The long-standing rules for assigning scientific names to bacteria and archaea are overdue for an update, according to a new consensus statement backed by 119 microbiologists from around the globe, including UNLV microbiologist Brian Hedlund and Desert Research Institute biologist Alison Murray.
Bacteria and archaea (single-celled organisms that lack cell nuclei) make up two of the three domains of life on Earth and are named according to the International Code of Nomenclature of Prokaryotes (the Code). At present, the Code only recognizes species that can be grown from cultures in laboratories – a requirement that has long been problematic for microbiologists who study bacteria and archaea in the wild.
Since the 1980s, microbiologists have used genetic sequencing techniques to sample and study DNA of microorganisms directly from the environment, across diverse habitats ranging from Earth’s icy oceans to deep underground mines, hot springs here in Nevada, and even the surface of human skin.
For a vast majority of these species, no method yet exists for cultivating them in a laboratory, and therefore, according to the Code, they cannot be officially named.
In an article published this week in the journal Nature Microbiology, an international consortium of scientists presents the rationale for updating the existing regulations for naming new species of bacteria and archaea. They also propose two possible paths forward.
“Consider what chemistry would be without a system to name and group all elements or chemical compounds,” says Hedlund, whose National Science Foundation grant funded a series of workshops that led to the article and proposed plans. “How can we communicate about microbiology without a common language?”
As a first option, the group proposes formally revising the Code to include uncultivated bacteria and archaea represented by DNA sequence information, in place of the live culture samples that are currently required. As an alternative, they propose creating an entirely separate naming system for uncultivated organisms that could be merged with the Code at some point in the future.
“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 to formally name them, which is creating a lot of chaos and confusion in the field,” says Murray, lead author on the article. “Being able to represent the diversity of uncultivated organisms known by their genome sequences in a common language is incredibly important.”
According to Hedlund, the benefits of moving forward with either of these options is a major step forward. “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,” he said.
For example, researchers who use DNA sequencing to study the human microbiome – the thousands of species of bacteria and archaea that that live inside and on the human body – would have a means of assigning formal names to the species they identify that are not yet represented in culture collections. This would improve the ability for researchers around the world to conduct collaborative studies on topics such as connections between diet and gut bacteria in different human populations, or to build off of previous research.
“It is incredibly important for those in our field to have a structured way to communicate with the global scientific community and the public about the vast untapped biodiversity of the microbial world,” says Anna-Louise Reysenbach, a biologist from Portland State University who was among the collaborating scientists. “That’s why this change is so important.”
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 statement and others around the world who want to help see this change enacted. So far, many have been eager to participate.
“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,” Murray says. “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.”
The move to update the classification system is not without controversy. Hedlund says one of the biggest arguments against the change is that experiments with purified species are an important part of learning enough about microbes to classify them.
“While I agree that there are limitations on what science can do without pure lab cultures, microbial ecology is becoming more sophisticated and in many cases we know more about some uncultivated prokaryotes than those that are studied in the lab,” says Hedlund. “Really, traditional microbial cultivation and taxonomy and modern microbial ecology are complementary and we should strive to do our best to learn about microorganisms whether or not they can be cultured in the lab.”
Note: View the original news release in the Desert Research Institute newsroom
