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Plant Biology: Roots and shoots. Peter Shaw. This is the jpg-free version, for rapid downloading. For pretty pics – come to the lecture! (Or ask me for the source file, if you have a pressing excuse…). Introduction.

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plant biology roots and shoots
Plant Biology: Roots and shoots

Peter Shaw

This is the jpg-free version, for rapid downloading.

For pretty pics – come to the lecture! (Or ask me for the source file, if you have a pressing excuse…)


Today we are going to look at the morphology and functions of the structural elements within plant bodies: shoots to support leaves, and roots for anchorage and uptake. Notice that (unlike photosynthesis or cell anatomy) these details are specific to the vascular plants, and do not apply to bryophytes etc. No tracheids, no mention in this lecture!!


These are supportive tissues, evolved to raise leaves and/or flowers above ground level.

(let’s expand on that and/or. Can you think of any plants with a stalk for the flowers but not the leaves?

This is quite common, ie dandelions, asphodels…

A stalk to support the leaves but ground-level flowers?

Much harder – Aspidestra has slug-pollinated ground level flowers (but no true stem). Some tropical forest climbers (passion flowers) have flowers at ground level.

Aspidistra (cast iron plant) flowers, which lie on the ground and are slug pollinated.

basic stem anatomical terms

Terminal bud with apical meristem

Basic stem anatomical terms

Axillary bud

An internode

A node




Stems bear buds, an embryonic shoot. Typically in a leaf axil, these contain meristematic tissue, and any bud is able to take over if the buds above it are mechanically removed. The only reason lateral buds do not shoot out is hormonal suppression from other more active buds. (More in a later lecture). Buds are the protected way that leaves overwinter, most obviously but not only in deciduous species.

Sometimes these buds are not obvious: in the cactacea the leaves and flowers come out of common buds, but these are known as areoles. A cut cactus will resprout from an areole. (There is one genus, Mammillaria, where the flowers emerge between the areoles, although internally they still derive from bud tissue).


We all know potatoes, Solanum tuberosum. Most of us know their Vavilov centre (=genetic home, where highest diversity is found: The Andes of course.) We know that the green shoots are toxic due to an heat-resistant alkaloid called solanine. (This is serious – never eat potato leaves or sprouts, and best avoid green tissue where a spud has sat in the light).

But how would you classify the tuber, the bit that you eat? The obvious answer is a root, but roots don’t make lateral buds, which is what potato eyes are, and in fact potato tubers are modifies stems!

bulbs rhizomes etc
Bulbs, rhizomes etc

Many plants find the soil a convenient safe place to store energy in swollen tissues. We are all familiar with bulbs – in fact these are accumulations of swollen leaf bases, safely out of harms way many cm below the soil surface. These can be remarkably water-retentive, many bulbs surviving a year without water. Think of onions (But never ever confuse ornamental bulbs with onions!)

Rhizomes are different. They make buds that emerge as new shoots, so must be stems. In plants like ginger or bracken the rhizome acts like a storage root. In many grasses and strawberries they become runners, creeping over the soil and putting down new roots at intervals.

monocot dicot stem cross sections
Monocot/dicot stem cross-sections

In dicot stems the vascular bundles lie in a ring

In monocot stems the vascular bundles are scattered throughout the stem.


These organs are traditionally said to have two functions:

1: structural anchorage, providing the mechanical support that enables the plant to put up its shoots,

2: To act as a nutrient uptake surface, collecting water and minerals from the soil solution.

As a mycologist I must add a third function:

3: To support infections by mycorrhizal fungi.

(It is true that most plants will grow perfectly well without these fungi. It is also true that very few wild plants actually do live without these beneficial infections).

types of root system

Fibrous roots – numerous thin roots, about the same diameter.

Typical of grasses, also rhododendrons.

Types of root system

Tuberous roots –few, short stubby roots. Useless for nutrient uptake! (These plants rely heavily on their mycorrhizal fungi, shown here as ). Bulbs, orchids, non-photosynthetic parasitic plants.

Tap roots – deep fat roots capable of nutrient/water storage. Lateral roots emerge from it. In biennials is often edible, accessing the energy stored as starch.

Tap root



Root hairs: these greatly increase SA for uptake. 1 rye plant has a root SA of 600m2!

Vascular tissue

Root apical meristem

Root cap. Here cells are continuously sloughed off by soil abrasion. This protects the apical meristem and (along with mucilage) lubricates the roots passage through the soil. (This is also the area which senses gravity)



Zone of cell differentiation


Zone of cell elongation

Stele (holds vascular tissue)


Zone of cell division

general root ts
General root TS

Stele, containing phloem and xylem embedded in pericycle cells.

Endodermis. These cells contain suberin to resist water flow, forcing it to pass symplastically.




The layout of the vascular tissues within the stele differs between monocots and dicots. In dicots the xylem forms a star shape (# points variable but 4-6 is typical) with phloem filling out the intervening spaces. In monocots the central spce is occupied by pith, with the vascular tissue in a ring.





Eudicot root Monocot root


The apical meristems in roots give rise to lateral meristems – side roots. These form part of the secondary body of the plant, along with the two lateral meristems which allow tree trunks to expand (the vascular cambium and the cork cambium). Roots give rise to more roots, but not generally to shoots.


Roots can pop out of odd places, such as high up on stems. These are called adventitious roots, and are what allow gardeners to strike cuttings.

On a larger scale, adventitious roots can act as stilts, supporting tree trunks. The sacred banyan tree (actually a strangler fig) Ficus benghalensis uses its adventitious roots to support the branches, and eventually can form a covered, stilted mini-forest! The Indian prince Gautama Siddhartha is said to have attained enlightenment under such a Banyan tree in Bodhgaya, India. (It’s still there, albeit as a rooted cutting).

Screwpines (Pandanus), which lean on their adventitious roots.

noteworthy roots
Noteworthy roots

A few bulbous plants go to remarkable lengths to protect their bulbs. Bluebells (Hyacintoides non-scripta) have contractile roots which pull their bulbs deeper into the soil after germination. Mature bulbs are often >20 deep despite have germinated at the surface!

Epiphytic plants (the moth orchid Phaloenopsis is a good example) have roots that adhere strongly to their substrate, allowing them to grow high up on tree trunks or stone surfaces. The degenerate bromeliad Tillandsia usneoides (‘Spanish moss’) makes a nuisance of itself by hanging off telegraph wires!!

mycorrhizal roots
Mycorrhizal roots

Many plants have roots which are so short fat and stubby as t appear useless for nutrient uptake. That’s because they are useless!

The work is done by paid helpers – mycorrhizal fungi. This trait has evolved many times (>=5), and often results in roots utterly smothered in hyphae.

Here we see the short, fat, dichotomously branched tips of a tree’s ectomycorrhizas.



Root hairs also get infected by mycorrhizal fungi, which act as extensions of the root system and collect nutrients (especially P) for the plant. This is the normal state for most wild plants. In exchange the plant supplies sugars to the fungus. (This sugar drain can be a detectable cost, if nutrients are supplied as chemical fertilisers).

The mycorrhizal condition has evolved at least 4 times, probably closer to 10, and can be over-simplified by shoehorning mycorrhizas into 2 groups: Sheathing (ecto) mycorrhizas, which envelop roots in a coat of hyphae, and endomycorrhizas which penetrate inside the cells inside a hosts’ root.

In both cases the increase in uptake area is huge – as much as 3m of hyphae from 1cm root. There are many trials showing how much better plants do with mycorrhizal infection in poor soils.


TS of an ectomycorrhizally infected root

Varieties of:

What you actually see


Hartig Net

(between root cells)



Or endomycorrhizas

vesicles - these are large and stain well.

Arbuscules are harder - really needing EM. It is not clear that all endos have these, casting doubt on the name VAM. Arbuscules die and are absorbed by the plant, only to have new arbuscules re-form. This seems to be how P is transferred to the plant.


Parasitic plants

Not all vascular plants have functional (green) chloroplasts. There is a polyphyletic group of plants called obligate parasitic plants that cannot photosynthesise, and instead rely on other plants for their energy supply.

Many of these are orchids, such as the coralroot, Corallorhiza trifida here, but others include toothwort Laethrea, Rafflesia, Cynomorium coccineum.

The Maltese fungus, Cynomorium coccineum

Fungus rock, Gozo, Malta.


Some of these parasitic are simple root-plug-ins (called haustoria), physically inserting the parasite’s vascular tissue into that of its host.

The western australian christmas tree Nuytsia floribunda (a mistletoe relative – loranthaceae) is a root parasite whose haustoria cut into tree roots. They are so effective that they have been reported cutting underground wires! (Like all mistletoes it lacks root hairs).

Many other plants (especially in the family Scrophulariaceae) are hemiparasitic, sucking water and sugars out of neighbouring plants while continuing to photosynthesise themselves.

Nuytsia floribunda

witchweeds striga
Witchweeds, Striga
  • Striga – the witchweeds (c. 40 species) - parasitic plants that plugs its root system into the roots of many crops
  • Is endemic in Africa, where it significantly stunts the yield of commercial crops. Traditionally it was said to ‘bewitch’ the crops into poor yields, hence its name.
  • S. asiatica was accidentally introduced into fields in Carolina -noted as a pest in 1950s, affecting 175000 acres. It has been almost eradicated here by an expensive herbicide regime.

Mycorrhizal parasites

You will find quaint old (and not-so-old) texts saying that the coral root orchid, ghost orchid, birds nest orchid are ‘saprotrophs’, meaning that they feed on decaying organic matter. We know that this is just plain wrong. Decomposer fungi are saprotrophs. Orchids are mycorrhizal. It’s just that some of them give nothing back to the mycorrhiza. In fact they plug into the mycorrhizal network which links together forest trees and act as a sugar-sink. The orchid lives by parasitising trees via their ectomycorrhizas.

Corallorhiza, the coral-root orchid. The coralling roots are highly infected by mycorrhizal fungi.

orchid mycorrhizas
Orchid mycorrhizas
  • These are weird!
  • If a science fiction writer produced this story, it would be rejected as being too implausible. In fact it’s true.
  • Orchids are notable for several things, including production of vast amounts of tiny seeds.;
  • These seeds are almost invisible - too small to carry useful reserves of energy.

So how do orchid seeds manage?

  • They need to be infected by a decomposer fungus. Quite a variety will do - Rhizoctonia is one of the commoner, but some really nasty pathogens are used - Armillaria, Fomes, Coriolus.
  • These fungi should kill the seed. In most cases they probably do. In some cases, the seed ends up parasitising the fungus!
  • Hyphae enter the plant cell, but are attacked and digested by the orchid.
  • This is the plant’s sole source of nutrients and energy until a leaf is produced, 2-8 (15) years later.
  • Some orchids never make green leaves, are purely parasitic on their fungi.

This means that orchids can colonise over large distances, and appear as if by magic years after actually colonising.

I have introduced soil + seeds, fungus to sites in 1991 - some orchid leaves appeared in 1995, while some flowers appeared de novo 1996 - 1999. They had been there all the time, invisible under the soil.