Microorganisms are organisms too small to be seen with the unaided eye, typically measured in micrometres, that include cellular life such as bacteria, archaea, many protists and fungi; viruses are acellular infectious agents often grouped with microbes for study though not considered living organisms. Found in virtually all habitats, microbes underpin global biogeochemical cycles, drive much of Earth’s primary production, and influence human health and disease. Britannica; Britannica—Types of microorganisms; Are Viruses Living?.

Antonie van Leeuwenhoek reported the first detailed observations of what he called “animalcules” in the 1670s, communicating findings to the Royal Society; a seminal letter read in 1677 described abundant microbes in infusions, marking the empirical discovery of the microbial world. Lens on Leeuwenhoek; Lens on Leeuwenhoek—Publication history; Britannica—Leeuwenhoek.

Definition and scope

A microorganism is an organism of microscopic size, often single-celled, such as Bacteria, Archaea, many microscopic fungi and protists; viruses, though acellular and not considered living by most definitions, are commonly covered in microbiology due to their size and relevance to infection. Britannica; Britannica—Are Viruses Living?; Britannica—Microbiology: Types of microorganisms.

Historical foundations

Microscopy enabled systematic study of microbes. The light (optical) microscope can resolve details down to roughly 0.2 μm, sufficient to visualize many bacteria, while electron microscopes—developed in the 20th century—achieve sub-nanometre resolution for ultrastructure. Britannica—Microscope; Britannica—Electron microscope. In the 19th century, Louis Pasteur linked fermentation and putrefaction to microorganisms, disproved spontaneous generation using swan‑neck flasks, and advanced germ theory; contemporaries including Robert Koch developed methods and causation criteria that established microbes as etiologic agents of specific diseases. Britannica—Pasteur’s contributions; Britannica—Spontaneous generation; Britannica—Germ theory. The Gram stain (1884) became a cornerstone of bacterial differentiation in clinical and research laboratories. Britannica—Gram stain.

Classification and diversity

Microorganisms occur across two cellular domains and among eukaryotes:

• –Bacteria are prokaryotes lacking a membrane‑bound nucleus; most cells are ~0.5–5 μm across, with diverse shapes, cell walls (Gram‑positive vs Gram‑negative), and metabolic strategies. Britannica—Types of microorganisms; Britannica—Bacteria: diversity and size.
• –Archaea are prokaryotes distinct from bacteria in genetics and biochemistry (e.g., ether‑linked membrane lipids; lack of peptidoglycan), a division clarified by small‑subunit rRNA phylogenetics that established the tripartite domains of life. Britannica—Types of microorganisms; PNAS—Woese & Fox 1977; Journal of Bacteriology editorial.
• –Eukaryotic microbes include many fungi (yeasts, molds) and protists (e.g., amoebae, flagellates, algae); some algae and fungi are macroscopic, but numerous species are microscopic for part or all of their life cycle. Britannica—Types of microorganisms; Britannica—Yeast.
• –Virus particles comprise nucleic acid within a protein capsid (sometimes enveloped), replicate only within host cells, and are generally regarded as nonliving entities. Britannica—Are Viruses Living?.

Molecular tools transformed microbial systematics. Comparative 16S rRNA gene sequencing underpins identification and phylogeny of bacteria and archaea (with caveats regarding resolution), while shotgun metagenomics profiles entire community DNA without cultivation. PNAS—Woese & Fox 1977; Microbiome (2022) on 16S gene limits; Nature Reviews Microbiology—CRISPR-Cas review.

Morphology and size

Bacterial sizes commonly range from ~0.5–5 μm (e.g., Escherichia coli ≈2 μm long), though exceptions span orders of magnitude, and morphologies include cocci, bacilli, spirilla, and spirochetes. Britannica—Types of microorganisms; Britannica—Bacteria: diversity and size. Yeasts are typically ~3–10 μm cells reproducing by budding or fission; many protozoa are tens of micrometres; most viruses are tens to hundreds of nanometres. Britannica—Yeast; Britannica—Electron microscopy overview.

Ecology and global roles

Microorganisms are ubiquitous, including extreme environments (acidic, hypersaline, high‑temperature, high‑pressure, or deep subsurface). Extremophiles—prevalent among archaea and bacteria—thrive at such extremes and produce enzymes useful under harsh industrial conditions. Britannica—Extremophile. A deep biosphere hosts slow‑growing communities kilometres below seafloor; single‑cell isotope tracing has shown active metabolism in ~2‑km‑deep Miocene coal and shale beds, with generation times from months to centuries under in situ conditions. PNAS—Trembath‑Reichert et al. 2017.

Microbes drive element cycling: diazotrophs fix atmospheric N₂ to ammonia; nitrifiers oxidize ammonia to nitrite/nitrate; denitrifiers return N to the atmosphere. Diverse microbes mediate sulfur and carbon transformations, including methanogenesis and methane oxidation. Britannica—Nitrogen‑fixing bacteria; Britannica—Biosphere: nitrogen cycle; OpenStax Microbiology—Biogeochemical cycles.

In the oceans, photosynthetic microorganisms (phytoplankton, including cyanobacteria and microalgae) account for roughly half of global primary production and contribute substantially to oxygen release and the biological carbon pump. NASA analyses and education resources attribute ~45–50% of global primary production to phytoplankton and highlight their carbon sequestration impacts. NASA Goddard—Why identify phytoplankton from space; NASA GMAO highlight; NASA Earth Observatory.

Microbial biomass constitutes a major share of non‑plant life. A global census estimated ≈550 Gt C total biomass, ~80% in plants, with bacteria ≈70 Gt C (~15% of total), and remaining groups (including archaea, fungi, protists, animals, viruses) contributing the balance; microbes dominate marine biomass. PNAS—Bar‑On, Phillips & Milo 2018.

Microorganisms and humans

The human body hosts vast microbial communities (the Microbiome) across body sites (gut, skin, oral, airway, urogenital). A 2016 quantitative analysis revised the often‑quoted 10:1 ratio, estimating ~3.8×10¹³ bacterial cells and ~3.0×10¹³ human cells in a 70‑kg reference adult—roughly a 1:1 ratio by cell count. PLOS Biology—Sender, Fuchs & Milo 2016. The U.S. Human Microbiome Project characterized microbial community composition and function in healthy volunteers and disease cohorts, catalyzing metagenomic approaches for human health research. NIH—HMP overview; NIH news release.

Pathogenic microbes cause infectious diseases (bacteria, many viruses, some fungi and protozoa), while the majority of environmental and commensal microbes are harmless or beneficial. Clinical and public health definitions emphasize transmission routes and the diversity of infectious agents. Britannica—Infectious disease; Cleveland Clinic—Infectious diseases.

Methods of study

Microscopy remains central: light microscopy for cell morphology and staining (e.g., Gram staining distinguishes thick peptidoglycan Gram‑positive from thin‑walled Gram‑negative bacteria), and electron microscopy for ultrastructure. Britannica—Gram stain; Britannica—Electron microscope. Culture techniques isolate and characterize microbes, though many environmental microbes elude standard cultivation (“great plate count anomaly”), prompting culture‑independent methods. Frontiers in Microbiology—Grand challenges. Molecular approaches include 16S/18S rRNA gene sequencing for community profiling and shotgun metagenomics for functional potential, enabling discovery of vast uncultured diversity. Microbiome (2022); Britannica—Microbiology overview of types.

Biotechnology, industry, and medicine

Microbes underpin fermented foods and beverages: yeasts (Saccharomyces cerevisiae) leaven bread and ferment beer and wine; lactic acid bacteria transform dairy and vegetables; many foods (e.g., yogurt, sauerkraut, soy sauce) rely on microbial starters. Britannica—Yeast; Britannica—Food microbiology; Britannica—Beer: yeast. Microbial metabolism yields enzymes, organic acids, solvents, and biofuels at industrial scale. Britannica—Food/industrial microbiology.

Many antibiotics are microbial products (e.g., penicillin from Penicillium, streptomycin from Streptomyces), inaugurating the antibiotic era and transforming infectious disease treatment; resistance evolution necessitates stewardship and new agents. Britannica—Penicillin; Britannica—Antibiotic. Adaptive immune systems in bacteria and archaea (CRISPR‑Cas) capture fragments of invader DNA and guide nucleases to degrade matching sequences; harnessed as genome‑editing tools, these systems trace to microbial defense. Nature—CRISPR‑Cas immunity review.

Notable milestones and techniques

• –First microscopic observations of microbes (1670s) by Antonie van Leeuwenhoek, via single‑lens microscopes and detailed Royal Society correspondence. Lens on Leeuwenhoek.
• –Foundations of germ theory and sterilization/pasteurization in the 19th century (Pasteur; Koch’s laboratory methods and postulates). Britannica—Germ theory; Britannica—Pasteur.
• –Gram staining (1884) to classify bacteria by cell wall architecture. Britannica—Gram stain.
• –rRNA phylogenetics (1977) revealing the tripartite domains: Bacteria, Archaea, Eukarya. PNAS—Woese & Fox 1977.
• –Culture‑independent community profiling and metagenomics enabling study of the uncultured majority in environmental and host‑associated microbiomes. Microbiome (2022); NIH—HMP.

Diversity at scale

Scaling laws applied to global datasets predict on the order of 10¹² (one trillion) microbial species on Earth, vastly exceeding the currently cultured and classified fraction; while debated and method‑dependent, such estimates underscore the immense, largely uncharted microbial diversity. PNAS—Locey & Lennon 2016; PNAS commentary.