School Science Lessons
Microbiology
2012-05-15 SPwp
Please send comments to: J.Elfick@uq.edu.au
9.7.0 Microbiology
Table of contents
3.44 Bacteria
9.213 Viruses
3.44 Bacteria
4.1.9 Bacillus, Presence of bactericidal substances using a coin and Bacillus mycoides
4.1.8 Bacillus, Streptomycin on Bacillus subtilis using the small disc test
1.1.0 Bacteria, Archaea, Archaebacteria
3.44.0 Bacteria in humans, bacterial diseases
19.3.6.14 Bacteria in food, the 2 hour and 4 hour rule
3.44.01 Bacteria classified by shape
3.44.02 Bacteria classified by diseases
1.2.0 Bacteria classified by phylum
3.44.03 Bacteria classified by physiology
19.3.6.14: Bacteria in food, the 2 hour and 4 hour rule
3.44.0 Bacteria in humans, bacterial diseases
6.6 Bacteria (Primary)
2.1.11 Bacteria NOT suitable for use in schools
9.1.2.5 Bacterial smear, Prepare heat-fixed stained bacterial smear
9.6.0 Bacteria, Species and possible experiments for schools
9.5.0 Bacterial infections, germ theory, Pasteur, Koch
4.5.1 Conjugation in bacteria, Escherichia coli
6.6 Different bacteria, (Primary)
9.210 Grass in water
4.5.2 Lenski's experiments with Escherichia coli
3.0 Microbiology, Procedures, materials and equipment
9.5.5 Pasteur's spontaneous generation experiment
9.71 Rhizobium in legumes
4.1.6 Soil bacteria that decompose urea
9.4.0 Sulfonamides, sulfa drugs
9.211 Teeth scrapings
9.212 VRE bacteria (Vancomycin Resistant Bacteria)
9.3.0 Yoghurt and lactic acid bacteria
9.3.0 Yoghurt and lactic acid bacteria
10.10.2 Candidiasis (Thrush) Candida albicans
1.5.1 Lactic acid, 2-hydroxypropanoic acid, CH3CH(OH)COOH
19.1.6.0 Leavening agents
4.2.1 Make yoghurt (activity for primary grade 4 students, about 9 years old)
4.2.1a Make yoghurt, a report from Turkey
4.3.17 Make yoghurt, test milk quality
3.44.03 Bacteria classified by physiology
[Items 3.44.1.0 to 3.44.199 based on the David Bergey classification]
3.44.12f Acetic acid bacteria
3.44.17 Actinomycetes and related bacteria
3.44.8a Bioluminescent and related bacteria
3.44.4 Budding bacteria / appendage bacteria (stalked bacteria)
3.44.12c Colourless sulfur-oxidizing bacteria
3.44.12.4 Denitrifying bacteria
3.44.2.0 Gliding bacteria, fruiting bacteria that leave a visible trail of slime
3.44.11 Gram-negative anaerobic cocci
3.44.7 Gram-negative aerobic rods and cocci
3.44.9 Gram-negative, anaerobic, straight, curved, and helical rods
3.44.12.0 Gram-negative chemolithotrophic bacteria
3.44.10 Gram-negative cocci and coccobacilli
3.44.8 Gram-negative facultative anaerobic rods
3.44.14 Gram-positive cocci
3.44.15 Gram-positive, endospore-forming rods and cocci
3.44.16 Gram-positive, non-sporing rods, asporogenous
3.44.12d Hydrogen-oxidizing bacteria
3.44.13 Methane-producing bacteria
3.44.12e Methanotrophs
3.44.19 Mycoplasmas
3.44.12.1 Nitrifying bacteria
3.44.12.2 "True" nitrifying bacteria
3.44.12.3 Nitrogen-fixing bacteria
3.44.1.0 Oxygenic phototropic bacteria
3.44.18 Rickettsias and chlamydias
3.44.3 Sheathed bacteria
3.44.6 Spiral and curved bacteria, aerobic, motile, helical / vibrioid, Gram-negative
3.44.5 Spirochetes (spirochaetes)
3.44.1.0 Oxygenic phototropic bacteria
3.44.1.8 Anaerobic chemotropic bacteria
3.44.1.2 Anoxygenic phototropic bacteria, purple sulfur bacteria, have internal sulfur granules
3.44.1.1 Cyanobacteria
3.44.1.5 Green nonsulfur bacteria
3.44.1.6 Green sulfur bacteria
3.44.1.7 Multicellular filamentous green bacteria
3.44.1.3 Purple sulfur bacteria, have external sulfur granules
3.44.1.4 Purple nonsulfur bacteria
3.44.2.0 Gliding bacteria, fruiting bacteria that leave a visible trail of slime
3.44.2.1 Myxobacteria
3.44.2.3 Nonphotosynthetic, nonfruiting gliding bacteria
3.44.2.2 Sulfate and sulfur-reducing proteobacteria
3.44.20 Sulfur-reducing bacteria
3.44.21 Archaeobacteria, Archaea [may also occur above]
3.44.23 Bordetella pertusssis
3.44.22 Endosymbionts
9.213 Viruses
9.213b Classification of viruses
10.9.3 Genital herpes, Herpes Simplex Virus (HSV) type 2
9.213.2 Herpes varicella-zoster, chicken pox, shingles
9.213.1 HSV-1 and HSV-2
10.9.8 Human Immunodeficiency Virus, HIV and Acquired Immunodeficiency Syndrome, AIDS
9.213a List of viruses
3.44.0 Bacteria in humans, bacterial diseases
See diagram 9.205: A bacterium | See diagram 9.205.1: Different bacteria
In the healthy person both the human genome and the microbiome (of bacteria) contribute to metabolic pathways.
Bacteria contribute to the health of a person in the following ways:
1. Toxin degeneration
2. Micronutrient synthesis
3. Glycan and amino acid metabolism.
Bacterial diseases
Actinomycosis, Anthrax, Bartonellosis, Brucellosis, Buruli ulcer, Campylobacter enteritis, Cat-scratch disease, Chancroid, Conjunctivitis / Keratitis, Diarrheal disease, Diphtheria, Ehrlichioses, Gonococcal infections, Granuloma inguinale, Leprosy, Leptospiros, Listeriosis, Melioidosis, Meningitis, Mycetomix, Nocardiosis, Parapertussis, Plague, Pneumonia, Rat bite fever, Rickettsioses, Salmonellosis, Shigellosis, Trench fever, Tub€erculosis, Tularemia, Typhoid fever, Vibrio cholera, Yersiniosis
6.6.0 Bacteria, Different bacteria
See diagram 9.205: Bacteria, (Singular: Bacterium)
Bacteria live like fungi but they are so small you cannot see them except with a microscope but you can see what they do. Dissolve soup powder or cube in a cup of hot water and pour evenly into 3 clean glasses. Add 1 teaspoon of salt to one glass. Add 1 teaspoon of vinegar (acetic acid) to the second glass. Add nothing to the third glass. Cover the glasses and leave them in a warm place for 2 -3 days. The first two glasses remain clear because they contain substances which stop bacteria growing. The liquid in the third glass is cloudy because it contains so many bacteria.
3.44.01 Bacteria classified by shape
1. Spherical shape bacteria, coccus
Staphylococcus, Streptococcus, Diplococcus, Gonococcus, Pneumococcus, Nitrococcus
Streptococcus mutans causes tooth decay. It needs both glucose and fructose from the breakdown of sucrose in food and soft drinks to produce plaque and lactic acid.
2. Rod shape bacteria, bacillus
Agrobacterium tumefaciens, Azotobacter, Bacillus amylobacter, Bacillus anthracis, Bacillus subtilis, Bacterium termo, Bacterium vermiforme, Brevibacterium vermiforme, Clostridium, Nitrobacter, Nitrosomonas, Nostoc, Rhizobium, Salmonella
Agrobacterium tumefaciens, non-pathogenic crown gall on base of stems or roots
Agrobacterium rhizogenes, pathogenic crown gall of peaches and roses
Agrobacterium rubi, pathogenic crown gall of grape
Bacillus anthracis, anthrax, in hoofed animals, rarely in humans as cutaneous anthrax black scab (eschar) but may become fatal.
Bacillus thuringiensis, produces the protein Cry5B, used as a crop pesticide and could be used to clear nematode parasites from people.
Escherichia coli, E. coli), (Theodor Escherich 1885), causes inflammation of the urethra (urethritis) and bladder (cystitis) "honeymoon disease", traveller's diarrhoea
Salmonella typhi, causes typhoid fever, intestinal and gall bladder infections, enlarged spleen
Clostridium botulinum, botulism, food poisoning often from canned food, destroyed by high temperature cooking, toxin may affect central nervous system
Clostridium tetani, tetanus, (lockjaw), from infected wounds, toxin causes contraction of muscles
3. Spiral, corkscrew shape bacteria, spirillum, spirochaete, spirochete
Leptospira, Treponema
4. Comma shape bacteria, vibrio
Nitrobacter oxidizes nitrite
Nitrosomonas oxidizes ammonia
Pseudomonas syringae bacterial gall on oleanders and lilac, angular leaf spot on cucurbits, e.g. cucumbers, halo blight of bean
Pseudomonas tumefaciens, crown gall organism
Vibrio cholerae, causes cholera, intestinal infection, diarrhoea, severe dehydration
3.44.02 Bacteria classified by diseases
Phylum Actinobacteria, Actinomycetes, are pathogens.
Phylum Actinobacteria are found in soils.
Corynebacterium michiganense bacterial canker of tomato, Solanum tuberosum
Phylum Chlamydiae are pathogens.
Phylum Bacteroidetes are pathogens in the human mouth.
Bacteroides thetaiotaomicron uses glycan metabolism in the colon to harvest additional energy from otherwise indigestible sugars, e.g. galactose and mannose.
 Phylum Chloroflexi are photosynthetic bacteria.
Phylum Cyanobacteria are the "blue-green algae".
Phylum Fusobacteria are Gram -ve pathogens and cause skin ulcers.
Phylum Planctomycetes are aquatic bacteria.
Phylum Proteobacteria are pathogens.
Burkholderia pseudomallei melioidosis disease often occurs after floods in tropical areas
Pseudomonas syringae bacterial blight of mulberry and pea, bacterial brown spot of bean, bacterial canker of stone fruit
Ralstonia solanacearum causes bacterial wilt disease in bananas.
Xanthomonas campestris bacterial black spot of mango, cucurbits, e.g. cucumbers
Phylum Spirochaetes are Gram -ve, pathogens.
3.44.1.0 Oxygenic phototropic bacteria
Purple phototropic bacteria get their energy from light but do not give off oxygen. They have their own type of chlorophyll and carotenoid pigments. Purple sulfur bacteria normally respire anaerobically and oxygen hinders their growth. They use hydrogen sulfide in an aquatic habitat that has light but no oxygen
3.44.1.1 Cyanobacteria
Anabaena, Calothrix, Chamaespiphon, Cyanothece, Gloeobacter, Gloeocapsa, Gloethece, Microcystis, Myxobaktron, Nodularia, Nostoc, Oscillatoria, Pleurocapsa, Prochlorothrix, Scytonema, Spirulina, Stigonema, Synechococcus, Synechocystis, Trichodesmium
3.44.1.2 Anoxygenic phototropic bacteria
These purple sulfur bacteria, have internal sulfur granules
Chromatium okenii, photosynthetic sulfur bacteria that deposit sulfur outside the cells
Amoebobacter, Lamprobacter, Lamprocystis, Thiocapsa, Thiocystis, Thiodictyon, Thiopedia, Thiospirillum
3.44.1.3 Purple sulfur bacteria
They have external sulfur granules
Ectothiorhodospira mobilis are photosynthetic sulfur bacteria that deposit sulfur outside the cells.
3.44.1.4 Purple nonsulfur bacteria
They are mostly anaerobic and do not use hydrogen sulfide. They are rods, curved rods, ovoid, flagellated, ring shaped or spiral and are used to treat odorous swine wastewater.
Rhodobacter adriaticus, Rhodomicrobium, Rhodopila, Rhodospirillum rubrum, Rhodopseudomonas capsulata, Rhodyclus
3.44.1.5 Green nonsulfur bacteria
Heliobacillus, Heliobacterium
3.44.1.6 Green sulfur bacteria
Anacalochloris, Chlorobium, Chloroherpeton, Pelodictyon, Prosthecochloris
3.44.1.7 Multicellular filamentous green bacteria
Chloroflexus, Chloronema, Heliothrix, Oscillochloris
3.44.1.8 Anaerobic chemotropic bacteria
Erythrobacter
3.44.2.1 Myxobacteria
They form rod-shaped aggregates to form fruiting bodies when nutrients are low.
Chondromyces crocatus, Mellitangium erectum, Myxococcus stipitatus
3.44.2.2 Sulfate and sulfur reducing proteobacteria
They are sulfur or sulfate reducers, anaerobic, and live in an oxygen free aquatic habitat.
Desulfomaculum is soil dwelling and causes tinned meat spoilage called "sulfide stinker".
3.44.2.3 Nonphotosynthetic, nonfruiting gliding bacteria
Archangium, Cytophaga, Leucothrix, Lysobacter, Pelonema, Simonsiella, Sorangium, Thermonema
Beggiatoa is a filamentous gliding bacterium that oxidizes sulfur compounds in sulfur springs, sewage works and hydrothermal vents, rotting seaweed, and the surface of plant roots in swamps.
3.44.3 Sheathed bacteria
They live within a sheath that becomes a tube, and are found in sewage works, and the blooms in autumn leaves.
Clonothrix, Crenothrix, Leptothrix, Sphaerotilus
3.44.4 Budding bacteria / appendage bacteria (stalked bacteria)
They have extensions (prosthecae) involved in reproduction.
Blastobacter, Caulobacter, Gallionella, Gemmata, Kuznezovia, Metallogenium
3.44.5 Spirochetes, spirochaetes
Borrelia, Cristispira, Leptospira, Spirochaeta, Treponema pallidum
Borrelia burgdorferi, carried by lice and ticks on mice and deer, causes relapsing fever and Lyme disease.
Leptospira causes leptosporosis, Weil's disease.
Treponema pallidum causes syphilis.
3.44.6 Spiral and curved bacteria, aerobic, motile, helical / vibrioid, Gram-negative
Alteromonas, Aquaspirillum, Azospirillum, Campylobacter, Cellvibrio, Halovibrio, Helicobacter, Herbaspirillum, Marinomonas, Micavibrio, Oceanospirillum, Spirillum, Sporospirillum, Vampirovibrio
Bdellovibrio are predators on other bacteria and are less than a tenth of their size.
Helicobacter pylori causes ulcers in the gastric lining, stomach ulcers.
Nonmotile Gram-negative curved bacteria
Ancyclobacter, Brachyarcus, Cyclobacterium, Flectobacillus, Meniscus, Microcyclus, Pelosigma, Runella, Spirosoma
3.44.7 Gram-negative aerobic rods and cocci
Acidiphilium, Acidomonas, Acidothermus, Acinetobacter, Afipia, Agrobacterium, Agromonas, Alcaligenes, Aminobacter, Azotobacter, Beijerinckia, Bordetella, Bradyrhizobium, Brucella, Chromohalobacter, Chryseomonas, Comoamonas, Cupriavidas, Deleya, Derxia, Ensifer, Erythrobacter, Flavimonas, Flavobacterium, Francisella, Frateuria, Gluconobacter, Halobacterium, Halococcus, Halomonas, Hydrogenophaga, Janthinobacterium, Lampropedia, Legionella, Marinobacter, Mesophilobacter, Methylobacillus, Methylobacterium, Methylophaga, Methylophilus, Methylovorus, Moraxella, Morococcus, Oligella, Phenylobacterium, Phyllobacterium, Psychrobacter, Rhizobacter, Roseobacter, Rugamonas, Serpens, Sinorhizobium, Sphingobacterium, Thermoleophilum, Thermomicrobium, Thermus, Variovorax, Volcaniella, Weeksella, Xanthanomonas, Xanthobacter, Xanthomonas, Xylella, Xylophilus, Zoogloea.
Free-living anaerobic nitrogen fixers live in soil or water and combine gaseous nitrogen with carbon and hydrogen to make organic molecules. Many organic molecules come from bacterially fixed nitrogen. Azotobacter, Azomonas, Azospirillum, Beyerinckia
Some are free-living inside animals and cause disease, e.g. Neisseria gonorrhoeae, Kingella, Moraxella, Acinetobacter.
Neisseria gonorrhoeae causes gonorrhoea, urethral / vaginal discharge, "the clap"
Enteric bacteria
Escherichia coli may release vitamin K but also pathogenic strains cause diarrhoea and urinary infections. Human faeces are 30% dry weight of dead bacteria.
Helicobacter causes enteritis, chronic gastritis and peptic ulcers.
Ancylobacter is a ring-shaped bacterium.
Magnetospirillum magnetobacterium is a curved rod-shaped bacterium containing magnetic particles, magnetite Fe3O4, or greigite Fe3S4.
Neisseria meningitidis causes meningococcal meningitis.
Xanthomonas campestris causes bacterial leaf spot on cucurbits, e.g. cucumbers, and lettuce, pelagoniums, black rot of crucifers, angular leaf spot of zinnia.
3.44.8 Gram-negative facultative anaerobic rods
Cardiobacterium hominis causes endocarditis.
Enterobacter causes urinary infections.
Klebsiella pneumoniae can produce klebsiella pneumoniae carbapenemases (KPC) that inactivate many types of antibiotics. Carbapenems are a type of beta-lactam antibiotics. An enzyme annuls the effectiveness of modern antibiotics and tends to infect patients have experienced surgery or other invasive procedures in hospitals. Klebsiella pneumoniae causes inflammation of the lungs, klebsiella pneumonia, urinary tract infections, and bacteremia. Infections are difficult to treat and are often fatal. Many strains of Klebsiella can fix nitrogen, i.e., they can reduce atmospheric nitrogen to ammonia and amino acids.
Proteus causes urinary infections.
Salmonella causes typhoid fever and gastro-enteritis.
Serratia is found in soil, water and the guts of insects and vertebrates.
Shigella dysenteriae causes gastric dysentery
Vibrio cholorae causes cholera
Vibrio parahemolyticus, in guts of fishes, causes gastro-enteritis
Photobacterium, rods and curved rods, fermentative metabolism
3.44.8a Bioluminescent and related bacteria
Bacteria may emit light with enzyme luciferase, oxidation reaction, in live fish, light-emitting reaction.
Actinobacillus, Aeromonas, Arsenophonus, Budvicia, Buttiauxella, Calymmatobacterium, Cedecea, Chromobacterium, Citrobacter, Edwardsiella, Eikenella, Enhydrobacter, Erwinia, Escherichia, Ewingella, Gardnerella, Haemophilus, Hafnia, Kluyvera, Leclercia, Leminorella, Moellerella, Obesumbacterium, Pantoea, Pasteurella, Plesiomonas, Pragia, Providencia, Rahnella, Streptobacillus, Tatumella, Xenorhabdus, Yersinia, Yokenella, Zymomonas
Erwinia carotovora causes bacterial soft rot on root and fleshy leaf bases, e.g. lettuce, celery, dahlia, black leg on potato
Gardnerella vaginalis causes bacterial vaginosis, nonspecific vaginitis (not associated with STDs) watery discharge.
Haemophilus ducreyi causes chancroid, soft chancres and inflammation of the inguinal lymph nodes.
Haemophilus influenzae causes haemophilus influenza (HIB) inflammation of the paranasal cavities, sinusitis, inflammation of the epiglottis, noisy breathing in children, meningitis in children
Yersinia pestis causes plague, bubonic plague, fever, swelling of lymph nodes (buboes) that burst releasing pus or bleed under the skin. The black death was caused by strains of the bacterium Yersinia pestis identified by analysis of ancient DNA obtained from bodies of plague victims in England, France, Germany, Italy and the Netherlands.
3.44.9 Gram-negative, anaerobic, straight, curved, and helical rods
Acetivibrio, Acetoanaerobium, Acetofilamentum, Acetogenium, Acetomicrobium, Acetothermus, Acidaminobacter, Anaerobiospirillum, Anaerorhabdus Anaerovibrio, Bacteroides, Butyrivibrio, Centipeda, Fervidobacterium, Fibrobacter, Fusobacterium, Haloanaerobium, Halobacteroides, Ilyobacter, Lachnospira, Leptotrichia, Malonomonas, Megamonas, Mitsuokella, Oxalobacter, Pectinatus, Pelobacter, Porphyromonas, Prevotella, Propionigenium, Propionispira, Rikenella, Roseburia, Ruminobacter, Sebaldella, Selenomonas, Sporomusa, Succinimonas, Succinivibrio, Syntrophobacter, Syntrophosmonas, Thermobacteroides, Thermospipho, Thermotoga, Tissierella, Wolinella, Zymophilus
3.44.10 Gram-negative cocci
Acinetobacter, Branhamella, Nisseria, Paracoccus
3.44.11 Gram-negative anaerobic cocci
Acidaminococcus, Megasphaera, Syntrophococcus, Veillonella
3.44.12.0 Gram-negative chemolithotrophic bacteria
(Mineral inorganic substrates are oxidized in the cell. Photolithotrops obtain energy from light.)
They oxidize ammonia and nitrite, metabolize sulfur and sulfur compounds, and precipitate iron oxides and manganese oxides.
Family Nitrobacteraceae: Nitrobacter, Nitrospina, Nitrococcus. Nitrosomonas, Nitrospira, Nitrosococcus, Nitrosolobus
Metabolize sulfur: Thiobacillus, Sulfolobus, Thiobacterium, Macromonas, Thiovulum, Thiospira
Family Siderocapsaceae: Sinderocapsa, Naumanniella, Ochrobium, Siderococcus
3.44.12.1 Nitrifying bacteria
Nitrosifyers, ammonia-oxidizing bacteria, reduce inorganic nitrogen compounds and oxidize ammonia to nitrite
Nitrosomonas europaea, Nitrosococcus oceani, Nitrosolobus multiformis, Nitrosospira, Nitrosovibrio
Aerobic gram negative bacteria that reduce inorganic nitrogen compounds
Nitrosomonas, Nitrosolobus, Nitrosococcus oxidize ammonia and ammonia compounds to nitrous acid and are called nitrosifyers.
2NH3 +3O2 + Nitrosomonas europaea --> 2HNO2 + 2H2O + energy
nitrous acid + bases --> nitrates
Nitrobacter, Nitrococcus, Nitrospira oxidize the nitrite to nitrate and are called true nitrifying bacteria or nitrate producing bacteria. Nitrobacter oxidizes nitrite to nitrate. Only Nitrobacter can grow on organic compounds.
2HNO2 + O2 + Nitrobacter --> 2HNO3 + energy
NO2- + 1/2O2 --> NO3-
No bacteria can change ammonia to nitrate.
3.44.12.2 "True" nitrifying bacteria
Nitrate-oxidizing bacteria, oxidize the nitrite to nitrate
Nitrobacter winogradskyi, Nitrococcus mobilis, Nitrospira, Nitrospina
3.44.12.3 Nitrogen-fixing bacteria
See diagram 9.209: Rhizobium in legumes
The free living soil bacteria anaerobe Clostridium pasteurianum and the aerobes Azotobacter, Azomonas, Azospirillumis, Beyerinckia fix aerobic nitrogen into combined nitrogen in the soil that is available to plants. They combine gaseous nitrogen with carbon and hydrogen to make organic molecules. Many organic molecules come from bacterially fixed nitrogen. Rhizobium radicicola enters the root hairs of some legumes and pass to the root cortex where nodules form. The fixed nitrogen compounds in the root nodules are available to other plants when the first plant dies. The strain of rhizobium found in peas, beans and clover has cilia over the whole cell. The strain of Rhizobium found in cowpea, peanut and Cassia has a single cilium at one end.
3.44.12.4 Denitrifying bacteria
Some soil bacteria, e.g. Bacillus denitrificans, decompose ammonia and nitrates to liberate nitrogen and thus reduce the available combined nitrogen in the soil.
3.44.12c Colourless sulfur-oxidizing bacteria
Reduce H2S, S and S2O32- + O2 or H2O –> SO42- and 2H+.
Thioploca, Thiotrix, Leucathrix live in marine habitats.
Thiobacillus ferrooxidans is rod-shaped that oxidizes ferrous iron, e.g. iron pyrites, FeS2.
Macromonas, Thermothrix, Thiobacterium, Thiodendron, Thiomicrospira, Thiosphaera, Thiospira, Thiovulum
Iron-oxidizing and manganese-oxidizing and /or iron-depositing bacteria and manganese-depositing bacteria
Aquaspirillum, Bilophococcus, Gallionella, Leptospirillum, Metallogenium, Naumaniella, Ochrobium, Siderocapsa, Siderococcus, Sulfobacillus
Hydrogen-bacteria
Hydrogenobacter
3.44.12d Hydrogen-oxidizing bacteria
They use H2 as an electron donor and O2 as an electron acceptor with nickel-containing hydrogenases. They may use CO2 as a carbon source and CO as an energy source.
O2 + 2H2 --> 2H2O
Carboxydotrophic bacteria oxidize CO to CO2, e.g. Pseudomonas carboxydororans in the soil.
3.44.12e Methanotrophs
They can oxidize methane to methanol in aerobic reactions. Some can use ethanol, methylamine and formate. They are found living symbiotically in marine mussels and sponges near hydrothermal vents.
Methylosinus, Methylocystis, Methanomonas, Methylomonas, Methanobacter, Methylococcus
Zymonas convert sugars to ethanol in the South American alcoholic drink, "pulque" made from the juice of the Agave cactus.
3.44.12f Acetic acid bacteria
They partially oxidize ethanol, into acetic acid, e.g. Acetobacter makes vinegar from grape wine. They also synthesize cellulose to be excreted as a covering.
3.44.13 Methane-producing bacteria
Anaerobic bacteria found in mud, sewage, sludge and the rumen of sheep and cattle. Iodophilic bacteria in the rumen stain blue with iodine because they contain starch from decomposition of cellulose.
Methanobacterium, Methanococcus jannaschii, Methanosarcina, Methanospirillum
3.44.14 Gram-positive cocci
Aerobic, Catalase-Positive Genera
Deinobacter, Deinococcus, Marinococcus, Micrococcus, Planococcus, Saccharococcus, Staphylococcus, Stomatococcus
Aerotolerant, Catalase-Negative Genera
Aerococcus (Enterococcus) Gemella, Lactococcus, Leuconostoc, Melissococcus, Pediococcus, Streptococcus, Trichococcus, Vagococcus
Anaerobic, Catalase-Negative Genera
Coprococcus, Peptococcus, Peptostreptococcus, Ruminococcus, Sarcina
 Streptococcus mutans, and other oral bacteria in dental plaque on teeth, produce acids that dissolve tooth enamel leading to cavities (caries) infection of the tooth pulp (pulpitis) infection of the gum (gingivitis) infection of the gums and bone (peridontitis) Vincent's disease (ulcerative gingivitis, trench mouth).
Streptococcus pneumoniae, inflammation of the respiratory system, sinusitis, laryngitis, bronchitis, inflammation of the lungs, pneumonia, streptococcal meningitis
Streptococcus pyrogenes, inflammation of the throat, sore throat, "strep throat"
Staphylococcus aureus, ("golden staph") inflammation of the lungs, pneumonia, infection of hair follicles (folliculitis) pimples, boils (furuncles) scalded skin syndrome of infants, impetigo pustules on skin, toxic shock syndrome, non-STD vaginitis
3.44.15 Gram-positive, endospore-forming rods and cocci
Amphibacillus, Bacillus, Brochothrix, Carnobacterium, Clostridium, Desulfotomaculum, Kurthia, Oscillospira, Renibacterium, Sporolactobacillus, Sporosarcina, Sulfidobacillus, Syntrophospora
Carnobacterium pleistocenium was discovered in Alaskan permafrost.
3.44.16 Gram-positive, non-sporing rods
Caryophanon, Erysipelothrix, Lactobacillus, Listeria
Lactobacillus, (over 120 species) converts lactose to lactic acid, in decaying plant substances, is benign in vagina and intestines, extensively used as a leavening agent to make fermentation products
Listeria monocytogenes causes listeriosis, affecting people with weakened immune systems, the elderly and pregnant women with fever, headache, tiredness, cramps, diarrhoea, nausea and premature birth. However, healthy people may not be affected.
Irregular, Gram-positive, non-sporing rods
Acetobacterium, Aeromicrobium, Agromyces, Arachnia, Arcanobacterium, Aureobacterium, Brachybacterium, Caseobacter, Clavibacter, Coriobacterium, Curtobacterium, Dermabacter, Exigouibacterium, Falcivibrio, Jonesia, Microbacterium, Mobiluncus, Mycobacterium, Pimelobacter, Rarobacter, Rubrobacter, Sphaerobacter, Terrabacter, Thermoanaerobacter
Cellulomonas biazotea is a cellulose-dissolving bacterium.
Mycobacterium leprae Hansen's disease (leprosy) affects skin, mucous membranes, nerves to cause skin numbness and lumps, deformed limbs.
Mycobacterium tuberculosis contagious lung infection that can spread to other tissues (TB)
3.44.17 Actinomycetes (acetomycetales) and related bacteria
Actinokineospora, Actinomadura, Actinomyces, Actinoplanes, Archina, Arthobacter, Bifidiobacterium, Brevibacterium, Cellumonas, Corynebacterium, Dermatophilus, Eubacterium, Frankia, Glycomyces, Micromonospora, Mycobacterium, Nocardia, Propionibacterium, Rothia, Saccarothrix, Streptomyces, Streptosporangia, Streptoverticillium, Thermoactinomyces, Thermomonospora
Streptomyces bacteria grow in damp soil and form a dust of spores when the soil becomes dry. When rain hits the dry ground, an aerosol of water and soil can be breathed in to cause the "rain smell" from the geosmin produced by Streptomyces antibioticus. In Australia, when heavy rain occurs after a long period of dry weather, a bad taste may develop in the drinking water caused by the high concentration of geosmin washed into water supply dams.
Streptomyces scabies common scab of potatoes, turnips, beetroot, "potato scab"
Corynebacterium diptheriae, inflammation of the pharynx, toxins affect heart, diphtheria
3.44.18 Rickettsias and chlamydias
They are obligate intracellular parasites and cannot be cultured. Typhus, Spotted Fever, French Fever, Q Fever and Ehrlichiosis, Potomac Fever in horses
Aegyptianella, Anaplasma, Bartonella, Chlamydia, Cowdria, Coxiella, Ehrlichia, Eperythrozoon, Grahamella, Haemobartonella, Neorickettsia, Rickettsia, Rickettsiella, Rochalimaea, Wollbachia
Rickettsia, typhus
Chlamydia trachomatis causes chlamydial pelvic inflammatory disease, PID.
3.44.19 Mycoplasmas
Acoleplasma, Anaeroplasma, Asteroleplasma, Mycoplasma, Spiroplasma, Thermplasma, Ureaplasma
Mycoplasma pneumoniae, inflammation of the alveoli in the lungs, pneumonia
Mycoplasma spp. big bud (greening, virescence), e.g. tomato, potato, dock (thick bushy stems, reduced fruit yield) yellow crinkle of papaya
3.44.20 Sulfur-reducing bacteria
Elemental sulfur is reduced to thiosulfate and dimethylsulfoxide.
Desulfobacter, Desulfobacterium, Desulfobulbus, Desulfococcus, Desulfomicrobium, Desulfomonas, Desulfomonile, Desulfonema, Desulfosarcina, Desulfotomaculum (also endospore-forming) Desulfovibrio, Desulfurella, Thermodesulfobacterium
Desulfuromonas reduces elemental sulfur
3.44.21 Archaeobacteria, Archaea [may also occur above]
Acidianus, Archaeoglobus, Desulfurococcus, Desulfurolobus, Haloarcula, Halobacterium, Halococcus, Haloferax, Hyperthermus, Metallosphaera, Methanobacterium, Methanobrevibacter, Methanococcoides, Methanococcus, Methanocorpusculum, Methanoculleus, Methanogenium, Methanohalobium, Methanohalophilus, Methanolacinia, Methanolobus, Methanomicrobium, Methanoplanus, Methanosarcina, Methanosphaera, Methanospirillum, Methanothermus, Methanothrix, Natronobacterium, Natronococcus, Pyrobaculum, Pyrococcus, Pyrodictium, Staphylothermus, Sulfolobus, Thermococcus, Thermodiscus, Thermofilum, Thermoplasma, Thermoproteus
3.44.22 Endosymbionts
Caedibacter, Holospora, Lyticum, Pseudocaedibacter
Tectibacter is an endosymbiont of Protozoa.
Blattabacterium is an endosymbiont of insects.
3.44.23 Bordetella pertusssis
Bordetella pertusssis contagious whooping cough in children
4.5.1 Conjugation in bacteria, Escherichia coli
The strain Escherichia coli GY767 (DSM-No. 1562) is streptomycin sensitive. The F plasmid is integrated into its chromosomal DNA, and it is able to transfer chromosomal genetic information to strains of E. coli that have no F plasmid. In this experiment, the recipient is E. coli AB1157 (DSM-No. 1563). This streptomycin resistant strain is characterized by a large number of mutations and can no longer produce for itself the amino acids proline, leucine, arginine, threonine, or histidine, or the vitamin thiamine, which it requires to survive. These substances must therefore be present in the culture medium if growth is to occur. In the following experiment, donor cells (E. coli GY767, DSM-No. 1562) and recipient cells (E. coli AB1157, DSM-No. 1563) are mixed in a ratio of 1:9. Within two hours the chromosomal genes for the biosynthesis of proline, threonine, and leucine are transferred from the donor to the recipient. Recipient cells are distinguished from the donor cells by their resistance to streptomycin. After transfer of the genes for biosynthesis of the amino acids proline, leucine, and threonine, recombinant recipient cells, now also called transconjugants, grow on minimal agar that contains arginine, histidine, thiamine, and streptomycin, but not proline, leucine, or threonine. Neither the donor, with its streptomycin sensitivity, nor the unchanged recipient, which would need the missing nutrients proline, leucine, and threonine, can grow on this minimal agar. Conjugation between E. coli GY767 (DSM-No. 1562) a wild strain with chromosomal integrated F-plasmid, and E. coli AB1157 (DSM-No. 1563) a multiple auxotrophic mutant. Neither strain can grow on streptomycin containing minimal agar. Transconjugants of E. coli AB1157 (DSM-No. 1563) develop on this medium only after conjugative transfer of genetic information
Equipment: Beaker, glass, 250 mL, Bunsen burner, Conical flask, 250 mL, Drigalski spatula, Incubator, Petri dishes × 3, Pipette, 5 mL, sterile, Pipette aids, Pipettes, 1 mL, sterile, × 4.
Materials:
9.1.2.20 Nutrient broth medium, for the overnight culture | 9.1.2.18 Minimal agar medium | Distilled water, Ethanol, 70%, Overnight culture of E. coli GY767 (DSM-No. 1562), Overnight culture of E. coli AB1157 (DSM-No. 1563), Streptomycin, 0.02 g.
1. Using the Erlenmeyer retort, prepare minimal agar with 100 mL distilled water and adjust to a pH value of 7.2 using 1 M NaOH. Seal the retort with aluminium foil and sterilize, then leave to cool to 55o3. Add 0.02 g streptomycin and firmly shake the retort to dissolve. Pour into three agar dishes.
2. Prepare 5 mL each of overnight culture of E. coli GY767 (DSM-No. 1562) and E. coli AB1157 (DSM-No. 1563).
3. Mix 0.3 mL E. coli GY767 (DSM-No. 1562) overnight culture and 2.7 mL E. coli AB1157 (DSM-No. 1563) overnight culture in a sterilized test-tube and incubate at 208 37oC for two hours.
4. Spread 0.1 mL of this mixture onto a minimal agar dish using the Drigalski spatula, sterilized with 70% alcohol and flamed in the Bunsen burner.
5. Prepare two control dishes with 0.1 mL of E. coli GY767 (DSM-No. 1562) and E. coli AB1157 (DSM-No. 1563) overnight culture respectively. Incubate all three dishes at 37oC for 72 hours. E. coli GY767 (DSM-No. 1562) shows no signs of growth on the nutritive medium, as it is streptomycin sensitive. Nor can E. coli GY767 (DSM-No. 1562) grow on this medium, because the amino acids required by this strain, proline, leucine, and threonine, are not present. Cells of E. coli AB1157 (DSM-No. 1563) can grow on this medium only when they have received from the donor the genes for biosynthesis of these amino acids. During the experiment, genes for arginine, histidine, and thiamine biosynthesis are also transferred, but not detected.
4.5.2 Lenski's experiments with Escherichia coli
Starting from an Escherichia coli bacterium twenty years ago, Richard Lenski of Michigan State University used it to establish twelve laboratory populations, then study succeeding generations of these separate populations for genotypic and phenotypic changes, e.g. changes in cell size and growth rates on glucose. Similar changes occurred in the twelve populations. After about 30,000 generations some of these bacteria were able to metabolize citrate which they had never done before. These experiment provide long-term data on the genetics of bacteria and the rate of evolutionary change.
9.71 Rhizobium in legumes
See diagram 9.209: T.S. Root nodule | See diagram 9.72: Root nodules
Rhizobium bacteria can enter the roots of legumes and cause lumps, root nodules, where they live. These bacteria can use the nitrogen gas from the air. We say Rhizobium can "fix" nitrogen from the air. Very few other living things can fix nitrogen. Some nitrogen goes into the stems and leaves of the legume plant. When the leaves fall off, some nitrogen compounds are added to the soil that other plants can then use. When the legume plants die, the nitrogen fixed by the Rhizobium can still be available to other plants. Some legumes, e.g. cowpea and lablab bean, are grown until the flowering stage and then dug into the soil as "green manure". When these plants rot, they leave nitrogen compounds in the soil both from the leaves and root nodules. Different crop plants require different strains of Rhizobium. Farmers can purchase commercial inoculum containing the strain appropriate for nodulation of their particular crop. Dig up different legume plants and count the number of nodules and note the sizes of the nodules. Cut open some nodules. The inside of a nodule that is fixing nitrogen is a pink-red colour. Inactive nodules are brown or green inside.
9.210 Grass in water
Put dead grass or fresh hay in a jar, cover with water and leave it uncovered to stand at room temperature for some days. Do not use mouldy hay because it may contain pathogenic fungi. After a few days, a skin forms on the surface of the water, the mould pellicle. After eight days, use a glass rod to transfer a part of the pellicle and some fluid to a microscope slide. Spread out the pellicle evenly and apply a coverslip. Examine the pellicle under the microscope. Observe rod-shaped or spherical unicellular bacteria. Observe unicellular organisms moving very rapidly through the field of view, e.g. Paramecium.
9.211 Teeth scrapings
1. Put white scrapings from the teeth on a microscope slide. Examine the scraping under a microscope and look for any bacteria. You may have to seek approval to work with samples from the human mouth because diseases may spread. Wear safety glasses and disposable surgical gloves.
2. Use a tooth pick to dislodge material on the tooth surface at the gum line or between ther teeth and put in a drop of water on a clean slide. Use the blunt end of the tooth pick to squash the material into tiny pieces. Fix the smear by briefly passing the slide through a flame. Stain the smear with a drop of methylene blue. Rinse the smear with tap water for 2 seconds to remove excess stain then blot it with absorbent paper. Dry the smear by briefly passing the slide through a flame. Examine the smear under a microscope.
9.212 VRE bacteria (Vancomycin Resistant Bacteria )
Vancomycin Resistant Bacteria are the species Enterococcus faecium and Enterococcus faecalis, resistant to the antibiotic Vancomycin. Enterococci bacteria usually occur in the bowel and the female genito-urinary tract. They can cause urinary tract infections if the peritoneal cavity is infected by bowel contents and if the bloodstream is infected by intravascular devices in hospitals used by unhygienic hospital staff .
9.3.0 Yoghurt and lactic acid bacteria
Lactic acid bacteria convert lactose to lactic acid by a form of fermentation and so are used to preserve milk and perhaps have the probiotic function of increasing pH in the intestine to lower the activity of harmful bacteria and other organisms. Lactic acid bacteria, (order Lactobacillales) are mainly Lactobacillus, Leuconostoc, Pediococcus, Lactococcus, and Streptococcus, but also my include Aerococcus, Carnobacterium, Enterococcus, Oenococcus, Sporolactobacillus, Tetragenococcus, Vagococcus, and Weisella.
Yoghurt is usually prepared from two species of bacteria, chains of cocci or diplococci of Streptococcus thermophilus and rod-shaped bacilli of Lactobacillus acidophilus or Lactobacillus bulgaricus, that both stain Gram positive, purple. The bacteria have been renamed Lactobacillus delbrueckii (subsp. bulgaricus) for (Lactobacillus bulgaricus) and Streptococcus salivarius (subsp. thermophilus) for Streptococcus thermophilus.
Lactobacillus casei is a species of non-starter lactic acid bacteria (NSLAB) found in ripening Cheddar cheese.  It was developed by Dr. Minoru Shirota (1899-1982) as Lactobacillus casei strain shirota for production of Yakult, the yogurt-like probiotic drink.
Probiotic organisms, usually lactic acid bacteria (LAB) and bifidobacteria (formerly Lactobacillus bifidus), are live microorganisms thought to be beneficial to the host organism that are usually consumed as part of fermented foods with specially-added active live cultures, e.g. yoghurt.
Lactobacillus acidophilus occurs naturally in the human gastrointestinal tract, mouth and vagina,  and may be used with Streptococcus salivarius (subsp. thermophilus) and with Lactobacillus delbrueckii (subsp. bulgaricus) to produce acidophilus-type yoghurt.
Leuconostoc citrovorum with Streptococcus lactis convert lactic acid to aldehydes and ketones to produce buttermilk with its characteristic flavour and aroma.
9.4.0 Sulfonamides, sulfa drugs
See diagram 14.12: Sulfanilamides, sulflilamide, sulfamethoxazole
The first of the antibacterial drugs, the sulfonamides, were found effective against the “cocci infections” caused by the bacteria streptococci, gonococci and pneumococci. The basic compound is called sulfanilamide. Many derivatives can be made from this compound by modifying the molecule to change its potency or reduce side effects or toxicity. The effectiveness of these drugs depends on maintaining the basic structure and shape of the molecule. One of the essential growth compounds for most bacteria susceptible to the sulfonamides is p-aminobenzoic acid. Bacteria absorb a sulfonamide because its shape and charge distribution is similar to p-aminobenzoic acid, and then they cannot metabolize it. Bacteria use p-aminobenzoic acid to produce folic acid, but, unlike humans, cannot absorb folic acid from their food. Prontosil sulfanilamide requires the patient to drink copious quantities of water at the same time because kidney damage was caused by earlier products. The term "sulfanilamides" refers to the family of molecules based on sulfanilamide, so it is a chemical term. The term sulfonamide (sulfa drugs) refers to drugs based on sulfanilamide, so a medical term. Sulfonamides (sulpha drugs) do not kill bacteria but prevent them growing and multiplying to allow natural immunity processes to deal with them.
Sensitivity to drugs determined by genes
Individual people fall into two genetic groups, those who acetylate drugs like sulfonamides fast and those who do so slowly. While 90% of Japanese and Chinese are fast acetylators, only 40% of Americans (both black and white) acetylate drugs fast. Acetylation is often the first step in metabolizing and thus deactivating a drug, so slow acetylators are exposed to higher levels of a drug given at the same dose. The acetyl derivative of sulfa thiazole is not very soluble. It tended to block kidney tubules and lead to death. It was replaced by sulfadiazine. The same acetylating enzyme deactivates some carcinogens, e.g. aromatic amines such as benzidene and o-tolidine, used in dyestuff manufacture and as analytical reagents in the detection of blood and chlorine levels in water. Slow acetylators are at higher risk of bladder cancer from these chemicals.
9.5.0 Bacterial infections, germ theory, Pasteur, Koch
See 19.3.6.12: Pasteurization and UHT
1. The symptoms of a bacterial infection are usually local redness, heat, swelling and local pain and sometimes the formation of pus. By contrast viral infections usually affect many parts of the body, e.g. blocked nose, cough and headache. However, local virus infections include conjunctivitis (pink eye, truck driver's eye) and herpes. Herpes is painful but most viral diseases feel more like an itch. Pus is a yellow white viscous fluid formed in infected tissue, containing white blood cells (polymorphonuclear leucocytes) remains of cells, dead tissue, and micro-organisms. Pus should be surgically drained as soon as possible. Normal body temperature = 36.8 ± 0.7°C (i.e. 36.1 °C to 37.5 °C). Fever is occurring if body temperature = or > 37.5 °C (in the mouth) 37.2 °C (under the arm) 38.0°C (in the rectum).
2. Infections of the skin by Staphylococcus aureus include the following:
2.1 Infection of the hair follicles as small white head pimples at the base of hair shafts or as a swollen red boil (furuncle, carbuncle)
2.2 Impetigo blisters then crusts on the surface of the skin of young children
2.3 Cellulitis infection below the skin surface
2.4 Infection of the eyelid glands, (hordeolum, stye)
3. Huge abscesses in the jaw are caused by Actinomyces israelii infecting humans man and animals, e.g. lumpy jaw in cattle.
4. Infections caused by fungi include superficial infections of the skin or mucous membranes, e.g. yeast vaginitis, oral thrush, athletes foot and rare systemic infections in the bloodstream of a person with a weak immune system, e.g. Cryptococcus fungus causes fungal meningitis in HIV affected patients. The Candida yeast is common but it may cause infections in the mouth, the gut, and the female reproductive system (Candida vaginitis). Aspergillus fungus causes Aspergillus asthma in patients with HIV infection, cancer and leukaemia. The Pneumocystis pneumonia fungus (PCP) is an opportunistic infection of HIV patients and malnourished children.
5. The germ theory developed by Louis Pasteur and Robert Koch identified the cause of diseases starting with anthrax and finishing with tuberculosis and plague. The principle of identification was set out in Koch's postulates in 1881:
1. The germ is always present in the disease.
2. The germ can be cultivated outside the body and preserved for generations.
3. The disease can be reproduced in experimental animals.
4. The organism causing the disease cannot be found in inoculated animals.
9.5.5 Pasteur's spontaneous generation experiment
See diagram 9.5.1: Pasteur's flask
It was believed that living organisms could develop from non-living matter without pre-existing living matter, e.g. Disease can develop spontaneously in damaged human tissue without any exterior organism being involved. In 1859 Louis Pasteur tested this belief by putting boiled clear meat soup into a swan-neck flask. Then swan neck was heated to kill any living things in it. The swan-neck flask was left standing while dust fell from the air and accumulated in the loop of the swan neck. Air from the atmosphere could still pass by the dust in the swan neck. The meat soup remained clear. Later he tipped the flask so that the dust in the loop of the swan neck fell into the flask. The meat soup in the flask became cloudy because of bacterial infection from the dust in the air.
9.6.0 List of bacteria and school experiments
Acetivibrio
Acetoanaerobium
Acetobacter aceti, spoils beers and wines, oxidizes ethanol, producing acetic acid
Acetobacterium
Acetofilamentum
Acetogenium
Acetomicrobium
Acetothermus
Acidaminobacter
Acidaminococcus
Acidianus
Acidiphilium
Acidomonas
Acidothermus
Acinetobacter
Acoleplasma
Actinobacillus
Actinokineospora
Actinomadura
Actinomyces
Actinoplanes
Aegyptianella
Aerococcus (Enterococcus)
Aeromicrobium
Aeromonas
Afipia
Agave
Agrobacterium rhizogenes
Agrobacterium rubi
Agrobacterium tumefaciens, induces tumours in plants, crown galls disease
Agromonas
Agromyces
Alcaligenes eutrophus, used to make biodegradable plastics
Alteromonas
Aminobacter
Amoebobacter
Amphibacillus
Anabaena
Anacalochloris
Anaerobiospirillum
Anaeroplasma
Anaerorhabdus
Anaerovibrio
Anaplasma
Ancyclobacter
Aquaspirillum
Arachnia
Arcanobacterium
Archaeoglobus
Archangium
Archina
Arsenophonus
Arthobacter
Asteroleplasma
Aureobacterium
Azomonas
Azospirillum
Azospirillumis
Azotobacter vinclandii, free-living nitrogen fixer
Bacillus amylobacter
Bacillus anthracis
Bacillus cereus NOT suitable for use in schools
Bacillus denitrificans
Bacillus licheniformis, decomposes protein
Bacillus megaterium, produces lipase, protease and PHB, has specific cell size
Bacillus mycoides, has specific tendency to form colonies
Bacillus stearothermophilus, grows at 65oC
Bacillus subtilis, decomposes starch to produces amylase, lipase and protease, Risk Group 1, Suitable for school use
Bacterium termo
Bacterium vermiforme
Bacteroides
Bacteroides thetaiotaomicron
Bartonella
Bdellovibrio
Beggiatoa
Beijerinckia
Beyerinckia
Bifidiobacterium
Bilophococcus
Blastobacter
Blattabacterium
Bordetella pertusssis
Borrelia
Borrelia burgdorferi
Brachyarcus
Brachybacterium
Bradyrhizobium
Branhamella
Brevibacterium vermiforme
Brochothrix
Brucella
Budvicia
Buttiauxella
Butyrivibrio
Caedibacter
Calothrix
Calymmatobacterium
Campylobacter
Cardiobacterium hominis
Carnobacterium pleistocenium
Caryophanon
Caseobacter
Cassia
Caulobacter
Cedecea
Cellulomonas biazotea, produces cellulase to decompose cellulose
Cellvibrio
Centipeda
Chamaespiphon
Chlamydia trachomatis
Chlorobium
Chloroflexus
Chloroherpeton
Chloronema
Chondromyces crocatus
Chromatium okenii, photosynthetic, anaerobic bacterium
Chromobactium (Janthinobacterium) violet colonies, grow at 20oC
Chromobacterium violaceum NOT suitable for use in schools
Chromohalobacter
Chryseomonas
Citrobacter
Clavibacter
Clonothrix
Clostridium botulinum
Clostridium pasteurianum
Clostridium perfringens (welchii) NOT suitable for use in schools
Clostridium tetani
Comoamonas
Coprococcus
Coriobacterium
Corynebacterium diptheriae
Corynebacterium michiganense
Cowdria
Coxiella
Crenothrix
Cristispira
Cupriavidas
Curtobacterium
Cyanothece
Cyclobacterium
Cytophaga
Datura
Deinobacter
Deinococcus
Deleya
Dermabacter
Dermatophilus
Derxia
Desulfobacter
Desulfobacterium
Desulfobulbus
Desulfococcus
Desulfomaculum
Desulfomicrobium
Desulfomonas
Desulfomonile
Desulfonema
Desulfosarcina
Desulfotomaculum
Desulfotomaculum
Desulfovibrio
Desulfurella
Desulfurococcus
Desulfurolobus
Desulfuromonas
Diplococcus
Ectothiorhodospira mobilis
Edwardsiella
Ehrlichia
Eikenella
Enhydrobacter
Ensifer
Enterobacter
Envinia carotovora, produces pectinase, rots fruit
Eperythrozoon
Erwinia carotovora, decomposes phospholipids
Erysipelothrix
Erythrobacter
Escherichia coli (E. coli) T4 bacteriophage attacks B strain, used for genetic experiments on bacteria, Risk Group 1, Suitable for school use
Eubacterium
Ewingella
Exigouibacterium
Falcivibrio
Fervidobacterium
Fibrobacter
Flavimonas
Flavobacterium
Flectobacillus
Francisella
Frankia
Frateuria
Fusobacterium
Gallionella
Gardnerella vaginalis
Gemella
Gemmata
Gloeobacter
Gloeocapsa
Gloethece
Gluconobacter
Glycomyces
Gonococcus
Grahamella
Haemobartonella
Haemophilus ducreyi
Haemophilus influenzae
Hafnia
Haloanaerobium
Haloarcula
Halobacterium
Halobacteroides
Halococcus
Haloferax
Halomonas
Halovibrio
Helicobacter pylori
Heliobacillus
Heliobacterium
Heliothrix
Herbaspirillum
Holospora
Hydrogenobacter
Hydrogenophaga
Hyperthermus
Ilyobacter
Janthinobacterium
Jonesia
Kingella
Klebsiella pneumoniae
Kluyvera
Kurthia
Kuznezovia
Lachnospira
Lactobacillus
Lactobacillus bulgaricus, used to produce yoghurt, curds, ferments glucose and lactose to produce lactic acid
Lactococcus lactis, used to produces yoghurt, curds
Lactococcus
Lamprobacter
Lamprocystis
Lampropedia
Leclercia
Legionella
Leminorella
Leptospira
Leptospirillum
Leptothrix
Leptotrichia
Leucathrix
Leuconostoc
Leuconostoc mesenteroides, converts sucrose to dextran, used to producing sauerkraut
Leucothrix
Listeria
Lysobacter
Lyticum
Macromonas
Magnetospirillum magnetobacterium
Malonomonas
Marinobacter
Marinococcus
Marinomonas
Megamonas
Megasphaera
Melissococcus
Mellitangium erectum
Mesophilobacter
Metallogenium
Metallosphaera
Methanobacter
Methanobacterium
Methanobrevibacter
Methanococcoides
Methanococcus jannaschii
Methanocorpusculum
Methanoculleus
Methanogenium
Methanohalobium
Methanohalophilus
Methanolacinia
Methanolobus
Methanomicrobium
Methanomonas
Methanoplanus
Methanosarcina
Methanosphaera
Methanospirillum
Methanothermus
Methanothrix
Methylobacillus
Methylobacterium
Methylococcus
Methylocystis
Methylomonas
Methylophaga
Methylophilus
Methylophilus methylotrophus, needs methanol to grow
Methylosinus
Methylovorus
Micavibrio
Microbacterium
Micrococcus
Micrococcus luteus (Sarcina lutea), has yellow colonies, specific colony colour, Risk Group 1, Suitable for school use
Microcyclus
Microcystis
Micromonospora
Mitsuokella
Mobiluncus
Moellerella
Moraxella
Morococcus
Mycobacterium leprae
Mycobacterium tuberculosis
Mycoplasma pneumoniae
Myxobaktron
Myxococcus stipitatus
Natronobacterium
Natronococcus
Naumanniella
Neisseria gonorrhoeae
Neisseria meningitidis
Neorickettsia
Nisseria
Nitrobacter winogradskyi
Nitrococcus mobilis
Nitrosococcus oceani
Nitrosolobus multiformis
Nitrosomonas europaea
Nitrosospira
Nitrosovibrio
Nitrospina
Nitrospira
Nocardia
Nodularia
Nostoc
Obesumbacterium
Oceanospirillum
Ochrobium
Oligella
Oscillatoria
Oscillochloris
Oscillospira
Oxalobacter
Pantoea
Paracoccus
Pasteurella
Pectinatus
Pediococcus
Pelobacter
Pelodictyon
Pelonema
Pelosigma
Peptococcus
Peptostreptococcus
Phenylobacterium
Photobacterium phosporeum NOT suitable for use in schools, bioluminescent, needs saline conditions
Photolithotrops
Phyllobacterium
Pimelobacter
Planococcus
Plesiomonas
Pleurocapsa
Pneumococcus
Porphyromonas
Pragia
Prevotella
Prochlorothrix
Propionibacterium
Propionigenium
Propionispira
Prosthecochloris
Proteus vulgaris NOT suitable for use in schools
Providencia
Pseudocaedibacter
Pseudomonas acruginosa NOT suitable for use in schools
Pseudomonas aeruginosa NOT suitable for use in schools, said to be responsible for one-in-ten hospital-acquired infections,
an opportunistic bacteria that attacks weakened immune systems. It mutates rapidly and is acquiring resistance to antibiotics, e.g. ciprofloxacin because of exposure to the disinfectant BSK, benzalkonium chloride.
Pseudomonas carboxydororans
Pseudomonas fluorescens, fluorescent, decomposes gelatine
Pseudomonas fluorescens, floating mats of bacteria
Pseudomonas solanacearum NOT suitable for use in schools
Pseudomonas syringae
Pseudomonas tabacci NOT suitable for use in schools
Pseudomonas tumefaciens
Psychrobacter
Pyrobaculum
Pyrococcus
Pyrodictium
Rahnella
Ralstonia solanacearum
Rarobacter
Renibacterium
Rhizobacter
Rhizobium leguminosarum, used to study symbiotic nitrogen fixation in nodules on legume roots
Rhodobacter adriaticus
Rhodomicrobium
Rhodopila
Rhodopseudomonas capsulata
Rhodopseudomonas palustris, red photosynthetic anaerobe
Rhodospirillum rubrum, Risk Group 1, Suitable for school use
Rhodyclus
Rickettsia typhus
Rickettsiella
Rikenella
Rochalimaea
Roseburia
Roseobacter
Rothia
Rubrobacter
Rugamonas
Ruminobacter
Ruminococcus
Runella
Saccarothrix
Saccharococcus
Salmonella typhi
Sarcina
Sarcina lutea, ( Micrococcus luteus), has yellow colonies, specific colony colour, Risk Group 1, Suitable for school use
Scytonema
Sebaldella
Selenomonas
Serratia marescens NOT suitable for use in schools
Shigella dysenteriae
Siderocapsa
Siderococcus
Simonsiella
Sinderocapsa
Sinorhizobium
Sorangium
Sphaerobacter
Sphaerotilus
Sphingobacterium
Spirillum
Spirillum serpens
Spirochaeta
Spiroplasma
Spirosoma
Spirulina
Sporolactobacillus
Sporomusa
Sporosarcina urea, decomposition of urea
Sporospirillum
Staphylococcus albus, ( S. epidermis), forms white colonies, Risk Group 1, Suitable for school use
Staphylococcus aureus NOT suitable for use in schools
Staphylothermus
Stigonema
Stomatococcus
Streptobacillus
Streptococcus faecalis (Enterococcus faecalis)
Streptococcus lactis, (Lactococcus), sours milk
Streptococcus mutans
Streptococcus pneumoniae
Streptococcus pyrogenes
Streptococcus thermophilus, ferments glucose and lactose at 50oC
Streptomyces antibioticus
Streptomyces griseus, earth odour of soil, produces streptomycin antibiotic
Streptomyces scabies
Streptosporangia
Streptoverticillium
Succinimonas
Succinivibrio
Sulfidobacillus
Sulfobacillus
Sulfolobus
Synechococcus
Synechocystis
Syntrophobacter
Syntrophococcus
Syntrophosmonas
Syntrophospora
Tatumella
Tectibacter
Terrabacter
Thermoactinomyces
Thermoanaerobacter
Thermobacteroides
Thermococcus
Thermodesulfobacterium
Thermodiscus
Thermofilum
Thermoleophilum
Thermomicrobium
Thermomonospora
Thermonema
Thermoplasma
Thermoproteus
Thermospipho
Thermothrix
Thermotoga
Thermplasma
Thermus
Thiobacillus
Thiobacillus ferrooxidans, leaches sulfur from coal, oxidizes iron(II)
Thiobacterium
Thiocapsa
Thiocystis
Thiodendron
Thiodictyon
Thiomicrospira
Thiopedia
Thioploca
Thiosphaera
Thiospira
Thiospirillum
Thiotrix
Thiovulum
Tissierella
Treponema pallidum
Trichococcus
Trichodesmium
Ureaplasma
Vagococcus
Vampirovibrio
Variovorax
Veillonella
Vibrio cholerae
Vibrio fischeri NOT suitable for use in schools
Vibrio natriegens (Beneckea natriegens) needs sodium chloride, used to study growth of micro-organisms
Vibrio parahemolyticus
Volcaniella
Weeksella
Wolinella
Wollbachia
Xanthanomonas
Xanthobacter
Xanthomonas campestris, produces a biopolymer
Xanthomonas phaseoli NOT suitable for use in schools
Xenorhabdus
Xylella
Xylophilus
Yersinia
Yersinia pestis
Yokenella
Zoogloea
Zymomonas
Zymonas
Zymophilus
9.213 Viruses
See 10.9.0: Sexually transmitted infections, STIs, HIV and AIDS
A virus is a strand or strand of nucleic acid covered by protein and sometimes a membrane. Viruses cause infected cells to produce progeny viruses. Retroviruses use the enzyme reverse transcriptase to copy the viral RNA (ribonucleic acid) into DNA (deoxyribonucleic acid). Plant viruses can usually be recognized by marks on leaves, e.g. mosaics, leaf streaks, and ring spots. Viruses are not affected by antibiotics. A bacteriophage is similar to a very small virus. It infects bacteria.
9.213a List of viruses
Bacteriophage (T type) (host E coli)
Broad bean wilt virus on legumes
Clover stunt virus on legumes
Cucumber mosaic virus
Cymbidium virus of orchids
Encephalitis virus causes headache, fever, inflammation of the brain, carried by mosquitoes, eastern equine encephalitis is fatal.
Infection variegation of Camellia japonica
Iris mosaic virus
Leaf roll of potato virus
Lettuce big vein virus
Lettuce necrotic yellows virus
Orthomyxovirus (influenza virus A, B, C) causes nasal obstruction, headache, sneezing, chest pain, cough.
Potato mosaic virus, Potato Virus X
Polio virus (poliomyelitis) attacks motor neurones, cause paralysis and atrophy of muscles.
Rabies virus infects peripheral nerves then central nervous system.
Rhinovirus (coronovirus) causes common cold, nasal obstruction, headache, sneezing.
Rose mosaic
Smallpox virus has been eradicated but some cultures exist in laboratories.
Tobacco mosaic virus
Tomato spotted wilt virus on tomato, capsicum, dahlia, chrysanthemum
Turnip mosaic virus
Woodiness of passion fruit virus
9.213b Classification of viruses
The classification of viruses can be based on the type and arrangement of the genetic material.
Group 1. dsDNA Double-strand DNA viruses include oral herpes, herpes zoster (shingles) genital herpes, chickenpox viruses, cold sore, Herpes simplex virus, types 1 and 2 (HSV-1 and HSV-2) Adenoviruses human adenoids, tonsils, Human Papilloma Virus (HPV) causes dermal warts and genital warts Condylomata acuminata, Molluscum Contagiosum Virus
Group 2. ssDNA Single-strand DNA viruses include some of the smallest viruses.
Group 9. dsRNA Double-strand RNA include viruses responsible for diarrhoea in children.
Group 4. positive sense ssRNA Single-strand RNA viruses include influenza, hepatitis A virus (HAV) infectious hepatitis from faecal contamination of food and water and possibly milk, shellfish, hepatitis C virus (HCV) from exchange of body fluid, blood transfusion, sexual contact, shared needles for intravenous drug use, severe acute respiratory syndrome (SARS) foot-and-mouth disease, yellow fever, rubella viruses and most plant viruses
Group 5. negative sense ssRNA Single-strand RNA viruses include influenza, measles (rubeola) mumps infection of salivary glands (paramyxovirus) rabies, Ebola virus, foot-and-mouth disease
Group 6. ssRNA Diploid single-strand RNA viruses that use reverse transcriptase, retroviruses, include HIV virus.
Group 7. ds DNA-RT Circular double-strand DNA viruses that use reverse transcriptase, include hepatitis B virus (HBV) serum hepatitis from exchange of body fluid, blood transfusion, sexual contact, pregnant mother to baby, shared needles for intravenous drug use
Human Immunodeficiency Virus, HIV, and AIDS, acquired immune deficiency syndrome.
9.213.1 HSV-1 (Herpes simplex 1) and HSV-2 (Herpes simplex 2)
HSV-1, herpes simplex virus causes cold sores, painful blemishes of the mouth (fever blisters). It can become dormant for years, when drugs cannot affect it, then, years later, be revived by excessive sunlight or fever to cause a cold sore in the same place as before.
HSV-2 causes painful genital sores that can return late in life as shingles.
9.213.2 Herpes varicella-zoster, chicken pox, shingles
The Herpes varicella-zoster virus causes chicken pox (varicella) in the skin of children as red spots that become small bubbles then become dry crusts. In adults, the Herpes varicella-zoster virus causes shingles (zoster) as painful lesions in a pattern along the sensory nerves.