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C.E.J. Botha 

 DF Cutler and DW Stevenson


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Organization & Classification of Plant Parts

The principle of tissue system organization


Exercise 1 The use of the microscope

Exercise  2
The stem - variation in structure

Exercise  3

Variations in root structure



Exercise  4
General leaf anatomy



Exercise  5
The origin and development of the secondary plant body, and the periderm



Exercise 6

Anomalous growth in plants


Exercise 7

The vascular system


Exercise 8

Structural adaptations

Online Glossary

Cell arrangement and the influence this has on morphology




Classification: Click here to get some practical help with the  classification of  stem, root and leaf.



The Appendices: Contain information and details of useful techniques and they provide help with sectioning, stain preparation, and staining technique.












What kind of section do you have?







The Seven Sessions











Core Objectives






Core Practical Outcomes



Tactical Outcome



Text Books



Click here for a detailed look at the appendices






Plant Form and Function:


The Virtual Plant  has been developed primarily as a a hands-on aid to student revision and is based on the introductory Plant Anatomy courses offered at several Universities, including  Rhodes University. The primary objectives are to introduce the reader to the internal structure of higher plants in their vegetative state. The Virtual Plant therefore includes information on plant structure-function interrelationships where this is appropriate. This material was produced as an adjunct to Plant Anatomy - an applied approach, in which we introduce the student to the principles of Plant anatomy, and examine some of its applications in more detail. Users are however advised to refer also to other texts, such as  Esau's Plant Anatomy and Anatomy of Seed Plants for additional reference material. The Virtual Plant is designed to give more comprehensive coverage of the discipline than is commonly allowed for in modern syllabi - which, sadly almost all neglect the importance of plant structure and associated issues.

The overall theme of The Virtual Plant is to introduce and to explore the anatomy of  stem, root and leaf - from a fundamental structure, function and adaptive perspective. We also introduce users to simple microscopic technique - we introduce the basic use of the microscope and explore some useful preparation techniques, which may be found by following the appropriate links to the appendices. The exercises present examples of some normal and some of the abnormal (anomalous) anatomical structures that exist amongst Angiosperms and Gymnosperms.

The philosophy behind The Virtual Plant was relatively simple -- not everyone works quickly enough to be able to finish a practical session within the allotted time; not all students are lucky enough to have after-hours access to a microscope; nor do all students absorb information at the same pace.  The Virtual Plant was designed to allow for self-paced, independent study, as these would  encourage key questions such as:-  "Why is the internal structure of plants so different?" or  "why is plant structure so regular and predictable in some, but not all plants?"

A further factor that encouraged the production of the The Virtual Plant was that plant anatomy is unfortunately, becoming less studied at school, college and university level. Perhaps because the discipline is perceived as being a less glamorous laboratory-based option, compared to many other fields in Plant Biology. Arguably, lack of anatomical knowledge is proving disastrous. Fewer scientists really understand what they are dealing with when examining plant structure. Molecular biology for example, requires understanding of the localization of gene complexes in plants. In some cases, the researchers do not know (or understand, or worse, comprehend)  the difference between the cortex and stele in stems in even the most commonly-used plants, let alone understand the ontogenetic differences between a bundle sheath and a mestome sheath!

 Those of us who have a genuine interest in plant anatomy, believe that students need to be given a thorough grounding in basic plant structure. At the very least you will then be able to recognize the difference between stems, roots and leaves and should be able to recognise the cell and tissue types within which your interest lies.

We hope that the information presented here will be useful and will help you learn about the intermixture of structures that make up some otherwise fairly common land plants.  If you make good use of The Virtual Plant and the information it contains, we believe that you will gain a great deal of insight into plant structure and the interactive functionality of the whole plant. Additionally you may gain a greater appreciation for  this subject, and just why it is so important to understand plant structure.   

The techniques section contains useful, quite straight-forward procedures, which should benefit teacher and student alike. This section explores basic methods used in the preparation, preservation, sectioning, and staining of plant material. By making use of these techniques, you will  enhance or improve the image detail in your own material and, we hope, this excites greater interest in this fundamental botanical discipline. 

Structural Organization




The study of plant structure requires a good understanding of basic plant anatomy. It also requires the ability to recognize various structures such as stems, leaves and roots and to understand their cellular makeup.

Anatomy is without doubt, a core discipline in Botany.

Through the study of the internal structure of plants, you will be able to explore and learn more about the interrelationships between cells, and the tissues that these make up. Tissues in turn, make up the organs of the plant -- root, stem leaf, flower and fruit. You will see that  the same cell types and tissues occur in simple and complex tissues that make up plants. Plant anatomy therefore, must  involve studies at the light and electron microscope level. We should not forget that many of the diverse structures which make up the plant body, have a particular visible shape (morphology) and that the morphology is, in part, dictated by the internal arrangement of cells into tissues and thus into organs.
p The  principle of tissue systems

One of the most useful schemes developed for understanding general topographical anatomy, was devised by the German Botanist, Julius von Sachs (1875). His classification system has a great deal of merit - firstly, because it was relatively simple, and second, due to its wide applicability to the juvenile and young  leaf, stem and root.

According to von Sachs' scheme, there are three principle tissue systems: (1) The epidermis and cork layers which comprise the dermal system, (2) the conducting strands of xylem and phloem, which make up the vascular system, and (3) the remaining non protective and non-conductive tissues, which make up the fundamental or ground system.



The way in which cells are grouped will influence the plant's morphology


For example:-

  • Angular stems may form discretely-localized mechanical (supporting) tissue - usually collenchyma and or sclerenchyma associated with the ridges in these stems.
  • Even though it floats on water, the water lily leaf requires some means of mechanical support. When we examine the internal structure of these leaves, we will find beautifully-adorned astro- and osteosclerieds
  • Canna leaves have large airspaces within their petioles and within the lamina of the leaf. These airspaces are formed by many-faceted, highly branched cells, termed aerenchyma.
  • Cut a pumpkin petiole, and immediately, lots of sticky 'goo' emerges from the cut surface. This sap is rich in a wide variety of soluble carbohydrate and soluble proteins including enzymes, as well as other substances that are transported within a highly nutritious watery matrix. Many of these molecules are involved in the transport processes in some way. The majority of this sap is transported within highly specialized conduits called sieve tubes, within the phloem tissue.

What is it? Stem? Root? Leaf? Helps you decide if a section was made from a stem, a root or a leaf. Click HERE to see some good arguments based upon microscopic examination that will help you make a decision for yourself!

Exploring the Virtual Plant


The Virtual Plant is organized into seven practical tasks. The first deals with the use of the microscope and the subsequent exercises explore issues relating to the basic concepts of the primary structure of the stem, root and leaf. The next two sessions deal with anomalous structures and the final session, is a brief overview of the evolutionary changes in vascularization. They may be approached in any order.  This version of The Virtual Plant does not cover all aspects of plant structure and  function -- hopefully, though you will become stimulated to look further, deeper and hence, understand more. The  sessions are described briefly below.

The Laboratory Sessions


The Microscope This introductory session is devoted to some of the basic principals needed (generally poorly explained and and often forgotten!) to enable you to make good use of a student microscope. We make use of simple examples and introduce the concept of magnification, field of view and  scale.

The Stem This session explores monocotyledon, dicotyledon and gymnosperm stems - you can look at at the differences and similarities between them and have an opportunity to examine examples of herbaceous and potentially woody stems as well.

The Root Here, the emphasis is on similarities and differences -- the monocot, the dicot and gymnosperm rooting systems. How do they differ? Are there features that they have in common, or is it simply cut and dried that they are all categorized and distinct from one another?

The Leaf This session serves as an introduction to mesomorphic and non-mesomorphic leaf structure. There is a fairly detailed examination of the differences and similarities between some "typical" monocot, dicot and gymnosperm leaves. You will be exposed to structural changes related to, and induced by,  the type of photosynthesis (C3 C4 and CAM), as well as by habitat and environment for example.

Secondary Growth in Plants  The emphasis in this session will be on structural changes that occur during secondary growth in roots and stems, including the changes that occur in the transition from an entirely primary plant body, to one in which new vascular tissues and new protective layers are formed. 

Anomalous Growth in Plants In this session we introduce the concept of anomalous growth using some examples of  roots and stems. The examples chosen are but few but hopefully they will stimulate a basic understanding of the concepts involved in anomalous growth.

The vascular system Vascularization was an essential step in the land migration, as well as the development of more efficient (but not necessarily larger) plants. This exercise examines some aspects of the evolution and development of the vascular systems in plants. We will look at some examples of hydrophytes, as well as some 'typical' land plants, which show variable structural features.

 Core objectives:


  • Gaining insight and ability by combining theoretical knowledge gained in lectures, with practical illustration through  observation of the images provided in the virtual plant, or from similar images observed using a compound microscope.
  •  Improving comprehension  by exploring the commonality of cells, cell distribution, tissues, organs - what do they have in common? Where & how do they differ? 
  • Improving perception of the variation seen in simple compared with complex interrelationships between the cells that make up tissues, and the tissues that make up organs of the plant.
  • Understanding more about plant structure and function relationships, through looking at architecture and the mechanics of plant construction.
  • Developing capacity to interpret the interrelationships between cells tissues and organs.
  • Learning about simple preparative techniques required for practical microscopic observation

Core practical outcomes:


  • Recognize the difference between the structure of stems, roots and leaves
  • Gain a clearer understanding & improve interpretive skills in correlating what you see under the microscope with what you  illustrate on paper. Understand the concept of cellular and tissue variation.
  • Apply simple preparative techniques, required in specimen preparation and to be able to evaluate structure and implied function from these preparations. 

Tactical Outcome:


  • To develop understanding and ability to work with botanical specimens, using a simple compound microscope.

Text Books:


In addition to the accompanying Plant Anatomy - an applied approach, we strongly encourage reference to texts such as Esau's The Anatomy of Seed Plants  and Plant Anatomy as these are sources of very valuable additional information.

The appendices:


The appendices have been compiled to help and assist you to make the most of general procedures which are needed to allow preparation and observation. How to cut sections, to stain them to draw what you see - this and more information is provided here.

Please remember: Many of the chemicals that are mentioned in the assignments and write-ups, which are used to fix, prepare and/or stain sections may well be hazardous to your health. Please exercise great care when using them.

Legal Notice:

The concepts and ideas expressed within the Virtual Plant and its associated electronic media are, unless otherwise stated, those of the authors. Whilst you are welcome to make use of the material, copying of images,  parts of images, or text, other than for normal use by an instructor, is expressly forbidden without the publisher's consent.

This material may not be copied to,  or inserted into any other text or hypertext document under any circumstances without express written approval of the authors and permission to make use of the material must be sought from the publisher. Many of the images are digitally signed and can be traced.