Germination

Germination is the process whereby growth emerges from a period of dormancy. The most common example of germination is the sprouting of a seedling from a seed of an angiosperm or gymnosperm. However, the growth of a sporeling from a spore, for example the growth of hyphae from fungal spores, is also germination. In a more general sense, germination can imply anything expanding into greater being from a small existence or germ.

Seed germination
Germination is the growth of an embryonic plant contained within a seed, it results in the formation of the seedling. The seed of a higher plant is a small package produced in a fruit or cone after the union of male and female sex cells. Most seeds go through a period of quiescences where there is no active growth, during this time the seed can be safely transported to a new location and/or survive adverse climate conditions until it is favorable for growth. The seed contains an embryo and in most plants stored food reserves wrapped in a seed coat. Under favorable conditions, the seed begins to germinate, and the embryonic tissues resume growth, developing towards a seedling.

Requirements for seed germination
The germination of seeds is dependent on both internal and external conditions. The most important external factors include: temperature, water, oxygen and sometimes light or darkness. Often different varieties of seeds require distinctive variables for successful germination; some seeds germinate while the soil is cold, while most germinate while the soil is warm. This depends on the individual seed variety and is closely linked to the ecological conditions of the plants' natural habitat.


 * Water - is required for germination. Mature seeds are often extremely dry and need to take in significant amounts of water, relative to the seeds dry weight, before cellular metabolism and growth can resume. Most seeds respond best when there is enough water to moisten the seeds but not soak them. The uptake of water by seeds is called imbibition which leads to the swelling and the breaking of the seed coat. When seeds are formed, most plants store food, such as starch, proteins, or oils, to provide nourishment to the growing embryo inside the seed. When the seed imbibes water, hydrolytic enzymes are activated that break down these stored food resources in to metabolically useful chemicals, allowing the cells of the embryo to divide and grow, so the seedling can emerge from the seed. Once the seedling starts growing and the food reserves are exhausted, it requires a continuous supply of water, nutrients and light for photosynthesis, which now provides the energy needed for continued growth.


 * Oxygen - is required by the germinating seed for metabolism: If the soil is waterlogged or the seed is buried within the soil, it might be cut off from the necessary oxygen it needs. Oxygen is used in aerobic respiration, the main source of the seedling's energy until it has leaves, which can photosynthesize its energy requirements. Some seeds have impermeable seed coats that prevent oxygen from entering the seeds, causing seed dormancy. Impermeable seed coats to oxygen or water, are types of physical dormancy which is broken when the seed coat is worn away enough to allow gas exchange or water uptake between the seed and its surrounds.


 * Temperature - affects cellular metabolic and growth rates. Different seeds germinate over a wide range of temperatures, with many preferring temperatures slightly higher than room-temperature while others germinate just above freezing and others responding to alternation in temperature between warm to cool. Often, seeds have a set of temperature ranges where they will germinate and will not do so above or below this range. In addition, some seeds may require exposure to cold temperature (vernalization) to break dormancy before they can germinate. As long as the seed is in its dormant state, it will not germinate even if conditions are favorable. Seeds that are dependent on temperature to end dormancy, have a type of physiological dormancy. For example, seeds requiring the cold of winter are inhibited from germinating until they experience cooler temperatures. For most seeds that require cold for germination 4C is cool enough to end dormancy, but some groups especially with in the family Ranunculaceae and others, need  less than -5C.  Some seeds will only germinate when temperatures reach hundreds of degrees, as during a forest fire. Without fire, they are unable to crack their seed coats, this is a type of physical dormancy.


 * Light or darkness - can be a type of environmental trigger for germination in seeds and is a type of physiological dormancy. Most seeds are not affected by light or darkness, but many seeds, including species found in forest settings will not germinate until an opening in the canopy allows them to receive sufficient light for the growing seedling.

Stratification mimics natural processes that weaken the seed coat before germination. In nature, some seeds require particular conditions to germinate, such as the heat of a fire (e.g., many Australian native plants), or soaking in a body of water for a long period of time. Others have to be passed through an animal's digestive tract to weaken the seed coat and enable germination.



Dormancy
Many live seeds have dormancy, meaning they will not germinate even if they have water and it is warm enough for the seedling to grow. Dormancy factors include conditions affecting many different parts of the seed, from the embryo to the seed coat. Dormancy is broken or ended by a number of different conditions and cues both internal and external to the seed. Environmental factors like light, temperature, fire, ingestion by animals and others are conditions that can end seed dormancy. Internally seeds can be dormant because of plant hormones such as absciscic acid, which affects seed dormancy and prevents germination, while the production and application of the hormone gibberellin can break dormancy and induces seed germination. This effect is used in brewing where barley is treated with gibberellin to ensure uniform seed germination to produce barley malt.

Seedling establishment
In some definitions, the appearance of the radicle marks the end of germination and the beginning of "establishment", a period that ends when the seedling has exhausted the food reserves stored in the seed. Germination and establishment as an independent organism are critical phases in the life of a plant when they are the most vulnerable to injury, disease, and water stress. The germination index can be used as an indicator of phytotoxicity in soils. The mortality between dispersal of seeds and completion of establishment can be so high, that many species survive only by producing huge numbers of seeds.

Germination rate
In agriculture and gardening, germination rate is the number of seeds of a particular plant species, variety or particular seedlot that are likely to germinate. This is usually expressed as a percentage, e.g. an 85% germination rate indicates that about 85 out of 100 seeds will probably germinate under proper conditions. Germination rate is useful in calculating seed requirements for a given area or desired number of plants.

Dicot germination
The part of the plant that emerges from the seed first is the embryonic root, termed radicle or primary root. This allows the seedling to become anchored in the ground and start absorbing water. After the root absorbs water, the embryonic shoot emerges from the seed. The shoot comprises three main parts: the cotyledons (seed leaves), the section of shoot below the cotyledons (hypocotyl), and the section of shoot above the cotyledons (epicotyl). The way the shoot emerges differs between plant groups.

Epigeous
In epigeous (or epigeal) germination, the hypocotyl elongates and forms a hook, pulling rather than pushing the cotyledons and apical meristem through the soil. Once it reaches the surface, it straightens and pulls the cotyledons and shoot tip of the growing seedlings into the air. Beans, tamarind, and papaya are examples of plant that germinate this way.

Hypogeous
Another way of germination is hypogeous (or hypogeal) where the epicotyl elongates and forms the hook. In this type of germination, the cotyledons stay underground where they eventually decompose. Peas, for example, germinate this way.

Monocot germination
In monocot seeds, the embryo's radicle and cotyledon are covered by a coleorhiza and coleoptile, respectively. The coleorhiza is the first part to grow out of the seed, followed by the radicle. The coleoptile is then pushed up through the ground until it reaches the surface. There, it stops elongating and the first leaves emerge through an opening as it is.

Precocious germination
While not a class of germination, this refers to germination of the seed occurring inside the fruit before it has begun to decay. The seeds of the green apple commonly germinate in this manner.

Pollen germination
Another germination event during the life cycle of gymnosperms and flowering plants is the germination of a pollen grain after pollination. Like seeds, pollen grains are severely dehydrated before being released to facilitate their dispersal from one plant to another. They consist of a protective coat containing several cells (up to 8 in gymnosperms, 2-3 in flowering plants). One of these cells is a tube cell. Once the pollen grain lands on the stigma of a receptive flower (or a female cone in gymnosperms), it takes up water and germinates. Pollen germination is facilitated by hydration on the stigma, as well as the structure and physiology of the stigma and style. Pollen can also be induced to germinate in vitro (in a petri dish or test tube).

During germination, the tube cell elongates into a pollen tube. In the flower, the pollen tube then grows towards the ovule where it discharges the sperm produced in the pollen grain for fertilization. The germinated pollen grain with its two sperm cells is the mature male microgametophyte of these plants.

Self-incompatibility
Since most plants carry both male and female reproductive organs in their flowers, there is a high risk for self-pollination and thus inbreeding. Some plants use the control of pollen germination as a way to prevent this selfing. Germination and growth of the pollen tube involve molecular signaling between stigma and pollen. In self-incompatibility in plants, the stigma of certain plants can molecularly recognize pollen from the same plant and prevents it from germinating.

Spore germination
Germination can also refer to the emergence of cells from resting spores and the growth of sporeling hyphae or thalli from spores in fungi, algae, and some plants.

Resting spores
In resting spores, germination involves cracking the thick cell wall of the dormant spore. For example, in zygomycetes the thick-walled zygosporangium cracks open and the zygospore inside gives rise to the emerging sporangiophore. In slime molds, germination refers to the emergence of amoeboid cells from the hardened spore. After cracking the spore coat, further development involves cell division, but not necessarily the development of a multicellular organism (for example in the free-living amoebas of slime molds).

Zoospores
In motile zoospores, germination frequently means a lack of motility and changes in cell shape, which allow the organism to become sessile.

Ferns and mosses
In plants such as bryophytes, ferns, and a few others, spores germinate into independent gametophytes. In the bryophytes (e.g. mosses and liverworts), spores germinate into protonemata, similar to fungal hyphae, from which the gametophyte grows. In ferns, the gametophytes are small, heart-shaped prothalli that can often be found underneath a spore-shedding adult plant.