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Plant Biology Basics – Guest Post by Daniel Fuller

basil leaf underside showing powres stomata macro photography

Most gardeners get by knowing how much water and fertiliser to put on their tomatoes, and when. But someone that has basic plant biology knowledge just understands plants in a way that’s hard to describe to people that don’t have basic plant biology knowledge.

It’s kind of like how some people really know cars. They have a totally different understanding of how a car works than most of us do; we simply keep ours serviced and fuelled and they generally take us to where we want to go. But a mechanically-knowledgeable person can tell you every part within that machine, and a really good one can hear what’s going wrong just by listening to the sound of the engine.

In this article, we’re going to take a look “under the hood” of plants and go over a few of the plant biology basics. We’re not going for our PhD here, we’re just learning a few things that are relevant to our work in the garden.

Listen to Professor Ros Gleadow, President of the Global Plant Council and Professor of Plant Science at Monash University, speaking about plant biology basics

What is a Plant?

It’s a great question, and one that we could discuss for a very long time. An obvious way that we can define a plant is that it’s a member of the plant kingdom, Plantae. That’s a pretty good definition, but it doesn’t really tell us very much about what a plant is, does it?

Another definition is a terrestrial organism that is connected to the earth and photosynthesises, but what about parasitic plants that get all of their energy from their hosts and don’t even have leaves to photosynthesise? Or what about aquatic plants – don’t they count?

Let’s go with this definition for all intents and purposes: a plant is a living organism that has roots, stems, leaves and reproductive parts. We can call bryophytes (mosses, liverworts, etc.) primitive plants because although they lack true roots and leaves, they are related to the sorts of organisms that gave rise to ferns, conifers and flowering plants.

Algae are the type of organism that bryophytes evolved from, and depending on the type of algae and the person you’re speaking to, algae may or may not be a plant. Let’s just forget about algal organisms for this article, and instead speak about land plants with a focus on monocots and dicots.


This is the bottom of the plant. Most of the time, anyway.

Primarily roots anchor a plant to the ground and uptake water, nutrients and oxygen. They also form relationships with a variety of organisms, for example rhyzobacterial connections that fix nitrogen in legumes, mycorrhyzal fungi that assist with a variety of functions and form the “wood wide web”.

In general, roots like to be in the soil, where they can access nutrients and moisture, but also oxygen which is part of the reason why it’s good to let the soil dry between watering your plants. Another reason is that overly moist environments provide an ideal environment for fungal pathogens.


It’s very interesting how the original plant stem prototype evolved differently to form the plant shapes and habits we see today. Tree trunks, branches, vines, rhizomes, stolons, and many tubers are all examples of true stems.

Their main purposes are to support the plant, and to move and store water, nutrients and energy.

Generally stems like to be in the air. You will find plants that don’t mind getting their stems submerged, but in general you want to avoid covering stems with water, soil, mulch, grass clippings, leaves, plastic, or any other medium that will prevent air from moving around the stem.

Many trees and shrubs will show a “root flare” at their base when they’ve been correctly planted. You don’t usually want to plant trees deeply so that they emerge from the earth like a telephone pole, nor do you want to volcano mulch a “cone of death” around the base of them.

Fun fact: the singular “leaves” on an acacia tree are not true leaves but in fact modified stems that are flattened and contain all of the necessary ingredients to photosynthesise. Only the “compound leaves” with tiny leaflets are the true leaves of the Acacia genus – other acacia leaves that seemingly have parallel leaf veins are, in fact, modified stems called “phyllodes”.


Leaves emerge from stems, contain the ingredients needed to photosynthesise, and have tiny holes called “stomata” (singular “stoma”), as well as guard cells that open and close the stomata as the conditions change around the plant.

So why do leaves need tiny holes that let that precious water escape? Because those pores in the leaves are what make it possible to transform water and carbon dioxide into sugars that can be used immediately or stored in the stems and roots.

If the stomata are too open, they lose too much moisture which can be deadly to a plant, especially in a dry heatwave. If they are too closed, the plant may not be able to photosynthesise as much as it needs to survive and grow. This is why the guard cells regulate the leaf holes in order to keep the plant producing carbon without dehydrating.

The colour of healthy leaves can tell us the sort of light frequencies that they are able to absorb. Green leaves contain high amounts of chlorophyll and are adept at sourcing energy from all light frequencies except for green, which they reflect into our eyes. Leaves that naturally have red, yellow or orange leaves, such as some cultivars of Japanese maple, usually contain higher levels of carotenoids and are better at absorbing green light but unable to absorb large amounts of red and yellow light frequencies which are reflected back to our eyes.

When leaves drop en masse, go limp, start to die (known as “necrosis”) or start to turn yellow (known as “chlorosis”) they can tell us about potential health problems that are developing.

Reproductive Parts

A plant can sexually reproduce in a number of different ways depending on which of the four types it is, which we will discuss in a second. The most primitive plants reproduce using spores, and more advanced plants use seeds.

Flowering plants are the most advanced plants, and they use flowers in their seed production. Often flowers will recruit specific or general pollinators to assist with combining male or female genetic material from one or two plants.

Some plants have flowers that have both male and female parts within the same flower, and these plants are said to have “bisexual” flowers. Plants that have separate male and females flowers on the same plant are said to be “monoecious“. And plants that have separate plants for each sex are said to be “dioecious“.

The Four Types of Plants

We can say that plants can be classified into 4 groups, depending on have their evolutionary lineage.

Bryophytes such as mosses and liverworts are the most primitive members of the plant kingdom in that they most resemble the types of plants that first evolved out of algae. They don’t have a vascular system, which we’ll define shortly, nor do they have true leaves, stems or roots which are all adaptations that evolved later on. They reproduce using spores.

Pteridophytes are ferns and fern-like plants; these guys evolved out of bryophytes and are more sophisticated due to their vascular system which gave them the ability to produce leaves, stems and roots. Like bryophytes, pteridophytes reproduce using spores.

Gymnosperms evolved out of pteridophytes and developed reproductive cones that use the wind to produce true seeds, which are uncovered by any kind of fruit or pod, but are exposed once the female cones open up.

Angiosperms are the flowering plants; anything that has a flower belongs to this most highly evolved group of plants, whether it’s an herbaceous weed, a vegetable or a giant tree. The seeds of flowering plants are covered by some kind of “true fruit”, whether that’s a juicy plum, a eucalyptus seed pod, or a rose hip.

Monocots and Dicots

Flowering plants have traditionally been broken down into monocots and dicots. This distinction works in the garden, but angiosperms have actually been reclassified and now there are monocots, eudicots and primitive (or basal) angiosperms.

Basically, what happened is that as flowering plants diversified out from that original flowering plant, certain plants broke off very early, in a similar way to how mosses and ferns broke off the evolutionary tree earlier than conifers and flowering plants.

Water lilies and magnolias are both example of basal angiosperms that are neither true monocots or eudicots.

With that being said, it’s fine to keep classifying flowering plants into monocots and dicots because they are still useful distinctions to make in the garden. It’s just a good power move when someone’s talking about dicots to correct them, especially if it’s your boss.

Monocot versus dicot seed structure

Monocots and dicots can be differentiated in a number of different ways which you can learn about through this article on the Plants Grow Here blog ( but perhaps the most interesting way they differ is in their vascular systems.

Angiosperm Vascular Systems

Animals aren’t they only organisms to have a vascular system – except for bryophytes, plants have veins too.

The vascular system of a dicot has a ring that separates sugar veins (phloem) on the outside and water veins (xylem) on the inside.

Botanists will tell you that there is a difference between conifer and dicot vascular systems but this isn’t really relevant for most gardeners except to say that conifers are said to have “soft wood” compared with the “hard wood” that flowering trees have.

Monocots, on the hand, have evolved a different tactic. Their vascular tissue is arranged in many bundles of xylem and phloem that act like a series of straws to move water and nutrients up, as well as to move sugar up and down. Each bundle does contain xylem and phloem vascular tissue, which is why you can ring bark a palm tree with a brushcutter and it will still be okay, whereas if you ring bark a dicot tree you may remove enough phloem tissue that the tree can’t move sugars and dies.

Monocot versus dicot stem vascular bundles
Monocot versus dicot root vascular system

Dicot plants do start out with vascular bundles in their “primary growth”, but their vascular bundles grow to form solid rings, whereas monocot vascular bundles are haphazard and do not form rings.

Secondary Growth

A dicot’s first year’s growth is called its primary growth, because it hasn’t had a full year’s cycle to reach the second phase of growth which is called secondary growth, or lateral growth.

Dicot primary growth versus secondary growth

Between the xylem and phloem in dicots (and gymnosperms) there is a ring (or rather, a pipeline) of stem cells, or meristematic tissue, called the vascular cambium. These stem cells produce new phloem cells to the outside, and new xylem cells to the inside. Xylem cells die as they mature but are still able to transport water one way up the trunk or branch toward the leaves through capillary action, which is the force that makes water travel up a tea towel if you leave a corner in a glass of water.

During the growing season, more lateral growth is produced than the off season, and this pattern is reflected in a tree’s rings. Dendochronology is the science of studying a tree’s rings to determine its age as well as the climatic and other conditions that have been recorded in the tree’s tissue throughout its lifetime.

As well as the vascular cambium, there can be a cork cambium which produces bark in some dicots. With that being said, “bark” is a non-technical term and can be made of different parts of the plant – sometimes it’s actually the phloem and by stripping the bark back we may prevent the plant from transporting sugars which can kill it, as in the case of ring barking a tree with a brushcutter.

Other Types of Meristematic Tissue

As a plant grows, it lays down cells that make up its body which can be broken into two categories. The first type are undifferentiated cells, which are stem cells, which as we’ve learnt can also be called meristematic cells. They are termed “undifferentiated” because they are able to produce different types of cells that may be needed, such as vascular and ground tissue in stems, roots, bark, leaves, flowers, and so on.

Differentiated cells, on the other hand, have already become what they’re going to be. For example, once a cell is a part of a juicy fruit, it can’t product a new branch off of the fruit skin (unless the seeds within, containing meristems sprout). Differentiated cells remain differentiated until they die.

Plant meristem structure

Meristematic tissue is present within the cambiums in dicots, as well as the apical tips of branches and roots and within the nodes and around the leaf axils of established plants. When trees get taller, they are growing from their apical tips – if you hammer a nail into the base of a tree, it will stay at the same height because the base of a tree only grows thicker, not taller.

A Plant is Like a River

Think of the way a plant grows: each limb is a river that moves water up, and moves sugars up and down. The tip of the branch is where new leaves are created, not from old parts of the stem.

When new growth appears from buds hidden under the bark (called epicormic growth), you’ll notice that they are part of new branches which can be called “water sprouts” or “suckers” rather than growing new leaves off an old stem. Epicormic growth is generally a sign of stress for the plant, such as hedge pruning or bushfire stress.

Pruning methods – non-selective heading, selective heading and thinning

If we prune a branch back to the fork, the energy in the “river” diverts to the other branch. However, if we cut a branch halfway along it, the energy has nowhere to go but to bust out the sides with epicormic growth as if we had put a dam in the middle of a river and forced the water to flood and create new courses to run.

The result for non-selective pruning is fuzzy water sprouts which is fine if you want to create bushy growth, but stick to selectively pruning to the forks if you want to keep natural shape.

The river can also be blocked by girdling (which means strangulation) by leaving ties around trees or allowing roots to become bound within a pot, disease, and basically any other way that the vascular system becomes blocked or cut off.


You can see how these basic biological principles give us an insight into the needs of our plants, and we’re able to see behind the matrix

In the same way a mechanic understands your car better than you do, now you’ll be able to walk into any garden and see beyond the outer form of plants and be able to imagine their inner workings. You’ll understand how plants use each of their parts, and some of the science behind the gardening clichés we’ve all heard, such as “don’t ring bark a tree” or “don’t paint the leaves”.

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