Purple Bacteria From Vietnam’s Acid Sulfate Paddies Cut Methane by Up to 75 Percent

Rice paddies feed billions of people, but they also leak enormous quantities of methane into the atmosphere. Now a team of Vietnamese researchers has found that a group of remarkably hardy microbes harvested from some of the country’s most hostile farmland could help plug that leak while simultaneously feeding the crop. In a study published in International Microbiology, scientists isolated 118 strains of purple nonsulfur bacteria from acid sulfate rice soils across the Mekong Delta and identified three strains capable of cutting methane emissions by as much as 75 percent under laboratory conditions.

The stakes are considerable. Agriculture, forestry, and other land-use sectors account for roughly 22 percent of total global greenhouse gas emissions, and rice cultivation alone releases more than 686 million tonnes of carbon dioxide equivalent each year, according to figures cited from the FAO. Methane is the dominant culprit among paddy emissions, and its global warming potential is 28 times greater than that of carbon dioxide. The problem is particularly acute when rice straw is returned to flooded fields, a practice that builds soil organic carbon but feeds the anaerobic archaea that generate methane as a metabolic byproduct.

The research team, led by Phan Thi Ngoc Nhanh and Nguyen Quoc Khuong, focused on a setting where the challenge is compounded by soil chemistry. Acid sulfate soils, widespread in the Mekong Delta, are characterized by very low pH and high concentrations of toxic aluminum, iron, and manganese. Soil pH values in the sampled fields ranged from 3.82 to 5.30, and aluminum concentrations in some locations exceeded 235 milligrams per kilogram, well above phytotoxic thresholds. These conditions suppress both rice productivity and the activity of most soil microbes, making conventional biological approaches difficult.

Purple nonsulfur bacteria, however, are metabolic generalists. They can grow aerobically, microaerobically, or anaerobically, in light or in darkness, using a wide range of organic substrates including acetate, succinate, and pyruvate. Crucially, that substrate flexibility overlaps with the carbon sources methanogenic archaea depend on, which means the bacteria can compete directly with methane producers for food in flooded soils. Previous work had shown that related strains could reduce methane emissions in saline and heavy-metal-contaminated paddies, but acid sulfate environments remained largely unexplored.

To find suitable candidates, the researchers collected 60 soil and 60 water samples from four representative acid sulfate rice-growing regions: the Plain of Reed and the Depressed of Hau River in Dong Thap and Hau Giang provinces, the Long Xuyen Quadrangle in An Giang, and the Ca Mau Peninsula in Bac Lieu. Samples were taken 30 days after sowing, near rice roots and below the water surface, and composited from 13 points per field. The team then cultured the samples in anaerobic, illuminated tubes and purified the resulting pink, red, and purple colonies until 118 distinct strains were obtained.

Screening was deliberately brutal. Each strain was tested for growth at pH 4.5 and in the presence of iron at 200 milligrams per liter, aluminum at 100 milligrams per liter, and manganese at 1,100 milligrams per liter, concentrations mirroring the worst field conditions. More than 90 percent of the isolates grew well under the acidic conditions, and 100 strains tolerated all three metals. Those survivors were then evaluated for traits valuable to farmers: nitrogen fixation, solubilization of three insoluble phosphate forms, and production of indole-3-acetic acid, a plant growth hormone. Nitrogen fixation rates reached up to 61.9 milligrams of ammonium per liter, phosphate solubilization exceeded 180 milligrams per liter for iron phosphate in the best strains, and hormone production peaked at 14.1 milligrams per liter.

The decisive test came in sealed glass bottles containing fresh acid sulfate soil, ground rice straw, and water, with or without bacterial inoculation. After five days, headspace gas was analyzed by gas chromatography. All 20 top-performing strains reduced methane under both microaerobic light and aerobic dark conditions, but three stood out. Strain WHA-9B achieved reductions of 61.3 percent under light and 75.2 percent in the dark, while WHA-1A reached 68.6 percent in the dark and SPL-4A achieved 45.9 percent under light. Genetic sequencing of the 16S rRNA gene identified WHA-1A and SPL-4A as Rhodobacter sphaeroides and WHA-9B as Blastochloris sulfoviridis.

The mechanism, the authors argue, is substrate competition. When rice straw decomposes anaerobically, it releases acetate, hydrogen, carbon dioxide, and dissolved organic carbon, the preferred fuels of methanogenic archaea. Purple nonsulfur bacteria consume many of the same compounds, diverting carbon into bacterial biomass instead of methane. The bacteria also raise environmental pH during growth, pushing conditions beyond the optimal range of 6.4 to 7.2 for methanogens. Earlier studies support this interpretation: experiments with Rhodopseudomonas palustris found a negative correlation between bacterial cell density and methane emission, and field applications of purple bacteria have cut emissions by the equivalent of roughly three tonnes of carbon dioxide per hectare per season.

The nutrient-supplying traits add a second layer of benefit. By fixing atmospheric nitrogen, the bacteria could reduce dependence on synthetic fertilizers, which themselves stimulate methanogenic activity in flooded soils. By solubilizing the insoluble iron, aluminum, and calcium phosphates that lock up phosphorus in acid sulfate soils, they make a critical nutrient available to rice roots. And by producing indole-3-acetic acid, they promote root development, which improves oxygen transport into the rhizosphere and further suppresses methane production. In principle, a single inoculant could detoxify the soil, feed the plant, and starve the methane producers all at once.

The authors are careful to note the limits of the work. The methane assays were conducted in controlled incubations, and the study did not directly measure changes in methanogen or methanotroph communities, so the proposed mechanisms remain inferential. They recommend follow-up research using quantitative PCR of methanogenic marker genes such as mcrA or high-throughput sequencing to confirm how the bacteria reshape the microbial food web. Even so, the identification of acid- and metal-tolerant strains that combine methane mitigation with plant growth promotion marks a promising step toward biofertilizers tailored to one of the world’s most challenging rice-growing environments, where the dual pressures of food security and climate change meet in the mud.

Subject of Research: Isolation of acid sulfate-tolerant purple nonsulfur bacteria that mitigate methane emissions and supply nutrients in Mekong Delta rice paddies

Article Title: Selection of acid sulfate purple nonsulfur bacteria for mitigating methane emissions from paddy soils in the Mekong Delta, Vietnam

Article References: Nhanh, P. T. N., Nhan, T. C., Bao, M. C., Quang, L. T., Thu, L. T. M., Trong, N. D., Nguyen, T. T. K., Xuan, L. N. T., Xuan, D. T., Phuc, N. T. H., & Khuong, N. Q. (2026). Selection of acid sulfate purple nonsulfur bacteria for mitigating methane emissions from paddy soils in the Mekong Delta, Vietnam. International Microbiology. https://doi.org/10.1007/s10123-026-00883-4

Image Credits: AI Generated

DOI: 10.1007/s10123-026-00883-4

Keywords: purple nonsulfur bacteria, methane emissions, acid sulfate soils, Mekong Delta, rice paddies, greenhouse gases, Rhodobacter sphaeroides, Blastochloris sulfoviridis, nitrogen fixation, phosphate solubilization, biofertilizer, soil microbiology