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Environmental Transformations and Interactions

When Studying Microbes, More Instruments Can Mean Better Results

First-of-its-kind approach combines analyses from different instruments into single workflow to study microbes at the single cell level 

microbes and film

While each type of advanced instrument gives scientists information about some aspect of microbial identity, structure, or function, a new approach combines outputs from multiple instruments into a single workflow for a much clearer picture. (Illustration by Michael Perkins | Pacific Northwest National Laboratory)

The Science  

Scientists often use microscopes, spectroscopes, and other advanced instruments to study tiny microbes, but each instrument looks at a different aspect of the way microbes function and provides different results in the form of data or images. Each instrument provides an incomplete part of the picture, limiting scientific understanding. To address the problem, researchers developed an innovative approach that combined results from multiple instruments. This first-of-its-kind correlative analysis allows scientists to peer down to the level of single cells and compare results for more in-depth analysis. 

The Impact 

Because microbes play a dominant role on Earth—from carbon cycling in the environment to unlocking nutrients for plants during drought—scientists seek to understand how they function in community and individually down to the cellular level. One type of advanced instrument can help scientists identify which microbes are in a particular community. Another instrument can offer the overall chemical composition of a community of cells. But the way the instruments obtain these results from populations of cells makes it challenging for scientists to bring all the results together into a single body of information. A new approach developed by a team of scientists overcomes the limitations of a single instrument by providing a workflow across multiple instruments, thereby providing a powerful tool to discover and compare multiple facets of microbial functioning. This new approach allows scientists to study individual cells with several different instruments, each revealing part of the microbes’ hidden secrets. 


Many experiments use a single advanced instrument that provides data on biology, chemistry, morphology, or other characteristics from microbial communities or individual cells. A multi-institutional team of scientists recognized that they needed to develop a process that would allow each instrument to be used on the same sample sequentially or in tandem. By combining stable isotope probing, fluorescence in situ hybridization imaging, scanning electron microscopy, confocal Raman microspectroscopy, and nano-scale secondary ion mass spectrometry (NanoSIMS), they illustrated how individual cells can be thoroughly studied to gather information about their identity, structure, physiology, and metabolic activity. The process combines results into a more holistic picture of individual microbes. The NanoSIMS work in particular was conducted at EMSL, the Environmental Molecular Sciences Laboratory, a U.S. Department of Energy Office of Science User Facility. To test their approach, they used an artificial community of two types of microbes–a human gut commensal and a cell producing the climate-active gas, methane. The combined analyses and results yielded a much more complete understanding about microbial functioning than results from each instrument alone. In an even more daunting test, they applied the approach to a microbial community of bacteria from a salt marsh that has proven challenging to study. Again, the results allowed them to clearly establish the identity and activity of the microbes down to the single-cell level. This correlative analysis or workflow enables scientists to more accurately identify and characterize diverse microbes in a range of different ecosystems, from the human gut to soils affected by industrial waste. 


Roland Hatzenpichler, Montana State University, 

George Schaible, Montana State University,  

John Cliff, Environmental Molecular Sciences Laboratory,  


This study was funded through the National Aeronautics and Space Administration and the Gordon and Betty Moore Foundation. A portion of this research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program and used resources at EMSL, the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility. 


G.A. Schaible, et al., “Correlative SIP-FISH-1 SEM-Raman-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes.” ISME Communications 2, 52 (2022). [DOI: 10.1038/s43705-022-00134-3]