Learning Series: Leveraging Plant-Microbe Synergy for Growing Healthier Crops

Watch “Leveraging Plant-Microbe Synergy for Growing Healthier Crops” with Jo Tobias here:

https://youtu.be/0jX-8JlSk6Q

Here is an audio version of the session for listening on the go.

Here is the slide deck used in Jo Tobias’s presentation on “Leveraging Plant-Microbe Synergy for Growing Healthier Crops”.

Introduction

Root Shoot Soils specializes in regenerative soil management and living compost to restore degraded landscapes and improve soil health. Since 2015, Jo has worked with farmers across British Columbia, Alberta, Saskatchewan, Manitoba, and Ontario to help land stewards develop a deeper connection to their soil through microbial activity, nutrient cycling, and decomposition. Well-managed compost is a key tool for kickstarting ecological processes, reducing synthetic inputs, and improving long-term soil fertility. Jo has a background in computing science and software development, applying data analysis and systems-thinking to agriculture, leading to a transition into permaculture and soil ecology. For Jo, a
visit to her family in the Philippines was a pivotal moment, revealing the negative effects of the Green Revolution:

• Hybridized rice cultivars required heavy fertilizer and pesticide use, displacing traditional farming methods and heirloom rice varieties.
• Farmers became dependent on chemical inputs, impacting long-term soil health.

Soil ecosystems operate in a complex web of life, where microbial communities, organic matter, and plant interactions shape soil health. Soil ecology tells a different story – one of life, death, interconnectedness, and symbiosis – emphasizing the need for regenerative practices.

Understanding Soil as an Ecosystem

Soil is not just dirt; it is a living ecosystem that supports plant, microbial, and animal life. Soil is an ecosystem, a community of living organisms merged with the non-living components, acting as a system. Soil consists of three main components:

• Solids – mineral matter, including sand, silt, and clay, as well as organic matter and living biota.
• Liquids – water that moves through the pore spaces, transporting nutrients.
• Gases – air that circulates in the soil, providing oxygen to organisms and roots.

Pore spaces within soil regulate air and water movement, supporting root penetration and microbial activity. Water plays a critical role:

• Enters the soil, filling pore spaces and transporting nutrients like a highway system.
• Drains out, allowing air to replace it, ensuring oxygen for aerobic organisms and plant roots.

A well-structured soil system supports sustained microbial communities and nutrient cycling. Soil health is driven by biology, as microbial interactions regulate decomposition and fertility.

Living Organisms

These are the key groups of living organisms in soil:

• Bacteria
• Fungi
• Algae
• Roots
• Protozoa
• Nematodes
• Microarthropods
• Earthworms
• Beetles
• Ants
• Millipedes

The soil food web is a complex relationship between diverse fauna and flora found in soil.

Defining Soil Health

Healthy soil supports the entire food web, retaining nutrients, filtering water, suppressing diseases, and fostering biodiversity. Soil health is defined as the continued capacity of soil to function as a vital living ecosystem that sustains plants, animals, and humans (USDA-NRCS, 2012). The principles of soil health are:

• Know your context: Soil health is different in every location.
• Keep the soil covered: Bare soil is vulnerable to erosion and degradation.
• Keep living roots in the soil: Living roots sustain microbial life.
• Minimize soil disturbance: Tillage disrupts microbial communities.
• Plant diversity encourages soil biodiversity: Different plants support different microbes.
• Integrate animals: Grazing and manure contribute to soil fertility.

The missing principle: restore and sustain a thriving soil food web to maintain long-term soil function.

Current State of Agriculture

Agricultural soils are now bacterial-dominated due to long-term intensive management. The loss of fungal biomass, soil organisms, and habitat complexity has weakened soil ecosystems. The causes of soil biodiversity loss are:

• Fast-growing plant selection reducing organic matter diversity.
• Simplified organic inputs limiting food sources for microbes.
• Tillage and soil disturbance breaking fungal networks and compact soil.
• Fertilizers inhibiting fungi, shifting microbial balance toward bacteria.
• Phosphate fertilizers suppressing mycorrhizae, reducing nutrient uptake.

Can soil health be restored?

• Recovery is a slow, long term process, as many soils have been intensively managed for 50+ years.
• Nine years of low-input farming may be needed before microbial balance improves.
• Some fungal species may take 30+ years to return after stopping intensive management.

Restore, Sustain, Thrive

Why is it important to restore and sustain a thriving soil food web?

• Retaining and cycling nutrients to support plant growth.
• Water – regulation, storage, and purification.
• Disease and pest management.
• Toxin decomposition (bioremediation).
• Supporting the production of food, feed, fiber, and fuel.

Rhizosphere

Lorenz Hiltner (1904) first described the rhizosphere as the region of soil surrounding plant roots. It
serves as an interface between plants, soil, and microbes. The size of the rhizosphere varies depending on plant species. It is a complex environment supporting a dense microbial community. More active and diverse microbial communities exist closer to the root zone compared to bulk soil. Microbial communities can also vary at different root locations.

Rhizodeposits

Rhizodeposition refers to root deposits released into the surrounding soil. Root deposits are
classified based on:

• Chemical structure
• Mode of release
• Function

Root border cells detach from the root cap but remain viable in the soil. These cells survive in the
soil, secreting enzymes and proteins. Over 90% of root border cells remain alive after detachment.
Studies on field maize show that border cells remain alive for several days after detachment. The
number of root border cells released varies by plant species:

• Peas: 4,000 – 21,000 cells per day
• Cotton: 8,000 – 10,000 cells per day
• Field mustard: 0 cells per day

Root border cells help engineer the root’s microbial ecology. They reduce friction at root tips by
secreting mucilage and enhance plant defense by secreting antimicrobial compounds. Root exudation is a strategy plants use to survive and adapt to their environment. Plants can modify exudate composition to selectively encourage specific microbial communities in the rhizosphere.

The Phyllosphere

The phyllosphere refers to the above-ground surfaces of plants, including leaves, stems, flowers,
fruits, and seeds. Different plant parts create distinct microbial habitats:

• Anthosphere = flowers
• Caulosphere = stems
• Carposphere = fruits
• Phylloplane = leaves
• Spermosphere = seeds

The phyllosphere hosts a diverse array of microorganisms, influenced by environmental conditions, plant species, and surface properties. Microbes in the phyllosphere can contribute to plant health, helping with stress tolerance and disease suppression.

Biological Inoculants: Compost, Compost Extracts, and Teas

Bio-inoculants are beneficial microbial inputs used to enhance soil health and plant resilience. The
types of bio-inoculants are:

• Compost: provides a diverse community of microorganisms to restore biological activity in the soil.
• Compost extracts: contain soluble nutrients and microorganisms that help boost soil microbial life.
• Compost teas: actively brewed solutions designed to multiply beneficial microbes before application.

Restore Soil Microbiome

The goal is to restore the soil microbiome by increasing beneficial microbial populations. Compost
extracts and teas are tools used to bring life back into the soil. Compost extract is made by extracting microbes, soluble nutrients, and organic compounds from high-quality compost. Compost tea is brewed to multiply beneficial organisms, creating an active microbial solution for soil and plant application. Both compost extract and compost tea improve microbial balance, support plant health, and enhance nutrient cycling. Proper application methods ensure that microbial communities establish and function effectively in the soil. Monitoring microbial activity over time is critical to assess progress and make necessary adjustments.

Power of Compost

Compost is a tool for soil restoration, not the end-all solution. It is essential to introduce microbes
into the soil, whether through livestock, compost, or other organic inputs. High-quality, biodiverse
compost is one of the most effective ways to restore soil health. Biologically-rich and diverse
compost production is critical for supporting microbial life.

Liquid Bio-Blends

The quality of compost extracts and teas depends on the quality of the base compost. Water acts
as a carrier for microorganisms, ensuring they reach plant roots and soil surfaces effectively. The
advantages of liquid bio blends are:

• Immediate nutrient availability.
• Flexible application methods.
• Cost-effective.
• Customizable recipes

Compost Extract vs. Compost Tea

Compost extract:

• Quick to make (5 minutes to 1 hour depending on concentration preference).
• Soil application.
• No foods added at the start, but can be added prior to soil application.
• Microbes do not grow in the solution.
• An effective means to get beneficial organisms into the rhizosphere.
• Soil organic matter level must be ≥ 5%.
• Nearly fool-proof.

Compost tea:

• Takes at least 24 hours to make.
• Primarily a foliar application, though some exceptions allow soil application.
• Requires microbial supplements at the start of the process.
• Microbes are activated and grown in the solution.
• Used to prevent disease-causing organisms or re-inoculate the phyllosphere.
• Can be used in soil with organic matter levels ≤ 3% (foods added and dead organism bodies act as organic matter).
• Easy to mess up.

Case Study: Stonecroft Farm

Stonecroft Farm is a mixed farming operation focused on soil regeneration through biological
management. The transition to microbial-driven nutrient cycling has been key to reducing synthetic
inputs and improving soil function. Compost is a key component of the transition, providing a biologically-rich amendment to increase soil microbial diversity and improve soil structure. The
composting process incorporates a mix of manure, woody material, and crop residues, ensuring a
balanced carbon-to-nitrogen ratio for microbial activity. Field and microbiology results:

• Increased soil microbial diversity, leading to better nutrient cycling and organic matter decomposition.
• Significant improvements in soil structure, with better aggregation, increased water retention, and reduced ponding.
• Shifts in plant communities, with more diversity and fewer problem weeds, indicating enhanced soil fertility and biological balance.