School Science Lessons
Biology experiments
Updated: 2008-06-25
Biology names
Table of contents
9.196 Fungi
9.209 Bacteria
9.207 Lichens
9.213 Viruses
9.213.1 HSV-1 and HSV-2
Biotechnology
4.1.0 Microbial systems
4.2.0 Fermentation processes in food production
4.3.0 Using in vitro culture techniques
4.4.0 Biotechnology genetics
4.5.0 Appendices
9.1.2.0 Techniques for studying bacteria
9.196 Fungi
3.43.00 Fungi classification
6.0 Culture media for routine cultivation and identification of fungi
6.5 Fungi (primary)
6.7 Mouldy bread and rotten fruit (primary)
9.203 Bathroom and kitchen mould
9.207 Lichens
9.208 Slide culture preparation to identify fungi
3.26.0 Yeast, Phylum Ascomycota
9.27 Red yeast rice, Monascus purpureus
3.28 Ginger beer "plant"
3.29 Cork taint of wine, "corky" wine (2,4,6-TCA)
9.201 Agaricus
9.214 Aspergillus
9.215 Candida
9.216 Cryptococcus
9.200 Eurotium
9.217 Fusarium
9.218 Microsporum
9.221 Monascus purpureus
9.199 Mucor
9.202 Penicillium
9.198 Pythium
9.197 Phytophthora
9.220 Puccinia
9.196 Rhizopus
9.219 Trichophyton
9.209 Bacteria
3.44 Bacteria classification
9.209 Rhizobium in legumes
9.210 Grass in water
9.211 Teeth scrapings
6.6 Bacteria (primary)
3.43.00 Fungi classification
See also 16.3.1.7: Chitin
Fungi have no chlorophyll and the main body, hypha, has with walls containing chitin. Fungi may be unicellular or filamentous so are generally classified as yeasts, moulds and mushrooms. Asexual spores, conidia, are cut off from the ends of conidiophore hyphae. A fungus infection of humans is called a mycosis. It is particularly dangerous in immunodeficient patients with AIDS. The main divisions of the fungi are the Basidiomycota, Ascomycota, Glomeromycota, Zygomycota and Deuteromycota, now called the "mitosporic fungi", also called "fungi imperfecti" because no sexual reproduction has been observed.
2.0.3 Plant cells and tissues, eukaryotic cells
3.43.01 Phylum Ascomycota, ascomycetes, ascus-producing fungi, sac fungi
3.43.02 Phylum Basidiomycota, basidiomycetes, basidium-producing fungi, club fungi
3.43.02a Rusts, Uredinales
3.43.02b Smuts
3.43.03 Phylum Zygomycota, zygomycetes, phaecomycota, phycomycetes
3.43.03a Class Microsporidia
In former classification systems, most of the following groups were classified together as the Phycomycetes, the algae-like fungi.
3.43.04 Deuteromycota (now called the "mitosporic fungi") deuteromycetes, imperfect fungi, fungi imperfecti, anamorphic fungi (They are Ascomycota and Basidiomycota in which sexual reproduction is unknown, so they are called "imperfect".)
The following groups are nowadays usually classified under the heterokontophyta division of the algae.
3.43.05 Class Mycetozoa (Phylum Myxomycota), Myxomycetes (acellular or plasmodial or coenocytic slime moulds), unit is a plasmodium slime fungus, fungus-like slime moulds, many micro-organisms but most not fungi, also giant kelps, Stemonitis, Physarum polycephalum
3.43.06 Class Oomycetes (Phylum Oomycota), water moulds, rusts, Kingdom Chromista, water mould, egg fungi, not a fungus but similar to brown algae. The zoospores have two cilia. (They are nowadays usually classified under the Heterokontophyta division of the Algae, or put in the Kingdom Chromista.)
3.43.07 Class Hyphochytridiomycetes (Phylum Hypochytridiomycota), zoospores with just one anterior flagellum (They are nowadays usually classified under the Heterokontophyta division of the Algae, or put in the Kingdom Chromista.)
3.43.08 Class Chytridiomycetes (Phylum Chytridiomycota), chytrids, Algae: Heterokontophyta zoosporic fungi, aquatic fungi
3.43.09 Phylum Glomeromycota, Glomerales, mycorrhizal associations, arbuscular, i.e. inside plant cells, mutualistic
3.43.10 Phylum Cerozoa, amoeboids and flagellates, slime mould, cabbage club root fungus, Plasmodiophora
3.43.01 Phylum Ascomycota, ascomycetes, ascus-producing fungi, sac fungi, truffle
Aleuria, orange peel cup fungus
Amanita, agaric mushroom, fly agaric, poisonous toadstool, muscimol, muscimole, muscarine
Armillariella mellea, honey-fungus
Aspergillus
Candida
Ceratocystis
Claviceps purpurea (Family Clavicipitaceae) ergine, d-lysergic diethylamide, ergot fungus, ergometrine causes abortions, ergotamine used for migraine headaches, natural LSD, plant pathogen of rye seed heads [d-lysergic acid amide, d-lysergic acid diethylamide, LSD]
See: LSD
Cordyceps sinensis, caterpillar fungus
Dipodascus
Endothia
Epidermophyton, causes tinea
Erysiphe, powdery mildew
Eurotium
Fusarium, Panama disease of bananas, Fusarium wilt
Geastrum, earth-stars
Histoplasma capsulatum, Darling's disease
Microsporum
Microsphaera
Monilinia
Morchella
Mycosphaerella fijiensis, black Sigatoka disease of bananas
Nematospora (formerly Eremothecium)
Neurospora crassa
Peziza, cup fungus, saprophytic in wood
Phallus, stink horns
Pneumocystis jirovecci, affects AIDS patients
Saccharomyces
Saccharomycodes
Schizosaccharomyces octosporus
Sphaerotheca
Taphrina, leaf curl disease
Trichoderma, soil mould
Trichophyton
Tuber, truffle, morel
Venturia
Zygosaccharomyces
3.43.02 Phylum Basidiomycota, basidiomycetes, basidium-producing fungi, club fungi, sexual spores are produced on a club-shaped basidium
Agaricus, mushroom
Amanita muscaria, poisonous mushroom
Boletus
Calvatia, giant puffball mushroom
Clavaria
Coprinus, on dung pads
Crucibulum laeve, bird's nest fungus
Cryptococcus
Cyathus
Diptoporus betulinus, "razor strap", bracket fungus on birch trees
Exidea glandulosa, "witches' butter"
Exobasidium
Ganoderma, bracket fungi
Geastrum
Lycoperdon, puff ball
Phlebopus boletes
Pleurotus ostreatus, oyster mushroom
Polyporus
Meripilus gigantaeus, bracket fungus
Merulius, dry rot of timber
Phallus, stink horn
Schizophyllum commune, split gill fungus
3.43.02a Rusts, Uredinales
wheat rust Puccinia triticina, wheat stem rust Puccinia graminis, soybean rust Phakopsora, white pine blister rust, apple cedar rust, hollyhock rust, asparagus rust, white pine blister rust
Puccinia
3.43.02b Smuts
maize smut (corn smut) Ustilago maydis, sugar cane smut Ustilago scitaminea, loose smut Ustilago nuda
Karnal bunt, partial bunt, caused by Tilletia indica
3.43.03 Phylum Zygomycota, zygomycetes, phaecomycota, phycomycetes, have no cross walls, septa
Encephalitozoon cuniculi, causes diarrhoea in AIDS patients
Mucor
Phallus, stink horn
Pilobolus
Polyporus stolonifera, bread mould
Rhizopus
Uromycladium, acacia gall rust fungus
3.43.03a Class Microsporidia
Tiny parasites with no mitochondria
Loma in fish, Abelspora in crab, Amblyspora in mosquito
3.43.04 Deuteromycota (now called the "mitosporic fungi") deuteromycetes, imperfect fungi, fungi imperfecti, anamorphic fungi (They are Ascomycota and Basidiomycota in which sexual reproduction is unknown.)
Arthrobotrys
Blastomyces dermatiidis, pathogen, cultures are a biohazard to laboratory personnel!
Candida
Cladosporium, brown food mould, soil mould
Dactylella
Epidermophyton
Fusarium
Histoplasma
Verticillium
3.43.05 Myxomycota, Mycetozoa, Myxomycetes slime fungi, fungus animals, fungus-like slime moulds, many micro-organisms but most not fungi, also giant kelps
1.1.1 Kingdom Protista - Heterotrophic protists
Fuligo, yellow slime mould, Protista, Mycetozoa
Sternonitis, Protista, Mycetozoa
 Physarum, many headed slime, "pet slime mould", Protista, Mycetozoa
3.43.06 Oomycota, oomycetes, water mould, egg fungi, but it is not a fungus. It is similar to brown algae. The zoospores have two cilia. (They are nowadays usually classified under the Heterokontophyta division of the Algae, or put in the Kingdom Chromista.)
1.1.2 Chromista
1.1.3 Heterokontophyta
Albugo candida (Cystopus), water mould, white rust
Monoblepharis
Peronospora, plant pathogen
Physarum, slime mould
Phytophthora infestans, potato blight
Pythium, root rot, damping-off fungus
Plasmopara, downy mildew of grapes
Saprolegnia, water mould, cotton mould
3.43.07 Hyphochtridiomycota, hyphochytridiomycetes, zoospores with just one anterior flagellum
(They are nowadays usually classified under the Heterokontophyta division of the Algae, or put in the Kingdom Chromista.)
1.1.2 Chromista
1.1.3 Heterokontophyta
Aimillaria, Lactarius, Tremella
3.43.08 Phylum Chytridiomycota, Chytridiomycetes, chytrids, Algae: Heterokontophyta zoosporic fungi, aquatic fungi, asexual, single cilium, saprophytic
1.1.3 Heterokontophyta
Allomyces
Batrachochytrium, kills frogs
Chytriomyces
Monoblepharis
Rhizophydium
Synchytrium endobioticum, potato wart disease, black scab
3.43.09 Phylum Glomeromycota, Glomerales, mycorrhizal associations, arbuscular, i.e. inside plant cells, mutualistic
 Acaulospora
Geosiphon
Glomus
Nostoc
Pacispora
Paraglomus
Physoderma
Siphonaria
3.26.0 Yeast, Phylum Ascomycota
(Bakers' yeast, Saccharomyces cerevisiae (beer yeast, S. ellipsoideus) (wine yeast, S. ludwigii, S. minor) (bread yeast, S. octosporus) (grape yeast S. pastorianus)
3.26.1 A yeast population
3.27 Red yeast rice, Monascus purpureus
3.28 Ginger beer "plant"
3.35.4 Yeast cells
3.38 Carbon dioxide and fermentation for brewing
9.204 Yeast population, bakers' yeast
9.205 Sampling yeast populations
9.206 Find wild yeasts in flowers
9.212 Ginger beer "plant"
4.1.2 Enrichment of wild yeast strains
4.3.22 Test for zymase and catalase in yeast
6.6.14 Heat of respiration, yeast, bakers' yeas
6.6.18 Alcoholic fermentation, yeast, Saccharomyces cerevisiae
11.3.3 Triple scale wine hydrometer
12.4.17 Test for zymase and catalase in yeast
17.4.2 Catalysts, fermentation with yeast
19.2.11 Yeast for fermentation and brewing
Appendix 2A. Fermentation
3.26.1 A yeast population
See diagram 9.204: Yeast cell forming bud
Natural sources of yeast include the wax-like coatings on smooth-skinned fruits, especially grapes. However, bakers' yeast is usually obtainable. It reproduces rapidly, making it a good subject for observing population changes under varying conditions.
Set up tubes of sugar, molasses or honey solutions and a water control. Place a quarter cake of crumbled yeast in each tube. Compare the results. Place a one-hole stopper with glass tubing in the sugar - yeast solution and allow the gas produced to bubble through a tube of clear lime water which will detect the presence of carbon dioxide. Yeasts reproduce asexually through a process called "budding". Place a drop of the sugar - yeast solution on a microscope slide and cover with a coverslip. Examine the slide with the high power objective. Look for cells with protrusions or buds. If you can see nuclei in the cells, look for their presence in the buds.
Sampling yeast populations
An effective method of studying population growth with micro-organisms is to start a culture each day and, on the final day, to sample and count all cultures. For example, a new yeast culture can be started each day for 10 days, using one grain of yeast for each culture. On the tenth day samples are taken from each culture and counted with a microscope. A special slide for counting blood cells is desirable, but not essential. If the population on a given day is too large to count, dilute a sample by adding 9 parts water to 1 part of sample.
3.27 Red yeast rice, Monascus purpureus
It is used to produce red-purple fermented rice called "red yeast rice" with the Chinese brand names "Xuezhikang (XZK)" or "Hypocol". Red yeast rice is used for food colouring, e.g. Peking duck and pickled tofu. Also, it is a Chinese herbal medicine. Clinical trials have shown that it may reduce the chance of repeated heart attacks after surgery better than other statins. However, it may cause liver damage.
3.28 Ginger beer "plant" is the yeast Saccharomyces florentinus (S. pyriformis) and the bacterium Lactobacillus hilgardii (Brevibacterium vermiforme).
3.29 Cork taint of wine, "corky" wine (2,4,6-TCA)
See 16.1.3.2: 3. Phenols (group: OH-C in a benzene ring) (phenol = C6H5O6)
The "damp cardboard" taste of corky wine is caused usually by 2,4,6-trichloroanisole (2,4,6-TCA) produced mainly by Trichoderma and Fusarium strains of fungi when in contact with chlorine used to bleach corks made from the bark of Quercus suber. The taint taste of 2,4,6-TCA may also cause the "Rio" defect in South American coffee and affect beer, sake and fish and prawns. Nowadays, the wine cork is being replaced by screw-top caps, e.g. the Stelvin cap that seals the bottle but allows a very small amount of air to touch the surface of the wine to allow maturation.
3.44 Bacteria classification
1.2 Phylogenetic classification
3.44.01 Bacteria classified by shape
3.44.02 Bacteria classified by diseases
3.44.03 Bacteria classified by physiology
9.1.2.0 Techniques for studying bacteria
See diagram 9.205 Bacteria diagrams
9.4 Sulfonamides, sulfa drugs
Sodium benzoate
9.209 Rhizobium in legumes
9.210 Grass in water
9.211 Teeth scrapings
9.212 Ginger beer plant
4.4.2 Conjugation in bacteria, Escherichia coli
6.9.14.0 Composting
Bacteria (primary)
3.44.01 Bacteria classified by shape
1. Spherical shape bacteria, coccus
Staphylococcus, Streptococcus, Diplococcus, Gonococcus, Pneumococcus, Nitrococcus
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
Escherichia coli (E. coli) causes cystitis, "honeymoon disease"
3. Spiral, corkscrew shape bacteria, spirillum, spirochaete, spirochete
Leptospira
Treponema pallidum causes syphilis
4. Comma shape bacteria, vibrio
Nitrobacter oxidizes nitrite
Nitrosomonas oxidizes ammonia
Pseudomonas tumefaciens, crown gall organism
Vibrio cholerae, causes cholera
3.44.02 Bacteria classified by diseases
Phylum Actinobacteria, Actinomycetes, are pathogens.
Gardnerella vaginalis causes bacterial vaginosis, nonspecific vaginitis.
Phylum Actinobacteria are found in in soils.
Phylum Chlamydiae are pathogens.
Chlamydia trachomatis causes chlamydial pelvic inflammatory disease, PID.
Phylum Bacteroidetes are pathogens in the human mouth.
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.
Neisseria gonorrhoeae causes gonorrhoea, urethral / vaginal discharge, "the clap".
Ralstonia solanacearum causes bacterial wilt disease in bananas.
Phylum Spirochaetes are Gram -ve, pathogens.
Leptospira causes leptosporosis, Weil's disease.
Treponema pallidum causes syphilis.
Borrelia, carried by lice and ticks, causes relapsing fever and Lyme disease.
3.44.03 Bacteria classified by physiology [Items 3.44.1.0 to 3.44.199 based on the David Bergey classification]
3.44.1.0 Oxygenic phototropic bacteria
3.44.2.0 Gliding bacteria, fruiting bacteria that leave a visible trail of slime
3.44.3 Sheathed bacteria
3.44.4 Budding bacteria / appendaged bacteria (stalked bacteria)
3.44.5 Spirochetes (spirochaetes)
3.44.6 Spiral and curved bacteria, aerobic, motile, helical / vibrioid, Gram-negative
3.44.7 Gram-negative aerobic rods and cocci
3.44.8 Gram-negative facultative anaerobic rods
3.44.8a Bioluminescent and related bacteria
3.44.9 Gram-negative, anaerobic, straight, curved, and helical rods
3.44.10 Gram-negative cocci and coccobacilli
3.44.11 Gram-negative anaerobic cocci
3.44.12.0 Gram-negative chemolithotrophic bacteria
3.44.12a Nitrifying bacteria
3.44.12b "True" nitrifying bacteria
3.44.12.1 Nitrifying bacteria
3.44.12.2 "True" nitrifying bacteria
3.44.12.3 Nitrogen-fixing bacteria
3.44.12.4 Denitrifying bacteria
3.44.12c Colorless sulfur-oxidizing bacteria
3.44.12d Hydrogen-oxidizing bacteria
3.44.12e Methanotrophs
3.44.12f Acetic acid bacteria
3.44.13 Methane-producing bacteria, methane-producing
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
3.44.17 Actinomycetes and related bacteria
3.44.18 Rickettsias and chlamydias
3.44.19 Mycoplasmas
3.44.20 Sulfur-reducing bacteria
3.44.21 Archaeobacteria, Archaea [may also occur above]
3.44.22 Endosymbionts
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 sulphur 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, 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, have external sulfur granules
Ectothiorhodospira mobilis are photosynthetic sulfur bacteria that deposit sulfur outside the cells.
3.44.1.4 Purple nonsulfur bacteria 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
3.44.2.0 Gliding bacteria, fruiting bacteria that leave a visible trail of slime
3.44.2.1 Myxobacteria form rod-shaped aggregates to form fruiting bodies when nutrients are low.
Chondromyces crocatus, Mellitangium erectum, Myxococcus stipitatus
3.44.2.2 Sulphate and sulphur reducing proteobacteria are sulphur or sulphate reducers, anaerobic, and live in an oxygen free aquatic habitat.
Desulfomaculum is soil dwelling and causes tinned meat spoilage called "sulphide 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 sulphur compounds in sulphur 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 / appendaged bacteria (stalked bacteria)
They have extensions called prosthecae that are involved in reproduction.
Blastobacter, Caulobacter, Gallionella, Gemmata, Kuznezovia, Metallogenium
3.44.5 Spirochetes, spirochaetes
Borrelia, Cristispira, Leptospira, Spirochaeta, Treponema pallidum
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.
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, Rhizobium, 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.
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.
3.44.8 Gram-negative facultative anaerobic rods
Cardiobacterium hominis causes endocarditis.
Enterobacter causes urinary infections.
Klebsiella pneumoniae can cause pneumonia, urinary tract infections, and bacteremia. 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
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.)
Oxidize ammonia and nitrite, metabolise sulfur and sulfur compounds, percipitate 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
3.44.12a Nitrifying bacteria
Nitrosifyers, ammonia-oxidizing bacteria, reduce inorganic nitrogen compounds and oxidize ammonia to nitrite
Nitrosomonas europaea, Nitrosococcus oceani, Nitrosolobus multiformis, Nitrosospira, Nitrosovibrio
3.44.12b "True" nitrifying bacteria
Nitrate-oxidizing bacteria, oxidize the nitrite to nitrate
Nitrobacter winogradskyi, Nitrococcus mobilis, Nitrospira, Nitrospina
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 which 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
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 founds 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 Colorless 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.
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
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
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 are cellulose-dissolving bacterium.
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.
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
3.44.19 Mycoplasmas
Acoleplasma, Anaeroplasma, Asteroleplasma, Mycoplasma, Spiroplasma, Thermplasma, Ureaplasma
3.44.20 Sulfur-reducing bacteria
Elemental sulphur is reduced to to thiosulfate and dimethylsulfoxide.
Desulfobacter, Desulfobacterium, Desulfobulbus, Desulfococcus, Desulfomicrobium, Desulfomonas, Desulfomonile, Desulfonema, Desulfosarcina, Desulfotomaculum (also endospore-forming) Desulfovibrio, Desulfurella, Thermodesulfobacterium
Desulfuromonas reduces elemental sulphur
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.
9.4 Sulfonamides, sulfa drugs
See diagram 14.12
The first of the antibacterial drugs, the sulfonamides, were found to be 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.
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.