Soil Fungi Give Drought-Stricken Purple Rice a Boost, and One Species Stands Out

Beneath the flooded paddies and dry upland fields of northeastern Thailand, an invisible partnership is quietly shaping the future of one of the world’s most nutritious staple crops. A new study published in the Journal of Agriculture and Food Research has shown that native arbuscular mycorrhizal fungi (AMF) isolated from Thai rice soils can dramatically improve the growth, drought resilience, and nutritional quality of Maled Phai, a prized purple-brown pigmented rice cultivar rich in health-promoting antioxidants. Remarkably, not all fungal partners performed equally: one species, Gigaspora margarita, consistently outshone its rivals, offering a glimpse of how carefully matched soil microbes could become a cornerstone of climate-resilient agriculture.

Rice feeds more than half of humanity, but pigmented varieties such as Maled Phai occupy a special niche. Their dark purple-brown grains accumulate anthocyanins, the same class of pigments found in blueberries and black rice, alongside phenolic compounds, flavonoids, carotenoids, and phytosterols. These bioactive molecules have attracted intense scientific interest because of their antioxidant potential and possible protective effects against coronary heart disease and cancer. Yet pigmented rice is as vulnerable as any cereal to drought, which disrupts photosynthesis, stunts growth, impairs grain filling, and can degrade the very compounds that make these varieties nutritionally valuable. As climate change intensifies water scarcity across Southeast Asia, researchers are searching for sustainable tools that protect both yield and grain quality without costly irrigation or chemical inputs.

The research team, led by Thanawan Gateta and Sophon Boonlue of Khon Kaen University, turned to an ancient biological solution: the mutualistic fungi that colonize the roots of most terrestrial plants. AMF penetrate root cortical cells and extend vast networks of hyphae into the soil, dramatically expanding the plant’s absorptive surface. In exchange for plant sugars, the fungi deliver water and nutrients, particularly phosphorus, which moves sluggishly through dry soil. The team collected rhizosphere soil from rice fields in three Thai provinces, Khon Kaen, Roi Et, and Buriram, and isolated ten native AMF isolates using wet-sieving and decanting techniques. Spore abundance ranged from just 1.00 to a striking 102.64 spores per gram of soil, and root colonization rates among the isolates spanned from 26.67 percent to 84.00 percent.

Three high-performing isolates were selected for rigorous identification. Morphological examination of spore shape, pigmentation, size, and wall structure, combined with SSU-ITS-LSU rDNA sequencing and maximum likelihood phylogenetic analysis, assigned the isolates to two genera: Acaulospora citrusnsis (RE-KKU-008), Acaulospora mellea (RE-KKU-009), and Gigaspora margarita (RE-KKU-010). Each was then multiplied in pot cultures using maize as a host plant, and standardized inocula of 200 spores were applied to rice seedlings at transplanting, ensuring that every pot received an equal fungal dose.

The greenhouse experiment was ambitious in scope. A factorial randomized complete block design crossed three water regimes, 100, 66, and 33 percent of available water, with the three AMF species and an uninoculated control, across nine replications. Soil moisture was monitored daily by gravimetric methods and maintained at target levels for the duration of the growing season. The researchers measured everything from plant height and tiller number to gas exchange, chlorophyll content, root architecture, biomass, yield components, nutrient concentrations, oxidative stress markers, antioxidant enzyme activities, and the full suite of grain bioactive compounds.

The results were striking. Inoculated plants grew taller, produced more tillers, and photosynthesized faster than their uninoculated counterparts, with the strongest effects under well-watered and moderately dry conditions. Under moderate drought at 66 percent available water, plants inoculated with A. mellea and G. margarita maintained growth and photosynthetic performance approaching those of well-watered controls, suggesting that this intermediate stress level represents an optimal operating range for the symbiosis. Root systems told a similar story: mycorrhizal plants developed longer roots with greater surface area and volume, and retained higher relative water content and chlorophyll levels as water became scarce. Biomass, both above and below ground, followed the same pattern, with A. citrusnsis and G. margarita producing the heaviest plants under full irrigation and all three fungi cushioning losses under drought.

Yield and nutrition benefited in parallel. Mycorrhizal plants produced more panicles and heavier grain loads, and their shoots carried significantly higher concentrations of nitrogen, phosphorus, and potassium, elements central to photosynthesis, energy transfer, and assimilate transport to developing grains. Microscopy confirmed that the fungi had genuinely taken hold: root sections stained with Trypan Blue revealed abundant intraradical hyphae, vesicles, and arbuscules, the tree-like exchange structures characteristic of successful colonization, while these structures were entirely absent in controls. Colonization exceeded 60 percent in all inoculated treatments, reaching 88 percent in plants treated with A. mellea.

Perhaps the most novel finding concerned grain quality. Under both moderate and severe drought, mycorrhizal plants maintained higher levels of total phenolic content, anthocyanins, and flavonoids, along with stronger DPPH radical-scavenging activity, than uninoculated plants. Under well-watered conditions, G. margarita produced the highest phenolic and anthocyanin concentrations. The researchers attribute this enhancement to activation of the phenylpropanoid pathway, the metabolic route that generates phenolics, flavonoids, and anthocyanins. In effect, the fungi helped the rice preserve its functional food value precisely when drought would normally erode it, a dual benefit for farmers growing premium pigmented rice.

The biochemical evidence revealed how the symbiosis shields plants at the cellular level. Drought triggers the accumulation of reactive oxygen species, which damage membranes and proteins, reflected in elevated hydrogen peroxide and malondialdehyde. Mycorrhizal plants under drought showed markedly lower levels of these oxidative stress markers, together with boosted activities of the detoxifying enzymes superoxide dismutase, peroxidase, and catalase, and increased proline, an osmoprotectant that helps cells retain water. Correlation analysis reinforced the picture: root colonization was positively associated with growth, physiological, and nutritional traits, and negatively correlated with oxidative damage. Principal component analysis cleanly separated treatments by water regime and fungal status, with the first two components explaining 68.5 percent of total variance.

Why did Gigaspora margarita dominate? The authors point to its biology: its large spores are packed with lipid droplets and storage reserves that fuel rapid germination and establishment, and its extensive extraradical hyphae excel at exploring dry soil for water and nutrients. Host-fungus compatibility likely plays a role as well, since symbiotic performance depends on the interplay of fungal species, plant genotype, and environment. Notably, most prior rice studies have focused on Glomus-type fungi, leaving the potential of Gigaspora largely unexplored. The study also moves beyond the typical two-level drought design by testing a three-point water gradient, revealing that fungal benefits peak at moderate stress rather than scaling linearly with severity, because severe drought starves the fungus of carbon while abundant water removes the plant’s need for the partnership. The team cautions that greenhouse results must now be validated in the field, and that transcriptomic and metabolomic work could illuminate the mechanisms behind G. margarita’s superiority. Still, the message is clear: the right native fungus, matched to the right crop, could help farmers grow more resilient, more nutritious rice on a warming, water-stressed planet.

Subject of Research: Species-specific effects of indigenous arbuscular mycorrhizal fungi on drought resilience and grain bioactive compounds in pigmented rice

Article Title: Species-specific effects of indigenous arbuscular mycorrhizal fungi on growth, drought resilience, and grain bioactive compound accumulation in Maled Phai rice ( Oryza sativa L.)

Article References: Gateta, T., Seemakram, W., Kamoshita, A., Ekprasert, J., Kokaew, U., Sawaengkaew, J., Jangpromma, N., & Boonlue, S. (2026). Species-specific effects of indigenous arbuscular mycorrhizal fungi on growth, drought resilience, and grain bioactive compound accumulation in Maled Phai rice (Oryza sativa L.). Journal of Agriculture and Food Research, 31, Article 103353. https://doi.org/10.1016/j.jafr.2026.103353

Image Credits: AI Generated

DOI: 10.1016/j.jafr.2026.103353

Keywords: arbuscular mycorrhizal fungi, Maled Phai rice, drought stress, anthocyanins, Gigaspora margarita, Acaulospora, antioxidant enzymes, phenolic compounds, grain quality, sustainable agriculture, phosphorus uptake, Thailand