Into the invisible, indispensable world of microbial biodiversity

Zooming in on the micro-organisms that populate our internal and external ecosystems

Ectomycorrhizal mycelium associated to Picea glauca roots. This fungus helps move nutrients between hosts and is an important food source for invertebrates. André-Ph. D. Picard, Wikimedia Commons
26 October 2020
26 October 2020

When American poet Walt Whitman wrote the line “I contain multitudes” in his 1855 poem Song of Myself, he almost certainly wasn’t referring to the trillions of microbes sharing his body. 

Microbes are micro-organisms, such as bacteria and viruses, which are too small for us to see without using a microscope. They were the first kind of life to appear on our planet, around 3.8 billion years ago, and they’ll be the last, too. Today, they’re present everywhere that life is found on Earth, including in places where no other organisms can survive, such as in boiling hot hydrothermal vents in the ocean, and in rocks deep under the planet’s surface. And, they play critical roles in human, animal, climate and planetary health – many of which we’re only just beginning to understand.  

Despite their importance and ubiquity – there’s about a billion microbes in a teaspoon of soil – there is a huge amount we still don’t know about these microscopic beings, and comparatively few researchers dedicated to the topic. In a 2016 study, biologists at Indiana University estimated that Earth could be home to as many as a trillion microbial species, of which 99.999% remain undiscovered. “Microbial biodiversity, it appears, is greater than ever imagined,” said co-author Jay T. Lennon in a press release about the research.

A hydrothermal vent spews hot water and bits of bacterial mat at Axial Seamount. Some microbes can survive in such extreme environments. Oregon State University, Flickr
A hydrothermal vent spews hot water and bits of bacterial mat at Axial Seamount. Some microbes can survive in such extreme environments. Oregon State University, Flickr

The microbial ecosystems within

We don’t need to travel to the deepest oceans or the most isolated rainforests to encounter new microbial species, either – they could be under your fingertips as you scroll this article, or quite literally on the tip of your tongue. Microbes are so prevalent and important in our own anatomies that today’s microbiologists are beginning to look anew at what we consider “us” and “other”. Faced with evidence that over half of the cells in “our” bodies are living microbial bacteria – and that these organisms influence our emotions, thoughts, choices and health in myriad ways we’re only just starting to understand – they’ve begun to reconceptualize the human body not as a discrete individual, but as a dynamic and extremely biodiverse ecosystem.

“I love thinking that I’m like a walking rainforest,” says Jacob Mills, a microbial ecologist at the University of Adelaide in Australia. “And there’s potential for that to be a very reconnecting thought. It’s like we’re Russian dolls: we’ve got ecosystems within us, and around us, and then that’s within the wider landscape, and that’s on the planet – so from personal to planetary health, it’s all linked, all the way down.”

For Mills, that’s more than just a nice idea – it’s a call to action. He’s working with colleagues to get microbial biodiversity front of mind for parents, community developers and urban planners. That’s because people who live in cities tend to have poorer microbial biodiversity in their bodies than those who live rurally, since there tend to be fewer types of microbes in urban environments – and because the people who live there usually have less contact with microbe “hot-spots” such as soil, animals and unprocessed food. That’s been linked to weaker immune systems, higher prevalence of certain immune disorders and higher rates of issues such as asthma and allergies. There is also mounting evidence of links between gut biome imbalances and mental health challenges such as anxiety and depression. 

“The establishment of our microbiome happens when we’re very young, starting even before birth,” says Mills, “and that exposure to microbial biodiversity is particularly important for those first three years of life, because that’s when the microbiome is developing the most. And the configuration of your microbiome has a lot to do with the functionality of your immune system.”

So, the researchers are working on ways to create more opportunities for urbanites to “re-wild” their microbiomes, through means such as planting fruit trees on public land for urban foraging; establishing green walls and roofs to inhibit pollution and noise and improve people’s sensory experience of being outside; and delivering “green prescriptions”, whereby medical professionals recommend patients with non-communicable diseases or mental health challenges take part in nature-based physical activities such as walking in a park or participating in a community gardening project.

Urban Gardening at Nodeulseom, South Korea. Urbanites tend to have less microbial biodiversity because of less contact with nature. travel oriented, Flickr
Urban Gardening at Nodeulseom, South Korea. Urbanites tend to have less microbial biodiversity because of less contact with nature. travel oriented, Flickr

The microbial ecosystems outside

Our cities certainly aren’t the only sites for scientists’ quests to know, understand and conserve microbial biodiversity. Microbes’ critical roles in all of Earth’s ecosystems are slowly being uncovered. Ninety percent of marine biomass is microbial, and these organisms produce almost half of the oxygen in our atmosphere; sit at the base of the marine food chain, serving as food for fish, krill and whales; and play a primary role in sequestering carbon and other greenhouse gases. For instance, microbial communities at undersea hydrothermal vents consume much of the methane that these vents emit, preventing it from rising to the ocean’s surface and escaping into the Earth’s atmosphere. 

On land, micro-organisms are critical for soil ecology and fertility – they regulate the flow of nutrients to plants, decompose organic matter, play a key role in nitrogen-fixing and help to detoxify pollutants. By colonizing plant roots and creating long fungal filaments called mycorrhizae, microbial fungi can extent those roots’ reach by up to a hundred times, channelling nutrients and water back to the plant and enabling it to communicate with other plants in the area. Healthy populations of beneficial soil microbes also help to ward off colonization by less-friendly versions, such as those that cause crop diseases; that’s one reason why sustainable agriculture advocates tend to avoid additives such as synthetic fertilizers, pesticides and insecticides, which can kill off those useful microbes alongside damaging ones.

Human-induced phenomena like pollution, ocean acidification, habitat destruction and climate change all impact the Earth’s microbial communities and are already jeopardizing their ability to carry out the functions so critical for the rest of species’ survival. In a 2019 “warning to humanity” consensus statement, 33 microbiologists stated that “[m]icroorganisms support the existence of all higher trophic life forms. To understand how humans and other life forms on Earth (including those we are yet to discover) can withstand anthropogenic climate change, it is vital to incorporate knowledge of the microbial ‘unseen majority’.”

As scientists, policymakers and civil society representatives gather this month to chart the global course for biodiversity conservation (through the Convention on Biological Diversity’s Post-2020 Biodiversity Framework) and restoration (through the upcoming UN Decade on Ecosystem Restoration), it may be useful to remain cognizant of our place in the living systems that surround us – and to take stock of how we are tending to our own personal ecosystems. “We can’t really begin to restore the land until we restore ourselves,” said Mills. “How can we pretend that we know what healthy land looks like, if we don’t even know what health for ourselves looks like?”


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