When you look at the Great Barrier Reef, it’s easy to focus on the spectacular things you can see.
Colourful corals. Giant clams. Sea turtles. Fish moving through the reef.
But beneath this visible ecosystem exists another world that is almost completely invisible to us.
The reef has a microbiome.
And scientists have now produced one of the most detailed maps yet of this microscopic ecosystem, revealing an astonishing diversity of bacteria, archaea and viruses living in the waters surrounding Australia’s Great Barrier Reef.
The researchers identified more than 800,000 microbial genomes, including hundreds of bacterial species that had never previously been recorded in scientific databases.
An ecosystem hiding in plain sight
A microbiome is a community of microorganisms living within a particular environment.
Humans have one.
Our skin, mouth and digestive system are home to enormous populations of bacteria and other microorganisms. Scientists have spent years studying how these microscopic communities influence our health.
But ecosystems have microbiomes too.
The Great Barrier Reef is essentially a gigantic biological city, and microorganisms are among its most numerous inhabitants.
Researchers collected seawater samples from 48 different reefs and used DNA sequencing to determine which microorganisms were present.
Rather than having to grow individual microbes in a laboratory, scientists can now analyse DNA directly from environmental samples.
This technique, known as metagenomics, allows researchers to study entire microbial communities simultaneously.
And what they found was extraordinary.
Hundreds of species unknown to science
The study identified 5,283 bacterial and archaeal genomes, representing 876 distinct species.
Around two-thirds of these species were not previously represented in public databases.
In other words, scientists had never properly catalogued them before.
The researchers also detected more than 300,000 different types of viruses in the reef’s waters.
That doesn’t mean there are 300,000 completely unknown viruses capable of infecting humans.
Most environmental viruses infect microorganisms rather than people.
And that’s precisely what makes them interesting.
Viruses are an important part of microbial ecosystems. They infect bacteria and other organisms, influencing which species thrive and helping recycle nutrients through the environment.
The reef’s invisible inhabitants are therefore not simply passengers in the water.
They are helping run the ecosystem.
Why do microbes matter to a coral reef?
Coral reefs depend on incredibly complicated biological relationships.
Corals themselves live in partnership with microscopic algae that provide them with energy through photosynthesis.
But this is only one part of the microbial story.
Bacteria and other microorganisms participate in processes involving carbon, nitrogen, phosphorus and other nutrients.
Some help break down organic material.
Others produce chemicals that can influence neighbouring organisms.
Some microbes can become particularly important when environmental conditions change.
That means the reef’s microbiome could potentially provide scientists with an early-warning system for the health of the ecosystem.
Instead of waiting until coral visibly bleaches or dies, researchers could potentially detect changes in its microbial community first.
A microscopic health check for the reef
Imagine being able to monitor a reef without relying solely on what you can see.
A coral might look relatively healthy to a diver while its surrounding microbial community is already changing.
If particular groups of microorganisms consistently increase or disappear when a reef experiences heat stress, pollution or other environmental pressures, scientists could potentially use those changes as biological indicators.
The Great Barrier Reef Microbial Genomes Database created by the researchers provides a huge new resource for investigating these relationships.
It’s similar to having a detailed medical record of the reef’s microscopic inhabitants.
Scientists can now begin asking questions such as:
Which microbes are associated with healthy reefs?
Which ones appear when reefs become stressed?
Which microorganisms are responsible for important chemical processes?
And perhaps most importantly:
How does this invisible ecosystem change as the planet changes?
We are still discovering most of the microbial world
One of the most fascinating aspects of this research is what it says about our understanding of life on Earth.
We tend to think of species discovery as something involving an animal or plant that nobody has ever seen before.
But enormous numbers of organisms remain unknown to science simply because they are microscopic.
Many cannot easily be cultured in a laboratory.
Others live in environments that are difficult to sample.
Modern DNA sequencing is changing that.
Instead of asking, “Can we catch this organism and grow it?”, scientists can increasingly ask:
“Can we find its DNA?”
That shift is revealing an enormous hidden layer of Earth’s biodiversity.
And the Great Barrier Reef is providing an excellent example.
The reef isn’t just coral
The phrase “coral reef” can make the ecosystem sound simpler than it really is.
A reef isn’t simply coral surrounded by fish.
It is a vast network of organisms interacting with one another at every scale imaginable.
There are animals large enough to see from space.
There are organisms smaller than the width of a human hair.
And between them exists a microscopic ecosystem containing thousands of different organisms that scientists are only beginning to understand.
The latest research gives us a glimpse into that hidden world.
The next time you look at a coral reef, remember that almost everything happening there is invisible to your eyes.
The colourful world above the surface may be spectacular.
But underneath it is an entire microbial civilisation.
And we’re only just beginning to map it.