Counting and imaging bacteria using fluorescent microscopy & Electron Microscopy and Atomic Force Microscopy (AFM)

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1 Counting and imaging bacteria using fluorescent microscopy & Electron Microscopy and Atomic Force Microscopy (AFM) Bruce E. Logan Kappe Professor of Environmental Engineering Department of Civil and Environmental Engineering The Pennsylvania State University

2 Viewing bacteria using a microscope Bacteria ~1 um in size Invisible using brightfield microscopy Use phase-contrast to see bacteria (wet mount) Staining bacteria can help differentiate them (gram stain) based on cell structure

3 Fluorescent staining Fluorescence increases light sensitivity Can stain cells for specific materials General stains: Acridine orange DAPI Viability/Respiration: CTC FISH- fluorescent in-situ hybridization (allows staining of specific types of bacteria)

4 Phase contrast image (isolate PDX)

5 Natural assemblage of bacteria- AO stain

6 Natural assemblage of bacteria- AO stain

7 Natural assemblage of bacteria- AO stain

8 Water from Lake Constance (Germany): DAPI

9 Soil bacteria: SYBR Green II stain) From: Weinbauer et al. Appl. Environ. Microbiol. 64, 5000.

10 Fluorescent redox probe (CTC) for actively respiring bacteria (P. putida) From: Rodriguez et al. Appl. Environ. Microbiol. 58, 1801.

11 Viewing particles in seawater on filters using cytoclear slides

12 Closeup of Chaetoceros (brightfield image, AO, AB)

13 Closeup of Chaetoceros (blue light, AO, AB)

14 Viruses in Seawater (stained with Yo-Pro-1, a cyanine-based nucleic stain) From: Hennes and Suttle, 1995, Limnol. Oceanogr. 40, 1050

15 Material specific stains Other stains can be used to view materials in cells Alcian blue (AB) stains only negatively charged polysaccharides Used to identify material responsible for large particle aggregation in the ocean (TEP- transparent exopolymer particles)

16 Alcian Blue stained phytoplankton culture

17 Alcian Blue stained phytoplankton culture- phase contrast

18 Using fluorecent in-situ hybridization (FISH) with 16s rrna-targed oligonucleotide probes

19 FISH Analysis of Nitrifying Biofilms Nitrosomonas (ammonia oxidizing) Nitrospira (nitrite oxidizing) From: Okabe et al. 1999, Appl. Environ. Microbiol. 65, 3182

20 FISH Analysis of Toluene-degrading Biofilms Acinetobacter sp Pseudomonas putida From:Moller et al. 1998, Appl. Environ. Microbiol. 64, 721.

21 Electron Microscopy Scanning Electron Microscopy (SEM) Transmission Electron Microscopy (TEM) Environmental SEM (ESEM)

22 SEM Images Burkholderia cepacia G4 Pseudomonas fluorescens P17

23 TEM Images Pseudomonas fluorescens P17

24 ESEM Images

25 ESEM Images

26 Atomic Force Microscopy (AFM)

27 Imaging with the Bioscope Atomic Force Microscope Bacteria are attached to glass slides and once attached, AFM experiments can be performed. Generate 3-D images of surfaces (topographic imaging) Provide information about surface properties such as adhesion properties and chemical composition (phase imaging)

28 Configuration of the AFM Sensor to measure cantilever position Laser Cantilever with silicon nitride tip Adapted from image on Digital Instruments web page

29 AFM imaging: use a silicon nitride tip mounted on a cantilever tips 100 μm = width of human hair! Spring constant of cantilever ~ 0.1 N/m 400 nm Made of silicon nitride Radius of tip = 5 50 nm 2.9 μm

30 BIOSCOPE: Atomic Force Microscope (AFM) is integrated with an inverted microscope

31 AFM Head on microscope stage

32 AFM Cantilever &Tip

33 AFM Cantilever &Tip

34 The Atomic Force Microscope (AFM) can be used to provide data on: - surface topography - surface heterogeneity - adhesion forces between tip and surface Data is obtained in different ways, that include: - Contact mode - Tapping mode - Phase (in tapping mode) - Approach/Retraction curves Samples can be imaged in water or in air

35 AFM- Contact Mode The topography of a surface is measured by monitoring the deflection of the tip (using a laser) as it is pulled across a surface. Cantilever Tip

36 AFM-Tapping Mode The topography of a surface is also measured but the tip oscillates during scanning.

37 Height image Deflection image Δh(x) Δd(x) d setpoint d setpo

38 Height image Deflection image Δh(x) Δd(x) d setpoint Δh piezo decreases d setpoin

39 Height images not as clear as Deflection images

40 Residuals on Surfaces TAPPING (Amplitude) PHASE AFM images of bacteria in air often show some sort of material adjacent to cells PHASE TAPPING

41 Bacteria imaged with AFM show a residual The side of the AFM tip makes contact with cell giving the appearance of a Shadow 1μm 0.95 μm 0.44 μm

42 Bacteria imaged in air do not have show artifacts (they have less height) Bacterium imaged while drying Water drops Dried bacterium No residuals when dr C

43 AFM studies of cell morphology Chemicals can be used to alter cell adhesion properties, but their effects on bacterial morphology are not well known. Objective: Use the AFM to probe morphological changes in response to chemical treatments.

44 Sodium Pyrophosphate Low IS water MOPS Buffer (Control) Lysozyme and EDTA Topographic Images of Pseudomonas stutzeri KC Disodium Tetraborate

45 Tapping Mode Free Amplitude Tapping Fluid Layer Amplitude Reduced

46 Tapping Mode Phase Imaging

47 AFM Images (in air): Burkholderia cepacia G4 exposed to Tween 20 Tapping mode image Phase image

48 Tapping Mode Phase Imaging Pseudomonas stutzeri KC Disodium Tetraborate Tween 20

49 Bacterial interaction forces Objectives: Use the AFM to measure forces between bacteria and surfaces.

50 What is the interaction force between a bacterium and a surface? Bacterium Repulsion? Surface Bacterium

51 A. Glass bead on a tipless cantilever B. Glass bead in front of the pyramid shape tip C. Glass bead behind the pyramid shape tip D. Too much glue on the bead (done intentionally)

52 Approach AFM- Force Measurement Attractive Force Distance from surface

53 Approach AFM- Force Measurement Repulsive Force Distance from surface

54 Approach AFM- Force Measurement Retraction Approach Retraction Distance from surface

55 Anatomy of a deflection curve

56 Anatomy of a deflection curve

57 Anatomy of a deflection curve

58 Anatomy of a deflection curve

59 Anatomy of a deflection curve

60 EXAMPLE: Show that force curves must be done on the top of the bacterium

61 First, Zoom in on a single bacterium

62 Now you are ready for deflection curve analysis

63 Deflection curve on E. coli D21f2

64 Deflection curve on E. coli D21f2

65 Deflection curve on E. coli D21f2

66 Deflection curve on E. coli D21f2

67 Deflection curve on E. coli D21f2

68 Deflection curve on E. coli D21f2

69 Deflection curve analysis Must be on the very top of a bacterium to obtain a good force curve X * X *

70 Understanding Force Curves Force, nn = k cantilever Δd cantilever Δd cantilever, nm Δh piezo, Challenge: Where nm is zero distance?

71 AFM Force Measurements (Non-interacting Sample and Tip, Hard Sample) spring constant, k [=] N/m 0 Tip-to-Sample Distance (nm) 0 constant compliance region

72 AFM Force Measurements (Non-interacting Sample and Tip, Soft Sample) spring constant, k [=] N/m 0? Tip-to-Sample Distance (nm) 0 constant compliance region?

73 (d) (c) (b) (a) k c i d h c d c i c d b i b z b h a z a d d z d k b d, Cantilever deflection (d) (c) (b) (a)

74 6 Approach Curves Force (nn) KT2442 in 1 mm MOPS Buffer ph=2.2 ph=4.75 ph=7.00 ph= Tip-to-Sample Distance (nm)

75 Surface roughness is important

76 AFM vs Electron Microscopy AFM does not require the use of formaldehyde or other fixative chemicals AFM does not require ultrahigh vacuum, or even any vacuum Morphology more clearly observed using AFM TEM is best for observing flagella In ESEM, samples need not be dried, but we found it very difficult to observe bacteria