Bacteria (2021 Edition)

Contents

Minimal Life

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 03 shows the minimum parts and functions for the first living bacterium aka LUCA. Here's a corresponding list to elaborate further :



	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).
Figure 02 Seawater Composition

		DNA and enzymes for replication. RNA and polymerase for the transcription of gene to mRNA. Ribosome and tRNA to translate genetic codes to protein. 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. Finally, when bacterium grows to certain size (when the surface area to volume ratio becomes unfavorable for transporting materials from
Figure 03 Minimal Life [view large image]	Figure 04 Minimal Genes	inside and to outside), it would reproduce through binary fission (See also "Binary Fission and other Forms of Reproduction in Bacteria").

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 + P_i + 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 -

   		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.

   The following evolutionary sequence (see Figure 08 for pictorial aid) is a probable scenario to explain the train of events that leads to the present day photosynthesis (see Figure 09) :
   
   
   • Green Sulfur Bacteria - Hydrogen sulfide H₂S is a close relative of water H₂O. They belong to the same group in the periodic table except that the electron configuration of H₂S is further away from the nucleus. Such structure makes H₂S easier to break into S + 2H⁺ + 2e^-. The conventional view is for the photosynthesising bacteria first exploited the easy-to-oxidise molecules as shown in Figure 08 (1) in the type-I reaction similar to the photosystem I in Figure 09 with H₂O replaced by H₂S (see examples of oxidation in Redox Gradients).
   
   
   • Proto-Cyanobacteria (H₂S) - Early in their history the green sulfur bacteria experienced some kind of genetic glitch which duplicated the entire set of genes for the type-I reaction. This spare copy was free to modify the codes (without harming its host). Eventually, it evolved an ability to recycle electrons but can only make the ATP molecule to store energy, it could also produce oxygen (Figure 08 (2)). This is called type-II reaction similar to the photosystem II in Figure 09 with H₂O replaced by H₂S. Thus, this kind of proto-cyanobacteria contained both the type-I and type-II reaction centers. However, they were not linked, only one type could be turned on at a time. The type-II reaction would be switched on when the H₂S concentration ran low. This theory will be vindicated if such "missing link" bacteria with no coupling between the two types have ever been found.
   
   
   • Proto-Cyanobacteria (Mn) - It happened on occasions that the proto-cyanobacteria got swept into shallow ponds with no H₂S but rich in manganese (Mn). They could duly switch on the type-II reaction to get the electron supply from Mn. However, it didn't help because the manganese produced too many electrons choking up the organisms (Figure 08 (3)).
   
   

   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).

   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.

   
   

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   Extra-Terrestrial Life

   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]

   Figure 12 shows the prebiotic condition between Mars and Earth. It illustrates further the possibility of life on Mars :
   
   
   • It shows that the condition between the 2 planets is very similar from their formation about 4.5 up to 3.5 GYA.
   • Mars suddenly dried up at about 3.5 GYA as indicated by craters (from LHB) on river channels (see "Why Did Mars Dry Out ?"). The "dry-up" is relatively swift with a time scale of about 0.1 billion years. Ultimately related to its smaller size, which leaded to sequence of processes eventually striped off its atmosphere and water splits into hydrogen escaping to space while the free oxygen combines with iron to form ferric oxide (Fe₂O₃) in red color. (see "This Is Why Mars Is Red And Dead", and "MAVEN").
   • Life emerged at about 3.6 GYA on Earth.
   • Thus, Mars barely have enough time to produce life.

   Even if it managed to overcome the adverse condition, life would be very primitive at the stage of prokaryote eking out an anaerobic and autotrophic living (do not breathe oxygen and made own food in the dark). They could hardly make it to the stage of cyanobacteria as they would live underground with no sun light to run photosynthesis. As it is still occurring on Earth today, prokaryotes in anoxic sediments produce methane, i.e., CH4 (see "Prokaryotic Metabolism"). Such gas has been detected and mapped on Mars (see Figures 07-09wa and 07-09wb), but is dismissed by scientists as usual because it can be produced by other means.

   Figure 12 Mars/Earth Comparison, Prebiotic [view large image]

   Of course, the scenario would be different depending on the "dry-up" time (see "Major Events of Life on Earth" to match).

   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]

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   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".
   
   

   Lag Phase - This is the beginning of the cycle with one bacterium at the stage of growth and preparation to do binary fission. 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.

   Figure 15 Bacterial Life Cycle [view large image]

   Stationary Phase - This is when the growth is balanced by decline due to over population. 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.

   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.

   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.

   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.

   Figure 17 Horizontal Gene Transfer [view large image]

   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

   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

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.

Here's a brief description on some of the bacterial processes in various environment :


• In Soil (see more details in "Soil microbiology") -
  
  
  • Bacteria and archaea are the most abundant microorganisms in the soil, and serve many important processes.
  • Autotrophic bacteria are responsible for nitrogen fixation, which is the conversion of atmospheric nitrogen into nitrogen-containing compounds (such as ammonia) that can be used by plants. This is very important because almost every plant and organism requires nitrogen in some way.
  • Algae (cyanobacteria) can make their own nutrients through photosynthesis producing oxygen. They can live below the soil surface in uniform temperature and moisture conditions. Some algae are also capable of performing nitrogen fixation. Photosynthetic bacteria and algae also fix larger amount of solar energy to chemical energy than the ~ 5% in plants.
  • Many species of Actinomycetes produce antimicrobial compounds under certain conditions and growth media. Almost two-thirds of the natural antimicrobial drug compounds used currently are produced by different species of Actinomycetes. These bacteria share characteristics with fungi but are more abundant in soil.
  • Chemolithotrophs belong to the domains Bacteria and Archaea. It includes "lithotroph" ('lithos' (rock) and 'troph' (consumer) - "eaters of rock" in Greek, Many but not all lithoautotrophs are extremophiles). The microbial oxidation of sulfur is an important link in the biogeochemical cycling of sulfur in environments hosting both abundant reduced sulfur species and low concentrations of oxygen, such as marine sediments, oxygen minimum zones (OMZs) and hydrothermal systems.

  In decomposition of dead body, the prime decomposers are bacteria or fungi. The process is very important to clean up the remains and to produce vital nutrients for ecosystem's primary producers — usually plants and algae. Remineralization further breaks down the parts into inorganic nutrient. In most forest ecosystems, soil microbe biomass comprises from 1 to 5% of the total soil organic matter pool. Because of the high concentrations of nutrients contained in microbial tissues, microbial biomass contains a disproportionate amount of the nutrient pool contained within organic matter, especially for nitrogen and phosphorus. As a result, the microbial biomass may contain from 3 to 15% of the nutrient pool within the soil organic matter. The deep subsurface holds ~ 15% of the total biomass in the biosphere. It is chiefly composed of bacteria and archaea, which are mostly surface-attached and turn over their biomass every several months to thousands of years.

  Figure 20 Soil Biomes [view large image]

• In Water (see more details in "Aquatic Organisms: Microorganisms") -
  • Freshwater microorganisms participate in various biogeochemical cycles, such as decomposing organic material into nutrients for other organisms and control the water quality. In deeper water, these microorganisms also play a critical job in remineralizing to restore the inorganic nutrients which influence the materials circulation in the system. Photosynthesising bacteria are one of the autotrophic components in phytoplanktons, which are the primary food producer at the surface of water. Bacteria play the role of decomposer at the bottom (the sediment) (see Figure 21,b).
  • Bacterial distribution and processes in the open seas are similar to those in the freshwater. The most impressive is a cyanobacterium called Prochlorococcus. It is estimated to be more abundant than any other photosynthesizer on the planet, and to be responsible for producing 20% of the oxygen in the atmosphere. At the other end in the oceanic sediment the usually negligible chemolithoauotrophic bacteria become important as primary food producers for higher form of life such as mussels, crabs and worms (Figure 21,a).

  In unpolluted running waters (streams, brooks, rivers), the number of bacteria is often so low (~ 106/mL) that the water appears crystal clear. As long as pollution remains low, the course of a river several kilometers long is sufficient to bio-mineralize the easily degradable organic materials introduced from neighboring settlements (the process is called self-purification, see "Effects of pollutants on the aquatic environment"). The appearance of water fleas is a good indicator for clean water.

  Figure 21 Aquatic Environment [view large image]

• In Air (see more details in "Airborne Microbes") -
  • The concentration of bacteria-like particles has been measured to be ~ 10⁵/m³ in environments including a classroom, a day-care center, a dining facility, a health center, three houses, an office, and outdoors.
  • Airborne microbes are biological airborne contaminants (aka bioaerosols) like bacteria, viruses or fungi as well as airborne

    	toxins passed from one victim to the next through the air, without physical contact. This usually happens when an infected subject sneezes, coughs, or just plain breathes. It is hard to prevent such a method of transmission. Airborne microbes are a major cause of respiratory ailments (Figure 22).
    Figure 22 Airborne Microbes	Other bacteria known as natural flora live in our bodies. The immune system recognize them as beneficial, we actually would not survive without them.

    Airborne bacteria mainly become suspended in the air column launched by air turbulence from terrestrial or aquatic environments . Winds are the primary means of transport for bioaerosols. They can be deposited by a number of mechanisms, including gravity pulling, or precipitating together with rain (Figure 23). Once suspended in the air column, the bioaerosols would have the opportunity to travel long distances with the help of wind and precipitation, increasing the occurrence of widespread disease by these microorganisms. Some microbes are able to withstand the extreme condition in clouds, where they are able to perform processes that alter the chemical composition of the cloud, and may even induce precipitation. Figure 23 illustrates such occurrence, the processes in green color indicate bacterial growth, while they may be eliminated in the red colored processes.

    Figure 23 Bacteria in Air [view large image]

• In Plants (See more details in "Plant pathology") -
  • Some bacteria benefit from the plant nutrients provided by the roots, but plants can also benefit from their rhizobacteria as well. Biofertilization accounts for about 65% of the nitrogen supply to crops worldwide. Nitrogen fixation is one of the most beneficial processes performed by rhizobacteria (Figure 25,a).
  • Not all bacteria are beneficial. Plant pathogenic bacteria cause many different kinds of symptoms that include galls and over-growths, wilts, leaf spots, specks and blights, soft rots, as well as scabs and cankers. Bacteria grow in the spaces between cells and do not invade them. The means by which plant pathogenic bacteria cause disease is as varied as the types of

    symptoms they cause. Some plant pathogenic bacteria produce toxins or inject special proteins that lead to host cell death or they produce enzymes that break down key structural components of plant cells and their walls. Still others colonize the water-conducting xylem vessels causing the plants to wilt and die. Agrobacterium species even have the ability to genetically modify or transform their hosts and bring about the formation of cancer-like overgrowths called crown gall.

    Figure 25 Bacteria in Plants [view large image]

    Figure 25,b shows the life cycles of the bacterial pathogen Xcc, which can propagate from the seeds of the plant and from the plant's dead body.

• In Animals (see more details in "Animals in a bacterial world, a new imperative for the life sciences") -
  • Host-microbe symbiosis exists in almost all animals, and the symbiotic bacteria can be profitable, harmful, or of no effect to the host. For example, the harmless Escherichia coli strains commonly found in intestine are a normal part of the gut flora and can be beneficial to their hosts by producing vitamin K and by keeping pathogenic bacteria from colonizing the intestine. By contrast, some Pathogenic E. coli strains such as O26 can cause disease in its host by producing potentially lethal toxins.
  • To cause disease, a pathogen must gain an access to the host, adhere to host tissues, penetrate or evade host defense system, and damage the host either directly or indirectly by accumulation of microbial wastes.
  • Many animal genes (~ 1/3) are homologs (similar structure) of bacterial genes, mostly derived by descent, but occasionally by gene transfer from bacteria.
  • In addition to quorum signals (cell–cell communication to determine population density triggering certain gene expression), bacteria use the host's cell surface–derived proteins to communicate with their hosts, affecting host processes both at the cellular level (e.g., apoptosis for programming cell death, Toll-like Receptor signaling in immune response), as well as at the organ-system level. Conversely, host-derived signal molecules like nitric oxide (NO) can be sensed directly by microbes.

  Infectious diseases are caused by pathogenic microbes that attack and obtain their nutrition from the host they infect. A pathogen is a microorganism that has the potential to cause disease. An infection is the invasion and multiplication of pathogenic microbes in an individual or population. An infection does not always result in a disease. When an infection causes damage to the individual’s vital functions in system, it leads to a disease. Ability to cause disease is pathogenicity, whereas the degree of pathogenicity is known as virulence. To cause disease, a pathogen must gain an access to the host, adhere to host tissues, penetrate or evade host defense system, and damage the host either directly or indirectly by accumulation of microbial wastes (see lists of "Animal bacterial diseases" some of which are shown in Figure 26).

  Figure 26 Bacteria in Animals [view large image]

  Animals use sophisticated mechanisms to manage their microbial environment. Physical barriers, such as capsules, chorions, and mucus are used to protect eggs; and chemical barriers, including antimicrobial peptides (AMPs) to shape the composition

  of the associated microbiota. Conversely, several animals recruit specific bacteria to their embryonic surfaces to provide protection against potential pathogens.
  
  
• In Human (See more details in "Human microbiome") -
  • The human body is inhabited by millions of tiny living organisms, which, all together, are called the human microbiota. It is estimated that the average human body is inhabited by as many non-human cells as human cells. Bacteria are microbes found

    on the skin (Figure 27), in the nose, mouth, and especially in the gut. We acquire these bacteria during birth and they live with us throughout our lives. We need a diverse and balanced microbiota in our intestines to keep us healthy. Some microorganisms that colonize humans are commensal, meaning they co-exist without harming humans; others have a mutualistic relationship with their human hosts. Conversely, some non-pathogenic microorganisms can harm human hosts via the metabolites they produce. Certain microorganisms perform tasks that are known to be useful to the human host but the role of most of them is not well understood. Those that are expected to be present, and that under normal circumstances do not cause disease, are sometimes deemed normal flora or normal microbiota.

    Figure 27 Bacteria in Human Skin [view large image]

    See "Three Lines of Defence" against the harmful bacteria in human, "Gut Flora", then a long "List of Human Microbiota". and the 2021 Nature, Outline article "The Skin Microbiome" by Unilevel.

  
  
• In Space (See more details in "List of microorganisms tested in outer space") -
  • The ISS Microbial Tracking series-2 continues the monitoring of the types of microbes that are present on the International Space Station (ISS). Microbial Tracking-2 (MT-2) seeks to catalog and characterize potential disease-causing microorganisms aboard the ISS. The study show that the microorganisms living on surfaces inside the space station so closely resembled those on an astronaut’s skin that scientists could tell when each new crew member arrived and departed by looking at the microbes left behind.

  Scientists have placed dried cell pellets (aggregates) of the radiation resistant bacteria Deinococcus (D.rad) in exposure panels attached to the outside of the International Space Station (ISS). They exposed the microbial cell pellets with different thickness to measure the effect. The results indicated the importance of the aggregated form of cells for surviving in harsh space environment. The experimental design enabled them to get and extrapolate the survival time of D.rad. The dried cell pellets of 500 µm thickness were alive after 3 years of space exposure and repaired DNA damage at cultivation.

  Figure 28 Bacteria in ISS [view large image]

  The formation of endospore could also help the bacteria to survive in space. See "DNA Damage and Survival Time Course of Deinococcal Cell Pellets During 3 Years of Exposure to Outer Space" and "Plucky Microbes".

  • One theory, called "panspermia", hypothesizes that extraterrestrial microorganisms lying dormant on the surface of comets or meteors crashed into Earth billions of years ago and kick started the development of life. A related theory, called "directed panspermia," poses the idea that an alien civilization could seed planets with life by purposefully sending bacteria over there.
  • Evidences accumulated over the years show that the emergence of life is a gradual process unlike something just appeared from nowhere (see "Origin of Viruses").