Plant Endophyte Research Center

Plant endophytes represent natural solutions to some of the greatest challenges facing agriculture. Overlooked for much of the last century, scientists and industry are quickly turning to biology once again to feed a growing population while protecting the environment. The study of the applied use of these organisms is only in its infancy.

Biostimulant research has really only started to gain attention within the last 20 years, but continues to grow as the need for and interest increases.



Global population growth is predicted to reach 9.5 billion by 2050, and feeding it is one of the greatest challenges facing society. Additionally, developing nations such as China and India will likely continue to expand their economies, creating wealth and higher purchasing power for many. This will result in increased materials consumption and a higher demand for meat, dairy, fish and vegetables, all of which will add pressure to the food system. Meanwhile, greater competition for land, water and energy will continue to stretch an already over-extended environment. To address these issues, humanity must simultaneously increase food production and environmental sustainability. Because these two goals have historically been mutually exclusive, we must radically rethink food production.

Agriculture was first “invented” in the Middle East approximately 15,000 years ago. For the first 14,900 years, the importance of soil health and biodiversity was common knowledge. While farmers did not realize it, they were encouraging growth and diversity of beneficial microorganisms in the soil. In the early part of the 20th century came the realization that we could mass produce chemical fertilizers and pesticides, apply them to fields and base breeding programs on higher inputs with significant success. In the early 1960s, at the beginning of the Green Revolution, it was predicted that world food production would not keep pace with population growth. The term “population bomb” was often used in literature. However, the authors did not take into account dramatic increases in food production per acre over the next 40 years driven by advances in breeding programs, increased utilization of agrochemicals and mechanization of farming operations.

Today we know the gains seen during the Green Revolution are diminishing. Plus, due to the real or perceived adverse effects of agrochemicals and genetically modified organisms (GMOs) on human health and the environment, their application is increasingly discouraged in favor of organic production practices. Therein lies the dilemma facing agriculture today, stagnating increases in yield per acre and increasing human discontent for applied chemical fertilizers, pesticides and GMOs. As a result, humanity must once again turn to biology to double agricultural production per acre, the amount it will take to feed the population in 2050.


Endophytes are microorganisms that live in plant tissue and cause no harm. In some cases, they can be very beneficial, acting as biostimulants or plant probiotics to increase plant health, deter disease and supply nutrients. Plants give these microorganisms a place to grow and thrive, and in turn, the bacteria provides what plants need to be healthy and successful in a harsh and unforgiving environment. At the most basic level, endophytes produce plant growth hormones when times are good, they provide nutrients in challenging environments and they even help plants deal with stress in multiple ways. On a deeper level, they have been found to control plant gene expression, serve as a communication system from one plant to another and act as an integral part of a plant’s immune system. As these interactions are both complex and multifaceted, the understanding of them and how they may improve agriculture is only beginning to evolve.

Biocontrol Agents

In the past few years, the “Agtech Boom” has focused on technology-based agricultural research and development among universities and industry. According to TechCrunch, investment in agtech tripled from 2016 to 2017, with a primary focus on early stage biological technologies. The market for commercial biofertility inoculants and biocontrol agents was more than $1 billion in 2012 and is expected to grow to over $7 billion by 2019, according to Transparency Market Research. By 2030, sales of biocontrol agents are expected to surpass chemical sales, currently valued at $48 billion.

Aside from consumer demand for safer and more sustainable food, biocontrol agents are also gaining in popularity due to the low cost of entry into the market. A new agent may be introduced to store shelves in less than two years and for less than $10 million, according to AgFunder News. Biocontrol agents also enjoy a regulatory advantage over chemicals. Many regulatory hurdles are waived altogether with the EPA’s recognition of the status “derived from natural materials.”

Plant Endophyte Research Center Figure 1

Simultaneously, chemical product research and development and product launches are falling (Figure 1), and giants like Dow, Monsanto and DuPont face a dilemma when it comes to entering the biocontrol agent market. These companies historically generated profit by synthesizing and patenting chemical structures. This approach is costly and carries with it the price tag of nearly $300 million to bring a new product to market, according to AgFunder News.  However, the payoff is big and long term, netting a significant return on investment. Biocontrol agents, on the other hand, are more difficult to patent, are less robust in nature due to the development of resistance, and are much more difficult to package. Biocontrol agents are also complex and can change over time, resulting in uncertainty. Uncertainty equals risk, and this risk is inhibitive when it comes to investing in product development. IALR’s Plant Endophyte Research Center has the chance to become a leader to fill this void, promoting cross-fertilization to strengthen pipelines.

Advanced Phenotyping

IALR’s Plant Endophyte Research Center focuses on beneficial bacteria that live inside plant tissues. Although great effort has recently been directed toward endophytes, the field of study is relatively new and much is to be learned, including plant species and cultivar specificity, complex genetic regulation of beneficial traits, protective compounds they produce, their interactions with plant genomics and their importance in plant breeding programs. Endophytes also represent a rich source of biologically active metabolites that find wide-ranging applications from natural agrochemicals to antibiotics. To take advantage of this untapped reservoir of beneficial organisms and byproducts, IALR scientists are currently focused on isolating bacteria from plants in the Blue Ridge Mountain Region. This region, one of the world’s oldest mountain ranges, is characterized by immense ecological diversity. Once isolated and purified, collected endophytes are then screened for promising agricultural traits such as IAA hormone production, ACC deaminase activity, nitrogen fixation, phosphate solubilization and antimicrobial activities. The most promising candidates are screened for growth promotion, drought resistance and disease inhibiting characteristics.

In addition to building the endophyte library, IALR is leveraging technology to measure the beneficial effects of endophytes. IALR’s robotic SMART tables are highly precise modified computer numerical control (CNC) gantry robots. Equipped with high-definition cameras, they are ideal for testing the effects of various biofertilizers on plant growth and health. Designed for high throughput screening, the tables have the potential to test hundreds of plants at once, primarily during their first month of growth. The images collected are then analyzed using pixel analysis to gain a reliable estimate of plant size. Additional equipment such as NIR meters and CO2 analyzers can also be used to get estimates of plant health.

 IALR’s precision agriculture program features the AgBot drone from Aerial Technology International, a phenotyping platform capable of precisely measuring and evaluating plant performance in the field. The unmanned aerial vehicle is fully autonomous and equipped with both multispectral and thermal cameras to monitor plant growth and health from the sky. The data collected is geotagged, allowing multiple layers to be combined to get a better estimate of plant health over time.

Plant Endophyte Library

IALR’s plant endophyte, or beneficial bacteria, library now totals 2,000 characterized endophytes and continues to grow. Endophytes are microorganisms that live in plant tissue and cause no harm. In some cases, they can be very beneficial, acting as biostimulants or plant probiotics to increase plant health, deter disease and supply nutrients. Plants give these microorganisms a place to grow and thrive, and in turn, the bacteria provides what plants need to be healthy and successful in a harsh and unforgiving environment.

Years of experience have allowed IALR scientists to hone collection practices from plant to plate. Some highlights regarding the program include:

  • The collection includes more than 2,000 strains.
  • Initiated an industry/producer driven targeted pest testing program using endophytes that produce antimicrobial compounds to fight strawberry, tobacco, grapevine and pepper diseases.
  • Developed targeted characterization steps focused on nutrient uptake and acquisition.

Collaboration Opportunities:

  • Provide a Pathway to Commercialization for Partners – IALR will work with university researchers to develop or validate potential microbial inoculants.
  • Grant Development with University Partners to Support the Initiative – Building on past research, IALR will continually seek partnerships for grant development leveraging its facilities and expertise.
  • Providing Testing Services for Industry – IALR may act as an independent laboratory to test and verify the effectiveness of microbial inoculants, IALR will partner with industry and growers to provide field trial services for validation of inoculants or to test promising crops and or inoculants, and IALR can provide a mid-Atlantic field trial location for companies to test their products or crops.
  • Developing Products – Once promising strains are identified, they can be marketed for licensing agreements; co-licensing agreements may be available to gain more knowledge of promising strains through genomics, etc.; and co-development/proof of concept testing may be conducted in the lab, greenhouse or field.