geobiology- 第七讲 chapter 3

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Geobiology-Geobiology- 第七讲第七讲

chapter 3chapter 3

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The universe is either matter or energy.

Earth system comprises the solid earth, atmosphere, hydrosphere and biosphere. The solid earth again shows spherical structures, consisting of core, mantle and crust. The upper mantle and crust form Earth’s outer rigid part, called lithosphere.

Earth’s matter in gaseous, liquid, or solid states.

Energy is what makes matter move.

Matter and energy cannot be created or destroyed. However, matter and energy can be transformed into different kinds of matter and energy. Any matter in our planet simply represents a temporary storage of matter in one place and in one form

Physical processes (such as evaporation), chemical processes (such as oxidation) or biological processes (such as photosynthesis) will cause the matter to be transported or change its chemical state in the Earth’s dynamic system of cycles.

Life on Earth is inextricably linked to the inanimate world through a variety of interacting cycles and feedback loops.

3.1 Introduction3.1 Introduction

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The first law of thermodynamicsThe first law of thermodynamics says that energy cannot says that energy cannot be created or destroyed, but can be transformed. be created or destroyed, but can be transformed.

The second law of thermodynamicsThe second law of thermodynamics says that when says that when energy is transformed from one kind to another, it is energy is transformed from one kind to another, it is degraded, meaning that the energy becomes less degraded, meaning that the energy becomes less capable of doing work. capable of doing work. . .

EntropyEntropy refers to the amount of low-quality energy in a refers to the amount of low-quality energy in a system. system.

If entropy is very high, matter will tend to If entropy is very high, matter will tend to disorganizedisorganize to simpler states. to simpler states.

The second law of thermodynamics is sometimes The second law of thermodynamics is sometimes called thecalled the law of entropy because all energy law of entropy because all energy transformations will increase the entropy of a transformations will increase the entropy of a system unless new high-quality energy, such as solar system unless new high-quality energy, such as solar energy, enters the system to replenish it. energy, enters the system to replenish it.

3.2 Energy flow- 3.2 Energy flow- basic lawsbasic laws

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• Eenergy loss is inevitable.

• New energy

• Sun, vast majority

• Moon

• Geothermal energy

3.2.2 Earth’s energy budget3.2.2 Earth’s energy budget

51%

19%

19% energy powers the hydrologic cycle by evaporation, generates wind, powers photosynthesis (0.06%), and in general drives many of the cycles within and between the spheres of the Earth

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3.3.1 A system approach3.3.2 Three key traits of the environmental system

3.3.2.1 Openness

3.3.2.2 Integration

3.3.2.3 Complexity

3.3 The environment as a system: an overview3.3 The environment as a system: an overview

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These cycles of chemical elements between living and nonliving matter (reservoirs) through complicated pathways are called biogeochemical cycles. The four earth’s surface spheres involved in these cycles are the atmosphere, the biosphere (the sum of all living things as well as formerly living things that have not yet decomposed), the hydrosphere (the entirety of Earth's water except for vapor in the atmosphere), and the lithosphere.

3.4 Biogeochemical cycles3.4 Biogeochemical cycles

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Elements are used for three general purposes:

Biomass production. The element is incorporated into cell

material, e.g. C, H, O, N, P. S, and many trace elements.

Energy source. Reduced carbon compounds such as sugars,

lipids, and amino acids are used as energy sources by

chemoorganotrophs. Chemolithotrophs can use reduced

inorganic molecules such as hydrogen sulfide (H2S),

ammonia (NH3), and hydrogen gas (H2).

Terminal electron acceptor. Electrons from the energy

source are transferred to an oxidized form of the element

during respiration. In aerobic conditions, O2 is used as a

terminal electron acceptor. In anaerobic conditions, some

prokaryotes can use nitrate (NO3-), nitrite (NO2

-), sulfate

(SO42-), and carbon dioxide (CO2) as terminal electron

acceptors.

3.4 Biogeochemical cycles3.4 Biogeochemical cycles

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3.4.2 Element abundance3.4.2 Element abundance

Table 3.1. Atomic composition by weight of three representative organisms

Element Human (%) Alfalfa (%) Bacterium (%)

OxygenCarbonHydrogenNitrogenPhosphorusSulfurtatal

62.81 19.37 9.31 5.14 0.63 0.64 97.90

77.90 11.34 8.72 0.83 0.71 0.10 99.60

73.68 12.14 9.94 3.04 0.60 0.32 99.72

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3.4.2 Element abundance3.4.2 Element abundance

Table 3.2 The relative abundance by weight of some chemical elements in the earth’s crust

Element (chemical symbol) Relative Abundance (%)

Oxygen (O) 42.6

Silicon (Si) 27.7

Aluminum (Al) 8.1

Iron (Fe) 5.0

Calcium (Ca) 3.6

Sodium (Na) 2.8

Potassium (K) 2.6

Magnesium (Mg) 2.1

Phosphorus (P) 0.07

Carbon (C) 0.03

Nitrogen (N) Trace

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3.4.3 Carbon cycle3.4.3 Carbon cycle

• The carbon cycle is a typical biogeochemical cycle, involving the transfer of carbon between reservoirs.

withdrawal from and addition to the atmosphere

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3.4.3.1 Carbon reservoirs3.4.3.1 Carbon reservoirs

• surficial reservoirs ： terrestrial biomass, carbon in soils, carbon dioxide in the atmosphere, dissolved inorganic carbon (DIC) in ocean waters, carbon in marine biomass, and carbon in the form of methane.

• geological reservoirs: stored in lithosphere, which dominate in terms of mass of carbon, and comprise carbon stored in both inorganic form (as carbonate) and organic form, principally kerogen in detrital sedimentary rocks, but also fossil fuels (petroleum, gas and coal) .

Table 3.3 Masses of carbon in different reservoirsReservoir Mass (Pg C = 1015g C)

Environmental reservoirs

Atmosphere 780

Oceans Inorganic 37400

Organic 1000

Terrestrial biomass 500

Soils 2000

Methane hydrates 10000

Geological reservoirs

Oxidized Carbonates >60×106

Reduced Kerogen 15×106

Fossil fuels 4130

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3.4.3.2 Withdrawal of carbon3.4.3.2 Withdrawal of carbon

• Geological processes

• Weathering of exposed rocks

• Silicate rocks: CaSiO3 + 2CO2 + 2H2O → Ca2+ + 2HCO3- + 2H+ + SiO3

2- (transport)

• Carbonate rocks: CaCO3 + CO2 + H2O → Ca2+ + 2HCO3- (transport)

• Precipitation of CaCO3 and formation of limestones and marls

• Ca2+ + 2HCO3- → CaCO3 + CO2 + H2O (sedimentation);

• Ca2+ + 2HCO3- + 2H+ + SiO3

2- → CaCO3 + CO2 + SiO2.H2O + H2O (sedimentation).

• Biological processes: photosynthesis (DIC and CO2)

• Net increase of living biomass in the aquatic and terrestrial environments

• Burial of organic carbon (including particulates) in sediments.

• Accumulation of organic carbon in the terrestrial soil reservoirs.

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3.4.3.33.4.3.3 Addition of carbonAddition of carbon

• Geological processes

• Volcanisms release CO2 gases to atmosphere

• Tectonic processes uplift the rocks and fossil carbon to surface. The burning of the fossil carbon releases CO2 back to atmosphere.

• Destabilization of methane hydrate (tectonics or climate change), oxidation releases CO2 to air

• Biological processes

• Respiration

• Methane is produced during the anaerobic breakdown of organic matter.

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3.4.3.43.4.3.4 Isotopic distributionsIsotopic distributions

• Exchange of CO2 between oceans and atmosphere controls the distribution of carbon isotopes between these reservoirs. Because the ocean DIC reservoir is the larger, it controls the isotopic composition of atmospheric CO2, an average fractionation around 8‰.

• bicarbonate in ocean surface waters, at around +1.5‰ V-PDB• bulk ocean DIC (dissolved CO2 plus bicarbonate), δ13C close to 0‰ • atmospheric CO2, around -7.8‰ V-PDB

• Photosynthesis with an average fractionation around 20‰.

• In terrestrial ecosystems, C3 photosynthetic carbon has δ13C around -27‰, C4 photosynthetic pathway has a smaller associated carbon isotopic fractionation

• Marine photosynthetic carbon has δ13C around -22‰.

• Biogenic methane δ13C is in a range of -110 to -60‰ in marine environments (CO2 reduction) and -65 to -50‰ in freshwater environments (acetoclasis).

• Precipitation of CaCO3 from marine DIC involves very little fractionation of carbon isotopes, thus limestones inherit the isotopic composition of contemporaneous marine DIC (δ13C of 0 ± 3‰).

• Bulk Earth carbon has δ13C of around -7 to -5‰. Carbonate (c. 0‰) and buried organic carbon (c. -21‰) imply that around twice as much carbon must be stored in carbonate form than is stored as organic carbon.

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CC33 and C and C44

•C3 植物是指在光合作用的暗反应过程中，一个 CO2 被一个五碳化合物 (1 ， 5- 二磷酸核酮糖，简称 RuBP) 固定后形成两个三碳化合物 (3- 碳酸甘油酸 ) ，即 CO2

被固定后最先形成的化合物中含有三个碳原子，所以称为 C3 植物，如米和麦。

•C4 植物是指在光合作用的暗反应过程中，一个 CO2 被—个含有三个碳原子的化合物 ( 磷酸烯醇式丙酮酸 ) 固定后首先形成含四个碳原子的有机酸（草酰乙酸），所以称为 C4 植物。 C4 植物具有两条固定 CO2 的途径，即 C3 途径和 C4 途径。 C4 植物主要是那些生活在干旱热带地区的植物 , 如玉米、茼蒿、白苋菜、小白菜、空心菜。

•C4 植物通常分布在热带地区，光合作用效率较 C3 植物高，对 CO2 的利用率也较C3 植物高 .植物分类场所

暗反应

途径反应过程

C3 叶肉细胞叶绿体 C3

C5+CO2→2C3+ATP+[H]→C5+ （ CH2

O ） +H2O

C4

叶肉细胞叶绿体 C4 C3 （ PEP ） +CO2→C4

维管束鞘细胞叶绿体 C3

C5+CO2→2C3+ATP+[H]→C5+ （ CH2

O ） +H2O

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Geobiology-Geobiology- 第八讲第八讲

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3.4.4 Oxygen cycle-3.4.4 Oxygen cycle-distributiondistribution

• Atmosphere.

• The partial pressure of oxygen in atmosphere is ~0.21 bar, corresponding to a total mass of ~34×1018 mol O2.

• There is a nearly uniform mixture of the main atmospheric gases (N2, O2, Ar) from the Earth's surface up to ~80 km altitude

• Because atmospheric pressure (and thus gas molecule density) decreases exponentially with altitude, the bulk of molecular oxygen in the atmosphere is concentrated within several kilometers of Earth's surface.

• Above this, in the thermosphere, gases become separated based on their densities. Molecular oxygen is photo-dissociated by UV radiation to form atomic oxygen, which is the major form of oxygen above ~120 km altitude.

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• The oceans • in the surface mixed layer (~0-60 m water depth), O2 concentrations

saturated to supersaturatedgreater in colder high-latitude surface waters than in waters near the equator vary strongly with season, especially in high productivity watersfalls to zero in some regions with restricted water circulation, biological

utilization of oxygen exceeding O2 resupply through advection and diffusion

• O2 concentrations drop below the surface mixed layer to form O2 minimum zones (OMZs), consumption exceeding resupply through advection and diffusion. Below the OMZs in the open ocean, O2 concentrations gradually increase again from 2000 m to the seafloor.

• There are also regions of the world oceans where stratification and anoxia are more permanent features (e.g. Black Sea).

• In several regions of the open ocean, strong O2-depletion is associated with deep-water upwelling, high rates of surface water primary productivity, and high dissolved oxygen demand in intermediate waters.

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• Air-sea O2 exchange

•High rates of marine primary productivity result in net outgassing of O2 from the oceans to the atmosphere in spring and summer, and net ingassing of O2 during fall and winter.

•These patterns of air-sea O2 transfer relate to latitude and season:

• Outgassing of O2 during northern hemisphere high productivity months (April through August) is accompanied by simultaneous ingassing in southern latitudes when and where the productivity is lowest.

• Low-latitude ocean surface waters show very little net air-sea O2 exchange and minimal change in outgassing or ingassing over an annual cycle.

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Marine sediments

•Oxygen concentrations in the pore fluids of sediments are controlled by a balance of entrainment of overlying fluids during sediment deposition, diffusive exchange between the sediment and the water column, and biological utilization.

• In marine sediments, there is a good correlation between the rate of organic matter supply and the depth of O2 penetration in the sediment.

• In coastal sediments and on the continental shelf, burial of organic matter is sufficiently rapid to deplete the sediment of oxygen within millimeters to centimeters of the sediment-water interface.

• In deeper abyssal sediments, where organic matter delivery is greatly reduced, O2 may penetrate several meters into the sediment before being entirely consumed by respiration.

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Surface freshwater

• In flowing freshwater environments O2 concentrations closely match air-saturated values.

• In static water bodies, however, O2-depletion can develop much like in the oceans.

• This is particularly apparent in some ice-covered lakes.

• Stratification: High productivity during spring and summer in shallow turbid aquatic environments can result in extremely sharp gradients from strong O2 supersaturation at the surface to near O2-depletion within a few meters of the surface.

• The high concentration of labile dissolved and particulate organic matter in many freshwater environments leads to rapid O2-depletion where advective resupply is limited.

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Soils and groundwater (Reading)

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3.4.4.3 O3.4.4.3 O22 production production

• Oxygenic photosynthesis

• Global net primary production ranges from 23×1015 mol yr-1 to 26×1015 mol yr-1, distributed between 14×1015 mol yr-1 O2 production from terrestrial primary production and 12×1015 mol yr-1 from marine primary production. It is estimated that ~50% of all photosynthetic fixation of CO2 occurs in marine surface waters by phytoplankton and thus half of all global photosynthetic oxygen production resulting from marine primary production.

• Photolysis of water

• In the upper atmosphere today, a small amount of O2 is produced through photolysis of water vapor.

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3.4.4.3 O3.4.4.3 O22 consumption consumption

Aerobic respiration

Oxidization of reduced volcanic gases. CO, H2, SO2, H2S, and CH4

Mineral oxidation (tectonic uplift) olivine, Fe2+ -bearing pyroxenes and amphiboles,

metal sulfides, and graphite.

Submarine oxidization of reduced substance. reduced metal sulfides dissolved reduced gases ferrous-iron silicates

Abiotic organic matter oxidation. dissolved and particulate organic matter and fossil

fuels, fires from burning vegetation and fossil fuels, and atmospheric methane oxidation.

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3.4.4.3 Global oxygen budgets and the global oxygen cycle

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3.4.5 Nitrogen cycle

• The conversion of nitrogenous compounds from one form to another by various communities results in what is called the nitrogen cycle. These metabolic activities represent essential steps in the nitrogen cycle, which are shown below.

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3.4.5 Nitrogen cycle

Nitrogen-fixing bacteria in root nodules

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3.4.5.5 Nitrogen reservoirs and their exchanges3.4.5.5 Nitrogen reservoirs and their exchanges

• Total ~5×1021 g N, 80% in the atmosphere. Sedimentary rocks contain almost all the remainder with just a trace (<1% of total) in oceans and living and dead organic matter.

• In the atmosphere: except for trace amounts of N2O, NOy, NHx, and organic N, it occurs as N2.

• In oceans and soils: organic nitrogen, nitrate, and ammonium.

• Transferred from land to the atmosphere

• The high-temperature processes: biomass combustion and fossil-fuel combustion;

• The low-temperature processes: volatilization of gases from soils and waters and turbulent injection of particulate matter into the atmosphere.

• Deposited to land and ocean surfaces

• Wet deposition includes rain, snow, and hail; the nitrogen can be inorganic or organic.

• Dry deposition includes gases and aerosols.

• Transferred from continents to the coastal ocean via discharge of rivers and groundwater, as NO3

- or particulate organic nitrogen.

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3.4.5.6 Remarks on nitrogen cycle3.4.5.6 Remarks on nitrogen cycle

• Both ammonium and nitrate are used by plants. Both ammonium and nitrate are used by plants. NitrateNitrate appears to be appears to be more readily available because it does not bind to clay particles in the soil more readily available because it does not bind to clay particles in the soil as ammonium does. as ammonium does.

• Microorganisms are intimately involved in nitrogen fixation, Microorganisms are intimately involved in nitrogen fixation, ammonification, nitrification, and denitrification.ammonification, nitrification, and denitrification.

• Farmers take advantage of the microbial activities that take place in soils. Farmers take advantage of the microbial activities that take place in soils. For example, plowing fields before fertilization and planting creates an For example, plowing fields before fertilization and planting creates an aerobic environment that promotes the growth of ammonifiers and aerobic environment that promotes the growth of ammonifiers and nitrifiers and discourages the growth of denitrifiers. nitrifiers and discourages the growth of denitrifiers.

• The disruption of the nitrogen cycle by human activity plays an important The disruption of the nitrogen cycle by human activity plays an important role in a wide-range of environmental problems:role in a wide-range of environmental problems:

• production of tropospheric smog. production of tropospheric smog. • Nitrous oxide, greenhouse gases , also destroys stratospheric ozone. Nitrous oxide, greenhouse gases , also destroys stratospheric ozone. • Nitrate rain is acidic and can cause ecological problems as well as serve as a Nitrate rain is acidic and can cause ecological problems as well as serve as a

fertilizer to vegetation. fertilizer to vegetation.

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3.4.6 Sulfur cycle3.4.6 Sulfur cycleAlthough a number of oxidation states are possible, only three form significant amounts of sulfur in nature, -2 (sulphydryl, R-SH, and sulfide,

HS-), 0 (elemental sulfur, S°), and +6 (sulfate, SO42-)

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3.4.6.13.4.6.1 Reservoirs and fluxesReservoirs and fluxes

• Three major reservoirs form the global sulfur cycle: sulfate dissolved in the world’s oceans; sulfate in ancient evaporite deposits; and sulfide (mainly in the form of pyrite FeS2) in marine sediments.

• constantly augmented by release of sulfur of volcanic origin, either as gases (SO2 and H2S) that ultimately rain out to

oceans via the hydrosphere or from weathering of igneous rocks.

• Other reservoirs of sulfur are all very small, including sulfur in

• atmosphere (1 x 1012 g),

• soil (3 x 1016 g),

• terrestrial biomass (1 x 1016 g)

• fossil fuels (7 x 1016 g)

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3.4.6.13.4.6.1 Reservoirs and fluxesReservoirs and fluxes

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3.4.6.2 Hydrogen sulfide and sulfate reduction

3.4.6.3 Sulfide and elemental sulfur oxidation

3.4.6.4 Organic sulfur compounds

3.4.6.5 Isotopic distributions (Reading)

3.4.6 Sulfur cycle3.4.6 Sulfur cycle

Homework

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3.4.7 Phosphorus cycle3.4.7 Phosphorus cycle

• Phosphorus, an essential nutrient for all life forms, is a component of several critical biological compounds including ：•nucleic acids

•Phospholipids

•ATP

• Most plants and microorganisms readily take up phosphorus as orthophosphate (PO4

3-), assimilating it into biomass. From there, the phosphorus is passed along the food web.

• When, plants and animals die, decomposers convert organic phosphorus back to inorganic phosphate.

• Most microorganisms do not alter the valence of the phosphorus atom. Some organisms, however, are able to use phosphate as an electron sink when oxygen, sulfate, and nitrate are not present.

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3.4.7.1 Reservoirs and flux-3.4.7.1 Reservoirs and flux-readingreading

• Phosphorus, an essential nutrient for all life forms, is a component of several critical biological compounds including ：•nucleic acids

•Phospholipids

•ATP

• Most plants and microorganisms readily take up phosphorus as orthophosphate (PO4

3-), assimilating it into biomass. From there, the phosphorus is passed along the food web.

• When, plants and animals die, decomposers convert organic phosphorus back to inorganic phosphate.

• Most microorganisms do not alter the valence of the phosphorus atom. Some organisms, however, are able to use phosphate as an electron sink when oxygen, sulfate, and nitrate are not present.

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3.4.7.1 Reservoirs and flux-3.4.7.1 Reservoirs and flux-readingreading

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3.4.7.2 Phosphorus limitation primary 3.4.7.2 Phosphorus limitation primary productionproduction

When bioavailable phosphorus is exhausted prior to more abundant nutrients, it limits the amount of sustainable biological productivity. This is the ecological principle often referred to as Liebig's Law of the Minimum.

Terrestrial ecosys tems: phosphorus-limited due to sorptive binding of phosphate by Fe- and Al-oxide and oxyhydroxide.

Phosphorus limitation in lakes: Microbial reduction and re-oxidation/re-precipitation of ferric oxyhydroxides controls P-release versus P-retention by sediments. It has also been shown that bacteria in surficial sediments directly take up and release phosphate in response to changes in redox state.

Phosphorus limitation in rivers: dissolved inorganic phosphorus (DIP) levels are set by sorption equilibrium with suspended sediments; this con trolling mechanism is known as the phosphate buffer mechanism.

Phosphorus limitation in oceans: the subject of controversy and debate. The limiting nutrient on long, geological time-scales or in the modern ocean.

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3.4.7.3 Diagenesis and burial of phosphorus in marine sediments3.4.7.3 Diagenesis and burial of phosphorus in marine sediments

The sources of particulate phosphorus to the seabed include:

• detrital inorganic and organic material transported by rivers.

• biogenic material produced in the marine water column that sinks to the seabed

• atmospheric dust that becomes entrained with sinking particulate material and is thus transported to the seabed.

Pore water phosphate source:

• breakdown via microbial respiration

• release of sorbed phosphate from host Fe-oxyhydroxides when these phases are buried into suboxic and anoxic zones within the sediment.

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3.4.7.5 Eutrophication-3.4.7.5 Eutrophication-discussiondiscussion

Phosphorus is a limited nutrient in some ecosystem. In the proper quantities, phosphorus is good for the environment. However, an overabundance of the element in the environment can lead to a phenomenon called eutrophication, a state of heightened biological productivity in a water body. One of the leading causes of eutrophication is a high rate of nutrient input, in the form of phosphates or nitrates.

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3.4.8 Iron cycle3.4.8 Iron cycle

Homework

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3.4.9 Major features of biogeochemical cycles3.4.9 Major features of biogeochemical cycles

A variety of pathways

Each biogeochemical cycle has many different pathways.

Each element has a different set of potential biogeochemical

pathways.

phosphorus and iron generally do not cycle

through the atmosphere because

they do not easily form gases

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Variable rates of cycling.

the chemical reactivity of the substance

whether it has a gas phase (occurs in the atmosphere) somewhere in the cycle.

H2O, 10 days in atmosphere

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The effects of human activity.

Acceleration of the cycles-depletion and environmental problems (e.g. P-eutrophication, N-smog, S-acid rain).

Carbon provides a prominent example of how humans are actively disturbing a major cycle, with potentially drastic consequences (global warming).

geobiology- 第七讲 chapter 3

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