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Chapter 16

Microbial Ecology

Book Version 6
By Boundless
Boundless Microbiology
Microbiology
by Boundless
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Section 1
Microbial Ecology
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Microbes and Ecosystem Niches

Every ecosystem on Earth contains microorganisms that occupy unique niches based on their specific metabolic properties.

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Organization of Ecosystems

Microorganisms serve essential roles in the complex nutrient exchange system that defines an ecological community.

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Role of Microbes in Biogeochemical Cycling

Microbes form the backbone of every ecological system by controlling global biogeochemical cycling of elements essential for life.

Microbial Environments and Microenvironments

The extraordinary biological diversity among microbes reflects their ability to occupy every habitable environment on the planet.

Section 2
Soil and Plant Microbiology
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Soil Composition

Soil is a mix of varying amounts of inorganic matter, organic matter, water, and air.

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Physical Properties of Soil

Soils are made up of combinations of four distinct layer types or horizons: O horizon, A horizon, B horizon, and C horizon.

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Mycorrhiza

A mycorrhiza is a symbiotic association between a fungus and the roots of a vascular plant.

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Wetland Soils

Wetlands are considered one of the most biologically diverse of all ecosystems.

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Endophytes and Plants

An endophyte is an endosymbiont, often a bacterium or fungus, that lives within a plant for at least part of its life without causing apparent disease.

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Mycorrhizae: The Symbiotic Relationship between Fungi and Roots

Many plants form associations called mycorrhizae with fungi that give them access to nutrients in the soil, protecting against disease and toxicities.

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Plant Pathogens

There are four main bacterial pathogenicity factors: cell wall degrading enzymes, toxins, phytohormones, and effector proteins.

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Nitrogen Fixation: Root and Bacteria Interactions

Plants cannot extract the necessary nitrogen from soil, so they form symbiotic relationships with rhizobia that can fix it as ammonia.

Section 3
Aquatic Microbiology
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Marine Habitats

The marine environment supplies many kinds of habitats that support marine life.

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Planktonic Communities

Plankton (singular plankter) are any organisms that live in the water column and are incapable of swimming against a current.

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Planktonic Food Webs

Plankton communities are divided into broad categories of producer, consumer, and recycler groups.

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Ocean Floor

Ocean floor extremophile chemosynthetic microbes provide energy and carbon to the other organisms in these environments.

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Cold-Seep Ecosystems

A cold seep is an area of the ocean floor where hydrogen sulfide, methane, and other hydrocarbon-rich fluid seepage occurs.

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The Deep Sea and Barophilism

A piezophile (also called a barophile) is an organism which thrives at high pressures, such as deep sea bacteria or archaea.

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Sea Coral and Sea Anemone Zooxanthellae

Zooxanthellae refers to a variety of species that form symbiotic relationships with other marine organisms, particularly coral.

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Sponge Communities

Sponge reefs serve an important ecological function as habitat, breeding and nursery areas for fish and invertebrates.

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Freshwater Environments

Fresh water is naturally occurring water on Earth which has low concentrations of dissolved salts and other total dissolved solids.

Section 4
Nutrient Cycles
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Sources and Sinks of Essential Elements

Biogeochemical cycles are pathways by which essential elements flow from the abiotic and biotic compartments of the Earth.

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The Carbon Cycle

The carbon cycle describes the flow of carbon from the atmosphere to the marine and terrestrial biospheres, and the earth's crust.

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Syntrophy and Methanogenesis

Bacteria that perform anaerobic fermentation often partner with methanogenic archea bacteria to provide necessary products such as hydrogen.

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The Phosphorus Cycle

Phosphorus, important for creating nucleotides and ATP, is assimilated by plants, then released through decomposition when they die.

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The Nitrogen Cycle

The nitrogen cycle is the process by which nitrogen is converted from organic to inorganic forms; many steps are performed by microbes.

The Sulfur Cycle

Many bacteria can reduce sulfur in small amounts, but some bacteria can reduce sulfur in large amounts, in essence, breathing sulfur.

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The Iron Cycle

Iron is an important limiting nutrient required for plants and animals; it cycles between living organisms and the geosphere.

Section 5
Microbial Symbioses
Mutualism vs. Symbiosis

Symbiosis is a relationship between two organisms: it can be mutualistic (both benefit), commensal (one benefits), or parasitic.

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The Rumen and Ruminant Animals

Ruminant animals (such as deer and cows) digest food in a four-chambered stomach with the help of special bacteria, protozoa, and fungi.

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Hydrothermal Vent Microbial Ecosystems

Hydrothermal vents are home to chemosynthetic bacteria, which are the basis of a unique ecosystem that thrives in total darkness.

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Squid-Aliivibrio Symbiosis

Squid host light-generating Allivibiro bacteria in a special organ so that they can illuminate themselves and blend in with the environment.

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Mutualistic Relationships with Fungi and Fungivores

Members of Kingdom Fungi form ecologically beneficial mutualistic relationships with cyanobateria, plants, and animals.

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Agrobacterium and Crown Gall Disease

Argobacterium causes Crown Gall Disease by transferring a DNA plasmid to the host plant, causing the host to make nutrients for it.

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The Legume-Root Nodule Symbiosis

Legumes have a symbiotic relationship with bacteria called rhizobia, which create ammonia from atmospheric nitrogen and help the plant.

Section 6
Microbial Bioremediation
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Microbial Ore Leaching

Microbial ore leaching is the process in which microorganisms are used to extract metals from ores.

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Petroleum Biodegradation

Petroleum oil can be degraded by microorganisms that use it as a source of energy.

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The Degradation of Synthetic Chemicals in Soils and Water

Microorganisms are crucial participants in the detoxification of water and soil.

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Diseases
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Microbial Ecology
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