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World of Microbes

Microbes / November 12, 2019

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
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.

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

Source: archive.bio.ed.ac.uk
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