Soil and Root Testing for Mycorrhizal Fungi in California

Soil and Root Testing for Mycorrhizal Fungi in California

Mycorrhizae, derived from the Greek words "mykes" (fungus) and "rhiza" (root), represent a symbiotic association between fungi and plant roots. These relationships are ancient, dating back to the early colonization of land by plants approximately 450 million years ago. Mycorrhizal fungi are integral to the health and productivity of most terrestrial ecosystems. They enhance plant nutrition, improve soil structure, and increase plant resistance to pathogens. This article delves into the types of mycorrhizal associations, their benefits to plants, the variety of plants involved, and methods for detecting these associations.

Types of Mycorrhizae

There are several types of mycorrhizal associations, categorized primarily based on their structural characteristics and the specific fungi involved. The major types include:

  1. Arbuscular Mycorrhizae (AM)

    • Fungi Involved: Glomeromycota
    • Structure: These fungi penetrate plant root cells, forming structures called arbuscules (branched, tree-like structures) and vesicles (storage organs).
    • Plants Involved: Predominantly herbaceous plants, including crops like wheat, maize, and legumes.
  2. Ectomycorrhizae (ECM)

    • Fungi Involved: Basidiomycota, Ascomycota
    • Structure: These fungi form a sheath around the root, called a mantle, and extend into the root cortex intercellularly, forming a Hartig net.
    • Plants Involved: Mostly woody plants, such as pine, oak, birch, and eucalyptus.
  3. Ericoid Mycorrhizae (ERM)

    • Fungi Involved: Ascomycota (primarily)
    • Structure: The fungi form loose coils inside the root cells.
    • Plants Involved: Heath family (Ericaceae), including heather and blueberries.
  4. Orchid Mycorrhizae

    • Fungi Involved: Basidiomycota
    • Structure: Fungi form pelotons (coiled structures) within the root cells.
    • Plants Involved: Orchids
  5. Monotropoid Mycorrhizae

    • Fungi Involved: Basidiomycota
    • Structure: Similar to ECM but specifically associated with non-photosynthetic plants in the Monotropoideae subfamily.
    • Plants Involved: Monotropes, such as Indian pipe.

Benefits to Plants

Mycorrhizal associations offer a multitude of benefits to plants, which can be broadly categorized into nutritional, physiological, and ecological advantages.

Nutritional Benefits

  • Enhanced Nutrient Uptake: Mycorrhizal fungi extend the root system through their hyphal networks, increasing the surface area for nutrient absorption. This is particularly beneficial for the uptake of phosphorus, nitrogen, and micronutrients like zinc and copper.
  • Improved Water Absorption: The extensive hyphal network also aids in water uptake, making plants more resilient to drought conditions.

Physiological Benefits

  • Increased Stress Tolerance: Mycorrhizal associations help plants cope with various environmental stresses, including salinity, heavy metals, and drought. The fungi can detoxify these elements and sequester them, reducing their impact on the plant.
  • Enhanced Root Growth: Mycorrhizal fungi secrete growth-promoting substances that can stimulate root branching and elongation, further improving nutrient and water absorption capabilities.

Ecological Benefits

  • Soil Structure Improvement: Mycorrhizal fungi produce glomalin, a glycoprotein that helps bind soil particles together, improving soil structure and stability. This enhances soil aeration, water retention, and reduces erosion.
  • Disease Resistance: Mycorrhizal fungi can protect plants from soil-borne pathogens through competitive exclusion, production of antifungal compounds, and induction of plant defense mechanisms.
  • Biodiversity Support: Mycorrhizal networks can connect different plants, facilitating nutrient exchange and communication, which can enhance ecosystem stability and biodiversity.

Plant Associations

Mycorrhizal associations are widespread and occur in nearly 90% of all land plants. Different types of mycorrhizae associate with various plant groups, as outlined previously. Here are some examples:

  • Arbuscular Mycorrhizae: Most crops (e.g., wheat, maize, rice), many vegetables (e.g., tomatoes, carrots), and many herbaceous plants.
  • Ectomycorrhizae: Many forest trees (e.g., pine, oak, spruce), woody shrubs, and some herbaceous plants.
  • Ericoid Mycorrhizae: Plants in the Ericaceae family (e.g., rhododendrons, blueberries, cranberries).
  • Orchid Mycorrhizae: All orchids, which rely on these fungi for seed germination and nutrient supply, especially in the early stages of growth.
  • Monotropoid Mycorrhizae: Non-photosynthetic plants like Indian pipe and other members of the Monotropoideae subfamily.

Detection of Mycorrhizal Associations

Detecting and studying mycorrhizal associations involves various methods, including visual microscopy and plate counts.

Visual Microscopy

Microscopy is a powerful tool for examining mycorrhizal structures within plant roots. The process involves several steps:

  1. Sample Collection: Roots are collected from the field or greenhouse, ensuring minimal disturbance.
  2. Clearing: Roots are cleared of pigments and cellular contents using a solution of potassium hydroxide (KOH) to make fungal structures more visible.
  3. Staining: Cleared roots are stained using dyes like trypan blue, acid fuchsin, or Schaeffer black ink, which selectively stain fungal structures.
  4. Mounting: Stained roots are mounted on microscope slides and examined under a compound microscope.

For different types of mycorrhizae, specific structures are identified:

  • Arbuscular Mycorrhizae: Look for arbuscules, vesicles, and hyphal networks within root cells.
  • Ectomycorrhizae: Identify the mantle around the roots and the Hartig net.
  • Ericoid Mycorrhizae: Look for hyphal coils within root cells.
  • Orchid Mycorrhizae: Identify pelotons within root cells.

Plate Counts

Plate counts are used to quantify and identify mycorrhizal fungi in soil or root samples. This method involves culturing fungi on selective media and counting the resulting colonies. The process includes:

  1. Sample Preparation: Soil or root samples are collected and homogenized.
  2. Dilution: Samples are serially diluted to reduce the density of fungal spores and hyphae.
  3. Plating: Diluted samples are spread onto agar plates containing selective media that favor the growth of mycorrhizal fungi while inhibiting other microorganisms.
  4. Incubation: Plates are incubated under conditions suitable for fungal growth, typically at 25-30°C for several days to weeks.
  5. Counting: Colonies that develop on the plates are counted and identified based on morphological characteristics. For precise identification, molecular techniques like DNA sequencing may be used.


Mycorrhizal associations are fundamental to plant health and ecosystem functioning. By forming symbiotic relationships with plants, mycorrhizal fungi enhance nutrient uptake, improve water absorption, increase stress tolerance, and protect against pathogens. The different types of mycorrhizae, including arbuscular, ectomycorrhizae, ericoid, orchid, and monotropoid mycorrhizae, associate with a wide range of plant species, from crops to forest trees and orchids. Detecting these associations through visual microscopy and plate counts provides valuable insights into the diversity and functionality of mycorrhizal fungi. As we continue to explore these intricate relationships, the potential for harnessing mycorrhizal fungi in sustainable agriculture and ecosystem management becomes increasingly apparent.

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Understanding Soil Health

Assessing soil health involves looking at physical, chemical, and biological components.

Soil health is a fundamental concept that underpins the success of agriculture, gardening, and land management practices. It refers to the overall well-being and vitality of the soil ecosystem, encompassing physical, chemical, and biological aspects. Understanding soil health is crucial for maintaining sustainable and productive landscapes while also contributing to environmental conservation.

  1. Physical
    The physical properties of soil play a critical role in its health. These properties include soil texture, structure, compaction, and water-holding capacity. Soil texture refers to the proportions of sand, silt, and clay particles in the soil. A balanced texture allows for adequate water drainage and retention, preventing waterlogging and drought stress. Soil structure influences root penetration, aeration, and nutrient movement. Healthy soil structure promotes a friable and well-drained medium for plant growth.
  2. Chemical
    Soil chemistry directly affects nutrient availability and plant growth. Key chemical factors include soil pH, nutrient content, and the presence of contaminants. Soil pH measures the soil's acidity or alkalinity and profoundly influences nutrient uptake by plants. Nutrient content, including macronutrients like nitrogen, phosphorus, and potassium, must be in balance to support healthy plant growth. Monitoring and maintaining proper nutrient levels through fertilization are essential for maximizing crop yields and preventing nutrient deficiencies.
  3. Biological
    The biological component of soil health pertains to the diverse array of microorganisms, insects, and other organisms that inhabit the soil ecosystem. These organisms play crucial roles in nutrient cycling, organic matter decomposition, and disease suppression. Soil microorganisms break down organic matter, releasing nutrients that are subsequently made available to plants. A rich and diverse soil microbiome contributes to enhanced nutrient availability and plant resilience against diseases.

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We provide a range of soil tests from basic chemistry, to texture/infiltration rate, all the way to biology.

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Basic Soil Health Test

The Basic Soil Health Test is an excellent starting point for understanding your soil's condition. It offers a comprehensive analysis encompassing pH levels, nutrient content, CEC (Cation Exchange Capacity), salts, and organic matter. This budget-friendly test is ideal for identifying potential soil health issues and establishing a solid foundation for further management.

Full Chemistry Test

Our Full Chemistry Test provides a detailed assessment of your soil's quality, guiding you towards healthy and sustainable soil management practices. Through an extensive analysis, we examine macro and micronutrient levels, pH, CEC, organic matter, and salinity. This comprehensive understanding empowers us to create tailored recommendations for soil amendments and treatments, optimized for the specific plants you intend to cultivate. By optimizing your soil's chemistry, you can expect to foster more robust and vibrant plant growth.

Complete Soil Health Test

Uncover a deeper understanding of your soil's health with the Complete Soil Health Test. This comprehensive analysis goes beyond the basics, measuring nutritional factors and examining soil texture. It covers macro and micronutrients, organic matter, pH, CEC, as well as sand, silt, and clay percentages. Additionally, we assess carbon sequestration levels, providing you with a holistic view of your soil's composition. The personalized recommendations derived from this test empower you to make precise adjustments to enhance your soil's health and productivity.

MWELO Soil Management Report

For those navigating California's MWELO guidelines, our MWELO Soil Management Report is an indispensable resource. This report not only ensures compliance but also promotes sustainable and thriving landscapes. It includes comprehensive data such as soil texture, infiltration rate, pH, total soluble salts, sodium content, and organic matter percentage. With amendment recommendations, optionally tailored to specific plant types, and annual maintenance tips, you'll be equipped to create landscapes that are both aesthetically pleasing and environmentally responsible.

Heavy Metals

The Heavy Metals analysis is a vital tool in assessing potential soil contamination. Given the uncertain history of properties, this analysis identifies the presence of heavy metals that might have accumulated due to past activities or nearby industrial sources. With results available in approximately nine business days, you'll gain insights to ensure the safety and health of your soil.

Soil Food Web

Explore the intricate world beneath the surface with our Soil Food Web analysis. By estimating population sizes of essential trophic groups—bacteria, fungi, protozoa, and nematodes—we unveil the microbiological health of your soil. Additionally, we identify specific organisms within these groups, providing insights into the soil's successional level and overall condition. This analysis is applicable to soil, compost, and compost tea samples, offering a holistic perspective on your soil's biological vitality.

Pesticide Screening

The Pesticide Screening can detect hundreds on common pesticides that may have been applied or drifted from nearby sources.

Herbicide Screening

The Herbicide Screening plays an important role in ensuring the safety of your soil and plants. By detecting the presence of herbicide residues, this test can indicated whether a soil has had history of herbicide applications.

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Regenerative Soil Management Practices

Working with nature to improve soil means implementing practices like cover cropping, mulching, and composting.

Cover Cropping

Cover cropping involves planting specific crops during non-growing seasons to cover and protect the soil. These crops enhance soil structure, prevent erosion, suppress weeds, and provide organic matter when incorporated into the soil. Leguminous cover crops also contribute nitrogen fixation, enriching soil fertility naturally. Cover cropping is a sustainable method that improves soil health and biodiversity.


Mulching entails covering the soil surface with organic materials like straw, leaves, or wood chips. Mulch conserves soil moisture, moderates temperature fluctuations, suppresses weeds, and prevents soil erosion. As the mulch breaks down, it contributes organic matter, enriching the soil's structure and fertility. Mulching is an effective and easy way to maintain soil health.


Composting transforms organic waste into nutrient-rich compost. Incorporating compost into the soil enhances its structure, moisture retention, and fertility. Compost also introduces beneficial microorganisms that aid in nutrient cycling and disease suppression. Composting not only reduces waste but also revitalizes soil, making it an essential component of sustainable gardening.

Water Conservation Techniques

Implementing water-efficient practices such as drip irrigation, rainwater harvesting, and utilizing drought-resistant plants minimizes water use and reduces soil erosion. Conserving water in landscapes maintains soil moisture, supports plant growth, and sustains overall soil health. Water conservation techniques are vital for responsible gardening in arid and water-scarce regions.

If you have any questions feel free to get in touch with the Alluvial Soil Lab team at (831) 216-1367 or at

This page was written with the help of AI.

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