Prokaryotes

Prokaryotes are primitive, one-celled organisms that have left an extensive fossil record in the form of sedimentary structures produced by physiological activity of cell communities. For billions of years, communities of prokaryotes made up the biosphere of the earth. They are a well-defined group of organisms and occupy a highly diverse variety of habitats.

Characteristics of Prokaryotes

From about 3.5 to 1 billion years ago, life on Earth, as determined from fossil records, consisted entirely of one-celled organisms that have a cell morphology and a metabolism different from those of all other life forms. These organisms, the prokaryotes, are characterized by their lack of a cell nucleus, their lack of sexual reproduction (meiosis), the small size of the prokaryotic cell, and their distinctive biochemistry. Prokaryotes are neither plants nor animals, although the aerobic photosynthetic forms, often called blue-green algae, have in the past been placed with the plants. Eukaryotes, organisms with a cell nucleus and a larger, more complex cell, make up animals, plants, fungi, and protists. Prokaryotes are thus quite separate from all other life forms in terms of their cell biology. Prokaryotes and eukaryotes are the two most basic categories of living things, exhibiting basic differences in their biologic processes that are greater than those that exist between animals or plants or between any of the other kingdoms.

Prokaryotes are mainly single-celled organisms, usually found living together in “colonies” consisting of immense numbers of cells. Their deoxyribonucleic acid (DNA) is distributed throughout the cell; it is not, as in the case of the eukaryotes, localized in a cell nucleus surrounded by a nuclear membrane. The prokaryotic cell is smaller by a factor of ten than the average eukaryotic cell. It lacks chloroplasts and mitochondria and consequently is considered primitive when compared with the eukaryotic cell.

Prokaryotes constitute the kingdom Monera, one of five kingdoms in modern taxonomy. (The other kingdoms are protists, fungi, animals, and plants, all of which have more complex eukaryotic-type cells.) Phyla, or categories, within the kingdom Monera include bacteria, cyanobacteria (or blue-green algae), the archaebacteria, and prochlorophytes. Bacteria, as well as the other moneran phyla, are further subdivided into a number of classes. Bacterial classes of the Monera include eubacteria, photosynthetic bacteria, myxobacteria (slime bacteria), actinomycetes (moldlike bacteria), and other groups, each characterized by its own distinctive metabolism and biochemistry. Bacteria consist of obligate or strict anaerobes and facultative anaerobes; the former include the photosynthetic bacteria, which differ from the cyanobacteria not only in their ability to function, if required, under anaerobic conditions and low light levels, but also in their different photosynthetic pigment.

The archaebacteria are considered by some to be the most primitive and ancient of the monerans. Archaebacteria have a number of biochemical and metabolic characteristics that allow them to live under very adverse conditions—conditions such as those that appear to have existed during the early history of the earth. The archaebacteria are defined from their ribosomal ribonucleic acid (RNA), which in sequencing is quite different from that of all other monerans. The archaebacteria differ fundamentally from the other bacteria classes in structural and biochemical aspects as well.

Geological Significance

Fossil prokaryote cells of great antiquity have become widely known from the fossil record. They were first reported in the 1910s by C. D. Walcott from 1.5-billion-year-old strata of western Montana (Belt series). However, the authenticity of these fossils was doubted until the discovery, in 1954, of one of the oldest known paleontological “windows” on life of the past, the 2-billion-year-old Gunflint biota. Since then, many occurrences of prokaryote cell fossils have been reported, most from very fine-textured flinty cherts associated with stromatolites of the Proterozoic (latter part of the Precambrian) eon and dating from as far back as 3.5 billion years.

The geologic significance of the prokaryotes is great. Not only do they (at present as well as in the geologic past) play an important part in the recycling of many chemical elements, but they also have a role in basic geologic processes such as weathering and other alteration of rocks. For example, prokaryotes are involved in the formation of stromatolites. Stromatolites are layered organosedimentary structures, frequently found fossilized in rock strata of many different geologic ages. Stromatolites come in a considerable variety of shapes and sizes. The different types have often been given Linnaean biological names because, when originally discovered, they were thought to be fossil organisms like corals or sponges. Most stromatolites are dome-shaped, finger-shaped, or laminar structures that have a characteristic “signature.” They can form significant parts of rock strata, particularly in limestone and dolomites. Stromatolites are found in rock strata as ancient as the Archean (former part of the Precambrian) eon and are particularly diverse and abundant in strata of the Proterozoic. Locally, they can be quite common in early Paleozoic marine strata as well.

The origin of stromatolites was debated for many years; as late as the 1950s, many paleontologists seriously doubted their biogenic origin. This doubt stemmed, at least in part, from the fact that stromatolites occur so much further in the geologic past than do any other fossils. Through thousands and thousands of meters of Precambrian strata, they are the only fossils that can be found. Early workers on stromatolites, such as Walcott, suggested a cyanobacterial origin for them. The discovery of the well-preserved cells of prokaryotic type in digitate (fingerlike) stromatolites of the Gunflint Chert of Ontario in the 1950s led to a gradual acceptance by most geologists and paleontologists of the organic origin of the majority of stromatolites. It became clear that, under the right conditions, small, fragile cells could be preserved in very ancient strata.

During the 1970s and 1980s, studies on Precambrian stromatolites and the prokaryotic organisms responsible for them became widespread. Stromatolite occurrences going as far back as 3.5 billion years have been documented. These ancient stromatolites yield not only morphological information but also carbon isotope ratios indicative of a biogenic origin. They sometimes supply biochemical information in the form of hydrocarbons, amino acids, and porphyrins (the latter is apparently a degradation product of original photosynthetic pigment). In 1999, studies of Proterozoic rocks from western Australia confirmed the presence of chemicals that could only have been synthesized by cyanobacteria.

The morphology of a prokaryotic organism is simple. Unlike fossils of eukaryotic organisms, fossils of most prokaryotes provide little specific information about the actual living organism. Prokaryotic cells can be single coccoid (spherical) forms, or they can be elongate chains of cells, as with the filaments, or trichomes, of the cyanobacteria.

Study of Prokaryotes

A standard petrographic thin section mounted on a glass slide is the common mount for observing cells preserved in a stromatolite. Oil immersion is usually required if fossil prokaryote cells are to be observed. Thin slivers of a stromatolite can also be examined under oil immersion; however, the best results are generally with well-made thin sections. Often, considerable trial and error is involved in finding stromatolites that preserve cells and then in actually locating those cells. Different parts of a particular stromatolite specimen usually have varying degrees of cell preservation. Very fine-grained sediments, such as those that occur with stromatolites preserved by black cherts or finely crystalline limestones, generally give the best results.

In these sections, under high optical magnification, a stromatolite may exhibit fossil cyanobacterial cells as either filaments or rod-shaped forms. If preservation of these small prokaryote cells is excellent, as in the stromatolites of the Gunflint formation, the biogenic origin of the cells will be clear, and distinct cell types can be observed. When most stromatolites are examined in thin sections under high magnification, however, the biogenicity of the small objects seen is usually not so certain. Often, small black globules of carbon, suggestive of macerated cells, are evident, but their origin usually cannot be proved. Contaminants such as spores, pollen grains, bacteria cells, and fungi fragments can be problematic, particularly in examination of suspected fossiliferous rocks when thin sections are not used. Even with most thin sections, the unequivocal verification of a biogenic origin for fossil cells is rare. In the case of the Gunflint prokaryotes, the detail preserved in these fossil cells is highly remarkable; some of them show internal cell structure and cells in the process of division.

The earliest stromatolites that yield these fossil cells are generally either broad domes or laminar forms. Associated cells either are single-cell coccoid forms or consist of probable chains of photosynthetic bacteria. Chains of cells of filamentous cyanobacteria generally first appeared about 2.3 billion years ago, and this appearance of filaments agrees fairly well with the first appearance of branched or digitate stromatolites, for which filamentous cyanobacteria seem to be responsible.

Chemical Signatures

Often more significant than single-cell morphology or the megascopic morphology of a stromatolite is the chemical signature left by a group of prokaryotes as a consequence of their metabolic activity. Prokaryotes are classified according to their type of metabolism; some prokaryotes have a metabolism that enables them to occupy a wider variety of ecological niches than do eukaryotic organisms. Anaerobic and aerobic forms are the two fundamental forms of prokaryotic metabolism. In these two categories are the autotrophs and the heterotrophs; heterotrophic prokaryotes require previously formed organic material on which to live, while autotrophs do not. The autotrophs obtain their energy from their environment either in the form of sunlight (photoautotrophs) or through chemical reactions such as oxidation, as in the sulfur-oxidizing bacteria; such bacteria are called chemoautotrophs. This type of metabolism is unique in the organic world, since all other life forms obtain their energy from photosynthesis or through utilization of the chemical energy contained in previously formed organic compounds. The cyanobacteria are photoautotrophs and are responsible for the formation of the various types of stromatolites. The process of photosynthesis changes the microenvironment around the photosynthesizing prokaryote; the mineral precipitation that results is responsible for the formation of stromatolite layers.

Some stromatolites contain oxidized manganese, cobalt, or other “transitional” elements, possibly incorporated into these fossil communities by oxidative metabolism of bacteria. Chemoautotrophic prokaryotes, which are various types of bacteria, may leave a chemical signature in the form of these oxides and precipitate their production of a layered stromatolite-like structure containing these oxidized metals. A number of bacteria oxidize manganese to higher oxidation states so that it is precipitated; deep-sea manganese nodules presently being formed are believed to have such an origin. Sectioning of these nodules shows a finely layered, stromatolite-like structure. Some of the heavy-metal-bearing stromatolites of the early Precambrian may reflect a similar chemoautotrophic metabolism. Analysis of organic residues present in many stromatolites in small quantities can sometimes shed light upon the specific organisms responsible for forming them. This technique, however, has met with only limited success, although degradation products of the photosynthetic pigment present in cyanobacteria have been identified, supporting the cyanobacterial origin of many ancient stromatolites.

The earliest stromatolites, those of Archean age (about 3.5 billion years old), exhibit certain distinctive morphological and chemical aspects. Some of these early stromatolites may be products of anaerobic assemblages of photosynthetic bacteria rather than of cyanobacteria communities. Geochemical evidence suggests that the atmosphere in the Archean may have been anoxygenic (oxygen-free) and that the photosynthetic bacteria, not being obligate aerobes, would have been favored by such an environment.

Principal Terms

aerobes: prokaryotes (usually bacteria) that live in the presence of elemental oxygen

anaerobes: prokaryotes that can live only in an atmosphere that is free of elemental oxygen

deoxyribonucleic acid (DNA): a molecule made up of two strands of nucleotides arranged in a double helix; the molecular basis of heredity

grazing and cropping eukaryotes: single-celled (protists) or multicelled (metazoans) eukaryotes (cells with a definite nucleus), which appear in the fossil record during the close of the Precambrian eon, about 1 billion years ago

nucleotide: a molecule made up of a series of amino acids that, when linked together, are capable of carrying genetic information

Precambrian eon: the first 3.5 billion years of the geologic record; it is followed by the Paleozoic era of the Phanerozoic eon

ribonucleic acid (RNA): a complex compound made up of nucleotide bases that acts as a template, or “messenger,” in the replication of DNA

ribosome: a large multienzyme found associated with cell nuclear materials, composed of RNA and protein molecules

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