Chapter Capsule

A. Ecosystem Organization

1. Living things inhabit only that area of the earth called the biosphere, which is made up of the hydrosphere (water), the lithosphere (soil), and the atmosphere (air).

2. The biosphere consists of terrestrial ecosystems of biomes and aquatic ecosystems.

3. Biomes contain communities, assemblages of coexisting organisms.

4. Communities consist of populations, groups of like organisms of the same species.

5. The space within which an organism lives is its habitat; its role in community dynamics is its niche.

B. Energy and Nutrient Flow

1. Organisms consume nutrients and derive energy.

2. Their collective trophic status relative to one another is summarized in a food or energy pyramid.

3. At the beginning of the chain or pyramid are producers—photosynthetic or lithotrophic organisms that synthesize large, complex organic compounds from small, simple inorganic molecules.

4. The levels above producer are occupied by consumers, organisms that feed upon other organisms.

5. Decomposers are consumers that obtain nutrition from the remains of dead organisms and help recycle and mineralize nutrients.

6. Organisms are usually not related in a linear food chain fashion; a cross-linked food web better reflects their ability to use alternative nutritional sources.

C. Microbial Interrelationships include:

1. Mutualism, a beneficial, dependent, two-way partnership.

2. Commensalism, a one-sided relationship that benefits one partner while neither benefiting nor harming the other.

3. Cometabolism, the by-product of one microbe becomes a nutrient for another.

4. Synergism, two microbes degrade a substrate cooperatively.

5. Parasitism, a host is harmed by the activities of its passenger.

6. Competition, the inhibition of one organism by another organism.

7. Predation, the seeking and ingesting of live prey.

D. Biogeochemical Cycles

1. The processes by which bioelements and essential building blocks of protoplasm are recycled between the biotic and abiotic environments are called biogeochemical cycles.

2. They require microorganisms that can remove elements and compounds from a nonliving inorganic reservoir and return them to the food web.

3. The Gaia hypothesis is a philosophical explanation for the self-sustaining and self-regulating nature of organisms and the environment.

E. Atmospheric Cycles

Key compounds in the carbon cycle include carbon dioxide, methane, and carbonates.

1. Carbon is fixed when autotrophs (photosynthesizers) add carbon dioxide to organic carbon compounds.

2. This is later returned to carbon dioxide by respiration and burning fossil fuels. Volcanic activity is one of several natural ways in which carbonates revert to carbon dioxide.

3. Anaerobic metabolism of methane by methanogens also contributes to carbon recycling.

4. The accumulation of a heat-trapping layer of carbon dioxide, methane, nitrous oxide, and water vapor in the upper atmosphere contributes to the greenhouse effect, which gives rise to global warming.

5. Photosynthesis takes place in two stages—light reactions (light-dependent) and dark reactions (light-independent).

a. During the light reactions, photons of solar energy are absorbed by chlorophyll, carotenoid, and phycobilin pigments in thylakoid membranes in chloroplasts or in specialized membrane lamellae. Captured light energy fuels a series of two photosystems that split water by photolysis and release oxygen gas and electrons to drive photophosphorylation. In this process, released light energy is used to synthesize ATP and NADPH.

b. Dark reactions occur during the Calvin cycle, which uses ATP to fix carbon dioxide to a carrier molecule, ribulose-1,5-bisphosphate, and convert it to glucose in a multistep process.

c. The type of photosynthesis commonly found in plants, algae, and cyanobacteria is called oxygenic because it liberates oxygen. Anoxygenic photosynthesis occurs in photolithotrophs, which do not produce oxygen.

6. The nitrogen cycle requires four processes and several types of microbes.

a. In nitrogen fixation, atmospheric N₂ gas (the primary reservoir) is combined with oxygen or hydrogen to form NO₂², NO₃², or NH₄¹ salts. Microbial fixation is achieved both by free-living soil and symbiotic bacteria (Rhizobium) that help form root nodules in association with legumes.

b. Ammonification is a stage in the degradation of nitrogenous organic compounds (proteins, nucleic acids) by bacteria to ammonium.

c. Some bacteria nitrify NH₄¹ by converting it to NO₂² and then to NO₃², which can be incorporated into protoplasm by still other microbes.

d. Denitrification is a multistep microbial conversion of various nitrogen salts back to atmospheric N₂.

F. Cycles in the Lithosphere

1. In the sulfur cycle, environmental sulfurous compounds are converted into useful substrates and returned to the inorganic reservoir through the action of microbes. The major inorganic forms of sulfur are S, H₂S, SO₄, and S₂O₃, and the chief organic forms are in certain amino acids.

2. The chief compound in the phosphorus cycle is phosphate (PO₄) found in certain mineral rocks. Microbial action on this reservoir makes it available to be incorporated into organic phosphate forms such as DNA, RNA, and ATP. Phosphate is often a limiting factor in ecosystems.

3. Microorganisms often cycle and help bioamplify (accumulate) heavy metals and other toxic pollutants that have been added to habitats by human activities.

4. Soil is a dynamic, complex ecosystem that accommodates a vast array of microbes, animals, and plants coexisting among rich organic debris, water and air spaces, and minerals.

a. The breakdown of rocks and the release of minerals are due in part to the activities of acid-producing bacteria and pioneering lichens, symbiotic associations between fungi and cyanobacteria or algae.

b. Humus is the rich, moist layer of soil containing plant and animal debris being decomposed by microorganisms.

c. An important habitat is the rhizosphere, a zone of soil around plant roots, which nurtures the growth of microorganisms.

d. Mycorrhizae are specialized symbiotic organs formed between specialized fungi and certain plant roots.

G. Cycles in the Hydrosphere

1. The surface water, atmospheric moisture, and groundwater are linked through a hydrologic cycle that involves evaporation and precipitation. Living things contribute to the cycle through respiration and transpiration.

2. Water that percolates into the earth accumulates in deep underground aquifers.

3. The diversity and distribution of water communities are related to sunlight, temperature, aeration, and dissolved nutrients.

a. The three strata occurring vertically are the photic zone, the profundal zone, and the benthic zone; horizontal sections are the littoral zone and the limnetic zone. Features of the marine environment include tidal and wave action and estuary, intertidal, and abyssal zones that harbor unique microorganisms.

b. Phytoplankton and zooplankton drifting in the photic zone constitute a microbial community that supports the aquatic ecosystem.

c. Temperature gradients in still waters cause stratified layers to form; the epilimnion and hypolimnion meet at an interface called a thermocline.

d. Currents brought on by temperature changes cause upwelling of nutrient-rich benthic sediments and outbreaks of abundant microbial growth (red tides).

e. Oligotrophic waters contain few nutrients and support a sparser population.

f. Waters artificially spiked with high levels of nutrients lead to eutrophication and explosive aquatic overgrowth of algae and other plants.

4. Water analysis:

a. Providing potable water is central to prevention of water-borne disease.

b. Water is constantly surveyed for certain indicator bacteria (coliforms and enterococci) that signal fecal contamination.

c. Assays for possible water contamination include the standard plate count, the most probable number (MPN) procedure, and membrane filter tests to enumerate coliforms.

5. Water and sewage treatment:

a. Drinking water is rendered safe by a purification process that involves storage, sedimentation, settling, aeration, filtration, and disinfection.

b. Sewage or used wastewater can be processed to remove solid matter, dangerous chemicals, and microorganisms.

c. Treatment occurs in three phases. Microbes biodegrade the waste material or sludge. Solid wastes are further processed in anaerobic digesters that can provide combustible methane and fertilizer.

d. Future solutions may involve bioremediation, the degradation of pollutants by microbial activities.

A. Food Microbiology

Microbes and humans compete for the rich nutrients in food. Although some microbes are present on food as harmless contaminants, others create favorable flavors and nutrients or unfavorable reactions.

1. Fermentations in foods: Microbes can impart desirable aroma, flavor, or texture to foods. Bread, alcoholic beverages, some vegetables, and some dairy products are infused with starter cultures of pure microbial strains to yield the necessary fermentation products.

a. Baker’s yeast, Saccharomyces cerevisiae, is used to leaven bread dough by giving off CO₂; bacteria contribute additional flavors.

b. Beer making involves the following steps: Barley is sprouted (malted) to generate digestive enzymes and then dried; malt is transformed to mash and heated with hops to produce a wort. Wort is fermented by yeast to a concentration of 3% to 6% alcohol and lagered in large tanks before it is carbonated and packaged.

c. Wine is started by fermentation of must (fruit juices) to yield 7% to 15% alcohol. Whiskey, vodka, brandy, and other alcoholic beverages are distilled to increase their alcohol content.

d. Vegetable products, including sauerkraut, pickles, and soybean derivatives, can be pickled in the presence of salt or sugar.

e. Vinegar is produced by fermenting plant juices first to alcohol and then to acetaldehyde and acetic acid.

f. Most dairy products are produced by microbes acting on nutrients in milk. In cheese production, milk proteins are coagulated with rennin to form solid curd that separates from the watery whey. Different cheeses are obtained by varying water, fat, acid, and salt content and by aging with bacteria and yeasts; yogurt and buttermilk are also processed with live cultures.

g. Mass-cultured microbes such as yeasts, molds, and algae can serve as food. Single-cell protein, pruteen, and mycoprotein are currently added to animal feeds; in some countries, large colonies of the cyanobacterium Spirulina are harvested to be used as food supplements.

2. Food-borne disease: Some microbes cause spoilage and food poisoning.

a. In food intoxication, damage is done when the toxin is produced in food, is ingested, and then acts on a specific body target; examples are staphylococcal and clostridial poisoning.

b. In food infection, the intact microbe does damage when it is ingested and invades the intestine; examples are salmonellosis and shigellosis.

3. Precautions for food:

a. Microbial growth that leads to spoilage and food poisoning can be avoided by high temperature and pressure treatment (canning) and pasteurization for disinfecting milk and other heat-sensitive beverages.

b. Refrigeration and freezing inhibit microbial growth.

c. Irradiation sterilizes or disinfects foods for longer-term storage.

d. Alternative preservation methods include additives (salt, nitrites), treatment with ethylene oxide gas, and drying.

B. Industrial Microbiology

1. Industrial microbiology involves the large-scale commercial production of organic compounds such as antibiotics, vitamins, amino acids, enzymes, and hormones using specific microbes in carefully controlled fermentation settings.

2. Microbes are chosen for their production of a desired metabolite; several different species can be used to biotransform raw materials in a stepwise series of metabolic reactions.

3. Fermentations are conducted in massive culture devices called fermentors that have special mechanisms for adding nutrients, stirring, oxygenating, altering pH, cooling, monitoring, and harvesting product.

4. Plant organization includes downstream processing (purification and packaging).