quiz 8: ch 28

decomposition of sulfur-containing amino acids produces ______ gas

H2S

dead zone

In a body of water, a region lacking fish and other aquatic life, usually due to insufficient dissolved O2.

terminal electron acceptor

In aerobic conditions, O2 is used as a terminal electron acceptor in respiration. In anaerobic conditions, some prokaryotes can use nitrate (NO3−), nitrite (NO2−), sulfate (SO4−), or carbon dioxide (CO2) as a terminal electron acceptor

ectomycorrhiza

Mycorrhizal association in which fungi grow around the plant cells, forming a sheath around the root. -These fungi associate mainly with certain trees, including conifers, beeches, and oaks. Over 5,000 species of fungi are involved in ectomycorrhizal relationships but many are restricted to a single type of plant.

the cyclic paths that elements take as they flow from living (biotic) and non-living (abiotic) components of ecosystems are _______

biochemical cycles

Within the biosphere, ecosystems vary in both

biodiversity (number and variety of species present and their evenness of distribution) and biomass (the weight of all organisms present).

chemoorganotrophs use reduced _______ compounds such as sugars, lipids, and amino acids as energy sources

carbon

In aquatic environments, the most significant nitrogen-fixers are

cyanobacteria -They are especially important in flooded soils such as rice paddies

The role an organism plays in a particular ecosystem is called its

ecological niche

the organisms in a given area and their interactions with each other and the non-living environment form the _______

ecosystem

the chemolithoautotrophs found near hydrothermal vents support the growth of clams and tube worms, providing these animals with the sources of _____

energy and carbon

Wet soils, dry soils, increases in acidity

wet soils: unfavorable for aerobic microbes dry soils: metabolic activity decreases; many microbes produce survival forms such as endospores and cysts increases in acidity: bacterial growth suppressed, allowing fungi to thrive

mycorrhiza

which are fungi growing in a symbiotic relationship with certain plant roots

Nitrogen fixation

is the process in which nitrogen gas (N2) is reduced to form ammonia (NH3), which can then be incorporated into cellular material. The process, catalyzed by the enzyme complex nitrogenase, requires a tremendous amount of energy because N2 has a very stable triple covalent bond. -prelatively few organisms—all of which are prokaryotes—can reduce this gaseous form of the element. Thus, just as humans and other animals depend on primary producers to fix carbon, they rely on prokaryotes to convert atmospheric nitrogen to a form they can assimilate to create biomass.

Metagenomic data provide two separate but related types of information about a microbial community:

taxonomic diversity and genetic capabilities

Microbial Mat

A type of microbial community characterized by distinct layers of different groups of microbes that together make up a thick, dense, highly organized structure.

Respiration and Fermentation

-When heterotrophs consume organic material, they break it down using respiration and/or fermentation to release energy, which is captured to make ATP. These processes usually also make CO2. -The type of organic material helps dictate which species degrade it. A wide variety of organisms use sugars, amino acids, and proteins as energy sources, but rapidly multiplying bacteria often play the dominant role in decomposing these substances. In contrast, relatively few organisms (primarily fungi) can break down lignin, a major component of wood (figure 28.9). Aerobic conditions are required for this degradation, so wood at the bottom of marshes resists decay. -The O2 supply has a strong influence on the carbon cycle. Not only does O2 allow degradation of certain compounds such as lignin, it also helps determine the types of carbon-containing gases produced. When organic matter is degraded aerobically, a great deal of CO2 is produced. When the O2 level is low, however, as is the case in marshes, swamps, and manure piles, the degradation is incomplete, generating some CO2 and also a variety of other products.

chemoorganotrophs

reduce carbon compounds

chemolithotrophs

reduce inorganic molecules

heterotrophs break down organic material using the processes of _______ and/or _______

respiration fermentation

biosynthesis

(biomass production). All organisms require elements for biosynthesis. As an example, nitrogen is required to produce amino acids. Plants and many prokaryotes assimilate nitrogen by incorporating ammonia (NH3) to synthesize the amino acid glutamate (see figure 6.29). Some prepare for this step by converting nitrate (NO3−) to ammonia. Once glutamate has been synthesized, the amino group can then be transferred to other carbon compounds to produce the other amino acids. Animals cannot incorporate ammonia, and instead require amino acids in their diet. Some prokaryotes can reduce atmospheric nitrogen to form ammonia—the process of nitrogen fixation. The ammonia can then be incorporated into cellular material.

Mycorrhizas

(myco means "fungus"; rhizo means "root") are fungi growing in symbiotic relationships with plant roots (figure 28.13). They enhance the competitiveness of plants by helping them take up phosphorus and other substances from the soil. In turn, the fungi gain nutrients for their own growth from root secretions. It is estimated that over 85% of vascular plants (plants with specialized water- and food-conducting tissues) have mycorrhizas.

eutrophic

(nutrient rich), photosynthetic organisms flourish, often forming a visible layer on the surface

Energy Sources for Ecosystems

-All chemotrophs harvest the energy trapped in chemical bonds to generate ATP. -Photosynthesis, carried out by chlorophyll-containing plants and microorganisms, converts radiant energy (sunlight) to chemical energy in the form of organic compounds, which can then be used by chemoorganotrophs. -A number of hydrothermal vents have been discovered some thousands of meters below the ocean surface. These vents form when water seeps into cracks in the ocean floor and becomes heated by the molten rock, finally spewing out in the form of mineral-laden undersea geysers. The hydrogen sulfide discharged supports thriving deep-sea communities, oases in the otherwise desolate ocean floor (figure 28.12). Large numbers of sulfur-oxidizing chemolithoautotrophs are Page 780found in and around the vents. Many of these bacteria and archaea are free-living but some live in symbiotic association with the large tube worms and clams that inhabit the areas. The chemolithoautotrophs obtain energy by oxidizing hydrogen sulfide, and they fix CO2, providing the animals with both a carbon and an energy source.

Organisms are categorized according to their trophic level (source of food), which is intimately related to the cycling of nutrients. There are three general trophic levels:

-primary producers -consumers -decomposers

microorganisms

-without microorganisms, nutrients would be depleted, halting growth and reproduction of other forms of life -microorganisms play crucial roles in energy capture and nutrient cycle -without microorganisms, the earth would quickly become buried by tons of wastes

carbon fixation

A fundamental part of the carbon cycle is carbon fixation, the defining characteristic of primary producers (figure 28.8). Fixation incorporates chemical elements into molecules that can be directly used by living organisms. Primary producers convert CO2 into an organic form, using mechanisms described in chapter 6. Without primary producers, no other organisms, including humans, could exist. We depend on them to generate the organic carbon compounds we use as an energy source and for biosynthesis.

rhizobia

A group of Gram-negative nitrogen-fixing bacteria that form symbiotic relationships with leguminous plants such as clover and soybeans. -are the most agriculturally important symbiotic nitrogen-fixing bacteria. These grow as endosymbionts within specialized organs called nodules on the roots of legumes (plants that bear seeds in pods), including alfalfa, clover, peas, beans, and peanuts (figure 28.14a). The input of soil nitrogen from rhizobia may be about 10 times the annual rate of nitrogen fixation by non-symbiotic organisms. To foster plant growth, farmers often add the appropriate symbionts to the seeds of certain legumes

Oligotrophic

A nutrient-poor environment.

_________ is a decomposition process that converts organic nitrogen into NH3

Ammonification

Eutrophic

An environment that is nutrient rich, supporting the excessive growth of algae and other organisms.

Hypoxic

An environment very low in dissolved O2.

Endomycorrhizas

Mycorrhizal association in which fungi penetrate root cells, growing as coils or tight, bushlike masses within the cells. -These are by far the most common mycorrhizal relationships and are found in association with most herbaceous plants. Relatively few species of fungi are involved, perhaps only 100 or so, and most appear to be obligate symbionts. Page 781The relationship for some plants is also obligate; for example, most orchid seeds will not germinate without the activities of a fungal partner.

fact about oligotrophic lakes

Oligotrophic lakes in temperate climates may have anaerobic layers due to thermal stratification resulting from seasonal temperature changes. During the summer months, the surface water warms. This decreases the density of the water, causing it to form a distinct layer that does not mix with the cooler, denser water below. The upper layer, called the epilimnion, is generally O2 rich due to the activities of photosynthetic organisms. In contrast, the lower layer, the hypolimnion, may be anaerobic due to the consumption of O2 by heterotrophs. Separating these two layers is the thermocline, a zone of rapid temperature change. As the weather cools, the waters mix, providing O2 to the deep water.

Primary Producers

Organisms that convert CO2 into organic compounds, sustaining other forms of life.

bacteriocins

Proteins made by bacteria that kill certain other bacteria.

energy source

Reduced carbon compounds such as sugars, lipids, and amino acids are used as energy sources by chemoorganotrophs. Chemolithotrophs can use reduced inorganic molecules such as hydrogen sulfide (H2S), ammonia (NH3), and hydrogen gas (H2)

sulfur-oxidizing prokaryotes can oxidize _______ to sulfate

S0 and H2S

most plants and microorganisms assimilate sulfur as ______

SO4 2-

diazotrophs

Some nitrogen-fixing prokaryotes, or diazotrophs, are free-living

Ecology

Study of interactions of organisms with one another and with their environment.

taxonomic diversity

Taxonomic diversity is studied by examining either the nucleotide sequence of 16S rRNA genes (18S rRNA genes for eukaryotes) or the deduced amino acid sequences of ribosomal proteins to classify and identify microorganisms.

decomposers

These are heterotrophs that digest the waste products and remains of primary producers and consumers. Decomposers specialize in digesting complex materials such as cellulose, converting them into small molecules that can more easily be used by other organisms. The complete breakdown of organic molecules into inorganic molecules such as ammonia, sulfates, Page 769phosphates, and carbon dioxide is called mineralization. Microorganisms, particularly bacteria and fungi, play a major role in decomposition because of their unique metabolic capabilities.

consumers

These are heterotrophs that eat primary producers or other consumers. Herbivores, which eat plants or algae, are primary consumers. Carnivores that eat herbivores are secondary consumers; carnivores that eat other carnivores are tertiary consumers. A chain of consumption is a food chain; interacting food chains form a food web.

sulfur reduction

Under anaerobic conditions, sulfate generated by the sulfur-oxidizers can then be used as a terminal electron acceptor by certain organisms. The sulfur- and sulfate-reducing bacteria and archaea use sulfate in the process of anaerobic respiration, reducing it to hydrogen sulfide (H2S). In addition to its unpleasant odor, the H2S is a problem because it reacts with metals, resulting in corrosion.

Hydrothermal Vents

Undersea geysers that spew out mineral-laden hot water.

The density and composition of the soil microbiome are dramatically affected by environmental conditions.

Wet soils, for example, are unfavorable for aerobic microbes because the spaces in the soil fill up with water, lowering the amount of air in the soil. When the water content of soil drops to a very low level, as during a drought or in a desert environment, the metabolic activity and number of soil microorganisms decrease. Many produce survival forms such as endospores and cysts that are resistant to drying. Other environmental influences that affect soil microbes include acidity, temperature, and nutrient supply. For example, acidity suppresses bacterial growth, allowing fungi to thrive with less competition for nutrients. This is why mushrooms often appear in a lawn fertilized with an acid-producing fertilizer such as ammonium chloride.

sulfur is found in all living organisms, primarily in the ________ acids methoi (didn't finish typing)

acids

plants and many prokaryotes assimilate nitrogen by incorporating _______ into the synthesis of glutamate

ammonia

sulfur-reducing and sulfate-reducing bacteria and archaea use sulfate as a terminal electron acceptor during ______, thereby reducing it to hydrogen sulfide

anaerobic respiration

the process by which ammonium is oxidized to molecular nitrogen under anaerobic conditions is called _______

anammox

phosphorous is not a component of _____

proteins but is ATP, phospholipids, and nucleic acids

microbial mat

is a thick, dense, highly organized structure composed of distinct layers. Frequently they are green, reddish-pink, and black, which indicate the growth of different microbial groups (figure 28.4). -The top green layer is typically composed of various species of cyanobacteria, and the color is due to their photosynthetic pigments. -Directly below the green layer is a reddish-pink layer consisting of purple sulfur bacteria. The light-harvesting pigments of these anoxygenic phototrophs can use wavelengths of light not collected by the cyanobacteria. -At the bottom is a black layer, resulting from iron molecules reacting with hydrogen sulfide produced by a group of bacteria called sulfate-reducers. These obligate anaerobes oxidize the organic compounds produced by the photosynthetic microbes growing in the mat's upper layers, using sulfate as a terminal electron acceptor.

Ammonification

is the decomposition process that converts organic nitrogen into ammonia (NH3). In alkaline environments, such as heavily limed soil, the gaseous ammonia may enter the atmosphere. In neutral environments, ammonium (NH4+) is formed. This positively charged ion adheres to negatively charged particles.

Nitrification

is the process that oxidizes ammonium (NH4+) to nitrate (NO3−). -Bacteria known as nitrifiers do this in a cooperative two-step process, using ammonium and an intermediate nitrite (NO2−) as energy sources. Nitrifiers are obligate aerobes, using O2 as a terminal electron acceptor. Consequently, nitrification does not occur in waterlogged soils or in anaerobic regions of aquatic environments.

________ are organisms that obtain energy through the oxidation of H2, use CO2 as a terminal electron acceptor, and produce CH4 (methane)

methanogens

microorganisms called _______ use methane as an energy source by oxidizing it to produce CO2

methylotrophs

the process by which N2 is reduced to form NH3 is called

nitrogen fixation

Phosphorus is a component of several critical biological compounds, including

nucleic acids, phospholipids, and ATP. -Most plants and microorganisms can take up phosphorus as orthophosphate (PO43−), incorporating it into biomass. From there, the phosphorus is passed along the food web. When plants and animals die, decomposers convert organic phosphate back to the inorganic form. -In many aquatic habitats, growth of algae and cyanobacteria—the primary producers—is limited by low concentrations of phosphorus. When phosphates are added from sources such as agricultural runoff, phosphate-containing detergents, and wastewater, eutrophication can result.

during aerobic respiration, microbes use _____ as their terminal electron acceptor

o2

nitrifies are

obligate aerobes

in many aquatic environments, the growth of algae and cyanobacteria is limited by low concentrations of __________, without which they are unable to produce sufficient critical biological components including nucleic acids, phospholipids, and ATP

phosphorous

Organisms of the same type in a given location make up a

population

nitrogen is a significant component of what macromolecules

proteins and nucleic acids

oligotrophic

A nutrient-poor environment. -the growth of photosynthetic organisms and other autotrophs is limited by the lack of inorganic nutrients, particularly phosphate, nitrate, and iron.

metagenomics

The cultivation-independent study of microbial communities or their members by analyzing the total microbial genomes in a sample taken directly from an environment.

There are two common types of mycorrhizal relationships:

Endomycorrhizas and Ectomycorrhizas

Rhizosphere

Zone around plant roots containing organic materials secreted by the roots.

most microorganisms grow as ______ attached to solid surfaces or at air-water interfaces

biofilms

All of the ecosystems on Earth make up the

biosphere

Denitrification

is the process that reduces nitrate (NO3−), converting it to gaseous forms such as nitrous oxide (N2O) and molecular nitrogen (N2). This happens when prokaryotes anaerobically respire using nitrate as a terminal electron acceptor. -Denitrification can have negative environmental and economic consequences. Under anaerobic conditions in wet soils, for example, denitrifying bacteria will reduce the oxidized nitrogen compounds of fertilizers, releasing gaseous nitrogen to the atmosphere. In some areas, this process may represent 80% of nitrogen lost from fertilized soil, a considerable economic loss to the farmer. In addition, nitrous oxide contributes to global warming.

Carbon Cycle

ll organisms are composed of organic molecules such as proteins, lipids, and carbohydrates. The carbon travels through the food chain as primary producers are eaten by primary consumers, which are then eaten by secondary consumers. Decomposers then use organic molecules in the remains of primary producers and consumers.

all organisms are composed of organic molecules such as proteins, lipids, carbohydrates, and nucleic acids. Ultimately, all life depends on the capability of ______ to fix carbon dioxide into organic molecules

primary producers

Microorganisms and Herbivores

Another mutualistic relationship occurs between microbes and certain herbivores. In order to live on grass and other plant material, herbivores such as cattle and horses rely on a microbial community that inhabits a specialized digestive compartment. The microbes digest cellulose and hemicellulose, two of the major components of plant material, releasing compounds that can then serve as a nutrient source for the animal. The specialized digestive compartment in ruminants such as cattle, sheep, and deer is called a rumen, and it precedes the true stomach. Non-ruminant herbivores such as horses and rabbits have a compartment called a cecum, which serves a similar purpose; it lies between the small intestine and the large intestine.

Primary producers are characterized by their ability to convert _______ into organic molecules, a process Called carbon fixation

CO2

anammox

Certain bacteria oxidize ammonium under anaerobic conditions, using nitrite as a terminal electron acceptor. This reaction, called anammox (for anoxic ammonia oxidation), forms N2 and might provide an economical means of removing nitrogen compounds during wastewater treatment.

Nitrogen Fixation

Conversion of nitrogen gas to ammonia.

_______ is the process that reduces NO3- to N2O or N2

Denitrification

Decomposers

Organisms that digest the remains of primary producers and consumers.

Consumers

Organisms that eat primary producers or other consumers.

genetic capabilities

The genetic capabilities of the community as a whole are determined by analyzing the entire spectrum of sequenced genes in a sample. A significant challenge is to link the two types of information, allowing researchers to determine which uncultivated microbes have a given genetic capability.

hypoxic

The heterotrophs consume dissolved O2 as they metabolize the organic material. Because O2 consumption can outpace the slow rate of diffusion of atmospheric O2 into the waters, the environment can become hypoxic (very low in dissolved O2). Insufficient O2 leads to the death of resident fish and other aquatic animals.

primary producers

These are autotrophs; they convert CO2 into organic materials. Producers include both photoautotrophs (use sunlight for energy) and chemolithoautotrophs (oxidize inorganic chemicals for energy). Primary producers serve as a food source for consumers and decomposers.

Biogeochemical cycles

are the cyclical paths that elements take as they flow through living (biotic) and non-living (abiotic) components of ecosystems. These cycles are important because a fixed and limited amount of the elements that make up living cells exists on the earth and in the atmosphere. Thus, in order for an ecosystem to sustain its characteristic life-forms, elements must continually be recycled.

When studying biogeochemical cycles, it is helpful to consider the role of a given element in a particular organism's metabolism. Elements are used for three general purposes:

biosynthesis energy source terminal electron acceptor

All of the different organisms in the location form a

community

consists of a community of organisms and the non-living environment with which they interact.

ecosystem

An especially important part of the soil microbiome is found in the

rhizosphere (the zone of soil that adheres to plant roots) -The concentration of microbes there, particularly Gram-negative bacteria, is generally much greater than in surrounding soil. This is because the root cells secrete organic molecules that serve as a nutrient source for microbes. Specific types of bacteria appear to preferentially interact with particular plants.