Difficulty: Introductory | Prerequisites: none
Tags: three domains of life, prokaryotes, eukaryotes, Bacteria, Archaea, Eukarya, extremophiles, microbe reproduction, transformation, conjugation, cyanobacteria, protists, fungi, spores, nutrient cycling, photosynthesis, binary fission
This topic introduces how biologists sort all living things into three domains (Bacteria, Archaea, Eukarya) and then zooms in on three groups that fall outside the plant-and-animal spotlight: microbes, protists, and fungi. You will need to know the structural difference between prokaryotic and eukaryotic cells, the ways microbes gain genetic variation without sexual reproduction, and the basic feeding and reproductive strategies of protists and fungi. The material underpins everything that follows in the Innovations sequence, because plants and animals evolved from lineages covered here.
Life is divided into three domains: Bacteria, Archaea (both prokaryotic), and Eukarya (eukaryotic). Microbes reproduce asexually but shuffle genes through transformation and conjugation. Protists are a grab-bag of unicellular and multicellular eukaryotes that feed in multiple ways, while fungi are heterotrophs that decompose organic matter and reproduce via spores.
Prokaryote
An organism whose cells lack a membrane-bound nucleus. DNA sits in a nucleoid region rather than inside a nuclear envelope.
In simple terms, the cell's genetic material floats freely in the cytoplasm instead of being sealed inside its own compartment.
Eukaryote
An organism whose cells contain a membrane-bound nucleus and other membrane-bound organelles (mitochondria, ER, etc.).
Think of it as the upgraded cell plan: DNA gets its own room, and other organelles get theirs.
Extremophile
A microorganism that thrives in conditions most life cannot tolerate, such as extreme heat, cold, acidity, or salinity.
These are the organisms that live in boiling hot springs or ultra-acidic environments and do just fine.
Transformation (microbial genetics)
The uptake of free DNA fragments from the surrounding environment by a bacterial cell.
In simple terms, the microbe picks up stray bits of DNA lying around outside and incorporates them into its own genome.
Conjugation
Direct transfer of genetic material between two bacterial cells through a physical connection (pilus). Sometimes called "microbe sex," though it is not true sexual reproduction.
One cell builds a bridge to another and passes a copy of some of its genes across.
Cyanobacteria
Photosynthetic bacteria that produce oxygen as a by-product. They are widely credited with oxygenating Earth's early atmosphere.
Think of them as the original oxygen factories, billions of years before land plants existed.
Protist
An informal grouping of eukaryotes that are not plants, animals, or fungi. Protists can be unicellular or multicellular and feed by absorption, ingestion, or photosynthesis.
This is essentially the "everything else" category of eukaryotic life.
Absorptive feeding
A mode of nutrition in which an organism takes up dissolved nutrients directly from its environment across cell membranes.
The organism soaks up food molecules from whatever it is sitting on or in, rather than eating something whole.
Ingestive feeding
A mode of nutrition in which an organism engulfs and internally digests food particles or other organisms.
The organism eats, in the everyday sense: it takes in another organism (alive or dead) and breaks it down inside.
Fungi
Eukaryotic heterotrophs that obtain nutrients by absorptive feeding. They cannot photosynthesise and play a central role in decomposition and nutrient cycling.
Fungi are the recyclers of the biological world: they break down dead material and return nutrients to the soil.
Spore (fungal)
A reproductive cell produced by fungi that can develop into a new organism. Spores are typically resistant to harsh conditions and can disperse widely.
Think of spores as the fungal equivalent of seeds, though structurally and developmentally they are quite different.
Bacteria and Archaea are both prokaryotic (no nuclear membrane)
Eukarya are eukaryotic (membrane-bound nucleus present)
The key structural dividing line is the nuclear membrane: prokaryotes lack one, eukaryotes have one
Extremophiles
Primarily microorganisms
Thrive in extreme temperatures, pH, salinity, or pressure
Found across Bacteria and Archaea
Reproduction
Microbes reproduce only asexually (binary fission)
They gain genetic variation through horizontal gene transfer:
Transformation: uptake of free DNA from the environment
Conjugation: direct transfer of genes between cells via a pilus (sometimes called "microbe sex")
Cyanobacteria
Photosynthetic prokaryotes that produce O2 and consume CO2
Likely responsible for the Great Oxygenation Event, transforming Earth's atmosphere from anoxic to oxygen-rich
Eukaryotes that do not fit into plants, animals, or fungi
Can be unicellular or multicellular
Reproduce sexually or asexually
Three feeding strategies:
Absorptive feeding: nutrients taken directly from the environment
Ingestive feeding: eating live or dead organisms
Photosynthesis: some protists (e.g. algae) are photosynthetic
Eukaryotic heterotrophs, cannot photosynthesise
Central role in nutrient cycling and decomposition
May reproduce sexually or asexually, typically via spores
Students often think Archaea are bacteria. They are not. Archaea and Bacteria are separate domains, despite both being prokaryotic. They differ in membrane chemistry, ribosomal RNA sequences, and many metabolic pathways.
Conjugation is frequently confused with sexual reproduction. Conjugation transfers genetic material between cells, but it does not involve gametes, meiosis, or the fusion of two cells into one. It is horizontal gene transfer, not sex.
Students sometimes assume all protists are single-celled. Many protists (e.g. kelp, certain algae) are multicellular.
Fungi are sometimes lumped in with plants because they are sessile. Fungi are heterotrophs, they cannot photosynthesise, and their cell walls contain chitin rather than cellulose.
Prof Dobkowski's exam material consistently tests your ability to distinguish between domains and between prokaryotic and eukaryotic features. Expect questions on horizontal gene transfer mechanisms and their names. The role of cyanobacteria in oxygenating the atmosphere is a classic exam target.
Know the difference between transformation and conjugation cold. Both names, both mechanisms.
Be able to list the four traits that define all animals (covered in Innovations 3) as distinct from protists and fungi.
Understand why fungi are not plants (no photosynthesis, chitin cell walls, heterotrophic).
True or False: Archaea and Bacteria belong to the same domain. (False, they are separate domains.)
Fill in the blank: Microbes gain new genetic material from the environment through a process called ________. (Transformation.)
True or False: All protists are unicellular. (False, some are multicellular.)
Fill in the blank: Fungi reproduce via ________. (Spores.)
True or False: Cyanobacteria are eukaryotes. (False, they are prokaryotes.)
Q: Name the three domains of life and state which are prokaryotic.
A: Bacteria, Archaea, and Eukarya. Bacteria and Archaea are prokaryotic; Eukarya is eukaryotic.
Q: What is the key structural feature that distinguishes prokaryotes from eukaryotes?
A: Eukaryotes have a membrane-bound nucleus; prokaryotes do not.
Q: Describe two mechanisms by which bacteria acquire new genetic information without sexual reproduction.
A: Transformation (uptake of free DNA from the environment) and conjugation (direct transfer of genes between cells via a pilus).
Q: What role did cyanobacteria play in Earth's early history?
A: Cyanobacteria performed photosynthesis, producing oxygen and consuming CO2. They are credited with oxygenating Earth's atmosphere (the Great Oxygenation Event).
Q: How do protists differ from fungi in their feeding strategies?
A: Protists can feed by absorption, ingestion, or photosynthesis. Fungi feed only by absorption and cannot photosynthesise.
Q: Why are fungi classified separately from plants?
A: Fungi are heterotrophs (they cannot photosynthesise), their cell walls contain chitin rather than cellulose, and they obtain nutrients through absorptive feeding.
This material connects directly to Innovations 2 (Plants), because land plants evolved from green algae, a photosynthetic protist lineage. The symbiosis between fungi and early land plants (mycorrhizae) reappears in the plant diversification material. Understanding prokaryotic vs eukaryotic cell structure also underpins the animal classification content in Innovations 3, where all animals are defined as multicellular eukaryotes.
three domains of life, Bacteria, Archaea, Eukarya, prokaryote, eukaryote, nuclear membrane, extremophile, thermophile, halophile, acidophile, binary fission, asexual reproduction, horizontal gene transfer, transformation, conjugation, pilus, cyanobacteria, Great Oxygenation Event, photosynthesis, protist, absorptive feeding, ingestive feeding, algae, fungi, chitin, cellulose, spore, nutrient cycling, decomposer, BIOL 180, Introduction to Biology, University of Washington, Prof Dobkowski