Chapter: Prokaryotes-Bacteria and Archaea

Bacteria and Archaea were only figments of our imagination before the advent of the microscope. However, current evolutionary theory suggests they form two of the main branches of the tree of life. However, to us they are quite difficult to differentiate between Bacteria and Archaea based on morphological characteristics.

Multicellular Bacteria?

Both bacteria and archaea are almost completely unicellular. There are some colonial species, in which cells have intercellular connective structures linking cells together. These can form strings or mats, known as colonies. However, there is no differentiation of cell, producing distinct tissues, common in most multicellular eukaryotic organisms.

Impact of Bacteria and Archaea

Bacteria and Archaea are EVERYWHERE, and have been on Earth for a really, really long time. They have been found in every ecosystem from the 40 miles above the Earth’s surface in the atmosphere, to the bottom of the oceans, from the boiling pools of Yellowstone to underneath the glacier at the North Pole. They are inside of us, all over us, in the air we breath and all over the food we eat.

At 3.5 billion years old, they are the oldest living organisms known. In fact, Bacteria and Archaea had the Earth to themselves for over half of their existence. Scientists have spent the past several centuries cataloging the species of the world and have come up with a current estimate of 1.8 million species of plants and animals (and is estimated to be around 9 million). In contrast, only 5,000 species of Bacteria and Archaea have been cataloged. This isn’t because they aren’t there. It is because they are REALLY hard to identify. With today’s technology, we will not even be close to being able to estimate the number of species, let alone the number of individual prokaryotes.

That didn’t stop a group of microbiologists from the University of Georgia from trying. The group, led by microbiologist William Whitman, estimates the number to be five million trillion trillion. That's a five with 30 zeroes after it. Look at it this way. If each bacterium were a penny, the stack would reach a trillion light years. These almost incomprehensible numbers give only a sketch of the vast pervasiveness of bacteria in the natural world. 

Humans and Bacteria

Did you remember to floss this morning? As it turns out, it is a continuing battle. In fact, an adult human has 10^14 human cells within its body. But your digestive tract alone has an order of magnitude more bacterial cells, AN ORDER OF MAGNITUDE. We have a little less living on our skin at only 10^12. So when some says they really aren’t feeling like themselves today, ask them if they think the bacteria might be trying to take control of their bodies (because it may be true)

Prokaryotes Live Everywhere

Prokaryotes are EVERYWHERE. They live in the outer reaches of the atmosphere, inside of our stomachs, in boiling water, underneath the glaciers of the north pole, at the bottom of the deepest part of the ocean, and even miles below the Earth’s surface. Even though they are super tiny, they are thought to make up over 10% of the world’s biomass.

This is a true-color picture of the Grand Prismatic Springs of Yellowstone National Park. It is really that color; this is not Photoshopped. It is a geologic feature that constantly oozes water superheated from the Earth’s interior. As the water oozes out, it flows in extremely shallow streams. All those colors you see (other than blue) are unique bacterial communities that thrive at different temperatures: lemon yellow, mustard yellow, light orange, dark orange, and even red. And there isn’t a plant in sight.

Medical Importance

Bacteria are the primary agents of disease. Bacteria that cause disease are said to be pathogenic. And they primarily contaminate tissues at entry points: such as mouths, eyes, and open wounds. In plants, bacteria can also cause disease: and they are also most susceptible to infection at entry points: Stomata (the breathing pores in the leaves) and any open wounds the plant may have. Periodontitis is a disease of the mouth that primarily causes gum decay, and it is the first discovered Archaean pathogen. Periodontitis involves progressive loss of the bone around the teeth, and if left untreated, can lead to the loosening and subsequent loss of teeth. With that said, there are very few pathogenic Archaea that affect human health.

Germ Theory of Disease

The germ theory of disease, also called the pathogenic theory of medicine, is a theory that proposes that microorganisms are the cause of many diseases. Although highly controversial when first proposed, germ theory was validated in the late 19th century and is now a fundamental part of modern medicine and clinical microbiology, leading to such important innovations as antibiotics and hygienic practices. Koch was the first scientist to devise a series of tests used to assess the germ theory of disease.Koch's Postulates were published in 1890, and derived from his work demonstrating that anthrax was caused by the bacterium Bacillus anthracis. postulates are still used today to help determine whether a newly discovered disease is caused by a microorganism.Koch's postulates are four criteria designed to establish a causal relationship between a causative microbe and a disease. The postulates were formulated by Robert Koch and Friedrich Loeffler in 1884 and refined and published by Koch in 1890. These postulates have been generalized to many other diseases.

Koch's postulates are:

1. The microorganism must be found in abundance in all organisms suffering from the disease, but should not be found in healthy organisms.

2. The microorganism must be isolated from a diseased organism and grown in pure culture.

3. The cultured microorganism should cause disease when introduced into a healthy organism.

4. The microorganism must be reisolated from the inoculated, diseased experimental host and identified as being identical to the original specific causative agent.

Sanitation and Nutrition 

Once Koch and other microbiologists brought attention to the fact that germs create disease, many cities around the world began instituting cleaning campaigns within the cities. And you can see the effect of this, the mortality rate has consistently dropped since the beginning of the 20th century. Everyone thinks antibiotics are what dramatically reduced mortality rates. However, Penicillin, which was the first antibiotic that was widely distributed wasn’t widely used until the late 1940s. By this time, the mortality rate had been cut from approximately 800 per 100,000 to 150 per 100,000. So sanitation was really the key component in controlling pathogenic prevalence. Antibiotics were the nail in the coffin, however. But they were not without their consequences.

Pathogenic Bacteria

The ability for a bacteria to resist disease is known as its virulence. And virulence varies among individuals of a population, which is why there is a such a concern about the overuse of antibiotics. Within a given population it Is known that certain individuals are going to be resistant to antibiotics. Subsequently, those individuals will reproduce and produce the next generation. This is a picture of E. coli. Interestingly its virulence depends on the length of its genome.

Escherichia has an amazing diversity in its genome. Of all the specimens sequenced of Escherichia within ins genus, only 20% of their DNA are identical. This means that 80% of the variance changes within this one genus. Compare that with humans and chimpanzees. We only differ by 3% in our genomes between chimps. Escherichia differs by 80%.

Antibiotics

Discovered in 1928, antibiotics were a game changer in modern medicine. In fact, they are what define modern medicine. By World War II, the use of antibiotics were so commonplace that they were be given out to young children as “preventative” medicine, much like we use vaccines today. However, this has led to an unfortunate conclusion. Simple natural selection theory propses that those individuals most fit to survive in a population do and reproduce, providing the seed for the next generation. What we have seen is that bacteria have become resistant to antibiotics because of normal evolutionary processes. This has led to antibiotic resistant strains of bacteria that are scary to think about the implications of.

Extremophiles

We live in an extreme world. The X games were created to celebrate that. We do 1080 Kickflip McNastys, double backflips off a bicylcle, surf in hurricanes and ski 89 degree slopes. However, Bacteria and Archaea are the original extremophiles. They can literally grow on salt crystals (where nothing else can), they can live and thrive in temperatures barely below boiling to temperatures barely above freezing. And they can exist in extremely high pressure environments, even 7 miles below the surface of the ocean.

These prokaryotes that grow in these extreme environments are really important to the biological sciences. They are the weirdest organisms that we know. And their ancestry is so old that looking at them may help explain how life on Earth came to be. It is likely that life began in the absence of sunlight. In these environments, geothermal energy is these physical source of energy that is used to generate chemical energy for life to carry out its functions.

These organisms are so weird, that they are our best guess as to what to look for on other planets for extraterrestrial life. In the movies, we always extraterrestrial life that looks an awful lot like us: bipedal, big forward looking eyes, and even a mouth and nose. However, the most likely organisms that we will actually find will probably look something more like prokaryotes. I could be wrong; but if I were a betting man, I’d bet on finding little boogers before finding little green men.

Researching extremophiles has tremendously advanced our knowledge of the history of life on Earth, and not just because it allowed us to see that there are truly 3 domains of life on Earth, not 5 kingdoms. Researchers looking at the bacterial mats in Yellowstone found a protein that allowed researchers to amplify segments of DNA of any organism, which allows us to sequence those organisms. Without this technology, genetic research would likely still be in its infancy, simply because we wouldn’t have all the As, Cs, Ts, and Gs that we need to compare taxa.

Finding New Bacterial Species

So how do we find new bacterial species? It isn’t as easy as finding a new insect species. If you want to find a new insect species, just go somewhere not a lot of entomologists have been (like North Korea) or someplace where there is a huge amount of biodiversity (like Brazil), take your butterfly net and start frolicking around the bushes. You are very likely to come up with a new species. And how do you know? You just look at it, and ask yourself…Self, does that look like a new species? If so, keep it and take it back to the lab for further testing. Just for the record, most entomologists choose sipping margaritas in sunny, tropical Brazil over the work encampments of North Korea.

To find a new bacterial species, we do have to do the above steps (but we have to do even more in the lab). We have to sample cells from a specific environment. The most studied environment is the human body, for obvious reasons. Of the 5,000 species we know over 10% live in the human mouth. Just think of all the other environments where bacteria live, and you might just go cross-eyed. So the cells are collected, but that is just the beginning. The cells are taken back to the lab, where they have to be enriched. They must be grown (usually in a petri dish) into a colony, simply so they is enough of the bacteria to actually study. And here is the tricky part, nearly all bacteria have to grown under very specific environmental conditions. If you get one of these wrong, the bacteria won’t grow.

Once you grow up a colony that is large enough, you have to sequence part of its genome. In this way nearly all bacterial species that have been identified have been identified using the phonetic approach under the phylogenetic species concept. So how do you sequence a gene. It is REALLY expensive and very time consuming to sequence the entire genome. So researchers have identified specific genes in which they isolate from the rest of the genome in order to compare with other species. That isolated part of the genome is then amplified to increase the abundance of it. Then the amplified genes are put into a sequence machine that can identify the sequence of nucleotides of the DNA. Then researchers can compare the new sequence to see their sequence “significantly” differs. If it does then it can be argued that you have discovered a new species. However, how significant does the DNA have to be in order to be consider a different species. This is extremely subjective and is a hot point of contention among microbiological geneticists.

Discovering Archaea

Until the 20th century, most biologists considered all living things to be classifiable as either a plant or an animal. But in the 1950s and 1960s, most biologists came to the realization that this system failed to accommodate the fungi, protists, and bacteria. By the 1970s, a system of Five Kingdoms had come to be accepted as the model by which all living things could be classified. At a more fundamental level, a distinction was made between the prokaryotic  bacteria and the four eukaryotic  (plants, animals, fungi, & protists). The distinction recognizes the common traits that eukaryotic organisms share, such as nuclei, cytoskeletons, and internal membranes.

The scientific community was understandably shocked in the late 1970s by the discovery of an entirely new group of organisms -- the Archaea. Dr. Carl Woese and his colleagues at the University of Illinois were studying relationships among the prokaryotes using DNA sequences, and found that there were two distinctly different groups. Those "bacteria" that lived at high temperatures or produced methane clustered together as a group well away from the usual bacteria and the eukaryotes. Because of this vast difference in genetic makeup, Woese proposed that life be divided into three domains: Eukaryota, Eubacteria, and Archaebacteria. He later decided that the term Archaebacteria was a misnomer, and shortened it to Archaea. The three domains are shown in the illustration above at right, which illustrates also that each group is very different from the others. 

Morphological Diversity

Prokaryotes are really diverse. They can vary in size from half a micron to 100 microns. That would be if humans varied from 5 cm to 10m. Their shapes have three major variations. They can look like rods, spheres, or even rotini pasta. And the way they get around can vary from whip-like flagella which allow certain bacteria to sort swim. Others have a gliding motion, reaching out to a destination and pulling into it, much like certain worms. Others have hairs on their membrane, called cilia, that make them move around with the efficiency of a hovercraft.

Some prokaryotes have a thicker cell wall that contains a lot of carbohydrates and when stained appear dark purple in color. These are said to be Gram stain positive. Other prokaryotes lack an abundance of carbohydrates and contain an extra phospholipid layer, and don’t absorb Gram stain, and are Gram stain negative.

Metabolic Diversity

Organisms that make their own food are said to be autotrophs. Let’s break down that word. Auto means “ones self” and troph means “to nourish”. So autotrophs nourish themselves. We know and love autotrophs every day. We know them as plants. Well, certain bacteria can produce their own carbon-containing compounds (usually sugars) as well and are also known as autotrophs. Organisms that rely on other organisms to produce carbon-containing compounds and consume those organisms for food are known as heterotrophs. Hetero means “different” and troph means “to nourish”. We are heterotrophs, deer are heterotrophs, and bacteria that can’t produce their own food are also heterotrophs.

Remember cellular respiration and Photosynthesis. In photosynthesis, plants utilize energy from the sun combining carbon dioxide with water to make sugars and oxygen gas. Plants break down the sugars (a C-containing compound) using oxygen as an electron receptor in order to synthesize ATP from ADP and a Phosphorous molecule, in a process known as cellular respiration. This is responsible for generating the energy needed for plants to go through life’s functions. Animals also break down sugars in exactly the same process.

Certain prokaryotes also have these metabolic processes. However of the six known metabolic processes known in living organisms, prokaryotes do all of them, whereas eukaryotes only do two. Prokaryotes can use another electron donor other than sugar and they can use another electron receptor other than oxygen.

Photophosphorylation

The production of ATP using the energy of sunlight is called photophosphorylation. Only two sources of energy are available to living organisms: sunlight and reduction-oxidation (redox) reactions. All organisms produce ATP, which is the universal energy currency of life.In photophosphorylation, light energy is used to create a high-energy electron donor and a lower-energy electron acceptor. Electrons then move spontaneously from donor to acceptor through an electron transport chain. An electron transport chain couples electron transfer between an electron donor (such as NADH) and an electron acceptor (such as O2) with the transfer of H+ ions (protons) across a membrane. The resulting electrochemical proton gradient is used to generate chemical energy in the form of (ATP). Electron transport chains are the cellular mechanisms used for extracting energy from sunlight in photosynthesis and also from redox reactions, such as the oxidation of sugars (respiration).

Chemoorganotrophs

Chemoorganotrophs are organisms which oxidize the chemical bonds in organic compounds (compounds containing carbon) as their energy source. Chemoorganotrophs also attain the carbon molecules that they need for cellular function from these organic compounds. The organic compounds that they oxidize include sugars (i.e. glucose), as well as fats and proteins). All animals are chemoheterotrophs (meaning they oxidize chemical compounds as a source of energy and carbon), as are fungi, protozoa, and some bacteria. The important differentiation amongst this group is that chemoorganotrophs oxidize only organic compounds while chemolithotrophs instead use inorganic compounds as a source of energy.A chemolithotroph is an organism that uses an inorganic substrate (usually of mineral origin) to obtain reducing equivalents for use in biosynthesis (e.g., carbon dioxide fixation) or energy conservation via aerobic or anaerobic respiration. Known chemolithotrophs are exclusively microbes; No known macrofauna possesses the ability to utilize inorganic compounds as energy sources. Macrofauna and lithotrophs can form symbiotic relationships, in which case the lithotrophs are called "prokaryotic symbionts." An example of this is chemolithotrophic bacteria in deep sea worms, in which the bacterial lithotrophs use the worms as a host body, but they produce ATP from the deep sea vents and share energy with their host.