Biology {microbiology}| can be about archaebacteria, bacteria, and other microscopic plants and animals.



Prokaryotes {archaebacteria} {extremophile} (Archaea) can live in deep sea at high pressure and heat.


Earliest archaebacteria {Korarchaeota} evolved into Crenarchaeota and Euryarchaeota.


Nanoarchaeum equitans {nanoarchae} {Nanoarchaeota} has 500,000-base DNA, has smaller cells than mycoplasmas, and lives in high temperature, and no oxygen. Perhaps, it is symbiotic or parasitic.



Later archaebacteria {Crenarchaeota} evolved from Korarchaeota. The oldest Crenarchaeota are Thermoproteales, then Sulfolobales, then Desulfurococcales, then Crenarchaeales, and then Caldisphaerales.


Thermophiles {sulfolobus} can metabolize sulfur.



Later archaebacteria {Euryarchaeota} evolved from Korarchaeota. The oldest Euryarchaeota are Thermoplasmatales, then Thermococcales, then Methanopyrales, then Methanosarcinales, then Methanomicrobiales, then Mathanococcales, then Methanobacteriales, then Halobacteriales, and then Archaeoglobi. Euryarchaeota include thermophiles.


Archaebacteria {haloferax} can metabolize halogens and iron.


Archaebacteria {halophile} can metabolize halogens.


Archaebacteria {methanogen}| can produce and use methane, live in oxygen-free environments, have unusual cell walls, have unusual lipids, and have different RNA nucleotides. They can be spheres or rods and are half of all Archaea.

Archaebacteria {methanobacterium} {methanococcus} can use methane.

Methanogens use hydrogen gas, carbon dioxide or acetate, phosphorus, and nitrogen. They make methane.


With no oxygen, methane does not break down quickly. With no oxygen, ammonia breaks down by ultraviolet light. If methane concentration is higher than carbon dioxide, methane molecules polymerize.

carbon dioxide

With no oxygen, carbon dioxide and iron react to make iron-carbonate siderite. Early-Earth air carbon dioxide was less than eight times current concentration, because rocks do not have siderite.


Very small bacteria-like cells {mycoplasm}| can cause disease, such as mycoplasmic pneumonia. Archaebacteria include the mycoplasm Thermoplasma.


Euryarchaeota include one-celled organisms {hyperthermophilic bacteria} {thermophile}| {thermoacidophile} that live in 180-C ocean vents and use halogens, methane, and/or iron. Thermophiles {archaeoglobus} {aquifex} can grow at 95 C.



One-celled organisms {bacteria}| can have rigid cell walls, surrounded by polysaccharide capsules.


Bacteria have one chromosome. Bacteria reproduce asexually by fission. Some bacteria form spores. Bacteria can have zero, one, or two no-membrane nuclei.


Bacteria have no mitochondria. Endoplasmic reticulum has no ribosomes.


Bacteria can have flagella.


Bacteria can be parasites, use fermentation, or be saprophytes.


Anaerobic bacteria can produce methane gas.

dormancy in bacteria

Bacteria can lose water, shrink, and stop metabolism {dormancy, bacteria}|.

Gram stain

Bacterial classification can depend on whether stain {Gram stain}| colors cell walls {Gram-positive bacteria} or not {Gram-negative bacteria}. Gram-negative bacteria include Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii.



Deinococcus radiodurans proteins {bacteriophytochrome}| can control gene expression, absorb red light, and fluoresce infrared light.

SOS response

Stressed bacteria first try to repair damaged DNA {SOS response}. Then they derepress genes that make proteins that cause high mutation rates. Bacterial cells can attach RecA protein to single-stranded DNA, which splits LexA regulatory protein, which derepresses genes that cause DNA mutations, which alter drug targets.

type IV secretion system

Gene regions can make secretion proteins {type IV secretion system} (TFSS). TFSS can inject protein toxins into host cells. Helicobacter has CagA gene, which makes CagA protein. Helicobacter injects CagA protein into stomach-lining cells. CagA protein increases stomach-cancer probability. CagA changes and affects cell shape, secretion, and signaling. For example, host cells make cytokines.


culture of bacteria

Bacteria can grow in tubes or on plates {culture, bacteria} {bacterial culture}.

Hfq protein

RNA-binding proteins {Hfq protein} can have more sensitivity in cultures with little fluid motion {low fluid shear}.


Bacteria cluster and attach to surfaces to form intercellular matrix {biofilm}|. They exchange signals and proliferate into microcolonies. Matrix can differentiate into different regions. Cells can leave to form new colonies. Substituted furanones block biofilm formation and break up existing ones, because they are similar to acylated homoserine lactones and mimic bacterial signals.

4-Microbiology-Bacteria-DNA Transfer

conjugation in bacteria

Bacteria pylus allows DNA transfer {conjugation, bacteria}|.


Bacteria have flagella-like parts {pylus} for conjugation.


DNA from one cell can enter and become part of another cell {transduction}|.



Bacteria exchange chemical signals {autoinducer} (AI-1), using special receptors, to determine bacteria density by quorum sensing. Autoinducers help make biofilms, make spores, regulate reproduction, release toxin, and emit light. Autoinducers can exchange boron sugars {autoinducer two} (AI-2) with other species. Gram-negative bacteria use signals {acylated homoserine lactone} (ACL). Gram-positive bacteria use peptide signals.

quorum sensing

Bacteria exchange chemical-signal autoinducers, using special receptors, to determine bacteria density {quorum sensing}. If density passes threshold, bacteria make virulence-factor proteins that harm hosts. Bacteria can then make biofilms.

virulence factor

If bacteria density passes threshold, bacteria make proteins {virulence factor} that harm hosts.



Organisms can have one cell or be very small {microbe}|.


Microbes {nanobe} can be 20 to 150 nanometers diameter, have inner and outer layers, have DNA, and have tendril-like colonies.


Soil bacteria {actinomycete} can make abyssomicin antibiotic.


Soil bacteria {myxobacteria} include Stigmatella aurantiaca, which makes myxochromide.


Bacteria {saprophyte}| can use putrefaction to get food.

Pelagibacter ubique

Bacteria {Pelagibacter} {SAR11 gene} can have no junk DNA and use ocean carbon. Pelagibacter is in all oceans at all depths. Total mass is more than all fish. Algae use its products. If species have large populations, they can minimize DNA.


Bacteria {pleuromona} can have only 300 to 1000 genes.


Small bacteria-like cells {rickettsia} can grow in other, mostly insect, cells. Rickettsia includes typhus and Rocky Mountain spotted fever, but most rickettsias are harmless.


Bacteria {Wolbachia} can kill fruitfly eggs and live three weeks.



Rod-like bacteria {bacillus}| include anthrax, diphtheria, typhoid, tuberculosis, and leprosy bacteria.


Bacteria {Chlamydomonas} can have two front flagella, which flex and extend to pull it through water. Flagella have ten microtubule pairs, with one pair in center. Outside nine slide along central pair. Front rhodopsin-like pigment has maximum sensitivity to blue-green light. As in rhodopsin, retinal is inside the seven membrane loops.

E. coli

Bacteria {E. coli bacteria} can inhabit human intestine.


E. coli can sense sugars, amino acids, toxic ions, and light, using at least twelve different membrane and cell-wall protein receptors. They can compare previous sense qualities to subsequent sense qualities over several seconds, to establish gradients. Gradients change signal strengths by varying loop structures inside receptor proteins.

Receptors signal to G-proteins, which eventually send to six flagella. Signals combine at flagella to move bacterium in same direction or stop, which causes tumbling and random direction. Movements thus find food or escape poisons.


Flagella use hydrogen-ion gradients to turn eight ratchets at 6000 rpm. Flagella can spiral clockwise or counterclockwise. Flagella can align parallel or radiate from cell in all directions. Aligning and spiraling in same rotation causes forward motion. Radiating, and spiraling in opposite rotation, causes stopping.


Bacteria {halobacteria} (Halobacterium salinarium) can have flagella. Like rhodopsin, retinal pigment lies inside seven loops through membrane. It has maximum sensitivity to orange light, because Halobacterium lives in salt marshes.


Non-invasive gram-negative rod bacteria {pseudomonas} can cause urinary tract infections, skin infections, and other infections.



Spherical bacteria {coccus}| can be streptococcus, staphylococcus, or single spheres, such as pneumonia and gonorrhea.


Spherical bacteria {staphylococcus} can form sphere clumps. Methicillin-resistant Staphylococcus aureus (MRSA) has antibiotic resistance to beta-lactams, by making enzyme that splits antibiotic. Vancomycin-resistant Staphylococcus aureus (VRSA) has antibiotic resistance to beta-lactams, by five-gene cassettes that alter cell-wall receptors.


Spherical bacteria {streptococcus} can form sphere chains.



Spiral-corkscrew bacteria {spirochete} include syphilis.


Spiral bacteria {borrelia} can cause Lyme disease.

Helicobacter pylori

Spiral bacteria {Helicobacter pylori} can live in high-acidity human stomachs, cause peptic ulcers, trigger stomach cancers, have cylindrical bodies, and have four flagellae. They can protect against acid reflux and esophagus cancer.


Genome has 1,700,000 bases, has 1550 genes, and varies by 6%. CagA gene makes CagA protein, which increases stomach-cancer probability. CagA gene region makes proteins for type IV secretion system (TFSS). TFSS can inject protein toxins into host cells, and Helicobacter injects CagA protein. In host cells, CagA changes and affects shape, secretion, and signaling. Host cells make cytokines. VacA gene makes VacA protein, which causes vacuoles and coats helper T cells.


Spiral-coil bacteria {spirilla} include cholera.

Related Topics in Table of Contents




Contents and Indexes of Topics, Names, and Works

Outline of Knowledge Database Home Page



Topic Index

Name Index

Works Index


Search Form

Database Information, Disclaimer, Privacy Statement, and Rights

Description of Outline of Knowledge Database



Copyright Not Claimed

Privacy Statement

References and Bibliography

Consciousness Bibliography

Technical Information

Date Modified: 2015.0704

Description: 4-Microbiology