BGS Collaborate with the nmRC using Electron Microscopy // by Joe Emmings

Joe Emmings (BGS) tells us about a recent FIB-SEM and TEM collaboration with the Nanoscale and Microscale Research Centre (nmRC), University of Nottingham. 

Black shales are organic-rich mudstones, hydrocarbon source rocks and can host accumulations of metals such as Vanadium (V), Molybdenum (Mo) and Uranium (U). The mechanism(s) for preservation of organic matter is a critical aspect of understanding the present-day distribution of hydrocarbons and metals through black shales. Despite this, the origin of organic matter in many black shales remains enigmatic. Life is subdivided into the prokaryotes and eukaryotes. Eukaryotic cells are relatively large (i.e. single to hundreds of micrometres) and are usually more refractory and complex compared to prokaryotic cells. Using conventional optical microscopy, organic matter in black shales usually lacks eukaryotic cellular structures. It is therefore often described as ‘amorphous’ and is difficult to interpret.

The JEOL 2100+ Transmitting Electron Microscope (TEM) at the Nanoscale and
Microscale Research Centre (nmRC), University of Nottingham
However, cells of the prokaryotes (i.e., bacteria or achaea) are usually much smaller, typically 10s nanometres to 1‑2 micrometres in diameter, and include a wide range of shapes and sizes, including chains or clusters of filamentous, spherical or rod-shaped forms. Therefore we hypothesised that the ‘amorphous’ organic matter present in black shales is associated with, or was generated by, prokaryotes (i.e., bacteria) with cells that are too small to image using conventional optical microscopy. In order to test this hypothesis, we investigated organic matter from the UK Bowland Shale in collaboration with the Nanoscale and Microscale Research Centre (nmRC) at the University of Nottingham. We imaged nanometre-scale structures within ‘amorphous’ particles of organic matter using Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) and Transmitting Electron Microscopy (TEM). 

Left: FIB-SEM chamber configuration. Right: image acquired at 52 stage tilt and following
deposition of platinum strip. Platinum is deposited in order to protect the target wafer from 
damage by the ion beam. This image was acquired during ion milling of the first trench.
A FIB is a beam of ions (such as gallium) that can be focused on a sample under high-vacuum within a SEM. The main use of FIB-SEM in geoscience is to prepare samples ahead of analysis using other techniques, such as TEM or synchrotron analysis. FIB-SEM is used to bombard and swath small areas of the sample surface, cutting nano-scale trenches into the sample, creating welds, and ultimately extracting nanometre-thick ‘wafers’ or ‘lift-outs’. The working rule is that the resolution of transmitted electron imaging of a geological sample is approximately one-tenth its thickness. Therefore analysis of thinned FIB-SEM wafers under TEM can achieve extremely high imaging resolution, and in some cases, revealing sub-nanometre features (i.e., scale of single ångströms). 

Left: a plan-view of the target shale wafer with milled trenches on three edges.
Right: extracted wafer (welded to omniprobe)
Imaging extremely small features in geological materials is intrinsically important, because many geological processes operate at the nano-scale. To paraphrase the idiom seeing is believing, electron microscopy at the nanoscale can greatly improve our understanding of rocks as records of processes and as resources. 

This research was supported by NanoPrime, an access scheme funded by the Engineering and Physical Sciences Research Council (EPSRC) and University of Nottingham. Two streams of funding are available; proof-of-concept studies (up to £2k) and pump-priming projects (up to £15k). Calls for proposals are quarterly. The scheme presently ends in March 2020. Many UK higher education institutes and partner research organisations (including BGS) are eligible to apply. If you are BGS staff and interested in applying, or you are an external researcher wishing to collaborate with BGS via NanoPrime, please contact Jeremy Rushton at Please also visit the website or contact for further information. 

Top: FIB 'lift-outs' welded to the sample holder prior to TEM analysis. Bottom: TEM imaging
of 'amorphous organic matter' extracted using FIB-SEM, including mineral inclusions, 
mineral imprints and possible remnants of rod-shape bacterial cells.

Joe Emmings is a Post-Doctoral Research Associate in Geochemistry at the British Geological Survey’s Stable Isotope Facility and Centre for Environmental Geochemistry. Please contact Joe if you are interested in his research field at