Like the ocean’s ‘gut flora’: we sailed from Antarctica to the equator to learn how bacteria affect ocean health


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Eric Jorden Raes, Dalhousie UniversityAboard an Australian research vessel, the RV Investigator, we sailed for 63 days from Antarctica’s ice edge to the warm equator in the South Pacific and collected 387 water samples.

Our goal? To determine how the genetic code of thousands of different micro-organisms can provide insights into the ocean’s functional diversity — the range of tasks performed by bacteria in the ocean.

Our research was published yesterday in Nature Communications. It showed how bacteria can help us measure shifts in energy production at the base of the food web. These results are important, as they highlight an emerging opportunity to use genetic data for large-scale ecosystem assessments in different marine environments.

In light of our rapidly changing climate, this kind of information is critical, as it will allow us to unpack the complexity of nature step by step. Ultimately, it will help us mitigate human pressures to protect and restore our precious marine ecosystems.

Why should we care about marine bacteria?

The oceans cover 71% of our planet and sustain life on Earth. In the upper 100 meters, the sunlit part of the oceans, microscopic life is abundant. In fact, it’s responsible for producing up to 50% of all the oxygen in the world.

A whale breaches the ocean
Marine bacteria provide the energy and food for the entire marine food web, from tiny crustaceans to whales.
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Much like the link recently established between human health and the human microbiome (“gut flora”), ocean health is largely controlled by its bacterial inhabitants.

But the role of bacteria go beyond oxygen production. Bacteria sustain, inject and control the fluxes of energy, nutrients and organic matter in our oceans. They provide the energy and food for the entire marine food web, from tiny crustaceans to fish larvae, whales and the fish we eat.

These micro-organisms also execute key roles in numerous biogeochemical cycles (the carbon, nitrogen, phosphorus, sulphur and iron cycles, to name a few).

So, it’s important to quantify their various tasks and understand how the different bacterial species and their functions respond to environmental changes.

Fundamental questions

Global ocean research initiatives — such as GO-SHIP and GEOTRACES — have been measuring the state of oceans in expeditions like ours for decades. They survey temperature, salinity, nutrients, trace metals (iron, cobalt and more) and other essential ocean variables.

Only recently, however, have these programs begun measuring biological variables, such as bacterial gene data, in their global sampling expeditions.

The author smiles in front of a blue and white ship, with 'Investigator' written on the side.
On board the RV Investigator, we departed Hobart in 2016, beginning our 63-day journey to sample microbes in the South Pacific.
Eric Raes, Author provided

Including bacterial gene data to measure the state of the ocean means we can try to fill critical knowledge gaps about how the diversity of bacteria impacts their various tasks. One hypothesis is whether a greater diversity of bacteria leads to a better resilience in an ecosystem, allowing it to withstand the effects of climate change.

In our paper, we addressed a fundamental question in this global field of marine microbial ecology: what is the relationship between bacterial identity and function? In other words, who is doing what?

What we found

We showed it’s possible to link the genetic code of marine bacteria to the various functions and tasks they execute, and to quantify how these functions changed from Antarctica to the equator.

The functions that changed include taking in carbon dioxide from the atmosphere, bacterial growth, strategies to cope with limited nutrients, and breaking down organic matter.




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Marine life is fleeing the equator to cooler waters. History tells us this could trigger a mass extinction event


Another key finding is that “oceanographic fronts” can act as boundaries within a seemingly uniform ocean, resulting in unique assemblages of bacteria with specific tasks. Oceanographic fronts are distinct water masses defined by, for instance, sharp changes in temperature and salinity. Where the waters meet and mix, there’s high turbulence.

The change we recorded in energy production across the subtropical front, which separates the colder waters from the Southern Ocean from the warmer waters in the tropics, was a clear example of how oceanographic fronts influenced bacterial functions in the ocean.

Dark blue water meets light blue water under a cloudy sky.
An oceanographic front, where it looks like two oceans meet.
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Tracking changes in our ecosystems

As a result of our research, scientists may start using the functional diversity of bacteria as an indicator to track changes in our ecosystems, like canaries in a coal mine.




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Half of global methane emissions come from aquatic ecosystems – much of this is human-made


So the functional diversity of bacteria can be used to measure how human growth and urbanisation impact coastal areas and estuaries.

For example, we can more accurately and holistically measure the environmental footprint of aquaculture pens, which are known to affect water quality by increasing concentrations of nutrients such as carbon, nitrogen and phosphorus – all favourite elements utilised by bacteria.

Likewise, we can track changes in the environmental services rendered by estuaries, such as their important role in removing excessive nitrogen that enters the waterways due to agriculture run-off and urban waste.

With 44% of the world’s population living along coastlines, the input of nitrogen to marine ecosystems, including estuaries, is predicted to increase, putting a strain on the marine life there.

Ultimately, interrogating the bacterial diversity using gene data, along with the opportunity to predict what this microscopic life is or will be doing in future, will help us better understand nature’s complex interactions that sustain life in our oceans.




Read more:
Humans are polluting the environment with antibiotic-resistant bacteria, and I’m finding them everywhere


The Conversation


Eric Jorden Raes, Postdoctoral researcher Ocean Frontier Institute, Dalhousie University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

We found methane-eating bacteria living in a common Australian tree. It could be a game changer for curbing greenhouse gases


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Luke Jeffrey, Southern Cross UniversityTrees are the Earth’s lungs – it’s well understood they drawdown and lock up vast amounts of carbon dioxide from the atmosphere. But emerging research is showing trees can also emit methane, and it’s currently unknown just how much.

This could be a major problem, given methane is a greenhouse gas about 45 times more potent than carbon dioxide at warming our planet.

However, in a world-first discovery published in Nature Communications, we found unique methane-eating communities of bacteria living within the bark of a common Australian tree species: paperbark (Melaleuca quinquenervia). These microbial communities were abundant, thriving, and mitigated about one third of the substantial methane emissions from paperbark that would have otherwise ended up in the atmosphere.

Because research on tree methane (“treethane”) is still in its relative infancy, there are many questions that need to be resolved. Our discovery helps fill these critical gaps, and will change the way we view the role of trees within the global methane cycle.

Wait, trees emit methane?

Yes, you read that right! Methane gas within cottonwood trees was first reported in 1907, but has been largely overlooked for almost a century.

Only in 2018 was a tree methane review published and then a research blueprint put forward, labelling this as “a new frontier of the global carbon cycle”. It has since been gaining rapid momentum, with studies now spanning the forests of Japan, UK, Germany, Panama, Finland, China, Australia, US, Canada, France and Borneo just to name a few.

Research on tree methane is still in its relative infancy.

In some cases, treethane emissions are significant. For example, the tropical Amazon basin is the world largest natural source of methane. Trees account for around 50% of its methane emissions.

Likewise, research from 2020 found low-lying subtropical Melaleuca forests in Australia emit methane at similar rates to trees in the Amazon.

Dead trees can emit methane, too. At the site of a catastrophic climate-related mangrove forest dieback in the Gulf of Carpentaria, dead mangrove trees were discovered to emit eight times more methane than living ones. This poses new questions for how climate change may induce positive feedbacks, triggering potent greenhouse gas release from dead and dying trees.

Aerial shot of river through trees in the Amazon
Trees account for around 50% of the total Amazon basin methane emissions.
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Treethane emissions most likely account for some of the large uncertainties within the most recent global methane budget, which tries to determine where all the methane in the atmosphere comes from. But we’re still a long way from refining an answer to this question. Currently, trees are not yet included as a distinct emissions category.

So where exactly is the treethane coming from?

Within wetland forests, scientists assumed most treethane emissions originate from the underlying soils. The methane is transported upwards via the tree roots and stems, then through to the atmosphere via their bark.

We confirmed, in other recent research, that wetland soils were indeed the source of methane emissions in lowland forest trees. But this wasn’t always the case.

Some lowland forest trees such as cottonwood can emit flammable methane directly from their stems, which is likely produced by microbes living within the moist trees themselves. Dry upland forest trees are also emerging as methane emitters too — albeit at much lower rates.

Paperbark trees surround a body of water
Paperbark forest in a wetland, where bark-dwelling methane-eating microbes were discovered.
Luke Jeffrey, Author provided

Discovering methane-eating bacteria

For our latest research, we used microbiological extraction techniques to sample the diverse microbial communities that live within trees.

We discovered the bark of paperbark trees provide a unique home for methane-oxidizing bacteria — bacteria that “consumes” methane and turns it into carbon dioxide, a far less potent greenhouse gas.

Remarkably, these bacteria made up to 25% of total microbial communities living in the bark, and were consuming around 36% of the tree’s methane. It appears these microbes make an easy living in the dark, moist and methane-rich environments.




Read more:
Emissions of methane – a greenhouse gas far more potent than carbon dioxide – are rising dangerously


This discovery will revolutionise the way in which we view methane emitting trees and the novel microbes living within them.

Only through understanding why, how, which, when and where trees emit the most methane, may we more effectively plant forests that effectively draw down carbon dioxide while avoiding unwanted methane emissions.

Author sampling microbes from paperbark tree
Microbe sampling techniques have advanced within the last few decades, allowing us to understand the diverse microbial communities living within trees.
Luke Jeffrey, Author provided

Our discovery that bark-dwelling microbes can mitigate substantial treethane emissions complicates this equation, but provides some reassurance that microbiomes have evolved within trees to consume methane as well.

Future work will undoubtedly look further afield, exploring the microbial communities of other methane-emitting forests.

A trillion trees to combat climate change

We must be clear: trees are in no way shape or form bad for our climate and provide a swath of other priceless ecosystem benefits. And the amount of methane emitted from trees is generally dwarfed by the amount of carbon dioxide they will take in over their lifetime.

However, there are currently 3.04 trillion trees on Earth. With both upland and lowland forests capable of emitting methane, mere trace amounts of methane on a global scale may amount to a substantial methane source.

As we now have a global movement aiming to reforest large swaths of the Earth with 1 trillion trees, knowledge surrounding methane emitting trees is critical.




Read more:
Half of global methane emissions come from aquatic ecosystems – much of this is human-made


The Conversation


Luke Jeffrey, Postdoctoral Research Fellow, Southern Cross University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Humans are polluting the environment with antibiotic-resistant bacteria, and I’m finding them everywhere



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Michelle Power, Macquarie University

Many of us are aware of the enormous threat of antibiotic- (or “antimicrobial”) resistant bacteria on human health. But few realise just how pervasive these superbugs are — antimicrobial-resistant bacteria have jumped from humans and are running rampant across wildlife and the environment.

My research is revealing the enormous breadth of wildlife species with superbugs in their gut bacterial communities (“microbiome”). Affected wildlife includes little penguins, sea lions, brushtailed possums, Tassie devils, flying foxes, echidnas, and a range of kangaroo and wallaby species.




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To combat antibiotic resistance, we need to use “One Health” — an approach to public health that recognises the interconnectedness of people, animals and the environment.

And this week’s appointment of federal Environment Minister Sussan Ley to the world’s first One Health Global Leaders Group on Antimicrobial Resistance, brings me confidence we’re finally heading in the right direction.

Where we’ve found superbugs

Tackling antimicrobial resistance with One Health requires studying resistance in bacteria from people, domesticated animals, wildlife and the environment.

Tasmanian devil standing on a rock
Tasmanian devils are among the species we’ve found harbouring resistant bacteria.
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Humans have solely driven the emergence and spread of antimicrobial-resistant bacteria, mainly through the overuse, and often misuse, of antibiotics.

The spread of superbugs to the environment has mainly occurred through human wastewater. Medical and industrial waste, which pollute the environment with the antibiotics themselves, worsen the issue. And the ability for antibiotic-resistant genes to be shared between bacteria in the environment has propelled antimicrobial resistance even further.




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How antibiotic pollution of waterways creates superbugs


Generally, wildlife closer to people in urban areas are more likely to carry antimicrobial-resistant bacteria, because we share our homes, food waste and water with them.

For example, our recent research showed 48% of 664 brushtail possums around Sydney and Melbourne tested positive for antibiotic-resistant genes.

Brushtailed possum in a tree
Hundreds of possums around Sydney and Melbourne have resistant bacteria.
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Whether animals are in captivity or the wild also plays a role in their levels of antimicrobial resistance.

For example, we found only 5.3% of grey-headed flying-foxes in the wild were carrying resistance traits. This jumps to 41% when flying-foxes are in wildlife care or captivity.

Likewise, less than 2% of wild Australian sea lions we tested had antibiotic-resistant bacteria, compared to more than 40% of those in captivity. We’ve found similar trends between captive and wild little penguins, too.

And more than 40% of brush-tailed rock wallabies in a captive breeding program were carrying antibiotic resistance genes compared to none from the wild.

So why is this a problem?

An animal with antibiotic-resistant bacteria may be harder to treat with antibiotics if it’s injured or sick and ends up in care. But generally, we’re yet to understand their full impact – though we can speculate.

Grey-headed flying-foxes hanging from a branch
We’ve found new types of resistant genes in flying-fox communities.
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For wildlife, resistant bacteria are essentially “weeds” in their microbiomes. These microbial weeds may disrupt the microbiomes, impairing immunity or increasing the risk of infection by other agents.

Another problem relates to how antimicrobial-resistant bacteria can spread their resistant genes to other bacteria. Sharing genes between bacteria is a major driver for new resistant bacterial strains.

We’ve been finding more types of resistant genes in an animal’s microbiome than we do in comparison to commonly studied bacteria, such as Escherichia coli. This means some wildlife bacteria may have acquired resistance genes, but we don’t know which.

Many of the wildlife species we’ve examined also carry human-associated bacterial strains — strains known to cause, for instance, diarrhoeal disease in humans. In wildlife, these bacteria could potentially acquire novel resistance genes making them harder to treat if they spread back to people.

This is something we found in grey-headed flying-fox microbiomes, which had new combinations of resistant genes. These, we concluded, originated from the outside environment.

How do we mitigate this threat?

Antimicrobial stewardship — using the best antibiotic when a bacterial infection is diagnosed, and using it appropriately — is a big part of tackling this global health issue.

This is what’s outlined in Australia’s National Antimicrobial Resistance Strategy: 2020 & Beyond, which the federal government released in March this year.

The 2020 strategy builds on a previous strategy by better incorporating the environment, in what should be a true “One Health” approach. The World Health Organisation’s appointment of Ley supports this.

Antimicrobial stewardship is equally important for those in veterinary fields as well as medical doctors. As Australia leads the world in wildlife rehabilitation, antimicrobial stewardship should be a major part of wildlife care.

For the rest of us, preventing our superbugs from spilling over to wildlife also starts with taking antibiotics appropriately, and recognising antibiotics work only for bacterial infections. It’s also worth noting you should find a toilet if you’re out in the bush (and not “go naturally”), and not leave your food scraps behind for wild animals to find.




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‘Deeply worrying’: 92% of Australians don’t know the difference between viral and bacterial infections


The 2020 strategy recognises the need for better communication to strengthen stewardship and awareness. This should include education on the issues of antimicrobial resistance, what it means for wildlife health, and how to mitigate it.

Citizens tackle antibiotic resistance in the wild.

This is something my colleagues and I are tackling through our citizen science project, Scoop a Poop, where we work with school children, community groups and wildlife carers who collect possum poo around the country to help us better understand antimicrobial resistance in the wild.

The power of working with citizens to better the health of our environment cannot be overstated.




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Explainer: what are superbugs and how can we control them?


The Conversation


Michelle Power, Associate Professor in the Department of Biological Sciences, Macquarie University

This article is republished from The Conversation under a Creative Commons license. Read the original article.