Basic Plant Biology: Keeping the Coffee Plant “Happy”

Basic Plant Biology: Keeping the Coffee Plant “Happy”

By EMMA SAGE, Coffee Science Manager at the SCA.

What Plants Need

A healthy, “happy” coffee plant is one that is able to produce the greatest number of quality seeds. There are three main factors influencing the “happiness” of a plant: genetics, the environment, and applied agricultural management. Since there is no exact formula to produce award-winning specialty coffee, farmers work to meet all the basic needs of plants so they are able to thrive. There are common biological necessities universal to all plants that make this possible. These essentials are sun, water, soil, and air; the four combine to provide the plant with the energy and nutrients necessary to sustain life. Certainly, different plants have adapted to require different specific conditions, depending on their histories and environments. However, all plants share these external factors that allow growth and reproduction—the only metrics of success a plant has.

Plants live in ecosystems. It doesn’t matter if the ecosystem is a natural one or an agricultural one. Either way, plants interact with their external surroundings and are dependent on soil, weather, microorganisms, temperature, humidity, and myriad other influences. Although a farmer may choose plants based on what is known about their genetics, the only factor that can be actively controlled each year after planting is the plantation’s agricultural management.

The following information is an introduction to plant biology and agricultural management on the coffee farm. It does not attempt to outline the difficult and high-risk situations that most coffee producers today are faced with. It is meant to present some basic biological factors to help non-agronomists understand some of the scientific complexities that go into maintaining a healthy, productive, high-quality coffee plantation. Use it as an overview, learn, and look to your producer relationships to get the human side of the story.

The Essentials for Life

It is critical to remember that whenever we take a “natural” plant out of the forest and use it for agricultural purposes, such as with coffee, its needs are changed. Agriculture is not nature. Coffea arabica is perhaps one of the more stubborn and sensitive of agricultural commodities. Since it is endemic to a very specific region (the highlands of Ethiopia and South Sudan), where it was born under an unusual set of genetic circumstances, it has a low level of genetic diversity with which to combat challenges (Lashermes, Combes, Robert, Trouslot, D’Hont, Anthony, et al., 1999). Also, it has only recently (in evolutionary time) been distributed throughout the world, which means that it has not had time to evolve to new climates and conditions. A C. arabica coffee plant in Indonesia, or Brazil, or Jamaica still grows best under the ideal conditions that its ancestors learned to love in the shaded understory of tropical forests in East Africa. This is one reason why it is so difficult to make C. arabica plants happy, and why this continues to challenge farmers all over the equatorial world.

To function, plants “inhale” and “exhale” the building blocks of life. The “inhale” is called photosynthesis, and the “exhale” is called respiration; both depend on water, energy from the sun, and nutrients. Plants take in nutrients and water from the soil through their roots.

There is always one major factor limiting a plant’s growth and reproduction (Larcher, 2003). This may sound bad, but in fact it is for the best—because we don’t want giant plants taking over the world and demolishing skyscrapers in a King-Kong-esque dramatic growth spurt. Usually, carbon (C), water (H2O), or nitrogen (N) will be the primary limiting factor. In the agricultural world, this often becomes macronutrients such as nitrogen (N), potassium (K+) and phosphorus (P). This is why farmers often have to irrigate or apply fertilizer to crops. In this day and age, perennial and wild plants are not often limited by carbon, as there is plenty of extra carbon in the atmosphere. However, in the case of annual crops (such as corn, soy, and wheat), carbon can become limiting, and adding peat or carbon-based composts can help alleviate this deficit. If you put a shade plant in sun, it will require more nutrients in order to keep up with the level of growth and production that will occur. If you add nitrogen, the plant will demand more phosphorus, potassium, and calcium to function properly. If you add more nutrients, the plant will therefore need more water. You get the idea. In this way, a plant is always, physiologically speaking, attempting to balance its available resources and allocate them to specific tasks relevant to sustaining life. What do humans do to make C. arabica coffee plants biologically happy? Plenty!

Adequate Growing Conditions: Site Choice

Location is key for growing C. arabica. Site selection is one of the most important choices a farmer can make to ensure success. That being said, not all farmers have a choice of site; they may simply have a piece of land in proximity to a known coffee-growing area. Slope and aspect, topography, temperature, weather pattern, rainfall, seasonal change, and soil texture are not easy factors to alter (unless you construct a giant greenhouse around your coffee plants, which doesn’t seem feasible). The condition of the soil and history of the land can also influence the potential of a site. Practical and logistical considerations must be made in light of local harvesting techniques, irrigation, pruning, and other management practices.

Seasonal changes (or the lack thereof, in equatorial regions) delineate the annual fruiting cycle of the plant. In growing areas such as Ethiopia, Hawaii, Central America, and Southern Brazil, the seasons generally result in a single cycle of fruit growth. In these areas, flowers are initiated in periods of slow growth (winter), and flowering and new stem growth occur with rain or sometimes a cold snap (spring). The specific temperature range of a potential plantation is key, as C. arabica prefers a temperature from 15-24°C and is very sensitive to cold and frost, with the latter destroying both leaves and fruit.

Adequate Water: Transpiration, Irrigation, and/or Soil Management

Creating an adequate water situation is key to maintaining a happy plantation of C. arabica plants. Many coffee farmers rely on rainfall as their only water source. Less frequently, irrigation systems are set up to maintain highly productive full-sun growing conditions. In these cases, commonly found in Brazil and Vietnam, where growth and therefore water demand are very high, automated systems have helped allow the expansion of coffee production (Snoeck & Lambot, 2009). In other instances, irrigation can be managed to facilitate flowering (Willson, 1999). The water balance of a coffee plantation is ideally maintained through soil and site selection. If this is adequate to begin with, a farmer is much less likely to need irrigation or soil additions to assure proper drainage. Coffee, like all plants, needs a minimum amount of water to remain healthy (i.e., not wilted) and functioning. This is because nutrients and minerals are absorbed by plants via capillary action, from their roots all the way up to the highest shoots. However, too much water in the soil can be detrimental. Roots need oxygen to survive and function, and shallow roots make erosion a topic of concern in certain coffee growing regions that experience periods of severe rainfall (Clifford & Willson, 1985; Snoeck & Lambot, 2009).

Evaporation and transpiration are affected by many things in an ecosystem, including the water status of a soil; the relative humidity; and the amount of sun, wind, and tree cover. Cloud cover can also influence the amount of transpiration that occurs and therefore the amount of water that is lost. Evapotranspiration is the term used to describe the process of water loss from plants (Larcher, 2003). C. arabica plants are evergreen, and thus lose water throughout the year (Clifford & Willson, 1985). Soil texture can have an impact on the water balance of a plant. In fact, soil can either naturally hold water or drain water, depending on its pore space (Hillel, 2004; Snoeck & Lambot, 2009). In order to pull water from the soil, plants exert an evaporative demand created by a difference in pressure between the air, plant, and soil. Soil texture also impacts the ability of C. arabica plants to withstand dry seasons, as water held deep in the soil is  used over periods of low rainfall (Clifford & Willson, 1985).

Adequate Sun: Shade Management

Photosynthesis requires energy from the sun to convert CO2 from the air into sugars, which are plant food (Raven, Evert, & Eichhorn, 1999). However, the intensity of sunlight is important to C. arabica plants, and difficult to regulate naturally. Because C. arabica evolved as an understory plant, it can only utilize a limited amount of sun. In fact, too much sun can damage the photosynthetic tissues over time, eventually leading to decreased growth and production (Clifford & Willson, 1985). Young plants, like human infants, are particularly sensitive, which is why you often see coffee seedlings under cover. High temperatures associated with strong sunlight can also slow down photosynthesis by causing the plant’s pores (called stomata) to close up (Larcher, 2003).


Many farmers attempt to regulate sun via a shade tree regime. However, there are trade-offs, as additional plants mean more work! There is no universal guide for shade tree management, as this depends upon local conditions and the microclimate of the plantation (Muschler, 2009). When strategically planned, shade trees can be beneficial in other ways, such as providing a food source for humans (banana or avocado trees) or plants (trees which add more nitrogen into the soil) (Snoeck & Vaast, 2009). Trees can also be planted in such a way as to serve as wind breaks for the plantation. Shade can be utilized to conserve water, lower temperature in hot regions, and protect against frost (Muschler, 2009; Snoeck & Lambot, 2009). Frequent cloud cover, often occurring at high altitudes, can act similarly to reduce the amount of light reaching leaves, at times lowering temperatures to the point that reductions in photosynthesis occur. Like all agricultural management, shade and sun balance is a continual process of assessment and adjustment for coffee farmers.

Adequate Nutrients: Soil Management

Nutrients beyond what a plant gets from air and water (carbon, oxygen, and hydrogen) are obtained through the soil. Roots act as little vacuums of water and nutrients, so that plants stay well hydrated AND healthy at the same time (Raven, Evert, & Eichhorn, 1999). Soil and its nutrients can be regionally specific, varying with local geology and parent material. So, depending on where a plantation sits in the world, soil management differs. In fact, it can be a micro-region-specific, very precise science, and some agronomists recommend having soils as well as foliar tissues analyzed multiple times a year to assure accurate nutrient management.

Figure 1. The basic nutrient cycle of Coffea arabica (and many other plants).

Nitrogen is one of the most important macronutrients, as it is used for essential functions such as photosynthesis and new tissue production, as well as other key processes (Carelli, Fahl, & Ramalho, 2006; Clifford & Willson, 1985). Nitrogen deficiencies commonly occur in unshaded and high-producing C. arabica plantations, due to the demand put on the photosynthetic tissues. A healthy amount of nitrogen in a plant results in healthy, dark green leaves. A deficiency can present with paling or yellowing leaves (termed chlorosis). On the other hand, it is possible to over-fertilize with nitrogen, and this can have different consequences in coffee, such as a higher caffeine content (Snoeck & Lambot, 2009). There are various forms of nitrogen that can be applied to soil, but each farmer and agronomist has to make an educated decision as to which is best for a particular site and situation.

After nitrogen, potassium and phosphorus are the most critical macronutrients to the basic biological functions of plants (Larcher, 2003). Potassium is important to the physiological development of fruit, and phosphorus is necessary for root, wood, and bud development. You may recognize these if you have spent time on any sort of farm, as most commercially available fertilizers aim for a specific N:P:K balance. Potassium deficiency can result in brown spots developing, especially on older leaves (Snoeck & Lambot, 2009). Phosphorus deficiency can occur after the coffee tree produces a heavy crop or suffers a water deficiency, and can present with leaf chlorosis or a bluish-green tint of the leaves (Rothfos, 1980).

Micronutrients, such as zinc, magnesium, boron, iron, and copper, all play small yet important roles in maintaining proper plant function. Deficits of these elements can result in various physical symptoms in C. arabica. Foliar nutrient sprays can also be applied to coffee plants to deliver nutrients directly into leaves, but these are labor intensive. This practice is not common in all coffee-growing regions, but can be especially beneficial in situations of specific nutrient deficiencies.

The pH of the soil, which results from the underlying geology, should also be taken into consideration. It can be labor-intensive—or even impossible—to significantly alter the long-term pH of soil, and certain areas must be annually managed (Snoeck & Vaast, 2009). Many tropical or semi-tropical coffee-growing regions of the world have slightly acidic soil, which is favorable for growing coffee (Wellman, 1961). However, C. arabica has been known to grow in a range of soil acidity conditions, from acidic to neutral (a pH of ~4-7) (Rothfos, 1980). The pH can also influence the ability of the soil to “let go” of its nutrients and allow plants to take them up. This is technically called the “cation exchange” capacity of the soil, and it also depends on soil texture and organic matter content (Larcher, 2003; Snoeck & Lambot, 2009).

Protecting the topsoil (where most C. arabica roots live) and all the nutrients that it holds, including those that farmers pay to add, is a very important consideration when managing a coffee plantation. Physical erosion can be a threat to coffee trees, the larger ecosystem, and farm workers. The susceptibility of a site to erosion and runoff can influence the recovery (or actual use) of nutrients added in the form of expensive compost and fertilizer. Organic matter, soil composition (silt, sand, and clay), and level of compaction all contribute to this (Snoeck & Vaast, 2009). However, unchangeable physical-site factors, such as slope, aspect, and rainfall, and unpredictable events are often responsible for soil erosion. Farmers can use many methods to conserve soil and combat nutrient loss and erosion, but it’s a perennial challenge.

Adequate Stimulation: Spacing and Pruning

Assuring that a coffee plantation will be healthy and productive for as long as possible requires active management, beginning with planting density, or plant spacing. It is essential to give each tree enough space to meet its needs, while at the same time considering yield per hectare. Depending on the cultivar utilized, adult C. arabica plants usually require 1-3 meters between plants. For example, when plants are spaced 2.5 meters apart, that results in 1600 plants per hectare; whereas, if spaced at 4 meters apart, the yield would be 625 plants per hectare (Rothfos, 1980). In situations where coffee is being intercropped with other types of plants, these decisions are more complex and depend on what sort of energy and water demands neighboring plants will have in relation to the needs of C. arabica.

C. arabica becomes less productive as it ages; therefore, pruning has emerged as a common way to stretch the lifespan of a coffee tree. The other option, re-planting, takes longer and is riskier for farmers as it depends on successful establishment of a seedling, followed by about two years of essentially no production, and therefore no income from those plants. There are two main methods of pruning that are common around the globe, depending on local agronomy and crop maintenance practices. These are single- and multi-stemmed pruning (Rothfos, 1980; Snoeck & Lambot, 2009). Under either of these methods, stumping or less drastic methods of rejuvenation can be deployed depending on the needs of the cultivar and coffee farm. Different agronomists recommend different objective guidelines for pruning, based on factors including tree height, decreased productivity, and tree age (Snoeck & Lambot, 2009). It is often recommended that a farm strategically prune sections of the coffee plantation each year, as opposed to pruning all trees at once. This way any loss of revenue due to regrowth periods is minimized. In addition to the main pruning strategy, maintenance pruning also takes place each year, usually during periods of slow growth (Clifford & Willson, 1985; Willson, 1999). Generally, two-year-old secondary stems are found to be most productive, and this motivates coffee farmers to maximize the number of these within their plantations each year (Clifford & Willson, 1985).

Farmer Challenges

Of course, the best-laid plans of mice and men (and plants), often go astray. A farmer can pick a regionally-specific coffee cultivar, plant it in a strategic location with good sunlight and well-drained soil, and in all other ways set up a “perfect” coffee plantation—and still be faced with insurmountable challenges. Unexpected weather, climate change, pest or pathogen outbreaks, and other “acts of God” and nature can turn a happy coffee plantation into a barren, bleak wasteland. There are risks in agriculture that can only be fully understood by those famers who live it every crop cycle. For those of us who work in the roasting, retailing, or consuming end of the value chain, it’s important to remember the limitations of our perspective.

“Farming looks mighty easy when your plow is a pencil, and you’re a thousand miles from the corn field.”
– President Dwight D. Eisenhower



emEmma Sage is SCA’s coffee science manager. Before moving into the coffee industry, she completed degrees in ecology and botany, and dabbled in the wine industry. She enjoys learning all there is to know about the science of coffee (and more importantly, sharing it with you).


Literature Cited & Further Reading


Carelli, M. L. C., Fahl, J. I., & Ramalho, J. D. C. (2006). Aspects of nitrogen metabolism in coffee plants. Brazilian Journal of Plant Physiology, 18, 9-21.

Clifford, M. N., & Willson, K. C. (1985). Coffee: Botany, Biochemistry, and Production of Beans and Beverage. Westport, CT: AVI.

Hillel, D. (2004). Introduction to Environmental Soil Physics. USA: Elsevier Academic Press.

Larcher, W. (2003). Physiological Plant Ecology (4th ed.). New York: Springer.

Lashermes, P., Combes, M. C., Robert, J., Trouslot, P., D’Hont, A., Anthony, F., & Charrier, A. (1999). Molecular characterisation and origin of the Coffea arabica L. genome. Molecular and General Genetics MGG, 261(2), 259-266.

Muschler, R. G. (2009). Shade Management and its Effect on Coffee Growth and Quality. In J. N. Wintgens (Ed.), Coffee: Growing, Processing, Sustainable Production 2nd ed.,  (pp. 395-422). Weinheim: Wiley-VCH Verlag GmbH & Co. kGaA, Weinheim.

Raven, P., Evert, R., & Eichhorn, S. (1999). Biology of Plants. New York: W.H. Freemand and Company.

Rothfos, B. (1980). Coffee Production. Germany: GORDIAN-Max-Rieck GmbH.

Snoeck, J., & Lambot, C. (2009). Crop Maintenance. In J. N. Wintgens (Ed.), Coffee: Growing, Processing, Sustainable Production 2nd ed.,  (pp. 250-327). Weinheim: Wiley-VCH Verlag GmbH & Co. KGaA.

Snoeck, J., & Vaast, P. (2009). Importance of Organic Matter and Biological Fertility in Coffee Soils. In J. N. Wintgens (Ed.), Coffee: Growing, Processing, Sustainable Production 2nd ed.,  (pp. 375-387): Wiley-VCH Verlag GmbH & Co. KGaA.

Wellman, F. L. (1961). Coffee: Botany, Cultivation, and Utilization. New York: Interscience Publishers Inc.

Willson, K. C. (1999). Coffee, Cocoa, and Tea. UK: CABI Publishing.