A New Naming System Proposed for Bacteria and Archaea

Actinobacteria like the ones shown here are the source of most clinical antibiotics, but resist cultivation. New environmental genomes will enable more microbial discoveries.
Actinobacteria like the ones shown here are the source of most clinical antibiotics, but resist cultivation. New environmental genomes will enable more microbial discoveries. Credit: Kristen M. DeAngelis

A new consensus statement in “Nature Microbiology” this month by 119 microbiologists from around the world, including Kristen DeAngelis, microbiology, say the long-standing rules for assigning scientific names to Bacteria and Archaea are overdue for an update.

Bacteria and less well-known Archaea – single-celled organisms with no nucleus – are two of the three domains of life on Earth, named according to the International Code of Nomenclature of Prokaryotes (ICNP). The third is Eukarya, cells with nuclei. The code only recognizes bacteria and archaea species that can be grown from cultures in laboratories, which is a problem for microbiologists who study wild bacteria and archaea, the authors explain.

Since the 1980s, microbiologists have used genetic sequencing techniques to sample and study DNA of wild microorganisms directly from the environment from habitats such as ocean volcanos, underground mines and human skin. Most of these cannot be cultivated in a laboratory, so according to the ICNP they cannot be officially named.

DeAngelis says, “Our ability to see and define the vast and mostly hidden microbial world has been transformed by sequencing technology, but our nomenclature rules haven’t kept pace. Names might seem silly, but we need them to talk about microbes, to research them to teach about them. The fact that this is such a broad consensus makes this extra special.”

She and her co-authors state, “We propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future.”

“Regardless of the path taken,” they say, “we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.” Their recommendations come out of a series of workshops supported by the National Science Foundation.

Brian Hedlund of the University of Nevada, Las Vegas, points out, “For researchers in this field, the benefits of moving forward with either of these options will be huge. We will be able to create a unified list of all of the uncultivated species that have been discovered over the last few decades and implement universal quality standards for how and when a new species should be named.”

Alison Murray, research professor of biology at the Desert Research Institute in Reno, Nevada, adds, “This is an exciting field to be in right now because we’re describing diversity of life on Earth and uncovering new phyla just like scientists were back in the 1800s when they were still discovering larger organisms. Lots of paradigms have been changing in how we understand the way the world works, and how much diversity is out there – and this is another change that needs to be made. We’re going to need to change it or we’re going to live in chaos.”