Chapter 7: How Bacteria & Archaea Grow

Welcome to Last Minute Lecture.

This free chapter overview is designed to help students review and understand key concepts.

These summaries supplement not replaced the original textbook and may not be redistributed or resold.

For complete coverage, always consult the official text.

Welcome to the Deep Dive.

We're here to take complex source material,

dense chapters really, and break them down into something you can actually use, something conversational.

Today, our mission is microbial growth and survival.

We're talking bacteria, archaea, the fundamentals of how they divide, grow, and basically conquer almost every environment on earth.

And just to set the stage, get this.

Scientists found microbes living almost two kilometers below the seabed in coal from the Mycenae era, still metabolically active after maybe 20 million years.

It's an incredible find.

And what's really mind bending is their estimated generation time.

We're talking months, maybe even over a hundred years for a single division.

Wow, a hundred years.

That completely redefines slow growth, doesn't it?

It highlights that growth in nature is often, well, really slow and nutrient limited or oligotrophic.

Exactly.

So today we're focusing on the basics from the source material, how these cells manage to divide with such precision, how we measure their population growth, you know, in the lab mainly, and the strategies they use to survive extreme conditions.

Okay, so we'll go step by step.

Division mechanisms, growth dynamics, and then survival in harsh places.

Let's unpack the division part first.

Sounds good.

The most common strategy, the one everyone learns first, is binary fission.

Pretty straightforward, right?

Cell gets longer, duplicates its stuff, builds a wall of septum down the middle, and boom, two daughter cells.

That's the classic picture, yes.

But it's worth remembering there's quite a bit of diversity out there.

Some bacteria, like listeria, actually reproduce by budding.

Ah, like yeast.

Sort of, yeah.

And then you have some cyanobacteria doing multiple fission, one big cell releasing lots of tiny ones called biocytes.

And streptomyces, they form long filaments that then break up into spores, so not always just a simple split.

Okay, good point.

But sticking with the standard bacterial cell cycle for a moment, it involves growth, copying the chromosome, moving those copies apart, and then the actual split for cytokinesis.

But unlike our cells, eukaryotes, these processes often overlap quite a bit in bacteria.

They really do.

It's much less compartmentalized in time.

Replication, partitioning the chromosomes, and building the septum can all be happening concurrently.

So how do they manage that?

Especially ensuring each daughter cell gets one complete chromosome before the wall closes?

That's where some elegant molecular machinery comes in.

For chromosome

partitioning, many bacteria use the Parabara system.

Think of PARA as a specific site, like a handle on the chromosome.

The PARA protein grabs onto that PARA handle.

Then the PARA protein, which kind of spreads through the cell, acts like a track or maybe a relay system.

It effectively pulls or guides the PARB DNA complex to the opposite end of the cell.

Like a little molecular tug of war ensuring separation.

Exactly.

Making sure one copy ends up at each pole before division.

Okay, so the DNA gets separated, but then there's the septum formation, the actual pinching in half.

It's driven by this ring of FDSC protein, right?

How does the cell make absolutely sure that ring forms precisely in the middle and crucially doesn't slice through the DNA before it's fully separated?

Right, that would be catastrophic.

Cells have evolved basically two key mechanisms to prevent that, often working together.

The first is the MinCDe system.

MinCD, okay, what does that do?

It's pretty cool, actually.

These Mn proteins, they oscillate back and forth from one pole of the cell to the other, like a biochemical pendulum.

Oscillating, really?

Yeah, and MnC, one of the proteins in the system, is an inhibitor of FDSC ring formation.

So by constantly sweeping back and forth, the Mn system ensures that MnC concentration is always high at the poles.

So the only place the FDSC ring can form is mid -cell, where the MnC concentration is lowest on average.

Precisely.

It restricts the ring formation to the center.

Clever.

What's the second failsafe?

It's called nucleoid occlusion.

This involves another protein, SLMA, in E.

coli, for instance.

Cell MA binds all over the chromosome, the nucleoid, except near the very end, the terminus of replication.

And while cell MA is bound to the DNA,

it physically prevents FTSC from polymerizing into a ring in that area.

So as long as the bulk of the chromosome is still in the middle of the cell, cell MA bound to it says, nope, can't build a wall here yet.

So the septum can only fully form once the chromosomes have moved out of the way, clearing that mid -cell zone.

That's the idea.

It's a spatial inhibitor linked directly to the DNA's position.

Between MnCE, keeping things away from the poles, and nucleoid occlusion, protecting the DNA itself, the cell gets the septum right where it needs to be when it needs to be there.

That's remarkably precise.

And you mentioned earlier that these processes overlap to speed things up.

Yes.

Think about E.

coli.

Replicating its entire chromosome takes about 40 minutes.

But under good conditions, the cell can divide every 20 minutes.

How does that work?

It initiates new rounds of DNA replication before the previous round is even finished.

So you can have multiple replication forks going at once on the same chromosome.

It's like starting the next step on the assembly line before the first product is fully complete.

Incredible efficiency.

OK, so let's connect this internal machinery to the outside.

The cell -shaped rod sphere, comma, that's determined by how it builds its cell wall, right, under the influence of trigger pressure.

Absolutely.

And the how involves bacterial versions of our own cytoskeleton proteins.

It's fascinating.

For Cochi, the spherical ones, new peptidoglycan, the wall material, is synthesized primarily at the septum guided by FTSE.

That naturally leads to spheres.

Makes sense.

But rods are more complex.

Right.

Rods need to elongate first, then divide.

They use two main machines.

For elongation, there's the elongosome.

This involves a protein called Mecrubi, which is structurally similar to eukaryotic actin.

Mecrubi forms filaments that run along the inside of the cell membrane and guide the synthesis of new wall material along the sides, pushing the cell longer.

So Mecrubi is key for the rod shape.

Totally.

If you experimentally deplete Mecrubi in a rod -shaped bacterium, it typically rounds up and becomes spherical.

Then, for the division, the bittily sum involving FTSE takes over at mid -cell to build the septum, just like in Cochi.

OK.

A longosome for length, divisome for division.

What about those curved or comma -shaped cells, like Vibrio?

Ah, Vibrio.

They add another layer.

They use FTSE and Mellibier.

But they also employ a protein called Crescentin.

Crescentin is similar to eukaryotic intermediate filaments.

It localizes specifically along one side of the cell, the side that will become the inner curve.

By being there, it seems to slow down or somehow modify peptidylglycan insertion on just that one side.

Causing the cell to curve as it grows.

Exactly.

A slight asymmetry in growth leads to the characteristic comma shape.

So what's the big picture here?

Why is understanding these bacterial cytoskeletal proteins so important?

Well, a couple reasons.

First, they're simpler, more tractable systems for studying fundamental processes of cell shape, determination, and division that are conserved in principle in eukaryotes.

Second, and maybe more practically, these proteins like FTSE and Metare are essential for bacterial survival.

Meaning drug targets.

Precisely.

Molecules that specifically inhibit FTSE, for example, can block cell division in pathogens like Staphylococcus aureus.

So they represent promising avenues for developing new antibiotics, which we desperately need.

Right.

Okay, let's shift gears.

We've looked inside one cell dividing.

Now let's think about the whole population.

How do we study microbial growth, usually in the lab?

Typically, we use what's called a batch culture.

It's basically a closed system.

You add microbes to a flask of sterile medium, seal it, and watch what happens over time.

And if you plot the number of viable cells, usually on a logarithmic scale, against time, you get that classic microbial growth curve.

Exactly.

And that curve shows several distinct phases reflecting the changing physiological state of the population.

First, there's the lag phase.

The slow start.

Right.

The cells aren't necessarily dividing much yet.

They're busy adapting to the new medium, maybe repairing damage, synthesizing enzymes they need for these new nutrients.

It's an adjustment period.

Then things take off.

Yes.

Then you hit the exponential phase, or log phase.

Here, the cells are dividing at a maximal constant rate for the given conditions.

The population is doubling regularly.

This is the healthiest state and the most uniform population, so it's ideal for biochemical experiments.

And this is where you calculate things like generation time.

Exactly.

Generation time, G.

The time it takes for the population to double, and the growth rate constant, K.

They're characteristic for a given organism under specific conditions.

Okay, so log phase.

Yeah.

But it can't last forever in a closed flask.

Nope.

Eventually, something becomes limiting.

Either essential nutrients run out, maybe oxygen gets depleted if they're aerobic, or toxic waste products build up, like acids from fermentation.

This leads to the stationary phase.

Where the population size levels off.

Correct.

The net population size is constant.

Either the division rate equals the death rate, or cells just stop dividing altogether, entering a kind of survival mode.

They actually down regulate things like initiating new DNA replication to consume energy.

Makes sense.

What happens after stationary phase?

If conditions don't improve, or get worse, you enter the death phase.

Here, the number of viable cells starts to decline, often exponentially, as cells suffer irreparable damage.

Grim.

Is that the end of the story?

Not quite.

There's often a fifth phase, particularly if you watch for a long time, called the long -term stationary phase.

This isn't just a slow decline, it's actually quite dynamic.

Dynamic how?

You can see successive waves of mutants arising.

A subpopulation might evolve that's better at scavenging nutrients released by dying cells, or more resistant to the accumulated toxins.

Whoa.

Like a mini -evolutionary battle playing out in the flask.

That's a good way to put it.

It's natural selection and action.

One genetic variant might take over for a while, only to be outcompeted later by another variant better suited to the harsh changing conditions.

Life finds a way, even in a dying culture.

Fascinating.

Okay, let's broaden out from the lab flask to the real world, often much tougher environments.

You mentioned extreme survival strategies.

Let's start with solutes and water.

Right.

Water availability is absolutely critical.

We talk about water activity, a measure of available water.

Pure water has an awe of 1 .0.

Most bacteria need an arm .98 or higher to actively grow.

Which explains why drying or adding lots of salt or sugar preserves food, right?

It lowers the water activity.

Exactly.

It makes water unavailable to microbes.

But some microbes, halophiles, actually love salt.

And extreme halophiles require really high salt concentrations like 3 molar in NCL or even saturation environments like the Dead Sea or salt evaporation ponds.

How do they survive that without shriveling up like raisins?

They fight osmotic stress by accumulating high internal concentrations of specific solutes called compatible solutes.

Things like potassium chloride or organic molecules like tain or proline.

Compatible meaning?

Meaning they can be kept at very high concentrations inside the cell to balance the external saltiness, keeping the cell turgid without interfering badly with the cell's enzymes and metabolic processes.

Clever adaptation.

What about temperature?

That's another major factor.

Huge factor.

Every microbe has its cardinal temperatures, a minimum below which it won't grow, an optimum where it grows fastest, and a maximum above which it dies.

Based on these optimal, we group them.

OK.

What are the main groups?

At the cold end, you have cyclophiles.

Their optimum is often below 15 degrees C.

Some can even grow below freezing.

They adapt by having cell membranes rich in unsaturated fatty acids, which stay fluid at low temperatures.

Some even make antifreeze proteins.

Then there are the ones we're most familiar with.

Masophiles.

Their optima are moderate, usually between 20 degrees and 45 degrees C.

This group includes most human pathogens, since our body temperature is around 37 degrees C.

And at the hot end?

You get thermophiles.

Optima 45, 80 degrees C.

And then hyperthermophiles.

Optima above 80 degrees C.

Some archaea can grow well above boiling point, up to 113 degrees C or even slightly higher under pressure.

How on earth do they keep their proteins and DNA from falling apart at those temperatures?

Several ways.

Their membranes have more saturated branched lipids for stability.

Their proteins have subtle structural differences, making them more heat stable, often helped by chaperone proteins.

And critically, for DNA stability, many hyperthermophiles use an enzyme called reverse DNA gyrase.

Reverse gyrase?

Yeah.

It introduces positive supercoils into the DNA, which helps prevent the strands from melting apart at extreme temperatures.

Amazing.

Okay, another big environmental factor.

Oxygen.

Oh yes.

Oxygen is a real double -edged sword for microbes.

We classify them based on their relationship with O2.

What are the categories?

You have obligate aerobes.

Phophiles need O2, but only at low levels.

Normal atmospheric levels are toxic.

Facultative anaerobes grow best with O2, but can switch to anaerobic metabolism if it's absent.

Okay, then there are the ones that don't use it.

Right.

Aerotolerant anaerobes ignore O2.

They don't use it or are harmed by it.

And finally, strict anaerobes, for whom O2 is lethal poison.

Why is oxygen toxic to some?

I mean, we breathe it.

Because oxygen metabolism inevitably generates nasty byproducts called reactive oxygen species, ROS.

Things like superoxide radicals, O2, and hydrogen peroxide, H2O2, which can damage DNA, proteins, lipids, basically everything in the cell.

So how do organisms that use oxygen deal with that?

They have protective enzymes.

The two main ones are superoxo dismutase, SOD, which converts superoxide into oxygen and hydrogen peroxide, and catalase, or sometimes peroxidase, which breaks down hydrogen peroxide into water and oxygen.

And the strict anaerobes lack these.

Generally, yes.

They don't have robust defenses against ROS, which is why even brief exposure to air can kill them.

Facultative and aerotolerant organisms usually have SOD and catalyst peroxidase, too.

Makes sense.

Let's quickly touch on pressure and radiation.

Sure.

For pressure, most surface microbes are fine.

But deep sea organisms experience immense Some are barotolerant, survive but don't prefer high pressure, while others are piezophilic or barophilic, meaning they actually require high pressure to grow optimally.

Adaptations often involve changes in membrane fatty acids, more unsaturated ones to maintain fluidity under pressure.

And radiation.

Radiation can be damaging, too.

Ionizing radiation, like gamma rays or X -rays, causes DNA breaks and protein damage.

Some bacteria, famously Deinococcus radiodurans, are incredibly resistant due to highly efficient DNA repair systems.

What about UV?

UV radiation, especially around 260 mm, is readily absorbed by DNA and causes specific damage like thymine dimers, disrupting replication.

That's why UV is used for sterilization.

And visible light.

Can that be harmful?

Surprisingly, yes, sometimes.

If a cell contains photosensitizer molecules, visible light can excite them, leading to the production of highly reactive singlet oxygen, a type of ROS.

Many photosynthetic or even non -photosynthetic microbes that are exposed to light produce carotenoid pigments.

Like the colors in carrots.

Exactly those kinds of pigments.

They're very effective at quenching singlet oxygen, providing protection against light -induced damage.

So much adaptation.

It's important to remember, though, as we discussed with the myosin microbes, that in many natural environments, microbes aren't actively growing like in log phase.

They're often in low -nutrient oligotrophic conditions.

Right.

They spend a lot of time in a state of growth arrest or dormancy, conserving energy.

They might even start breaking down their own ribosomes to recycle the components when starved.

And when they do grow in nature, they rarely exist as free -floating single cells, like in a lab broth.

That's a key point.

Most microbes in nature live attached to surfaces in complex communities called biofilms.

Not just a random slime layer, right?

Definitely not.

Biofilms are highly structured communities.

Microbes attached to a surface start producing extracellular polymeric substances, EPS, which is that slimy matrix of polysaccharides, proteins, DNA, that encases the community.

What's the advantage of living in a biofilm?

Huge advantages.

The EPS matrix protects them from physical stress, from drying out, from UV radiation, from toxic substances, and importantly, from antibiotics and disinfectants.

It also helps trap nutrients.

That sounds like a major problem in medicine.

Absolutely is.

Biofilms readily form on medical implants, catheters, teeth.

Debil plaque is a biofilm.

The cells inside are much harder to kill with antibiotics, partly due to the physical barrier of the EPS, and partly because some cells within the biofilm enter a dormant, highly resistant state called persister cells.

So biofilms require coordination.

How do microbes in these communities talk to each other?

They use a process called quorum sensing.

It's essentially cell -density -dependent communication.

Sensing a quorum.

Like having enough members present to vote.

Kind of, yeah.

The classic example is the bioluminescent bacterium Vibrio fishery.

Each cell produces a small signaling molecule, an auto -inducer, in this case, and a sol -homocerein lactone, or AHL.

When there are only a few cells around, low density, this AHL molecule just diffuses away into the environment.

But as the population grows denser, the concentration of AHL builds up outside the cells.

To the point where it starts diffusing back into the cells.

Exactly.

Once the intracellular AHL concentration reaches a certain threshold,

the quorum binds to regulatory proteins and triggers a collective response.

In Vibrio fishery's case, it switches on the genes for bioluminescence, so the whole population starts glowing together.

So they coordinate group behaviors.

Does this happen between different species, too?

Yes, absolutely.

There's inter -domain communication as well.

A fantastic example is the symbiosis between rhizobium bacteria and lagoon plants.

For nitrogen fixation.

Right.

The plant root releases specific chemical signals, flavonoids.

The rhizobium bacteria detect these signals, and in response they produce their own signals called nod factors.

These nod factors cause the plant root hair to curl and allow the bacteria to infect, ultimately forming the nitrogen fixing nodule.

It's a chemical conversation between kingdoms.

That's really cool.

Okay, let's wrap up with a quick look at how we actually study these microbes in the lab, focusing on culturing.

Culturing is the cornerstone of microbiology, even though we know it has limitations.

As we mentioned, estimates are that we can currently only culture maybe one to five percent of the microbes out there in standard lab conditions.

So when we do culture them, we need media.

What are the basic types?

Broadly, we distinguish between defined or synthetic media, where every single chemical component and its exact concentration is known.

This is great for controlled physiological studies versus complex media.

These contain ingredients like beef extract, yeast extract, or peptones, which are enzymatic digests of proteins.

We know they provide lots of nutrients, but the exact chemical composition is variable and not fully known.

They're good for growing many different types of microbes, especially ones with complex nutritional requirements, fastidious ones.

And media can also be designed for specific functions, right?

Selective or differential.

Yes.

Selective media contain ingredients that inhibit the growth of some microbes while allowing others to grow, like adding antibiotics to select for resistant strains.

Differential media contain indicators, usually dyes, that allow you to distinguish between different types of microbes based on their metabolic activities.

Like Maconchi agar.

Perfect example.

Maconchi agar is both selective, inhibits gram -positives, and differential.

Lactose fermenters turn pink -rid, non -fermenters stay colorless.

And getting a pure culture, just one type of microbe, is crucial.

How is that usually done?

Often starts with an enrichment culture, using specific conditions or media to favor the growth of the desired microbe from a mixed sample.

Then you need isolation techniques.

The streak plate method is the workhorse, physically spreading cells out on agar, so individual cells form isolated colonies.

Spread plates and pore plates are used for counting.

Which brings us back to counting.

Why are plate counts reported as colony -forming units, CFU, instead of just cells?

Because we can't be sure that each colony arose from a single cell.

Maybe two or three cells stuck together, landed in the same spot, and grew into one colony.

So CFU acknowledges that uncertainty.

It reflects the number of viable units capable of forming a colony.

And this relates to the great plate count anomaly.

Exactly.

If you take a sample, say soil or water, and count the cells directly under a microscope using a counting chamber like a Petrov -Hauser chamber,

you almost always see vastly more cells than you get colonies when you plate the same sample on agar media.

Why the discrepancy?

Many reasons.

Some cells might be dead, some might be viable but not culturable on the specific medium used, some might be injured and unable to grow, or they might require neighbors to grow.

Consortia.

Besides direct microscopic counts and plate counts, what's another common way to estimate population size?

Turbidity measurement using a spectrophotometer.

As microbes grow in a liquid culture, they make it cloudy or turbid.

The spectrophotometer measures how much light is scattered by the suspension.

More cells mean more scattering, higher turbidity.

It's fast and non -destructive, but it measures total biomass,

living in dead cells, not necessarily viable cells.

And finally, you mentioned batch culture limitations.

Are there ways to keep cells growing exponentially for longer?

Yes, using continuous culture systems.

A chemostat, for example, continuously adds fresh medium at a slow, controlled rate while simultaneously removing spent medium and excess cells.

This keeps the nutrient concentration constant and low and the population density stable, maintaining cells and exponential growth, often mimicking those low -nutrient natural environments better than batch culture.

Wow, okay, that's quite a journey.

We've gone from a 100 -year division, times deep underground, down to the nanoscale precision of min proteins and FTSEs rings, ensuring perfect division through population dynamics, extreme survival, and even social networking via quorum sensing.

It really covers the fundamentals of microbial existence.

And understanding these processes is crucial whether you're developing antibiotics, targeting cell wall synthesis, predicting how pathogens might spread, or even harnessing microbes for biotechnology.

So much packed into such tiny organisms.

Absolutely.

And maybe a final thought for you to consider.

We talked about the great plate count anomaly and how many microbes are viable, but not culturable BBNC on standard lab media.

These BBNC cells are dormant, but they can potentially wake up and resume growth if conditions become favorable again.

Like microbial sleeper cells.

Exactly.

So the question is how do our current methods for ensuring safety testing, water purity, checking food for contamination need to evolve to better detect or account for potentially hidden, dormant, but still dangerous microbes?

That's a really important point.

A lot to think about.

Thank you for joining us on this deep dive into the remarkable world of microbial growth and survival.