19 December 2022

A new research technique may unlock the secrets of soil microbes


A study from the US paves the way for more in-depth investigations into the role of soil microbes. By improving the stable isotope survey, researchers highlighted the “food web” of interactions stimulated by soil microorganisms

by Matteo Cavallito


An innovative method of analyzing microbes could pave the way for new insights into the complex interactions that continuously take place in the soil, explains a study published in recent weeks by scientists at Lawrence Livermore National Laboratory, a research center based in California. The authors, assisted by colleagues at the U.S. Department of Energy’s Joint Genome Institute and UC Berkeley, have developed a technique that allows for more effective use of what is known as SIP, or Stable Isotope Probing.

The new version of this method, according to a statement from the California Laboratory, “automates several steps in the process of stable isotope probing, allowing investigations of microbial activity of microorganisms under realistic conditions, without the need for lab culturing.”

A novel technique

The SIP method is usually based on the incorporation of isotopes into microbial biomass. This allows researchers to identify active microbes in a complex community by defining their physiological traits including cell biochemistry, metabolism, growth and mortality. However, the analysis takes place in the laboratory, is labor-intensive and allows only a small number of samples to be processed.

LLNL scientists, says the statement, have made major innovations to the method, significantly reducing the manual labor required and starting to process 16 samples simultaneously.

“Our semi-automated approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of SIP,” said Erin Nuccio, co-author and research coordinator. “We have now used this approach to process over a thousand samples, including some from very understudied soil microhabitats.”

New perspectives

According to the authors, the technique allows the dynamic activities of microbial communities to be studied more effectively. This is highlighted by the same results of the study that focused on the mycorrhizosphere that hosts arbuscular mycorrhizal fungi, or AMFs. These particular microbes, an Indiana University research previously observed, interact with plants by providing them with increased carbon storage capacity.

The fungi identified by the researchers, the study says, “highlight the potential for cross-kingdom trophic interactions in the AMFs hyphosphere, including predation, decomposition of fungal necromass or plant detritus, and archaeal ammonia oxidation that may utilize ammonium or CO2 released from the aforementioned processes.”

By combining the new method with other disciplines such as metatracriptomics, which studies the gene expression of microbes, and proteomics, which provides essential information about proteins, it will be possible to obtain “an important genomic resource for future experiments exploring interactions between arbuscular mycorrhizal fungal hyphae (filamentous structure of, ed.) and their native microbiome.”

Microbes and carbon

MFAs, the researchers recall, form symbiotic relationships with 72 percent of all terrestrial plants. In exchange for carbon, the fungus provides essential resources such as nitrogen, phosphorus and water. This study thus made it possible to highlight the “food web” of interactions stimulated by the same microorganisms in the soil.

Peculiar role of microbes in the carbon cycle has long been the subject of various studies.

In January 2021, for example, researchers at the University of Massachusetts Amherst revealed how microbial diversity promotes growth in carbon use efficiency, i.e., the balance between the amount assimilated by fungi and bacteria and the amount emitted into the atmosphere

The survey, explains Jennifer Pett-Ridge, one of the co-authors, shows “a major route for how plant carbon gets broadly distributed into soil.” The soil itself “holds the largest pool of actively cycling organic carbon on the planet.” And the study, which is based on sequencing “a tiny amount of DNA,” has “determined the active organisms and then reconstructed their genomes and potential interactions.” The application of these techniques now opens the way for new research.