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EYE ON CHINA
Sequencing the Soil Microbiome One Cell at a Time
Scientists from the Single-cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT) developed a technique to sort and sequence soil bacteria genome one cell at a time, while also determining its function in the soil environment.

A part from just housing your regular Monstera plant, the soil is also home to billions––bacteria, fungi, protozoa, and viruses. Their metabolic processes provide the foundation for the industrial production of numerous compounds of value.

Given the importance of the microbiome to industrial production, it would be of great value to recognise “who is doing what” and identify the key players in the soil microbiome. However, up until this point, pinpointing the resolution of a single cell has been challenging as typically millions of cells are analysed at the same time.

Published in the journal mSystems, researchers from the Single-Cell Centre at the Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT) of the Chinese Academy of Sciences have developed a new scientific instrument called a Raman-activated Cell Sorter-Sequencer or RACS-Seq. It is the first instrument that can recognise cells and its functions at precisely a one-cell resolution in a complex ecosystem.

The RACS-Seq is based upon their previously developed bacteria-profiling technique called Raman-Activated Gravity-driven single-cell Encapsulation and Sequencing, or RAGE sequencing. This technique utilises laser “tweezers” and gravity to facilitate the analysis of bacteria cells one at a time. The form and structure of a bacterium are then examined using ‘Raman spectroscopy,’ a method of analysis that uses light interactions with chemical bonds in a molecule for identification.

With the Raman spectra of one microbial cell, a structural fingerprint is captured and can be used as a representation of its metabolic activity. When this single-cell Raman spectra is coupled with isotopes involved in this activity, we can tell the amount of chemical that the cell is taking up from its environment.

Feeding bacteria with isotopes of carbon, hydrogen, or nitrogen allows us to detect the chemical processes within the cells. This metabolic tracking can then be linked via the RAGE technique to individual cells whose genome can be sequenced.

“This should allow researchers to ‘mine’ soil to find bacteria of interest that are in the business of producing particular carotenoids, lipids, polysaccharides, protein and even antibiotics,” said Jing Xiaoyan, a microbiome scientist with the QIBEBT Single-Cell Center and the article’s lead author.

Future work would look at improving the throughput of the technique from a few cells per minute to fully automating the process, accelerating the process for mechanistic dissection and bioresource mining.

“Our goal ultimately is to keep optimising the RACS-Seq instrument, so that it becomes a universal and highly versatile tool for precisely probing target cells or metabolic activities of interest,” added Xu Jian, the article’s corresponding author and Director of the QIBEBT Single-Cell Center. “And not just from soil, but from any other complex natural ecosystem.”


Source: Jing et al. (2021). One-Cell Metabolic Phenotyping and Sequencing of Soil Microbiome by Raman-Activated Gravity-Driven Encapsulation (RAGE). Msystems, 6(3), e00181-21.

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