Biochemical ‘memory’ can help bacteria to grow

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When we think of ‘memory’ we typically think of the brain being able to recall facts and events, but ‘memory’ can take other forms: some plastics can ‘remember’ particular shapes, material shapes or magnetic alignment can be used for storing digital data and our immune systems also have a capacity to ‘remember’ past infections.

Bacteria are also believed to display a kind of ‘memory’ too, which helps them to digest nutrients they have encountered recently. A new study by researchers in the US explores this ‘memory’ in E. coli to see how it impacts on their ability to grow in environments where the food source changes.

So, what’s the point?

Bacteria are hardy survivors – the Mad Max of organisms. They are thought to be one of the very first forms of life to have evolved, and will certainly be around long after humans have gone (in fact, they’ll almost certainly have eaten our physical remains).

Central to their incredible capacity to survive is their ability to eat different things. Now while this might not seem particularly impressive to us – a species that invented the bacon ice-cream sundae or the cheeseburger in a can – species of bacteria have evolved to eat substances as unappetising as concrete, petroleum and nuclear waste (although no peer-reviewed tests have been conducted to see if any can eat the cheeseburger in a can).

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When a bacterium is exposed to a new food source, it typically takes a while to become adjusted to it (the so-called ‘lag phase’). In this phase, the bacterium is generating the biochemical machinery (enzymes etc.) needed to digest the new nutrients it finds itself surrounded by.

During the ‘lag phase’ the bacteria are not dividing and so growth of the bacterial population is temporarily stunted. The researchers wanted to see if bacteria could, in effect, be trained to grow on more than one food source and reduce or eliminate the ‘lag phase’.

This idea is not completely crazy – the authors claim that ‘memory’ has been previously observed in bacteria, as some of the metabolic machinery for the original food source will still kick around inside the cell even after the bacterium has adjusted to the new food source.

Figuring out whether or not bacterial ‘memory’ helps them to quickly adapt to changing environments could be important in understanding how to control the growth and spread of bacteria. This is not just useful for killing harmful bacteria that we don’t want, but also for culturing or harvesting bacteria that we do want, for instance those used in waste treatment or for producing therapeutic molecules such as human insulin.

What did they do?

The researchers developed a microfluidic device, which fed a culture of bacteria (E. Coli) a stream of either glucose or lactose, with the feed changing every 4 hours for 3 complete glucose/lactose cycles (24 hours in total).

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As the feed flows past the culture, individual bacteria are washed away, and are measured at a point downstream. The number of bacteria washed away in the stream is used as an indication of the total size of the population.

In a second experiment, they tested how long this ‘memory’ persists by growing bacteria on lactose for four hours, switching to glucose for a varying time (4, 5.5, 7, 9 and 12 hours) then measuring the ‘lag phase’ (if any) when the feed was switched back to lactose.

Did they prove anything?

The first time lactose was introduced (after 4 hours of glucose), there was a significant ‘lag phase’ as the bacteria adjusted to the new food (see Graph A below). However, the next time glucose was introduced, the ‘lag phase’ was much shorter and in subsequent changes of glucose/lactose there was no ‘lag phase’ at all, with the transitions described as ‘seamless’ (see Graph B below).

bacterial phenotypic memory

However, in the second experiment where the exposure time to glucose was varied, they found that when the bacteria were deprived of lactose for longer than four hours, the ‘lag phase’ reappeared. The ‘lag phase’ generally increased as the time away from lactose increased (see Graph C above).

In further tests, they looked at the lactose-digesting machinery (specifically proteins known as LacY and LacZ). They stated that LacY and LacZ are degraded extremely slowly, so this alone is unlikely to be the cause of the increase in ‘lag phase’.

However, they reckoned that LacY and LacZ are passed on from mother cell to daughter cell as each bacterium divides, causing ‘dilution’ of these proteins in each resulting cell (all of the residual LacY/LacZ of the mother cell would be shared between mother and daughter after division).

This can explain why there is little change in the length of the ‘lag phase’ at lactose-deprivation times below 4 hours (not much cell division occurs), but above this time there is a general increase in the ‘lag-phase’ as the number of cells dividing increases with time (sharing roughly the same amount of LacY and LacZ between a larger number of cells).

So, what does it mean?

There certainly appears to be a link between the length of time since the bacteria were exposed to lactose and the length of the ‘lag phase’, and the reasoning that cell-division is responsible appears to be consistent with the results.

This study could help scientists to better understand the mechanisms behind the growth behaviour of bacteria – important information in trying to control them. This is essential for harnessing their incredible capabilities technologically and curtailling their potential to harm us too.

Original article in PLoS Genetics Sep 2014


All images are open-source/Creative Commons licence.Credit: Bobjgalindo (First); A Gatilao (Second); NIH/NIAID (Third); G Lambert and E Kussel (Fourth)


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Lambert, G., & Kussell, E. (2014). Memory and Fitness Optimization of Bacteria under Fluctuating Environments PLoS Genetics, 10 (9) DOI: 10.1371/journal.pgen.1004556

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The physics of a free-kick, the uses of lasers and the logic behind a ‘fish cannon’.

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The World Cup might be over, but scientists in Japan have modelled the way footballers kick a ball in an effort to see if boots can be designed to improve curl. They found that while technique is important, the material of the boot makes no difference. So it looks like you can’t blame your ability on your boots – if you’re rubbish, you’re just rubbish.

But computers can do more than just tell us about football (although all other uses do seem rather unimportant by comparison), scientists in the US have tried to develop a computational model that can understand exaggeration in language. The model weighs up ‘measured background knowledge, principles of communication, and reasoning about communicative goals’ to recognise the use of hyperbole when referring to the price of everyday objects. They hope that in the future, they can extend their work to cover other non-literal language, such as ‘irony and metaphor’.

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So while it a computer might not yet understand if you’re as ‘sick as a parrot’, a smartphone app could help you to avoid becoming so – US scientists have developed an app that uses a special form of light scattering to estimate populations of E. Coli bacteria on a piece of meat. It’s still in the development stage, but they claim it can detect colonies of bacteria that are many times smaller than those needed to make people sick. [Read the full TSiC article HERE]

But while some bacteria can make you ill, others can be useful: A study by scientists in India shows that bacteria can improve the efficiency of ‘laser driven ion accelerators’. Basically a laser is fired at a target, converting some of it into plasma (ionised gas), which drives the target forwards. The poor bacteria act as small ‘bags of water’ which aid laser energy coupling and results in a hotter plasma being produced (almost certainly getting fried in the process).

Lasers can do more than just burn bacteria, they can be used to tell different chemicals apart – as different chemical groups scatter the laser light in different ways. Researchers in the US have demonstrated a system where a single laser pulse can distinguish between similar chemical compounds from a distance of up to 400m, which they hope could one day be used to detect ‘potentially hazardous chemicals from a safe distance.’

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And finally, hydroelectric dams can be extremely hazardous to migrating salmon, potentially turning the river into an ad hoc sushi restaurant (see a TSiC article about it HERE), but a novel way of helping the intrepid piscines avoid a messy demise has been developed – firing the fish over the dam using a giant cannon. Yes, really. Each cannon (developed by a company called Whooshh Innovations can fire up to 40 fish per minute and will no doubt confuse lots of hungry bears.

All images are open-source/Creative Commons licence.Credit: H Ishii et al. (First); P-S Liang et al. (Second); W Baxter (Third)


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DNA nets could be ‘ancient defence weapon’

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DNA is essential to complex life – it is a complex set of instructions on how to build every protein in your body, from the signaling hormones in your head to the (unwanted) hairs on your feet.

But the code of life for us could well be the code of death for pathogens invading our bodies: a recently discovered process involves our immune cells trapping invaders in microscopic nets made of DNA.

But although this immune process is relatively new to science, it may be an extremely old method of fighting off infection. A new study by scientists from the UK reckons that it could be used by some of the most ‘ancient’ organisms on the planet, and have been preserved right through the evolutionary process.

So, what’s the point?

Our immune system is complex, with many different cells performing different tasks in order to prevent entry, slow down movement and ultimately destroy invaders such as bacteria and viruses. Different cells produce substances from bacteria-bursting antibodies to sticky mucous to contribute to this effort.

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Some cells (neutrophils) are now known to generate nets of DNA. These neutrophil extracellular traps (which form the highly appropriate acronym, NETs) are thought to form a physical barrier to prevent movement of pathogens, but also contain anti-microbial chemicals to help kill them too.

Because NETs are a fairly recent discovery, their origins are still little-understood. The authors claim they have been observed in other mammals, as well as in birds and fish, but has not been ‘studied in detail’ in invertebrates.

A better understanding of what NETs are can help us not only to understand how they evolved, but also may help in understanding certain auto-immune diseases which are linked to NETs.

What did they do?

The authors of the paper reckoned that if NETs are indeed an ‘ancient’ defence system, then it would be used by creatures that evolved much earlier than vertebrates. So they ran tests on crabs, mussels and sea anemones to see if they deployed NETS too.

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Certain immune cells were extracted from the creatures examined and certain chemicals, known to stimulate immune cells into responding were added to them.

A stain (dye that becomes visible when bound to specific chemicals) for DNA was also added. The stain cannot cross cell membranes so would only stain DNA in cells where the membrane was disrupted (i.e. dead cells) or DNA which was outside the cells.

To see how similar the immune cells’ reaction processes are to vertebrates, they also tested three different chemicals known to disrupt the production of NETs in mammals to see if they have the same effect in crabs (they didn’t test the other two).

Did they prove anything?

Stimulating the immune cells of the crabs ‘resulted in expulsion of material’ (a line worthy of the Bad Sex in Fiction Award) which stained positively (it just gets worse!) with the dye.

In addition, the material could be ‘dissolved’ with an enzyme used to break down DNA (DNAse-1). Similar observations were seen in the cells of the mussels and sea anemones too.

NET (chromatin)

Electron microscope images of the ‘material’ reveal a ‘mesh’ structure ‘studded with small granules’, which they said was a ‘similar structure to mammalian NETS’, although with a few slight differences were noticed.

To show that this reaction is a genuine immune response, they added L. Anguillarum (an infectious bacterium to crabs) to the cells, which did indeed trigger the production of the same material.

They also found that the same chemicals known to disrupt NET production in mammals did the same in the crab cells.

So, what does it mean?

This is certainly evidence that NETs (or similar DNA-based defences) are used in invertebrates as well as vertebrates.

The authors argue that because the same chemicals were able to disrupt NET production in creatures as diverse as humans and crabs, it suggests that the immune response occurs by similar biochemical pathways.

This leads them to suggest that NETs are an ‘evolutionary ancient defence weapon’.

If this is the case, it would be interesting to see just how far up the evolutionary ladder NETs can be found – it seems like quite a generic response that could defend against a wide range of pathogens, so it may be the case that it is used by even simpler organisms than sea anemones.

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If anything this shows how much in common we have with ancient organisms – many cellular processes and biochemicals have proven to be so successful that they have remained largely unchanged throughout evolution.

So perhaps it shouldn’t be such a surprise that a process which is one of the most important things an organism needs to do – protect itself – appears to also have stood the test of time.

Original article in Nature Communications Aug 2014


All images are open-source/Creative Commons licence.Credit: ynse (First); BruceBlaus (Second); Ar rous (Third); C T Robb et al. (Fourth); G Beard (Fifth)


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Robb C.T., Dyrynda E.A., Gray R.D., Rossi A.G. & Smith V.J. (2014). Invertebrate extracellular phagocyte traps show that chromatin is an ancient defence weapon., Nature communications, PMID: http://www.ncbi.nlm.nih.gov/pubmed/25115909

How your smartphone can tell you if meat is tainted

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Digging around in the back of your fridge can sometimes uncover a cornucopia of forgotten tasty nuggets (like cheese that has had extra time to ‘mature’ or even actual nuggets), but sometimes you’ll come across a potential dilemma: the Russian-roulette meat.

You bought it on impulse while it was on special offer at the supermarket, but kinda just forgot about it as tastier or more convenient meals presented themselves, and now you’ve no idea for how long it’s been sitting there.

Do you risk it? It doesn’t smell bad, and the best-by date is only out by a couple of days so if you cook it to death it’ll be fine, right? Do you throw away what could be a perfectly safe and tasty piece of food or do you run the risk of spending the next day or so in gut-wrenching agony?

Well fortunately a new solution might be just around the corner – a team of researchers from the US has developed a method that they claim can sense bacteria on meat, using nothing more than the (not-so-humble) smartphone.

So, what’s the point?

While I may have made a trashy and cynical attempt to make light of food wastage so far, it is not a trivial matter: according to a report by the UN Food and Agriculture Organisation in 2011, around 10% of meat (see figure 7) in Europe, North America and Oceania is wasted by the consumer.

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On the other hand, eating tainted meat can cause illnesses such as food poisoning in humans. While proper cooking of tainted meat should kill all of the bacteria and other microorganisms alive in it, you can still become sick if they have left behind particular toxic biochemicals or microspores.

While no meat can ever be 100% bacteria-free, one of the important factors in whether meat is safe to eat is how much of the micro-critters there are – more bacteria, more toxins.

So a device that can give you an indication of how much bacteria are currently crawling around on your dodgy buffalo wings or Aberdeen Angus steak could help you to decide whether or not it’s a good idea to chance it.

What did they do?

The techology is based on an interesting quirk of light: it is scattered in a very particular way by certain shapes such as spheres and cylinders (Mie scattering).

Cells such as mammalian tissue (i.e. meat) and different species of bacteria (which can be a range of different shapes) scatter light in ever-so-slightly different ways from one another.

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Normally the scatter of bacteria and mammalian cells are difficult to tell apart, but the scientists reckoned that by measuring the scatter at a range of different angles, they could distinguish bacterial colonies from the background noise (scattering caused by mammalian cells).

A set of samples was prepared: ground beef with solutions containing varying concentrations of E. coli (ground beef with deionised water was used as the control sample).

To scan the beef, the researchers developed a smartphone app that shines an LED (the light source) onto the samples and allows the user to take pictures at a specific distance and at 4 specific angles.

The angles are measured by the smartphone’s in-built gyroscope and two dotted lines appear on the screen for the user to match up to make sure the phone is at the right distance from the sample.

The app can then analyse the pictures to give an estimate of the E. coli concentration.

Did they prove anything?

The researchers found that samples containing different concentrations of bacteria scattered light most intensely at different tilt angles. They suspect this is because higher concentrations usually mean that the colonies of bacteria formed will be larger.

This is good news because it mean the technique can be used to estimate how much bacteria are in each sample.

scattering graphs

Strangely, previous research highlighted by the authors suggest that at low concentrations (less than 105 CFU/mL), normal bacterial colonies should be too small in number to be detectable by this method.

They suggest that at low concentrations, the bacteria may interact with the mammalian cells to produce small structures which they call ‘pseudo-colonies’ which are individually large enough to scatter the LED light and numerous enough to produce a detectable signal.

They provide an electron microscope image of what they believe is a pseudo-colony (which they point out very conveniently!).

pseudo colony

So, what does it mean?

By all accounts it looks as if their experiment has worked. Their app was able to analyse Mie scattering from various samples and to build up profiles of scattering at different angles to enable different concentrations of E. coli to be distinguishable from one another.

The researchers claim that the lowest detection limit of the app is about 100,000 times lower than the ‘infectious dose’ of E. coli, meaning that the app could comfortably detect if levels of this bacteria were indeed dangerous.

However, this has only worked so far for one species of bacteria – and distinguishing between bacterial species by this method may prove to be much more difficult, if not impossible. This is important because some species need a smaller concentration than E. coli to be infectious.

It is a step in the right direction, obviously more work needs to be done – but unlike many other technologies, it is one that seems ready-made for the general public: being an app means that if the technology is perfected it could be used by anyone with a smartphone.

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So perhaps in a couple of years’ time, your smartphone could help you to make a more informed decision about whether that slightly off-colour steak is still good to eat. But for now, I might just stick with a salad…

…who am I kidding, I’ll just make sure it’s well-done!

Original article in Scientific Reports Aug 2014


All images are open-source/Creative Commons licence.
Credit: P-S Liang et al. (First and Fifth); jbloom (Second); Rocky Mountain Laboratories NIAID/NIH (Third); P-S Liang et al. edited and anotated by TSiC (Fourth); MCB/Maggie O (Sixth).


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Citation:

Liang P.S., Park T.S. & Yoon J.Y. (2014). Rapid and reagentless detection of microbial contamination within meat utilizing a smartphone-based biosensor., Scientific reports, 4 PMID: http://www.ncbi.nlm.nih.gov/pubmed/25092261

Scientists figure out fashion, jealousy in dogs and how high a Lego tower can be built

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Who’d Have Thunk It? 31.07.14
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We begin this edition with a question which has plagued mankind for decades: How high can you build a Lego tower? At the behest of the BBC (good to see licence-fee-payers’ money put to good use!), engineers from the Open University have conducted tests to work it out. By placing 2×2 bricks in a metal ram, they found each one can withstand a compressive force of over a third of a tonne before becoming squashed into a pile of plastic ‘Camembert’. They calculated that theoretically the tower could reach up to 3,591m (about 11 Eiffel towers), although they say that in reality it would probably just buckle and fall sideways way before this, because it would be almost impossible to build completely straight.

From down-to-Earth bricks to extraterrestrial boulders: A team of astrophysicists reckons it has solved the mystery of why asteroids seem to have loads of large boulders on their surfaces – using a bag of mixed nuts. The ‘Brazil Nut Effect‘ works on the principle that if you shake a mixed bag of nuts, the smaller ones can maneuver through the spaces to the bottom, leaving the larger ones on top. They reckon a similar thing is happening on asteroids with rocks of different sizes.

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The Deepwater Horizon disaster of 2010 was described as ‘the worst environmental disaster the world has ever faced’ by Barack Obama no less, but the oil slick hasn’t just affected photogenic creatures such as pelicans and turtles – bacteria that live in beach sand also appear to have been affected. A study by US scientists found that some species of bacteria (including some which can cause illness in humans) have been partially replaced by those that can (quite usefully) break down hydrocarbons. They reckon this could be due to the clean up operation as well as the slick itself. [See full TSiC article HERE].

While the unfortunate residents of the Gulf Coast are acutely aware of mankind’s impact on the environment, it appears that people who live close to the sea are more likely to believe that climate change is real. A study in New Zealand surveyed nearly 6,000 people and found a link between belief in climate change and distance to the coast, after accounting for factors such as wealth and conservative views. They reckon that by living near the coast, people would be less removed from the issue and the perceived effects of climate change would ‘become more concrete and local’.

From changing climates to changing clothes: scientists have also tried to tackle the world of fashion in a delightful paper entitled ‘The Science of Style‘. US researchers surveyed almost 250 people, asking them to score how ‘fashionable, good and liked’ various combinations of colours were in both men’s and women’s clothing. The conclusion? Combinations which either clash or are too similar are bad – the ideal colour sets are ones which ‘match moderately’. So now we finally know which clothes to wear under our labcoats. Thanks science!

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And finally, while designer clothes might illicit envy in humans, it looks like we’re not the only species that can experience visits from the green-eyed monster: Dogs can apparently show ‘jealous behaviour’ too. Dogs whose owners were instructed by (rather heartless) researchers to show affection to a stuffed-toy dog in front of them were observed to ‘snap’, ‘whine’ and ‘push or touch’ their owners more often than if the owners’ attention was directed towards a ‘nonsocial object’ such as a book. Perhaps this shouldn’t be such a surprise – after all, some humans probably snap and whine when they get jealous too.

Read more Who’d Have Thunk It? Articles HERE

All images are open-source/Creative Commons licence.

Credit: M Manske (First); MassDEP (Second); D Stockman (Third).

Text © thisscienceiscrazy. If you want to use any of the writing or images featured in this article, please credit and link back to the original source as described HERE.

Two ways to make bacteria directionless

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Bacteria are sometimes thought of as simple, or if they cause illness: simple and annoying. But these tiny critters are arguably the most successful organisms on Earth, surviving in all sorts of unpleasant and extreme environments including sulfurous hot springs, clouds and, most extreme of all, the human gut!

Central to the success of many species is the ability to sense food and move towards it. In humans, we use our eyes, noses and ears to guide us directly to the veritable bounty of an all-you-can-eat buffet, but some bacteria use a different, and much more jumbled method to reach food sources.

And a new study by German scientists has found two ways of limiting the ability of a certain species of bacteria to spread by affecting their jumbled walk. One involves breaking their legs (well, their equivalent of legs) and the other disrupting the link between sensing food and producing the movement required to reach it.

So, what’s the point?

Named after the Latin word for whip, flagella are long appendages that certain cells (including some species of bacteria and mammalian sperm cells) use to move themselves around.

At the base of each flagellum is a biological structure sometimes described as a ‘motor‘. The flow of charged particles (ions) across the cell membrane causes the ‘motor’, and therefore parts of the whole structure, to rotate (each proton moves part of the motor around a little bit as it passes through). This turns the appendage like a propeller, to make the cell move.

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The complexity and intricacy of the flagellum has led some using it as an example of intelligent design (i.e. It was designed by God). However, different species have different proteins making up the structure of their flagella, and many of these proteins actually have other functions in the cell too.

What is more, other structures exist in nature, such as ATP synthase, which also have rotating ‘motors’ but don’t actually exploit them for locomotion. So it is actually quite easy to see how the flagellum could have evolved (and could potentially be evolved again in species which don’t currently have them).

So apart from debunking the theories of creationists, what is this research about? Well in order to survive and proliferate, bacteria need to eat. Moving about allows them to find richer sources of food, as well as avoiding poisonous chemicals, and it turns out that many species of bacteria do indeed have the ability to sense important chemicals which they either want to move toward or flee away from – a process known as chemotaxis.

But their ‘walk’ isn’t straightforward. Bacteria use their flagella in two modes: they either propel them forwards or cause them to ‘tumble’ to face a new direction randomly. By moving then tumbling over and over again, they maneuver themselves to a new position. It’s a bit like drunk-walking towards a kebab.

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The scientists say that some species of bacteria that normally have flagella at their ‘back’ (primary flagella) sometimes develop secondary sets of flagella at their sides when the liquid in which they are swimming becomes thicker (more viscous) or if they encounter a surface, which ‘provides superior performance’ in these conditions.

But they say they recently saw a particular species (the rather unpleasant-sounding S. putrefaciens) which use these secondary flagella under normal (‘planktonic’) conditions, and wanted to figure out what advantage they conferred to the bacteria in this case.

Understanding how bacteria work is not only important in treating certain diseases, but also for technologies where we exploit them, such as in the food industry and for producing biomolecules for therapeutic use such as insulin, and chemotaxis is an important mechanism by which bacterial populations grow and thrive.

What did they do?

The scientists compared normal (wild-type) S. putrefaciens with a mutant strains which had either their primary or secondary flagella disabled.

The bacteria were initially placed (‘inoculated’) in the centre of a petri-dish, and their positions checked again after 12 hours. The bacteria were expected to spread out across the dish, as nutrients would soon be depleted in the centre, meaning the outer edge of the dish would be richer in food.

They then re-ran this experiment, but in mutants with impaired reactions to chemical sensing (in other words, they could sense food, but could not move in reaction to their senses). Again, one set had both sets of flagella functioning while the others had either the primary or secondary flagella disabled.

They did this by altering a gene to produce a defective version of the CheY protein, which is thought to interact with part of the flagellum ‘motor’ to induce tumbling. A bacterium with working CheY will tumble more when it senses it is heading away from food, in the hope that it will eventually land facing the right direction.

Did they prove anything?

The researchers found that wild-type bacteria spread the furthest, followed by mutants with disabled secondary flagella, with those with disabled primary flagella spreading the least.

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However, in a separate test, they found that the bacteria with the disabled secondary flagella actually swam faster (in a straight line) than the wild-types. So swimming-speed was not the reason why the wild-types were better spread out.

The researchers then analysed the angles at which the bacteria tumbled whenever they changed direction. They found that the mutants with the secondary flagella disabled made turns at much larger angles (on average around 90o) than the wild type and tumbled about twice as often.

They speculate that these reasons combined mean that the wild-type, with working secondary flagella, by turning less and moving forwards more, actually manage to spread themselves further over time than the mutants, despite being slower straight-line swimmers.

Bacteria with defective CheY spread out about as poorly as the mutants with disabled primary flagella, even if both sets of flagella were working properly. But those with defective CheY and disabled secondary flagella barely spread out at all.

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In a third experiment, they found that mutants with a boosted CheY function but disabled secondary flagella did actually spread out a bit, whereas boosting CheY function had no effect on those with disabled primary flagella. The researchers concluded that CheY must interact with the primary flagella, but has less or even no effect on the secondary flagella.

So, what does it mean?

The researchers say that, in this species at least, the primary flagella provide the ‘main propulsion’ for chemotaxis, and their switch to ‘tumbling’ mode is affected by the CheY protein. The secondary flagella help to control reorientation when the bacteria tumble and are relatively less affected by CheY.

The first weird thing to note is that the combination of disabled secondary flagella and defective CheY result in such a small spread of bacteria. In theory, the primary flagellum should still be propelling the bacteria forwards, but without CheY or the secondary flagella they would not change direction.

The researchers reckon that these bacteria may use a slightly different movement pattern than just run-and-tumble. Some bacteria use a run-reverse-flick pattern, where they move forwards, then backwards (by spinning the primary flagellum in the opposite direction) before tumbling.

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If they don’t tumble, they are pretty much just moving backwards and forwards, and so are unlikely to spread that quickly. The mutant with both sets of flagella working but defective CheY will also move backwards and forwards, but the functioning secondary flagella will push it sideways as well.

Moving backwards and forwards, in this case, appears to be similar to not moving at all: the mutants with disabled primary flagella spread a similar amount to the ones which had both sets of flagella working but didn’t tumble.This rather cool video shows that when the primary flagellum is disabled, the spinning of the secondary flagella will cause the bacteria to wander round in circles. Note the bacterium in the middle which is believed to have a secondary flagellum stuck to the bottom of the dish and so just spins round and round.

So it’s likely that if the bacteria don’t tumble, both mutants with working secondary flagella are just running around in circles, and those without working secondary flagella just move backwards and forwards, although more videos proving this would have been good as well as pretty interesting to watch (if you’re as sad as I am).

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In any case, it seems the scientists have shown two ways of controlling the spread of this type of bacteria: disabling flagella and disabling CheY. Controlling how bacteria spread affects how quickly they can grow and reproduce and so is vital knowledge in applications where we want to either limit their growth (e.g.medicine) or boost it (e.g. biomanufacturing).

So do bacterial loan sharks threaten to break their debtors flagella? No, but we can if we want to… mwhahaha!

Original article in PNAS Jul 2014

All images are open-source/Creative Commons licence. Credit: AJ Cann (First); LadyofHats (Second); TSiC (Third); S Bubendorfer et al. edited by TSiC (Fourth, Fifth and Seventh); J Taktikos et al. annotated by TSiC (Sixth).

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How Deepwater Horizon and its clean-up have changed beach microbe populations

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The Deepwater Horizon disaster is considered to be the largest marine oil spill in history, turning vast swathes of the southern US coast into tar pits, and helpless marine critters into bewildered balls of bitumen.

“But what of the poor bacteria?” I hear absolutely nobody cry. Well it turns out some people are interested in the microorganisms that populate these beaches – for one thing they form an important part of the wider ecosystem.

A new study by US scientists looks at how populations of microorganisms have been affected, with certain types of bacteria seemingly replaced by others, and suggests that not only the slick itself, but also the clean-up operation have played a role in this ecological shift.

So, what’s the point?

Deepwater Horizon was a floating oil rig based in the Gulf of Mexico. On April 20th, 2010 an explosion on the rig killed 11 workers and resulted in the catastrophic leakage of oil into the sea. The leak was not properly stemmed until around three months later, by which time around 90-180 million US gallons of oil were thought to have spilled into the Gulf of Mexico.

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While most of the attention of the media regarding the environmental impact of the disaster was focused on oil-drenched photogenic animals, less-glamorous organisms were also affected. The ecosystems that exist on sandy beaches are diverse and complex, and the tiniest creatures – microorganisms – form a vital cog of these systems.

So in order to understand the full effects of the disaster, figuring out what has happened to the microorganisms is key – and this study sets out to do precisely that.

But they weren’t just interested in the effects of the spill itself – they also wanted to see whether some of the clean-up techniques also affected the microbial populations.

What did they do?

The scientists took samples from two sandy beaches – one in Louisiana and the other in Alabama, and assessed the different types and relative numbers of microorganisms present in the sand. They took samples at different locations on each beach (from the swash up to the dunes) and at various points throughout the year following the explosion.

Crucially, the first set of samples was taken before the oil reached the shore, providing an idea of what sort of microbes lived there before the disaster.

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They also looked at how the local environment (the sand) changed over time, analysing not just how much oil (strictly speaking, ‘total organic content’) was in there, but also factors such as the size of the sand grains (sand was tilled, cleaned or replaced in various areas, as well as being disturbed by heavy vehicles) which affects things such as water content and pH in-between the sand grains.

Did they prove anything?

On both beaches, they found that the microbial communities in the dunes did not vary much over time, but closer to the water (areas of the beach more affected by the slick) they did.

They found that the communities around the swash shifted to favour microorganisms that thrive in higher carbon and water content environments – which could suggest that in this area, both the slick itself and the replacement of the sand with coarser grains may have had an effect.

At the backshore, they found that microbial communities were influenced by grain size more than the other variables,’ again suggesting that the change in the sand composition due to the clean-up operation has actually had an effect.

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They also suggest that the act of washing the sand – which they say is typically done with ocean water, could physically replace the native microorganisms in the sand with those present in the ocean water.

Interestingly, among the bacterial groups that were reduced in number were Enterobacteriales, which can cause unpleasant gut-related illnesses in humans, while numbers of hydrocarbon-degrading bacteria (certain species of Oceanospirillales) increased.

So, what does it mean?

This study suggests two very interesting things:

1. The clean-up effort may have impacted on the microbial communities.

2. Enterobacteria that can cause illnesses in humans have actually been reduced in number.

The researchers reckon that it is likely that the remediation and cleaning of sand is responsible for some of the changes to the community, because the changes were not ‘smooth’ and natural processes (even Hurricane Alex) were unlikely to have caused such a huge shift in populations.

The oil spill itself was also insufficient to explain these changes, as some occurred on areas of the beaches that were not reached by the slick, but which were cleaned or otherwise disturbed nonetheless.

microbe communities on beach

This is an interesting conclusion – that the clean-up itself is an important environmental impact – and this may need to be considered in the future.

The fact that Enterobacteria have been reduced in number is perhaps not surprising – after all, the sand was cleaned to remove the oil. But considering that on the beach they tested in Louisiana, 7.5% of samples exceeded state limits for these bacteria in 2010 (this fell to 4.4% in 2011), perhaps the clean-up was overdue.

The researchers say that ‘in general, beaches are not routinely physically remediated if fecal indicator (illness-causing bacteria) counts exceed state standards’, whereas obviously a massive clean-up operation took place in response to the oil slick.

Managing the clean-up of the ‘worst environmental disaster America has ever faced‘ was of course no easy task, but it has thrown up some interesting points about how the clean-up operation itself may impact the ecosystem too, and hopefully this will help with the planning and execution of disaster responses in the future.

Original article in PLOS ONE Jul 2014


All images are open-source/Creative Commons licence.
Credit: US Coast Guard (First); Louisiana GOHSEP (Second); Louisiana GOHSEP (Third); MassDEP (Fourth); A S Engel and A A Gupta (Fifth).


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