Winter flooding of paddy rice production is characterized by flooding of paddy fields during the winter fallow season. It has attracted attention in terms of its ecological function, supporting the biodiversity of paddy field ecosystems. Therefore, recent winter flooding in Japan has been conducted by organic farming. However, it is not well documented how organic farming with winter flooding affect the productivity of rice. We conducted field experiments to examine changes in rice yield in organic farming with winter flooding compared with those in conventional and organic farming over the period of 5 and 9 years. The yields in organic farming with winter flooding were lower than those in conventional farming but were almost the same as those in organic farming. We found a trend that shows the relative yield of organic farming with winter flooding compared to that of conventional farming increased during the first several years after the conversion from conventional farming to organic farming with winter flooding, but that it decreased after several years. This trend may be caused by the flourishing of weeds during continuous organic farming with winter flooding. Therefore, we tested four weed control methods: rice bran application, mechanical weeding, repeated puddling, and side-row fertilizer application. Although each method suppressed weeds to certain extents, some combinations of different weeding methods more effectively suppressed weed growth, thereby resulting in enhanced rice yields. We found a trend in rice yield and a possibility of combining several weed control methods in organic farming with winter flooding.
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