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Does Trichoderma change root microbes in rockwool?
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Rockwool goes into a glasshouse sterile, with no organic matter in it, but soilless systems are colonised by microbes, especially bacteria, soon after planting. A team at the University of New England in Armidale, New South Wales, set out to describe the microbes living around the roots of glasshouse tomatoes in rockwool, and to see what a Trichoderma-based biocontrol product did to them (Thomas et al., 2026).
What this means for your grow
The root zone of a rockwool crop is not empty. In this trial the authors found a species-rich bacterial community around mature tomato roots, and they conclude that mineral substrates in a hydroponic system can support a complex and resilient root microbiome. Treating the slabs with a Trichoderma product did not significantly change the root-zone bacteria over the sampling period, and the Trichoderma itself showed up only at low levels. The study did not measure plant health or yield, so it cannot tell you whether the product helped the crop.
What did the team do?
The team grew 24 grafted tomato plants in a temperature-controlled glasshouse at the university, set up to copy a commercial rockwool system. Seedlings started in rockwool propagation cubes and were then planted on rockwool slabs, three plants to a slab, with eight slabs across two hydroponic channels. Water and a two-part fertiliser went in by drip irrigation, in an open (drain-to-waste) system, and plants were watered only in daylight. As the plants matured, the irrigation solution was adjusted to the levels used in a commercial glasshouse, with a target pH of 5.5 to 6.5 and a target EC (electrical conductivity) of 2.8 to 3.0 mS per centimetre.
At 68 days after planting, when the first trusses were mature, four randomly chosen slabs were treated with a commercial biocontrol product containing multiple strains of Trichoderma, poured onto the propagation cubes. The other four slabs were left untreated as controls. The team then sampled the root zone on four occasions between 68 and 79 days after planting, taking small cores from the propagation cube and from two places in the slab, and cutting roots that had grown outside the slab. They identified the bacteria and fungi in each sample from their DNA.
What did they find?
- Lots of bacterial species, but a few dominate. Samples held an average of 553 unique bacterial amplicon sequence variants (ASVs). The 10 most dominant ASVs accounted for more than 25% of all the sequences, so the authors describe the community as species-rich but unevenly distributed. The biggest groups were Alphaproteobacteria (mean 38.9%), Gammaproteobacteria (22.8%) and Bacteroidia (15.1%).
- Fewer kinds of fungi. The fungal community was less diverse and consisted almost exclusively of Ascomycota (mean 64%) and Rozellomycota (29%). Within the Ascomycota, Plectosphaerella (mean 51%) and Fusarium (11%) were the most common. The authors note that Plectosphaerella can be pathogenic to plants.
- The bacteria did not notice the treatment. There was no significant difference in bacterial diversity or composition between treated and untreated plants.
- Trichoderma arrived, but only just. It was not detected before treatment. Afterwards it was found in all four treated slabs, and in one control slab, at low relative abundance (about 0.1% of the fungal reads). Apart from Trichoderma itself, the treatment made no significant difference to how common the dominant fungi were.
- The community changed anyway. In treated and untreated plants alike, bacterial diversity dropped significantly between day 2 and day 7 after treatment, then came back to levels like the first samples. The make-up of the community had changed significantly by day 7 and stayed different from the first samples.
What could it mean?
The authors say the uneven spread of species in rockwool can reduce microbiome stability, so encouraging a wider range of the plant-associated bacteria already present is a potential way to lower the risk of root-borne pathogens in rockwool. They suggest the fertigation solution, which is mostly or entirely mineral ions, could be enriched with more varied organic compounds to support a wider variety of plant-associated microbes. They also caution that a biological treatment tested on soil crops may not suit a soilless system, and that if a beneficial organism cannot compete with the microbes already there and persist, or needs frequent reapplication, its benefits are likely to be negligible.
The authors call this a preliminary study. For now it is most useful to researchers and to commercial glasshouse growers thinking about how biological products behave in rockwool, rather than a guide to what a product will do in a home setup.
What were the limitations?
- The study did not look at the plants themselves, such as their health or yield. The authors say identifying links between plant health and the microbiome is an important target.
- It used a single plant variety and a short sampling period of 11 days. The authors say a longer sampling period is needed, since the microbiome has been seen to change over the life of a rockwool crop.
- Samples were pooled to get DNA of good enough quality for sequencing, which reduced the statistical power of the results.
- Sampling focused on the rhizosphere and did not aim to recover endophytic organisms, which the authors say may explain the low Trichoderma readings. They say a more specific assay method should be used to quantify root-colonising biocontrol agents such as Trichoderma.
- Differences between studies in sampling intervals and diversity measures meant the authors could not conclude whether the changes they saw over time are common in hydroponic systems or specific to their own setup.
- The paper's figures do not always agree in small details. The sampling period is called 12 days in the results and 11 days in the discussion, and the test comparing treated and untreated bacterial communities is given as p = 0.68 in the text and p = 0.66 in the figure caption. Neither changes the finding of no significant difference.
Trial details
- Where: a temperature-controlled glasshouse at the University of New England, NSW, Australia, designed to replicate a commercial rockwool hydroponic system. All plants were in the same glasshouse compartment.
- Crop: tomato (Solanum lycopersicum) cultivar 'Endeavour', grafted on rootstock 'DRO141'. Plants were grown to maturity and sampled while bearing mature trusses.
- How long: treatment at 68 days after planting (DAP); sampling on four occasions between 68 and 79 DAP.
- System and substrate: nursery stage in rockwool propagation cubes (Plantop, Grodan), then rockwool slabs (GT Master, Grodan). 24 plants on two parallel hydroponic channels, four slabs per channel, three plants per slab. Open (drain-to-waste) drip irrigation with municipal water, irrigated only during daylight, with the frequency and duration of irrigation shots adjusted to the time of day and light intensity.
- Nutrition: two-part fertiliser added by proportional injectors. As plants matured, target pH 5.5 to 6.5 and target EC 2.8 to 3.0 mS cm−1.
- Climate: 25°C day and 18°C night at first, then 23°C day and 16°C night once the first trusses were mature.
- Treatment: a commercial biocontrol agent containing multiple strains of Trichoderma (PlantMate, Agrimm, New Zealand), 180 mg mixed in 10 L of tap water and poured onto the propagation cubes of plants in four randomly selected slabs (two per channel), at 68 DAP. Four slabs were left as untreated controls. The manufacturer recommends reapplication every 10 to 14 days.
- Sampling: horizontal cores (9 mm diameter, 100 mm long) from the propagation cube, the slab below the plant stem and the slab between plants, plus bare roots growing outside the slab, pooled for each plant. Groups: before treatment (n = 6), untreated control (n = 12) and treated (n = 12).
- Methods: Illumina MiSeq sequencing of the 16S rRNA gene V4 region (bacteria) and the ITS1 region (fungi). Diversity compared with Kruskal-Wallis tests and PERMANOVA; differences in abundance tested with ANCOM-BC2 and DESeq2.
- Results, bacteria: average 553 unique ASVs per sample (SD 61.2); top 10 ASVs more than 25% of sequences. No difference between treated and untreated plants in alpha diversity (Shannon-Wiener index, Χ2(2) = 0.3, p = 0.87) or composition (PERMANOVA of weighted Unifrac distances, n = 24, F = 0.67, p = 0.68). Significant drop in diversity between day 2 and day 7 after treatment (Faith's phylogenetic diversity, Χ2(3) = 20.1, p < 0.001); composition changed by day 7 (PERMANOVA, n = 32, F = 5.81, p = 0.001). In later samples Novosphingobium was enriched (log2-fold-change 2.10, q < 0.001), while Emticicia (LFC −1.72, q = 0.02) and Cellvibrio (LFC −2.62, q = 0.0054) were depleted.
- Results, fungi: Ascomycota mean 64% (SD 22%), Rozellomycota 29% (SD 16%), Plectosphaerella 51% (SD 27%), Fusarium 11% (SD 10%), unclassified 7.6% (SD 7.1%). Trichoderma the only genus significantly differentially abundant between treated and untreated plants (DESeq2, log2-fold-change = 5.0, p-adj = 0.01). Unweighted composition differed between treated and untreated plants (PERMANOVA, n = 24, F = 2.31, p = 0.008); weighted composition did not (F = 1.53, p = 0.195). Shannon-Wiener diversity, control against treated, Χ2(1) = 3.6, p = 0.056 (approached significance).
- Funding and conflicts of interest: supported by the Australian Government, and by Future Food Systems Cooperative Research Centre (CRC) Ltd. under the Australian Commonwealth Government CRC Program, project P2-007, 'Microbial rhizosphere diversity in glasshouse hydroponic crops'. The authors thank project partners from Costa Tomato Exchange. The authors declare no conflicts of interest.
- Publication: Environmental Microbiology Reports 18(3), e70380, published online 21 June 2026, https://doi.org/10.1111/1758-2229.70380. Licence: CC BY 4.0.
- Not reported in the paper: the dates or year of the trial; lighting (any supplementary light, light levels, photoperiod); relative humidity and CO2; the fertiliser recipe; whether the Trichoderma product was applied again; and any measure of plant growth, health or yield.
Links
- The study: Diversity, Composition and Resilience of the Root Microbiome of Tomato Plants in a Hydroponic Rockwool System (free full text also on PubMed Central)
- The project: Microbial rhizosphere diversity in glasshouse hydroponic crops, Future Food Systems CRC
References
- Thomas, P., Sindel, B., & Winter, G. (2026). Diversity, composition and resilience of the root microbiome of tomato plants in a hydroponic rockwool system. Environmental Microbiology Reports, 18(3), e70380. https://doi.org/10.1111/1758-2229.70380