Germination: The Challenge of Emerging from the Seed

by Guido Masé June 11, 2019

A deeper look into how a new plant is born

The seeds plants make encapsulate the future: a new generation, a whole world of potential. While starting seeds indoors, or scattering them over bare ground, or pushing them into furrows and feeling the cool soil on our fingers, we hope that this potential will turn into reality through the process of germination: maybe, if we're lucky, in a few days or weeks seedlings will sprout and we can watch new life unfold. 

Whether your seedlings are waiting to emerge, or you're already busy watering and tending fresh baby plants, late spring serves as an opportunity to take an in-depth look at the process of germination. What's happening in those seeds as they swell and crack and send out their first green? While the answers are fascinating, they also show us yet again how, despite our differences, we and the plants face similar challenges as we grow and explore new horizons. Taking a look at the way plants handle the challenge of germination may yield some useful insights for us, too.


Before germination, the seed is a perfect packet of potential. There are all different types: some, like angelica (Angelica archangelica), must germinate quickly, and rarely maintain their potential for more than one season 1. Others seem to last hundreds of years or more (a seed from the date palm, Phoenix dactylifera, germinated after close to 2,000 years of storage)2. Many seeds, like those from echinacea (Echinaceaspp.) or lavender (Lavandulaspp.) flowers, require a few weeks of freezing temperatures to germinate (a safeguard against sprouting during a warm spell in late fall)3. Still others won't sprout at all until special conditions are met: belladonna (Atropa belladonna), for example, needs its seeds to experience an acid bath, 8-10h of warm (90F) temperatures, and some "roughing up" (rubbing between two sheets of sandpaper can do the trick, a process known as scarification)4. This mimics belladonna seeds' natural cycle, where a bird eats the toxic fruit, passes the seeds through gullet and stomach, and then dies from the plant's poison (leaving its body as fertilizer). These differences are likely due to different types of coatings found around the seed. These coatings serve as the interface between the outside world and what's locked away inside: the embryo(a tiny, curled-up seedling), some food for that embryo to use (sugars and fats, usually), and all-important water.

seed embryo

The embryo has fully-formed structures ready to create energy for the cell: a tiny radicle that will push down into the soil to harvest water and minerals by interacting with the soil environment; and baby leaves called cotyledons ready to unfurl in the sun and start photosynthesis. The embryo houses genetic instructions that serve as a roadmap not only for germination, but also for everything the plant will need during the course of its life. Crucially, strands of messenger RNA--the first step in turning DNA into new structures for the emerging seedling--are also present, ready and waiting inside the embryo, along with cellular organelles like mitochondria for making energy5. All that's missing is water: the cells in the embryo are relatively dry, with water content around 5-15%. At these concentrations, the fatty membrane that surrounds the embryo's cells is in a "gel" state. This is essential for the long-term preservation of the embryo in the relatively dry conditions of the seed, and it's analogous to what happens in the cells of certain worms, amphibians, and even mammals during hibernation. When water enters the seed, all this changes6. It's the first stage of germination, a process known as imbibition.

There are a few factors that determine how much water a seed will imbibe 7. One is the "pull" that the relatively dry embryonic cells exert on water found outside the seed: by osmosis, water will travel into the seed to dilute the concentrated material found inside. Another is the "push" that the seed exerts on the outside world: seed contents are under relatively high pressure, which slows the influx of water. A final factor comes from specialized structures seeds possess to facilitate the entry of water during imbibition: beans and peas, for example, have extensive micro-structures on their seed coat that channel water more quickly to the micropyle, the place on the seed where water enters. At any given time, the combination of these factors determines whether, and how quickly, water enters the seed.

There are some interesting implications here: first, adequate and continuous moisture is essential for successful imbibition. But good contact between the moist soil and the seed is important, too: this helps maximize any capillary effects on the seed coat. It is sound advice to press your seeds firmly into the soil: this will speed imbibition, and as water enters the seed more quickly, you'll see faster germination. Regardless, once water begins to enter the seed, the real magic starts.

Seed planting

Remember that there are already strands of messenger RNA and cellular organelles waiting inside the embryo's cells, ready to spring into action. As water moves in, they do just that: proteins start to form, following the instructions stored in the RNA. The embryo begins to "breathe", using oxygen and the seed's stores of sugar and fat to support protein synthesis with abundant energy. All this starts to happen while water is entering, so that by the time the seed reaches equilibrium with the moisture in the soil, its metabolism is revved up and ready. At the same time, the embryo does some "housekeeping": it repairs any damage its DNA sustained before germination, and as best it can patches up damage that occurred during imbibition.

This is fascinating: it points to the fact that the act of germination carries risk, especially during that initial phase of water uptake. Remember that, as a seed, most of the cell membranes in the embryo exist as a gel. This gel isn't particularly flexible, and it is more porous than a normal cell membrane. So if water enters too quickly, flooding embryonic cells before their membranes have a chance to change to their more flexible form, you see widespread cellular damage, which (if excessive) can kill or rot the embryo. This can be visible to the naked eye: if you look at bean sprouts, you can see what look like little "cracks" or "blisters" on the seed leaves, evidence of the damage the embryo endured during imbibition8. This reminds me of what happens to athletes as they train to improve: muscles and connective tissue can suffer, especially if the training volume increases too quickly. But we see this with any challenge we might encounter on the road to actualize our potential: rush in too fast, and you might sustain some damage. Again the plants remind us, starting at the very earliest moment of their lives, to follow a moderate pace. 

Once imbibition is complete and the embryo works through its housekeeping chores, water uptake stalls until the embryo is ready to start growing--that is, making new cells. Before doing so, it rearranges a strong lattice-work of proteins inside its cells for two main purposes: first, to start moving the radicle down and out of the seed; second, to set the stage for cell division (a strong protein skeleton is needed to divide a cell in two during mitosis)9. When everything is ready, the radicle cracks the seed and emerges, opening the new-born plant to a steady influx of moisture so that growth can begin in earnest. Now, "breathing" becomes essential: cellular respiration, which as with us happens in the seedling's mitochondria, takes energy reserves and oxygen to fuel cell division, which elongates the embryonic stem and eventually pushes the seed-leaves out of the ground to harvest solar energy. A new plant is alive and thriving.

spinach plant

One final, remarkable parallel between humans and plants comes to light during this time: if a germinating plant finds oxygen levels are below ideal (a condition called hypoxia), it can slow down its metabolism, reducing the rate of protein synthesis and cell division. While this slows germination, it also prevents hypoxia-induced damage and increases chances for long-term survival. To control this balance, the embryo uses a short-acting hormone, a gas called nitric oxide(NO). As oxygen levels drop, the levels of NO increase, metabolism drops, and anti-inflammatory, anti-aging genes kick in 10. Those of you familiar with cardiovascular health will recognize that humans use NO in a very similar way: as oxygen levels drop (for example, when a muscle is exercising hard), NO levels increase, opening up the circulation and bringing more blood and oxygen to the area. Just as with plants, NO regulates animals' response to hypoxia. To me, this is further evidence of a long-standing connection with the green world.

As you watch your seedlings grow this spring, as you think about stretching yourself to meet the challenges that the rush of summer brings, think of what we can learn from plants. The enthusiasm of following a dream or new idea will certainly lead to growth, but there may be a little damage along the way. Breathing deeply can help, allowing sufficient oxygen to support every process of growth. And as we unconsciously regulate our blood flow while we garden and take in the greening world, we can think that the newly-emerging seedlings are doing a very similar thing, using the exact same hormone we do. May your dreams grow with success into the light of the summer sun.


  1. Ojala, Arja. "Seed dormancy and germination in Angelica archangelica subsp. archangelica (Apiaceae)." Annales Botanici Fennici. The Finnish Botanical Publishing Board, 1985
  2. Sallon, Sarah, et al. "Germination, genetics, and growth of an ancient date seed." Science 320.5882 (2008): 1464-1464.
  3. Romero, Fredy R., Kathleen Delate, and David J. Hannapel. "The effect of seed source, light during germination, and cold-moist stratification on seed germination in three species of Echinacea for organic production." HortScience 40.6 (2005): 1751-1754.
  4. Genova, Elena, Gergana Komitska, and Yundina Beeva. "Study on the germination of Atropa bella-donna L. seeds." Bulgarian Journal of Plant Physiology 23.1-2 (1997): 61-66.
  5. Bewley, H. Nonogaki GW Bassel JD. "Germination—still a mystery." Plant Sci179 (2010): 574-581.
  6. Crowe, John H., Folkert A. Hoekstra, and Lois M. Crowe. "Membrane phase transitions are responsible for imbibitional damage in dry pollen." Proceedings of the National Academy of Sciences 86.2 (1989): 520-523.
  7. Bradford, Kent J. "Manipulation of seed water relations via osmotic priming to improve germination under stress conditions." HortScience (USA) (1986).
  8. Morris, J. L., W. F. Campbell, and L. H. Pollard. "Relation of imbibition and drying on cotyledon cracking in snap beans, Phaseolus vulgaris L." Journal of the American Society of Horticultural Science 95 (1970): 541-3.
  9. de Castro, Renato D., et al. "Cell division and subsequent radicle protrusion in tomato seeds are inhibited by osmotic stress but DNA synthesis and formation of microtubular cytoskeleton are not." Plant Physiology 122.2 (2000): 327-336.
  10. Borisjuk, Ljudmilla, et al. "Low oxygen sensing and balancing in plant seeds: a role for nitric oxide." New Phytologist 176.4 (2007): 813-823.


Guido Masé
Guido Masé

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