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| Changes in structure and function that improve an organism's survival in a given environment. Microbes survive in their habitats through the process of gradual adjustment of their anatomy and physiology. It is this adaptability that allows microbes to inhabit all parts of the biosphere |
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| is a process by which chemical substances (nutrients) are acquired from the environment and used in cellular activities such as metabolism and growth. |
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| In general, all living things have an absolute need for the bio-elements, traditionally listed as carbon, hydrogen, oxygen, phosphorus, potassium, nitrogen, sulfur, calcium, iron, NaCl (salt) and magnesium |
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| CHOPKINS, NaCl (salt) Mgood |
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Definition
| carbon, hydrogen, oxygen, phosphorus, potassium, nitrogen, sulfur, NaCl (salt), magnesium |
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| Any substance, whether an element or compound, that must be provided to the organism. Once absorbed, nutrients are processed and transformed into the chemicals of the cell |
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| required in relatively large quantities and play principal rolls in cell structure and metabolism. ex: sugars and amino acids that contain carbon, hydrogen, and oxygen (carbs!) |
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| aka trace elements, present in much smaller quantities and are involved in enzyme function and maintenance of protein structure. ex: manganese, zinc, nickel |
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| molecules that contain a basic framework of carbon and hydrogen. Natural organic nutrients are almost always the products of living things. They range from the simplest organic molecule, methane (CH4), to large polymers such as carbohydrates, lipids, proteins, and nucleic acids |
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a nutrient compound that is composed of an element or elements OTHER than carbon and hydrogen.
The natural reserviors of many inorganic compounds are mineral deposits in the soil, water, and atmosphere.
ex: metals and their salts (magnesium sulfate, ferric nitrate, sodium phosphate), gases (oxygen, carbon dioxide), and water. |
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| carbon based nutritional type; a heterotroph is an organism that must obtain it's carbon in an organic form; heterotrophs are nutritionally dependent on other life forms since organic carbon usually originates from living organisms. |
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| an organism that uses inorganic CO2 as its carbon source; because autotrophs can convert inorganic CO2 into organic compounds, they are not nutritionally dependent on living things. |
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| carbon source vs carbon function |
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Definition
| Although a distinction is made between the type of carbon cells absorb as nutrients (extracellular source; organic vs inorganic), the majority of carbon compounds involved in the normal structure and metabolism of all cells is organic (intracellular function). So even microbes that use carbon dioxide (CO2) as their primary source of carbon will convert this CO2 into organic compounds once it gets into the cell. |
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| an organic compound such as an amino acid, nitrogenous base, or vitamin that cannot be synthesized by an organism and must be provided as a nutrient. Many fastidious bacteria lack the genetic and metabolic mechanisms to synthesize every organic compound needed for survival. |
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| Microbes that synthesize energy from the sun via photosynthesis |
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| microbes that synthesize energy from chemical compounds |
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| organisms that gain energy from the nonliving environment via sunlight through photosynthesis; ex: algae, plants, cyanobacteria |
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| organisms that gain their energy from a nonliving environment via simple inorganic chemicals; have adapted to the most stringent nutritional strategy on earth; only certain bacteria and archaea that require neither light nor organic nutrients; survive totally on inorganic nutrients ie: minerals and gases; such as methanogens and deep sea vent bacteria |
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| organisms that gain energy via metabolic conversion of the nutrients from other organisms; ex: protozoa, fungi, many bacteria, animals two subtypes of microbes: saprobes and symbiotics |
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| metabolize the organic matter from dead organisms; fungi, bacteria, some protozoa (decomposers) |
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| obtain organic matter from living organisms; ex: parasites, commensals, mutualistic microbes, |
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Definition
| derive energy from sunlight OR organic matter; ex: purple and green photosynthetic bacteria |
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Definition
this type of photosynthesis occurs in plants, algae, and cyanobacteria and uses chlorophyll as the primary agent. Carbohydrates formed by the reaction can be used by the cell to synthesize other cell components. Since these organisms are the primary producers in most ecosystems, they constitute the basis of food chains by providing nutrition for heterotrophs
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Term
| anoxygenic photosynthesis |
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Definition
uses a unique pigment, bacteriochlorophyll; its hydrogen source is hydrogen sulfide gas; and it gives off elemental sulfur as one product. the reactions all occur in the absence of oxygen (coincidental) ex: purple and green sulfur bacteria that live in aquatic habitats, often in mixtures with other photosynthetic microbes.
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Definition
unique type of chemoautotroph widely distributed in the earth's habitats; all known methanogens are archaea; many are found in extreme habitats such as deep sea vents and hot springs; others are common in soil, swamps, and even human/animal intestines; metabolism is adapted to produce methane gas (CH4 or swamp gas) by reducing CO2, using hydrogen gas under anaerobic conditions:
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Definition
| oxygenic photosynthesis: oxygen is produced |
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| anoxygenic photosynthesis: no oxygen produced |
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| metabolism of methanogens resulting in methane gas aka swamp gas |
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| the majority of heterotrophic microorganisms; derive both carbon and energy from organic compounds; processing these organic molecules by respiration or fermentation releases energy in the form of ATP. ex: aerobic respiration |
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| Glucose [C6H12O6] + 6O2 ---> 6CO2 + 6H2O + Energy (ATP) |
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| a saprobe that has adapted to and invades a susceptible host; because such an infection usually occurs when the host is compromised; also called an opportunistic pathogen; ex. Psuedomonas aeruginosa naturally lives in water and soil but can cause disease when carried into a hospital |
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Definition
| free-living microbes that feed primarily on organic detritus released by dead organisms; primary niche is as decomposers of plant litter, animal matter, and dead microbes; most (esp bacteria and fungi) have a rigid cell wall and cannot engulf large particles of food; they release enzymes into environment to digest food into smaller pieces that can be transported into the cell; many exist strictly on dead matter in soil/water and are unable to adapt to the body of a live host. |
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Definition
| are so dependent that they are unable to grow outside of a living host; ex: leprosy bacillus and the syphilis spirochete; Less strict parasites such as the gonococcus and pneumococcus can be cultured artificially if provided with the correct nutrients and environmental conditions. |
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Definition
| the structure specialized for transport; cells must transport waste materials out of the cell (and into the environment); this is true even in organisms with cell walls (bacteria, algae, and fungi), because the cell wall is usually only a partial, nonselective barrier |
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| The dispersal of molecules, ions, or microscopic particles propelled down a concentration gradient by spontaneous random motion to achieve a uniform distribution; net movement of molecules down their concentration gradient by random thermal motion; ex: A drop of perfume released into one part of a room is soon smelled in another part, or a lump of sugar in a cup of tea spreads through the whole cup without stirring |
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Definition
| this means that the cell does not expend extra energy for them to function. The inherent energy of the molecules moving down a gradient does the work of transport. |
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| the diffusion of water across a selectively permeable membrane in the direction of lower water concentration; under the laws of diffusion, water will diffuse at a faster rate from the side that has more water to the side that has less water. As long as the concentrations of the solutions differ, one side will experience a net loss of water and the other a net gain of water until equilibrium is reached and the rate of diffusion is equalized. |
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| Two solutions having the same osmotic pressure such that, when separated by a semipermeable membrane, there is no net movement of solvent in either direction. Isotonic solutions are generally the most stable environments for cells, because they are already in an osmotic steady state with the cell. Parasites living in host tissues are most likely to be living in isotonic habitats. |
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| Having a lower osmotic pressure than a reference solution. the solute concentration of the external environment is lower than that of the cell's internal environment. Pure water provides the most hypotonic environment for cells because it has no solute. Because the net direction of osmosis is from the hypotonic solution into the cell, cells without walls swell and can burst when exposed to this condition. |
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| Having a greater osmotic pressure than a reference solution. Because hypertonicity will force water to diffuse out of a cell, it is said to create high osmotic pressure or potential. In cells with a wall, water loss causes shrinkage of the protoplast away from the wall, a condition called plasmolysis.* Although the whole cell does not collapse, this event can still damage and even kill many kinds of cells. The effect on cells lacking a wall is to shrink down and usually to collapse. |
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| In cells with a wall, water loss due to being in a hypertonic environment, causes shrinkage of the protoplast away from the wall. Although the whole cell does not collapse, this event can still damage and even kill many kinds of cells. The growth-limiting effect of hypertonic solutions on microbes is the principle behind using concentrated salt and sugar solutions as preservatives for food, such as in salted hams and fish. |
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Definition
| The passive movement of a substance across a plasma membrane from an area of higher concentration to an area of lower concentration utilizing specialized carrier proteins in the membrane that will bind a specific substance. This binding changes the conformation of the carrier proteins in a way that facilitates movement of the substance across the membrane. Once the substance is transported, the carrier protein resumes its original shape and is ready to transport again. |
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Definition
| carrier proteins bind and transport only a single type of molecule. |
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| The rate of transport of a substance is limited by the number of binding sites on the transport proteins. As the substance's concentration increases, so does the rate of transport until the concentration of the transported substance causes all of the transporters' binding sites to be occupied. Then the rate of transport reaches a steady state and cannot move faster despite further increases in the substance's concentration. |
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Definition
Nutrient transport method that requires carrier proteins in the membranes of the living cells and the expenditure of energy.
Features are 1. the transport of nutrients against the diffusion gradient or in the same direction as the natural gradient but at a rate faster than by diffusion alone; 2. the presence of specific membrane proteins; 3. the expenditure of additional cellular energy in the form of ATP-driven uptake. Examples of substances transported actively are monosaccharides, amino acids, organic acids, phosphates, and metal ions. |
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| Carrier-mediated active transport |
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Definition
| functions with specific membrane proteins that bind both ATP and the molecules to be transported. Release of energy from ATP drives the movement of the molecule through the protein carrier. This can occur in either direction. Some bacteria transport certain sugars, amino acids, vitamins, and phosphate into the cell by this mechanism. Other bacteria can actively pump drugs out of the cell, thereby providing them resistance to the drugs. Other active transport pumps can rapidly carry ions such as K+, Na+, and H+ across the membrane. |
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Definition
| A form of active transport in which the substance being transported is altered during transfer across a plasma membrane; couples the transport of a nutrient with its conversion to a substance that is immediately useful inside the cell; This method is used by certain bacteria to transport sugars (glucose, fructose) while simultaneously adding phosphate molecules that activate them in preparation for a metabolic cycle. |
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| The substances transported do not pass physically through the membrane but are carried into the cell by the cell enclosing the substance in its membrane, simultaneously forming a vacuole and engulfing it. |
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| A type of endocytosis in which the cell membrane actively engulfs large particles or cells via flexible cell extentions (psuedopods) into vesicles. A phagocyte is a cell specialized for doing this. Ex: Amoebas and certain white blood cells ingest whole cells or large solid matter |
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| The engulfment, or endocytosis, of liquids by extensions of the cell membrane, very fine protrusions called microvilli. |
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| The term biologists use to describe the totality of adaptations organisms make to their habitats. |
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| the lowest temperature that permits a microbe's continued growth and metabolism; below this temperature, its activities are inhibited |
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| The highest temperature at which an organism will grow. If the temperature rises slightly above maximum, growth will stop. If it continues to rise beyond that point, the enzymes and nucleic acids will eventually become permanently inactivated—a condition known as denaturation—and the cell will die. This is why heat works so well as an agent in microbial control. |
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| the enzymes and nucleic acids will eventually become permanently inactivated |
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| covers a small range, intermediate between the minimum and maximum, which promotes the fastest rate of growth and metabolism. Only rarely is the optimum a single point. |
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| a microorganism (bacterium, archaea, fungus, or alga) with an optimum temperature below 15°C (59°F) but generally can grow at 0°C (32°F). It is obligate with respect to cold and generally cannot grow above 20°C (68°F). Inoculations have to be done in a cold room because ordinary room temperature can be lethal to these organisms. True psychrophiles are not capable of surviving in the human body and do not cause infections. |
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Definition
organisms that grow at intermediate temperatures. Although an individual species can grow between the extremes of 10°C and 50°C (50°F and 122°F), the optimum growth temperatures (optima) of most mesophiles fall into the range of 20°C to 40°C (68°F to 104°F). Organisms in this group inhabit animals and plants as well as soil and water in temperate, subtropical, and tropical regions. Most human pathogens have optima somewhere between 30°C and 40°C (human body temperature is 37°C or 98°F). |
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| a microbe that grows optimally at temperatures greater than 45°C (113°F). Such heat-loving microbes live in soil and water associated with volcanic activity, in compost piles, and in habitats directly exposed to the sun. Thermophiles generally range in growth temperatures from 45°C to 80°C (113°F to 176°F). Most eukaryotic forms cannot survive above 60°C (140°F), but a few bacteria and archaea, called hyperthermophiles, grow at between 80°C and 121°C (250°F, currently thought to be the highest temperature limit endured by enzymes and cell structures). Strict thermophiles are so heat tolerant that researchers may use a heat-sterilizing device to isolate them in culture. |
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Definition
destructive metabolic by-products of oxygen, represented by O2−; peroxide (H2O2), and hydroxyl radicals (OH) are other destructive metabolic by-products of oxygen. To survive these toxic oxygen products, many microorganisms have developed enzymes capable of scavenging and neutralizing these chemicals. The complete conversion of superoxide ion into harmless oxygen involves a two-step process and at least two enzymes:
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| chemical representation of superoxide ion, destructive metabolic by-products of oxygen |
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| In this series of reactions essential for aerobic organisms, the superoxide ion is first converted to hydrogen peroxide and normal oxygen by the action of an enzyme called superoxide dismutase. Because hydrogen peroxide is also toxic to cells (it is used as a disinfectant and antiseptic), it must be degraded by an enzyme—either catalase or peroxidase—into water and oxygen. If a microbe is not capable of dealing with toxic oxygen by these or similar mechanisms, it will be restricted to habitats free of oxygen. |
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| (aerobic organism) can use gaseous oxygen in its metabolism and possesses the enzymes needed to process toxic oxygen products |
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| An organism that cannot grow without oxygen. Most fungi and protozoa, as well as many bacteria (genera Micrococcus and Bacillus), have strict requirements for oxygen in their metabolism. |
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| an aerobe that does not require oxygen for its metabolism and is capable of growth in the absence of it. This type of organism metabolizes by aerobic respiration when oxygen is present, but in its absence, it adopts an anaerobic mode of metabolism such as fermentation. Facultative anaerobes usually possess catalase and superoxide dismutase. A number of bacterial pathogens fall into this group. This includes gram-negative intestinal bacteria and staphylococci. |
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Definition
| does not grow at normal atmospheric concentrations of oxygen but requires a small amount of it (1%–15%) in metabolism. Most organisms in this category live in a habitat such as soil, water, or the human body that provides small amounts of oxygen but is not directly exposed to the atmosphere. |
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| (anaerobic microorganism) lacks the metabolic enzyme systems for using oxygen gas in respiration. Because strict, or obligate, anaerobes also lack the enzymes for processing toxic oxygen, they cannot tolerate any free oxygen in the immediate environment and will die if exposed to it. Strict anaerobes live in highly reduced habitats, such as deep muds, lakes, oceans, and soil. |
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| do not utilize oxygen gas but can survive and grow in its presence. These anaerobes are not harmed by oxygen, and some of them possess alternate mechanisms for breaking down peroxide and superoxide. For instance, lactobacilli, which are common residents of the intestine, inactivate these compounds with manganese ions. |
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| grow best at higher CO2 tensions (3%–10%) than are normally present in the atmosphere (0.033%). This becomes important in the initial isolation of some pathogens from clinical specimens, notably Neisseria (gonorrhea, meningitis), Brucella (undulant fever), and Streptococcus pneumoniae. Incubation is carried out in a CO2 incubator that provides the correct range of CO2. Keep in mind that CO2 is an essential nutrient for autotrophs, which use it to synthesize organic compounds. |
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| a series of numbers ranging from 0 to 14, pH 7 being neither acidic nor alkaline. As the pH value decreases toward 0, the acidity increases, and as the pH increases toward 14, the alkalinity increases. The majority of organisms live or grow in habitats between pH 6 and pH 8 because strong acids and bases can be highly damaging to enzymes and other cellular substances. |
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| microorganisms living in the range of pH 5.5 to 8; usually found living in soil, fresh water, or the bodies of plants and animals |
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| include Euglena mutabilis (featured in Case Study 7), an alga that grows in acid pools between 0 and 1.0 pH, and Thermoplasma, an archaea that lives in hot coal piles at a pH of 1 to 2, and will lyse if exposed to pH 7. A few species of algae, archaea, and bacteria can actually survive at a pH near that of concentrated hydrochloric acid near a pH of 0. Not only do they require such a low pH for growth but particular bacteria actually help maintain the low pH by releasing strong acid. Because many molds and yeasts tolerate moderate acidity, they are the most common spoilage agents of pickled foods. |
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| live in hot pools and soils that contain high levels of basic minerals. Probably the upward limit of tolerance is shown by proteobacteria in California's Mono Lake that have adapted to pH 12. Bacteria that decompose urine create alkaline conditions, because ammonium (NH4+) can be produced when urea (a component of urine) is digested. Metabolism of urea is one way that Proteus spp. can neutralize the acidity of the urine to colonize and infect the urinary system. |
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| live in habitats with a high solute concentration. |
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| A microbe whose growth is either stimulated by salt or requires a high concentration of salt for growth. Obligate halophiles such as Halobacterium and Halococcus inhabit salt lakes, ponds, and other hypersaline habitats. They grow optimally in solutions of 25% NaCl but require at least 9% NaCl (combined with other salts) for growth. These archaea have significant modifications in their cell walls and membranes, and will lyse in hypotonic habitats. |
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Definition
| microbes adapt to wide concentrations in solutes. Such organisms are remarkably resistant to salt, even though they do not normally reside in high-salt environments. For example, Staphylococcus aureus can grow on NaCl media ranging from 0.1% up to 20%. Although it is common to use high concentrations of salt and sugar to preserve food (jellies, syrups, and brines), many bacteria and fungi actually thrive under these conditions and are common spoilage agents. A particularly hardy sugar-loving or saccharophilic yeast withstands the high sugar concentration of honey and candy. |
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| A microorganism that thrives under high (usually hydrostatic) pressure. Deep-sea microbes exist under pressures many times that of the atmosphere. Marine biologists sampling deep-sea trenches 7 miles below the surface isolated unusual eukaryotes called foraminifera that were being exposed to pressures 1,100 times normal. These microbes are so strictly adapted to high pressures that they will rupture when exposed to normal atmospheric pressure. |
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| Because of the high water content of cytoplasm, all cells require water from their environment to sustain growth and metabolism. Water is the solvent for cell chemicals, and it is needed for enzyme function and digestion of macromolecules. A certain amount of water on the external surface of the cell is required for the diffusion of nutrients and wastes. Even in apparently dry habitats, such as sand or dry soil, the particles retain a thin layer of water usable by microorganisms. Only dormant, dehydrated cell stages (for example, spores and cysts) tolerate extreme drying because of the inactivity of their enzymes. |
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| defined as close associations between organisms that are advantageous to at least one of the members. Recall that the members of symbiotic relationships are termed symbionts. Symbioses can be obligatory or nonobligatory, involve animals, plants, and other microbes, and can include complex multipartner interactions. Some symbionts live internally (endosymbionts), whereas others are affixed to the outside surfaces of their partners (ectosymbionts). |
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| a term that implies all members share in the benefits of the relationship. Many mutualistic associations have developed over hundreds of millions and even billions of years of shared evolution, a process termed coevolution. Coevolving symbionts remain in very close contact and must evolve together to sustain themselves. Any changes in partner A exert a selective pressure on partner B to adapt to these changes, and vice versa. |
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| hundreds of millions and even billions of years of shared evolution; Coevolving symbionts remain in very close contact and must evolve together to sustain themselves. Any changes in partner A exert a selective pressure on partner B to adapt to these changes, and vice versa. These adaptations occur at the genetic level, and in some cases, genes are exchanged between the partners. Over very long periods, the mutualists can become completely interdependent. We see this in Buchneraendosymbionts of certain aphids. These bacteria provide the aphid with needed amino acids and the aphid provides them a protective habitat. The bacteria are now so obligate that they have lost a large part of their genome and cannot survive outside the aphid. The aphids too have come to require the bacteria for survival. |
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| Organisms are so intimately associated that they require each other to survive. Root nodules (a1) have nitrogen-fixing endosymbiotic bacteria that supply the plant with usable nitrogen and provide a nurturing habitat for the bacteria (a2 inset). Jellyfish (b1) and corals rely on endosymbiotic algae called dinoflagellates (b2 inset) for survival. |
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| Organisms interact at the cellular level for mutual benefit, but they can be separated and live apart. The protozoan in (c) engulfs the algae but absorbs the nutrients they release and shelters them. (d) The plant supplies nutrients to the fungus and the fungus protects the plants against drying and insects. |
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| The members have an unequal relationship. One partner is favored by the association and the other is not harmed or helped. (e) Tiny colonies of Haemophilus absorb required growth factors given off by Staphylococcus. (f1 and 2) Human commensals associated with the epidermis make a living off flakes and excretions, generally with neutral effects. |
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| A microbe invades the sterile regions of a host and occupies its tissues and cells, causing some degree of damage. (g) All viruses are parasites that invade cells and take over their function. (h) Malaria shows multilevel parasitism. Mosquitoes (h1) are blood-sucking ectoparasites of humans that carry their own parasites (h2) that can also infect humans. |
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Microbes sharing a habitat feed off substances released by other organisms.
(i) Azotobacter releases NH4 that feeds Cellulomonas, and Cellulomonas degrades cellulose that feeds Azotobacter. (j) A dust mite lives in human settings and feeds off dead skin flakes. |
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| One member of an association produces a substance that harms or kills another. (k) Ants have complex symbiotic relationships that involve mutualism and amensalism with fungi and bacteria. (l1 and l2) In the amensal phase of their ecology, the ants cultivate actinomycetes to protect their habitat from microbial pests. |
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| The nondependent forms of mutualism. Organisms gain mutual benefit from their association, but they can survive independently outside of the partnership. In many cases, such cooperative relationships are coevolving to greater dependency. One example is the protozoan Euplotes, which harbors endosymbiotic algae in its cells. Both members can survive apart from their mutualistic habit but have a well-developed affinity for each other. |
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| obligate intracellular parasitism |
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Definition
| The most extreme form of parasitism, which means the microbe spends all or most of its life cycle inside the host cell, from which it derives essential nutrients and other types of support. Viruses are genetic and metabolic parasites; Rickettsia and Chlamydia bacteria are energy parasites; and apicomplexan protozoans like Plasmodium (cause of malaria) are hemoglobin parasites. The kinds of harm that parasites do to their hosts varies from superficial damage (ringworm on the skin from a fungal infection) to death (rabies virus). |
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| cross-feeding, is communal feeding of organisms sharing a habitat In essence, products given off by one organism are usable by another. The organisms involved do not require this relationship for survival but they generally benefit from it. Many syntrophic associations occur in aquatic habitats and soils within biofilms and are related to nutrient and bioelement recycling. A simple example involves a pair of free-living soil bacteria that share their metabolic products cyclically.Cellulomonas uses its enzymes to digest plant cellulose into glucose, but it cannot fix nitrogen.Azotobacter fixes nitrogen gas from the air and releases ammonium, but it does not digest cellulose. The glucose is a source of carbon for Azotobacter, and the ammonium supplies Cellulomonas with usable nitrogen. Even more complex interactions occur in the cycling of elements such as sulfur, phosphorus, and nitrogen |
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| An action of one microbe that causes an adverse effect in another microbe. It usually involves antagonism or competition of some type and occurs in a community where microbes are sharing space and nutrient sources. Some microbes effectively compete by using up a vital nutrient to grow faster and dominate the habitat. |
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| The release of natural chemicals or antibiotics—that inhibit or kill microbes. Many fungi and bacteria are adapted to this survival strategy. An intriguing example can be found in the complex symbiosis of certain ants. These ants have been shown to cultivate specialized gardens of fungi as a source of food. To protect the fungi from other microbes, the ants also cultivate species of filamentous bacteria called actinomycetes that produce antibiotics. The ants spread the chemical in their gardens to protect the fungi from invasion by parasites. |
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| Biofilms result when organisms attach to a substrate by some form of extracellular matrix that binds them together in complex organized layers. Biofilms are so prevalent that they dominate the structure of most natural environments on earth. In a sense, these living networks operate as “superorganisms” that influence such microbial activities as adaptation to a particular habitat, content of soil and water, nutrient cycling, and the course of infections. |
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Definition
| An activity among bacteria in a biofilm in which the members signal each other and coordinate their functions. This process occurs in several stages, including self-monitoring of cell density, secretion of chemical signals, and genetic activation |
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