Protein fragments ID two new 'extremophile' microbes--and may help find alien life

Perfectly adapted microorganisms live in extreme environments from deep-sea trenches to mountaintops. Learning more about how these extremophiles survive in hostile conditions could inform scientists about life on Earth and potential life on other planets. In ACS' Journal of Proteome Research, researchers detail a method for more accurate extremophile identification based on protein fragments instead of genetic material. The study identified two new hardy bacteria from high-altitude lakes in Chile -- an environment like early Mars.

Even though humans tend to avoid settling in extremely hot, cold or high-altitude areas, some microorganisms have adapted to live in such harsh locations.

These extremophile microbes are of interest to astrobiologists who are searching for life on other planets.

Researchers currently use individual gene sequencing to identify Earth-bound microbes, based on their DNA.

However, current methods can't distinguish closely related species of extremophiles.

So, Ralf Moeller and colleagues investigated whether they could identify an extremophile by using its protein signature rather than a gene sequence.

The researchers started their demonstration with water samples from five high-altitude Andean lakes more than 2.3 miles above sea level in the Chilean Altiplano.

(For reference, Denver is about one mile above sea level.) From the samples, the researchers cultivated 66 microbes and then determined which of two methods better identified the microorganisms:

• Traditional gene sequencing compared the nucleotides of the 16s rRNA gene (a typical gene for sequence-based microbe analysis) from each sample to a database for identification.
• The newer "proteotyping" technique analyzed protein fragments known as peptides to produce peptide signatures, which the team used to identify microorganisms from proteome databases.

With these methods, the researchers identified 63 of the 66 microorganisms that were cultivated from the high-altitude lake samples.

For the three microorganisms that gene sequencing failed to identify because their genetic information wasn't in the available database, proteotyping identified two potentially new types of extremophile bacteria.

These results suggest proteotyping could be a more complete solution for identifying extremophile microorganisms from small biological samples.

The team says protein profiling could someday help us search for and identify extraterrestrial life and better explore the biodiversity on our own planet.

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Researchers discover potential microbiome links to skin aging

The effects of aging and external factors like UV exposure on skin are well documented. As people age or spend more time in the sun, their skin tends to become drier and more wrinkled,

Recent findings have identified an exciting potential new link to signs of skin aging -- the skin microbiome, the collection of microorganisms that inhabits our skin. The results come from a collaborative study carried out by researchers at the Center for Microbiome Innovation (CMI) at the University of California San Diego (UC San Diego) and L'Oréal Research and Innovation.

Their work was published in Frontiers in Aging on January 11, 2024, in an article entitled "A multi-study analysis enables identification of potential microbial features associated with skin aging signs." To the best of the team's knowledge, the study is the first to isolate microbes associated specifically with signs of skin aging and skin health, rather than chronological age.

Combining CMI's sophisticated data analysis abilities with L'Oréal's knowledge and expertise in skin health assessment, the study comprehensively examined data collected during 13 studies that L'Oréal had carried out in the past, consisting of 16S rRNA amplicon sequence data and corresponding skin clinical data for over 650 female participants, aged 18 -- 70. While each of the studies included in the analysis had focused on one particular area of interest -- for example, crow's feet wrinkles or moisture loss -- this multi-study analysis collated the data to search for trends related to specific microbes while accounting for other variables, such as age.

"Previous studies have shown that the types of microbes on our skin change fairly predictably with age," said corresponding author Se Jin Song, the CMI Director of Research. "Our skin also changes physiologically with age; for example, we gain wrinkles and our skin gets drier. But there is variation in what this looks like in people -- you've probably noticed that there are some people who have younger or older looking skin than many others their age. Using advanced statistical methods, we were able to tease apart the microbes that are associated with these types of aging signs for skin, like crow's feet wrinkles, from those that are associated with simply age as a chronological number."

Two notable trends emerged from the analysis. First, the team found a positive association between skin microbiome diversity and lateral cantonal lines (crow's feet wrinkles), which are generally viewed as one of the key signs of skin aging. Second, they observed a negative correlation between microbiome diversity and transepidermal water loss, which is the amount of moisture that evaporates through the skin. In further exploring the trends, the researchers identified several potential biomarkers that warrant investigation as microorganisms of interest. It would be premature to infer causation or actionable insights, but the study's results have provided researchers with directions on the next steps to hone in on better understanding microbial associations with skin aging.

"At L'Oréal, our commitment is to create beauty products that meet the unique needs of each individual. Our recent collaboration with the Center for Microbiome Innovation has shed light on the role of the skin microbiome in aging, particularly in how it affects wrinkles and overall skin quality," said co-author Qian Zheng, Head of Advanced Research, North America at L'Oréal. "This research is groundbreaking in identifying new microbial biomarkers linked to visible signs of aging like crow's feet wrinkles. It marks a significant step towards developing technologies for healthier, more youthful skin. We look forward to sharing new results as they become available, furthering the scientific community's understanding and contributing to advancing new skincare solutions."

Future paths of investigation the team has suggested include metabolomics work to discover chemical biomarkers related to skin aging, as well as meta-transcriptomics research into potential targets for genetic engineering. Research into other layers of the skin has also been considered, as many studies focus on the outer skin due to the ease of sample collection.

"While the study's findings represent an advance of our knowledge of the skin microbiome, we view them as just the beginning of a new phase of research," said co-author Rob Knight, the CMI Faculty Director and Professor of Pediatrics, Bioengineering, Computer Science & Engineering and Data Science at UC San Diego. "By confirming a link between the microbiome and skin health, we've laid the groundwork for further studies that discover specific microbiome biomarkers related to skin aging, and, one day, show how to modify them to generate novel and highly targeted recommendations for skin health."

Read more at Science Daily

Researchers discover that the ice cap is teeming with microorganisms

There are no plants, and only very few animals: people rarely come here. The large glaciers in Greenland have long been perceived as ice deserts. Gigantic ice sheets where conditions for life are extremely harsh.

But now, it seems, we have been wrong. There is much more life on the glaciers than we thought.

Headed by Professor Alexandre Anesio, a group of researchers from the Department of Environmental Science at Aarhus University have discovered that the glaciers are teeming with life. Microbes that have adapted to life on the ice. And not just one or two species. Several thousand different species.

"A small puddle of melt-water on a glacier can easily have 4,000 different species living in it. They live on bacteria, algae, viruses and microscopic fungi. It's a whole ecosystem that we never knew existed until recently," says Alexandre Anesio.

What do the microbes live on?

Over the past 50 years, researchers have repeatedly been surprised by the hardiness of life. Life has been found several kilometres underground -- where there is neither sun nor oxygen. Billions of microorganisms "eat" minerals in the bedrock and so can survive.

Researchers have shown that life can even survive in space. In 2007, European researchers placed a colony of more than 3,000 microscopic water bears (tardigrades) outside a satellite and sent them into orbit around the Earth. The orbit lasted 10 days, after which the satellite returned to Earth. No less than 68 per cent of the microbes survived the vacuum of space and the lethal radiation.

Therefore, it might not come as a surprise that life also thrives on the glaciers. After all there is sun, oxygen and water. Nevertheless, until recently, researchers believed that the ice had too little nourishment to sustain life. But they were wrong.

There is nourishment. Just in incredibly small quantities, explains Alexandre Anesio.

Black algae

One of the microorganisms on the ice that the researchers spent most time investigating is a small black algae. The algae grows on top of the ice and tinges it black. There is a reason why the black algae so interesting for the researchers.

"When the ice darkens, it becomes more difficult to reflect sunlight. Instead, heat from the sun's rays is absorbed by the ice, which starts to melt. The more the ice melts, the warmer the temperature on Earth. The algae therefore play an important role in global warming," says Alexandre Anesio.

In recent years, larger and larger areas of the ice have become stained by the algae, making the ice melt even faster. Alexandre Anesio has calculated that the algae are increasing the ice melt by about 20 per cent.

The algae on the ice also existed before people kicked off global warming through industrialisation. However, climate change means spring arrives ever earlier to the Arctic and as a result the algae have a longer season to grow and spread.

"The algae spread a little more every year. When I travel to Greenland, I now see vast areas where the ice is completely dark because of the algae," he says.

Looking for an algaecide

Alexandre Anesio and his colleagues are spending a lot of time on the black algae because they are trying to find out whether the algae growth can be slowed down in some way or another.

The is a balance In most ecosystems -- a kind of equilibrium -- because the various organisms keep each other in check. So Alexandre Anesio wants to learn more about the relationship between the different microbes.

"The various microorganisms on the ice affect each other. Some leave nutrition that others live off. Small viral particles attack and consume bacteria. We believe that some of the fungal spores could eat the black algae. This is what we're looking for," he says.

However, he stresses that, even if they do find a way to curb algae growth, this will not solve climate change. Although it could slow it down.

Algae growth is a consequence of our releasing too many greenhouse gases into the atmosphere. And this is where the problem must be solved. We need to focus on slowing down our emissions.

The same pigment as in black tea

Algae is found virtually everywhere. In the sea, in lakes, on trees and rocks, and even as small spores in the air. Most algae are greenish. Like plants and trees, they are green because of chlorophyll. A molecule that enables them to photosynthesise.

But it's different for the black algae.

"Because the algae live on the ice, they're bombarded with sunlight and radiation. To protect themselves, they produce a lot of black pigment. It's actually the same pigment as in black tea. The pigment forms a protective layer outside the algae and protects the chlorophyll molecules against the dangerous radiation," says Alexandre Anesio. When the pigment absorbs the sun's rays, it generates heat. This heat makes the ice around the algae melt. And this actually benefits the algae. They need both water and micronutrients from the ice to live.

And they can only use the water when it is liquid.

NASA also has an eye on his research

Alexandre Anesio's research into life on the ice is important for a better understanding of climate change. However, NASA is also following his research results closely. The results may be crucial in the hunt for life in space.

"NASA has approached us several times because we're working with life that lives in one of the most inhospitable places on Earth. If life thrives on and under the ice, there's a probability that we'll also find life in the ice on Mars or Jupiter's and Saturn's ice moons, for example," he says.

Before NASA sent their Perseverance rover to Mars, they even invited Alexandre Anesio to a meeting.

"They were afraid that the rover would take with it microbes from Earth. Microbes that may be able to survive on Mars and pollute the samples they were going to take from Mars. So, they wanted to know what conditions life can survive in. What are the boundaries for life?"

Can give an indication of what they should look for

NASA is so interested in the research of life in the ice because we haven't found liquid water on any other planets in the solar system. Not yet, anyway. But we've found plenty of ice.

However, there is evidence to suggest that there are liquid oceans beneath the frozen surface of Saturn's moon, Enceladus and Jupiter's moon, Europa -- and one of the necessities of life, as we know it, is liquid water.

Therefore, NASA and other space agencies are very interested in learning more about the type of life that can live on and under the ice. Because organisms that resemble those in Greenland are probably those they'll be looking for on the ice moons.

Read more at Science Daily

Searching for life with space dust

Following enormous collisions, such as asteroid impacts, some amount of material from an impacted world may be ejected into space. This material can travel vast distances and for extremely long periods of time. In theory this material could contain direct or indirect signs of life from the host world, such as fossils of microorganisms. And this material could be detectable by humans in the near future, or even now.

When you hear the words vacuum and dust in a sentence, you may groan at the thought of having to do the housework. But in astronomy, these words have different connotations. Vacuum of course refers to the void of space. Dust, however, means diffuse solid material floating through space. It can be an annoyance to some astronomers as it may hinder their views of some distant object. Or dust could be a useful tool to help other astronomers learn about something distant without having to leave the safety of our own planet. Professor Tomonori Totani from the University of Tokyo's Department of Astronomy has an idea for space dust that might sound like science fiction but actually warrants serious consideration.

"I propose we study well-preserved grains ejected from other worlds for potential signs of life," said Totani. "The search for life outside our solar system typically means a search for signs of communication, which would indicate intelligent life but precludes any pre-technological life. Or the search is for atmospheric signatures that might hint at life, but without direct confirmation there could always be an explanation that does not require life. However, if there are signs of life in dust grains, not only could we be certain, but we could also find out soon."

The basic idea is that large asteroid strikes can eject ground material into space. There is a chance that recently deceased or even fossilized microorganisms could be contained in some rocky material in this ejecta. This material will vary in size greatly, with different-sized pieces behaving differently once in space. Some larger pieces might fall back down or enter permanent orbits around a local planet or star. And some much smaller pieces might be too small to contain any verifiable signs of life. But grains in the region of 1 micrometer (one-thousandth of a millimeter) could not only host a specimen of a single-celled organism, but they could also potentially escape their host solar system altogether, and under the right circumstances, maybe even venture to ours.

"My paper explores this idea using available data on the different aspects of this scenario," said Totani. "The distances and times involved can be vast, and both reduce the chance any ejecta containing life signs from another world could even reach us. Add to that the number of phenomena in space that can destroy small objects due to heat or radiation, and the chances get even lower. Despite that, I calculate around 100,000 such grains could be landing on Earth every year. Given there are many unknowns involved, this estimate could be too high or too low, but the means to explore it already exist so it seems like a worthwhile pursuit."

There may be such grains already on Earth, and in plentiful amounts, preserved in places such as the Antarctic ice, or under the seafloor. Space dust in these places could be retrieved relatively easily, but discerning extrasolar material from material originating in our own solar system is still a complex matter. If the search is extended to space itself, however, there are already missions that capture dust in the vacuum using ultralight materials called aerogels.

Read more at Science Daily

A window of opportunity for methane to slip by nature's filters

Warmer oceans can lead to large amounts of methane being released from the seabeds, which may amplify climate warming. A new study develops a method to understand the role of microorganisms in increasing emissions of methane from seabeds.

Vast reservoirs of the potent greenhouse gas methane are stored beneath the sea in a solid ice-like combination with water. This solid is known as methane hydrate. For over three decades, various concerns have been raised that warming the seafloor may cause this methane to be rapidly released, perhaps even reaching the atmosphere where it would cause further climate warming. Happily, this methane hydrate is mostly located beneath the seafloor and under hundreds of meters of seawater. Even if warming melts this methane hydrate and releases methane gas, the natural microbial filters present in the seafloor were expected to destroy most of the methane before it ever reaches the open seawater.

However, there have been some gaps in our knowledge of the relevant seafloor processes. In particular, can seafloor warming be rapid enough that methane hydrate could melt so fast that the released methane would overwhelm and ultimately bypass the natural microbial filters? "The microbial filter layer in the sediment -- we call it the 'sulfate-methane transition', where methane is removed -- is somewhat delicate," explains Assistant Professor Christian Stranne at the Department of Geological Sciences, Stockholm University. "The filter layer takes many years to form and reach peak methane-consuming efficiency. The filter is a living thing, made of microorganisms that consume methane under anaerobic (no-oxygen) conditions. The filter also moves up and down within the sediment, depending on the rate at which methane is reaching it."

In a new study, just published in Communications Earth and Environment, Stranne and colleagues from Stockholm University and Linnaeus University have combined a new model of the biological behaviour and vertical movements of this microbial filter with existing models of seafloor sediments' physical behaviour. The physical parts of the model include processes such as how cracks form and methane can move up thorough the sediment after methane hydrates melt.

Christian Stranne explains: "Imagine that the amount of methane rising through the sediment suddenly increases, as might happen if methane hydrate begins to melt faster. It can take decades for the filter to adjust itself to consume methane at the new rate. Our new study shows that during the time that the filter is not reestablished, substantial methane can leak past the filter, and into the ocean water."

Despite this "window of opportunity," methane from melting hydrates that reaches the seawater faces further methane-destroying processes. These processes make it nearly impossible for substantial methane from methane hydrate melting to reach the atmosphere. However, methods as demonstrated in this study can be applied to other regions where seafloor-released methane is much shallower and is more likely to reach the atmosphere, such as the Arctic continental shelves, according to Christian Stranne.

"Methane hydrates are a massive storehouse of carbon, so it remains important to understand how they interact with ocean changes, and potentially, the atmosphere, over long and, in the case of our study, rather short timescales. We now know that there is indeed a possible process for melting methane hydrates to temporarily bypass what was previously thought to be a strong filter in the sediment," says Christian Stranne.

The warming rate is, however, of great importance: "Our results suggest that if our oceans warm at a pace significantly lower than 1 °C per 100 years, the filter can keep up with the pace and remain highly efficient. Unfortunately, we see higher warming rates than that in some of our oceans."

Read more at Science Daily

New 'vertical map' of airborne microorganisms indicates how global warming will impact global ecosystems

In a landmark study of airborne microorganisms from ground level up to 3,500 metres, scientists from the Singapore Centre for Environmental Life Sciences Engineering (SCELSE) at Nanyang Technological University, Singapore (NTU Singapore) have found that bacteria and fungi populate the planet's lower atmosphere in very specific ways and if changed, may negatively impact human health and food supply.

Using a combination of a 200-metre meteorological tower and a research aircraft that circled at different heights from 300 metres to 3,500 metres to gather the necessary measurements, the researchers found that temperature was the single most important factor influencing the composition of airborne microbial communities.

As the temperature of the air changes, the species found and the ratio of bacteria to fungi change significantly. These findings suggest that the currently observed increase in global temperature will have an impact on the atmospheric microbial ecosystem, as well as planetary terrestrial and aquatic ecosystems.

The study was published today in the peer-reviewed journal Proceedings of the National Academy of Sciences (PNAS) by a team of interdisciplinary scientists led by NTU Professor Stephan Schuster, Research Director (Meta-'omics & Microbiomes) at SCELSE.

Atmospheric microorganisms, collectively known as the air microbiome, consist of bacteria and fungi, and largely remain suspended in air once they are blown off the planet's surface.

Only a fraction of these microorganisms find their way back down to the surface, when they are washed down by rain droplets or fall back down together with larger particles such as sand grains or dust.

"Our research generated a comprehensive 'vertical map' of airborne microorganisms in the planet's atmosphere," said Prof Schuster, the study's corresponding author.

"We found that the composition of the air microbiome in our atmosphere is determined by the temperature. As global air temperatures are rising due to climate change, this could lead to very significant changes in the air microbiome with serious consequences for people and the planet."

"If the composition of the air microbiome changes globally, it may affect human health, exacerbating respiratory syndromes in susceptible patients, or it could affect the yield of agricultural crops, which then threatens our food security. Natural processes that have worked for thousands of years such as carbon cycling of this planet may also be changed."

"With our latest research paper, we are a step closer to showing that air has its own microbial ecosystem, much like those on land and in the sea. We expect that changes in the air microbiome will also have knock-on effects on terrestrial and aquatic ecosystems," adds Prof Schuster.

The vertical map of microorganisms also provides a starting point for future ecological surveys and the necessary measures not only for the protection of global environments, but also for agricultural production sites, which may be negatively impacted by changes to the airborne microbial communities.

With the new dataset as a baseline, scientists can also model and predict the changes in the air microbiome if temperatures were to rise by two degrees or more, said the research team.

Key discoveries

To measure the air microbiome high above the ground, the team used a specialised research aircraft from the Technische Universität Braunschweig, Germany, to collect synchronised measurements of meteorological parameters and airborne biomass samples up to a height of 3,500 metres.

The research team on the aircraft coordinated the sampling times with a team stationed at the 200-metre-high meteorological tower at the Karlsruhe Institute of Technology (KIT) in Karlsruhe, Germany.

A total of 480 vertical air samples were collected from Germany, which were brought back to Singapore to be analysed. The team was surprised to find that the composition of microorganisms above 1,000 metre was stable, independent of day or night. These air layers act as a "sink in the sky," where bacteria accumulate in higher numbers than at the ground. The team identified over 10,000 different species of airborne microbes from the samples taken above 1,000 metres.

This was very different from the air samples that were taken below 300 metres, which were shown to follow the 24-hour day and night cycle (called the diel cycle), where the air composition changes from bacteria and some fungi dominating during the day, to wood-rotting fungi dominating in the night.

The discovery of the diel cycle of airborne microorganisms was first published in PNAS in 2019[1][1], when the same research team studied the tropical air in Singapore using air samples taken at various levels of a 50-storey high-rise residential building named Pinnacle@Duxton.

In its latest study, the team also reported that atmospheric turbulence -- wind and weather -- is the primary driver of microbial aerosol dynamics, which determines how microorganisms in the air are distributed.

Driven by the day/night temperature changes, air masses become layered (stratified) at night and mixed during the day, resulting in the stratification of the air microbiome across different heights of the lower part of atmosphere.

"For the first time, meteorological and biological data of the atmosphere were measured in unison, allowing us to develop a comprehensive hypothesis about the effects of atmospheric turbulence on the dispersal of microorganisms in the lower atmosphere," said Prof Schuster.

Researchers further noticed that higher air layers contained an up-to-20-times higher concentration of radio-tolerant bacteria, which are known to withstand ionising radiation, desiccation, UV radiation, or oxidising agents. Of these bacteria, one species known as Deinococcus radiodurans is known to withstand a 1,000-fold higher radiation dose than the human body.

The team hypothesised that the ionising rays from sun and space had contributed to the development of radioactive tolerance in these bacteria at greater height, whereas bacteria on the ground have not been exposed to such levels of radiation.

Sampling for airborne life on Mars?

Based on their experiments, the researchers comment that their air sampling technologies could in principle, be used for investigating the atmosphere of neighbouring planets, such as Mars.

By tapping on the knowledge that microorganisms will aggregate in a planet's atmosphere, it could provide an alternative to the current method of sampling, which is done by a robotic vehicle drilling and collecting soil samples.

For instance, a robot with an air sampler could collect microorganisms from the atmosphere by trapping them in an air filter, and sending the filter back to earth, in a potential future Mars sample-return mission.

The air microbiome study is one of SCLESE's flagship research projects together with its research into terrestrial and aquatic ecosystems. The project was carried out over eight years, and has resulted in more than 40 papers, culminating with these results. The air microbiome research was supported by a Singapore Ministry of Education Tier 3 grant, SCELSE, and NTU.

Sustainability, climate change and the environment are key research pillars for NTU Singapore and are part of its Sustainability Manifesto launched last year. The University will continue fundamental and applied research to develop sustainable solutions that can mitigate the effects of natural disasters and climate change, and to meet the demand for food with alternative food sources.

Over the last two years during the pandemic, Prof Schuster and his team have pivoted to use their air sampling technology to detect and analyse the SARS-COV-2 virus from indoor air, a technique that demonstrated greater sensitivity than surface swab tests.

Read more at Science Daily

Being clean and hygienic need not impair childhood immunity

The theory that modern society is too clean, leading to defective immune systems in children, should be swept under the rug, according to a new study by researchers at UCL and the London School of Hygiene & Tropical Medicine.

In medicine, the 'hygiene hypothesis' states that early childhood exposure to particular microorganisms protects against allergic diseases by contributing to the development of the immune system.

However, there is a pervading view (public narrative) that Western 21st century society is too hygienic, which means toddlers and children are likely to be less exposed to germs in early life and so become less resistant to allergies.

In this paper, published in the Journal of Allergy and Clinical Immunology, researchers point to four significant reasons which, they say, disprove this theory and conclude we are not "too clean for our own good."

Lead author, Emeritus Professor of Medical Microbiology Graham Rook (UCL Infection & Immunity), said: "Exposure to microorganisms in early life is essential for the 'education' of the immune and metabolic systems.

"Organisms that populate our guts, skin and airways also play an important role in maintaining our health right into old age: so throughout life we need exposure to these beneficial microorganisms, derived mostly from our mothers, other family members and the natural environment.

"But for more than 20 years there has been a public narrative that hand and domestic hygiene practices, that are essential for stopping exposure to disease-causing pathogens, are also blocking exposure to the beneficial organisms.

"In this paper, we set out to reconcile the apparent conflict between the need for cleaning and hygiene to keep us free of pathogens, and the need for microbial inputs to populate our guts and set up our immune and metabolic systems."

In a review of evidence, the researchers point to four factors.
 

• Firstly, the microorganisms found in a modern home are, to a significant degree, not the ones that we need for immunity.
• Secondly, vaccines, in addition to protecting us from the infection that they target, do a lot more to strengthen our immune systems, so we now know that we do not need to risk death by being exposed to the pathogens.
• Thirdly, we now have concrete evidence that the microorganisms of the natural green environment are particularly important for our health; domestic cleaning and hygiene have no bearing on our exposure to the natural environment.
• Finally, recent research demonstrates that when epidemiologists find an association between cleaning the home and health problems such as allergies, this is often not caused by the removal of organisms, but rather by exposure of the lungs to cleaning products that cause a type of damage that encourages the development of allergic responses.

Professor Rook added: "So cleaning the home is good, and personal cleanliness is good, but, as explained in some detail in the paper, to prevent spread of infection it needs to be targeted to hands and surfaces most often involved in infection transmission. By targeting our cleaning practices, we also limit direct exposure of children to cleaning agents.

Read more at Science Daily

Modern microbes provide window into ancient ocean

 Step into your new, microscopic time machine. Scientists at the University of Colorado Boulder have discovered that a type of single-celled organism living in modern-day oceans may have a lot in common with life forms that existed billions of years ago -- and that fundamentally transformed the planet.

The new research, which will appear Jan. 6 in the journal Science Advances, is the latest to probe the lives of what may be nature's hardest working microbes: cyanobacteria.

These single-celled, photosynthetic organisms, also known as "blue-green algae," can be found in almost any large body of water today. But more than 2 billion years ago, they took on an extra important role in the history of life on Earth: During a period known as the "Great Oxygenation Event," ancient cyanobacteria produced a sudden, and dramatic, surge in oxygen gas.

"We see this total shift in the chemistry of the oceans and the atmosphere, which changed the evolution of life, as well," said study lead author Sarah Hurley, a postdoctoral research associate in the departments of Geological Sciences and Biochemistry. "Today, all higher animals need oxygen to survive."

To date, scientists still don't know what these foundational microbes might have looked like, where they lived or what triggered their transformation of the globe.

But Hurley and her colleagues think they might have gotten closer to an answer by drawing on studies of naturally-occurring and genetically-engineered cyanobacteria. The team reports that these ancient microbes may have floated freely in an open ocean and resembled a modern form of life called beta-cyanobacteria.

Studying them, the researchers said, offers a window into a time when single-celled organisms ruled the Earth.

"This research gave us the unique opportunity to form and test hypotheses of what the ancient Earth might have looked like, and what these ancient organisms could have been," said co-author Jeffrey Cameron, an assistant professor of biochemistry.

Take a breath

You can still make the case that cyanobacteria rule the planet. Hurley noted that these organisms currently produce about a quarter of the oxygen that comes from the world's oceans.

One secret to their success may lie in carboxysomes -- or tiny, protein-lined compartments that float inside all living cyanobacteria. These pockets are critical to the lives of these organisms, allowing them to concentrate molecules of carbon dioxide within their cells.

"Being able to concentrate carbon allows cyanobacteria to live at what are, in the context of Earth's history, really low carbon dioxide concentrations," Hurley said.

Before the Great Oxidation Event, it was a different story. Carbon dioxide levels in the atmosphere may have been as much as 100 times what they are today, and oxygen was almost nonexistent. For that reason, many scientists long assumed that ancient microorganisms didn't need carboxysomes for concentrating carbon dioxide.

"Cyanobacteria have persisted in some form over two billion years of Earth's history," she said. "They could have been really different than today's cyanobacteria."

To find out how similar they were, the researchers cultured jars filled with bright-green cyanobacteria under conditions resembling those on Earth 2 billion years ago.

Hurley explained that different types of cyanobacteria prefer to digest different forms, or "isotopes," of carbon atoms. As a result, when they grow, die and decompose, the organisms leave behind varying chemical signatures in ancient sedimentary rocks.

"We think that cyanobacteria were around billions of years ago," she said. "Now, we can get at what they were doing and where they were living at that time because we have a record of their metabolism."

Resurrecting zombie microbes

In particular, the team studied two different types of cyanobacteria. They included beta-cyanobacteria, which are common in the oceans today. But the researchers also added a new twist to the study. They attempted to bring an ancient cyanobacterium back from the dead. Hurley and her colleagues used genetic engineering to design a special type of microorganism that didn't have any carboxysomes. Think of it like a zombie cyanobacterium.

"We had the ability to do what was essentially a physiological resurrection in the lab," said Boswell Wing, a study coauthor and associate professor of geological sciences.

But when the researchers studied the metabolism of their cultures, they found something surprising: Their zombie cyanobacterium didn't seem to produce a chemical signature that aligned with the carbon isotope signatures that scientists had previously seen in the rock record. In fact, the best fit for those ancient signals were likely beta-cyanobacteria -- still very much alive today.

The team, in other words, appears to have stumbled on a living fossil that was hiding in plain sight. And, they said, it's clear that cyanobacteria living around the time of the Great Oxygenation Event did have a structure akin to a carboxysome. This structure may have helped cells to protect themselves from growing concentrations of oxygen in the air.

"That modern organisms could resemble these ancient cyanobacteria -- that was really counterintuitive," Wing said.

Scientists, they note, now have a much better idea of what ancient cyanobacteria looked like and where they lived. And that means that they can begin running experiments to dig deeper into what life was like in the 2 billion-year-old ocean.

"Here is hard evidence from the geological record and a model organism that can shed new light on life on ancient Earth," Cameron said.

Read more at Science Daily

Clay subsoil at Earth's driest place may signal life on Mars

 Earth's most arid desert may hold a key to finding life on Mars.

Diverse microbes discovered in the clay-rich, shallow soil layers in Chile's dry Atacama Desert suggest that similar deposits below the Martian surface may contain microorganisms, which could be easily found by future rover missions or landing craft.

Led by Cornell University and Spain's Centro de Astrobiología, scientists now offer a planetary primer to identifying microbial markers on shallow rover digs in Martian clay, in their work published Nov. 5 in Nature Scientific Reports.

In that dry environment at Atacama, the scientists found layers of wet clay about a foot below the surface.

"The clays are inhabited by microorganisms," said corresponding author Alberto G. Fairén, a visiting scientist in the Department of Astronomy at Cornell University. "Our discovery suggests that something similar may have occurred billions of years ago -- or it still may be occurring -- on Mars."

If microbes existed on Mars in the past, their biomarkers likely would be preserved there, Fairén said. "If microbes still exist today," he said, "the latest possible Martian life still may be resting there."

The red planet will see rovers cruising across the surface there in the next few years. NASA's rover Perseverance will land on Mars in February 2021; Europe's Rosalind Franklin rover will arrive in 2023. Both of those missions will seek microbial biomarkers in the clay below the planet's surface.

"This paper helps guide the search," Fairén said, "to inform where we should look and which instruments to use on a search for life."

In the Yungay region of the Atacama desert, the scientists found the clay layer, a previously unreported habitat for microbial life, is inhabited by at least 30 salt-loving microbial species of metabolically active bacteria and archaea (single-cell organisms).

The researchers' Atacama discovery reinforces the notion that early Mars may have had a similar subsurface with protected habitable niches, particularly during the first billion years of its history.

"That's why clays are important," he said. "They preserve organic compounds and biomarkers extremely well and they are abundant on Mars."

Read more at Science Daily

Evolution in the gut

They are a part of us: we all carry about ten times as many bacteria and archaea as our own cells. The bacterial ecosystem in our digestive tract, the so-called microbiome, is not only of great importance for our metabolism, but also for the immune system and even our behaviour. The same is true to animals, but the composition of the microbiome differs greatly between animal species. For the first time, a large-scale study was carried out to explain the development of the microbiome using faecal samples from free-living animals. 128 different species from very classes fish, amphibians, reptiles, birds and mammals were examined. The research groups involved were able to show how evolution and dietary habits interact and determine the composition of bacteria in the digestive tract. Many microorganisms in the intestine seem to have developed in sync with their host animals over millions of years. These results should also help in the characterisation of faecal pollution in water by allowing attribution to certain animal species in a much more precise way in the future.

Samples from all branches of the family tree

"So far there have been studies on the microbiome of humans, or special data for individual species such as rats. However, we wanted to select many animal species that were as representative as possible of the entire evolutionary tree of vertebrates -- from birds to mammals to fish," says Prof. Andreas Farnleitner, Co-Leader of the Interuniversity Research Centre "Water and Health" at the TU Wien (ICC Water & Health) and Professor of Microbiological Diagnostics in extension of the ICC Water & Health group at Karl Landsteiner Private University in Krems.

It was important to get samples from wild animals, as zoo animals can have a completely different microbiome than their wild counterparts. The Institute for Wildlife Science and Ecology of the University of Veterinary Medicine Vienna was the lead partner for the sample collection. The DNA of the microorganisms studied was then sequenced -- partly at the TU Wien and partly at the Max Planck Institute for Developmental Biology in Tübingen.

"A total of more than 400 samples from 180 different species were analysed, resulting in 20 million gene sequences," said Dr. Georg Reischer (TU Vienna). The cooperation partners of the MPI in Tübingen contributed their know-how in bioinformatic data analysis and evolutionary biology to the study. This revealed striking relationships that can be explained by evolutionary history: The microbiome has developed over many millions of years in co-evolution with the host animals. Closely related species that are close to the evolutionary family tree also have similarities in the microbiome. "Nutrition also plays a role, but it is never the only decisive factor," explains Georg Reischer. "If a mammal eats the same food as a bird, it still does not have the same bacteria in its intestines."

The contamination bio-detector
The data collected in this study not only allows the interpretation of the co-evolution of host animals and the microorganisms in their digestive tract, it also facilitates the development of methods to assist in the provision of clean water. In recent years, a technology has been developed at the TU Wien that uses DNA tests to provide information on the source of fecal pollution in water. Thus it became possible to find out whether the contamination was caused by human wastewater or grazing animals. "Now we have a very extensive data set at our disposal that will make such tests possible in a much more comprehensive and accurate way," says Andreas Farnleitner.

From Science Daily

Bacteria may help frogs attract mates

Adult female (left) and calling male of Boana prasina.

Brazilian scientists have discovered that the strong odor released by some amphibian species is produced by bacteria and that attracting a mate is one of its purposes. The bacteria in question are a noteworthy example of symbiosis as they assist in the animal's mating process. A paper recounting the discovery of this role of microorganisms isolated from the skin of frogs has been published in the journal Proceedings of the National Academy of Sciences (PNAS).

"Frogs emit a pungent odor. Sometimes a particular species can be recognized by its scent, but until now, the function of this odor was unknown. It was typically assumed to be an aposematic smell, meaning a chemical warning sign that served to repel predators, as in the case of skunks [Mephitis mephitis] among mammals, for example," said Célio Haddad, a professor at São Paulo State University's Rio Claro Bioscience Institute (IBRC-UNESP) in Brazil and a coauthor of the article.

According to Haddad, who is also affiliated with the university's Aquaculture Center (CAUNESP) in Jaboticabal, this hypothesis was considered plausible because many amphibian species, especially when poisonous, are brightly colored, and this serves as a visual alert to frighten predators. "We thought odor might play a similar role among anurans [frogs and toads]," he said.

The new study resulted from the postdoctoral research of Argentinean biologist Andrés Eduardo Brunetti, supervised by Professor Norberto Peporine Lopes. Conducted at the University of São Paulo's Ribeirão Preto School of Pharmaceutical Sciences (FCFRP-USP), the research was supported by FAPESP.

"The importance and originality of Brunetti's research is that for the first time it shows a pronounced difference in the odors emitted by frogs of opposite sexes," Haddad said. "No other studies of anurans have ever described this type of behavior. The results suggest that the odor serves to permit mutual recognition between males and females of the same species for mating purposes."

The research was also supported by the FAPESP Research Program on Biodiversity Characterization, Conservation, Restoration and Sustainable Use (BIOTA-FAPESP) and by the University of São Paulo (USP), the National Council for Scientific and Technological Development (CNPq) and Brazil's Coordination for the Improvement of Higher Education Personnel (CAPES).

"In anurans, you often see different species sharing a lake or marsh. In such places, there are 30 male frogs for every female of the same species on average. The question is how the females recognize males of their own species among a multitude of males belonging to several species while they're all vocalizing at the same time," Brunetti said.

"It's well-known that the function of the call of anuran males is to attract females and that every species has a characteristic song. Our findings suggest that odor appears to play a similar role, serving as an olfactory signal that enables females to recognize males of their own species."

Biologists were also unaware of a difference in the scents of male and female frogs. Brunetti discovered this difference during his research, whose primary goal was to understand the chemical composition of the volatile components emitted by the skin of various frog species.

His working hypothesis suggested that smell was a chemical warning sign that served to repel predators. To verify the hypothesis, Brunetti conducted field surveys at several sites in São Paulo state and Rio de Janeiro state, collecting specimens of the tree frog Boana prasina.

"It's very hard to collect females in the wild. Initially, we managed to collect only males. When we noticed what appeared to be a sexual difference in their odors, I went into the field again with the specific aim of capturing females for comparison," he said.

"During my doctoral research at the Argentinian Natural Science Museum in Buenos Aires, while investigating the volatile compounds in two other frog species, I discovered that the secretions were made up of a blend of 35 to 42 compounds in nine different chemical classes. We then realized that some of the compounds had the specific signature of compounds produced by bacteria."

Brunetti came to Brazil to investigate whether the selected tree frogs had skin bacteria that produced the characteristic odor of each species, and if so, which compounds they produced. His laboratory research proceeded on two fronts: analysis of the volatile compounds released by the skin of these frogs and identification of the bacteria on their skin.

Brunetti and colleagues used gas chromatography and mass spectrometry to analyze the diversity of the volatile components secreted by the skin of B. prasina. They found that adult males and females secrete a blend of 60-80 compounds, including alcohols, aldehydes, alkenes, ethers, ketones, methoxypyrazines, terpenes and thioethers.

The compounds were exactly the same in both males and females, but the researchers were surprised to find a pronounced sexual difference in the levels of methoxypyrazines, terpenes, and thioethers.

"These three components were responsible for the difference between males and females. Thioethers and methoxypyrazines are typically produced by microorganisms," Brunetti said.

They decided to determine whether microorganisms were the source of these compounds in B. prasina. To do so, they isolated, cultivated and identified bacteria associated with the skin of these frogs and analyzed their volatile components.

No fewer than 128 different components were detected. Analysis of each component revealed that four methoxypyrazines present in males and females were produced by a single bacterium of the genus Pseudomonas.

In B. prasina, Brunetti discovered, methoxypyrazines were much more abundant in females than in males. Two of the four types of methoxypyrazines were measured at higher levels in females, while two were found at higher levels in males.

Symbiotic relationship

"The interesting thing about Pseudomonas sp. is that these bacteria live on the skin of males and females, where they metabolize the same volatile compounds but at different levels of concentration according to the sex of the host," Brunetti said.

The levels of methoxypyrazine measured in these frogs, he added, suggest the existence of a complex mechanism of metabolic interactions that creates a different environment on the skin of males and females, favoring the synthesis of characteristic methoxypyrazines in each sex.

"These frogs and bacteria have a symbiotic relationship. In exchange for the service provided by the bacteria, entailing sexual differentiation by scent, the frogs provide an environment -- their own skin -- on which the bacteria can proliferate," he explained.

The function of this sexual difference in methoxypyrazine levels is unknown. "However, we assume that the difference in scent helps male frogs of this species recognize females of the same species in places inhabited by other frog species," Brunetti said.

"We know that many anurans use visual communication [bright skin colors] to repel predators as well as acoustic communication [vocalization] to attract female mates. Perhaps B. prasina uses a form of olfactory communication for the same purpose."

Brunetti will attempt to confirm this hypothesis in future research. If correct, it will have major repercussions. "Only one anuran, in Madagascar, is currently known to communicate by odor. Among amphibians, salamanders, which are distant relatives of anurans, are known to use this form of communication," Haddad said.

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Blood-sucking flies have been spreading malaria for 100 million years

Mosquitoes in the amber.

The microorganisms that cause malaria, leishmaniasis and a variety of other illnesses today can be traced back at least to the time of dinosaurs, a study of amber-preserved blood-sucking insects and ticks show.

In addition to demonstrating the antiquity of vectors and their long-term association with parasitic microorganisms, the findings are remarkable for several reasons.

First, bloodsuckers like mosquitoes, fleas, sand flies, ticks and biting midges aren't frequently found in amber, and rarer yet is evidence of any microorganisms they might have been carrying.

But a review by entomologist George Poinar of Oregon State University showed that amber from five regions around the world contained hematophagous arthropods carrying preserved, identifiable pathogens and parasites.

"Feeding on vertebrate blood evolved as an efficient way for certain insects and acarines to get protein for growth and reproduction," said Poinar, professor emeritus in the College of Science and an international expert on plant and animal life forms found preserved in amber. "It's likely that primitive mosquitoes and other arthropod vectors were present back in the Jurassic and were even transmitting pathogens at that period. This would have resulted in widely dispersed diseases, many of which were probably fatal to vertebrates when they first appeared."

Poinar looked at bloodsucking insects and ticks encased in Dominican, Mexican, Baltic, Canadian and Burmese amber dating back from 15 million to 100 million years.

Among the vectors were mosquitoes, sand flies, biting midges, bat flies, black flies, fleas, kissing bugs and ticks. They carry a cornucopia of microorganisms that today cause diseases such as filariasis, sleeping sickness, river blindness, typhus, Lyme disease and, perhaps most significantly, malaria.

Malaria remains a relentless public health concern, with multiple nations reporting increases in infections for 2018. In Venezuela alone, Poinar notes, more than 650,000 new cases of malaria have been reported this year.

"Numerous malaria species parasitize vertebrates today, and we now know that over the past 100 million years, malaria was being vectored by mosquitoes, biting midges, bat flies and ticks," Poinar said. "Obtaining fossil records of pathogens carried by biting arthropods establishes a timeline when and where various diseases appeared and how they could have affected the survival, extinction and distribution of vertebrates over time."

Poinar stresses, however, that while his research shows what parasites and pathogens specific bloodsuckers were transmitting at particular periods and locations in the past, "these fossils are not old enough to tell us when and how associations between vectors, pathogens and vertebrates originated."

Poinar believes that the microorganisms first infected blood-sucking arthropods and only after equilibria had been reached between them were the microorganisms then vectored to vertebrates.

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Bursting bubbles launch bacteria from water to air

MIT researchers have found that bacteria can affect a bubble's longevity.

Wherever there's water, there's bound to be bubbles floating at the surface. From standing puddles, lakes, and streams, to swimming pools, hot tubs, public fountains, and toilets, bubbles are ubiquitous, indoors and out.

A new MIT study shows how bubbles contaminated with bacteria can act as tiny microbial grenades, bursting and launching microorganisms, including potential pathogens, out of the water and into the air.

In the study, published in the journal Physical Review Letters, the researchers found that bacteria can affect a bubble's longevity: A bacteria-covered bubble floating at the water's surface can last more than 10 times longer than an uncontaminated one can, persisting for minutes instead of seconds. During this time, the cap of the contaminated bubble thins. The thinner the bubble, the higher the number of droplets it can launch into the air when the bubble inevitably bursts. A single droplet, the researchers estimate, can carry up to thousands of microorganisms, and each bubble can emit hundreds of droplets.

"We discovered bacteria can manipulate interfaces in a manner that can enhance their own water-to-air dispersal," says Lydia Bourouiba, assistant professor of civil and environmental engineering and director of the Fluid Dynamics of Disease Transmission Laboratory.

Bourouiba's co-author on the paper is graduate student Stephane Poulain.

Something in the water

Bourouiba has spent the past several years meticulously generating, imaging, and characterizing clean, uncontaminated bubbles, with the goal of establishing a baseline of normal bubble behavior.

"We first had to understand the physics of clean bubbles before we could add organisms like bacteria to see what effect they have on the system," Bourouiba says.

As it happens, the researchers first noticed bacteria's effect somewhat by accident. The team was in the midst of moving to a new lab space, and in the shuffle, a beaker of water had been left out in the open. When the researcher used it in subsequent experiments, the results were not what the team expected.

"The bubbles produced from this water lived much longer and had a peculiar thinning evolution compared to that of typical clean water bubbles," Poulain says.

Bourouiba suspected the water had been contaminated, and the team soon confirmed her hypothesis. They analyzed the water and found evidence of bacteria that are naturally present indoors.

The juice effect

To directly study bacteria's effect on bubbles, the team set up an experiment in which they filled a column with a solution of water and various bacteria species, including E. coli. The researchers developed a system to generate bubbles with an air pump, one at a time, inside the column, in order to control the volume and size of each bubble. When a bubble rose to the surface, the team used high-speed imaging coupled with a range of optical techniques to capture its behavior, at the surface and as it burst.

The researchers observed that, once a bubble contaminated with E. coli made it to the water's surface, its own surface, or cap, immediately started to thin, mostly by draining back into the water, like a melting shell of chocolate. This behavior was similar to that of uncontaminated bubbles.

But the contaminated bubbles remained on the surface more than 10 times longer than uncontaminated bubbles. And after a critical period of time, the bacteria-laden bubbles started thinning much faster. Bourouiba suspected that it might not be the bacteria themselves, but what they secrete, that holds the bubble in place for longer.

"Bacteria are alive, and like anything alive, they make waste, and that waste typically is something that potentially could interact with the bubble's interface," Bourouiba says. "So we separated the organisms from their 'juice.'"

The researchers washed bacteria away from their secretions, then repeated their experiments, using the bacteria's secretions. Just as Bourouiba suspected, the bubbles containing the secretions alone lasted much longer than clean bubbles. The secretions, the group concluded, must be the key ingredient in extending a bubble's lifetime. But how?

Again, Bourouiba had a hypothesis: Bacterial secretions may be acting to reduce a bubble's surface tension, making it more elastic, more resistant to perturbations, and in the end, more likely to live longer on a water's surface. This behavior, she noted, was similar to surface-active compounds, or surfactants, such as the compounds in detergents that make soap bubbles.

To test this idea, the researchers repeated the experiments, this time by swapping out bacteria for common synthetic surfactants, and found that they too produced longer-lasting bubbles that also thinned dramatically after a certain time period. This experiment confirmed that bacteria's secretions act as surfactants extending the lifetime of contaminated bubbles.

The researchers then looked for an explanation for the drastic change in a contaminated bubble's rate of thinning. In clean bubbles, the thinning of the cap was mostly the result of drainage, as water in the cap mostly drains back into the fluid from which the bubble rose. Such bubbles live on the order of seconds, and their drainage speed continuously slows down as the bubble thins.

But if a bubble lasts past a critical time, evaporation starts playing a more dominant role than drainage, essentially shaving off water molecules from the bubble's cap. The researchers concluded that, if a bubble contains bacteria, the bacteria and their secretions, make a bubble last longer on a water's surface -- long enough that evaporation becomes more important than drainage in thinning the bubble's cap.

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Synthetic microorganisms allow scientists to study ancient evolutionary mysteries

A genetically modified yeast containing an endosymbiotic bacterium.

Scientists at Scripps Research and their collaborators have created microorganisms that may recapitulate key features of organisms thought to have lived billions of years ago, allowing them to explore questions about how life evolved from inanimate molecules to single-celled organisms to the complex, multicellular lifeforms we see today.

By studying one of these engineered organisms-a bacterium whose genome consists of both ribonucleic acid (RNA) and deoxyribonucleic acid (DNA)-the scientists hope to shed light on the early evolution of genetic material, including the theorized transition from a world where most life relied solely on the genetic molecule RNA to one where DNA serves as the primary storehouse of genetic information.

Using a second engineered organism, a genetically modified yeast containing an endosymbiotic bacterium, they hope to better understand the origins of cellular power plants called mitochondria. Mitochondria provide essential energy for the cells of eukaryotes, a broad group of organisms-including humans-that possesses complex, nucleus-containing cells.

The researchers report engineering the microbes in two papers, one published October 29, 2018 in the Proceedings of the National Academy of Sciences (PNAS) and another published August 30, 2018 in Journal of the American Chemical Society (JACS).

"These engineered organisms will allow us to probe two key theories about major milestones in the evolution of living organisms-the transition from the RNA world to the DNA world and the transition from prokaryotes to eukaryotes with mitochondria," says Peter Schultz, PhD, senior author on the papers and president of Scripps Research. "Access to readily manipulated laboratory models enables us to seek answers to questions about early evolution that were previously intractable."

The origins of life on Earth have been a human fascination for millennia. Scientists have traced the arc of life back several billion years and concluded that the simplest forms of life emerged from Earth's primordial chemical soup and subsequently evolved over the eons into organisms of greater and greater complexity. A monumental leap came with the emergence of DNA, a molecule that stores all of the information required to replicate life and directs cellular machinery to do its bidding primarily by generating RNA, which in turn directs the synthesis of proteins, the molecular workhorses in cells.

In the 1960s, Carl Woese and Leslie Orgel, along with DNA pioneer Francis Crick, proposed that before DNA, organisms relied on RNA to carry genetic information, a molecule similar to but far less stable than DNA, that can also catalyze chemical reactions like proteins. "In science class, students learn that DNA leads to RNA which in turn leads to proteins-that's a central dogma of biology-but the RNA world hypothesis turns that on its head," says Angad Mehta, PhD, first author of the new papers and a postdoctoral research associate at Scripps Research. "For the RNA world hypothesis to be true, you have to somehow get from RNA to a DNA genome, yet how that might have happened is still a very big question among scientists."

One possibility is that the transition proceeded through a kind of microbial missing link, a replicating organism that stored genetic information as RNA. For the JACS study, the Scripps Research-led team created Escherichia coli bacteria that partially build their DNA with ribonucleotides, the molecular building blocks typically used to build RNA. These engineered genomes contained up to 50 percent RNA, thus simultaneously representing a new type of synthetic organism and possibly a throwback to billions of years ago.

Mehta cautions that their work so far has focused on characterizing this chimeric RNA-DNA genome and its effect on bacterial growth and replication but hasn't explicitly explored questions about the transition from the RNA world to the DNA world. But, he says, the fact that E. coli with half its genome comprised of RNA can survive and replicate is remarkable and seems to support the possibility of the existence of evolutionarily transitional organisms possessing hybrid RNA-DNA genomes. The Scripps Research team is now studying how the mixed genomes of their engineered E. coli function and plans to use the bacteria to explore a number of evolutionary questions.

For instance, one question is whether the presence of RNA leads to rapid genetic drift-large changes in gene sequence in a population over time. Scientists theorize that massive genetic drift occurred quickly during early evolution, and the presence in the genome of RNA could help explain how genetic change occurred so quickly.

In the paper published in PNAS, the researchers report engineering another laboratory model for an evolutionary milestone thought to have occurred more than 1.5 billion years ago. They created a yeast dependent for energy on bacteria living inside it as a beneficial parasite or "endosymbiont." This composite organism will allow them to investigate the ancient origins of mitochondria-tiny, bacteria-like organelles that produce chemical energy within the cells of all higher organisms.

Mitochondria are widely thought to have evolved from ordinary bacteria that were captured by larger, single-celled organisms. They carry out several key functions in cells. Most importantly, they serve as oxygen reactors, using O2 to make cells' basic unit of chemical energy, the molecule ATP. As crucial as mitochondria are to cells, their origins remain somewhat mysterious, although there are clear hints of descent from a more independent organism, widely assumed to have been a bacterium.

Mitochondria have a double-membrane structure like that of some bacteria, and-again, like bacteria-contain their own DNA. Analyses of the mitochondrial genome suggest that it shares an ancient ancestor with modern Rickettsia bacteria, which can live within the cells of their hosts and cause disease. Stronger support for the bacterial origin of mitochondria theory would come from experiments showing that independent bacteria could indeed be transformed, in an evolution-like progression, into mitochondria-like symbionts. To that end, the Scripps Research scientists engineered E. coli bacteria that could live in, depend upon, and provide key assistance to, cells of Saccharomyces cerevisiae, also known as baker's yeast.

The researchers started by modifying E. coli to lack the gene encoding thiamin, making the bacteria dependent on the yeast cells for this essential vitamin. At the same time, they added to the bacteria a gene for ADP/ATP translocase, a transporter protein, so that ATP produced within the bacterial cells would be supplied to their yeast-cell hosts-mimicking the central function of real mitochondria. The team also modified the yeast so that their own mitochondria were deficient at supplying ATP. Thus the yeast would be dependent on the bacteria for normal, mitochondria-based ATP production.

The team found that some of the engineered bacteria, after being modified with surface proteins to protect them from being destroyed in the yeast, lived and proliferated in harmony with their hosts for more than 40 generations and appeared to be viable indefinitely. "The modified bacteria seem to accumulate new mutations within the yeast to better adapt to their new surroundings," says Schultz.

With this system established, the team will try to evolve the E. coli to become mitochondria-like organelles. For the new E. coli endosymbiont, adapting to life inside yeast could allow it an opportunity to radically slim its genome. A typical E. coli bacterium, for example, has several thousand genes, whereas mitochondria have evolved a stripped-down set of just 37.

The Scripps Research team rounded out the study with further gene-subtraction experiments, and the results were promising: they found they could eliminate not just the E. coli thiamin gene but also the genes underlying the production of the metabolic molecule NAD and the amino acid serine, and still get a viable symbiosis.

"We are now well on our way to showing that we can delete the genes for making all 20 amino acids, which comprise a significant part of the E. coli genome," says Schultz. "Once we've achieved that, we'll move on to deleting genes for the syntheses of cofactors and nucleotides, and within a few years we hope to be able to get a truly minimal endosymbiotic genome."

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Ancient Mars had right conditions for underground life, new research suggests

New research shows that ancient Mars likely had ample chemical energy to support the kinds of underground microbial colonies that exist on Earth.

A new study shows evidence that ancient Mars probably had an ample supply of chemical energy for microbes to thrive underground.

"We showed, based on basic physics and chemistry calculations, that the ancient Martian subsurface likely had enough dissolved hydrogen to power a global subsurface biosphere," said Jesse Tarnas, a graduate student at Brown University and lead author of a study published in Earth and Planetary Science Letters. "Conditions in this habitable zone would have been similar to places on Earth where underground life exists."

Earth is home to what are known as subsurface lithotrophic microbial ecosystems -- SliMEs for short. Lacking energy from sunlight, these subterranean microbes often get their energy by peeling electrons off of molecules in their surrounding environments. Dissolved molecular hydrogen is a great electron donor and is known to fuel SLiMEs on Earth.

This new study shows that radiolysis, a process through which radiation breaks water molecules into their constituent hydrogen and oxygen parts, would have created plenty of hydrogen in the ancient Martian subsurface. The researchers estimate that hydrogen concentrations in the crust around 4 billion years ago would have been in the range of concentrations that sustain plentiful microbes on Earth today.

The findings don't mean that life definitely existed on ancient Mars, but they do suggest that if life did indeed get started, the Martian subsurface had the key ingredients to support it for hundreds of millions of years. The work also has implications for future Mars exploration, suggesting that areas where the ancient subsurface is exposed might be good places to look for evidence of past life.

Going underground

Since the discovery decades ago of ancient river channels and lake beds on Mars, scientists have been tantalized by the possibility that the Red Planet may once have hosted life. But while evidence of past water activity is unmistakable, it's not clear for how much of Martian history water actually flowed. State-of-the-art climate models for early Mars produce temperatures that rarely peak above freezing, which suggests that the planet's early wet periods may have been fleeting events. That's not the best scenario for sustaining life at the surface over the long term, and it has some scientists thinking that the subsurface might be a better bet for past Martian life.

"The question then becomes: What was the nature of that subsurface life, if it existed, and where did it get its energy?" said Jack Mustard, a professor in Brown's Department of Earth, Environmental and Planetary Sciences and a study coauthor. "We know that radiolysis helps to provide energy for underground microbes on Earth, so what Jesse did here was to pursue the radiolysis story on Mars."

The researchers looked at data from the gamma ray spectrometer that flies aboard NASA's Mars Odyssey spacecraft. They mapped out abundances of the radioactive elements thorium and potassium in the Martian crust. Based on those abundances, they could infer the abundance of a third radioactive element, uranium. The decay of those three elements provides the radiation that drives the radiolytic breakdown of water. And because the elements decay at constant rates, the researchers could use the modern abundances to calculate the abundances 4 billion years ago. That gave the team an idea of the radiation flux that would have been active to drive radiolysis.

The next step was to estimate how much water would have been available for that radiation to zap. Geological evidence suggests there would have been plenty of groundwater bubbling about in the porous rocks of the ancient Martian crust. The researchers used measurements of the density of the Martian crust to estimate roughly how much pore space would have been available for water to fill.

Finally, the team used geothermal and climate models to determine where the sweet spot for potential life would have been. It can't be so cold that all water is frozen, but it also can't be overcooked by heat from the planet's molten core.

Combining those analyses, the researchers conclude that Mars likely had a global subsurface habitable zone several kilometers in thickness. In that zone, hydrogen production via radiolysis would have generated more than enough chemical energy to support microbial life, based on what's known about such communities on Earth. And that zone would have persisted for hundreds of millions of years, the researchers conclude.

The findings held up even when the researchers modeled a variety of different climate scenarios -- some on the warmer side, others on the colder side. Interestingly, Tarnas says, the amount of subsurface hydrogen available for energy actually goes up under the extremely cold climate scenarios. That's because a thicker layer of ice above the habitable zone serves as a lid that helps to keep hydrogen from escaping the subsurface.

"People have a conception that a cold early Mars climate is bad for life, but what we show is that there's actually more chemical energy for life underground in a cold climate," Tarnas said. "That's something we think could change people's perception of the relationship between climate and past life on Mars."

Exploration implications

Tarnas and Mustard say the findings could be useful in thinking about where to send spacecraft looking for signs of past Martian life.

"One of the most interesting options for exploration is looking at megabreccia blocks -- chunks of rock that were excavated from underground via meteorite impacts," Tarnas said. "Many of them would have come from the depth of this habitable zone, and now they're just sitting, often relatively unaltered, on the surface."

Mustard, who has been active in the process of selecting a landing site for NASA's Mars 2020 rover, says that these kinds of breccia blocks are present in at least two of the sites NASA is considering: Northeast Syrtis Major and Midway.

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Why does a Yellowstone microorganism prefer meager rations over rich ones?

In Yellowstone National Park's Dragon Spring, part of the Norris Geyser Basin, scientists have found a microorganism that behaved in an unexpected way.

Arizona State University geoscientist Everett Shock has collaborated with a team of life scientists from Montana State University to discover a puzzle at the junction of geochemistry and biology.

The puzzle, which has no solution yet, is: Why would a microorganism thriving in a hot spring draw its energy from low-quality sources instead of rich ones?

Shock, who is a professor in geochemistry in ASU's School of Earth and Space Exploration and the School of Molecular Sciences, has long studied questions of habitability as they apply to life on Earth, and to the potential for life on other planets.

"The team isolated this organism, which is a member of the Acidianus genus, from a hot spring in Yellowstone National Park and cultured it in the laboratory," he said. "There it was given a choice of three different geochemical energy supplies."

This microbe, Shock said, can get energy from combining hydrogen with sulfur, or hydrogen with iron, or sulfur with iron. In the experiments the team carried out, hydrogen and sulfur supplied the least energy, while hydrogen and iron provided the most.

"Surprisingly, the organism grew best on the lowest energy supply -- and it grew the worst with the richest energy material," Shock said.

The scientists' report was published July 3 in Nature Geoscience. The lead author is Maximiliano Amenabar of Montana State University; besides Shock, the other authors are Eric Roden (University of Wisconsin), and John Peters and Eric Boyd (both Montana State).

Rich diet: Genetically costly?

"The results were quite counterintuitive," said Shock. "It's only natural to expect that in any environment, the 'big deal' energy sources will be supporting the most organisms, and the feeble sources -- well, you wonder if they are supporting anything at all."

It turns out, he explained, that in a genetic sense, it may be costly for the organism to go after the big-energy supply.

"It's like mining," he said. "You can have a rich ore deposit, but if extracting it costs more than you can get for it, it's not worth pursuing."

And in microorganism terms, Shock said, "biological cost may come down to availability. Perhaps the low-energy source is more reliable in nature than the high-energy one."

Shock suggested that reliability could "tune" the microorganism's metabolism to the energy source that's always available.

But apparently not exclusively, he added. "The organism is also capable of using these other energy sources. However, maybe using them takes more work, so the organism grows more slowly with them."

The focus of future research on this organism will be to assess in detail its energy costs. A recently completed genome for it will aid the research.

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