Microbiome Management in soil & plants

The root zone is a living environment.

A field or a greenhouse, a row of young plants, and under each one a root system working through the soil. Living roots release carbon that feeds the microbes around them, and water connects every scale, from rain on the field to the thin layer of water around a mineral grain.

Follow the roots downExamine the research

Seen and unseen

A plant, and the living soil around its roots.

A plant, the living soil around its roots, and a millimetre of the rhizosphere: the root, the carbon it releases, bacteria, fungal hyphae and a soil crumb. A teaspoon of productive soil generally holds 100 million to 1 billion bacteria.2

Environmental conditions

Resources, physical conditions and management.

Microbial activity

Functions and interactions within the community.

Observable function

What can be measured in the host or wider system.

A young plant in outline above the soil line, its roots spreading through soil aggregates below. A small box marks a lateral root among the aggregates.

  1. The root zone

    Magnified view of the root zoneA root along the top with two root hairs reaching down into the soil, the carbon compounds the root releases (small dots), and bacteria clustered in the soil just below its surface. Fungal hyphae thread through the soil, one into a soil aggregate. A green tint marks the soil closest to the root, where microbial numbers and activity are highest.abcde
    • a Root
    • b Root exudates
    • c Bacteria
    • d Hyphae
    • e Aggregate

    Observable function Root mass and leaf tissue analysis

  1. Root mass and leaf tissue analysis
Illustration. Magnified views are conceptual and not to scale.

Why this system is investigated. A living root changes the chemistry of the soil around it, and humic and fulvic substances are reactive in that same water: they carry charge, hold nutrient ions and bind metals. The questions here run from the root environment to the material’s chemistry, to the plant’s response, and to the microbes that live on what the root releases.

Across 81 studies, humic substances raised early plant growth on average, with wide variation, and field trials range from small gains to none, so the material, the soil and the measurement are read together.

Why the setting matters

From a field to a mineral grain, by way of a living root.

Five scales, one system. Living roots and the water around them connect each scale to the next, which is why a question about a crop is also a question about the soil it grows in.

  1. 1 Field or greenhouse

    Where the roots grow sets everything that follows: the soil or substrate, how water arrives, how nutrients are supplied. A greenhouse is a setting, and its plants may grow in soil, in a substrate or in a nutrient solution.

    Water. Rain or irrigation enters the root zone. Some is taken up by roots; some drains away with whatever is dissolved in it.

  2. 2 Plant

    Leaves fix carbon from the air. Part of that recently fixed carbon travels to the roots, and part of what reaches the roots passes into the soil, released directly or through the fungi that partner with them.3

    Water. Water moves up from root to leaf and leaves through the leaves, so the roots keep drawing more from the soil.

  3. 3 Roots

    Roots branch through soil crumbs and the pores between them. Each living root changes the soil immediately around it.1

    Water. Roots take up water and the nutrients dissolved in it.

  4. 4 Rhizosphere

    The soil a living root influences. Roots release carbon compounds that feed the microbes around them, and bacteria crowd where those compounds land. Mycorrhizal fungi take carbon from the root and pass nutrients back.1,3

    Water. What the root releases moves through the water around it.

  5. 5 Mineral surface

    At the smallest scale, organic matter meets a mineral grain. Soluble compounds, much of them already processed by microbes, attach to mineral surfaces in patches, and what attaches is protected from decomposers. How long carbon stays depends on these surroundings more than on its chemistry.4,5

    Water. Dissolved compounds reach the mineral surface in water.

Illustration. Each frame looks into the box in the one before. Organisms enlarged; not to scale. The last frame shows soil organic matter as a mixture of fragments on a mineral grain, attached in patches.

What is happening here

A root is part of a wider living system.

The rhizosphere is the region of soil influenced by a living root. Compounds released by roots help shape microbial activity nearby, connecting the plant with its surrounding soil community.1,2

It is one of four places a microbe can live in relation to a root, and the research below keeps them apart: a change in the soil community, on the root surface and inside the root are different findings.

Cross-section of a root in soilA root seen in cross-section. 1, surrounding soil: particles with pore spaces between them. 2, rhizosphere: a gradual zone around the root, shaded more strongly close to the root, where compounds released by the root are most concentrated. 3, root surface: the outer boundary of the root, with root hairs. 4, root interior: plant tissue, with a central vascular cylinder. An inset enlarges the zone at the root edge: a, root boundary; b, microorganisms; c, compounds released near the root; d, soil particles and pores.abcd1234
  • aRoot boundary
  • bMicroorganisms
  • cCompounds released near the root
  • dSoil particles and pores
Conceptual illustration. Organisms and features are enlarged and not drawn to scale.
  1. 1

    Surrounding soil

    The wider setting of particles, pores, organic material and organisms.

  2. 2

    Rhizosphere

    The soil region influenced by the living root.

  3. 3

    Root surface

    The interface between the root and its surroundings.

  4. 4

    Root interior

    Plant tissue, distinct from the soil and the root surface. Microbes that live inside plant tissue are called endophytes.

Define the growing system

The setting changes the questions.

Start by identifying where the roots are growing and how water, nutrients and environmental conditions are managed. Field soil, growing substrates and nutrient solutions require different descriptions and measurements.

  • Field soils

    Consider the soil profile, crop history, rooting conditions, water movement, fertility program and seasonal conditions.

    Questions

    • What varies across the field?
    • Which management changes occurred?
    • What comparisons would make a response easier to interpret?

  • Substrate-based production

    Consider the growing medium, container or bed, irrigation pattern, drainage, nutrient program and crop stage.

    Questions

    • What is supplied to the root zone?
    • What is retained or drained?
    • How consistent are conditions between plants and growing areas?

  • Nutrient-solution systems

    Consider solution management, root-zone oxygen, nutrient supply, temperature, recirculation and system hygiene.

    Questions

    • Where and how is the solution measured?
    • Which parts of the system share the same water?
    • What else changes when an input is introduced?

Protected growing can use soil, substrates or nutrient solutions. “Greenhouse” describes the growing setting, not a single root environment.

The framework in this setting

One field study, read through the framework.

The framework sorts what to examine: the conditions, the biological activity, and what can be observed in the plant and the system. Applied to the Iowa maize study featured below, it shows which part of the explanation was measured and which was not.12

  1. Growing conditions

    Eroded upland soil and a seasonally wet lowland in the same rainfed Iowa fields, over four site-years with dry and wet seasons.

  2. Biological activity

    Not measured in this study. The framework keeps it as the open part of the explanation, not an assumed cause.

  3. Plant and system observations

    Grain yield read along each strip by soil position: no field-wide effect, and gains of 7 to 19 percent on the upland soil.

Observe and reassessThe link to dry seasons is the authors’ reading of a correlation. A design that also logged soil water would test it.

A greener leaf, larger root system or higher yield is an observation. Establishing why it changed requires suitable measurements and comparisons.

Read the framework

What is established

Measured at the root: gains, and no effect.

Across 81 studies, humic substances raised shoot dry weight by an average of 22 percent and root dry weight by 21 percent, with wide spread: about half the shoot studies found less than a 5 percent gain. Compost-derived materials raised shoot growth; peat-derived materials did not; stressed plants responded more than unstressed ones. Most studies measured early growth, not field yield.8

One interaction, traced at the root.

In rice seedlings grown short of phosphate, a fulvic preparation raised phosphorus uptake by about 20 percent at three of four doses. The gain ran through the root: roots acidified the solution around them. When the researchers held the solution’s pH steady, the gain disappeared.10

The measurement is phosphorus taken up by the plant. It says nothing about the fulvic material itself entering the root.

Panel A. A rice root in nutrient solution with a fulvic preparation added and the pH free to change. Protons released at the root acidify the solution beside it, and phosphate moves into the root. Phosphorus uptake was about 20 percent higher.AFulvic preparation addedH+H+H+H+H+H+PPPP

A pH free to change: the solution beside the root acidifies, and phosphorus uptake rose by about 20 percent.

Panel B. The same root and fulvic preparation with the solution’s pH held steady by a buffer. The solution beside the root does not acidify, and phosphorus uptake showed no gain.BFulvic preparation added, pH held steadyPPPP

B pH held steady: no gain.

Illustration of the comparison in Lv et al. 2024: rice seedlings in nutrient solution, short of phosphate. H+ marks protons released at the root; P marks phosphate. Not to scale; amounts are not drawn. The fulvic preparation is named, not drawn.

At the root tip

In laboratory maize seedlings, a humic acid from vermicompost lengthened roots, increased lateral root emergence and raised root proton pump activity.9

Inside the plant

Tritium from a labelled leonardite humic acid entered wheat seedling roots within 24 hours. Most stayed in the roots; a small portion reached the shoots. The label may travel on breakdown products, so it does not show the intact material crossing into the plant.11

What is being investigated

Does the carbon in a fulvic material feed the microbes inside the plant?

Measured
Humic and fulvic treatments have shifted which bacteria live inside stevia leaves and tomato roots.16,17
Not measured
Whether any of those endophytes used carbon from the added material. A change in who is present is not evidence of what they ate; tracing the carbon would answer it.
Read the science

Selected research

One controlled study, one field study.

A controlled experiment can isolate a response; a field study shows whether it survives soil, weather and scale. In the field, results divide. A micronized leonardite product raised Iowa maize yield only on eroded upland soil; in replicated Iowa production fields a leonardite extract raised it by 1 to 4 percent. University trials in processing tomato, and 35 Ontario trials in dry bean, found no effect.12,13,14,15

  • Published studyControlled study · Hydroponic cucumber

    In nutrient solution, root and leaf applications reached similar growth by different routes.

    De Hita and colleagues applied a sedimentary humic acid to cucumber roots in nutrient solution, or sprayed it on the leaves. Both routes improved shoot and root growth, but the short-term root responses differed: root application raised root proton pump activity and root abscisic acid; leaf application did not.

    Limitation. A short-term hydroponic experiment in one species; the responses concern this preparation and these conditions.

    Funding. Cátedra Timac Agro grant; one author is at the Roullier Group’s innovation centre.

    Interpretation. Similar growth outcomes did not mean identical mechanisms. The findings apply to this preparation, this species and these hydroponic conditions, not to field soils.

    Study design
    Controlled experiment in hydroponic culture
    Material
    Sedimentary humic acid extracted from leonardite
    Source
    De Hita et al., 2020. Discriminating the Short-Term Action of Root and Foliar Application of Humic Acids on Plant Growth: Emerging Role of Jasmonic Acid
    Read evidence summary

  • Published studyField study · Rainfed maize, Iowa

    In the field, the response depended on where the maize grew.

    Olk and colleagues sprayed a micronized leonardite product on rainfed maize in replicated, field-long strips on two Iowa farms over four site-years. No year showed a field-wide yield effect. On eroded upland soil, yields rose 7 to 19 percent, mostly in drier seasons; a wet lowland showed a small fall that was not significant.

    Limitation. The link to weather rests on correlation and was not tested directly; significance was set at P < 0.10.

    Funding. American Colloid Company and USDA-ARS; two authors were employed by Minerals Technologies.

    Interpretation. A field result belongs to its soil, season, product and rate. The design could not identify a mechanism, and plant nutrient concentrations did not respond consistently.

    Study design
    Replicated field experiment (strip plots)
    Material
    Micronized leonardite suspension (at least 180 g/kg humic acid and 15 g/kg fulvic acid)
    Source
    Olk et al., 2021. Maize Growth and Grain Yield Responses to a Micronized Humic Product Across Soil Types and Annual Weather Patterns in Central Iowa, United States
    Read evidence summary

In this collection. Four records for soil and plants: these two, a meta-analysis of 81 studies, and a tomato study run in greenhouse soil and in hydroponics.

Browse soil & plant evidence

What is being investigated

Sustainability, as questions that can be measured.

Whether a humic or fulvic material makes a growing system more sustainable is a comparison, not a label. The organic matter a soil builds for itself and an extracted commercial material are different things, and a product’s footprint runs from sourcing and extraction through transport and application. Each question names what would have to be measured.

  • Nutrient loss

    Does less nitrogen or phosphorus leave the root zone?

    Measure Nitrate and phosphorus in drainage, leachate or runoff, against an untreated comparison, through a season.

  • Water use

    Does the crop produce more for the water it receives?

    Measure Water applied or received, soil moisture and yield, from the same plots in the same season.

  • Carbon balance

    Does the soil end up holding more carbon than the material brought, after the cost of making and moving it?

    Measure Soil organic carbon at fixed depths over several years, the carbon in the material applied, and the emissions from extracting and transporting it.

None of the four soil and plant records in this collection measured nutrient loss, water use or a carbon balance. Faster growth is not, on its own, lower emissions, and a carbon stock is context, not a removal result.

Propose a measurement

For practitioners: what to record

What to document when observing a growing system, so that a change can be read in context.

Start with a baseline and a useful question.

Choose observations that match the crop, growing system and decision. Record the conditions alongside the plant response so that a change can be interpreted in context.

AreaExamples to document
Crop and stageSpecies, cultivar, planting or transplant date, development stage.
Growing environmentSoil or substrate, rooting volume and relevant environmental conditions.
Water and nutritionIrrigation, nutrient program and appropriate measurements at defined locations.
Root and plant developmentConsistently collected observations of roots, canopy and growth.
ProductionRelevant yield, quality or marketability measures at an appropriate stage.
Concurrent changesWeather, management, pest pressure and other inputs or interventions.

Use consistent methods and suitable comparisons. Photos can support a record, but visual differences alone do not establish a mechanism or treatment effect.

For recirculating or shared systems, the experimental unit may be the reservoir, bench or system rather than each individual plant. A formal evaluation should account for the actual arrangement.

Discuss an evaluation

Where to learn or contribute

The soil and plant publications.

Cover of The Microbiome Management Guide, Plant and Soil Edition

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The Microbiome Management Guide

Plant and Soil Edition

Understanding the living relationships behind plant growth, and the role of humic and fulvic substances.

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Handbook

Bring soil and plant expertise to the work.

Review a publication, interpret a record, or help design the measurements above: which parts of a humic or fulvic material soil microbes use as carbon, and whether a field loses less nitrogen, uses water better or holds more carbon.

Contribute expertiseReview a publication

Associated brand. Quad AG, run by the project’s founders, sells products for soil and plants. No study on this page tested its products.

How the project relates to its brands

Sources and further reading

  1. USDA Natural Resources Conservation Service. Soil Health Management. www.nrcs.usda.gov/conservation-basics/soil/soil-health/soil-health-managementLiving roots, soil communities and the rhizosphere.
  2. USDA Natural Resources Conservation Service. Soil Biology Primer. www.nrcs.usda.gov/resources/education-and-teaching-materials/soil-biology-primerThe wider soil community.
  3. Kaiser C, et al. Exploring the transfer of recent plant photosynthates to soil microbes: mycorrhizal pathway vs direct root exudation. New Phytologist. 2014 online, 2015 in print. doi.org/10.1111/nph.13138Recently fixed carbon reaches soil microbes through roots and through mycorrhizal fungi.
  4. Cotrufo MF, et al. Formation of soil organic matter via biochemical and physical pathways of litter mass loss. Nature Geoscience 8:776 to 779. 2015. doi.org/10.1038/ngeo2520Soluble compounds processed by microbes end up attached to minerals.
  5. Lehmann J, Kleber M. The contentious nature of soil organic matter. Nature 528:60 to 68. 2015. doi.org/10.1038/nature16069Organic matter on mineral surfaces is protected from decomposers; persistence is set by the surroundings.
  6. De Hita D, Fuentes M, Fernández V, Zamarreño AM, Olaetxea M, García-Mina JM. Discriminating the short-term action of root and foliar application of humic acids on plant growth: emerging role of jasmonic acid. Frontiers in Plant Science 11:493. 2020. doi.org/10.3389/fpls.2020.00493The controlled study: root and foliar application of a humic acid in hydroponic cucumber.
  7. Zhang P, et al. Dose-dependent application of straw-derived fulvic acid on yield and quality of tomato plants grown in a greenhouse. Frontiers in Plant Science 12:736613. 2021. doi.org/10.3389/fpls.2021.736613The straw-derived fulvic preparation and the tomato experiments.
  8. Rose MT, Patti AF, Little KR, Brown AL, Jackson WR, Cavagnaro TR. A meta-analysis and review of plant-growth response to humic substances: practical implications for agriculture. Advances in Agronomy 124:37 to 89. 2014. doi.org/10.1016/B978-0-12-800138-7.00002-4The 81-study meta-analysis: average gains, their spread, and the role of source and stress.
  9. Canellas LP, et al. Humic acids isolated from earthworm compost enhance root elongation, lateral root emergence, and plasma membrane H+-ATPase activity in maize roots. Plant Physiology 130:1951 to 1957. 2002. doi.org/10.1104/pp.007088Laboratory maize seedlings: root length, lateral roots and proton pump activity.
  10. Lv X, Li Q, Deng X, et al. Fulvic acid application increases rice seedlings performance under low phosphorus stress. BMC Plant Biology 24:703. 2024. doi.org/10.1186/s12870-024-05435-4Rice seedlings short of phosphate: phosphorus uptake, and the pH buffer that removed the gain.
  11. Kulikova NA, Abroskin DP, Badun GA, et al. Label distribution in tissues of wheat seedlings cultivated with tritium-labeled leonardite humic acid. Scientific Reports 6:28869. 2016. doi.org/10.1038/srep28869Tritium from a labelled leonardite humic acid in wheat seedling roots and shoots.
  12. Olk DC, Dinnes DL, Scoresby JR, Darlington JW, Hurburgh CR, Rippke GR. Maize growth and grain yield responses to a micronized humic product across soil types and annual weather patterns in central Iowa, United States. Frontiers in Plant Science 12:672078. 2021. doi.org/10.3389/fpls.2021.672078The field study, and the worked framework example: Iowa maize strip plots, no field-wide effect, gains on eroded upland soil.
  13. Olk DC, Dinnes DL, Callaway CR. Maize growth responses to a humic product in Iowa production fields: an extensive approach. Frontiers in Plant Science 12:778603. 2022. doi.org/10.3389/fpls.2021.778603Replicated Iowa production fields: yield gains of 1 to 4 percent.
  14. Hartz TK, Bottoms TG. Humic substances generally ineffective in improving vegetable crop nutrient uptake or productivity. HortScience 45:906 to 910. 2010. doi.org/10.21273/HORTSCI.45.6.906University trials in processing tomato with no effect.
  15. Mahoney KJ, McCreary CM, Depuydt D, Gillard CL. Fulvic and humic acid fertilizers are ineffective in dry bean. Canadian Journal of Plant Science. Published online 2016. Abstract read. doi.org/10.1139/cjps-2016-014335 Ontario dry bean trials with no effect.
  16. Yu X, Yang J, Wang E, Li B, Yuan H. Effects of growth stage and fulvic acid on the diversity and dynamics of endophytic bacterial community in Stevia rebaudiana Bertoni leaves. Frontiers in Microbiology 6:867. 2015. doi.org/10.3389/fmicb.2015.00867Endophyte communities in stevia leaves shifted with fulvic acid.
  17. Lengrand S, Dubois B, Pesenti L, Debode F, Legrève A. Humic substances increase tomato tolerance to osmotic stress while modulating vertically transmitted endophytic bacterial communities. Frontiers in Plant Science 15:1488671. 2024. doi.org/10.3389/fpls.2024.1488671Endophyte communities in tomato roots shifted with a humic product.

Prepared by Carbon Biome Project, 19 October 2026; revised 22 October 2026. External scientific review of this page has not been completed. Citing the USDA Natural Resources Conservation Service does not imply its endorsement of the project.

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