Biogeochemical Cycles and Earth History

CHNOPS Elements

Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur; six biogenic elements that form ~95% of living biomass.

Potassium, Sodium, Calcium Role

Macro-nutrients necessary for biological functions, but NOT part of the core CHNOPS six elements.

Ecological Niche

The functional role, position, and resource utilization of an organism within its community (its "profession").

Habitat

The specific physical location or environment where an organism lives (its "address").

Levels of Biological Organization (Highest to Lowest)

Biosphere -> Ecosystem -> Community -> Population -> Organism -> Organ System -> Organ -> Tissue -> Cell -> Organelle -> Molecule -> Atom.

Biosphere

The global ecological system integrating all living beings and their physical environment.

Ecosystem

A biological community interacting with its abiotic physical environment.

Community

All interacting populations of different species occupying a defined geographic area.

Population

A group of interbreeding individuals of the same species living in a specified area.

Organism

An individual living entity (e.g., a single animal, plant, or bacterium).

Keystone Species

A species that exerts a disproportionately large influence on ecosystem structure and stability relative to its abundance.

Endemic Species

A species natively restricted to a single specific, defined geographic region.

Invasive Species

Non-native organisms introduced to an ecosystem that outcompete native species and disrupt ecological balance.

Indicator Species

Organisms whose presence, absence, or health reflects environmental conditions or ecosystem quality.

Mutualism (+/+)

A symbiotic interaction where both participating species benefit (e.g., mycorrhizal fungi and plant roots).

Commensalism (+/0)

A symbiotic interaction where one species benefits while the other is neither helped nor harmed (e.g., barnacles on whales).

Parasitism (+/-)

A symbiotic interaction where one organism benefits at the direct expense of its host.

Predation & Competition

Non-symbiotic interspecific interactions driving natural selection and food web structure.

Habitable Zone ("Goldilocks Zone")

The distance range from a star where surface temperatures allow liquid water to persist under an atmosphere.

LUCA (Last Universal Common Ancestor)

The inferred shared ancestor of all modern life, identified via shared genes across Archaea, Bacteria, and Eukaryota.

LUCA Environment

Oxygen-free, high-temperature environment harvesting energy from deep-sea chemical gradients.

Prokaryotes vs. Eukaryotes

Prokaryotes lack a membrane-bound nucleus and organelles; Eukaryotes possess linear DNA within a nucleus and complex organelles.

Autotrophs vs. Heterotrophs

Autotrophs synthesize organic carbon directly from inorganic sources; Heterotrophs consume organic carbon from other organisms.

Endosymbiosis

Evolutionary process where host cells engulfed free-living prokaryotes, transitioning them into organelles (mitochondria & chloroplasts).

Evidence for Endosymbiosis

Circular DNA, double membranes, independent binary fission, and genetic homology with bacteria.

Cambrian Radiation (Explosion)

Rapid biological diversification (~542-540 Ma) yielding major animal phyla, exoskeletons, and compound eyes.

Mass Extinctions

Catastrophic events causing widespread species loss, altering ecosystems and triggering adaptive radiation among survivors.

Bioenergetics

The flow of energy through living systems at cellular and ecosystem levels.

Metabolism

The sum of all energy-consuming (anabolic) and energy-generating (catabolic) chemical reactions in a cell or organism.

First Law of Thermodynamics

Energy cannot be created or destroyed; it can only be transferred or transformed from one form to another.

Second Law of Thermodynamics

Energy transfers are inefficient, producing unusable heat energy and increasing systemic entropy.

Entropy

A measure of randomness or disorder in a system; living organisms require continuous energy inputs to maintain low entropy.

Open System

A physical system that freely exchanges both energy and matter with its surroundings (all living organisms are open systems).

Potential Energy

Stored energy associated with an object's position, spatial structure, or chemical state.

Chemical Energy

A form of potential energy stored within molecular bonds (e.g., ATP, sugars) released when bonds break.

Kinetic Energy

The energy associated with motion (e.g., flowing water, cellular movement, heat).

Photoautotroph

Organism that uses solar radiation to synthesize organic compounds from CO2 (e.g., plants, cyanobacteria).

Chemoautotroph

Organism (bacteria/archaea) that oxidizes inorganic compounds (H2S, methane) for energy in lightless environments.

Trophic Level

The positional step or energy level an organism occupies within a food chain or web.

Producers

Autotrophic organisms forming the foundational base of a food chain.

Primary Consumers

Herbivores that feed directly on producers.

Secondary Consumers

Carnivores that feed on primary consumers.

Tertiary Consumers

Carnivores that feed on secondary consumers.

Apex Consumer

Top predators at the highest trophic level with no natural predators.

Decomposers & Detritivores

Organisms in detrital food webs that break down decaying organic matter, recycling abiotic nutrients.

Biome

A major regional ecological community defined by climate conditions (temperature and precipitation) and characteristic plant/animal adaptations.

Tundra Biome

Extremely cold, dry biome; permafrost layer prevents deep rooting; dwarf shrubs, mosses, lichens; treeless plains with low vegetation.

Savanna Biome

Warm tropical biome with distinct wet/dry seasons; grasslands scattered with drought-tolerant trees (acacias); grazing herbivores.

Desert Biome

Arid biome (

Deciduous Forest Biome

Moderate rain with 4 distinct seasons; broadleaf trees (oak, maple) shedding leaves in autumn; rich leaf litter/humus.

Wetlands Biome

Biome with permanently/seasonally saturated hydric soils; hydrophytic vegetation (reeds, mangroves); standing water and high biodiversity.

Biomass

Total mass of living organic matter per unit area or volume in a habitat or ecosystem.

Production

The absolute amount of energy or organic material fixed by a system (measured in grams or Joules).

Productivity

The rate at which organic matter is produced per unit area per unit time (e.g., g/m²/yr or kcal/m²/yr).

Primary Production

Generation of new organic biomass via direct CO2 fixation by autotrophs.

Photosynthesis Equation

6CO2 + 6H2O + Sunlight -> C6H12O6 + 6O2 (Light reactions split H2O in thylakoids; Calvin cycle fixes CO2 in stroma).

Chemosynthesis

Synthesis of organic matter by chemoautotrophs using inorganic chemical oxidation (e.g., H2S) near deep-sea vents.

Respiration (R) Equation

C6H12O6 + 6O2 -> 6CO2 + 6H2O + ATP (Releases chemical bond energy for work, yielding metabolic heat).

Biogeochemical Cycles Definition

Systems describing the movement and recycling of essential elements through the atmosphere, hydrosphere, lithosphere, and biosphere.

Biogeochemical Cycle Origin & Purpose

Originated alongside early planetary formation and volcanic outgassing; purposed with endlessly recycling finite matter to maintain ecosystem habitability.

Carbon Cycle Type & Reservoirs

Gaseous cycle; primary reservoirs include atmosphere (CO2), oceans, biosphere, rock formations, and fossil fuel reserves.

Carbon Cycle Purpose

Builds organic molecules (carbohydrates, lipids, proteins, nucleic acids) and regulates planetary temperature via atmospheric CO2.

Carbon Cycle Processes

Photosynthesis fixes CO2; respiration/decomposition release CO2; geological weathering and volcanism store or release carbon over deep time.

Nitrogen Cycle Type & Reservoirs

Gaseous cycle; primary reservoirs include atmosphere (N2 gas ~78%), soil, freshwater/marine waters, and living tissue.

Nitrogen Cycle Purpose

Essential structural constituent for amino acids, proteins, nucleotides, and DNA/RNA.

Nitrogen Cycle Origin

Originated via ancient volcanic outgassing forming Earth's primeval N2 atmosphere, later harnessed by early prokaryotic microbes.

Nitrogen Fixation

Diazotrophic bacteria (Rhizobium in legume roots, Azotobacter, cyanobacteria) convert inert N2 gas into ammonia (NH3) or ammonium (NH4+).

Nitrification

Conversion of ammonium (NH4+) into nitrites (NO2-) and then nitrates (NO3-) by specialized soil bacteria for autotroph uptake.

Assimilation (Nitrogen)

Absorption of nitrates (NO3-) by plants to synthesize organic proteins and nucleic acids, passed to consumers via feeding.

Ammonification

Breakdown of nitrogenous wastes and decaying organisms back into ammonium (NH4+) by bacterial/fungal decomposers.

Denitrification

Anaerobic soil bacteria convert nitrates (NO3-) back into inert N2 gas, completing the gaseous atmospheric loop.

Phosphorus Cycle Type & Reservoirs

Sedimentary cycle (no atmospheric gas phase); primary reservoirs are phosphate rocks, soil minerals, aquatic sediments, and biological tissue.

Phosphorus Cycle Purpose

Essential for the structural backbone of DNA, RNA, ATP energy transfers, and cell membrane phospholipids.

Phosphorus Cycle Origin & Processes

Originated from tectonic uplifting and igneous rock erosion; rock weathering releases PO4(3-), absorbed by plants, passed up food webs, and returned via decomposition or oceanic sedimentation.

Sulfur Cycle Type & Reservoirs

Sedimentary/gaseous hybrid cycle; stored long-term in rocks, minerals, and ocean sediments, with atmospheric exchange (SO2, H2S).

Sulfur Cycle Purpose

Required for sulfur-containing amino acids (cysteine, methionine) crucial for protein folding, enzymes, and tertiary protein structure.

Sulfur Cycle Processes

Volcanic outgassing and bacterial reduction release H2S/SO2; oxidation yields sulfates (SO4^2-); plants absorb sulfate; decomposition and fossil fuel combustion release sulfur.

Interconnection: Water Cycle Link

Precipitation and runoff leach soluble nitrates, sulfates, and phosphates from land into rivers, soils, and ocean systems.

Interconnection: Ocean Role

Oceans function as giant reservoirs storing massive quantities of dissolved inorganic carbon and sediments while exchanging sulfur gases with the air.

Human Impacts on Biogeochemical Cycles

Fossil fuel burning overloads carbon/sulfur cycles (acid rain/climate change); synthetic fertilizers cause excess nitrogen/phosphorus runoff (eutrophication); deforestation reduces terrestrial carbon sinks.

Early Earth Atmosphere

Young Earth (~4.0 Ga) possessed an anoxic atmosphere rich in CH4, NH3, H2, and CO2, with intense surface UV radiation.

Hydrothermal Vent Life Origin

Deep-sea vents shielded early life from surface UV radiation, providing minerals and chemical/thermal gradients.

White Smokers vs. Black Smokers

White Smokers are alkaline, lower-temperature, methane-rich vents (Lost City) ideal for life's origin; Black Smokers are superheated, highly acidic vents.

G Stars (Sun-like)

Solar-type stars; rare (~7%); ~10 billion year lifespan; luminous and supports life, but shorter lived than smaller stars.

M Dwarfs (Red Dwarfs)

Most abundant stars (~75%); burn extremely slowly for trillions of years; close orbital zones expose planets to violent flares and radiation.

K Dwarfs (Orange Dwarfs)

"Goldilocks stars"; 3x more abundant than G stars; 15-45 billion year lifespan; stable radiation without severe flares.

Hadean Eon (4.5 - 4.0 Ga)

Earth formation; heavy bombardment, severe volcanism, and no initial liquid surface water.

Archean Eon (4.0 - 2.5 Ga)

Origin of first single-celled prokaryotes (~3.8-4.0 Ga); anoxic atmosphere; oldest fossil evidence in stromatolites (~3.5 Ga).

Proterozoic Eon (2.5 Ga - 542 Ma)

Great Oxidation Event (~2.5 Ga); Banded Iron Formations; first aerobic eukaryotes (~1.0-1.5 Ga); soft-bodied multicellularity (~650 Ma).

Great Oxidation Event (~2.5 Ga)

Cyanobacteria flood atmosphere with O2 via photosynthesis; causes global glaciation and mass die-offs of obligate anaerobes.

Phanerozoic Eon (542 Ma - Present)

Eon marked by the emergence and diversification of complex, visible multicellular life.

Cambrian Period (542 - 485 Ma)

Cambrian Explosion; hard shells, Trilobite compound eyes, early chordates (Pikaia).

Ordovician-Silurian (485 - 419 Ma)

Life colonizes land (~400 Ma); fungi (Tortotubus - 440 Ma) build soil; early spore plants and invertebrates.

Devonian Period (419 - 359 Ma)

"Age of Fishes"; armored Placoderms dominate; evolution of first tetrapods from lobe-finned fish.

Carboniferous Period (359 - 299 Ma)

Extensive coal swamps; high atmospheric O2 allows giant arthropods; evolution of the amniotic egg.

Permian Period (299 - 251 Ma)

Dominated by synapsids (Dimetrodon); ends with the End-Permian Mass Extinction (~96% marine species lost).

Mesozoic Era (251 - 65 Ma)

Dominance of Archosaurs and Dinosaurs across Pangaea; ends with Cretaceous-Tertiary (K-T) asteroid extinction (~65 Ma).

Cenozoic Era (65 Ma - Present)

Mammalian adaptive radiation and diversification; first ancestral hominids appear (~5 Ma).

Oxygen Revolution Evolutionary Impact

Toxic O2 forced surviving lineages to evolve aerobic respiration, yielding vastly higher ATP energy outputs.

Cambrian Arms Race Drivers

Rising O2 permitted higher metabolic rates; compound vision and active predation selected for protective shells and exoskeletons.