X-ray fluorescence nanotomography provides high resolution elemental map of bacteria

Using X-rays instead of visible light can allow you to get an idea of the biochemistry in microbial communities

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Dec 07, 2018

This is a slightly older article but I recently saw it in the news which got me very excited. Since I started working at a synchrotron just over a year ago, I've been trying to get microbiologists to be more interested in the techniques that you can do there.

In this paper, a team from Brookhaven National Laboratory used X-ray fluorescence to study E. coli. In essence, they used X-rays instead of light to perform a type of microscopy. This then allowed them to tune the energy of the X-rays and build up a map of the different chemical species within the cell. It works because different metal atoms absorb X-rays with different energies. If you cycle through a range of different energies with your X-ray beam and raster scan across the sample, you can quickly find out which pixels contain which metals. You can also do this with different chemical species, such that you can differentiate between carbohydrates in the cell wall and lipids in the membrane. If you do this in slices and get a single image, it's called X-ray fluorescence microscopy. The team at Brookhaven did tomography which meant that they rotated their sample and built up a 3D elemental map instead of a single plane. The also performed ptychography which was done on the same instrument and is a method to get very high resolution structural information about the cell.

I think it would be fascinating to study microbial communities using these methods. The biggest question I have is would you be able to do label-free imagining? You get so much information from each pixel and each bacterial cell, it might be possible to identify the bacterium in a mixture purely based on this. That's not to say that no sample preparation is needed. As the authors point out, using high-energy X-rays like this can damage samples so it's safer to use dried or cryo-cooled bacterial cultures.

It looks like this technique is becoming more popular among the microbiology community which makes me very happy. I can't wait to see what exciting findings are next.


X-ray Fluorescence (XRF) microscopy is a growing approach for imaging the trace element concentration, distribution, and speciation in biological cells at the nanoscale. Moreover, three-dimensional nanotomography provides the added advantage of imaging subcellular structure and chemical identity in three dimensions without the need for staining or sectioning of cells. To date, technical challenges in X-ray optics, sample preparation, and detection sensitivity have limited the use of XRF nanotomography in this area. Here, XRF nanotomography was used to image the elemental distribution in individual E. coli bacterial cells using a sub-15 nm beam at the Hard X-ray Nanoprobe beamline (HXN, 3-ID) at NSLS-II. These measurements were simultaneously combined with ptychography to image structural components of the cells. The cells were embedded in small (3–20 µm) sodium chloride crystals, which provided a non-aqueous matrix to retain the three-dimensional structure of the E. coli while collecting data at room temperature. Results showed a generally uniform distribution of calcium in the cells, but an inhomogeneous zinc distribution, most notably with concentrated regions of zinc at the polar ends of the cells. This work demonstrates that simultaneous two-dimensional ptychography and XRF nanotomography can be performed with a sub-15 nm beam size on unfrozen biological cells to co-localize elemental distribution and nanostructure simultaneously.


X-ray Fluorescence Nanotomography of Single Bacteria with a Sub-15 nm Beam
Tiffany W. Victor, Lindsey M. Easthon, Mingyuan Ge, Katherine H. O’Toole, Randy J. Smith, Xiaojing Huang, Hanfei Yan, Karen N. Allen, Yong S. Chu & Lisa M. Miller
Scientific Reports volume 8, Article number: 13415 (2018)

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Ben Libberton

Science Communicator, Freelance

I'm a freelance science communicator, formally a Postdoc in the biofilm field. I'm interested in how bacteria cause disease and look to technology to produce novel tools to study and ultimately prevent infection.

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