At the heart of this bacterium-plant relationship lies the soil bacterium Agrobacterium tumefaciens. Agrobacterium lives in the rhizosphere, the region in the soil close to plant roots. This area is full of secreted molecules from the plant as well as plenty of other soil microorganisms.

Agrobacterium tumefaciens is a versatile bacterium with two distinct lifestyles. In its free-living state, it happily lives and grows in the soil.

However, the bacterium also responds to some plant molecules, like sugars and acids, through its sensors on the surface. These molecules are often a sign of a wound within the plant root.

Once Agrobacterium tumefaciens detects such a molecule, it activates its virulence and makes it move toward the plant. The otherwise harmless bacterium is now a pathogen and can sneak into the plant where it goes on a big mission.

But just like animals, plants have defence mechanisms against bacterial pathogens as they recognise their bacterial surface. Depending on the plant’s immune system, the plant can be resistant or susceptible to the incoming intruder.

Luckily, Agrobacterium tumefaciens has the right weapons to counterattack, which is why it can infect many different plants.

Agrobacterium transfers its DNA into plants

Agrobacterium’s remarkable capability lies in its unique ability to transfer its own DNA into plant cells. For this, the bacterium has a special exporting machine sitting in its outer envelope.

Through this machinery, the bacterium sends some of its DNA. But not just any part. Agrobacterium tumefaciens has a special DNA portion in the form of a circle for this process. And on this so-called T-plasmid are only genes that help the bacterium during the plant-infection process.

When arriving in the plant cell, the T-plasmid is coated with specific bacterial proteins. These help the plasmid find its way to the nucleus of the plant cell.

Once landed in the nucleus, some of the plant’s systems are hijacked to destroy the proteins around the bacterial plasmid. This sets the plasmid free and it can now interact with the DNA of the plant cell.

Since the bacterial DNA-plasmid contains similar sequences as the plant DNA, these overlap so that the bacteria-DNA can integrate into the plant-DNA. Now, the bacteria-DNA is part of the plant-DNA and the plant activates the bacterial genes just as they were its own.

Transformed plants grow tumours as bacterial houses

Some of these activated bacterial genes cause the plant to produce certain plant hormones at very high levels. This hormonal imbalance triggers the cells to divide rapidly without control. The plant grows plant tumours, or so-called galls. You have probably seen them on the stems of plants or trees.

But Agrobacterium tumefaciens doesn’t merely cause tumours. Some of its genes – now present within the plant DNA – become factories to produce opines. Opines are an exclusive food source for the bacterium, allowing it to grow and thrive within its newly established plant-tumour home.

With Agrobacterium tumefaciens from microbiology to biotechnology

Once Agrobacterium tumefaciens’ superpower to transfer DNA into plant cells was discovered and understood, researchers used it extensively in the biotechnology field. They learned to introduce random pieces of DNA into plants, uncovering plant physiology and paving the way for genetically modified organisms.

By engineering specific DNA segments in the bacterium, researchers can transfer desirable traits and functions into plants. This technique, known as plant transformation, has enabled the development of genetically modified plants that resist pests, withstand harsh conditions or produce pharmaceutical proteins and vaccines.

A bacterium helps us unravel plant physiology

As we’ve seen so often in the microbial world, the smallest actors often have the grandest roles. Agrobacterium tumefaciens, a humble soil bacterium, is a true superhero when it comes to plant interactions.

Its ability to infect plants, exchange signals and transform its own genetic material has offered us valuable insights into the fascinating partnership between bacteria and plants. From the soil to the laboratory, Agrobacterium tumefaciens is at the forefront of illuminating the mysteries of nature and guiding us toward a deeper understanding of both the botanical and microbial worlds.

The post Learning with Agrobacterium tumefaciens: Understanding plants better appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

And some of these microbes learned to adapt to these special – or extreme – conditions. They can’t even cope in normal environments.

Extreme conditions or extreme environments can be anything that we consider uninhabitable for us. This can be extremely high or low temperatures, extremely high or low pressure, radiation or toxicity.

Some of these microbes actually love the extremes. And these so-called extremophiles have special superpowers that help them survive in hostile places – like the bottom of the sea.

What are extremophiles

For example, so-called thermophiles live and grow at temperatures above 50 °C and hyperthermophiles even at temperatures above 80 °C. On the other hand, psychrophiles love temperatures below 10 °C. Plus, researchers keep finding interesting new species in the permafrost soils of the Arctic and Antarctic.

Some extremophiles also have superpowers to survive in extremely salty or acidic places like saline lakes or acid mine drainages. And other extremophile microbes grow in places with high metallic or toxic concentrations or high pressure like at the deep sea of the ocean.

These extreme environments put a lot of pressure on microbes, which means they need to adapt to these conditions or they won’t survive. Hence, in these extreme environments, microbes are mutating more often or exchanging more DNA with other species to learn to cope with these challenging conditions.

Here, we will look at microbes and extremophiles that live and grow in the deep sea. In this dark place, microbial communities have developed fascinating mechanisms to adapt. And from here, they can also impact our global climate.

Extremophiles living in the deep sea

Imagine the bottom of the sea about 30 km underwater: It is dark since sunlight cannot shine this far. It is 2 – 3 °C cold while close to hydrothermal vents, it can be up to 400 °C all of a sudden. And the pressure at the sea bottom is extremely high since all that water is extremely heavy pushing everything down.

And yet, the bottom of the sea is full of happily-living, growing microbes that enjoy their times together, feeding each other and stabilising our ecology. These microbes can swim around in the open sea. Most of them attach to dirt or sediment particles on which they form biofilms.

As you can imagine, this environment doesn’t offer much food or energy. So, it is incredibly important that microbes interact with each other here to exchange meals and information. That’s why many microbes in the deep sea feed each other with one microbe producing a special substrate that another microbe likes to eat.

These microbial food webs are very important for our global nutrient cycles as deep-sea microbes sequester atmospheric gasses, like CO2, and degrade contaminants and pollutants. For example, thermophilic bacteria like Desulfovulcanus ferrireducens and Oceanithermus profundus live close to hydrothermal vents which is why they grow best at about 65 °C. These extremophiles get their energy from hydrogen gas and organic acids that swim in the ocean.

Also, during oil spillages in the ocean over recent years, researchers found many bacteria and fungi that can eat and degrade oil or petroleum. Hence, their need for food cleans our oceans of these harmful components.

How extremophiles adapt to the deep sea

The deeper you are in the ocean, the less oxygen is available for microbes to breathe. Hence, microbes had to become creative about where to get their energy from. For example, Desulfovulcanus ferrireducens mainly uses iron components for respiration and growth while Oceanithermus profundus prefers nitrogen gas. All over the oceans, there are SO MANY microbes eating these iron components and nitrogen gas. Hence, all their metabolic activities impact the iron and nitrogen cycles of the whole planet.

But microbes and bacteria in the deep sea did not only have to adapt their meals to these conditions. Deep-sea extremophiles also had to develop mechanisms to withstand the pressure and the cold of this hostile place.

At very low temperatures, proteins often get out of shape so that they lose their functions. This can mess up the whole bacterial cell, which is why psychrophilic bacteria have so-called chaperones that constantly check the bacterium for proteins that are out of shape. These chaperones then help the protein get back into normal shape and thus to its normal functioning state.

Extremophile bacteria have different membranes

Another way to adapt to hot and cold temperatures is for bacteria to change their membranes. As you might know from experience, fat gets solid when it’s cold and fluid when it’s hot. And since bacterial membranes are mainly made out of lipids and fats, thermophilic and psychrophilic bacteria need to make sure their membranes can cope with the extreme temperatures.

To prevent membranes from becoming too fluid and leaky at high temperatures, thermophilic microbes solidify their membranes. On the contrary, psychrophilic bacteria like Psychromonas and Marinomonas need to make sure that their membranes stay flexible at cold temperatures.

Luckily, this special cold-adapted membrane also helps bacteria withstand the high pressure in the deep sea. And to counteract the pressure inside the cell, piezophile bacteria produce a lot of stuff and basically crowd their cells with proteins. This aims to keep the cell pressure inside high against the high pressure from the outside.

However, investigating such high pressure is extremely difficult in the lab. That’s why researchers still don’t know much about the pressure adaption of extremophiles in the deep sea.

What we can learn from extremophiles in the deep sea

Even though we still don’t know much about the fascinating microbial life underwater, researchers are optimistic that they will find lots of helpful microbes. Whether adapted to the cold or to the heat, deep-sea microbes have incredible mechanisms to grow at extreme temperatures.

This means they contain proteins that function perfectly on either side of the temperature spectrum. So, researchers hope that we could use that knowledge to design tailor-made proteins for our daily lives. We could for example use them in households or in biotechnology applications, for example, to improve cleaning efficiency or reduce energy input.

Another important aspect is to explore how microbes in the deep sea affect our global climate. With climate change, our oceans are getting warmer and thus they contain less oxygen. This means that also microbes are likely adapting to these changes which in turn influences the global climate.

Hence, understanding how microbes cope with the conditions in the deep sea helps us comprehend the full impact of climate change. This might then give us an idea about how to prevent more damage to our beautiful planet. With the help of microbes.

The post Even at the dark and cold bottom of the sea, microbes flourish appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

Energy to grow, to move, to fight, to produce stuff and also to reproduce.

Generally, living organisms get this energy from food. It fuels us, just as it fuels animals, plants and bacteria.

But where exactly is this energy in food? How do bacteria and other living organisms access this energy? And what do they do if their favourite food is not around?

To answer these questions, let’s look at how molecules store energy.

How do living organisms gain energy?

Each chemical bond between atoms contains energy. Hence, a molecule that is made of many atoms and thus many chemical bonds, contains energy. When such a chemical bond opens, it releases energy in the form of electrons.

Depending on the kind of chemical bond within the molecule, these electrons can have higher or lower energy levels. Thus, they contain more or less energy.

So, to obtain energy from molecules, organisms need to break apart molecules and extract the electrons with high energy. But this is not as easy as it sounds. Chemical bonds are quite tight and it actually requires energy to break them open.

Hence, organisms need to have the right sets of proteins that can break open specific chemical bonds in molecules. These kinds of proteins are called enzymes. So, only if an organism has enzymes to break apart glucose, it can use glucose to extract its electrons and obtain energy.

Interestingly, most organisms do exactly that. They break apart glucose into smaller products and take the freed electrons. In that case, glucose is the so-called electron donor.

Now, these electrons need to go somewhere, since they are full of energy. So, organisms save this energy by transferring these electrons onto other molecules. These molecules have lower energy levels, hence they like to take up electrons. We call these molecules electron acceptors.

But finding the right electron acceptor is not as easy as it sounds.

The many steps from an electron donor to an electron acceptor

Imagine you stand on a high wall and want to get down onto the ground. You could take one big jump to reach the ground. But then you would risk that this high fall would give you so much energy that you might break your knees.

So, you could take a set of stairs, that brings you to the ground in multiple steps. Each step only releases a small chunk of energy but they would definitely not hurt you.

It is the same with electrons from donors with a lot of energy. Transferring these electrons to a final electron acceptor would free up too much energy at once. This could actually burn a cell. Hence, organisms transfer these electrons onto intermediate electron acceptors.

Each of these transfer steps only releases a small chunk of energy that keep organisms warm but also fuel cellular processes. In bacteria, these transfer processes happen in their membranes, where the released energy is directly used.

Here, the released electrons energise flagella so that bacteria can swim. Electrons can also activate transporters so that bacteria can import or export stuff. Not needed electrons and their energies are stored in energy-saving molecules like ATP.

This whole process of electron transfer from a donor to its final acceptor is generally what researchers call cellular or – more specifically – bacterial respiration.

Which molecules do bacteria use for cellular respiration?

Cellular respiration fuels most living organisms. And glucose is a molecule with one of the highest energy levels. Hence, breaking down glucose to extract its electrons is the most common in living organisms.

Animals do it. Fungi do it. So, bacteria are no exception to it.

And as a final electron acceptor, most organisms use oxygen. This molecule has a very low energy level and is basically everywhere so most organisms transfer their electrons to it.

This is what we call aerobic respiration (which is what we generally do as well). But it comes with great risk.

The downside of aerobic bacterial respiration

As soon as an oxygen molecule is fuelled with just one electron, it becomes hyperreactive. Such a semi-activated oxygen molecule can basically react with any compound in a cell and damage it.

This is what makes aerobic respiration quite dangerous. So, every organism aims to hide these reactive oxygen molecules in the membrane.

Yet, it can happen that such a reactive oxygen molecule escapes the membrane. In this case, a special protein binds it and breaks it apart. So, every organism that does aerobic respiration has this same kind of protective protein to get rid of reactive oxygen molecules.

This means that whenever scientists find a new microbe, they first test whether this new microbe has these proteins. To test this, they add a bit of hydrogen peroxide to the bacterial colony. When bubbles come out of the bacteria, it means that they do aerobic respiration. In this case, they have the enzymes to break apart the reactive oxygen molecule and produce oxygen from it.

Which other molecules can bacteria use as energy source?

As we said, most bacteria use glucose as an energy source for cellular respiration. However, there are also many fancy exceptions. And these exceptions make the bacterial – and microbial – world so colourful and diverse.

While many bacteria can extract electrons from many different organic acids and amino acids, some use sulphur compounds. Some bacteria also break apart greenhouse gases like methane, carbon monoxide or even hydrogen gas. Since these bacteria might be helpful in tackling our climate problems, they are of particular interest to researchers!

What does bacterial respiration look like without oxygen?

We surely need our oxygen for respiration. Yet, many bacteria and fungi can live with only small amounts of it or even no oxygen at all.

In this case, they do anaerobic respiration. This basically means that they don’t transfer their electrons to oxygen as an electron acceptor.

Instead, many bacteria have enzymes to transfer their electrons to different electron acceptors. And these depend on what the bacteria have available around them. These electron acceptors can be nitrate or sulphate compounds, salts like arsenate or even metals like iron and gold.

Also, in many microbes, anaerobic respiration is closely related to microbial fermentation. In this case, the bacteria break apart glucose but produce molecules that do not require oxygen.

Just think about yeast that produces ethanol in beer and wine. Or lactic acid bacteria in your sauerkraut and yoghurt that produce lactic acid to make the food more acidic. Lastly, there are fungi like Zymomonas mobilis that produce huge amounts of ethanol from glucose.

Bacterial respiration makes the microbial world diverse

As we have seen, bacteria learned to use various sources to gain energy. They created the right enzymes to extract electrons from fancy high-energy molecules.

And then they learned to transfer these electrons onto even fancier molecules to gain the most energy. Some of these processes even involve bacteria producing shiny gold!

In my opinion, these truly amazing superpowers make the bacterial world so incredibly colourful and fascinating!

The post How bacteria gain energy from cellular respiration to fuel life appeared first on Bacterialworld.
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

But what do bacteria and fungi use antibiotics for? Why do they produce them? And what are the advantages of microbes having antibiotics as molecular weapons?

What are antibiotics?

The father of antibiotics, Selman Waksman, first used the word antibiotics for any small molecule made by a microbe that can inhibit the growth of other microbes.

So, microbes – especially bacteria and fungi – use antibiotics to kill other microbes. These other microbes can be bacteria, fungi or bigger organisms. Not viruses though!!!

Why not viruses?

Because antibiotics bind and inhibit cellular machines in living organisms. These molecules often bind to so-called targets. Antibiotic targets can be proteins or enzymes that make for example the cell wall, other proteins or components of the respiration complex.

These proteins are generally essential. So, when antibiotics inhibit the proteins, the cells are missing these essential functions. And without them, they cannot survive and die.

Hence, like other bacterial toxins, antibiotics are lethal.

Interestingly though, bacteria and fungi make antibiotics from simple building blocks. These are present in every cell and can be amino acids, lipids or even sugars.

But instead of using these building blocks for their normal functions, microbes link them together in different ways. With this, they create new – and fancier – molecules that barely resemble the original blocks.

Then, they transport these antibiotics to the outside or send them off in outer membrane vesicles. When the antibiotic hits another microbe, there are two possibilities: either the microbe is resistant to the activity of the antibiotic or it dies from it.

But what about the microbe that produces the antibiotic? Is it resistant to the antibiotic itself?

Why are microbes that produce antibiotics not get killed?

Since antibiotics are meant to KILL other microbes, then why do producing microbes not get killed by their own antibiotics? The answer is self-protection!

Whenever bacteria or fungi produce antibiotics, they always also produce some sort of self-protective means. Just as when bacteria produce other toxins, they always need to make sure they are not killed by their own weapons.

These self-protectors usually keep the antibiotic in an inactive state. For example, they completely surround the antibiotic molecule so that it cannot bind to its usual target within the cell. Another strategy is to add a small molecule to the antibiotic – again to keep it from binding to its target.

Then, when the microbe is ready to transport the antibiotic outside of the cell, it takes the self-protection off the antibiotic. This releases only the toxic part – the antibiotic itself – into the surrounding.

Note, however, that these self-protection mechanisms are not antibiotic resistance mechanisms. Self-protection mechanisms are meant to inactive antibiotics only temporarily. Hence, these mechanisms are reversible. The antibiotic can still become active and thus toxic.

Resistance mechanisms, on the other hand, are meant to inactive antibiotics permanently. Hence, these mechanisms are irreversible. Since this usually completely destroys the antibiotic, it cannot become active anymore.

But what triggers microbes and especially bacteria to produce antibiotics? How do antibiotics help the producing cell in their daily circumstances?

Why do bacteria produce antibiotics?

To answer this question, we need to look at where the bacteria live that make antibiotics. And two-thirds of the known antibiotics are made by bacteria from the Actinobacteria family. Within this family, Streptomyces is the best-known member that produces half of all known antibiotics.

Another example is bacteria from the Myxococcus family. So, where do Streptomyces and Myxococcus bacteria live? Interestingly, these bacteria call the soil their home.

And in the soil, they often confront lots of friends and foes. And they need to constantly fight for their own survival.

Myxococcus is known as a wolf-pack predator because it kills its prey in massive attacks. Colonies of Myxococcous roll over their prey, secrete antibiotics and thus kill them and feed on them.

Streptomyces, on the other hand, uses its antibiotics a bit more civil.

To move in the environment, Streptomyces bacteria grow as long filaments throughout the soil. They build long chains and branch out into the soil as multicellular organisms. These branches are filled with Streptomyces cells but also spores so that the bacteria can extend to new places.

When the bacteria hit a period of bad weather or don’t find much food, they release their spores as a survival strategy. Plus, they start releasing nutrients for the spores. But these nutrients also attract other organisms like bacteria.

Hence, at the same time, Streptomyces produces a huge amount of antibiotics to fend off these putative food-stealers. Like this, Streptomyces makes sure their spores are safe and can survive in their new homes for a while.

How do antibiotics produced by bacteria help others?

Like Streptomyces, lots of bacteria use antibiotics to fight off predators. This assures their own survival and that of their species.

Yet, more and more research finds that bacteria not only kill other species with antibiotics so they can survive. The killing also benefits their hosts.

For example, the bacterium Janthinobacterium lividum lives on frogs where it produces the antibiotic violacein. This antibiotic kills fungi so that the bacterium protects the frog from deadly fungal infections.

Also, a bacterium that lives in our noses is the harmless Staphylococcus lugdunensis. This bacterium produces the antibiotic lugdunin. That inhibits the harmful Staphylococcus aureus from settling down in our noses. Now, scientists look into how we could use the harmless Staphylococcus lugdunensis to protect us from infections.

Another example of microbes that produce antibiotics to help others is the three-member association of ants, Streptomyces and a fungus. Several species of ants grow fungi for food. They feed their fungi with fresh plants and let them grow in special underground gardens.

To not contaminate these fungal gardens, ants carry symbiotic Streptomyces that produce antibiotics. Like this, the antibiotics kill other microbes and keep the fungal gardens free of harmful intruders. As a thank you, the ants feed the Streptomyces and give them a place to live.

About antibiotic-producing microbes

So, just as we use antibiotics to kill harmful bacteria and fungi, antibiotic-producing microbes do the same. They want to fight off predators and assure their own survival.

When you think about it: we use their own killer weapons against them. Poor microbes!

The post Bacteria use antibiotics to kill their foes and protect others appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

And when it comes to the size of an organism, one thing is quite clear: The bigger, the more food they need.

This is also true for bacteria. Depending on the shape of a bacterium, bacterial cells are differently big or small. And the bigger a bacterium is, the more energy they need.

So, in a location where there is not much food, this might be a problem.

Not for superhero bacterium Thiovulum majus. This one is a huge bacterium with an incredibly amazing mechanism to find and get food for itself and its brothers and sisters.

Read on to find out what this bacterium does to not run out of food.

Large bacteria run out of food easily

Thiovulum majus is one of the bigger bacteria with about 10 – 15 μm cell length. Average-sized bacteria are usually around 1 μm in length and the smallest nanobacteria even only 0.2 μm.

This makes Thiovulum majus a giant under the bacteria. It is about 10 – 15 times bigger than other bacteria. And this means it also needs a lot more energy and nutrients.

Thiovulum majus also has an interesting lifestyle. It lives at the bottom of salt marshes, close to water sediments. Here, the water contains a lot of sulfur, which Thiovulum majus uses to gain energy.

However, Thiovulum majus also needs oxygen to live. Hence, within water, it needs to be in the perfect spot with the right oxygen and sulfur concentrations. Sounds easy, but is pretty complicated if you’re a bacterium drifting in water.

First, to find the optimal spot in water, Thiovulum majus uses chemotaxis to follow the right oxygen concentration. As soon as they are satisfied with a location, they need to make sure to stay in this position. And Thiovulum majus found an amazing mechanism to achieve that.

A floating veil keeps bacteria in place

Interestingly, Thiovulum majus produces a so-called tether or stalk. This is a strong but flexible string made of mucus. It is pretty sticky and works like the superglue of Caulobacter crescentus.

When Thiovulum majus swims in water, it carries this stalk at its end. Here, it can grow up to ten times as long as the bacterial cell itself. And the stalk can stick to stalks from other bacteria or particles in the water.

When many stalks stick to each other and to particles, they form a net-like layer in the water. This layer, or a white veil, floats above the sediment in the water and can become several centimetres in size.

Now, the bacteria are attached to this veil since their stalks are stuck within this mesh of stalks. Scientists found that on a veil with the surface area of your fingernail, around 100’000 Thiovulum majus bacteria are attached.

Every once in a while one such stalk breaks and thus releases the bacterium. However, Thiovulum majus uses its chemotaxis to swim in a U-shaped pattern which brings it back to the veil. Growing a new stalk, the bacterium attaches to the veil again to make sure it stays in the right location.

Hence, using chemotaxis and attaching to the veil keeps Thiovulum majus in a more or less fixed position in the water. And this location has the optimal concentration of both oxygen and sulfur.

High-speed rotating bacteria bring nutrients to the population

Now imagine, lots of Thiovulum majus bacteria live at this location of optimal oxygen concentration. At some point, the bacteria have used the available oxygen in that surrounding.

How to bring in new oxygen?

Looking at the Thiovulum majus bacteria, you can see that they have many flagella on their cell surfaces. And by rotating these flagella, the bacteria start to rotate as well. And by rotating the whole bacterial cells, the bacteria induce a water flow. This flow draws water from above towards the bacterial cells and the veil. And this freshwater brings a lot of oxygen to the bacterial population.

This rotation is incredibly fast and researchers studied this movement in the lab. They attached the bacteria to a glass surface and let them rotate. Through the rotation, it looked as if the bacteria formed little cells around them and they also pulled neighbouring cells close. This started to look like crystals of rotating bacterial cells.

This rotation of flagella lets Thiovulum majus swim with a speed of up to 600 μm/s. Don’t forget that Thiovulum majus is about 10 μm long. This means it can swim 60 times its own cell length in one second!

It’s as if you could swim about 100 m in one second. Yet, the World Record for swimming 100 m freestyle is currently at just below 45 seconds.

This high swimming speed makes Thiovulum majus the second-fastest bacterium that we know of. And this superpower explains why this bacterium is so powerful in inducing a water flow. With this constant mixing of water, the bacteria make sure they always have enough oxygen and nutrients to live.

Bacteria found ways to survive in different environments

I’m always impressed by the superpowers that bacteria have and their resilience. They learned to make the best out of each situation, found ways to use whatever they come across and adapted to live anywhere.

The question that remains now is: Why did Thiovulum majus become such a big bacterium? When they started using their rotating mechanism they brought in more nutrients. Did this help them become bigger because they had all the nutrients at hand?

Or did the bacterium grow big and then needed to find a mechanism to find and bring in more food? These are the kinds of questions scientists are probably looking into right now. And I can’t wait to learn the answer.

The post Floating veils for large bacteria to attach to and fetch nutrients appeared first on Bacterialworld.
Bacterialworld - A blog about bacteria: from scientific studies to vivid stories about the fascinating bacterial world

So, they talked of cocci and bacilli based on the spheres and rods that they saw under the microscope.

And they classified microbes and bacteria based on these shapes.

It came only with later, modern technologies that scientists learned that there was more to bacteria than their shapes. Even though bacteria looked similar, they had different superpowers.

Yet, some of these bacterial superpowers are indeed influenced by their cell shapes.

So, what is it about bacterial shapes? Why do bacteria look differently? And how do the different shapes of bacteria help them survive and thrive?

What gives bacteria their shapes?

To protect themselves from the environment, bacteria as well as all other organisms have cell envelopes. These keep the cellular machines and internal parts together so that a bacterium can function within this envelope.

And this envelope also gives bacteria their shape.

Both Gram-positive and Gram-negative bacteria have a layer of so-called peptidoglycan within their envelope. This peptidoglycan layer is made of sugars that are linked together by very strong bonds. This is why the peptidoglycan layer is pretty rigid and stiff and has a specific shape in each bacterium.

Either on the inside or on the outside, the peptidoglycan layer is linked to the cellular membranes. Together, these make up the bacterial envelope with a specific cell shape.

What different shapes do bacteria have?

Microbiologists have different ways to classify known bacterial shapes. Here, I will introduce you to the bacterial shapes according to what makes the most sense to me.

Rod-shaped bacteria

As the name suggests, these bacteria have a rod or cylindrical shape. Examples of rod-shaped bacteria are Escherichia coli and Bacillus subtilis.

Scientists are also convinced that rod-shaped bacteria are the evolutionary ancestors of all other bacterial shapes.

The shape comes from proteins that form long cables within the bacterial cell. These span out the whole bacterium from one end to the other.

Rod-shaped bacteria grow by two modes that we talk about in Why bacteria divide into two and grow with the help of a strong ring: First, they extend their cell size by growing the peptidoglycan, the cable proteins and the membrane.

Second, the cable proteins determine the middle of the cell, where the bacterium produces a special ring. Eventually, this ring narrows so that the bacterium divides and two bacterial cells form.

Spherical bacteria

The spherical bacteria – or so-called cocci – include many pathogenic bacteria like Staphylococcus aureus, Streptococcus pneumoniae and Neisseria gonorrhoeae.

Microbiologists think that spherical bacteria were once rod-shaped as well. However, spherical bacteria do not have these long cable proteins that extend their cell bodies. Thus, they stay spherical and grow by dividing their spherical cells right in the middle.

However, sometimes the two daughter cells do not completely divide and they stay attached to each other. This is why some spherical bacteria live as so-called diplococci.

Curved bacteria

Curved bacteria have the shape of a comma or banana and are sometimes also slightly twisted. Examples of curved or banana-shaped bacteria are Caulobacter crescentus and Vibrio cholerae.

These curved bacteria usually live in watery environments where there are flows. Here, the curved shape helps the bacteria to align with the flow while staying attached to a surface.

In the case of Caulobacter crescentus, one end of the bacterium is glued to a surface with a strong super glue. When this bacterium divides in the middle, one daughter cell remains attached to the surface, while the other one can swim away and find a new location to settle down.

Spiral bacteria

Spiral bacteria are a mix of rods and curves which give them a helical twist. Hence, these bacteria have a corkscrew shape.

Many pathogenic bacteria use their corkscrew shape to swim through gel-like solutions. This includes Helicobacter pylori and Campylobacter jejuni.

Since spiral – or helical – bacteria are also thinner, they can reach locations that are too narrow for other bacteria to reach. They also use their flagella to push themselves forward and “wriggle” through narrow pores.

Star-shaped bacteria

Some bacteria look even fancier than others: They are real stars – yes, bacteria with a star shape.

While we don’t know much yet about star-shaped bacteria, they belong to the so-called Stella species or are Methylomirabilis oxyfera. These usually grow in freshwater, soil and sewage.

The star shape comes from six little arms that extend out of the bacterial cell. These push and grow to the outside giving these bacteria a shiny star shape.

Why do bacteria have different shapes?

Now that we have seen the different shapes of bacteria, you might ask yourself, why do bacteria have these different shapes? How do they help them?

As always in biology, it comes down to how a property helps a bacterium survive in a certain location. Often, the cell shape gives a bacterium advantages over other bacteria and it is easier for them to settle down and face harsh environments.

For example, spherical cells have the lowest surface-to-volume ratio. This means they have a large envelope surface through which they can take up a lot of nutrients. All this while their cell volume is relatively small. So they don’t actually need that many nutrients. This helps cocci to grow in locations where there are little amounts of nutrients.

On the other hand, rod-shaped bacteria often have flagella. And thanks to their shapes, they are efficient swimmers. This allows them to swim to new places in cases of danger or the lack of nutrients.

Bacterial cell shapes help face harsh environments

Also, straight rod cells can pack into biofilms more efficiently and build organised structures. This helps them colonise different locations and resist dangerous environments.

Many rod-shaped bacteria also form longer filamentous organisms. These stronger and larger structures protect bacteria from being eaten by other organisms. Another advantage of these multicellular organisms is that they allow more cells to attach to surfaces and colonise hosts.

Lastly, both curved and helical bacteria use their shapes to get better around their environments. Curved bacteria grow in watery environments but also in our guts. Here, their shapes help them align with the flow of water or our gut content while they stay attached to a surface or the gut wall. This keeps them at their preferred location and protects them from being flushed away.

Spiral bacteria use a fascinating helical movement to screw through gel-like or viscous fluids. This for example helps pathogens swim through the mucus of our stomach and guts and colonise us and make us sick.

Bacteria and their shapes

Here, we looked at the different shapes that bacteria have and how these help them survive. Bacteria always face harsh and new environments and conditions and only survive if they have the right tools or means.

So, by adapting their shapes, bacteria often have advantages over other bacteria. Plus, they look cool and fabulous!

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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.

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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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However, some bacteria found a way to become invisible in front of the immune cell army. They put on an invisibility cloak so that they can sneak into the human body without being seen. This invisibility cloak is a so-called bacterial capsule. And pathogenic bacteria use capsules to trick the immune system to infect our bodies.

Here, we will explore what bacterial capsules are and how bacteria use them to overcome our immune systems.

About bacteria with capsules

Bacteria that produce capsules are generally pathogens. These are bacteria that can infect us, cause disease and make us sick. And bacterial pathogens use capsules for the infection process. Without capsules, pathogenic bacteria would be eaten and killed by our immune cells.

Bacteria with capsules are for example Klebsiella pneumoniae, Mycobacterium tuberculosis, Haemophilus influenzae, pathogenic and uro-pathogenic Escherichia coli, Neisseria meningitidis and Porphyromonas gingivalis.

Many people carry Klebsiella pneumoniae in their gastrointestinal tract or nose without having any symptoms. However, in some people, this bacterium can enter the blood circulation and cause infections like pneumonia, sepsis, urinary tract infections, bacteremia or meningitis.

The pathogen Mycobacterium tuberculosis causes the devastating disease tuberculosis with almost 1.4 million deaths every year. Haemophilus influenzae infections lead to sinusitis and uro-pathogenic Escherichia coli causes urinary tract infection. Another awful pathogen is Neisseria meningitidis. This bacterium infects the membrane around our brain and leads to the disease meningitis. Lastly, Porphyromonas gingivalis is an oral pathogen that infects and destroys the tissue around our teeth. You might know this disease as periodontitis.

This list of pathogenic bacteria might sound a bit frightening. But it is to highlight the one feature they all have in common: These bacteria use their capsules to enter our bodies and cause these diseases.

So, let’s have a look at what this capsule actually is.

What are bacterial capsules

The bacterial capsule is a thick layer of a sugar-water mix that surrounds the bacterial cell.

The capsule layer consists of long chains of sugar molecules that are attached to the bacterial cell surface. These sugar molecules have different lengths, lots of branches and different attachments. The sugar chains absorb water molecules so that a gooey slime develops. Researchers can even see this under the microscope.

Interestingly, different bacteria can produce chemically identical capsules. But the same bacteria can also produce different capsules. In this case, bacteria add little attachments to the outer tip of their sugar branches. Now, this bacterium “looks” completely different from the outside.

Generally, antibodies bind to these sugars, which is why we call these sugars antigens. However, when bacteria change their sugar tips, they also change their antigens. Hence, another antibody is needed to recognise this new antigen – even though it might still be the same sugar. In this case, we call the bacterium with the new sugar antigen a serotype.

For example, researchers found 80 different antigens and thus serotypes in Escherichia coli based on their capsule sugars. And for Streptococcus pneumoniae, they even identified 93 serotypes.

Now, you might ask yourself what is the function of capsules in bacteria?

Bacterial capsules are invisibility cloaks

A bacterial capsule works like an invisibility cloak. As soon as a bacterium enters the dark halls of our human bodies, it puts on the cloak. Now it won’t be seen by the immune guardians. Like this, bacterial pathogens follow the model of “the best defence for a pathogen is a good defence”.

The players of our immune system recognise and bind to specific molecules on the surface of bacteria. This activates the immune system and attracts more phagocytes. These immune cells eat intruding pathogens and destroy them. Like this, our immune army is always ready to fight the bad guys.

However, the bacterial capsule hides these surface molecules that our immune system usually recognises. Like this, our immune players cannot bind these sugar-coated pathogens. This keeps the immune army deactivated. Now, bacteria can escape the immune system, sneak into our bodies and cause infections.

Our immune system can also fight intruding bacteria by producing antimicrobials. Yet, the sugar capsule of some bacteria can absorb these small molecules and make them useless. Hence, the bacterial capsule acts as a protective layer against immune attacks.

Neisseria meningitidis even has a “capsule-switch”. Once activated, it can cover itself with another sugar layer that looks completely different from the outside. The immune players need to learn again to recognise this new layer, which takes time. Hence, with this “hyper-encapsulation”, Neisseria meningitidis can escape the immune system again.

Overcoming bacterial capsules

Because bacterial capsules are at the outer surface of a bacterium, researchers want to use these components as targets for vaccines. However, since bacteria can change their capsular components, these targets are not very reliable. So, researchers are working on developing vaccines that recognise different serotypes.

For example, a vaccine that recognised different antigens of the capsule in Klebsiella pneumoniae was developed and reached clinical trials. However, the high costs of such an efficient vaccine made this project difficult.

Another approach is to better understand how pathogenic bacteria regulate their “capsule-switch”. If we can prevent bacteria from putting on another cloak, we can help our immune system do its job and kill intruding bacteria. Hence, researchers are looking for ways to achieve this.

Bacterial invisibility cloaks – another way for bacteria to survive

You might now think how nasty bacteria are for using such a capsule to escape our immune system and infect us. However, for bacteria, this is another survival mechanism. If they do not put on their invisibility cloak, the immune system will eat and kill them. So, some bacteria developed this mechanism to overcome their foes.

And I think it is a pretty smart way to survive.

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