Skip to content
Search AI Powered

Latest Stories

Scientists Just Expanded the Tree of Life

Scientists Just Expanded the Tree of Life
Genetics, Dna, Double Helix Strand With Its Sub-Units, The Nucleobases, Adenine, Thymine, Cytosine, And Guanine, Yellow, Pink, Orange And Purple Respectively. (BSIP/UIG via Getty Images)

Researchers have increased the number of known microbial genomes by nearly 10 percent and see likelihood for additional widespread discovery. The new microbes have added 20 new branches on the tree of life and could lead to substantial progress in evolutionary discoveries and practical advancements in various industries.

An Australian study recently plunged into the world of dark matter, using new technology to identify a multitude of microbial species. As a result, scientists have now added new 20 phyla to the tree of life.

Expanding the tree of life

Researchers at the University of Queensland used advances in gene sequencing technology and mathematics to study microbial genomes obtained straight from environmental samples, without the necessity of cultivation in the lab. The new technology is called metagenomics, whereby researchers gather specimens of all the genetic material—for instance, in a sample of soil, ocean water or baboon feces—and then piece them together using computational models to identify the microorganisms they represent.


“It’s like getting a mix-up of lots of different jigsaw puzzles, and then trying to put together the pieces of each individual puzzle,” says Donovan Parks at the University of Queensland in Australia.

Metagenomics has been key to this process because 90 percent of Earth’s microbes cannot exist outside of their own environment, such as a cow’s gut bacteria. In the study, published in Nature Microbiology, the ability to recover and organize genetic material directly from the environment may reveal the mystery behind so-called “dark matter” microbes. Every environment contains bacteria, but the limitations of technology have prevented scientists from studying them. Thus, they’ve been known as “dark matter.”  

Referring to these microbial genomes, Deputy Director of the Australian Center for Ecogenomics Professor Gene Tyson explained: “Less than one per cent can be cultured, due to challenging factors including slow growth rates, fastidious growth requirements, and the need to cross-feed off other species.”

But through metagenomics, the study produced 7280 bacterial and 623 archaeal genomes, approximately one-third of which were new to science, increasing the total recovered number in storage to 80,000—nearly 10 percent.

Tyson said, “The approximately 8000 genomes recovered move us closer to a comprehensive genomic representation of the microbial world, but also show that much remains to be discovered.”

In fact, while this study was ongoing, others were busy reporting dozens or even hundreds of diverse genomes from various environments. Prior studies had approximated the number of microbial species around 1 trillion, with only two percent yet identified.

“But this is probably an underestimate, as we’ve recently found that existing methods for estimating this actually miss a lot of organisms,” according to ACE co-researcher Dr. Donovan Parks.

“There’s still a whole lot that we don’t know,” Nicholas Coleman at the University of SydneyColeman said. “There are so many crazy environments out there, and even two patches of dirt side-by-side can have different organisms.”

Moreover, thestudy’s discovery of microbes differed so greatly from anything previously categorized by our scientific system of identification, it required researchers to add 20 new phyla to the tree of life. Phyla sit right below biological kingdoms in the order of things, and yet the microbes were no more closely related than humans and insects.  

“To give this context, every single insect on Earth belongs to just one phylum, and every single animal with a backbone belongs to one phylum, so this is crazy new levels of stuff,” Coleman said.

Next, scientists need to learn more about the new microbes. One place to start in sorting out the function of various microbes is to compare them to more familiar ones.

“For example, they might have a gene that looks similar to a methane metabolism gene,” Parks said.

But the unusual nature of these new microbes may lengthen the time required to fully absorb their functionality and capability.

“This study has put names on that dark matter,” Coleman explained. “Now we need to figure out what it’s actually doing and how we can benefit from it.”

Applications for the discovery of the new microbes

Scientists are hopeful that the bacterial microbes may lead to the development of new antibiotics. Various microbes could help in industry or environmental services—breaking down plastics, or in the creation of fuels or other chemicals.

“The better we can grasp the diversity of microbes, the more we can go looking for things that are useful,” Coleman said.

Researchers are continuing to survey other public data banks of metagenomes, and are locating tens of thousands more microbial species, according to the study’s co-author Philip Hugenholtz.

“This is just the beginning,” he said. “It’s going to go off the charts.”

Hugenholtz clarifies that this ongoing research indicates that while the number of new microbial species are numerous, the number of new phyla appears to be slowing down. These next steps in the discovery process may begin to fill in smaller gaps, rather than drawing wholly new branches, creating a more complete picture of the tree of life.

Parks said, “Constructing a comprehensive genomic repository of microbial diversity lays the foundation for furthering our understanding of the role of microorganisms in critical biogeochemical and industrial processes.”

However, Tyson is focusing on a more philosophical perspective to the discovery. “The real value of these genomes is that many are evolutionarily distinct from previously recovered genomes.” He explains, “They increase the evolutionary diversity spanned by both bacterial and archaeal genome trees by over 30 per cent, and are the first representatives within 17 bacterial and three archaeal phyla.” By way of comparison, a single phylum contains all vertebrates, and another, all flowering plants.

Parks, too, recognizes this connection between this expansion of the tree of life and how the functions of these particular microbes’ will provide insight into evolutionary development. Eventually, the ability to fill in the tree of life will help us trace the origins of humanity.

Parks said, “All the questions we have about ancient evolutionary events – what our last common ancestor looked like, when methane metabolism arose, when oxygen-producing organisms evolved – they really benefit from having more genomes to look at and a more detailed tree.”

More from News

Screenshots of Kamala Harris and J.D. Vance
C-SPAN; NBC News

Kamala Harris Calls Out JD Vance For 'What He Didn't Say' During RNC Speech In Epic Takedown

In a fiery speech to supporters in North Carolina, Vice President Kamala Harris called out what J.D. Vance—former President Donald Trump's freshly selected running mate—"didn't say" in his speech accepting the VP nomination on Night 3 of the Republican National Convention.

Amid much talk about key conservative issues like immigration, the ongoing border crisis, and "law and order," he did not once mention what the GOP has explicitly laid out and is now attempting to distance itself from: Project 2025.

Keep ReadingShow less
Screenshot of Daniel Dale; Donald Trump
CNN; Chip Somodevilla/Getty Images

CNN Fact-Checker Debunks Trump's RNC Speech Lies For 2 Minutes Straight—And Yeah, It's A Lot

CNN fact-checker Daniel Dale debunked lies former President Donald Trump told during his acceptance speech at the Republican National Convention, dedicating two minutes to picking apart Trump's many falsehoods.

Trump made numerous oddball remarks during his speech, particularly his reference that the world was "at peace" when he was in office until his political opponents "turned it into a planet of war," declaring that the planet is now "blowing up around us" due to Democratic policies.

Keep ReadingShow less
Screenshots of Donald Trump and Tiffany Trump
C-SPAN

Trump Snubbed Daughter Tiffany As She Went In For A Kiss At The RNC—And People Are Team Tiffany

Social media users were sympathetic to Tiffany Trump after her father, former President Donald Trump, appeared to snub her as she went in for a kiss before his climactic speech accepting the GOP's presidential nomination.

Footage from early in the evening shows a smiling Tiffany walking up the stairs toward Trump, who clearly saw her. She then attempted to greet him with a kiss only to be ignored, as he looked out at the crowd beyond her, as she walked away looking dejected.

Keep ReadingShow less
Picture of Marjorie Taylor Greene seen on "The Daily Show" with Jon Stewart
The Daily Show

Jon Stewart Just Pointed Out The Weird Noise MTG Made During Her RNC Speech—And Now We Can't Unhear It

Jon Stewart had a lot to unpack on Tuesday's airing of The Daily Show, given a wild week that included the shocking assassination attempt on former Republican President Donald Trump as well as the Republican National Convention in Milwaukee, which kicked off on Monday.

One specific highlight from the opening night of the RNC that Jon couldn't help but fixate on was far-right Georgia Representative Marjorie Taylor Greene making strange sounds while addressing delegates during her speech.

Keep ReadingShow less
Justin Long and wife Kate Bosworth
Slaven Vlasic/Getty Images for Smile Train

Justin Long Shares Wife Kate Bosworth's 'Really Romantic' Reaction To Him Pooping The Bed

Warning: soiler alert. Graphic bowel movement descriptions ahead.

Actor Justin Long had a romantic e-poo-phany about how much he loved his wife, actor Kate Bosworth, when he soiled the bed after suffering from food poisoning during a trip to Mexico.

Keep ReadingShow less