Thursday, May 6, 2021

A new field guide for Earth’s wild microbes

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It was once believed that only high quality DNA could be obtained directly from animals or from well-preserved bones and specimens, but from the 1990s microbiologists began to sequence DNA directly. from spoons of soil, mud and seawater. They searched for genetic material called environmental DNA, or eDNA, which is shed by living things. Instead of having to grow microbes in the lab to get their genomes, they are now using eENA and a technique called metagenomics to directly sequence discarded pieces of DNA. Nayfatch says it has “really revolutionized the way scientists study microbial diversity.”

Nayfatch is a researcher at the Joint Genome Institute, which provides DNA sequencing services to scientists around the world. Over the past 15 years, the institute has sequenced eDNAs of researchers studying deep seabed thermal vents, arctic permafrost, ocean mud, Greek lagoons, deep African gold mines, human intestines and animals, etc. This database, which is the culmination of research by all of these groups, has enabled Eloe-Fadrosh and her colleagues to discover more branches of the tree of life.

Included in the The new database, which will be made public, is a treasure trove of new genes encoding useful compounds called “secondary metabolites”. These are small organic compounds found in nature that have therapeutic properties, such as the opium produced by the poppy or the penicillin of the Penicillium mushrooms. Soil bacteria are also a powerful source of therapeutic products. The soil bacterial strain Streptomyces, for example, has given rise to many antibiotics and even anti-cancer drugs. In fact, some of its compounds that were developed into drugs, like the antibiotics chloramphenicol and spectinomycin, are now considered essential drugs by the World Health Organization.

“Personally, I’m very interested in the diversity that exists and how we can catalog it,” says Eloe-Fadrosh. As a researcher at the Department of Energy, she is particularly interested in the roles that these microbes play in biogeochemical processes in the environment and in the carbon cycle. Microbes that reside in the soil break down organic matter and release carbon dioxide and methane, which contribute greenhouse gases to the atmosphere.

A big question right now in microbial ecology is what will happen to microbes in arctic permafrost when warm global temperatures and that starts to thaw. Will they release a carbon flood in the atmosphere as they wake up and feast on the frozen plants and animals buried there? “People often want to know how the microbiota will react to climate change? And we have a hard time answering those questions because we still just understand which of them live there and what they do, ”says Allison Murray, a microbial ecologist at the Desert Institute, who was not involved in. study.

This catalog is an important first step in understanding this, as it contains several new species of microbes with genes involved in methane production. Additionally, says Eloe-Fadrosh, she has found many archaea that have genes that metabolize methane, taking it out of the atmosphere and using it for energy. She is excited about the future potential of using these microbes to sequester atmospheric carbon.

Karen Lloyd, a microbiologist at the University of Tennessee Knoxville who was not involved in the project, says this source of new genetic sequences is “mind-boggling” in its potential to expand our options for useful biological molecules. For Lloyd, the study “shows us the full extent of the microbial world, and it shows us that the microbial landscape is vast and remains to be discovered.

Eisen, an avid ornithologist, compares this database to a first draft of a field guide for non-domesticated microbes on Earth. But he says this is only the first step in understanding the function of these organisms and their importance in the ecosystem. The next step is to learn something about their biology.

Eloe-Fadrosh agrees. “By better cataloging the diversity of microbes, we hope to be better able to identify all of the different metabolisms and unique features that are encoded throughout the tree of life,” she says.


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