Supplemental Lecture (98/04/14 update) by Stephen T. Abedon (abedon.1@osu.edu)

  1. Chapter title: Bacteria
    1. A list of vocabulary words is found toward the end of this document
    2. Procaryotes tend to be small, have short generation times, and display, in total, a biochemically adeptness not matched by their eucaryote counterparts. These facts, not one of which is entirely independent of the others, explains both the diversity of procaryotes and their astonishingly large overall population sizes. Procaryotes, as a collection of diverse species, simply do more and in more places than collectively do eucaryotes, though their small size does limit them to niches in which excessive size is not a factor (e.g., the ability to chew or engulf is not a procaryotic forte) .
    3. Procaryotes play numerous important roles in various environmental chemical cycles as well as the mineralization of, especially, dead animals. The world would be a far different place in the absence of procaryotes. Indeed, arguably, eucaryotes could not survive the loss of all the world's free living procaryotes, though one could readily imagine a world consisting solely of procaryotes. Such a world, in fact, would be equivalent to that which existed prior to the rise of the eucaryotic lineage, a span which includes a majority of the time on earth during which life existed.
    4. In this lecture we will concentrate on discussing the physiology and ecology of those procaryotes which are of the eubacteria lineage, the bacteria (we will save archaeobacteria for a later lecture). Only a minority of the eubacteria cause all of the procaryote-caused human diseases. Nevertheless, such bacteria tend to be greatly over-represented in microbial research simply because of biases in human interests and granting mechanisms. In fact, bacteria which do not cause any known disease exist in far larger numbers than bacteria which do cause disease. Included among these latter bacteria are many free-living bacteria as well as bacteria which form symbiotic (mutual or commensal) relationships with eucaryotes (the most extreme example being the obligate endosymbiotic relationship between eucaryotic cells and mitochondria as well as chloroplasts in the case of algae and plants).
    5. Elsewhere in these notes there also exists a glossary of bacteria listed alphabetically by binomial designation. In addition, see "lecture: procaryote cell walls and membranes I," "lecture: procaryote cytoplasmic organelles," "lecture: procaryote extracellular appendages," and "lecture: bacterial cell shapes and arrangements" for a detailed look at the procaryotic cell as it occurs among common bacteria. Finally, see also the lecture on eubacterial classification.
  2. Bacterial abundance
    1. High diversity:
      1. A single gram of rich, undisturbed soil may contain as many as 5,000 different species of bacteria (more bacterial species, even, than all those that have been described by science).
      2. In fact, the health, and therefore the biological diversity of a given environment may be measured, in part, in terms of the sheer numbers of bacterial species present, per gram.
    2. High total numbers:
      1. The total number of bacteria of all types present in that gram of soil numbers in the billions (109).
      2. Though this number is huge, the concentration of bacteria in mammalian feces is hundreds of times even greater.
      3. The total number of bacteria living in or on the average human consist of more cells than the total number of human cells making up the human body.
      4. Bacteria numbers, in short, are immense.
  3. Bacterial sex
    1. Transfer of DNA snippets:
      1. Though bacteria neither undergo meiosis nor mitosis, and do not require cellular fusion in order to initiate reproduction (indeed, bacteria are not diploid), many bacteria nonetheless maintain active sex lives.
      2. This is done through the transfer of snippets of genomic DNA from cell to cell by various mechanisms.
      3. Following uptake, these DNA snippets may be incorporated into the recipient cell's DNA by a process of molecular recombination. In other words, the basic mechanisms of sex, recombination between DNA sourced from different parents, are employed by bacteria.
    2. Various mechanisms of transfer:
      1. Various mechanisms are utilized by which DNA may be taken up by bacteria.
      2. These mechanisms range from the active uptake to passive mechanisms which result in random gene exchange.
      3. It is not certain just what, if any, short term evolutionary advantage bacteria receive from engaging in sex. However, repair of DNA damage certainly has been suggested.
    3. Evolutionary leaps:
      1. By participating in sex, bacteria may be capable of more rapid evolutionary leaps than they would otherwise be capable of.
      2. Particularly, novel mutational combinations may be achieved through bacterial sex.
      3. Though operating less frequently per individual than that achieved among eucaryotes participating in obligate sexual reproduction, the much shorter generation times and high numbers associated with bacteria can nevertheless make such transfers significant contributors to the evolution of bacterial populations.
    4. Species genetic cohesiveness:
      1. It is almost certain that DNA exchange between related bacteria can maintain the cohesiveness of bacterial species
      2. In other words, some form of the biological species concept may actually operate among otherwise asexually reproducing bacteria.
    5. Plasmids: important but not quite sex:
      1. Exchange of DNA also occurs when plasmids (small, circular pieces of DNA) are transferred by various processes from bacteria to bacteria.
      2. Exchange of plasmid DNA does not necessarily result in recombination and therefore in increased species cohesiveness.
      3. By being a means by which fully novel, evolved genes are brought into novel genetic backgrounds, this mechanism of horizontal plasmid DNA transfer contributes to the ability of bacterial species to rapidly adapt to new niches such as those associated with antibiotic resistance.
    6. Sex among bacteria (less strictly, i.e., gene exchange with or without recombination) therefore appears to:
      1. contribute to the ability of bacteria to adapt to changing environments
      2. genetically explore unoccupied niches (such as that associated with antibiotic resistance in pathogenic bacteria)
      3. help maintain the cohesive of bacterial species
  4. Rapid evolutionary adaptation
    1. Mutation rates scale:
      1. Mutation rate tends to scale.
      2. Most organisms measured, regardless of genome size, have a mutation rate on the order of one mutation per genome per generation.
    2. The actual rate represents some compromise between the costs of increasing polymerase fidelity and the costs in producing defective progeny consequent to increased mutation rates.
    3. Profoundly more mutations:
      1. Procaryotes have both very short generation times (on the order of 1 to a few hours long in the wild) and smaller genomes (on the order of a 1000 times smaller than most eucaryotes).
      2. This works out to perhaps 1,000 times more mutations per gene, per unit time, per individual than are available to a given eucaryote.
      3. The amount of genetic variation which enters into bacteria populations as a result of mutation is enormous.
      4. Bacteria additionally have greater population sizes resulting in the the absolute amount of mutational variation entering the population being even more enormous.
    4. Profoundly more evolutionarily adaptable:
      1. Because of their high mutations rates, bacteria are very adaptable to environmental change.
        1. the small size and simple structure of bacteria
        2. results in their ability to maintain short generation times
        3. thus leading to their enormous capacity to adapt
        4. and therefore to invade new niches
      2. These features are key to the evolutionary success of procaryotes.
      3. See figure below for a more detailed discussion of these concepts.
  5. Bacterial biochemical diversity
    1. Novel biochemical diversity niche:
      1. What bacteria are best at is evolving diverse biochemistries.
      2. This allows bacteria to exploit a large variety of nutrient sources.
      3. Any given bacteria may have a characteristically wide or narrow spectrum of sources of energy and carbon.
      4. As a whole bacteria exploit a far greater spectrum of energy and carbon sources than are biochemically available to eucaryotes (also as a whole).
    2. Inventors of basic pathways:
      1. Bacteria were the inventors of major metabolic pathways found in both eucaryotes (which arose from procaryotes) and procaryotes.
      2. These pathways include:
        1. glycolysis
        2. electron transport chains
        3. chemiosmosis
        4. cellular respiration
        5. photosynthesis
    3. Carbon and energy source diversity:
      1. Today there are few compounds which may supply carbon or energy that are not available to bacteria.
      2. These compounds not available metabolically to bacteria tend to be man-made and therefore are only very recently even potentially available to bacteria.
      3. Presumably, given enough time and chemical abundance, bacteria will figure out (evolutionarily) how to exploit most if not all of the incorrectly disposed of organic compounds synthesized by man.
    4. Bacteria are similarly varied in their chemical source of nitrogen as well as their oxygen requirements.
    5. Evolution of biochemical diversity:
      1. See the evolution of biochemical diversity illustration (supplemental material) for an explanatory sketch of just why bacteria are such significant sourses of biochemical diversity.
      2. Arguments stemming from "small size" in this illustration applies more to bacteria than to the other unicellular organisms: protozoa, yeasts, and algae.
      3. Many of the arguments presented in this illustration are nevertheless approximately applicable to fungi.
      4. It is particularly argument number 4 which typically does not apply to protozoa.
  6. Cellular diversity
    1. Numerous shapes:
      1. Bacteria may be found in numerous shapes.
      2. Basic shapes include spheres (cocci), rods (bacilli), spirals (spirochetes), etc. as well as many variations on these basic shapes.
    2. The majority of bacteria live either as individuals cells, or cells which remain superficially attached following division (e.g., as chains, sheets, or three dimensional blobs).
    3. Little differentiation:
      1. Only a very few bacteria display even some degree of cellular differentiation in which different members of an aggregate perform different tasks.
      2. Presumably differentiation of labor increases the fitness of an aggregate as a whole thus implying that procaryotes are not entirely incapable of a rudimentary multicellular existence.
    4. Typically small:
      1. The vast majority of bacteria are small with cell diameters of 1 to 5 micrometers.
      2. At least one bacteria is known which has a cell length of 500 micrometers (0.5 mm), however.
  7. Gram staining
    1. Profound evolutionary distinction:
      1. A major morphological/evolutionary split among eubacteria is between those which are stained by a procedure known as gram-staining and those which are not.
      2. Gram-staining thus divides eubacteria into those which stain (gram-positive) and those which do not stain (gram-negative).
      3. Even eubacteria which give ambiguous gram-stains (or lack cell walls) can often be grouped into gram-negative or gram-positive taxa based on other characteristics particularly including DNA sequence data.
    2. Positives have simpler envelopes:
      1. Gram-positive bacteria have simpler cell envelopes than gram-negative bacteria, particularly consisting of a plasma membrane and a thick cell wall.
      2. Gram-negative bacteria, in contrast, have cell envelopes consisting of a thinner cell wall as well as a membrane external to the cell wall (outer membrane) which is in addition to the plasma membrane found inside the cell wall.
    3. Negatives are more pathogenic:
      1. In terms of pathogenicity, gram-negative bacteria tend to be more dangerous than gram-positive bacteria.
      2. This is because the body reacts more explosively (and badly) to gram-negative bacteria, particularly to components of their outer membrane (specifically, the lipid A portion of lipopolysaccharide, also known as endotoxin).
      3. The body also has more difficulty clearing gram-negative infections.
  8. Germ theory of disease
    1. Microscopic organisms cause disease:
      1. The germ theory of disease, developed particularly in the 19th century, codifies today's understanding that the greatest, pre-antibiotic and vaccination contributor to human morbidity and mortality were microscopic organisms which are capable of infecting living bodies.
      2. We now know that the majority of these disease-causing microorganisms are classified as bacteria or viruses.
    2. The germ theory of disease is the greatest contribution science has made to the practice of medicine, ever, period!
  9. Illustration, evolution of biochemical diversity

    1. Illustration key:
      1. Lower complexity, lower total nutrient demands. Absolute requirements for replication are low. High surface to volume ratios. Result: short generation times.
        1. Small spaces can support large numbers of small individuals.
        2. The ratio mutation / genome = C (i.e., some constant) for most cellular organisms. This results in the gene / mutation ratio being lower in smaller genomed organisms. This means that the mutation / gene ratio is higher in these organisms. Result: small size, small genome, higher per gene rate of mutation.
        3. The niche of small individuals is predominantly as absorbers and new niches for absorbers are found predominantly through either an increase in the spectrum of nutrient utilization or an increase in the efficiency of nutrient utilization, both consequences of increases in biochemical diversity.
        4. Short generation times result directly in rapid increases in numbers and hence large populations.
        5. Selection for short generation times provides counter pressure to selection for higher DNA polymerase fidelity, and hence for greater mutation rates.
        6. Mutation is the means by which novel variation (e.g., biochemical novelty) is input into system.
        7. Large numbers assure relatively complete explorations of possible mutational variation by populations.
        8. Short generation times assure rapid increases in the absolute numbers of favorable mutants.
        9. The original organisms were small in size. This means that small sized individuals have simply existed longer and therefore have had a longer time to diverge and explore niches requring novel biochemistries than have larger organisms.
  10. Vocabulary
    1. Bacterial abundance
    2. Bacterial biochemical diversity
    3. Bacterial sex
    4. Cellular diversity
    5. Germ theory of disease
    6. Gram-staining
    7. Rapid evolutionary adaptation
  11. Practice questions
    1. In molecular terms, give two details which differentiate bacteria sex from human sex? [PEEK]
    2. What is meant by the phrase Germ Theory of Disease? [PEEK]
    3. How does bacterial sex differ from eucaryote sex? Give two reasons. [PEEK]
    4. The small size of bacteria results, through various steps, in bacteria displaying an extreme of biochemical diversity. Many of these steps explain how it is that bacteria are capable of either rapidly evolving or obtaining a large degree of evolutionary divergence. However, only one of those steps actually explains why it is that it is biochemistries of bacteria (or fungi but not protozoa) which are doing so much of the evolving. Explain why this is so.[PEEK]
    5. In terms of the fidelity of DNA polymerases, explain how it is that the mutation rate of bacteria, per genome, is not significantly greater nor lesser than that seen humans. [PEEK]
    6. Describe four distinctive characteristics of Bacillus subtilis (i.e., less general than "is a eubacteria" or, for example, "has a plasma membrane"). [PEEK]
    7. Which of the following characteristics associated with the majority of bacteria is not responsible for the high level of biochemical diversity displayed by bacteria in general (choose best answer)? [PEEK]
      1. their small size
      2. their short generations times
      3. their tendency to cause human disease
      4. their tendency to obtain nutrients from dissolved matter found in the environment
      5. all of the above
      6. none of the above
    8. Bacterial sex basically involves the integration of snippets of other bacteria's DNA into the reference bacterium's chromosome, via a process called recombination. How does the acquisition of R plasmids differ from bacterial sex? [PEEK]
    9. Approximately how many species of bacteria can you expect to find in a single gram of otherwise undisturbed soil? [PEEK]
      1. 5
      2. 500
      3. 5000
      4. 10
      5. 100
      6. 1000
    10. As a whole, which group of cellular organisms would you expect to display the most biochemical diversity (e.g., able to derive nutrition from the greatest variety of chemical sources). [PEEK]
      1. the protozoa
      2. the bacteria
      3. the viruses
      4. the eucaryotic algae
      5. the cyanobacteria
      6. the chlamydias
  12. Practice question answers
    1. bacteria sex (i) is not tied to bacteria reproduction, (ii) involves the recombination of snippets of DNA into the recipient genome, (iii) tends not to be reciprocal (i.e., exchange between two chromosomes) in any sense, (iv) is not associated with either meiosis or fertilization, (v) does not always respect even good species boundaries, (vi) depending on the bacteria species, can occur as a consequence of numerous mechanisms of gene transfer.
    2. idea that some fraction of diseases have a microorganismal etiology (cause).
    3. Does not directly involve replication, does not involve meiosis, does not involve cell fusion, involves movement of "snippets" of DNA between organisms rather than whole genomes.
    4. Due to their inability to engulf or ingest large chunks of food, the nutrient obtaining strategies available to very small creatures are limited to various mechanisms of absorption. The digestion or transduction of energies from nutrients requires first and foremost sophisticated biochemistries. To expand their nutrient acquisition spectrum, bacteria therefore must either expand their biochemical prowess (and thereby broaden the range of nutrients they may utilize) or become larger (and become something else, e.g., a eucaryote) in order to engulf or ingest. Over evolutionary time, bacteria have done both.
    5. In order to maintain the same rate of mutation per genome, the fidelity of bacterial DNA polymerases, given their much smaller genomes, need not be nearly as great as those of humans. However, since bacterial genomes are smaller, the per genome bacterial mutation rate is spread over fewer genes, resulting in more mutations per nucleotide and therefore per gene.
    6. gram-positive, bacilli, soil bacteria, endospore-former, aerobic, naturally competent, non-pathogenic.
    7. iii, their tendency to cause human disease. If nothing else, the overwhelming majority of bacteria do not cause human disease.
    8. Plasmids do not generally integrate into the host chromosome via recombination. Thus, acquisition of R plasmids resembles bacterial sex in that "snippets" of DNA from other bacteria are making it into the reference bacterium's cytoplasm, but fails to fully resemble bacterial sex in that subsequent recombination into the host chromosome and replacement of host DNA does not occur.
    9. iii, 5000
    10. ii, the bacteria
  13. References
    1. Black, J.G. (1996). Microbiology. Principles and Applications. Third Edition. Prentice Hall. Upper Saddle River, New Jersey. pp. ???.
    2. Campbell, N.A. (1996). Biology. Fourth Edition. Benjamin/Cummings Pub. Co. Menlo Park, CA. p. 498-499.
    3. Olson, G.J. (1995). Eubacteria. in The Tree of Life. http://phylogeny.arizona.edu/tree/eubacteria/eubacteria.html
    4. Postlethwait, J.H., Hopson, J.L. (1995). The Nature of Life. Third Edition. McGraw Hill, Inc. p. 455.
    5. Prescott, L.M., Harley, J.P., Klein, D.A. (1996). Microbiology. Third Edition. Wm. C. Brown Pub. Dubuque, Iowa. pp. 415-476, 416-437,491-502.
    6. Raven, P.H., Johnson, G.B. (1995). Biology (updated version). Third Edition. Wm. C. Brown publishers, Dubuque, Iowa. pp. 589-609.
    7. Tortora, G.J., Funke, B.R., Case, C.L. (1995). Microbiology. An Introduction. Fifth Edition. The Benjamin/Cummings Publishing, Co., Inc., Redwood City, CA, pp. 273-294.
    8. Woese, D.J. (1987). Towards a natural system of organisms: Proposal for the domains archaea, bacteria, and eucarya. Microbiological Reviews 51:221-227.