To grow and produce crops under almost any condition, plants need to make good use of all nutrients available to them. While they are masters at absorbing some nutrients from the air and soil, they are struggling with others.

One such problematic element is nitrogen. Even though nitrogen makes up about 80% of the atmosphere, it is mainly present as dinitrogen gas N₂.

This means two nitrogen atoms are tightly bound to one another via three strong and energy-rich bonds. In this form, plants can neither take up the nitrogen nor use any of the nitrogen atoms to make other molecules from them.

Yet, they need nitrogen since it is part of every DNA molecule, protein, the energy provider ATP and many vitamins. Hence, plants need a way to acquire that element in a simple way that does not cost them too much energy.

Enter bacteria.

Diazotrophic bacteria fix nitrogen

The so-called diazotrophs have developed a highly efficient enzyme complex to capture, or fix, dinitrogen from the atmosphere and break up its energy-rich bonds. This complex is the nitrogenase, and all diazotrophs use one of three types of nitrogenase.

The most efficient nitrogenase contains a molybdenum ion at its core, while other nitrogenases use vanadium or iron. These metals are extremely rare in the environment. Hence, depending on which one is available, bacteria regulate which of the three nitrogenases to produce.

After capturing a dinitrogen molecule, the nitrogenase enzyme transfers energy in the form of protons and electrons to it. This eventually breaks up the bond between the two nitrogen atoms and produces two ammonium ions NH₃⁺.

Bacteria then use the ammonium ions for their own growth and share the surplus with their friends and partners. In Nature, several symbiotic relationships exist between bacteria and other organisms which are based around the nitrogen-fixating superpower of bacteria.

Soil bacteria share fixed nitrogen with plants

The best known nitrogen-fixing organisms are soil bacteria from the families Bradyrhizobium, Frankia, Bacillus, Clostridium, Burkholderia and Pseudomonas. These either live freely in the soil or form symbiotic relationships with plants.

Especially important are symbiotic rhizobia like Bradyrhizobium and Frankia. Plants attract these soil bacteria to their roots by sending out special molecules, which the bacteria respond to via their quorum sensing receptors. Within the root network of legume plants, the bacteria then build little nodules in which they live protected from the surrounding.

Within the nodules, bacteria fix and convert nitrogen with their enzyme complexes, which requires a lot of energy. Gladly, the host plant provides this energy in the form of sugars and organic acids that it produces with photosynthesis. The plant then transports these molecules into the root nodules, where the bacteria break them up, extract their electrons and thus gain the necessary energy.

After breaking up the nitrogen using these very electrons, the bacteria transport the produced ammonium from the nodules into the plant. With the ammonium, the plant makes DNA, proteins and vitamins; everything that it needs to grow and produce crops and fruiting bodies. Hence, rhizobia bacteria are highly important for the health of plants as well as crop production and yield.

Marine bacteria can fix nitrogen

Soil bacteria are not the only nitrogen-fixing organisms; marine bacteria are also important for global nutrient cycles. For example, cyanobacteria form long filamentous multicellular organisms, with some cells specialised in nitrogen fixation.

Often, cyanobacteria are closely associated with other marine bacteria with which they share nitrogen. So far, scientists do not fully understand these types of interactions but are sure that nitrogen-fixing organisms are crucial for the marine food web and the survival of many species under water.

When temperatures are high enough and nitrogen concentrations are optimal, you can pretty much see the nitrogen-fixation process. A green blanket on the water surface is a sign for cyanobacteria that power both photosynthesis and nitrogen fixation with the carbon dioxide and nitrogen from the air. This so-called algae bloom is mainly due to cyanobacteria like Aphanizomenon, Dolichospermum, Anabaena and Synechococcus bacteria.

Soil bacteria as biofertilisers for sustainable food production

Since some soil bacteria are so efficient in fixing nitrogen and providing it to the plant, they have also become valuable in agriculture. Some so-called biofertilisers consist of bacteria that are added to soil or plants to build symbiotic relationships with them, helping them grow better and produce bigger crops.

Hence, biofertilisers containing bacteria are an efficient and sustainable way to produce more food and in higher quality. With this, farmers will rely less on synthetic fertilisers while maintaining high crop yields. Additionally, using nitrogen-fixing bacteria as biofertilisers helps protect the health of the soil and the environment.

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Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

And only thanks to pigments, life on Earth is possible. Pigments were the first molecules that microbes used to harvest sunlight. Microbes could then transform the light energy into chemical energy and produce oxygen.

Even the brown-reddish haemoglobin in your blood is an essential pigment as it transports oxygen within your body. Also for bacteria, pigments and their colours have life-saving functions. Here, we will look at how biopigments colour the bacterial world and what bacteria gain from producing them.

Bacterial pigments bring colour to the world of bacteria

Biopigments are molecules with complex chemical structures and at least one excited electron. Depending on the electron’s arrangement, a pigment absorbs light at a specific wavelength. It reflects the colour of the unabsorbed wavelength, which gives the pigment its colour.

As the function of pigments depends on the incoming light, sunlight plays a crucial role for bacteria with pigments. By adding certain pigments to their membrane, bacteria can adapt to environments that are directly affected by sunlight or the lack of it. This gives them an advantage over those bacteria that lack these pigments.

However, some bacteria also use pigments for other purposes, which we discuss further in this article.

Microbes harness photosynthetic power with colourful pigments

Sunlight is incredibly powerful since each light photon contains energy. Bacteria adapted to harvest energy from sunlight with special pigments.

Pigments can capture the incoming photon and transfer its energy to other molecules. This process transforms the incoming light energy into chemical energy. So-called phototrophic microbes are those that gain their energy from light.

The best-known example of a photosynthetic biopigment is chlorophyll in plants, algae and cyanobacteria. Cyanobacteria produce several complexes of bacteriochlorophylls to absorb blue and red light. As the green light is not absorbed, it is reflected, which is why chlorophyll – and thus cyanobacteria, algae and plants – are green.

Some bacteria harvest more light by producing several pigments of different types. They then arrange them in an optimal formation according to the incoming light.

For example, carotenoids capture energy in the green-blueish range and pass it on to the associated chlorophyll. Together, these photosynthetic complexes absorb light energy from almost the entire wavelength spectrum.

Halophilic bacteria and archaea are microbes that produce carotenoids to capture sunlight. You may have seen salt ponds with a reddish colour. This comes from the red and pink-coloured archaea Halobacteria, bacteria Salinibacter or algae Dunaliella. Thanks to their colourful carotenoids, these microbes adapt to salty waters that are exposed to direct sunlight.

Cyanobacteria in the deep sea, lagoons, lakes, ponds or rivers produce similar molecules to chlorophyll. These absorb the blue-green light in water, which allows these bacteria to survive in these dark environments. If you have ever seen a lagoon shining yellow or orange, this was probably due to the colourful cyanobacteria inside.

Bacterial biopigments protect from too much light

As light is full of energy, bacteria also need to protect themselves from getting burned. For this, they produce pigments that take up the excess light energy. Like this, the main photosynthetic complex does not get damaged.

Carotenoids and xanthomonadins are the colourful sun blockers of the microbial world. These molecules absorb high-energy light to protect chlorophyll from damage. Over 600 different carotenoids were described and they usually come in yellow-orange-reddish colours.

The yellow xanthomonadins absorb wavelengths within the energy-rich UV spectrum. Bacteria like Xanthomonas campestris live on plant leaves where they are exposed to direct sunlight. Hence, their yellow xanthomonadin coats are like self-made sunblocks protecting the bacteria.

Also, the pigment melanin shields the producing cell from energy-rich sunlight. Many bacteria living in the soil or bacterial spores produce these pigments. Here, melanin absorbs light from a wide range of the light spectrum to protect the inner of the cell. Hence, melanin-producing bacteria, like Vibrio cholerae and Streptomyces bacteria, are brown or black.

Bacterial pigments let electrons flow and save energy

Since bacterial pigments allow electrons to flow, they can also be energy conductors. Hence, some pigments are important components of energy complexes and synthesis machineries.

For example, yellow flavins are pigments involved in cellular metabolism. The main flavin is riboflavin, which you may know as vitamin B12. This essential molecule – produced only by bacteria – allows our bodies to work.

Phenazines are unique bacterial pigments with yellowish-green fluorescent colours. Pyocyanin, exclusively produced by Pseudomonas bacteria, shuttles electrons – and thus energy – during the respiration process. Hence, pyocyanin is essential for Pseudomonas as it keeps the bacteria healthy and alive.

Some biopigments have anti-oxidant effects

Bacterial pigments don’t just help adapt to external environmental conditions like the sunlight. They also guard the inner bacterial cell from stressful situations.

Excess or uncaptured energy or escaped light photons can react with oxygen. This process produces so-called oxygen radicals, which can damage molecules inside the bacterium. Known as oxidative stress, oxygen radicals can even become life-threatening for bacteria.

Carotenoids and xanthomonadins protect bacterial cells from oxidative stress. These pigments transform the free oxygen radicals into harmless molecules. Since carotenoids and their product vitamin A have similar functions in humans, it is only healthy for us to take up a lot of these with our diet.

In the bacterium Gemmatimonas aurantiaca, orange carotenoids also work like sunscreen and oxidative shield. These pigments both give the bacterium its bright orange colour and protect it from too much sunlight.

Bacteria combat microbial enemies with coloured pigments

As night falls, many bacterial pigments reveal their darker sides. They become important weapons for microbial warfare. Without sunlight, several pigments take on roles as virulence factors and antimicrobials as they mess up cells’ energy and oxygen household.

For example, prodigiosin is the red weapon of Serratia marcescens. As prodigiosin inhibits the growth of several bacterial, fungal and insecticidal pathogens, Serratia marcescens is an important biocontrol bacterium of plant disease.

You may have seen prodigiosin-producing Serratia bacteria on contaminated food. They develop these red, blood-like dots.

Violacein is a purple pigment with anti-viral, anti-bacterial and anti-cancer properties. For example, Chromobacterium violaceum sends membrane bubbles filled with violacein to kill bacterial enemies.

Similarly, Janthinobacterium lividum protects frogs and salamanders as it lives on their skins. Here, the bacterium throws violacein at pathogenic fungi that would otherwise infect and harm the animals.

Pyocyanin, the fluorescent electron-shuttling pigment in Pseudomonas, is also very sensitive to oxygen. It even turns Pseudomonas aeruginosa cultures in the lab blueish just by shaking and airing them.

Yet, not all bacteria have an appropriate coping mechanism for pyocyanin. Hence, these bacteria suffer oxidative stress when they come into contact with this pigment. This is why Pseudomonas uses pyocyanin also to fight bacterial and fungal enemies.

Vivid pigments colour the bacterial world

The Bacterial World is colourful – one of this blog’s taglines. You may have asked yourself what this is about and why bacteria have so many different colours.

From the dazzling pink of halophilic microorganisms to the sunny yellow of phytopathogens, bacterial pigments give their producers shiny and vibrant colours. But thanks to the colourful biopigments, bacteria also gain abilities to survive in new and challenging environments.

Some of these bacterial pigments are essential for us humans and even life on Earth. From some of these colourful biopigments, we produce vitamins that we need for our own metabolism. Also, every oxygen molecule that you just took up with your last breath, at some point, was transformed by a bacterial chlorophyll pigment.

So, I guess it is yet again time to be grateful to bacteria and their vibrant and life-enabling activities!

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Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

And more and more people become aware that a plant-based diet is not only better for your health, but also for our planet. Hence, the focus on agriculture right now is to become more sustainable to grow enough plant-based food for everyone.

This means that we need to find better ways to support plant growth and protect plants from diseases. Unfortunately, several plants pathogens make plants sick, so they die or do not grow enough crops.

Currently, we use fertilizers and pesticides to protect plants from pathogens. However, these chemicals are bad for the environment long-term as they contaminate the soil and water.

Hence, we need to find ways to protect plants by either getting rid of dangerous intruders or by strengthening the immune systems of plants.

Enter bacteria and their superpowers.

They do both.

What is biocontrol?

Some bacteria that live in or on plants are called biocontrol agents. These organisms are harmless to the plant and have two main functions: They protect the plant from pests and diseases and support its growth and crops.

Some of these organisms additionally strengthen the plant’s immune system or resistance – again to protect the plant from disease and help it grow.

One such biocontrol agent is the bacterium Pseudomonas putida. It grows near the roots of many plants where it produces helpful molecules for the plant.

And plants are clever too as they make sure that only the right types of bacteria grow near them. For this, several plants release specific molecules through their roots that help Pseudomonas putida grow. The bacterium senses these molecules so that they activate the bacterium’s chemotaxis system.

Now, Pseudomonas putida uses its flagellum to swim towards these molecules. This movement ultimately leads the bacterium to the plant that released the molecules.

Pseudomonas putida as a biocontrol agent

Once the bacterium “found” the plant, it settles down near it and starts building biofilms. Within these biofilms, the bacteria are connected with each other and with the plant. Like this, they can easily exchange molecules and information with each other and with the plant and build close relationships.

Pseudomonas putida now produces molecules to help the plant grow. For example, some molecules extend the tips of the roots so that the plant can better take up nutrients from the soil.

Pseudomonas putida also breaks down complex nutrients in the soil that the plant use. This basically feeds the plant the needed nutrients. Other molecules from the bacterium activate the overall immune system of plants so that plant pathogens have a harder time infecting the plant.

Altogether, Pseudomonas putida has similar features as biofertilizers that help plants grow.

How does bacterial biocontrol protect plants against intruders?

Pseudomonas putida can also directly fight off plant pathogens to protect their plant hosts. For this, it uses two strategies: It either holds back essential nutrients from plant pathogens or kills the intruder.

Not sure which strategy is more evil though…

Pseudomonas putida keeps essential nutrients to inhibit plant pathogens

All living organisms need iron to live and grow. And one efficient strategy to prevent other microbes from growing is by stealing iron from them.

Our immune system does it as well: All iron in our body is bound to specific transporters. Like this, no free iron swims in our blood for microbes to use. This defence mechanism is one of the first strategies of our immune systems to keep harmful bacteria from growing inside our bodies.

Similarly, Pseudomonas putida produces many different iron transporters that bind iron very efficiently. Like this, no free iron is present in the soil that other microbes could use.

Yet, this is not all. Pseudomonas putida is quite a naughty one since it can also steal iron-loaded transporters from other bacteria. This not only prevents the other bacteria from using the iron, but it also helps Pseudomonas putida grow.

Pseudomonas putida kills intruding plant pathogens

Lastly, Pseudomonas putida is a real fighter when it comes to protecting its host plant. This bacterium uses a special nanoweapon to kill plant pathogens.

Our bacterial fighter carries a bow and arrow and is not afraid of using them to keep intruders off the plant. Pseudomonas putida actively shoots arrows together with lethal toxins into other bacteria to kill them. Many bacteria use this killer machine, called the type 6 secretion system. But interestingly, Pseudomonas putida seems to have a more efficient killing device than others.

Scientists proved that with a simple experiment. When different plant pathogens were growing inside plant leaves, the leaves got sick. However, when Pseudomonas putida was additionally living in the leaves, the plant leaves did not get sick.

Finally, the scientists let the plant pathogens grow together with a Pseudomonas putida bacterium that could not shoot its bow and arrow. Now, the plant leaves got sick again and the plants suffered from the plant pathogens.

These results show that Pseudomonas putida uses its bow and arrow to actively kill other harmful bacteria to protect plants. Even though the experiment was done in plant leaves, scientists are convinced that something similar happens in the root area of plants.

Bacteria as biocontrol agent to save our planet?

As soon as we better understand how exactly this plant warden protects its host from harmful bacteria, we could use Pseudomonas putida on a large scale. This would improve the health of plants so that they can grow more and better crops.

Hence, such a biocontrol agent would eventually help us have more food available for everyone.

The post Bacterial killer weapons as biocontrol to protect plants appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

Yes, also plants have a lot of delicious and nutritious food for bacteria.

And just as bacteria can be good or bad for us and our bodies, bacteria can be good or bad for plants. Some bacteria help plants grow while other bacteria harm plants. These are the so-called plant-pathogenic bacteria.

These plant-pathogenic bacteria can infect plant leaves, roots or fruit. You might have seen weird spots on plant leaves or on crops or opened a spoiled piece of fruit.

You can imagine that some bacteria developed some really smart ways to live in or on our bodies. Similarly, some bacteria found methods to live and thrive in and on plants and protect themselves from their immune attacks.

This means that plant-pathogenic bacteria learned to recognise that they landed on plants, enter them and cause diseases to use the plant’s nutrients. But before any of that happens, let’s have a look at where plant-pathogenic bacteria come from.

How do bacteria land on plants?

Bacteria are everywhere around us. They live on almost any surface – be it alive or not – but also in the air we breathe.

And some bacteria even live in clouds or on sand dust. Hence, through rain or sand storms, these bacteria are transported to new areas and arrive on new soils.

Other bacteria use animals or little bugs to get transported. When the transporting animal comes into contact with plants, it can brush off the hitchhiking bacteria.

When a bacterium comes into contact with a plant leaf, it uses special adhesion proteins to link to the plant surface. These proteins bind specifically to proteins on the plant.

After this happened, some plant-pathogenic bacteria like Xanthomonas form biofilms. These work like slimy houses that surround the bacteria and protect them from weather, sunshine or drought.

So, for now, the bacteria are safe inside their biofilm houses. In there, they can grow and reproduce and get ready for their big attacks.

How do bacteria know when they arrived on plants?

Before launching an attack to infect a plant, the bacterium needs to know that it actually IS on a plant. And for that, some bacteria learned to speak the language of plants.

Yes, also plants send out words to tell themselves and other plants what is going. These words are chemical molecules. And some bacteria developed special antennae or receptors on their surfaces to bind these molecules.

This means bacteria can listen to and understand what plants say. And this tells bacteria that they actually arrived on a plant.

However, one bacterium cannot launch a plant-destroying attack by itself. It needs to know that it has support from its sibling bacteria. And for that, bacteria also talk to each other.

So, bacteria also send out words in the form of chemicals. And they listen to their own words so that they know that they are not alone. Now, they can start their attacks to make their way into the plant.

But plants also know how to protect themselves: Plants can interfere with bacterial chatter. For that, plants produce chemicals that bind these bacterial words. Now, bacteria cannot talk to each other anymore and think they are on their own, so an attack is probably not worth it.

And then there is the plant microbiome that protects the plant from bad things like harmful bacteria. However, plant-pathogenic bacteria learned to fight off the plant protection shields.

How do plant-pathogenic bacteria make their way into plants?

Even though plants have special protection mechanisms to keep bacteria from entering, plant-pathogenic bacteria found clever ways around them. Just as pathogenic bacteria can fight off our immune defences and end up making us sick.

As one way to protect against pathogenic bacteria, plants cover their surfaces with a waxy layer. This is a physical barrier for bacteria while it also prevents the water inside the plant from evaporating.

However, the bacterium Pseudomonas syringae developed its very own bacterial superpower to circumvent this barrier: This plant pathogen produces ice crystals even above freezing temperatures.

These ice crystals harm the waxy layer, cut open the plant envelope and cause the so-called frost injury. With such an injury, the plant loses water and the bacteria can enter the plant through the open wound.

Other plant pathogens move specifically towards the stomata on the surface of plants. These are the gates that let gases like carbon dioxide enter the plant. And interestingly, these bacteria produce certain chemicals that keep these gates open so that the bacteria can enter the plant.

Once the bacteria are inside the plant, they can start their attacks. For this, they use special bacterial weapons that transport toxins into the plant. These toxins then disrupt the plant from functioning properly and make them sick.

So, just as pathogenic bacteria learned to bind to and enter our human bodies, plant-pathogenic bacteria developed mechanisms to specifically enter plant organs. Hence, one goal of researchers is to understand how bacteria achieve this. The idea is to create plants that are resistant to plant-pathogenic bacteria.

The post How plant-pathogenic bacteria understand plant language and make them sick appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

Even though about 70% of the Earth’s surface is covered by water, a majority of that water we cannot drink.

The water that is available to drink can also be contaminated with toxic chemicals or certain microorganisms that would sicken us.

But not all microbes are bad. In fact, many microbes are helping us save our planet. One way of doing this is by cleaning up our drinking water.

We don’t have enough clean freshwater

Everyone needs water to drink.

Humans can only drink freshwater, which makes up less than 3% of the world’s water supply. Freshwater is found in lakes, rivers, and streams. It is also locked away in the icecaps as glaciers, up in the atmosphere as water vapor, and deep in the soil as groundwater.

Of the small amount of freshwater easily accessible to us, we have used or contaminated much of that freshwater. Agricultural practices have diverted many sources of freshwater for animals and crops. Climate change and warmer temperatures cause farmers to use more freshwater resources as well. And global industrial practices can lead to toxic chemicals entering the environment and water.

This means that now we have less freshwater available to drink than ever.

We have learned ways to clean our drinking water, but this requires a lot of chemicals, energy, and money. Good thing microbes can help us decontaminate our drinking water in faster, easier, and cheaper ways.

Microbes clean water by filtering out bad bacteria

Drinking certain types of bacteria can make us sick. You have probably heard of outbreaks of E. coli or Salmonella leading to people being ill.

These microbes normally live in animals’ digestive tracks and are excreted in their wastes. They can enter the water system from runoff from farms, and ingesting them can make us really unwell. Luckily, microbes can help remove pathogenic bacteria from our water.

A simple method of water filtration includes having water flow over a bed of microbes and sand to remove any contaminates, called ‘slow sand filtration.’ At the top of the sand is a gelatinous layer of microbes, known as a biofilm. In such a biofilm live various bacteria, fungi, protozoa, archaea, and other aquatic microorganisms.

This layer is the so-called Schmutzdecke, which is German for “dirty layer.” As water flows over this biofilm, microbes in the Schmutzdecke trap and consume particles and pathogenic microbes. Every Schmutzdecke layer has a unique community of microbes based on the contaminants in the water. In this way, beneficial microbes remove harmful ones and decontaminate our drinking water.

Slow sand filters can purify away 90-99% of contaminating bacteria! The Schmutzdecke removes most of the fecal contaminating bacteria like E. coli. This system does not involve the use of chemical disinfectants, which can select possibly pathogenic bacteria that become resistant to decontamination efforts.

Also, the Schmutzdecke feeds on the microbes and organic matter found in the contaminated water. Hence, slow sand filters are a cheap and low-maintenance way to filter water in resource-limited areas throughout the world.

Microbes clean our drinking water by preventing bacterial build-up

The Schmutzdecke is an example of a community of microbes filtering water to remove pathogenic microbes and make the water safe to drink. But decontaminating water does not always need a whole community of microbes. Sometimes just one part of a microbe is enough to clean the water. In fact, researchers have found a protein from bacteria that can help stop bacterial contamination.

Pathogenic bacteria like Pseudomonas aeruginosa can contaminate water lines that carry water to homes and businesses. To let other P. aeruginosa know they have found a place to stay, bacterial cells send messages to each other in the form of chemical molecules. This communication system, called quorum sensing, allows bacteria to ‘sense’ the number of other bacteria, (a ‘quorum’) around them.

If enough P. aeruginosa cells grow in the same area and send the same message, they will start to form a biofilm. Just like the Schmutzdecke, biofilms act as a gelatinous layer and are difficult to break up. That’s where that special bacterial protein comes in to help stop biofilm formation.

This protein is called AiiA_DH82 and comes from the deep-sea bacterium Bacillus velezensis (DH82 strain). AiiADH82 binds and degrades the chemical messages that bacteria use to communicate with each other.

Without those chemical signals, bacteria do not know they should start forming a biofilm. Adding AiiA_DH82 to P. aeruginosa cultures decreased bacterial growth and significantly inhibited biofilm formation in P. aeruginosa-contaminated water. Scientists hope one day to apply the AiiA_DH82 protein to water lines and drinking fountains. In these, bacteria could group to reduce bacterial contamination and keep our drinking water safe.

Microbes clean our drinking water

People everywhere need clean water for cooking, cleaning, and drinking. However, clean drinking water is a limited resource. Toxic chemicals or pathogenic microbes can pollute our water. Current methods to purify water cost a lot of energy and money.

We are fortunate that microbes are here to help us clean up our water and our environment. As the global population increases, using microbes to clean drinking water is a cheaper, sustainable and more environmentally friendly way to produce the needed levels of clean water. A great example of how microbes are making our world better.

Along with microbes, we can save the planet!

Take away messages from this week’s article:

• Clean drinking water is a limited and necessary resource for everyone on the planet
• Microbes can clean polluted drinking water by reducing the growth of pathogenic bacteria
• Microbial decontamination of drinking water is a sustainable and inexpensive way to provide clean drinking water to our increasing global population

The post How Microbes Clean our Drinking Water appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

So, yes, also bacteria are always trying to find their siblings and communicate with them. And once they know they are not alone, they start reacting as a group.

Some bacteria start building biofilms – houses to keep the bacteria inside safe. Others like to talk to each other and produce goodies that everyone can enjoy. And other bacteria even form multicellular organisms with new superpowers.

Yet, some bacterial species like to move only in groups. Researchers call this bacterial movement twitching.

Bacteria can only twitch and move in groups when they have so-called twitching pili. Not all bacteria have these types of pili and – unfortunately for us – many bacterial pathogens produce them. And these bacteria use their pili to infect us and make us sick.

So, let’s have a look at what these bacterial pili are.

What are bacterial pili?

Bacterial pili look like little hair that grow out of bacterial cells.

This hair is anchored to the bacterial cell envelope and can be attached to any site of the bacterial surface. Some bacteria only have on pilus, others have two pili at opposite ends and some bacteria even produce bundles of pili that work together.

The pilus hair is a helix of an endless number of the same protein: the so-called pilin protein. This pilin works like a perfect puzzle piece: Each end of the pilin fits the next pilin piece. Like this, endless pilin puzzle pieces attach to each other in a circular manner and form a stable hair-like helix structure.

But not to lose their precious hair, bacteria need to attach the pilus to their cell envelope. For this, bacteria have a huge anchoring complex on the inside of their cell envelope. And this anchor holds the pilus at the correct location.

To make this pilus dynamic, bacteria link the anchor to a tiny motor. This motor has a ring shape that surrounds the anchor and thus the hair. And bacteria need this motor for the actual moving process.

How do bacteria move with pili?

This circular motor on the inside of the cell envelope has two main functions: to extend and retract the pilus. Endless circles of extending the pilus, attaching to a surface and retracting the pilus allow bacteria to move.

To extend or lengthen the pilus hair, the motor (orange) binds the pilin proteins inside the bacterium (grey circles) and transports them outside of the cell. This costs energy, which is why bacteria need this little motor. Hence, by adding more pilin protein to the pilus from the inside, the pilus hair (grey) extends towards the outside.

On the outside at the end of the pilus hair sits a protein (green) that can stick to surfaces. When this protein attaches to a surface, the motor on the inside of the bacterium changes its direction. Instead of adding pilins to the pilus and lengthening the hair, the motor takes pilins off the pilus and thus shortens the hair.

Now, the bacterium is attached to a surface while the pilus shortens. Like this, the bacterium pulls itself towards that surface.

This means that the attachment to the surface has to be so strong, that it can pull the bacterial cell towards this new location. This works like the bacterial superglue that some bacteria use to grow and survive.

What is the function of bacterial pili?

Bacterial pili can attach to all sorts of surfaces. Mainly, bacteria use this movement in environments of low water or on wet surfaces like human tissue.

For example, a bacterium can connect with its pilus to another bacterial cell. Now, when the bacterium retracts the pilus, it pulls the other bacterium closer. Like this, bacteria can form aggregates which helps them in the first steps of settling down and building biofilm houses.

Also, when several bacteria stick together and form bigger groups, they can move along a surface in a coordinated manner. This helps bacteria conquer new environments quicker and find new resources. For example, the bacterium Pseudomonas aeruginosa can reach out in swarms trying to find more space and new places to live in.

Interestingly, multicellular Myxobacteria move as huge cell aggregates to attack their prey. These bacteria use their twitching pili to glide along a surface, attach to a prey and pull the whole aggregate towards the prey. Like this, the Myxobacteria quickly run over their prey so it does not stand a chance.

However, bacterial pathogens also use pili to infect us. The bacterium Neisseria gonorrhoeae can attach its pilus to human epithelial and endothelial cells. When the bacterium then retracts the pilus, it pulls itself closer to the cell and attaches to it more tightly. Now, it can infect the cell and eventually the host.

But not all is lost with bacteria and their pili. Currently, researchers are trying to better understand how bacteria use their pili and how this machine works mechanistically. They will then try to find drugs that inhibit the pili. This could be an alternative way to inhibit bacterial pathogens and maybe even drug-resistant bacteria.

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Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

And with an increasing global population, it will be important to find ways to increase the world’s food supply in sustainable ways.

Adding microbial communities, called biofertilizers, to soil can increase crop yield and plant health all without adding any toxic chemicals.

Lucky for us that microbes once again can help save our planet by addressing our global food crisis.

A global challenge

While the global population grows to almost 8 billion people, the land for agriculture remains limited. One way to meet this growing challenge is to increase the quantity of food produced on the same amount of land.

In the past, farmers added expensive chemical fertilizers to their crops. These meant to increase important soil nutrients – specifically nitrogen and phosphorus – and help the plants produce more food.

Unfortunately, these chemicals enter and pollute nearby water systems, harming our health as well as the health of our planet. Plus, producing these chemical fertilizers releases greenhouse gases that add to climate change.

One sustainable method to increase crop production is to add microbial communities to agricultural plants; so-called microbial biofertilizers.

Microbes as biofertilizers

These biofertilizers are soil microorganisms that provide nutrients, stimulate growth, and improve plant health. Also, biofertilizers are more sustainable, less toxic, and cheaper than traditional fertilizers.

Here, we will look at what biofertilizers actually do and how these microbes work for the plants.

Helping plants get nutrients

All living organisms need nitrogen, but not all nitrogen found in the soil is in a useable form. In fact, nitrogen is a major limiting nutrient for plants because most nitrogen in the soil is in a form that plants cannot use.

Hence, microorganisms first need to “fix” the nitrogen and then convert it into a usable form. For this, bacteria make an enzyme called nitrogenase that converts nitrogen from atmospheric nitrogen (N₂) to ammonia (NH₃). Now, plants can absorb this nitrogen form and use it for energy and growth.

Some plants have evolved to work with bacteria to make it easier for them to absorb the fixed nitrogen. For example, the roots of certain legume plants include special root nodules. In these live nitrogen-fixing bacteria called Rhizobia. When chickpea seeds were grown together with these bacteria, their yield increased 250%. Also, adding Bradyrhizobium species to mung bean plants promoted plant growth and yield and plants had a higher tolerance to insecticides.

Cyanobacteria also help plants fix nitrogen. When wheat plants grew together with cyanobacteria species Calothrix ghosei, Hapalosiphon intricatus, and Nostoc species, they grew higher and had more grain. Additionally, co-cultivation with Nostoc or Anabaena species resulted in increased root length and wheat plant nitrogen levels. Cyanobacteria are important nitrogen-fixing bacteria in aquatic environments too, especially for rice production.

Helping plants grow

Besides nitrogen, soil bacteria can provide plants with many nutrients, vitamins, and plant hormones. These are called phytohormones. Phytohormones promote plant growth by acting as signaling molecules to regulate plant metabolism and stress response.

When Rhizobia bacteria grew together with the mustard plant Brassica juncea and produced phytohormones, the plants grew better. Also, in corn (maize), inoculation with Azospirillum brasilense resulted in increased plant growth correlated with elevated phytohormone levels.

Over 80% of Rhizobia bacteria produce the major phytohormone indole-3-acetic acid (IAA). This phytohormone regulates plant growth, cell differentiation, and stress response. Thus, when bacteria secrete indole-3-acetic acid, it promotes root growth. This helps plants take up nutrients better.

In addition to a single bacterial species, communities of microbes help plants stay healthy and grow. Archaea, bacteria and fungi all associate with the roots of plants and synergistically provide nutrients to the plant. Researchers are studying these communities to understand important microbial interactions. The aim is to design microbial communities specific to each crop that promote higher crop production in the future. Just think, one day you could order a biofertilizer optimized for your unique climate, soil, and plant!

Fighting plant enemies

Not only do microbes provide their hosts with nutrients to promote growth, they also protect their hosts from deadly pathogens. Especially fungal pathogens are known enemies that threaten plants.

For example, Pseudomonas and Bacillus strains release toxic chemicals such as hydrogen cyanide to inhibit fungi that infect coffee plants. Other Bacillus strains produce antifungal molecules and simultaneously increase corn (maize) seedling growth. The bacterium Ochrobactrum anthropi TRS‐2 can fight fungi, and application of this bacterium on tea plants decreased brown root rot caused by the fungi Phellinus noxius.

Some bacteria even produce biofilms on the roots of plants as a barrier against invading fungal pathogens!

Agricultural crops are also prone to infection by nematodes, commonly called roundworms. Nematophagous bacteria can deter nematode growth by sending out toxins, and competing for nutrients. For example, Pasteuria penetransbacteria infects nematodes, while Pseudomonas strains can produce antibiotics against nematodes that infect potato plants. No matter the pathogen, soil bacteria have evolved ways to promote and protect their host plant.

Microbial biofertilizers assist our global challenge

As the world’s population increases, we will need sustainable and inexpensive ways to increase agricultural production. Just as microbes add nutrients and flavors to our meals, bacteria can nourish our crops as well. Plus, biofertilizers are a greener, healthier, and less expensive alternative to traditional chemical fertilizers.

So, next time you go out into your garden, think about adding some biofertilizers like compost or manure instead of chemicals to help your fruits and vegetables grow.

Along with bacteria, we can help save the planet!

Take away messages from this week’s article:

• The increasing human population is creating a global food crisis 
• Microbes can act as biofertilizers by providing important nutrients and helping promote plant growth
• Microbial biofertilizers are a sustainable and inexpensive way to increase global food production

The post Microbes as biofertilizers appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

Some microbes come to make their hosts sick. Other microbes are there to help and protect them.

This is a story of both types of microbes and an unusual host: amphibians.

Yes, also frogs and salamanders and other amphibians carry microbes on their skins.

And some of these microbes mean to kill the animals. But, luckily, the animals are protected by helpful bacteria that produce colourful antibiotics.

Read on to find out how bacteria and fungi do not get along on the skin of amphibians. We will also explore how bacteria protect amphibians from extinction.

About fungi that infect the skins of their hosts

Many frogs, salamanders and other amphibians have gone extinct because of a deadly fungal infection. And it seems that many more animals are already infected and sick from that same pathogen.

The bad guys? The two fungal species Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans. They cause a deadly skin disease on frogs and other exotic amphibians.

Similarly, the fungus Trichophyton rubrum can infect our skin and hair. This pathogen causes a disease that you may know as ringworm or athlete’s foot. Typically, you can see such a fungal infection as a red, itchy and circular rash.

But luckily there is a new weapon around to keep these fungal intruders at bay: Bacteria that get rid of the fungus to protect their hosts.

Bacteria produce colourful antibiotics…

Few microbes can grow and thrive on the gloomy skin of frogs or salamanders. One such microbe is the bacterium Janthinobacterium lividum.

This bacterium has an interesting taste for food. It eats the released skin when the amphibians shed their skin. And it also really likes the mucus on the surface of the amphibians.

As a thank you for the good meal, the bacteria help the amphibians in the fight against the deadly fungus.

How?

Generally, bacteria produce antibiotics to get rid of annoying competitors. For example, Janthinobacterium produces the antibiotic violacein, which has a dark violet colour. This antibiotic also kills the fungi that make the frogs sick.

It is still unclear to researchers, how Janthinobacterium transports the antibiotic to the fungus. We already know that the bacterium Chromobacterium violaceum produces membrane bubbles filled with violacein. And that it throws these purple bubbles at its competitors. So, one idea is that Janthinobacterium uses a similar strategy and throws violacein bubbles at the fungus.

Also, when Janthinobacterium grows on the skin of frogs, it triggers the frog to produce more anti-fungal molecules. These molecules kill the fungus and other pathogenic bacteria that are dangerous to the frog.

… and protect them from deadly fungi

Janthinobacterium is not the only bacterium that produces colourful antibiotics to protect its host.

You might have seen red dots in your shower every once in a while. These come from the bacterium Serratia marcescens which makes a red antibiotic. Interestingly, this bacterium can also live on the skins of amphibians. And here, the red antibiotic also protects from deadly fungi.

Other bacteria, like allrounder Pseudomonas, also live on the skins of some amphibians. And these bacteria produce many different antifungals to protect their hosts.

Hence, it looks as if the right skin bacteria protect frogs and salamanders from deadly fungi. And these bacteria keep throwing around colourful bubbles filled with antibiotics – sounds like a bacterial festival to celebrate their hosts?

Colourful bacterial antibiotics to save amphibians?

Now, researchers are trying to save amphibians from the deadly fungus with a process called bioaugmentation. With this strategy, researchers introduce special bacterial communities to the environment. And they hope that the bacteria will jump over to different amphibians.

Bacteria like Janthinobacterium then hopefully establish stable communities on the skins of amphibians and protect them from fungal infections. And let’s hope that these bacterial parties will save more frog species from extinction!

The post Bacteria produce colourful antibiotics to protect frogs appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

What’s your New Year’s resolution?

Are you trying to eat healthier by eating microbially fermented foods full of nutrients?

Or do you want to be more friendly to the environment by using green bio-plastics?

Keeping this planet green and healthy is a great New Year’s resolution. And one that microbes can help us with.

For example, microbes can degrade and remove the toxic pollution that we have produced. They do that in a process called microbial bioremediation.

Just another way microbes help save the planet.

Our pollution problem

Oil spills, chemical leaks, industrial discharge. We hear about these types of toxic pollution all too often. Increased urbanization, industrialization, and utilization of natural resources pollute and contaminate the environment, which is unhealthy to humans and the planet.

Unfortunately, it is much easier to spill oil or leak a chemical than it is to clean it up. Especially, if the pollution compound is toxic. Cleaning up these types of pollution is costly and may be harmful to the environment.

Why microbial bioremediation?

How lucky are we that microbes can make cleaning up these messes easier? Our microbial friends can degrade and detoxify environmental pollution. This process is called microbial bioremediation.

Microbes absorb or eat toxic pollutants. They then break them down into harmless compounds. This process is a more cost-effective and environmentally friendly method to clean up toxic pollution.

Cleaning up after oil spills

We use petroleum oil in multiple ways, from powering our cars and homes to manufacturing plastics and medicines. Most petroleum oil is found deep in the ground and it takes much energy and expense to pump the oil to the surface.

Unfortunately, sometimes we spill some of that oil. The 2010 Deepwater Horizon oil spill in the Gulf of Mexico is the largest known oil spill and it released 4.9 million barrels of oil into the ocean! What an environmental disaster!

Petroleum oil is a type of fossil fuel full of different organic compounds called hydrocarbons. They contain hydrogen (“hydro”) and carbon molecules. For us humans, ingesting these compounds would be deadly.

So, when that oil disaster happened in 2010, microbiologists and their microbial friends came to the rescue. Luckily, some microbes have special enzymes that recognize and degrade hydrocarbons into smaller compounds. They then use these smaller compounds to grow and reproduce.

Microbes eating hydrocarbons

Many bacteria can degrade petroleum oil. For example, a special Pseudomonas aeruginosa strain can break down oil droplets and grow on petroleum oil with nothing else to eat.

Additional Pseudomonas strains as well as Bacillus subtilis strains are capable of eating hydrocarbons too.

Researchers have also found communities of bacteria working together to degrade and remove petroleum oil. And they are now developing ways to implement these bacterial communities for cleaning up oil spills from contaminated soil and water.

Fungi are also used for bioremediation, called mycoremediation (“myco” refers to fungus). Researchers discovered 16 different fungi species that degrade hydrocarbons in crude oil.

The superhero fungi Trichoderma viridae, Aspergillus flavus and Varicosporium elodeae have the highest rates of degradation. And the Exophiala xenobiotica fungus degrades a hydrocarbon compound found in car gasoline.

Scientists are working to use these microbes in larger bioremediation projects as greener and cheaper ways to clean up oil spills.

Detoxifying heavy metal contamination

Oil spills are not the only toxic pollution generated by us humans. Through many industrial processes, we release heavy metals such as copper, lead, and mercury. Once in the environment, heavy metals can enter the food supply and accumulate in our bodies. Unfortunately, these can lead to health issues and sometimes even cancer.

Removing heavy metals from contaminated water and soils is costly, time-consuming, and ineffective at low concentrations of the contaminate. Good thing microbes can make this process faster and more efficient.

They help remove heavy metals through a process called biosorption. Microbial cell walls are made up of proteins and sugars with a slightly negative charge. Metals have a positive charge.

Thus, microbes can attract and bind these toxic metals. This means microbes act like magnets and pull out the toxic metals from the environment.

Many microbes can absorb a variety of metals. But these microbes also need to protect themselves from toxic metals. For this, they have special enzymes that transform the metals into less toxic forms inside the cell.

However, even microbes cannot survive if the concentration of toxic metals is too high. So, it is important to find microbes that can tolerate high levels of metals and detoxify them. Scientists have discovered some Aspergillus species that can survive high concentrations of copper and nickel metals.

These microbes must also be superb at decontaminating. One rockstar strain of Aspergillus flavus removed over 97% of mercury contamination. And two Pseudomonas species strains removed over 75% of copper, lead, and zinc contamination. Microbes like these will be vital for removing future heavy metal contamination.

Microbes creating a cleaner future

There are a lot of toxic materials in our world. As human activity increases, so too does the amount of toxic pollution we create on our planet. The results of oil spills and heavy metal contamination hurt our human health as well as the health of our planet.

Luckily, microbes have evolved ways to survive and detoxify these types of pollution. Our microbial friends can help remove these toxins and clean up messes created by us. By harnessing the power of microbes, bioremediation projects address our pollution problem and work to make our planet a greener and healthier place. And that’s a great New Year’s resolution!

Along with microbes, we can save the planet!

Take away messages from this week’s article:

• Toxic pollution is a major problem for the health of humans and our planet
• Microbes can detoxify environmental pollution in a process called microbial bioremediation
• Microbial bioremediation is an environmentally friendly and relatively inexpensive way to clean up toxic pollution

The post Microbial bioremediation: microbes cleaning-up our toxic messes appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

They need food, more space and are just annoyed by intruding competitors.

So, when they decide to bring out the big (tiny) killer machines, they aim to hurt their opponents badly.

One of these killer weapons is the so-called type 6 secretion system. It looks like a crossbow that sits within a bacterial cell waiting to fire lethal arrows.

And these arrows are the real deal in this killer weapon. They punch holes into the membrane of the opposing microbes and carry lethal toxins into the cell.

Here, we will focus on these arrows and how they work.

Bacteria fire lethal spikes to kill

This type 6 secretion system crossbow is made up of two parts. One part – the base – stays within the firing bacterium. You can understand this as a stem inside the bacterium.

On top of this stem sits the second part – the arrow. This arrow is ready to be fired and will actually leave the bacterium. It consists of three parts, that you can also see in the picture below:

Such an arrow has a long thin spike (red) that is connected to the stem (black). Onto this spike, different toxins (purple) are glued and hang around the arrow. On the top of the spike, the arrow has a pointy tip (pink) that pokes the membrane of the prey bacterium.

So, when bacteria shoot these type 6 secretion system arrows into other bacteria, they shoot all these different parts: the tips, the spikes and the toxins. And the toxins are what ultimately kill the prey bacteria.

Now, bacteria actually have several different proteins for these parts of the arrow lying around in their cells. And for long, it was not clear how bacteria decide how to assemble such an arrow. So, different studies looked at these different parts and how they interact with each other to better understand how bacteria build their lethal arrows.

Let’s start at the top.

A master hat protein decides for the assembly of the arrow

The protein at the very end of the arrow is called the PAAR protein. It is very sharp and has the shape of a hat. The bacterium uses this pointy end to punch a hole into the prey bacterium’s membrane.

Our bacterium of interest, Pseudomonas aeruginosa, contains seven of these hat PAAR proteins and ten different spike proteins. Generally, one PAAR protein sits on the top of one arrow spike while the spike is actually made of three VgrG proteins. So, one study looked at which of these pointy PAAR proteins belongs to which arrow spike.

To do this, researchers made different versions of the same bacterium – so-called mutants. These did not have certain hat proteins anymore so they could not kill their opponents that efficiently anymore. Also, these bacteria were unable to fire their arrows in the first place.

With these experiments, the researchers could then identify the different hat-spike pairs in Pseudomonas aeruginosa. They also learned that the PAAR protein actually determines which arrow the bacterium will fire next.

Lethal toxins stick to the spike protein

Next, the spike proteins are incredibly important since they carry the different toxins into the prey cell. And for a toxin to stick to a spike, they both have specific patches. And these patches are unique for each spike-toxin pair.

Researchers showed this by swapping the patches for the toxins between different spike proteins. They looked at the spikes G4b and G5 in the bacterium Pseudomonas aeruginosa. Usually, the G4b spike has a patch for the toxin A and the G5 spike has a patch for the toxin B.

So, Pseudomonas aeruginosa uses spike G4b to kill with toxin A and if it feels like killing with toxin B, it shoots spike G5.

The researchers then interchanged those patches. Now the G4b spike had the patch for toxin B and the G5 spike the patch for toxin A. And they showed that G4b could not fire toxin A anymore and G5 could not fire toxin B anymore.

Instead, Pseudomonas aeruginosa now fired toxin B with the G4b spike and toxin A with the G5 spike.

This helped the scientists better understand how bacteria shoot their toxins out of the cell. Another study then looked at how this patch works and how exactly the toxin is glued to the type 6 secretion system spike.

Bacteria can (sometimes!) fire spikes with random stuff

Other studies then look at whether bacteria could use random toxins and glue them to the type 6 secretion system spikes. This idea might give us tools to shoot whatever we want with this killer machine. However, in practice, it is a bit tricky.

So, researchers tried different versions of this concept in the bacterium Pseudomonas aeruginosa.

First, they took a toxin from the same bacterium but from a different part to the arrow. Instead, they glued this toxin to the spike of the bacterium and looked at whether it would fire an arrow with this toxin. Indeed, the bacterium could now shoot this new arrow into other bacteria, even though it was not as efficiently.

In a second try, they tried to patch a toxin from a different bacterium to the spike in Pseudomonas aeruginosa. This new arrow was not able to shoot that toxin into other bacteria. So, there are some limitations about how the spikes and their patches work to make toxins stick.

Understanding bacteria and their spikes for new strategies

This bacterial nanoweapon is an incredibly handy tool for bacteria. They can deliver lethal proteins into almost any organism. If we managed to understand this weapon better, we might be able to modify it and deliver whatever we want with this.

We might be able to transport therapeutics, drugs or even anti-cancerous agents. But until we’re there, still quite a bit of research is needed.

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Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world