Tag Archives: microorganisms

Wild microorganisms are evolving to eat plastic pollution

Microorganisms around the world are likely evolving to be able to degrade and consume plastic materials.

Image via Pixabay.

A new global assessment of microorganism genomes, the largest study of its kind, found that wild bacteria and microbes are evolving to be able to consume plastics. Overall, the authors report that an average of one in four of the organisms analyzed in the study carried at least one enzyme that could degrade plastic. Furthermore, the number and types of enzymes matched the amount and type of plastic pollution at the location where samples of different organisms were collected — suggesting that this is a natural, ongoing process, caused by the presence of plastic in the environment.

These results are evidence that plastic pollution is producing “a measurable effect” on the world’s microbes, the authors conclude.

Plastic bacteria

“We found multiple lines of evidence supporting the fact that the global microbiome’s plastic-degrading potential correlates strongly with measurements of environmental plastic pollution — a significant demonstration of how the environment is responding to the pressures we are placing on it,” said Prof Aleksej Zelezniak, at Chalmers University of Technology in Sweden.

Millions of tons of plastic are dumped in the oceans and landfills every year, and plastic pollution has become endemic everywhere on Earth. Addressing this issue will be one of the defining challenges of future generations along with efforts to reduce our reliance on such materials and improve our ability to recycle and cleanly dispose of used plastic. However, plastics are hard to degrade — that hardiness is one of their selling points to begin with.

According to the findings, microbes in soils and oceans across the globe are also hard at work on the same project. The study analyzed over 200 million genes from DNA samples taken from environments all around the world and found 30,000 different enzymes that could degrade 10 different types of plastics. such compounds could serve us well in our efforts to recycle plastics, breaking them down into their building blocks. Having more efficient recycling methods on hand would go a long way towards cutting our need to produce more plastics.

“We did not expect to find such a large number of enzymes across so many different microbes and environmental habitats. This is a surprising discovery that really illustrates the scale of the issue,” says Jan Zrimec, also at Chalmers University, first author of the study.

The team started with a dataset of 95 microbial enzymes already known to degrade plastic; these compounds were identified in species of bacteria found in dumps and similar places rife with plastic.

They then looked at the genes that encode those enzymes and looked for similar genes in environmental DNA samples collected at 236 sites around the world. To rule out any false positives, they compared the enzymes with enzymes from the human gut — all of which are known to be unable to degrade plastic.

Roughly 12,000 new enzymes were identified from ocean samples. Higher levels of degrading enzymes were routinely found in samples taken at deeper points, which is consistent with how plastic pollution levels vary with depth. Some 18,000 suitable genes were identified in soil samples. Here, too, the researchers underscore the effect of environmental factors: soils tend to contain higher levels of plastics with phthalate additives than the ocean, and more enzymes that can attack these substances were identified in soil samples.

Overall, roughly 60% of the enzymes identified in this study did not fit into a previously-known class, suggesting that they act through chemical pathways that were previously unknown to science.

“The next step would be to test the most promising enzyme candidates in the lab to closely investigate their properties and the rate of plastic degradation they can achieve,” said Zelezniak. “From there you could engineer microbial communities with targeted degrading functions for specific polymer types.”

The paper “Plastic-Degrading Potential across the Global Microbiome Correlates with Recent Pollution Trends” has been published in the journal Microbial Ecology.

Deep burial in sub-seafloor sediments seems to ‘freeze’ microorganism evolution

Scientists at the Center for Geomicrobiology at the Aarhus University, Denmark, have sequenced the genome of several bugs living in the subsurface seabed in Aarhus Bay. They found that because of the extreme energy deprivation, evolution can slow down or even grind to a halt in such environments.

The researchers used gravity coring to analyze sediment stacks up to 10 m long.
Image credits Nils Risgaard-Petersen.

For the most part, microorganisms are notoriously prone to proliferate. This huge speed of multiplication, combined with selective and accidental mutational processes, makes them hugely adaptable and quick to differentiate into new strains, or speciate.

That is, unless they live in the subsurface seabed, according to Danish researchers.

By analyzing sediment cores reaching back up to 10,000 years ago (roughly the end of the last glaciation) taken from Aarhus Bay, researchers at the Center for Geomicrobiology at Aarhus University, Denmark, have found that the extreme environments at that depth can “arrest” evolution for millennia under layers of mud.

Old folks

The team was able to show that microorganisms living in the deep seabed have generation times (the gap between two successive generations) of up to 100 years. Which is a lot even by human standards. But it’s immense when you consider that bacteria in your gut, for example, have generation times of about 20 minutes. A low rate of division also means that these bugs are relatively genetically stable over time.

“This means that these buried microorganisms presumably have a very low adaptability, unlike the microbial life that otherwise surrounds us in our environment” says Kasper U. Kjeldsen, associate professor at the Center for Geomicrobiology, who participated in the research project.

It probably comes down to harsh environmental conditions (especially pressure) but most of all, the team says, to scarce energy sources. Simply put, the bacteria have nothing to eat at that depth so they don’t do much and they reaaaally think about the state the economy’s in before they divide. Their low rate of division doesn’t just make them slow to adapt but also conserves their genetic material — essentially “freezing” their species’ evolution in time.

So why do these bugs live down here if it’s so spectacularly bad for them? Well, they may not have a say in the matter. Genetic sequencing of these populations shows that they’re made up of the hardier species which inhabited the seafloor over the last thousands of years and were subsequently buried under sediment. Unlike the majority of today’s surface dwellers, they can survive deep burial, although the scientists don’t know exactly why, only that it’s a skill they had before burial.

“Here we use [genetic] sequencing to explore changes of microbial communities during burial and isolation from the surface […] and identify a small core set of mostly uncultured bacteria and archaea that is present throughout the sediment column. These persisting populations constitute a small fraction of the entire community at the surface but become predominant in the subsurface,” the team writes.

“Our results indicate that subsurface microbial communities predominantly assemble by selective survival of taxa able to persist under extreme energy limitation [and] that the ability of subseafloor microbes to subsist in the energy-deprived deep biosphere is not acquired during burial but that these microbes were already capable of living in this unique environment.”

The researchers hope that their new findings could help us better understand and reconstruct past environmental and climatic conditions based on analysis of the microbial species composition in deep marine sediment cores.

The full paper “Microbial community assembly and evolution in subseafloor sediment” has been published in the journal Proceedings of the National Academy of Sciences.

Microorganisms can survive in space and on other planets, safe behind dried-up biofilms

A new paper from the University of Edinburgh shows that by banding together into biofilms, microbial communities can live far longer than isolated individuals when exposed to Mars-like brines. The bugs survived even better when dried out first, such as would happen on the surface of a spaceship in transit.

What kind of film was this picture snapped with? Biofilm.
Image credits NASA / Wikimedia.

The findings offer hope for discovering alien life, as well as showing the dangers of contaminating alien planets with Earth microorganisms.

Traveling buddies

Mostly bone-dry and with little atmosphere to protect its surface from radiation or keep temperature in check, Mars is a world decidedly hostile to life. Still, it does have some very attractive qualities. The red planet is really close (by astronomical standards) to Earth and harbors ice caps — even seasonal streams of liquid water. So a lot of people have their sights set on Mars for potential colonization. Even more, in the end Mars may surprise us with its own indigenous life — which would be great.

One problem arises however. Every time we send a craft to the planet, we run the risk of infecting/seeding it with microorganisms from Earth. If these get a foothold on Mars, they could endlessly frustrate scientists trying to determine the planet of origin — or they could overtake the native inhabitants altogether. But are microbes even capable of surviving the trip through space, and then on Mars?

A new research paper by Dr Adam Stevens at the University of Edinburgh and colleagues shows that biofilms (colonies protected by a slime-like casing) can survive for long periods of time in Mars-like brines — even longer if they’ve been dried out by space-flight first.

The team submerged biofilm samples in seven brines of various chemical compositions and concentrations. In the most diluted brines, all of the biofilms survived well past the 5-hour observation time. In more concentrated brines (the last being 70 times as salty as the weakest one), desiccated biofilms survived for much longer than those whose water content wasn’t altered.

 

Alien invasion with a twist

After an initial shock, these dried out biofilms actually started to grow — presumably in an effort to protect themselves from the environment, the team writes. This may be caused by cells communicating through the biofilm, with cells exposed on the outside layer sending warning signals to those further down in the colony. These insulated cells could then either produce more insulating slime, or reproduce more quickly and build the barrier through sheer numbers.

Still, 5 hours into the experiment, all the microbes in the dried biofilms were dead. The hydrated biofilm cells didn’t even make it to the one hour mark, with some samples dying out in under half an hour.

This research helps us better understand how to look for, and protect, possible alien life. Areas on Mars that have water are the most likely spots for finding alien life, so they’re designated as ‘special regions’ by the international Committee on Space Research. At the same time, these characteristics also make them the most readily-contaminated spots on the planet. Stevens’ research shows that biofilms could allow microorganisms to survive in these conditions. This means that in case of contamination, it would be impossible to study special regions with any semblance of accuracy — so we should be very careful when sending any drones or rovers to these areas.

The same paper also shows there’s hope in finding life nestled in Mars’ briny slopes, as well as on the moons further out in the solar system.

“This research gives us some information about what we could possibly look for if we do go and investigate these brines – which, on the flip side, we’re saying maybe we shouldn’t,” says Stevens.

“To me, this is a kind of a call to pick up the baton of this area that we really need to understand as we launch into an era of space travel,” says Jennifer Macalady at Penn State University in University Park.

The full paper “Biofilms Confer Resistance to Simulated Extra-terrestrial Geochemical Extremes” has been published in the journal bioRxiv.

home-dust

How many germs you can find in your home: about 9,000 different species

After they analyzed dust samples collected from 1,200 US households, researchers at University of Colorado at Boulder identified over 9,000 different species of microbes, bacteria and fungus. The exact makeup depends on where the home is located, the gender of the people living inside and whether or not pets are present.

home-dust

Image: Red Beacon

What if I told you there were germs cramming every inch of your home? Most people are already aware of this, thankfully. Others freak out, partly because they might not understand that’s it perfectly natural this way. You weren’t affected by the germs until your heard the news, and you shouldn’t be after you find out. Nevertheless, there have been countless studies that document the germs living inside your home. This is, however, the most extensive by far revealing the extent of the biological makeup that comprises a typical American home.

The research is also another success story of citizen science coming to the rescue, as all the samples were collected by regular folks who then mailed them to the university. About 1,200 households responded to the call and sent dust collected from obscure locations people never usually bother cleaning, like the ledges above the door. The participants also filled out a questionnaire which asked what were their living and household habits, whether or not they were vegetarian, had pets and so on.

Some of the key findings:

  • The average American household has more than 2,000 different species of fungus and 7,000 species of bacteria.
  • Some of the fungus species include common strains like Aspergillus, Penicillium, Alternaria and Fusarium. 
  • Most of the fungus comes from outside the home so the fungus makeup of a home depends on where this is located.
  • Distinct bacteria were found in homes where only women or men lived. That’s because some types of bacteria are more common in women than men, and vice-versa. For instance, in male-dominant homes scientists found two types of skin-dwelling bacteria belonging to the genuses Corynebacterium and Dermabacter, as well as the fecal-associated genus Roseburia, in greater abundance than in female-dominant homes. The researchers attribute the difference in hygiene habits.
  • Having a dog or cat for a pet significantly altered the bacteria makeup of a home. In fact, having pets was the most influential factor that determine the biological ecosystem of your home. The researchers could determine whether or not dogs or cats lived in a home with an accuracy of 92% and 83%, respectively.

The researchers say that most of these microorganisms and fungi they identified are harmless.

“People do not need to worry about microbes in their home. They are all around us, they are on our skin, they’re all around our home – and most of these are completely harmless.

“It is just a fact of life that we are surrounded by these microbes,” concludes Dr Noah Fierer, associate professor of ecology and evolutionary biology at University of Colorado at Boulder.

 

Exotic extreme microbes played a role in Earth’s early atmosphere

Some species of bacteria can survive virtually anywhere: in acids, in nuclear waste, at extremely low or high temperatures, at extreme pressures, and so on; extreme microbes that survive on gases thrown out by Siberian hot springs may have played an extremely important role in the formation of our planet’s atmosphere and its composition, a new study concludes.

Extreme exotic microbes

Living now only in isolated places, in only (for them) a few oases, these little guys were once all over the place, and in fact, you can even say that they ruled the Earth, in its early period. What is absolutely stunning about them is that they feed on carbon monoxide, but they also eliminate carbon monoxide, which at a first glance seems to make no sense whatsoever. The microbes called anaerobic carboxydotrophs were found in the Kamceatka Peninsula in Siberia, and researchers were surprised to see that a lot of the carbon monoxide in the area wasn’t produced by hot volcanic gases, but it was in fact produced by the microbes.

“We targeted geothermal fields,” University of Chicago geophysicist Albert Colman said, “believing that such environments would prove to be prime habitat for carboxydotrophs due to the venting of chemically reduced, or in other words, oxygen-free and methane-, hydrogen-, and carbon dioxide-rich volcanic gases in the springs.”

Why is this important ? Well, the processing of carbon monoxide has huge implications for the air’s composition billions of years ago, in a time called the Archaean.

The early atmosphere

Artistic depiction of an early atmosphere

It is belived that in the Archaean, the atmosphere contained an almost insignificant amount of oxygen, and was filled instead with large amounts of carbon dioxide and possibly methane. After that, an event called the Great Oxidation occured, about 2.3-2.5 billions of years ago, and the atmosphere started changing, and the sparse amount of oxygen became a small, but significant fraction of the composition.

“This important transition enabled a widespread diversification and proliferation of metabolic strategies and paved the way for a much later climb in oxygen to levels that were high enough to support animal life,” Colman said.

If these microbes were not only eating, but also eliminating carbon dioxide, this means that probably levels of the gas were much higher than thought during the Archean period.

“Our work is showing that you can’t consider microbial communities as a one-way sink for carbon monoxide,” Colman said. His calculations suggest that carbon monoxide may have nearly reached concentrations of 1 percent in the atmosphere, tens of thousands of times higher than current levels.

Also, another thing that should be taken into consideration is that the carbon monoxide would have been toxic for a lot of the early microorganisms, thus placing an incredible amount of evolutionary pressure on the early inhabitants of the Earth.

“A much larger fraction of the microbial community would’ve been exposed to higher carbon monoxide concentrations and would’ve had to develop strategies for coping with the high concentrations because of their toxicity,” Colman said.

This line of research will probably be continued by more and more studies, given the unexpected twist it gives to the early atmosphere; it also sheds a new light on Earth’s atmosphere, while showing us just how little we know about the period when life on our planet existed only in the form of microorganisms.