The science behind rice cultivation in Japan

Daniel Kowalski (Kumamoto)

Whether amidst towering mountains or one of the rare, flat floodplains that speckle the coastline, one constant feature defines the Japanese landscape. In a country of such varied habitats, the flooded rice paddies create patchworks crisscrossed by narrow country roads on the plains and stacked terraces climbing the mountainsides. 

My area of Kumamoto Prefecture is surrounded by lowland paddies. A glance at a map reveals the area sectioned into neat, albeit irregular, rectangles, and my daily journeys to and from work are illuminated by observing the flora and fauna change with the seasons. Rice plants start as seedlings in dry soil, sunning themselves for a while until they are firmly established, and are then partially submerged as the fields are flooded.With the arrival of summer, the dogged intensity of the sun eventually bleaches their stalks yellow, bowing them under the weight of budding rice. The diverse wildlife drawn to this shifting habitat has been a favorite aspect of my life in Japan; from herons stalking at harvest, to shoaling fish of all sizes, miniature mud-brown frogs, cascading flocks of sparrows, and dragonflies floating like distant dust motes above sun-drenched summer fields.

Japanese rice farming is thought to have begun in the Yayoi period (somewhere between 300 BCE to 250 CE). At that time, Japan experienced heavy cultural influence from China and Korea, and rice farming techniques likely arrived via the Asian mainland. In feudal times, rice was so highly valued that a proportion of the crop was collected as tax by the government. 

In Japan or beyond, show someone a picture of a water-logged field filled with grassy green stems and they’ll quickly identify it as rice. This is an iconic image—no other common crop is grown under the same conditions.

Rice is unique, with distinct adaptations, benefits, and problems.

Poolside plants

So, why do most other plants not like being waterlogged? For the same reason that you or I wouldn’t enjoy being sat underwater—it makes it rather hard to breathe. 

Plants photosynthesise, taking carbon dioxide from the air and using sunlight to transform the gas into sugars. This converts sunlight into tangible, easily-stored chemical energy. The sugars formed can be broken back down into gases to release the chemical energy they store. This is respiration—the same process we humans use to power ourselves. Both photosynthesis and respiration generate energy for the plant, but photosynthesis is only an option when there’s sunlight. So plants must also respire to augment their energy during the day and to allow themselves to survive the long, dark night. 

Respiration requires oxygen gas from the air, and the plant can absorb it in two places: the green leaves and stems, and the roots. As plants don’t have lungs to manage gas exchange, often they need to absorb oxygen all over the plant itself, so that it reaches the various tissues that need it. This is why standing water is a big problem for a lot of plants. That layer of water above the soil reduces the speed that oxygen gas caught between grains of soil is replaced, and so there is quickly nothing available to be absorbed by roots. Photosynthesis is not an option: there isn’t a lot of light underground. The green leaves and stalks of plants can also absorb oxygen from the air, but, as most are not built to move that absorbed gas between roots and stem, the roots cannot create energy. 

Rice plants are an exception. Their stalks have spongy tubes (called aerenchyma literally meaning “air infusion”) that allow for the movement of oxygen from the top of the plant to the base, and so they are pretty happy in waterlogged conditions that would have other plants wither. Some strains can even survive being fully submerged by either growing quickly until they break the surface of the water or entering a hibernation-like state to conserve resources.

This also explains why we often grow rice in waterlogged conditions. It stops or destroys the pesky weeds that would exist in a dry field. They simply cannot cope with standing water in the way rice plants can. This doesn’t require any agrochemical weed killers, which might have negative impacts on the local environment and water system. It’s low-tech and green—what more could you want?

A lurking menace

The lack of oxygen in waterlogged fields also affects the microbes that live in that soil. Just like plants and animals, some microbes use oxygen to power themselves and aren’t able to keep operating without it. But unlike plants and animals, not all of these oxygen-using microbes rely on sugars as fuel.

Beneath rice paddies are certain microbes that use the methane gas produced by other communities of microorganisms instead. Methane is best known for its role as a greenhouse gas—a component of the atmosphere that helps the planet retain heat and, when the levels of it increase, contributes to global warming. Methane is roughly 200 times less prevalent in the atmosphere than carbon dioxide, but far more effective at trapping heat. Each gram of methane in the atmosphere is thought to trap about 30 times more heat than the same amount of carbon dioxide over a 100 year time-frame.

Agriculture is the largest source of anthropogenic methane emissions. Most of this comes from livestock (a little under 80% in 2021) but the remainder is almost entirely due to rice cultivation. Worldwide, this is slowly increasing, and production will likely continue growing alongside the human population. Large-scale, intensivist farming is also likely to increase, to the further detriment of the environment. Therefore, reducing these emissions can only have a positive effect, even if other greenhouse gas sources can have their emissions figures further reduced in absolute terms. 

Although the low-oxygen soils under rice paddies are veritable methane factories, they show a relative reduction in the amounts of a different greenhouse gas emitted. Nitrous oxide is less prevalent than carbon dioxide or methane, but much more efficient when it comes to warming the planet. Methane, on average, lingers in the atmosphere for about 12 years, while nitrous oxide can remain in our skies for 109. This longevity contributes to its absurd warming effect; gram for gram it traps about 273 times as much heat as carbon dioxide over 100 years. It also contains, as the name might suggest, oxygen—something that rice fields are relatively deficient in. For fields that are cycled between wheat and rice over the course of a year, studies have consistently shown a tendency for higher nitrous oxide production during the wheat season (up to 70% of the annual total). 

Careful management of crop rotation and flooding of rice fields has the potential to minimize the production of both methane and nitrous oxide, and that’s not the only good news for Japanese rice fields.

A haven of diversity

A large proportion of Japan’s red list of threatened species live in wetlands (50% as of 2011). Following a reduction in naturally-occurring wetlands with increasing land management, many of these rare flora and fauna now exist in a kind of symbiosis with the well-managed aquacultural landscape produced by rice farming. 

The creation of paddies usually involves forming earthen banks as a retaining wall for the area to be flooded, particularly to form the terraces in upland farms. The roots of colonizing grasses add much needed stability to what would otherwise be a long pile of dirt, and so plant life is encouraged to grow here. Mowing two or three times a year keeps the vegetation in check. But it also has a secondary effect. The repeated cutting prevents any single hardier species from dominating the habitat formed, and helps to maintain plant diversity. This has a knock-on effect to promote diversity further up the food chain. 

This style of land management may have further benefits in upland farms. Fertilizer is naturally washed downhill in these environments, leaving the higher terraces relatively nutrient-poor. Some plant species favor these growing conditions, and several species of rare plants have been shown to be more common in these elevated terraces. The introduction of wetland habitat also adds diversity to the existing grassland and forest habitats found in Japan’s mountains, allowing for more complex ecosystems to develop.

The active management of rice fields is crucial to their benefits. Simply letting nature take the wheel results in a loss of biodiversity, as the hardier or invasive plants take over. 

Europe has similar issues with rewilding in its woodlands. Simply allowing a woodland to develop without human intervention creates a primary woodland with a relatively low biodiversity. Repurposing farmland to new woodland is not the solution to maintaining the diversity of animals and plants. Instead, the maintenance of older, existing woodland (secondary woodland) is vital to ensure this biodiversity survives. However, some have suggested that abandonment of farmland in Australia or North America could have the opposite effect. The methods of farming employed in these areas are a legacy of European colonialism, and it is thought that farmland could revert to pre-settlement conditions if nature is given the chance to allow the native landscape to recover. 

The future of rice farming in Japan

For Japan, the survival of many endangered species currently relies on the practice of traditional rice farming. But this too is endangered. 

As the country’s population contracts, younger people are rapidly moving away from the sparsely-inhabited countryside to the relative affluence, opportunity, and companionship offered by larger cities. This shift has effectively crippled the potential labor force for traditional farming methods. The number of workers in Japan’s agricultural sector is decreasing by around 50,000 a year, with the average age of workers over 65 years old as of 2022. Many of these farmers also maintain side jobs to ensure a steady income. Alongside a shift in dietary preference to bread and pasta, brought about by Western influence, the future for rice farming is uncertain.

These, though, are changes at the national level. Kyushu in general, and my area of central Kumamoto specifically, have increasing birth rates. My local population is growing, both from this and migration into the satellite towns surrounding the city of Kumamoto itself. Yet there is still rice farming here.

Japan isn’t homogeneous – it has a mixed character, just as rice paddies have a mixed character. Their role as maintained wetland habitats offers refuge to endangered plants and animals, while contributing to significant greenhouse gas emissions. Rice is Japan’s only self-sufficient staple food, and with international conflicts bringing domestic food security into sharper focus, the Japanese government has invested heavily in subsidy programs to support the industry. However, Japan is distinct in lacking the centralized, intensivist farming of other major rice-producing countries. Despite this bringing challenges in competitiveness, it is vital for lower greenhouse gas emissions and higher biodiversity.  

In the future, it will be important to preserve this balance of the natural and the constructed in areas such as mine. I hope that I can visit Japan in five, 10, or even 20 years, and still find great open seas of waving stalks stretching to the distant mountains, green and verdant enough to make the grass look bland in comparison, and still with the drifting motes of distant dragonfly wings reflecting the morning sunlight.


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Daniel Kowalski is currently an ALT in Kumamoto Prefecture. Prior to moving to Japan, he spent half a decade working as a research chemist and still gets a little buzz from learning more about how the world works. He enjoys reading, hiking, and Daiso.

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