Tag Archives: bacteria

A lot of plant genes actually come from bacteria. And this may explain the success of early land plants

The evolution of land plants (simplified). Around 500 million years ago land plants started to spread from water to land. Credit: IST Austria.

When we think of gene transfer, the first thing that pops into our mind is inheritance. We tend to physically resemble our parents, be it in terms of height, skin tone, eye color, or facial traits, because we inherited genes from each parent, who in turn got their genes from their parents, and so on. Some organisms, however, find sexual reproduction counterproductive for their needs and opt for cloning, creating perfect genetic copies of themselves in perpetuity, apart from the occasional mutated offspring that refuses to be another chip off the old block. But that’s not all there is to it.

Sometimes DNA jumps between completely different species, and the results can be so unpredictable, they can dramatically alter the course of the evolution of life on Earth. Case in point, a new study makes the bold claim that genes jumping from microbes to green algae many hundreds of millions of years ago, shifted the tides and drove the evolution of land plants. Hundreds of genes found in plants thought to be essential to their development may have originally appeared in ancient bacteria, fungi, and viruses and became integrated into plants via horizontal gene transfer.

Speaking to ZME Science, Jinling Huang, a biologist at East Carolina University and corresponding author of the new study, said there could have been two major episodes of horizontal gene transfer (HGT) in the early evolution of land plants.

“Many or most of the genes acquired during these two major episodes have been retained in major land plant groups and affect numerous aspects of plant physiology and development,” the researcher said.

Sharing (genes) is caring

Genome-swapping events are rather common in bacteria. In fact, HGT is one of the main reasons why antibiotic resistance is spreading rapidly among microbes. This exchange of genetic material can turn otherwise harmless bacteria into drug-resistant ‘superbugs’.

Until not too long ago, HGT was thought to occur only among prokaryotes like bacteria, but recent evidence suggests that it can also happen in plants and even some animals. For instance, a 2021 study made the bold claim that herrings and smelts, two groups of fish that commonly roam the northernmost reaches of the Atlantic and Pacific Oceans, share a gene that couldn’t have been transferred through normal sexual channels — in effect, the researchers claim that HGT took place between two vertebrates.

“In genetics classes, we learn that genes are transmitted from parents to offspring (as such, kids look similar to their parents). This is called vertical transmission. In horizontal gene transfer, genes are transmitted from one species to another species. Although the importance of HGT has been widely accepted in bacteria now, there are a lot of debates on HGT in eukaryotes, particularly plants and animals. The findings of this study show that HGT not only occurred in plants, but also played an important role in the evolution of land plants,” Huang told ZME Science.

In order to investigate the role of HGT in early plant evolution, Huang and colleagues from China analyzed the genomes of 31 plants, including mosses, ferns, and trees, as well as green algae related to modern terrestrial plants. The researchers suspected quite a few genes transferred over from bacteria, but the results were totally surprising. They suggest that nearly 600 gene families — far more than researchers had expected — found in modern plants were transferred from totally foreign organisms like bacteria and fungi.

Many of these genes are thought to be involved in important biological functions. For instance, the late embryogenesis abundant genes, which help plants adapt to drier environments, are bacterial in origin. The same is true for the ammonium transporter gene that’s essential for a plant’s ability to soak up nitrogen from the soil to grow. And if you just despise cutting tear-jerking onions, you have HGT to blame too. The researchers found that the genes responsible for the biosynthesis of ricin toxin and sulfine (the irritating substance released when we cut onions) are also derived from bacteria.

“We were a little surprised to find those genes,” Dr. Huang told me, adding that his team was able to reconstruct the phylogenies (the history of the evolution of a species) for the genes using independent lines of evidence to determine whether a gene is derived from bacteria and the result of some inherited mutation.

“For instance, an ABC complex in plants consists of two subunits. Phylogenetic analyses show that both genes were acquired from bacteria. We also found that the two genes are positioned next to each other on the chromosomes of both bacteria and some plants, suggesting that the two genes might have been co-transferred from bacteria to plants,” the scientist added.

The establishment of plant life on land is one of the most significant evolutionary episodes in Earth history, with evidence gathered thus far indicating that land plants first appeared about 500 million years ago, during the Cambrian period, when the development of multicellular animal species took off.

This terrestrial colonization was made possible thanks to a series of major innovations in plant anatomy and biochemistry. If these findings are true, bacteria must have played a major role. Due to HGT, the earliest plants could have gained advantageous traits that make them more adapted to their novel terrestrial environment almost immediately, rather than having to wait for who knows how many thousands or even millions of years to develop similar genetic machinery.

The findings appeared today in the journal Molecular Plant.

Gut bacteriophages associated with improved cognitive function and memory in both animals and humans

A growing body of evidence has implicated gut bacteria in regulating neurological processes such as neurodegeneration and cognition. Now, a study from Spanish researchers shows that viruses present in the gut microbiota can also improve mental functions in flies, mice, and humans.

Credit: CDC.

They easily assimilate into their human hosts — 8% of our DNA consists of ancient viruses, with another 40% of our DNA containing genetic code thought to be viral in origin. As it stands, the gut virome (the combined genome of all viruses housed within the intestines) is a crucial but commonly overlooked component of the gut microbiome.

But we’re not entirely sure what it does.

This viral community is comprised chiefly of bacteriophages, viruses that infect bacteria and can transfer genetic code to their bacterial hosts. Remarkably, the integration of bacteriophages or phages into their hosts is so stable that over 80% of all bacterial genomes on earth now contain prophages, permanent phage DNA as part of their own — including the bacteria inside us humans. Now, researchers are inching closer to understanding the effects of this phenomenon.

Gut and brain

In their whitepaper published in the journal Cell Host and Microbe, a multi-institutional team of scientists describes the impact of phages on executive function, a set of cognitive processes and skills that help an individual plan, monitor, and successfully execute their goals. These fundamental skills include adaptable thinking, planning, self-monitoring, self-control, working memory, time management, and organization, the regulation of which is thought, in part, to be controlled by the gut microbiota.

The study focuses on the Caudovirales and Microviridae family of bacteriophages that dominate the human gut virome, containing over 2,800 species of phages between them.

“The complex bacteriophage communities represent one of the biggest gaps in our understanding of the human microbiome. In fact, most studies have focused on the dysbiotic process only in bacterial populations,” write the authors of the new study.

Specifically, the scientists showed that volunteers with increased Caudovirales levels in the gut microbiome performed better in executive processes and verbal memory. In comparison, the data showed that increased Microviridae levels impaired executive abilities. Simply put, there seems to be an association between this type of gut biome and higher cognitive functions.

These two prevalent bacteriophages run parallel to human host cognition, the researchers write, and they may do this by hijacking the bacterial host metabolism.

To reach this conclusion, the researchers first tested fecal samples from 114 volunteers and then validated the results in another 942 participants, measuring levels of both types of bacteriophage. They also gave each volunteer memory and cognitive tests to identify a possible correlation between the levels of each species present in the gut virome and skill levels.

The researchers then studied which foods may transport these two kinds of phage into the human gut -results indicated that the most common route appeared to be through dairy products.

They then transplanted fecal samples from the human volunteers into the guts of fruit flies and mice – after which they compared the animal’s executive function with control groups. As with the human participants, animals transplanted with high levels of Caudovirales tended to do better on the tests – leading to increased scores in object recognition in mice and up-regulated memory-promoting genes in the prefrontal cortex. Improved memory scores and upregulation of memory-involved genes were also observed in fruit flies harboring higher levels of these phages.

Conversely, higher Microviridae levels (correlated with increased fat levels in humans) downregulated these memory-promoting genes in all animals, stunting their performance in the cognition tests. Therefore, the group surmised that bacteriophages warrant consideration as a novel dietary intervention in the microbiome-brain axis.

Regarding this intervention, Arthur C. Ouwehand, Technical Fellow, Health and Nutrition Sciences, DuPont, who was not involved in the study, told Metafact.io:

“Most dietary fibres are one way or another fermentable and provide an energy source for the intestinal microbiota.” Leading “to the formation of beneficial metabolites such as acetic, propionic and butyric acid.”

He goes on to add that “These so-called short-chain fatty acids may also lower the pH of the colonic content, which may contribute to an increased absorption of certain minerals such as calcium and magnesium from the colon. The fibre fermenting members of the colonic microbiota are in general considered beneficial while the protein fermenting members are considered potentially detrimental.”

It would certainly be interesting to identify which foods are acting on bacteriophages contained within our gut bacteria to influence cognition.

Despite this, the researchers acknowledge that their work does not conclusively prove that phages in the gut can impact cognition and explain that the test scores could have resulted from different bacteria levels in the stomach but suggest it does seem likely. They close by stating more work is required to prove the case.

Your microbiota will be having non-stop sex this Valentine’s Day

Even if you’re alone this Valentine’s Day, there’s no need to worry: some parts of your body will be getting plenty of action. In fact, your body will host a veritable carnival of the sensual in your tummy, as your microbiota will engage in an orgy of sex and swinger’s parties — where they’ll be swapping genes instead of keys.

A medical illustration of drug-resistant, Neisseria gonorrhoeae bacteria. Original image sourced from US Government department: Public Health Image Library, Centers for Disease Control and Prevention. Image in the public domain.

The salacious gene

Imagine you have a severe disease with a very unusual cure: you can treat by making love with someone who then passes on the necessary genes to cure your ailment. It is, as they say, sexual healing. Using sex to protect or heal themselves is precisely what bacteria can do, and it’s a crucial defense mechanism.

In the past, the research community thought bacterial sex (or conjugation, as scientists call it) was a terrible threat for humans, as this ancient process can spread DNA capable of conveying antibiotic resistance to their neighbors. Antibiotic resistance is one of the most pressing health challenges the world is facing, being projected to cause 10 million deaths a year by 2050.

But there’s more to this bacterial sex than meets the eye. Recently, scientists from the University of Illinois at Urbana-Champaign and the University of California Riverside witnessed gut microbes sharing the ability to acquire a life-saving nutrient with one another through bacterial sex. UCR microbiologist and study lead Patrick Degnan says:

“We’re excited about this study because it shows that this process isn’t only for antibiotic resistance. The horizontal gene exchange among microbes is likely used for anything that increases their ability to survive, including sharing vitamin B12.”

For well over 200-years, researchers have known that bacteria reproduce using fission, where one cell halves to produce two genetically identical daughter cells. However, in 1946, Joshua Lederberg and Edward Tatum discovered bacteria could exchange genes through conjugation, an entirely separate act from reproduction.

Conjugation occurs when a donor and a recipient bacteria sidle up to each other, upon which the donor creates a tube, called a pilus that attaches to the recipient and pulls the two cells together. A small parcel of DNA is then passed from the donor to the recipient, providing new genetic information through horizontal transfer.

Ironically, it wasn’t until Lederberg met and fell in love with his wife, Esther Lederberg, that they made progress regarding bacterial sex.

Widely acknowledged as a pioneer of bacterial genetics, Esther still struggled for recognition despite identifying the horizontal transfer of antibiotic resistance and viruses, which kill bacteria known as bacteriophages. She discovered these phages after noticing small objects nibbling at the edges of her bacterial colonies. Going downstream to find out how they got there, she found these viral interlopers hiding dormant amongst bacterial chromosomes after being transferred by microbes during sex.

Later work found that environmental stresses such as illness activated these viruses to replicate within their hosts and kill them. Still, scientists assumed that bacterial sex was purely a defense mechanism.

Esther Ledeberg in her Stanford lab. Image credits: Esther Lederberg.

Promiscuity means longevity

The newly-published study builds on Esther’s work. The study authors felt this bacterial process extended beyond antibiotic resistance. So they started by investigating how vitamin B12 was getting into gut microbial cells, where the cells had previously been unable to extract this vitamin from their environment — which was puzzling as, without vitamin B12, most types of living cells cannot function. Therefore, many questions remained about how these organisms survived without the machinery to extract this resource from the intestine.

The new study in Cell Reports uses the Bacteroidetes species, which comprise up to 80% of the human microbiome in the intestines, where they break down complex carbohydrates for energy.

“The big, long molecules from sweet potatoes, beans, whole grains, and vegetables would pass through our bodies entirely without these bacteria. They break those down so we can get energy from them,” the team explained.

This bacteria was placed in lab dishes mixing those that could extract B12 from the stomach with some that couldn’t. The team then watched in awe while the bacteria formed their sex pilus to transfer genes enabling the extraction of B12. After the experiment, researchers examined the total genetic material of the recipient microbe and found it had incorporated an extra band of DNA from the donor.

Among living mice, something similar happens. When the group-administered two different subgroups of Bacteroidetes to a mouse – one that possessed the genes for transferring B12 and another that didn’t — they found the genes had ‘jumped’ to the receiving donee after five to nine days.

“In a given organism, we can see bands of DNA that are like fingerprints. The recipients of the B12 transporters had an extra band showing the new DNA they got from a donor,” Degnan said.

Remarkably, the team also noted that different species of phages were also transferred during conjugation, exhibiting bacterial subgroup specificity in some cases. These viruses also showed the capacity to alter the genomic sequence of its bacterial host, with the power to promote or demote the life of its microbic vessel when activated.

Sexual activity in our intestines keeps us healthy

Interestingly, the authors note they could not observe conjugation in all subgroups of the Bacteroidetes species, suggesting this could be due to growth factors in the intestine or a possible subgroup barrier within this large species group slowing the process down.

Despite this, Degnan states, “We’re excited about this study because it shows that this process isn’t only for antibiotic resistance.” And that “The horizontal gene exchange among microbes is likely used for anything that increases their ability to survive, including sharing [genes for the transport of] vitamin B12.”

Meaning that bacterial sex doesn’t just occur when microbes are under attack; it happens all the time. And it’s probably part of what keeps the microbiome and, by extension, ourselves fit and healthy.

Researchers successfully use viruses to clear years-old, antibiotic-resistant infection

Drug-resistant bacteria are a very concerning, and growing, threat. Now researchers at the Erasmus Hospital, Belgium, are working to recruit viruses in our fight against them.

Stylized bacteriophages. Image via Pixabay.

The researchers report successfully treating an adult woman, who was infected with drug-resistant bacteria, using a combination of antibiotics and bacteriophages (bacteria-killing viruses). Such experiments are the product of several decades’ worth of research into the use of bacteriophages in humans. The results are encouraging and could pave the way towards such viruses having a well-established role in the treatment of drug-resistant bacteria.

Viral helpers

The patient had been severely injured by the detonation of a bomb during a terrorist attack. She suffered multiple injuries, including one to her leg, that damaged it down to the bone. After surgery to have some of the tissue removed, she developed a bacterial infection on the leg. The bacteria responsible was Klebsiella pneumoniae, which is known to be resistant to antibiotics. It also creates biofilms that physically insulate affected areas from antibiotics.

Doctors tried to clear the infections, with no success, for several years. Left with no other options to try, her medical team suggested bacteriophage therapy, which they performed with assistance from researchers at the Eliava Institute in Tbilisi.

Bacteriophage therapy is not in medical use today as there are still concerns around the safety of using such viruses to treat humans with already-weakened immune systems, and many unknowns regarding when and how to best employ them.

To employ a bacteriophage in this role, one must be found that attacks the exact strain of bacteria that causes the infection. The researchers carried out a thorough search and testing process, and eventually found a suitable virus in a sample of sewer water. This was then isolated and grown in the lab, mixed into a liquid solution, and applied directly to the site of the infection. At the same time, the patient was put on a heavy antibacterial regimen.

Although it took three years of treatment, the patient is now free of the infection and able to walk again.

The team notes that their results showcase that such approaches can be effective treatment options when other avenues fail. However, they also explain that a better way of finding suitable bacteriophages must be developed before these interventions become viable in a practical sense. It simply takes too much time and effort to perform this search the same way the team did here for hospitals to realistically do this for multiple patients. There are currently no guarantees that a suitable virus will be found even if such a search is performed, as well.

The paper “Combination of pre-adapted bacteriophage therapy and antibiotics for treatment of fracture-related infection due to pandrug-resistant Klebsiella pneumoniae,” has been published in the journal Nature Communications.

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.

Why kids hate broccoli: a foul combination with oral bacteria

Credit: Pixabay.

Your first memory of eating Brussels sprouts and broccoli is likely not a very happy one. Many children dislike these sorts of vegetables, known as Brassica, and some may even find them disgusting. There are a couple of reasons why broccoli can taste really bad, especially for children who are more sensitive, including bitter-taste compounds and gene variants.

Now, scientists have found yet another factor that makes these plants unpalatable: enzymes in broccoli can combine with bacteria in our saliva to produce very unpleasant sulfurous odors. The higher the levels of these compounds, the more likely children were to say they dislike the vegetables. Furthermore, the levels of these volatile compounds were found to be similar in parent-child pairs, which suggests the oral biome is shared.

In the mouth, broccoli can produce putrid odors in some people

Broccoli, cauliflower, and Brussels sprouts all contain a glucosinolate compound that makes them taste bitter. But to some people, their taste can be especially foul. For some time, scientists have known that the TAS2R38 gene is responsible for regulating how humans sense bitterness in food, with huge evolutionary implications.

The bitter taste, along with sourness, is thought to be protective, an early sign that is supposed to communicate ‘be careful, this food may be toxic’. This warning system is quite robust, being capable of identifying thousands of different compounds, some of which could poison and even kill us.

Sensitivity to bitter compounds is a little bit higher in very young humans. Children have around twice as many taste buds as adults, for instance. Also, there’s quite a bit of genetic variance in how people express TAS2R38.

Of course, broccoli isn’t toxic. On the contrary, it’s a ‘superfood’, very rich in nutrients and antioxidants, while being low on calories. It just so happens that our body mistakes it for something that may be toxic, and this sensitivity is within a spectrum, meaning there’s significant variation among people. To some people broccoli and other vegetables like it are palatable, to others it’s simply not approachable.

Normally the Glucosinolates get all the attention, but Damian Frank, a Research Fellow in Food Chemistry and Sensory Food Scientist at the University of Sydney, found that another compound called S-methyl-ʟ-cysteine sulfoxide shouldn’t be overlooked when it comes to Brassica bitterness. When these compounds combine with enzymes in the plant’s tissue and people’s saliva, they produce sulfurous odors.

Frank and colleagues investigated differences in sulfur volatile production in saliva from 98 child/parent pairs. Using gas chromatography-olfactometry-mass spectrometry, the researchers first measured the main odor-active compounds in raw and steamed cauliflower and broccoli. They then mixed saliva samples from each participant with raw cauliflower powder and analyzed the produced volatile compounds. Each sample was then associated with taste ratings self-reported by the parent or child.

Unsurprisingly, dimethyl trisulfide, which smells rotten, sulfurous and putrid, was the least liked odor by both children and adults. But what was intriguing was that there were large differences in sulfur volatile production between child/parent pairs while children had very similar sulfurous odor production to their parents. This makes sense since people tend to have similar microbiomes when sharing the same diet, household, and ancestry.

“There were big differences between the amount of volatiles formed between individuals. But there was a significant correlation between children and adults; the parents of children with high enzyme activity tended to also have high activity. This suggested similarity in the amount and type of bacteria present,” Frank told ZME Science.

Although children whose saliva produced the highest amount of sulfur volatiles predictably disliked raw Brassica vegetables the most, this relationship wasn’t as strong for their parents. This is perhaps due to less taste sensitivity with age and an acquired tolerance of the flavor with repeated exposure through life. That being said, many parents likely hate broccoli as much as their kids do.

“Sometimes the parent has to overcome their own dislike to give their child “healthy” food like brassicas. They want to be a good parent and do the right thing, but it goes against the grain!” said Frank.

The researchers also measured common genetic differences in bitter sensing receptor genes among the participants, the results of which will be published soon. These will likely help explain why some people like Brassica vegetables and others, well, not so much.

“Not sure whether I will be doing further work in this interesting area.  But a better characterization of the type of bacteria present in individual oral microbiomes is a worthwhile research area. Also more research on how bacteria in the mouth affect taste and perception is super fascinating,” Frank said.

The findings were reported in the Journal of Agricultural and Food Chemistry.

Sewage sludge dry.

Purple bacteria turn sewage into hydrogen fuel

Purple bacteria are poised to turn your toilet into a source of energy and useable organic material.

Desiccation cracks sludge.

Dried sewage sludge.
Image credits: Hannes Grobe.

Household sewage and industrial wastewater are very rich in organic compounds, and organic compounds can be very useful. But there’s a catch: we don’t know of any efficient way to extract them from the eww goo yet. So these resource-laden liquids get treated, and the material they contain is handled as a contaminant.

New research plans to address this problem — and by using an environmentally-friendly and cost-efficient solution to boot.

The future is purple (and bacterial)

“One of the most important problems of current wastewater treatment plants is high carbon emissions,” says co-author Dr. Daniel Puyol of King Juan Carlos University, Spain.

“Our light-based biorefinery process could provide a means to harvest green energy from wastewater, with zero carbon footprint.”

The study is the first effort to apply purple phototrophic bacteria — phototrophic means they absorb photons, i.e. light, as they’re feeding — together with electrical stimulation for organic waste recovery. The team showed that this approach can recover up to 100% of the carbon in any type of organic waste, supplying hydrogen gas in return — which is very nice, as hydrogen gas can be used to create power cells or energy directly.

Although green is the poster-color for photosynthesis, it’s far from the only one. Chlorophyll’s role is to absorb energy from light — we perceive this absorption as color. Green chlorophyll, for example, absorbs the wavelengths we perceive as red (which sits opposite green on the color wheel). If you’ve ever toyed around with the color-correction feature in graphical software (a la Photoshop, for example), you know that taking out the reds in a picture will make it look green. The same principle applies here.

Plants are generally green because red wavelengths carry the most energy — and plants need energy to create organic molecules. But the substance comes in all sorts of colors in a variety of different organisms. Phototrophic bacteria also capture energy from sunlight, but they use a different range of pigment — from orange, reds, and browns, to shades of purple — for the job. However, the color itself isn’t important here.

“Purple phototrophic bacteria make an ideal tool for resource recovery from organic waste, thanks to their highly diverse metabolism,” explains Puyol.

These bacteria use organic molecules and nitrogen gas in lieu of CO2 and water as food. This supplies all the carbon, electrons, and nitrogen they need for photosynthesis. The end result is that they tend to grow faster than other phototrophic bacteria or algae and generate hydrogen gas, proteins, and a biodegradable type of polyester as waste.

But what really sealed the deal for the team is that they can decide which of these waste products the bacteria churn out. Depending on environmental conditions such as light intensity, temperature, and the nutrients available, one of these products will predominate in the material they excrete.

The team doubled-down on this property by flooding the bacteria’s environment with electricity.

“Our group manipulates these conditions to tune the metabolism of purple bacteria to different applications, depending on the organic waste source and market requirements,” says co-author Professor Abraham Esteve-Núñez of University of Alcalá, Spain.

“But what is unique about our approach is the use of an external electric current to optimize the productive output of purple bacteria.”

This concept — a “bioelectrochemical system” — works because all of the purple bacteria’s metabolic pathways use electrons as energy carriers. They use up electrons when capturing light, for example. On the other hand, turning nitrogen into ammonia releases electrons, which the bacteria need to dissipate. By applying an electrical current to the bacteria (i.e. by pumping electrons into their environment) or by taking electrons out, the team can cause the bacteria to switch from one process to the other. It also helps improve the overall efficiency of both processes (see Le Chatelier’s principle).

The team included an analysis of the optimum conditions for hydrogen production in the paper (it relies on a mixture of purple bacteria species). They also tested the effect of a negative current (electrons supplied by metal electrodes in the growth medium) on the metabolic behavior of the bacteria.

Their first key finding was that the nutrient blend that fed the highest rate of hydrogen production also minimized the production of CO2 — this would allow the bacteria to recover biofuel from wastewater with a low carbon footprint, the team explains. The negative current experiment proved that these bacteria can use cathode electrons to perform photosynthesis.

Even more striking were the results using electrodes, which demonstrated for the first time that purple bacteria are capable of using electrons from a negative electrode, or “cathode“, to capture CO2 via photosynthesis.

“Recordings from our bioelectrochemical system showed a clear interaction between the purple bacteria and the electrodes: negative polarization of the electrode caused a detectable consumption of electrons, associated with a reduction in carbon dioxide production,” says Esteve-Núñez.

“This indicates that the purple bacteria were using electrons from the cathode to capture more carbon from organic compounds via photosynthesis, so less is released as CO2.”

The paper “Biological and Bioelectrochemical Systems for Hydrogen Production and Carbon Fixation Using Purple Phototrophic Bacteria” has been published in the journal Frontiers in Energy Research.

How art restorers in Italy used bacteria to clean up pesky grime on Michelangelo sculptures

The marble sarcophagus of Giuliano di Lorenzo de’ Medici sculpted by Michelangelo. The sarcophagus is flanked by the representations of Night and Day. Credit: Flickr, Aleksandr Zykov.

Whilst some of Michelangelo’s most famous marble sculptures, such as the exquisite David housed at the Galleria dell’Accademia in Florence and Pietà found in St. Peter’s Basilica in Vatican City, have been restored and preserved across the centuries, the same can’t be said about all the master’s great works.

After years of gathering grime that blemished Michelangelo’s marble statues in the Medici Chapel at the Basilica of San Lorenzo, Florence, art restorationists finally embarked on a delicate cleanup process. To this aim, the team employed an innovative method whereby specialized strains of bacteria were set loose to feed on the grime, restoring the luster of the marble molded by the maestro.

The tiniest art restorers in the world

Experts at Italy’s National Research Council had been restoring the sarcophaguses at the final resting place of the Medicis for nearly a decade. After years of painstaking and careful work, most of the blemishes on the artwork were safely removed — all but a few stubborn stains that didn’t seem to respond to conventional restoration methods.

The mess is attributed to Alessandro Medici, a former ruler of Florence who was assassinated in 1537 and his body was buried in his family’s chapel without being properly eviscerated. Over the centuries, compounds from Alessandro’s remains seeped into the marble of some of Michelangelo’s statues in the chapel, leading to deep stains that no known cleaning product could remove.

Ultimately, it was decided to employ microbes to good purpose, essentially turning the marble decorations into huge petri dishes. But first, they had to pick the right strains.

Biologist Anna Rosa Sprocati evaluated a catalog of over 1,000 strains. It was of the utmost importance that she selected the right bacteria for the job. For instance, some strains ate the grime — but also ate the marble of Michelangelo’s masterpieces. One wrong move and the restoration process could have turned into a disaster.

Ultimately, Sprocati settled for a shortlist of eight candidates, which she tested on a sample section behind the altar of the chapel. One of the bacteria called Serratia ficaria SH7 was particularly voracious — it ate oils, glue, and all of Alessandro’s phosphates, leaving Michelangelo’s marble sparkling white. The bacterium is non-hazardous to human health and doesn’t leave spores.

The bacteria was first used to clean the marble in the tomb of Giuliano di Lorenzo, Duke of Nemours, which is graced by the personification of Night and Day. Previously, Night’s hairs and ears were covered in black grime, which was successfully cleared away by two different strains Pseudomonas stutzeri CONC11, a bacterium isolated from the waste of a tannery near Naples, and Rhodococcus sp. ZCONT, a bacterium collected from soil contaminated with diesel in Caserta. Night’s face was treated with a stabilizer often found in toothpaste and cosmetics derived from Xanthomonas campestris bacteria. 

Then work suddenly stopped because of COVID, resuming sometime mid-October 2020. Sprocati went back at it, spreading gels with the SH7 bacteria on the grimy sarcophagus of Lorenzo di Piero, Duke of Urbino, the father of the assassinated Alessandro.

A stain on the family name

Photo featuring Dawn, with its pair Dusk in the background, flanking a sarcophagus in the tomb of Lorenzo de’ Medici in Florence, Italy. Credit: Flickr, George M. Groutas.

All of these now squeaky clean masterpieces were commissioned by Pope Leo X, the first Medici pope, also known as Giovanni di Lorenzo de Medici, who desired a marvelous new sacristy as the final resting place for his noble family. Of course, they selected Michelangelo, the greatest artist of his time and a protege of the Medici family since he was a teenage boy.

After Leo X suddenly died of pneumonia, Michelangelo continued work on the marvelous mausoleum until 1527, the date Rome was sacked by the mutinous troops of Charles V, Holy Roman Emperor. Seeking to seize the opportunity, Florentines staged a coup to overthrow the Medicis and instate a Republic. Michelangelo supported this initiative that saw Alessandro, among many other Medicis, ousted from the city.

Alessandro was rough and uncultured, a lover of sensual pleasures who enriched himself personally through taxes and duties and was determined to make his authority absolute beyond all question. Many saw him as a tyrant. According to various historical sources, Michelangelo simply couldn’t stand Alessandro.

Michelangelo didn’t pick the winning side though, and it wasn’t long before the Medicis were back in town. In 1531, Pope Clement VII, another Medici pope (this is the kind of tremendous influence this banking family could command!), pardoned the exiled Michelangelo, who hastily went back to work to complete the family chapel. But by that time, Alessandro had become Duke of Florence. Michelangelo couldn’t sit in the same town as Alessandro, let alone in the same room, so it was time for the great Renaissance artist to flee once more.

In 1537, the loathsome Alessandro was murdered by a relative. His body was rolled up in a carpet and dropped into a sarcophagus without many honors. This time, when Michelangelo returned, he finished the job at the chapel. But even centuries later, Alessandro would stain his family’s name — quite literally.

Fortunately, some very hungry bacteria helped restorers finish the chapel’s much-needed cleanup. Tourists can now admire some of Michelangelo’s finest works in new light, as the chapel has been reopened to visitors.

This isn’t the first time microbes were used for art restoration. Sulphur-eating strains were used to clean black crusts from the Milan Cathedral. Bacteria were also used to clean a fresco on a cathedral dome in Pisa and a cemetery close to the Leaning Tower.

Plastic-eating bacteria turns waste into vanilla flavoring

Example of PET waste. Credit: pixabay.

The invention of plastic has been one of the most important cornerstones to raising our standard of living in the past century. However, the same qualities that make plastic so desirable to consumers — in particular, its very low cost and high durability — also make it a bane to the environment. This is why scientists across the world are busy researching sustainable solutions to our growing plastic litter problem, either at the source (i.e. finding biodegradable alternatives) or during waste treatment.

One such effort focused on the latter. Researchers at the University of Edinburgh in Scotland devised an experimental method that converts treated polyethylene terephthalate (PET) — the lightweight plastic used to package everything from beverages to food — into vanillin, the primary ingredient extracted from vanilla beans that creates the characteristic taste and smell of vanilla.

To do so, the researchers turned to the common E. coli bacteria, which is found virtually everywhere, including your lower intestines. They engineered a strain to consume terephthalic acid, a molecule derived from PET, and transform the substance in vanillin, through a series of chemical reactions.

During one experiment, the E. coli turned a used plastic bottle into vanillin which should be fit for human consumption. Subsequent research will determine whether or not this plastic-derived vanilla compound is indeed safe to eat.

“This is the first example of using a biological system to upcycle plastic waste into a valuable industrial chemical and this has very exciting implications for the circular economy. “The results from our research have major implications for the field of plastic sustainability and demonstrate the power of synthetic biology to address real-world challenges,” said study first author Joanna Sadler of the School of Biological Sciences at the University of Edinburgh.

This research is exciting because it could solve two problems in one go. Every year, people across the globe produce about 50 million tonnes of PET waste with important economic and environmental consequences. Whilst PET is one of the most easily recyclable plastics, most still ends up in landfills or, worse, the ocean.

Meanwhile, people love vanilla! In 2018, global demand for vanillin was in excess of 37,000 tonnes. The compound is not only used in food but also in other industries from cosmetics to herbicides.

Thus, using bacteria to convert a harmful waste into a valuable product is a fantastic one-two punch.

“Our work challenges the perception of plastic being a problematic waste and instead demonstrates its use as a new carbon resource from which high-value products can be obtained,” said Stephen Wallace, co-author of the new study and a researcher at the School of Biological Sciences at the University of Edinburgh.

In the future, the researchers in Scotland plan on performing further strain engineering, process optimization, and extend the pathway to other metabolites so they might turn plastic into useful compounds other than vanillin.

The findings appeared in the journal Green Chemistry.

Trained bacteriophages could help us with our drug resistance issues

Antibiotic-resistant bacteria are giving our medicine an increasingly-harder time. Bacteriophages however, viruses that prey on bacteria, could help us regain the upper hand.

A bacteriophage model made out of digital Lego blocks. Image credits Pascal / Flickr.

We’re quite spoiled in this modern day and age. Things as minor as cutting a finger are dealt with a wash, bandage, and an antibiotic at most — but they could be very deadly for our ancestors even 100 years ago. But as time passes, bacteria adapt to the drugs they’re exposed to, developing resistance.

It’s estimated that by 2050, antibiotic-resistant bacteria will claim over 10 million lives, as our existing therapies lose effectiveness and patients are left vulnerable.

Bacteria eaters

“Antibiotic resistance is inherently an evolutionary problem, so this paper describes a possible new solution as we run out of antibiotic drug options,” says Joshua Borin, lead author of the study. “Using bacterial viruses that can adapt and evolve to the host bacteria that we want them to infect and kill is an old idea that is being revived. It’s the idea of the enemy of our enemy is our friend.”

Bacteriophages, or phages for short, are viruses that specialize in infecting and reproducing using bacteria. They’re quite like the viruses that make us sick, only with a different ‘meal’ preference.

A new project led by researchers at the University of California San Diego, Biological Sciences department, have shown that phages can be trained, so to speak, to make them better able to attack and destroy bacteria. These pre-trained phages could help delay the onset of antibiotic resistance in groups of bacteria by physically destroying them (rather than chemically, as drugs do), and the team showcases this potential in their experiments. The study also included researchers at the University of Haifa in Israel and the University of Texas at Austin

The experiment was carried out in a series of unassuming laboratory flasks. Boiled down, it involved training specialized phages to recognize and attack certain bacterial strains, in preparation for a final ‘target’. The secret here is that the phages are given an opportunity to better adapt to their prey while kept in the flasks (through natural evolutionary processes). Phages that were ‘trained’ for 28 days, the team explains, were 1,000 times more efficient at suppressing the bacterial colony than untrained ones, and for between three to eight times as long.

“The trained phage had already experienced ways that the bacteria would try to dodge it,” said Associate Professor Justin Meyer, the study’s corresponding author. “It had ‘learned’ in a genetic sense. It had already evolved mutations to help it counteract those moves that the bacteria were taking. We are using phage’s own improvement algorithm, evolution by natural selection, to regain its therapeutic potential and solve the problem of bacteria evolving resistance to yet another therapy.”

While the findings are encouraging, they’re still quite preliminary — more of a proof of concept, if you will. Moving forward, the team wants to test their approach on strains of bacteria important in clinical settings, such as E. coli. Its viability as a treatment option will also be checked using animal models.

The paper “Coevolutionary phage training leads to greater bacterial suppression and delays the evolution of phage resistance” has been published in the journal PNAS.

Silver nanoparticles change shape and get ‘consumed’ when destroying bacteria

New research is looking into the interaction between silver nanoparticles and E. coli bacteria as a possible solution to the growing levels of antibiotic resistance seen in pathogens. Although the antibacterial effect of silver has been known for some time now, we didn’t understand why it had this effect.

Silver bars. Image via Pixabay.

Silver has seen growing use for pathogen control in the last few years, in things such as antimicrobial coatings, for example. So far, it definitely seems to be good at the job of killing these tiny threats. Still, a better understanding of how and why it can protect from microbes could help us better apply silver to the task.

In order to glean this information, a team of researchers monitored the interactions between silver nanoparticles and a culture of E. coli bacteria. According to the results, silver nanoparticles undergo several dramatic changes in properties such as size and shape while interacting with bacteria.

Silver for monsters

Concerning the issue of antibiotic resistance, silver poses a very exciting prospect in that it physically kills bacteria, not chemically, as our drugs do. In other words, pathogens don’t have any way of defending themselves against silver.

An international team of researchers with members from Italy, the United States, and Singapore report that silver nanoparticles go through “several dramatic” changes when interacting with E. coli bacteria. This goes against the current prevailing wisdom that the metal remains unaltered during such interactions.

These changes seem to originate in electrostatic interactions between the silver and the bacteria. This causes some of the nanoparticles to dissolve and spread as ions in the environment, eventually making their way into the bacterial cells. Their shape changes as they dissolve, getting smaller and more rounded (they start out as triangular shapes).

After observing these mechanisms, the team treated their E. coli colony with a substance that increased the permeability of the bacteria’s membranes, and then tested them again. In this case, the effects on the silver were more pronounced, they explain.

“It seems from this study that silver is ‘consumed’ from the interaction,” said Guglielmo Lanzani, one of the authors on the paper and director of the Center for Nano Science and Technology of IIT-Istituto di Tecnologia.

“We think this does not affect the efficiency of the biocidal process and, due to the tiny exchange of mass, the lifetime is essentially unlimited,” said Giuseppe Paternò, a researcher at IIT and co-author of the study. “The structural modifications, however, affect the optical properties of the metal nanostructures.”

Although the findings help us better understand the interactions between bacteria and silver nanoparticles, they’re likely not the entire story, the authors note. Laboratories are highly controlled environments, and as such cannot begin to capture everything that’s going on in the wild. These factors that are left out might have an important hand to play in shaping the final interaction between bacteria and silver.

Even so, the team will continue to explore this topic, with a particular interest in studying the chemical machinery (‘chemical pathways’) inside the bacteria that cause these structural changes in silver. They also want to understand why silver is a more powerful antibacterial agent than other materials, and why bacterial membranes seem to be so vulnerable to it while our cells are almost unaffected.

The paper “The impact of bacteria exposure on the plasmonic response of silver nanostructured surfaces” has been published in the journal Chemical Physics Reviews.

Scientists Find New Technique to Defeat Antibiotic-Resistant Bacteria

Petri Dish Bacteria
Photo by Andrian Lange/Unsplash

Stress often causes bacteria to form biofilms. The stress can be in the form of a physical barrier, ultraviolet light, or a toxic substance such as antibiotics. These biofilms take from hours to days to form and can be of various shapes, sizes, colors, and textures depending on the species of bacteria involved.

Being in the state of a biofilm protects them from hazardous substances in their environment — biofilms have a unique outer wall, with different physical and chemical properties than their individual cells. They can coordinate metabolically, slow their growth, and even form an impenetrable barrier of wrinkles and folds.

This is one way they achieve high antibiotic resistance. Researchers from the United Kingdom recently studied the bacteria B. Sultilis transition from a free-moving swarm to a biofilm as a defense mechanism and published what they did to combat its antibiotic resistive properties in eLife.

Photo by Clemencedg/CC BY-SA 3.0/Wikimedia

To determine if their test strain behaves as others do, they recreated first performed stress tests on them. They tested the bacteria’s response to a physical barrier, ultraviolet light, and an antibiotic. The addition of a physical barrier led to a single-to-multi-layer transition of the bacteria, followed by an increase in cell density and the formation of multilayer islands near the barrier. Later, wrinkles developed on the islands near the barrier in the area the islands had started to appear initially.

When they applied ultraviolet light to the swarm, they again observed a drop in cell speed and an increase in density. And after the scientists added a large dose of the antibiotic kanamycin the bacterial cells formed a biofilm. The researchers then devised a strategy to tackle this bacteria biofilm.

They added kanamycin to the environment of a new batch of swarming bacterial cells and watched as a biofilm began to take shape. They then re-administered the antibiotic in a much larger dose than the first one, just before the completion of the biofilm’s formation. The breakdown of the partially formed biofilm and the death of the bacterial cells occurred as a result.

This shows that antibiotic-resistant bacteria lose their resistance to antibiotics when they undergo a phase transition, right before transitioning to a biofilm, where they would become much more resilient. So with proper timing of the administering of antibiotics, bacteria can be attacked in their most vulnerable state and eliminated. Researchersbelieve similar swarm-to-biofilm transitions occur in other bacterial species too.

Their research could pave the way to finding more effective ways of managing clinically relevant bacteria. Such as Salmonella enterica which spreads to the bloodstream and is transmitted by contaminated food. Or the multidrug-resistant Pseudomonas aeruginosa which causes infections in the blood, lungs (pneumonia), and other parts of the body after surgery and is spread in hospitals.

Photosynthesis could be as old as life itself

Photosynthesis has been supporting life for longer than previously assumed, according to a new paper. The finding suggests that the earliest bacteria that wiggled their way around the planet were able to perform key processes involved in photosynthesis.

Image via Pixabay.

Exactly how the earliest organisms on our planet lived and evolved is an area of active interest and research — but not answers are few and scarce. However, a new paper could fundamentally change how we think about this process.

The advent of photosynthesis on a large scale is one of the most significant events that shaped life on Earth. Not only did this process feed bacteria and plants that would then support for entire ecosystems, but it also led to a massive increase in atmospheric oxygen levels, basically making our planet livable in the first place. Oxygen that we and other complex life still breathe to this day.

To the best of our understanding , it took life several billion years to evolve the ability to perform photosynthesis. However, if the findings of this new study are confirmed, it means complex life could have appeared much earlier.

A light diet

“We had previously shown that the biological system for performing oxygen-production, known as Photosystem II, was extremely old, but until now we hadn’t been able to place it on the timeline of life’s history. Now, we know that Photosystem II show patterns of evolution that are usually only attributed to the oldest known enzymes, which were crucial for life itself to evolve.”

The team led by researchers from Imperial College London studied the evolutionary process of certain proteins that are crucial for photosynthesis. Their findings show that these could possibly have first appeared in the very early days of life on Earth.

They traced the ‘molecular clock’ of key proteins involved in the splitting of water molecules. This approach looks at the time between ‘evolutionary moments’, events such as the emergence of different groups of cyanobacteria or land plants that carry a version of these proteins. They then used this to calculate the rate at which the proteins evolved over time — by backtracking this rate, researchers can estimate when a protein first appeared.

A comparison with other known proteins, including some used in genetic data manipulation that should (in theory) be older than life itself, as well as comparison with more recent events, suggests that these photosynthesizing enzymes are very old. According to the team, they have nearly identical patterns of evolution to the oldest enzymes — suggesting they evolved at a similar rate for a similar time.

Based on what we know so far, type II photosynthesis (which produces oxygen) likely appeared around 2.5 billion years ago in cyanobacteria (blue-green algae), with type I likely evolving some time before that. But there’s something that doesn’t really mesh with that timeframe: we know that there were pockets of atmospheric oxygen before this time. This means that biological communities were around to produce said oxygen even before the 2.5 billion years ago mark, since oxygen is extremely reactive and doesn’t last long in nature without binding to something. Researchers have been trying to reconcyle this for a while.

The current findings could help make everything fit. According to the team, key enzymes that underpin photosynthesis were likely present in the earliest bacteria on Earth. There’s still some uncertainty about this, as life on our planet is at least 3.4 billion years old, but it could be older than 4 billion years.

The first versions of the process were probably simplified, very inefficient versions of the one seen in plants and algae today. It took biology around one billion years to tweak and refine the process, which eventually led to the appearance of cyanobacteria. From there, it took two more billion years for plants and animals to colonize dry land, with the latter breathing oxygen produced by the former.

One interesting implication of these findings is that it could mean life would evolve much quicker and easier on other planets than previously assumed. We tend to estimate this based on how quickly and easily life appeared and then developed on Earth.

The paper “Time-resolved comparative molecular evolution of oxygenic photosynthesis” has been published in the journal Biochimica et Biophysica Acta (BBA) – Bioenergetics.

Researchers find four strains of bacteria on the ISS — three are completely new to science

Life finds a way, the old saying goes. According to a new paper, that includes ‘living on a spaceship’.

Transmission electron micrograph of strain S2R03-9T Methylobacterium jeotgali, a relative of the new strains. Image via Wikimedia.

A team of researchers from India and the US working in collaboration with NASA report discovering four bacterial strains living on the International Space Station (ISS). Three of these were completely unknown to science until now. Three of these strains were isolated in 2015 and 2016 — one in an overhead panel in a research lab, the second in the station’s Cupola, and the third on the surface of the crew’s dining table. The fourth strain was isolated from an old HEPA filter that was brought back to Earth in 2011.

All of these strains belong to a ‘good’ family of bacteria found in soil and freshwater here on Earth. They’re involved in nitrogen fixation processes, plant growth, and in fighting plant pathogens.

Out of this world

These bacteria likely made their way onto the ISS when the crew first started growing a small number of plants aboard to supplement their diets. Plants don’t develop and live on their own, but generally rely on bacterial communities for several essential services; as such, finding plant-related microbes in their environment (the space station) isn’t very surprising.

However, only one of these was previously identified by researchers: the one from the used HEPA filter. This strain was identified as belonging to the species Methylorubrum rhodesianum. The other three were genetically sequenced and found to all belong to the same, new species. They were temporarily christened IF7SW-B2T, IIF1SW-B5, and IIF4SW-B5.

The team, led by University of Southern California geneticist Swati Bijlani, proposes the name Methylobacterium ajmalii for the species, after Indian biodiversity scientist Ajmal Khan. The new species is closely related to the already-known M. indicum bacteria. The genetic sequencing of these bacteria was meant to help us better determine how they relate to other bacteria, but also to help us determine the genetic elements that make them suited to life in the unusual conditions aboard the ISS.

“To grow plants in extreme places where resources are minimal, isolation of novel microbes that help to promote plant growth under stressful conditions is essential,” Kasthuri Venkateswaran and Nitin Kumar Singh from NASA’s JPL, two members of the team, explained in a press statement.

“The whole-genome sequence assembly of these three ISS strains reported here will enable the comparative genomic characterization of ISS isolates with Earth counterparts in future studies,” the team explains in their study. “This will further aid in the identification of genetic determinants that might potentially be responsible for promoting plant growth under microgravity conditions and contribute to the development of self-sustainable plant crops for long-term space missions in future.”

At least one of the strains, IF7SW-B2T, shows promise in our search for genes involved in plant growth, they add. Still, we’re only just beginning to understand the wealth of bacteria living aboard the ISS. Collecting samples isn’t hard, but taking them to Earth for proper examination is. The crew has taken over 1,000 samples so far, but they’re all still awaiting transport back to Earth.

The paper “Methylobacterium ajmalii sp. nov., Isolated From the International Space Station” has been published in Frontiers in Microbiology.

One of the largest ecosystems on Earth lives beneath the seafloor and eats radiation byproducts

Researchers at the University of Rhode Island’s (URI) Graduate School of Oceanography report that a whole ecosystem of microbes below the sea dines not on sunlight, but on chemicals produced by the natural irradiation of water molecules.

Image credits Ely Penner.

Whole bacterial communities living beneath the sea floor rely on a very curious food source: hydrogen released by irradiated water. This process takes place due to water molecules being exposed to natural radiation, and feeds microbes living just a few meters below the bottom of the open ocean. Far from being a niche feeding strategy, however, the team notes that this radiation-fueled feeding supports one of our planet’s largest ecosystems by volume.

Cooking with radiation

“This work provides an important new perspective on the availability of resources that subsurface microbial communities can use to sustain themselves. This is fundamental to understand life on Earth and to constrain the habitability of other planetary bodies, such as Mars,” said Justine Sauvage, the study’s lead author and a postdoctoral fellow at the University of Gothenburg who conducted the research as a doctoral student at URI.

The process through which ionizing radiation (as opposed to say, visible light) splits the water molecule is known as radiolysis. It’s quite natural and takes place wherever there is water and enough radiation. The authors explain that the seafloor is a particular hotbed of radiolysis, most likely due to minerals in marine sediment acting as catalysts for the process.

Much like radiation in the form of sunlight helps feed plants, and through them most other life on Earth, ionizing radiation also helps feed a lot of mouths. Radiolysis produces elemental hydrogen and oxygen-compounds (oxidants), which serve as food for microbial communities living in the sediment. A few feet below the bottom of the ocean, the team adds, it becomes the primary source of food and energy for these bacteria according to Steven D’Hondt, URI professor of oceanography and a co-author of the study.

“The marine sediment actually amplifies the production of these usable chemicals,” he said. “If you have the same amount of irradiation in pure water and in wet sediment, you get a lot more hydrogen from wet sediment. The sediment makes the production of hydrogen much more effective.”

Exactly why this process seems to be more intense in wet sediment, we don’t yet know. It’s likely the case that some minerals in these deposits can act as semiconductors, “making the process more efficient,” according to D’Hondt.

The discovery was made after a series of experiments carried out at the Rhode Island Nuclear Science Center. The team worked with samples of wet sediment collected from various points in the Pacific and Atlantic Oceans by the Integrated Ocean Drilling Program and other U.S. research vessels. Sauvage put some in vials and then blasted these with radiation. In the end, she compared how much hydrogen was produced in vials with wet sediment to controls (irradiated vials of seawater and distilled water). The presence of sediment increased hydrogen production by as much as 30-fold, the paper explains.

“This study is a unique combination of sophisticated laboratory experiments integrated into a global biological context,” said co-author Arthur Spivack, URI professor of oceanography.

The implications of these findings are applicable both to Earth and other planets. For starters, it gives us a better understanding of where life can thrive and how — even without sunlight and in the presence of radiation. This not only helps us better understand the depths of the oceans, but also gives clues as to where alien life could be found hiding. For example, many of the minerals found on Earth are also present on Mars, so there’s a very high chance that radiolysis could occur on the red planet in areas where liquid water is present. If it takes place at the same rates it does on Earth’s seafloor, it “could potentially sustain life at the same levels that it’s sustained in marine sediment.”

With the Perseverance rover having just landed on Mars on a mission to retrieve samples of rocks and to keep an eye out for potentially-habitable environments, we may not have to wait long before we can check.

At the same time, the authors explain that their findings also have value for the nuclear industry, most notably in the storage of nuclear waste and the management of nuclear accidents.

“If you store nuclear waste in sediment or rock, it may generate hydrogen and oxidants faster than in pure water. That natural catalysis may make those storage systems more corrosive than is generally realized,” D’Hondt says.

Going forward, the team plans to examine how the process takes place in other environments, both on Earth and beyond, with oceanic crust, continental crust, and subsurface Mars being of particular interest to them. In addition to this, they also want to delve deeper into how the subsurface communities that rely on radiolysis for food live, interact, and evolve.

The paper “The contribution of water radiolysis to marine sedimentary life” has been published in the journal Nature Communications.

Scientists store information in DNA of living cells

The message ‘Hello world!’ was encoded in the DNA of the E. coli bacteria. Credit: Wikimedia Commons.

One milliliter droplet of DNA can theoretically store as much information as two Walmarts full of data servers. Naturally, many scientists see the blueprint of life as the ultimate medium for storing information — but that’s a bit easier said than done.

Previously, scientists encoded the entire book The Wizard of Oz, images, and even GIFs into the iconic double-helix “twisted ladder,” which they could then decode.

Now, a team at Columbia University in New York have taken things to the next level. Rather than storing information in DNA molecules isolated in the lab, the scientists used gene-editing tool CRISPR to encode and store information inside living bacteria.

DNA kept outside cells tends to degrade fast, which is exactly what you don’t want to happen to your precious data. Bacteria, on the other hand, are remarkably resilient in the face of harsh conditions and can adapt to changing environments. Essentially, the bacteria act as a buffer between the information stored in its DNA and the harsh environment.

The researchers inserted specific DNA sequences of the four bases — adenine (A), cytosine (C), thymine (T), and guanine (G) — that encode binary data (the 1s and 0s that computers use) into the cells of E. coli bacteria. Different arrangements of these four bases can be used, for instance, to encode different letters of the alphabet, which is how the scientists managed to store the 12-byte text message ‘Hello world!’ in the bacterial cells.

The message was read by extracting and sequencing the bacterial DNA. Obviously, this is all a much more laborious and prone to error process than encoding 1s and 0s on a flash or hard drive. However, DNA storage will probably never be meant for average digital users. Instead, it might see use when long-term storage of important information is required, such as archives, even for up to thousands of years.

“We demonstrate multiplex data encoding into barcoded cell populations to yield meaningful information storage and capacity up to 72 bits, which can be maintained over many generations in natural open environments. This work establishes a direct digital-to-biological data storage framework and advances our capacity for information exchange between silicon- and carbon-based entities,” the researcher wrote.

The findings appeared in the journal Nature Chemical Biology.

Could bacteria take up jobs mining in space? Turns out, they could

This year has certainly been all about microbes, and a new paper keeps this trend going — but not how you’d expect.

Sphingomonas desiccabilis growing on basalt rock.

Microbes can help extract economically-important materials from rocks in zero-gravity, a new paper reports. The findings showcase the potential of microscopic life in such applications even in space. They also point to the possibility of ‘biomining’ being used as a critical transition step before settling another planet.

The smallest miners

Rare earth elements are, as their name suggests, quite rare. But they’re also critical for high-tech applications due to their often-unique physical and chemical properties. Due to their rarity, such elements are very challenging and expensive to mine and refine, and we’re limited in how much we can produce. Demand for such materials will soon outstrip supply. One solution, however, may lie just above the skies.

Having the ability to identify and isolate rare earth elements will be extremely important for humanity as we seek to expand to other worlds — bonus points if we can do it easily and cheaply. Microbes are already used in this role on Earth, and the new study reveals that they can work just as well in low- or zero-gravity conditions.

The team worked with three species of bacteria (Sphingomonas desiccabilis, Bacillus subtilis, and Cupriavidus metallidurans) in microgravity conditions that simulated the environment aboard the ISS or that on Mars. They measured how efficiently these could leech 14 rare earth elements from basalt rocks, which are very similar to those on the surface of the Moon and Mars. Trials on Earth were carried out in parallel with these experiments to give the team a control group in normal gravity conditions.

All in all, S. desiccabilis successfully extracted the elements from rocks in all three gravity conditions. It was quite effective across all conditions and showed the highest extraction efficiency (around 70%) of all the bacteria tested with the elements Cerium and Neodymium. The other two species were either less effective in low gravity conditions (compared to normal gravity), or were completely unable to perform the task.

The findings suggest that not all the species we use for mining here on Earth would function well, or at all, in other gravity conditions. However, they also clearly show that some of these species would. Identifying which ones these are will be a species-by-species process, but it would definitely pay off in the long term.

That being said, the idea of carrying microorganisms from Earth to another planet is quite a philosophical can of worms. While it may definitely help us extract the things we need from deposits far away, such a step risks fundamentally altering (or replacing) a celestial body’s biosphere.

The paper “Space station biomining experiment demonstrates rare earth element extraction in microgravity and Mars gravity” has been published in the journal Nature Communications.

Hospital floors are full of bacteria, posing a risk to patients’ health

While they might be cleaned regularly, floors in hospital rooms can (and frequently do) quickly get contaminated with antibiotic-resistant bacteria. This process happens mere hours after patient admission, according to a new study. This creates a route through which patients can be exposed to potentially dangerous organisms.

Credit SIM Flickr

Floors aren’t often given the same care as surfaces that patients or health care workers regularly touch, such as bed rails and various buttons. In many cases, floors aren’t cleaned when new patients are admitted to hospital rooms unless they’re visibly dirty or soiled. This can create health problems across the hospital, previous studies have found.

“If bacteria stayed on floors this wouldn’t matter, but we’re seeing clear evidence that these organisms are transferred to patients, despite our current control efforts,” said Curtis Donskey, co-author of the study. “Hand hygiene is critical, but we need to develop practical approaches to reduce underappreciated sources of pathogens.”

A team of researchers from the Northeast Ohio VA Healthcare System tracked contamination levels in 17 hospital rooms with newly-admitted patients to study how and how fast these could transfer to the patients. Before testing, the rooms were cleaned and sanitized, with all patients screened for healthcare-associated bacteria (and found negative).

For the study, the researchers looked at the interactions between patients and healthcare workers and portable equipment. They collected samples one to three times per day from patients, their socks, beds, and other often-touched surfaces, as well as key sections of the floor that could have been contaminated.

Almost half the rooms tested positive for methicillin-resistant Staphylococcus aureus (MRSA) in the first 24 hours. At the same time, vancomycin-resistant enterococci (VRE) pathogens were identified in 58% of patient rooms within four days of admission. The contamination spread from the floors to other surfaces, the findings showed.

“While we’re showing that these scary-sounding bugs can make their way into a patient’s room and near them, not everyone who encounters a pathogen will get an infection,” said Sarah Redmond, lead author of the study. “With that in mind, are there simple ways to address these areas of exposure without placing too much emphasis on the risk?”

The researchers had reported similar findings in a previous study in August, explaining that SARS-CoV-2 nucleic acid (genetic material) was frequently identified on floors and on the shoes of personnel on a COVID-19 ward. Still, they said further research is needed to clarify the role of floor contamination in the transmission of both bacterial and viral pathogens and to identify ways to address contamination.

The study does however have a set of limitations. This included a small sample size and variables in characteristics among patients and healthcare personnel that may affect how applicable the study findings are to other hospitals, among others

The study was published in the journal Infection Control & Hospital Epidemiology.

Scientists synthesize antibiotics to conquer resistant microbes

Credit: Pixabay.

The COVID-19 pandemic is on everyone’s mind right now. However, there’s another medical crisis looming that may be far more dangerous and consequential for decades to come. Scientists have been warning for years that microbes are becoming resistant to even the strongest antibiotics we throw at them. According to a new study, our silver lining might lie in the chemical synthesis of antibiotics that neutralize microbial adaptations.

Revisiting shelved antibiotics

After Alexander Fleming’s discovery of penicillin in 1928, the world entered the golden age of antibiotics. Within a remarkably small timeframe, the wide-scale adoption of antibiotics post-WWII changed the leading cause of death in the United States from communicable diseases to non-communicable diseases (cardiovascular disease, cancer, and stroke), and raised the average life expectancy at birth from 48 years to 78.8 years.

But microbes haven’t stayed idle. Some bacteria developed proteins or other molecules that allow them to multiply despite the presence of antibiotics. When such adaptations occur in a population, they quickly proliferate. This is why tens of thousands of preventable deaths occur each year due to drug-resistant strains of common bacteria like Staphylococcus aureus and Enterococcus faecium.

Until not too long ago, streptogramins, a class of antibiotics, used to be very effective against S. aureus infections. But then the bacteria started to produce proteins called virginiamycin acetyltransferases (Vats), which recognize streptogramins and will chemically deactivate these drugs before they can bind to the cell’s ribosome. This is why streptogramins are considered to be useless in many cases, especially for hospital-acquired bacterial infections.

But we shouldn’t cross out streptogramins just yet. Like most antibiotics, streptogramins are derived from naturally occurring compounds produced by other bacteria, which are later tweaked for optimized performance in the human body.

Assembling antibiotics like LEGO bricks

Researchers at the University of California San Francisco employed a different approach to antibiotic production, which enabled them to synthesize streptogramins that can overcome the resistance conferred by Vat enzymes.

However, the scientists didn’t create new antibiotics from scratch. That would be too time-consuming, expensive, and prone to failure. Instead, the team led by Ian Seiple, an assistant professor in the UCSF School of Pharmacy’s Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute (CVRI), took a modular approach, redesigning existing streptogramins by altering and joining together precursor molecules like LEGO pieces. The resulting “rebuilds” of existing drugs blocked Vats from deactivating the antibiotics.

“The aim is to revive classes of drugs that haven’t been able to achieve their full potential, especially those already shown to be safe in humans,” said Seiple in a statement. “If we can do that, it eliminates the need to continually come up with new classes of drugs that can outdo resistant bacteria. Redesigning existing drugs could be a vital tool in this effort.”

“This system allows us to manipulate the building blocks in ways that wouldn’t be possible in nature,” added the researcher, who is the lead author of the new study published today in the journal Nature . “It gives us an efficient route to re-engineering these molecules from scratch, and we have a lot more latitude to be creative with how we modify the structures.”

In order to determine which LEGO bricks they would have to modify, the researchers employed cryo-electron microscopy and x-ray crystallography to create three-dimensional pictures of the drug at near-atomic resolution. They also modeled the bacterial ribosome and the Vat protein. This way, the researchers could isolate molecules that are essential to antibiotic function.

The team of researchers found that two of the seven building blocks for streptogramins were promising targets for chemical modification. After tweaking these regions, the researchers came up with a new promising candidate against streptogramin-resistant S. aureus. Experiments on mice showed that the antibiotic was over 10 times more effective than classical streptogramins.

According to Seiple, the same approach can be applied to other classes of antibiotics that have been shelved due to microbial resistance.

“We learned about mechanisms that other classes of antibiotics use to bind to the same target,” he said. “In addition, we established a workflow for using chemistry to overcome resistance to antibiotics that haven’t reached their potential.”

“It’s a never-ending arms race with bacteria,” said James Fraser, a professor in the School of Pharmacy’s Department of Bioengineering and Therapeutic Sciences in the UCSF School of Pharmacy. “But by studying the structures involved— before resistance arises—we can get an idea of what the potential resistance mechanisms will be. That insight will be a guide to making antibiotics that bacteria can’t resist.” 

Bacteria can survive interplanetary travel between Earth and Mars

The bacterial exposure experiment took place from 2015 to 2018 using the Exposed Facility located on the exterior of Kibo, the Japanese Experimental Module of the International Space Station. Credit: JAXA/NASA.

Some scientists are of the opinion that life might have not originated on this planet. Instead, it could be that microscopic organisms hitched rides on asteroids and meteorites, traveled through the cosmos, and eventually slammed into Earth, germinating life as we know it. This theory, called “panspermia”, has one obvious flaw: how could life survive in outer space long enough for it to reach a safe harbor?

Although definitely controversial, panspermia isn’t as wacky as it may sound at first glance. Japanese researchers, for instance, recently showed that some bacterial species can survive exposure to outer space, incredible as that may sound. What’s more, they may be able to do so for decades and even much more.

For Dr. Akihiko Yamagishi, a Professor at Tokyo University of Pharmacy and Life Sciences and lead author of the new study, these findings raise enticing possibilities. They suggest that panspermia may indeed be possible, which would make life much more common in the universe than previously thought.

Yamagishi’s inquiries were inspired by previous studies from 2018 when his team detected microbes floating at an altitude of up to 35 kilometers above Earth’s surface. That was pretty surprising, and the researchers naturally wondered just how high these microbes could migrate.

“If the microbes can go up to space, there may be a possibility that the microbes can be transferred from a planet to another,” Prof. Yamagishi told ZME Science.

In order to test this hypothesis, the Japanese researchers placed dried Deinococcal bacteria aggregates in exposure panels outside the International Space Station. Deinococcus are known to form relatively large colonies and be resistant to ultraviolet radiation. They were also the most abundant species found in the highest layers of Earth’s atmosphere.

This experiment wasn’t as straightforward as it sounds, though. But Yamagishi and colleagues were fortunate enough to find a solution.

“We were announced that our space experiment cannot be done because extravehicular activity is not available because of the retirement of the shuttle, while our experiment relied on extravehicular activity. But, JAXA has developed the system to expose samples to ExHAM without extravehicular activity, using robotic arms,” the researcher told me.

Japanese astronaut Kimiya Yui set up the exposure experiment module ExHAM on the International Space Station. Credit: JAXA/NASA>

The bacterial samples, which had varying thicknesses, were exposed to the same environment outside the space station for one, two, or three years.

Even after three years of exposure to space, the bacteria still survived, although those at the surface of the aggregate died. On the upside, the dead surface bacteria acts like a protective layer shielding the surviving bacteria beneath.

By extrapolating survival data for aggregates larger than 0.5 millimeters in thickness, the Japanese researchers concluded that Deinococcal colonies could survive for between 15 and 45 years in a state of stasis right outside the space station.

That’s ample time for the bacteria to hitch a ride during interplanetary travel from Earth to Mars, or from Earth to Pluto for that matter.

Of course, conditions on the ISS are not the same as interplanetary space, which is why the researchers plan to conduct more experiments.

“The experiments were done at the low Earth orbit, which is about 400 km above the surface of Earth, but within the van Allen radiation belt which protects against ionization radiation. Though the ionization radiation is not expected to be harmful to our radioresistant microbe, the survival outside the van Allen radiation belt should be tested by an exposure experiment with the spacecraft or on Deep Space Gateway. We are also looking for the opportunity to search for life on Mars, building the automatic microscope to search for bacteria on Mars’ surface,” Yamagashi said.

This isn’t the first study to show that bacteria may survive in outer space — however, it provides the first bit of evidence that bacteria can survive in space as aggregates, without shielding from rock or other materials. And that’s a pretty big deal for what’s possibly one of the most important scientific inquiries out there: how did life first appear and are we alone out there?

“The origin of life is the biggest mystery of human beings. Recently, researches have revealed the scenario of an RNA world, where the RNA has appeared in nature and started replication of genetic information. However, there are a lot of arguments and missing pieces in the scenario. Especially the probability of the origin of life is totally different between scientists: Some think the origin is very rare and happened only once in the Universe, while others think the origin is very easy and can happen on every planet that is suitable for life. If panspermia is possible, life must exist much more often, in either case,” Yamagashi said.

The findings appeared in the journal Frontiers in Microbiology.