Why we need to think small
Microbes aren’t the most obvious conservation priority, but a lot depends on them – including us. HANNAH THOMASY reports.
TO SAVE THE EARTH WE HAVE TO START THINKING SMALL
MOST LISTS of the world’s endangered species don’t include Prochlorococcus – but they just might be the most important of all.
It’s estimated that these photosynthetic bacteria produce 10% of the Earth’s oxygen, but a recent study by Macquarie University shows that their growth and ability to photosynthesise are being significantly affected by plastic leachates – chemicals that leach out of plastic when it’s exposed to sea water. That’s important to know, but we need to know a lot more.
“There is very little research into how Prochlorococcus, or indeed any marine photosynthetic bacteria, are affected by human pollutants – that was one of the key drivers for us to undertake our research,” says lead author Sasha Tetu, a professor in the university’s Molecular Sciences Department.
US microbial ecologist Jack Gilbert agrees. “Bacteria in the ocean produce 50% of the world’s oxygen,” he says.
“If you thought trees were important – yeah, they are, but they’re only half the story. Without microbial photosynthesis in the ocean, you don’t have enough oxygen on the planet to breathe.”
Gilbert, a professor in both oceanography and paediatrics at University of California San Diego, has studied microbial communities in everything from the Arctic Ocean and mangrove forests to the human gut. He says oxygen production is just one of many ways that microbes help sustain life on Earth, and it is imperative that we learn more about them so we can conserve them and ensure they keep providing vital services.
Microbe is a catch-all term for any organism that is too small to be seen with the naked eye. This extremely diverse group includes viruses, bacteria, archaea, and protists, as well as very small or single-celled plants, animals, and fungi.
As well as producing oxygen, microbes perform many functions that are essential for life as we know it. Both on land and in the ocean, they are at the bottom of many food webs, serving as lunch for many animals.
Microbes also perform essential decomposition services.
“Microbes remove all of our waste; without them we would be knee deep in waste,” says Gilbert. “And the air and the water would be toxic. We couldn’t drink it or breathe it.”
Noah Fierer, a microbial ecologist from the University of Colorado Boulder in the US, says microbes in the soil are essential for plant growth, both in agriculture and natural ecosystems.
“They have a huge influence, directly and indirectly, on how well plants grow,” he says.
“The microbes that associate with plants can defend them from pathogens… There’s also a strong influence of soil microbes on nutrient availability.
“Microbes break down organic matter and make nitrogen and phosphorous available to plants. They can even influence moisture availability. So, for example, most plants associate with fungi that can help plants scavenge water from the soil.”
It’s estimated that at least 20,000 species of plants directly depend on microbes for survival; in some ecosystems, they provide up to 86% of the nitrogen plants need to survive.
Despite their size, microbes also have a surprisingly large influence on the planet’s climate, in both positive and negative ways. Some break down organic matter, releasing greenhouse gases like carbon dioxide, nitrous oxide, and methane, which could increase the temperature of the planet; but others could help cool the planet.
Microbes in soils and in the oceans play a huge role in carbon sequestration. In fact, just two types of marine bacteria – one of them Prochlorococcus – remove around 10 billion tonnes of carbon from the atmosphere each year.
Others, found in soils and aquatic environments, can remove methane from the atmosphere.
Microbes can also produce an anti-greenhouse gas called dimethyl sulfide (DMS), which is important for cloud formation. And that’s just the valuable functions we know about.
“If there’s a way to make a living, a microbe has figured out how to do it… because they’ve had three billion years of evolution to figure it out,” says Fierer. Almost every year, there’s totally new metabolic processes that we discover.”
The risk is not that human influence will kill all the microbes, but that we will sufficiently alter their communities in ways that are detrimental to the survival of plants, animals or us.
Plastic in the ocean is a good example. Plastics don’t indiscriminately kill bacteria, says Gilbert, but “if you pump the environment full of plastics and microplastics, you select for bugs that can actually out-compete some of the bugs that are helping to recycle our nutrients, to capture our carbon, to produce our oxygen.
“You change the ecosystem and the ecosystem no longer supports the services that we rely on.”
Mangrove trees that live along tropical coastlines are a perfect example, he adds. “When we have organic matter pollution in mangrove swamps, one of the reasons the trees don’t survive very well is that we kill off some of the bacteria in the sediments which help to recycle the nutrients which feed the trees and keep them healthy.
“You select for an entirely new environment, which is not ideal for supporting the resilience and resistance of those trees to stress. So, the mangroves start dying and when the mangroves start dying, you completely decimate the local fish nurseries. When fish nurseries disappear, the fishing industry disappears.”
Other pollutants such as heavy metals, pesticides and crude oil also can alter microbial communities, and deforestation and agricultural practices can influence the numbers and types of microbes in a given location.
Not every situation is the same and there may be situations where the loss of a particular microbe does not have too great an impact because others are able to fill in for its core functions. But we don’t really know enough about it yet.
“We know that microbes are sensitive to how we’re treating the environment, but what that means in terms of the function of those microbes is an area of active research,” says Fierer.
So, what should we do? As in many conservation projects, one of the first steps is figuring out what’s out there. The Earth Microbiome Project is an ambitious attempt to do just that.
Founded by Gilbert, the Pacific Northwest National Laboratory’s Janet Jansson, and University of California San Diego’s Rob Knight in 2010, the project’s mission is to characterise microbial life in 200,000 samples obtained from different environments across the globe.
Nicole Webster, a principal research scientist at the Australian Institute of Marine Science, says another important step is to figure out how to minimise the harmful effects of human activities on microbes.
“We have these conservation guidelines for our more charismatic animals like corals,” she says. “So, we know for instance that corals spawn during a certain part of the year and that the spawn can be particularly sensitive to suspended sediments and therefore a lot of the dredging activity that happens near coral reefs is actually shut down for that period around coral spawnings…
“From our understanding of biology, we change our management practices to best conserve the environment… We’re not having the same conversation about microbes despite the fact that microbial ecologists know how fundamentally important these microbes are to the ecosystem processes.”
Policy changes are sorely needed to help protect microbes from threats such as pollution, harmful agricultural practices, and climate change, but many fear these won’t happen soon enough to preserve important microbial communities.
That’s why the concept of a Microbiota Vault was developed: to serve as a sort of back-up server, storing microbial data in case we horribly mess up the system and need to re-boot.
Inspired by the Svalbard Global Seed Vault in Norway, the Microbiota Vault is being managed by an international group of scientists, including Gilbert, Knight, and Rutgers professors Maria DominguezBello and Martin Blaser.
Gilbert says the project was initially focused on the human gut microbiome but will be expanding into microbes of every environment. The goal, he says, is, “to create a vault for the microbiome of all the soils on the planet, the microbiome of all the sediments on the planet, even the deep ocean ones, the microbiome of every animal’s poop, every plant’s root and rhizosphere, the air we breathe, the lakes that we swim in, the rivers that we use for our navigation.
“The entire system needs preservation and if we can’t be trusted to not keep on disrupting it, we better protect it and preserve it in vitro, outside of that environment now, so that we can figure out ways to repair it when it becomes irreparably damaged and our lives are threatened.”
In places where this damage has already occurred, scientists are investigating whether it is, in fact, possible to use microbes to restore ecosystem health. Gilbert says one of his current collaborative projects involves taking soil and sediment – and the resident microbes – from healthy mangrove forests and using these soils to help restore dead areas.
Adding this soil along with its microbes before planting new mangroves will hopefully help the new trees to recolonise the area and speed up restoration. At the MPG Ranch in western Montana, scientists are studying if microbes can hinder invasive plant species. Others want to know if microbes can help corals become more resilient in the face of stress.
There’s no doubt that it’s time to include microbes in our conversations about conservation, restoration, and the future of our planet.
It’s understandably easier to inspire people to conserve cuddly pandas or majestic whales or striking pangolins than to get them care about species we can’t even see, but microbes are essential for the health of every ecosystem and the animals within them.