Issues Magazine

A Bug’s Life

By Bonnie Laverock

From health to life on Earth as we know it, our relationship with microbes is far more complex than you might think.

What Is a Microbe?

In the 21st century, we grow up knowing that there are microbes all around us, portrayed as an invisible enemy ready to attack. We know we need to wash our hands, to clean the spaces around us, to cook our meat properly – or risk serious illness. We also know that there are such things as “friendly bacteria” in our guts that help us to digest our food properly.

Mostly, when we talk about microbes we really mean bacteria – small, single-celled organisms invisible to the naked eye. But we also interact with other types of microbe on a daily basis – microscopic fungi such as the yeasts we use to bake bread, and the Archaea.

To us, Archaea seem very similar to bacteria – tiny single cells, capable of doing many of the same things, such as breaking down carbohydrates into methane in the gut. However, the Archaea make up a domain of life that is completely separate to the domain occupied by bacteria.

As humans, we belong to the third domain of life, Eukaryota, which includes plants, animals, fungi and a large number of other microbes, such as amoebae. It’s weird to think that even though they look (and behave) so similar to bacteria, on the tree of life Archaea are actually more closely related to us eukaryotes.

The Microbial Human

The human body contains at least ten times more bacterial cells than human cells (about 1014 compared with 1013). And that’s just the bacteria – we are also home to microscopic fungi (mostly on the skin) and Archaea (in the gut). An alien observer with very powerful vision might classify a person not as a single organism but as an entire ecosystem capable of movement.

This is the idea behind the Human Microbiome Project run by the United States National Institutes of Health, which is characterising the microbes that are found on humans. Scientists working on the Human Microbiome Project have shown that healthy humans have distinct populations of different bacteria living on different areas of the skin.

For example, our faces, ears, necks and noses are mostly home to microbes called actinobacteria. Meanwhile, our arms and hands have a higher proportion of proteobacteria. It seems that the reason for this may be the availability of different carbohydrates (sugars) in different areas of the human body.

One amazing finding of the Human Microbiome Project is that every human is an individual habitat; for example, bacteria break down sugars on our tongues, but you may have a completely different community of bacteria performing this job than the person sitting next to you.

The greatest numbers of microbes in the human body live in the large intestine, where they are able to break down certain carbohydrates that our bodies wouldn’t otherwise be able to digest. It seems that gut microbes are incredibly important for human health – changes in the composition of animal gut microbial communities have been linked to cancer, obesity and even anxiety and depression.

Most of the microbes that live on our skin or inside our bodies are either neutral (they have no good or bad effect on our health) or they are beneficial in some way (such as the ones that aid our digestion). However, when our immune systems are lowered or when the microbes are in a body part they don’t normally inhabit, they can become pathogens that cause disease or infection.

An example of this is the bacterium Staphylococcus epidermidis, which normally inhabits our skin with no harmful effects. However, it can infect wounds in the human body, and because it has been found to grow very easily on plastic devices it can be a particular problem for people with catheters or prosthetic limbs.

Another example is Clostridium difficile, which normally inhabits the colon. This bacterium has received some attention because it causes antibiotic-associated diarrhoea, which occurs when a course of antibiotics has wiped out the other normal gut bacteria, allowing C. difficile to become more abundant.

We call these microbes opportunistic pathogens, because they take advantage of the right conditions (a wound, low immunity or a change in diet) to grow far more abundant than normal, and thereby become infectious.

The most important thing to realise about these microbes is that they are part of a normal, healthy body. It is only the explosion in their abundance in relation to other competing microbes that causes harm to humans.

As microbiologists we can see these changes as a change in the community structure and diversity of the microbes. In a healthy human we might observe a mix of many different species, with some more abundant than others, whereas in a diseased human we would see one dominant species while some species might disappear altogether.

Microbes Making and Using Oxygen

Microbial ecologists – scientists who study the activity and interactions of microbes in the environment – know that microbes are everywhere. From the deepest, darkest parts of the ocean, where boiling hot water bubbles out of vents in the seafloor, to the extremely dry, cold valleys of Antarctica, microbes live and thrive. And as we study them, we learn more about how life began on Earth, how life may adapt to our changing world, and even whether life can exist on other planets.

When the Earth was still only about a billion years old there was very little oxygen in the atmosphere. Archaea and bacteria evolved in the oceans, and used sunlight to gain energy by converting carbon dioxide to oxygen through photosynthesis. It was this process, driven by the microbes, that completely changed the Earth and allowed the evolution of oxygen-breathing life forms (including us).

This process wasn’t sudden. The build-up of oxygen in the oceans took about another billion years. During this time, any oxygen produced by the microbes reacted with iron and precipitated onto the seafloor, forming large deposits of iron oxide. These sedimentary rocks, which are deep red to dark brown in colour, are characteristic sources of iron ore, including those found in the Pilbara region of Western Australia. You could say that the recent mining boom in Australia owes everything to the much earlier microbial boom!

Western Australia is also home to living examples of some of the earliest life on Earth. The stromatolites of Shark Bay are microbial structures that form in shallow, warm seas, where photosynthetic microbes called cyanobacteria form colonies on the seafloor. Bacterial colonies are often sticky – think of the film (called a biofilm) of plaque on your teeth after a night’s sleep. These biofilms of bacteria trap sediment from the sea, which slowly builds up and forms cauliflower-like limestone rocks, with the outer layers always colonised by living microbes “breathing” carbon dioxide and pumping out oxygen. Stromatolite fossils have been dated to 3.5 billion years old, around the time when oxygen started building up in the Earth’s atmosphere.

Even today, a group of microbes living in our oceans – tiny photosynthetic organisms called phytoplankton – are responsible for around half of the oxygen produced by photosynthesis each year. They are the lungs of this planet, and continue to contribute to the health of the oceans. However, just like the opportunistic pathogens of the human body, certain species of phytoplankton can be harmful when they become too abundant. In lakes, rivers, estuaries and coastal regions, the number of phytoplankton can explode – we call this a bloom – so much that they become visible as a green, red or brown “tide”.

The usual effect of these blooms is to rapidly use up most of the oxygen in the water, and to block sunlight from reaching the deeper water, causing plants and fish to die. This process is called eutrophication, a problem normally associated with areas where the concentration of nutrients in the water is unusually high from agricultural and industrial run-off of nitrate and phosphate.

Sometimes the bloom has other harmful effects. Some phytoplankton called dinoflagellates (such as Karenia brevis) can be harmful to human health, causing eye and lung infections in swimmers, or causing fish and shellfish to be toxic when eaten.

The “Garbos” of Land and Sea

The Earth would be a very different place without recycling, in this case the recycling of important elements such as carbon, nitrogen, phosphorus and sulfur, as well as many trace metals and gases. A lot of this work is carried out by bacteria and Archaea, the “garbos” of our world. They are so useful because they have a wide range of different metabolisms – they are not restricted to respiring oxygen for energy, but can instead use different compounds such as nitrate or sulfate.

Because of their size, these microbes tend to live relatively close to each other, so they are able to work together and exchange the products of their metabolism. For example, certain groups of bacteria and Archaea are able to perform nitrification, which converts ammonia to nitrate. The denitrification process, which is carried out by a wide range of microbes, then converts nitrate into nitrogen gas.

These reactions are part of the nitrogen cycle, and are extremely important in most of the Earth’s ecosystems. Nitrogen is an essential element in all living things – it is present in key molecules in our bodies, such as amino acids and proteins.

Nitrogen gas is “fixed” into microbial cells through nitrogen fixation. This process occurs in soils and sediments, freshwater and seawater; a lot of nitrogen-fixing bacteria live symbiotically with plants, for example in the roots of legumes (on land) or seagrasses (in the oceans). Microbes fix nitrogen into a form that can then be taken up by the plant, and in return they are able to use the sugars excreted by the plant. Without these relationships, many plants would not be able to gain the amount of nitrogen they need to grow.

Microbe Relationships

Such relationships exist between microbes and many different forms of life. For example, most types of coral rely on a symbiotic relationship with microscopic algae called zooxanthellae. These algae are photosynthetic and produce nutrients and oxygen needed by the corals to grow and respire. Much of the beautiful colour seen on a coral reef is actually due to these microbes – when the relationship breaks down, the corals often lose their community of microbes and become “bleached”. Many of the corals on the Great Barrier Reef are now bleached due to environmental stresses such as eutrophication, an excess of sediment on the reef (which shuts out the light), or increasing seawater temperatures.

Many other marine life forms have symbiotic relationships with bacteria. For example, a lot of bacteria can communicate with each other using chemical signals and change their behaviour when they have reached the right population density.

Many bacteria in the sea are able to move using a flagellum. This allows bacteria to settle on a sea sponge, for example. When they have reached a high enough density, a chemical cue can cause the bacteria to “switch off” their ability to move so that they form a biofilm on the sponge.

This bacterial communication is called quorum sensing, and the way it works can give us important information about human diseases. Many human diseases and infections are caused by bacteria that form biofilms – on catheters and prostheses, as previously mentioned, but also on heart valves and contact lenses, in the lungs of patients with cystic fibrosis, and on the teeth and gums of people with periodontal disease.

Investigating the ways in which bacteria communicate – to form a biofilm, or to break it down – allow us to understand how disease works in our bodies.

A Question of Balance

Microbes are everywhere – indeed, we couldn’t live without them – but they can also cause problems, both for human health and for the environment. Our growing population continues to put more pressure on the natural environment, and has already led to changes in the Earth’s ecosystem. Examples in Australia include large-scale coral bleaching events or the death of seagrass meadows. Both of these habitats support food webs that are vital to Australian life, from fishing, commerce or tourism. They also have an intimate relationship with microbes, some of which can even give us more information about our own bodies.

As the planet changes, it is likely that many microbes will thrive – but as we have seen, often disease is the result of a particular type of microbe being able to thrive. Understanding and maintaining the balance of microbes – both in our bodies and in our environment – may be the best strategy for us to continue to thrive on Earth.