Bacteria

Life Processes ... continued

E

Excretion

Excretion = Exit

If it exits the body it's excretion

So when you do a number 1 or a number 2 - both excretion

However, when you breath out - that's also excretion

Sweat and tears are not. The distinction is whether or not the thing exiting the body is waste

Carbon dioxide that you exhale is waste, so it is excretion

Undigested cellulose that makes up the bulk of feces is waste

Urea in Urine is waste

Excretion by bacteria is done through one of two methods

  1. Diffusion

  2. Facilitated transport

  3. Active transport

  4. Exocytosis

Diffusion

This is when small molecules simply move down their concentration gradient. Stuff that is made by chemical reactions in the cell, such as carbon dioxide, will be in a higher concentration within the cell. So diffusion will favor their movement out of the cell. This is also how we get rid of our carbon dioxide.

Facilitated transport

This is when the molecule is either too large to diffuse through the lipid membrane. Or it is repelled by the lipid membrane. So, the cell 'facilitates' the transport of the compound through a tunnel made of protein that spans the membrane. This channel will move was down its concentration gradient.

Active transport

This is when the waste needs to be pushed through a channel to the outside of the cell. This is similar to facilitated transport as it uses a channel. However it needs to be pushed due to it going against its concentration gradient. This is 'active' as it uses ATP. This is 'active' because the cell needs to use energy to get ride of the waste

Exocytosis

Exocytosis = exit cell. This is when the waste to large to diffuse or to be pushed out of a channel. In this case it is packaged into a little ball (vesicle) which is made from lipid. This merges with the membrane and the ball is popped, throwing the waste away from the cell

There are lots of things chemicals that need to leave a bacterial cell.

These are the 5 compounds that we will look at. Three are from Respiration, then Nitrogen and Toxins.

The three from Respiration are Carbon dioxide (aerobic), Lactic Acid (anaerobic), Methane (anaerobic)

Excretion of Carbon

These are the 3 that are due to Respiration:

  1. Carbon dioxide (aerobic)

    • If the bacteria is a obligate aerobe or a facultative anaerobe in an oxygen rich environment, then it will conduct aerobic respiration.

    • Aerobic respiration: glucose + oxygen = Carbon dioxide + water (+ lots of energy)

    • The Carbon Dioxide diffuses out of the bacteria and re enters the air

  2. Lactic Acid (anaerobic)

    • If the bacteria is a obligate anaerobe or a facultative anaerobe in a hypoxic (low O2) or anoxic (no O2) environment then it will conduct anaerobic respiration

    • Lactic acid Anaerobic respiration: Glucose = Lactic Acid + Lactic Acid (+ little bit of energy)

  3. Methane (anaerobic)

    • If the bacteria is a methanogenic bacteria then it will be an obligate anaerobe that produces methane

    • Methanogenic Anaerobic respiration: Glucose = Methane + Carbon Dioxide

Carbon Cycle

Parthenon, Greece, 447BC

What remains of human civilization from the B.C's.

Where is the material of life from over 2000 years ago?

What structures did they live in

What sturctures of theirs remain

What ancient structures can you think of?

What are they made of?

Have a look here for interest if you like: https://en.wikipedia.org/wiki/List_of_oldest_known_surviving_buildings

The only things left are made from stone

So where is everything else? Where are the millions of animal skin tents, wooden huts, wooden houses?

Only the rich and powerful, of whom there were very few, could build from stone, or those that lived where trees were scare.

Wood is easier to build with: no mining required, no brick-making. Just cut down cut it into planks, stick them together and you have a house. But where are all the things millions of people lived in? Where are their spears and arrows. Their clothes. Where is it all?

Its in the air

All of it, is in the air

Ash to Ash, Dust to Dust.

How does it get there?

The bacteria and Fungi digested the wood.

Absorbed the digested complex carbon structures and broke these down, gaining their energy through cellular respiration, into simple carbon compounds: Carbon dioxide mainly, and some Methane (anaerobic)

This process of turning everything that was alive, like wood, back into Carbon dioxide is called the Carbon cycle.

It is a cycle, because eventually trees will absorb this carbon dioxide and use the carbon to make more wood and grow.

They will then die, their wood will be fed on by bacteria and fungi, through digestion, cellular respiration, and excretion, the carbon will re-enter the air again and so continues the cycle

But it is not just trees. Grass takes in carbon dioxide and uses the carbon to build itself. Zebra eat the grass and use the carbon to build themselves bigger. Some of this carbon becomes part of the fat of the Zebra. The zebra also does cellular respiration, so it takes in oxygen and releases carbon dioxide in its breath.

A lion eats the zebra and it is assimilated the carbon into its body. Becoming part of a muscle. The lion grows old and passes away. The bacteria that has lived happily in its gut for throughout its life now eat it, they digest, respire, then excrete the carbon dioxide back into the air.

Carbon enters living systems through Photosynthesis

It then moves through the food chains through Digestion

It only enters back into the atmosphere via Respiration... or fire

Carbon going into the air slowly

Carbon going into the air very quickly (Australian bush fires 2020)

Chatham Islands Whaling station, 1880s.

Where are the wooden structures? In the air!!!

Coromandel Gold Mine, 1880s.

Where are the wooden structures? In the air!!!

Richard Henry's house, jetty and conservation pen, 1890

Where did Richards house and pens go? In the air!!

Hurleyville Dairy, South Taranaki. Abandoned 1970s. How long till its in the air??

Meat at Pak'n Save, 2019. Where is the meat now? Its in the air!!

Fresh Meat in Africa... where is it now?

Death, Food and Carbon Dioxide

When something dies, its carbon will only become carbon dioxide if something eats it and releases the carbon dioxide through respiration.

If we have a cow and it dies then there are 3 options:

  1. eaten by us

    • when have you ever eaten something alive? Everything you eat is dead

    • When we eat it, most of the carbon will be released via cellular respiration and we breath it out as carbon dioxide. Only a very small amount of what we eat remains in our bodies, otherwise we'd get very fat very quickly.

    • Carbon reenters the atmosphere via respiration

  2. eaten by scavengers

    • includes rats

    • Carbon reenters the atmosphere via respiration

  3. eaten by insects and worms

    • these are often included as decomposers

    • maggots and worms are busy here

    • Carbon reenters the atmosphere via respiration

  4. eaten by bacteria and fungi

    • these are decomposers

    • we call this rotting or decomposition

      • decomposition - the opposite of composition

        • decomposition = break down

    • Bacteria eat it. Some of the carbon atoms remain in the bacteria allowing it to grow.

    • Carbon reenters the atmosphere via respiration

  5. it is preserved

    • This is when bacteria cannot digest it

    • The main way happens is to get rid of moisture. Dry it out. Think of the Egyptian preservation.

    • Carbon is trapped

Carbon atoms moving through natural living systems

Carbon is the basis of life on the planet

Carbon is trapped in rocks, like:

  1. Graphite (graphite mine): pure carbon, found in pencils

  2. Diamonds - pure carbon, arranged differently

  3. Metal Carbonates (CO3) such as Calcium carbonate found in

    • Chalk (fine limestone):'white cliffs of Dover'

    • Limestone (compacted chalk):

        • Waitomo Caves

        • Auckland Clock Tower and Auckland Museum

    • Marble bench tops and statues

  4. The largest store on the planet is in the earths core as Iron Carbon Alloys.

    • As these alloys move towards earths surface they combine with oxygen rich compounds, to make carbon dioxide and dihydrogen oxide (water). This makes the carbon dioxide and water for our planet

    • https://www.nature.com/articles/s43247-021-00222-7

    • Interestingly, we make steel, this is a iron carbon alloy

Water that can very slowly dissolve limestone, releasing the Carbon dioxide back into the atmosphere - this is how the Waitomo caves formed

The bulk of the Carbon in our Atmosphere has come from Volcanoes.

Volcanoes release carbon dioxide from the super heated rocks into the atmosphere. This is the original source of carbon dioxide. Our first atmosphere which was full of carbon dioxide and nitrogen.

Photosynthetic bacteria and later algae turned this carbon dioxide rich atmosphere of the very early earth into the oxygen rich one we have today (78% Nitrogen, 21% oxygen, 0.01% Carbon dioxide)

We need this 0.01% Carbon dioxide to keep out planet warm, and to sustain plant life - if photosynthesis stopped, everything would die.

Carbon atoms move through this cycle, going from living systems to the air, then back into living systems

This is a perfect balance

CO2 - plants - animals - bacteria/fungi - CO2

CO2 - Photosynthesis - Respiration - CO2

Combustion

Looking at the side of the chart we can see combustion, fire.

Naturally occurring fires are due to dry lightening and friction of branches in extremely dry and hot conditions. So Combustion was a relatively rare event

Carbonification

Looking on the chart we can also see 'Carbonification'

Carbonification occurs when dead organisms are buried before the bacteria and fungi have consumed all of the carbon.

This often happens with large trees in jungles. The huge tree falls, bacteria and fungi start to work on the trunk, but the surrounding trees drop leaves onto it. Eventually the trunk is buried under the leaf litter. Other trees fall on top of it, more leaf litter and then it is completely buried. Oxygen can no longer get to it, so all that is left is slow anaerobic respiration. Some carbon still escapes as methane from this slow anaerobic respiration. As the trunk gets buried deeper and deeper the water is squeezed out by pressure and also it becomes harder for ground water to get that deep. With reducing levels of water, fewer and fewer bacteria can survive until they are all gone. Now you have a layer of carbon compounds. These carbon compounds have been squeezed together under the pressure of millions of years of other trees falling on top of them. This makes a solid carbon compound.

These carbon compounds also have hydrogen attached so they are called hydrocarbons. These hydrocarbons are made from dead things, so they are also called fossil fuels.

All fossil fuels are hydrocarbons. There are 3 types depending on their state; solid, liquid, gas.

These carbon compounds are coal, oil and gas.

Coal = trees

Oil = dead sea life

Gas = dead sea life

These buried fossils are too deep for bacteria to get to in numbers of significance

So this is deep stored carbon

Coal - lots of carbon, all fused together making a very complex molecule. Which means it has incredible amounts of stored energy way more than wood or cellulose

Crude oil is a mixture of different sized hydrocarbons

Size refers to the number of Carbon atoms. The more Carbon atoms, the hotter

Crude oil is separated using heat and gravity.

By heating the oil, convection currents form. The smallest compounds float up the highest, whilst the long carbon chain ones can absorb more heat energy and are heavier so they come out the bottom.

Petrol has up to 10 Carbons. Diesel up to 20. And bitumen tar has over 70.

Because Tar or bitumen has so many Carbons it is hard to vaporize and for oxygen to collide with it. It needs to be extremely hot to vaporize. Because of its very high melting point, bitumen tar used on roads even through it is from crude oil. In fact fire from blow torches is often used to soften it back into a liquid. Fire is also used to heat it so that it can be poured onto roads.

However, given the right conditions it actually can burn, as proven in the Skycity tar roof fire. Though it did need a blowtorch left on it for a long time.

Humans stuffed it up

The carbon cycle was in a nice balance

Then Humans discovered the energy of fossils.

They dug it up and burnt it.

That burning it released heaps of energy. And so they did, all of them.

To burn petrol, diesel and coal you combine the hydrocarbon with with oxygen to make carbon dioxide and water

So now Combustion of fossils is adding heaps of Carbon into the atmosphere.

This carbon dioxide in the air traps heat, causing global warming

The only way to remove this carbon dioxide is through photosynthesis.

However, humans cut down 15 billion trees per year

The amazon rainforest is being deforested so fast that it might be gone by the end of the century.


https://www.nature.com/articles/d41586-020-00508-4

This causes Global Warming

Global warming causes the ice caps to melt, bush fires to occur and more Global warming to occur. Droughts and severe storms occur more frequently and global food supply is at greater risk. This is Bad for all species, including humans.

This extra combustion added Carbon to the atmosphere, causing global warming. In the diagram above, it is the peach 'Anthropogenic' carbon.

We cut down the worlds forests stopping the world from healing itself. But we weren't finished causing damage

Then invented something wont rust away and that bacteria and fungi cannot decompose! Plastic!

Then humans discovered how to turn petrol into plastic and their impact on the planet got way worse because bacteria and fungi can NOT digest plastic

Because plastic cannot be eaten by bacteria it does not decompose and turn back into carbon dioxide.

Paper can decompose and turn back into carbon dioxide

Wood and wooden houses decompose and turn back into carbon dioxide

But plastic does not

Plastic can be broken into smaller pieces by waves smashing it on beaches, by UV light breaking some of the polymers. By animals taking bites out of it. But all it does is get smaller and smaller until it enters food chains

These food chains include us. Furthermore, as we start eating plastics we get the toxins of plastics. BPA is part of plastics. It is called Bisphenol A. This is a very large chemical compound with 15 carbons, C15H16O2 . Bacteria can not break this down. But it can enter the food chains, be eaten by humans and enter our blood. This has consequences such as the chemical castration of the human male

Too keep plastic out of our food chains our choices are

  1. Burn it

    • This contributes to global warming

  2. Bury it very deep

    • Make sure it is very deep or it will get out

    • There is a problem of it leaching (leachate) from the dump into the underground water.

  3. Turn it back into oil though plastic pyrolysis

  4. Recycle it, upcycle it or reuse it

By working together, Humans are smart enough to fix the problem

Especially if we get a little help from plants, bacteria and fungi

Sir David Attenborough has seen the changes that humans have done to the planet, and the speed of these changes.

He has worked to raise awareness of the destruction that we are causing on earth

As humans have become aware of the issues, there is a effort of unprecedented scale to harness the intellectual capabilities of our entire species and to solve the problems that we have created

As people become aware they want to help. Human behavor changes. We buy products that use less plastic. We buy food that doesn't have palm oil. We drive cars that burn less petrol, perhaps even drive EVs.

Though the biggest change can only be done with a bit of a push from governments.

We can fix the climate problems.

  1. Drive Electric Vehicles

  2. Make the Electricity with renewable energy

    • hydropower

    • solar power

    • wind power

  3. Stop using Fossils as fuel

  4. Plant trees. Lots of trees.

Going electric, using renewable electricity and planting trees. Good, climate change solved.

What about plastics?

In terms of plastics, we need to invent things that can do the same jobs that plastic do, but they need to be eaten by bacteria once we have finished with them

These things are bioplastics.

This makes the cycle natural again

Bacteria and fungi to the rescue!

Bacteria and fungi will digest the bioplastic, respire - turning it into carbon dioxide and water, and then excrete the carbon dioxide

This carbon dioxide is then absorbed by the extra trees that we have planted

Future humans or aliens will find plastic. A lot of it.

They will find the stone remnants of our buildings, especially those with reinforced steel

A lot of our steel things will slowly rust away

All of our wooden structures will rot

This decay will be slow in the dry places, like Los Vegas

This decay will be faster in wet places, like Auckland

Decay is digestion, respiration and excretion by bacteria and fungi

They keep the nutrients cycling.

The anthropogenic carbon cycle

Now the carbon cycle runs with significant modification by humans

We now need to account for

  1. deforestation

  2. mining of fossils

  3. burning of fossils

The diagram shows human input in red

As you can see, also in red, humans are increasing the amount of carbon in the atmosphere by 4 Billion Tonnes per year

4 PgC = 4 Billion tonnes


Excretion of Nitrogen

Nitrogen compounds

    • From the breaking down of amino acids

    • For us, we release this as urea, CH4N2O in urine. but bacteria do not (in fact some can digest urea to get the carbon)

    • For bacteria, they release the nitrogen as either

      • Ammonium, NH4

            • most bacteria do this.

            • Looking at the structure of an amino acid, you can see why this is

            • This can be absorbed through the roots of plants and used to create amino acids

      • Nitrite ions, NO2-

            • This is done by special Nitrifying bacteria

            • Nitrifying bacteria can take in ammonia and turn it into nitrate

      • Nitrate ions, NO3-

            • The Nitrifying bacteria mentioned above, can also turn nitrite ions into nitrate ions

            • This Nitrate can then be taken up through the roots of plants

            • Plants can also use this nitrate, NO3- to build amino acids

    • This cycle of nitrate is extremely important to the cycling of nitrogen through living systems

amino acid → bacteria → ammonium / nitrate → plant → amino acid

(plants can also take up urea as their nitrogen source, which is why its good to pee on the roots of a lemon tree)


    • A group of anaerobic bacteria called denitrifying bacteria they can use NO3- as a source of oxygen, their version of anaerobic respiration is:

            • Glucose or methane + Nitrate = Nitrogen + Carbon dioxide + Water

            • these are denitrifying bacteria and they are used in the Mangere sewage treatment to reduce the amount of nitrate entering the Manukau harbor

            • Denitrifying bacteria can take this nitrate and turn it back into Nitrogen gas, N2

    • A special group of aerobic bacteria called nitrogen fixing bacteria can turn Nitrogen gas N2, into Ammonia, NH4 , and into nitrate ions

            • These nitrogen fixing bacteria are fundamental to life on our planet as they are the only things that can take nitrogen directly from our atmosphere and turn it into something that plants can use. So they start the cycle

The movement of Nitrogen is called the The Nitrogen Cycle

Nitrogen Cycle

Excretion of Toxins

Imagine that you are in a tribe of humans trying to find food. Walking for years from place to place. Then you find a place that has food, enough for you and your tribe. What would you do to protect your find? To secure food for you and your tribe? You might make weapons and traps to keep others away.

For Bacteria, they can secrete Toxins. These are their weapons.

These weapons will be either excreted: exotoxin

Or released when they die: endotoxin

Bacteria excrete their exotoxin weapons for 2 reasons

  1. Competition (War)

    • To keep the food for only their species

    • once the bacteria have found a new food supply, the release of toxins will stop other species from becoming established

    • These toxins will Kill other bacterial species

  2. Hunting and killing

    • To turn other cells into food

    • some of the toxins are designed to kill other cells so that they can become food

Competition - the use of Toxins in the War for food

The use of exotoxins to prevent bacterial to bacteria competition is used in agar art

Bacteria can be 'drawn' onto the agar plate. They then secrete toxins stopping the other bacteria from coming over to their 'space'.

Sometimes one bacteria's toxin might be more effective than the others, it will then be able to kill of the other species and take the whole plate for its descendants

Hunting and killing - the use of Toxins to turn cells into food

This toxin is designed to turn cells into food

It is a pore forming toxin.

The bacteria excretes this toxin. It is safe from it due to its capsule and slime layer

The toxin then arrives at a cell, and bores a tunnel into the cells membrane, a pore

This tunnel causes water to pour into the cell

The cell can not stop the water from pouring in

The cell swells, then bursts

The bacteria moves over and digests the remnants of the burst cell.


Flesh eating bacteria secrete a pore forming toxin, as well as others that cause blood cells to burst and all the cells in the flesh to die. This all becomes food for the bacteria, which then eat, grow, reproduce, repeat.

Bacterial Toxins in Human Disease

Botulism toxin is a exotoxin that is one of the deadliest

Luckily, it is easily destroyed by cooking

As are the toxins from Salmonella and Campylobacter

This is why cooking your food thoroughly is so important.

However, not all toxins can be destroyed through cooking.

This is why once food is 'off' cooking it will not make it safe. Despite killing the bacteria and destroying many of the toxins, there will still be many toxins that will retain their toxicity.

Exposure to very high levels of bacterial toxins can cause 'toxic shock' which is when the immune system goes nuclear on the toxins. The chaos that follows causes multi-organ failure and death die

Botumlism is a disease where people make home canned goods but haven't sterilized the food properly.

Cloxtridium botulinum is an anaerobic bacteria that can live in these cans

It secretes the botulism toxin

When eaten, this toxin goes into nerve fibers and neurons and stops them from releasing neurotransmitters

This stops your brain from communicating with your muscles

This blocks the signal from your brain telling your ribs and diaphragm to move, thus you stop breathing!

Scientists have isolated the toxin, and now people have it directed into the muscles in their forehead to block the signal from their brain to their forehead so they no longer frown.

Another really nasty one is Tetanus. It is also a anaerobic bacterium that releases a exotoxin that blocks nerve to muscle signaling.

The symptoms are different as only some neurotransmitters are blocked rather than all of them. It blocks the relaxing neurotransmitters but not the contract neurotransmitters - so all of the muslces contract!

This can also kill by stopping the rib cage from moving.

Luckily the vaccine for it is extremely effective

Notice how many of the 5 deadliest substances are bacterial toxins