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Plants Background: What's New?

Recent discoveries change forever our notions of plant life as essentially passive and helpless organisms.

The traditional concept of plant life does not include much about roots, except that they are both anchors and pumps. What's new about roots is below, under Rhizosphere.

The traditional concept of plant life does not include the many survival-based associations plants have with other kinds of life in their communities, except that legumes fix nitrogen with bacterial help. What's new about plant symbiosis, especially with fungi, is below, under Mycorrhiza Symbiosis Plus.

Rhizosphere: The Inter-Active Root Zone

The rhizosphere is the zone of soil influenced by growing plant roots.

Until recently, only the above-ground part of plants has been much studied. "Out of sight, out of mind" is more than an old adage. Science has just begun to grasp the workings of this intimate root zone.

The rhizosphere extends out from the growing root just a few millimeters. It is an incredibly busy soil habitat, and most of its busy-ness is microbial. Within this root zone plants interact chemically with bacteria, fungi, and soil nutrients. Root tips are magnets for life. Bacteria of many kinds assemble in biofilms that surround the root surface. Think of the rhizosphere as an interface between living root and living soil.

The rhizosphere of a particular plant may be small, even microscopic, but consider for a moment how many uncountable billions of trees and forbs penetrate the soil in all the continents of Earth, and consider that no animal life can survive without green plants, and you begin to grasp how centrally important this micro-habitat is to the whole web of ecosystems we call the biosphere.

Here are some graphic introductions to growing root tips.

parts of a root tip and areas of the rhizosphere
graphic from Raina Maier et al, 2000, Environmental Microbiology


Greatly enlarged growing root, showing the multitude of organisms active here

Growing root tip--Root hairs look transparent here.
As the root pushes into soil, tip cells wear off, providing food for microbes
Credit: No. 53 from Soil Microbiology and Biochemistry Slide Set.
1976 J.P. Martin, et al., eds. SSSA, Madison WI.

Above, we mentioned "living soil." What lives in soil near plant roots? From tiny to huge:

bacteria and archaea
fungal hyphae (tubes) growing in all directions
single-celled algae
protozoans, especially the shelled amoebae
nematode worms (microscopic)
arthropods such as barely visible springtails and mites;
insect larvae, beetles; earthworms, millipedes, snails and slugs

Relatively enormous animals such as pocket gophers, moles, mice and voles play a role in aerating and loosening soil. Soil is a kind of crucible where organic materials such as leaves are shredded by detritus feeders such as snails, and finally decomposed by fungi and bacteria. The result is humus, source of much of a soil's fertility and its capacity to hold water.

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A Gallery of Soil Life:


Incredibly small
bacteria and archaea,

in one gram of soil


Frankia filamentous soil bacteria
actinomycetes bacteria give soil its earthy aroma


400,000 in one gram of soil

fungal hyphae in soil, image credit Tim Wilson,
bacteria colonizing surface of fungal hyphae


Soil Algae,
two of many kinds of the
algae in one gram of soil

Chlamydomonas flagellated soil algae; green in life
Chlorokybus soil algae, dividing


amoeba and ciliates, two kinds of the 30,000
in one
gram of soil

testate or shelled amoeba Arcella
image by Wim Van Egmond

soil ciliate protozoans
image by Agatha Sabine, U. Salzburg

life in soil


We still can't see them, but they are much larger than above

tardigrade or water bear
nematode roundworm

Macro soil life

visible to the naked eye

globular springtail, barely visible
soil mite, some are barely visible




Macro soil life

highly visible to the naked eye

sow bugs, isopod crustaceans
Macro-life: tiny but just visible globular springtails feed on a newly emerged mushroom (enlarged)
Image credit John Caddy


Root Exudates

There are many players at the roots. Their interactions are largely chemical. Roots manufacture and  exude (give off) a wide variety of compounds that regulate the soil microbial community in their vicinity. Root exudates act as messengers that stimulate the microbial community.  Some compounds made by the plant encourage the growth of beneficial bacteria; others weaken and repel harmful bacteria.

One group of compounds exuded from roots are sugars made in the leaves and transferred downward to the rhizosphere to feed bacteria and fungi. These organisms, in turn, act as living fertilizers; they can dissolve phosphates locked in soil and free them so roots can absorb them. Bacteria and fungi also dissolve minerals from rock grains (sand) and make them available. Trichoderma fungi act against attacking fungi as well as activating plant defenses by priming defense genes. Nitogen-fixing bacteria, of course, are well-known symbiotes of roots, providing essential fertilization.

In addition to fungi and bacteria, protozoans play an active role in the rhizosphere. They eat bacteria, and check overgrowth of bacterial populations. Tiny nematode worms are also efficient predators of bacteria. The presence of protozoa in the rhizosphere can increase plant growth.  When bacteria are digested by protozoans such as amoebas, more nitrogen becomes available to roots. Nematode digestion has a similar effect. We are just beginning to grasp the incredible complexity of plants' many interactions with microbes in soils.

One set of interactions plants have with other life forms, especially with fungi, are explored in the next section on plant symbiosis.

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Symbiosis: Mycorrhiza Plus

Gardeners and farmers have long known that masses of fungus are associated with plant roots, but only recently has the earthwide importance of this association become known.

Some fungi and 95% of plants depend on each other for nourishment. Plants without their fungal partners do not thrive; they barely stay alive.

Observe the two redwood seedlings
. The one without mycorrhiza is not a survivor.

Plants evolved from freshwater algae that were already symbiotes of fungi. When land plants left their freshwater origin and colonized land, they carried symbiotic partners with them, on them and inside them. The partners are microscopic fungi.

This mutually beneficial partnership or symbiosis is called mycorrhiza. The word means “fungus-root.”  A mass of tiny fungal tubes expands the working area of roots.

These tubes or hypae extend the plants’ reach and makes them strong and growing, by giving them more access to water and necessary minerals. This makes them more resilient against environmental stresses such as drought.

Without mycorhizzal help, few plants can thrive. Without thriving plant life, of course, animal life cannot survive. Mycorrhizza names an earthwide interdependency that is so vast it is hard to comprehend. To thrive, plants—grains, grasses, trees, vegetables—require fungal partners, or symbiotes. Most of these fungal partners cannot even reproduce outside symbiosis. This suggests the antiquity of the association, probably 475-500 million years old. This partnership for mutual benefit is of central importance to the entire biosphere.

The news: fungi are centrally important to the food supply of animals. This means you.


Seven Aspects of Mycorrhizal Symbiosis

Mycorrhizae increase a plant’s root surface by a factor of ten. Fungal hyphae act like a massive root hair system, scavenging minerals and water from the soil and supplying them to the plant. This greatly improves a plant’s resilience and ability to resist drought.
From the fungal partner, the plant receives phosphorus, nitrogen, potassium, and micronutrients such as copper, sulfur and zinc.
The fungus receives nutrients via the roots. Sugars created in leaves move downward and into the fungal hyphae.
Mycorrhizal plants develop tolerance to pH changes and temperature extremes. They also develop stronger resistance to attacking bacteria and fungi.
Many plants can’t survive  without their fungal associate. Important must-have-mycorrhiza plants in western North America include sagebrush, bitterbrush, and native bunchgrasses. Orchid plants can’t even germinate without their fungal symbiotes.
Many plants have more than one fungal partner; oak trees tend to partner with several kinds simultaneously.
Mycorrhizal fungi are symbiotic with many kinds of plants at once, so beneath our feet in a meadow or a woodland are networks of plants all physically connected in a kind of networked sharing. Parent trees can share nutrients with their saplings.




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Two Types of Mycorrhizal Symbiosis


Arbuscular Mycorrhiza: Endo(inside)-symbiosis


Forbs and grasses (grasses, grains, vegetables, herbs—most flowering plants) partner with fungi that penetrate into the root and create structures inside the root.

finely-branched arbuscule inside root
photo credit Mark Brundrett© 2008 from
Mycorrhizal Associatons: The Web Resource

These structures (arbuscules) are where plant and fungus exchange phosphorus, carbohydrates, water and other nutrients. Each partner in these ancient symbioses has developed the ability to "switch on" certain genes in the other. Symbiotic partners must be able to signal each other for the partnership to work. Most mycorrhyzal fungi in non-woody plants belong to one fungal group, the Glomeromycota. Mosses and ground pines also partner with mycorrhizal fungi, using their rhizomes rather than true roots. Epiphyte plants that live on trees also have mycorrhizal symbiotes, which are also prevalent in wetlands, even in salt marshes.

Trees & Shrubs: Ecto(external)-mycorrhizae

The fungi that partner with trees and shrubs form a sheath on the outside of growing roots.

These fungi supply plant hormones that promote growth. They also produce chemicals that protect the plant from attacking soil bacteria and fungi. Mycorrhizal trees form networks of fungi in the soil which connect many species of forbs and trees. Seedlings of parent trees automatically hook into this network, which assures them of water and nutrients.

Many trees, such as oaks, form mycorrhizal symbioses with dozens of different fungi species. Mycorrhizal fungi must live with a partner symbiont or they die. As a result, many are generalists that can partner with different kinds of trees. For instance, the poisonous fly agaric mushroom partners with both spruce and birch.

Many of these fungi form mushrooms above ground; their spores are spread by wind and water. Many also form fruiting bodies underground--various kinds of truffles.

Truffles are closed fruits that give off aromas attractive to small animals such as voles, chipmunks and flying squirrels. They dig up the truffles and excrete the spores, often at some distance from the host tree. If a jay or squirrel buries and forgets an acorn a few hundred feet from the parent tree, they may be outside the mycorrhizal network, unless it is extended by enterprising rodents spreading spores in their droppings. An elegant solution. Truffle fungi recruit unknowing animal symbionts to disperse their spores.

Sample Fungal Symbiotes

Laccaria mushroom symbiont of rainforest spruce

deadly fly agaric, symbiont of birch and conifers
pine roots sheathed with fungal symbiont. The image does not show the micro-hyphae that extend beyond the roots
tundra mushroom symbiont of dwarf birch and blueberry.The fungal symbionts receive 8-16% of the plants’ photosynthesis carbohydrates. The plants receive 70% of their nitrogen from the fungi.

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Fungal Symbiosis in Leaves

Fungal spores are everywhere in air. Plant leaves are bombarded by them constantly. Thousands of spores land each day on every leaf. Each spore wants to grow there. Some are spores of wilts, blights, and rusts, that want to eat the plant. These fungi are called saprophytes. But other fungi just want to find a home where they can have a symbiont and make a living.

Microshaeropsis symbiont attacking white pine blister rust fungi in a red currant leaf. Photo credit: J. Bérubé, NRCan 

Scientists were long puzzled by the knowledge that many kinds of fungal cells are found living inside leaves, but doing no apparent harm. Gradually, scientists found out that the fungi were doing good. It turns out that many fungal cells are powerful protectors, living symbiotically with the plant and fending off plant diseases, especially saprophyte fungi. Cacao trees, the source of chocolate, depend on these fungal partners for their lives. Plant life is a continual struggle between fungi that want to eat plants, and fungi that eat the attackers.

Many insects eat plants. These fungal cells living inside leaves produce alkaloid compounds that are poisonous to insects and to many microbes. Alkaloids so produced also deter browsing and grazing mammals.


Tall Fescue Example

Grasses are eaten by livestock and insects, and to the grass, herbivores such as cattle, sheep, horses, and grasshoppers are attackers. Tall fescue grasses have found a solution to herbivore grazing. Tall fescue lives in symbiosis with a fungus that produces alkaloids. These fungal hyphae are coiled inside the grass leaf cells. When the grass is eaten, it tastes bad and makes the eater ill, so they won’t eat it again. The plant defends itself from animal teeth. From the human point of view, tall fescue is infected and diseased. From fescue’s point of view, it’s a winner.


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Nitrogen Uptake Symbiosis


Plants must have nitrogen to grow. Nitrogen in the form of such compounds as nitrates is necessary for building amino acids and proteins essential to all life. Nitrogen as a two molecule gas comprises 78% of our atmosphere.  In elemental form, however, nitrogen can’t be used by living organisms. Its molecules  have very strong bonds that have  to be broken apart and bonded to other elements, such as oxygen, sodium, and potassium, in order to become usable by life. Some microbes can break those bonds. Other microbes are efficient collectors and re-cyclers of nitrogen released into soils by death and decomposition. For example, when amoebae eat and digest bacteria, plant-ready nitrogen is released into the soil.

Since nitrogen is so central to existence, most obviously in the growth of plants, scientists have explored several paths that plants use to uptake nitrogen. Most of it becomes available through symbiosis.

Rhizobia Bacteria Nitrogen fixers

We have known for centuries that legume plants enrich the soil. Until recently, we didn’t know exactly how that happened. Certain groups of soil bacteria are able to convert nitrogen into nitrates. The symbiotic bacteria group called Rhizobia form nodules on the roots of legumes (clovers, peas, alfalfa, soy, etc.). Plant roots chemically “invite” the bacteria to come on in. The nodules formed are filled with ammonium, which supplies the plant with nitrogen, and fertilizes the soil when the plant dies. Inside the nodules, the rhizobia receive food (carbohydrates & proteins), oxygen, and protection from predators such as amoebas.



Actinomycetes Bacteria Nitrogen fixers

Many kinds of plants form symbiosis with a different group of bacteria that live in their roots, the Actinomycetes, which can also convert nitrogen from the air into a form that plants can use. The most common is a bacteria group called Frankia. Many of these symbiotic plants are shrubs and trees that supply nitrogen to desert soils and old-growth forests, where nitrogen is scarce.Like Rhyzobia, Actinomycetes form nodules on roots.

desert paloverde tree has photosynthetic bark
and symbiotic Frankia nodules on its roots
Bitterbrush gets its nitrogen from symbiotic Frankia nodules on its roots.
Image credit Clinton and Shock
red alder pioneers nitrogen-poor soils aided by symbiotic Frankia bacteria
Frankia nodules on red alder roots

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Cyanobacteria Nitrogen Fixers Gallery

Cyanobacteria combine two critical abilities: to photosynthesize and to make nitrogen available to plants. Many lichens consist of a fungus plus a cyanobacterium instead of an algal partner. Such lichens are the primary source of nitrogen in old growth forests on the Pacific Coast of  North America.

Lobaria lichen fixes nitrogen on an alder branch
with Nostoc cyanobacteria
green dog lichen on the forest floor
fixes nitrogen with Nostoc cyanobacteria
Collema jelly lichens fix nitrogen with the cyanobacteria Nostoc
Peltigera lichens fix nitrogen in northern forests around the earth.
Biological soil crusts with cyanobacteria (in lichens and living solo) provide nitrogen to the desert

Biological soil crusts are the living surfaces of deserts worldwide. They are composed partly of cyanobacteria and supply much desert nitrogen. Nitrogen is released to soil by rains and flooding.LINK TO PAGE

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Explore Further in Plant Pages

Plants: What's New? Including Symbiosis with Fungi and Bacteria
Plant Diversity: Major Kinds (Images)
Plant Defense including Symbiosis with Wasps
Plant Pollination including Symbiosis with
Insects, Mammals and Birds
Seed Dispersal Including 'Compelled Symbiosis' with Birds, Insects and Mammals

Explore Further in the Biosphere

Biosphere: Introduction
Biosphere as Place: Introduction
Biosphere as Ocean: Life Zones
Biosphere as Ocean Floor: Benthic Biomes One
Biosphere as Ocean Floor: Benthic Biomes Two
Biosphere on Land: Terrestrial Biomes
Biosphere on Land: Anthropogenic Biomes
Biosphere as Process: Introduction
Biosphere Process: Floating Continents, Tectonic Plates
Biosphere Process: Photosynthesis
Biosphere Process: Life Helps Make Earth's Crust
Biosphere Process:
Rock Cycle--Marriage of Water and Rock
Biosphere Process: Marriage of Wind and Water
Biosphere Process: Gas Exchange
Biosphere as An Expression of Spirit
The Ecological Function of Art
The Earth Goddess
The Tree of Life
The Green Man
Earth Art
Biosphere as Community
Biosphere Microcosm: Bacteria and Archaea
The Procaryote Domain
Biosphere Microcosm: Germs
Biosphere Community: The Eucaryote Domain
Biosphere Community: Protists 1: Algae
  Biosphere Community: Protists 2: Protozoa
Biosphere Community: Plants: What's New?
Biosphere Community: Plant Diversity--Major Groups
Biosphere Community: Plant Defense
Biosphere Community: Plant Pollination
Biosphere Community: Plant Seed Dispersal
Biosphere Community: Kingdom Animals
Biosphere Community: Kingdom Fungi
Biosphere Community: Six Great Extinctions
Return to Ecology Index