The Best Time to Apply Mycorrhizal Fungi Based on Your Crop Rotation

Adding mycorrhizal fungi to your fertility program isn’t just about picking the right product, it’s about applying it at the right time. And in rotational systems, timing is everything.  With arbuscular mycorrhizal fungi(AMF) your fertilizer efficiency sky-rockets!

Different crops can either support or suppress AMF development. Some, like corn, small grains, sunflowers, and beans, form strong symbiotic relationships. Others, especially those in the brassica family, do not. If you’re growing crops like sugar beets, canola, mustard, or radish, knowing when to reintroduce fungi into your soil is the key to long-term soil health and sustainable yields.

Here’s how to time your application for maximum impact, based on what’s in your rotation.

Know Which Crops Support Fungal Colonization

First, understand the difference between mycorrhizal and non-mycorrhizal crops.

Mycorrhizal crops include:

• Corn
• Small Grains
• Soybeans/Dry Beans
• Alfalfa
• Sorghum
• Peanuts
• Cotton
  

Non-mycorrhizal crops include:

• Sugar beets
• Canola
• Mustard
• Radish
• Turnips
• Kale
  

Brassicas, in particular, rely more on bacterial processes and do not form relationships with mycorrhizal fungi. Planting these crops without follow-up biological management can severely diminish fungal populations in your soil.

After Non-Mycorrhizal Crops: Rebuild Immediately

According to New Age Farming’s founder, Brady Krchnavy, the ideal time to apply mycorrhizal fungi is immediately after harvesting a non-mycorrhizal crop, especially one like sugar beets or canola.  Where possible, a post harvest cover crop inoculated with AMF would be ideal but treating the following spring’s cash crop is the next best option.

Why? Because the harvest and tillage required for those crops are biologically destructive. The soil is often worked multiple times:

• Once to incorporate lime and fertilizer
• Again for planting
• A possible third time for cultivation
• Again post-harvest
  

Each pass reduces soil fungal populations. And since brassicas don’t support mycorrhizal fungi, the fungi lie dormant or die off.

Applying arbuscular mycorrhizal fungi after the post harvest tillage in a winter cover crop allows those spores to begin colonizing roots in the soil of a mycorrhizal crop like rye or barley.

Even in winter, Farm Fungi’s strains survive harsh conditions, from -50°F to 140°F, ensuring they’re alive and ready when spring roots start growing.

At Planting: The Most Effective Application Point

If you’re coming into a corn, wheat, or soybean year, your best bet is to apply mycorrhizal fungi at planting. By either treating the seed(liquid or dry) or applying in-furrow, root colonization can happen upon germination and this ensures a healthy robust plant.

There are two main methods:

• In-furrow application: Delivers the fungi directly into the root/seed zone
  
• Seed treatment: Allows colonization to begin immediately as the seed germinates
  

This early colonization widens and deepens the root system, enhances phosphorus uptake, and improves drought resilience. Trials show fungi-treated corn plants produce more nodal roots, thicker stalks, and greater leaf area within just weeks of emergence.

These benefits are amplified when fungi are introduced into biologically suppressed soils—like those following brassicas or heavily tilled systems.

Timing Tips Based on Common Rotations

Corn – Soybean Rotation

• Apply at planting in the corn year.
  
• Residual fungi can benefit soybeans the following year.
  

Wheat–Canola Rotation

• Inoculate the wheat at each planting.
  

Sugar Beet–Corn Rotation

• Apply to corn at planting.
  
• Avoid deep fall tillage that disrupts fungal establishment.
  

Cover Crop Systems

• Use mycorrhizal-friendly covers like rye, oats, clover.
  
• Avoid full-season brassica covers without post-season inoculation.
  

Avoiding Common Timing Mistakes

Some farmers mistakenly apply fungi before planting non-mycorrhizal crops. While the product won’t harm those crops, it also won’t colonize them. More importantly, follow-up tillage and chemicals can destroy the spores before they have a chance to work.

Instead, plan your fungi application to coincide with a compatible crop and minimal soil disturbance. Strip-till, shallow till, or no-till systems are particularly effective for supporting fungal growth across seasons.

If you’ve made significant soil improvements with fungi in past years, don’t let one poorly timed application undo your progress.

Why Timing Matters for ROI

Applying mycorrhizal fungi at the wrong time is like spraying herbicide in the rain, it wastes your money and doesn’t give the product a chance to work.

But with proper timing, fungi offer:

• Better nutrient absorption
• Improved drought tolerance
• Faster canopy development
• More resilient crops across variable years
  

Farmers who integrate fungi strategically into their rotations report steady profit gains and more consistent performance across their fields – even under stress.

Plan your program like you plan your fertility. Apply where it matters, when it matters.

Sources 

• Kise, Sam. “New Age Farming and the Power of Mycorrhizal Fungi.” Future Farmer Magazine, March-April 2023.
  
• Petersen, Mike. “Trip Report of the VT Crop Stage Plots.” Soils Consultant Report, Wood River Interchange, 2022.
  
• Petersen, Mike. “Trip Report of the V4-V5 Crop Stage Plots.” Soils Consultant Report, Wood River Interchange, 2022.
  
• Soil Food Web School. “The Magnificent Mycorrhizal Fungi.” soilfoodweb.com.