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Brock Biology of Microorganisms

Twelfth Edition

Madigan / Martinko Dunlap / Clark

Chapter 1
Nutrient Cycles, Bioremediation, and Symbioses
Lectures by Buchan & LeCleir
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24.1 The Carbon Cycle

Carbon is cycled through all of Earths major carbon reservoirs


i.e., atmosphere, land, oceans, sediments, rocks, and

biomass
Reservoir size and turnover time are important parameters in understanding the cycling of elements

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The Carbon Cycle

Figure 24.1

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Major Carbon Reservoirs on Earth

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24.1 The Carbon Cycle


CO2 in the atmosphere is the most rapidly transferred carbon reservoir

CO2 is fixed primarily by photosynthetic land plants and


marine microbes CO2 is returned to the atmosphere by respiration of animals and chemoorganotrophic microbes as well as human activities
Microbial decomposition is the largest source of CO2 released to the atmosphere

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24.1 The Carbon Cycle


The carbon and oxygen cycles are intimately linked

Phototrophic organisms are the foundation of the carbon


cycle Oxygenic phototrophic organisms can be divided into two groups: plants and microorganisms Plants dominant phototrophic organisms of terrestrial

environments
Phototrophic microbes dominate aquatic environments

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24.1 The Carbon Cycle

Photosynthesis and aerobic respiration are reverse reactions Photosynthesis


CO2 + H2O (CH2O) + O2

Aerobic Respiration
(CH2O) + O2 CO2 + H2O

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Redox Cycle for Carbon

Figure 24.2

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24.2 Syntrophy and Methanogenesis

On a global basis, biotic processes release more CH4 than abiotic processes

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Estimates of CH4 Released into the Atmosphere

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II. Nitrogen, Sulfur, and Iron Cycles

24.3 The Nitrogen Cycle 24.4 The Sulfur Cycle 24.5 The Iron Cycle

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24.3 The Nitrogen Cycle

Nitrogen
A key constituent of cells, particularly proteins Exists in a number of oxidation states

NH3 > NO2- > NO3 Ammonia > nitrite > nitrate

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Redox Cycle for Nitrogen

Figure 24.5

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24.3 The Nitrogen Cycle


N2 is the most stable form of nitrogen and is a major reservoir
The ability to use N2 as a cellular nitrogen source (nitrogen fixation) is limited to only a few prokaryotes Denitrification is the reduction of nitrate to gaseous nitrogen products and is the primary mechanism by which N2 is produced biologically

Ammonia produced by nitrogen fixation or ammonification can be


assimilated into organic matter or oxidized to nitrate

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24.3 The Nitrogen Cycle

Anammox is the anaerobic oxidation of ammonia to N2 gas Denitrification and anammox result in losses of nitrogen

from the biosphere as N2 and other gaseous products

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24.4 The Sulfur Cycle

Sulfur transformations by microbes are complex


H2S > S0 > SO4= Hydrogen sulfide > elemental sulfur > sulfate The bulk of sulfur on Earth is in sediments and rocks (lithosphere) as sulfate and sulfide minerals (e.g., gypsum, pyrite) The oceans (hydrosphere) represent the most significant

reservoir of sulfur (as sulfate) in the biosphere

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Redox Cycle for Sulfur

Figure 24.6

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24.4 The Sulfur Cycle

H2S oxidation by autotrophs Aerobic by chemolithotrophs Anaerobic by anoxygenic photosynthesis

SO4 reduction by anaerobic respiration

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24.5 The Iron Cycle


Iron is one of the most abundant elements in the Earths crust On the Earths surface, iron exists naturally in two

oxidation states
Ferrous (Fe2+) Ferric (Fe3+)

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Redox Cycle of Iron

Figure 24.7

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24.5 The Iron Cycle

Fe3+ can be used by some microbes as electron acceptors in anaerobic respiration In aerobic acidic pH environments, acidophilic

chemolithotrophs can oxidize Fe2+ (e.g. Acidithiobacillus)

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A Microbial Mat Containing High Levels of Ferrous Iron (Fe2+)

Figure 24.8b

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24.5 The Iron Cycle

Pyrite (FeS2)
One of the most common forms of iron in nature Its oxidation by bacteria can result in acidic conditions in

coal-mining operations

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Role of Iron-Oxidizing Bacteria in Oxidation of Pyrite

Figure 24.10a

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Role of Iron-Oxidizing Bacteria in Oxidation of Pyrite

Figure 24.10b

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24.5 The Iron Cycle

Acid Mine Drainage


An environmental problem in coal-mining regions Occurs when acidic mine waters containing sulfuric acid

are mixed with natural waters in rivers and lakes


Bacterial oxidation of sulfide minerals is a major factor in its formation

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Acid Mine Drainage from a Bituminous Coal Region

Figure 24.11

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III. Microbial Bioremediation

24.6 Microbial Leaching of Ores 24.7 Mercury and Heavy Metal Transformations 24.8 Petroleum Biodegradation

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24.6 Microbial Leaching of Ores

Bioremediation
Refers to the cleanup of oil, toxic chemicals, or other pollutants from the environment by microorganisms

Often a cost-effective and practical method for pollutant


cleanup

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24.6 Microbial Leaching of Ores

Microbial Leaching
The removal of valuable metals, such as copper, gold, uranium & mercury from sulfide ores by microbial

activities
Particularly useful for copper ores

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24.6 Microbial Leaching of Ores

In microbial leaching, low-grade ore is dumped in a large pile (the leach dump) and sulfuric acid is added to maintain a low pH

The liquid emerging from the bottom of the pile is enriched in


dissolved metals and is transported to a precipitation plant Bacterial oxidation of Fe2+ is critical in microbial leaching as Fe3+ itself can oxidize metals in the ores

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The Microbial Leaching of Low-Grade Copper Ores

Recovery of Copper as a Metallic Copper

Figure 24.14c

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Arrangement of a Leaching Pile and Reactions

Figure 24.15

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24.8 Petroleum Biodegradation

Prokaryotes have been used in bioremediation of several major crude oil spills

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Environmental Consequences of Large Oil Spills

Contaminated Beach in Alaska containing oil from the Exxon Valdez spill of 1989

Figure 24.19a

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Environmental Consequences of Large Oil Spills

Center rectangular plot (arrow) was treated with inorganic nutrients to stimulate bioremediation

Figure 24.19b

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24.8 Petroleum Biodegradation

Diverse bacteria, fungi, and some cyanobacteria and green algae can oxidize petroleum products aerobically Oil-oxidizing activity is best if temperature and inorganic

nutrient concentrations are optimal


Hydrocarbon-degrading bacteria attach to oil droplets and

decompose the oil and dispense the slick

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Hydrocarbon-Oxidizing Bacteria in Association with Oil

Figure 24.20

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IV. AnimalMicrobia Symbioses

24.10 The Rumen and Ruminant Animals 24.11 Hydrothermal Vent Microbial Ecosystems

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Bacteria in Ruminants Aid in Digestion in Vegetation

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Biogeochemical Cycling and Energy Flow

Microorganisms and herbivores


Relationship between microorganisms and herbivores relies on community of microbes that inhabit specialized compartment in digestive tract of the animal.
In ruminants such as cows and sheep the compartment is called the rumen
Rumen is located in front of the true stomach

In non-ruminants such as horses compartment is called cecum


Cecum lies between small and large intestine

Microbes that inhabit these compartments digest cellulose and hemicellulose to compounds that can be used as nutrients
Cellulose and hemicellulose are major components of plants

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Diagram of the Rumen and Gastrointestinal System of a Cow

Figure 24.27a

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24.10 The Rumen and Ruminant Animals


The rumen contains 1010-1011microbes/g of rumen constituents Microbial fermentation in the rumen is mediated by celluloytic microbes that hydrolyze cellulose to free glucose

that is then fermented, producing volatile fatty acids (e.g.,


acetic, propionic, butyric) and the CH4 and CO2 Fatty acids pass through rumen wall into bloodstream and are utilized by the animal as its main energy source

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Biochemical Reactions in the Rumen

Figure 24.28

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24.10 The Rumen and Ruminant Animals

Rumen microbes also synthesize amino acids and vitamins for their animal host Rumen microbes themselves can serve as a source of

protein to their host when they are directly digested


Anaerobic bacteria dominate in the rumen

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Characteristics of Some Rumen Prokaryotes

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Hydrothermal Vents

Figure 24.29

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24.11 Hydrothermal Vent Microbial Ecosystems

Deep-sea hot springs (hydrothermal vents) support thriving animal communities that are fueled by chemolithotrophic microbes

Diverse invertebrate communities develop near


hydrothermal vents, including large tube worms, clams, mussels

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Invertebrates Living Near Deep-Sea Thermal Vents

Tube Worms (Family Pogonophora)

Figure 24.30a

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Invertebrates Living Near Deep-Sea Thermal Vents

Mussel Bed in Vicinity of Warm Vent

Figure 24.30c

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24.11 Hydrothermal Vent Microbial Ecosystems

Chemolithotrophic prokaryotes that utilize reduced inorganic

materials emitting from the vents (primary producers) form


endosymbiotic relationships with vent invertebrates Vent tube worms harbor several features that facilitate the growth

of their endosymbionts (e.g., trophosome, specialized


hemoglobins, high blood CO2 content)

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A Hydrothermal Vent Black Smoker

Figure 24.32

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24.11 Hydrothermal Vent Microbial Ecosystems

Thermophilic and hyperthermophilic microbes live in gradients that form as hot water mixes with cold seawater

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V. PlantMicrobial Symbioses

21.13 Lichens and Mycorrhizae

24.15 The LegumeRoot Nodule Symbiosis

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24.13 Lichens and Mycorrhizae


Lichens
Leafy or encrusting microbial symbiosis Often found growing on bare rocks, tree trunks, house roofs, and the surfaces of bare soils Consist of a mutalistic relationship between a fungus and an alga (or cyanobacterium)
Alga is photosynthetic and produces organic matter for the fungus The fungus provides a structure within which the phototrophic partner can grow protected from erosion by rain or wind

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Lichens

Figure 24.35

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Mutualisitic Relationships Between Microorganisms and Eukaryotes


Lichen are an association between an alga and a fungus

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Lichens

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24.13 Lichens and Mycorrhizae

Mycorrhizae
Mutalistic associations of plant roots and fungi Two classes
Ectomycorrhizae fungi colonize outside of root Endomycorrhizae fungi grow into root tissue

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24.13 Lichens and Mycorrhizae

Ectomycorrhizae
Fungal cells form an extensive sheath around the outside of the root with only a little penetration into the root tissue

Found primarily in forest trees, particularly boreal and


temperate forests

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Mycorrhizae

Figure 24.37b

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24.13 Lichens and Mycorrhizae

Endomycorrhizae
Fungal mycelium becomes deeply embedded within the root tissue

Are more common than ectomycorrhizae


Found in >80% of terrestrial plant species

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24.13 Lichens and Mycorrhizae

Mycorrhizal fungi assist plants by


Improving nutrient absorption
This is due to the greater surface area provided by the fungal mycelium

Helping to promote plant diversity

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Effect of Mycorrhizal Fungi on Plant Growth

Figure 24.38

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Biogeochemical Cycling and Energy Flow


Symbiotic nitrogen-fixers and plants
Significant relationship in plant growth and crop production

Important in both terrestrial and aquatic habitats


Organisms collectively called rhizobia Most agriculturally important nitrogen fixers Tend to be associated with leguminous plants Association between plants and rhizobia involves chemical communication between partners
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Leguminous Plants with Root Nodules


Peas Clover Alfalfa Peanuts

Soybeans
Lentils

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24.15 The LegumeRoot Nodule Symbiosis


The mutalistic relationship between leguminous plants and nitrogen-fixing bacteria is one of the most important symbioses known Rhizobia are the most well-known nitrogen-fixing

bacteria engaging in these symbioses

Animation: Root Nodule Bacteria and Symbioses with Legumes

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24.15 The LegumeRoot Nodule Symbiosis

Infection of legume roots by nitrogen-fixing bacteria leads to the formation of root nodules where nitrogen fixation occurs
Leads to significant increases in combined nitrogen in soil

Nodulated legumes grow well in areas where other plants would not

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Soybean Root Nodules

Figure 24.42

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Effect of Nodulation on Plant Growth

Figure 24.43

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24.15 The LegumeRoot Nodule Symbiosis

Rhizobium sp. need O2 to generate energy for N2 fixation, but nitrogenases are inactivated by O2 In the nodule, O2 levels are controlled by the O2-binding protein leghemoglobin

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Major Cross-Inoculation Groups of Leguminous Plants

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Steps in the Formation of a Root Nodule in a Legume

Figure 24.45

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24.15 The LegumeRoot Nodule Symbiosis

The legumebacterial symbiosis is characterized by several metabolic reactions and nutrient exchange

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N2 fixation in legumes
Appropriate bacterial species colonize root cells Substances from root cells cause bacteria to produce nod factors
Induce root hairs to curl

Bacteria invade root hair


Move into root cell by infection thread

Bacterioids fix nitrogen and release ammonia that diffuses into root cells
Ammonia is assimilated into amino acids for use by plant

Bacteria cell for bacterioid inside cell


Division of root cell and bacterioids produce root nodules

Bacteria gain nutrients from plant


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The Root Nodule Bacteriod

Figure 24.49

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Termites w/ N2-fixing Bacteria in Their Gut Aids in Cellulose Decomposotion

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