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Endophytes and Our Gardens

Endophytes are the living organisms, either bacteria or fungi (rarely viruses), that live between the living plant cells. They establish a symbiotic association with the plants without transmitting any disease. Endophytes are known to be present in many plants that have been studied and have been found to enhance the plant’s ability to tolerate abiotic stresses and resistance to pathogens, disease, and insect pest attacks.

Table of Contents

Classification of Endophytes

Endophytes are classified into two groups depending upon the physiology and functioning nature. 

Systematic and Non-Systematic Endophytes

Systematic Endophytes (SE)

  • The organisms live within the plant tissues throughout their life cycle and do not harm their host.
  • SE do not change their host for the entirety of their life cycle i.e., their diversity and concentration would not change.                         

Non-Systematic Endophytes (NSE)

  • Non-Systematic endophytes are the organisms that live within the plant tissues as far as the host is providing enough food.
  • NSE harm their host under resource-limited or undesirable conditions, i.e., become pathogenic endophytes.

 Clavicipitaceous and Non-Clavicipitaceous

 Clavicipitaceous Endophytes

  • These endophytes live and proliferate in cool and warm-season grasses.
  • They develop varied relationships with the plants ranging from pathogenic to symbiotic.
  • Improve plant biomass
  • Improve drought-tolerance
  • Decrease herbivory (release toxic chemicals that make plants un-appetizing for the predators).
  • Do not cause any disease/harm to the host

Non-Clavicipitaceous Endophytes

  • These endophytes are typically Ascomycota fungi and can live either dependent upon the host plant or independently.
  • They are adapted to colonize both the below ground, above-ground plant tissues.
  • Develop resistance against habitat-specific stresses such as salinity, temperature, and pH, etc.
  • These endophytes have been the most widely researched organisms due to the unusual benefits that they provide to their host plants.

Advantages and Applications of Endophytes

Endophytes are an essential component of Integrated Pest Management due to their eco-friendly nature. They protect plant commodities, inhibit pest attacks, and do no harm to the soil and environment. For example, inoculation of Acromonium Lolli and Acromonium in grass species of Lolium perenne and Festuca is commercially available, giving the grasses tolerance against foliar lawn pests (chinch bugs, armyworms, webworms, etc.).

Endophytes have become a primary concern of all plant-development-related research. Endophytes play an essential role in improving plant yield, combating stresses, inhibiting disease and pest attack through nitrogen fixation, inheriting resistance, and through alkaloid productions, respectively.


Phytoremediation through endophytes is the use of plant-microbe interaction to remediate polluted oil, water, and the atmosphere. 

Phytoremediation of Crude-oil contaminated soils:

Two endophytic bacteria, “Pseudomonas aeruginosa strain BRRI 54 and Acinetobacter strain BRSI 56,” have been inoculated into the two types of grass “Leptochloa fusca and Brachiaria mutica.” The metabolic activity and colonization patterns of endophytic bacteria enhanced the plant growth and the degradation of crude oil for remediating the vegetated soils. Research results showed that the maximum crude oil degradation was achieved through B. mutica compared with the L. fusca. The use of these grasses in lawns and gardens not only absorbs heavy metals from the soil but also filters polluted air through phytoextraction and phyto-absorption. (Fatima, Imran, Amin, Khan, & Afzal, 2016)

Remediation of Saline Soils:

Bioaugmentation of endophytic strains in Helianthus annuus has been studied for its reclamation of saline and Ni-affected soil properties. “P. libanensis TR1arbuscular mycorrhizal fungi, and Claroideoglomus BEG2210″ are the bacterial strains that were used. The results showed improved plant growth, improved nickel-sodium accumulation potential, and better physiological status. (Ma, Rajkumar, Oliveira, Zhang, & Freitas, 2019)


Modern agriculture aims at producing better quality crops both in yield and nutrition. 

  • In New Zealand, the attack of Argentine stem weevil on ryegrass has been controlled through the insertion of AR1 and AR37 strains of endophytic bacteria. The additional advantage of this association is that the grass does remain palatable for the livestock. (Fletcher, 1999)
  • The use of living organisms to control and suppress the pest population, diseases, and plant growth is a successful effort towards sustainable agriculture . Bio-inoculated varieties of grasses (ryegrass, Festuca grass species, etc.), evergreen trees (poplar tree) have been introduced in agriculture and forestry to bring innovation in overall agriculture. (Jain & Pundir, 2017)
  • The alarming use of insecticides and pesticides in controlling common garden pests has become a major concern among environmentalists. Because the damage these chemicals are causing to the soil, air, and ecosystem is drastic. In this situation, the introduction of various endophytes having insecticidal properties proved to be efficient. For example, Indole Diterpenes (Insecticide effective against Blowfly weevil), known as nodulisporic acid, is present in wild olive. 

Medicinal Properties:

Bioprospecting has uncovered natural products derived from endophytes. These have anti-parasitic, antimicrobial, insulin, neuro-protective, immune-suppressant, and cytotoxic, and antibiotic properties. (Egan et al., 2016)

  • The alkaloid “Beauvericin” has cytotoxic action against tumor cells found and harvested from the fungus F. oxysporum.
  • “Pestalotiopsis” has resistance against multi-drug resistant tuberculosis Staphylococcus aureus and many other antimicrobial effects.

Plant use Endophytic Fungi in Defense:

Endophytic fungi develop a symbiotic relationship with plants and help to activate the plant’s defense mechanism against herbivores. Endophytes improve the nutrient uptake capability of plants through secondary metabolite production. This alteration in chemical composition aids in discouraging herbivory and non-herbivory damage. (Mengistu, 2020)

Herbivory prevention:

The plants bearing endophytic association are less likely to be damaged by the substantial herbivores. Endophytes control invertebrate and vertebrate herbivores through reduced reproductive rate, avoidance, reduced feeding, and decreased immunity. (Bamisile, Dash, Akutse, Keppanan, & Wang, 2018)

Disadvantages of Endophytes to livestock:

Resistance to fungal infections caused by herbivores provides an environmentally sustainable alternative against pesticides. The result was beneficial for the plants but not for the livestock. The endophytic defense chemicals have reported decreasing pregnancy rates and increased birth issues in livestock, especially in cows. The use of endophytes in the enhancement of yield must be considered before their application. (Gundel, Pérez, Helander, & Saikkonen, 2013)

Q: what plants have endophytes?

A: Endophytes have been found in few evergreen trees and most grass species such as ryegrass, fescue grass, etc. However, the presence in all kinds of plants has not been reported yet. 

Q: Are endophytes harmful?

A: Not all endophytes are harmful, and not all are beneficial. Scientists have characterized the beneficial endophytes as “selective or animal-friendly.”

Q: How do plants obtain endophytes?

A: Endophytes are transmitted through three ways: 1) Vertical Transmission: through infected plant’s seeds. 2) Horizontal transmission: i.e., through sexual spores of infected plants. 3) Mixture of vertical and horizontal life cycles.

Q: What are endophytic algae?

A: Endophytic algae are microscopic organisms that live inside macroscopic seaweeds. For example, Ulvella leptochaeta is an endophytic algae known to enhance its host’s immunity against several diseases. 

Q: Describe the role of endophytes in plants?

 A: Endophytes develop a symbiotic association with their host plants, i.e., they obtain food and shelter from the plants and, in response, develop immunity against pathogens, insects, and diseases and enhance their growth and development.

Q: Are endophytes harmful?

A: Endophytes in fodder are harmful to livestock. However, the native grass species and those that develop without symbiotic association with the beneficial endophytes are not harmful to the plants.

Q: What are bacterial endophytes?

A: Endophytes are the microbial symbionts that live within the plants. They develop tolerance in plants against the abiotic stresses and are responsible for the development of healthy plants. When the plant is healthy, diseases will not attack.


Bamisile, B. S., Dash, C. K., Akutse, K. S., Keppanan, R., & Wang, L. (2018). Fungal endophytes: beyond herbivore management. Frontiers in microbiology, 9, 544.

Egan, J. M., Kaur, A., Raja, H. A., Kellogg, J. J., Oberlies, N. H., & Cech, N. B. (2016). Antimicrobial fungal endophytes from the botanical medicine goldenseal (Hydrastis Canadensis). Phytochemistry Letters, 17, 219-225.

Fatima, K., Imran, A., Amin, I., Khan, Q., & Afzal, M. (2016). Plant species affect colonization patterns and metabolic activity of associated endophytes during phytoremediation of crude oil-contaminated soil. Environmental science and pollution research, 23(7), 6188-6196.

Fletcher, L. (1999). “Non-toxic” endophytes in ryegrass and their effect on livestock health and production. NZGA: Research and Practice Series, 7, 133-139.

Gundel, P. E., Pérez, L. I., Helander, M., & Saikkonen, K. (2013). Symbiotically modified organisms: non-toxic fungal endophytes in grasses. Trends in plant science, 18(8), 420-427.

Jain, P., & Pundir, R. K. (2017). Potential role of endophytes in sustainable agriculture-recent developments and future prospects. Endophytes: biology and biotechnology, 145-169.

Ma, Y., Rajkumar, M., Oliveira, R. S., Zhang, C., & Freitas, H. (2019). Potential of plant beneficial bacteria and arbuscular mycorrhizal fungi in phytoremediation of metal-contaminated saline soils. Journal of hazardous materials, 379, 120813.

Mengistu, A. A. (2020). Endophytes: Colonization, behaviour, and their role in defense mechanism. International Journal of Microbiology, 2020.