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Chapter 14 - Biogeochemical Cycling Objectives Be able to give an explanation of why biogeochemical cycles are important Be able to explain what the GAIA.

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Presentation on theme: "Chapter 14 - Biogeochemical Cycling Objectives Be able to give an explanation of why biogeochemical cycles are important Be able to explain what the GAIA."— Presentation transcript:

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 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 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? Compare atmospheres and temperatures on Earth, Venus, and Mars. 0.03% 79% 21% 1% 1.7ppm 13 98% 1.9% 0 0.1% % 2.7% 0.13% 1.6% % 3.5% Trace 70 ppm Carbon dioxide Nitrogen Oxygen Argon Methane Surface temperature 0 C Earth with life Earth no lifeMarsVenusGas Atmosphere and Temperatures found on Venus, Mars, and Earth

5 Biogeochemical activities are: unidirectional on a geologic time scale cyclical on a contemporary scale To understand cycling of elements, the size and cycling activity level of the reservoirs of the element must be defined. atmospheric CO 2 is a relatively small reservoir of carbon that is actively cycled. Such small, actively cycled reservoirs are most subject to perturbation. The concept of a reservoir

6 Physical transformations dissolution precipitation volatilization fixation Chemical transformations biosynthesis biodegradation oxidoreductive-biotransformations What reactions drive biogeochemical cycling? 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 Description of ecosystem Net primary productivity (g dry organic matter/m 2 /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 Up to 1,500 1,200 – 1,600 Up to 2,800 2, – 1, ,900 1,000 – 6, – 1,200 up to 9,400 Net primary productivity of some natural and managed ecosystems

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 N 2 was present, it was not in a usable form for microbes.

9 Carbon ReservoirMetric tons carbon Actively cycled Atmosphere CO 2 Ocean Biomass Carbonates Dissolved and particulate organics Land Biota Humus Fossil fuel Earths crust 6.7 x x x x x x x x Yes No Yes No Global Carbon Reservoirs

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 CO 2 reservoir beginning with industrialization. As a result, the level of CO 2 in the atmosphere has increased 28% in the past 150 years. Carbon source metric tons carbon/yr Release by fossil-fuel combustion 7 x 10 9 Land clearing 3 x 10 9 Forest harvest and decay 6 x 10 9 Forest regrowth -4 x 10 9 Net uptake by oceans -3 x 10 9 Annual flux 9 x 10 9

11 Natural sources of CO 2 respiration ocean degassing terrestrial degassing wildfires Anthropogenic sources of CO 2 fossil fuel combustion cement production land use changes Natural sinks for CO 2 terrestrial uptake by plants uptake by soils oceanic partitioning biomass production Anthropogenic sinks for CO 2 chemical production biological materials Natural and anthropogenic CO 2 sources and sinks

12 CO 2 (ppm) CH 4 (ppm) N 2 O (ppm) SF 6 (ppt) PFC (ppt) Preindustrial Atmospheric Lifetime (years) ,20050,000 Global Atmospheric Concentrations of Selected Greenhouse Gases CO 2 is not the only problem! CH 4 is 22 times stronger as a greenhouse gas than CO 2

13 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 15 – 60% hemicellulose10-30% lignin5- 30% protein/nucleic acids2-15% fungal cell walls/arthropods chitin Carbon cycling on the habitat scale

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 H 2 O 2 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. 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, CO 2 (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 CO 2, 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 CO 2 to methane (use CO 2 as a terminal electron acceptor) both chemoautotrophically or heterotrophically using small MW molecules such as methanol or acetate. 4H 2 + CO 2 CH 4 + 2H 2 O G 0 = 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 CO 2 in trapping heat.

20 Anthropogenic 190 – % of total

21 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. CH 4 + O 2 CH 3 OH HCHO HCOOH CO 2 + H 2 O methanol formaldehyde formic acid MMO

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. 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. CO CO 2 CO CO 2 CO CO 2

23 The Nitrogen Cycle N is cycled between: NH 4 + (-3 oxidation state) and NO 3 - (+5 oxidation state)

24 Nitrogen ReservoirMetric tons nitrogenActively cycled Atmosphere N 2 Ocean Biomass Soluble salts (NO 3, NO 2 -, NH 4 + ) Dissolved and particulate organics Dissolved N 2 Land Biota Organic matter Earths crust 3.9 x x x x x x x x No Yes No Yes Slow No Global Nitrogen Reservoirs

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

26 Free-living bacteria must also protect nitrogenase from O 2 complex is membrane associated slime production high levels of respiration conformation change in nitrogenase when O 2 is present Azotobacter - aerobic Beijerinckia - aerobic, likes acidic soils Azospirillum - facultative Clostridia - anaerobic Examples of free-living bacteria:

27 Summary for nitrogen fixation: energy intensive inhibited by ammonia occurs in aerobic and anaerobic environments end-product is ammonia nitrogenase is O 2 sensitive Fate of ammonia (NH 3 ) produced during nitrogen fixation plant uptake microbial uptake adsorption to colloids (adds to CEC) fixation within clay minerals incorporation into humus volatilization nitrification } assimilation and mineralization

28 NH 3 is assimilated by cells into: proteins cell wall constituents nucleic acids Ammonia assimilation and ammonification Release of assimilated NH 3 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 Ammonification predominates at C:N ratios < 20 Assimilation predominates at C:N ratios > 20 Fate of ammonia (NH 3 ) produced during nitrogen fixation plant uptake microbial uptake adsorption to colloids (adds to CEC) fixation within clay minerals incorporation into humus volatilization nitrification

31 Nitrification - Chemoautotrophic aerobic process Nitrosomonas Nitrobacter NH 4 + NO 2 - NO 3 - Nitrosomonas: 34 moles NH 4 + to fix 1 mole CO 2 Nitrobacter: 100 moles NH 4 + to fix 1 mole CO 2 Summary for nitrification Nitrification is an chemoautotrophic, aerobic process Nitrification in managed systems can result in nitrate leaching and groundwater contamination 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 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.

32 What is the fate of NO 3 - 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 N 2 and N 2 O inhibited by oxygen not inhibited by ammonium

34 Denitrification requires a set of 4 enzymes: nitrate reductase nitrite reductase High [NO 3 - ] favors N 2 production Low [NO 3 - ] favors N 2 O production nitric oxide reductase nitrous oxide reductase

35 Denitrification NO, N 2 O deplete the ozone layer Reaction of N 2 O with ozone O 2 + UV light O + O O + O 2 O 3 (ozone generation) N 2 O + UV light N 2 + O * N 2 O + O * 2NO (nitric oxide) NO + O 3 NO 2 + O 2 (ozone depletion) NO 2 + O * NO + O 2 returns fixed N to atmosphere: get formation of NO, N 2 O NO 3 NO N 2 O N 2

36 Summary for nitrate reduction Nitrate assimilated must be reduced to ammonia for use. Oxygen does not inhibit this process Nitrate assimilation is inhibited by ammonia 1. Assimilatory nitrate reduction 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 N 2 and N 2 O Many heterotrophs denitrify

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

38 Sulfur ReservoirMetric tons sulfurActively cycled Atmosphere SO 2 /H 2 S Ocean Biomass Soluble inorganic ions (primarily SO 4 2- ) Land Biota Organic matter Earths crust 1.4 x x x x x x Yes Slow Yes No Global Sulfur Reservoirs

39 1. Assimilatory sulfate reduction The form of sulfur utilized by microbes is reduced sulfur. However, sulfide (S 2- ) is toxic to cells. Therefore sulfur is taken up as sulfate (SO 4 2- ), 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 SO 4 2- to S 2- ) SO ATP APS + Ppi adenosine phosphosulfate APS + ATP PAPS + ADP 3 – phosphoadenosine – 5-phosphosulfate PAPS + 2e - SO PAP SO H + + 6e - S 2- S 2- + serine cysteine + H 2 O

40 Sulfur Mineralization SH – CH 2 - CH - COOH + H 2 O NH 2 - OH – CH 2 - CH – COOH + H 2 S NH 2 - terrestrial environments cysteineserine marine environments algae dimethylsulfoniopropionateDimethylsulfide (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) H 2 S and DMS are photooxidized to SO 4 2- in the atmosphere Normal biological production = 1 kg SO 4 /ha/yr Rural production = 10 kg SO 4 /ha/yr Urban production = 100 kg SO 4 /ha/yr acid rain – pH < 5.6 Both the H 2 S and the DMS generated during sulfur mineralization are volatile and therefore significant amounts are released to the atmosphere. Here they are photooxidized to sulfate. SO water H 2 SO 4 (sulfuric acid) fossil fuel burning releases SO 2 H 2 SO 3 (sulfurous acid)

42 Aerobic sulfur oxidation H 2 S + 1/2O 2 S 0 + H 2 0G = kcal/mol Chemolithotrophic bacteria Beggiatoa Thioplaca Thiothrix Thermothrix Thiobacillus H 2 S not released to the atmosphere acts as substrate for sulfur-oxidizers. Under aerobic conditions: What unusual community is based on the chemoautrophic sulfur oxiders?

43 What is the conundrum for these organisms? Most of these microbes deposit S 0 as granules inside the cell. They can further oxidize S 0 but this is not preferred. However, there are some sulfur oxidizers most notably Thiobacillus thiooxidans that are acidophilic and prefer to oxidize S 0 to SO 4 2-.

44 Acidothiobacillus - obligate aerobes acid intolerant spp. Acidophilic sulfur-oxidizers: H 2 S + 1/2O 2 S 0 + H 2 O acid tolerant spp. S 0 + 3/2O 2 + H 2 O H 2 SO 4 G = kcal/mol All sulfur oxidizers are aerobic with the exception of: Acidothiobacillus denitrificans - uses nitrate as TEA 4NO S 0 3SO N 2

45 Phototrophic oxidation anaerobic photoautotrophic process: Chromatium Ectorhodospirillum Chlorobium Under anaerobic conditions, H 2 S is utilized by photosynthetic bacteria: CO 2 + H 2 S C(H 2 O) + S 0 Anaerobic photosynthesis CO 2 + H 2 O C(H 2 O) + O 2 Aerobic photosynthesis 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 S 0 reduction 2. dissimilatory SO 4 2- reduction anaerobic heterotrophic limited number of electron donors (substrates) lactic acid pyruvic acid H 2 small MW alcohols

47 Desulfuromonas acetoxidansCH 3 COOH + 2H 2 O + 4S 0 2CO 2 + 2H 2 S Desulfovibrio Desulfotomaculum H 2 + SO 4 2- H 2 S + 2H 2 O - + 2OH - Example of a heterotrophic sulfate reducer: Examples of autotrophic sulfate reducers: Summary - Sulfate Reduction: inhibited by oxygen can result in gaseous losses to atmosphere produces H 2 S 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 CaCO 3, 1 g CaSO 4, 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 Initial conditions – aerobic, but O 2 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 SO 4 as the TEA. SO 4 H 2 S (black) + CO 2 Sulfate reducers Fourth population – anaerobic, photoautotrophs photosynthesize using H 2 S and CO 2. CO 2 + H 2 S S 0 + C(H 2 O) Green and purple sulfur bacteria Population development

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

51 10/17/03

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