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Bacteria (2021 Edition)


Minimal Life
Evolution of Bacteria
Extra-Terrestrial Life
Life Cycle and Reproduction
Bacterial Distribution and Process in Soil, Water, Air, Plants, Animals, Human, Space

Minimal Life

As portrayed in Figure 01, starting from some simple building blocks, complex molecules proceeded to assemble soon after a stable
History of Physics hydrosphere was developed. It requires the assistance of enzyme to advance to further complicity. Usually, it is a special kind of protein having a shape to match both reactants that provides the function. However, there is a special kind of genetic molecule called RNA which can serve both functions of replication and catalyst. The advance of chemical complicity occurred during that period is called "RNA World".
Figure 01 Transition to Life [view large image]
    Life emerged as the role of RNA replication is taken over by DNA and its catalytic function by protein. Figure 03a shows the minimum parts and functions for the first living bacterium aka LUCA. Here's a corresponding list to elaborate further :

    Seawater Composition
  1. Cytoplasm is the internal environment to keep the organism alive. Its functions are to support and suspend cellular molecules. The gelatinous liquid composed of water (~96%), salts (dissolved into ions), and organic molecules (for supporting life). Such environment suggests that life arose from the sea (see Figure 02).
  2. Figure 02 Seawater Composition
    Minimal Life Minimal Genes
  3. DNA and enzymes for replication.
  4. RNA and polymerase for the transcription of gene to mRNA.
  5. Ribosome and tRNA to translate genetic codes to protein from mRNA.
  6. A membrane with pumps which acquire useful substance, eject waste and maintain ionic gradient. It is the location where the ATP (aka "battery of life") is made to keep life in an non-equilibrium state.
  7. Finally, when bacterium grows to certain size (when the surface area to volume ratio becomes unfavorable for transporting materials from
  8. Figure 03a Minimal Life
    [view large image]

    Figure 03b Minimal Genes

    inside and to outside), it would reproduce through binary fission (See also "Binary Fission and other Forms of Reproduction in Bacteria").

The Craig Venter Institute started working on a minimal genome in 2006. It tried to synthesize an artificial bacterium having minimum number of genes. The first version contains 428 genes while the next one in 2016 has 473 (see Figure 03b, the numerals in red identify the corresponding parts in the list for minimal life, and the original article : "Design and Synthesis of a Minimal Bacterial Genome").

September, 2021 Update.

It is expected that every single gene in this minimal cell is essential. The cell has zero degree of freedom. As a result, any mutations that arise would be harmful. Nevertheless, it is demonstrated in 2021 that it can still mutate and the rates of adaptation are equivalent to the non-minimal cell, except the cell size. The un-evolved minimal cells become really sick and are easily out competed by the non-minimal version. Following is a summary of the original article "Evolution of a Minimal Cell" : Thus, life is robust once started. That's why it is so hard to eliminate certain bacteria and viruses.


Evolution of Bacteria

    As indicated in Figure 10, there are 4 evolutionary stages from 3.6 - 2.4 billion years ago. Each stage can be identified by the method of ATP production as explained in the following :

  1. LUCA - Normally, the sodium pump on the surface of modern cell membrane runs forward to establish the sodium (high Na+ concentration outside the cell) / potassium (high K+ inside, Figure 05) gradient which is very important for cellular processes. The pump is powered by hydrolyzing ATP :
    ATP + H2O ADP + Pi + 0.32 ev ----- (1).
    However, when ATP supplies are running low, it takes over the function of ATP production by running the process backward.
    If in the beginning of life, only the simpler sodium pump was available to produce ATP, then it would explain the chemical composition in the Interstitial Fluid (the body fluid outside the cell, i.e., the internal sea in modern life) which has the similar high proportion of Na+, Cl- as in sea water (Figure 02). Modern life retains the original environment where it was born. The saline bag in ICU is a morbid reminder for the role of NaCl in life.
    Figure 05 Sodium Pump in Action [view large image]

    A bagful of chemicals however suitable for a living organism is not enough to start the process of life. The substances within would be in thermal equilibrium. It requires infusion of energy to run living processes in non-equilibrium state (see "Why ATP?" to appreciate the role of ATP).

  2. Anoxygenic Autotrophy - Autotrophy (self-nourishment) means the ability of an organism to live on inorganic materials, i.e., a special kind of ATP generation process in absence of oxygen (an-oxygenic - the very early atmospheric condition). The most general form of such process is shown in Figure 06, where electron is transferred from one compound to another. A proton gradient for the production of ATP is established in the process, while the electron eventually settles down to a state of lower energy.
    An example is the Methanogenesis associated with the Archaea Methanogen :

    4H2 + CO2 2H2O + CH4 + 0.25 ev ----- (2)

    where CO2 is the electron acceptor, CH4 the product (reduced acceptor), the electron releases an energy of 0.25 ev. This kind of reaction is called redox (reduction-oxidation).
    Figure 06 Redox Reaction Methanogens are primitive gram-positive organisms, some of them have a layer of pseudopeptidoglycan. ATP generation occurs om the membrane next to the cytoplasm.
    Figure 07 shows the different cell envelop structure for different kind of prokaryotes (archaea and bacteria). The simpler one can be considered as more primitive and hence evolved earlier. The methanogens are still living today with this mode in certain environmental niche such as in the digestive tracts of animals, ....
    Figure 07 Structures of Cell Envelop
    [view large image]

    Note that gram-stain of violet color is positive when the outer-most layer is peptidoglycan or pseudopeptidoglycan (polymers) for archaea. It is otherwise negative in pink color with a membrane or polysaccharide as the outer-most layer (Figure 07).

  3. Anoxygenic Photosynthesis -
    Photosynthesis Photosynthesis, Modern Fossil evidences have been accumulated over the years that anoxygenic photosynthesis were used by bacteria 3.4 billion years ago in a sulfuric environment such as the hot spring. It is also known that oxygen-producing form of photosynthesis emerged about one billion years later. The question is : why it takes so long ?

    Figure 08 Photosynthesis Evolution [view large image]

    Figure 09 Photosynthesis, Modern
    [view large image]

    See the chart in Figure 10.

  4. Oxygenic Photosynthesis - Until one day the type-I and type-II centers were turned on and coupled, then the excessive electrons could go over to the type-I reaction to relieve the blockage. The modern version of photosynthesis were in place with the manganese getting the electrons from H2O (Figure 08 (4)). Since this kind of modification involving two coincidences (the use of Mn and the link between the two types) is highly improbable, therefore it took a long time (about 1 billion years) to institute.

    According to a paper on "Long-term phenotypic evolution of bacteria", bacterial phenotypic evolution can be described by a two-stage process with a rapid initial phenotypic diversification followed by a slow long-term exponential divergence. In this case, it is the evolution of the green sulfur bacteria to cyanobacteria (see Figure 13a,b for its cell wall structure).
  5. Figure 10 Evolution of Bacteria
    [view large image]

    There is a chart in Figure 10 to relate the time scale for the 4 evolutionary stages of bacterial evolution. It also includes a family tree for some bacteria labeled with corresponding stages.


    Extra-Terrestrial Life

    Ancient Atmosphere Figure 11 shows a bacteria-like feature inside a rock ejected from Mars (a Martian meteorite called ALH84001) and collected on Earth in 1984. It looks similar to the cyanobacteria in filament form (Figure 10). Age of the rock is about 4.5 billion year old while the sample's diameter ~ 10-5 cm, which is considered to be too small for a viable living organism
    (dcyano ~ 10-4 cm) by some scientists, and all the bio-signatures in ALH84001 have been proven to be reproducible by non-biological means, while morphology is not a good indicator. Thus, the search for life on Mars remains inconclusive.

    Figure 11 Bacteria on Mars [view large image]

    Europa That brings up some ideas about life in the universe. It seems that unicellular organisms such as the cyanobacteria are the earliest life form that can adjust to environmental stress readily because of simpler body plan but enough bio-functions to respond. They can live in all sorts of extremely harsh condition even in other worlds such as Europa (Figure 13). But they would never be able to send out radio signals to announce their presence. It is no wonder that the current search for Extra-Terrestrial Life by big radio telescopes have turned up nothing so far. The chance of detecting human-like creatures is very slim as we are the product of environmental changes under sequence of unique circumstances. Statistically, it can never be reproduced.

    Figure 13 Europa
    [view large image]

    Table 01 below lists some major events about life on Earth to show the process and duration for its development with pictorial illustration in Figure 14.

    Event Time (GYA) Interval (GYA) Comments
    Big Bang 13.8 ~ 0 Beginning of the Universe
    Solar System 4.5 9.3 Formation of the Earth
    LUCA, ancestor of prokaryotes 3.6 0.9 Hydrosphere + Chemical reactions + RNA world (see "Prebiotic")
    Cyanobacteria 2.4 1.2 Mutations + Proliferation + Photosynthesis Oxygenic atmosphere
    Eukaryotes 1.6 0.8 Novelty by mixing parts or whole from prokaryotes
    Cambrian Explosion 0.54 1.06 From uni- to multi-cellular, cause not clear (see Figure 14)
    Present 0 0.54 Darwinian evolution with adoption to changing environment

    Table 01 Major Events of Life on Earth


    Figure 14 Ascending Complexity of Life on Earth [view large image]


    Life Cycle and Reproduction

    Bacterial growth and reproduction require the supply of the "Building Blocks of Life" including water (H2O), carbon dioxide (CO2), and certain nitrogen compounds, i.e., the H, C, N, O. Nutrients enter the bacterium through pores in its membrane and undergo a series of chemical transformations, converting them into new cellular components; these chemical transformations are collectively known as metabolism. Bacteria can exist only in certain range of temperature, pH level, ... (see "What bacteria need to grow and multiply" from the perspective of food preservation). The bacterial life cycle in a closed system with a fixed supply of nutrients is often used to illustrate the effect of limited resource (Figure 15). BTW, such effect is also applicable to human society as shown in "Future of the Human Race - Limit to Growth".

      Bacterical Life Cycle
    1. Lag Phase - This is the beginning of the cycle with one bacterium at the stage of growth and preparation to do binary fission.
    2. Exponential Phase - This is the phase of unlimited reproduction (if there is a never ending supply of resources). The number of progenies is N = 2n, where n is the number of successive binary fission. The elapsed time t = n/r, where r is the rate of change between successive generations. Note that the curve for this phase in Figure 15 is a straight line for
      n = log2N with slope r. For example, r = 1/(20 minutes) for E. coli, which doubles its population every 20 minutes under optimal conditions.
    3. Figure 15 Bacterial Life Cycle [view large image]

    4. Stationary Phase - This is when the growth is balanced by decline due to over population.
    5. Death Phase - Depletion of resource and adverse effects of over population finally finished off the colony.

    Asexual reproduction produces offspring that are genetically identical to the parent. This is a very efficient way to propagate under stable environment. In an unstable or unpredictable environment, asexually-reproducing species have to depend on mutations to cope (normally the mutation rate is rather slow in the range of 10-6 to 10-9 per nucleotide per bacterial generation). Somehow it works out because of the rapid multiplication of the bacteria, there has to be a few that can survive the change (such as introduction of antibiotic drug). Genetic error can be wiped out rapidly too. There must be diverse attempts in bacterial reproduction over the past 3.6 billion years. Eventually, only 4 types remain viable into the modern age (Figure 16) :

    1. Binary Fission -
      • The first step is to duplicate a copy of the DNA and segregate the two copies to opposite sides of the cell.
      • Division apparatus (proteins) then assemble a ring-like structure (FtsZ ring) at the center of the cell.
      • Then the cytoplasm is cleaved in two, and new cell walls are synthesized.
      • The process finally produces two identical copies of the bacteria.
    2. Baeocyte Formation -
      • It starts out as a small cell (baeocyte).
      • During vegetative (non-reproductive) growth, the cell enlarges and produces a thick extracellular matrix.
      • Within the growing cell, DNA replicates and the nucleoids (the nucleus-like region of the prokaryotic cell) segregate.
      • Reproductive phase begins by rapid succession of cytoplasmic fissions leading to the formation of several baeocytes.
      • Eventually, the extracellular matrix breaks open, releasing the baeocytes.
    3. Budding -
      • It starts out as swarmer cell (capable of swimming by means of a flagellum). It cannot replicate its DNA or reproduce; its role is dispersal.
      • It ejects the polar flagellum and in its place grows a single prostheca (A cellular appendage that is an extension of the cellular membrane and contains cytosol).
      • The prosthecate cell can replicate its DNA and produce offspring. During reproduction, the body of the stalked cell does not grow markedly, but instead, an offspring cell buds from the distal end of the stalk.
      • The mature offspring assembles a flagellum and swims away.
    4. Bacterical Reproduction
    5. Intra-cellular Offspring (another version of binary fission with the daughter cells appear at the poles instead of in the middle of the mother cell) -
      • FtsZ rings appear near both cell poles.
      • Two small offspring cells grow at these locations.
      • DNA is generated in these smaller cells.
      • The internal offsprings grow within the cytoplasm of the mother cell.
      • Once offspring development is complete the mother cell dies and releases the offsprings.
    6. Figure 16 Reproduction, Bacterial [view large image]

    Some bacteria have evolved gene renewal or repair capacity called "Horizontal Gene Transfer", which is a primitive (but faster) way to cope with stress by acquiring genetic materials from outside. Eventually, it invented coupling (conjugation) between 2 bacteria for the process - a method akin to sexual reproduction (see also "Sex and Death").

      Here's the 3 types which are still being used in modern time (Figure 17) :

    1. Transformation -
      • The first requirement is the availability of DNA fragment (usually about 10 genes long) from a dead, degraded bacterium.
      • Transformation can be performed only by live competent recipient bacterium, which means the cell is ready to accept extra-chromosomal DNA or plasmids (small circular DNA) from the environment.
      • Transformation usually is also limited to homologous (similar DNA sequence) recombination (exchange). Typically this involves similar bacterial strains of the same species. Special proteins would then perform breakage and reunion of paired DNA segments to complete the transformation.
    2. Horizontal Gene Transfer
    3. Transduction -
      • A bacteriophage mistakenly assembles with a fragment of the donor bacterium's chromosome or a plasmid instead of a phage genome.
      • The bacteriophage carrying the donor bacterium's DNA gains entry to a recipient bacterium.
      • The bacteriophage inserts the donor bacterium's DNA it is carrying into the recipient bacterium.
      • Homologous recombination occurs and the donor bacterium's DNA is exchanged for some of the recipient's DNA.
    4. Figure 17 Horizontal Gene Transfer
      [view large image]

    5. Conjugation - This is a mechanism similar to the transformation and transduction except that it involves cell-to-cell contact through a pilus (a hair-like appendage found on the surface of many bacteria and archaea).

    Endospore is a dormant cell formed by some bacteria as protection against harsh environments such as extreme cold/heat, nutrient depletion, desiccation, UV exposure, stomach acid, ... Figure 18,a shows the process of endospore formation in 6 steps for a
    Endospore duration of about 15 hours to produce a dormant endospore of six layers (Figure 18,b). Bacteria can also develop resistance to some of the medical treatment to eradicate them including washing, boiling, disinfection, and all kinds of antibiotic (Figure 18,c shows some bacterial strategies to neutralize antibiotics). Eventually, there would be a new strain with modified genome which would render the drug useless.

    Figure 18 Endospore and Antibiotic Resistance


Bacterial Distribution and Process in Soil, Water, Air, Plants, Animals, Human, Space

There is more extensive coverage on this subject by an essay on "Microbes and Environment". Here's only a very brief summary.

Distribution While invisible to the naked eye and thus somewhat intangible, the sheer number (~1030 total number of bacteria and archaea in this world) and diversity of microorganisms underlie their role in maintaining a healthy global ecosystem. Microorganisms have key roles in carbon and nutrient cycling, animal (including human) and plant health, agriculture and the global food web. Microorganisms live in all environments on Earth, i.e., they are ubiquitous (everywhere) as shown in Figure 19, which also illustrates the importance of bacteria in climate change via CO2 cycling and CH4 production (see "Scientists’ warning to humanity: microorganisms and climate change").

Figure 19 Distribution

Micro-Biome is a community of micro-organisms occupying a major habitat.