Hidden Microbes Beneath Thailand’s Sacred Red Rice Could Replace Chemical Fertilizers

Deep in the paddy fields of Phatthalung Province in southern Thailand, a humble red-grained rice variety called Sangyod has been cultivated for generations, prized for its distinctive aroma, its cultural significance, and its nutritional richness. Now, a team of researchers from Prince of Songkla University has peered into the soil surrounding its roots with an unusually powerful combination of tools, and what they found could help reshape how rice is grown across the region. By pairing long-read shotgun metagenomic sequencing with traditional culture-based screening, the scientists have mapped the bacterial communities living in the rhizosphere of Sangyod rice and identified a shortlist of bacterial strains that could one day serve as living, self-replicating fertilizers.

The study, published in the journal Current Research in Biotechnology, addresses a pressing agricultural dilemma. Conventional rice farming depends heavily on synthetic fertilizers and chemical pesticides, which deliver rapid results but degrade soil structure, reduce microbial diversity, and accumulate toxic residues and heavy metals such as zinc in soil and water. Organic farming, by contrast, avoids these inputs and supports beneficial soil microorganisms, but often yields less in the short term. As fertilizer costs climb and global supply chains wobble, the search for sustainable alternatives has intensified, and one of the most promising candidates is a group of soil bacteria known as plant growth-promoting rhizobacteria, or PGPR.

These bacteria occupy the narrow zone of soil surrounding plant roots, where they promote growth through several well-characterized mechanisms. Some fix atmospheric nitrogen into a biologically usable form, effectively manufacturing fertilizer on site. Others solubilize insoluble phosphates, unlocking a nutrient that plants otherwise cannot access, since most soil phosphorus exists in mineral forms unavailable for direct uptake. Still others produce indole-3-acetic acid, or IAA, an auxin hormone that stimulates root elongation, lateral root formation, and root hair development, thereby improving the plant’s capacity to take up water and nutrients. Bacteria combining these traits have been shown in previous studies to enhance the growth and grain yield of maize and rice, and even to help plants tolerate heavy metal contamination in soils.

To capture the full picture of who lives in the Sangyod rhizosphere, the researchers turned to Oxford Nanopore sequencing, a long-read technology that reads entire stretches of DNA in one pass. They collected rhizosphere soil from three organic and three chemically cultivated Sangyod fields, all located within a few hundred meters of one another in Tamode District, and extracted DNA using a bead-beating lysis protocol. Sequencing on a GridION instrument generated between roughly 91,000 and 175,000 raw reads per sample, corresponding to 149 to 297 megabases of sequence data. After quality filtering, which raised the median read length from under about 1,000 base pairs to between roughly 2,400 and 2,900 base pairs, the reads were classified taxonomically using Kraken2 and abundance was estimated with Bracken, with stringent mapping checks to remove any reads from human, rice, or contaminant sources.

The taxonomic results revealed a community dominated by two bacterial phyla: Pseudomonadota, which accounted for roughly 42 to 53 percent of classified reads, and Actinomycetota, which made up roughly 31 to 43 percent. At the genus level, Streptomyces reigned supreme in every single sample, comprising 21 to 31 percent of reads, followed by Bradyrhizobium, a genus famous for its nitrogen-fixing symbioses. At the species level, the community fragmented into a long tail of taxa, with Pseudomonas putida, Stenotrophomonas maltophilia, Pseudomonas aeruginosa, and Sorangium cellulosum among the most abundant individually represented species. Interestingly, the organic fields showed numerically higher richness and Shannon diversity than the chemical fields, but none of these differences reached statistical significance, suggesting that at the sequencing depth achieved, the two cultivation systems hosted broadly similar bacterial communities.

Metagenomics, however, only tells you who is present, not what they can do. To bridge that gap, the team cultivated bacteria from the soil on two different media: nutrient agar, a general-purpose medium, and yeast extract mannitol agar, a semi-selective medium designed to favor rhizobacteria with nitrogen-fixing potential. From these plates they recovered 18 isolates from YEM agar and 56 from nutrient agar, and subjected all 74 to a battery of functional screens. The results were striking. Sixteen of the 18 YEM isolates, and all 56 nutrient agar isolates, grew on nitrogen-free medium, a preliminary indication of nitrogen-fixing ability. IAA production was detected in every single isolate, with concentrations ranging from under 2 micrograms per milliliter to a remarkable 83.12 micrograms per milliliter in one nutrient agar isolate.

Phosphate solubilization proved rarer but no less interesting. On Pikovskaya agar, where a clear halo around a colony signals the dissolution of insoluble calcium phosphate, 14 of the YEM isolates and 15 of the nutrient agar isolates tested positive. The standout was SSY16, a YEM-derived isolate with a phosphate solubilization index of 1.80, the highest recorded in the study. Molecular identification based on 16S rRNA gene sequencing revealed that SSY16 most closely matches Streptomyces sp. PB-64, with 99.56 percent sequence identity, and phylogenetic analysis placed it firmly within the Streptomyces lineage. This finding carries a satisfying symmetry: the most abundant genus in the metagenomic dataset was also the source of the most powerful phosphate solubilizer recovered in culture, hinting at consistency between the two approaches.

Notably, SSY16 could be grown on YEM medium but was never recovered on nutrient agar, a detail the authors highlight as evidence that culture medium choice fundamentally shapes which rhizobacteria are captured and tested. Streptomyces species are renowned for producing bioactive compounds, including antibiotics, volatile metabolites, and siderophores, iron-scavenging molecules that enhance plant iron nutrition and suppress pathogens by competing for iron. Meanwhile, the highest IAA producer, isolate SSN43, was closely related to Bacillus subtilis subsp. stercoris, while other top performers included relatives of Bacillus stratosphericus, Cytobacillus firmus, Priestia megaterium, and Paenibacillus polymyxa, all genera with documented plant growth-promoting credentials.

The final challenge was compatibility. A bacterial consortium only works if its members cooperate rather than fight. Using a reciprocal agar disc diffusion assay, the researchers tested the six highest IAA-producing isolates against SSY16, the primary phosphate solubilizer. Three isolates, SSN17, SSN28, and SSN43, produced clear inhibition zones against SSY16 in one or both directions, with the strongest antagonism coming from SSN28, a Bacillus altitudinis relative that generated an inhibition radius of over 5 millimeters. But three others, SSN34, SSN18, and SSN52, showed no detectable antagonism in either reciprocal combination. SSN34, which produced 38.96 micrograms per milliliter of IAA and grew on nitrogen-free medium, emerged as the leading candidate to pair with SSY16, with SSN18 and SSN52 as secondary options.

The authors are careful to frame these results as preliminary. The agar-based antagonism assay reflects only in vitro conditions, the sequencing depth was limited relative to the staggering diversity of soil, and the culture conditions, two media, one temperature, and short incubation periods, inevitably captured only a subset of the total microbial community. Growth on nitrogen-free medium indicates potential nitrogen fixation but does not confirm it biochemically. The real test will come in co-culture experiments, greenhouse trials, and eventually field validation, where the candidate consortium must prove it can boost Sangyod rice growth under real plant-associated conditions. Still, the study offers a compelling template for sustainable agriculture: by combining the census power of long-read metagenomics with the functional precision of targeted cultivation, researchers can move from anonymous soil DNA to named, characterized, and compatible bacterial partners, bringing the vision of microbe-powered rice farming one step closer to the paddy.

Subject of Research: Rhizosphere microbiome and plant growth-promoting rhizobacteria of Sangyod rice under organic and chemical cultivation

Article Title: Integrated shotgun metagenomic and culture-based characterization of plant growth-promoting rhizobacteria associated with Sangyod Rice

Article References: Rangchai, J., Moolika, N., Chanasongkhram, K., Sathapondecha, P., Iewkittayakorn, J., & Sangket, U. (2026). Integrated shotgun metagenomic and culture-based characterization of plant growth-promoting rhizobacteria associated with Sangyod Rice. Current Research in Biotechnology, Article 100427. https://doi.org/10.1016/j.crbiot.2026.100427

Image Credits: AI Generated

DOI: Not provided

Keywords: Sangyod rice, plant growth-promoting rhizobacteria, shotgun metagenomics, Oxford Nanopore sequencing, rhizosphere microbiome, phosphate solubilization, indole-3-acetic acid, nitrogen fixation, Streptomyces, Bacillus, biofertilizers, sustainable agriculture