Ecosystems and Biodiversity Notes

Unit 1: The Living World - Ecosystems

Introduction to Ecosystems

Interactions between living organisms and their physical environment define an ecosystem.
Biotic Factors: Living components such as plants, animals, microorganisms, fungi, and protists.
Abiotic Factors: Nonliving (physical) components like the hydrosphere, atmosphere, geosphere, nutrients, pH, salinity, dissolved oxygen (DO), wind speed, temperature, and depth.
Biosphere: The region of Earth where life exists, encompassing all ecosystems.
Ecosystem: A community of living organisms and the physical conditions in a specific area.
Ecosystem boundaries can be distinct (e.g., caves, lakes) or indistinct, making it difficult to determine where one ends and another begins.
Ecosystems interact with their surroundings through energy and matter exchange.
Competition: The struggle among individuals to obtain limited shared resources.
Competitive Exclusion Principle: Two species competing for the same limiting resource cannot coexist.
If two species have the same realized niche, the superior competitor will drive the other to extinction.

Resource Partitioning

Species divide a resource based on behavioral or morphological differences.
Natural selection favors individuals in each species that minimize resource overlap. Over generations, species evolve to reduce overlap and partition resource use.

Predation

One animal kills and consumes another.
Prey species evolve defenses to avoid predators.

Parasitism

One organism lives on or in another.
Parasites rarely cause the death of their host.
Pathogen: A parasite that causes disease in its host.
Parasitoid: A predator that lays eggs inside other organisms (the host).

Herbivory

An animal consumes plants or algae.
Abundant herbivores can significantly impact producers.
Producers evolve defenses like spines or distasteful chemicals.

Mutualism

An interaction where both species benefit.
Example: Acacia trees provide food and shelter to ants, which protect the trees from herbivores and competitors.
Example: Coral reefs provide a home for algae, and algae provide corals with sugars through photosynthesis.
Example: Lichens consist of algae and fungi; fungi provide nutrients to algae, and algae provide carbohydrates to fungi via photosynthesis.

Commensalism

One species benefits while the other is neither harmed nor helped.
Example: Birds perch on trees to find food and nest, without affecting the tree.

Species Classification

Native Species: Species living within their historical range for thousands or millions of years.
Exotic (Alien) Species: Species living outside their historical range.
Example: Honeybees were introduced to North America in the 1600s.
Example: Red foxes were introduced to Australia for hunting.

Invasive Species

Species introduced accidentally (e.g., rats on cargo ships) or intentionally (e.g. Fungi introduced to the US, killing American Elm and Chestnut trees).
Many exotic species fail to thrive in new regions.
An exotic species that thrives and harms other species is considered an invasive species.
Examples in the US: rats, zebra mussels, and kudzu.

Terrestrial Biomes

Biomes: Categorized by average annual temperature and precipitation combinations.
Examples: Tropical rainforest, tropical seasonal forest, subtropical desert, woodland/shrubland, temperate grassland, temperate seasonal forest, temperate rainforest, boreal forest, tundra, and polar ice cap.
Terrestrial Biome: Geographic region with a particular combination of average annual temperature, annual precipitation, and distinctive plant growth forms on land.
Plants and animals adapt to the specific climate of the biome.

Aquatic Biomes

Aquatic Biome: Region characterized by salinity, depth, and water flow combination.

Climate Diagrams

Display monthly temperature and precipitation values to help determine a biome's productivity.

Freshwater Biomes

Include streams, rivers, lakes, ponds, and freshwater wetlands.
Often a source of drinking water.

Rivers and Streams

Rivers have high oxygen (O2) levels due to flowing water and air, carrying nutrient-rich sediment to deltas and flood plains.
Flowing fresh water originates from underground springs or runoff from rain/melting snow.
Streams are narrow with small water volumes, while rivers are wider with larger water volumes.

Lakes and Ponds

Contain standing water, some too deep to support emergent vegetation.
Littoral Zone: Shallow water with rooted plants.
Limnetic Zone: Deeper water where plants do not emerge.
Profundal Zone: Deepest water with limited oxygen due to minimal sunlight penetration.
Benthic Zone: Sediments beneath the littoral, limnetic, and profundal zones.

Lake Classification

Classified by fertility levels.
Oligotrophic Lakes: Low phytoplankton due to low nutrients (nitrogen and phosphorus), appearing very clear.
Mesotrophic Lakes: Moderate fertility level.
Eutrophic Lakes: High fertility level, turbid (murky) due to increased algae growth from human-introduced nutrients (fertilizers).

Freshwater Wetlands

Aquatic biome submerged/saturated by water for part of the year, shallow enough to support emergent vegetation.
Among Earth's most productive biomes.
Benefits: Store excess water during storms (reducing floods), recharge groundwater by absorbing rainfall, filter pollutants via plant roots, and support high plant growth due to abundant water and decaying organic matter nutrients.

Biogeochemical Cycles

Movement of matter within and between ecosystems.
Energy flows, and matter cycles.
Reservoir: Stores carbon or other substances.
Movement of matter occurs between sources and sinks.
Source: Releases more greenhouse gas into the atmosphere than it absorbs
Sink: Takes up a chemical element or compound from another part of its natural cycle and holds it a long time (long term reservoir)

The Carbon Cycle

Reservoirs can hold carbon for varying durations.
Largest carbon reservoir: rocks/sediments in the ocean.
7 processes: photosynthesis, respiration, exchange, sedimentation, burial, extraction, and combustion.
Fast parts: living organisms (short carbon storage), CO2 exchange between air/water, combustion of organic carbon.
Slow parts: carbon in rocks, soils, and fossil fuels (millions of years storage).

Photosynthesis

Plants, algae, and phytoplankton remove carbon dioxide ( $CO_2$ ) from the atmosphere and convert it to glucose.
Considered a CO2 sink.

Cellular Respiration

Plants and animals release stored energy.
Uses oxygen ( $O2$ ) to break down glucose, releasing energy and $CO2$ .
Considered a $CO_2$ source.
Both processes are quick and balance carbon in the atmosphere.

Ocean and Atmosphere Exchange

$CO_2$ moves directly between the ocean and atmosphere, dissolving into and out of the ocean surface.
This quick process maintains balance.
Increased $CO_2$ leads to ocean acidification due to increased exchange.

Sedimentation and Burial

Algae and phytoplankton use $CO_2$ for photosynthesis.
Coral reefs and marine organisms use $CO_2$ to make calcium carbonate exoskeletons.
Marine organisms die, sink, and decompose into sediments with carbon (C).
Over time and under pressure, sediments turn into sedimentary stone (e.g., limestone, sandstone), a long-term carbon reservoir.

Extraction and Combustion

Humans extract fossil fuels and combust them (burn).
Combustion (natural fires) releases carbon into the atmosphere.

Human Impacts

Without human influence, the cycle is balanced.
$CO_2$ combustion contributes to global warming.
Greenhouse gases absorb heat emitted from Earth's surface.
$CO_2$ significantly contributes to warming.
Humans accelerate the movement of fossilized carbon to the atmosphere, disrupting the balance.
Tree harvesting increases $CO_2$ in the atmosphere because trees store carbon.
$CO_2$ levels increased from 280 ppm in 1800 to over 420 ppm today.

The Nitrogen Cycle

Nitrogen moves from the atmosphere into soils through fixation pathways, including fertilizer production by humans.
Nitrogen exists in multiple forms in the soil.
Denitrifying bacteria release nitrogen gas back into the atmosphere.
Most reservoirs hold nitrogen for short times; the atmosphere is a major reservoir.
Nitrogen is crucial for plant and animal nutrients, required for DNA and proteins.
Nitrogen Fixation: Converts atmospheric nitrogen gas ( $N2$ ) into usable forms (ammonium ( $NH4$ +) and nitrate ( $NO_3$ −)).
- Available for plant uptake and tissue synthesis.

Types of Nitrogen Fixation

Bacteria Fixation: Soil bacteria (free-living or symbiotic with root nodules) convert $N_2$ into ammonia.
- Cyanobacteria (blue-green algae) and bacteria in legume roots (peas, beans, some trees).
Synthetic Fixation: Humans use fossil fuels to convert $N2$ into $NO3$ (nitrates) for fertilizers.

Nitrification

Conversion of $NH4$ + into nitrite ( $NO2$ −) and then nitrate ( $NO_3$ −) by soil bacteria.

Assimilation

Plants take in nitrates and ammonia from the soil.
Animals obtain them by eating plants and other animals.

Ammonification

Fungi and bacterial decomposers break down organic nitrogen in dead bodies/waste, converting it into ammonia and returning it to the soil.

Denitrification

Conversion of nitrate ( $NO3$ −) into nitrous oxide ( $N2O$ ) and nitrogen gas ( $N_2$ ) by bacteria in anaerobic conditions.

Human Impacts on the Nitrogen Cycle

$N_2O$ (nitrous oxide) is a greenhouse gas, contributing to climate warming.
$N_2O$ is produced by nitrate denitrification in agricultural soils.
Ammonia Volatilization: Excess fertilizer leads to $NH_3$ entering the atmosphere, causing acid precipitation and respiratory irritation.
Leaching and Eutrophication: Synthetic fertilizer use causes nitrates ( $NO_3$ −) to leach out of soil, running into waterways and causing algae blooms.

The Phosphorus Cycle

Begins with weathering/mining of phosphate rocks and use of phosphate fertilizer, releasing phosphorus into soil and water.
Phosphorus is used by producers and moves through the food web.
In water, phosphorus can precipitate and form sediments, transforming into new phosphate rocks over time.
Major reservoirs: rocks and sediments with phosphorus-bearing minerals.
Lacks an atmospheric component.
Limited transfer from ocean to land.
Scarce in aquatic and terrestrial biomes.
Phosphorus is often a limiting factor in undisturbed ecosystems.
Cycle is slow compared to carbon and nitrogen cycles.

Human Impacts on Phosphorus Cycle

Humans mine phosphorus to make fertilizer.
Fertilizer applied to lawns, gardens, and agricultural fields can leach into water bodies.
Leached phosphorus leads to algae growth, causing algal blooms.
Some algae produce toxins during blooms.
After the bloom, algae die and decompose, consuming large amounts of oxygen.
Water becomes hypoxic (low in oxygen), leading to dead zones where fish and other aquatic organisms die.
One of the largest dead zones is at the Mississippi River's mouth in the Gulf of Mexico.
Phosphates in detergents are another source, now banned in some states and the European Union.

The Hydrologic (Water) Cycle

Movement of water between sources and sinks in different states (solid, liquid, gas).
Solar energy drives the water cycle.
Ocean is the largest reservoir.
Ice caps and groundwater are major freshwater reservoirs.

Transpiration

Plants draw groundwater from roots to leaves.
Water evaporates into the atmosphere through leaf openings (stomata).
Evapotranspiration combines evaporation and transpiration for total water entering the atmosphere.

Precipitation Pathways

Runoff: Flows over the surface into water bodies.
Infiltration: Trickles through soil into groundwater aquifers.
Groundwater (aquifers) and surface water (lakes/rivers) are freshwater reservoirs for humans and animals.
Precipitation recharges groundwater if the soil is permeable or runoff recharges surface water.

The Sulfur Cycle

Sulfur exists mostly in rocks.
Weathering releases sulfate ions ( $SO_4^{2-}$ ) that producers assimilate and pass through the food web.
Volcanoes, fossil fuel burning, and copper mining release sulfur dioxide ( $SO_2$ ) into the atmosphere.
Sulfur dioxide combines with water to form sulfuric acid ( $H2SO4$ ), which returns to Earth via rain or snow.

Primary Productivity

Photosynthesis: Plants, algae, and bacteria use solar energy to produce usable sugars, converting carbon dioxide and water into glucose and oxygen.
Cellular Respiration: Cells unlock chemical energy.
- Aerobic Respiration: Conversion of glucose and oxygen into energy, carbon dioxide, and water.
- Anaerobic Respiration: Conversion of glucose into energy without oxygen (less energy produced).
Primary Productivity: Rate of converting solar energy into organic compounds.
Gross Primary Productivity (GPP): Total amount of solar energy producers capture via photosynthesis over time.
Net Primary Productivity (NPP): Energy captured by producers minus the energy producers use for respiration.
Measured in units of energy per area per time (e.g., kcal/m2/year).
Producers typically capture about 1% of available solar energy.
NPP of an ecosystem is about 25-50% of GPP.
Biomass: Total mass of living matter in a specific area.
Standing Crop: Amount of biomass present in an ecosystem at a particular time.

Trophic Levels

1st Law of Thermodynamics: Energy is neither created nor destroyed; it only changes form.
When a tree dies, its carbon, nitrogen, phosphorus, and water return to the soil.
2nd Law of Thermodynamics: Usable energy decreases as you move up a food chain.
Ecological Efficiency: Proportion of consumed energy passed from one trophic level to another.
Trophic Pyramid: Representation of the distribution of biomass, numbers, or energy among trophic levels.
Ecosystems require a continuous inflow of high-quality energy to maintain structure and function.
Energy flows from sun to producers (lowest trophic levels) and then upward in terrestrial and near-surface marine communities.
On average, about 10% of energy moves from one level to the next, with the other 90% used by the organism and lost as heat.
Graphing the numbers of individuals or biomass within each trophic level produces a similar pyramid.

Food Chains and Food Webs

Food Chain: A simple linear diagram linking producers and consumers, illustrating the movement of energy and matter through trophic levels.
Food Web: A model of interlocking food chains showing the flow of energy and nutrients in two or more food chains.

Trophic Level Categories

Producers
Primary Consumers
Secondary Consumers
Scavengers
Detritivores
Decomposers

Feedbacks

Negative Feedback Loop: A system responds to a change by returning to its original state or decreasing the rate of change.
- Example: Mono Lake water level drops, reducing the lake surface area, which decreases evaporation causing the lake level to rise again.
Positive Feedback Loop: Change in a system is amplified.
- Example: Population growth, where more offspring lead to more reproduction, increasing the population size.

Unit 2: The Living World - Biodiversity

Introduction to Biodiversity

Number of species is a common measure of biodiversity.
Estimating the total number of species on Earth is challenging.
Approximately 2 million species have been named.

Levels of Biodiversity

Ecosystem Diversity: Variety of ecosystems within a region.
Species Diversity: Variety of species within an ecosystem.
Genetic Diversity: Variety of genes among individuals of a species.
Habitat Diversity: Variety of habitats within an ecosystem.

Species Types

Specialists: Organisms that live only under a narrow range of biotic or abiotic conditions (e.g., koalas eating only eucalyptus leaves).
Generalists: Organisms that can live under a wide range of biotic and abiotic conditions (e.g., white-tailed deer).
Species Richness (r): Total number of species in a given area. Higher richness indicates good ecosystem health.
Species Evenness: Relative proportion of individuals within different species in an area.

Ecosystem Services

Processes by which life-supporting resources (clean water, timber, fisheries, agricultural crops) are produced.

Categories of Ecosystem Services

Provisions
Regulating Services
Support Systems
Resilience
Cultural Services

Provisions

Goods humans can use directly (e.g., lumber, food crops, medicinal plants, natural rubber, furs).
About 70% of the top 150 prescription drugs in the United States come from natural sources.

Regulating Services

Natural ecosystems regulate environmental conditions.
Tropical rainforests and oceans remove carbon from the atmosphere.
Ecosystems regulate nutrient and hydrologic cycles.

Support Services

Natural ecosystems provide support services like pollination of food crops.
Ecosystems provide natural pest control by providing habitat for predators that prey on agricultural pests, and filter harmful pathogens and chemicals from water.

Cultural Services

Awe-inspiring beauty of nature provides aesthetic benefits.
Scientific funding supports biodiversity research with no guaranteed economic gain.

Threats to Biodiversity (HIPPO)

Habitat Loss (H)
Invasive Species (I)
Pollution (P)
Population (P)
Overharvesting (O)
Habitat Loss: Major cause of declining species diversity, primarily due to human development. Specialized habitats are prone to population declines, with species declining even without complete habitat destruction.
Exotic Species: Moved worldwide by humans, posing threats to biodiversity as predators, pathogens, or superior competitors to native species.
Pollution: Toxic contaminants (pesticides, heavy metals, acids, oil spills), endocrine disruptors, nutrients causing algal blooms and dead zones, and thermal pollution make water bodies too warm for species to survive.
Human Population: Exponential increase in the human population leads to a decrease in biodiversity.
Climate Change: Affects temperature and precipitation patterns, threatening biodiversity.
- Species may migrate to suitable climates, but this isn't always possible.
Overharvesting: Hunting, fishing, and harvesting remove individuals faster than the population can replace them, potentially causing extinction.

Island Biogeography

Habitat size and distance determine species richness.
Larger islands support more total species.
Species richness increases with habitat size.
Islands closer to the mainland support more species due to easier colonization.
Islands have been colonized by new species in the past.
Many island species have evolved to be specialists with limited resources.
Specialists can be threatened by invasive generalist species that outcompete them.

Ecological Tolerance

Range of conditions (temperature, salinity, flow rate, sunlight) an organism can endure before injury or death.
Applies to both individuals and species.

Tolerance Ranges

Optimal Range: Organisms survive, grow, and reproduce.
Zone of Physiological Stress: Organisms survive but experience stress (infertility, lack of growth, decreased activity).
Zone of Intolerance: Organisms will die.
Fundamental Niche: Abiotic conditions under which a species can survive, grow, and reproduce.
Realized Niche: Abiotic and biotic conditions under which a species actually lives.
All species have an ideal range, declining under extreme conditions.
Resilience: Rate at which an ecosystem returns to its original state after a disturbance.
Different species may perform similar functions but vary in disturbance susceptibility.

Natural Disruptions to Ecosystems

Sea level varies with glacial ice changes over geological time.
Environmental change/upheaval results in habitat changes.
Wildlife migrates due to natural disruptions.
Intermediate Disturbance Hypothesis: Ecosystems with intermediate disturbance levels are more diverse than those with high or low levels.

Niche Specialization

Niche Generalist: Can survive under a wide range of conditions.
Niche Specialist: Adapted to a specific habitat or food source.
Niche specialists thrive under constant conditions but are vulnerable to habitat or food source loss.
Niche generalists fare better under changing conditions.
Mass Extinctions: Five global mass extinction events have occurred in the past 500 million years.

Adaptations

Organisms adapt over time (short and long term) through incremental genetic changes.
Environmental changes can be sudden or gradual, threatening a species' survival.
Individuals alter behaviors, move, or die.
Evolution: Change in the genetic composition of a population over time.
Microevolution: Evolution below the species level.
Macroevolution: Evolution that leads to new species, genera, families, classes, or phyla.

Types of Evolution

Evolution by Artificial Selection: Humans determine which individuals breed, selecting for desired traits, yielding numerous livestock breeds and pets, and modern agricultural crops. Can produce unintended results such as herbicide resistance.
Evolution by Natural Selection: The environment determines which individuals survive and reproduce.
Excess offspring are produced, but not all survive.
Individuals differ in their traits which can be passed on.
Trait differences are associated with survival and reproduction differences.

Random Processes of Evolution

Mutation
Gene flow
Genetic drift
Bottleneck effects
Founder effects

Mutation

Random change in the genetic code. Mutations in reproductive cells are passed on.
Some mutations improve survival or reproduction, adding genetic diversity.

Gene Flow

Individuals move from one population to another, altering genetic composition.
High gene flow can prevent adaptation to natural or artificial selection.
Can introduce genetic variation to lacking populations.

Genetic Drift

Change in genetic composition due to random mating.
It is a nonadaptive, random process particularly important in small populations.
Bottleneck Effect: Reduction in genetic diversity due to population size reduction.
- Reduced genetic variation increases disease risk and lowers fertility, reducing ability to adapt to future changes causing decline and extinction.
Extinction: Death of the last member of a species.

Founder Effect

Change in genetic composition due to descent from a small number of colonizing individuals (a subset of the original population's genotypes).

Speciation

Allopatric Speciation: Speciation occurs with geographic isolation, with new species occurring from the larger population if the region differs enough and evolution occurs.
Sympatric Speciation: Evolution of one species into two without geographic isolation, typically due to polyploidy (three or more sets of chromosomes).
- Humans have altered plant species for larger yield, found in some snails and salamanders.

Ecological Succession

Primary Succession: Ecological succession on bare rock surfaces with no soil.
- Pioneer species like algae, lichens, and mosses colonize unoccupied habitats.
Secondary Succession: Succession in disturbed areas retaining their soil.
In lakes, succession fills them with sediments, transforming them into terrestrial habitats over hundreds/thousands of years.

Species Roles

Keystone Species: A significant role in determining community structure, (sea otter, lion, gray wolf, sea star, elephant).
Indicator Species: Indicates ecosystem character or quality through presence, abundance, scarcity, or chemical composition (amphibians, fish, grizzly bears, prairie dogs).
Ecosystem Engineer: A keystone creates/maintains habitat for others.
Pioneer Species: that colonize previously uncolonized land, (lichens, fungi, bacteria, lyme grass).