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Algae is a broad name for several photosynthetic eukaryotic groups, rather than one exclusive clade. The older name blue-green algae for cyanobacteria is misleading in a comparison of cellular organization: cyanobacteria are bacteria, with neither chloroplasts nor a cell nucleus.

A chloroplast is a compartment in photosynthetic plant and algae biological cells. Its internal thylakoids carry out light-dependent reactions; its surrounding chloroplast stroma contains the enzymes of the Calvin cycle. Cyanobacteria perform oxygenic photosynthesis without chloroplasts. See Alberts et al., Molecular Biology of the Cell: chloroplasts and photosynthesis.

Detritus is nonliving organic material, including dead remains and organic wastes. It is a resource for decomposers, not itself an organism or a predator. In the illustrative food web, the dashed arrow from algae to detritus denotes a material transfer; the solid arrow from detritus to decomposers denotes resource use.

The goal of ecology is to explain where organisms live, how many there are, and how their interactions with one another and their surroundings change those patterns. Living partners include prey, predators and parasites; nonliving conditions include light, temperature and water. An ecosystem brings these interacting parts into one study system. See Clark, Douglas and Choi, Biology 2e, 44.1: the scope of ecology.

Start with an invented aquatic food web: photosynthetic algae feed zooplankton, which feed small fish, which feed large fish. That food chain has four feeding positions and three feeding arrows. Dead material also reaches decomposers through detritus, so the food web branches rather than forming a single ladder.

The appeal of ecology is that an organism's surroundings include other organisms that change those surroundings. Photosynthesis links light to living material; predation transfers that material between organisms; decomposers return its constituent chemical elements to forms that can be used again. These connections help explain why changing one part of an ecosystem can affect distant parts of its food web, although an arrow alone does not predict the size or even the direction of an indirect change. Population dynamics supplies quantitative tools when the question concerns changing counts.

In 1866, Ernst Haeckel's Generelle Morphologie der Organismen included a section titled Oecologie und Chorologie in volume 2, beginning on page 286. This places the terminology of ecology in an early systematic treatment of organisms and their relationships. See Haeckel, Generelle Morphologie der Organismen, volume 2 (1866), contents and p. 286. A later quantitative landmark is Raymond L. Lindeman's 1942 treatment of ecosystems through feeding relationships and energy flow. See Lindeman, The Trophic-Dynamic Aspect of Ecology, Ecology 23 (1942), 399–417.

An ecosystem is a system of interacting organisms and their nonliving surroundings. A pond study might include algae, fish, bacteria, water, dissolved chemical compounds and incoming light. The useful step is to state the boundary and time interval: the pond surface, bottom and shoreline might enclose the study region, but water, organisms and energy can cross them. The chosen boundary specifies what counts as internal storage, input or output; it does not make the ecosystem sealed. See Clark, Douglas and Choi, Biology 2e, 46.1: ecosystems and their components.

For a toy pond water budget over one day, begin with $1000{\mathrm{m}}^3$, add $120{\mathrm{m}}^3$ crossing inward, and remove $90{\mathrm{m}}^3$ crossing outward. With all other transfers omitted by assumption, the final amount is $1000+120-90=1030{\mathrm{m}}^3$. The same bookkeeping asks whether a change inside an ecosystem came from internal processes or exchanges with its surroundings. Changing the boundary to include an upstream reservoir changes which transfers are internal, while preserving the accounting.

Endosymbiosis is an ecological association in which one organism, the endosymbiont, lives inside another. The definition specifies location, not that both partners benefit, nor that the internal partner has become an organelle. An intracellular association can remain an association between distinct organisms. Endosymbiotic theory addresses a different question: how particular ancestral bacteria became inherited, functionally integrated organelles during evolution.

The striking consequence is that a eukaryotic biological cell can combine histories: its nuclear lineage and its mitochondria need not have the same ancestry. Mitochondria have bacterial ancestry related to Alphaproteobacteria; the plastids of plants and many algae, including chloroplasts, have ancestry within cyanobacteria. These are ancestral lineages, not a claim that a named living bacterial species is the literal ancestor. Present-day bacteria and organelles have both evolved since their shared ancestors. ^[ref]

A eukaryote is an organism belonging to the lineage characterized by a membrane-bounded cell nucleus and extensive cellular compartmentalization. A nuclear envelope surrounds the nuclear genome; nuclear chromosomes are typically linear. Ribosomes perform biological translation outside the cell nucleus. See OpenStax Microbiology, 3.4: nuclear organization and protein synthesis. Specialized biological cells can lose their cell nucleus, as mature mammalian red blood cells do, while remaining parts of eukaryotic organisms; see OpenStax Biology 2e, 40.2: mature red blood cells.

Yeasts, plants and animals are all eukaryotes. Typical cells in these groups have mitochondria, but chloroplasts belong to photosynthetic plant and algae lineages, not to every eukaryote. A cell wall occurs in typical plant and fungus cells but is absent from animal cells. These are comparisons of representative cells, not a checklist every specialized cell must satisfy. See OpenStax Biology 2e, 4.3: nucleus, organelles and representative cells.

The interesting feature is controlled separation: cell membranes and organelle membranes let different cellular processes occupy distinct compartments while membrane transport connects them. The evolution of eukaryotes also involved partnership: mitochondria descend from a bacterial endosymbiosis. Modern phylogenetics supports an archaeal ancestry for the nuclear lineage, alongside this bacterial contribution; see two-domain system. Thus the history of a whole eukaryote cannot be read as the history of just one of its genes.

Oxygenic photosynthesis uses water as an Electron source and releases molecular oxygen. Plants, algae and cyanobacteria provide examples. The defining distinction from anoxygenic photosynthesis is molecular oxygen release, not merely capture of light.

Photosynthesis captures light energy and transforms it into chemical forms that a biological cell can use. In plants, algae and cyanobacteria, this supports carbon fixation: incorporation of carbon from carbon dioxide into chemical compounds used to build living material. Capturing light and incorporating carbon are distinct processes coupled through metabolism. See OpenStax Biology 2e, 8.1: overview of photosynthesis.

For oxygenic photosynthesis, a simplified net equation writes a six-carbon sugar, glucose, as the representative product:This is net stoichiometry, not a one-step mechanism. A worked bookkeeping check counts six carbon chemical atoms, twelve hydrogen chemical atoms, and eighteen oxygen chemical atoms on each side: the product side has six oxygen chemical atoms in the sugar and twelve in molecular oxygen. The light label supplies energy, not additional chemical atoms.

Crucially, the released molecular oxygen comes from water, not carbon dioxide. Cancelling water made and consumed in different steps hides this distinction in the net equation. The Calvin cycle supplies a net three-carbon triose phosphate, such as glyceraldehyde 3-phosphate, for subsequent sugar synthesis; it does not directly export glucose. See OpenStax Biology 2e, 8.2: light-dependent reactions and OpenStax Biology 2e, 8.3: using light energy to make organic molecules.

The useful achievement is connecting incoming light to both usable energy and new biological material. ATP is an immediate energy currency; NADPH supplies Electrons for synthesis; carbon dioxide supplies the carbon incorporated into carbohydrates. These roles are complementary. Conservation of energy still holds: photosynthesis transforms energy, never creates it, and some absorbed energy is dissipated as heat. A plant also carries out cellular respiration, including in biological cells that perform photosynthesis. Gas exchange reflects both processes. Oxygenic photosynthesis remains central to interpreting terrestrial molecular oxygen as an atmospheric biosignature gas. See OpenStax Biology 2e, 8.3: photosynthesis and respiration.

A primary producer builds organic chemical compounds from inorganic sources. Photosynthetic algae, plants and cyanobacteria use light energy for this role through photosynthesis and carbon fixation. The role supplies new living material to a food web; it does not mean that the organism creates energy.

Zooplankton are drifting aquatic consumers, including small animals. In the illustrative food web, the chosen zooplankton feed on algae and serve as prey for small fish; this assumed diet is not a claim about every kind of zooplankton.