LC

Study Notes – Bacteria, Archaea, Protists, Fungi, and Conservation Biology (

Chapter 27 – Bacteria & Archaea

Masters of Adaptation

  • Prokaryotes inhabit almost every environment, including those too acidic, salty, hot, or cold for other life.
    • Example: Laguna Salada de Torrevieja (Spain) is many times saltier than seawater; its pink color is caused by trillions of halophilic prokaryotes.
  • Because of their adaptability, prokaryotes are the most abundant organisms on Earth and were the first life-forms to appear.
  • Two modern domains: Bacteria and Archaea.

Structural & Functional Adaptations

  • Most prokaryotes are unicellular and smaller than eukaryotic cells.
  • Three common shapes
    • Cocci (spheres)
    • Bacilli (rods)
    • Spirals (helical or corkscrew-shaped)
Cell-Wall Composition (Gram Stain)
  • Gram-positive bacteria
    • Thick peptidoglycan layer retains crystal violet dye → appear purple.
  • Gram-negative bacteria
    • Thin peptidoglycan layer plus an outer membrane rich in lipopolysaccharides (LPS).
    • Outer membrane impedes entry of many antibiotics ⇒ greater intrinsic resistance.
Additional Surface Features
  • Capsule (sticky polysaccharide or protein layer)
    • Adheres to substrates & host tissues; shields pathogens from immune attack.
  • Endospores
    • Metabolically inactive, extremely durable cellular structures.
    • Can survive centuries; e.g., \textit{Bacillus anthracis} spores have infected farmers unearthing old carcasses.
  • Fimbriae
    • Short, numerous appendages for attachment to surfaces or other cells.
  • Pili (Sex pili)
    • Longer than fimbriae; draw two cells together for DNA transfer (conjugation).
Motility
  • ~50 % of prokaryotes exhibit taxis—directed movement relative to a stimulus (e.g., chemotaxis, phototaxis).
  • Flagella
    • Rotary motors powered by proton gradients; may be scattered or localized at cell poles.
Internal Organization & DNA
  • No membrane-bound nucleus; DNA in a nucleoid region.
  • Genome: single circular chromosome + small, independently replicating plasmids.

Genetic Diversity & Evolution (Concept 27.2)

Three processes accelerate diversity:

  1. Rapid binary fission (short generation times)
  2. Spontaneous mutation (even low per-division rates accumulate quickly)
  3. Genetic recombination
    • Transformation – uptake of naked DNA; may introduce multiple genes at once; mismatched bases repaired after integration, yielding one mutant and one non-mutant progeny.
    • Transduction – bacteriophages transfer host genes; can disseminate virulence loci (e.g., pathogenic E. coli strains).
    • Conjugation – one-way transfer via sex pilus; requires F factor; Hfr strains donate chromosomal segments; R plasmids confer antibiotic resistance → selected in drug-rich environments.
  • Horizontal gene transfer (HGT) moves genes across species boundaries, blurring phylogenies.

Metabolic Diversity

  • Energy & carbon sources define four major nutritional modes:
    • Photoautotrophs – light + CO_2 (e.g., cyanobacteria)
    • Chemoautotrophs – inorganic chemicals (e.g., NH3, H2S) + CO_2; unique to some prokaryotes like \textit{Sulfolobus}.
    • Photoheterotrophs – light + organic carbon; rare, found in salt-loving bacteria.
    • Chemoheterotrophs – organic energy + organic carbon; includes most pathogens, decomposers, animals, fungi.
  • Oxygen relationships
    • Obligate aerobes require O_2.
    • Obligate anaerobes poisoned by O_2; use fermentation or anaerobic respiration with alternate final e- acceptors.
    • Facultative anaerobes switch between aerobic and anaerobic metabolism.
  • Biofilms – surface-associated colonies with cooperative metabolic interactions; dental plaque dominated by Streptococcus mutans.

Phylogeny & Major Bacterial Clades

  • Proteobacteria (Gram-negative; defined by rRNA)
    • Metabolically diverse; includes E. coli (gut commensal), Rhizobium (N₂-fixing legume symbiont), pathogens Campylobacter (blood poisoning), Helicobacter pylori (ulcers), Neisseria gonorrhoeae.
  • Chlamydias – intracellular parasites; C. trachomatis causes blindness & STI urethritis.
  • Spirochetes – helical heterotrophs; include Treponema pallidum (syphilis) and Borrelia burgdorferi (Lyme disease).
  • Gram-positive bacteria
    • Actinomycetes (soil decomposers), Bacillus anthracis, Clostridium botulinum, Staph/Strep, Mycoplasmas (wall-less, tiniest cells).

Archaea Highlights

  • Share traits with both bacteria and eukaryotes, plus unique features (e.g., ether-linked lipids).
  • Extremophiles
    • Halophiles (salt lakes), Thermophiles (hot springs), Methanogens (anaerobic; produce CH_4 in swamps, guts, ice).
  • Marine archaeal nitrifiers significant in global N cycle.

Ecological & Human Relevance

  • Chemical recycling: decomposers releasing elements; loss of prokaryotes would cripple life.
  • Symbiosis: mutualism (gut microbes), commensalism, parasitism.
  • Pathogenesis: virulence factors—exotoxins, endotoxins (LPS), fimbriae, flagella, capsules.
  • Biotechnology: bioremediation; industrial fermentation (yogurt, vinegar); GM E. coli produces human insulin.

Chapter 28 – Protists

Living Small & Big Picture

  • "Protist" = informal, polyphyletic term for mostly unicellular eukaryotes; no longer a formal kingdom.
  • Eukaryotes possess membrane-bound organelles & cytoskeleton; most lineages are protists; most protists are microscopic.
  • Reproduction varies—sexual, asexual, or both.

Nutritional Diversity

  • Photoautotrophs (algae) with chloroplasts.
  • Heterotrophs that absorb or ingest food.
  • Mixotrophs combine both modes.

Representative Clades & Biology

Apicomplexans
  • Obligate animal parasites; apex organelles penetrate host cells.
  • Complex life cycles require multiple hosts.
  • Plasmodium causes malaria (~200 M cases; 600 k deaths annually). First vaccine (2015) gives partial protection.
Ciliates
  • Large, diverse group; move/feed using cilia.
  • Predatory on bacteria & other protists; possess dual nuclei (macro- & micronucleus).
Amoebozoans
  • Amoebas with lobe/tube-shaped pseudopodia.
  • Include slime molds, tubulinids, Entamoeba histolytica (amebic dysentery; 3rd-leading eukaryotic parasite death cause).

Ecological Roles

  • Protists act as symbionts (e.g., dinoflagellates in corals, wood-digesters in termites) and producers (major aquatic primary producers).
  • Some are parasitic (e.g., Plasmodium, Giardia, Phytophthora potato blight).

Chapter 31 – Fungi

Hidden Networks & Nutritional Modes

  • Heterotrophs that absorb nutrients.
    • Decomposers of non-living material.
    • Parasites of living hosts.
    • Mutualists (e.g., mycorrhizae, lichens).
  • Ecosystem recyclers; essential for nutrient cycling.

Body Structure

  • Multicellular fungi form hyphae (chitin-walled filaments) aggregated into a mycelium ⇒ high surface area for absorption.

Reproduction

  • Produce vast numbers of spores (sexual or asexual) dispersed by wind/water.
  • Sexual cycle: fusion of hyphae of compatible mating types; pheromone signaling; haploid most of life with transient diploid stage.
  • Asexual cycle: molds (mitotic spores); yeasts bud by cell division; dimorphic species switch forms.

Evolutionary Context

  • Closest relatives to animals; ancestor was aquatic, single-celled, flagellated.
  • Fossil record to 460 M y ago.
  • Classification often based on reproductive structures.

Major Phyla & Examples

  • Zoopagomycetes – parasites/commensals; influence insect behavior.
  • Mucoromycetes – fast-growing molds on foods; many plant associations.
  • Ascomycetes (sac fungi) – marine, freshwater, terrestrial; include edible morels, pathogens, and Penicillium (antibiotic producer); form lichens & mycorrhizae.
    • Ergot on rye (ascomycete) produced toxins causing medieval ergotism; ergots contain lysergic acid → LSD precursor.
  • Basidiomycetes (club fungi) – mushrooms, puffballs, shelf fungi; wood decomposers; rapid mushroom formation; “fairy rings”; some psychoactive (“magic” mushrooms) with psilocybin.

Ecological Functions

  • Decomposition of cellulose & lignin—critical for element recycling.
  • Mutualisms
    • Lichens (fungus + alga/cyanobacterium).
    • Mycorrhizae supply phosphate & minerals to >90 % of vascular plants.
  • Pathogens/Mycoses
    • Plant losses (10-50 % of fruit harvest); human infections like ringworm, athlete’s foot, oral/vaginal thrush (\textit{Candida albicans}).
    • Emerging heat-tolerant pathogen Candida auris; hospital outbreaks; multi-drug resistance.

Human Uses & Hazards

  • Food: edible mushrooms, truffles, blue cheese mold.
  • Fermentation: bread, beer, wine.
  • Pharmaceuticals: Penicillin (antibiotic), Lovastatin (cholesterol-lowering), Ciclosporin (immunosuppressant).
  • Poisonous mushrooms (Amanita “Destroying Angel”, “Death Cap”) cause liver failure; folk identification rules unreliable.

Chapter 56 – Conservation Biology & Global Change

Scope & Fields

  • Conservation biology integrates ecology, physiology, molecular biology, genetics, and evolution to preserve biodiversity at all levels.

Biodiversity Crisis (Concept 56.1)

  • Extinction is natural, but current rates ((100–1000\times) background) signal crisis; >1,000 species lost in last 400 years; current threat level exceeds dinosaur-era extinctions.
Three Levels of Biodiversity
  1. Genetic diversity – variation within & between populations; wild genes saved rice from viruses.
  2. Species diversity – variety of species; endangered (on brink), threatened (likely to become endangered); 12 % birds, 21 % mammals threatened.
  3. Ecosystem diversity – variety of habitats; example: Wisconsin prairie reduced from 800,000 → 800 ha.
Ecosystem Services
  • Natural processes sustaining human life:
    • \textit{Purification} of air & water
    • \textit{Detoxification} & waste decomposition
    • \textit{Pollination}, pest control, soil preservation
    • \textit{Moderation} of weather extremes

Major Threats to Biodiversity ("HIPPO")

  1. Habitat loss & fragmentation – biggest factor (e.g., grizzly range shrink: 500 M → 5 M ha).
  2. Introduced species – lack native controls (brown tree snake on Guam eliminated native birds).
  3. Overharvesting – e.g., >80 % decline in Atlantic bluefin tuna within a decade.
  4. Global change – pollution, climate change; acid rain when precipitation \text{pH} < 5.2.

Small Population Biology

  • Minimum viable population (MVP) – smallest size for long-term survival; genetic drift & inbreeding pose risks when below MVP.

Socio-Ecological Conflicts

  • Balancing species conservation vs. human jobs/income (wolves/grizzlies vs. grazing, mining).

Agriculture & Soil

  • Farming depletes nutrients, water, and promotes erosion; Dust Bowl (1930s) exemplar.
  • 30 % of farmland currently shows reduced productivity due to soil degradation.
  • Organic fertilizers (manure, fishmeal, compost) replenish nutrients.

Irrigation

  • 75\% of global freshwater use → agriculture.
  • Dependent on groundwater; aquifer depletion causes land subsidence & salinity.

Toxins & Biomagnification

  • Biological magnification concentrates persistent toxins at higher trophic levels.
    • Rachel Carson’s "Silent Spring" (1960s) exposed DDT effects; bird recovery after US ban (1971).
  • Pharmaceutical runoff: estrogenic compounds feminize fish populations.

Carbon Cycle & Climate Change

  • Anthropogenic CO_2 from fossil fuels & deforestation adds \approx8 Gt C /yr; net atmospheric increase ≈ 4 Gt C /yr.
  • Greenhouse effect: heat re-radiated from Earth trapped by gases (CO2, CH4), maintaining habitable temps.
  • Rapid change is too fast for many organisms to adapt.
  • Arctic amplification: polar regions warming ≈2× global average; shrinking sea ice threatens polar bear seals hunting.
  • Ocean acidification: CO2 + H2O \rightarrow H2CO3; ↓ pH by 0.071 (1982-2022) ⇒ 18 % increase in acidity; reduces CaCO_3 availability for shells & corals.

Mitigation & Personal Actions

  • Reduce consumption: reusable bottles, skip disposables, bring bags, cut food waste.
  • Conserve water & electricity.
  • Participate in conservation programs; plant native flora for pollinators.

Cross-Chapter Connections & Themes

  • Adaptation & Evolution: rapid genetic mechanisms (HGT in prokaryotes, sexual/asexual cycles in fungi) enable survival in changing environments, mirroring conservation concerns about adaptation pace.
  • Symbiosis threads through domains—biofilms, coral-dinoflagellate mutualism, mycorrhizae—highlighting interdependence in ecosystems threatened by global change.
  • Human Health & Economy: pathogens (bacterial, protistan, fungal) and ecosystem services illustrate direct stakes in biodiversity; biotechnology harnesses these organisms for medicine and industry.
  • Climate & Chemical Cycling: prokaryotes (methanogens, nitrifiers), protists (photosynthetic plankton), and fungi (decomposers) are integral in biogeochemical cycles underpinning climate regulation and soil fertility.

Key Formulae & Values (LaTeX syntax)

  • Change in ocean pH: \Delta pH = -0.071\;(1982!\rightarrow!2022) ⇒ \text{Acidity}\uparrow18\%.
  • Simple carbon fluxes (in Gt C yr^{-1}):
    \text{Photosynthesis}: 122,\; \text{Respiration}: 120,\; \text{Anthropogenic}: 8,\; \text{Net atmospheric gain}: 4.
  • Biomagnification conceptually: C{\text{trophic n+1}} > C{\text{trophic n}}\quad(\forall\;n) if toxin is persistent & lipophilic.