For many years, the mention of microbes or bacteria elicited responses of “EWWW!”
More recently, we have broadened our understanding to realize that microbes can be beneficial to us, especially in food production, and, in fact, they can enhance sustainability in agriculture.
To dive deeper, we questioned Jane Fife, PhD and CTO for 3BarBio, about changing attitudes toward microbes, their innovative uses in agriculture, and recent developments in agriculture.
I. PERCEPTION PIVOT
Q: How has the traditional perception of microbes in agriculture shifted over the years, and what prompted this change?
Microbes have been viewed historically as pathogens – agents of disease. Overuse of antibiotics and pesticides to kill pathogens has led to antibiotic resistance of disease-causing microbes in numerous cases.
Q: What are some of the misconceptions about microbes?
Many microbes are actually more helpful than harmful to people and the planet.
Since microbes cannot be seen with the naked eye, it is hard for us to fully understand what they are doing and directly see their benefits.
Q: What is the best way to address those misconceptions?
Instances where the value of microbes can be clearly demonstrated make for great educational opportunities. For example, the increasing use of probiotics (rather than antibiotics) in our own diets has brought a more positive perception of microbes and their contributions to our wellness.
As science has advanced, more tools have been developed to understand microbes and the microbiomes that exist in nature – showing there are a lot more “good” or “neutral” microbes than bad in the environment. High-throughput sequencing and meta-omic (genomic, proteomic, transcriptomic) technologies have been instrumental in revealing microbial diversity and composition to better understand the functional role of the microbiome and deciphering microbe interactions with plants, animals and humans. These recent advancements in meta-omics have shown that the soil microbiome influences “one-health” – soil, plant, animal and human health (Banerjee and van der Heijden 2023).
II. GET THE DIRT ON SOIL
Q: What are some key historical beliefs and practices surrounding the use of microbes in agriculture, and how have they transformed?
Enhancing soil health requires maintaining a fertile and biologically active top layer of soil. Early on, when farmers cultivated a crop in a new area of land, they would transfer productive soils (and the microbes that came along with it) from one field to another to positively affect crop productivity. During the mid-1800s, symbiotic nitrogen fixation was starting to be understood by the presence of nodules on legumes believed to be induced by soil bacteria. In 1888, Rhizobium leguminosarum was first isolated; and by late-1890s, a Rhizobium-based bioinoculant was commercialized named “Nitrogin” (Nobbe and Hiltner, 1896). Evidence of soil microorganisms involved with phosphorous solubilization similarly date back to early 1900s (Kishore et al 2015).
Related to soil health, soil microbial communities can directly influence a multitude of processes occurring in the soil, including nutrient cycling (predominately of nitrogen, phosphorous, sulfur and iron), organic matter dynamics, soil structure, carbon transformations and sequestration. Soil microbe diversity and biological activity are key components of soil health.
Healthy soils are linked to global food and water security, and have important implications for mitigating climate change (Lehmann et al 2020). Degradation of soils has occurred due to land-use changes, erosion, compaction, and fertilizer and pesticide contamination. Agricultural soils are typically more homogenous than natural environments due to lower plant diversity and frequent disturbance. Agricultural practices that have been shown to improve soil health include conservation or no-tillage practices, crop diversification (including use of cover crops), and reductions in mineral fertilizers and synthetic pesticides.
Soil health is a systematic representation of the physical, chemical, and biological functions of the soil – all three act together as a system, and if one is off they can all be off. Typical physical and chemical indicators are well-studied and may be seen (e.g., soil aggregation) or are fairly easily measured (e.g., pH, electrical conductivity). Biological indicators tend to be less well defined (e.g., organic matter). Recent recommendations of more descriptive microbial indices for soil health include measurements such as overall microbial diversity, degree of pathogen occurrence, and presence of specific soil functional groups (Lehmann et al 2020).
III. SOIL HEALTH AS HERO
Q: What scientific discoveries have led to a better understanding of the role of microbes in soil health and plant growth?
Recent advancements in metagenomic analyses (whole genome sequencing) have made it possible to not only understand the complete taxonomic profile of microorganisms in a soil environment, but also reveal novel microbe species and their potential mechanisms involved in plant growth promotion and biocontrol.
Microbial composition differs considerably between the bulk and rhizosphere soil. Plant roots secrete organic compounds (known as root exudates) that recruit certain microbes from the bulk soil to the rhizosphere. Subsequently, the number of microbes present in the rhizosphere is approximately 10- to 100-times higher than that in bulk soil and will vary for different plant species (Vincze et al 2024). Successful root colonization by the bacteria is essential for beneficial effects to be exerted on the plant. The main environmental factors affecting the structure of the rhizosphere microbiome are moisture, temperature, pH, salinity, and nutrient content (C-N ratio and other nutrients). Root exudates are dynamic and change according to plant development, subsequently altering the rhizosphere microbial community and function throughout different plant development stages.
Plant growth promoting rhizobacteria (PGPR) (a term first coined by Dr. Joseph Kloepper during PhD research; Kloepper and Schroth, 1978) colonize plant roots and can contribute significantly to improve plant growth and yield. Rhizobacteria strains of various genera are designated as PGPRs, including Acinetobacter, Aeromonas, Agrobacterium, Allorhizobium, Arthrobacter, Azoarcus, Azorhizobium, Azospirillum, Azotobacter, Bacillus, Bradyrhizobium, Burkholderia, Caulobacter, Chromobacterium, Delftia, Enterobacter, Flavobacterium, Frankia, Gluconacetobacter, Klebsiella, Mesorhizobium, Micrococcus, Paenibacillus, Pantoea, Pseudomonas, Rhizobium, Serratia, Streptomyces, Thiobacillus, and others.
Through a variety of mechanisms, PGPR species can promote plant growth by fixing atmospheric nitrogen, mobilizing soil phosphorous, solubilizing minerals (phosphorous, potassium, zinc, etc), production of siderophores for iron chelation, plant growth hormones (auxins, cytokinins, and gibberellins), enzymes, and volatile compounds. Some PGPRs can also suppress plant diseases by antibiotic production, lytic enzymes, competition, and induction of systemic resistance. Additionally, PGPRs can help plants tolerate abiotic stress by inducing the plant’s systemic tolerance.
In addition to soil rhizobacteria, arbuscular mycorrhizal fungi (AMF) occur naturally in soil environments and widely form root symbiosis with many plant species. AMF form a hyphal network with plant roots that significantly enhances the access of roots to a much larger soil surface area, contributing directly to increased uptake of water and essential nutrients in the bulk soil.
Advanced research for improving plant-microbe interactions and PGPR performance has included various emerging synthetic biology approaches including “microbiome engineering” to create synthetic communities (“syncoms”), genetic engineering of PGPRs to enhance certain functions, and plant genome engineering to enable recruitment of the desired microbiome (Kumar and Dubey 2020; Bano et al 2021; Haskett et al 2021).
IV. BENEFICIAL “BUGS”
Q: How do microbes contribute to improved nutrient availability and uptake by plants, leading to increased crop yields?
The Green Revolution introduced new high-yielding seed varieties and increasing use of synthetic fertilizers, pesticides, and other agrochemicals. Overuse of synthetic agrochemicals (particularly fertilizers) for increasing crop productivity has subsequently deteriorated soil health. Heavy long term use of fertilizers results in acidification and accumulation of harmful substances in the soil, causing a decrease in the fertility of the soil. Between 30-50% or more of total applied fertilizer is lost to the environment through leaching or valorization, leading to increasing water and air pollution.
Biofertilizer use in place of synthetic fertilizers has been viewed as a healthier, more sustainable approach in agricultural production to lessen environmental and health consequences. Biofertilizer products contain living microorganisms (primarily bacteria or fungi)
that convert important nutrients from unavailable to available forms in the soil through biological processes like nitrogen fixation, phosphorus solubilization and mineralization.
Nutrients are required by every living organism on the planet. A total of 17 essential plant nutrients (C, H, O, N, P, K,… ) are needed for proper plant development. Nitrogen is one of the most important nutrients for plant growth and applied heavily (100 million metric tons annually) in crop production. The two main forms used in fertilizers are ammonium (NH4+) and nitrate (NO3–). Nitrate does not adhere to negatively charged soil particles and easily leaches in soil water, becoming unavailable for plants. Through nitrification, ammonium is converted to nitrate via nitrite (NO2–) by soil microorganisms, which can also lead to nitrate leaching and gaseous nitrous oxide (N2O) production. Nitrous oxide is a greenhouse gas 300 times more potent than carbon dioxide. The soil conditions most favorable for nitrification involve neutral soil pH, moisture at 50% water holding capacity, and a soil temperature of 80oF. Application of denitrification inhibitors is a current strategy for reducing nitrogen losses from soil (Beeckman et al 2018).
Biological nitrogen fixation is receiving intense attention to help reduce nitrogen application. Biological nitrogen fixation is an energy expensive process for bacteria, requiring 16 ATP molecules to break down a single N2 molecule. The reaction is catalyzed by the enzyme complex nitrogenase. Nitrogenase is extremely oxygen sensitive and inactivates in aerobic environments. Challenges with biological N-fixation largely stem from the energy expense to the bacteria, coupled with oxygen sensitivity of the bacteria’s nitrogenase complex required for reducing dinitrogen to ammonia. This oxygen sensitivity further complicates energy requirements of the bacteria as energy is most efficiently produced by the bacteria using aerobic respiration in the presence of oxygen (the “oxygen paradox”; Marchal et al 2000).
Phosphorous is another key nutrient used by plants. Historically, phosphorous fertility recommendations have involved a “build and maintain” approach, applying fertilizer at a rate to build soil phosphorous to a critical level and then maintaining that level through application at crop removal rates. Consequently, accumulation of phosphorous has occurred in the soil and has become known as “legacy P”. These legacy P stores are retained in soils in a continuum of phosphorous availabilities, including non-labile forms that must be mobilized into solution by microbial activity in the rhizosphere. Maintaining plant available phosphorous is essential for efficient utilization in cropping systems.
V. SOYBEAN SUCCESSES
Q: What specific examples exist of microbes being used successfully in modern agricultural practices, and how have these instances driven change?
Soybean inoculants were the first generation of microbial products to have a large-scale market, having widespread adoption in Brazil and Argentina during the 1990s. Key to Brazil’s success was intense research dating back to the 1950s and 1960s by the Brazilian Agricultural Research Corporation (EMBRAPA) that led to the identification of four elite Bradyrhizobium strains that were effectively adapted to Brazil’s soil, climate, and soybean genotypes. Today, nearly all soybeans in Brazil are inoculated, limiting the need for nitrogen fertilizer in soybean production.
Widespread adoption of soybean inoculants in Brazil was enabled by strict commercial standards and quality control, ensuring product quality to achieve high levels of performance in the field. From the beginning, Brazil created legislation requiring soybean inoculants to contain minimal concentrations of 109 CFU/mL, purity, shelf-life greater than 6 months, and the absence of biological contaminants at the 10-5 dilution (MAPA, 2011). In addition, in every state, Brazil set up an extension-like system to help growers learn how to use these new products. EMBRAPA has since developed elite Azospirillum brasilense strains, which support nitrogen fixation (not as efficiently as Bradyrhizobium) and plant root growth primarily by producing phytohormones. Elite Azospirillum strains are being co-inoculated with Bradyrhizobium in soybean or as an inoculant for corn.
Soybean inoculation is more common in South America than in the United States. In the United States, only about 15% of farmers use soybean inoculants. Factors that have contributed to less use of soybean inoculants in the United States include planting soybean varieties with limited response to inoculation and limited yield increases in soils with soybean history, due to the established symbiotic bacteria populations in the soil (Graham et al, 2004).
After 2015, the next generation of microbe products including biofertilizers and biofungicides became available, which has driven interest in the biological market in recent years.Nitrogen fixation in corn has been actively researched for several decades. Several new non-symbiotic N-fixing products were recently introduced to the US corn market. Together these new microbial inoculants are impacting several million acres, only a small fraction of the ~90 million acres of corn planted in the United States and ~500 million acres planted worldwide each year.
Success in the field depends on a number of factors, including species compatibility with the environment, the degree of competition with other soil organisms (including macroorganisms and microorganisms), and timing of application.
VI. MICROBE MAGICIANS
Q: How has the adoption of microbial solutions impacted soil structure, water retention, and overall ecosystem health?
Microbial activity in the soil improves soil health by promoting nutrient cycling and soil structure formation. Microbes tend to thrive in a less disturbed environment, where they can effectively break down organic matter, releasing essential nutrients for plant uptake and producing organic compounds that help bind soil particles together.
Microbial activity in the soil is also responsible for carbon sequestration. Microbial carbon use efficiency can promote soil carbon storage to impact reduction in greenhouse gas emissions of carbon dioxide (Tao et al 2023). Microbes use carbon for growth and metabolism. When used for growth, carbon becomes sequestered in microbial cells and ultimately in the soil; and when used for metabolism, carbon is released as a side product in the air as carbon dioxide. Thus, growth of microbes versus metabolism is desired for increasing soil carbon storage.
Q: What role do microbes play in pest and disease management, and how has this influenced the need for reduced chemical interventions?
Overuse of agrochemicals in agriculture has resulted in deterioration of soil fertility and health.Harmful microbes that cause disease can become more rampant when chemicals are overused due to built up resistance to the chemical and loss of biodiversity in the soil. Beneficial microbes can help reduce disease incidence through competition for resources, production of antibiotics and siderophores to lower iron availability for other microbes.
Q: How do microbes foster plant resilience against environmental stresses, such as drought and extreme temperatures?
Microbes can help plants become more resilient to environmental stresses like drought and extreme temperatures throughincreasing nutrient availability, water use efficiency, and enhanced plant growth. Microbes can help plants accumulate more nutrients, like nitrogen and phosphorous, either directly through nitrogen fixation and phosphorous solubilization, or indirectly by increasing root biomass. Microbes can enhance water retention by producing biofilms along the root surface. Microbes also produce phytohormones that promote plant growth and help modulate stress levels in the plant. An intricate “cross-talk” occurs between plants and microbes in the rhizosphere, facilitated by chemical signal molecules produced by the plant in root exudates and secondary metabolites produced by the microbes.
VII. TOMORROW’S TECH TODAY
Q: What advancements in technology have facilitated the widespread application of microbial solutions in agriculture?
Advancements in drying technologies and formulation are leading to improvements in microbial shelf-life and quality for improved product performance in the field. More dry microbial inoculants are being developed and commercialized, with high concentration and longer shelf-lives of one year and greater. Keeping the microbes dormant in a dry state is advantageous as it limits active metabolism and death of the microbes during storage and distribution. Dry formulations also are less expensive to distribute because of lower weight and volume. Active metabolism of microbes in liquid formulations can limit their shelf-life and fitness by the time products are used and are more prone to contamination.
Recent meta-analyses (Barbosa et a 2021, Barbosa et al 2022) of microbial inoculants in Brazil found peat-based inoculants had slightly higher yield responses compared to liquid inoculants. Dry carrier materials can provide protection and nutrients to the microorganisms for survival during application and in the soil environment. Further, application of dry inoculants avoids desiccation loss during application, if the dry carrier can provide a protective environment.
Farmers are more accustomed to working with liquids. In South America, liquid formulations make up over 80% of the market because liquids are easier to produce by industry and easier to use by farmers (Cassan et al 2020). Dry formulations can be delivered as liquids. Revitalization of the microbes in an appropriate liquid solution is recommended prior to use to avoid loss of viability and fitness of the microbes after rehydration.
Technical breakthroughs in delivery of microbial inoculants are just beginning.Making biologicals simpler for farmers to use and more effective in the field is key to these breakthroughs. Planter box additives have become more common as it provides the farmer flexibility for seed treatment. More recently, layering seed lubricants with microbial inoculants is gaining traction. Application of dry microbial products with the seed lubricant is advantageous because it fits with existing practice for seed singulation and avoids microbe desiccation losses typically experienced with liquid seed treatment.
VIII. BATTLE: MICROBES VS. CHEMICALS
Q: Is there a misconception that biologicals/microbes must replace all chemical products, and are there efforts to promote combining the two types of products?
Biologicals won’t replace chemicals, but rather must be integrated using a “systems” approach to increase agricultural productivity in a way that is safer for people and the planet. Microbe products must be evaluated for compatibility with chemical fertilizers and pesticides. Microbes are often applied as a seed treatment or in-furrow with conventional fungicides, insecticides, and/or starter fertilizers. Some chemicals can decrease the viability and performance of the microbe when tank mixed and delivered together. For example, the starter fertilizer 10-34-0 has a salt index of 20, which is too high and causes harm to many microbes. A lower salt index starter fertilizer or diluting 10-34-0 in half has shown better results across a wide range of microbes applied with starter fertilizer.
IX. RESEARCH TO THE RESCUE
Q: How are agribusinesses and researchers collaborating to develop innovative microbial products that cater to diverse farming needs?
Collaboration remains critical for developing new innovative microbial products. Many new microbe technologies are being discovered, largely in research organizations and startups.Advancing new technologies more quickly can be helped by partnering with other organizations through joint development and/or involving contract development and manufacturing organizations (CDMO).
Recently, a big shift in biologicals has come from distributors working with microbe manufacturers to develop new product combinations. Innovation in new formulations and protective packaging that fit farmer practices is leading to increased options and market growth. For example, two new products were introduced into the US market in 2023 using seed lubricants to deliver dry microbial products: BioWakeTM Seed Lubricant (AMVAC, Newport Beach CA) and Hopper ThrottleTM (Meristem Crop Performance, Powell, OH).
X. NATURE LOVE: ORGANICS AND REGENERATIVE
Q: In what ways has the growing interest in organic and regenerative agriculture boosted the adoption of microbial practices?
A growing focus on soil health and increasing biological activity in the soil has also increased interest in, and use of, microbials. Regenerative agriculture aims to restore soil health and biodiversity in the soil through practices such as conservation tillage (e.g., no-tilling), cover crops, application of manures, and reduction in use of chemical fertilizers and pesticides. At a field level, microorganisms’ role in soil fertility and health is crucial for biological activity to break down organic matter and nutrient cycling. At the plant level, application of microbials helps increase plant growth and resilience to support increased biological activity in the soil.
Research on the plant and soil microbiome has led to interest in “microbiome engineering” to modify the microbial communities in the soil to increase effectiveness of microbial inoculants (Nadarajah and Rahman, 2023). Newly introduced microbes must be able to thrive in the environment and maintain a stable community. A major hurdle for effectiveness is the microorganisms’ ability to colonize plant roots in the environment, and very little is known about colonization of microbes in agricultural crops. In the short term, application of microbiome engineering in controlled environment agricultural production would be beneficial.
XI. FUTURE FOCUS
Q: What challenges and barriers still exist in fully embracing microbial-based solutions in agriculture, and how are these being addressed?
Education remains a major barrier to widespread use of microbial-based solutions. Numerous biological products have flooded the market, leading to confusion with growers on what a product is and how it is supposed to be used. Growers must consider the specific needs of each zone in their fields and then seek appropriate biological solutions to meet those needs. For example, a low-producing zone may benefit from addition of a PGPR to enhance plant root growth and abiotic stress mitigation.
Q: How has the evolving perspective on microbes influenced the development of novel ag biologicals, such as biofertilizers and biopesticides?
Biological products are the fastest growing segment in agriculture. There’s genuine interest by growers, trying to better understand what biological products are and how they best work. Interest is being driven by the potential to produce higher yields while building soil health and helping plants be more resilient to abiotic stressors like drought and extreme temperatures.
Q: What does the future hold for the integration of microbes in agriculture, and how might continued innovation shape sustainable farming practices?
Integration of microbes into agriculture will require continued innovation in formulation, distribution, and delivery. A supply chain created for agrochemicals and seed inputs needs to be adapted to better handle living microorganisms. Increased use of dry formulations supports better shelf-life and improved storage and distribution. Bulk concentrates of dry microbes can be stored under refrigerated conditions until needed, then blended with dry carriers and packaged in finished product format. A “smarter” supply chain manages inventories in a more on-demand manner to ensure the most viable microbes are being packaged and delivered to the farmer when needed.
JANE FIFE, PhD, Chief Technical Officer of 3BarBio
Dr. Fife’s research focuses on improving formulation and delivery of biologics for more effective application of beneficial microbes to promote plant growth and biological disease control. Prior to joining 3Bar Biologics, she has more than 15 years of expertise in application technology and agricultural biologics through her leadership role managing technology development in agribusiness at Battelle Memorial Institute. Dr. Fife holds a PhD in Agricultural Engineering from The Ohio State University, where she currently serves as an Adjunct Faculty and teaches courses in engineering design.
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