Key takeaways for organic greenhouse operators
Build and manage living soil. The 2026 Canadian Organic Standards place greater emphasis on soil biological function, including maintaining active microbial and macroorganism communities in container soils. Fertility management should therefore consider the long-term development of soil health, not just immediate nutrient availability.
Consider replacing animal-based fertilizers with plant-based fertilizers. Research showed that yields were maintained when alfalfa meal replaced 50% or 100% of the nitrogen from a standard animal-based fertilizer program. Alfalfa meal also reduced N₂O and NH₃ losses and increased indicators of soil health.
Recognize how management shapes the soil microbial community. Research showed that alfalfa meal and silage influenced microbial abundance and function differently from animal-based fertilizer, and that responses varied between mineral soil and peat-based systems. Growers should therefore consider the interactions between fertilizer source, the growing medium and conditions experienced by the existing microbial community.
From growing medium to living soil
The 2026 Canadian Organic Standards (COS) mark an important clarification in expectations for organic greenhouse production. While growing crops in containers remains permitted, the updated standards explicitly require that the growing medium function as a living soil by supporting microorganisms and macroorganisms that contribute to nourishing plants through natural biological processes.
The requirements for the composition of soil used in organic container systems remain largely unchanged (Box 1). However, the 2026 standards now require the soil to be reused for at least three consecutive years, placing greater importance on building and maintaining a functioning biological community within the soil over time.
Box 1. Minimum requirements for soil used in an organic container system. CAN/CGSB-32.310–2026
The soil used in a container must contain:
- at least 2% mineral material (by dry weight or volume);
- at least 10% compost (by volume); and
- (new in 2026) a biological fraction that supports root-soil interaction and soil health.
The standards also tighten the use of highly soluble nitrogen and phosphorus fertilizers. These inputs are now limited to no more than 20% of a crop’s nutrient requirements, based on realistic yield expectations. This further emphasizes that organic production should rely primarily on biological nutrient cycling. Hydroponic and aeroponic systems, in which crops receive nutrients through soluble nutrient solutions, continue to be prohibited under the COS.
Research by Dr. Martine Dorais and her colleagues is helping to develop management practices that support greenhouse productivity while remaining aligned with organic principles. Rather than focusing only on crop yield, their research considers the greenhouse as an agroecosystem and examines how management practices affect a broad range of ecosystem services. One aspect of this research is the use of plant-based fertilizers as alternatives to animal-based fertilizers.
Can plant-based fertilizers replace animal-based fertilizers?
Interest in using plant-based fertilizers such as alfalfa meal is increasing. Not only do plant-based fertilizers reduce reliance on commercial animal-based fertilizers sourced from conventional agriculture, they may also benefit soil ecosystem services.
As part of OSC4, Charlotte Giard-Laliberté, a PhD student working with Dr. Dorais, has been evaluating plant-based fertilizers in two commercial organic greenhouse production systems: a soil-based system and a container system (Box 2).
In one study, researchers replaced 50% or 100% of the nitrogen in the standard animal-based fertilizer program with alfalfa meal. They evaluated crop production and several ecosystem services, including nitrogen losses, soil carbon and nitrogen storage and biological soil health.
Box 2. Research study production systems
Soil-based system: Native mineral soil
Container system: Peat-based growing medium (referred to as a “soilless” system in the linked journal articles)
Standard fertilizer program: 80% nitrogen from feather meal and 20% nitrogen from pelleted poultry manure
Crops: Cucumber (cycle 1) and tomato (cycle 2)
Across both production systems, alfalfa meal resulted in a tighter coupling between nitrogen release and crop demand. It also reduced two important forms of nitrogen loss: nitrous oxide (N₂O), a potent greenhouse gas, and ammonia (NH₃). Although alfalfa meal did not reduce nitrogen leaching, it improved several indicators of soil health including soil carbon and nitrogen storage and populations of earthworms, beneficial bacteria and fungi.
Importantly, these benefits were achieved without sacrificing crop yields.
In the soil-based system, crops had access to soil nitrogen reserves. Crops recovered only about 28% of the applied fertilizer nitrogen but fertilizer nitrogen not taken up by crops was largely retained in the soil rather than being lost to the environment. This potentially contributes to longer-term soil fertility. In this system, complete replacement of standard fertilizer with alfalfa meal had little effect on yield.
The situation was different in the container system. Because the peat-based medium provided relatively little available nitrogen, crops depended much more heavily on fertilizer inputs. Crops recovered about 75% of the applied fertilizer nitrogen. Even in this system, replacing up to 50% of the standard fertilizer nitrogen with alfalfa meal maintained crop yields.
For greenhouse growers this is an important finding: alfalfa meal has the potential to successfully replace a substantial portion of animal-based fertilizer in both intensive soil-based and container greenhouse systems.
Fertilizer choice changes the soil microbial community
A second study examined an aspect of organic greenhouse production that is becoming increasingly important under the new standards: the soil microbial communities.
Researchers compared two plant-based fertilizers – alfalfa meal and silage – with the standard animal-based fertilizer program. They analyzed procaryotic and fungal DNA to determine how fertilizer treatments affected soil microbial communities and their potential patterns of nutrient use.
One indicator they examined was the number of ribosomal RNA (rrn) gene copies in bacteria. Microorganisms with more rrn gene copies generally have greater potential for rapid growth when nutrients are abundant; these are known as copiotrophs. In contrast, microorganisms with fewer rrn gene copies tend to be better adapted to lower-nutrient conditions and are more efficient at decomposing complex compounds; these are known as oligotrophs.
The researchers expected the plant-based fertilizers – with their higher carbon-to-nitrogen ratios and greater amounts of complex carbon compounds such as cellulose – to favour microbes adapted to breaking down these materials.
The results showed that fertilizer choice did, in fact, influence which microorganisms were most abundant, but the response depended on the resource conditions of the growing system, particularly carbon and nitrogen availability.
In the mineral soil, as expected, alfalfa meal encouraged oligotrophic microorganisms that are good at breaking down more complex forms of carbon and linking carbon and nitrogen cycling. In the peat-based medium, microbes were already accustomed to a carbon-rich but nitrogen-poor environment. In this case, microbes responded mainly to the additional nitrogen supplied by the fertilizers; the proportion of copiotrophic microorganisms increased as did nitrogen cycling.
Silage, and to a lesser extent alfalfa meal, also brought new microorganisms into the system, acting as microbial inocula. This had particularly noticeable effects in the container soil. Whether these changes are temporary or not remains unclear.
For greenhouse growers, it is important to recognize that the fertilizer effects on the soil microbiome depend not only on the fertilizer source but also on the growing medium and conditions experienced by the existing microbial community.
Managing organic greenhouses as agroecosystems
The 2026 COS reinforce a shift toward managing organic greenhouses as functioning agroecosystems. For growers, this means considering how management practices influence the biological processes that support crop nutrition and soil health. Dr. Dorais’ research, which evaluates a broad range of ecosystem services, provides a more comprehensive picture than yield measurements alone and helps identify management practices that strengthen the long-term resilience of organic greenhouse systems.
This article is based on the following scientific journal articles:
Giard-Laliberté C, Madore-Millette G, Pelster DE, Messiga AJ, Dessureault-Rompré J, Dorais M. 2026. Improving ecosystem services with alfalfa meal in highly intensive organic soil-based and soilless greenhouse systems. Agronomy for Sustainable Development 46: 40. https://doi.org/10.1007/s13593-026-01112-y.
Giard-Laliberté C, Thomas J, Nguyen Thi Thuy An, Hogue R, Tekeu H, Dunfield K, Dorais M. 2026. Plant-based fertilization leads to distinct shifts in bacterial trophic strategies, microbial functional potential, and enzyme activity in soil-based and soilless organic greenhouse systems. Applied Soil Ecology. 277. https://doi.org/10.1016/j.apsoil.2026.107350
Stay tuned for more findings from Dr. Martine Dorais’ research team as they continue exploring innovative greenhouse practices – including biochar and intercropping!
Published September 29, 2026
Organic Science Cluster 4 is an industry-led research and development endeavour co-managed by the Organic Federation of Canada and the Organic Agriculture Centre of Canada at Dalhousie University and supported by the AgriScience Program under Agriculture and Agri-Food Canada’s Sustainable Canadian Agricultural Partnership together with over 80 funding partners.
