Green Manure Can Backfire: Too Much of a Good Thing Boosts Toxic Gas and Cuts Rice Yields

Green manure has long been celebrated as one of agriculture’s most environmentally friendly tools. Farmers plow nitrogen-rich cover crops into their fields, feeding the soil, reducing synthetic fertilizer needs, and building organic matter in a single operation. Across China and much of Asia, the practice is central to efforts aimed at making rice production more sustainable. But a new mesocosm-scale study published in the journal Plant and Soil reveals a hidden cost that has largely escaped scrutiny: when green manure is applied at high rates, paddy soils begin to emit substantially more hydrogen sulfide, a toxic and foul-smelling gas that can damage rice plants and undermine the very yields the practice is meant to improve.

The research, led by Sheng-Nan Hou and corresponding author Hui Zhu of the Northeast Institute of Geography and Agroecology at the Chinese Academy of Sciences, together with colleagues from Fujian Normal University and Nanjing Normal University, set out to answer a deceptively simple question. What happens to hydrogen sulfide emissions in flooded rice paddies when green manure is incorporated at different rates, and how do those emissions connect to the microbial machinery of the sulfur cycle and to the final harvest? The answer, it turns out, is a story of thresholds, trade-offs, and a delicate microbial balance that farmers ignore at their peril.

The team designed a mesocosm experiment with four treatments representing a gradient of green manure inputs: a control with no incorporation, and three levels of 15,000, 30,000, and 45,000 kilograms per hectare. Mesocosms, essentially contained experimental ecosystems, allowed the researchers to track gas emissions, soil chemistry, plant performance, and microbial communities under controlled conditions that mimic real paddy environments. This scale of experimentation sits comfortably between laboratory incubations and full field trials, giving the results a robustness that smaller studies often lack.

The headline finding is stark. Cumulative hydrogen sulfide emissions rose in lockstep with the amount of green manure incorporated. Compared with the control, the low, medium, and high application rates produced 2.39-fold, 7.10-fold, and 8.75-fold increases in cumulative emissions, respectively. In other words, tripling the green manure input from the low to the high rate more than tripled the gas released. The timing of these emissions followed a clear and predictable pattern: hydrogen sulfide release peaked within the first 30 days after incorporation, when fresh organic matter was decomposing most rapidly, then declined steadily and essentially ceased after about 55 days.

Why does adding plant biomass to a waterlogged soil generate this toxic gas? The mechanism lies in the biology of sulfate-reducing bacteria, a group of microorganisms that thrive in the oxygen-starved conditions of flooded paddies. These bacteria respire sulfate rather than oxygen, converting it to sulfide as a metabolic byproduct. Fresh green manure delivers a surge of easily degradable carbon and nutrients into the soil, and the study found that this influx promoted the accumulation of soil nutrients including total nitrogen, total phosphorus, and total organic carbon. Those enriched conditions, in turn, enhanced the abundance of key sulfate-reducing bacteria and boosted the abundance of functional genes known as cysD and cysN, which are involved in sulfur assimilation and metabolism. More microbial capacity for sulfur processing meant more hydrogen sulfide escaping into the atmosphere.

The consequences for the rice crop were equally striking, and they reveal a Goldilocks dynamic. The low green manure rate of 15,000 kilograms per hectare enhanced rice yield by 6.02 percent compared with the control, delivering exactly the kind of benefit that has made green manuring popular. But the medium rate reduced yield by 12.25 percent, and the high rate was catastrophic, cutting yields by 42.59 percent. The pattern suggests that at moderate to high inputs, hydrogen sulfide toxicity and associated soil conditions overwhelm any nutritional benefit the added biomass provides. Hydrogen sulfide is well known to interfere with root respiration and nutrient uptake in plants, and previous work by some of the same researchers has examined the physiological mechanisms and recovery thresholds of rice plants under hydrogen sulfide stress.

What makes this study particularly valuable is that it connects the dots across multiple levels of the system simultaneously. Rather than measuring emissions in isolation, the researchers linked the gas fluxes to soil nutrient accumulation, to shifts in sulfur-cycling microbial communities, to the abundance of specific functional genes, and finally to the agronomic outcome that matters most to farmers: the size of the harvest. This chain of evidence, from organic input to nutrient enrichment to microbial proliferation to gene expression to gas emission to yield loss, provides a mechanistic narrative that few studies in this field have achieved. It transforms what could have been a simple observational correlation into a causal explanation grounded in microbial ecology.

The implications for agricultural practice are immediate and geographically specific. The authors conclude that the 15,000 kilograms per hectare treatment achieved the most favorable combination of rice yield and soil fertility performance under their mesocosm conditions, offering concrete guidance for agronomic practices in Northeast China, where the research group is based. The message is not that green manure should be abandoned, but that its application rate matters enormously. Moderate incorporation appears to hit the sweet spot, improving fertility and boosting yields without triggering the microbial sulfur cascade that produces harmful emissions at higher doses. Excessive application, by contrast, risks both environmental harm and economic loss.

Beyond the immediate agronomic recommendations, the findings open a broader window onto an underexplored dimension of agricultural greenhouse and trace gas emissions. Hydrogen sulfide from managed ecosystems has received far less attention than carbon dioxide, methane, or nitrous oxide, yet it affects plant health, contributes to odor problems, and participates in atmospheric sulfur chemistry. Related research has documented biogenic hydrogen sulfide emissions from mangrove forests and linked eutrophication in lake sediments to increased sulfur biotransformation and gas release. The new study extends this picture to one of the world’s most important cropping systems, suggesting that as organic amendments become more prevalent in sustainable agriculture, sulfur gas dynamics deserve a place alongside carbon and nitrogen in emissions accounting.

There are also important caveats and directions for future work. The experiment was conducted at mesocosm scale, and while this provides strong internal validity, field-scale confirmation across seasons, soil types, and climates will be needed to refine application thresholds for different regions. The study was supported by the National Natural Science Foundation of China, and the authors note that data will be made available on request. Nonetheless, the core insight stands: the microbial sulfur cycle in paddy soils is highly sensitive to the amount of organic carbon farmers add, and the functional genes that track this sensitivity offer a potential molecular indicator for managing green manure intelligently. As agriculture worldwide pivots toward organic and regenerative practices, this research serves as a timely reminder that sustainability is not simply a matter of adding more nature to the field. It is a matter of dose, timing, and understanding the invisible microbial economies that convert what we bury in the soil into what we breathe from it. Getting that balance right could mean the difference between a greener harvest and a stinking, sulfurous failure.

Subject of Research: Hydrogen sulfide emissions from paddy soils under varying green manure incorporation rates and their effects on rice yield

Article Title: Mechanistic insights into hydrogen sulfide emissions in paddy soils under green manure incorporation and their effects on rice yield

Article References: Mechanistic insights into hydrogen sulfide emissions in paddy soils under green manure incorporation and their effects on rice yield. (n.d.). https://doi.org/10.1007/s11104-026-09148-5

Image Credits: AI Generated

DOI: 10.1007/s11104-026-09148-5

Keywords: green manure, hydrogen sulfide, paddy soil, rice yield, sulfate-reducing bacteria, soil microbiology, sulfur cycle, cysD, cysN, soil fertility, sustainable agriculture, Northeast China