Transcript The Carbon Cycle

Chapter 24
Nutrient Cycles, Bioremediation,
and Symbioses
I. The Carbon and Oxygen Cycles
 24.1 The Carbon Cycle
 24.2 Syntrophy and Methanogenesis
24.1 The Carbon Cycle
 Carbon is cycled through all of Earth’s major carbon
reservoirs
 i.e., atmosphere, land, oceans, sediments, rocks, and
biomass
The Carbon Cycle
Figure 24.1
 Reservoir size and turnover time are important
parameters in understanding the cycling of elements
Major Carbon Reservoirs on Earth
 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 anthropogenic
activities
 Microbial decomposition is the largest source of CO2
released to the atmosphere
 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
 Photosynthesis and respiration are reverse reactions
 Photosynthesis
CO2 + H2O
(CH2O) + O2
 Respiration
(CH2O) + O2
CO2 + H2O
Redox Cycle for Carbon
Figure 24.2
 The two major end products of decomposition are CH4
and CO2
24.2 Syntrophy and Methanogenesis
 Methanogenesis is central to carbon cycling in anoxic
environments
 Most methanogens reduce CO2 to CH4 with H2 as an
electron donor; some can reduce other substrates to
CH4 (e.g., acetate)
 Methanogens team up with partners (syntrophs) that
supply them with necessary substrates
Anoxic Decomposition
Figure 24.3
Rxns of Anoxic Conversion of Organic Compounds to CH4
 Methanogenic symbionts can be found in some protists
 Believed that endosymbiotic methanogens benefit
protists by consuming H2 generated from glucose
fermentation
Termites and Their Carbon Metabolism
Hindgut and termite larva
Fluoresces due to F420
Methanogens
Figure 24.4
 On a global basis, biotic processes release more CH4
than abiotic processes
Estimates of CH4 Released into the Atmosphere
 Acetogenesis is a competing H2-consuming process to
methanogenesis in some environments
 e.g., termite hindgut, permafrost soils
- Methanogenesis from H2 (-131 kJ) is energetically more
favorable than acetogenesis (-105 kJ)
- Acetogens position themselves in the termite gut nearer to the
source of H2 produced from cellulose fermentation than
methanogens
- Acetogens can ferment glucose and methoxylated aromatic
compounds from lignin whereas methanogens cannot
 Sulfate-reducing bacteria outcompete methanogens and
acetogens in marine environments
II. Nitrogen, Sulfur, and Iron Cycles
 24.3 The Nitrogen Cycle
 24.4 The Sulfur Cycle
 24.5 The Iron Cycle
24.3 The Nitrogen Cycle
 Nitrogen
 A key constituent of cells
 Exists in a number of oxidation states
Redox Cycle for Nitrogen
Figure 24.5
 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
 Anammox is the anaerobic oxidation of ammonia to N2
gas
 Denitrification and anammox result in losses of nitrogen
from the biosphere
24.4 The Sulfur Cycle
 Sulfur transformations by microbes are complex
 The bulk of sulfur on Earth is in sediments and rocks as
sulfate and sulfide minerals (e.g., gypsum, pyrite)
 The oceans represent the most significant reservoir of
sulfur (as sulfate) in the biosphere
Redox Cycle for Sulfur
Figure 24.6
 Hydrogen sulfide is a major volatile sulfur gas that is
produced by bacteria via sulfate reduction or emitted
from geochemical sources
 Sulfide is toxic to many plants and animals and reacts
with numerous metals
 Sulfur-oxidizing chemolithotrophs can oxidize sulfide
and elemental sulfur at oxic/anoxic interfaces
 Organic sulfur compounds can also be metabolized by
microbes
 The most abundant organic sulfur compound in nature is
dimethyl sulfide (DMS)
 Produced primarily in marine environments as a degradation
product of dimethylsulfoniopropionate (an algal osmolyte)
 DMS can be transformed via a number of microbial
processes
24.5 The Iron Cycle
 Iron is one of the most abundant elements in the
Earth’s crust
 On the Earth’s surface, iron exists naturally in two
oxidation states
 Ferrous (Fe2+)
 Ferric (Fe3+)
Redox Cycle of Iron
Figure 24.7
 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)
Oxidation of Ferrous Iron (Fe2+)
Figure 24.8a
A Microbial Mat Containing High Levels of Ferrous Iron (Fe2+)
Figure 24.8b
 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
Pyrite and Coal
Figure 24.9
Role of Iron-Oxidizing Bacteria in Oxidation of Pyrite
Figure 24.10a
 Acid Mine Drainage
 An environmental problem in coal-mining regions
 Occurs when acidic mine waters are mixed with natural
waters in rivers and lakes
 Bacterial oxidation of sulfide minerals is a major factor in
its formation
Acid Mine Drainage from a Bituminous Coal Region
Figure 24.11
Ferroplasma acidarmanus
Streamers of F. acidarmanus, an extremely acidophilic iron-oxidizing
archaeon
Figure 24.12
Ferroplasma acidarmanus
Scanning electron micrograph of F. acidarmanus
Figure 24.12
III. Microbial Bioremediation
 24.6 Microbial Leaching of Ores
 24.7 Mercury and Heavy Metal Transformations
 24.8 Petroleum Biodegradation
 24.9 Biodegradation of Xenobiotics
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
 Microbial Leaching
 The removal of valuable metals, such as copper, from
sulfide ores by microbial activities
 Particularly useful for copper ores
Effect of the Acidithiobacillus ferrooxidans on Covellite
Figure 24.13
 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
The Microbial Leaching of Low-Grade Copper Ores
A Typical Leaching Dump
Effluent from a Copper Leaching Dump
Figure 24.14a
The Microbial Leaching of Low-Grade Copper Ores
Recovery of Copper as a Metallic Copper
Small Pile of Metallic Copper Removed from
the Flume
Figure 24.14c
Arrangement of a Leaching Pile and Reactions
Figure 24.15
 Microbes are also used in the leaching of uranium and
gold ores
Gold Bioleaching tanks in Ghana
24.7 Mercury and Heavy Metal Transformations
 Mercury is of environmental importance because of its
tendency to concentrate in living tissues and its high toxicity
 The major form of mercury in the atmosphere is elemental
mercury (Hgo) which is volatile and oxidized to mercuric ion
(Hg2+) photochemically
 Most mercury enters aquatic environments as Hg2+
Biogeochemical Cycling of Mercury
Figure 24.17
 Hg2+ readily absorbs to particulate matter where it can
be metabolized by microbes
 Microbes form methylmercury (CH3Hg+), an extremely
soluble and toxic compound
 Several bacteria can also transform toxic mercury to
nontoxic forms
 Bacterial resistance to heavy metal toxicity is often
linked to specific plasmids that encode enzymes
capable of detoxifying or pumping out the metals
- Transform CH3Hg+ to Hg2+ and Hg2+ to Hg0
Mechanism of Hg2+ Reduction to Hgo in P. aeruginosa
The mer operon
Transport and Reduction of Hg2+
Figure 24.18a
24.8 Petroleum Biodegradation
 Prokaryotes have been used in bioremediation of
several major crude oil spills
Environmental Consequences of Large Oil Spills
Contaminated Beach in Alaska containing
oil from the Exxon Valdez spill of 1989
Figure 24.19a
Environmental Consequences of Large Oil Spills
Oil Spilled into the Mediterranean Sea from a Power Plant
Figure 24.19c
Center rectangular plot (arrow) was treated with
inorganic nutrients to stimulate bioremediation
Figure 24.19b
Taean Oil Spills
Taean Oil Spills
Taean Oil Spills
Taean Oil Spills
 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
Hydrocarbon-Oxidizing Bacteria in Association with Oil
Figure 24.20
 Gasoline and crude oil storage tanks are potential
habitats for hydrocarbon-oxidizing microbes
- If sufficient sulfate is present, sulfate-reducing bacteria can
grow and consume hydrocarbons
 Some microbes can produce petroleum
 Particularly certain green algae
Botryococcus braunii excreting oil droplets
24.9 Biodegradation of Xenobiotics
 Xenobiotic Compound
 Synthetic chemicals that are not naturally occurring
 e.g., pesticides, polychlorinated biphenyls, munitions,
dyes, and chlorinated solvents
 Many degrade extremely slowly
24.9 Biodegradation of Xenobiotics
 Pesticides
 Common components of toxic wastes
 Include herbicides, insecticides, and fungicides
 Represent a wide variety of chemistries
 Some of which can be used as carbon sources and
electron donors by microbes
Examples of Xenobiotic Compounds
Figure 24.23
Persistence of Herbicides and Insecticides in Soils
Table 24.4
Table 24.4
 Some xenobiotics can be degraded partially or
completely if another organic material is present as a
primary energy source (cometabolism)
 Chlorinated xenobiotics can be degraded anaerobically
(reductive dechlorination) or aerobically (aerobic
dechlorination)
 Reductive dechlorination is usually a more important
process as anoxic conditions develop quickly in polluted
environments
Biodegradation of the Herbicide 2,4,5-T
Growth of Burkoholderia cepacia on 2,4,5,-trichlorophenoxyacetic acid
Figure 24.24a
Pathway of Aerobic Herbicide 2,4,5-T Biodegradation
Figure 24.24b
 Plastics of various types are xenobiotics that are not
readily degraded by microbes
Chemistry of Synthetic Polymers
Figure 24.25
 The recalcitrance of plastics has fueled research efforts
into a biodegradable alternative (biopolymers)
Bacterial Plastics
Poly-β-hydroxyvalerate and poly-β-hydroxybutyrate
Figure 24.26a
Bacterial Plastics
Shampoo Bottle Made of
the PHB/PHV Copolymer
Figure 24.26b
IV. Animal–Microbia Symbioses
 24.10 The Rumen and Ruminant Animals
 24.11 Hydrothermal Vent Microbial Ecosystems
 24.12 Squid-Alvibrio Symbiosis
24.10 The Rumen and Ruminant Animals
 Microbes form intimate symbiotic relationships with
higher organisms
 Ruminants
 Herbivorous mammals (e.g., cows, sheep, goats)
 Possess a special digestive organ (the rumen) within
which cellulose and other plant polysaccharides are
digested with the help of microbes
Diagram of the Rumen and Gastrointestinal System of a Cow
Figure 24.27a
Photo of Fistulated Holstein Cow
Figure 24.27b
 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
Biochemical Reactions in the Rumen
Figure 24.28
 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
Characteristics of Some Rumen Prokaryotes
 Abrupt changes in an animal’s diet can result in
changes in the rumen flora
 Rumen acidification (acidosis) is one consequence of
such a change
 Anaerobic protists and fungi are also abundant in the
rumen
- Many perform similar metabolisms as their prokaryotic
counterparts
 Cecal Animals
 Herbivorous animals that possess a cecum
 A cecum is
 An organ for celluloytic digestion
 Located posterior to the small intestine and anterior
to the large intestine
24.11 Hydrothermal Vent Microbial Ecosystems
 Deep-sea hot springs (hydrothermal vents) support
thriving animal communities that are fueled by
chemolithotrophic microbes
Hydrothermal Vents
Figure 24.29
 Diverse invertebrate communities develop near
hydrothermal vents, including large tube worms, clams,
mussels
Invertebrates Living Near Deep-Sea Thermal Vents
Tube Worms (Family Pogonophora)
Figure 24.30a
Close-up Photograph Showing Worm Plume
Figure 24.30b
Mussel Bed in Vicinity of Warm Vent
Figure 24.30c
 Chemolithotrophic prokaryotes that utilize reduced inorganic
materials emitting from the vents 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)
Chemolithotrophic Sulfur-Oxidizing Bacterial Symbionts
SEM of Trophosome Tissue
TEM of Bacteria in Sectioned
Throphosome Tissue
Figure 24.31a
 Black Smokers
 Thermal vents that emit mineral-rich hot water (up to
350°C) forming a dark cloud of precipitated material on
mixing with cold seawater
 Thermophilic and hyperthermophilic microbes live in
gradients that form as hot water mixes with cold
seawater
Phylogenetic FISH Staining of Black Smoker Chimneys
Bacteria
Archaea
Figure 24.33
24.12 Squid-Aliivibrio Symbiosis
 A mutualistic symbiosis between the marine bacterium
Aliivibrio fischeri and the Hawaiian bobtail squid Euprymna
scolopes is a model for how animal–bacterial symbioses are
established
 The squid harbors large populations of the bioluminescent A.
fischeri in a specialized structure (light organ)
 Bacteria emit light that resembles moonlight penetrating
marine waters, which camouflages the squid from predators
Squid-Aliivibrio Symbiosis
Hawaiian bobtail squid, Euprymna scolopes
Figure 24.34a
Thin-sectioned TEM through the E. scolopes light organ
Figure 24.34b
 The symbiotic relationship is highly specific and benefits
both partners
 Transmission of bacterial cells is horizontal
 The light organ is colonized by A. fischeri from surrounding
seawater shortly after juvenile squid hatch
 Bioluminscence is controlled quorum sensing
 A. fischeri is supplied with nutrients by the squid
V. Plant–Microbial Symbioses
 21.13 Lichens and Mycorrhizae
 24.14 Agrobacterium and Crown Gall Disease
 24.15 The Legume–Root Nodule Symbiosis
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
Lichens
Figure 24.35
Lichen Structure
Figure 24.36
 Mycorrhizae
 Mutalistic associations of plant roots and fungi
 Two classes
 Ectomycorrhizae
 Endomycorrhizae
 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
Mycorrhizae: Typical Ectomycorrhizal Root of Pinus Rigida
Figure 24.37a
Mycorrhizae
Figure 24.37b
 Endomycorrhizae
 Fungal mycelium becomes deeply embedded within the
root tissue
 Are more common than ectomycorrhizae
 Found in >80% of terrestrial plant species
 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
Effect of Mycorrhizal Fungi on Plant Growth
Figure 24.38
24.14 Agrobacterium and Crown Gall Disease
 Agrobacterium tumefaciens forms a parasitic symbiosis
with plants causing crown gall disease
 Crown galls are plant tumors induced by A. tumefaciens
cells harboring a large plasmid, the Ti (tumor induction)
plasmid
Crown Gall Tumors on a Tobacco Plant
Figure 24.39
Structure of the Ti Plasmid of Agrobacterium
vir genes: Encode proteins that are essential for T-DNA transfer.
ops genes: Encode proteins that produce opines in plant cells transformed by
T-DNA. Opines are used as a source of carbon, nitrogen, and phosphate
for the parasitic agrobacteria.
Transmissability genes: Involved in the transfer of Ti-plasmid by conjugation from
agrobacteria to another.
Figure 24.40
 To initiate tumor formation, A. tumefaciens cells must
attach to the wound site on the plant
 Attached cells synthesize cellulose microfibrils and
transfer a portion of the Ti plasmid to plant cells
 DNA transfer is mediated by Vir proteins
Mechanism of Transfer of T-DNA to the Plant Cell
(a) Phenolic compounds are synthesized by
metabolites synthesized by wounded plant
tissues and induce the transcription of vir
genes.
(b) VirD is an endonuclease.
(c) VirB functions as a conjugation bridge.
VirE is a single-strand binding protein that
assists in T-DNA transfer.
Figure 24.41
 The Ti plasmid has been used in the genetic
engineering of plants
24.15 The Legume–Root Nodule Symbiosis
 The mutalistic relationship between leguminous plants
and nitrogen-fixing bacteria is one of the most important
symbioses known
 Examples of legumes include soybeans, clover, alfalfa,
beans, and peas
 Rhizobia are the most well-known nitrogen-fixing
bacteria engaging in these symbioses
Animation: Root Nodule Bacteria and Symbioses with Legumes
 Infection of legume roots by nitrogen-fixing bacteria
leads to the formation of root nodules that fix nitrogen
 Leads to significant increases in combined nitrogen in soil
 Nodulated legumes grow well in areas where other
plants would not
Soybean Root Nodules
Figure 24.42
Effect of Nodulation on Plant Growth
Figure 24.43
 Nitrogen-fixing bacteria 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
Root Nodule Structure
Figure 24.44
 Cross-Inoculation Group
 Group of related legumes that can be infected by a
particular species of rhizobia
Major Cross-Inoculation Groups of Leguminous Plants
 The critical steps in root nodule formation are as follows:
 Step 1: Recognition and attachment of bacterium to root hairs
 Step 2: Excretion of nod factors by the bacterium
 Step 3: Bacterial invasion of the root hair
 Step 4: Travel to the main root via the infection thread
 Step 5: Formation of bacteroid state within plant cells
 Step 6: Continued plant and bacterial division, forming the
mature root nodule
Steps in the Formation of a Root Nodule in a Legume
Figure 24.45
The Infection Thread and Formation of Root Nodules
Bacteria
Figure 24.46a
Figure 24.46b
Figure 24.46e
 Bacterial nod genes direct the steps in nodulation
 nodABC gene encode proteins that produce
oligosaccharides called nod factors
 Nod factors
 Induce root hair curling
 Trigger plant cell division
Nod Factors: General Structure and Structural Differences
General structure
Structural differences
Figure 24.47
 NodD is a positive regulator that is induced by plant
flavonoids
Plant Flavonoids and Nodulation
A flavonoid molecule that is an
inducer of nod gene expression
A flavonoid molecule that is an
inhibitor of nod gene expression
Figure 24.48b
 The legume–bacterial symbiosis is characterized by
several metabolic reactions and nutrient exchange
The Root Nodule Bacteriod
Figure 24.49
 A few legume species form nodules on their stems
 Nonlegume nitrogen-fixing symbiosis also occurs
 The water fern Azolla contains a species of
heterocystous nitrogen-fixing cyanobacteria known as
Anabaena
 The alder tree (genus Alnus) has nitrogen-fixing root
nodules that harbor the nitrogen-fixing bacterium
Frankia
Root nodules of the common
alder Alnus Glutinosa
Frankia culture purified from
nodules of Comptonia peregri