Microbial Symbioses

Mutualism vs. Symbiosis

Symbiosis is a relationship between two organisms: it can be mutualistic (both benefit), commensal (one benefits), or parasitic.

Learning Objectives

Compare Mutualism and Symbiosis

Key Takeaways

Key Points

  • Mutualism, a relationship in which both species benefit, is common in nature. In microbiology, there are many examples of mutualistic bacteria in the gut that aid digestion in both humans and animals.
  • Commensalism is a relationship between species in which one benefits and the other is unaffected. Humans are host to a variety of commensal bacteria in their bodies that do not harm them but rely on them for survival (e.g. bacteria that consume dead skin).
  • Parasitic relationships, in which one species benefits and the other suffers, are very common in nature. Most of the microorganisms studied in medical microbiology are parasitic and feed on human tissue. For example, cholera, leshmaniasis, and Giardia are all parasitic microbes.
  • Symbiotic relationships can also be classified by the physical relationship between the two species. Endosymbionts live inside the tissues of the host, while ectosymbionts live outside of their partner species.

Key Terms

  • commensalism: A class of relationship between two organisms in which one organism benefits without affecting the other
  • symbiosis: A close and often long-term interaction between two or more different biological species
  • mutualism: A relationship between individuals of different species in which both individuals benefit

Symbiosis is any relationship between two or more biological species. Such relationships are usually long term and have a strong impact on the fitness of one or both organisms. Symbiotic relationships are categorized by the benefits and physical relationships experienced by each species.

Common types of symbiosis are categorized by the degree to which each species benefits from the interaction:

  • Mutualism: In mutualistic interactions, both species benefit from the interaction. A classic example of mutualism is the relationship between insects that pollinate plants and the plants that provide those insects with nectar or pollen. Another classic example is the behavior of mutualistic bacteria in ecology and human health. Gut bacteria in particular are very important for digestion in humans and other species. In humans, gut bacteria assist in breaking down additional carbohydrates, out-competing harmful bacteria, and producing hormones to direct fat storage. Humans lacking healthy mutualistic gut flora can suffer a variety of diseases, such as irritable bowel syndrome. Some ruminant animals, like cows or deer, rely on special mutualistic bacteria to help them break down the tough cellulose in the plants they eat. In return, the bacteria get a steady supply of food.
  • Commensalism: In commensalism, one organism benefits while the other organism neither benefits nor suffers from the interaction. For example, a spider may build a web on a plant and benefit substantially, while the plant remains unaffected. Similarly, a clown fish might live inside a sea anemone and receive protection from predators, while the anemone neither benefits nor suffers.
  • Parasitism: Parasites are organisms that harm their symbiotic partners. Parasitism is incredibly common in nature: depending on the definition, more than half of all species may go through at least one parasitic stage in their life cycle. There are many well-documented examples of parasitic bacteria and microorganisms throughout this text.

Symbiosis can also be characterized by an organism's physical relationship with its partner.

  • Endosymbiosis: a relationship in which one of the symbiotic species lives inside the tissue the other. For example, Coral polyps have special algae called zooxanthelle that live inside their cells. Zooxanthelle provide sugars to the coral through photosynthesis. Similarly, nitrogen-fixing fungi often live inside the cells of plants, providing nitrogen in exchange for the sugars of photosynthesis.
  • Ectosymbiosis: a relationship in which one species lives on the outside surface of the other. Barnacles that live on whales and bromeliads that live on tropical trees are examples of endosymbionts.

These categories can be paired with the above terms to better describe the species' interactions. For example, you might say that a gut bacteria is an "endosymbiotic mutualist," or that a flea is an "ectosymbiotic parasite. "

The Rumen and Ruminant Animals

Ruminant animals (such as deer and cows) digest food in a four-chambered stomach with the help of special bacteria, protozoa, and fungi.

Learning Objectives

Identify how ruminant animals host symbiotic bacteria

Key Takeaways

Key Points

  • Ruminant animals use a special four-chambered stomach with a unique microbial flora to digest tough cellulose found in the plants in their diets. Most vertebrates cannot make cellulase, the enzyme that breaks down cellulose, but microbes in the rumen produce it for them.
  • Ruminants chew and ingest plant matter and then swallow it. The plant matter is separated into liquids and solids in the rumen, and liquids drain into the reticulum. Solids in the rumen are then regurgitated into the mouth to be chewed and further broken down.
  • Liquids pass from the reticulum into the omasum, where sugars, fatty acids, and other nutrients are absorbed into the blood stream.
  • After the omasum, food passes into the abomasum, which is much like the stomach in non-ruminant (monogastric) animals, and from there moves into the small intestine, where it is digested.

Key Terms

  • Rumen: The first chamber in the alimentary canal of ruminant animals. It serves as the primary site for microbial fermentation of ingested feed.
  • Abomasum: The fourth and final stomach compartment in ruminants. It secretes rennin - the artificial form of which is called rennet, and is used in cheese creation.
  • Omasum: The third compartment of the stomach in ruminants. Though its functions have not been well-studied, it appears to primarily aid in the absorption of water, magnesium, and the volatile fatty acids produced.

A Ruminant's Multi-chambered Stomach

Ruminants are mammals that digest plant based food by processing it in a series of chambers in their stomachs. There are about 150 species of ruminants, including both domestic and wild species. Ruminating mammals include cattle, goats, sheep, giraffes, bison, moose, elk, yaks, water buffalo, deer, camels, alpacas, llamas, and antelope.

Ruminants differ from non-ruminants (called monogastrics) because they have a four-chambered stomach. The four compartments are called the rumen, the reticulum, the omasum, and the abomasum. The rumen and the reticulum are connected and work in concert and are therefore sometimes called the "reticulorumen".


The digestive tract of a ruminant: The ruminant digestive tract has four compartments, the rumen, the reticulum, the omasum, and abomasum.

The Ruminant Digestive Process

  • Ruminants chew plant matter to mix it with saliva and swallow. The food then enters the first two stomach chambers, the reticulum and rumen (or reticulorumen).
  • The reticulum and rumen work together to separate solids and liquids. Contractions push solid food particles back up into the rumen, while liquids are drained into the reticulum. Specialized microbe species live in the rumen and help ruminants break down cellulose.
  • Solids are formed into a bolus, called "cud," in the rumen and the solid cud is regurgitated back up to the mouth where it is chewed a second time, and returned to the reticulorumen to repeat the process.
  • Liquid digesta in the reticulum is passed into the omasum where nutrients and water are absorbed into the blood stream.
  • After this, digesta is passed into the abomasum, which is similar to the stomach of other animals. After the abomasum, digesta moves through the large and small intestines.

Ruminants are of interest to microbiologists because they have unique species of bacteria, yeasts, protozoa, and fungi in their rumens. The plant matter consumed by ruminants is high in cellulose, but vertebrates cannot produce cellulase which is the enzyme required to break down cellulose. Thus ruminants depend on the symbiotic microbes in their guts to break down cellulose for digestion. There is no oxygen in the rumen, so bacteria in the rumen are typically anaerobes or facultative anaerobes.

Hydrothermal Vent Microbial Ecosystems

Hydrothermal vents are home to chemosynthetic bacteria, which are the basis of a unique ecosystem that thrives in total darkness.

Learning Objectives

Describe hydrothermal vent microbial ecosystems

Key Takeaways

Key Points

  • Hydrothermal vents emit nutrient rich, geothermally heated water. Mats of chemosynthetic bacteria grow around the vents and synthesize carbohydrates from the carbon dioxide ejected by the vent.
  • Many species of crabs, worms, snails, and tube worms depend on these bacterial mats for food. These species are often specially adapted to life in the lightless, high pressure, and hot environment of the vent.
  • Vents are the target of exploitation of the mining industry, which is a cause for concern among marine biologists. Mining could damage these very unique and diverse ecosystems.

Key Terms

  • chemosynthesis: The production of carbohydrates and other compounds from simple compounds such as carbon dioxide, using the oxidation of chemical nutrients as a source of energy rather than sunlight; it is limited to certain bacteria and fungi.
  • geothermal: Pertaining to heat energy extracted from reservoirs in the earth's interior.

Hydrothermal Vents and Their Microbial Communities

A hydrothermal vent is a fissure in the earth's surface from which geothermally heated water issues. They are typically found deep below the surface of the ocean. Hydrothermal vents are of interest to microbiologists because they have unique microbial communities found nowhere else on earth.


Hydrothermal Vents: Hydrothermal vents are cracks in the earth's crust where geothermally heated water leaks out.

In most shallow water and terrestrial ecosystems, energy comes from sunlight, but in the deep ocean there is total darkness. However, hydrothermal vents often expel nutrient rich water, containing methane and sulfur compounds. Vent bacteria can synthesize all the compounds they need to live from these nutrients, a process called chemosynthesis. These bacteria form the basis of the entire hydrothermal vent ecosystem.

The chemosynthetic bacteria grow into a thick mat, covering the hydrothermal vent, and this is the first trophic level of the ecosystem. Snails, shrimp crabs, tube worms, and fish feed on the bacterial mat and attract larger organisms such as squid and octopuses. Many of these species are specially adapted to live in the dark and lack eyes. Hydrothermal vents are biodiversity hot spots because they have many species that are uniquely adapted to live in this harsh environment. For example, the Pompeii tube worm Alvinella pompejana can resist temperatures up to 176°F. These ecosystems are almost entirely independent of sunlight (although the dissolved oxygen used by some animals does ultimately come from plants at the surface ).


Tubeworms Living Near A Hydrothermal Vent: Some species of tube worms are specially adapted to withstand the high temperatures found at hydrothermal vents.


Crabs near a hydrothermal vent: The ecosystems around hydrothermal vents rely on mats chemosynthetic bacteria, and many species feed on the bacteria. Hydrothermal vents are some of the most unique ecosystems in the world

Despite being some of the most remote ecosystems in the world, hydrothermal vents are under threat from mining companies. As mineral resources on land have become depleted, mining companies have turned to deep sea geothermal vents to extract metals and sulfur. Although the technology for deep sea mining is new, conservation biologists are concerned that mining hydrothermal vents will destroy these fragile and unique ecosystems.

Squid-Aliivibrio Symbiosis

Squid host light-generating Allivibiro bacteria in a special organ so that they can illuminate themselves and blend in with the environment.

Learning Objectives

Explain the symbiotic relationship of squid and aliivibrio

Key Takeaways

Key Points

  • Squid rely on Allivibrio bacteria to generate light that allows them to blend in with the light coming from above. Animals below them cannot see their shadow when they view the squid from below.
  • Squid use mucus to attract many species of bacteria into their light organ, but they sort out Aliivibiro in several ways. Ciliated cells in the light organ create a current that expels most bacteria, and the squid uses hydrogen peroxide to create a hostile environment that Aliivibrio can resist.
  • Once inside the light organ, the Aliivibrio bacteria receive sugars and amino acids from the squid. However, this is costly to the squid, and the squid clears out its light organ during the day so that it does not have to constantly maintain a colony of Aliivibrio bacteria.

Key Terms

  • cilia: Organelles found in eukaryotic cells. Cilia are slender protuberances that project from the much larger cell body.
  • BIoluminescence: The emission of light by a living organism.


A special category of symbiotic relationships involve bioluminescence, where light producing bacteria are hosted by another organism. One of the best studied examples of bioluminescence is the Hawaiian bobtail squid (Euprymna scolopes) and its mutualistic bacteria, Aliivibrio fischeri. Aliivibrio fischeri inhabits a special light organ in the squid's mantle. The bacteria are fed a sugar and amino acid solution by the squid. In return, they produce light to hide the squid's silhouette when viewed from below, allowing the squid to match ambient light conditions.


Bobtail Squid: Bobtail squid rely on their mutualist bacteria Allivibrio fischerii to generate light. The bacteria inhabits a special light organ in the squid's mantle and receives sugars and amino acids in exchange for light.

Bobtail squid hatchlings do not have Aliivibrio fischeri naturally in their bodies. They are born with a special light organ structure, with cilliated cells at the opening designed to trap passing A. fischeri, but must obtain the bacteria from sea water. To do this, the squid secretes a special mucus whenever its cells detect peptidoglycan (which is found in the cell walls of bacteria). The mucus collects near the opening of the light organ which traps passing bacteria. The squid weeds out unwanted bacteria in several ways. For instance, A. fischeri is able to survive in the mucus better than other species. It is also a very mobile bacteria, and is able to swim against the current created by the cilia at the mouth of the light organ.

The squid also creates a hostile environment at the entrance to the light organ by secreting an enzyme that splits hydrogen peroxide, creating a toxic environment for most bacteria. Aliivibrio fischeri can capture hydrogen peroxide before the squid can use it as a toxin, and thus can survive in the hostile chemical environment. Once A. fischeri has passed these hurdles at the opening of the light organ, it can colonize chambers of the light organ and begin enjoying the benefits of symbiosis.

Despite all the effort that goes into obtaining Aliivibrio fischeri, the squid ejects 95% of its bacteria every day. It not fully understood why the squid cleans out its light organ, but the bacteria require a great deal of sugar and amino acids, so it may be most useful to the squid to host bacteria only when they are needed. It may also provide a supply of bacteria for squid hatchlings.

Mutualistic Relationships with Fungi and Fungivores

Members of Kingdom Fungi form ecologically beneficial mutualistic relationships with cyanobateria, plants, and animals.

Learning Objectives

Describe mutualistic relationships with fungi

Key Takeaways

Key Points

  • Mutualistic relationships are those where both members of an association benefit; Fungi form these types of relationships with various other Kingdoms of life.
  • Mycorrhiza, formed from an association between plant roots and primitive fungi, help increase a plant's nutrient uptake; in return, the plant supplies the fungi with photosynthesis products for their metabolic use.
  • In lichen, fungi live in close proximity with photosynthetic cyanobateria; the algae provide fungi with carbon and energy while the fungi supplies minerals and protection to the algae.
  • Mutualistic relationships between fungi and animals involves numerous insects; Arthropods depend on fungi for protection, while fungi receive nutrients in return and ensure a way to disseminate the spores into new environments.

Key Terms

  • mycorrhiza: a symbiotic association between a fungus and the roots of a vascular plant
  • lichen: any of many symbiotic organisms, being associations of fungi and algae; often found as white or yellow patches on old walls, etc.
  • thallus: vegetative body of a fungus

Mutualistic Relationships

Symbiosis is the ecological interaction between two organisms that live together. However, the definition does not describe the quality of the interaction. When both members of the association benefit, the symbiotic relationship is called mutualistic. Fungi form mutualistic associations with many types of organisms, including cyanobacteria, plants, and animals.

Fungi & Plant Mutualism

Mycorrhiza, which comes from the Greek words "myco" meaning fungus and "rhizo" meaning root, refers to the association between vascular plant roots and their symbiotic fungi. About 90 percent of all plant species have mycorrhizal partners. In a mycorrhizal association, the fungal mycelia use their extensive network of hyphae and large surface area in contact with the soil to channel water and minerals from the soil into the plant, thereby increasing a plant's nutrient uptake. In exchange, the plant supplies the products of photosynthesis to fuel the metabolism of the fungus.

Mycorrhizae display many characteristics of primitive fungi: they produce simple spores, show little diversification, do not have a sexual reproductive cycle, and cannot live outside of a mycorrhizal association. There are a number of types of mycorrhizae. Ectomycorrhizae ("outside" mycorrhiza) depend on fungi enveloping the roots in a sheath (called a mantle) and a Hartig net of hyphae that extends into the roots between cells. The fungal partner can belong to the Ascomycota, Basidiomycota, or Zygomycota. In a second type, the Glomeromycete fungi form vesicular–arbuscular interactions with arbuscular mycorrhiza (sometimes called endomycorrhizae). In these mycorrhiza, the fungi form arbuscules that penetrate root cells and are the site of the metabolic exchanges between the fungus and the host plant. The arbuscules (from the Latin for "little trees") have a shrub-like appearance. Orchids rely on a third type of mycorrhiza. Orchids are epiphytes that form small seeds without much storage to sustain germination and growth. Their seeds will not germinate without a mycorrhizal partner (usually a Basidiomycete). After nutrients in the seed are depleted, fungal symbionts support the growth of the orchid by providing necessary carbohydrates and minerals. Some orchids continue to be mycorrhizal throughout their lifecycle.


Mycorrhizal fungi: (a) Ectomycorrhiza and (b) arbuscular mycorrhiza have different mechanisms for interacting with the roots of plants.


Lichens display a range of colors and textures. They can survive in the most unusual and hostile habitats. They cover rocks, gravestones, tree bark, and the ground in the tundra where plant roots cannot penetrate. Lichens can survive extended periods of drought: they become completely desiccated and then rapidly become active once water is available again. Lichens fulfill many ecological roles, including acting as indicator species, which allow scientists to track the health of a habitat because of their sensitivity to air pollution.


Lichen: fungi and cyanobateria: Lichens have many forms. They may be (a) crust-like, (b) hair-like, or (c) leaf-like.

Lichens are not a single organism, but, rather, an example of a mutualism in which a fungus (usually a member of the Ascomycota or Basidiomycota phyla) lives in close contact with a photosynthetic organism (a eukaryotic alga or a prokaryotic cyanobacterium). Generally, neither the fungus nor the photosynthetic organism can survive alone outside of the symbiotic relationship. The body of a lichen, referred to as a thallus, is formed of hyphae wrapped around the photosynthetic partner. The photosynthetic organism provides carbon and energy in the form of carbohydrates. Some cyanobacteria fix nitrogen from the atmosphere, contributing nitrogenous compounds to the association. In return, the fungus supplies minerals and protection from dryness and excessive light by encasing the algae in its mycelium. The fungus also attaches the symbiotic organism to the substrate.


Thallus of lichen: This cross-section of a lichen thallus shows the (a) upper cortex of fungal hyphae, which provides protection; the (b) algal zone where photosynthesis occurs, the (c) medulla of fungal hyphae, and the (d) lower cortex, which also provides protection and may have (e) rhizines to anchor the thallus to the substrate.

The thallus of lichens grows very slowly, expanding its diameter a few millimeters per year. Both the fungus and the alga participate in the formation of dispersal units for reproduction. Lichens produce soredia, clusters of algal cells surrounded by mycelia. Soredia are dispersed by wind and water and form new lichens.

Fungi & Animal Mutualism

Fungi have evolved mutualisms with numerous insects. Arthropods (jointed, legged invertebrates, such as insects) depend on the fungus for protection from predators and pathogens, while the fungus obtains nutrients and a way to disseminate spores into new environments. The association between species of Basidiomycota and scale insects is one example. The fungal mycelium covers and protects the insect colonies. The scale insects foster a flow of nutrients from the parasitized plant to the fungus. In a second example, leaf-cutting ants of Central and South America literally farm fungi. They cut disks of leaves from plants and pile them up in gardens. Fungi are cultivated in these disk gardens, digesting the cellulose in the leaves that the ants cannot break down. Once smaller sugar molecules are produced and consumed by the fungi, the fungi in turn become a meal for the ants. The insects also patrol their garden, preying on competing fungi. Both ants and fungi benefit from the association. The fungus receives a steady supply of leaves and freedom from competition, while the ants feed on the fungi they cultivate.

Agrobacterium and Crown Gall Disease

Argobacterium causes Crown Gall Disease by transferring a DNA plasmid to the host plant, causing the host to make nutrients for it.

Learning Objectives

Summarize the symbiotic relationship between plants and agrobacterium

Key Takeaways

Key Points

  • Crown Gall Disease is caused by Agrobacterium tumefaciens, a bacteria that infects plants. The bacteria causes tumors on the stem of its host.
  • Agrobacterium tumefaciens manipulates its hosts by transferring a DNA plasmid to the cells of its host. Plasmids are normally used to transfer DNA from bacteria to bacteria.
  • Once in the host cell, the plasmid integrates itself into the host plant cell's genome and forces the host to produce unique amino acids and other substances which nourish the bacteria. These compounds are unusable by most bacteria, so Argobacteria can out-compete other species.

Key Terms

  • plasmid: A circle of double-stranded DNA that is separate from the chromosomes, which is found in bacteria and protozoa.
  • pilus: A hair-like appendage found on the cell surface of many bacteria.

Crown Gall Disease is caused by a bacteria called Agrobacterium tumefaciens. The disease manifests as a tumor-like growth usually at the junction of the root and shoot. A. tumefaciens can transfer part of its DNA to the host plant, through a plasmid - a bacterial DNA molecule that is independent of a chromosome. The new DNA segment causes the plant to produce unusual amino acids and plant hormones which provide the bacteria with carbon and nitrogen.


Smart plants cue farmers to nutrient deficiencies: A. tumefaciens attaching itself to a plant cell

Bacteria normally use plasmids for horizontal gene transfer, so they can share genes with related bacteria to help them cope with stressful environments. For example, plasmids can confer on bacteria the ability to fix nitrogen, or to resist antibiotic compounds. Typically bacteria transfer plasmids through conjugation: a donor bacteria creates a tube called a pilus that penetrates the cell wall of the recipient bacteria and the plasmid DNA passes through the tube. The other bacteria either integrates the plasmid into its chromosomes, or it remains free-floating in the cytoplasm. In either case, the recipient bacteria receives new genetic material.

In the case of Crown Gall Disease, A. tumefaciens transfers a plasmid containing T-DNA into the cells of its host plant through conjugation, as it would with another bacteria. However, once inside the plant cell, the DNA integrates semi-randomly into the genome of the plant and changes the behavior of the celll.

The new plasmid genes are expressed by the plant cells, and cause them to secrete enzymes that produce the amino acids octopine or nopaline. It also carries genes for the biosynthesis of the plant hormones, auxin and cytokinins, and for the biosynthesis of opines, providing a carbon and nitrogen source for the bacteria.

These opines can be used by very few other bacteria and give A. tumefaciens a competitive advantage.

The Legume-Root Nodule Symbiosis

Legumes have a symbiotic relationship with bacteria called rhizobia, which create ammonia from atmospheric nitrogen and help the plant.

Learning Objectives

Evaluate legume and nitrogen-fixing bacteria symbiosis

Key Takeaways

Key Points

  • Rhizobia normally live in the soil, but when there is limited soil nitrogen, legumes release flavonoids which signal to rhizobia that the plant is seeking symbiotic bacteria.
  • When exposed to flavonoids, the Rhizobia release nodulation factor, which stimulates the plant to create deformed root hairs. Rhizobia then form an " infection thread" which allows them to enter the root cells through the root hairs.
  • Once the rhizobia are inside the root cells, the root cells divide rapidly, forming a nodule.
  • The rhizobia create ammonia from nitrogen in the air, which is used by the plant to create amino acids and nucleotides. The plant provides the bacteria with sugars.

Key Terms

  • Nodulation Factor: Signaling molecules produced by bacteria known as rhizobia during the initiation of nodules on the root of legumes. A symbiosis is formed when legumes take up the bacteria.

Legumes and their Nitrogen-Fixing Bacteria

Many legumes have root nodules that provide a home for symbiotic nitrogen-fixing bacteria called rhizobia. This relationship is particularly common in nitrogen-limited conditions. The Rhizobia convert nitrogen gas from the atmosphere into ammonia, which is then used in the formation of amino acids and nucleotides.


Root Nodules: Root nodules are formed when nitrogen fixing bacteria called rhizobia enter the cells of a host plant.

Rhizobia normally live in the soil and can exist without a host plant. However, when legume plants encounter low nitrogen conditions and want to form a symbiotic relationship with rhizobia they release flavinoids into the soil. Rhizobia respond by releasing nodulation factor (sometimes just called nod factor), which stimulates nodule formation in plant roots. Exposure to nod factor triggers the formation of deformed root hairs, which permit rhizobia to enter the plant. Rhizobia then form an infection thread, which is an intercellular tube that penetrates the cells of the host plant, and the bacteria then enter the host plants cells through the deformed root hair. Rhizobia can also enter the root by inserting themselves between cracks between root cells; this method of infection is called crack entry. Bacteria enter the root cells from the intercellular spaces, also using an infection thread to penetrate cell walls. Infection triggers rapid cell division in the root cells, forming a nodule of tissue.

The relationship between a host legume and the rhizobia is symbiotic, providing benefits to both participants. Once the rhizobia have established themselves in the root nodule, the plant provides carbohydrates in the form of malate and succinate, and the rhizobia provide ammonia for the formation of amino acids. Many legumes are popular agricultural crops specifically because they require very little fertilizer: their rhiziobia fix nitrogen for them. Used properly some legumes can even serve as fertilizer for later crops, binding nitrogen in the plant remains in the soil.


Soy Beans: Soy beans are a type of legume crop that rely on rhizobia

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