Tag Archives: microbe

Fossil Friday: microbes discovered deep underground remain virtually unchanged since 175 million years ago

New research has identified what’s very likely the tiniest living fossils so far — a group of microbes that feed off radioactive decay.

Abandoned tin mine in Vredehoek, Cape Horn, South Africa. Image credits jbdodane / Flickr.

The team, led by the Bigelow Laboratory for Ocean Sciences, an independent, non-profit oceanography research institute, reports that the microbes have been frozen, evolutionary-speaking, for millions of years. Finding such a case could upturn our current understanding of how microbes evolve and why, and could potentially help guide biotechnology applications in the future (since you want these to not evolve/change over time).

We’re fine as we are

“This discovery shows that we must be careful when making assumptions about the speed of evolution and how we interpret the tree of life,” said Eric Becraft, the lead author on the paper. “It is possible that some organisms go into an evolutionary full-sprint, while others slow to a crawl, challenging the establishment of reliable molecular timelines.”

The microbe species is known as Candidatus Desulforudis audaxviator, and was first discovered in 2008 by a group of researchers led by Tullis Onstott, a co-author on the new study. They live in a gold mine in South Africa almost two miles beneath the surface, swimming merrily in the water-filled cavities inside the rock walls. They feed on chemical products formed by natural radioactive decay processes in minerals at the site, creating a completely independent ecosystem that doesn’t even rely on sunlight to function.

Given their very peculiar living arrangement, the team understandably wanted to know how the microbes evolved to where they are today. They checked other underground samples recovered from around the world and found the species in Siberia, California, and in several other mines in South Africa. Each of these environments was chemically different, the team explains, which spurred them to look for differences among the populations at each site. These groups were obviously separated, and have likely been separate for millions of years, and every one of them had unique conditions they lived in — which would make you think they evolved their own unique quirks.

“We wanted to use that information to understand how they evolved and what kind of environmental conditions lead to what kind of genetic adaptations,” said Bigelow Laboratory Senior Research Scientist Ramunas Stepanauskas, the corresponding author on the paper and Becraft’s postdoctoral advisor.

“We thought of the microbes as though they were inhabitants of isolated islands, like the finches that Darwin studied in the Galapagos.”

So they analyzed the genetic code of 126 individuals retrieved at sites on three different continents — and they were flabbergasted to find that all of them were almost completely identical.

They ruled out the possibility that these microbes could have traveled between the sites. The species is anaerobic and can’t live long in the presence of oxygen, they don’t survive well on the surface; the team also ruled out cross-contamination between these sites.

The best explanation they have so far, the team explains, is that these communities didn’t change all that much, genetically, since they first became separated about 175 million years ago as the supercontinent Pangaea split. In essence, they’re living fossils.

“They appear to be living fossils from those days. That sounds quite crazy and goes against the contemporary understanding of microbial evolution,” says Stepanauskas.

The findings offer a unique counterpoint to the much more accelerated rates of mutation and evolution seen in other microbial communities. Populations of bacteria such as E. coli have been noted to evolve (in response to environmental changes) in as little as a few years. The growing antibiotic resistance issue is an example of just how fast bacteria can evolve.

The team’s current hypothesis is that the species’ genetic freeze is due to powerful anti-mutation mechanisms in its genome. We don’t yet know whether that’s true, but if it is, we could have just discovered an extremely rare feature that we can copy and exploit. Developing this into a tool could pave the way towards more stable DNA polymerases (molecules that copy DNA strands), which are a key component of our biotechnology kit. Essentially, it would allow us to make the biological machinery that copies DNA much more stable over time, which sounds unimpressive but is actually a very big deal for the field.

But the findings also have deep implications for how we think about microbial genetics and the rate at which such microscopic organisms mutate.

“There’s a high demand for DNA polymerases that don’t make many mistakes,” Stepanauskas said. “Such enzymes may be useful for DNA sequencing, diagnostic tests, and gene therapy.”

“These findings are a powerful reminder that the various microbial branches we observe on the tree of life may differ vastly in the time since their last common ancestor,” Becraft said. “Understanding this is critical to understanding the history of life on Earth.”

The paper “Evolutionary stasis of a deep subsurface microbial lineage” has been published in The ISME Journal.

The Bacteria Files: Pseudomonas — What it is and why you should know about it

It may not be a household name on the level of E. coli or Salmonella, but this troublesome bacterium is very well known. In medicine and manufacturing, Pseudomonas is high on the list of things you don’t want to have nearby. It all comes down to one particular tendency it has: like a freeloader, a rash, or that one gray hair, once Pseudomonas shows up, it simply will not go away.

Pseudomonas is a genus of gram-negative, rod-shaped bacteria which use flagella for movement. They are typically found in soil and water as obligate aerobes (needing oxygen for survival), but also colonize plant and animal tissues. A colorful group, many of them produce blue-green pigments called pyocyanins. P. fluorescens, as the name suggests, produces a pigment that even glows in the dark. In a lab setting, seeing growth media turn green is a suspicious sign that the organism may be present.

Pseudomonas fluorescens under UV light. Image credits: Biotech Michael / Wikipedia.

A Hospital Hazard

When it comes to Pseudomonads as pathogens, P. aeruginosa is the star of the show. It likes to spend its time in hospitals, thriving on medical equipment, such as catheters and ventilators. It will settle on a surface, get comfortable, and form a large extended family — but it won’t be content to remain there. This microbial opportunist is simply waiting for the right moment to strike.

Supervillain that it is, it has quite a few accomplishments under its belt. Pseudomonas aeruginosa alone is associated with sepsis, pneumonia, dermatitis, urinary tract infections, and infections in cystic fibrosis patients and the otherwise immunocompromised. It’s also special within its genus because it is one of the only Pseudomonads that can maintain metabolism in the absence of oxygen. This is what enables it to stay functional in damaged lung tissue.

In cystic fibrosis, a genetic disorder causes cells to produce a much thicker, more viscous mucus than is typical. In the lungs, this blocks ducts and passageways, and generally makes it difficult for the natural defenses (such as cilia) to function. This is when your opportunist sees its chance. It enters with moist air from a contaminated ventilator, or simply from unwitting, unclean hands touching your face, and settles in the altered mucus of the lung. Now it can do the thing it’s most hated for: it forms a structure called a biofilm.

Scanning electron micrograph of P. aeruginosa. Image credits: Janice Haney Carr, USCDCP.

Once settled, the cells rapidly reproduce and then literally stick together, releasing cellular products to form a slimy matrix. In the end, you have layers and layers of bacteria forming on top of one another until all medication can truly do is cut away at the upper surface. And if the fact that it’s so anchored wasn’t enough, along with Staphylococcus aureus and Klebsiella species, P. aeruginosa is among the best known bacteria in the world for laughing in the face of antibiotics.

As it turns out, P. aeruginosa isn’t limited to only affecting humans from within. It can be the bane of any water bottling plant. Since they tend to live in springs, wells, and other natural sources, with one small error in the process, Pseudomonas could become attached to a factory line. And once the biofilm fully establishes on the equipment, no amount of scrubbing will make it go away. Heavy-duty chemical treatment is required. Their presence can be so pervasive, that manufacturers have been known to just toss out expensive equipment, rather than waste further resources trying to rid themselves of this plague.

Silver Linings

Still, it isn’t all bad news. Many Pseudomonads have made significant positive contributions to human activity as well — from antibiotics and research opportunities to even cleaning up our messes:

P. fluorescens, can be cultured to produce an antibiotic called Mupirocin, used in the treatment of highly resistant bacterial species. It is also found around plant roots and acts to protect them from fungal growths.

P. deceptionensis lives in the Antarctic and has provided multiple avenues of interest. Strain M1T has presented with a previously unknown internal structure called a stack, meanwhile strain DC5 produces silver particles during metabolic processes.

P. aeruginosa, P. putida and a few other species can decompose hydrocarbons and are used in bioremediation. In fact, a strain of P. putida is the first organism to be patented (with much difficulty) because of its potential for use in degrading toluene and naphthalene in soil, as well as converting styrene to a biodegradable plastic, without being a threat to human health.

Deception Island, Antarctica where P. deceptionensis was discovered. Image credits: W. Bulach / Wikipedia.

So, you see, even the worst of them can be used for positive things – it can break down hydrocarbons and is an excellent model for biofilm formation. As with most bacteria, the majority are harmless to humans. But it is always good to be informed and Pseudomonas is just one more thing you should know about.

Astronauts identify microbes in space for the first time

The International Space Station is becoming more and more independent. Now, astronauts can carry out microbial DNA sampling, which opens up exciting avenues for practical research.

NASA astronaut Kate Rubins poses for a picture during the first sample initialization run of the Biomolecular Sequencer investigation. Credits: NASA.

Space Germs

The mere idea of identifying microbes in space, without sending a probe back to Earth, was only a dream a few years ago. Now, thanks to the Genes in Space-3 project, NASA astronauts and biochemists have the ability to not only identify and treat microbial ailments in outer space but also potentially identify life on other planets. This also means that they can carry out a number of practical experiments in outer space — which they’ve already started.

The identification process has two parts: first, astronauts gather the microbial samples and subject them to Polymerase Chain Reaction — a technique commonly used in modern molecular biology to amplify copies of DNA segments across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence — then, they sequence and identify the microbes.

The first batch they sampled turned out to be regular microbes, like the ones commonly found in houses or anywhere that humans live. We truly tend to contaminate everything, and outer space seems to be no exception. What was somewhat surprising though was the sheer number of microbes they found on the space station.

“We have had contamination in parts of the station where fungi was seen growing or biomaterial has been pulled out of a clogged waterline, but we have no idea what it is until the sample gets back down to the lab,” said Sarah Wallace, NASA microbiologist and the project’s principal investigator at the agency’s Johnson Space Center in Houston.

“On the ISS, we can regularly resupply disinfectants, but as we move beyond low-Earth orbit where the ability for resupply is less frequent, knowing what to disinfect or not becomes very important,” said Wallace.

Independent sampling

The need for on-site germ sampling became even more evident after the Johnson Space Center was damaged by Hurricane Harvey. The ISS was unable to send samples back to Earth — including microbial samples. Furthermore, as future manned missions are expected to be longer and longer, monitoring microbial activity aboard a shuttle will be much more important.

However, that’s still far off. For now, the most exciting prospect is studying microbial behavior and distribution in microgravity. Previous research has shown that floating in microgravity can give some microbes an unexpected genetic boost. Basically, researchers have found an increase in expression of virulence factors in Salmonella Typhimurium and increased biofilm production in Staphylococcus aureus. However, it’s unclear if this stays true for other microbes, or if different species behave in different ways. Bacterial response to microgravity is an increasingly useful area of study, and it’s one which NASA is tackling head-on.


That ATM keyboard you’ve touched earlier is covered in germs from all over town

ATMs may be excellent city-wide DNA repositories, a new New York University study concludes. Their keypads are a melting pot for bugs from human skin, household surfaces, even traces of food.


Image credits Emma Blowers / Pixabay.

News just in: ATM keyboards are just littered with germs, bits of people, and all sorts of DNA. With how much use these things see, it’s hardly surprising; but the range of what you can find here is. NYU scientists went around Manhattan, Queens, and Brooklyn, swabbing off of ATMs in eight neighborhoods. That netted them a total of 66 samples which they then compared with known microbial markers.

Just like the germs on our smartphones’ screens can tell a lot about our individual lifestyle, the germs on the ATM tell the story of a city. The team found a wide range of human skin microbes, most of which can be traced back to household surfaces such as TVs, restroom and kitchen surfaces, as well as pillows. Microbes associated with bony fish, mollusks, and chicken were also found in different neighborhoods, suggesting that residues from meals can find their way to the keypads upon use.

The team also points out that the data suggests a geographic zoning, but only for certain types of microbes.

“The sampling strategy was designed to target geographic areas with distinct ethnic and population demographics, known as neighborhood tabulation areas,” the paper reads.

Store- and laundromat-based ATM keypads showed the highest number of biomarkers, with Lactobacillales (lactic acid bacteria) being the most prominent. This kind of bacteria is usually found in spoiled or rotting milk products and plants — it’s what makes milk go sour and pickles become pickled. Samples taken in Manhattan tested positive for the biomarker Xeromyces bisporus, a mold that grows on spoiled backed goods. There was no significant difference in the biomarkers of indoor or outdoor ATMs.

“Our results suggest that ATM keypads integrate microbes from different sources, including the human microbiome, foods, and potentially novel environmental organisms adapted to air or surfaces,” explains senior author Jane Carlton, director of the Center for Genomics and Systems Biology and professor of biology at NYU.

“DNA obtained from ATM keypads may therefore provide a record of both human behavior and environmental sources of microbes.”

While most of you are probably going through an ew-fueled bristling right now, from a microbiologist’s point of view the findings are actually quite exciting. Because each machine sees probably hundreds of uses each day and come in direct contact with air, water, and microbes adapted to live on different types of urban surfaces, the communities sampled here represent an “average” — a snapshot of each city‘s own microbial footprint. Each ATM effectively pools strains from a lot of different sources together.

Still, the machine samples showed low diversity and apart from the few bugs I’ve mentioned earlier, there was no obvious geographic clustering. The team believes this low diversity comes down to periodic cleaning of the ATMs — which would wipe out some of the bugs. Tourists and commuters also have a hand to play in mixing the communities throughout town, the team said.

Such mixing is probably limited to an in-city range, so in the end, each city might actually be unique — they may each have their own DNA.

The full paper “Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City” has been published in the journal mSphere.

World leaders pledge to fight drug-resistant bacteria

Meeting at the United Nations, world leaders agreed that we are facing an unprecedented threat from drug-resistant bacteria and agreed to fight it together.

Scanning electron micrograph of Methicillin-resistant Staphylococcus aureus (MRSA). Image credits: NIAID

UN Secretary-General Ban Ki-moon said that without a doubt a fundamental threat to human development and security.

“It is not that it may happen in the future. It is a very present reality – in all parts of the world, in developing and developed countries; in rural and urban areas; in hospitals; on farms and in communities,” Mr. Ban noted.

He went on to present a few “sobering examples” and figures of what drug-resistant bacteria is already doing:

  • “More than 200,000 newborn children are estimated to die each year from infections that do not respond to available antibiotics.
  • An epidemic of multidrug-resistant typhoid is now sweeping across parts of Africa, being spread through water.
  • Resistance to HIV/AIDS drugs is on the rise.
  • Extensively drug-resistant tuberculosis has been identified in 105 countries.
  • Resistance to antimalarial medicines is an urgent public health concern in the Greater Mekong sub-region.
  • The spread of antibiotic-resistant infections from live farm animals to meat and people has been documented.
  • Furthermore, dangerous new genetic mechanisms for the spread of resistance are emerging and spreading quickly throughout the world.”

The magnitude and nature of this problem make it impossible for any one country to deal with it. It simply must be an international effort – and that’s exactly what was agreed.

Leaders of the world pledged to make a joint effort to fight this threat, and for the first time developed a coordinated plan aimed at the root of the problem. According to the recently-signed document, UN countries have agreed to:

  • develop multisectorial programs and policy initiatives focused on antimicrobial resistance;
  • mobilize and coordinate investment into new therapeutic technologies, surveillance and research;
  • increase awareness of antimicrobial resistance to encourage positive behavior from the general public; and
  • request the establishment of an ad hoc interagency coordination group in consultation with WHO, FAO and the World Organization for Animal Health.

Now arguably, that’s still pretty vague and could be much more detailed, but it’s still a start. Expert organizations, including the WHO, applauded the move and said that it’s high time something like this was agreed to.

“Antimicrobial resistance poses a fundamental threat to human health, development, and security. The commitments made today must now be translated into swift, effective, lifesaving actions across the human, animal and environmental health sectors. We are running out of time,” said Dr. Margaret Chan, the Director-General of WHO.

Recently, the WHO announced that gonorrhea is becoming untreatable, becoming resistant to more and more drugs. I’m really happy something like this is happening, and hopefully we’ll see concrete measures soon.

Oil seeps create thriving micro-ecosystem

Natural hydrocarbon seeps are providing the nutrients for vast microbial communities to thrive in the Gulf of Mexico. Although the oil itself is not particularly beneficial, the nutrients it brings up enable the micro-ecosystem to flourish.

Researchers from Columbia University have discovered how bubbles formed by naturally-occurring oil seeps in the Gulf of Mexico attract large volumes of microorganisms known as phytoplankton. They believe this is because of the amount of nutrients from the ocean floor that the bubbles bring with them to the surface.
(Photo : Ajit Subramaniam | Columbia University)

Petroleum seeps are quite common in many areas of the world, though many of them have already been exploited completely. In fact, oil seeps have been exploited since ancient times, by both humans and microorganisms. However, marine seeps are relatively understudied, and only in recent years have we become better at detecting them through remote sensing.

Seeps generally flow at a very slow and steady rate; the material that flows is generally toxic, but some organisms that live nearby have adapted to the conditions and even take advantage of them. This seems to be the case with phytoplankton communities gather in areas of the Gulf .

“This is the beginning of evidence that some microbes in the Gulf may be preconditioned to survive with oil, at least at lower concentrations,” oceanographer Ajit Subramaniam from Columbia’s Lamont-Doherty Earth Observatory said.

The theory is that rising oil and gas bubbles are bringing up deep-water nutrients that phytoplankton need to grow. This would explain why the biggest blooms are located above the seeps, but at a distance. The highest phytoplankton concentration was located several hundred feet below the water surface – twice higher than the average.

“In this case, we clearly see these phytoplankton are not negatively affected at low concentrations of oil, and there is an accompanying process that helps them thrive. This does not mean that exposure to oil at all concentrations for prolonged lengths of time is good for phytoplankton.”

Following a series of lab experiments, Subramaniam found that while the organisms can tolerate low quantities of oil in their environment, it does nothing good for them. In this case, it remains to be seen what the long-term impact will be on the plankton.

“The direct effect of oil is usually negative, but in some cases small amounts of oil can be outweighed by the positive effect of the nutrients that are tagging along,” added Andy Juhl, an aquatic ecologist at Lamont and coauthor.

For now, researchers are trying to obtain a broader view of the seeps in the Gulf and how they affect microbial activity. They don’t know what types of plankton thrive under these conditions and what (if any) damage long-term exposure does. This ecosystem consisting both of plankton and oil-degrading bacteria and other microbes is likely very complex and it’s not clear how this influx of nutrients affects its internal balance.

“Satellite radar data have given us a detailed picture of where natural seeps are concentrated across deep seafloor of the Gulf of Mexico,” said co-author Ian MacDonald, an oceanographer and professor at Florida State University. “Building on this, the present, novel results show biological effects near the ocean surface in areas where seeps are most prolific.”

Journal Reference: Elevated surface chlorophyll associated with natural oil seeps in the Gulf of Mexico.

DNA survey of New York subway finds traces of Anthrax, the plague and Mozzarella Cheese

The most extensive DNA survey of the NYC subway has revealed that New Yorkers really like pizza and mozzarella, but also that drug-resistant microbes are widespread. They also found traces of the plague, anthrax, and learned that a tasmanian devil never took the subway in the city.

Subway stations are teeming with life – microbial life – of which we know very little.

In a way, the human body is very similar to the subway – both harbor a rich biodiversity when it comes to microbes and other microscopic living creatures. The average human, for example, contains about 100 trillion microbial cells – 10 times more than it contains human cells. Even in the bloodstream, about a third of all cells are microbial. We may think ourselves as being human, but in a way, we are like a petri dish, tightly connected to the microbes that live, breathe, feed and reproduce on and inside our bodies; we couldn’t live without them.

“A city is like an organism,” said IBM Corp. computational biologist Robert Prill, who is among those at the company investigating ways to better collect and analyze these immense new public-health genome databases. “It has a circulating system consisting of the movement of people.”

Also, as we move, we leave behind a trace – we basically shed our skin, dropping about 1.5 million skin cells every hour. If you look really carefully, you could find plenty of human skin cells, as well as the microbial cells that come along with them. This is what this survey aimed to do: see what microbial populations inhabit the subway, in order to better understand how they behave and develop in urban environments. These areas are very understanding, despite playing a key role in events such as disease outbreaks.

“We know next to nothing about the ecology of urban environments,” evolutionary biologist Jonathan Eisen at the University of California at Davis told the WSJ. “How will we know if there is something abnormal if we don’t know what normal is?”

This is where the PathoMap project steps in. PathoMap is a research project by Weill Cornell Medical College to study the microbiome and metagenome of the built environment of NYC. This huge project involved tests at 466 open stations in New York City, including on the kiosks, benches, turnstiles, garbage cans, and railings, over an 18-month period. Researchers dug their way through rats, vomit, and condoms to gather the DNA they needed for the survey.

By its end, researchers had over 10 billion fragments of biochemical code, which they then fed into a supercomputer armed with the extensive genetic databases of all known plants, animals, viral and bacterial life. With it, they were able to create an amazing map with 15,152 different types of life-forms this DNA belonged to were spread throughout the city. Here are just some of the results:

  • 46.9 DNA came from bacteria, mostly harmless
  • 48 percent did not match any known organism
  • harmful drug resistant bacteria were found at almost half of all the stations
  • a trace of anthrax and three traces of the bubonic plague were found, but this doesn’t mean that there’s a risk of these diseases actually developing
  • food poisoning bacteria are plentiful in the subway
  • cross the measured sites, genetic material from beetles and flies was the most prevalent – the cockroach genome hasn’t been sequenced yet so that DNA wasn’t identified
  • the cucumber DNA ranked third (of the known ones), probably due to left over foods
  • no Tasmanian devils, Himalayan yaks and Mediterranean fruit flies have ever traveled with the NY subway.

See the results in an interactive map here. Raw data is also online here.

The results, which were published in the journal Cell Systems, paints a very interesting (and expected) picture of the microbial life and DNA traces from the NY subway. I really hope this kind of survey would be conducted in other areas as well, because as Eisen said, we need to know what are the “normal” microbial levels in heavily used areas such as subways. Different subways with different environmental conditions are likely to harbor different microbial populations.

“Unintentionally, architects and engineers are creating ecosystems without much thought at all as to whether they are healthy or harmful to humans,” said biologist Jessica Green, director of the University of Oregon’s Biology and The Built Environment Center. “Different urban conditions might promote the growth of different microbial ecosystems.”

It is a monumental task, but one which might prove to be very important in the future. As Science Alert brilliantly puts it, scientists are the real heroes.

Scientific Article.

“Copper kills everything”: A Copper Bedrail Could Cut Back On Infections For Hospital Patients

As modern medicine can be quite paradoxical sometimes, checking into a hospital can actually boost your chances of an infection; and if you’re thinking that this only happens in poorer, underdeveloped countries – you’re wrong. No matter where you check in at a hospital, you are vulnerable to infections which have nothing to do with your original problem. Now, a team from Chile studying this issue believe they have found a solution for this problem: copper.

A copper bedrail can kill germs on contact.
Courtesy of CopperBioHealth

The World Health Organization estimates that “each year, hundreds of millions of patients around the world are affected” by healthcare-acquired infections. These are called healthcare-acquired infections, healthcare-associated infections or hospital-acquired infections. Most of them can be very dangerous, and there doesn’t seem to be a correlation between how well the hospital is equipped and how likely you are to get an infection. However, in developing countries, the rate of hospital infection seems to be higher.

The source of these infections can come as quite a surprise – Constanza Correa, a Chilean researcher and her team found that bed safety railings are major source of infections. They replaced the railings with copper ones, and the effect was immediate and visible.

“Bacteria, yeasts and viruses are rapidly killed on metallic copper surfaces, and the term “contact killing” has been coined for this process,” wrote the authors of an article on copper in Applied and Environmental Microbiology. That knowledge has been around a very long time. The journal article cites an Egyptian medical text, written around 2600-2000 B.C., that cites the use of copper to sterilize chest wounds and drinking water.

Indeed, this is called the “Oligodynamic effect” – many metals have a strong antimicrobial effect, being toxic not only for microbes, but also for algae, molds, spores, fungi, prokaryotic and eukaryotic microorganisms, even in relatively low concentrations. Most heavy metals exhibit this effect, but also silver, iron, and of course, copper. Silver and copper actually have the strongest antimicrobial effect.

Correa and her team hasn’t yet assessed the entire impact that bed railings can have, but a study of the effects of copper-alloy surfaces in U.S. hospitals’ intensive care units, published last year in Infection Control and Hospital Epidemiology, showed promising results: Their presence reduced the number of healthcare-acquired infections from 8.1 percent in regular rooms to 3.4 percent in the copper rooms. That’s a reduction of almost 60 percent.

“Healthcare-acquired infections are a huge problem. People come to the hospital with a sickness, and they get another one in the hospital. Then they have to stay longer and spend more money on treatment. Sometimes it can cause death. Eighty percent of these infections come from touching hospital surfaces. In the hospital room, the most contaminated surface is the bed rail. It’s the most manipulated by medical staff and patients. It’s in direct contact with the patient. That’s the most critical surface in the room”, Correa said in an interview published on NPR.


“Copper kills everything”, she says, so why not use it more in hospitals? There is a huge number of ways in which you can use it. You can have copper IV poles, feeding tables, night tables, even mattress covers (a copper additive).

“Copper kills everything. Why wouldn’t you use it? It has so much sense for people.”

New Device Harnesses Sun and Sewage to Produce Hydrogen Fuel

It almost seems too good to be true – a novel device that uses only sunlight and wastewater to produce hydrogen gas could provide a sustainable energy source, while also improving the efficiency of the waste water system.

A sustainable, self-driven system

deviceIn a paper published in the American Chemical Society journal ACS Nano, a team led by Yat Li, associate professor of chemistry at the University of California, Santa Cruz described how they developed the hybrid solar-microbial device which combines a microbial fuel cell (MFC) and a type of solar cell called a photoelectrochemical cell (PEC).

In the Microbial (MFC) component, bacteria generate electricity by degrading the organic material in the waste water. The biologically generated energy is then delivered to the PEC to assist the solar-powered splitting of water (electrolysis) that generates hydrogen and oxygen.

Strictly speaking, both MFC and PEC could be used individually to generate hydrogen gas; the problem however, is that both require a small additional voltage (an “external bias”) to overcome the thermodynamic energy barrier for proton reduction into hydrogen gas. When used together, the two elements are sustainable and self driven, because the combined energy from the organic matter (harvested by the MFC) and sunlight (captured by the PEC) is sufficient to drive the electrolysis of water.

“The only energy sources are wastewater and sunlight,” Li said. “The successful demonstration of such a self-biased, sustainable microbial device for hydrogen generation could provide a new solution that can simultaneously address the need for wastewater treatment and the increasing demand for clean energy.”

Unusual bacteria, scaling, and commercial use

The microbial cells feature some rather unusual bacteria, which are able to generate electricity by transferring metabolically-generated electrons across their cell membranes to an external electrode. In order to develop this component, Li teamed up with researchers at Lawrence Livermore National Laboratory (LLNL) who have been studying electrogenic bacteria and working to enhance MFC performance. As it turns out, waste water is a perfect environment, as it contains both rich organic nutrients and a diverse mix of microbes that feed on those nutrients, including naturally occurring strains of electrogenic bacteria.

When fed with wastewater and illuminated in a solar simulator, the PEC-MFC device showed continuous production of hydrogen gas at an average rate of 0.05 cubic meters per day. Of course, in order to become actually useful, this invention has to be scaled, and considering that researchers also reported a drop in hydrogen as bacteria used up the organic matter in the wastewater, cuold this become commercially viable?

Scientists are optimistic. They are already in the process of scaling up the small laboratory device to make a larger 40-liter prototype continuously fed with municipal wastewater. This is the intermediary step, and if everything works out fine with that, then they can finally take their results to the municipality.

“The MFC will be integrated with the existing pipelines of the plant for continuous wastewater feeding, and the PEC will be set up outdoors to receive natural solar illumination,” Qian said.

“Fortunately, the Golden State is blessed with abundant sunlight that can be used for the field test,” Li added.

Journal Reference: Hanyu Wang, Fang Qian, Gongming Wang, Yongqin Jiao, Zhen He, Yat Li. Self-Biased Solar-Microbial Device for Sustainable Hydrogen Generation. ACS Nano, 2013; 130916123121001 DOI: 10.1021/nn403082m

A section of mouse colon is shown with gut bacteria (outlined in yellow) residing within the crypt channel. Credit: Caltech / Mazmanian Lab

How bacteria colonize the human gut – study reveals important insights

Our bodies are hosts to some hundreds of thousands of bacteria that live in harmony with each other, helping the body be healthy, in return for the food and shelter it provides to these tiny organisms . Collectively, all the microorganisms inside the human body are referred to as the microbiome, most of whom are found in the  gastrointestinal (GI) tract – in particular, the colon. Scientists have known for many years that the bacteria inside our bodies are indispensable for human health, but what has always bothered them is a pestering puzzle that until recently has remained largely unsolved. Considering the gut is such a flexible system where food, fecal matter and other fluids are constantly interchanged, how do bacteria thrive in such a system – namely, how do they manage  stable microbial colonization of the gut?

A recent study performed by researchers at California Institute of Technology (Caltech), led biologist Sarkis Mazmanian, may have finally come up with an answer. After studying one common group of bacteria, the scientists found evidence that  a set of genes is paramount to gut colonization. In addition, the Caltech researchers also found out that the bacteria, some of them at least, are in direct contact with the host body – something that was  unperceivable until of late. These advances in our understanding of how the bacteria inside the gut work and flourish might help scientists devise ways to correct for abnormal changes in bacterial communities—changes that are thought to be connected to disorders like obesity, inflammatory bowel disease and autism.

Colonizing the human gut

A section of mouse colon is shown with gut bacteria (outlined in yellow) residing within the crypt channel. Credit: Caltech / Mazmanian Lab

A section of mouse colon is shown with gut bacteria (outlined in yellow) residing within the crypt channel.
Credit: Caltech / Mazmanian Lab

The focus of the researchers’ experiments was on  a genus of microbes called Bacteriodes,  a group of bacteria that has several dozen species and which can be found in the greatest abundance in the human microbiome. Bacteriodes wasn’t chosen because of its popularity, however, instead because it also makes for an excellent lab  pet – it  can be cultured in the lab (unlike most gut bacteria), and can be genetically modified to introduce specific mutations, fundamental criteria in order to test what effects and consequences these bacteria pose in the human body.

A few different species of the bacteria were added to one mouse, which was sterile (germ-free), to see if they would compete with each other to colonize the gut. They appeared to peacefully coexist, as expected, but then the researchers first  colonized a mouse with one particular species, Bacteroides fragilis, and inoculated the mouse with the same exact species as in the first instance, to see if they would co-colonize the same host.  To the researchers’ surprise, the newly introduced bacteria could not maintain residence in the mouse’s gut, despite the fact that the animal was already populated by the identical species.

“We know that this environment can house hundreds of species, so why the competition within the same species?” says Lead author S. Melanie Lee (PhD ’13), who was an MD/PhD student in Mazmanian’s lab at the time of the research. “There certainly isn’t a lack of space or nutrients, but this was an extremely robust and consistent finding when we tried to essentially ‘super-colonize’ the mice with one species.”

To explain the results, Lee and the team developed what they called the “saturable niche hypothesis.” The idea is that by saturating a specific habitat, the organism will effectively exclude others of the same species from occupying that niche. It will not, however, prevent other closely related species from colonizing the gut, because they have their own particular niches. A genetic screen revealed a set of previously uncharacterized genes—a system that the researchers dubbed commensal colonization factors (CCF)—that were both required and sufficient for species-specific colonization by B. fragilis.

“Melanie hypothesized that this saturable niche was part of the host tissue”—that is, of the gut itself—Mazmanian says. “When she postulated this three to four years ago, it was absolute heresy, because other researchers in the field believed that all bacteria in our intestines lived in the lumen—the center of the gut—and made zero contact with the host…our bodies. The rationale behind this thinking was if bacteria did make contact, it would cause some sort of immune response.”

“We are not alone…”

Upon using advanced imaging techniques and technology to survey colonic tissue in B. fragilis colonized mice, the researchers found a small population of microbes living in tiny pockets called crypts. The discovery is extremely important because it explains how the bacteria protect themselves from the constant flow of matter that passes through the GI tract. An even more important discovery came later on. In order to test if these CCF genes had anything to do with how the bacteria colonize the crypts that shelter them from harm, the researchers injected mutant bacteria (without CCF) into the colons of sterile mice. Those bacteria couldn’t colonize the crypts, proving they’re indispensable to the colonization mechanism of gut bacteria.

“There is something in that crypt—and we don’t know what it is yet—that normal B. fragilis can use to get a foothold via the CCF system,” Mazmanian explains. “Finding the crypts is a huge advance in the field because it shows that bacteria do physically contact the host. And during all of the experiments that Melanie did, homeostasis, or a steady state, was maintained. So, contrary to popular belief, there was no evidence of inflammation as a result of the bacteria contacting the host. In fact, we believe these crypts are the permanent home of Bacteroides, and perhaps other classes of microbes.”

The discovery doesn’t however explain however how other bacteria colonize the gut, considering  they don’t have CCF genes at all. A hypothesis proposed by the Caltech researchers is that  Bacteroides are keystone species—a necessary factor for building the gut ecosystem.

“This research highlights the notion that we are not alone. We knew that bacteria are in our gut, but this study shows that specific microbes are very intimately associated with our bodies,” Mazmanian says. “They are living in very close proximity to our tissues, and we can’t ignore microbial contributions to our biology or our health. They are a part of us.”

The findings appeared in the journal Nature.

Life found deep in the oceanic crust for the first time

For the first time in history, researchers have found microbes living deep inside Earth’s oceanic crust – the black basalts that make some 60% of our planet’s surface – potentially the largest habitat on our planet.

Engineering and microbes

navaMicrobiologist Mark Lever is on board the Integrated Ocean Drilling Program’s research vessel JOIDES Resolution to examine rock samples from the depths – and the engineering problems are numerous. Drilling beneath 2.5 km of water and hundreds of meters of sediment and then onto the crust is no easy feat.

They drilled through 265 metres of sediment and 300 metres of crust to collect (geologically) young basalts that were formed some through 265 metres of sediment and 300 metres of crust to collect samples which contained microbes that metabolize sulphur compounds and some that produce methane.

So how do the microbes survive down there? The key is a process called chemosynthesis; you’ve most likely heard of photosynthesis, which is the process through which plants use sunlight to gain energy. Well chemosynthesis does the same thing, but uses chemical instead of solar energy. It is basically the biological conversion of one or more carbon molecules (usually carbon dioxide or methane) and nutrients into organic matter using the oxidation of hydrogen (or other inorganic molecules). Chemosynthesis also fuels other unlikely places which harbor life, such as hydrothermal vents.


The thing is, the oceanic crust is relatively homogeneous as a habitat throughout our planet, and if you find microbes at one site, the odds are you’re gonna find them throughout its entire extent. If this is indeed the case, the crust “would be the first major ecosystem on Earth to run on chemical energy rather than sunlight”, says Mark Lever, an ecologist at Aarhus University in Denmark, who led the study.

An unlikely habitat

“This study is highly significant in that it confirms the existence of a deep-subsurface biosphere that is populated by anaerobic microorganisms,” says Kurt Konhauser, a geomicrobiologist at the University of Alberta in Edmonton, Canada.

oceanic crust1

Oceanic crust is called this way well, because it’s typically under the oceans. It is much thinner than continental crust and it is constantly formed at spreading centres on oceanic ridges. To put it this way, it’s not an oceanic crust because there is an ocean above it, there’s an ocean above it because it’s an oceanic crust. It consists of several layers, the topmost which is usually 0.5 km thick, made of basalts.

The team included scientists from six different countries. To test if the microbes were still active, the team heated the rock samples to 65 °C in water rich in chemicals found on the sea floor. Over time, more and more methane was produced, showing that the little buggers were still well and active.

Lever is convinced that the microbes are not just accidentally there, hitching a ride from someplace else – despite initial doubts.

“When I went on this expedition, I thought it would be impossible to get contamination-free samples,” he says.

He changed his opinion quickly after analyzing the samples. The team had added small amounts of marker chemicals to the fluid they used to drill for samples, but although they basically painted the outside with this fluid, the rocks were so compact that none of it reached the inside. Lever now plans to analyse fragments of crust collected from other sites in the Pacific Ocean and the north Atlantic. We’ll keep you posted with any future updates on the matter.

“Given the large volume of sub-sea-floor crust, one can’t help but wonder how the amount of living biomass there compares to that at the Earth’s surface,” says Konhauser.

Via Nature

Microbes thrive in high altitude stormy clouds – could play role in global climate

It’s a bird! No, it’s a plane! No, it’s… microbes ?! High up in the atmosphere, 10.000 meters above ground, researchers have found over 100 species of bacteria doing just fine in stormy clouds.

The eye of Hurricane Earl in the Atlantic Ocean, seen from a NASA research aircraft on Aug. 30, 2010. This flight through the eyewall caught Earl just as it was intensifying from a Category 2 to a Category 4 hurricane. Researchers collected air samples on this flight from about 30,000 feet over both land and sea and close to 100 different species of bacteria.

The eye of Hurricane Earl in the Atlantic Ocean, seen from a NASA research aircraft on Aug. 30, 2010. This flight through the eyewall caught Earl just as it was intensifying from a Category 2 to a Category 4 hurricane.

Each year, hundreds of millions of tons of dust, water and man-maned pollutans make their way into the atmosphere, often traveling between distant locations or even between continents on jet streams. Of course, along with these massive quantities, some microbes get sucked up too – but even though bacteria have been known to survive in the most extreme environments, researchers weren’t expecting them to do so good high up in the air. It’s suspected that some of them are able to feed up there, creating a thriving ecosystem 10 km above our heads.

The discovery came up rather accidentally; a team of scientists based at the Georgia Institute of Technology in Atlanta hitched a ride on nine NASA airplane flights aimed at studying hurricanes. Previous studies had identified some microorganisms in those environments, but no attempt had been made to catalog and understand them – especially while driving your plane through a raging hurricane.

But despite extremely dangerous conditions and several other practical issues, scientists are a sturdy bunch; they managed to collect thousands upon thousands of airborne microorganisms floating in the troposphere about 10 kilometers over the Caribbean, as well as the continental United States and the coast of California; no difference was found between microbes above air or land.

The first surprise was to see that over 60% of the samples they collected were still alive; they cataloged a total of 314 different families of bacteria in their samples, but it’s not yet clear if any of them are pathogens. This research seems to back up the idea that storms act as “elevators” for microbes, plucking them off Earth’s surface and carrying them high into the sky, says Dale Griffin, an environmental and public health microbiologist with the U.S. Geological Survey in St. Petersburg, Florida, who was not involved in the study.

soil and sky

What’s interesting is that 2 of the 17 most common families of bacteria in the upper troposphere feed on oxalic acid – one of the most common chemical compounds in the sky, raising a pertinent question: is the high atmosphere actually an ecosystem?

“That’s a big question in the field right now,” Griffin says. “Can you view [the atmosphere] as an ecosystem?”

We shouldn’t jump to conclusions too soon though warns David Smith, a microbiologist at NASA’s Kennedy Space Center in Florida. He has studied bacteria in the air above Oregon’s Mount Bachelor in a separate study, and found that they hibernate during their long, aerial trip.

“While it’s really exciting to think about microorganisms in the atmosphere that are potentially making a living, there’s no evidence of that so far.”

Even if they spend their atmospheric trip in dormancy, they could still play a key role in climate. How so? Well, most microbial cells are the perfect size and texture to cause water vapor to condense or even form ice around them, which means they could actually “seed” clouds, having a substantial effect on weather and climate.

Via ScienceMag

NASA scientists find evidence of life in meteorites

Wherever it’s possible, life finds a way; the old saying seems to be more and more actual these days, with NASA and other space agencies reporting interesting discoveries that point towards life existing in many more other places other than our own planet. After rewriting the biology books with the arsenic eating microbe, NASA researchers claim to have found evidence of fossilized bacteria in meteorites that landed on Earth.

Dr Richard Hoover, an astrobiologist at the space agency’s Marshall Space Flight Centre in Alabama sparked the discussion after he said he found a bacteria in an extremely rare type of meteorite, of which only nine are currently known to us. He reported finding traces of nitrogen, which couldn’t have come from the rock sample, which absolutely lacked that particular element.

“I interpret it as indicating that life is more broadly distributed than restricted strictly to the planet Earth.”, he briefly said, igniting the imagination of numerous scientists and not only.

However, this is still a matter of certain debate, and an impressive number of experts have been called to shed more light on this findings. This discovery was published in the Journal of Cosmology; editor-in-chief Rudy Schild said:

“Given the controversial nature of his discovery we have invited 100 experts, and have issued a general invitation to over 5,000 scientists from the scientific community, to review the paper and to offer their critical analysis.”

Given the huge number of people involved, it will definitely stir up discussion throughout the scientific community, so we probably shouldn’t have too much to wait until we get more details on this matter.

Woman has an intestinal infection. She has her husband’s stool inserted into her. She is cured

Two years ago, Dr. Alexander Khoruts took on a patient suffering from an awful infection of Clostridium difficile; she was suffering from diarrhea. Now we’ve all probably had our bad moments, but this is not your average case. It was so bad that she was practically stuck in a wheelchair wearing diapers. She was also losing massive weight and she was practically on the road to death, since no antibiotics treatment worked. But Dr. Khoruts had an idea.

He thought the time had come for a transplant; but he didn’t think of transplanting a part of intestine, or stomach, or any other organ. Instead, he transplanted some of her husband’s bacteria. Bacteria from his stool, that is. He mixed it with some saline solution and implanted it into her colon. According to the doctor and his colleagues, the diarrhea dissapeared within a day and did not return.

The procedure is not without precedent, and has been carried out a few times throughout the past decades. However, pretty much nobody expected it to actually work – even the doctors themselves. But they were able to do something that is a premiere: take a genetic survey of her gut flora before and after the procedure.

“The normal bacteria just didn’t exist in her,” said Dr. Khoruts. “She was colonized by all sorts of misfits. hat community was able to function and cure her disease in a matter of days,” said Janet Jansson, a microbial ecologist at Lawrence Berkeley National Laboratory and a co-author of the paper. “I didn’t expect it to work. The project blew me away.”

This is yet another proof that we have still many to understand about the microbes that live inside of us, some of which play a vital role in our own survival.

“We have over 10 times more microbes than human cells in our bodies,” said George Weinstock of Washington University in St. Louis. But the microbiome, as it’s known, remains mostly a mystery. “It’s as if we have these other organs, and yet these are parts of our bodies we know nothing about.”

Now that’s something worth thinking about when you go to sleep at night.


Low level of antibiotics cause drug resistance in ‘superbugs’

For years and years (good) doctors have warned about the dangers of taking antibiotics too lightly, which generally causes ‘bugs’ to be more resistant. More recently, a study conducted by researchers from Boston University showed that microbes are a lot like us: what doesn’t kill them makes them stronger, and this could have extreme consequences. Here’s what it’s about.

You’re sick, you go to the doctor, he gives you a prescription. You start taking it, after a couple of days feel all better, and stop taking it. The result is likely a strain of bacteria (or virus) that will be resistant to a whole number of drugs. The same thing could happen if you’re sick and instead of going to the doctor just take those pills you’ve got, and avoid going to the doctor alltogether.

superbugBasically, when administered in lethal levels, antibiotics trigger a fatal chain reaction within the bacteria that shreds the cell’s DNA. However, when the level is less than the lethal one, the results are not only the survival of the bacteria and the further resistance to this drug, but also to a whole series of other ones too.

“In effect, what doesn’t kill them makes them stronger,” said Collins, who is also a Howard Hughes Medical Institute investigator. “These findings drive home the need for tighter regulations on the use of antibiotics, especially in agriculture; for doctors to be more disciplined in their prescription of antibiotics; and for patients to be more disciplined in following their prescriptions.”

“We know free radicals damage DNA, and when that happens, DNA repair systems get called into play that are known to introduce mistakes, or mutations,” said Collins. “We arrived at the hypothesis that sub-lethal levels of antibiotics could bump up the mutation rate via the production of free radicals, and lead to the dramatic emergence of multi-drug resistance. The sub-lethal levels dramatically drove up the mutation levels, and produced a wide array of mutations,” Collins observed. “Because you’re not killing with the antibiotics, you’re allowing many different types of mutants to survive. We discovered that in this zoo of mutants, you can actually have a mutant that could be killed by the antibiotic that produced the mutation but, as a result of its mutation, be resistant to other antibiotics.”