What we’ve discovered about amazing microbes

When I look into the microbial world, I imagine it’s a bit like an astronomer looking into the universe. It’s equally as wondrous, daunting and humbling when you realise that in every single gram of soil, there’s billions of microbes with all sorts of different forms and functions. It’s even more mind-boggling how much they influence our world and how they’ve shaped our own evolution.

Anything is possible for microbes. We’ve observed them just about everywhere: from the smouldering craters of volcanoes to the frozen wilderness of Antarctica, to the deep dark depths of the ocean.

One reason they’re so widespread is that, unlike us, they don’t require organic foods and instead can get energy from just about anything. Wherever there is the slightest glimmers of sunlight, toxic gases like carbon monoxide, or even radioactive metals like uranium, you can guarantee there’ll be a microbe out there thriving. I imagine that if you transplanted some of them onto the surface of Mars, they wouldn’t necessarily thrive, but some would survive for quite a while.

Scientists such as myself haven’t yet been able to identify and catalogue all the different species of microbes, but we’re getting there. There have been huge advances in the last 10 to 20 years, especially with metagenomics. Through this we can look at the DNA content of all the microbes in any environment and reconstruct what they’re doing. We’ve uncovered a whole new life on this planet, with potential applications for dealing with some of the biggest challenges of our time.

Scientists such as myself haven’t yet been able to identify and catalogue all the different species of microbes, but we’re getting there

Microbiology was something I stumbled into. I was interested in a lot of things, but I didn’t really have a clear plan. It was only in the very last stages of my PhD when I finally realised that microbes are amazing and the work I was doing was really interesting. And that I was actually pretty good at it.

What clicked for me was the realisation that through science, you’re not just following in someone else’s footsteps, learning what’s been done before. Instead, you’re actually creating new knowledge. There are so many things we don’t understand about the world that are waiting to be discovered, and there are many ways we can use that knowledge to do good. Most people, especially those who struggle with confidence like I did, don’t realise that they can play an active part in making discoveries. When that realisation finally dawned on me, it was an incredible moment. It wouldn’t have been possible without an empowering mentor, my PhD supervisor Professor Greg Cook at the University of Otago, New Zealand.

Microbes were the first life forms on Earth and have been around for 3.5 billion years. Microbes also formed the first eukaryotic cells – and all humans are eukaryotes. We have all ultimately descended from them.

It’s thought that those first life forms were not powered by organic foods, but by gas. The earliest microbes ate the hydrogen seeping out of deep-sea hydrothermal vents. This rich source of energy allowed them to grow, diversify, and gradually develop complexity. From my own work, we now know that this very same gas, hydrogen, continues to sustain many trillions of bacterial cells in all sorts of environments today.

One of our biggest discoveries is that hydrogen found in our atmosphere powers microbes. When we think of air, we normally think of it as a source of oxygen for breathing, nitrogen for nitrogen fixation, and carbon dioxide for photosynthesis. But it’s not conventionally thought of as a source of energy. Yet there’s tiny amounts of hydrogen always circulating through our air – about one molecule in every million. It’s too low to power our bodies or cars, but more than enough to sustain countless microbes in our soils.

This discovery was totally unexpected

This discovery came from asking a very simple question: how do microbes live for literally decades without their preferred organic foods? It’s generally thought that microbes simply “hibernate” when they’ve exhausted their preferred foods. However, we showed they in fact broaden their appetites and will scavenge anything they find. The tiny amounts of hydrogen provide a sort of indefinite lifeline to them. The idea is that, if there’s nothing else around in your environment to sustain you, there’s always going to be a little bit of hydrogen in the atmosphere. So if you’re a microbe that can do this, your chances of survival are very good.

To discover this, we took a microbe called Mycobacterium smegmatis (found in soil and certain human tissues!) and let it eat all the organic foods to the point that it stopped growing. During survival, this microbe turned off expression of the genes for using organic foods, but switched on a bunch of other genes, including those for using hydrogen.

Then I had my eureka moment!

When the microbe had used up all the organic energy sources we supplied it, I observed it still took up energy, but from the atmosphere instead. When we deleted the genes responsible for this process, the microbe could no longer scavenge hydrogen and was unable to survive for long periods.

This discovery was totally unexpected.

We’ve shown microbes guzzle atmospheric carbon monoxide too, helping keep air pollution in check.

We also now have a good understanding of how this process happens at the atomic level, but also why it’s important at the global scale. This hidden process controls the composition of the atmosphere, helping to reduce climate change, and supports the biodiversity of our land and waters worldwide.

About a third of all climate change is caused by emissions from microbes due to increased human activity

In fact, these discoveries have helped us uncover how life on an entire continent exists. It’s been known for decades that there’s lots of life in Antarctica’s cold, dry, exposed soils, but it’s mainly microbial in nature.

In most of the continent, the conditions are too extreme for plants to grow and thrive by conventional photosynthesis. Instead, gas-guzzling microbes are at the basis of the food chain. Rather than use solar energy, these microbes meet their energy and carbon needs by consuming hydrogen and carbon dioxide straight from the atmosphere. They even make vast amounts of water through this process. So it explains why life can exist in the coldest, driest continent.

About a third of all climate change is caused by emissions from microbes due to increased human activity. They produce vast amounts of methane and nitrous oxide every day through the agricultural and waste sectors. But given microbes also use gases like methane as energy sources, we can also harness them to mop up some of the mess we’ve created. This will help to build a more circular economy.

We’re partnering with several sectors, namely the energy, agricultural, and waste, to see if we can not only cut emissions, but also bypass and recycle them. Microbes offer a solution because they’re already doing this, without any need for additional power, and that’s how they’ve lived for billions of years. It’s also possible to harness them at scale, as reflected by the incredible treatment plants that use microbes to detoxify the billions of litres of wastewater each day.

Ultimately, microbes haven’t just determined our past, but also hold the keys to our future. By using them for good and at scale, we might just be able to counteract some of the biggest problems we’ve created.

As told to Cosmos contributor Graem Sims.