A technique to isolate active microbes in the soil and understand its large-scale cycles

Charles Paradis with a soil core sample (Photo courtesy Lance E. King/Y-12 National Security Complex. All rights reserved)
Charles Paradis with a soil core sample (Photo courtesy Lance E. King/Y-12 National Security Complex. All rights reserved)

An article published in the journal “Nature Communications” reports the first use of a technique called BONCAT+FACS to isolate the active microbes present in a soil sample. A team of scientists led by the Lawrence Berkeley National Laboratory (Berkeley Lab) adapted a technique developed to isolate proteins produced in cells to transform it into a tool that could identify single active microbes. This will help to understand in new details parts of ecosystems difficult to investigate, also obtaining information on large-scale cycles existing in the environment.

Estelle Couradeau, the study’s lead author, explained that the soil probably contains the most diverse microbial communities on the planet. Each gram of soil contains billions of cells belonging to tens of thousands of species that, all together, perform important world nutrient cycles. They form the backbone of ecosystems and a healthy soil microbiome is the key to sustainable agriculture.

Since 2009, Berkeley Lab managed ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies), a multi-institutional consortium that aims to advance our understanding of microbial biology and the impact of microbial communities on their ecosystems. One of the big problems in this type of research is that most soil microbes don’t grow in lab. Trent Northen of ENIGMA, one of the authors of this study, explained that for example the microbiomes that remove waste from underground water reserves are found a few hundred meters below the surface with the consequent problems in taking samples. Another problem is that in some ecosystems up to 95% of the microbes are inactive at any given time.

Typically, microbiologists take samples from the environment and analyze the DNA of the microbes they found. However, most of the commonly used techniques don’t distinguish active microbes from dormant ones among those found in soil and sediments. To try to find a solution to this problem, the authors of this new research adapted a technique called BONCAT (Bioorthogonal Non-Canonical Amino Acid Tagging), invented in 2006 to obtain a tool that could identify groups of symbiotic marine microbes from ocean sediments. The technique was further refined in the version called BONCAT Fluorescent Activated Cell Sorting (BONCAT+FACS), which can detect single active microbes.

The BONCAT+FACS technique is based on the use of a fluorescent tagging molecule that binds to a modified version of the amino acid methionine. When a fluid containing the modified methionine is introduced into a sample of microbes, the active ones are those that are creating proteins and in that activity they will incorporate the modified methionine into their cells. The process takes only a few hours so it can tag active cells even if they are not replicating.

Trent Northen and some other members of that eam that conducted this research were also involved in a previous one, published in January 2018 in the journal “Nature Communications”, which aimed to try to understand how microorganism communities can adapt to the biocrust, which is in the biological crusts of soil in very dry and arid environments. Those are all important research to learn about an important element of ecosystems with practical consequences. For example, Estelle Couradeau spoke about the possible applications of the BONCAT+FACS technique to improve agriculture. By bringing together the expertise of scientists from various disciplines, we’re really getting to know the secrets of the soil.

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