Presentation on theme: "Chapter 14 - Biogeochemical Cycling"— Presentation transcript:
1 Chapter 14 - Biogeochemical Cycling ObjectivesBe able to give an explanation of why biogeochemical cycles are importantBe able to explain what the GAIA hypothesis isBe able to list three major biogeochemical changes between early and modern earthBe able to define the term reservoir and give an example of a small easily perturbed reservoir and a large stable reservoirBe able to list the three major plant polymersBe familiar with all parts of the carbon, nitrogen, and sulfur cyclesBe able to draw each cycle and describe the microbial activities associated with each leg of the cyclesBe 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 cellMajor elementsCarbonOxygenHydrogenNitrogenSulfurPhosphorusMinor elementsPotassiumCalciumMagnesiumChlorineIronTrace elementsManganeseMolybdenumCobaltCopperZinc50208141320.050.2All trace elements combined comprise 0.3% of dry weight of cellChemical compositionof 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 EarthGasVenusMarsEarthno lifeEarthwith lifeCarbon dioxideNitrogenOxygenArgonMethaneSurface temperature 0C96.5%3.5%Trace70 ppm45995%2.7%0.13%1.6%-5398%1.9%0.1%290 500.03%79%21%1%1.7ppm13
5 The concept of a reservoir Biogeochemical activities are: unidirectional on a geologic time scalecyclical on a contemporary scaleThe concept ofa reservoirTo 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 transformationsdissolutionprecipitationvolatilizationfixationChemical transformationsbiosynthesisbiodegradationoxidoreductive-biotransformationsDriving force for biogeochemical cycles is sunlightThe 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 ecosystemsDescription of ecosystemNet primary productivity(g dry organic matter/m2/yr)TundraDesertTemperate grasslandTemperate forestTropical rainforestCattail SwampFreshwater pondOpen oceanCoastal seawaterUpwelling areaCoral reefCorn fieldRice paddySugarcane field400200Up to 1,5001,200 – 1,600Up to 2,8002,500950 – 1,5001006004,9001,000 – 6,000340 – 1,200up to 9,400
8 The Carbon CycleThe 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 carbonActively cycledAtmosphereCO2OceanBiomassCarbonatesDissolved and particulate organicsLandBiotaHumusFossil fuelEarth’s crust6.7 x 10114.0 x 1093.8 x 10132.1 x 10125.0 x 10111.2 x 10121.0 x 10131.2 x 1017YesNo
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/yrRelease by fossil-fuel combustion x 109Land clearing x 109Forest harvest and decay x 109Forest regrowth x 109Net uptake by oceans x 109Annual flux x 109
11 Natural and anthropogenic CO2 sources and sinks Natural sources of CO2respirationocean degassingterrestrial degassingwildfiresAnthropogenic sources of CO2fossil fuel combustioncement productionland use changesNatural sinks for CO2terrestrialuptake by plantsuptake by soilsoceanicpartitioningbiomass productionAnthropogenic sinks for CO2chemical productionbiological materials
12 CO2 is not the only problem! Global Atmospheric Concentrations of Selected Greenhouse GasesCO2(ppm)CH4N2OSF6(ppt)PFCPreindustrial19922783560.7001.7140.2750.3113270Atmospheric Lifetime(years)50-200121203,20050,000CH4 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. microorganismssimple vs. simple to complex substratesaerobic vs. aerobic/anaerobic redox conditionsWhat are the major carbon inputs into the environment?plant materials (through photosynthesis)cellulose – 60%hemicellulose %lignin %protein/nucleic acids 2-15%fungal cell walls/arthropodschitin
14 CelluloseCellulose degradation begins outside the cell with a set of three exoenzymes:β-1,4- endoglucanseβ-1,4- exoglucanaseβ-1,4- glucosidase
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 generationThe 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 = kJAlthough 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.
21 CH4 + O2 CH3OH HCHO HCOOH CO2 + H2O Methane utilizationIn 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.MMOCH O CH3OH HCHO HCOOH CO2 + H2Omethanol 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.COCO2COCO2In 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.COCO2In 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 CycleN is cycled between: NH4+ (-3 oxidation state) and NO3- (+5 oxidation state)
24 Global Nitrogen Reservoirs Metric tons nitrogenActively cycledAtmosphereN2OceanBiomassSoluble salts (NO3, NO2-, NH4+)Dissolved and particulateorganicsDissolved N2LandBiotaOrganic matterEarth’s crust3.9 x 10155.2 x 1086.9 x 10113.0 x 10112.0 x 10132.5 x 10101.1 x 10117.7 x 1014NoYesSlow
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 fixationland 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 FixationN2 fixing systemNitrogen fixation(kg N/hectare/yr)Rhizobium-legumeAnabaena-AzollaCyanobacteria-mossRhizosphere assoc.Free-living30-402-251-21-2 kg N/hec/yr kg/N/hec/yr
26 Examples of free-living bacteria: Azotobacter- aerobicBeijerinckia- aerobic, likes acidic soilsAzospirillum- facultativeClostridia- anaerobicFree-living bacteria must also protect nitrogenase from O2complex is membrane associatedslime productionhigh levels of respirationconformation change in nitrogenase when O2 is present
27 } Summary for nitrogen fixation: energy intensive end-product is ammoniainhibited by ammoniaoccurs in aerobic and anaerobic environmentsnitrogenase is O2 sensitiveFate of ammonia (NH3) produced during nitrogen fixation}assimilation and mineralizationplant uptakemicrobial uptakeadsorption to colloids (adds to CEC)fixation within clay mineralsincorporation into humusvolatilizationnitrification
28 Ammonia assimilation and ammonification NH3 is assimilated by cells into:proteinscell wall constituentsnucleic acidsRelease of assimilated NH3 is called ammonification. This process can occur intracellularly or extracellularlyproteaseschitinasesnucleasesureases
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 formsAssimilation predominates at C:N ratios > 20Ammonification predominates at C:N ratios < 20Fate of ammonia (NH3) produced during nitrogen fixationplant uptakemicrobial uptakeadsorption to colloids (adds to CEC)fixation within clay mineralsincorporation into humusvolatilizationnitrification
31 Summary for nitrification Nitrification - Chemoautotrophic aerobic processNitrosomonas NitrobacterNH4+NO2-NO3-Nitrosomonas:34 moles NH4+ to fix 1 mole CO2Nitrobacter:100 moles NH4+ to fix 1 mole CO2Nitrification 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 nitrificationNitrification is an chemoautotrophic, aerobic processNitrification 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 mineralsleaching (groundwater contamination)dissimilatory nitrate reductionnitrate ammonificationdenitrificationplant uptakemicrobial uptakebiological uptake (assimilatory nitratereduction)}Assimilatory nitrate reductionmany 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 ammoniumnitrate is more mobile than ammonium leading to leaching lossmicroorganisms 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 producedinhibited by oxygennot inhibited by ammoniumfound in a limited number ofcarbon rich environmentsstagnant watersewage plantssome sedimentsDenitrificationuse of nitrate as a TEA(anaerobic process) – more energy producedmany heterotrophic bacteria are denitrifiersproduces a mix of N2 and N2Oinhibited by oxygennot inhibited by ammonium
34 Denitrification requires a set of 4 enzymes: nitrite reductasenitrous oxidereductasenitrate reductasenitric oxidereductaseHigh [NO3-] favors N2 productionLow [NO3-] favors N2O production
35 Denitrificationreturns fixed N to atmosphere:get formation of NO, N2ONO NO N2O N2NO, N2O deplete the ozone layerReaction of N2O with ozoneO2 + UV light O + OO + 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 reductionNitrate assimilated must be reduced to ammonia for use.Nitrate assimilation is inhibited by ammoniaOxygen does not inhibit this process2. Dissimilatory nitrate reduction to ammonia (DNRA)Anaerobic respiration using nitrate as TEAInhibited by oxygenLimited to a small number of carbon-rich, TEA poor environmentsFermentative bacteria predominate3. Dissimilatory nitrate reduction (denitrification)Anaerobic respiration using nitrate as TEAInhibited by oxygenProduces a mix of N2 and N2OMany heterotrophs denitrify
37 Sulfur Cycle 10th most abundant element average concentration = 520 ppmSulfur Cycleoxidation states range from +6 (sulfate) to -2 (sulfide)
38 Global Sulfur Reservoirs Metric tons sulfurActively cycledAtmosphereSO2/H2SOceanBiomassSoluble inorganic ions(primarily SO42- )LandBiotaOrganic matterEarth’s crust1.4 x 1061.5 x 1081.2 x 10158.5 x 1091.6 x 10101.8 x 1016YesSlowNo
39 adenosine phosphosulfate 1. Assimilatory sulfate reductionThe 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 Ppiadenosine phosphosulfateAPS + ATP PAPS ADP3’ – phosphoadenosine – 5-phosphosulfatePAPS + 2e SO PAPSO H e S2-S serine cysteine + H2O
40 Sulfur Mineralization terrestrial environmentsSH – CH2- CH - COOH + H2OOH – CH2- CH – COOH + H2S--NH2cysteineNH2serinemarine environmentsalgae dimethylsulfoniopropionateDimethylsulfide (DMS)At a C:S ratio < 200:1, sulfur mineralization is favoredAt 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 atmosphereSO42- + water H2SO4 (sulfuric acid)acid rain – pH < 5.6fossil fuel burning releases SO H2SO3 (sulfurous acid)Normal biological production = 1 kg SO4/ha/yrRural production = 10 kg SO4/ha/yrUrban 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 + 1/2O2S0 + H20G = -50.1kcal/molChemolithotrophic bacteriaBeggiatoaThioplacaThiothrixThermothrixThiobacillusWhat 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 aerobesacid intolerant spp.H2S + 1/2O S0 + H2Oacid tolerant spp.S0 + 3/2O H2OH2SO4G = kcal/molAll sulfur oxidizers are aerobic with the exception of:Acidothiobacillus denitrificans - uses nitrate as TEA4NO S SO N2
45 Under anaerobic conditions, H2S is utilized by photosynthetic bacteria: Phototrophic oxidationanaerobic photoautotrophic process:CO2 + H2S C(H2O) + S0Anaerobic photosynthesisCO2 + H2O C(H2O) + O2Aerobic photosynthesisChromatiumEctorhodospirillumChlorobiumGreen and purple sulfur bacteria
46 Summary - Consequences of Sulfur Oxidation Solubilization and leaching of minerals, e.g., (phosphorus) due to decreased pHAcid mine drainageAcid rainDissimilatory sulfate reduction and sulfur respirationHeterotrophic reduction of sulfur1. respiratory S0 reduction2. dissimilatory SO42- reductionanaerobicheterotrophiclimited number of electron donors (substrates)lactic acidpyruvic acidH2small MW alcohols
47 Summary - Sulfate Reduction: Example of a heterotrophic sulfate reducer:Desulfuromonas acetoxidansCH3COOH + 2H2O + 4S CO2 + 2H2SExamples of autotrophic sulfate reducers:DesulfovibrioDesulfotomaculumH2 + SO42-H2S + 2H2O- + 2OH-Summary - Sulfate Reduction:inhibited by oxygencan result in gaseous losses to atmosphereproduces 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 chemoheterotrophsSecond population – anaerobic, chemoheterotrophs ferment cellulose to low molecular weight fatty acids and alcoholsThird population – anaerobic, chemoheterotrophs respire the low molecular weight fatty acids and alcohols using SO4 as the TEA.SO H2S (black) + CO Sulfate reducersFourth population – anaerobic, photoautotrophs photosynthesize using H2S and CO2.CO2 + H2S S C(H2O) Green and purple sulfurbacteria