User:Changla/sandbox

An endophyte is an endosymbiont, often a bacterium or fungus, that lives within a plant for at least part of its life cycle without causing apparent disease. Endophytes are ubiquitous and have been found in all species of plants studied to date; however, most of the endophyte/plant relationships are not well understood. Endophytes are also known to occur within lichens and algae. Some endophytes may enhance host growth, nutrient acquisition and may improve the plant's ability to tolerate abiotic stresses, such as drought, and enhance resistance to insects, plant pathogens and herbivores. As often with other organisms associated with plants such as mycorrhizal fungus, endophytes gain carbon from their association with the plant host.

Transmission
Endophytes may be transmitted either vertically (directly from parent to offspring) or horizontally (among individuals). Vertically transmitted fungal endophytes are typically considered clonal and transmit via fungal hyphae penetrating the embryo within the host’s seeds (e.g., seed transmitting forms of Epichloë). Conversely, reproduction of the fungi through asexual conidia or sexual spores leads to horizontal transmission, where endophytes may spread between plants in a population or community. Some endophytes that frequently transmit vertically may also produce spores on plants that can be transmitted horizontally (e.g., Epichloë festucae).

Plant Host Benefits
Endophytes and plants often engage in mutualism, with endophytes primarily aiding in the health and survival of the host plant with issues such as pathogens and disease, water stress, heat stress, nutrient availability and poor soil quality, salinity, and herbivory. Plant-microbe interactions are not strictly mutualistic, with endophytic fungi potentially becoming pathogens or saprotrophs that only become active and reproduce under specific environmental conditions or when their host plants are stressed or begin to senesce. These plant-microbe symbiotic interactions can instead be viewed as a continunm between pathogenic and mutualistic with any particular interactions influenced by factors such as environmental conditions, genetics, and plant tissue age. Redman et al. advanced the hypothesis of 'habitat adapted symbiosis' where plants are proposed to associate with particular endophytes that increase tolerance or resistance to the predominant biotic or abiotic stresses of their habitats. Fungal and bacterial endophytes make up communities that may increase a plant's capacity to survive and thrive in its habitat.

Endophytes may benefit host plants by preventing pathogenic or parasitic organisms from colonizing them, by extensively colonizing plant tissues and competitively excluding potential pathogens. Endophytes may also produce chemicals which inhibit the growth of competitors, including pathogenic organisms. The presence of endophytes is also known to increase expression of defense-related genes in plants, making plants more resistant to many potential pathogens. Certain microbial endophytes may also help plants to continue growing despite root herbivory.

Some fungal and bacterial endophytes have proven to increase plant growth and improve overall plant hardiness. They can aid in a plant's ability to deal with abiotic stresses including salt, drought or heat. Endophytes have also been shown to enhance plant development and increase nutrient (phosphorus and nitrogen) uptake into plants.

Medicinal Applications
Endophytes as a whole can produce a wide variety of medically useful compounds or aid in the production of medically important plants. Certain fungal endophyte secondary metabolites have anti-fungal, anti-microbial, anti-viral, anti-oxidant, and anti-cancer properties; examples of this include taxol, torreyanic acid, exopolysaccharides, and solamargine. Manipulations of a plant's endosymbiots can also affect plant development, growth and ultimately the quality and quantity of compounds harvested from the plant.

Industrial and Environmental Applications
The main quality selected for use in biofuel is high productivity. Through the above benefits use of endophytes can potentially increase productivity and allow production to occur on land otherwise unsuitable. Inoculating plants with certain endophytes may provide increased disease or parasite resistance while others may possess metabolic processes that convert cellulose and other carbon sources into "myco-diesel" hydrocarbons and hydrocarbon derivatives. Common species used in biofuel in the US are Zea mays (corn), Salix species (poplars and willows), and sugarcane species.

In restoration ecology, endophytes can assist native species in outcompeting non-native invasive species and, colonizing barren land in secondary ecological succession, and restoring ecosystems degraded by pollutants. As with in biofuel production, in phytoremediation high productivity species are often used. Plants are able to contain, store, potentially break down, and stimulate microorganisms in the soil to break down certain pollutants. With phytoremediation the main challenge is the growth of plants in soil contaminated with organic pollutants and inorganic pollutants such as heavy metals. In this endophytes assist plants in converting pollutants into less biologically harmful forms such as breaking down TCE of PAHs in their metabolic pathways, and assist plants in tolerating higher levels of soil contamination with pollutants such as toluene. Endophytes degrade organic pollutants, and help plants themselves interact with pollutants.

The roots of plant communities to varying degrees help hold soil together by creating a network of roots that trap soil within. This in turn helps prevent soil erosion, stabilizes slopes and prevent landslides, helps prevent desertification in vulnerable areas, and controls pollution into waterways by acting as part of riparian buffers. Many of the areas where plants could help most are those with harsher abiotic conditions which endophytes would help the plants tolerate.

Agricultural Applications
Among the many promising applications of endophytic microbes are those intended to increase agricultural use of endophytes to produce crops that grow faster and are more resistant and hardier than crops lacking endophytes. Epichloë endophytes are being widely used commercially in turf grasses to enhance the performance of the turf and its resistance to biotic and abiotic stresses. Piriformospora indica is an interesting endophytic fungus of the order Sebacinales, the fungus is capable of colonising roots and forming symbiotic relationship with many plants. P. indica symbiosis has been shown to increase crop yield for a variety of crops (barley, tomato, maize etc.) and provide a measure of protection against pathogens and abiotic stresses. Recent evidence suggests that communities of bacterial and fungal endophytes may work in functional consortia to promote growth and protect plants in natural populations; while plants in intensive cultivation may lose these defensive and growth promotional microbiome components. Some scientists propose that restoration of defensive and growth promotional endophytes in agricultural crops could result in reduction of agrochemical inputs to control pests and diseases and result in crops that would better tolerate droughts and other stresses. There is some evidence that some bacterial endophytes may establish symbiosis with both plants and animals. This raises the possibility that crops could one day be produced that carry probiotic endophytes to enhance human health.

Endophytes Identification
Endophytes can be identified in several ways, usually through amplifying and sequencing a small piece of DNA. Some endophytes can be cultured from a piece of their host plant in an appropriate growth medium. An important step in culturing endophytes is to surface disinfect plant tissues prior to placement on culture media; this kills epiphytic microbes, ensuring only growth of endophytic microbes. Not all endophytes can be cultured in this way, as shown by discovery of cryptic, unculturable endophyte species through DNA based analysis of leaf tissue. Many fungal endophytes do not sporulate when cultured, as the plant host is necessary for them to complete their life cycle. Since fungal identification by morphology is based primarily on spore-bearing structures, this fact makes visual identification of some endophytic cultures challenging.

It is speculated that there may be many thousands of endophytes useful to mankind but since there are few scientists working in this field, and since environmental contamination, deforestation and biodiversity loss are widespread, many endophytes might be permanently lost before their utility is explored.

Diversity
Endophytic species are very diverse; only a small minority of existing endophytes have been characterized. A single plant organ (leaf, stem or root) of a plant can harbor many different species of endophytes, both bacterial and fungal. Additionally, some endophytic bacteria may live within endophytic fungi.

Diversity of Fungal Endophytes
From within the phylums Basidiomycota and Ascomycota endophytic fungi may be from Hypocreales and Xylariales of the Sordariomycetes (Pyrenomycetes) class or from the class of Loculoascomycetes. Endophytes are diverse taxonomically, and as such classification based on broader ecological categories or functional classes has been proposed.

One group of fungal endophytes are the arbusbuclar mycorrhizal fungi involving biotrophic Glomeromycota associated with various plant species. Though the fungi does not breach the plant's cellular membrane or share cytoplasm, the fungi grows an arbuscule pushing aside the membrane and increasing the surface area for resource exchange. AM fungi have a long history of co-evolution with land plants showing up in the fossil record in plants of the Devonian Period.

Diversity of Algal Endophytes
A number of endophytes are now known that grow within seaweeds and algae. One such example is Ulvella leptochaete, which has recently been discovered from host algae including Cladophora and Laurentia from India.

Diversity of Bacterial Endophytes
Bacterial endophytes are polyphyletic, belonging to broad range of taxa, including α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Firmicutes, Actinobacteria, etc... Bacterial endophytes have been found to become intracellular in root and shoot cells of many plants, with entry into cells in the meristems. In this intracellular form bacteria lose cell walls but continue to divide and metabolize, these wall-less intracellular forms of bacteria are called L-forms. Paungfoo-Lonhienne et al. observed the degradation of intracellular microbes within root cells and hypothesized that intracellular microbes may be a source of organic nutrients or vitamins for plants; they termed this process 'rhizophagy'.