Life › The microbial world
Bacteria & archaea: the microbial world
from at least 3.5 billion years ago· Organism or group· Microbes & cells
Well establishedStrong fossil, genetic or geological evidence.
The two great domains of simple single cells without a nucleus, which made up all of life for roughly two billion years.
See it on the Life map →What happened
Bacteria and archaea look alike under a microscope: small cells with no nucleus. In 1977 Carl Woese showed, by comparing ribosomal RNA, that they are as different from each other as either is from us. They differ in membrane fats, cell walls and gene machinery. Together they number an estimated 10³⁰ cells, living everywhere from deep rock to human guts. Eukaryotes, the cells of plants and animals, later arose from a merger of an archaeon and a bacterium.
Why it matters
They invented most of life's core chemistry, including photosynthesis and nitrogen fixation, and still run Earth's carbon, nitrogen and oxygen cycles; complex life is built on them.
Think of it like
Like a building's mechanical systems: rarely noticed, yet every tenant depends on them.
The evidence (fossils, genes, rocks)
Fossils such as stromatolites and the Gunflint Chert microfossils, chemical traces in ancient rocks, and DNA comparisons among living species.
Still debated
Which domain is older, how many species exist (estimates run from millions to a trillion), and where exactly eukaryotes branch off.
Inside this (3)
Connections (10)
▸LUCA, the last universal common ancestor split into Bacteria & archaea: the microbial worldStrong evidence
The connection
LUCA's descendants split into two great lineages, bacteria and archaea, which differ in membrane fats, cell walls and gene-copying machinery. Every later cell traces to one or the other. Complex cells like ours came from a much later merger of an archaeon and a bacterium.
When and how
Soon after LUCA, perhaps 4 billion years ago; the split was recognized from ribosomal RNA by Carl Woese and George Fox in 1977.
How sure are we?
Gene trees built from many genes consistently place the root between bacteria and archaea, though rooting such ancient trees is technically hard.
Debates and open questions
Exactly where the root lies, and why the two lineages ended up with completely different membrane chemistry.
▸Bacteria & archaea: the microbial world built StromatolitesWell established
The connection
Stromatolites are built by layered communities, not single species: sunlight-using microbes on top, others living off their waste below. Their sticky slime traps grains and helps minerals form, and the community keeps growing up through each new layer of sediment.
When and how
From at least 3.48 billion years ago in the Pilbara, Western Australia; still forming today at Shark Bay, Western Australia, studied since the 1950s.
The evidence
Living Shark Bay stromatolites grow this way and resemble ancient ones; fossil examples preserve microscopic layering and organic matter.
Debates and open questions
Which microbes built the earliest ones, and how to tell microbial layers from layers that minerals can form on their own.
▸Apex Chert 'microfossils' controversy concerns possible fossils of Bacteria & archaea: the microbial worldDebated
The connection
Thread-like structures in 3.46-billion-year-old Australian chert were described as fossil microbes and once billed as Earth's oldest fossils. If biological, they are direct remains of early bacteria or archaea. Critics argue they are mineral and carbon artifacts formed by hot fluids.
When and how
J. William Schopf of UCLA described them in 1993; Martin Brasier of Oxford challenged them in 2002; the debate continued into the late 2010s.
How sure are we?
In 2017 Schopf's team reported carbon isotope patterns fitting different microbes; other teams showed minerals can form similar shapes. Neither side has fully won.
Debates and open questions
Whether the threads are life at all and, if so, which microbes; Schopf's original claim that some were cyanobacteria has been largely dropped.
▸Bacteria & archaea: the microbial world share genes through Horizontal gene transferWell established
The connection
Their DNA floats free in the cell, with no nucleus around it, and each cell reproduces by splitting, so a gene picked up today passes straight to its descendants. The result is a shared gene pool: two strains of E. coli can differ by more than a thousand genes.
When and how
Throughout microbial history; first shown by Frederick Griffith in 1928 and by Joshua Lederberg and Edward Tatum in 1946.
The evidence
Lab experiments show transfer directly; genome comparisons find many genes whose family tree does not match their host's, a sign they were borrowed.
Debates and open questions
How much transfer blurs the deep tree of life; some researchers think most microbial gene families have moved between lineages at least once.
▸Gunflint Chert microfossils preserves fossils of Bacteria & archaea: the microbial worldWell established
The connection
The Gunflint Chert captured a whole community of microbes about 1.88 billion years ago. Silica-rich water seeped into cells and hardened around them, preserving filaments and spheres from shallow seas. It gave scientists their first convincing snapshot of the microbial world long before animals.
When and how
Gunflint Iron Formation, northwestern Ontario, Canada; found by Stanley Tyler in 1953 and described with Elso Barghoorn in 1954.
The evidence
The microfossils have cell walls, sizes and shapes matching living bacteria, sit within the original rock fabric, and contain organic carbon.
Debates and open questions
Fossil bacteria rarely reveal metabolism; whether some were cyanobacteria or iron-oxidizers is debated, and archaea are almost impossible to recognize as fossils.
▸Asgard archaea: the host cell are a branch of Bacteria & archaea: the microbial worldStrong evidence
The connection
Asgard archaea belong to the archaea, one of the two great domains of microbes alongside bacteria. They went unnoticed until DNA was sequenced straight from environmental samples, showing how much of the microbial world was hidden and suggesting eukaryotes are an offshoot of archaea.
When and how
Seafloor sediments, hot springs and microbial mats worldwide; first described from sediment near Loki's Castle, Arctic Ocean, in 2015.
How sure are we?
Their genomes carry the core archaeal genes, and gene trees consistently group them with other archaea, including the strain grown in the lab in 2020.
Debates and open questions
How many Asgard groups exist, and whether eukaryotes should formally be counted as a branch within the archaea.
▸Bacteria & archaea: the microbial world supplied the partner that became Mitochondria: endosymbiosisWell established
The connection
The mitochondrion began as a free-living bacterium related to today's alphaproteobacteria. It ended up inside an archaeal host, perhaps as a partner trading chemicals, and was never expelled. Over many generations it handed most of its genes to the host and became a permanent part of the cell.
When and how
Roughly 2.0–1.6 billion years ago, location unknown; the idea dates to the early 1900s and was championed by Lynn Margulis from 1967.
The evidence
Mitochondrial DNA, ribosomes and membranes are bacterial; gene sequencing since the late 1970s places mitochondria among or beside the alphaproteobacteria.
Debates and open questions
Which exact bacterial group was the ancestor, and whether the relationship began as partnership, parasitism or the host trying to eat it.
▸Carl Woese showed the deep split within Bacteria & archaea: the microbial worldWell established
The connection
Before Woese, all microbes without a nucleus were lumped together as bacteria. Comparing ribosomal RNA sequences, he showed that methane-producing microbes, and later many salt- and heat-loving ones, formed a separate group as distant from bacteria as from humans. The single microbial world became two deep lineages: bacteria and archaea.
When and how
University of Illinois at Urbana-Champaign, 1977, by Carl Woese and George Fox; published in the Proceedings of the National Academy of Sciences.
The evidence
Archaea have chemically different cell membranes and gene-reading machinery closer to ours; whole-genome sequencing from 1996 onward confirmed the split.
Debates and open questions
What the last common ancestor of bacteria and archaea was like, and where exactly the root of the tree of life lies.
▸Antibiotic resistance evolves in Bacteria & archaea: the microbial worldWell established
The connection
Antibiotics kill bacteria, so any bacterium carrying a gene that blocks, breaks down or pumps out the drug survives and multiplies. Resistance genes are ancient, because microbes fought each other with natural antibiotics long before humans did, and they spread quickly by gene swapping. Archaea are mostly unaffected by common antibiotics.
When and how
Alexander Fleming found penicillin in 1928 and warned of resistance in 1945; resistant strains spread in hospitals within years of mass use in the 1940s.
The evidence
Hospital and lab tracking of resistant strains; resistance genes recovered from 30,000-year-old Yukon permafrost (2011) show such genes predate medicine.
Debates and open questions
How fast resistance will outpace new drugs, and how much farm antibiotic use contributes compared with medical use.
▸Viruses: on the edge of life constantly infect and reshape Bacteria & archaea: the microbial worldWell established
The connection
Viruses that infect microbes outnumber cells perhaps tenfold. In the oceans they kill an estimated fifth of microbial life each day, releasing nutrients and shaping which species thrive. They also carry genes between hosts, and microbes evolved defences such as CRISPR in response, an arms race running for billions of years.
When and how
Bacteria-infecting viruses (phages) were discovered by Frederick Twort in 1915 and Félix d'Hérelle in 1917; their huge ocean role became clear from the late 1980s.
The evidence
Seawater counts of about 10 million virus particles per milliliter; microbial genomes full of viral DNA and CRISPR records of past infections.
Debates and open questions
How far back the arms race goes; viruses leave no fossils, so their deep history must be pieced together from genes.