9.1 Cycles and waste #
The study of Cycles and waste provides fundamental principles governing cellular architecture, molecular interactions, and physiological regulation.
Lysogentic Cycle
9.1.1 Carbon and nitrogen #
Global fluxes are not quoted. Oxygenic photosynthesis fixes CO2. Respiration and fermentation return it. In anaerobic mud, fermenters supply H2, CO2, and acetate to methanogenic archaea, and the fermentations stay favourable only while methanogens remove the H2. That partnership is syntrophy. Methanotrophs oxidise methane with oxygen and methane monooxygenase; other archaea oxidise it anaerobically, often with sulfate reducers. A Winogradsky column is the same stack: oxygenic phototrophs on top, purple and green sulfur bacteria where light meets sulfide, sulfate reducers and methanogens in the mud.
| Step | Change | Who |
|---|---|---|
| Fixation | N2 to ammonia | nitrogenase, free-living or symbiotic |
| Ammonification | organic N to ammonia | decomposers |
| Nitrification | ammonia to nitrite to nitrate | Nitrosomonas, then Nitrobacter; archaea do the first step in the sea; some Nitrospira do both |
| Assimilation | nitrate to biomass ammonia | plants, fungi, many bacteria; costs energy |
| Denitrification | nitrate to N2 | Pseudomonas, Paracoccus; anaerobic respiration |
| Anammox | ammonium plus nitrite to N2 | planctomycetes, in an anammoxosome |
Nitrification feeds both plants and, once oxygen disappears, denitrifiers. Incomplete denitrification leaks nitrous oxide. Fixation is the only biological return from N2. Industrial fixation is chemistry, and a nodulated legume is the biological alternative.
9.1.2 Wastewater as a microbial process #
Biochemical oxygen demand is the oxygen microbes will use in oxidising a water’s organic load. Raw sewage can strip a river of dissolved oxygen. Primary treatment screens and settles. Secondary treatment is aerobic oxidation, either as activated sludge — a floc of bacteria and grazing protozoa, aerated, settled, and partly returned — or as a trickling-filter biofilm. Protozoa clarify the effluent by eating free bacteria. Sludge is then digested by hydrolysis, fermentation, and methanogenesis to methane plus CO2. If methanogens stop, acids and hydrogen accumulate and digestion fails. Tertiary treatment removes nitrogen by nitrification plus denitrification, or by anammox, and phosphorus as polyphosphate stored under alternating anaerobic and aerobic conditions. Final disinfection is Chapter 7. E. coli indicates faeces. It is not itself the pathogen of concern, and it does not stand in for viruses or for chlorine-resistant cysts such as Cryptosporidium.
9.2 Food, industry, and clean-up #
9.2.1 Food fermentations #
Acid or ethanol, and a heavy starter population, preserve food and make the flavour. Preservation fails if the pH stays high, if oxygen suits a dangerous organism better than the wanted one, or if toxin was already present. Low-acid anaerobic protein-rich conditions are the C. botulinum concern, because spores can then germinate and toxin can be formed. That is a warning from spore biology, not a canning schedule.
Yoghurt is lactic fermentation. Streptococcus thermophilus and Lactobacillus delbrueckii subspecies bulgaricus, and in other dairy foods Lactococcus, convert lactose to lactic acid. Casein denatures and many competitors stop. Penicillium roqueforti may finish a cheese. Bread, wine, and beer are Saccharomyces: sugar to ethanol and CO2, two ATP for the yeast. Bread keeps the gas and loses the alcohol in the oven. Wine keeps the alcohol. Oxygen early builds yeast by respiration; oxygen later prevents the ethanol. No recipe is implied. Vinegar is Acetobacter oxidising ethanol with oxygen. It is aerobic, so it is not a fermentation, and it is what happens to wine left open. Fermented vegetables repeat the lactic pattern. A starter, a chemistry the organism itself imposes, and stability from that chemistry are the three shared features.
9.2.2 Industrial metabolites #
The vessel is a batch, a fed batch, or a chemostat. Scale adds oxygen transfer, heat, and the price of contamination. Aeration, cooling, and Chapter 7 are the microbiological answers. Media and impeller speeds are not given. A primary metabolite is made during growth: amino acids, ethanol, citric acid. A secondary metabolite is made after growth slows and is not required for central metabolism. Antibiotics are secondary, so a harvest in early exponential phase finds little of them.
Aspergillus niger excretes citric acid and is a source of enzymes such as glucoamylase. Penicillium of the chrysogenum group makes penicillin. Fleming in 1929 saw the colony lyse staphylococci; Florey and Chain made the drug. Streptomyces, filamentous Gram-positive soil bacteria, have supplied a large share of natural-product antibiotics, streptomycin among the first, from genomes rich in such pathways. Corynebacterium glutamicum excretes glutamate it makes in excess, a primary metabolite. Recombinant insulin and similar proteins use these hosts with a constructed genome. Cloning is biotechnology. A Gram-negative host that lyses at harvest also releases lipid A, which is why Chapter 2 still matters to the process.
9.2.3 Biodegradation and bioremediation #
Mineralisation is breakdown to CO2, water, and inorganic ions. A molecule is recalcitrant if no enzyme attacks it or if it never reaches one, which is why many hydrophobic plastics persist while fungi slowly degrade lignin. Pollutant stuck to clay, or sitting as a separate oil, is not the concentration an enzyme sees. Some pollutants are foods and need an acceptor. Others are the acceptor: Dehalococcoides dechlorinates chlorinated ethenes by anaerobic respiration, and aeration removes the conditions it needs. Co-metabolism can turn a molecule the cell cannot eat into something more toxic. Biostimulation supplies what residents lack — after an oil spill, often nitrogen, phosphorus, or oxygen. Bioaugmentation adds organisms, which helps only if they reach the pollutant. Catabolic plasmids spread a pathway as resistance plasmids spread a drug. Metals are transformed or sequestered, not destroyed. Ideonella sakaiensis cuts one polyester with a PETase. That does not make plastics, as a class, biodegradable. Deploying the enzyme is biotechnology.
9.3 Key terms, summary, and self-check #
Key terms. Methanogenesis; syntrophy; nitrification; denitrification; anammox; biochemical oxygen demand; activated sludge; indicator; primary metabolite; secondary metabolite; biostimulation; bioaugmentation; co-metabolism.
Summary. Photosynthesis fixes carbon; respiration, fermentation, and methanogenesis return it. Nitrogenase, nitrifiers, denitrifiers, and anammox are the nitrogen cycle. Sewage treatment is those guilds arranged on purpose, with E. coli as a sign of faeces rather than as the pathogen. Lactic and ethanolic fermentations preserve food; vinegar is an oxidation with oxygen. Secondary metabolites such as penicillin are harvested after growth. Bioremediation works when the physiology matches and the pollutant is available. Constructing the producer is biotechnology.
Self-check.
1. From N2, which steps reach nitrate, and which two routes return N2?
2. Why does a digester fail when methanogens stop, even if fermenters are alive?
3. Which of yoghurt, bread, and vinegar is not a fermentation, and what is its electron acceptor?
4. Why is penicillin taken after exponential growth? Name the organism group for penicillin, citric acid, and streptomycin.
5. Why can air help an oil spill and hinder dechlorination of an ethene? Say which pollutant is the donor and which is the acceptor.
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# Closing: how the chapters fit together
A microbe here is a cell with its energy metabolism in the plasma membrane, or a particle with no metabolism, or a eukaryote living as one cell. Chapter 1 fixed the evidence: Pasteur on microbes from microbes, Koch on a pure culture that can fail. Carriage, unculturable agents, and preformed toxin open into viruses and virulence.
Chapter 2 is the structure the rest uses. Peptidoglycan is the target of lysozyme and beta-lactams, and it is absent from archaea, mycoplasmas, and animals. Lipid A is why Gram-negative lysis inflames. A dehydrated spore is why boiling is not sterilisation. Flagella, capsules, and pili are motility and adhesion. Ether lipids let archaeal membranes survive where bacterial ones do not.
Chapter 3 makes a population. Nutritional class is the guild of a cycle. N = N0 × 2^n is why killing must be exponential and why a chemostat is not a batch curve. Oxygen class is superoxide dismutase and catalase. Chapter 4 is the ATP inside that curve: substrate-level phosphorylation, a chain with oxygen or nitrate or sulfate, or fermentation. Cyanobacteria split water; purple sulfur bacteria use sulfide. Nitrogenase starts the nitrogen cycle and forces either a heterocyst or leghaemoglobin.
Chapter 5 is not a small cell. Baltimore classes are routes to mRNA. Eclipse and burst are assembly. cI versus Cro is how a toxin gene can sit silent in a chromosome. Influenza shows what eight negative-sense segments can do. HIV shows what reverse transcription costs: three enzyme targets and a provirus that outlasts drugs aimed only at replication.
Chapter 6 adds eukaryotic microbes without redrawing organelles. Fungal spores are reproductive. Plasmodium has a definitive host, the mosquito, and a hypnozoite that blood-stage clearance misses. An oomycete’s hypha does not make it a fungus. Chapter 7 writes the spore as a D-value and the wall as a drug target. Resistance is that target list read backwards, moving on plasmids. An antibacterial drug does not treat a virus.
Chapter 8 puts the structures in a host. An AB toxin is delivery plus a catalyst. Falkow asks whether a gene, not a species name, is responsible. R0 and herd immunity are left unnumbered. The adaptive system is the next subject. Chapter 9 runs the same physiology as cycles, sewage, food, and clean-up. Where a gene is inserted on purpose, the subject has become biotechnology.
Revision checklist #
1. State Koch’s four postulates and a limit of carriage, of culture, and of toxin.
2. Mark, on a Gram-negative envelope and an endospore, the beta-lactam target and the reason boiling fails.
3. Place the three main nutritional classes and write N = N0 × 2^n with the meaning of n.
4. Give the ATP situation and one product of lactic fermentation, and the site of a bacterial respiratory chain.
5. Contrast cyanobacteria and purple sulfur bacteria, and say why a heterocyst lacks photosystem II.
6. Assign dsDNA, −ssRNA, and HIV to Baltimore classes, and say which particles carry a polymerase.
7. Narrate Plasmodium from sporozoite to sporozoite, including the definitive host and the hypnozoite.
8. Define D, say why autoclave pressure is used, and name four drug targets with one resistance mechanism for two of them.
9. Compare exotoxin and endotoxin, and give the reaction of diphtheria toxin.
10. Draw the nitrogen cycle as six arrows with a guild on each, and say which of yoghurt, bread, and vinegar is not a fermentation.
Selected sources #
These notes are an original teaching summary, not a transcript of any textbook.
- Madigan MT, Bender KS, Buckley DH, Sattley WM, Stahl DA. Brock Biology of Microorganisms. Pearson. Recent edition.
- Tortora GJ, Funke BR, Case CL. Microbiology: An Introduction. Pearson.
- Willey JM, Sandman KM, Wood DH. Prescott’s Microbiology. McGraw-Hill.
- Flint SJ, Racaniello VR, Rall GF, Hatziioannou T, Skalka AM. Principles of Virology. ASM Press.
- Pasteur L. Mémoire sur les corpuscules organisés qui existent dans l’atmosphère. Examen de la doctrine des générations spontanées. Annales des sciences naturelles (Zoologie) (1861).
- Koch R. Die Ätiologie der Tuberkulose. Berliner Klinische Wochenschrift (1882).
- Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences of the USA 74:5088–5090 (1977).
- Baltimore D. Expression of animal virus genomes. Bacteriological Reviews 35:235–241 (1971).
- Ellis EL, Delbrück M. The growth of bacteriophage. Journal of General Physiology 22:365–384 (1939).
- Falkow S. Molecular Koch’s postulates applied to microbial pathogenicity. Reviews of Infectious Diseases 10:S274–S276 (1988).
- Prusiner SB. Novel proteinaceous infectious particles cause scrapie. Science 216:136–144 (1982).
- Fleming A. On the antibacterial action of cultures of a Penicillium, with special reference to their use in the isolation of B. influenzae. British Journal of Experimental Pathology 10:226–236 (1929).
- Ptashne M. A Genetic Switch. Cold Spring Harbor Laboratory Press.
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# Part C. Visual Figures & Scientific Diagrams Gallery
Comprehensive high-resolution visual reference repository for Microbiology from the B10logy Visual Atlas.
Average Prokaryote Cell
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# Part C. Visual Figures & Scientific Diagrams Gallery
Essential high-resolution reference diagrams for Microbiology from the B10logy Visual Atlas.