#FEMSmicroBlog: Growing rice with less water – how do microbes like it?


Rice is a staple food for more than half of the world’s population. It is cultivated on millions of hectares’ land worldwide. In conventional practice, rice fields are permanently flooded during cultivation. This makes it the largest water consumer in the agricultural sector and, due to the activity of anaerobic microbes, an immense contributor to greenhouse gas emissions. The study “Effect of water management on microbial diversity and composition in an Italian rice field system” published in FEMS Microbiology Ecology investigates the impact of an alternative water-saving cultivation strategy. Claudia Lüke explains for #FEMSmicroBlog how adapted water management affects the microbial communities in the rice field ecosystem. #FascinatingMicrobes


How do microbes impact rice fields?

Microbes play key roles in rice fields since they impact nutrient cycling and greenhouse gas emissions. Some beneficial organisms also support rice plants by improving their health and growth.

To water rice fields, farmers permanently cover the soil with water making the soil environment anoxic. Under these conditions, microorganisms that can use alternative electron acceptors to oxygen – such as nitrate, ferric iron and sulfate – are thriving.

In such anoxic soil, anaerobic and fermenting microorganisms degrade organic matter with methanogenic archaea producing methane as an end product. As a result, flooded rice fields are great contributors to global methane emissions.

Due to microbial fermentation, flooded rice fields are great contributors to global methane emissions.

Next to the anoxic bulk soil, rice roots can release oxygen to the soil thus forming small aerobic niches. In the rhizosphere – the soil around the roots – microbes can accumulate, interact with the root and stimulate plant growth.


How to save water in rice agriculture?

Preventing the accumulation of anaerobic microorganisms by growing rice with less water is not easy. Reducing watering can have huge impacts on crop productivity while pest control becomes more difficult.

One alternative strategy of rice field watering is ‘Alternate Wetting and Drying’, which is the focus of the study “Effect of water management on microbial diversity and composition in an Italian rice field system” published in FEMS Microbiology Ecology. Instead of permanently covering the fields with water, they are initially flooded, then allowed to dry and re-flooded again. This strategy tries to find a balance between using as little water as possible and sufficient amounts for optimal crop yields.

A field experiment was set up at the Research Centre for Cereal and Industrial Crops in Vercelli (Northern Italy) consisting of different field blocks. These were either cultivated conventionally – meaning continuously flooded – during plant growth or cultivated under the ‘Alternate Wetting and Drying’ conditions.

The experimental field site at the Research Centre in Vercelli.

The samples for the study were taken from the bulk soil and from the rice roots. Since each rice variety reacts differently to changing growth conditions, they can have impacts on microbes around the roots. Therefore, the study also tested two different rice varieties (Vialone Nano and Centauro). The diversity of bacteria and archaea in all individual samples was analysed by amplifying and sequencing 16S rRNA genes.


How does alternate watering affect microbes in rice fields?

The study showed that the composition of microbes in the bulk soil was very different from that of the rice roots. Interestingly, very specialised and less diverse microbial communities surrounded the roots. However, these microbiomes also seemed more vulnerable to changes or disturbances.

Schematics of microbial communities in the soil of rice fields.
Microbial communities in rice field soil. Illustrated by Juliane Lüke.

Whereas the bulk soil communities stayed similar in all treatments, the water management strategy strongly affected the microbes attached to the roots. For instance, taxa of the Sphingomonadaceae and Rhizobiaceae (Alphaproteobacteria), Enterobacteriaceae and Xanthomonadaceae (Gammaproteobacteria), as well as many Flavobacteriaceae (Bacteroidetes) were enriched during the ‘Alternate Wetting and Drying’ treatment. These families comprise many strains with plant-growth-promoting activities.

In general, microbes with an overall anaerobic lifestyle, including methanogens, were less abundant in rice fields treated with the ‘Alternate Wetting and Drying’ approach. These results suggest that they produce less methane and emit it into the atmosphere – a promising hypothesis to achieve our climate goals.


About the author of this blog

Claudia Lüke is a microbial ecologist. She obtained her PhD at the Max Planck Institute for Terrestrial Microbiology in Marburg (Germany) and worked as a Postdoc at the Radboud University in Nijmegen (the Netherlands).

About this blog section

The section #FascinatingMicrobes for the #FEMSmicroBlog explains the science behind a paper and highlights the significance and broader context of a recent finding. One of the main goals is to share the fascinating spectrum of microbes across all fields of microbiology.

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