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Profiles of microorganisms: the microbial world

The Microbial World
Microorganisms and microbial activities

Produced by Jim Deacon
Institute of Cell and Molecular Biology, The University of Edinburgh

This site was developed as a resource to support my teaching. All material is copyright of the author or other contributors BUT CAN BE USED FREELY FOR NON-PROFIT EDUCATIONAL PURPOSES. An acknowledgement would be appreciated.

I welcome comments and suggestions at:

DISCLAIMER. The information in these pages is believed to be accurate, but the author provides no warranty to this effect and will not be liable for the consequence(s) of any reliance placed on the information.


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The microbial world. I. Activities of microorganisms

Microorganisms are everywhere - a largely unseen world of activities that helped to create the biosphere and that continue to support the life processes on earth. So, Welcome to the Microbial World. In fact, you are part of it!

Of all the cells that make up the normal, healthy human body, more than 99 per cent are the cells of microorganisms living on the skin or in the gut, etc. This normal resident microbial population includes potential pathogens as well as organisms that help to keep the potential pathogens in check (see Yeasts and yeast-like fungi).

Here are a few more examples of the impact of microorganisms.

  • Look at the scene below - part of the Lower Sonoran desert of Arizona. Every one of these plants depends on microorganisms. Microbes play a vital role in creating desert soils (see Cyanobacteria). All of these plants have mycorrhizal fungi in their roots, serving for mineral nutrient uptake and probably also for water uptake (see Mycorrhizas). The large feather-like bush (paloverde) to the right of the giant saguaro cactus is a member of the Leguminosae, with nitrogen-fixing Rhizobium in its root nodules (see Nitrogen fixation). These plants, in turn, create the environment for desert animals - the kangaroo rat, cactus wren, Harris' hawk, Gila woodpecker, coyote, etc. [If you want to know more about desert environments and desert organisms, visit our Desert Ecology website]

The main plants seen here are: the giant saguaro cactus (Carnegiea gigantea, about 6 metres tall), various species of Opuntia (large jointed pads of the prickly pear to the left and right of the saguaro, teddy bear cholla in the foreground, the purple coloured pencil cholla to the left of the saguaro), bursage (Ambrosia deltoidea) in much of the foreground, and paloverde (Parkinsonia), the green-stemmed tree to the right of the saguaro. [Image supplied by Sharon von Broembsen, Oklahoma State University]

  • Microorganisms (including viruses) have major impact on human health (for example, see Airborne microbes; Proteus) and crop yields (for example, Biotrophs; Vascular wilts). But microorganisms also can be exploited to control disease, through production of antibiotics (see Penicillin) or by acting as biological control agents (for example, see Heterobasidion; Pythium oligandrum; Agrobacterium).
  • Microorganisms are a major source of useful products, including pharmaceuticals (e.g. cyclosporins from fungi are used as immunosuppressants in transplant surgery), food supplements (see Xanthan), and insecticidal compounds (see Bacillus thuringiensis).
  • Microorganisms have key environmental roles in regulating the populations of pest organisms (see Biological control, Catenaria), in the cycling of mineral nutrients (see Winogradsky column; Lichens) and in decomposition of organic matter, including wood decay (see Armillaria mellea) and the processing of human wastes (for example, Thermophilic microorganisms). It is estimated that one-third of all the "fixed" nitrogen that supports plant (and therefore animal) growth on earth (nitrogen in the form of nitrates, ammonium compounds and amino acids, etc.) is lost to the atmosphere each year as a result of denitrification by microbial activities. But a similar amount of atmospheric nitrogen gas (N2) is fixed into plant-available forms each year by the many types of nitrogen-fixing bacteria. If these estimates are anywhere near correct, then microbes really do keep our world turning.

Our list could go on, but we end this section by noting the astonishing diversity of physiology and metabolism that enables microbes to grow in every environment that will support life on earth.

  • We find fungi in environments too dry to support any other life form.
  • We find archaea (see below) - growing at temperatures over 100oC.
  • Other archaea grow only in highly saline environments, where nothing else will grow.
  • Some bacteria - the chemoautotrophs - grow in the simplest of all life-supporting conditions: they gain their energy by oxidising hydrogen or other inorganic substances, their nitrogen by fixing N2 gas, and all their carbon requirements from CO2.

Continue on this page for: The Microbial World. II. Origins and Diversity
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The Microbial World. II. Origins and Diversity

Here we consider microorganisms in geological time - how they evolved and diversified, and how they created the world that we know today. We also see the place of microorganisms in the scheme of life as a whole, based on gene sequencing to analyse the relatedness of organisms.

History of life on earth

An approximate history of life on earth is shown in the table below, based on information in Encyclopaedia Britannica (1986). There may be more up-to-date information, but the major points would still apply.

The evidence is fragmentary, and is obtained from three major sources:

  • the fossil record, consisting of the preserved remains of organisms themselves (of limited value for microorganisms)
  • geological deposits that are believed to result from biological activities
  • changes in the oxidation states of sediments (e.g. banded iron formation) indicating the progressive development of an oxygenic atmosphere.

Millions of years before present

Geological / fossil record

[abstracted from Encyclopaedia Britannica, 1986]

about 4,600 Planet earth formed
3,500-3,400 Microbial life present, evidenced by stromatolites (sedimentary structures known to be formed by microbial communities) in some Western Australian deposits
2,800 Cyanobacteria capable of oxygen-evolving photosynthesis (based on carbon dating of organic matter from this period). They would have been preceded by bacteria that perform anaerobic photosynthesis.
2,000-1,800 Oxygen begins to accumulate in the atmosphere
1,400 Microbial assemblages of relatively large unicells (25 - 200 micrometres) found in marine siltstones and shales, indicating the presence of eukaryotic (nucleate) organisms. These fossils have been interpreted as cysts of planktonic algae. [Eukaryotes are thought to have originated about 2,000 million years ago]
800-700 Rock deposits containing about 20 different taxa of eukaryotes, including probable protozoa and filamentous green algae
640 Oxygen reaches 3% of present atmospheric level
650-570 The oldest fossils of multicellular animals, including primitive arthropods
570 onwards The first evidence of plentiful living things in the rock record
400 onwards Development of the land flora
100 Mammals, flowering plants, social insects appear

From this table we see several key points.
  1. There has been life on earth for much of the planet's history. It is difficult to say when life first evolved or arrived here, but microbial life has been present for at least 3,500 million years, and the earth itself was only formed about 4,600 million years ago, after which its surface would need to have cooled to physiological temperatures.
  2. The early organisms would have been anaerobes. There is no primary source of oxygen on the earth, and any oxygen formed in the photodissociation of water by UV rays (with escape of hydrogen from the earth's gravitational field) would have combined rapidly with reduced substances. The early organisms would have been heterotrophs, using the accumulated organic matter formed by photochemical reactions. In the absence of oxygen and microbes, organic compounds would have persisted wherever they were sheltered from irradiation.
  3. Organisms resembling today's cyanobacteria probably existed about 2,800 million years ago. These organisms perform oxygen-evolving photosynthesis, like the green plants of today. But any oxygen that they produced would combine rapidly with chemically reduced substances in rocks and waters, so free oxygen would not accumulate in the atmosphere. These cyanobacteria almost certainly were preceded by organisms that performed anaerobic (non-oxygen-evolving) photosynthesis, like today's purple and green sulphur bacteria (see Winogradsky column).
  4. Eukaryotic organisms - those with a nucleus and with much larger cells than the bacteria or cyanobacteria - are found in rocks from about 1,400 million years ago, and perhaps occurred as early as 2,000 million years ago. It is assumed that they developed in an oxygenic atmosphere.
  5. From about 650 million years ago we find the first evidence of primitive multicellular organisms, and from about 400 million years we see the development of primitive land plants.
  6. There is strong evidence that fungi were associated with these primitive land plants, giving rise to the mycorrhizal associations typical of much of the world's vegetation today (see Mycorrhizas).
Microorganisms and the "Tree of Life"

Biologists have always striven to find a universal "tree of life" - a tree that reflects the natural, evolutionary relationships of living organisms and that, hopefully, extends back to the very origins of life.

Prokaryotes and eukaryotes

An important step along the path was the recognition that living organisms can be separated into two basic types: those with cells that contain a nucleus (the eukaryotes) and those that lack a nucleus (prokaryotes). Essentially, all the multicellular life forms are eukaryotes (with larger cells, containing organelles and a relatively large genome distributed between several chromosomes) whereas all bacteria and bacterium-like organisms are prokaryotes (with small cells, no internal membrane-bound organelles and a single circular chromosome). The geological record shows that organisms resembling today's prokaryotes have existed on earth for probably 3,500 million years, whereas eukaryotes have existed for perhaps only 1,500-2,000 million years.

The "Five Kingdoms"

In recent years biologists have tended to recognise five Kingdoms of organisms: the Monera (bacteria and bacterium-like organisms) representing prokaryotes, and plants, animals, fungi and protists (mainly unicellular nucleate organisms) representing eukaryotes.

The Five Kingdom approach is attractive in its simplicity, but has significant problems. One of these concerns the protists - a wide range of disparate organisms such as amoebae, slime moulds, ciliates, algae, etc. that are grouped together as a kingdom with little justification. Another problem stems from the recognition in the 1980s that some bacterium-like organisms (first given the name archaebacteria, and now called archaea) are so different from the true bacteria that they can be separated as a group. They are prokaryotes, and they look like bacteria, but in terms of cellular biochemistry and genetics the archaea differ from both eukaryotes and bacteria (see below).

DNA sequencing

DNA sequencing has provided a new approach for studying evolutionary relationships, since:

1. all organisms have a genome,

2. the genes that code for vital cellular functions are conserved to a remarkable degree through evolutionary time,

3. even these genes accumulate random changes with time (usually in the regions that are not vital for function). In this respect the gene changes are rather like the scars on a boxer's face - a record of the accumulated impact of time.

So, by comparing the genes that code for vital functions of all living organisms, it should be possible to assess the relatedness of different organisms. The gene most commonly used for this codes for the RNA in the small subunit (SSU) of the ribosome. [Ribosomes are the structures on which proteins are synthesised]. Some regions of this SSU rRNA (also termed 16S rRNA) are highly conserved in all organisms, whereas other regions are more variable.

By comparing the DNA sequences for 16S rRNA, Woese and his colleagues constructed a proposed universal phylogenetic tree, shown in simplified form below.

Proposed universal phylogenetic tree, based on nucleotide sequence comparisons of the DNA coding for the RNA of the small ribosomal subunit of different organisms. Only some of the microbial groups are shown here. [Based on a diagram in R Woese (1994) Microbiological Reviews 58, 1-9.]

We should note a technical point about this tree: the comparison of ribosomal RNA gene sequences can show the possible relatedness of organisms, but other information is needed to provide the root of a tree. One of the principal modes of evolution is thought to involve gene duplication followed by divergence. The original gene retains its vital function, while the copy can change and ultimately can encode a new function. If these paralogous gene pairs can be identified by sequence similarity, then the original gene should be present in all organisms whereas the new version will be present only in the more recently derived organisms. The root for the tree in the diagram above was determined by using paralogous genes for translation elongation factors involved in synthesis of protein chains on the ribosomes.

Domains and Kingdoms

The proposed universal phylogenetic tree recognises three Domains of organisms (Bacteria, Archaea and Eucarya) above the traditional level of Kingdoms. These domains seem to have diverged from one another a long time ago, presumably from an extinct or as yet undiscovered ancestral line. As shown in the diagram above, the archaea and eucarya seem to have arisen from a common line more recently than the divergence of these two groups from the bacteria. However, we should note that this tree is only provisional - it can look quite different if it is rooted by other methods. There will be many changes before we arrive at a universally acceptable tree, if ever!

For further details and discussion, see:

DM Williams & TM Embley (1996). Annual Review of Ecology and Systematics 27, 569-595.

The Tree of Life Project (not on this server)

University of California Museum of Paleontology (not on this server)

What should we now recognise as Kingdoms? Perhaps all the terminal branches of the tree represent kingdoms or taxa of similar major rank, and more will be added as the sequences of other organisms become available. Clearly, some of these kingdoms (or potential kingdoms) have advanced and expanded much more than others - the plants, animals and fungi are major groups of organisms with distinctive lifestyles, whereas the slime moulds and ciliates, for example, have not expanded to the same degree.

Origin and evolution of eukaryotes

Eukaryotes must have arisen from prokaryotic ancestors. Many aspects of this are still unknown, but there is persuasive evidence that the mitochondria and plastids (chloroplasts) of today’s eukaryotes are derived from prokaryotes. For example, both mitochondria and plastids have a single circle of DNA (the vestige of a bacterial chromosome) which codes for some of their functions. Also, mitochondria and plastids have ribosomes that resemble those of prokaryotes (termed 70S ribosomes) and that are sensitive to antibacterial antibiotics. Gene sequencing shows that:

  • the mitochondrial genome almost certainly arose from a purple bacterium (see the tree above)
  • the plastid genome almost certainly arose from a cyanobacterium.

Thus, it is believed that these organelles of eukaryotes represent bacteria that once lived inside the cells of other bacteria. Over evolutionary time, the endosymbionts (ntermal dwellers) lost the ability for an independent life and became reduced to the state of serving particular functions (oxidative energy metabolism, and photosynthesis) in eukaryotes.

It is much more difficult to trace the origins of two other characteristic features of eukaryotes - the nucleus and the cytoskeleton (which is composed or microtubules and associated proteins).

Lateral gene transfer

Genealogies based on the genes coding for small subunit ribosomal RNA (as in the diagram above) provide a rather simple view of an ordered sequence of evolutionary progression. However, the situation becomes more complex when these findings are supplemented with the DNA sequence data for other genes, such as those encoding important enzyme functions. Then it becomes clear that the genomes of eukaryotes are chimeric - they have some gene sequences that clearly resemble those of the archaea and some that resemble those of bacteria. In other words, there does not seem to be an ordered, linear sequence of genetic change during the early evolution of the major groups of eukaryotes. Instead, there is likely to have been one or more gene transfer events between the evolving lines of bacteria, archaea and eucarya. One way in which this could have happened is by engulfment of one organism by another (perhaps followed by endosymbiosis), then some of the engulfed organism's genes might have been retained while others were lost over time.

For further discussion of all these points, see:

Symposia of the Society for General Microbiology Volume 54. Evolution of Microbial Life (1996) Cambridge University Press.

Laura A Katz (1998) Changing perspectives on the origin of eukaryotes. Trends in Ecology and Evolution Volume 13, 493-497.

The archaea

The archaea are a fascinating group of organisms. Although they look like bacteria, and have simple cells with a prokaryotic structure, they have biochemical and genetic features quite different from those of bacteria. For example:

  • they do not have peptidoglycan in their walls;
  • at least some of them have sterols in the cell membrane (a feature of eukaryotes),
  • and they have different membrane lipids from those of either eukaroytes or bacteria (including ether linkages rather than ester linkages).

In terms of physiology and behaviour, the archaea fall into three major types.

  • Extreme thermophiles, growing at temperatures of 80oC or more. These organisms typically occur near geothermal vents (see Thermophilic microorganisms).
  • Halophiles, growing in extremely saline environments - they require solutions of at least 10% sodium chloride for their growth.
  • Methanogens (methane-generators), which grow in anaerobic conditions, gaining energy by oxidising hydrogen. For this, they use CO2 as the oxidant, reducing it to methane (CH4) in the process. The methanogens use simple organic acids such as acetate for synthesis of their cellular components. These organic acids are produced by other anaerobic bacteria as the end-products of growth on cellulose and other polymers. So, the methanogens are abundant wherever organic matter is present in anaerobic conditions - land-fill sites, the rumen of cows, etc.

The growth conditions for the archaea are thought to resemble those that existed in the early stages of the earth's history. Thus, these organisms were termed archaebacteria (ancient bacteria) when they were first discovered. But we should not assume that they were necessarily the first microorganisms.

Newly discovered microbes

We have always known that the current methods of sampling and culturing of organisms from natural environments are deficient - these methods tend to select for the fastest-growing organisms in the culture conditions that are used. But the DNA sequencing methods discussed earlier have been a powerful new tool for detecting and ultimately isolating unknown (and even unsuspected) microorganisms.

Basically, DNA is extracted from an environmental sample, split into single strands and mixed with a primer - a short DNA sequence that will combine with the complementary sequence on DNA in the sample. Then by the polymerase chain reaction the DNA in the environmental sample will be synthesised, starting at the primer and copying along the DNA strand. By using a primer from a highly conserved region of the gene for SSU rRNA, any ribosomal genes in the sample will be copied and their sequences can be compared with the sequences of known organisms. Any new gene sequences will represent new organisms, and these can be placed within the SSU rRNA gene tree.

In this way, two new types of archaea have been discovered from marine environments in the last decade. They seem to be remarkably common around the world, and the abundance of their DNA in coastal surface waters suggests that they can represent about 34% of the prokaryote biomass at certain times of the year.

See: DM Williams & TM Embley (1996). Annual Review of Ecology and Systematics 27, 569-595.

Further reading: websites

For more on the archaea and molecular evolution, some good starting points are:

The Scientist (not on this server)

The Tree of Life Project (not on this server)

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About this site

Aims and history

This site was first mounted on 8 October 1997, and is periodically updated (last update August 2003). The site is intended to provide a Microbiology resource for students and teachers. Any material on this site can be downloaded and used freely (with acknowledgement of the source) for educational purposes. However, the author and other contributors retain the copyright for all other purposes. Suggestions and contributions will be welcomed.


The following people contributed images or other materials for this site and are gratefully acknowledged:

lan Sutherland, Aline Robertson, Alan Isbister, Lucy Skillman, Nick Read, David Grayson, Patricia McCabe, Sion Wyn Jones (all of University of Edinburgh)

Professor Sharon von Broembsen, Oklahoma State University.

Fairfax Biological Laboratories, Clinton Corners, NY.

Dr Michael Carlile, Imperial College, London

Dr Eric McKenzie, Landcare Research, Mt. Albert, New Zealand

Dr Robby Roberson, Arizona State University

Professor Mel Fuller, University of Maine

John Wexler and his team at the EUCS Graphics and Multimedia Resource Centre provided much valuable advice and guidance.

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Links to Microbiology and related websites

The following have extensive links to microbiology sites

Society for General Microbiology (not on this server)

American Society for Microbiology (not on this server)

Cells Alive (not on this server)

Washington State University (Level 1 Microbiology course) (not on this server)

"Brock’s" Biology of Microorganisms textbook, 8th edn. (not on this server)

Sanger Centre for Genome research:information on some microbial gene sequences, plus some images of microbes. (not on this server)

Medical Microbiology Dept. University of Cape Town: virus images. (not on this server)

University of Texas (Houston) Medical School: techniques in clinical microbiology. (not on this server)

Fungal websites

British Mycological Society ( (not on this server)

Mycological Society of America ( (not on this server)

Plant pathology websites

American Phytopathological Society ( (not on this server)

The Fungal Web
Fungal zoospores: plasmodiophorids and chytrids
Armillaria and other wood-decay fungi
Fungal zoospores: Oomycota
Slime moulds
Fungal tip growth
Yeasts and yeast-like fungi
Bacterial colony and cell types
Bacillus thuringiensis
Proteus and clinical diagnostics
Agrobacterium tumefaciens
Cyanobacteria and 'cryptobiotic crust'
Airborne microorganisms
Thermophilic microorganisms
Penicillin and other antibiotics
Nitrogen fixation
Winogradsky column: life in a tube
Biofilms: development and significance
Exopolysaccharides and their commercial roles
Facial eczema, and mycotoxins
Biological control: Bacillus popilliae
Biotrophic plant pathogens
Vascular wilts: Panama disease
Dutch elm disease
Mycorrhizas and their significance
Pythium oligandrum and other mycoparasites
Catenaria anguillulae: a nematode parasite
Biocontrol of pine root rot
Biology and control of take-all
Bacillus thuringiensis
Fruit-rot pathogens (necrotrophs)
Potato blight

This site is no longer maintained and has been left for archival purposes

Text and links may be out of date