The distinction between prokaryotes and eukaryotes represents the most fundamental division in cellular life, separating organisms into two fundamentally different levels of cellular organisation. Prokaryotes (from Greek: pro=before, karyon=nucleus): cells lacking a membrane-bounded nucleus; genetic material (typically a single circular chromosome) is located in an irregular region of the cytoplasm called the nucleoid. Prokaryotes also lack the membrane-bound organelles characteristic of eukaryotic cells (no mitochondria, no ER, no Golgi apparatus, no chloroplasts), have 70S ribosomes, and typically have a cell wall (peptidoglycan in bacteria, pseudomurein in some archaea). Prokaryotes include all bacteria and archaea. Eukaryotes (from Greek: eu=true, karyon=nucleus): cells with a true membrane-bounded nucleus enclosing the genetic material (multiple linear chromosomes); in addition, eukaryotes have numerous membrane-bound organelles (mitochondria for aerobic respiration, chloroplasts in photosynthetic cells, endoplasmic reticulum, Golgi apparatus, lysosomes, peroxisomes), 80S ribosomes in the cytoplasm, and undergo mitosis and meiosis with a complex cell cycle. Eukaryotes include protists, fungi, plants, and animals.

Cyanobacteria (also called blue-green algae — though they are not true algae as they are prokaryotes) are one of the most ecologically significant groups of prokaryotes. They are the only prokaryotes capable of oxygenic photosynthesis (using water as the electron donor and releasing O2 — the same overall photochemistry as plant chloroplasts). Key features: Prokaryotic — no membrane-bound nucleus, 70S ribosomes, no chloroplasts; instead, photosynthetic pigments (chlorophyll a, phycocyanin, phycoerythrin) are on internal membrane systems. Produce oxygen — historically responsible for the Great Oxidation Event approximately 2.4 billion years ago when cyanobacterial evolution dramatically increased atmospheric oxygen levels. Nitrogen fixation — many species fix atmospheric nitrogen (N2 → NH4+), either in specialised anaerobic cells called heterocysts (in Anabaena, Nostoc — needed because nitrogenase enzyme is O2-sensitive) or in normal vegetative cells (in some non-heterocystous species). Ecological roles — form algal blooms in eutrophic water; are components of soil crusts; form symbioses in lichens (as phycobionts), in cycad coralloid roots, and in Azolla water fern.

Mycoplasma and related genera (Ureaplasma, Spiroplasma, Phytoplasma) form the class Mollicutes, a unique group of bacteria distinguished by their complete lack of a cell wall — they have only a plasma membrane bounded by a cholesterol-containing phospholipid bilayer (unique among bacteria in having cholesterol, which they must obtain from their hosts since they cannot synthesise it). Consequences of lacking a cell wall: pleomorphic shape (irregular, variable forms rather than fixed coccoid or bacilloid morphology); resistance to all beta-lactam antibiotics (penicillins, cephalosporins) which work by inhibiting cell wall synthesis; filterable through filters that retain typical bacteria (historically confused with viruses); intracellular or cell-surface parasitism (cannot survive independently in the environment — must be associated with host cells). Despite these unusual features, Mycoplasma is unambiguously prokaryotic: 70S ribosomes, no membrane-bound nucleus, circular chromosome, lack of histones. Pathogenic Mycoplasma species include: M. pneumoniae (atypical/walking pneumonia), M. genitalium (urethritis, pelvic inflammatory disease), Ureaplasma urealyticum (urogenital infections, implicated in preterm birth).

Despite some superficial similarities to prokaryotes (both can grow as filaments, both reproduce by spores), fungi are definitively eukaryotes as demonstrated by multiple lines of evidence. Nucleus: fungi have a true, membrane-bound nucleus with linear chromosomes, nuclear pores, and a nucleolus — completely different from the prokaryotic nucleoid. Ribosomes: cytoplasmic ribosomes of fungi are 80S (with 60S and 40S subunits), just like other eukaryotes; this is why antibiotics targeting prokaryotic 70S ribosomes do not affect fungi (explaining why bacterial infections and fungal infections require different antimicrobial drugs). Organelles: fungi have mitochondria (with their own 70S ribosomes, reflecting bacterial endosymbiotic origin), endoplasmic reticulum, Golgi apparatus, and vacuoles. Cell cycle: fungi undergo true mitosis and meiosis with spindle formation and chromosomal condensation. Cell wall chemistry: although both bacteria and fungi have cell walls, their chemistry is completely different — bacterial walls use peptidoglycan while fungal walls use chitin (and glucans), reflecting entirely different evolutionary origins. Molecular phylogeny: DNA sequencing shows fungi are most closely related to animals, with both groups forming the Opisthokonta clade within eukaryotes, far more distant from any prokaryote than from other eukaryotes.