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Chapter 14 - Biogeochemical Cycling

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1 Chapter 14 - Biogeochemical Cycling
Objectives Be able to give an explanation of why biogeochemical cycles are important Be able to explain what the GAIA hypothesis is Be able to list three major biogeochemical changes between early and modern earth Be able to define the term reservoir and give an example of a small easily perturbed reservoir and a large stable reservoir Be able to list the three major plant polymers Be familiar with all parts of the carbon, nitrogen, and sulfur cycles Be able to draw each cycle and describe the microbial activities associated with each leg of the cycles Be able to give an example of a microbe associated with each leg of the cycle

2 Chemical composition of an E. coli cell Elemental Breakdown
% dry mass of an E. coli cell Major elements Carbon Oxygen Hydrogen Nitrogen Sulfur Phosphorus Minor elements Potassium Calcium Magnesium Chlorine Iron Trace elements Manganese Molybdenum Cobalt Copper Zinc 50 20 8 14 1 3 2 0.05 0.2 All trace elements combined comprise 0.3% of dry weight of cell Chemical composition of an E. coli cell


4 How has earth maintained conditions favorable for life
How has earth maintained conditions favorable for life? Compare atmospheres and temperatures on Earth, Venus, and Mars. Atmosphere and Temperatures found on Venus, Mars, and Earth Gas Venus Mars Earth no life Earth with life Carbon dioxide Nitrogen Oxygen Argon Methane Surface temperature 0C 96.5% 3.5% Trace 70 ppm 459 95% 2.7% 0.13% 1.6% -53 98% 1.9% 0.1% 290  50 0.03% 79% 21% 1% 1.7ppm 13

5 The concept of a reservoir Biogeochemical activities are:
unidirectional on a geologic time scale cyclical on a contemporary scale The concept of a reservoir To understand cycling of elements, the size and cycling activity level of the reservoirs of the element must be defined. atmospheric CO2 is a relatively small reservoir of carbon that is actively cycled. Such small, actively cycled reservoirs are most subject to perturbation.

6 What reactions drive biogeochemical cycling?
Physical transformations dissolution precipitation volatilization fixation Chemical transformations biosynthesis biodegradation oxidoreductive-biotransformations Driving force for biogeochemical cycles is sunlight The ability to photosynthesize allows sunlight energy to be trapped and stored. This is not an efficient process although some environments are more productive than others. Only 10-15% of the energy trapped in each trophic level is passed on to the next level.

7 Net primary productivity (g dry organic matter/m2/yr)
Net primary productivity of some natural and managed ecosystems Description of ecosystem Net primary productivity (g dry organic matter/m2/yr) Tundra Desert Temperate grassland Temperate forest Tropical rainforest Cattail Swamp Freshwater pond Open ocean Coastal seawater Upwelling area Coral reef Corn field Rice paddy Sugarcane field 400 200 Up to 1,500 1,200 – 1,600 Up to 2,800 2,500 950 – 1,500 100 600 4,900 1,000 – 6,000 340 – 1,200 up to 9,400

8 The Carbon Cycle The development of photosynthesis allowed microbes to tap into sunlight energy and provided a mechanism for the first carbon cycle. At the same time the carbon cycle evolved, the nitrogen cycle emerged because nitrogen was limiting for microbial growth. Although N2 was present, it was not in a usable form for microbes.

9 Global Carbon Reservoirs
Metric tons carbon Actively cycled Atmosphere CO2 Ocean Biomass Carbonates Dissolved and particulate organics Land Biota Humus Fossil fuel Earth’s crust 6.7 x 1011 4.0 x 109 3.8 x 1013 2.1 x 1012 5.0 x 1011 1.2 x 1012 1.0 x 1013 1.2 x 1017 Yes No

10 The carbon cycle is a good example of one that is undergoing a major perturbation due to human activity. Human activity has had a large impact on the atmospheric CO2 reservoir beginning with industrialization. As a result, the level of CO2 in the atmosphere has increased 28% in the past 150 years. Carbon source metric tons carbon/yr Release by fossil-fuel combustion x 109 Land clearing x 109 Forest harvest and decay x 109 Forest regrowth x 109 Net uptake by oceans x 109 Annual flux x 109

11 Natural and anthropogenic CO2 sources and sinks
Natural sources of CO2 respiration ocean degassing terrestrial degassing wildfires Anthropogenic sources of CO2 fossil fuel combustion cement production land use changes Natural sinks for CO2 terrestrial uptake by plants uptake by soils oceanic partitioning biomass production Anthropogenic sinks for CO2 chemical production biological materials

12 CO2 is not the only problem!
Global Atmospheric Concentrations of Selected Greenhouse Gases CO2 (ppm) CH4 N2O SF6 (ppt) PFC Preindustrial 1992 278 356 0.700 1.714 0.275 0.311 32 70 Atmospheric Lifetime (years) 50-200 12 120 3,200 50,000 CH4 is 22 times stronger as a greenhouse gas than CO2

13 Carbon cycling on the habitat scale
The term reservoir can be used on a global scale or on a smaller scale such as a habitat. How does carbon cycle within a habitat? Macro vs. microorganisms simple vs. simple to complex substrates aerobic vs. aerobic/anaerobic redox conditions What are the major carbon inputs into the environment? plant materials (through photosynthesis) cellulose – 60% hemicellulose % lignin % protein/nucleic acids 2-15% fungal cell walls/arthropods chitin

14 Cellulose Cellulose degradation begins outside the cell with a set of three exoenzymes: β-1,4- endoglucanse β-1,4- exoglucanase β-1,4- glucosidase

15 Hemicellulose Chitin

16 For the more complex polymers such as lignin a variety of oxidizing enzymes are used. A specific example is the combination of lignin peroxidase and oxidase which produce H2O2 to aid in degradation of lignin. Lignin due to its complexity is generally degraded much more slowly than cellulose or hemicellulose.


18 The most complex organic polymer found in the environment is humus
The most complex organic polymer found in the environment is humus. Formation of humus is a two-stage process that involves the formation of reactive monomers during the degradation of organic matter, followed by the spontaneous polymerization of some of these monomers into the humus molecule.

19 Ultimately, these large polymers are degraded and produce new cell mass, CO2 (which returns to the atmosphere), and contribute to the formation of a stable organic matter fraction, humus. Humus turns over slowly, at a rate of 3 to 5% per year. In addition to mineralization to CO2, a number of small carbon molecules are formed largely as a result of anaerobic activities and in some instances as a result of anthropogenic activity. These include: Methane generation The methanogens are a group of obligately anaerobic Archaea that can reduce CO2 to methane (use CO2 as a terminal electron acceptor) both chemoautotrophically or heterotrophically using small MW molecules such as methanol or acetate. 4H2 + CO CH H2O G0 = kJ Although much methane is microbially produced, there are other sources as well. What happens to the methane? This is of concern because methane is a greenhouse gas 22 times more effective than CO2 in trapping heat.

20 Anthropogenic 190 – 405 54 - 49% of total

Methane utilization In most environments, the methane produced is utilized by methanotrophic microbes as a source of carbon and energy. The first enzyme in the biodegradation pathway of methane is methane monooxygenase (MMO). This enzyme is of interest because it can aid in the degradation of highly chlorinated materials such as TCE (trichloroethylene). The oxidation of TCE does not provide energy for the microbe, it is simply a result of nonspecific catalysis by the MMO enzyme. This is also called cometabolism. MMO CH O CH3OH HCHO HCOOH CO2 + H2O methanol formaldehyde formic acid

22 Carbon monoxide- a highly toxic molecule that is produced largely as a result of fossil fuel burning and photochemical oxidation of methane in the atmosphere. Despite the fact that this is a highly toxic molecule, some microbes can utilize is as a source of energy. CO CO2 CO CO2 In a compost system, the total emissions over a rotting period of twenty days (Table 1), values between 22 and 173 g per kg substrate were observed as total CO2- emissions. For carbon monoxide, the values between 1.0 and 18.6 mg per kg substrate were found. Nutrient Cycling in Agroecosystems 60: 79–82, 2001. CO CO2 In summary, there is huge variety in the types of carbon-containing molecules found in the environment. Similarly microbes have developed an equal variety in their metabolic approaches to deriving carbon and energy from these compounds.

23 The Nitrogen Cycle N is cycled between: NH4+ (-3 oxidation state) and NO3- (+5 oxidation state)

24 Global Nitrogen Reservoirs
Metric tons nitrogen Actively cycled Atmosphere N2 Ocean Biomass Soluble salts (NO3, NO2-, NH4+) Dissolved and particulate organics Dissolved N2 Land Biota Organic matter Earth’s crust 3.9 x 1015 5.2 x 108 6.9 x 1011 3.0 x 1011 2.0 x 1013 2.5 x 1010 1.1 x 1011 7.7 x 1014 No Yes Slow

25 Nitrogen must be fixed before it can be incorporated into biomass
Nitrogen must be fixed before it can be incorporated into biomass. This process is called nitrogen fixation. Biological inputs of nitrogen from N2 fixation land million metric tons/yr (microbial) The enzyme that catalyzes nitrogen fixation is nitrogenase. marine - 40 million metric tons/yr (microbial) fertilizers - 30 million metric tons/yr (anthropogenic) Rates of Nitrogen Fixation N2 fixing system Nitrogen fixation (kg N/hectare/yr) Rhizobium-legume Anabaena-Azolla Cyanobacteria-moss Rhizosphere assoc. Free-living 30-40 2-25 1-2 1-2 kg N/hec/yr kg/N/hec/yr

26 Examples of free-living bacteria:
Azotobacter - aerobic Beijerinckia - aerobic, likes acidic soils Azospirillum - facultative Clostridia - anaerobic Free-living bacteria must also protect nitrogenase from O2 complex is membrane associated slime production high levels of respiration conformation change in nitrogenase when O2 is present

27 } Summary for nitrogen fixation: energy intensive
end-product is ammonia inhibited by ammonia occurs in aerobic and anaerobic environments nitrogenase is O2 sensitive Fate of ammonia (NH3) produced during nitrogen fixation } assimilation and mineralization plant uptake microbial uptake adsorption to colloids (adds to CEC) fixation within clay minerals incorporation into humus volatilization nitrification

28 Ammonia assimilation and ammonification
NH3 is assimilated by cells into: proteins cell wall constituents nucleic acids Release of assimilated NH3 is called ammonification. This process can occur intracellularly or extracellularly proteases chitinases nucleases ureases

29 At high N concentrations
At low N concentrations

30 Summary for ammonia assimilation and ammonification
Assimilation and ammonification cycles ammonia between its organic and inorganic forms Assimilation predominates at C:N ratios > 20 Ammonification predominates at C:N ratios < 20 Fate of ammonia (NH3) produced during nitrogen fixation plant uptake microbial uptake adsorption to colloids (adds to CEC) fixation within clay minerals incorporation into humus volatilization nitrification

31 Summary for nitrification
Nitrification - Chemoautotrophic aerobic process Nitrosomonas Nitrobacter NH4+ NO2- NO3- Nitrosomonas: 34 moles NH4+ to fix 1 mole CO2 Nitrobacter: 100 moles NH4+ to fix 1 mole CO2 Nitrification is important in areas that are high in ammonia (septic tanks, landfills, feedlots, dairy operations, overfertilization of crops). The nitrate formed is highly mobile (does not sorb to soil). As a result, nitrate contamination of groundwater is common. Nitrate contamination can result in methemoglobenemia (blue baby syndrome) and it has been suggested (not proven) that high nitrate consumption may be linked to stomach cancer. Summary for nitrification Nitrification is an chemoautotrophic, aerobic process Nitrification is sensitive to a variety of chemical inhibitors and is inhibited at low pH. (There are a variety of nitrification inhibitors on the market) Nitrification in managed systems can result in nitrate leaching and groundwater contamination

32 } What is the fate of NO3- following nitrification?
accumulation (disturbed vs. managed) fixation within clay minerals leaching (groundwater contamination) dissimilatory nitrate reduction nitrate ammonification denitrification plant uptake microbial uptake biological uptake (assimilatory nitrate reduction) } Assimilatory nitrate reduction many plants prefer nitrate which is reduced in the plant prior to use however, nitrogen in fertilizer is added as ammonia or urea. assimilatory nitrate reduction is inhibited by ammonium nitrate is more mobile than ammonium leading to leaching loss microorganisms prefer ammonia since uptake of nitrate requires a reduction step

33 Dissimilatory nitrate reduction
Dissimilatory reduction of nitrate to ammonia (DNRA) use of nitrate as a TEA (anaerobic process) – less energy produced inhibited by oxygen not inhibited by ammonium found in a limited number of carbon rich environments stagnant water sewage plants some sediments Denitrification use of nitrate as a TEA (anaerobic process) – more energy produced many heterotrophic bacteria are denitrifiers produces a mix of N2 and N2O inhibited by oxygen not inhibited by ammonium

34 Denitrification requires a set of 4 enzymes:
nitrite reductase nitrous oxide reductase nitrate reductase nitric oxide reductase High [NO3-] favors N2 production Low [NO3-] favors N2O production

35 Denitrification returns fixed N to atmosphere: get formation of NO, N2O NO NO N2O N2 NO, N2O deplete the ozone layer Reaction of N2O with ozone O2 + UV light O + O O + O O3 (ozone generation) N2O + UV light N2 + O* N2O + O* NO (nitric oxide) NO + O NO2 + O2 (ozone depletion) NO2 + O* NO + O2

36 Summary for nitrate reduction
1. Assimilatory nitrate reduction Nitrate assimilated must be reduced to ammonia for use. Nitrate assimilation is inhibited by ammonia Oxygen does not inhibit this process 2. Dissimilatory nitrate reduction to ammonia (DNRA) Anaerobic respiration using nitrate as TEA Inhibited by oxygen Limited to a small number of carbon-rich, TEA poor environments Fermentative bacteria predominate 3. Dissimilatory nitrate reduction (denitrification) Anaerobic respiration using nitrate as TEA Inhibited by oxygen Produces a mix of N2 and N2O Many heterotrophs denitrify

37 Sulfur Cycle 10th most abundant element
average concentration = 520 ppm Sulfur Cycle oxidation states range from +6 (sulfate) to -2 (sulfide)

38 Global Sulfur Reservoirs
Metric tons sulfur Actively cycled Atmosphere SO2/H2S Ocean Biomass Soluble inorganic ions (primarily SO42- ) Land Biota Organic matter Earth’s crust 1.4 x 106 1.5 x 108 1.2 x 1015 8.5 x 109 1.6 x 1010 1.8 x 1016 Yes Slow No

39 adenosine phosphosulfate
1. Assimilatory sulfate reduction The form of sulfur utilized by microbes is reduced sulfur. However, sulfide (S2-) is toxic to cells. Therefore sulfur is taken up as sulfate (SO42-), and in a complex series of reactions the sulfate is reduced to sulfide which is then immediately incorporated into the amino acid serine to form cysteine. Sulfur makes up approx. 1% of the dry weight of a cell. It is important for synthesis of proteins (cysteine and methionine) and co-enzymes. Assimilatory sulfate reduction (requires a reduction of SO42- to S2-) SO ATP APS Ppi adenosine phosphosulfate APS + ATP PAPS ADP 3’ – phosphoadenosine – 5-phosphosulfate PAPS + 2e SO PAP SO H e S2- S serine cysteine + H2O

40 Sulfur Mineralization
terrestrial environments SH – CH2 - CH - COOH + H2O OH – CH2 - CH – COOH + H2S - - NH2 cysteine NH2 serine marine environments algae dimethylsulfoniopropionate Dimethylsulfide (DMS) At a C:S ratio < 200:1, sulfur mineralization is favored At a C:S ratio > 400:1, sulfur assimilation is favored

41 Sulfide oxidation (nonbiological)
Both the H2S and the DMS generated during sulfur mineralization are volatile and therefore significant amounts are released to the atmosphere. Here they are photooxidized to sulfate. Sulfide oxidation (nonbiological) H2S and DMS are photooxidized to SO42- in the atmosphere SO42- + water H2SO4 (sulfuric acid) acid rain – pH < 5.6 fossil fuel burning releases SO H2SO3 (sulfurous acid) Normal biological production = 1 kg SO4/ha/yr Rural production = 10 kg SO4/ha/yr Urban production = 100 kg SO4/ha/yr

42 Aerobic sulfur oxidation
H2S not released to the atmosphere acts as substrate for sulfur-oxidizers. Under aerobic conditions: H2S + 1/2O2 S0 + H20 G = -50.1 kcal/mol Chemolithotrophic bacteria Beggiatoa Thioplaca Thiothrix Thermothrix Thiobacillus What unusual community is based on the chemoautrophic sulfur oxiders?

43 What is the conundrum for these organisms?
Most of these microbes deposit S0 as granules inside the cell. They can further oxidize S0 but this is not preferred. However, there are some sulfur oxidizers most notably Thiobacillus thiooxidans that are acidophilic and prefer to oxidize S0 to SO42-.

44 Acidophilic sulfur-oxidizers:
Acidothiobacillus - obligate aerobes acid intolerant spp. H2S + 1/2O S0 + H2O acid tolerant spp. S0 + 3/2O H2O H2SO4 G = kcal/mol All sulfur oxidizers are aerobic with the exception of: Acidothiobacillus denitrificans - uses nitrate as TEA 4NO S SO N2

45 Under anaerobic conditions, H2S is utilized by photosynthetic bacteria:
Phototrophic oxidation anaerobic photoautotrophic process: CO2 + H2S C(H2O) + S0 Anaerobic photosynthesis CO2 + H2O C(H2O) + O2 Aerobic photosynthesis Chromatium Ectorhodospirillum Chlorobium Green and purple sulfur bacteria

46 Summary - Consequences of Sulfur Oxidation
Solubilization and leaching of minerals, e.g., (phosphorus) due to decreased pH Acid mine drainage Acid rain Dissimilatory sulfate reduction and sulfur respiration Heterotrophic reduction of sulfur 1. respiratory S0 reduction 2. dissimilatory SO42- reduction anaerobic heterotrophic limited number of electron donors (substrates) lactic acid pyruvic acid H2 small MW alcohols

47 Summary - Sulfate Reduction:
Example of a heterotrophic sulfate reducer: Desulfuromonas acetoxidans CH3COOH + 2H2O + 4S CO2 + 2H2S Examples of autotrophic sulfate reducers: Desulfovibrio Desulfotomaculum H2 + SO42- H2S + 2H2O- + 2OH- Summary - Sulfate Reduction: inhibited by oxygen can result in gaseous losses to atmosphere produces H2S which can result in anaerobic corrosion of steel and iron set in sulfate-containing soils

48 Winogradsky column – great illustration of sulfur cycling
Set up: Soil is mixed with 1 g CaCO3, 1 g CaSO4, and shredded paper (cellulose). Soil is added to a column and saturated with water. A soil-water slurry is poured on top of this layer to the desired thickness. Column is incubated under lights or in a window.

49 Population development
Initial conditions – aerobic, but O2 is used up quickly – aerobic chemoheterotrophs Second population – anaerobic, chemoheterotrophs ferment cellulose to low molecular weight fatty acids and alcohols Third population – anaerobic, chemoheterotrophs respire the low molecular weight fatty acids and alcohols using SO4 as the TEA. SO H2S (black) + CO Sulfate reducers Fourth population – anaerobic, photoautotrophs photosynthesize using H2S and CO2. CO2 + H2S S C(H2O) Green and purple sulfur bacteria

50 9/12/03 9/19/03 10/2/03 9/5/03 9/26/03

51 10/17/03

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