1. Nutrient Cycles, Bioremediation, and Symbioses
Chapter 24
Nutrient Cycles, Bioremediation, and Symbioses

2. I. The Carbon and Oxygen Cycles
24.1 The Carbon Cycle
24.2 Syntrophy and Methanogenesis

3. 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

4. The Carbon Cycle
Figure 24.1

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

6. Major Carbon Reservoirs on Earth

7. 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

8. 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

9. Photosynthesis and respiration are reverse reactions Photosynthesis
CO2 + H2O (CH2O) + O2
Respiration
(CH2O) + O CO2 + H2O

10. Redox Cycle for Carbon
Figure 24.2

11. The two major end products of decomposition are CH4 and CO2

12. 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

13. Anoxic Decomposition
Figure 24.3

14. Rxns of Anoxic Conversion of Organic Compounds to CH4

15. Methanogenic symbionts can be found in some protists
Believed that endosymbiotic methanogens benefit protists by consuming H2 generated from glucose fermentation

16. Termites and Their Carbon Metabolism
Hindgut and termite larva
Fluoresces due to F420
Methanogens
Figure 24.4

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

18. Estimates of CH4 Released into the Atmosphere

19. 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

20. Sulfate-reducing bacteria outcompete methanogens and acetogens in marine environments

21. II. Nitrogen, Sulfur, and Iron Cycles
24.3 The Nitrogen Cycle
24.4 The Sulfur Cycle
24.5 The Iron Cycle

22. 24.3 The Nitrogen Cycle Nitrogen A key constituent of cells
Exists in a number of oxidation states

23. Redox Cycle for Nitrogen
Figure 24.5

24. 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

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

26. 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

27. Redox Cycle for Sulfur
Figure 24.6

28. 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

29. Sulfur-oxidizing chemolithotrophs can oxidize sulfide and elemental sulfur at oxic/anoxic interfaces

30. 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

31. 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+)

32. Redox Cycle of Iron
Figure 24.7

33. 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)

34. Oxidation of Ferrous Iron (Fe2+)
Figure 24.8a

35. A Microbial Mat Containing High Levels of Ferrous Iron (Fe2+)
Figure 24.8b

36. 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

37. Pyrite and Coal
Figure 24.9

38. Role of Iron-Oxidizing Bacteria in Oxidation of Pyrite
Figure 24.10a

39. 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

40. Acid Mine Drainage from a Bituminous Coal Region
Figure 24.11

41. Ferroplasma acidarmanus
Streamers of F. acidarmanus, an extremely acidophilic iron-oxidizing archaeon
Figure 24.12

42. Ferroplasma acidarmanus
Scanning electron micrograph of F. acidarmanus
Figure 24.12

43. 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

44. 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

45. Microbial Leaching
The removal of valuable metals, such as copper, from sulfide ores by microbial activities
Particularly useful for copper ores

46. Effect of the Acidithiobacillus ferrooxidans on Covellite
Figure 24.13

47. 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

48. The Microbial Leaching of Low-Grade Copper Ores
A Typical Leaching Dump
Effluent from a Copper Leaching Dump
Figure 24.14a

49. 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

50. Arrangement of a Leaching Pile and Reactions
Figure 24.15

51. Microbes are also used in the leaching of uranium and gold ores
Gold Bioleaching tanks in Ghana

52. 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+

53. Biogeochemical Cycling of Mercury
Figure 24.17

54. 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

55. 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

56. Mechanism of Hg2+ Reduction to Hgo in P. aeruginosa
The mer operon
Transport and Reduction of Hg2+
Figure 24.18a

57. 24.8 Petroleum Biodegradation
Prokaryotes have been used in bioremediation of several major crude oil spills

58. Environmental Consequences of Large Oil Spills
Contaminated Beach in Alaska containing
oil from the Exxon Valdez spill of 1989
Figure 24.19a

59. Environmental Consequences of Large Oil Spills
Oil Spilled into the Mediterranean Sea from a Power Plant
Figure 24.19c

60. Center rectangular plot (arrow) was treated with inorganic nutrients to stimulate bioremediation
Figure 24.19b

61. Taean Oil Spills

62. Taean Oil Spills

63. Taean Oil Spills

64. Taean Oil Spills

65. 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

66. Hydrocarbon-Oxidizing Bacteria in Association with Oil
Figure 24.20

67. 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

68. Some microbes can produce petroleum
Particularly certain green algae
Botryococcus braunii excreting oil droplets

69. 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

70. 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

71. Examples of Xenobiotic Compounds
Figure 24.23

72. Persistence of Herbicides and Insecticides in Soils
Table 24.4

73. Table 24.4

74. Some xenobiotics can be degraded partially or completely if another organic material is present as a primary energy source (cometabolism)

75. 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

76. Biodegradation of the Herbicide 2,4,5-T
Growth of Burkoholderia cepacia on 2,4,5,-trichlorophenoxyacetic acid
Figure 24.24a

77. Pathway of Aerobic Herbicide 2,4,5-T Biodegradation
Figure 24.24b

78. Plastics of various types are xenobiotics that are not readily degraded by microbes

79. Chemistry of Synthetic Polymers
Figure 24.25

80. The recalcitrance of plastics has fueled research efforts into a biodegradable alternative (biopolymers)

81. Bacterial Plastics Poly-β-hydroxyvalerate and poly-β-hydroxybutyrate
Figure 24.26a

82. Bacterial Plastics Shampoo Bottle Made of the PHB/PHV Copolymer
Figure 24.26b

83. IV. Animal–Microbia Symbioses
The Rumen and Ruminant Animals
Hydrothermal Vent Microbial Ecosystems
Squid-Alvibrio Symbiosis

84. 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

85. Diagram of the Rumen and Gastrointestinal System of a Cow
Figure 24.27a

86. Photo of Fistulated Holstein Cow
Figure 24.27b

87. 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

88. Biochemical Reactions in the Rumen
Figure 24.28

89. 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

90. Characteristics of Some Rumen Prokaryotes

91. 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

92. Anaerobic protists and fungi are also abundant in the rumen
- Many perform similar metabolisms as their prokaryotic counterparts

93. 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

94. 24.11 Hydrothermal Vent Microbial Ecosystems
Deep-sea hot springs (hydrothermal vents) support thriving animal communities that are fueled by chemolithotrophic microbes

95. Hydrothermal Vents
Figure 24.29

96. Diverse invertebrate communities develop near hydrothermal vents, including large tube worms, clams, mussels

97. Invertebrates Living Near Deep-Sea Thermal Vents
Tube Worms (Family Pogonophora)
Figure 24.30a

98. Close-up Photograph Showing Worm Plume
Figure 24.30b

99. Mussel Bed in Vicinity of Warm Vent
Figure 24.30c

100. 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)

101. Chemolithotrophic Sulfur-Oxidizing Bacterial Symbionts
SEM of Trophosome Tissue
TEM of Bacteria in Sectioned
Throphosome Tissue
Figure 24.31a

102. 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

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

104. Phylogenetic FISH Staining of Black Smoker Chimneys
Bacteria
Archaea
Figure 24.33

105. 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

106. Squid-Aliivibrio Symbiosis
Hawaiian bobtail squid, Euprymna scolopes
Figure 24.34a

107. Thin-sectioned TEM through the E. scolopes light organ
Figure 24.34b

108. Transmission of bacterial cells is horizontal
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

109. V. Plant–Microbial Symbioses
Lichens and Mycorrhizae
Agrobacterium and Crown Gall Disease
The Legume–Root Nodule Symbiosis

110. 24.13 Lichens and Mycorrhizae
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

111. Lichens
Figure 24.35

112. Lichen Structure
Figure 24.36

113. Mycorrhizae Mutalistic associations of plant roots and fungi
Two classes
Ectomycorrhizae
Endomycorrhizae

114. 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

115. Mycorrhizae: Typical Ectomycorrhizal Root of Pinus Rigida
Figure 24.37a

116. Mycorrhizae
Figure 24.37b

117. Endomycorrhizae
Fungal mycelium becomes deeply embedded within the root tissue
Are more common than ectomycorrhizae
Found in >80% of terrestrial plant species

118. 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

119. Effect of Mycorrhizal Fungi on Plant Growth
Figure 24.38

120. 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

121. Crown Gall Tumors on a Tobacco Plant
Figure 24.39

122. 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

123. To initiate tumor formation, A
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

124. Mechanism of Transfer of T-DNA to the Plant Cell
Phenolic compounds are synthesized by metabolites synthesized by wounded plant tissues and induce the transcription of vir genes.
VirD is an endonuclease.
VirB functions as a conjugation bridge.
VirE is a single-strand binding protein that assists in T-DNA transfer.
Figure 24.41

125. The Ti plasmid has been used in the genetic engineering of plants

126. 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

127. Nodulated legumes grow well in areas where other plants would not
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

128. Soybean Root Nodules
Figure 24.42

129. Effect of Nodulation on Plant Growth
Figure 24.43

130. 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

131. Root Nodule Structure
Figure 24.44

132. Cross-Inoculation Group
Group of related legumes that can be infected by a particular species of rhizobia

133. Major Cross-Inoculation Groups of Leguminous Plants

134. 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

135. Steps in the Formation of a Root Nodule in a Legume
Figure 24.45

136. The Infection Thread and Formation of Root Nodules
Bacteria
Figure 24.46a

137. Figure 24.46b

138. Figure 24.46e

139. 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

140. Nod Factors: General Structure and Structural Differences
Figure 24.47
Structural differences

141. NodD is a positive regulator that is induced by plant flavonoids

142. 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

143. The legume–bacterial symbiosis is characterized by several metabolic reactions and nutrient exchange

144. The Root Nodule Bacteriod
Figure 24.49

145. A few legume species form nodules on their stems

146. Nonlegume nitrogen-fixing symbiosis also occurs
The water fern Azolla contains a species of heterocystous nitrogen-fixing cyanobacteria known as Anabaena

147. 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