rigid biofilm. Next the medium was replaced by the fresh one after double washing to remove nonadherent cells; antibiotics were added as indicated followed by 24 h incubation. Afterwards the number of viable cells was evaluated by staining the cells with propidium iodide and acridine orange. The estimated percentage of nonviable cells is given in the lower right corner of each panel. Magnification ×63.

Techniques Used: Incubation, Staining

The biofilm formation by S. aureus and S. epidermidis when growing on Basal medium (BM), Luria-Bertani broth (LB), Mueller-Hinton broth (MH), or Trypticase soy broth (TSB). 72-hour-old biofilms were stained by crystal violet.
Figure Legend Snippet: The biofilm formation by S. aureus and S. epidermidis when growing on Basal medium (BM), Luria-Bertani broth (LB), Mueller-Hinton broth (MH), or Trypticase soy broth (TSB). 72-hour-old biofilms were stained by crystal violet.

Techniques Used: Staining

The antibacterial effect of bisphosphonium salts of pyridoxine against biofilm-embedded S. aureus and S. epidermidis cells. Bacteria were grown for 72 h to form a rigid biofilm. Next the medium was replaced by the fresh one after double washing to remove nonadherent cells; compounds were added as indicated followed by 24 h incubation. Afterwards the number of viable cells was evaluated by staining the cells with propidium iodide and acridine orange. The estimated percentage of nonviable cells is given in the lower right corner of each panel. Magnification ×40.
Figure Legend Snippet: The antibacterial effect of bisphosphonium salts of pyridoxine against biofilm-embedded S. aureus and S. epidermidis cells. Bacteria were grown for 72 h to form a rigid biofilm. Next the medium was replaced by the fresh one after double washing to remove nonadherent cells; compounds were added as indicated followed by 24 h incubation. Afterwards the number of viable cells was evaluated by staining the cells with propidium iodide and acridine orange. The estimated percentage of nonviable cells is given in the lower right corner of each panel. Magnification ×40.

Techniques Used: Incubation, Staining

The effect of pyridoxine derivatives on the thickness of preformed biofilms of (a) S. aureus and (b) S. epidermidis . Three-day-old biofilms were washed twice by sterile broth, exposed for 24 h to antimicrobials at concentrations as indicated and then stained by crystal violet. Wells incubated with pure medium served as a control (indicated as E). Standard deviations in each case did not exceed 15% and are not provided. The values for 3 – 6 significantly differ from the control value (without any antimicrobials) that were indicated with P
Figure Legend Snippet: The effect of pyridoxine derivatives on the thickness of preformed biofilms of (a) S. aureus and (b) S. epidermidis . Three-day-old biofilms were washed twice by sterile broth, exposed for 24 h to antimicrobials at concentrations as indicated and then stained by crystal violet. Wells incubated with pure medium served as a control (indicated as E). Standard deviations in each case did not exceed 15% and are not provided. The values for 3 – 6 significantly differ from the control value (without any antimicrobials) that were indicated with P

Techniques Used: Staining, Incubation

The antibacterial effect of quaternary ammonium salts of pyridoxine against biofilm-embedded S. aureus and S. epidermidis cells. Bacteria were grown for 72 h to form a rigid biofilm. Next the medium was replaced by the fresh one after double washing to remove nonadherent cells; compounds were added as indicated followed by 24 h incubation. Afterwards the number of viable cells was evaluated by staining the cells with propidium iodide and acridine orange. The estimated percentage of nonviable cells is given in the lower right corner of each panel. Magnification ×63.
Figure Legend Snippet: The antibacterial effect of quaternary ammonium salts of pyridoxine against biofilm-embedded S. aureus and S. epidermidis cells. Bacteria were grown for 72 h to form a rigid biofilm. Next the medium was replaced by the fresh one after double washing to remove nonadherent cells; compounds were added as indicated followed by 24 h incubation. Afterwards the number of viable cells was evaluated by staining the cells with propidium iodide and acridine orange. The estimated percentage of nonviable cells is given in the lower right corner of each panel. Magnification ×63.

Techniques Used: Incubation, Staining

7) Product Images from "The impact of absorbed photons on antimicrobial photodynamic efficacy"

Article Title: The impact of absorbed photons on antimicrobial photodynamic efficacy

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2015.00706

Enzyme-linked lectinsorbent assay (ELLA) . ELLA applied on 72 h E. faecalis and A. naeslundii monospecies biofilms for confirmation of EPS. Blue dots represent original measured values, red solid line represents the fit of the sigmoideal curve and red dashed lines depict 95% confidence intervals. r 2 denotes the correlation coefficient. (A) ELLA on E. faecalis monospecies biofilm. (B) ELLA on A. naeslundii monospecies biofilm.
Figure Legend Snippet: Enzyme-linked lectinsorbent assay (ELLA) . ELLA applied on 72 h E. faecalis and A. naeslundii monospecies biofilms for confirmation of EPS. Blue dots represent original measured values, red solid line represents the fit of the sigmoideal curve and red dashed lines depict 95% confidence intervals. r 2 denotes the correlation coefficient. (A) ELLA on E. faecalis monospecies biofilm. (B) ELLA on A. naeslundii monospecies biofilm.

Techniques Used:

Photodynamic inactivation of AN and EF monospecies biofilms . All PIB results are shown as CFU medians with 25 and 75% quantiles depicted on a log 10 scaled ordinate. Medians on or below the solid and dashed lines represent CFU reductions of ≥ 3 log 10 and ≥ 5 log 10 steps, respectively, compared to untreated control groups PS-L-. (A) PIB against E. faecalis monospecies biofilm using SAPYR (number of absorbed photons: 6.78 × 10 18 ; energy dose: 30 J/cm 2 ): PIB group PS+L+ (yellow) shows a reduction by 5.1 log 10 steps CFU. (B) PIB against A. naeslundii monospecies biofilm using SAPYR (number of absorbed photons: 6.78 × 10 18 ; energy dose: 30 J/cm 2 ): PIB group PS+L+ (yellow) shows a reduction by 6.5 log 10 steps CFU. PS-L+ group shows a reduction by 0.5 log 10 steps CFU. (C) PIB against E. faecalis monospecies biofilm using MB (adjusted energy dose: 30 J/cm 2 ; corresponding number of absorbed photons: 56.5 × 10 18 ): PIB group PS+L+ (blue) shows a reduction by 3.4 log 10 steps CFU. (D) PIB against A. naeslundii monospecies biofilm using MB (adjusted energy dose: 30 J/cm 2 ; corresponding number of absorbed photons: 56.5 × 10 18 ): PIB group PS+L+ (blue) shows a reduction by 4.2 log 10 steps CFU. PS-L+ group shows a reduction by 1.2 log 10 steps CFU. (E) PIB against E. faecalis monospecies biofilm using MB (adjusted number of absorbed photons: 6.78 × 10 18 ; corresponding energy dose: 3.6 J/cm 2 ): PIB group PS+L+ (blue) shows no reduction of CFU. (F) PIB against A. naeslundii monospecies biofilm using MB (adjusted number of absorbed photons: 6.78 × 10 18 ; corresponding energy dose: 3.6 J/cm 2 ): PIB group PS+L+ (blue) shows no reduction of CFU.
Figure Legend Snippet: Photodynamic inactivation of AN and EF monospecies biofilms . All PIB results are shown as CFU medians with 25 and 75% quantiles depicted on a log 10 scaled ordinate. Medians on or below the solid and dashed lines represent CFU reductions of ≥ 3 log 10 and ≥ 5 log 10 steps, respectively, compared to untreated control groups PS-L-. (A) PIB against E. faecalis monospecies biofilm using SAPYR (number of absorbed photons: 6.78 × 10 18 ; energy dose: 30 J/cm 2 ): PIB group PS+L+ (yellow) shows a reduction by 5.1 log 10 steps CFU. (B) PIB against A. naeslundii monospecies biofilm using SAPYR (number of absorbed photons: 6.78 × 10 18 ; energy dose: 30 J/cm 2 ): PIB group PS+L+ (yellow) shows a reduction by 6.5 log 10 steps CFU. PS-L+ group shows a reduction by 0.5 log 10 steps CFU. (C) PIB against E. faecalis monospecies biofilm using MB (adjusted energy dose: 30 J/cm 2 ; corresponding number of absorbed photons: 56.5 × 10 18 ): PIB group PS+L+ (blue) shows a reduction by 3.4 log 10 steps CFU. (D) PIB against A. naeslundii monospecies biofilm using MB (adjusted energy dose: 30 J/cm 2 ; corresponding number of absorbed photons: 56.5 × 10 18 ): PIB group PS+L+ (blue) shows a reduction by 4.2 log 10 steps CFU. PS-L+ group shows a reduction by 1.2 log 10 steps CFU. (E) PIB against E. faecalis monospecies biofilm using MB (adjusted number of absorbed photons: 6.78 × 10 18 ; corresponding energy dose: 3.6 J/cm 2 ): PIB group PS+L+ (blue) shows no reduction of CFU. (F) PIB against A. naeslundii monospecies biofilm using MB (adjusted number of absorbed photons: 6.78 × 10 18 ; corresponding energy dose: 3.6 J/cm 2 ): PIB group PS+L+ (blue) shows no reduction of CFU.

Techniques Used:

8) Product Images from "Evaluation of Phototrophic Stream Biofilms Under Stress: Comparing Traditional and Novel Ecotoxicological Endpoints After Exposure to Diuron"

Article Title: Evaluation of Phototrophic Stream Biofilms Under Stress: Comparing Traditional and Novel Ecotoxicological Endpoints After Exposure to Diuron

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2018.02974

FC-CS in diuron-treated stream biofilms. (A) Biofilms were assessed by flow cytometry after sampling on d 0 , d 7 , d 14 , and d 21 , and altogether mapped by viSNE. viSNE maps are shown in single color, with each point in the viSNE map representing a single cell or particle from the biofilms or (B) ). (C) ) allowed for assigning subpopulations to types of organisms and potentially decaying cells.
Figure Legend Snippet: FC-CS in diuron-treated stream biofilms. (A) Biofilms were assessed by flow cytometry after sampling on d 0 , d 7 , d 14 , and d 21 , and altogether mapped by viSNE. viSNE maps are shown in single color, with each point in the viSNE map representing a single cell or particle from the biofilms or (B) ). (C) ) allowed for assigning subpopulations to types of organisms and potentially decaying cells.

Techniques Used: Flow Cytometry, Cytometry, Sampling

Extracellular polymeric substances (EPS) extraction of stream biofilm samples after diuron exposure. (A) EPS composition as % of total DOC after 3 weeks. BP, biopolymers; BB, building blocks of humic substances; LMW acids, low molecular weight acids; N/A, neutral/amphiphilic compounds. (B) Protein concentration per extracted DOC (μg/mg) over time. Data is presented as box plots according to Tukey. ∗ , ∗∗ , and ∗∗∗ represent the significant difference between the control and diuron-treated community at d21 ( ∗ P ≤ 0.05, ∗∗ P ≤ 0.01, ∗∗∗ P ≤ 0.001), n = 5.
Figure Legend Snippet: Extracellular polymeric substances (EPS) extraction of stream biofilm samples after diuron exposure. (A) EPS composition as % of total DOC after 3 weeks. BP, biopolymers; BB, building blocks of humic substances; LMW acids, low molecular weight acids; N/A, neutral/amphiphilic compounds. (B) Protein concentration per extracted DOC (μg/mg) over time. Data is presented as box plots according to Tukey. ∗ , ∗∗ , and ∗∗∗ represent the significant difference between the control and diuron-treated community at d21 ( ∗ P ≤ 0.05, ∗∗ P ≤ 0.01, ∗∗∗ P ≤ 0.001), n = 5.

Techniques Used: Molecular Weight, Protein Concentration

9) Product Images from "Antimicrobial Activity and Cell Selectivity of Synthetic and Biosynthetic Cationic Polymers"

Article Title: Antimicrobial Activity and Cell Selectivity of Synthetic and Biosynthetic Cationic Polymers

Journal: Antimicrobial Agents and Chemotherapy

doi: 10.1128/AAC.00469-17

Antibiofilm properties of cationic polymers. A PAO1-gfp biofilm was grown on a microslide for 24 h and treated with various cationic polymers at 10× MIC. The MIC of εPL against this strain was 16 μg/ml. Live/Dead cell staining was imaged by using confocal fluorescence microscopy. (a) Untreated cells; (b) εPL-treated cells; (c) LPEI-treated cells; (d) polymyxin B (PM B)-treated cells; (e) dead biovolume estimated from six different fluorescence images; (f) biomass reduction as shown by a resazurin assay ( AR 560 ) after treatment with the polymers/antiseptic agents for 24 h; (g) bacterial viability after the addition of polymers/antiseptic agents to preformed biofilms. A.U, arbitrary units.
Figure Legend Snippet: Antibiofilm properties of cationic polymers. A PAO1-gfp biofilm was grown on a microslide for 24 h and treated with various cationic polymers at 10× MIC. The MIC of εPL against this strain was 16 μg/ml. Live/Dead cell staining was imaged by using confocal fluorescence microscopy. (a) Untreated cells; (b) εPL-treated cells; (c) LPEI-treated cells; (d) polymyxin B (PM B)-treated cells; (e) dead biovolume estimated from six different fluorescence images; (f) biomass reduction as shown by a resazurin assay ( AR 560 ) after treatment with the polymers/antiseptic agents for 24 h; (g) bacterial viability after the addition of polymers/antiseptic agents to preformed biofilms. A.U, arbitrary units.

Techniques Used: Staining, Fluorescence, Microscopy, Resazurin Assay

10) Product Images from "Potentiation of Azole Antifungals by 2-Adamantanamine"

Article Title: Potentiation of Azole Antifungals by 2-Adamantanamine

Journal: Antimicrobial Agents and Chemotherapy

doi: 10.1128/AAC.00294-13

Potentiation of miconazole action against C. albicans biofilms by AC17. (A) Dose response of AC17 in combination with a subinhibitory miconazole concentration (50 μg/ml). Percent inhibition of resazurin reduction was calculated based on miconazole-alone
Figure Legend Snippet: Potentiation of miconazole action against C. albicans biofilms by AC17. (A) Dose response of AC17 in combination with a subinhibitory miconazole concentration (50 μg/ml). Percent inhibition of resazurin reduction was calculated based on miconazole-alone

Techniques Used: Concentration Assay, Inhibition

11) Product Images from "Direct Comparison of Physical Properties of Bacillus subtilis NCIB 3610 and B-1 Biofilms"

Article Title: Direct Comparison of Physical Properties of Bacillus subtilis NCIB 3610 and B-1 Biofilms

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.03957-15

Surface stiffness of different B. subtilis biofilms. Young's modulus values were obtained for 1-day-old biofilms of the wild-type strains B. subtilis B-1 (red) and NCIB 3610 (blue) and three mutant strains of NCIB 3610 (blue). Error bars are Gaussian
Figure Legend Snippet: Surface stiffness of different B. subtilis biofilms. Young's modulus values were obtained for 1-day-old biofilms of the wild-type strains B. subtilis B-1 (red) and NCIB 3610 (blue) and three mutant strains of NCIB 3610 (blue). Error bars are Gaussian

Techniques Used: Mutagenesis

Bulk viscoelasticity of B. subtilis biofilms. (A) Storage modulus values for 1-day-old biofilms of wild-type strains B. subtilis B-1 (red) and NCIB 3610 (blue) and three mutant strains of NCIB 3610 (blue); (B) storage modulus values for 1-day-old biofilms
Figure Legend Snippet: Bulk viscoelasticity of B. subtilis biofilms. (A) Storage modulus values for 1-day-old biofilms of wild-type strains B. subtilis B-1 (red) and NCIB 3610 (blue) and three mutant strains of NCIB 3610 (blue); (B) storage modulus values for 1-day-old biofilms

Techniques Used: Mutagenesis

One-day-old B-1 biofilms express the genes ywsC , blsA , tasA , and epsH .
Figure Legend Snippet: One-day-old B-1 biofilms express the genes ywsC , blsA , tasA , and epsH .

Techniques Used:

Surface roughness of different B. subtilis biofilms. The root mean squared surface roughness was determined for 1-day-old biofilms of wild-type B. subtilis strains B-1 (red) and NCIB 3610 (blue) and three mutant strains of NCIB 3610 (blue). (A) Profilometer
Figure Legend Snippet: Surface roughness of different B. subtilis biofilms. The root mean squared surface roughness was determined for 1-day-old biofilms of wild-type B. subtilis strains B-1 (red) and NCIB 3610 (blue) and three mutant strains of NCIB 3610 (blue). (A) Profilometer

Techniques Used: Mutagenesis

mRNA production of genes for biofilm matrix proteins in B. subtilis strain B-1. Gene expression analyses were performed for biofilms generated by wild-type strain B-1, at 10 h (A) and 18 h (B) of biofilm growth. The mRNA production of genes corresponding
Figure Legend Snippet: mRNA production of genes for biofilm matrix proteins in B. subtilis strain B-1. Gene expression analyses were performed for biofilms generated by wild-type strain B-1, at 10 h (A) and 18 h (B) of biofilm growth. The mRNA production of genes corresponding

Techniques Used: Expressing, Generated

Images of plated B. subtilis biofilms immediately after the application of 99% ethanol. Images were obtained for the wild-type strains B. subtilis B-1 (red) and NCIB 3610 and three mutant strains of NCIB 3610 (blue). Scale bars, 1 mm.
Figure Legend Snippet: Images of plated B. subtilis biofilms immediately after the application of 99% ethanol. Images were obtained for the wild-type strains B. subtilis B-1 (red) and NCIB 3610 and three mutant strains of NCIB 3610 (blue). Scale bars, 1 mm.

Techniques Used: Mutagenesis

Comparison of normalized total and dry masses of biofilms formed by the wild-type strains NCIB 3610 and B-1. This bar plot shows the total produced masses of 1-day-old biofilms of the wild-type strains NCIB 3610 (blue) and B-1 (red), as well as the dry
Figure Legend Snippet: Comparison of normalized total and dry masses of biofilms formed by the wild-type strains NCIB 3610 and B-1. This bar plot shows the total produced masses of 1-day-old biofilms of the wild-type strains NCIB 3610 (blue) and B-1 (red), as well as the dry

Techniques Used: Produced

12) Product Images from "In vivo biofilm formation on stainless steel bonded retainers during different oral health-care regimens"

Article Title: In vivo biofilm formation on stainless steel bonded retainers during different oral health-care regimens

Journal: International Journal of Oral Science

doi: 10.1038/ijos.2014.69

Scanning electron micrographs of 1-week-old biofilms formed in vivo during use of a toothpaste without antibacterial claims. ( a – c ) Single-strand wire. ( d – f ) Multi-strand wire.
Figure Legend Snippet: Scanning electron micrographs of 1-week-old biofilms formed in vivo during use of a toothpaste without antibacterial claims. ( a – c ) Single-strand wire. ( d – f ) Multi-strand wire.

Techniques Used: In Vivo

13) Product Images from "Flagellated but Not Hyperfimbriated Salmonella enterica Serovar Typhimurium Attaches to and Forms Biofilms on Cholesterol-Coated Surfaces ▿ Serovar Typhimurium Attaches to and Forms Biofilms on Cholesterol-Coated Surfaces ▿ †"

Article Title: Flagellated but Not Hyperfimbriated Salmonella enterica Serovar Typhimurium Attaches to and Forms Biofilms on Cholesterol-Coated Surfaces ▿ Serovar Typhimurium Attaches to and Forms Biofilms on Cholesterol-Coated Surfaces ▿ †

Journal: Journal of Bacteriology

doi: 10.1128/JB.01620-09

Overexpression of type 1 fimbriae inhibits biofilm formation on cholesterol-coated surfaces, while normal or decreased expression of type 1 fimbriae has no effect. Biofilm formation by serovar Typhimurium strains grown with 3% crude ox bile extract
Figure Legend Snippet: Overexpression of type 1 fimbriae inhibits biofilm formation on cholesterol-coated surfaces, while normal or decreased expression of type 1 fimbriae has no effect. Biofilm formation by serovar Typhimurium strains grown with 3% crude ox bile extract

Techniques Used: Over Expression, Expressing

Schematic diagram of Tn 10 d transposon insertion sites in serovar Typhimurium cholesterol biofilm mutants with mutations affecting type 1 fimbria and flagellum structure and biogenesis. The arrows indicate the sizes and orientations of neighboring genes,
Figure Legend Snippet: Schematic diagram of Tn 10 d transposon insertion sites in serovar Typhimurium cholesterol biofilm mutants with mutations affecting type 1 fimbria and flagellum structure and biogenesis. The arrows indicate the sizes and orientations of neighboring genes,

Techniques Used:

Dead salmonellae bound to cholesterol provide a scaffold for biofilm formation by live cells.
Figure Legend Snippet: Dead salmonellae bound to cholesterol provide a scaffold for biofilm formation by live cells.

Techniques Used:

Flagella are necessary for biofilm formation on cholesterol-coated surfaces, whereas motility is dispensable. Serovar Typhimurium strains were grown with and without 3% crude ox bile extract and added to cholesterol-coated Eppendorf tubes. Biofilms
Figure Legend Snippet: Flagella are necessary for biofilm formation on cholesterol-coated surfaces, whereas motility is dispensable. Serovar Typhimurium strains were grown with and without 3% crude ox bile extract and added to cholesterol-coated Eppendorf tubes. Biofilms

Techniques Used:

14) Product Images from "Epiphytic bacterial community composition on two common submerged macrophytes in brackish water and freshwater"

Article Title: Epiphytic bacterial community composition on two common submerged macrophytes in brackish water and freshwater

Journal: BMC Microbiology

doi: 10.1186/1471-2180-8-58

Biofilm composition in Lake Constance (left) and Schaproder Bodden (right) . A and B, M. spicatum upper section; C and D, C. aspera upper section; E and F, M. spicatum lower section; G and H, C. aspera lower section. n = 3; errors bars indicate SD. ALF: alphaproteobacteria; BET: betaproteobacteria; GAM: gammaproteobacteria; PLA: planctomycetes; HGC: actinomycetes; CFB: Cytophaga-Flavobacteria-Bacteroidetes.
Figure Legend Snippet: Biofilm composition in Lake Constance (left) and Schaproder Bodden (right) . A and B, M. spicatum upper section; C and D, C. aspera upper section; E and F, M. spicatum lower section; G and H, C. aspera lower section. n = 3; errors bars indicate SD. ALF: alphaproteobacteria; BET: betaproteobacteria; GAM: gammaproteobacteria; PLA: planctomycetes; HGC: actinomycetes; CFB: Cytophaga-Flavobacteria-Bacteroidetes.

Techniques Used: Proximity Ligation Assay

15) Product Images from "Microcosm biofilms cultured from different oral niches in periodontitis patients"

Article Title: Microcosm biofilms cultured from different oral niches in periodontitis patients

Journal: Journal of Oral Microbiology

doi: 10.1080/20022727.2018.1551596

Bray-Curtis (BC) similarity between the subgingival inoculum and all other inocula and all biofilms (a). BC similarity between the subgingival inoculum and the other inocula. (b). BC similarity between the subgingival inoculum and 14 d biofilms. (c). BC similarity between the subgingival inoculum and 28 d biofilms.
Figure Legend Snippet: Bray-Curtis (BC) similarity between the subgingival inoculum and all other inocula and all biofilms (a). BC similarity between the subgingival inoculum and the other inocula. (b). BC similarity between the subgingival inoculum and 14 d biofilms. (c). BC similarity between the subgingival inoculum and 28 d biofilms.

Techniques Used:

Bray-Curtis (BC) similarity between inocula and their corresponding biofilms. BC similarity between inocula and 14 d biofilms and between 14 d biofilms and 28 d biofilms shown per patient and per niche, respectively.
Figure Legend Snippet: Bray-Curtis (BC) similarity between inocula and their corresponding biofilms. BC similarity between inocula and 14 d biofilms and between 14 d biofilms and 28 d biofilms shown per patient and per niche, respectively.

Techniques Used:

Principal component analysis (PCA) plots from biofilms. (a). PCA plot per niche. Each color represents a different niche, as follows: Black – Saliva, Aqua – Subgingival, Blue – Tongue (brush), Green – Tongue (scraper), Red – Tonsils. Differences between niches were statistically significant (PERMANOVA; p = 0.0001; F = 6.93). Pairwise comparisons showed significant differences between biofilms from all niches (p = 0.0001) except between biofilms grown from saliva and tongue (scraper) (p = 0.08) and biofilms grown from tongue (brush) and tongue (scraper) (p = 0.12). (b). PCA plot per patient. Each color represents a different patient, as follows: Black – Patient 1, Aqua – Patient 2, Blue – Patient 3, Green – Patient 4, Red – Patient 5. Differences between patients were statistically significant (PERMANOVA; p = 0.0001; F = 33.72) and pairwise comparisons showed significant differences as well (p = 0.0001 in all cases).
Figure Legend Snippet: Principal component analysis (PCA) plots from biofilms. (a). PCA plot per niche. Each color represents a different niche, as follows: Black – Saliva, Aqua – Subgingival, Blue – Tongue (brush), Green – Tongue (scraper), Red – Tonsils. Differences between niches were statistically significant (PERMANOVA; p = 0.0001; F = 6.93). Pairwise comparisons showed significant differences between biofilms from all niches (p = 0.0001) except between biofilms grown from saliva and tongue (scraper) (p = 0.08) and biofilms grown from tongue (brush) and tongue (scraper) (p = 0.12). (b). PCA plot per patient. Each color represents a different patient, as follows: Black – Patient 1, Aqua – Patient 2, Blue – Patient 3, Green – Patient 4, Red – Patient 5. Differences between patients were statistically significant (PERMANOVA; p = 0.0001; F = 33.72) and pairwise comparisons showed significant differences as well (p = 0.0001 in all cases).

Techniques Used:

16) Product Images from "Red fluorescent biofilm: the thick, the old, and the cariogenic"

Article Title: Red fluorescent biofilm: the thick, the old, and the cariogenic

Journal: Journal of Oral Microbiology

doi: 10.3402/jom.v8.30346

Principal component analysis (PCA) plot of microbiome samples from all time points. The drawn lines link two samples from the same condition group: at day 7 between different pans, at day 10 and 21 within one pan. Biofilm age is indicated with different colors for the three times-a-day sucrose group (closed circles) and the eight times-a-day sucrose group (open circles). The thickness of all biofilms was 600 µm.
Figure Legend Snippet: Principal component analysis (PCA) plot of microbiome samples from all time points. The drawn lines link two samples from the same condition group: at day 7 between different pans, at day 10 and 21 within one pan. Biofilm age is indicated with different colors for the three times-a-day sucrose group (closed circles) and the eight times-a-day sucrose group (open circles). The thickness of all biofilms was 600 µm.

Techniques Used:

The effect of sucrose frequency on mineral loss and red fluorescence. Mineral loss from dentin plotted against intensity of red fluorescence (total amount of peaks within the red area of the spectrum) in arbitrary units. Biofilm age is indicated with different colors for the three times-a-day sucrose group (closed circles) and the eight times-a-day sucrose group (open circles). Remarkable is the increase in red fluorescence intensity at day 24 (red circles) in both groups. The thickness of all biofilms was 600 µm.
Figure Legend Snippet: The effect of sucrose frequency on mineral loss and red fluorescence. Mineral loss from dentin plotted against intensity of red fluorescence (total amount of peaks within the red area of the spectrum) in arbitrary units. Biofilm age is indicated with different colors for the three times-a-day sucrose group (closed circles) and the eight times-a-day sucrose group (open circles). Remarkable is the increase in red fluorescence intensity at day 24 (red circles) in both groups. The thickness of all biofilms was 600 µm.

Techniques Used: Fluorescence

The effects of biofilm thickness and age on red fluorescence, biofilm grown on Teflon. (a) Example of one CDFF pan per time point (screw thread for pan removal covered), (b) different depth settings of the plugs. (c) Intensity of red fluorescence (peak amplitudes for the different peak wavelengths within the red area of the spectrum) in arbitrary units per biofilm thickness. (d) Intensity of red fluorescence (peak amplitudes for the different peak wavelengths within the red area of the spectrum) in arbitrary units per biofilm age.
Figure Legend Snippet: The effects of biofilm thickness and age on red fluorescence, biofilm grown on Teflon. (a) Example of one CDFF pan per time point (screw thread for pan removal covered), (b) different depth settings of the plugs. (c) Intensity of red fluorescence (peak amplitudes for the different peak wavelengths within the red area of the spectrum) in arbitrary units per biofilm thickness. (d) Intensity of red fluorescence (peak amplitudes for the different peak wavelengths within the red area of the spectrum) in arbitrary units per biofilm age.

Techniques Used: Fluorescence

17) Product Images from "Phenalen-1-one-Mediated Antimicrobial Photodynamic Therapy: Antimicrobial Efficacy in a Periodontal Biofilm Model and Flow Cytometric Evaluation of Cytoplasmic Membrane Damage"

Article Title: Phenalen-1-one-Mediated Antimicrobial Photodynamic Therapy: Antimicrobial Efficacy in a Periodontal Biofilm Model and Flow Cytometric Evaluation of Cytoplasmic Membrane Damage

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2018.00688

Exemplary visualization of polymicrobial biofilms by means of scanning electron microscopy. Exemplary SEM visualization of randomly selected fields of untreated biofilms (PS-L–), biofilms treated with aPDT using SAPYR (SAPYR+L+) or SAGUA (SAGUA+L+) or treated with CHX (CHX 0.2%) in 3,000-fold, 12,000-fold, and 24,000-fold magnification. In the CHX-treated biofilms white arrows show debris most likely originating from killed cells on the top layer of the biofilms.
Figure Legend Snippet: Exemplary visualization of polymicrobial biofilms by means of scanning electron microscopy. Exemplary SEM visualization of randomly selected fields of untreated biofilms (PS-L–), biofilms treated with aPDT using SAPYR (SAPYR+L+) or SAGUA (SAGUA+L+) or treated with CHX (CHX 0.2%) in 3,000-fold, 12,000-fold, and 24,000-fold magnification. In the CHX-treated biofilms white arrows show debris most likely originating from killed cells on the top layer of the biofilms.

Techniques Used: Electron Microscopy

Spectroscopic measurements for release of nucleic acids. OD medians, 1st and 3rd quartiles of the supernatants of biofilms treated with phenalen-1-one mediated aPDT (groups: PS-L–, PS-L+, SAPYR+L-, SAPYR+L+, SAGUA+L-, and SAGUA+L+) or positive control (lysozyme treatment followed by Proteinase K digestion), as measured at 260 nm for release of nucleic acids.
Figure Legend Snippet: Spectroscopic measurements for release of nucleic acids. OD medians, 1st and 3rd quartiles of the supernatants of biofilms treated with phenalen-1-one mediated aPDT (groups: PS-L–, PS-L+, SAPYR+L-, SAPYR+L+, SAGUA+L-, and SAGUA+L+) or positive control (lysozyme treatment followed by Proteinase K digestion), as measured at 260 nm for release of nucleic acids.

Techniques Used: Positive Control

18) Product Images from "Alternative Mating Type Configurations (a/? versus a/a or ?/?) of Candida albicans Result in Alternative Biofilms Regulated by Different PathwaysA Tale of Two Biofilms"

Article Title: Alternative Mating Type Configurations (a/? versus a/a or ?/?) of Candida albicans Result in Alternative Biofilms Regulated by Different PathwaysA Tale of Two Biofilms

Journal: PLoS Biology

doi: 10.1371/journal.pbio.1001117

Alternative models for the regulation of a/α and a/a or α/α biofilms. (A) a /α cells undergo homozygous to a/a or α/α. (B) Regulation of a /α biofilm formation. Question marks refer to unknown signal and receptor of this signal transduction pathway. (C) Regulation of a/a (or α/α) biofilm formation. Regulation of α/α biofilms is assumed to be similar to that of a/a biofilms, for which we have presented evidence. Similar permeability and penetrability characteristics have been demonstrated for a/a and α/α biofilms. pm, plasma membrane.
Figure Legend Snippet: Alternative models for the regulation of a/α and a/a or α/α biofilms. (A) a /α cells undergo homozygous to a/a or α/α. (B) Regulation of a /α biofilm formation. Question marks refer to unknown signal and receptor of this signal transduction pathway. (C) Regulation of a/a (or α/α) biofilm formation. Regulation of α/α biofilms is assumed to be similar to that of a/a biofilms, for which we have presented evidence. Similar permeability and penetrability characteristics have been demonstrated for a/a and α/α biofilms. pm, plasma membrane.

Techniques Used: Transduction, Permeability

The MAP kinase response pathway plays no role in a/α biofilm formation. Deletion mutants generated in a /α cells of strain SC5314 for the α-pheromone receptor ( ste2/ste2 ) and the MAP kinases ( ste11/ste11 , hst7/hst7 , cek1/cek1 cek2/cek2 ), components of the upstream portion of the pheromone response pathway (see Table S2 for mutant origins and genotypes), formed normal a /α biofilms. The deletion mutant of CPH1 , which encodes the targeted transcription factor in the opaque cell pheromone response, also formed normal biofilms. Overexpression of STE11 in a wild type background by adding doxycycline to strain SC5314- TETp - STE11 did not enhance biofilm formation. However, deletion of TEC1 , which encodes the targeted transcription factor in the pheromone response pathway of white a/a cell biofilm formation, blocked a /α biofilm formation, as previously described [31] . (A) Quantitation of adhesion to a plastic surface after 16 h. (B) Images of adhesion of select strains to the plastic surface of wells after 16 h. (C) Biomass of biofilms formed after 48 h on a silicone elastomer surface. (D) ß-glucan released into the medium by 48 h biofilms. (E) Thickness of 48 h biofilms. (F) Cell density at the substratum (0 µm) and 20 µm above the substratum (20 µm) for 48 h biofilms of select strains. Data in panels A, C, D, and E are presented as mean ± standard deviation (error bar). Data are from eight measurements, two per biofilm preparation. Dox, doxycycline. Scale bar in panel H equals 100 µm.
Figure Legend Snippet: The MAP kinase response pathway plays no role in a/α biofilm formation. Deletion mutants generated in a /α cells of strain SC5314 for the α-pheromone receptor ( ste2/ste2 ) and the MAP kinases ( ste11/ste11 , hst7/hst7 , cek1/cek1 cek2/cek2 ), components of the upstream portion of the pheromone response pathway (see Table S2 for mutant origins and genotypes), formed normal a /α biofilms. The deletion mutant of CPH1 , which encodes the targeted transcription factor in the opaque cell pheromone response, also formed normal biofilms. Overexpression of STE11 in a wild type background by adding doxycycline to strain SC5314- TETp - STE11 did not enhance biofilm formation. However, deletion of TEC1 , which encodes the targeted transcription factor in the pheromone response pathway of white a/a cell biofilm formation, blocked a /α biofilm formation, as previously described [31] . (A) Quantitation of adhesion to a plastic surface after 16 h. (B) Images of adhesion of select strains to the plastic surface of wells after 16 h. (C) Biomass of biofilms formed after 48 h on a silicone elastomer surface. (D) ß-glucan released into the medium by 48 h biofilms. (E) Thickness of 48 h biofilms. (F) Cell density at the substratum (0 µm) and 20 µm above the substratum (20 µm) for 48 h biofilms of select strains. Data in panels A, C, D, and E are presented as mean ± standard deviation (error bar). Data are from eight measurements, two per biofilm preparation. Dox, doxycycline. Scale bar in panel H equals 100 µm.

Techniques Used: Generated, Mutagenesis, Over Expression, Quantitation Assay, Standard Deviation

Deletion mutants of EFG1 and BCR1 in a/α cells have aberrant phenotypes similar to those of ras1/ras1 , cdc35/cdc35 , and tpk2/tpk2 . See Table S2 for origins and genotype of strains. (A) Quantitation of adhesion to a plastic surface after 16 h. (B) Images of adhesion of select strains to the plastic surface of wells after 16 h. (C) Biomass of biofilms formed on an elastomer surface after 48 h. (D) ß-glucan released into the medium by 48 h biofilms. (E) Thickness of 48 h biofilms. (F) Representative images of cell density at the substratum and 20 µm above the substratum for 48 h biofilms of select strains. Data in panels A, C, D, and E are presented as mean ± standard deviation (error bars). Data are from eight measurements, two per biofilm preparation. (−Dox), in the absence of doxycycline; (+Dox), in the presence of doxycycline. Scale bar in panel F equals 100 µm.
Figure Legend Snippet: Deletion mutants of EFG1 and BCR1 in a/α cells have aberrant phenotypes similar to those of ras1/ras1 , cdc35/cdc35 , and tpk2/tpk2 . See Table S2 for origins and genotype of strains. (A) Quantitation of adhesion to a plastic surface after 16 h. (B) Images of adhesion of select strains to the plastic surface of wells after 16 h. (C) Biomass of biofilms formed on an elastomer surface after 48 h. (D) ß-glucan released into the medium by 48 h biofilms. (E) Thickness of 48 h biofilms. (F) Representative images of cell density at the substratum and 20 µm above the substratum for 48 h biofilms of select strains. Data in panels A, C, D, and E are presented as mean ± standard deviation (error bars). Data are from eight measurements, two per biofilm preparation. (−Dox), in the absence of doxycycline; (+Dox), in the presence of doxycycline. Scale bar in panel F equals 100 µm.

Techniques Used: Quantitation Assay, Standard Deviation

a/α biofilms differ from a/a and α/α biofilms in permeability, antifungal susceptibility, and human leukocyte penetration. Laser scanning confocal microscopy of biofilms was used to image the permeability of SYPRO Ruby and penetration by DiI-labeled human PMNs. The strains had been transformed so that each expressed green fluorescent protein (GFP) under the regulation of the actin promoter. See Table S1 for genotypes. (A, C, E, G, I) GFP fluorescence for assessing biofilm thickness and continuity. (B, D, F, H, J) SYPRO Ruby penetration 30 min after application to top of biofilms. (K through T) Penetrance by DiI-stained PMNs of two representative biofilms of each strain 3 h after the PMNs were dispersed on the top of biofilms. All images are representative of 9 biofilms for each strain and condition. (U) Biofilm thickness, permeation by SYRPO Ruby and penetration by PMNs. (V) Susceptibility to fluconazole, measured by percent cell death assessed with the dye Dead Red. In panels U and V, values are given as means ± standard derivatives. Scale bar for all biofilms (A through T) in panel A equals 50 µm.
Figure Legend Snippet: a/α biofilms differ from a/a and α/α biofilms in permeability, antifungal susceptibility, and human leukocyte penetration. Laser scanning confocal microscopy of biofilms was used to image the permeability of SYPRO Ruby and penetration by DiI-labeled human PMNs. The strains had been transformed so that each expressed green fluorescent protein (GFP) under the regulation of the actin promoter. See Table S1 for genotypes. (A, C, E, G, I) GFP fluorescence for assessing biofilm thickness and continuity. (B, D, F, H, J) SYPRO Ruby penetration 30 min after application to top of biofilms. (K through T) Penetrance by DiI-stained PMNs of two representative biofilms of each strain 3 h after the PMNs were dispersed on the top of biofilms. All images are representative of 9 biofilms for each strain and condition. (U) Biofilm thickness, permeation by SYRPO Ruby and penetration by PMNs. (V) Susceptibility to fluconazole, measured by percent cell death assessed with the dye Dead Red. In panels U and V, values are given as means ± standard derivatives. Scale bar for all biofilms (A through T) in panel A equals 50 µm.

Techniques Used: Permeability, Confocal Microscopy, Labeling, Transformation Assay, Fluorescence, Staining

Efg1 functions downstream of the Ras1/cAMP pathway, but upstream of Tec1. To assess the order of function, wild type genes were placed under the regulation of a tetracycline (doxycycline)-inducable promoter in deletion mutant backgrounds, and tested for biofilm formation in the absence or presence of doxycycline. See Table S2 for origins and genotypes of mutants. (A) Adhesion when EFG1 was overexpressed in the deletion mutants efg1/efg1-TETp-EFG1 , ras1/ras1-TETp-EFG1 , cdc35/cdc35-TETp-EFG1 , tpk1/tpk1-TETp-EFG1 , and tpk2/tpk2-TETp-EFG1 . (B) Gene expression assessed by RT-PCR when EFG1 was overexpressed. (C) Adhesion when TEC1 or BCR1 was overexpressed in mutants efg1/efg1-TETp-TEC1 and efg1/efg1-TETp-BCR1 . (D) Gene expression assessed by RT-PCR when TEC1 or BCR1 was overexpressed in the deletion efg1/efg1 mutant background. (E) Adhesion when EFG1 was overexpressed in the mutant tec1/tec1-TETp-EFG1 or bcr1/bcr1-TETp-EFG1 mutant. (F) Gene expression assessed by RT-PCR when EFG1 was overexpressed in the tec1/tec1 or bcr1/bcr1 mutant background. Data in panels A, C, and E are presented as mean ± standard deviation for data from eight measurements, two per biofilm. Dox, doxycycline.
Figure Legend Snippet: Efg1 functions downstream of the Ras1/cAMP pathway, but upstream of Tec1. To assess the order of function, wild type genes were placed under the regulation of a tetracycline (doxycycline)-inducable promoter in deletion mutant backgrounds, and tested for biofilm formation in the absence or presence of doxycycline. See Table S2 for origins and genotypes of mutants. (A) Adhesion when EFG1 was overexpressed in the deletion mutants efg1/efg1-TETp-EFG1 , ras1/ras1-TETp-EFG1 , cdc35/cdc35-TETp-EFG1 , tpk1/tpk1-TETp-EFG1 , and tpk2/tpk2-TETp-EFG1 . (B) Gene expression assessed by RT-PCR when EFG1 was overexpressed. (C) Adhesion when TEC1 or BCR1 was overexpressed in mutants efg1/efg1-TETp-TEC1 and efg1/efg1-TETp-BCR1 . (D) Gene expression assessed by RT-PCR when TEC1 or BCR1 was overexpressed in the deletion efg1/efg1 mutant background. (E) Adhesion when EFG1 was overexpressed in the mutant tec1/tec1-TETp-EFG1 or bcr1/bcr1-TETp-EFG1 mutant. (F) Gene expression assessed by RT-PCR when EFG1 was overexpressed in the tec1/tec1 or bcr1/bcr1 mutant background. Data in panels A, C, and E are presented as mean ± standard deviation for data from eight measurements, two per biofilm. Dox, doxycycline.

Techniques Used: Mutagenesis, Expressing, Reverse Transcription Polymerase Chain Reaction, Standard Deviation

The activity of Efg1 is regulated by phosphorylation of a threonine, at amino acid 206. The deletion mutant efg1/efg1 was transformed with EFG1T206A , in which threonine was replaced with alanine, thus mimicking the constitutively unphosphorylated state, or with EFG1T206E , in which threonine was replaced with glutamic acid, thus mimicking the constitutively phosphorylated state. Both EFG1T206A and EFG1T206E were placed under the regulation of the tetracycline (doxycycline)-inducible promoter to generate strains efg1/efg1-TETp-EFG1T206A and efg1/efg1-TETp-EFG1T206E. The transform ation constructs were tagged with GFP (see Table S2 for genotypes). Efg1 had previously been shown to be regulated by phosphorylation at threonine 206 [60] . (A) Levels of expression of Efg1 measured by western blot staining with anti-GFP antibody. (B) Quantitation of adhesion to a plastic surface after 16 h. (C) Images of adhesion by selective strains to the plastic surface after 16 h. (D) Biomass of biofilms formed on a silicone elastomer surface after 48 h. (E) ß-glucan released into the medium by 48 h biofilms. (F) Gene expression using RT-PCR of 48 h biofilms. Data in panels B, D, and E are presented as the means ± standard deviation. Data are from eight measurements, two per biofilm preparation.
Figure Legend Snippet: The activity of Efg1 is regulated by phosphorylation of a threonine, at amino acid 206. The deletion mutant efg1/efg1 was transformed with EFG1T206A , in which threonine was replaced with alanine, thus mimicking the constitutively unphosphorylated state, or with EFG1T206E , in which threonine was replaced with glutamic acid, thus mimicking the constitutively phosphorylated state. Both EFG1T206A and EFG1T206E were placed under the regulation of the tetracycline (doxycycline)-inducible promoter to generate strains efg1/efg1-TETp-EFG1T206A and efg1/efg1-TETp-EFG1T206E. The transform ation constructs were tagged with GFP (see Table S2 for genotypes). Efg1 had previously been shown to be regulated by phosphorylation at threonine 206 [60] . (A) Levels of expression of Efg1 measured by western blot staining with anti-GFP antibody. (B) Quantitation of adhesion to a plastic surface after 16 h. (C) Images of adhesion by selective strains to the plastic surface after 16 h. (D) Biomass of biofilms formed on a silicone elastomer surface after 48 h. (E) ß-glucan released into the medium by 48 h biofilms. (F) Gene expression using RT-PCR of 48 h biofilms. Data in panels B, D, and E are presented as the means ± standard deviation. Data are from eight measurements, two per biofilm preparation.

Techniques Used: Activity Assay, Mutagenesis, Transformation Assay, Construct, Expressing, Western Blot, Staining, Quantitation Assay, Reverse Transcription Polymerase Chain Reaction, Standard Deviation

The Ras1/cAMP pathway regulates a/α biofilm formation. (A) Key to the mutants used in the analysis of the Ras1/cAMP pathway in panels B through H. SC5314 ( a /α) was the parent strain (see Table S2 for origins and genotypes of mutants). (B) Quantitation of adhesion to a plastic surface after 16 h. (C) Images of adhesion of select strains to the plastic surface of wells after 16 h. (D) Biomass of biofilms formed on a silicone elastomer surface after 4 h. (E) Thickness of 48 h biofilms. (F) ß-glucan released into the media by 48 h biofilms. (G) The expression of three genes ( BCR1 , SUN41 , ALS3 ), which are involved in a /α biofilm formation, assessed by reverse transcription-polymerase chain reaction (RT-PCR). Actin 1 expression is constitutive and used to assess loading. (H) Representative images of cell density at the substrate and 20 µm above the substratum for 48 h biofilms of select strains. Data in panels B, D, E, and F are presented as mean ± standard deviation (error bar). Data are from eight measurements, two per biofilm preparation. (−Met, −Cys), in the absence of methionine and cysteine, a condition that activates the methionine promoter (Metp); (+Dox), in the presence of doxycycline, which activates the tetracycline-inducible promoter (TETp). Scale bar in panel H equals 100 µm.
Figure Legend Snippet: The Ras1/cAMP pathway regulates a/α biofilm formation. (A) Key to the mutants used in the analysis of the Ras1/cAMP pathway in panels B through H. SC5314 ( a /α) was the parent strain (see Table S2 for origins and genotypes of mutants). (B) Quantitation of adhesion to a plastic surface after 16 h. (C) Images of adhesion of select strains to the plastic surface of wells after 16 h. (D) Biomass of biofilms formed on a silicone elastomer surface after 4 h. (E) Thickness of 48 h biofilms. (F) ß-glucan released into the media by 48 h biofilms. (G) The expression of three genes ( BCR1 , SUN41 , ALS3 ), which are involved in a /α biofilm formation, assessed by reverse transcription-polymerase chain reaction (RT-PCR). Actin 1 expression is constitutive and used to assess loading. (H) Representative images of cell density at the substrate and 20 µm above the substratum for 48 h biofilms of select strains. Data in panels B, D, E, and F are presented as mean ± standard deviation (error bar). Data are from eight measurements, two per biofilm preparation. (−Met, −Cys), in the absence of methionine and cysteine, a condition that activates the methionine promoter (Metp); (+Dox), in the presence of doxycycline, which activates the tetracycline-inducible promoter (TETp). Scale bar in panel H equals 100 µm.

Techniques Used: Quantitation Assay, Expressing, Reverse Transcription Polymerase Chain Reaction, Standard Deviation

19) Product Images from "A Novel RNase 3/ECP Peptide for Pseudomonas aeruginosa Biofilm Eradication That Combines Antimicrobial, Lipopolysaccharide Binding, and Cell-Agglutinating Activities"

Article Title: A Novel RNase 3/ECP Peptide for Pseudomonas aeruginosa Biofilm Eradication That Combines Antimicrobial, Lipopolysaccharide Binding, and Cell-Agglutinating Activities

Journal: Antimicrobial Agents and Chemotherapy

doi: 10.1128/AAC.00830-16

Effects against established P. aeruginosa biofilms, determined via confocal microscopy. Live/Dead stain (green and red cells, respectively) and DAPI-FITC and WGA stains (blue and green, respectively) were used. White arrows show bacterial agglutination on the biofilm at a protein/peptide concentration of 10 μM. Bars, 20 μm.
Figure Legend Snippet: Effects against established P. aeruginosa biofilms, determined via confocal microscopy. Live/Dead stain (green and red cells, respectively) and DAPI-FITC and WGA stains (blue and green, respectively) were used. White arrows show bacterial agglutination on the biofilm at a protein/peptide concentration of 10 μM. Bars, 20 μm.

Techniques Used: Confocal Microscopy, Staining, Whole Genome Amplification, Agglutination, Concentration Assay

20) Product Images from "Impact of Nanoclays on the Biodegradation of Poly(Lactic Acid) Nanocomposites"

Article Title: Impact of Nanoclays on the Biodegradation of Poly(Lactic Acid) Nanocomposites

Journal: Polymers

doi: 10.3390/polym10020202

Absorbance (600 nm) of ( a ) PA at 23 °C, and ( b ) CE at 58 °C for second biofilm test. Columns with the same letter within a group (i.e., wells, films, or total) are not significantly different at p ≤ 0.05 (Tukey test).
Figure Legend Snippet: Absorbance (600 nm) of ( a ) PA at 23 °C, and ( b ) CE at 58 °C for second biofilm test. Columns with the same letter within a group (i.e., wells, films, or total) are not significantly different at p ≤ 0.05 (Tukey test).

Techniques Used:

21) Product Images from "Transfer of Microorganisms, Including Listeria monocytogenes, from Various Materials to Beef"

Article Title: Transfer of Microorganisms, Including Listeria monocytogenes, from Various Materials to Beef

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.68.8.4015-4024.2002

Slopes of two-phase curves obtained by plotting the logarithm of the number of CFU transferred to beef as a function of the number of serial contacts with biofilms of Comamonas sp., L. monocytogenes , S. sciuri ( Staph. sciuri ), and P. putida ( Ps. putida ) grown on stainless steel and polymers. (a) Slope 1 ( k 1 ) characterizes the first 3 contacts, and (b) slope 2 ( k 2 ) characterizes the last contacts. The bars represent the confidence intervals from two duplicate experiments.
Figure Legend Snippet: Slopes of two-phase curves obtained by plotting the logarithm of the number of CFU transferred to beef as a function of the number of serial contacts with biofilms of Comamonas sp., L. monocytogenes , S. sciuri ( Staph. sciuri ), and P. putida ( Ps. putida ) grown on stainless steel and polymers. (a) Slope 1 ( k 1 ) characterizes the first 3 contacts, and (b) slope 2 ( k 2 ) characterizes the last contacts. The bars represent the confidence intervals from two duplicate experiments.

Techniques Used:

Differences between the logarithm of the bacterial populations of biofilms of Comamonas sp., L. monocytogenes , S. sciuri ( Staph. sciuri ), and P. putida ( Ps. putida ), and the logarithm of the bacterial populations of the same biofilms, calculated from a count after swabbing (VSD). The bars represent the confidence intervals from two duplicate experiments.
Figure Legend Snippet: Differences between the logarithm of the bacterial populations of biofilms of Comamonas sp., L. monocytogenes , S. sciuri ( Staph. sciuri ), and P. putida ( Ps. putida ), and the logarithm of the bacterial populations of the same biofilms, calculated from a count after swabbing (VSD). The bars represent the confidence intervals from two duplicate experiments.

Techniques Used:

Total CFU transferred to beef by 12 contacts with biofilms of Comamonas sp. (C sp), L. monocytogenes (Lm), S. sciuri , and P. putida ( Ps putida ) on stainless steel (a), on PU (b), and on PVC (c). The bars represent the confidence intervals of two duplicate experiments. The straight line is the bisector.
Figure Legend Snippet: Total CFU transferred to beef by 12 contacts with biofilms of Comamonas sp. (C sp), L. monocytogenes (Lm), S. sciuri , and P. putida ( Ps putida ) on stainless steel (a), on PU (b), and on PVC (c). The bars represent the confidence intervals of two duplicate experiments. The straight line is the bisector.

Techniques Used:

Contact angles measured on the surfaces of cleaned materials; conditioned materials; conditioned and rinsed materials; biofilms of Comamonas sp., L. monocytogenes , S. sciuri ( Staph. sciuri ), and P. putida ( Ps. putida ) on stainless steel, PVC, and PU; and on the surfaces of pieces of beef. Contact angles with water (a), formamide (b), and di-iodomethane (c) are shown. The bars represent the confidence intervals. The results are from two duplicate experiments and 10 measurements per experiment.
Figure Legend Snippet: Contact angles measured on the surfaces of cleaned materials; conditioned materials; conditioned and rinsed materials; biofilms of Comamonas sp., L. monocytogenes , S. sciuri ( Staph. sciuri ), and P. putida ( Ps. putida ) on stainless steel, PVC, and PU; and on the surfaces of pieces of beef. Contact angles with water (a), formamide (b), and di-iodomethane (c) are shown. The bars represent the confidence intervals. The results are from two duplicate experiments and 10 measurements per experiment.

Techniques Used:

Percentage of objects in each of the five object area classes defined for analyzing the two-dimensional structure of biofilms of Comamonas sp., L. monocytogenes , S. sciuri ( Staph. sciuri ), and P. putida ( Ps. putida ) on stainless steel, PU, and PVC. The results are from two duplicate experiments.
Figure Legend Snippet: Percentage of objects in each of the five object area classes defined for analyzing the two-dimensional structure of biofilms of Comamonas sp., L. monocytogenes , S. sciuri ( Staph. sciuri ), and P. putida ( Ps. putida ) on stainless steel, PU, and PVC. The results are from two duplicate experiments.

Techniques Used:

Comparison of the logarithm of the concentration of ConA and WGA required to achieve an OD 405 of 0.8 for biofilms of Comamonas sp., L. monocytogenes , S. sciuri ( Staph. sciuri ), and P. putida ( Ps. putida ). The bars represent the individual standard deviations from one duplicate experiment. When exopolysaccharides were not detectable, the threshold value was used to perform the statistical analysis.
Figure Legend Snippet: Comparison of the logarithm of the concentration of ConA and WGA required to achieve an OD 405 of 0.8 for biofilms of Comamonas sp., L. monocytogenes , S. sciuri ( Staph. sciuri ), and P. putida ( Ps. putida ). The bars represent the individual standard deviations from one duplicate experiment. When exopolysaccharides were not detectable, the threshold value was used to perform the statistical analysis.

Techniques Used: Concentration Assay, Whole Genome Amplification

22) Product Images from "Bacteriophages ?MR299-2 and ?NH-4 Can Eliminate Pseudomonas aeruginosa in the Murine Lung and on Cystic Fibrosis Lung Airway Cells"

Article Title: Bacteriophages ?MR299-2 and ?NH-4 Can Eliminate Pseudomonas aeruginosa in the Murine Lung and on Cystic Fibrosis Lung Airway Cells

Journal: mBio

doi: 10.1128/mBio.00029-12

(A) Growth of lux -tagged Pseudomonas biofilms on the surface of the CFBE410- cell monolayer. Light was measured 1, 5, and 24 h (before and after the monolayer was washed with MEM). (B) Readings from 6 wells are shown. Values are shown as means ± standard deviations (SD) (error bars).
Figure Legend Snippet: (A) Growth of lux -tagged Pseudomonas biofilms on the surface of the CFBE410- cell monolayer. Light was measured 1, 5, and 24 h (before and after the monolayer was washed with MEM). (B) Readings from 6 wells are shown. Values are shown as means ± standard deviations (SD) (error bars).

Techniques Used:

23) Product Images from "Biohybrid Nanostructured Iron Oxide Nanoparticles and Satureja hortensis to Prevent Fungal Biofilm Development"

Article Title: Biohybrid Nanostructured Iron Oxide Nanoparticles and Satureja hortensis to Prevent Fungal Biofilm Development

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms140918110

SEM micrographs indicating the C. albicans biofilm development comparatively on control WDs (after 24 h— a 1 , 48 h— b 1 and 72 h— c 1 incubation time) and on MNP@18-SH coated WDs (after 24 h— a 2 , 48 h— b 2 . and 72 h— c 2 incubation) (2500×). The Candida biofilms developed on the coated WDs are strongly damaged and drastically reduced.
Figure Legend Snippet: SEM micrographs indicating the C. albicans biofilm development comparatively on control WDs (after 24 h— a 1 , 48 h— b 1 and 72 h— c 1 incubation time) and on MNP@18-SH coated WDs (after 24 h— a 2 , 48 h— b 2 . and 72 h— c 2 incubation) (2500×). The Candida biofilms developed on the coated WDs are strongly damaged and drastically reduced.

Techniques Used: Incubation

Graphic representation of viable cell counts analysis after removing C. albicans biofilm embedded cells at 24 h, 48 h and 72 h post inoculation of control and nanobiocoated WDs. * p
Figure Legend Snippet: Graphic representation of viable cell counts analysis after removing C. albicans biofilm embedded cells at 24 h, 48 h and 72 h post inoculation of control and nanobiocoated WDs. * p

Techniques Used:

24) Product Images from "Phenalen-1-one-Mediated Antimicrobial Photodynamic Therapy: Antimicrobial Efficacy in a Periodontal Biofilm Model and Flow Cytometric Evaluation of Cytoplasmic Membrane Damage"

Article Title: Phenalen-1-one-Mediated Antimicrobial Photodynamic Therapy: Antimicrobial Efficacy in a Periodontal Biofilm Model and Flow Cytometric Evaluation of Cytoplasmic Membrane Damage

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2018.00688

Exemplary visualization of polymicrobial biofilms by means of scanning electron microscopy. Exemplary SEM visualization of randomly selected fields of untreated biofilms (PS-L–), biofilms treated with aPDT using SAPYR (SAPYR+L+) or SAGUA (SAGUA+L+) or treated with CHX (CHX 0.2%) in 3,000-fold, 12,000-fold, and 24,000-fold magnification. In the CHX-treated biofilms white arrows show debris most likely originating from killed cells on the top layer of the biofilms.
Figure Legend Snippet: Exemplary visualization of polymicrobial biofilms by means of scanning electron microscopy. Exemplary SEM visualization of randomly selected fields of untreated biofilms (PS-L–), biofilms treated with aPDT using SAPYR (SAPYR+L+) or SAGUA (SAGUA+L+) or treated with CHX (CHX 0.2%) in 3,000-fold, 12,000-fold, and 24,000-fold magnification. In the CHX-treated biofilms white arrows show debris most likely originating from killed cells on the top layer of the biofilms.

Techniques Used: Electron Microscopy

Spectroscopic measurements for release of nucleic acids. OD medians, 1st and 3rd quartiles of the supernatants of biofilms treated with phenalen-1-one mediated aPDT (groups: PS-L–, PS-L+, SAPYR+L-, SAPYR+L+, SAGUA+L-, and SAGUA+L+) or positive control (lysozyme treatment followed by Proteinase K digestion), as measured at 260 nm for release of nucleic acids.
Figure Legend Snippet: Spectroscopic measurements for release of nucleic acids. OD medians, 1st and 3rd quartiles of the supernatants of biofilms treated with phenalen-1-one mediated aPDT (groups: PS-L–, PS-L+, SAPYR+L-, SAPYR+L+, SAGUA+L-, and SAGUA+L+) or positive control (lysozyme treatment followed by Proteinase K digestion), as measured at 260 nm for release of nucleic acids.

Techniques Used: Positive Control

25) Product Images from "Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources"

Article Title: Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources

Journal: PLoS ONE

doi: 10.1371/journal.pone.0231238

Average relative abundance of different archaeal taxa in DNA (left) and RNA (right) libraries from biofilm (upper panels) and sediment (lower panels) after incubation for 7 days ( n = 4) and 30 days ( n = 2) under the different treatment conditions. Con: Control (no addition of organic carbon); D-Arg: D-Arginine; L-Arg: L-Arginine; Trp: Tryptophan; Ptc: Protocatechuate; HA: Humic Acids; Pec: Pectin. The relative abundance of each phylogenetic group is depicted as a percentage of total reads. NOTE: the taxonomical level is not consistent across the displayed taxa to better illustrate changes in the abundance of groups within the phylum Bathyarchaeota and the class Thermoplasmata.
Figure Legend Snippet: Average relative abundance of different archaeal taxa in DNA (left) and RNA (right) libraries from biofilm (upper panels) and sediment (lower panels) after incubation for 7 days ( n = 4) and 30 days ( n = 2) under the different treatment conditions. Con: Control (no addition of organic carbon); D-Arg: D-Arginine; L-Arg: L-Arginine; Trp: Tryptophan; Ptc: Protocatechuate; HA: Humic Acids; Pec: Pectin. The relative abundance of each phylogenetic group is depicted as a percentage of total reads. NOTE: the taxonomical level is not consistent across the displayed taxa to better illustrate changes in the abundance of groups within the phylum Bathyarchaeota and the class Thermoplasmata.

Techniques Used: Incubation

26) Product Images from "Exopolymer Diversity and the Role of Levan in Bacillus subtilis Biofilms"

Article Title: Exopolymer Diversity and the Role of Levan in Bacillus subtilis Biofilms

Journal: PLoS ONE

doi: 10.1371/journal.pone.0062044

Size exclusion liquid chromatography (HPSEC) representative chromatograms of EPS isolated from biofilm (A) and from spent medium below the biofilms (B) grown in three media. SYM (—––); Czapek (– – –), and MSgg (- - - - - -). The molecular weight (M) distributions were graphically split into five size fractions. Their chemical composition and relative abundance of polysaccharides (▪), proteins (▪) and nucleic acids (▪) in these size fractions is graphically represented in A1 and B1. Chemical composition of EPS size fractions was determined from RI (refractive index) chromatograms shown in A and B and from UV 280 and 260 nm chromatograms (not shown).
Figure Legend Snippet: Size exclusion liquid chromatography (HPSEC) representative chromatograms of EPS isolated from biofilm (A) and from spent medium below the biofilms (B) grown in three media. SYM (—––); Czapek (– – –), and MSgg (- - - - - -). The molecular weight (M) distributions were graphically split into five size fractions. Their chemical composition and relative abundance of polysaccharides (▪), proteins (▪) and nucleic acids (▪) in these size fractions is graphically represented in A1 and B1. Chemical composition of EPS size fractions was determined from RI (refractive index) chromatograms shown in A and B and from UV 280 and 260 nm chromatograms (not shown).

Techniques Used: Liquid Chromatography, Isolation, Molecular Weight

Fractions of polysaccharides (▪), proteins (▪) and nucleic acids (▪) in EPS isolated from biofilms (A) and corresponding spent medium below the biofilm (B) grown in three different media. SYM, Czapek, MSgg. The error bars represent standard deviation of the mean (n≥4).
Figure Legend Snippet: Fractions of polysaccharides (▪), proteins (▪) and nucleic acids (▪) in EPS isolated from biofilms (A) and corresponding spent medium below the biofilm (B) grown in three different media. SYM, Czapek, MSgg. The error bars represent standard deviation of the mean (n≥4).

Techniques Used: Isolation, Standard Deviation

Macroscopic (top row) and microscopic (bottom row) images of biofilms (pellicles) grown for 24 h at 37°C in petri dishes in three different media. (A) SYM, (B) Czapek and (C) MSgg. Scale bar represents 10 mm (top row) and 10 µm (bottom row).
Figure Legend Snippet: Macroscopic (top row) and microscopic (bottom row) images of biofilms (pellicles) grown for 24 h at 37°C in petri dishes in three different media. (A) SYM, (B) Czapek and (C) MSgg. Scale bar represents 10 mm (top row) and 10 µm (bottom row).

Techniques Used:

Biofilm (pellicle) thickness at different time points during growth in (A) Czapek (———), Czapek + sucrose (▪ ▪ ▪ ▪ ▪); (B) MSgg (———), MSgg + sucrose (▪ ▪ ▪ ▪ ▪). The errors represent standard deviation of the mean (n≥4).
Figure Legend Snippet: Biofilm (pellicle) thickness at different time points during growth in (A) Czapek (———), Czapek + sucrose (▪ ▪ ▪ ▪ ▪); (B) MSgg (———), MSgg + sucrose (▪ ▪ ▪ ▪ ▪). The errors represent standard deviation of the mean (n≥4).

Techniques Used: Standard Deviation

Images of 9-day old biofilms disintegrated by vortex stirring as observed under stereomicroscope. Scale bar corresponds to 1 mm. Biofilms from (A) MSgg + sucrose, (B) Czapek + sucrose, (C) SYM, (D) MSgg and (E) Czapek growth medium.
Figure Legend Snippet: Images of 9-day old biofilms disintegrated by vortex stirring as observed under stereomicroscope. Scale bar corresponds to 1 mm. Biofilms from (A) MSgg + sucrose, (B) Czapek + sucrose, (C) SYM, (D) MSgg and (E) Czapek growth medium.

Techniques Used:

Expression of the epsA-O-gfp operon in biofilms grown in SYM (▪), Czapek (▪) and MSgg (▪) media given as weighted average of mean normalized fluorescence intensities of individual objects determined by fluorescence microscopy (n≥5).
Figure Legend Snippet: Expression of the epsA-O-gfp operon in biofilms grown in SYM (▪), Czapek (▪) and MSgg (▪) media given as weighted average of mean normalized fluorescence intensities of individual objects determined by fluorescence microscopy (n≥5).

Techniques Used: Expressing, Fluorescence, Microscopy

27) Product Images from "Expression and Purification of Chemokine MIP-3α (CCL20) through a Calmodulin-Fusion Protein System"

Article Title: Expression and Purification of Chemokine MIP-3α (CCL20) through a Calmodulin-Fusion Protein System

Journal: Microorganisms

doi: 10.3390/microorganisms7010008

( A ) The MBIC of tobramycin (circles) or MIP-3α (squares) was determined by the standard crystal violet assay for the quantification of growth inhibition. ( B ) The MBRC of tobramycin (black) or MIP-3α (gray) was determined by an assay with crystal violet, and percentage reduction of the 24-h-old- P. aeruginosa PAO1 biofilm resulting from MIP-3α or tobramycin at 10 dosage levels with 24 h treatment exposures. ( C , D ) The MBEC of tobramycin (circles) or MIP-3α (squares) was determined by an assay with the Calgary biofilm device. P. aeruginosa PAO1 biofilms were exposed to tobramycin or MIP-3α for 24 h. The killing of P. aeruginosa PAO1 biofilms were determined by plate counts.
Figure Legend Snippet: ( A ) The MBIC of tobramycin (circles) or MIP-3α (squares) was determined by the standard crystal violet assay for the quantification of growth inhibition. ( B ) The MBRC of tobramycin (black) or MIP-3α (gray) was determined by an assay with crystal violet, and percentage reduction of the 24-h-old- P. aeruginosa PAO1 biofilm resulting from MIP-3α or tobramycin at 10 dosage levels with 24 h treatment exposures. ( C , D ) The MBEC of tobramycin (circles) or MIP-3α (squares) was determined by an assay with the Calgary biofilm device. P. aeruginosa PAO1 biofilms were exposed to tobramycin or MIP-3α for 24 h. The killing of P. aeruginosa PAO1 biofilms were determined by plate counts.

Techniques Used: Crystal Violet Assay, Inhibition

28) Product Images from "Expression and Purification of Chemokine MIP-3α (CCL20) through a Calmodulin-Fusion Protein System"

Article Title: Expression and Purification of Chemokine MIP-3α (CCL20) through a Calmodulin-Fusion Protein System

Journal: Microorganisms

doi: 10.3390/microorganisms7010008

( A ) The MBIC of tobramycin (circles) or MIP-3α (squares) was determined by the standard crystal violet assay for the quantification of growth inhibition. ( B ) The MBRC of tobramycin (black) or MIP-3α (gray) was determined by an assay with crystal violet, and percentage reduction of the 24-h-old- P. aeruginosa PAO1 biofilm resulting from MIP-3α or tobramycin at 10 dosage levels with 24 h treatment exposures. ( C , D ) The MBEC of tobramycin (circles) or MIP-3α (squares) was determined by an assay with the Calgary biofilm device. P. aeruginosa PAO1 biofilms were exposed to tobramycin or MIP-3α for 24 h. The killing of P. aeruginosa PAO1 biofilms were determined by plate counts.
Figure Legend Snippet: ( A ) The MBIC of tobramycin (circles) or MIP-3α (squares) was determined by the standard crystal violet assay for the quantification of growth inhibition. ( B ) The MBRC of tobramycin (black) or MIP-3α (gray) was determined by an assay with crystal violet, and percentage reduction of the 24-h-old- P. aeruginosa PAO1 biofilm resulting from MIP-3α or tobramycin at 10 dosage levels with 24 h treatment exposures. ( C , D ) The MBEC of tobramycin (circles) or MIP-3α (squares) was determined by an assay with the Calgary biofilm device. P. aeruginosa PAO1 biofilms were exposed to tobramycin or MIP-3α for 24 h. The killing of P. aeruginosa PAO1 biofilms were determined by plate counts.

Techniques Used: Crystal Violet Assay, Inhibition

29) Product Images from "Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules"

Article Title: Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules

Journal: mSystems

doi: 10.1128/mSystems.00058-17

Hierarchical cluster analysis of reproducible parent masses (MS) representative of produced SMs from oral in vitro -grown biofilm representing > 100 bacterial species. MS profiles from replicate growth medium extracts were obtained from several growth stages: from 0 h (the time point when saliva was inoculated into SHI medium) to 21 h of incubation in SHI medium and sucrose. Pearson correlation distances are shown at tree branches. Distinct clusters of MS profiles are shown as colored leaves on the tree. Yellow leaves, 0 h of growth (0H) with saliva inoculated in SHI medium and sucrose; red leaves, 3 and 6 h of growth (3H and 6H, respectively); blue leaves, 9 and 13 h of growth (9H and 13H, respectively); black leaves, 17, 19, and 21 h of growth (17H, 19H, and 21H, respectively).
Figure Legend Snippet: Hierarchical cluster analysis of reproducible parent masses (MS) representative of produced SMs from oral in vitro -grown biofilm representing > 100 bacterial species. MS profiles from replicate growth medium extracts were obtained from several growth stages: from 0 h (the time point when saliva was inoculated into SHI medium) to 21 h of incubation in SHI medium and sucrose. Pearson correlation distances are shown at tree branches. Distinct clusters of MS profiles are shown as colored leaves on the tree. Yellow leaves, 0 h of growth (0H) with saliva inoculated in SHI medium and sucrose; red leaves, 3 and 6 h of growth (3H and 6H, respectively); blue leaves, 9 and 13 h of growth (9H and 13H, respectively); black leaves, 17, 19, and 21 h of growth (17H, 19H, and 21H, respectively).

Techniques Used: Mass Spectrometry, Produced, In Vitro, Incubation

Hierarchical cluster analysis and multidimensional scaling (MDS) analysis of replicate parent mass profiles of growth extracts from oral isolates and the in vitro biofilm community from liquid chromatography mass spectrometry (LC-MS). The tree topography shows Pearson correlation distance measures at tree branches (left panel). MDS ordinations for each time point are presented in the right panel. (a) Clustering of replicate growth extracts (a and b) from bacterial isolates and the in vitro biofilm community (Bio24a and -b) at 24 h of growth. (b) Clustering of replicate growth extracts (a and b) from bacterial isolates and the in vitro biofilm community (Bio72a and -b) at 72 h of growth. Abbreviations: Ab, Actinomyces bovis ; An, Actinomyces naeslundii ; Ao, Actinomyces odontolyticus ; Bio, in vitro biofilm community; Fn, Fusobacterium nucleatum ; Fp, Fusobacterium periodonticum ; Lf, Lactobacillus fermentum SHI-2; Pg, Porphyromonas gingivalis ; Si, S. infantis ; Spn, S. pneumoniae ; Sv, S. vestibularis ; Sm, S. mitis ; So, S. oralis ; Ss, S. salivarius SHI-3; Spa, S. parasanguinis ; Vp, Veillonella parvula SHI-1.
Figure Legend Snippet: Hierarchical cluster analysis and multidimensional scaling (MDS) analysis of replicate parent mass profiles of growth extracts from oral isolates and the in vitro biofilm community from liquid chromatography mass spectrometry (LC-MS). The tree topography shows Pearson correlation distance measures at tree branches (left panel). MDS ordinations for each time point are presented in the right panel. (a) Clustering of replicate growth extracts (a and b) from bacterial isolates and the in vitro biofilm community (Bio24a and -b) at 24 h of growth. (b) Clustering of replicate growth extracts (a and b) from bacterial isolates and the in vitro biofilm community (Bio72a and -b) at 72 h of growth. Abbreviations: Ab, Actinomyces bovis ; An, Actinomyces naeslundii ; Ao, Actinomyces odontolyticus ; Bio, in vitro biofilm community; Fn, Fusobacterium nucleatum ; Fp, Fusobacterium periodonticum ; Lf, Lactobacillus fermentum SHI-2; Pg, Porphyromonas gingivalis ; Si, S. infantis ; Spn, S. pneumoniae ; Sv, S. vestibularis ; Sm, S. mitis ; So, S. oralis ; Ss, S. salivarius SHI-3; Spa, S. parasanguinis ; Vp, Veillonella parvula SHI-1.

Techniques Used: In Vitro, Liquid Chromatography, Mass Spectrometry, Liquid Chromatography with Mass Spectroscopy

Flowchart of approaches employed to putatively annotate PMSs secreted from oral bacteria. (Step 1) A highly diverse in vitro biofilm community and single isolates of bacteria were grown in 1-ml cultures in a 24-well format. For the experimental setup, see Fig. S1 . To identify parent masses and their corresponding ion fragment profiles in each sample, growth extracts were analyzed with an UltiMate 3000 UHPLC system and a Maxis qTOF mass spectrometer equipped with an electrospray ionization (ESI) source. (Steps 2A and B) Parent masses obtained from replicate samples were sorted into bucket tables and compared between time points (step 2A) and between bacterial isolates (step 2B) by using Venn diagrams and cluster analyses. (Steps 3A and B) The Global Natural Products Social Networks infrastructure ( 22 ) was employed to putatively annotate MS/MS spectra by spectral alignments of query spectra with ~20,000 benchmarked MS/MS spectra in the GNPS library (step 3A). GNPS networks revealed associations between query spectra and benchmark spectra, which contributed to level 2 annotations of ~50 PSMs (step 3B). (Steps 4A and B) The DEREPLICATOR tool ( 23 ) was used to annotate MS/MS spectra and predict the probability of each annotation by calculating false discovery rate (FDR) scores (step 4A). These annotations were based on structural homologies with PMS in databases such as PubMed and correspond to level 2 annotation standards (step 4B).
Figure Legend Snippet: Flowchart of approaches employed to putatively annotate PMSs secreted from oral bacteria. (Step 1) A highly diverse in vitro biofilm community and single isolates of bacteria were grown in 1-ml cultures in a 24-well format. For the experimental setup, see Fig. S1 . To identify parent masses and their corresponding ion fragment profiles in each sample, growth extracts were analyzed with an UltiMate 3000 UHPLC system and a Maxis qTOF mass spectrometer equipped with an electrospray ionization (ESI) source. (Steps 2A and B) Parent masses obtained from replicate samples were sorted into bucket tables and compared between time points (step 2A) and between bacterial isolates (step 2B) by using Venn diagrams and cluster analyses. (Steps 3A and B) The Global Natural Products Social Networks infrastructure ( 22 ) was employed to putatively annotate MS/MS spectra by spectral alignments of query spectra with ~20,000 benchmarked MS/MS spectra in the GNPS library (step 3A). GNPS networks revealed associations between query spectra and benchmark spectra, which contributed to level 2 annotations of ~50 PSMs (step 3B). (Steps 4A and B) The DEREPLICATOR tool ( 23 ) was used to annotate MS/MS spectra and predict the probability of each annotation by calculating false discovery rate (FDR) scores (step 4A). These annotations were based on structural homologies with PMS in databases such as PubMed and correspond to level 2 annotation standards (step 4B).

Techniques Used: In Vitro, Mass Spectrometry

Venn diagrams showing unique and shared molecular masses produced at different growth stages of in vitro biofilms (Bio) and 14 of the total 27 studied bacterial isolates. Abbreviations: An, Actinomyces naeslundii ; Fn, Fusobacterium nucleatum ; Lf, Lactobacillus fermentum ; Pg, Porphyromonas gingivalis ; Sg, S. gordonii ; Si, S. infantis ; Sm, S. mitis ; Smu, S. mutans ; So, S. oralis ; Spa, S. parasanguinis ; Spn, S. pneumoniae ; Ssal, S. salivarius SHI-3; Va6, Veillonella sp. strain 6127; and Vp, Veillonella parvula . See Fig. S1 for detailed strain abbreviations. Number of parent masses are reported for time points 5, 24, 48 or 52, and 72 h.
Figure Legend Snippet: Venn diagrams showing unique and shared molecular masses produced at different growth stages of in vitro biofilms (Bio) and 14 of the total 27 studied bacterial isolates. Abbreviations: An, Actinomyces naeslundii ; Fn, Fusobacterium nucleatum ; Lf, Lactobacillus fermentum ; Pg, Porphyromonas gingivalis ; Sg, S. gordonii ; Si, S. infantis ; Sm, S. mitis ; Smu, S. mutans ; So, S. oralis ; Spa, S. parasanguinis ; Spn, S. pneumoniae ; Ssal, S. salivarius SHI-3; Va6, Veillonella sp. strain 6127; and Vp, Veillonella parvula . See Fig. S1 for detailed strain abbreviations. Number of parent masses are reported for time points 5, 24, 48 or 52, and 72 h.

Techniques Used: Produced, In Vitro

Related Articles

DNA Extraction:

Article Title: New Methods for Analysis of Spatial Distribution and Coaggregation of Microbial Populations in Complex Biofilms
Article Snippet: .. For DNA extraction, the biofilm was brushed off with a toothbrush and suspended in 1× phosphate-buffered saline (PBS) in 1.5-ml Eppendorf tubes. ..

Article Title: Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms
Article Snippet: .. The sectioned biofilm samples were then placed separately in 1 ml Eppendorf tubes containing 0.5 ml of phosphate-buffered saline (PBS) (containing 137 mM NaCl, 2.7 mM KCl, 10 mM Na2 HPO4 , and 2 mM KH2 PO4 ) for DNA extraction. .. Genomic DNA was extracted using a FastDNA SPIN kit for soil according to the manufacturer's instructions (Q-Bio gene; Australia).

Sonication:

Article Title: Reduced ability to detect surface-related biofilm bacteria after antibiotic exposure under in vitro conditions
Article Snippet: .. Removal of biofilm by sonication After exposure to antibiotic, the beads were transferred to individual Eppendorf tubes with 1 mL saline, vortexed for 30 s with maximum power (Vortex Genie 2; Scientific Industries), sonicated for 60 s (BactoSonic; Bandelin Electronic), and vortexed for 30 s again to dislodge biofilm-embedded bacteria. .. For conventional culture, 50-μL samples of the resulting sonication fluid were serially diluted and plated on blood agar plates.

Sampling:

Article Title: Differential Colonization Dynamics of Marine Biofilm-Forming Eukaryotic Microbes on Different Protective Coating Materials
Article Snippet: .. Afterwards, the triplicated biofilm samples collected from the same material surface and sampling date were put into one sterile Eppendorf tube together as a representative of all fouling replicates, and then they were maintained at −80 °C for the subsequent analysis. ..

other:

Article Title: Evaluation of Phototrophic Stream Biofilms Under Stress: Comparing Traditional and Novel Ecotoxicological Endpoints After Exposure to Diuron
Article Snippet: Biomass To assess the biomass of the sampled biofilm, 8 mL of biofilm suspension of each sample were centrifuged at 2000 g for 10 min at room temperature and the resulting pellet was placed in a 2 ml Eppendorf tube and stored at -20°C for ∼72 h. Subsequently, the pellets were freeze-dried (LYOVAC GT2) for 24 h and dry weight measured.

Staining:

Article Title: New Derivatives of Pyridoxine Exhibit High Antibacterial Activity against Biofilm-Embedded Staphylococcus Cells
Article Snippet: .. Biofilm Staining with Crystal Violet Biofilm formation was assessed either in 35 mm polystyrol tissue culture treated plates (Eppendorf) or in 96-well polystyrol tissue culture treated plates (Eppendorf) and analyzed with crystal violet staining as described previously [ ]. .. After 72 h of incubation, the culture liquid was removed; the plates were washed twice with phosphate-buffered saline (PBS) pH 7.4 and dried for 20 min. Then either 1 or 0.2 mL of 0.2% crystal violet solution (Sigma) in 96% ethanol was added per plate or well, respectively, followed by 20 min incubation.

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    Eppendorf AG biofilm formation
    Confocal laser scanning microscopy (CLSM) images (A) and SEM images (B) of the <t>biofilm</t> states of the H. alvei strain on zinc surfaces after different treatments. (a) 20 μg/mL C 6 -HSL, (b) control, (c–f) L -carvone treatments at concentrations of 0.0625, 0.125, 0.25, and 0.5 μL/mL.
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    Confocal laser scanning microscopy (CLSM) images (A) and SEM images (B) of the biofilm states of the H. alvei strain on zinc surfaces after different treatments. (a) 20 μg/mL C 6 -HSL, (b) control, (c–f) L -carvone treatments at concentrations of 0.0625, 0.125, 0.25, and 0.5 μL/mL.

    Journal: Frontiers in Microbiology

    Article Title: Reducing Quorum Sensing-Mediated Virulence Factor Expression and Biofilm Formation in Hafnia alvei by Using the Potential Quorum Sensing Inhibitor L-Carvone

    doi: 10.3389/fmicb.2018.03324

    Figure Lengend Snippet: Confocal laser scanning microscopy (CLSM) images (A) and SEM images (B) of the biofilm states of the H. alvei strain on zinc surfaces after different treatments. (a) 20 μg/mL C 6 -HSL, (b) control, (c–f) L -carvone treatments at concentrations of 0.0625, 0.125, 0.25, and 0.5 μL/mL.

    Article Snippet: In contrast, biofilm formation in the C6 -HSL-treated group was visibly higher than that in the control group, which proves that the biofilm formation of H. alvei is positively regulated by the AHL-based QS system.

    Techniques: Confocal Laser Scanning Microscopy

    Clustering pattern of pioneer biofilm-forming eukaryotic communities formed on the C0, P 0 and P F surfaces. ( a–c ) the clustering patterns of pioneer biofilm-forming the eukaryotic communities adhering to the C 0 , P 0 and P F surfaces (EC 0 , EP 0 and EP F ) based on the Unweighted Pair-Group Method with Arithmetic means (UPGMA) method. ( d ) the multidimensional scale (MDS) analysis of the clustering patterns of the early pioneer eukaryotic communities (EC 0 , EP 0 and EP F ) on the C 0 , P 0 and P F surfaces.

    Journal: Polymers

    Article Title: Differential Colonization Dynamics of Marine Biofilm-Forming Eukaryotic Microbes on Different Protective Coating Materials

    doi: 10.3390/polym11010161

    Figure Lengend Snippet: Clustering pattern of pioneer biofilm-forming eukaryotic communities formed on the C0, P 0 and P F surfaces. ( a–c ) the clustering patterns of pioneer biofilm-forming the eukaryotic communities adhering to the C 0 , P 0 and P F surfaces (EC 0 , EP 0 and EP F ) based on the Unweighted Pair-Group Method with Arithmetic means (UPGMA) method. ( d ) the multidimensional scale (MDS) analysis of the clustering patterns of the early pioneer eukaryotic communities (EC 0 , EP 0 and EP F ) on the C 0 , P 0 and P F surfaces.

    Article Snippet: Afterwards, the triplicated biofilm samples collected from the same material surface and sampling date were put into one sterile Eppendorf tube together as a representative of all fouling replicates, and then they were maintained at −80 °C for the subsequent analysis.

    Techniques:

    The Single-stranded Conformation Polymorphism (SSCP) patterns of the early biofilm-forming eukaryotic microbial communities developed on the C 0 , P 0 and P F surfaces.

    Journal: Polymers

    Article Title: Differential Colonization Dynamics of Marine Biofilm-Forming Eukaryotic Microbes on Different Protective Coating Materials

    doi: 10.3390/polym11010161

    Figure Lengend Snippet: The Single-stranded Conformation Polymorphism (SSCP) patterns of the early biofilm-forming eukaryotic microbial communities developed on the C 0 , P 0 and P F surfaces.

    Article Snippet: Afterwards, the triplicated biofilm samples collected from the same material surface and sampling date were put into one sterile Eppendorf tube together as a representative of all fouling replicates, and then they were maintained at −80 °C for the subsequent analysis.

    Techniques:

    FC-CS in diuron-treated stream biofilms. (A) Biofilms were assessed by flow cytometry after sampling on d 0 , d 7 , d 14 , and d 21 , and altogether mapped by viSNE. viSNE maps are shown in single color, with each point in the viSNE map representing a single cell or particle from the biofilms or (B) colored according to fluorescence intensity at 695 nm and according to the forward scatter (full set of scattering and fluorescence intensities displayed in Supplementary Figure S4 ). (C) Subpopulations (SP 1–20) categorized based on the viSNE map and optical scatter and fluorescence intensities. Some cells (4.7%) were not assigned due to lack of distinct properties. Comparison of subpopulation properties with data acquired from reference species and pigment-bleached reference samples (Supplementary Figure S5 ) allowed for assigning subpopulations to types of organisms and potentially decaying cells.

    Journal: Frontiers in Microbiology

    Article Title: Evaluation of Phototrophic Stream Biofilms Under Stress: Comparing Traditional and Novel Ecotoxicological Endpoints After Exposure to Diuron

    doi: 10.3389/fmicb.2018.02974

    Figure Lengend Snippet: FC-CS in diuron-treated stream biofilms. (A) Biofilms were assessed by flow cytometry after sampling on d 0 , d 7 , d 14 , and d 21 , and altogether mapped by viSNE. viSNE maps are shown in single color, with each point in the viSNE map representing a single cell or particle from the biofilms or (B) colored according to fluorescence intensity at 695 nm and according to the forward scatter (full set of scattering and fluorescence intensities displayed in Supplementary Figure S4 ). (C) Subpopulations (SP 1–20) categorized based on the viSNE map and optical scatter and fluorescence intensities. Some cells (4.7%) were not assigned due to lack of distinct properties. Comparison of subpopulation properties with data acquired from reference species and pigment-bleached reference samples (Supplementary Figure S5 ) allowed for assigning subpopulations to types of organisms and potentially decaying cells.

    Article Snippet: Biomass To assess the biomass of the sampled biofilm, 8 mL of biofilm suspension of each sample were centrifuged at 2000 g for 10 min at room temperature and the resulting pellet was placed in a 2 ml Eppendorf tube and stored at -20°C for ∼72 h. Subsequently, the pellets were freeze-dried (LYOVAC GT2) for 24 h and dry weight measured.

    Techniques: Flow Cytometry, Cytometry, Sampling, Fluorescence

    Extracellular polymeric substances (EPS) extraction of stream biofilm samples after diuron exposure. (A) EPS composition as % of total DOC after 3 weeks. BP, biopolymers; BB, building blocks of humic substances; LMW acids, low molecular weight acids; N/A, neutral/amphiphilic compounds. (B) Protein concentration per extracted DOC (μg/mg) over time. Data is presented as box plots according to Tukey. ∗ , ∗∗ , and ∗∗∗ represent the significant difference between the control and diuron-treated community at d21 ( ∗ P ≤ 0.05, ∗∗ P ≤ 0.01, ∗∗∗ P ≤ 0.001), n = 5.

    Journal: Frontiers in Microbiology

    Article Title: Evaluation of Phototrophic Stream Biofilms Under Stress: Comparing Traditional and Novel Ecotoxicological Endpoints After Exposure to Diuron

    doi: 10.3389/fmicb.2018.02974

    Figure Lengend Snippet: Extracellular polymeric substances (EPS) extraction of stream biofilm samples after diuron exposure. (A) EPS composition as % of total DOC after 3 weeks. BP, biopolymers; BB, building blocks of humic substances; LMW acids, low molecular weight acids; N/A, neutral/amphiphilic compounds. (B) Protein concentration per extracted DOC (μg/mg) over time. Data is presented as box plots according to Tukey. ∗ , ∗∗ , and ∗∗∗ represent the significant difference between the control and diuron-treated community at d21 ( ∗ P ≤ 0.05, ∗∗ P ≤ 0.01, ∗∗∗ P ≤ 0.001), n = 5.

    Article Snippet: Biomass To assess the biomass of the sampled biofilm, 8 mL of biofilm suspension of each sample were centrifuged at 2000 g for 10 min at room temperature and the resulting pellet was placed in a 2 ml Eppendorf tube and stored at -20°C for ∼72 h. Subsequently, the pellets were freeze-dried (LYOVAC GT2) for 24 h and dry weight measured.

    Techniques: Molecular Weight, Protein Concentration