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.

The post About twitching bacteria and their pili appeared first on Bacterialworld.
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

For a virus to survive, it needs another living organism. Viruses infect any organism that has its own metabolism: animals, humans, fungi or even bacteria.

But none of these organisms likes being infected by a virus. It makes them sick.

Therefore, each organism developed its own way to fight off viruses. For example, you have your immune system that is trying to protect you from bad viruses.

And so do bacteria.

The bacterial immune system is not as complex and sophisticated as ours. But still, bacteria developed several mechanisms to fight off viruses and protect the community.

Here, we will look at the different ways of how bacteria become immune to viruses.

How a virus infects a bacterium

First, let’s have a look at how a virus infects a bacterium and reproduces.

Most viruses can only infect one specific bacterium. This is because each bacterium has a slightly different coat around its cell. And viruses recognise specific components on the outside of these coats.

When a virus binds to such a specific component on the bacterium, it cuts a little hole into the coat. Now, the virus can inject its genome through the hole into the bacterium.

The bacterium recognises the genome and starts producing virus particles from the viral genome.

After the bacterium produced many virus particles and they assembled into full viruses, the bacterium bursts and dies. This releases the produced viruses from the bacterium. The viruses now spread and infect other bacteria and the cycle begins again.

How bacteria fight off viruses

Each infected bacterium is a risk to the whole bacterial community. An infected bacterium produces many viruses that can infect many more bacteria in a community.

This is why, bacteria developed several ways to defend themselves against viruses. And many bacteria use different modes of defence against viral attacks.

So, what does a bacterium do to defend itself against viruses?

Preventing the virus from binding

The first line of defence against a viral intruder is to prevent a virus from binding to the coat of the bacterium.

A virus recognises and binds to a specific component on the coat of the bacterium. So, a bacterium can mutate this component and change it to prevent the virus from binding.

Another option is for the bacterium to produce biofilm. Biofilm is a slime that covers the bacterium and all its bacterial friends and protects them from harmful components like antibiotics, chemicals and viruses.

Sending out bacterial decoys

A really smart way of bacteria is to mislead viruses. Bacteria can produce bubbles from their coats that still contain the specific components that viruses bind to.

A virus can bind to these specific components and infect the bubbles. But the bubbles do not contain machines to produce viruses. Therefore, the bacterium does not get infected and will not produce any viruses.

Smart bacteria!

Destroying what is coming in

After a virus attached to a bacterium, the actual infection starts when a virus injects its genome into the bacterium. This can be DNA or RNA.

Some of our little bacterial friends developed smart devices to recognise any DNA or RNA that does not belong to the bacteria. When a bacterium “sees” viral DNA or RNA inside the cell, it activates huge destruction machineries. These work like scissors and cut viral DNA or RNA into tiny pieces to make them non-functional. Now, the bacterium will not even start producing viral components.

Many bacteria have different kinds of anti-viral scissors. And each one machinery recognises and cuts one specific piece of viral DNA or RNA.

The interesting thing is that bacteria use these scissors also to learn to fight new viruses. With the so-called CRISPR-Cas system, a bacterium learns to recognise new pieces of viral DNA or RNA when it first “sees” it. The next time the bacterium is infected with that same virus, it already knows how to fight it.

This is similar to how our body learns to fight a virus after we gave it a vaccine. We show our bodies what a certain virus looks like and it can develop the right weapons against it. The next time this virus attacks our body, we already have powerful weapons to fight the intruding virus.

Inhibiting the viral genome

If a virus was indeed successful and injected its DNA or RNA into a bacterium, some bacteria can still handle this. In this case, the bacterium produces specific molecules that bind to the viral DNA and prevent it from functioning properly.

This prevents the bacterium from producing viral components from the viral genome.

If nothing else works there is still one way out

Imagine, a virus was indeed lucky and managed to inject its DNA or RNA into a bacterium. And then imagine, the bacterium did not destroy the viral DNA or RNA and it produced viral components.

Now, the bacterium needs to prevent that these particles assemble into full viruses so that it does not kill the bacterium and spread into the surrounding.

In this case, bacteria have one last line of defence. And this defence mechanism is a truly altruistic weapon: Kill itself to protect the others.

Yes, an infected bacterium is prepared to sacrifice itself so that the whole community survives.

Just before virus particles assemble to full viruses, a bacterium can activate a suicidal mechanism. Like this, no full viruses will be released into the surrounding. No other bacteria will get infected with this virus. Everyone is safe.

Because bacterial suicide is such a drastic mechanism, bacteria only activate it after all other defence mechanisms failed.

Multiple lines of defence to protect the whole community

As you can see, bacteria developed several ways to protect themselves from viral attacks.

Don’t forget that also viruses mutate and can become resistant to any of these mechanisms. So it is a constant microscopic war between all the different microbial players.

Interestingly, not one bacterium has all the described mechanisms and is perfectly protected. But each bacterium has a few of these anti-viral weapons. Therefore, by working together, the whole bacterial community knows how to fight off most viruses. This teamwork can indeed protect the whole community.

How much we can learn from our microbial friends about how to fight off nasty viruses :)

The post How bacteria fight off viruses appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

Microbes are necessary for many of our favorite foods, such as bread, cheese, and chocolate, and the beverages we wash them down with, like beer and wine!

With the holidays fast approaching, let’s look at how microbes play a central role in the holiday menu.

Microbes Help Make What You Eat

Microbes are everywhere, including your food. Not only known for food spoilage, but some microbes also help preserve and add flavor to foods. In a process called microbial fermentation, microbes convert sugars in foods into different compounds, such as alcohols or acids.

Bread

Microbes are also necessary to produce our foods. Many holiday meals include special bread that depends on the microorganism yeast. Bread making usually uses the yeast Saccharomyces cerevisiae to eat the sugar in bread dough to make carbon dioxide (CO₂) bubbles that expand and rise the bread.

Microbes can also give bread some of its flavors. Sourdough bread gained popularity during the COVID-19 pandemic because of the ease of culturing the sourdough yeast, called a starter. Sourdough’s unique flavor comes from the starter’s mixture of yeast and lactic acid bacteria. These Lactobacillus bacteria ferment and produce lactic acid, which gives sourdough that ‘sour’ taste and helps to prevent the bread from going stale.

Cheese

After making your holiday loaf, you will need to put something on those slices. Cheese is one of my favorite bread sidekicks and appears on many holiday menus.

Like bread, cheese requires a starter culture of bacteria to convert the sugars in the milk into acids such as lactic acid. Next, during cheese ‘ripening,’ added secondary microbial cultures give each cheese its unique flavor and texture. These secondary cultures can include bacteria, yeast, or even mold, like in the case of blue cheese, and all help produce those much-loved flavors.

Microbes Help Make What You Drink

Bread and cheese are delicious, but they are even better when paired with a nice beverage. Luckily, microbes help make some delicious drinks as well.

Beer

One of the oldest microbially-made drinks is beer. Beer dates back over 5,000 years, though recent evidence suggests people first fermented beer over 13,000 years ago! Like today’s beer, ancient cultures ground grains in large vats and exposed them to yeast that would eat the sugars and ferment it into alcohol and CO₂.

This process adds flavor to the drink as well as many nutrients and essential B vitamins. Most importantly, the alcohol kills possible contaminates and makes the water safe to consume. Adding hops aids its antimicrobial activity by inhibiting Gram-positive bacteria.

While the first beers relied on wild yeast strains naturally found in the air and dust, today’s brewers add specific strains of yeast for desired alcohol and flavor profiles. Or they might add bacteria. Many Belgian ales have Brettanomyces yeasts to produce their notable sour flavor, while German Berliner Weisse beers are fermented by Saccharomyces cerevisiae and Lactobacillus bacteria.

Wine

If beer is not your thing, possibly you will want a nice glass of wine this holiday season. You can thank microbes for that too.

Wine is produced when yeast ferment grapes, yielding both alcohol and CO₂ like for beer. Microbes are important not only for fermenting grapes, but specific yeast, fungi, and bacteria are important for keeping grapes healthy.

Additionally, some fungi are critical to produce specific wines. Botrytis cinerea is a fungus that helps to dry out and concentrate the sugars of a grape through a so-called ‘noble rot’. These grapes produce a sweet dessert wine called a botrytized wine. However, if Botrytis cinerea infects grapes during moist conditions, this ‘gray rot’ destroys the grape crop. Thus, having the right microbiome is important for agriculture just as it is for humans.

Kombucha

If you don’t like beer or wine, you can always try kombucha. This non-alcoholic beverage is produced from acetic acid bacteria and yeasts called a “tea fungus” that ferment tea. The bacteria and yeasts live symbiotically in a biofilm clump called a scoby (“symbiotic culture of bacteria and yeast”). Here, microbes work together to convert the sugars into acids that give the tea a nice tart flavor.

And don’t forget dessert!

Cakes, candies, and cookies are all staples of the holidays. These sweet treats would not be the same without microbes to add flavor and rise.

My favorite sweet, chocolate, comes from cacao beans that are initially fermented for many days by wild yeasts and bacteria. This process breaks down the beans and leads to the production of those oh so yummy chocolate flavors. Just another reason to love microbes!

Welcome Microbes to Your Next Meal

Microbes are vital for giving us so many of the foods and flavors we love. From foods like bread, cheese, and chocolate or drinks like beer, wine or kombucha, microbial fermentation plays an important role in many of our favorite dishes. Fermented foods give us flavors, vitamins, and additional food preservation.

These foods can also help maintain healthy digestive systems. Yoghurt, which is another fermented milk product, contains beneficial bacteria that can help maintain a balanced microbiome.

Not only do microbes help save the planet, but they also save our meals and our health too. So this holiday season, remember to incorporate microbial dishes into your menu.

The post Microbially Powered Meals: How microbes help make our foods appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

They have killer weapons to deliver lethal toxins into other microbes.

And by killing their surrounding competitors, they make space for themselves.

Like this, they conquer new places and environments wherever they go.

But some bacteria are even more sneaky than that. They don’t kill bacteria directly. Rather, they destroy the houses that bacteria live in.

This leaves the prey exposed to the harsh environment. And the attacker can claim the now available space.

Where do these kinds of battles happen? According to researchers, they might even happen in or on our bodies.

Let’s have a look at how bacteria fight by destroying each other’s houses.

Bacteria build biofilm houses

Just like us, when bacteria feel comfortable in a place, they start building houses to settle down. They grow within these houses, multiply, invite their neighbours and become social.

A happy life.

One bacterium that is a master in biofilm house building is the Escherichia coli UPEC. This pathogenic bacterium can grow in the urinary tracts of people and cause nasty bladder infections.

In bladders or on catheters, UPEC can also build biofilms. Here, it wraps itself into a thick layer of slime to protect itself from the surrounding. In this biofilm house, no molecules, like antibiotics, or other bacteria can harm UPEC.

It seems to be protected from almost any attack.

Almost.

Bacteria fight microscopic battles

Now, researchers found that even UPEC has bacterial competitors. These live in similar places like UPEC, so they already know each other.

That’s why UPEC’s opponents came up with a special strategy to make UPEC miserable. They learned to destroy UPEC’s biofilm houses. This is meant to weaken UPEC so that other antibacterial factors now have an effect.

What does that mean?

The UPEC bacterium is pretty nasty for us since we need high doses of antibiotics to get rid of it. And we know that taking antibiotics is not a good thing. So, researchers are looking for new weapons to fight this bacterium.

The idea is that if we understand how other bacteria fight UPEC, we could learn from them. Maybe we could work out similar ways to fight UPEC.

Bacteria fight by destroying biofilms

Researchers found that some bacteria produce compounds that stop UPEC from producing biofilm. One of these attackers is Salmonella enterica Typhimurium. This bacterium even developed a strategy to exclude UPEC from its own biofilm house.

Researchers showed that Salmonella produces a toxic sugar that inhibits UPEC from forming a biofilm. Like this, Salmonella directly stops UPEC from colonising new spaces.

Another bacterium, Lactobacillus acidophilus, produces a similar sugar. Researchers showed that this toxin also stops UPEC from building a biofilm.

However, it is still not clear how these sugars exactly work to inhibit biofilm production.

Bacteria fight by producing biofilm

The researchers also found that Salmonella and UPEC did not grow well together. Separated from each other, they were happy. Together, they were just fighting.

But something else was interesting: In a mixed biofilm, Salmonella managed to outgrow UPEC. It was growing faster and produced a lot more biofilm than UPEC.

This could mean that Salmonella tries to suffocate UPEC with biofilm. The researchers thought that the Salmonella bacteria grow on top of the biofilm, where they have more oxygen. Like this, the UPEC bacteria would be buried by all this biofilm slime and get less oxygen and eventually die.

Surely not a nice way to go!

What can we learn from these bacterial battles?

This study told us a lot about how bacteria live together and fight each other. Researchers are constantly looking for new ways to kill those bacteria that we cannot fight with antibiotics anymore. Based on this, we can even use bacteria as biocontrol agents to fight other pathogenic bacteria.

For example, Salmonella produces a compound that stops UPEC from forming biofilms. If we better understand how this toxin works, we might have a new method to inhibit bacteria from colonising surfaces in hospitals.

Also, UPEC and Salmonella are pathogenic bacteria and they can survive in wastewater even after cleaning. This is a major health issue. Hence, finding new ways to fight these bacteria will help us live healthier and safer.

This study was a small step in the grand fight against superbug bacteria. But those small steps are often the most important ones.

The post Bacteria fight by destroying each other’s biofilm houses appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

Everywhere in the world, you can find plastics, from grocery bags to pens to spandex leggings.

We use plastics because they are lightweight, flexible, and durable.

But their durability is also their biggest drawback. Plastic takes a long time to decompose, which becomes a huge burden for our environment and planet.

The plastic problem

But let’s start by looking at what plastic exactly is.

Plastics are made up of smaller monomer units that link together and form a chain called a polymer. Different monomers have different chemical structures. Different combinations of these plastic monomers make different types of plastics. That’s how a flexible grocery bag and a sturdy toothbrush can both be made from plastic.

It is like a brick building. There are many types of bricks, and different varieties of bricks are combined to build different sorts of buildings.

No matter the type of plastic, the links between two plastic monomers are very strong. This is what makes plastic so sturdy but also why it takes so long for plastics to break down naturally.

A typical plastic grocery bag takes 10-20 years to break down while a plastic bottle can take 100-450 years.

Currently, recycling plastics requires a lot of heat and chemicals to break the strong bonds between the monomers. Once those bonds are broken, the monomers can be reused to make something new.

As you can see, the recycling process is very energy-dependent, so we generally manage to recycle less than 10% of plastics. That means most plastic waste ends up burned (12%) or in landfills or oceans (79%) where it can sicken wildlife. One group predicted that 4.8 to 12.7 million metric tons of plastic had ended up in the oceans in 2010 alone! This causes major problems for aquatic life.

Plastic-degrading bacteria to the rescue

Gladly, we have some super bacteria that help us find new ways to degrade and recycle plastic. This will make the whole process easier, greener and less energy-intensive.

The key is plastic-degrading bacteria that have special enzymes to break down different types of plastics. Even though enzymes are proteins that speed up chemical reactions, most of these are fairly slow when it comes to degrading plastic polymers. Many of them still need high temperatures to perform best, which means a lot of energy input for recycling.

But recently, scientists discovered the bacterium Ideonella sakaiensis 201-F6 that can ‘eat’ plastic.

Yes, you read correctly.

Ideonella sakaiensis secretes an enzyme that breaks down the links between plastic monomers. These smaller monomers give the bacterium energy and building blocks. Just like how humans cut bread into slices to make it easier to eat, Ideonella sakaiensis breaks down plastic into smaller pieces to eat.

But Ideonella sakaiensis isn’t the only bacterium that loves eating plastic.

A recent study found that a strain of Pseudomonas eats polyurethane, another commonly used plastic polymer.

Other microbes like eating plastic too

And it’s not only bacteria that can be found in plastic-rich environments to degrade our plastic pollution. Also, other microorganisms evolved to eat plastic.

Isolated from landfill soil, the fungi Trichoderma viride breaks down plastic found in the landfill. The marine fungus Zalerion maritimum degraded small pieces of plastic, called microplastics, found throughout the oceans.

Harnessing microbial superpowers

Gladly, researchers are well on the way to using the power of microbes to help recycle plastics.

The bacterium Ideonella sakaiensis uses the enzyme PETase to break down a common type of plastic called polyethylene terephthalate (PET). Scientists hope to use the bacteria with their PETase enzymes in bioreactors to degrade plastic polymers. This would reduce the energy input needed for recycling.

But to achieve this, scientists need to better understand how PETase binds and degrades PET. For this, they determined the 3-D structure of the enzyme.

Based on these data, scientists tried to increase the efficiency of PET degradation, for which they slightly changed the protein structure of the enzyme. This already improved the degradation rate of the enzyme, but they continue to modify and improve PETase activity. Hopefully, this ongoing improvement will bring us a much more efficient plastic-degrading PETase enzyme that we can use for recycling plastics.

The plastic-degrading power of microbial communities

Additionally, communities of bacteria and microbes have the possibility of acting as plastic-degrading bioreactors. Researchers found a marine microbial biofilm that broke down weathered plastics. They then added bacteria, which they already knew would degrade plastic, to the biofilm. This addition increased the plastic degrading efficiency of the community.

And it looks as if nature already evolved a system to address our plastic waste. A bacterial community isolated from a plastic-processing plant degraded plastic at higher levels as compared to a formulated community of laboratory bacterial strains.

Why was that?

Well, when scientists looked at the genes of the native community, they found new bacterial strains. And these strains of bacteria most likely evolved to degrade plastic better than known strains.

Just imagine what types of plastic-degrading microbes scientists may find if they continue to look for them!

Let’s hope that one day we can implement microbial enzymes and communities in plastic recycling processing.

A cleaner future thanks to plastic-degrading bacteria

Plastics continue to pollute our planet. As these items fill landfills and oceans, they break into smaller and smaller pieces that are easily consumed by and sicken wildlife. Small microplastics can act as a surface for pathogenic and antibiotic-resistant bacteria to live on and spread. And microplastics have even been found in human drinking water.

Plus, the more plastic we lose to pollution the less plastic is available to recycle and reuse. This means more plastic needs to be produced using non-renewable fossil fuels. And we all know that fossil fuels are not sustainable as they contribute to air and water pollution as well as climate change. All of these factors compound the present plastic problem the planet faces today.

With more research, let’s hope we can find more bacteria that are able to degrade plastic polymers. By using microbes and microbial enzymes, possibly we can reduce overall plastic waste. However, even with microbes’ help, we can all play a part and reduce our plastic consumption. That means, buying reusable over disposable products and recycling plastics appropriately.

Along with microbes, we can save the planet!

Take-away messages from this week’s article

• Plastic pollution is a major problem for the planet
• Plastic is hard to break down, but some bacteria degrade plastic thanks to their special enzymes
• Communities of bacteria and microbes can work together to degrade and recycle plastic

The post Plastic Degrading Microbes For a Cleaner Future appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

Phages are basically genomic information – DNA or RNA – within a lipid-protein shell. Distributing their DNA or RNA into as many hosts as possible allows the phages to survive. They then reprogram the host to produce more phages packed with more phage DNA or RNA.

These newly produced phages then trigger the host to release themselves which can even kill the bacterium. With the release, the phages are spread further into the surrounding until they encounter another host and the cycle begins again.

Of phages and bacteria

Many different bacteriophages exist that specifically infect certain bacteria. So, just as their hosts differ, the phages differ as well. They come in different shapes, sizes and reproductive mechanisms.

Some phages have very simple shapes as in the picture below. Here, we will focus on the filamentous phages that can be even longer than the host bacterium itself.

Filamentous phages are very common in bacteria and they also have a special ability: They program the bacteria in a way that bacteria do not always produce the phage. They control the bacterium and wait until the right moment comes for them to be produced.

This means that these bacteria have DNA of the phages inside their own DNA. And only when the phage DNA is activated, the bacteria actually produce the phages. Until then, the phage is a so-called silent phage within the bacterium.

Let me be your phage

One bacterium that is infected with a silent phage is the pathogenic bacterium Pseudomonas aeruginosa. Within its genome, Pseudomonas aeruginosa contains the DNA for the filamentous Pf4 phage. However, it only produces this phage when the bacteria live in a biofilm community.

So, it seemed that the phages must somehow help the bacteria in the biofilm. As a new study found these phages actually help the bacterium become more resistant to antibiotics and chemical and toxic substances inside the biofilm.

But the way the phages achieve that is a fantastic antibiotic resistance mechanism that was not known before. To learn about the strategy, researchers took images with the microscope of the Pf4 filamentous phage. And they found these long phage filaments.

I wrap around you

While these structures were pretty impressive, they didn’t explain how the phages would actually behave within the biofilm together with Pseudomonas aeruginosa.

So, the researchers added some artificial biofilm from the bacterium to the phages. They then looked at the phages again in the microscope and they saw that the phage assembled and formed ordered filaments. These looked like highly organised nets of phages.

I protect you

The researchers then wanted to see how the bacteria could fit into these nets. So, they took images of the phages together with the bacteria. And they saw that the phages form their nets close to the bacterial cells just as in the picture below.

It seemed that the phage nets wrapped closely around the bacterial cells. Like this, the phages would form a droplet shape around the bacterial cell and separate it from the surrounding.

And these droplets are the foundation for the resistance to antibiotics of the bacteria. When researchers added different antibiotics to the phage-bacteria-droplets, the bacteria survived.

On the contrary, the bacteria on their own were dying from the antibiotic attack.

This means, that the phage net works as a wall to protect the encapsulated bacterium from toxic molecules in the surrounding. This is a completely new and remarkable mechanism of bacteria to protect themselves from environmental dangers. And they use their very own phages to do that!

It seems that another race against antimicrobial resistance just started…

And then I start again

Let’s put it all together and have a look at the life cycle of these phages:

Pseudomonas aeruginosa carries genes for the Pf4 phage in its genome and only activates them when it grows within a biofilm. At this moment, Pseudomonas produces both biofilm material and the Pf4 phage. These released phages then form nets around the bacterial cells. With this net, the phages protect bacteria from antibiotics and other toxic substances.

So, it seems that phages protect their own hosts from environmental dangers. After having hijacked the bacteria’s cell for their own production, it’s actually a pretty nice thing to do.

The post Love thy host: Phages protect bacteria from antibiotics appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world