Micronutrients from volcanic ash influence the tomato root microbiome and fruit production

Rajnish Khanna
9 min readApr 2, 2022


Rajnish Khanna, Ph.D., Brigid McNally, M.A., Elijah C. Mehlferber, Ph.D. Candidate, Kent F. McCue, Ph.D., Britt Koskella, Ph.D., Jon E. Ferrel, M.S., M.B.A.

Figure 1: Model depicting the predicted impact of Azomite treatment on biochemical composition in the roots leading to changes in root-associated bacterial community structure. Drawing by E. Mehlferber.

Key Words: Soil health, volcanic ash, microbiome, micronutrients, tomato

FOREWORD by Rajnish Khanna, Founder & CEO, i-Cultiver

Why is it important to examine how soil amendments effect soil and plant associated microbial communities?

Microbes play essential roles in nutrient cycles and in sustaining soil and plant health. Many types of soil treatments are commercially available and are routinely applied randomly without knowledge of their impacts on soil and plant health. There have been significant technical advances in our abilities to analyze the effects of these treatments on microbiota associated with soils and crops, but these tools are not yet easily accessible to the majority of agricultural industry. It is relatively easier to measure physical parameters, such as pH, moisture and nutrient (N, P, K content), etc. It is not surprising that increasingly, new companies are being established to offer different types of sensors and extended abilities to capture limited chemical, physical and environmental data, followed by advise on how to manage soils and crop treatments. While these are efforts in the desired direction, mostly the data interpretation is poorly managed and often skewed towards monetization.

Soil and crop relationships are complex and dynamic. Soil is often treated as a physical system, which it is not. Interpretation and making sense of such data is an important next step, and it must take into account the health of microbial communities and plants, which will then naturally ensure soil health. Along the same line of thought, obtaining a list of bacterial or fungal strains present in the soil is not sufficient without a robust ability to interpret the data. It is still too early in our understanding to deploy systems (data mining or “Artificial Intelligence”) based approaches to make conclusions, but there are companies that offer such services as well. When it comes to microbial functions, the vast majority are still unknown and any treatments with known bacterial strains must include the ability to assess whether those bacteria survive in the treated environments. There is a need for independent assessment of data in the industry, along with stronger ties within academic and industry efforts to achieve measurable goals. The work described here is designed to advance the understanding of how commercially available amendments such as Azomite may act in modifying the extraordinary soil and plant-associated biomes.

Azomite, volcanic ash fertilizer selectively modifies tomato associated microbiome

Commercially available fertilizer, AZOMITE® (name derived from “A to Z Of Minerals Including Trace Elements”) is a surface-mined, 38-million-year-old volcanic ash deposit. Multiple greenhouse based studies were performed over several years with tomatoes grown with or without Azomite. Treatment with Azomite caused a significant change in the composition of microbes associated with tomato roots (see proposed Model drawn in Figure 1). Azomite was applied as a supplement to the normal fertilizer program to tomato plants grown in the greenhouse. Azomite-treated plants showed a significant increase in fruit production at measured intervals (Figure 2). Azomite significantly increased the total number of tomatoes produced per plant. Future studies will determine the benefits of Azomite with reduced and non-conventional fertilizer programs.

Figure 2: Total number of tomatoes produced per week were counted. Results show that Azomite increased the number of tomatoes produced per plant.

Since Azomite is added to soil, we examined its impact on the composition of below-ground microbial communities. We particularly focused on those bacterial members that were present at higher levels in the plant associated compartments than the surrounding soil, and that were found to be associated with the plant more frequently than we would expect at random. These bacteria, dubbed “core taxa,” suggesting that they were enriched due to some selective process in the soil or by the plant under their respective conditions. We examined the rhizosphere (bacterial community tightly associated to root surface) and root endosphere (bacterial community inside the roots), compared to bulk soil (bacterial communities in the soil). This analysis revealed that Azomite had little effect on bulk soil or rhizosphere microbial composition overall, but it had a temporally (time-dependent) selective influence on the rhizosphere and root associated “core taxa.” Furthermore, changes in the composition of the core taxa could be correlated to a computationally inferred functional pathway enrichment of carbohydrate metabolism (Figure 3), suggesting that there may have been a shift of available microbial carbon sources within the roots. This finding supports the idea that different nutrient inputs can specifically alter the functional capacity of root-associated bacterial taxa, with potential to improve crop productivity.

Figure 3: Computationally inferred functional groups of “core taxa” that were differentially abundant in treated or Control samples. Left panel shows functions that were more abundant in Azomite treated samples and right panel shows functions that were identified as more abundant in Control samples in Rhizosphere* (a) and Root (b) in 8 weeks and 18 weeks as indicated. (*Rhizosphere: Bacteria tightly associated to the surface of roots.)

Based upon these observations, we hypothesize that the treated roots may have relatively higher levels of glucose or related sugar substrates. This change in biochemical composition may act to recruit different bacteria from the surrounding soil. We are continuing to investigate the underlying mechanisms of these changes.

Importance of These Findings

Different types of soil fertilizers are used routinely to increase crop yields globally. Companies frequently use comparative photos of treated and untreated plants to show superior performance or benefits that their products may provide, with little to no understanding of the impact their products may have on the environment, the microbial communities, or the crops. As a commercial endeavor, these practices can be successful in sales and marketing efforts. However, there exists a gap in our understanding of how soil fertilizers act on the plant-associated microbial communities, which have direct and long-lasting consequences on soil health, crop performance, and sustainable productivity for the growers. The underlying mechanisms of nutrient uptake are complex and thus difficult to evaluate fully but have critical influences on both soil and plant health. We developed a systematic approach to analyze the effects of a fertilizer on core microbial communities in soil and plants, yielding predictions that can be tested empirically and used to develop simple and affordable field tests. By focusing on the core bacterial taxa (i.e. those found more often than would be expected by chance within these communities), we were able to specifically look at the subset of the microbiome that is likely recruited by the plant under different environmental conditions. The methods described here can be used for any fertilizer and crop system. Continued effort in advancing our understanding of how fertilizers affect plant and microbe relations is needed to advance scientific understanding and help growers make better-informed decisions.

Globally, our food crops, like tomatoes, are grown with fertilizers containing nitrogen, phosphorus, and potassium (macronutrients), along with micronutrients such as magnesium, calcium, boron, and zinc. Plants, as living organisms absorb inputs as needed and as available in absorbable forms at different ratios throughout their growth. It is well established that certain soil and plant associated microbes are capable of promoting plant growth, stress tolerance, and productivity. However, there is a high degree of variability across agricultural environments, which makes it difficult to assess the possible influences of nutrient fertilizers on soil and plant-associated microbial communities. Recent advances in research have made it possible for us to uncover the underlying mechanisms, which can be used to achieve consistently improved food quality and productivity with minimal environmental impacts from nature based (instead of synthetic) soil inputs.

REFERENCE to Full Text of Published Article (Open Access)

  • Mehlferber, E.C., McCue, K.F., Ferrel, J.E., Koskella, B., Khanna, R. (2022) Temporally Selective Modification of the Tomato Rhizosphere and Root Microbiome by Volcanic Ash Fertilizer Containing Micronutrients. Applied and Environmental Microbiology. DOI:https://doi.org/10.1128/aem.00049-22

Download PDF: https://journals.asm.org/doi/epub/10.1128/aem.00049-22

Watch on YouTube, TerreScience (S1. E5.): Azomite Volcanic Ash Modifies Root Microbiomes | New Research With Jon Ferrel. https://youtu.be/OqzcxVOtXOc

Meet The Authors

Rajnish Khanna, M.Sc. Ph.D.

Rajnish Khanna, M.Sc. Ph.D. is founder and Chief Executive Officer of i-Cultiver, Inc. and Global Food Scholar, Inc., Senior Investigator at Carnegie Science, and Science Advisor at The Chopra Foundation. Rajnish is a strategic biotechnology consultant, plant and soil health scientist applying multidisciplinary approaches for research and development. Known for empowering the industry through strategic partnerships with academic institutions, facilitating technology transfer into real world applications, and deploying advanced technologies such as CLASlite, a unique software to quantify and monitor crop and tree health at global scale for agro-eco projects. Rajnish is creating an innovative online food platform, TerreLocal, to integrate the entire local food supply with local demand. Rajnish is a photobiologist, interested in how information, such as light, is perceived and translated by organisms into biological responses, and underlying mechanisms that may link information to our experience of consciousness. www.rajnishkhanna.com

Brigid McNally, M.A.

Brigid McNally, M.A., Creative Content Developer and Public Relations Consultant with Global Food Scholar, Inc. Brigid is passionate about communication, public education and nutrition. She is the founder and owner of PVX Farms. Brigid is a specialized vertical farmer, known for offering a variety of microgreens and sprouts with longer preserved vigor. Brigid obtained an M.A. in Communication from University of the Pacific, and she is leading the public communication and education effort for TerreLocal, a new online platform developed by Global Food Scholar, Inc.

Elijah C. Mehlferber, Ph.D. Candidate

Elijah C. Mehlferber, Ph.D. Candidate is a 5th year PhD Candidate in Integrative Biology at UC Berkeley who is interested in host-microbiome interactions, focusing on bacteria in the phyllosphere (the above-ground portion of the plant). Broadly, he wants to understand the mechanisms by which certain bacterial communities provide functions for their host, such as growth promotion or disease resistance.

Kent F. McCue, Ph.D.

Kent F. McCue, Ph.D. is a plant metabolic engineer. He has spent the last 35 years elucidating and manipulating metabolic pathways involved in adaptation of plants to biotic and abiotic stress, food safety and nutrition. He has helped develop methods for precision gene expression and molecular breeding. More recently studies have included the effects of nutrition and microbial communities on plant stress and disease resistance.

Britt Koskella, Ph.D.

Britt Koskella, Ph.D. is an Associate Professor at the University of California, Berkeley. She is an evolutionary ecologist interested in the role that microbial interactions play in shaping the host-associated microbiome. Using a combination of experimental approaches from in vitro to in vivo and observational field studies, her research program seeks to unravel the dynamic ecological and evolutionary relationships between hosts, symbionts and their pathogens. By focusing on how plant-associated microbiomes assemble, interact, and impact host phenotype, her goal is to leverage these interactions for increased agricultural sustainability. https://naturesmicrocosm.com/

Jon E. Ferrel, M.S., M.B.A.

Jon E. Ferrel, M.S., M.B.A. is the Vice President of Research & Development and Technical Services for Azomite Mineral Products, LLC, Nephi, UT, 84648 as well Adjunct Associate Administrative Professional Staff, Animal Sciences, Purdue University. Jon graduated from Purdue University with a master’s degree in Agricultural Economics, as well as an MBA from Indiana University’s Kelly School of Business. Jon mentors and collaborates with graduate students and faculty at several universities, as a consortium of scientists, focusing on applied nutrition of food animal production and plant sciences. Within his current responsibilities, Jon links aspects of basic and applied research for Azomite amongst animals and plants to the specific mechanisms of action and derived outcomes that support discovery, application, and implementation initiatives. The focus of Jon’s work has included allergenic and innate immune system responses to nutritional components, gene expression, digestibility, and gut architecture. Jon directly relates research findings to estimate the difference in optimal levels of return to management and operator labor under alternative employed technology assumptions through linear, non-linear, and stochastic risk-based statistical modeling.

Contact Rajnish Khanna: raj@i-cultiver.com



Rajnish Khanna

Rajnish Khanna is founder and CEO of i-Cultiver and Global Food Scholar; Senior Investigator at Carnegie Science; Science Advisor at The Chopra Foundation.