Shining a light on microbial dark matter

On 22 May 2017, 21 new members were elected to the Australian Academy of Science for their outstanding achievements in a wide range of scientific disciplines. We spoke to newly inducted Fellow Professor Philip Hugenholtz, a microbiologist from The University of Queensland (UQ), about how he came to be a part of such a prestigious group.

Like many of the new Fellows, Professor Hugenholtz was inspired to become a scientist at an early age. In his case it was way back in primary school, when he was tasked to do a project on the microorganisms that live in pond water.

“I remember being fascinated by the fact that there were all these little swimming organisms, that I couldn’t see by eye, that I could see under the microscope,” he said. “That unseen world was very appealing to me.”

Hugenholtz claims that microorganisms have been somewhat underappreciated throughout history, with plants and animals seen as “the crowning achievements of evolution” according to the narrative set by Charles Darwin.

“But in fact, it’s the other way around — most of the diversity on the planet is microbial, and all the things that you and I can see are pretty recent innovations,” said Professor Hugenholtz. “And that makes sense when you think about it, in terms of evolutionary timescales, because microorganisms have been around a lot longer than we have.”

Professor Hugenholtz’s fascination with the unseen world is more literal than one might expect, with the esteemed scientist taking a particular interest in ‘microbial dark matter’ — the vast majority of microorganisms that have not be grown on an agar plate.

“I was doing a postdoc in the States in the mid-90s with Norman Pace, and my job was to identify bacteria present in a hot spring at Yellowstone National Park by sequencing a little piece of their genomes, the 16S rRNA gene,” he recalled. “The important point is that we didn’t need to grow the bacteria on an agar plate in order to identify them, the same way that you can identify a loaf of bread or packet of biscuits at the supermarket by their barcodes alone.

“And when we compared these sequences against the ones known from bacteria we can grow on a plate, there was a huge disconnect. Many had nothing closely related to them at all. They were essentially indicating that there were huge groups of microorganisms that had never been characterised, because we hadn’t grown them.

“It’s estimated now, 20 years on, that only about 15% of all the diversity in the microbial world has actually got a cultured representative. The other 85% is waiting to be described, and that’s called microbial dark matter.”

Luckily for Professor Hugenholtz, the past 20 years have also seen the rise of whole genome sequencing — the process of determining the complete DNA sequence of an organism’s genome at a single time. “We can now obtain near complete genomes of uncultured organisms directly from their environmental settings, which tells us what they’re able to do, rather than just that they’re present,” he said.

Professor Hugenholtz’s team has applied this whole genome sequencing approach to many different habitats, including the notable discovery of microorganisms that are contributing to climate change. As part of a team led by Professor Gene Tyson, he and his colleagues extracted DNA from a permafrost environment, which was subsequently sequenced.

“We found a novel uncultured methane-producing organism that blooms in response to permafrost thawing,” he said. “It’s not a good idea to have something that can make methane when it’s woken up from sleep, because methane’s a potent greenhouse gas.”

This groundbreaking research, published in the journal Nature Microbiology, indicates that this previously unknown group of methane-metabolising microorganisms appears to be widespread in permafrost. It also led the researchers to wonder if this organism can be grown in the lab — because while the practice of culturing organisms has been somewhat overtaken by genome sequencing, microbial isolates are of great practical use.

“For instance, if you identify an uncultured bacterium in the guts of mice that you think might be important in causing a disease, you could test this by putting it into germ-free mice if you can grow it in the lab first,” Professor Hugenholtz noted. “So there are lots of experiments you can do with cultured organisms.”

These days, Professor Hugenholtz is based at UQ’s Australian Centre for Ecogenomics, which he co-founded with Professor Tyson. He is currently occupied working on the Genome Taxonomy DataBase (GTDB) — an Australian Research Council-funded project that seeks to use genome sequences to reclassify all microbial life.

“At the moment it’s kind of a mess, because there are a lot of microbial species that don’t form evolutionary coherent groups and the classification is very uneven,” Professor Hugenholtz said. “So we’re fixing up these issues using the genomes as a guide.”

Even though classification is a human-made construct, it’s very useful. As an example of this, Professor Hugenholtz used the analogy of time.

“We break down time into years, months, weeks, days, hours and minutes — it’s a hierarchical classification system — so you and I knew to talk on this day, at this time. And it’s the same with classification. We’re organising microorganisms in a similar way, so that they’re classified in robust and standardised heirachical system that reflects their evolution. This is particularly important as the mountains of microbial dark matter genomes come in the door — it provides the necessary framework for their classification.”

He is also investigating the human gut microbiome — the trillions of microbes that live in our digestive systems — an area that is currently of intense interest to the public as it becomes increasingly apparent that the microorganisms that live in and on us play important roles in our health and wellbeing.

“We’re applying the whole genome sequencing approach to the human gut and getting really high-resolution pictures of what’s in the gut to find out how it works,” Professor Hugenholtz said. “So I’m very excited by that too.”

Professor Hugenholtz and 20 other researchers were elected to the Australian Academy of Science by their peers, following a rigorous evaluation process. Joining esteemed names such as Australia’s Chief Scientist Alan Finkel, Nobel Prize winner Brian Schmidt and Dame Bridget Ogilvie, they bring the Academy’s total fellowship up to 524 scientists.

Image credit: ©stock.adobe.com/au/Maksym Yemelyanov