Comprehensive Biology Notes on Biomes, Ecology, and Earth Systems

Course Organization and Logistics

• Course Identification: General Biology (BIO 105) — Introduction to Biomes, instructed by Dr. Nick Lorusso (Fall 2026).

• Key Upcoming Deadlines:

  • Individual Graphing Assignment: Due Monday, September 14.

  • Group Assignments: Due Saturday, September 19.

• Group Communication Protocols: Group assignments and member coordination are organized through Canvas using direct messaging or in-class interaction.

• Core Agenda Topics:

  • Definition and core parameters of biomes.

  • Survey of planetary environments and global distribution.

  • Methodologies for quantitative and biological biome description.

  • Allocation of time for course policy review and assignment group formation.

Note-Taking Methodologies

• Cornell Method:

  • Structure: Divide the note page into three distinct areas: a main notes area, a narrow cue/question column on the left, and a summary section across the bottom.

  • Implementation: Record lecture details in the main section during class. Formulate review questions and key keywords in the cue column shortly after class, and write a concise summary at the bottom to convert raw notes into an interactive self-testing tool.

  • Reference: Cornell University — Cornell Note-Taking System.

• Outline Method:

  • Structure: Hierarchical organization using bullet points and progressive indentation levels.

  • Flow: Major Topics $\rightarrow$ Key Concepts $\rightarrow$ Supporting Details.

  • Application: Best suited for highly structured lectures moving sequentially through explicit topics.

  • Reference: OpenStax — Outlining Notes.

• Charting Method:

  • Structure: Tabular format organizing information into rows and columns defined by specific categories or characteristics.

  • Application: Ideal for synthesizing, comparing, and contrasting multiple concepts, anatomical structures, or physiological processes across common dimensions.

  • Reference: University of Minnesota — Note-Taking Forms.

• Concept Mapping:

  • Structure: Non-linear visual web starting with central major ideas connected to secondary concepts using labeled arrows, lines, linking words, and structural diagrams.

  • Application: Optimal for understanding complex relationships, biochemical pathways, feedback loops, and multi-step ecological processes.

  • Reference: University of Minnesota — Concept Mapping.

• Sentence Method:

  • Structure: Record content as a series of distinct, numbered or bulleted standalone statements.

  • Application: Useful when lectures present dense information rapidly without immediate structural cues.

  • Reference: OpenStax — Sentence Notes.

• Visual Note-Taking:

  • Structure: Integration of concise written text with sketch diagrams, symbols, directional arrows, and spatial layouts.

  • Application: Maximizes retention when material involves physical structures, spatial relationships, or geographic distributions.

  • Reference: OpenStax — Visual Note-Taking.

Biological Hierarchy and Principles of Ecology

• Biological Levels of Organization: Biological systems are organized hierarchically across distinct scalar levels. Scientific inquiry selects the specific level of organization matching the scale of the question being investigated:

  • Atom $\rightarrow$ Molecule $\rightarrow$ Cell Organelles $\rightarrow$ Cell $\rightarrow$ Tissue $\rightarrow$ Organ $\rightarrow$ System of Organs $\rightarrow$ Organism $\rightarrow$ Population $\rightarrow$ Ecosystem $\rightarrow$ Biome (Bioma) $\rightarrow$ Biosphere.

• Definition of Ecology: Ecology is the scientific study of the complex interactions occurring between living organisms (biotic factors) and their physical and chemical environments (abiotic factors).

Earth System Science (ESS) and Historical Climate Drivers

• Earth System Science (ESS) Framework: ESS integrates principles across traditional academic disciplines (meteorology, geology, biology, chemistry) to analyze Earth as a continuously dynamic, interconnected global system.

• Core Earth System Phenomena:

  • Temperature and precipitation dynamics.

  • Biogeochemical and nutrient cycling ($C$, $N$, $P$, $S$).

  • Phenology (the timing of cyclical and seasonal biological events).

  • Hydrological cycles and chemical transport.

  • Biological rhythms, including circadian rhythms and light/dark photoperiod cycles.

• The Biosphere: The highest level of ecological organization, encompassing the sum of all global ecosystems and living organisms on Earth.

• Biotic and Abiotic Modifiers of Global Climate:

  • Biotic Driving Forces: Biological activity directly alters global abiotic conditions. A primary historical example is the Great Oxidation Event ("Oxygen Revolution"), where the evolution of oxygenic photosynthesis by early cyanobacteria fundamentally transformed Earth's atmosphere and surface chemistry.

  • Solar Energy Input: The Sun serves as the primary external energy driver for Earth's climate system:

  • Approximately $\frac{1}{3}$ ($\sim 30\%$) of incoming solar radiation is immediately reflected back into space by clouds, atmospheric aerosols, and high-albedo surface features (ice, snow).

  • The remaining $\sim 70\%$ of solar energy is absorbed by the atmosphere, continental landmasses, and the hydrosphere.

  • Absorbed solar energy directly powers the global hydrological cycle, atmospheric circulation, surface heating, and weather phenomena.

• Deep Time Geologic Eons and Atmospheric Evolution:

  • Pre-Accretion / Accretion ($\sim 4.5\text{ billion years ago [bya]}$): Formation of Earth; extreme impact rates from solar system debris gradually declined following accretion.

  • Hadean Eon ($4.5 - 4.0\text{ bya}$): High impact rates; solar luminosity was reduced compared to present levels (starting around $\sim 70\%$ of modern intensity).

  • Archean Eon ($4.0 - 2.5\text{ bya}$): Formation of the world's oldest sedimentary rocks (e.g., Isua marine sediments, Barberton and Pilbara formations). Atmospheric carbon dioxide ($CO_2$) and methane ($CH_4$) levels were very high, providing greenhouse warming despite lower solar luminosity. Oldest physical evidence of life emerges near $\sim 3.8\text{ bya}$.

  • Proterozoic Eon ($2.5 - 0.541\text{ bya}$): Marked by the Great Oxidation Event ($\sim 2.4 - 2.3\text{ bya}$), where atmospheric free oxygen ($O_2$) accumulated rapidly, leading to a collapse in atmospheric $CH_4$, severe global glacial intervals ("Snowball Earth" events), and the emergence of eukaryotic fossils.

  • Phanerozoic Eon ($0.541\text{ bya - Present}$): Rapid expansion of multicellular life (Cambrian Explosion), diversification of land plants, fluctuation of atmospheric $O_2$ and $CO_2$, and multi-million-year glacial/interglacial oscillations.

Atmospheric Carbon Dioxide Trends and Global Climate Change

• The Keeling Curve (Mauna Loa Observatory, Hawaii):

  • Continuous long-term atmospheric $CO_2$ monitoring initiated by Charles David Keeling under the Scripps Institution of Oceanography in 1958.

  • Baseline measurements in 1958 began at approximately $315\text{ ppm}$ (parts per million) and exceeded $410\text{ ppm}$ by June 2018.

  • Observations: Measurements revealed two distinct patterns:

  1. Secular Upward Trend: A continuous, accelerating rise in average atmospheric $CO_2$ driven by fossil fuel combustion and industrial land-use changes.

  2. Seasonal Oscillations: A regular annual saw-tooth fluctuation caused by seasonal photosynthesis and respiration in the vast landmasses of the Northern Hemisphere (drawn down in northern spring/summer, releasing $CO_2$ in autumn/winter).

  • Significance: Hawaii was chosen for its isolation to capture pristine, well-mixed global atmospheric air, proving that atmospheric $CO_2$ elevation was a global phenomenon, not a local industrial artifact.

• Empirical Indicators of Contemporary Global Warming:

  • Global Temperature Anomaly ($1850 - 2019$): Combined land (Berkeley Earth) and ocean (UK Hadley Centre) surface temperature datasets show a global temperature anomaly relative to the $1951 - 1980$ baseline exceeding $+0.85\,^\circ\text{C}$ to $+1.0\,^\circ\text{C}$ by 2019.

  • Climatic Research Unit Data ($1860 - 2000$): Mean global surface temperatures rose from a baseline average of $\sim 15.08\,^\circ\text{C}$ ($14.48\,^\circ\text{C} - 14.88\,^\circ\text{C}$ range in late 19th century) up to $\sim 15.68\,^\circ\text{C}$ by the end of the 20th century.

  • GISTEMP Global Gridded Analysis ($1990:2010$\text{ vs }$1901:1920$): Demonstrates a global mean warming of $0.84\,^\circ\text{C}$. Spatial analysis reveals polar amplification, where high Northern Hemisphere latitudes experience significantly higher rate increases ($> 1.5\,^\circ\text{C} - 2.0\,^\circ\text{C}$) compared to equatorial ocean regions.

  • NOAA Recent Trends ($1990 - 2019$): Decadal surface temperature change maps confirm warming rates up to $+1.0\,^\circ\text{F}/\text{decade}$ across vast continental land masses, particularly in the Arctic and sub-Arctic regions.

Biome Fundamentals and Classification Systems

• Definition of Biomes: Biomes are major, broad-scale regional ecological units defined by their predominant vegetation growth forms (terrestrial biomes) or physical and chemical environmental attributes (aquatic biomes).

• Primary Biome Categories:

  • Terrestrial Biomes: Defined and delineated by dominant plant communities, which are constrained by macroclimate patterns and natural disturbance regimes (e.g., fire, grazing, windstorm).

  • Aquatic Biomes: Defined primarily by chemical salinity (freshwater vs. marine ecosystems) and secondarily by light penetration, water depth, flow dynamics, and dominant primary producers.

• Quantitative Biome Delineation Parameters:

  • Primary Abiotic Factors:

  1. Mean Annual Precipitation ($\text{cm}$).

  2. Mean Annual Temperature ($^\circ\text{C}$).

  • Secondary Abiotic Modifiers: Soil properties (pH, nutrient status, mineral composition), light availability, wind exposure (evapotranspiration rates), and disturbance dynamics.

• Whittaker Biome Framework: Maps major terrestrial biomes along continuous axes of annual temperature (ranging from $-15\,^\circ\text{C}$ to $30\,^\circ\text{C}$) and annual precipitation (ranging from $0\text{ cm}$ to $> 400\text{ cm}$):

  • Tropical Rainforest: High annual temperatures ($20\,^\circ\text{C} - 30\,^\circ\text{C}$), extremely high precipitation ($200 - 450\text{ cm}$).

  • Savanna / Tropical Seasonal Forest: High annual temperatures ($20\,^\circ\text{C} - 30\,^\circ\text{C}$), moderate precipitation ($50 - 150\text{ cm}$) with distinct dry seasons.

  • Subtropical Desert: Warm-to-hot temperatures ($15\,^\circ\text{C} - 30\,^\circ\text{C}$), extremely low precipitation ($< 25\text{ cm}$).

  • Chaparral / Mediterranean: Moderate temperatures ($10\,^\circ\text{C} - 20\,^\circ\text{C}$), low-to-moderate winter-dominated rainfall ($30 - 70\text{ cm}$).

  • Temperate Grassland: Moderate-to-cool temperatures ($0\,^\circ\text{C} - 20\,^\circ\text{C}$), low-to-moderate precipitation ($30 - 100\text{ cm}$).

  • Temperate Deciduous / Broadleaf Forest: Moderate annual temperatures ($5\,^\circ\text{C} - 20\,^\circ\text{C}$), moderate-to-high precipitation ($75 - 200\text{ cm}$).

  • Northern Coniferous Forest (Boreal Forest / Taiga): Cold annual temperatures ($-5\,^\circ\text{C}$ to $5\,^\circ\text{C}$), low-to-moderate precipitation ($40 - 100\text{ cm}$).

  • Arctic and Alpine Tundra: Extremely cold temperatures ($-15\,^\circ\text{C}$ to $0\,^\circ\text{C}$), low precipitation ($< 25 - 50\text{ cm}$).

• Alternative Climate Classification Systems:

  • Thornthwaite System: Classifies climates based on potential evapotranspiration, effective precipitation, and vegetation water requirements.

  • Bergeron System: Classifies climate based on air mass characteristics and source regions (e.g., continental polar, maritime tropical).

  • Köppen Climate Classification System: Uses a standardized three-letter code to categorize regional climates based on monthly temperature and precipitation thresholds:

  • First Letter (Major Climate Group):

    • A: Tropical climates (all months average temperature $\ge 18\,^\circ\text{C}$).

    • B: Dry (Arid and Semiarid) climates (precipitation is below potential evapotranspiration).

    • C: Mild Temperate / Mesothermal climates (coldest month average between $-3\,^\circ\text{C}$ and $18\,^\circ\text{C}$).

    • D: Snow / Continental / Microthermal climates (coldest month average $< -3\,^\circ\text{C}$, warmest month $\ge 10\,^\circ\text{C}$).

    • E: Polar climates (all months average temperature $< 10\,^\circ\text{C}$).

  • Second Letter (Precipitation Seasonality): f (fully humid / no dry season), m (monsoonal), s (dry summer), w (dry winter), W (desert), S (steppe), T (tundra), F (frost/ice cap).

  • Third Letter (Temperature Detail): a (hot summer), b (warm summer), c (cool summer), d (extremely cold continental winter), h (hot arid), k (cold arid).

• Case Study: La Crosse Location Biome Identification:

  • Geographic and Physical Parameters: Elevation = $220\text{ m}$, Latitude = $44\,^\circ\text{N}$, Mean Annual Precipitation = $86\text{ cm}$, Mean Annual Temperature = $8\,^\circ\text{C}$.

  • Biome Mapping Result: Overlaying $86\text{ cm}$ annual precipitation and an $8\,^\circ\text{C}$ mean annual temperature onto the Whittaker biome classification places La Crosse within the Temperate Broadleaf / Deciduous Forest biome (located along the ecological transition zone bordering temperate grassland/savanna systems).

Abiotic and Solar Drivers of Global Climate

• Climate vs. Weather:

  • Weather: Short-term, day-to-day atmospheric conditions at a specific location.

  • Climate: Long-term aggregated pattern of weather, including averages, extremes, seasonal timing, variability, and spatial distribution over multi-decade periods.

  • Primary Focus Variables: Temperature, precipitation, sunlight irradiance, and wind vectors (Holdren NCES, 2008).

• Latitudinal Solar Energy Gradients:

  • Earth's spherical shape results in variation in solar angle of incidence relative to latitude:

  • Equator and Tropics ($23.5\,^\circ\text{N}$ to $23.5\,^\circ\text{S}$): Sunlight strikes directly overhead ($\sim 90\,^\circ$ angle), concentrating solar flux density into a small surface area, delivering intense radiant energy per unit area.

  • High Latitudes ($30\,^\circ\text{N/S}$, $60\,^\circ\text{N/S}$, Poles): Solar radiation strikes Earth at an oblique, shallow angle, distributing the energy over a much larger surface area and traversing a thicker atmospheric layer, which increases attenuation and reflection.

  • Axial Tilt and Seasonality: Earth's rotational axis is tilted at $23.5\,^\circ$ relative to its orbital plane. As Earth orbits the Sun, changes in the orientation of Northern and Southern Hemispheres toward the Sun produce pronounced seasonal cycles in solar input and day length.

• Global Atmospheric Circulation and Hadley Cells:

  1. Intense solar heating at the equator warms the surface air, causing high rates of surface water evaporation.

  2. Warm, humid air expands, drops in density, and rises vertically into the upper troposphere at the equator ($0\,^\circ$ latitude).

  3. As the warm air mass ascends, it cools adiabatically. Cool air holds less water vapor than warm air, leading to moisture condensation, heavy cloud formation, and massive rainfall in equatorial regions (driving tropical rainforest biomes).

  4. The high-altitude air mass, now dry, is displaced poleward north and south toward $30\,^\circ$ latitudes.

  5. At approximately $30\,^\circ\text{N}$ and $30\,^\circ\text{S}$, the cold, dry air mass descends toward the Earth's surface. As it descends, it warms adiabatically and absorbs moisture from the land surface, creating hyper-arid belt zones (driving global deserts such as the Sahara, Arabian, and Australian deserts).

Regional Climate Modifiers: Topography and Oceans

• Moderating Effect of Large Water Bodies: Water possesses a high specific heat capacity ($\sim 4.184\text{ J/g}\,^\circ\text{C}$). Oceans and large lakes absorb vast quantities of heat during warm periods without experiencing major temperature shifts, and slowly release heat during cold periods, creating moderate maritime climates along coastal margins.

• Mountain Topography and the Orographic Rain Shadow Effect:

  1. Prevailing winds transport cool, moist air masses inland from oceans toward mountain ranges.

  2. Air encounters the windward slope of the mountain range and is forced upward.

  3. As the air rises, atmospheric pressure decreases, causing the air to expand and cool adiabatically ($\sim 6.5\,^\circ\text{C}$ per $1,000\text{ m}$ elevation gain). Water vapor condenses, producing heavy rain or snow on the windward side.

  4. Dry air passes over the crest and descends down the leeward side of the mountain range.

  5. As the dry air descends, it compresses and warms adiabatically, increasing its moisture-holding capacity and drawing moisture out of the surrounding soil and vegetation.

  6. This process creates a dry region known as a rain shadow on the leeward side of the range.

• Case Study: Atacama Desert (Chile):

  • Located on the western coast of South America, the Atacama Desert is one of the driest places on Earth, with some weather stations recording zero rainfall history.

  • Mechanisms of Aridity:

  • Rain shadow effect: The massive Andes Mountain range blocks moist trade winds blowing from the Amazon basin to the east.

  • Off-shore ocean currents: Cold Humboldt Current flowing northwards cools coastal air, stabilizing the lower atmosphere and suppressing vertical convection required for precipitation.

  • Primary Hydrological Input: Seasonal coastal fog (camanchaca) provides the primary source of ambient moisture for specialized desert vegetation.

• Microclimate: Highly localized atmospheric conditions existing within small-scale spatial zones (e.g., underneath a decaying log, beneath a specific canopy gap, along north- vs. south-facing slopes).

Marine Ecosystems and Environmental Zonation

• General Overview: Marine biomes cover approximately $71\%$ of Earth's surface and are defined by high mean dissolved salt concentration ($\sim 3.5\%$ or $35\text{ g/L}$, dominated by $Na^+$ and $Cl^-$).

• Light Penetration Profiles:

  • Water absorbs and scatters incoming solar radiation exponentially with depth; long red/orange wavelengths are absorbed within upper layers, while short blue/green wavelengths penetrate deepest.

  • Photic Zone: Upper ocean water column where light penetrates.

  • Euphotic Zone: Surface layer receiving sufficient solar light intensity for net photosynthetic carbon fixation to exceed respiratory losses ($\text{P} > \text{R}$).

  • Dysphotic Zone (Twilight Zone): Layer receiving faint solar light; insufficient intensity for photosynthetic balance ($\text{R} > \text{P}$).

  • Aphotic Zone: Deep layer characterized by total absence of sunlight.

• Marine Environmental Zonation Framework:

  • Distance-from-Shore Zonation:

  • Intertidal Zone: Marine margin periodically submerged and exposed by astronomical daily tide cycles.

  • Neritic Zone: Shallow marine environment extending from the low-tide mark to the outer edge of the continental shelf ($\sim 200\text{ m}$ depth).

  • Oceanic Zone: Deep open ocean region beyond the continental shelf break.

  • Depth and Substrate Zonation:

  • Pelagic Province: The open water column ecosystem above the sea floor.

  • Benthic Province: The organic and inorganic sediment bottom substrate underlying the water column.

  • Abyssal Zone: Deep ocean benthic floor extending between $4,000\text{ m}$ and $6,000\text{ m}$ depth.

  • Deep-Sea Trenches (Hadal Zone): Oceanic trench environments extending from $6,000\text{ m}$ to extreme depths of $\sim 11,000\text{ m}$ (e.g., Mariana Trench).

  • Pelagic Vertical Stratification:

  • Epipelagic Zone: Surface down to $200\text{ m}$ (corresponds to photic zone).

  • Mesopelagic Zone: $200\text{ m}$ down to $1,000\text{ m}$ ($650\text{ ft}$ to $3,300\text{ ft}$).

  • Bathypelagic Zone: $1,000\text{ m}$ down to $4,000\text{ m}$ ($3,300\text{ ft}$ to $13,000\text{ ft}$).

  • Abyssopelagic Zone: $4,000\text{ m}$ down to the benthic ocean floor.

Coastal and Dynamic Marine Habitats

• Intertidal Zones:

  • Environmental Dynamics: Extremely harsh ecosystem subject to variable inundation. Organisms face daily fluctuations in thermal shock, fluctuating salinity (dilution via rain, concentration via evaporation), desiccation stress, and high mechanical kinetic forces from breaking ocean waves.

  • Nutrient and Oxygen Availability: High levels of dissolved oxygen due to constant wave mixing and rapid nutrient turnover.

  • Substrate Types: Typically divided into exposed rocky shorelines or mobile sandy/muddy sediments.

  • Biological Community: Includes sessile organisms (barnacles, mussels) anchored to rocks, macroalgae, and predatory invertebrates (sea stars, sea anemones).

• Estuaries:

  • Definition: Semi-enclosed coastal ecosystems where freshwater discharged from rivers and streams mixes directly with ocean saltwater.

  • Physiochemical Characteristics: Variable salinity gradients (fluctuating with tide stage and river flow), shallow water column, high terrestrial sediment loading, and intense nutrient richness.

  • Productivity: Exceptionally high biological productivity; acts as essential nursery grounds for diverse marine invertebrate and fish species.

  • Major Types: Salt marshes, mangrove forests, and tidal river estuaries.

Freshwater Ecosystems: Lakes, Ponds, and Trophic Dynamics

• Freshwater System Characteristics: Environments containing low dissolved salt concentrations ($< 0.1\%$ or $< 0.5\text{ ppt}$).

• Freshwater Lake Zonation:

  • Littoral Zone: Shallow, warm, well-lit surface water directly adjacent to the shoreline where light penetrates to the bottom sediment. Supports rooted emergent (e.g., cattails) and floating-leaved aquatic macrophyte plants.

  • Limnetic Zone: Open, well-lit water column away from the shore, dominated by microscopic floating primary producers (phytoplankton) and zooplankton.

  • Profundal / Aphotic Zone: Deep water layer below the depth of effective light penetration ($< 1\%$ surface light intensity); dominated by decomposers and heterotrophic organisms.

  • Benthic Zone: Soil and organic mud substrate at the bottom inhabited by benthos organisms.

  • Photic Zone Variation: Depth of the photic zone varies from a few centimeters in highly turbid/eutrophic waters up to $\sim 5\text{ m}$ or more in clear systems. Shallow ponds lack an aphotic zone entirely.

• Lake Trophic Classification and Ecological Challenges:

  • Oligotrophic Lakes:

  • Characteristics: Low nutrient concentrations (low $N$ and $P$), low primary algal biomass, clear transparent water, high dissolved oxygen ($O_2$) concentration throughout the water column year-round.

  • Morphology: Typically deep basin profile with steep sides and a low watershed surface area to lake volume ratio.

  • Ecological Challenge: Extreme nutrient limitation restricts primary productivity, limiting food chain carrying capacity.

  • Eutrophic Lakes:

  • Characteristics: High nutrient concentrations (high $N$ and $P$), high phytoplankton/algal density, reduced water clarity, high organic sediment accumulation.

  • Morphology: Often shallower basins with extensive littoral zones.

  • Ecological Challenge: Cultural eutrophication (excess human fertilizer runoff) triggers intense algal blooms. When dense algal biomass dies, microbial decomposers consume vast amounts of oxygen, causing severe hypoxia/anoxia in deeper waters, resulting in mass fish kills and biological "dead zones".

Lake Stratification and Seasonal Turnover

• Physical Properties of Water Density: Pure liquid water exhibits an anomalous density curve, reaching maximum density at $4\,^\circ\text{C}$ ($\sim 1.000\text{ g/mL}$). Water cools below $4\,^\circ\text{C}$ down to $0\,^\circ\text{C}$ becomes less dense ($0.9998\text{ g/mL}$), enabling ice to float on liquid water.

• The Thermocline: A distinct vertical temperature gradient layer in a stratified water body, separating warmer, lower-density, oxygenated upper surface water from colder, denser, nutrient-rich bottom water.

• Annual Four-Season Turnover Cycle (Dimictic Temperate Lakes):

  • Winter Stratification: Ice covers the lake surface at $0\,^\circ\text{C}$. Below ice, temperature increases with depth: surface water $2\,^\circ\text{C}$, bottom water $4\,^\circ\text{C}$. High dissolved oxygen is trapped under ice at the top; organic debris and nutrients concentrate at the bottom sediment layer.

  • Spring Turnover: Surface ice melts and water warms up to $4\,^\circ\text{C}$. The entire water column reaches uniform temperature ($4\,^\circ\text{C}$) and uniform density ($1.000\text{ g/mL}$). Spring wind shear across the surface easily mixes the entire lake column, driving oxygen to deep waters and re-suspending bottom nutrients to the surface photic zone.

  • Summer Stratification: Solar warming heats upper surface water (Epilimnion, e.g., $22\,^\circ\text{C}$). Deep water (Hypolimnion) remains cold ($4\,^\circ\text{C}$). A sharp Thermocline forms between $8\,^\circ\text{C}$ and $5\,^\circ\text{C}$. Density differences prevent wind mixing; upper waters remain oxygen-rich but nutrient-depleted, while deep waters become nutrient-rich but oxygen-depleted.

  • Fall Turnover: Air temperatures drop, cooling surface waters down to $4\,^\circ\text{C}$. Density uniformity ($4\,^\circ\text{C}$ throughout) is restored across the lake depth. Fall winds cause vertical mixing, thoroughly re-distributing nutrients and oxygen prior to winter ice cover.

Lotic Ecosystems: River Continuum and Flow Dynamics

• Definition: Lotic ecosystems are running, flowing freshwater systems moving unidirectionally under gravity, ranging from headwater trickles to wide river systems.

• River Continuum Concept (Longitudinal Gradient):

  • Headwaters (Source / Upper Reaches):

  • Physical Attributes: High slope elevation, narrow bedrock/boulder channels, steep hydraulic gradients.

  • Water Characteristics: Fast-moving current, clear, cold temperatures, nutrient-poor, extremely high dissolved oxygen ($O_2$).

  • Biological Adaptations: Organisms possess structural adaptations to withstand current drag (e.g., flattened bodies, suction cups, silk anchorage).

  • Middle Reaches:

  • Physical Attributes: Channel widens, channel slope flattens out.

  • Water Characteristics: Flow velocity decreases, water temperature warms slightly, sediment and nutrient loading increases, dissolved oxygen decreases relative to headwaters.

  • Downstream Reaches (River Mouth / Lower Reaches):

  • Physical Attributes: Flat, wide floodplain, meandering channels, thick fine sediment deposits.

  • Water Characteristics: Slow-moving, warm water, turbid/muddy, highly nutrient-rich, low dissolved oxygen ($O_2$).

  • Productivity: High phytoplankton and fish biomass adapted to silty, warmer habitats.

Wetland Ecosystems: Marshes, Swamps, and Bogs

• General Definition: Wetlands are transitional land areas flooded, covered, or saturated with water for periods long enough to support aquatic-adapted vegetation (hydrophytes) and hydric anaerobic soils.

• Three Primary Types of Wetlands:

  • Marshes:

  • Vegetation: Dominated by non-woody, herbaceous emergent vascular plants (grasses, sedges, reeds, cattails).

  • Conditions: High nutrient availability, neutral-to-slightly alkaline pH, shallow water levels with high biological productivity.

  • Swamps:

  • Vegetation: Dominated by woody vegetation, including flooded trees (e.g., Bald Cypress) and shrubs.

  • Conditions: Located along low-lying river floodplains and saturated basins; nutrient-rich with continuous water saturated conditions.

  • Bogs:

  • Vegetation: Dominated by mat-forming Sphagnum peat mosses, ericaceous shrubs, and specialized carnivorous plants.

  • Conditions: Stagnant, waterlogged basins fed primarily by rain precipitation rather than runoff. Characterized by acidic conditions, low mineral nutrient levels, and low oxygen levels. Microorganism decomposition is severely suppressed, causing dead plant matter to accumulate over time as thick layers of peat.

Course Organization and Logistics

• Course Identification: BIO 105 (General Biology) — Introduction to Biomes, instructed by Dr. Nick Lorusso (Fall 2026).

• Key Deadlines: Individual Graphing Assignment due Monday, September 14; Group Assignments due Saturday, September 19.

• Communication: Coordinated via Canvas direct messaging or in-class interaction.

Note-Taking Methodologies

• Cornell Method: Main note section paired with a left cue/question column and a bottom summary section for interactive self-testing.

• Outline Method: Hierarchical bulleted organization ($\text{Major Topics} \rightarrow \text{Key Concepts} \rightarrow \text{Supporting Details}$).

• Charting Method: Tabular row/column format for comparing concepts across standardized dimensions.

• Concept Mapping: Non-linear visual web connecting ideas via labeled arrows, ideal for multi-step processes.

• Sentence Method: Sequential numbered or bulleted statements for fast-paced lectures.

• Visual Note-Taking: Merges text with diagrams, symbols, and spatial layouts to boost memory retention.

Biological Hierarchy and Principles of Ecology

• Biological Levels: $\text{Atom} \rightarrow \text{Molecule} \rightarrow \text{Cell Organelles} \rightarrow \text{Cell} \rightarrow \text{Tissue} \rightarrow \text{Organ} \rightarrow \text{System of Organs} \rightarrow \text{Organism} \rightarrow \text{Population} \rightarrow \text{Ecosystem} \rightarrow \text{Biome} \rightarrow \text{Biosphere}$.

• Definition of Ecology: Scientific study of interactions between living organisms (biotic factors) and their non-living physical/chemical environment (abiotic factors).

Earth System Science (ESS) and Historical Climate Drivers

• ESS Framework: Integrates atmospheric, biological, chemical, and geological disciplines to study Earth as an interconnected dynamic system; the Biosphere encompasses all global ecosystems.

• Solar Drivers & Biotic Modifiers: Sun is the primary climate driver ($\sim 30\%$ reflected, $\sim 70\%$ absorbed). Biological events alter climate, such as cyanobacteria driving the Great Oxidation Event.

• Deep Time Geologic Eons:

  • Hadean ($4.5 - 4.0\text{ bya}$): High planetesimal impacts, lower solar luminosity.

  • Archean ($4.0 - 2.5\text{ bya}$): High greenhouse gases ($CO_2$, $CH_4$), oldest rocks, emergence of life ($\sim 3.8\text{ bya}$).

  • Proterozoic ($2.5 - 0.541\text{ bya}$): Great Oxidation Event ($\sim 2.4 - 2.3\text{ bya}$), drop in $CH_4$, global glaciations ("Snowball Earth"), eukaryotic fossils.

  • Phanerozoic ($0.541\text{ bya - Present}$): Explosion of multicellular life, land plant diversification, climate oscillations.

Atmospheric Carbon Dioxide Trends and Global Climate Change

• Keeling Curve (Mauna Loa): Continuous $CO_2$ measurements showing a continuous secular upward trend ($315\text{ ppm}$ in 1958 to $> 410\text{ ppm} in 2018) driven by fossil fuels, plus annual seasonal oscillations from Northern Hemisphere vegetation photosynthesis/respiration.\n- **Empirical Warming Indicators:** Mean surface global temperatures have increased by +0.85\,^\circ\text{C}$to$+1.0\,^\circ\text{C} relative to mid-20th-century baselines, exhibiting strong polar amplification.\n\n### Biome Fundamentals and Classification Systems\n- **Biome Definition:** Large regional ecological units classified by dominant vegetation growth forms (terrestrial) or physical/chemical traits (aquatic).\n- **Key Delineation Parameters:** Primary drivers are mean annual precipitation (\text{cm}$) and mean annual temperature ($^\circ\text{C}), modified by soil, light, wind, and disturbances.\n- **Whittaker Framework:** Categorizes biomes (e.g., Tropical Rainforest, Savanna, Subtropical Desert, Chaparral, Temperate Grassland, Temperate Deciduous Forest, Boreal Forest, Tundra) across temperature and precipitation axes.\n- **Köppen Classification:** Standardized three-letter system designating major climate groups (`A`-`E`), precipitation seasonality (`f`, `m`, `s`, `w`, etc.), and temperature detail (`a`-`d`, `h`, `k`).\n- **La Crosse Case Study:** Elevation 220\text{ m}$, Latitude$44\,^\circ\text{N}$, precip$86\text{ cm}$, temp$8\,^\circ\text{C}$$\rightarrow **Temperate Broadleaf / Deciduous Forest** biome.\n\n### Abiotic and Solar Drivers of Global Climate\n- **Weather vs. Climate:** Weather is short-term atmospheric behavior; climate represents multi-decadal patterns, averages, and extremes.\n- **Solar Geometry:** Direct solar flux hits the tropics (\sim 90\,^\circ$angle), while high latitudes receive oblique solar angles. Earth's$23.5\,^\circ axial tilt creates seasons.\n- **Hadley Cells:** Intense equatorial heating causes warm air to ascend, cool adiabatically, condense, and produce heavy rainfall. Dry air is displaced poleward and descends at 30\,^\circ\text{N/S}, warming adiabatically to create major desert belts.\n\n### Regional Climate Modifiers: Topography and Oceans\n- **Water Moderation:** Oceans have high specific heat (\sim 4.184\text{ J/g}\,^\circ\text{C}), buffering coastal maritime temperatures.\n- **Orographic Rain Shadow:** Windward mountain slopes force air upward, causing adiabatic cooling and precipitation; descending air on leeward slopes warms adiabatically, drying the region (e.g., Atacama Desert behind the Andes).\n- **Microclimate:** Micro-scale atmospheric conditions within small spatial zones (e.g., under decaying logs).\n\n### Marine Ecosystems and Environmental Zonation\n- **General Overview:** Oceans cover \sim 71\%$of Earth with$\sim 3.5\% salinity.\n- **Light Profiles:** Euphotic zone (\text{P} > \text{R}$), Dysphotic zone ($\text{R} > \text{P}), and Aphotic zone (total darkness).\n- **Zonation:**\n - **Shore Distance:** Intertidal, Neritic (over continental shelf to 200\text{ m}), Oceanic.\n - **Depth/Substrate:** Pelagic (open water column), Benthic (sediment bottom), Abyssal (4,000 - 6,000\text{ m}$), Hadal ($> 6,000\text{ m} trenches).\n - **Pelagic Layers:** Epipelagic (0-200\text{ m}$), Mesopelagic ($200-1,000\text{ m}$), Bathypelagic ($1,000-4,000\text{ m}$), Abyssopelagic ($> 4,000\text{ m}).\n- **Coastal Habitats:**\n - **Intertidal:** Extreme physical challenges including tidal exposure, thermal shock, desiccation, and wave action.\n - **Estuaries:** Highly productive transition zones where river freshwater mixes with ocean saltwater.\n\n### Freshwater Systems, Lake Dynamics, and Wetlands\n- **Freshwater Traits:** Low salinity (< 0.1\%).\n- **Lake Zonation:** Littoral (shallow, rooted macrophytes), Limnetic (open photic water), Profundal/Aphotic (deep water), Benthic (bottom sediment).\n- **Trophic Status:**\n - **Oligotrophic:** Low nutrients (N$,$P$), clear water, high dissolved oxygen ($O_2), low biological productivity.\n - **Eutrophic:** High nutrients, dense algal blooms; decomposition can cause severe hypoxia/anoxia and fish kills.\n- **Seasonal Turnover (Dimictic Lakes):** Water reaches maximum density at 4\,^\circ\text{C}$. Summer features warm upper water (**Epilimnion**) separated from cold bottom water (**Hypolimnion**) by a **Thermocline**. Spring and fall turnovers mix the entire lake at uniform$4\,^\circ\text{C}, redistributing nutrients and oxygen.\n- **Lotic Systems (Rivers):** Headwaters are cold, steep, fast, clear, and high in O_2$; downstream reaches are wider, warmer, slower, silty, and nutrient-rich.</p></li><li><p><strong>Wetlands:</strong></p><ul><li><p><strong>Marshes:</strong> Non-woody emergent herbaceous plants, high nutrients.</p></li><li><p><strong>Swamps:</strong> Woody trees and shrubs, nutrient-rich flooded soils.</p></li><li><p><strong>Bogs:</strong> Acidic, stagnant, nutrient-poor waters dominated by <em>Sphagnum</em> moss and accumulating peat.</p></li></ul></li></ul><p></p><h5 id="b4fc106f-1138-4015-a391-8e6d1404dd83" data-toc-id="b4fc106f-1138-4015-a391-8e6d1404dd83" collapsed="false" seolevelmigrated="true">Course Organization and Logistics</h5><ul><li><p><strong>Course Identification:</strong> General Biology (BIO 105) — Introduction to Biomes, instructed by Dr. Nick Lorusso (Fall 2026).</p></li><li><p><strong>Key Upcoming Deadlines:</strong></p><ul><li><p>Individual Graphing Assignment: Due Monday, September 14.</p></li><li><p>Group Assignments: Due Saturday, September 19.</p></li></ul></li><li><p><strong>Communication:</strong> Organized through Canvas direct messaging or in-class interaction.</p></li></ul><h5 id="e28b79c2-252c-432e-b5d1-bbbd91dfea22" data-toc-id="e28b79c2-252c-432e-b5d1-bbbd91dfea22" collapsed="false" seolevelmigrated="true">Note-Taking Methodologies</h5><ul><li><p><strong>Cornell Method:</strong> Divides page into notes, left cue column, and bottom summary section for interactive self-testing.</p></li><li><p><strong>Outline Method:</strong> Hierarchical structure using bullet points ($\text{Major Topics} \rightarrow \text{Key Concepts} \rightarrow \text{Details}$).</p></li><li><p><strong>Charting Method:</strong> Tabular layout comparing concepts across standardized categories.</p></li><li><p><strong>Concept Mapping:</strong> Non-linear visual web connecting ideas via labeled arrows.</p></li><li><p><strong>Sentence Method:</strong> Standalone statements recorded sequentially for fast-paced lectures.</p></li><li><p><strong>Visual Note-Taking:</strong> Merges text with diagrams and symbols to enhance spatial retention.</p></li></ul><h5 id="4398278e-c525-43e2-a01f-54eca691697d" data-toc-id="4398278e-c525-43e2-a01f-54eca691697d" collapsed="false" seolevelmigrated="true">Biological Hierarchy and Principles of Ecology</h5><ul><li><p><strong>Biological Hierarchy:</strong> Scientific inquiry selects the scalar level that matches the question:</p><ul><li><p>$\text{Atom} \rightarrow \text{Molecule} \rightarrow \text{Organelle} \rightarrow \text{Cell} \rightarrow \text{Tissue} \rightarrow \text{Organ} \rightarrow \text{Organ System} \rightarrow \text{Organism} \rightarrow \text{Population} \rightarrow \text{Ecosystem} \rightarrow \text{Biome} \rightarrow \text{Biosphere}$</p></li></ul></li><li><p><strong>Definition of Ecology:</strong> The study of interactions between living organisms (biotic factors) and their non-living environment (abiotic factors).</p></li></ul><h5 id="0e0ac347-6a0d-4258-a944-0784a7ffc4ea" data-toc-id="0e0ac347-6a0d-4258-a944-0784a7ffc4ea" collapsed="false" seolevelmigrated="true">Earth System Science (ESS) and Historical Climate Drivers</h5><ul><li><p><strong>ESS Framework:</strong> Combines scientific disciplines to study Earth as an interconnected global system.</p></li><li><p><strong>The Biosphere:</strong> The sum of all global ecosystems on Earth.</p></li><li><p><strong>Solar Radiation:</strong> The primary climate driver ($\sim 30\%$reflected,$\sim 70\%$absorbed to power global weather and water cycles).</p></li><li><p><strong>Geologic Eons Summary:</strong></p><ul><li><p><strong>Hadean ($4.5 - 4.0\text{ bya}$):</strong> High asteroid impacts and lower solar luminosity.</p></li><li><p><strong>Archean ($4.0 - 2.5\text{ bya}$):</strong> High atmospheric$CO_2$and$CH_4$; oldest life evidence emerges ($\sim 3.8\text{ bya}$).</p></li><li><p><strong>Proterozoic ($2.5 - 0.541\text{ bya}$):</strong> Great Oxidation Event ($\sim 2.4\text{ bya}$) driven by cyanobacteria, triggering global glaciations ("Snowball Earth") and eukaryotic evolution.</p></li><li><p><strong>Phanerozoic ($0.541\text{ bya - Present}$):</strong> Rapid expansion of multicellular life and land plants.</p></li></ul></li></ul><h5 id="d0782af1-9428-4d45-8bea-a70e796983a4" data-toc-id="d0782af1-9428-4d45-8bea-a70e796983a4" collapsed="false" seolevelmigrated="true">Atmospheric Carbon Dioxide Trends and Global Climate Change</h5><ul><li><p><strong>The Keeling Curve (Mauna Loa Observatory):</strong> Long-term atmospheric$CO_2$tracking initiated in 1958 ($315\text{ ppm}$) showing:</p><ul><li><p><strong>Secular Upward Trend:</strong> Continuous rise driven by fossil fuel combustion ($> 410\text{ ppm}$by 2018).</p></li><li><p><strong>Seasonal Oscillations:</strong> Annual fluctuations caused by Northern Hemisphere photosynthetic drawdown and respiration.</p></li></ul></li><li><p><strong>Empirical Warming Indicators:</strong> Mean global surface temperature has increased by$+0.85\,^\circ\text{C}$to$+1.0\,^\circ\text{C}$relative to mid-20th-century baselines, showing strong polar amplification.</p></li></ul><h5 id="d75b901e-313b-4dfd-a623-867ab196f01a" data-toc-id="d75b901e-313b-4dfd-a623-867ab196f01a" collapsed="false" seolevelmigrated="true">Biome Fundamentals and Classification Systems</h5><ul><li><p><strong>Biome Definition:</strong> Large regional ecological units defined by vegetation growth forms (terrestrial) or physical/chemical attributes (aquatic).</p></li><li><p><strong>Primary Drivers:</strong> Mean annual precipitation ($\text{cm}$) and mean annual temperature ($^\circ\text{C}$).</p></li><li><p><strong>Whittaker Framework:</strong> Classifies biomes (e.g., Tropical Rainforest, Savanna, Desert, Chaparral, Temperate Grassland, Deciduous Forest, Boreal Forest, Tundra) across temperature and precipitation axes.</p></li><li><p><strong>Köppen System:</strong> Uses a 3-letter code denoting major climate group (<code>A</code>–<code>E</code>), precipitation seasonality, and temperature profile.</p></li><li><p><strong>La Crosse Location Case Study:</strong> Elevation$220\text{ m}$, Latitude$44\,^\circ\text{N}$, precipitation$86\text{ cm}$, temperature$8\,^\circ\text{C}$$\rightarrow$<strong>Temperate Broadleaf / Deciduous Forest</strong>.</p></li></ul><h5 id="9419e8c5-1e11-470b-bc21-6c0d78a45b68" data-toc-id="9419e8c5-1e11-470b-bc21-6c0d78a45b68" collapsed="false" seolevelmigrated="true">Abiotic and Solar Drivers of Global Climate</h5><ul><li><p><strong>Weather vs. Climate:</strong> Weather is short-term daily atmospheric condition; climate is the long-term pattern over decades.</p></li><li><p><strong>Solar Geometry:</strong> Direct overhead sunlight hits the tropics ($\sim 90\,^\circ$angle), concentrating heat energy. High latitudes receive oblique sunlight spread over larger areas.</p></li><li><p><strong>Earth's Axial Tilt ($23.5\,^\circ$):</strong> Produces pronounced seasonal changes during Earth's orbit.</p></li><li><p><strong>Hadley Cells:</strong> Intense solar heating at the equator causes warm, humid air to ascend, cool adiabatically, and drop rain (tropical rainforests). Dry air descends at$30\,^\circ\text{N/S}$latitude, creating major desert belts.</p></li></ul><h5 id="d692a169-4c3c-4120-be0e-286cd3873742" data-toc-id="d692a169-4c3c-4120-be0e-286cd3873742" collapsed="false" seolevelmigrated="true">Regional Climate Modifiers: Topography and Oceans</h5><ul><li><p><strong>Ocean Water Moderation:</strong> High specific heat ($\sim 4.184\text{ J/g}\,^\circ\text{C}$) allows oceans to buffer coastal maritime temperatures.</p></li><li><p><strong>Orographic Rain Shadow Effect:</strong></p><ul><li><p>Windward slope forces moist air upward$\rightarrow$cools adiabatically$\rightarrow$precipitation.</p></li><li><p>Leeward slope receives dry descending air$\rightarrow$warms adiabatically, drawing moisture from the land (e.g., Atacama Desert).</p></li></ul></li><li><p><strong>Microclimate:</strong> Small, highly localized environmental conditions (e.g., under a decaying log).</p></li></ul><h5 id="3195bc6d-d695-4e7f-8855-4949d363381d" data-toc-id="3195bc6d-d695-4e7f-8855-4949d363381d" collapsed="false" seolevelmigrated="true">Marine Ecosystems and Environmental Zonation</h5><ul><li><p><strong>General Traits:</strong> Oceans cover$\sim 71\%$of Earth with an average salinity of$\sim 3.5\%$($35\text{ g/L}$).</p></li><li><p><strong>Light Profiles:</strong></p><ul><li><p><strong>Euphotic Zone:</strong> Net photosynthesis exceeds respiration ($\text{P} > \text{R}$).</p></li><li><p><strong>Dysphotic Zone:</strong> Faint light, respiration exceeds photosynthesis ($\text{R} > \text{P}$).</p></li><li><p><strong>Aphotic Zone:</strong> Complete darkness.</p></li></ul></li><li><p><strong>Zonation Parameters:</strong></p><ul><li><p><strong>Shore Distance:</strong> Intertidal, Neritic (continental shelf to$200\text{ m}$), Oceanic.</p></li><li><p><strong>Depth/Substrate:</strong> Pelagic (open water), Benthic (sea floor), Abyssal ($4,000 - 6,000\text{ m}$), Hadal ($> 6,000\text{ m}$trenches).</p></li></ul></li></ul><h5 id="82d5aa2b-79b7-4e04-951d-b56962fee74f" data-toc-id="82d5aa2b-79b7-4e04-951d-b56962fee74f" collapsed="false" seolevelmigrated="true">Coastal Habitats</h5><ul><li><p><strong>Intertidal Zone:</strong> Periodically submerged and exposed by daily tides; organisms adapt to thermal shock, salinity changes, desiccation, and wave impact.</p></li><li><p><strong>Estuaries:</strong> Highly productive transition zones where river freshwater mixes with ocean saltwater.</p></li></ul><h5 id="3301070e-90cf-4aff-b4bb-f31ce2d840e2" data-toc-id="3301070e-90cf-4aff-b4bb-f31ce2d840e2" collapsed="false" seolevelmigrated="true">Freshwater Ecosystems and Lake Dynamics</h5><ul><li><p><strong>Freshwater Traits:</strong> Low dissolved salt concentration ($< 0.1\%$).</p></li><li><p><strong>Lake Zonation:</strong> Littoral (shallow, rooted plants), Limnetic (open photic water), Profundal/Aphotic (deep unlit water), Benthic (bottom substrate).</p></li><li><p><strong>Trophic Classification:</strong></p><ul><li><p><strong>Oligotrophic:</strong> Low nutrients, clear water, high dissolved oxygen, low biological productivity.</p></li><li><p><strong>Eutrophic:</strong> Nutrient-rich (high$N$and$P$), dense algal blooms; decomposition depletes oxygen, creating dead zones and fish kills.</p></li></ul></li><li><p><strong>Seasonal Turnover (Dimictic Lakes):</strong> Water is densest at$4\,^\circ\text{C}.

  • Summer Stratification: Warm upper layer (Epilimnion) is separated from cold bottom layer (Hypolimnion) by a Thermocline.

  • Spring & Fall Turnover: Uniform 4\,^\circ\text{C}$$ temperature across the water column allows wind to mix the lake, redistributing oxygen and nutrients.