As early as when soil taxonomists in China had different opinions on the formation and classification of paddy soil, Chen Huagui took the lead in studying the seasonal changes of ammonia nitrogen and nitrate nitrogen in paddy soil during the drought in summer and winter, aiming at the importance of rice production and the particularity of paddy soil fertility in China, which opened up a new field of biological cycle of nutrient elements in paddy soil in China. 1948 The paper published in Science Quarterly of Wuhan University pointed out that ammoniation can be carried out in both dry season and wet season of paddy fields in the Yangtze River basin, and ammonia nitrogen is the only important source of elemental nitrogen under the condition of water storage. In winter, with the improvement of aeration conditions, nitrification is significantly enhanced, and nitrate nitrogen and ammonia nitrogen occupy the same important position. However, after irrigation in spring, due to denitrification, nitrate nitrogen is greatly reduced, leaving only traces. In the mid-1950s, he led four graduate students to study the growth and decline of microbial population in paddy soil after ploughing green manure and storing water to plant rice, including: dominant species; The strain developed from facultative anaerobic to strict anaerobic; Dominant species of ammonifying bacteria; The decomposition of cellulose is mainly the function of cellulose-eating bacteria; The decomposition of lecithin is mainly the function of Bacillus cereus. At the 6th International Conference on Soil Science (Paris) held in 1956, the microbiological characteristics of paddy soil were discussed. During the period of 1957, the academic report "Biological Cycle of Plant Nutrient Elements in Paddy Soil" was given at the Sino-Soviet Rice Planting Scientific Seminar (Wuhan), which comprehensively summarized the biological cycle of plant nutrient elements in rice, discussed the biological changes of carbon, nitrogen, phosphorus, sulfur and iron in paddy soil, and pointed out five characteristics of biological cycle of paddy soil under the conditions of rice and dry farming: humus. The decomposition speed of organic matter is fast; Oxidation-reduction potential (Eh value) and its change category characteristics; The circulation of nitrogen, sulfur and iron is different from that of dry land soil; Applying a small amount of sulfuric acid fertilizer in some paddy soils has a good effect on seedling greening. These conclusions are of pioneering significance to the early research work of microbial and plant nutrient cycling in paddy soil in China.

Another outstanding contribution of Chen Huagui to the study of paddy soil microorganisms is that there are anaerobic nitrifying microorganisms in paddy soil for nitrosation. Since Velogradsky emphasized the necessity of aeration for nitrification of nitrifying microorganisms in 1890, no one has ever doubted that over-nitrification and nitrifying microorganisms are absolutely aerobic. Chen Huagui and his colleague qi zhou discovered anaerobic nitrite bacteria from paddy soil and obtained a pure culture of nitrite bacteria. This discovery has been recorded in the paper "Anaerobic Nitrification and Nitrifying Microorganisms" read by the Eighth International Conference on Soil Science (Bucharest) held in 1964, and published in the American Journal of Soil Science (1983), which aroused strong response from scholars all over the world and received letters from more than 20 related experts and scholars, praising and soliciting contributions. From the discovery of facultative anaerobic nitrification in paddy soil and the identification of high oxidation potential on rice root surface, the general law that nitrifying microorganisms and nitrification have been considered as absolute aerobic since the end of last century was denied, and the classic schema of paddy soil stratification and inorganic nitrogen transformation and loss by Japanese scholar (1956) in 1950s was developed and revised.

In the 1990s, although Chen Huagui was over 70 years old, he still led scientific and technical personnel to engage in molecular genetics research of nodule nitrogen fixation, and continued to contribute his intelligence and wisdom to the great cause of the four modernizations of the motherland, giving full play to his light and heat.