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Journal of Integrative Agriculture  2023, Vol. 22 Issue (3): 923-934    DOI: 10.1016/j.jia.2022.08.036
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Changes in the activities of key enzymes and the abundance of functional genes involved in nitrogen transformation in rice rhizosphere soil under different aerated conditions

XU Chun-mei*, XIAO De-shun*, CHEN Song, CHU Guang, LIU Yuan-hui, ZHANG Xiu-fu, WANG Dan-ying#

The State Key Laboratoty of Rice Biology, China National Rice Research Institute, Hangzhou 310006, P.R.China

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土壤微生物在氮转化过程中具有很重要的作用。本实验的目的是研究根际增氧方式处理后水稻根际土壤氮转化功能基因(硝化、反硝化以及固氮基因)丰度和关键酶(脲酶、蛋白酶、氨氧化酶、硝酸还原酶以及亚硝酸还原酶)活性变化。试验设计三种增氧方式(长淹处理:又称厌氧灌溉,水稻整个生育期保持3-5 cm水层;长淹增氧处理:种植方式同长淹。水稻种植之前,在土培盆中埋入打过孔的PVC管并接到增气泵上。首次通气2小时,此后每天间隔2小时通气10分钟(由计时器控制);干湿交替处理:又称好氧灌溉,自浅水层自然落干到土壤水势达-15 kPa 时,灌水 1~2 cm,再自然落干至土壤水势为-15 kPa,再上浅层水,如此循环),研究水稻主要生育期(分蘖期、齐穗期和成熟期)根际土壤氮转化功能基因丰度和关键酶活性变化,并分析各微生物活性指标间的相关性。结果表明,各处理水稻根际土壤氮转化功能基因丰度和关键酶活性均以齐穗期最高。增氧(长淹增氧和干湿交替处理)后水稻根际土壤硝化功能基因、固氮基因丰度增加、反硝化功能基因丰度降低;脲酶、蛋白酶和氨氧化酶活性提高,硝酸还原酶和亚硝酸还原酶活性降低,干湿交替处理尤其明显。干湿交替处理后水稻整个生育期根际土壤氨氧化古菌(AOA)和氨氧化细菌(AOBamoA基因以及固氮基因丰度的平均值分别是长淹处理的2.875.752.97倍,反硝化功能基因nirS, nirK丰度分别比长淹处理减少73.61%84.41%;脲酶、蛋白酶和氨氧化酶活性分别比长淹处理增加1.130.51和0.72倍,硝酸还原酶和亚硝酸还原酶活性分别比长淹处理减少10.30%36.48%。相关分析结果显示:硝化功能基因和固氮基因丰度与脲酶、蛋白酶和氨氧化酶活性呈极显著正相关;反硝化功能基因丰度与硝酸还原酶活性呈极显著正相关。上述指标和土壤微生物碳、微生物氮含量均呈正相关。综上,水稻根际土壤氮转化相关的微生物活性在齐穗期最高。增氧可以提高大多数氮素转化微生物活性和土壤微生物氮含量,从而促进水稻根际土壤氮素的转化。


Soil microorganisms play important roles in nitrogen transformation.  The aim of this study was to characterize changes in the activity of nitrogen transformation enzymes and the abundance of nitrogen function genes in rhizosphere soil aerated using three different methods (continuous flooding (CF), continuous flooding and aeration (CFA), and alternate wetting and drying (AWD)).  The abundances of amoA ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), nirS, nirK, and nifH genes, and the activities of urease, protease, ammonia oxidase, nitrate reductase, and nitrite reductase were measured at the tillering (S1), heading (S2), and ripening (S3) stages.  We analyzed the relationships of the aforementioned microbial activity indices, in addition to soil microbial biomass carbon (MBC) and soil microbial biomass nitrogen (MBN), with the concentration of soil nitrate and ammonium nitrogen.  The abundance of nitrogen function genes and the activities of nitrogen invertase in rice rhizosphere soil were higher at S2 compared with S1 and S3 in all treatments.  AWD and CFA increased the abundance of amoA and nifH genes, and the activities of urease, protease, and ammonia oxidase, and decreased the abundance of nirS and nirK genes and the activities of nitrate reductase and nitrite reductase, with the effect of AWD being particularly strong.  During the entire growth period, the mean abundances of the AOA amoA, AOB amoA, and nifH genes were 2.9, 5.8, and 3.0 higher in the AWD treatment than in the CF treatment, respectively, and the activities of urease, protease, and ammonia oxidase were 1.1, 0.5, and 0.7 higher in the AWD treatment than in the CF treatment, respectively.  The abundances of the nirS and nirK genes, and the activities of nitrate reductase and nitrite reductase were 73.6, 84.8, 10.3 and 36.5% lower in the AWD treatment than in the CF treatment, respectively.  The abundances of the AOA amoA, AOB amoA, and nifH genes were significantly and positively correlated with the activities of urease, protease, and ammonia oxidase, and the abundances of the nirS and nirK genes were significantly positively correlated with the activities of nitrate reductase.  All the above indicators were positively correlated with soil MBC and MBN.  In sum, microbial activity related to nitrogen transformation in rice rhizosphere soil was highest at S2.  Aeration can effectively increase the activity of most nitrogen-converting microorganisms and MBN, and thus promote soil nitrogen transformation. 

Keywords:  rhizosphere aeration        gene abundance       enzyme activities        soil microbial biomass carbon        soil microbial nitrogen  
Received: 23 March 2022   Accepted: 26 May 2022

This research was supported by the Key Research and Development Program of Zhejiang Province, China (2022C02008), the National Natural Science Foundation of China (31401343), the earmarked fund for China Agriculture Research System (CARS-01), and the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences (CAAS-ZDRW202001).

About author:  XU Chun-mei, E-mail:; #Correspondence WANG Dan-ying, Tel: +86-571-63370276, E-mail: wangdanying * These authors contributed equally to this study.

Cite this article: 

XU Chun-mei, XIAO De-shun, CHEN Song, CHU Guang, LIU Yuan-hui, ZHANG Xiu-fu, WANG Dan-ying. 2023.

Changes in the activities of key enzymes and the abundance of functional genes involved in nitrogen transformation in rice rhizosphere soil under different aerated conditions . Journal of Integrative Agriculture, 22(3): 923-934.

Akter M, Deroo H, Grave E D, Alboom T V, Sleutel S. 2018. Link between paddy soil mineral nitrogen release and iron and manganese reduction examined in a rice pot growth experiment. Geoderma, 326, 9–21.
Behrendt T, Braker G, Song G Z, Pommerenke B, Drsch P. 2017. Nitric oxide emission response to soil moisture is linked to transcriptional activity of functional microbial groups. Soil Biology & Biochemistry, 115, 337–345.
Braker G, Fesefeldt A, Witzel K P. 1998. Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Applied and Environmental Microbiology, 64, 3769–3775.
Cao H, Feng F, Xun M, Huang P, Li Y, Ji T, Wei G, Zhang W, Yang H. 2018. Effect of carbonized apple wood on nitrogen-transforming microorganisms and nitrogen oxides in soil of apple tree root zone. European Journal of Soil Science, 69, 545–554. 
Che R, Qin J, Tahmasbian I, Wang F, Zhou S, Xu Z, Cui X. 2018. Litter amendment rather than phosphorus can dramatically change inorganic nitrogen pools in a degraded grassland soil by affecting nitrogen-cycling microbes. Soil Biology & Bichemistry, 120, 145–152.
Chen J, Shen W J, Xu H, Li Y D, Luo T S. 2019. The composition of nitrogen-fixing microorganisms correlates with soil nitrogen content during reforestation: A comparison between legume and non-legume. Frontiers in Microbiology, 10, 1–10.
Chen Y C, Li F S, Li L B. 2018. Effects of different irrigation methods and ratios of urea pig manure on microbial activity related to nitrogen transformation in paddy soil. Journal of South China Agricultural University, 39, 31–39. (in Chinese) 
Coskun D, Britto D T, Shi W, Kronzucker H J. 2017. How plant root exudates shape the nitrogen cycle. Trends in Plant Science, 22, 661–673.
Erisman J W, Galloway J N, Dise N B, Bleeker M A S A, Vries W D. 2015. Nitrogen: Too Much of a Vital Resource. Science Brief. WWF Netherlands Zeist, the Netherlands. pp. 2–48.
Francis C A, Roberts K J, Beman J M, Santoro A E, Oakley B B. 2005. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proceedings of the National Academy of Sciences of the United States of America, 102, 14683–14688. 
Galloway J N, Townsend A R, Erisman J W, Bekunda M, Cai Z C, Freney J R, Martinelli L A, Seitizinger S P, Sotton M A. 2008. Transformation of nitrogen cycle: Recent trends, questions and potential solutions. Science, 320, 889–892.
Ghiloufi W, Seo J, Kim J, Chaieb M, Kang H. 2019. Effects of biological soil crusts on enzyme activities and microbial community in soils of an arid ecosystem. Microbial Ecology, 77, 201–216.
Gregory L G, Karakas-Sen A, Richardson D J, Spiro S. 2000. Detection of genes for membrane-bound nitrate reductase in nitrate-respiring bacteria and in community DNA. FEMS Microbiology Letters, 183, 257–279.
Gruber N, Galloway J N. 2008. An earth-system perspective of the global nitrogen cycle. Nature, 451, 293–296. 
van der Heijden M G A, Bardgett R D, Bardgett, van Straalen N M. 2008. The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystmes. Ecollogy Letters, 11, 296–310.
Jangid K, Williams M A, Franzluebbers A J, Sanderlin J S, Reeves J H, Jenkins M B, Endale D M, Coleman D C, Whitman W B, 2008. Relative impacts of land-use, management intensity and fertilization upon soil microbial community structure in agricultural systems. Soil Biology and Biochemistry, 40, 2843–2853.
Jin K, Sleutel S, Buchan D, Neve S D, Cai D X, Gabriels D, Jin J Y. 2009. Changes of soil enzyme activities under different tillage practices in the Chinese Loess Plateau. Soil and Tillage Research, 104, 115–120.
Kuypers M M M, Marchant H K, Kartak B. 2018. The microbial nitrogen-cycling network. Nature Reviews Microbiology, 16, 263–276.
Levy-Booth D J, Prescott C E, Grayston S J. 2014. Microbial functional genes involved in nitrogen fixation, nitrification and denitrification in forest ecosystems. Soil Biology and Bichemistry, 75, 11–25.
Li Z L, Tian D S, Wang B X, Wang J S, Wang S, Chen H Y H, Xu X F, Wang C H, He N P, Niu S L. 2019. Microbes drive global soil nitrogen mineralization and availability. Global Change Biology, 25, 1078–1088.
Liu Y, He N P, Wen X F, Wen X F, Yu G R, Gao Y, Jia Y L. 2016. Patters and regulating mechanisms of soil nitrogen mineralization and temperature sensitivity in Chinese terrestrial ecosystems. Agriculture, Ecosystems Ecosystems & Environment, 215, 40–46.
Lu R K. 2000. Soil Agricultural Chemical Analysis Methods. Agricultural Science and Technology Press, Beijing, China. (in Chinese)
Michotey V, Mejean V, Bonin P. 2000. Comparison of methods for quantification of cytochrome cd1-denitrifying bacteria in marine samples. Applied and Environmental Microbiology. 66, 1564e1571.
Ni L X, Xu J J, Chu X L, Li S Y, Wang P F, Li Y P, Li Y, Zhu L, Wang C. 2016. Correlation among soil enzyme activities, root enzyme activities, and contaminant removal in two-stage in situ conxtructed wetlands purifying domestic wastewater. Bulletin of Environmental Contamination and Toxicology, 97, 131–137.
OkanoY, Hristova K R, Leutenegger C M, Jackson L E, Denison R F, Gebreyesus B, Lebauer D, Scow K M. 2004. Application of real-time PCR to study effects of ammonia, on population size of ammoniaoxidizing bacteria in soil. Applied and Environmental Microbiology, 70, 1008–1016.
Rosch C, Bothe H. 2005. Improved assessment of denitrifying, N2-fixing, and total community bacteria by terminal restriction fragment length polymorphism analysis using multiple restriction enzymes. Applied and Environmental Microbiology, 71, 2026–2035. 
Rotthauwe J H, Witzel K P, Liesack W. 1997. The ammonia monooxygenase structural gene amoA as a functional marker: molecular finescale analysis of natural ammonia-oxidizing populations. Applied and Environmental Microbiology, 63, 4704–4712.
Schimel J P, Bennett J. 2004. Nitrogen mineralization: Challenges of a changing paradigm. Ecology, 85, 591–602. 
Sharma S, Singh P, Choudhary O P, Neemisha. 2021. Nitrogen and rice straw incorporation impact nitrogen use efficiency, soil nitrogen pools and enzyme activity in rice–wheat system in north-western India. Fields Crops Research, 266, 108131.
Si G H, Yuan J F, Xu X G, Zhao S J, Peng C L, Wu J S, Zhou Z Q. 2018. Effects of an integrated rice-crayfish farming system on soil organic carbon, enzyme activity, and microbial diversity in waterlogged paddy soil. Acta Ecologica Sinica, 38, 29–35.
Song X J, Wu H J, Wu X P, Li Q, Wang B S, Li S P, Liang G P, Li J, Liu C C, Zhang M N. 2018. Long-term conservation tillage improves surface soil carbon and nitrogen content and rhizosphere soil enzyme activities. Journal of Plant Nutrition and Fertiliers, 24, 1588–1597. (in Chinese)
Streit K, Hagedorn F, Hiltbrunner D, Portmann M, Saurer M, BuchmannN, Wild B, Richter A, Wipf S, Siegwolf R T W. 2014. Soil warming alters microbial substrate use in alpine soils. Global Chang Biology, 20, 1327–1338.
De la Torre J R D L, Walker C B, Ingalls A E, Knneke M, Stahl D A. 2008. Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environmental Microbiology, 10, 810–818.
Turner S, Meyer-Stüve S, Schippers A, Guggenberger G, Schaarschmidt F, Wild B, Richter A, Dohrmann R, Mikutta R. 2017. Microbial utilization of mineral-associated nitrogen in soils. Soil Biology & Biochemistry, 104, 185–196.
Wang S, Pablo G P, Ye J, Huang D F. 2012. Abundance and diversity of nitrogen-fixing bacteria in rhizosphere and bulk paddy soil under different duration of organic management. World Journal of Microbiology & Biotechnology, 28, 493–503.
Xu C M, Chen L P, Chen S, Chu G, Wang D Y, Zhang X F. 2020. Rhizosphere aeration improves nitrogen transformation in soil and nitrogen absorption and accumulation in rice plants. Rice Science, 27, 162–174.
Xu C M, Wang D Y, Chen S, Chen L P, Zhang X F. 2013. Effects of aeration on root physiology and nitrogen metabolism in rice. Rice Science, 20, 148–153.
Yang Y J, Zhang J B, Cai Z C. 2016. Nitrification activities and N mineralization in paddy soils are insensitive to oxygen concentration. Acta Agriculturae Scandinavica (Section B: Soil & Plant Science), 66, 272–281.
Yi N, Gao Y, Zhang Z, Wang Y, Liu X, Zhang L, Yan S. 2015. Response of spatial patterns of denitrifying bacterial communities to water properties in the stream inlets at Dianchi Lake, China. International Journal of Denomics, 2015, 1–11.
Zhang J P, Zhou X H, Chen L, Chen Z G, Chu J Y, Li Y M. 2016. Comparison of the abundance and community structure of ammonia oxidizing prokaryotes in rice rhizosphere under three different irrigation cultivation modes. World Journal of Microbiology & Biotechnology, 32, 85. 
Zhang Y, Li Q, Chen Y L, Dai Q, Hu J. 2019. Dynamic change in enzyme activity and bacteial community with long-term rice cultivation in mudflats. Current Microbiology, 76, 361–369.
Zhao F, Wang D Y, Xu C M, Zhang W J, Li F B, Mao H J, Zhang X F. 2010. Response of morphological, physiological and yield characteristics of rice (Oryza sativia L.) to different oxygen-increasing patters in rhizosphere. Acta Agronomica Sinica, 36, 303–312. (in Chinese)
Zilio M, Motta S, Tambone F, Scaglia B, Boccasile G, Squartini A, Adani F. 2020. The distribution of functional N-cycle related genes and ammonia and nitrate nitrogen in soil profiles fertilized with mineral and organic N fertilizer. PLoS ONE, 2, 1–19.
Zumstein M T, Helbling D E. 2019. Biotransformation of antibiotics: Exploring the activity of extracellular and intracellular enzymes derived from wastewater microbial communities. Water Research, 155, 115–123. 

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