Sunflower time lapse with soil. cross section, showing how the roots and the upper part of the plant grow

Germination is the process by which an organism grows from a seed or spore. The term is applied to the sprouting of a seedling from a seed of an angiosperm or gymnosperm, the growth of a sporeling from a spore, such as the spores of fungi, ferns, bacteria, and the growth of the pollen tube from the pollen grain of a seed plant.

A seed tray used in horticulture for sowing and taking plant cuttings and growing plugs

Germination is usually the growth of a plant contained within a seed; it results in the formation of the seedling. It is also the process of reactivation of metabolic machinery of the seed resulting in the emergence of radicle and plumule. The seed of a vascular plant is a small package produced in a fruit or cone after the union of male and female reproductive cells. All fully developed seeds contain an embryo and, in most plant species some store of food reserves, wrapped in a seed coat. Some plants produce varying numbers of seeds that lack embryos; these are empty seeds which never germinate. Dormant seeds are viable seeds that do not germinate because they require specific internal or environmental stimuli to resume growth. Under proper conditions, the seed begins to germinate and the embryo resumes growth, developing into a seedling.[clarification needed]

Disturbance of soil can result in vigorous plant growth by exposing seeds already in the soil to changes in environmental factors where germination may have previously been inhibited by depth of the seeds or soil that was too compact. This is often observed at gravesites after a burial.[1]

Seed germination depends on both internal and external conditions. The most important external factors include right temperature, water, oxygen or air and sometimes light or darkness.[2] Various plants require different variables for successful seed germination. Often this depends on the individual seed variety and is closely linked to the ecological conditions of a plant's natural habitat. For some seeds, their future germination response is affected by environmental conditions during seed formation; most often these responses are types of seed dormancy.

Most common annual vegetables have optimal germination temperatures between 75-90 F (24-32 C), though many species (e.g. radishes or spinach) can germinate at significantly lower temperatures, as low as 40 F (4 C), thus allowing them to be grown from seeds in cooler climates. Suboptimal temperatures lead to lower success rates and longer germination periods.

Some live seeds are dormant and need more time, and/or need to be subjected to specific environmental conditions before they will germinate. Seed dormancy can originate in different parts of the seed, for example, within the embryo; in other cases the seed coat is involved. Dormancy breaking often involves changes in membranes, initiated by dormancy-breaking signals. This generally occurs only within hydrated seeds.[5] Factors affecting seed dormancy include the presence of certain plant hormones, notably abscisic acid, which inhibits germination, and gibberellin, which ends seed dormancy. In brewing, barley seeds are treated with gibberellin to ensure uniform seed germination for the production of barley malt.[2]

In some definitions, the appearance of the radicle marks the end of germination and the beginning of "establishment", a period that utilizes 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.[2] The germination index can be used as an indicator of phytotoxicity in soils. The mortality between dispersal of seeds and completion of the establishment can be so high that many species have adapted to produce large numbers of seeds.

In agriculture and gardening, the germination rate describes how many seeds of a particular plant species, variety or seedlot are likely to germinate over a given period. It is a measure of germination time course and 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 over the germination period given. Seed germination rate is determined by the seed genetic composition, morphological features and environmental factors.[citation needed] The germination rate is useful for calculating the number of seeds needed for a given area or desired number of plants. For seed physiologists and seed scientists "germination rate" is the reciprocal of time taken for the process of germination to complete starting from time of sowing. On the other hand, the number of seed able to complete germination in a population (i.e. seed lot) is referred to as germination capacity.

Seed quality deteriorates with age, and this is associated with accumulation of genome damage.[6] During germination, repair processes are activated to deal with accumulated DNA damage.[7] In particular, single- and double-strand breaks in DNA can be repaired.[8] The DNA damage checkpoint kinase ATM has a major role in integrating progression through germination with repair responses to the DNA damages accumulated by the aged seed.[9]

The stages of germination of a pea plant: A. seed coat, B. radicle, C. primary root, D. secondary root, E. cotyledon, F. plumule, G. leaf, H. tap root

The part of the plant that first emerges from the seed is the embryonic root, termed the radicle or primary root. It allows the seedling to become anchored in the ground and start absorbing water. After the root absorbs water, an embryonic shoot emerges from the seed. This 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 among plant groups.[2]

In epigeal germination (or epigeous 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 plants that germinate this way.[2]

Germination can also be done by hypogeal germination (or hypogeous germination), where the epicotyl elongates and forms the hook. In this type of germination, the cotyledons stay underground where they eventually decompose. Peas, gram and mango, for example, germinate this way.[10]

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.[2]

When a seed germinates without undergoing all four stages of seed development, i.e., globular, heart shape, torpedo shape, and cotyledonary stage, it is known as precocious 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 by the structure and physiology of the stigma and style.[2] Pollen can also be induced to germinate in vitro (in a petri dish or test tube).[11][12]

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.[2]

Since most plants carry both male and female reproductive organs in their flowers, there is a high risk of self-pollination and thus inbreeding. Some plants use the control of pollen germination as a way to prevent this self-pollination. 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 prevent it from germinating.[13]

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.

Conidia are asexual reproductive (reproduction without the fusing of gametes) spores of fungi which germinate under specific conditions. A variety of cells can be formed from the germinating conidia. The most common are germ tubes which grow and develop into hyphae. The initial formation and subsequent elongation of the germ tube in the fugus Aspergillus niger has been captured in 3D using holotomography microscopy. Another type of cell is a conidial anastomosis tube (CAT); these differ from germ tubes in that they are thinner, shorter, lack branches, exhibit determinate growth and home toward each other. Each cell is of a tubular shape, but the conidial anastomosis tube forms a bridge that allows fusion between conidia.[14][15]

3D-visualization of Aspergillus niger spore germination. This image has been captured using holotomography microscopy.

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).[2]

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.[2]

Bacterial spores can be exospores or endospores which are dormant structures produced by a number of different bacteria. They have no or very low metabolic activity and are formed in response to adverse environmental conditions.[16] They allow survival and are not a form of reproduction.[17] Under suitable conditions the spore germinates to produce a vital bacterium. Endospores are formed inside the mother cell, and, exospores are formed at the end of the mother cell as a bud.[18]

As mentioned earlier, light can be an environmental factor that stimulates the germination process. The seed needs to be able to determine when is the perfect time to germinate and they do that by sensing environmental cues. Once germination starts, the stored nutrients that have accumulated during maturation start to be digested which then supports cell expansion and overall growth.[19] Within light-stimulated germination, Phytochrome B (PHYB) is the photoreceptor that is responsible for the beginning stages of germination. When red light is present, PHYB is converted to its active form and moves from the cytoplasm to the nucleus where it upregulates the degradation of PIF1. PIF1, phytochrome-interaction-factor-1, negatively regulates germination by increasing the expression of proteins that repress the synthesis of gibberellin (GA), a major hormone in the germination process.[20] Another factor that promotes germination is HFR1 which accumulates in light in some way and forms inactive heterodimers with PIF1.[21]

Although the exact mechanism is not known, nitric oxide (NO) plays a role in this pathway as well. NO is thought to repress PIF1 gene expression and stabilizes HFR1 in some way to support the start of germination.[19] Bethke et all (2006) exposed dormant Arabidopsis seeds to NO gas and within the next 4 days, 90% of the seeds broke dormancy and germinated. The authors also looked at how NO and GA effects the vacuolation process of aleurone cells that allow the movement of nutrients to be digested. A NO mutant resulted in inhibition of vacuolation but when GA was later added the process was active again leading to the belief that NO is prior to GA in the pathway. NO may also lead to the decrease in sensitivity of Abscisic acid (ABA), a plant hormone largely responsible for seed dormancy.[22] The balance between GA and ABA is important. When ABA levels are higher than GA then that leads to dormant seeds and when GA levels are higher, seeds germinate.[23] The switch between seed dormancy and germination needs to occur at a time when the seed has the best chances of surviving and an important cue that begins the process of seed germination and overall plant growth is light.