A New Naming System for Uncultivated Bacteria and Archaea is proposed

2020-06-08

Figure: spores (arrows), celles grouped into or more numerous mass chains of cells make up microbial communities in nature and of which only 1% can be grown in the laboratory. Credit: CAB-INTA-CSIC.


An International Consortium of Scientists, of Which several researchers from the Center for Astrobiology (CAB, CSIC-INTA) are part, has proposed the creation of a new naming system for bacteria and archaea that cannot be grown in the laboratory. The statement has been endorsed by 119 microbiologists around the world.


Bacteria and archaea (single-celled organisms that lack cell nuclei) make up two of three domains of life on Earth, and are named according to the International Code of Nomenclature of Prokaryotes (ICNP; the Code). At present, the Code only recognizes species that can be grown from cultures in laboratories -a requeriment that has long been problematic for microbiologists who study bacteria and archaea in the wild.

Since the 1980's, microbiologists have used genetic sequencing techniques to sample and study DNA of microorganisms directly from the envirnment, across diverse habitats ranging from Earth's icy oceans to deep underground mines to the surface of human skin. For a vast majority of this species, no method yet exists for cultivating them in a laboratory, and thus, according to the Code, they cannot be officially named.

"There has been a surge in recent years in genome-based discoveries for archaea and bacteria collected from the environment, but no system in place for formally name them, which is creating a lot of chaos and confusion in the field", said Alison Murray, Ph.D., Research Professor of Biology at the Desert Research Institute (DRI) in Reno (USA). "Being able to represent the diversity of uncultivated orgnisms known by their genome sequences in a common language is incredibly important".

In an article published today in the journal Nature Microbiology, Murray and her collaborators, including microbiologists from the Spanish Center for Astrobiology, presente the rationale for updating the existing regulations for naming new species of bacteria and archaea, adn propose two possible paths forward.

As a first option, the group proposed formally revising the Code to include uncultivated bateria and archaea represented by DNA sequence information, in place of the live culture samples that are currently required. As an alternative, the propose creating an entirely spearate naming system for uncultivated orgnisms that could be merged with the Code at some point in the future.

In environmental microbiology, and in particular in Astrobiology, DNA sequencing extrated from rocks from the depths of the Eart, from salt crusts, or icy blocks of glaciers, is used to understand biodiversity and microbial metabolisms and their relevance in biogechemical cycles. For Victor Parro, CAB researcher an co-author of the publication, "the mayority of these microorganisms cannot be cultivated in the lab, but we can know thir genome and inferir their metabolic capabilities. We know they're there, what they look like and what the do, and we want to register the with a name we all undestand."

The next step, says Murray, is to figure out an implementation strategy for moving forward with one of the two proposed plans, while engaging the many microbiologists who contributed to this consensus and others around the world who want to help see this change enacted. So far, many have been eager to participate.

 

Fuente: UCC-CAB

Fecha: 2020-06-08

 

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