Science.-Environmental DNA discovers new bacteria and marine natural products – Publimetro México

Madrid, 22 (European press)

The oceans are teeming with countless forms of life, from the world’s largest creature – the blue whale – to tiny microorganisms. In addition to their large number, these microorganisms are necessary to ensure the proper functioning of the entire ecosystem and climate. For example, there are photosynthetically active species, such as cyanobacteria, which produce about 50% of the oxygen in the atmosphere. In addition, by removing carbon dioxide from the atmosphere, microorganisms are helping to counteract global warming.

Despite this important role, research on the diversity of microorganisms present in the ocean has so far been only rudimentary. For this reason, a group of researchers led by Shinichi Sunagawa, Professor of Microbiome Research at ETH Zurich, is collaborating closely with Jörn Piel’s group to investigate this diversity.

To detect new natural products made by bacteria, Sunagawa and his team examined publicly available DNA data from 1,000 water samples collected at various depths throughout the world’s ocean regions. The data came from sources such as ocean voyages and marine monitoring platforms.

Thanks to modern technologies, such as the analysis of environmental DNA (eDNA), it has become easier to search for new species and discover known organisms that can be found in the place. But what little is known is about the special effects of marine microorganisms, that is, the chemical compounds that they make and that are important for interactions between organisms. At best, these compounds will benefit humans as well. The research is based on the assumption that the ocean microbiome harbors great potential for potentially beneficial natural products, for example through their properties as antibiotics.

The extracted DNA present in the samples was sequenced by the original researchers of the various expeditions. By reconstructing entire genomes on a computer, the scientists were able to decode the encoded information, the blueprints of proteins. Finally, they combined this new data with the 8,500 existing microorganism genome datasets in a single database.

In this way, they obtained 35,000 genomes to search for new microbial species and, in particular, the most promising bio-gene clusters (BGCs). BGC is a group of genes that provide the pathway for the synthesis of a natural product.

In this genome data, the researchers discovered not only many potentially beneficial BGCs – about 40,000 in total – but also previously undiscovered bacterial species belonging to the phylum Eremiobacterota. This group of bacteria was known to exist only in terrestrial environments and did not exhibit any particular biodiversity.

Named a new family of these bacteria Eudoremicrobiaceae, Sunagawa and his team were also able to show that the bacterium is widespread and widespread: one species in this family, Eudoremicrobium malaspinii, accounts for up to 6 percent of all bacteria found in certain areas of the ocean.

“The ocean relatives possess what is considered a giant genome for bacteria. Deciphering it completely has been a technical challenge because the organisms have not been bred before,” Sunagawa said in a statement. In addition, the new bacteria were shown to belong to the group of microorganisms presenting the greatest diversity in BGC among all the samples examined. “As it stands, they are the most biodiverse families in the oceanic water column,” he says.

The researchers examined two BGCs from Eudoremicrobiaceae in detail. One of them was a group of genes containing the genetic code for enzymes that Sunagawa said had never been found in this constellation in bacterial BGC. Another example examined was a natural, bioactive product that inhibits proteolytic enzyme.

In collaboration with the group led by Jörn Piel, the researchers used the experiments to validate the structure and function of each of the natural products. Like ‘E. malaspinii’ could not be cultured, Piel’s team had to inoculate the genes into a model bacteria to serve as blueprints for natural products. Then these bacteria produced the corresponding substances. Finally, the researchers isolated the molecules from the cells, determined the structure and validated the biological activity.

This was necessary because in one case the enzyme activity predicted by the computer programs did not match the results of the experiments. “Computer predictions about the chemical reactions an enzyme will provoke have their limitations, so validate those predictions in the lab if there is any doubt,” Sunagawa says.

Doing so is a time-consuming and expensive endeavor that is simply not feasible for a database of 40,000 potential natural products. “However, our database has a lot to offer, and it is accessible to all researchers who wish to use it,” Sunagawa says.

Besides collaborating continuously with the Piel Group to discover new natural products, Sunagawa wants to investigate unresolved questions about the evolution and ecology of ocean microorganisms. Among them, how microorganisms spread in the ocean, because they can only passively spread over long distances. He also wants to discover the ecological or evolutionary benefits that specific genes for microbes create. Sunagawa thinks BGCs may play a role.