Diatoms belong to the kingdom Chromista (sometimes called Protista in older classification schemes), not to the plant kingdom, despite being photosynthetic and producing a substantial share of the oxygen you breathe. They sit within a larger group called the stramenopiles, or heterokonts, which also includes brown seaweeds and some parasitic organisms like oomycetes. The classification can be confusing because diatoms look and act like tiny plants in many ways, but their evolutionary history, cell structure, and genetics tell a very different story.
Why Diatoms Are Not Plants
The confusion is understandable. Diatoms photosynthesize, they live in water where you might expect algae, and they turn sunlight into organic carbon just like land plants do. But the similarities are superficial. Plants belong to the kingdom Plantae and trace their chloroplasts back to a single ancient event in which a eukaryotic cell swallowed a cyanobacterium. Diatoms got their photosynthetic machinery through a more convoluted route: their ancestor engulfed a red alga that already had chloroplasts, in what biologists call secondary endosymbiosis.1PubMed. Genomic footprints of a cryptic plastid endosymbiosis in diatoms That means the chloroplast inside a diatom is wrapped in extra membranes, a leftover from being inside the engulfed alga, which itself had engulfed a cyanobacterium long before. Plants have two membranes around their chloroplasts. Diatoms have four.
This distinction places diatoms in an entirely separate branch of the tree of life. The stramenopile supergroup they belong to is one of the most diverse lineages of protists, encompassing everything from the giant kelp you see washed up on beaches to microscopic parasites that cause potato blight.2Molecular Biology and Evolution. A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts) Within the stramenopiles, diatoms are placed in the ochrophytes, a large subgroup of photosynthetic members. Recent phylogenomic work has reorganized the ochrophytes into two clades called Chrysista and Diatomista, with diatoms falling into Diatomista alongside bolidophytes, a group of tiny flagellated algae that appear to be their closest relatives.3Molecular Biology and Evolution. A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts)
The Red Algal Connection
The story of how diatoms acquired photosynthesis is one of the stranger chapters in evolutionary biology. Somewhere between roughly 1.3 billion and 620 million years ago, the ancestor of the ochrophyte lineage (the group containing diatoms) picked up a plastid derived from a red alga through secondary endosymbiosis.4Nature Communications. A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids That red algal donor belonged to a stem lineage that split off after the divergence of the hot-spring-loving Cyanidiophyceae from the rest of the red algae, and the donor lineage itself existed somewhere between about 1.7 billion and 1.3 billion years ago.5Nature Communications. A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids This event did not just hand diatoms a chloroplast. It came with a flood of genes from the engulfed alga, many of which were repurposed for entirely new jobs in the host cell.
The genetic fallout goes further. Genomic studies across nine sequenced diatom species have found that roughly 3 to 5 percent of their protein-coding genes were acquired horizontally from bacteria, not from the endosymbiont.6Molecular biology and evolution. Comprehensive and Functional Analysis of Horizontal Gene Transfer Events in Diatoms Over 90 percent of these bacterial genes are actively used, and they play roles in environmental sensing and expanding the metabolic toolkit. One striking example involves cobalamin (vitamin B12), a cofactor that only bacteria can synthesize but that roughly half of all diatom species need. In the Southern Ocean diatom Fragilariopsis cylindrus, five consecutive enzymes in the final steps of cobalamin synthesis appear to have been acquired from bacteria, which could give these diatoms a competitive edge in an ocean region where the vitamin is scarce.7Molecular biology and evolution. Comprehensive and Functional Analysis of Horizontal Gene Transfer Events in Diatoms
Living in a Glass House
Perhaps the most immediately distinctive thing about diatoms is not their kingdom classification but their cell wall: a rigid, intricate shell made of silica, the same material as glass. This structure, called a frustule, consists of two interlocking halves that fit together like a petri dish with its lid. The patterns etched into these silica walls are stunningly complex and species-specific, which is why diatom taxonomy has historically relied heavily on examining frustule geometry under a microscope.
The frustule is not a simple hard shell. Nanomechanical testing has revealed that different layers of the frustule have different mechanical properties, and the overall behavior depends on how hydrated the silica is and how much organic material is woven through the structure.8Scientific Reports. Revealing the static and dynamic nanomechanical properties of diatom frustules—Nature’s glass lace In other words, the frustule is a composite material, part glass, part organic matrix, engineered by evolution into shapes that are lightweight yet strong. These properties have attracted serious interest from materials scientists and biomedical researchers. The high surface area, thermal stability, biocompatibility, and easy surface modification of diatom silica make it a promising candidate for drug delivery systems.9PubMed Central. Diatoms Green Nanotechnology for Biosilica-Based Drug Delivery Systems Frustules are also abundant as fossil material (diatomaceous earth, or diatomite) in deposits around the world, which means the raw material is cheap and plentiful.10PubMed. Nature engineered diatom biosilica as drug delivery systems
The requirement for silica also sets diatoms apart ecologically. Unlike most other phytoplankton, diatoms need dissolved silicic acid to build their walls. This makes them uniquely dependent on the ocean’s silicon cycle, and the availability of silicic acid is a major factor controlling where and when diatoms dominate the plankton community.11Global Biogeochemical Cycles. Role of diatoms in regulating the ocean’s silicon cycle
A Metabolic Mashup
Diatoms’ odd evolutionary history, part heterotroph ancestor, part red algal endosymbiont, part bacterial gene donor, has given them a metabolism that looks nothing like a plant’s. One of the most surprising discoveries is that diatoms have a functional urea cycle, a metabolic pathway familiar from animal biochemistry but absent in green algae and land plants. In diatoms, this cycle is not about waste disposal the way it is in your liver. Instead, it serves as a hub for shuffling carbon and nitrogen between different parts of the cell’s biochemistry, linking the carbon-fixing reactions of photosynthesis with nitrogen assimilation.12Nature. Evolution and metabolic significance of the urea cycle in photosynthetic diatoms This turns out to be critical for surviving in the ocean, where nitrogen supply is often feast-or-famine. The urea cycle allows diatoms to recover rapidly after prolonged nitrogen starvation, giving them a burst of growth when nutrients suddenly become available.13Nature. Evolution and metabolic significance of the urea cycle in photosynthetic diatoms
This metabolic flexibility is one reason diatoms are such fierce competitors. In nutrient-rich coastal upwelling zones where iron is also available, massive diatom blooms can strip the water of dissolved nutrients, producing some of the highest chlorophyll concentrations in the ocean.14Limnology and Oceanography. Iron and macronutrients in California coastal upwelling regimes: Implications for diatom blooms Their metabolic diversity also extends to producing lipids, omega-3 fatty acids, pigments, antioxidants, and various polysaccharides, which has made them targets for industrial cultivation and bio-manufacturing.15PubMed Central. Diatoms for Carbon Sequestration and Bio-Based Manufacturing
Shape, Size, and the Centric-Pennate Divide
Diatoms come in two broad body plans: centric diatoms, which tend to be round or radially symmetrical, and pennate diatoms, which are elongated and bilaterally symmetrical. Pennates often have a slit called a raphe running along their length that lets them glide across surfaces. This division is more than cosmetic; it maps loosely onto ecology. Centric diatoms dominate the open-ocean plankton, while many pennate species are benthic, living attached to rocks, sediment, or other organisms.
But the boundary is not always clean. The genus Toxarium, for instance, has an elongated shape and benthic lifestyle that would seem to mark it as a pennate diatom. Yet when researchers examined its valve structure, they found it lacked all the hallmarks of true pennates: no raphe, no sternum, no organized rows of pores radiating from a midrib. Its pores are scattered irregularly, and molecular phylogenetics places it squarely within the centric lineage.16Journal of Phycology. PHYLOGENETIC POSITION OF TOXARIUM, A PENNATE‐LIKE LINEAGE WITHIN CENTRIC DIATOMS (BACILLARIOPHYCEAE) Cases like this underscore that body shape alone can be misleading and that the evolutionary relationships among diatoms are still being worked out.
The Shrinking Cell Problem
Diatom reproduction involves one of the stranger quirks in biology. When a diatom divides by mitosis, each daughter cell inherits one half of the parent’s silica frustule and builds a new, smaller half to fit inside it. This means one daughter cell stays the same size as the parent, but the other is slightly smaller. Over many generations, the average cell size in a population progressively shrinks. Once cells reach a critically small size, diatoms switch from asexual division to sexual reproduction. The resulting zygote develops into an auxospore, a specialized expanding cell that restores the original large size.17Journal of Phycology. AUXOSPORE FORMATION BY THE SILICA‐SINKING, OCEANIC DIATOM FRAGILARIOPSIS KERGUELENSIS (BACILLARIOPHYCEAE)
The details of sexual reproduction vary across species. In the pennate diatom Eunotia, mating requires two clones of different mating types; clones of the same type do not interact sexually. The gametes are not visibly different from each other, and fertilization happens through a copulation canal formed by outgrowths from both cells. The resulting zygote swells into a curved, sausage-shaped auxospore.18Journal of Phycology. MATING SYSTEM, SEXUAL REPRODUCTION, AND AUXOSPORULATION IN THE ANOMALOUS RAPHID DIATOM EUNOTIA (BACILLARIOPHYTA) Even bacteria seem to play a role: the marine diatom Odontella produces significantly more sexual cells and auxospores when cultured with specific bacteria from the Flavobacteriaceae family than when grown bacteria-free or with other bacterial species.19PLOS ONE. Specific bacterial microbiome enhances the sexual reproduction and auxospore production of the marine diatom, Odontella
How Old Are Diatoms
The fossil record of diatoms is surprisingly contentious. The oldest undisputed diatom fossils come from Lower Cretaceous deposits in eastern Australia, dated to about 125 to 120 million years ago. Those assemblages already contain dozens of species across multiple genera, suggesting diatoms had been diversifying for a long time before their first clear appearance in the rock record.20Scientific Reports. Uncertainties surrounding the oldest fossil record of diatoms Molecular clock estimates push the origin of crown-group diatoms back to around 200 million years ago, creating a roughly 75-million-year gap between when genetic evidence says diatoms arose and when their frustules first show up as fossils.21Scientific Reports. Uncertainties surrounding the oldest fossil record of diatoms One possible explanation is that the earliest diatoms either did not produce silica walls or produced walls too thin to survive fossilization.
When Diatoms Turn Toxic
Not all diatoms are harmless oxygen factories. Species in the pennate genus Pseudo-nitzschia produce domoic acid, a potent neurotoxin responsible for amnesic shellfish poisoning in humans and mass die-offs of marine mammals and seabirds. The toxin accumulates in shellfish and anchovies that feed on the diatoms, then concentrates further up the food chain.
Toxin production is not constant. It increases sharply when the cells are stressed. Iron limitation can boost domoic acid output roughly eightfold compared to optimal growth conditions, and copper stress pushes it even higher, to about twenty times the baseline rate.22Limnology and Oceanography. The effect of Fe and Cu on growth and domoic acid production by Pseudo-nitzschia multiseries and Pseudo‐nitzschia australis Modeling work suggests that the general pattern is straightforward: excess light combined with silicon or phosphorus limitation favors toxin production, as long as nitrogen is still available.23Harmful Algae. Factors controlling the production of domoic acid by Pseudo-nitzschia (Bacillariophyceae): A model study Under those conditions, the cells are capturing more light energy than they can channel into growth, and domoic acid appears to be a secondary metabolic outlet for the excess. The practical concern is that the nutrient conditions that trigger higher toxin production, particularly low iron combined with unused nitrate, are common in coastal upwelling systems where Pseudo-nitzschia blooms coincide with commercially important fisheries.
Diatoms as Environmental Sentinels
Because different diatom species have distinct preferences for water chemistry, temperature, and nutrient levels, the community of diatoms living in a river or lake acts as a running biological report card. Environmental scientists use diatom-based indices to assess water quality, and these indices have become standard tools in regulatory monitoring in Europe and elsewhere. A study modeling one widely used index, the Specific Pollution Sensitivity Index, found that phosphates, nitrites, and water temperature were the main environmental factors driving its variability.24PubMed Central. What do diatom indices indicate? Modeling the specific pollution sensitivity index In plain terms, the species composition shifts predictably as nutrient pollution and warming increase, so counting which diatoms are present tells you a lot about the health of a waterway without needing to run extensive chemical tests.
Ocean Acidification and the Silicon Squeeze
Diatoms’ dependence on dissolved silica makes them vulnerable to a climate-related threat that gets less attention than warming: ocean acidification. As seawater pH drops due to rising CO₂, silica dissolves more slowly. That might sound like good news for diatoms, since their glass walls would last longer. But the flip side is that less recycled silicic acid makes it back into surface waters for new diatoms to use. A series of in-situ mesocosm experiments with natural plankton communities found that ocean acidification increased the silicon-to-nitrogen ratio of sinking material by about 17 percent under conditions projected for the year 2100.25PubMed Central. Enhanced silica export in a future ocean triggers global diatom decline Earth system model simulations building on that finding project a global decline of diatoms by 13 to 26 percent due to acidification-driven silica scarcity by the year 2200.26PubMed Central. Enhanced silica export in a future ocean triggers global diatom decline Since diatoms are major carbon exporters whose heavy silica shells help them sink rapidly to the deep ocean, a decline of that magnitude could weaken one of the ocean’s most important biological carbon pumps.
Industrial Cultivation and Commercial Uses
Diatoms’ metabolic versatility and fast growth rates have made them attractive for commercial cultivation. In aquaculture, diatom biomass is already used as feed for shellfish larvae and juvenile fish because of its high lipid and amino acid content.27PubMed. Diatom cultivation and biotechnologically relevant products. Part II: current and putative products Beyond aquaculture, researchers are investigating diatoms as platforms for producing biofuels, though the economics remain challenging. Diatoms can be grown in both purely photosynthetic (autotrophic) and mixed-feeding (mixotrophic) modes, and their higher photosynthetic efficiency and faster biomass accumulation compared to many land-based energy crops are often cited as advantages.28Oceans. Microalgae (Diatom) Production — The Aquaculture and Biofuel Nexus The carbon captured during cultivation can be redirected into lipids, omega-3 fatty acids, pigments, and antioxidants, giving producers multiple revenue streams from a single organism.29PubMed Central. Diatoms for Carbon Sequestration and Bio-Based Manufacturing Cosmetics and pharmaceutical applications are at earlier stages of development, but the biocompatibility and low cost of diatom-derived silica continue to draw research interest.30PubMed. Diatom Silica for Biomedical Applications: Recent Progress and Advances