Eukaryote

• 1. Introduction

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  A picozoan drifts through seawater, smaller than three micrometers across. A coast redwood rises 120 meters into the air. A blue whale, up to 190 tonnes and 33.6 meters long, moves through the deep. These three organisms share almost nothing in size, yet they belong to the same domain of life: the eukaryotes. The word names every organism whose cells carry a membrane-bound nucleus. Animals, plants, fungi, seaweeds, and a vast crowd of single-celled creatures all qualify. The Greek roots tell a quiet story. "Eu" means "true" or "good", and "karyon" means "nut" or "kernel", a reference to that walled-off nucleus at the cell's center. Eukaryotes are outnumbered by the other forms of life. Counted one by one, they are a small minority of all organisms. So how did a rare cell type come to weigh so much, build so much complexity, and emerge in the first place? The answers run from ancient rock and contaminated biomarkers to a fusion of two unrelated microbes, and to the question of how many domains of life there really are.

• 2. A Tale Of Two Mergers

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  Mitochondria are commonly called "the powerhouse of the cell". They oxidize sugars or fats to produce ATP, the energy-storing molecule that keeps a eukaryote running. Each mitochondrion is wrapped in two membranes, each a phospholipid bilayer, and the inner one folds into invaginations called cristae where aerobic respiration happens. The strangest fact about them is that they carry their own DNA, structurally close to bacterial DNA. That DNA encodes rRNA and tRNA genes whose RNA resembles bacterial RNA more than it does eukaryote RNA. The leading explanation is symbiogenesis. An anaerobic archaeon from the phylum Promethearchaeota took in an aerobic proteobacterium, and that bacterium became the mitochondria. The merger is thought to have happened when prokaryotic cells became endosymbionts living inside their host. A second, much later union followed the same script. A cyanobacterium was taken in, and it became the chloroplast, giving rise to the plants. Some eukaryotes appear to have no mitochondria at all. The metamonads Giardia and Trichomonas, and the amoebozoan Pelomyxa, instead carry mitochondrion-derived organelles such as hydrogenosomes or mitosomes, and they draw energy from enzymatic action in the cytoplasm.

• 3. The Cell's Inner Architecture

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  The nucleus stores the cell's DNA, divided into linear bundles called chromosomes. During nuclear division, a microtubular spindle separates them into two matching sets, the process called mitosis. Around that nucleus sits a double membrane, the nuclear envelope, pierced by nuclear pores that let material pass in and out. Tube- and sheet-like extensions of this membrane form the endoplasmic reticulum, which handles protein transport and maturation. Ribosomes coat the rough endoplasmic reticulum and synthesize proteins, which enter an interior space called the lumen. From the smooth endoplasmic reticulum, protein-carrying vesicles bud off. In most eukaryotes, those contents are modified further inside stacks of flattened vesicles known as the Golgi apparatus. Vesicles can be specialized; lysosomes, for instance, hold digestive enzymes that break down biomolecules in the cytoplasm. The cytoskeleton gives the cell its shape and provides anchor points for movement. Its motor structures are microfilaments of actin paired with actin-binding proteins, including α-actinin, fimbrin, and filamin. Motor proteins of microtubules, dynein and kinesin, plus myosin of actin filaments, keep the whole network dynamic. Many eukaryotes wave long flagella or shorter cilia, built mainly of tubulin and supported by microtubules in a pattern of nine doublets surrounding two singlets, arising from a centriole. These projections are entirely distinct from prokaryotic flagella.

• 4. Walls, Plastids, And Sex

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  Cellulose, hemicellulose, and pectin make up the primary cell wall of land plants. The cellulose microfibrils link together with hemicellulose, embedded in a pectin matrix, and the most common hemicellulose there is xyloglucan. Plants, algae, fungi, and most chromalveolates carry such a wall, though animals do not. The wall supports the cell, protects it, filters what enters, and prevents over-expansion when water rushes in. Plastids belong to plants and various algae alongside their mitochondria. Like mitochondria, plastids hold their own DNA and descend from endosymbionts, here cyanobacteria. They often appear as chloroplasts, which contain chlorophyll and make organic compounds such as glucose through photosynthesis. Not all plastid-bearing groups are close kin; some eukaryotes acquired plastids from other eukaryotes through secondary endosymbiosis or ingestion. The capture and sequestering of photosynthetic cells and chloroplasts, called kleptoplasty, still occurs across many modern eukaryotes. Reproduction in this domain swings between a haploid phase, with one copy of each chromosome, and a diploid phase, with two. Two haploid gametes, such as eggs and spermatozoa, fuse into a zygote, which may grow by mitosis and later make new gametes through meiosis. Sex may be ancient here. Dacks and Roger proposed that facultative sex existed in the group's common ancestor. Core meiotic genes turn up in Trichomonas vaginalis and Giardia intestinalis, two organisms once thought asexual, hinting that sex was present in the common ancestor of all eukaryotes.

• 5. Naming The Living World

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  Aristotle and Theophrastus, in antiquity, recognized the two lineages of animals and plants. Linnaeus, in the 18th century, gave those lineages the taxonomic rank of kingdom, folding fungi in with plants though with some reservations. Fungi were later judged distinct enough to warrant their own kingdom. The single-celled eukaryotes posed a harder problem, first lumped in with plants or animals as they were discovered. In 1818, the German biologist Georg A. Goldfuss coined "Protozoa" for organisms such as ciliates. Ernst Haeckel expanded the idea in 1866 into a kingdom called Protista, gathering all single-celled eukaryotes. That left four kingdoms: Protista, Plantae, Fungi, and Animalia, with protists regarded as "primitive forms" united by their unicellular nature. DNA sequencing reshaped the picture entirely. In 1990, Carl Woese, Otto Kandler, and Mark Wheelis proposed domains rather than kingdoms as the top rank, uniting the eukaryote kingdoms in the domain "Eucarya" while allowing "eukaryotes" as a synonym. In 1996, the evolutionary biologist Lynn Margulis pushed for "inclusive" names and a symbiosis-based phylogeny, describing the group as "Eukarya (symbiosis-derived nucleated organisms)". By the early 21st century, phylogenomics settled into a rough consensus around two large clades, Amorphea and Diphoda, while the old Excavata was abandoned as paraphyletic. Newer surprises kept arriving, including the Provora, a group of microbial predators discovered in 2022.

• 6. Reading The Oldest Rocks

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  Steranes, eukaryotic-specific biomarkers, once seemed to place eukaryotes in Australian shales dated at 2.7 billion years old. Those Archaean biomarkers were later rebutted as contaminants that arrived afterward, and the oldest valid biomarker records run only around 800 million years old. The trouble deepens because some bacteria produce sterols too. A molecular clock analysis, by contrast, pushes the emergence of sterol biosynthesis back as far as 2.3 billion years ago. Fossils that clearly tie to modern groups begin appearing an estimated 1.2 billion years ago as red algae. Fossilized Vindhyan filamentous algae have been suggested to reach 1.6 to 1.7 billion years old, rather than the Cambrian age once assumed. Fossils from the Ruyang Group of China, roughly 1.8 to 1.6 billion years old, may be the oldest known eukaryotes. Qingshania magnifica from North China, which lived 1.635 billion years ago, stands as one possible earliest multicellular eukaryote, suggesting crown group eukaryotes arose in the late Paleoproterozoic. Other contenders carry their own tangled stories. Grypania, perhaps an alga, may be 2.1 billion years old. The "problematic" fossil Diskagma turns up in paleosols 2.2 billion years old. The Francevillian biota of Gabon, dated at 2.1 billion years, was proposed as "large colonial organisms", though some authors argue these are pseudofossils. Even after they appeared, eukaryotes may not have become ecologically dominant for ages. A massive rise in the zinc composition of marine sediments, attributed to growing eukaryote populations that take up zinc more readily than prokaryotes, came roughly a billion years after their origin.

• 7. Weight Of The Living World

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  468 gigatons. That is the collective global biomass of eukaryotes, set against just 77 gigatons for the prokaryotes. The gap exists despite eukaryotes being the smaller crowd by sheer count, because so many of them are large. Plants alone account for over 81 percent of all biomass on Earth. A single eukaryotic cell holds a volume around 10,000 times greater than that of a bacterium or archaeon. Complexity, though, has been rarer than size. Multicellularity in some form evolved independently at least 25 times within the eukaryotes. Complex multicellular life, setting aside the amoebae that aggregate into slime molds, arose in only six lineages: animals, symbiomycotan fungi, brown algae, red algae, green algae, and land plants. The deepest root of all this is the last eukaryotic common ancestor, or LECA, which was most likely a biological population rather than a single individual. The LECA is believed to have been a protist with a nucleus, at least one centriole and flagellum, facultatively aerobic mitochondria, sex through meiosis and syngamy, a dormant cyst walled in chitin or cellulose, and peroxisomes. In 2022, cryo-electron tomography revealed that Promethearchaeota archaea carry a complex actin-based cytoskeleton, the first direct visual evidence of the archaeal ancestry that one ancient merger set in motion.