Soil Microbes in the Spotlight

May 2, 2018 | Sustainable Agriculture |

The Dirt:

The beneficial qualities of soil microbes are enabling farmers to use fewer agricultural inputs and increase yield. This helps them do more with less to provide food for a growing population. And they might just be the best thing for your home garden or lawn. Let’s dig in…

As we have discussed on D2D, farmers face numerous growing challenges that include pest and disease threats as well as regulatory pressure to use less water and less fertilizer. But sometimes these big ag challenges can hit closer to home! Since the spring temperatures are here to stay, we want to make sure your lawn and home garden are flourishing! Are microbes the answer?

Microbes have been around a long time, in fact, we live in their world!  Microbes grow and reproduce in and on your body, in soil and on rocks, within plant roots and on their leaves, in wetlands, oceans and fresh waterways, and even in space!

As consumers, we may be more familiar with the trillions of intestinal bacteria that make up our gut microbiome than soil microbes. The microbes in our gut play a very significant role in the digestion of food, metabolism, inflammation and immune function. Similarly, the billions of microscopic bacteria, algae, fungi, protozoa, nematodes, and earthworms, in soil microbiomes play a vital role in the health of soil and plants. One cup of soil may hold as many bacteria as the gastrointestinal tracts of the 7.2 billion people on earth!

Did you know? Over 500 antibiotics have been cultivated from soil microbes, including penicillin and tetracycline, and streptomycin, all of which are responsible for saving human lives.

Just like the human body, when soil is healthy it is able to absorb and retain water, nutrients and minerals more efficiently. While farmers have always understood that healthy soil leads to a healthier crop, the why and how is only recently becoming better understood thanks to the rapid advances in DNA sequencing technologies.

Video: The Living Soil: How Unseen Microbes Affect the Food We Eat

Microbes can help farmers use less water and less fertilizer

DNA sequencing provides soil scientists with valuable genetic information that helps them to identify and understand the specific roles of microorganisms in the soil microbiome such as how bacteria and fungi interact. For example, ever wonder why plants are able to grow in the desert? With little or no available water, the plant is able to protect itself from heat and drought. The microbial community in and around the roots of that plant are very different from the microbial community surrounding the roots of a plant in an area with plenty of rainfall. By identifying the microorganisms responsible for preserving water and protecting the plant from heat, scientists can then isolate that microbe and apply it to crops in threat of drought conditions.

Harnessing the natural power of microbes, microbe-containing products can be applied to the surface of seeds or the soil itself to complement or provide an alternative to chemical agricultural inputs.

Some examples of beneficial bacteria and fungi:

Nitrogenfixing bacteria help a plant draw nitrogen from the air. Nitrogen is a critical element for plant growth but is not readily available to plants in its atmospheric form. Nitrogen-fixing bacteria help a plant draw nitrogen from the air by converting or “fixing” it to a usable form for healthy growth and development.

Mycorrhizal fungi help a plant by increasing its root surface area so that it can absorb more water and nutrients.

Microbes perform critical functions in soil food webs, such as decomposing organic materials, cycling nutrients, and improving soil structure. (USDA NRCS).

“Nature’s toolbox of beneficial bacteria and fungi can help us produce healthier crops with higher yields while reducing the need for fertilizer and other chemicals.”

Ejner Bech Jensen, Novozymes’ Vice President for BioAg Research.

Agricultural Microbials: Huge Market Potential

According to marketing research firm Research and Markets, the agricultural microbials market is projected to reach $6.01 billion by 2022 from $3.09 billion in 2017.

“The reduced development cost and time associated with microbial pesticides, reduction in the availability of chemical or synthetic active ingredients, and increase in pest resistance to several chemical pesticides is pushing the market growth toward microbial crop protection.”
(PR News Wire)

Land grant universities and researchers are committed to microbial crop protection and the EPA looks favorably upon them as well. This effectively shortens the timeline for development by years! In turn, the cost of product development decreases by millions of dollars.

Custom Microbes: Ecosystem in a Bottle

One of the new players in this space is a company called Holganix.  Holganix creates plant probiotics products that incorporate over 800 soil microbes, microbe food, and nutrient enhancers to build a powerful microbiological support system for plants and healthier soils. These products increase crop yield while simultaneously reducing the need for water, fertilizer and other chemical inputs. Holganix products have also shown promising results in controlling nematodes, which are a parasitic worms that burrow in the roots of plants, sapping them of their energy.

Holganix creates plant probiotics products that incorporate over 800 soil microbes, microbe food, and nutrient enhancers to build a powerful microbiological support system for plants and healthier soils.

With Holganix…and without Holganix

Holganix products have had measured success in field trials, which typically last three years. Customers are reporting increased yields, a reduction in fertilizer usage as well as reduced nematode pressure and crops with higher brix readings. (Brix readings measure the amount of sugar content in the plant tissue).

Custom Microbes: Seed Coatings

In addition to the Holganix approach— where microbes live in interactive “biomes— there are many companies that create microbial seed products.

One of the bigger players in this space is the BioAg Alliance, which represents the combined forces of Monsanto and Novozymes. BioAg Alliance makes seed coating products covering corn, forage, peanuts, pulse, soybean and wheat. Researchers screen thousands of microbes from different soil biomes to find out which ones help a plant fix nitrogen or absorb phosphorus more efficiently or protect a plant from a fungal disease. Those microbes which perform the best get selected for use as seed coatings. This specific blend of bacteria and fungi, coated directly onto the seeds, help the plants flourish naturally despite facing tough environmental conditions.

Other large players in this agricultural microbials market include BASF, Bayer, BioWorksCertis, DowDuPont and Syngenta. Some emerging players in the US agricultural microbials market include Agbiome,  AgrinosArystaLifeScience Bioconsortia, IndigoAgMarrone Bio InnovationsPivotBio, Plant Impact and Valent BioSciences.

Indigo’s microbe coatings have boosted cotton yields by an average of 14 percent in commercial trials in Texas. Source: Indigo Ag.

Bringing Microbes Home — What does this mean to you?

If you maintain a lawn or a garden, you have hard working soil microbes already as friendly neighbors! If either of those areas struggle with pests and diseases, there is most likely an imbalance in the soil microbiome. A product like Holganix, which was originally developed for turf grass, can help reestablish a healthy support system and make your fertilizer applications more efficient, which will reduce the amount of fertilizer and water required!

The Bottom Line: 

World food security and the environment face a number of pressures, not least through climate change and a growing population. Products that harness the powerful natural benefits of microbes are exciting tools for sustainable agriculture. Microbial agriculture products represent a new frontier in soil science, and will help farmers grow more food with less impact on the environment.


Soils &  Organisms : USDA ARS,

Mycorrhizal Applications,

Nature News, Nature Publishing Group,

Soil Science Society of America, 2015.   When Soil Won the Nobel Prize in Medicine. (pptx)

“BioConsortia Inc.” BioConsortia Inc – BioConsortia Inc,

Dunn, Elizabeth G. “Indigo’s Scientists Are Replacing Pesticides With Bacteria.”, Bloomberg, 16 Apr. 2018,

“Nutrient Pollution.” EPA, Environmental Protection Agency, 20 Feb. 2018,

Ramírez-Puebla, Shamayim T., et al. “Gut and Root Microbiota Commonalities.” Applied and Environmental Microbiology, html.

Reese, Matt. “Ohio Ag Net | Ohio’s Country Journal.” Ohio Ag Net Ohios Country Journal,

Savage, Steven. “Update On The Rapidly Growing Biologicals Sector In Agriculture.” Forbes, Forbes Magazine, 15 Mar. 2018,

Society, Microbiology. “Society Publishes New Briefing on Food Security from the Soil Microbiome.” Microbiology Society,

Sonon, Leticia S, and L. Mark Risse. “Soil Inoculants.” UGA Cooperative Extension, 1 June 2012, Inoculants.

“The BioAg Alliance Readies New Seed Coatings to Help Farmers Achieve Better Harvests.” Novozymes,

“The Factory of Life: Why Soil Biodiversity Is Important.” 2010,

“The Holganix Blog.” Update: Holganix Agriculture Trial Results,