Nutrient Cycles, Bioremediation, and Symbioses 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

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

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 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 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 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

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

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

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 Figure 24.47 Structural differences

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