Endophyte

Endophytes were first described by the German botanist Johann Heinrich Friedrich Link in 1809. They were thought to be plant parasitic fungi and they were later termed as "microzymas" by the French scientist Béchamp. There was a belief that plants were healthy under sterile conditions and it was not until 1887 that Victor Galippe discovered bacteria normally occurring inside plant tissues.^[2] Though, most of the endophytic studies reports the mutualistic relationship of bacteria and fungus, Das et al., (2019) reported about endophytic virome and their probable function in plant defense mechanisms.^[3]

Transmission

Endophytes may be transmitted either vertically (directly from parent to offspring) or horizontally (among individuals).

Most endophyte-plant relationships are still not well understood.^[7] However, recently it was shown that endophytes are transmitted from one generation to another via seeds, in a process called vertical transmission.^[8] 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,^[9] water stress, heat stress, nutrient availability and poor soil quality, salinity, and herbivory.^[2] In exchange the endophyte receives carbon for energy from the plant host. Plant-microbe interactions are not strictly mutualistic, as endophytic fungi can potentially become pathogens or saprotrophs, usually when the plant is stressed.^[10] Endophytes may become active and reproduce under specific environmental conditions or when their host plants are stressed or begin to senesce, thereby limiting the amount of carbon provided to the endophyte.^[11][12]

Endophytes may benefit host plants by preventing other pathogenic or parasitic organisms from colonizing them. Endophytes can extensively colonize plant tissues and competitively exclude other potential pathogens.^[13][14] Some fungal and bacterial endophytes have proven to increase plant growth and improve overall plant hardiness.^[15]

Studies have shown that endophytic fungi grow in a very intimate interaction with their host plant cells. Fungal

There are various behaviors that have been studied that resulted from endophyte symbiosis with plants. Through association with fungal endophytes, the root and shoot structures of Pseudotsuga menziesii (Douglas-fir) saplings in low-nutrient conditions have been shown to be elongated, as well as undergo overall biomass increases.^[20] The proposed mechanisms behind this include high inorganic phosphate solubilization ability by the fungi as well as organic phosphate mineralization, increased mycorrhizal associations through root colonization, and enhanced nitrogen and phosphorus uptake.^[20] Specific endophyte species can also stimulate root growth by increasing the flux of auxin to where the endophyte is.^[21]

Additionally, various reports on endophyte interactions have shown increased photosynthetic capacities of host plants as well as improved water relations.^[22] Improvements in water use efficiency were observed in higher CO₂ concentrations and a further increase was seen in water deficit conditions.^[22] In addition, other various physiological pathways were activated upon endophytes interactions with host plants, enabling tighter water control and further water management, which are to be the main reasons behind improved water relations.^[22] Specifically, evidence points to endophytes producing ABA to affect stomatal conductance as well as microbial respiration and plants recycling CO₂.^[23]

However, the specific biochemical mechanisms behind these behavioral changes are still largely unknown and lower-level signal cascades have yet to be discovered. Furthermore, while the benefits of endophyte relations are well-studied, the costs of these relations are less well understood, such as the specific carbon costs, the system of endophyte governance, and the environmental conditions that facilitate a proper plant-endophyte relationship.^[22]

In an experiment investigating the interaction between Miscanthus sinensis and the plant endophyte Herbaspirillum frisingense, a roughly 20% increase in fresh biomass was observed in M. sinensis following inoculation with H. frisingense.^[24] However, unique to this experiment was the mode by which this was thought to happen. Inoculation saw an upregulation in the genes relevant to jasmonate and ethylene production in the plant roots, although the mechanism to this is still unknown.^[24] Specifically, H. frisingense was shown to upregulate ethylene receptors and repress ethylene response factors, overall leading to an increase in root growth.^[24] Additionally, H. frisingense is known to produce indoleacetic acid (IAA),^[25] and was also shown to manage IAA genes, indicating that there is an intricate balance maintained between ethylene and IAA by H. frisingense.^[24]

Diversity

Endophytic species are very diverse; only a small minority of existing endophytes have been characterized.^[26][27] Many endophytes are in the phyla Basidiomycota and Ascomycota. Endophytic fungi may be from Hypocreales and Xylariales of the Sordariomycetes (Pyrenomycetes) class or from the class of Loculoascomycetes.^[28] One group of fungal endophytes are the arbuscular mycorrhizal fungi involving biotrophic Glomeromycota associated with various plant species.^[29] As often with other organisms associated with plants such as mycorrhizal fungus, endophytes gain carbon from their association with the plant host. Bacterial endophytes are polyphyletic, belonging to broad range of taxa, including α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Firmicutes, Actinobacteria.^[30]

One or more endophytic organisms are found in nearly every land plant.^[31] It is suggested that areas of high plant diversity such as tropical rainforests may also contain the highest diversity of endophytic organisms that possess novel and diverse chemical metabolites.^[32] It has been estimated that there could be approximately 1 million endophytic fungi that exist in the world.^[32]

A diazotrophic bacterium isolated in lodgepole pines (Pinus contorta) in British Columbia, Canada, is Paenibacillus polymyxa, which may help its host by fixing nitrogen.^{[33][34][35][36][37][38]}

Classification

Endophytes include a wide variety of microorganisms including fungi, bacteria and viruses. There are two different means of classifying endophytes.

Systemic and non-systemic

The first method divides endophytes into two categories: systemic (true) and nonsystemic (transient). These categories are based on the endophyte's genetics, biology, and mechanism of transmission from host to host.^[39] Systemic endophytes are defined as organisms that live within plant tissues for the entirety of its life cycle and participate in a symbiotic relationship without causing disease or harm to the plant at any point. Additionally, systemic endophytes concentrations and diversity do not change in a host with changing environmental conditions.^[39] Non-systemic or transient endophytes on the other hand vary in number and diversity within their plant hosts under changing environmental conditions. Non-systemic endophytes have also been shown to become pathogenic to their host plants under stressful or resource limited growing conditions.^[39] An example of this would be Colletotrichum fioriniae, which is an endophyte of many temperate broadleaved trees and shrubs, but can also be a pathogen on many fruits and some leaves.^[40][41]

Clavicipitaceous and non-clavicipitaceous

The second method divides fungal endophytes into four groups based on taxonomy and six other criteria: host range, host tissues colonized, in planta colonization, in planta biodiversity, mode of transmission and fitness benefits.^[42] These four groups are divided into clavicipitaceous endophytes (Class 1) and non-clavicipitaceous endophytes (Class 2, 3, and 4).

Class 1 endophytes are all phylogenetically related and proliferate within cool and warm season grasses. They typically colonize plant shoots where they form a systemic intercellular infection. Class 1 endophytes are mainly transmitted from host to host by vertical transmission, in which maternal plants pass fungi on to their offspring through seeds. Class 1 endophytes can further be divided into Types I, II and III. Among these three types of clavicipitaceous endophytes are different interactions with their plant hosts. These interaction range from pathogenic to symbiotic and symptomatic to asymptomatic. Type III clavicipitaceous endophytes grow within their plant host without manifesting symptoms of disease or harming their host. Class 1 endophytes typically confer benefits on their plant host such as improving plant biomass, increasing drought tolerance and increasing the production of chemicals that are toxic and unappetizing to animals, thereby decreasing herbivory. These benefits can vary depending on the host and environmental conditions.^[42]

Non-clavicipitaceous endophytes represent a

A strain of endophytic fungi which appeared to be closely related to Nigrograna mackinnonii which was isolated from a stem of the plant Guazuma ulmifolia collected in Ecuador was found to produce a variety of volatile organic compounds including terpenes and odd chain polyenes. The polyenes isolated from the fungus have properties that are sought in gasoline-surrogate biofuels.^[54]

Phytoremediation

Plants are potentially able to break down or sequester, or stimulate micro-organisms in the soil to break down or sequester, certain organic pollutants and inorganic pollutants such as

Two strains of the endophytic fungi Pestalotiopsis microspora isolated from stems of plants from the Ecuadorian rainforest were shown in laboratory experiments to be able to digest polyurethane plastic as the fungus's sole carbon source in anaerobic conditions, although many other non-endophytic fungi have demonstrated this ability, and most isolates of endophytic fungi in this experiment could perform this to some degree.^[56]

Drug discovery

Endophytes produce a wide variety of

A well known example of the discovery of chemicals derived from endophytic fungi is from the fungus Taxomyces andreanae isolated from the pacific yew Taxus brevifolia. T. andreanae produces paclitaxel, also known as taxol. This drug is important for the treatment of cancer. Other endophytes since have been discovered that also produce paclitaxel in other host species, but to date there has been no successful industrial source of paclitaxel created.^[62]

Endophytes have been discovered with various anti-tumor properties. Endophytic fungi produce many secondary compounds such as alkaloids, triterpenes and steroids which have been shown to have anti-tumor effects.^[59] The alkaloid beauvericin has been isolated from the fungus Fusarium oxysporum and has shown cytotoxicity against the tumor cells PC3, PANC-1, and A549.^[64][65] Two fusarubin derivatives: anhydrofusarubin and methyl ether of fusarubin were isolated from endophytic fungus Cladosporium sp. and have shown cytotoxicity against human leukemia (K-562).^[59] Three triterpenes were found in the endophyte Xylarialean sp., all three of these compounds displayed mild cytotoxic effects on tumor cells.^[65]

Some of the antimicrobial compounds produced by endophytic fungi are of interest in their effectiveness against pathogens which have developed resistances to antibiotics. Different fractions of