Cracking Soil’s Microbiome: Biopesticides and Plant Biostimulants

Cracking Soil’s Microbiome: Biopesticides and Plant Biostimulants

March 28, 2017SCP-M03-17-NI-001
Speciality Chemicals, March 2017

Nigel Walker, of That's Nice LLC/Nice Insight explains how new research into plant microbiome has led to increased potency of biopesticides and plant biostimulants, giving rise to new companies with novel biological approaches to increasing crop yields. 

Harnessing the Microbiome

The human population is expected to swell to 11 billion by 2100%.1 How the global food supply will meet this forecast in a sustainable way has led researchers to think past synthetic fertilizers and pesticides to more environmentally sound biopesticides and plant biostimulants. For years — since the 1920s, actually — farmers have used Bacillus thuringiensis (Bt), a species of bacteria that paralyses the digestive tract of insects by producing crystal proteins called +-endotoxins, as a natural pesticide. This biopesticide was so effective that scientists genetically engineered a species of corn (Bt corn) to produce the crystal proteins on its own.

But Bt is only one species of bacteria in a plant microbiome that is increasingly known to be region-specific and diverse. A single leaf can contain thousands of different species of bacteria, and the root system of a plant can contain two to ten times that variety. That is to say nothing of the complex fungal networks that have been known to be protective against drought, and are essential for the plants’ well-being, acting as living conduits for the transmission of water and essential minerals (and perhaps also organic compounds) not only between the plants and fungi but from plant to plant. The latest research on the plant microbiome has shown divergent microbiota populations in cropland separated by what previously were considered insignificant differences, such as elevation changes of 3,500 feet.2

Biopesticides and Biostimulants

The by-products of biopesticides and plant biostimulants are known to be anti-pest and/or promote plant growth. Microbial biopesticides and plant biostimulants can include three different kingdoms of microorganisms  the single-celled eukaryotes, fungi and related organisms, and prokaryotes  as well as viruses. The diversity and interconnectedness in the way that these three kingdoms interact with plants and animals are largely unknown, as is the microbiome of the soil. Even in the small landmass of New York’s Central Park, over 80% of the microbes have yet to be identified.3

In an agricultural sector historically dominated by six giant seed and chemical companies, 2015 was a strange year. 499 agricultural technology companies raised USD $4.6 billion in investments, doubling 2014 numbers, making the industry almost unrecognizable from $500 million invested in 2012.4 Some of these investments were joint ventures between smaller start-ups and bigger, established firms. An example of one such dual-venture is Monsanto and Novozymes’ partnership, which is in the process of sequencing and testing 2,000 bacteria isolated from soils around the world in hopes of finding “the next Bt.”

A company with a similar approach is Agbiome, which is unusual for an agrochemical company in that it is partially supported through grants awarded by the Bill and Melinda Gates foundation. Agbiome describes Howler as a “living microbe” fungicide that has been shown to be comparable to its synthetic chemical competitor, which is a substantial claim for a biopesticide since they are historically known to be less effective than their chemical counterparts. Agbiome also has an extensive network of field-sampling partners that have sequenced 26,000 (and counting) unique strains of crop-associated microbes, a proprietary library that will be used to discover new biologics and trait genes.7

It Just… Works!

Although these types of ventures will certainly bring to fruition species of bacteria and microbes that have anti-pest attributes, as well as others (and or the same) that will have stimulatory effects on plant growth, ultimately the isolation of a particular species may be shortsighted. The complex interactions between microbes in surprisingly different microbiomes may hold the key to improving crop yields and protecting against disease. The latest research in the plant microbiome is finding striking similarities between plants and humans.

One example of a mechanistic similarity between plant and human microbiomes is the faecal transplant procedure in humans and the idea of ‘community-steering’ in agricultural. Faecal transplants work by taking a stool sample of a ‘healthy patient’, mixing it with saline, and then spraying the length of the recipient's colon, via a colonoscopy, with the prepared solution. According to a New York Times article published in July of last year, the results of the procedure are profound. Clostridium difficile colitis, a complication of antibiotic therapy, has a reoccurrence of 20-60% of patients after initial episode but, following faecal transplant, 90% of patients were free of recurrence.

The most interesting aspect of this procedure is that even the leading doctors in the field are uncertain as to exactly how the treatment works. This is not surprising considering that a gram of fecal matter contains perhaps “100 billion bacteria, 100 million viruses and a million spores of fungi.” The leading theory is that competition for space and resources creates a delicate balance in which the good microbes use up the resources, thereby starving the bad microbes. Another theory is that the transduction of bile acid, which many good bacteria feed of, may be the reason for the effectiveness of the treatment. Possibly there is not one right answer but instead an amalgamation of dynamic factors.5


A paper published in July of 2016 in Nature Plants found a similar procedure to be true of crops. The group tested the possibility of community steering through application of soil inocula in the field by analyzing a large-scale, well-replicated, soil inoculation experiment on soils that had been used for arable farming for several decades. The term "community steering" is arguably the most revelatory. The group hypothesized that transplanting soil from one type of land into an entirely different type of land (if the recipient soil has limited fertility being that it has been “used for arable farming for several decades”) could transform recipient soil into soil that more resembles the donor. And in fact, their findings supported the hypothesis. The group found that not only did soil inoculation promote community development of the land, reinvigorating fertility, but that the land was in fact steered toward the plant and soil community of the respective donor.6

Essentially, crop-steering is harnessing the power of the microbiota in the microbiome to do whatever it is they’re doing. Investments in soil and crop technology startups increased 290% in the first half of 2016,with Indigo and PivotBio, two companies that are founded exclusively on accumulating knowledge about the microbiome to produce biopesticides and plant biostimulants, receiving a bulk of that funding. PivotBio is a firm that specializes in using knowledge of specific soil microbiome to improve the productivity of crops through improved nutrient delivery as well as providing protection against pests, specifically dealing microbes associated with corn.

More is known of Indigo Agriculture, which uses the knowledge they have obtained by sequencing over 40,000 microbes to create seed-coatings that will, according to their claims, help plant growth and provide protection against pests. Their website features a section titled ‘Harnessing Nature’ in which they attribute the inspiration for their hypothesis (that microbes living inside that plant are vital to the plant's health) from insights into the human microbiome.


Perhaps the movement toward biopesticides and plant biostimulants that harness the microbiome will follow a similar trajectory as the pharmaceutical sector’s cellular and gene therapy markets, in that it will be a more (to anthropomorphize the word) ‘personal’ approach to treatment. The future might see crop protection and stimulation that begins with sequencing the microbiome of a specific cropland followed by an individual approach to aid. This could mean anything from a unique coating on the seeds that infuse crops with specific bacteria, viruses, fungi, or other multicellular microorganisms (or perhaps a heterogeneous population of any of the above), to a kind of community steering that follows nature’s lead.

Ultimately, the shift in both the healthcare and agricultural sectors is a humble one for humanity, one that comes to grips with the fact that what we have been able to isolate and produce artificially cannot compare to understanding the complexity that nature has cultivated over the last 4 billion years of life. Still, it will be many more years before we know enough about the makeup of a diverse and varied microbiome in order to make biopesticides and plant biostimulants that are comparable to synthetic, chemical pesticides and fertilizers.


  1. Smith, Robin A. "Disentangling the Plant Microbiome." Duke Today. July 12, 2016. Accessed January 28, 2017.

  2.  Sacks, Oliver. Oaxaca Journal (New York: Random House, 2002), p. 55. Print.

  3.  Arnold, Carrie. "Soil Has a Microbiome, Too." Smithsonian. Web. August 11, 2016. Accessed January 28, 2017.

  4.  Pollack, Andrew. “Agriculture Start-Ups Get Boost From Big Firms and Investors.” The New York Times. Web. May 4, 2016.

  5. Zimmer, Carl. “Fecal Transplants Can Be Life-Saving, but How?” The New York Times. Web. July 15, 2016.

  6. Wubs, E. R. Jasper, Wim H. Van Der Putten, Machiel Bosch, and T. Martijn Bezemer. "Soil inoculation steers restoration of terrestrial ecosystems." Nature Plants 2 (July 11, 2016). doi:10.1038/nplants.2016.107.

  7.  Burwood-Taylor, Louisa. “Where Are They Now? AgBiome, One-Year On From Series B, Nears First Product Launch.” Agfunder News. Web. August 31, 2016


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