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Ecosystems & biodiversity. Feedbacks through biota Chapters 9, 13, & 18. Evolution of life & biogeochemistry. Biota mediate the cycles of many elements that cycle between various reservoirs with different residence times Biology – transfer energy through food chains/webs

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ecosystems biodiversity

Ecosystems & biodiversity

Feedbacks through biota

Chapters 9, 13, & 18

evolution of life biogeochemistry
Evolution of life & biogeochemistry
  • Biota mediate the cycles of many elements that cycle between various reservoirs with different residence times
  • Biology – transfer energy through food chains/webs
  • Geochemistry – lead to steady state systems far from chemical equilibrium
  • Records on Earth – atm composition, sediments
  • Diversity of microbial metabolisms
    • Higher organisms mostly aerobic
    • Present day cycles can deviate from rock record

Complex processes cycle elements

among different reservoirs

- involves biology

- has geochemical consequences

Different communities store and cycle

material and energy differently

- diversity differences

- different biogeochemical results

- different storage of biomass


What it means to be Alive

  • Auto conservation
    • The main function of every living organism is making sure that it can continue it's existence.
  • Auto reproduction
    • Any living system can reproduce or proceeds from a reproduction.
  • Storage of information
    • Each organism contains genetic information. This appears stored in DNA, and is read and translated by proteins according to a universal genetic code, which is common to all creatures.
  • Breathing-fermentation
    • Every living being must have a metabolism that will transform energy and matter taken from the environment into energy and compounds that can be used by the different parts of the living organism.
  • Stability
    • Through the creation and control of it's own internal environment, all creatures remain stable in front of the perturbations of the external world.
  • Control
    • The distinct parts of an organism contribute to the survival of a group and, therefore, to the conservation of it's identity.
  • Evolution
    • The mutations in the hereditary material and natural selection permit the perfection, adaptation and complexity of living beings. For many, life is a mere product of evolution.
  • Death

What it Means to be Alive

  • Capable of transforming energy
    • Photosynthesis and respiration
      • For homeostasis
      • For growth
      • For reproduction
  • Life and the second law of thermodynamics
    • Transformation of energy leads to disorder
    • Life requires the maintenance of order
    • Homeostasis, growth and reproduction occur at the expense of increased disorder (entropy) of the whole system
  • Life is characterized by:
    • Cells
    • Common metabolic pathways
    • Common genetic code
  • Living things include
    • Bacteria
    • Algae
    • Plants
    • Animals
  • Non-living things include
    • Viruses
    • Prions
    • Organic molecules
      • Proteins and amino acids
      • Nucleic acids
      • Fats
      • Sugars

The Origin of Life on Earth

  • The earth is 4.6 billion years old
  • Life on earth has existed for more than 3.8 billion years
  • All life requires liquid water
  • The basic molecules of life can be made from a primitive reducing atmosphere
    • Methane, ammonia water, hydrogen, and energy
    • No oxygen - anoxic

The Origin of Life

  • Growing evidence supports the idea that the emergence of catalytic RNA was a crucial early step. How that RNA came into being remains unknown.
  • Catalysts are essential for the chemistry of life
  • RNA acts as a genetic ‘messenger’ in modern cells
  • The ‘Central Dogma’ of Modern Biology
    • DNA makes RNA, RNA makes protein, proteins are the common biological source of enzymatic catalysis

Two Critical Steps in the Origin and Evolution of Life

  • Organic catalysis and self-replication
    • Catalytic RNA?
  • Photosynthesis
    • A mechanism for capturing energy and converting it into food
structure of the biosphere
Structure of the biosphere
  • Hierarchy
    • Species – reproductive group
    • Population – members of a single species that live in a given area
    • Community – assemblage of interacting species in a given area
    • Biome – a region with a characteristic plant community (e.g. rainforest, desert)
    • Ecosystem – a community of animals, plants, microbes, etc, together with the physical environment that supports it

Structure of the biosphere

  • Ecosystem
    • Assemblage of organisms that interact with each other and the environment
    • Some can be defined by their environment (rain forest, desert)
  • Interactions between organism and environment
    • Daisyworld example
  • Alteration of environments can impact ecosystems
    • ENSO events – food web effects
    • Cessation of upwelling – food web effects
  • Physiological versus ecological growth optima
    • Not always the same – optimal niche versus realized niche
    • High productivity oceanic regions are often high latitude or upwelling
    • Related to ocean physics and nutrient availability rather than growth optima; compromise between mixing (promoting nutrient availability) and temperature (promoting stratification)
  • Many ecosystems defined by the environment
  • Organisms subdivide that environment
  • Organisms that share habitats find niches within those habitats
    • Strategies and living habits
  • High productivity
    • Upwelling; low latitudes
  • Low productivity
    • Central gyres; downwelling


Upwelling – productive

No upwelling - collapse

La Nina

El Nino


Fig. 15-13 & 14

  • Nt = Noekt
  • Add resource limitation to set limits to population size (Nt)
  • Oh, and life pollutes…

Phytoplankton growth in the ocean


Temperature optima in the lab are 20-25 deg


Highest productivity at higher latitudes!

Ecological growth optimum is 8 deg C – due to ocean physics and nutrient availability

phytoplankton productivity
Phytoplankton productivity
  • Related to physics, light, & nutrient supply
  • If surface waters are too warm, water stratifies & limits nutrient resupply from bottom waters
  • High turbulence increases mixing up of nutrients
  • Compromise between nutrients & temp
  • On land, photosynthesis proceeds just above ground level
  • In water, communities may be vertically stratified
  • In the water, photosynthesis proceeds to considerable depths, depending on
    • Water clarity
    • Sun angle
    • Sea state
  • Unlike the atmosphere, water attenuates light, especially green and red
  • The depth to which light penetrates depends on the amount and nature of dissolved and suspended constituents
  • Oceanic waters contain few particles and are blue
  • Coastal waters contain high phytoplankton populations and are green
  • Estuarine waters contain lots of suspended sediments and look brown
Light penetrates deepest in oceanic waters
  • Blue light penetrates best
  • Red light is rapidly attenuated
Light penetration is shallower in plankton-rich coastal waters
  • Phytoplankton absorb blue light for photosynthesis
  • Water absorbs red light
  • Coastal ocean looks green
  • Depends on the amount of light up to saturation
  • Depends on the color of light – not all photons are equivalent
  • Most efficient with blue and red light, least efficient with green light
  • Ocean temperature varies with
    • Depth
    • Latitude
  • Temperature controls rate of chemical reactions
    • Slower at low temperature because molecules carry less energy
      • Fewer collisions
      • Less energy per collision
    • Metabolism is defined by chemical reactions
  • Most organisms are ectothermic – don’t regulate body temperature
  • Some organisms are endothermic – regulation of body temperature requires
    • lots of energy
    • good insulation
  • Salinity can vary with rainfall and evaporation
  • Changes in salinity (up or down) can affect metabolic function, energy consumption and cell viability.
  • Different organisms have very different salinity tolerances

Marine Communities Store Less Organic Carbon and Turnover Rates are Faster than Terrestrial Communities


Trophic Relationships

  • Energy Transfer
  • Primary Producers are Autotrophs
    • harvest sunlight
  • Heterotrophs are Consumers
    • eat organic matter
exploitation efficiency
Exploitation efficiency
  • Autotroph – plants & microbes
    • Photosynthesis or chemosynthesis
    • Produce organic matter from inorganic C sources
  • Heterotroph – accelerate chem reactions to gain energy
    • Herbivores - ~ 20%
    • Carnivores - ~ 0.2% (not very efficient at converting food to biomass!)
  • Mutualism – both organisms benefit
that s biology but biodiversity
That’s biology but… biodiversity
  • Linked to ecosystem health and stability
    • Number of species per unit area or ecosystem
  • Often think of deforestation
    • Destruction of tropical habitats
  • Number of species in a community
  • Diversity indices
    • Simpson diversity = 1 – [(proportion of species A)2 + (proportion of species B)2 + …..]
biodiversity over time
Biodiversity over time
  • Natural changes in diversity due to evolution and extinction of species
  • General increase in diversity over time
  • Interupted by extinction events
    • 26 my periodicity in extinction events?
    • Extraterrestrial cause?
  • Extinction is natural
    • Over 90% of species that have evolved are extinct

26 my periodicity


Figs. 13-4 & 13-10

recent changes in biodiversity
Recent changes in biodiversity
  • Present day rates exceed geological rates of extinction
  • Present day extinction is across the board – affects many groups
  • Other extinction events affected species within particular groups – other groups survived
    • Example is K-T extinction of dinosaurs; mammals and plants survived to reradiate
  • Modern extinction associated with spread of human populations
    • Over hunting/fishing
    • Habitat destruction – deforestation & coral bleaching

Fig. 18-1 - Extinction of large mammals and birds corresponds to the spread of human populations

deforestation biodiversity
Deforestation & biodiversity
  • Poster child
  • The tropics is the area of greatest rate of species loss
  • Concern for more than biodiversity
    • Addition of CO2
    • Loss of CO2 uptake mechanism
  • Impact on regional climate
deforestation and soil nutrients
Deforestation and soil nutrients
  • Distinct differences in storage of biomass & nutrient cycling between temperate & tropical forests
  • Temperate forests have thick, rich topsoils
    • Humus layer of organic detritus on top of subsoil
    • Nutrients stored in soils
  • Tropical soils are highly weathered (lots of rain)
    • Lateritic clays depleted in nutrients
    • Thin humus layer
    • Nutrients stored in biomass

Tropical above ground

storage of biomass & nutrients


Model results – decrease forest cover, increase albedo,

decrease winter temperatures, increase sea ice,

increase albedo, decrease temperatures….

deforestation and recovery
Deforestation and recovery
  • Rainforests – loss of rainforest trees leads to loss of nutrients & changes in the water cycle
  • Temperate forests recover because nutrients retained in the soils
deforestation water cycle climate
Deforestation & water cycle & climate
  • Elimination of tropical rainforests disrupts regional water cycle
    • Minimizes evapotranspiration (source of H2O to atm)
    • Decreases soil moisture and increases runoff
  • Increases erosion rates
    • Soils form slowly
    • 200-1500 yrs to form 2.5 cm of topsoil from bedrock
  • General circulation models to predict
    • Net temperature increase
    • Decrease in soil moisture

Tropical rain forests - high Net Primary Production but low nutrient residence times (as compared to other biomes)

High recycling sustains high productivity



(change in albedo)


Decrease forest cover

Increase runoff

Decrease nutrient supply

Decrease forest cover

Decrease forest cover

Increase albedo

Decrease net radiation

Decrease temp

Decrease evapotranspiration

Increase temperature

Decrease clouds

Increase temperatures

biodiversity and deforestation in tropical areas
Biodiversity and deforestation in tropical areas
  • Half of the living species are found in rainforests
  • Forest plants have medical value
    • Treatment of diseases
  • Forest plants have agricultural value
    • Need genetic diversity for long-term health (Darwinian evolution)
    • Need variety to limit vulnerability to diseases and pests
    • Modern agricultural practices limit diversities
    • Centers of genetic diversity for crops come from areas threatened by development, population pressures, deforestation
    • Seed banks
biodiversity and ecosystem stability
Biodiversity and ecosystem stability
  • Relationship is complex
    • In some settings environmental stability leads to high diversity
    • In others, high diversity is thought to result from disturbances of intermediate frequency and intensity
  • How does loss of biodiversity impact ecosystem?
    • Remove enough species and ecosystem collapses (removal of predators; invasive species)
    • May be that some species aren’t necessary – system maintained by a few keystone species
causes of deforestation
Causes of deforestation
  • Social, political, and economic drivers
  • Economic arguments – people and countries need hard currency (Nepal)
    • Motivation not to
    • Who will bear the costs of not exploiting resources?
  • Earth will recover, will humans survive?
biodiversity over time geologic
Biodiversity over time - geologic
  • Natural changes due to new species evolving and extinction
  • General increase that should theoretically occur over time
    • Extinction events – cleans the slate
    • Natural extinction – 90% of species ever alive are extint now

26 my periodicity


Fig. 13-4

darwin s main points
Darwin’s main points
  • In any population, more offspring are produced that can survive to reproduction
  • Genetic variation occurs in populations
  • Some inherited traits increase the probability of survival
  • Bearers of those traits are more likely to leave offspring to the next generation – those traits accumulate
  • Environmental conditions determines which traits are favorable

Biogeochemical Cycles

  • Elements cycle between organisms, the water, the sediments and the land
  • The maintenance of life requires continued access to these elements
  • Only a few are of biogeochemical significance
  • C, N, P, Si, Fe
  • Elemental ratios in living organisms are fairly constant
  • Redfield Ratio C:N:P 106:16:1

The Elements of Life

  • In addition to energy, life requires certain material substances
  • All organisms require 23 basic elements
  • Availability of these elements can limit growth and survival

The Carbon Cycle

  • A basic building block of life
  • Largest of all biogeochemical cycles
  • Availability rarely limits marine productivity
    • Seagrasses are important exceptions

The Nitrogen Cycle

  • N is a critical component of proteins, nucleic acids and pigments (e.g. chlorophyll)
  • Traditionally viewed as the most limiting nutrient in the sea
  • Liebig’s Law of the Minimum –
    • Growth is limited NOT BY THE TOTAL RESOURCES AVAILABLE but by the single resource in shortest supply,

The Nitrogen Cycle

  • Free N2 comprises 80% of the atmosphere
    • Not generally biologically available
    • Biological availability requires FIXATION
    • For most of earth’s history, N fixation was mediated by small microbes – cyanobacteria - and was generally in short supply
    • Cyanobacteria are photosynthetic but N2 fixation is inhibited by oxygen. How can this be?
    • Humans now use industrial processes to FIX more N2 than nature on an annual basis
    • Most of the anthropogenically fixed N ultimately winds up in our rivers, estuaries & coastal waters where it promotes HARMFUL ALGAL BLOOMS

The Phosphorus and Silicon Cycles

  • Phosphorus is necessary for nucleic acids (DNA, RNA, ATP etc.), bone, teeth and some shells
  • Silicon (NOT silicone) is used by diatoms and radiolarians to make their skeletons

P and Si cycles involve 3 loops

  • Most rapid cycle involved daily feeding, death and decay of organisms
  • Some organisms fall below the pycnocline where it can take hundreds of years to return to the sunlit portion of the sea
  • Some organisms get buried in the sediments; it may take millions of years –and tectonic activity to return the Si to the surface water
iron and other trace metals
Iron and other trace metals
  • Used in minute quantities
  • Long thought to be in excess supply
    • Iron is very abundant but not very soluble
    • Iron ships and sampling gear contaminated early samples
  • John Martin first showed that iron could limit ocean productivity
  • High nutrient – low chlorophyll (HNLC) areas limited by iron
    • Subarctic Pacific
    • Equatorial Pacific
    • Antarctic convergence
continental dust is a major source of iron to ocean waters

Continental dust is a major source of iron to ocean waters

HNLC areas are far from iron inputs from land runoff or continental dust