NEW HEALTH GUIDE – TYPES OF BACTERIA
Origins
It would be easy for us to assume that bacteria are the simplest form of life and thus presumably would have been the original life form on this planet. This may be true but it is not a simple equation. Bacteria are single-cell organisms and are what are known as prokaryotic cells. These differ considerably from the cells of both animals and plants inasmuch as there are no visible discrete compartments within the cell. They are also usually considerably smaller than the cells of animals and plants.
So how did bacteria first emerge? This looks like a classic ‘chicken and egg’ conundrum. Bacteria, like all cells, contain DNA and they function by the decoding of this DNA into proteins, which comprise the enzymes that control all the major processes within the organism. In this respect, they are similar to other cells and thus probably have a common origin. The link between DNA decoding and protein production is RNA. RNA does not differ greatly in structure from DNA and some believe that RNA is the origin of life. This is plausible as RNA is the messenger; it is the molecule that is transcribed from DNA and from which protein is translated. It was the discovery of ribozymes by Thomas Cech, at the University of Colorado, and Sydney Altman of Yale University that strongly suggested that RNA was the origin of life. Ribozymes are RNA molecules that have a 3D (tertiary) structure and they can act as catalysts, similar to enzymes. Therefore RNA could act not only as the store of genetic material but also as the ‘enzyme’ that decodes it into the structures of life.
We may never be able to confirm this hypothesis but if we assume that it is plausible, then we can start to examine how bacteria emerged and where they fit in the evolutionary tree. Approximately 4.3 billion years ago, the first cells are thought to have arisen, probably with RNA as an essential catalytic role and later as a self-replicating molecule. The basic integrity of a cell is the formation of a cell membrane, composed of lipid bilayers. As these can form spontaneously, they could have surrounded early RNA molecules. Their continued presence may have been promoted through mutation of the RNA, which would have been passed on to succeeding generations through self-replication. This basic system does have significant disadvantages because a mistake made in the replication of RNA would immediately have an effect not only on the replication of the genetic material but also on the ability to act as a catalyst-largely, it may be assumed, in a detrimental manner. The separation of the self-replicating machinery from the enzymes they encode would have resulted in far fewer abortive stages.
Consequently, we must assume that DNA largely took over the role of the carrier for the self-replicating genes and proteins of the enzymes that they eventually encoded. RNA merely remained as the messenger that carried the instructions from DNA to the formation of the proteins.
The early bacteria emerged approximately 1.5 billion years after the creation of the planet. For the next three billion years, bacteria were probably the planet’s sole living inhabitant. The fossil record shows that there were huge numbers of bacteria often collecting in large colonies, attached to many surfaces; their imprint can still be seen. Approximately one billion years ago, however, the numbers of these colonies in the fossil record began to fall and this could be evidence that bacteria had become the source of food for some other life form. Certainly, this was before the Cambrian explosion of half a billion years ago, when the diversity of life forms increased rapidly, but it does suggest that, for the first three-quarters of life on Earth, bacteria had it all their own way.
What were these bacteria?
1. Timescale of bacteria emergence
The common view is that prokaryotic cells, such as bacteria, and eukaryotic cells, such as those that comprise our bodies, had a common ancestor. The last universal common ancestor (LUCA) or cenancestor is considered to be the most recent ancestor of all life on Earth and possibly was living some 3.5 billion years ago. It is thought to have been a prokaryotic, single-celled organism possibly similar to simple bacteria found today. By this time, it has been concluded that the genetic code must have become DNA rather than RNA, and that the catalysts had become true enzymes (proteins) composed of the twenty amino acids. Furthermore, the machinery for dividing the DNA, maintaining its integrity, and expressing the genes through RNA was already established.
These bacteria would have been exclusively anaerobic; they did not respire oxygen as there was little or no available oxygen in the atmosphere at the time. These bacteria could produce energy from the available nutrients but this was an extremely inefficient process. About 3.2 billion years ago, photosynthetic bacteria or cyanobacteria first emerged. These bacteria could use energy from the sun to make sugars, which were used for further metabolism. The by-product of this photosynthesis was oxygen, which began to accumulate in the atmosphere. Oxygen is toxic to many cells, particularly the early anaerobic bacteria, which probably started to decline. About 2.5 billion years ago, the fossil record shows that aerobic bacteria emerged, able to use the newly available oxygen and use it to convert sugars into energy, usually in the form of adenosine-5’-triphosphate (ATP). The use of oxygen vastly increased the energy obtained from a single sugar molecule, and these bacteria soon predominated.
The main eukaryotic cells may have derived from an early example of Archaea bacteria, which themselves derived from LUCA. They probably evolved about 1.5 billion years ago. These were distinguishable from prokaryotic cells by having a defined nucleus, usually comprising discrete chromosomes, that contained the DNA. However, having emerged from bacteria, the evolution of these eukaryotic cells did not proceed independently of prokaryotes, but with a degree of symbiosis.
Eukaryotic cells possess distinct organelles; most animal cells possess mitochondia and most plant cells contain chloroplasts. Both these organelles are approximately the same size as bacteria and possess their own DNA. Mitochondria probably originated from oxygen-utilizing bacteria, such as early examples of proteobacteria or cyanobacteria, which have been captured by eukaryotic cells to provide energy through oxidative phosphorylation. Chloroplasts probably originated from photosynthetic bacteria in order to produce energy from light. In both cases, the eukaryotic cells ingested the bacteria but did not destroy them; allowing coexist is a good example of this known as endosymbiosis. Both animal and plant eukaryotic cells were taking up the energy-generating machinery of bacteria, which had evolved over millions of years, thus obviating the need for their separate evolution in eukaryotic cells. This certainly accelerated the development of eukaryotic cells. It is believed that the incorporation of mitochondria and chloroplasts into eukaryotic cells also occurred 1.5 billion years ago as eukaryotic cells emerged. The mitochondria-containing cells became the cells of animals and the chloroplast-containing cells those of plants. Both mitochondria and chloroplasts still contain their ancient DNA, which replicates independently from the nuclear DNA of the eukaryotic cell itself. Similarly, this DNA is not affected by the sexual reproduction of the host and carries unaltered DNA from generation to generation. The acquisition of these energy-producing organelles rapidly increased the evolution of the eukaryotic cells, resulting in the Cambrian explosion of multicellular, eukaryotic animals and plants 500 million years ago.
What else distinguishes a bacterial cell from a eukaryotic cell? The size is an obvious distinction: the bacterial cell could be two microns in length whereas a mammalian cell may be fifteen times longer and 1,000 times greater in volume. However, one striking feature is the maintenance of the self-replicating genetic material, DNA. In bacteria, it is maintained as a single genome, with the genes closely packed and genes controlling related functions often clustered together. On the other hand, most eukaryotic cells have their DNA divided up into several chromosomes and are diploid, receiving one set of chromosomes from each parent. Therefore the chromosomes are homologous pairs, basically carrying the same genes in the same order. This arrangement can compensate for errors in the DNA as recombination of a damaged gene with the duplicate intact gene can rectify the error. The single copy of the bacterial genome means that if a mistake is made, it is likely to be permanent and often is lethal. The reason for this may be that many eukaryotic cells form part of a much larger organism where disastrous mutations could cause major damage, such as cancer. So the duplication may have evolved to minimize this. Bacteria, on the other hand, although they are single-celled organisms, are usually not in isolation but form colonies. Each cell is capable of regenerating the colony. So if, during DNA division, mutations do occur which are lethal for the host cell, there will be enough members of the colony, in which mutations have not occurred, to keep the colony thriving.
Bacteria and their own fight for survival
Normally bacteria divide by binary fission, whereby a single cell expands by creating macromolecules that make up the components of the cell and the cell wall. When the cell reaches approximately double its size, a septum is formed between the two halves of this enlarged cell. The septum is essentially part of the cell wall that, when complete, forms two complete daughter cells, which are able to separate from each other. In ideal conditions, this cell division can take place once every twenty minutes; so, in theory, a single bacterial cell could produce more than sixteen million progeny in eight hours. Although cell division time is short, the time taken to replicate the DNA of the cell is longer, often twice as long. In order to keep up with cell division, new replication cycles of DNA are started before the previous round has finished. Indeed, multiple copies of DNA are being replicated within a fast-growing culture. Rapid replication of DNA promotes mutations. Many of these will be lethal but some will be beneficial. In particular, the mutations have allowed individual bacterial species increased capability to compete for nutrients, often to the disadvantage of neighbouring bacteria, resulting in some local ‘warfare’, particularly in environments such as the soil. This led to the development of ‘weapons’, chemicals known as secondary metabolites that are excreted by the bacteria. Bacteriocins are released by bacteria to destroy surrounding bacteria of similar species, but they are quite limited in their effect. This capability has been refined by, for example, the Actinomyces, which are able to release chemicals that kill most bacteria; it is from these that we get most of our antibiotics.
By many small advantageous mutations, bacteria have been able to adapt to almost every environment and this has been the primary method of survival and evolution; however, the evolution of bacteria has not been without its own struggles. A hundred years ago, Frederick Twort and Félix d’Hérelle independently discovered small elements capable of killing bacteria. These were bacterial viruses or bacteriophages, simply called phages for short. Their existence had been implied since the earliest medical documentation which reported that some river waters could cure some bacterial infections. Recent metagenomic studies have shown that these viruses are profuse in most aqueous environments, making them as abundant as bacteria themselves.
2. Structure of a T4 bacteriophage
The conventional lytic phage, which is composed of DNA surrounded by a protein coat, follows a cycle; it starts when the phage attaches to the bacterial cell and injects its DNA. This takes over the normal replication machinery of the bacteria and results in the production of many, sometimes hundreds, of new phage protein particles. These particles pick up the replicated phage DNA; they are released, killing the host bacterial cell in the process, and are able to infect new bacterial cells. Bacteria have had to defy this attack and, quite quickly in some cases, the bacteria become resistant, often by alterations in the cell surface so that the phage cannot attach. There has been a continuous struggle between bacteria and these viruses but, as with viruses that attack humans, a balance is usually reached.
At some points in this process, there would that have a predisposition towardsQ5n have been an inevitable exchange of genes. The new phage particles may pick up some bacterial genes along with, or rather than, new phage DNA which they can pass on to other bacterial cells on subsequent infection.
Some phages can become parasitic after infection; instead of replicating and producing new phages, the DNA integrates into the bacterial DNA. In this case, the phage DNA is replicated every time the bacterial DNA is replicated and so every daughter-cell DNA carries a copy of the phage DNA. It is often kept integrated by a repressor protein encoded by the DNA itself. This is known as a lysogenic phage. If this protein is compromised by a chemical, ultraviolet light, or some other insult, then the phage DNA initiates the production of new phage particles, the DNA replicates and is incorporated into these particles, and they are released to invade other bacteria. Often, the bacterial genes, surrounding the inserted phage DNA, are incorporated into these particles and these are spread to new bacterial cells.
Bacteria and their place in the world
Bacteria are, of course, still evolving; however, if we move out of geological time and into a time frame with which we are more familiar, the role of bacteria appears more static. They currently have an important role to play within some of the biogeochemical cycles that allow other living organisms to survive; these include the carbon, nitrogen, and sulphate cycles.
Carbon is the essential element in all living matter and it has to be converted into different forms. Carbon dioxide produced by animals and as a by-product of industry would soon render the world uninhabitable; plants fix carbon dioxide but so do bacteria. These bacteria, known as autotrophs, can produce their own organic compounds using the sun’s radiation and carbon dioxide and water. They convert them to sugars by photosynthesis. These can either be used by the bacteria themselves or by other organisms. Some carbon is taken up as methane and there are methane-oxidizing bacteria that convert it to carbon dioxide. Bacteria are also primarily responsible for the removal of carbon from dead tissue and plants. On the other hand, some bacteria can use organic carbon, particularly sugars, for the production of energy with the release of carbon dioxide. So different bacterial species are on opposite sides of the cycle and the success of each will depend on the availability of the nutrients they require. If there is an increase in carbon dioxide, the photosynthetic bacteria will prosper, whereas if too much has been converted into sugar, and there is an abundance of oxygen, respiring bacteria will thrive. The burning of fossil fuels and the high quantities of carbon dioxide it produces appear to upset this balance.
Nitrogen is an important component of proteins and nucleic acids, such as DNA. Most nitrogen on Earth is available as a gaseous molecule, comprising two nitrogen atoms, in the atmosphere but this is relatively inaccessible for plants, and thus eventually ourselves. The atmospheric nitrogen has to be ‘fixed’ and this is mainly performed by bacteria that contain a nitrogenase enzyme that can break the bond between the nitrogen atoms. These atoms can be converted to an ammonium salt or nitrates, which are usable by plants. Indeed, the nitrogen-fixing bacteria are often found clustered around the roots of plants. Bacteria are used for most of the interconversions of the various forms of nitrogen. Some bacteria, such as Pseudomonas species, are even able to convert nitrite back into molecular nitrogen, which is released into the atmosphere, so equilibrium is established. This balance is upset when large quantities of nitrates are used as fertilizers and there are insufficient bacteria to convert the excess back into atmospheric molecular nitrogen, resulting in general comparison of endotoxin and exotoxin actionzn lution.
Sulphur is an essential component of proteins and some co-factors. Plants require sulphates but this sulphur derivative is often not readily available. Sulphur is abundant as inorganic sulphides and thiosulphates, which can be oxidized by the bacterial genus Thiobacillus to form sulphates. These can be used directly by plants and incorporated into proteins that, in turn, can become incorporated into animal proteins. On the other hand, the balance can be maintained by anaerobic bacteria, such as the genus Desulfovibrio, that are able to reduce sulphates to hydrogen sulphide, which can then be oxidized to elemental sulphur.
Bacteria and the evolution of Man
The presence of bacteria must have had a major impact on the development of all species and not just because of their capability to cause disease. It is difficult to determine how this was manifested before the Cretaceous extinction sixty-five million years ago; however, when we examine modern animals, we can see how bacteria have lived in a symbiotic relationship with other organisms. Grass did not emerge until after the Cretaceous extinction and became widespread as the Earth became drier. This provided probably the greatest worldwide food resource but many animals could not access it because grass contains fibrous celluose. Many animals, such as ourselves, are simply unable to digest it. Some animals, such as cattle, evolved a system that relied upon bacteria. Their stomachs are made up of four compartments. The grass enters the rumen, which is essentially a large fermentation chamber. There are billions of bacteria including the species Ruminococcus flavefacians, Ruminococcus albus, Bacteriodes succinogenes, Butyrivibrio fibrisolvens. These bacteria break up the fibre of grass cells.
Cattle then regurgitate to grind the products with their teeth (chewing the cud) to try and break up the fibre further. The bacterial digestion of the grass releases nutrients that are, of course, used by the bacteria themselves but the excess is available to the animals as it is passed on to the abomasum, which contains acid similar to that in our own stomachs. The nutrients are further broken down and absorbed by the small intestine. Without bacteria, grass could not be a food source.
How have bacteria affected the evolution and development of Man? They clearly are not as crucial to the acquisition of nutrients from food as they are in ruminants, and the human gut can survive without them. When a child is born, the gastrointestinal tract is sterile but soon becomes colonized. The early colonizers are mainly aerobic bacteria such as Escherichia coli (E. coli) but quickly change during development. The gut of the infant has a low oxygen level and is soon colonized by anaerobic bacteria, similar to those found in the adult. It is estimated that up to 500 different species can colonize the gut, though probably only thirty are found in any significant numbers. The vast majority of these, more than 99 per cent, are anaerobes. Why are they in the gastrointestinal tract and are they important?
They are often seen as commensal (not harmful) or even mutualistic (beneficial) bacteria and they do perform a number of important functions required for the evolution of the human population, which has learnt to live on a very varied diet. While we still do not possess enzymes to digest some carbohydrates, some bacteria do possess these enzymes and can convert them into short-chain fatty acids that we can utilize. It is estimated that we would need to ingest 30 per cent more food to maintain our body weight if we did not have bacteria fermenting in our gut. They can, of course, cause problems. Flatulence after eating baked beans is caused by the bacterial fermentation of specific bean.
As a further by-product, the gut bacteria can also produce vitamins. We usually ingest these whole in our food, because we cannot make them, but some gut bacteria can produce vitamins such as vitamins K and H (biotin). The presence of large numbers of commensal bacteria in our guts also ensures that any pathogenic bacteria have a competitive disadvantage, so these bacteria go some way in protecting us against food-poisoning bacteria. The final role of these bacteria may be as stimulants to the gastric immune system, ensuring that it is primed against invasion by more pathogenic bacteria.
3. Microbiome of the human body
Moving further along the gastrointestinal tract, bile is released into the duodenum from the gall bladder. This is alkaline, which neutralizes the stomach acid, but it is bactericidal to many bacteria.
There are, however, bile-tolerant bacteria, such as Escherichia coli, that thrive in this environment.The large numbers of these predominantly aerobic bacteria suppress the establishment of pathogenic bacteria; for instance, they will curb Clostridium difficile (colloquially known as C. diff.) or the bacteria causing typhoid or dysentery.
There are also significant numbers of bacteria in the mouth. We are aware of those that cause tooth decay under certain conditions but it is not clear whether these bacteria perform a useful task or whether they are just a remnant of an earlier role that these bacteria had had in our evolutionary development. In some reptile species, such as Varanus komodoensis (Komodo dragon), the mouth bacteria contain deadly bacteria (Salmonella species), which produce toxins, sufficient to be fatal with a single bite to their victims.
The skin is the largest organ in the body, covering an area of nearly two square metres. It provides a natural barrier against bacterial infection, which, when penetrated, can cause infection either within the skin, dermatitis, or deeper within the body. We have up to 1,000 different species of bacteria able to survive on the skin. Most are located on the surface and in the upper areas of the hair follicles. The surface of the skin is generally acidic and has a high salt concentration, and some bacteria, such as Propionibacterium and Staphylococcus species, thrive in this environment.
