Exam: Wednesday April 9 Chapters: 1-8

1. Exam: Wednesday April 9Chapters: 1-8 Not open for discussion

2. Chapter 7: Pathways of Elements in the Ecosystem Robert E. Ricklefs The Economy of Nature, Fifth Edition

3. Background • Cycling of elements and flux of energy in ecosystems are fundamentally different: • chemical elements are reused repeatedly • energy flows through the system only once • Many aspects of elemental cycling make sense only when we understand that chemical transformations and energy transformations go hand in hand.

4. Assimilatory and Dissimilatory Processes • Assimilatory processes: • incorporate inorganic forms of elements into organic forms, requiring energy • example: photosynthesis (reduction of carbon) • Dissimilatory processes: • transform organic forms of elements into inorganic forms, releasing energy • example: respiration (oxidation of carbon)

5. Energy transformations and element cycling are linked. • Organisms play important roles in cycling of elements when they carry out chemical transformations: • most biological energy transformations are associated with biochemical oxidation and reduction of C, O, N, and S • these assimilatory and dissimilatory processes are often linked, one providing energy for the other

6. Coupled reactions are the basis of energy flow in ecosystems. • A typical coupling of assimilatory/ dissimilatory reactions might involve: • oxidation (dissimilation) of carbon in carbohydrate (energy-yielding), linked to • reduction (assimilation) of nitrate-N to amino-N (energy-requiring) • Some processes may involve many steps. • Energy is lost at each step (inefficiency).

7. Energy-releasing / energy-requiring

8. Ecosystems may be modeled as linked compartments. • An ecosystem may be viewed as a set of compartments among which elements are cycled at various rates: • photosynthesis moves carbon from an inorganic compartment (air or water) to an organic compartment (plant) • respiration moves carbon from an organic compartment (organism) to an inorganic compartment (air or water)

9. Elements move among compartments at different rates. • Inorganic carbon released through respiration may be taken up quickly through photosynthesis. The organic carbon fixed may be respired again quickly by plants. • Organic carbon stored in deposits of coal, oil, or peat is not readily accessible and may remain in storage for millions of years. • Inorganic carbon may also be taken out of circulation for millions of years by precipitation as calcium carbonate in aquatic systems.

10. Generalized compartment model of the cycling of elements within ecosystems

11. A Physical Model for the Water Cycle • The biosphere contains 1,400,000 teratons (TT, 1012 metric tons) of water, 97% of which resides in the oceans. • Other water compartments include: • ice caps and glaciers (29,000 TT) • underground aquifers (8,000 TT) • lakes and rivers (100 TT) • soil moisture (100 TT) • water in atmosphere (13 TT) • water in living things (1 TT)

12. Global water cycle; units in billion billion grams (10^18)

13. The water cycle is solar-powered. • The water cycle consumes one-fourth of the total solar energy striking the earth during a year: • precipitation over land exceeds evaporation by 40 teratons/yr; surplus returns to the ocean in rivers • evaporation over the oceans exceeds precipitation by 40 teratons/yr; surplus is delivered by winds to the land masses • The residence time of water varies by compartment. • The atmosphere contains 2.5 cm of moisture at any time; annual flux into and out of the atmosphere is 65 cm/yr: • residence time is compartment size/flux, or 2.5 cm / 65 cm/yr = 0.04 yr, about 2 weeks. • Soils, rivers, lakes and oceans have same flux rates as atmosphere, but they contain about 100,000 times as much water, yielding a mean residence time of 2,800 yr.

14. The carbon cycle is linked to global energy flux. • The carbon cycle is the focal point of biological energy transformations. • Principal classes of carbon-cycling processes: • assimilatory/dissimilatory processes (mainly photosynthesis and respiration) • exchange of CO2 between atmosphere and oceans • sedimentation of carbonates

15. Global carbon cycle; units in billions of metric tons or gigatons (GT) and GT/yr

16. First class of carbon cycling: Photosynthesis and Respiration • Approximately 85 GT of carbon enter into balanced assimilatory/dissimilatory transformations each year. • Total global carbon in organic matter is about 2,650 GT (living organisms plus organic detritus and sediments). • Residence time for carbon in biological molecules = 2,650 GT / 85 GT/yr = 31 years. • Figure 7.6 – good representation

17. Second class of carbon cycling: Ocean-Atmosphere Exchange • Exchange of carbon across the atmosphere-ocean interface links carbon cycles of terrestrial and aquatic ecosystems. • Oceans contain 50 times as much CO2 as the atmosphere (oceans as sink. Oceans as source?) • Dissolved carbon pool is 30,000 GT, nearly 50 X that of atmosphere (640 GT). • Net atmospheric flux (assimilation/ dissimilation and exchange with oceans) is 119 GT/yr for mean atmospheric residence time (640 GT / 119 GT/yr) of about 5 years. • By 1990: combustion of fossil fuels -> 6 GT / year = ~ 1% of total atmospheric carbon dioxide • Read up on climate change

18. Third class of carbon cycling: Precipitation of Carbonates • Precipitation (and dissolution) of carbonates occurs in aquatic systems: • precipitation (as calcium and magnesium carbonates) leads to formation of limestone and dolomite rock • turnover of these sediments is far slower than those associated with assimilation/dissimilation or ocean-atmosphere exchange • carbonate sediments represent the single largest compartment of carbon on planet (18,000,000 GT)

19. Most of the earth’s carbon is in sedimentary rocks (southern Texas)

20. Precipitation of Calcium and Carbon Through the Ages • CO2 dissolves in water to form carbonic acid, which dissociates into hydrogen, bicarbonate, and carbonate ions: CO2 + H2O  H2CO3 H2CO3 H+ + HCO3- 2H+ + CO32- • Calcium ions combine with carbonate ions to form slightly insoluble calcium carbonate, which precipitates: Ca2+ + CO32- CaCO3 • When precipitation> respiration (as in algal blooms) – calcium tends to precipitate out of the system

21. Slow Release of Sedimentary Calcium and Carbon • Calcium removed from the water column in the oceans is replaced by calcium dissolved from limestone sediments on land by slightly acidic water of rivers and streams. • Carbon is also slowly released from oceanic sediments as limestone is subducted beneath continental plates, and CO2 is outgassed in volcanic eruptions.

22. Reef-Builders extract carbon from water. • In neutral conditions of marine ecosystems, extraction of CO2 from water column drives precipitation of CaCO3: CaCO3 + H2O + CO2 Ca2+ + 2HCO3- • Reef-building algae and coralline algae incorporate calcium carbonate into their hard structures, forming reefs.

23. Skeleton of caralline algae made of calcium carbonate

24. Changes in the Carbon Cycle Over Time • Atmospheric CO2 concentrations have varied considerably over earth’s history: • during the early Paleozoic era (550-400 Mya), concentrations were 15-20 X those at present • concentrations declined to ca. present level by 300 Mya (during which saw development of forests on land), then increased again to 5 X present level through the early Mesozoic era (250-150 Mya) and have declined gradually since • early Paleozoic and early Mesozoic eras were extreme greenhouse times (hot temperatures), unlikely to be equaled by effects of current human enhancement of atmospheric CO2

25. Yes • Read: ‘Ecologists in the Field’ • Read it carefully. All of them • 

26. Nitrogen - A Most Versatile Element! • Ultimate source (largest reservoir) of this essential element is molecular N2 gas in the atmosphere, which can also dissolve in water to some extent. • Nitrogen is absent from native rock. • Nitrogen enters biological pathways through nitrogen fixation: • these pathways are more complicated than those of the carbon cycle because nitrogen has more oxidized and reduced forms than carbon

27. Biological pathways of the nitrogen cycle

28. Ammonification • Plants assimilate inorganic nitrogen into proteins, which may be passed through various trophic levels. • Ammonification (dissimilation of N) is carried out by all organisms: • initial step is breakdown of proteins into constituent amino acids by hydrolysis • carbon (not nitrogen) in amino acids is then oxidized, releasing ammonia (NH3)

29. Nitrification • Nitrification is oxidation of ammonia: • first step is oxidation of ammonia to nitrite (NO2-), carried out by Nitrosomonas in soil and Nitrosococcus in oceans • nitrite is then oxidized to nitrate (NO3-) by Nitrobacter in soil and Nitrococcus in oceans • nitrification is an aerobic process; the nitrifying organisms involved are chemoautotrophic bacteria

30. Denitrification • Denitrification is the reduction of nitrate to nitric oxide (NO), which escapes as a gas: • occurs in waterlogged, anaerobic soils, oxygen-depleted sediments, and bottom waters in aquatic ecosystems • carried out by heterotrophic bacteria such as Pseudomonas denitrificans • further N-reductions may lead to production of nitrous oxide (N2O) and molecular nitrogen (N2), both gases • denitrification may be one of the principal causes of low availability of nitrogen in marine systems

31. Nitrogen Fixation • Loss of nitrogen to atmosphere by denitrification is offset by nitrogen fixation: • fixation is carried out by: • free-living bacteria such as Azotobacter • symbiotic bacteria such as Rhizobium, living in root nodules of legumes and other plants • cyanobacteria • N-fixation is an energy-requiring process, with energy supplied by oxidation of organic detritus (free-living bacteria), sugars supplied by plants (bacterial symbionts), or photosynthesis (cyanobacteria)

32. Significance of Nitrogen Fixation • Nitrogen fixation balances denitrification on a global basis: • these fluxes amount to about 2% of total cycling of nitrogen through ecosystems • Nitrogen fixation is often very important on a local scale: • N-fixers dominate early colonizers on nitrogen-poor substrates, such as lava flows or areas left bare by receding glaciers

33. The Phosphorus Cycle • Phosphorous is an essential element, constituent of nucleic acids, cell membranes, energy transfer systems, bones, and teeth. • Phosphorus may limit productivity: • in aquatic systems, sediments act as a phosphorus sink unless oxygen-depleted • in soils, phosphorus is only readily available between pH of 6 and 7

34. Phosphorus Transformations • Phosphorus undergoes relatively few transformations: • plants assimilate P as phosphate (PO43-) and incorporate this into organic compounds • animals and phosphatizing bacteria break down organic forms of phosphorus and release the phosphorus as phosphate • phosphorus does not: • undergo oxidation-reduction reactions in the ecosystem • circulate through the atmosphere, except as dust

35. Phosphorus cycle

36. The Sulfur Cycle 1 • Sulfur is an essential element and, like nitrogen, has many oxidation states and follows complex chemical pathways. • Sulfur reduction reactions include: • assimilatory sulfate reduction to organic forms and dissimilatory oxidation back to sulfate by many organisms • reduction of sulfate when used as an oxidizer for respiration by heterotrophic bacteria in anaerobic environments

37. The Sulfur Cycle 2 • Sulfur oxidation reactions include: • oxidation of reduced sulfur when used as an electron donor (in place of oxygen in water) by photosynthetic bacteria • oxidation of sulfur by chemoautotrophic bacteria that use the energy thus obtained for assimilation of CO2

38. Sulfur in Coal and Oil Deposits • Iron sulfide (FeS) commonly associated with coal and oil deposits can result in environmental problems: • oxidation of sulfides in mine wastes to sulfate, which combines with water to form sulfuric acid, associated with acid mine drainage • oxidation of sulfides in coal and oil releases sulfates into atmosphere, which then form sulfuric acid, a component of acid rain

39. Sulfur cycle

40. Acidic streams from refuse of coal mines (Pennsylvania)

41. Microorganisms assume diverse roles in element cycles. • Decomposition in anaerobic organic sediments is dependent on certain specialized microbes, the denitrifiers: • these heterotrophic organisms use oxidized forms of N, S, and Fe as electron acceptors (oxidizers) in the absence of oxygen • for example, some anaerobic bacteria utilize nitrate as an alternative electron acceptor for the oxidation of glucose: glucose + NO3- CO2 + H2O + OH- + N2 + energy

42. Biological Nitrogen Fixation • Biological nitrogen fixation (by bacteria and cyanobacteria) is essential to counterbalancing N losses associated with denitrification. • Nitrogen is often implicated as a limiting nutrient in terrestrial and aquatic systems. • Nitrogen fixation is critical to ecosystem development in primary succession. • Continued nitrogen input is essential for long-term health of natural ecosystems.

43. Autotrophic Diversity • All autotrophs are capable of assimilating (reducing) carbon in CO2 into organic forms (initially glucose): • photoautotrophs accomplish this by capturing energy from sun through photosynthesis: • green plants, algae, and cyanobacteria use water as an electron donor (reducing agent) and are aerobic • purple and green bacteria use H2S or organic compounds as electron donors and are anaerobic

44. Chemoautotrophs • Chemoautrophs are not photosynthetic, reducing inorganic carbon (from CO2), but using energy obtained from aerobic oxidation of inorganic substrates: • methane - Methanosomonas, Methylomonas • hydrogen - Hydrogenomonas, Micrococcus • ammonia - nitrifying bacteria Nitrosomonas, Nitrococcus • nitrite - nitrifying bacteria Nitrobacter, Nitrococcus • hydrogen sulfide, sulfur, sulfate - Thiobacillus • ferrous iron salts - Ferrobacillus, Gallionella

45. Deep-Sea Vent Ecosystems • Deep-sea vent ecosystems are far below the penetration of any light, dependent on chemoautotrophic production: • hot water coming from vents is charged with hydrogen sulfide, H2S ; the hot water is their source of energy • chemoautrophic bacteria use oxygen from seawater to oxidize H2S, then use the energy thus obtained for assimilatory carbon reduction • other members of vent communities (clams, worms, crabs, fish) ultimately depend on primary production of these bacteria

46. Living things are intimately involved in elemental cycles. • Elements are cycled through ecosystems primarily because metabolic activities result in chemical transformations. • Each type of habitat presents a different chemical environment, especially with respect to: • presence/absence of oxygen • possible sources of energy • Numerous adaptations have arisen to meet these challenges.

47. Summary 1 • Unlike energy, nutrients are retained in ecosystems and may cycle indefinitely. • The movements of energy and elements, especially carbon, parallel one another in ecosystems. • Energy transformations result from the coupled oxidation and reduction reactions of various elements.

48. Summary 2 • The water cycle is a physical analogy for element cycling in ecosystems; many elements are also transported by the water cycle. • The carbon cycle involves both biological and nonbiological processes fundamental to functioning of the biosphere. • The nitrogen cycle involves many transformations and oxidation states. Microorganisms play essential roles throughout.

49. As usual • Do quiz for chapter 7 by Monday • We do chapter 8 on Monday • Exam on Wednesday. • (note: make-ups are harder)