The effects of organic fertilizers as a fraction substitute to chemical fertilizers on rice yield and quality, greenhouse gas emissions, and microbial diversity in soil | [Pakistan Journal of Botany • 2025]

Author(s):

1. BING HAO: Anhui Engineering Research Center for Smart Crop Planting and Processing Technology, Anhui Science and Technology University,Chuzhou ,China

2. MAN ZHANG: Anhui Engineering Research Center for Smart Crop Planting and Processing Technology, Anhui Science and Technology University,Chuzhou 233100,China

3. HONGZHI MIN: Anhui Engineering Research Center for Smart Crop Planting and Processing Technology, Anhui Science and Technology University,Chuzhou 233100,China

4. QINGQIN SHAO: Anhui Engineering Research Center for Smart Crop Planting and Processing Technology, Anhui Science and Technology University,Chuzhou 233100,China

5. CECE QIAO: Anhui Engineering Research Center for Smart Crop Planting and Processing Technology, Anhui Science and Technology University,Chuzhou 233100,China

6. JIKAI LIU: Anhui Engineering Research Center for Smart Crop Planting and Processing Technology, Anhui Science and Technology University,Chuzhou 233100,China

7. XINWEI LI: Anhui Engineering Research Center for Smart Crop Planting and Processing Technology, Anhui Science and Technology University,Chuzhou 233100,China

8. LUIS ALEJANDRO JOSE MUR: Department of Life Sciences,Penglais Campus, SY23 2DA, Aberystwyth, Wales,UK

9. WANG JIAN FEI: College of Resource and Environment / Anhui Province Agricultural Waste Fertilizer Utilization and Cultivated Land Quality Improvement Engineering Research Center, Anhui Science and Technology of University,Chuzhou 233100,China

10. LANTIAN REN: Anhui Engineering Research Center for Smart Crop Planting and Processing Technology, Anhui Science and Technology University,Chuzhou ,China

11. SHIMEI WANG: Rice Research Institute, Anhui Academy of Agricultural Sciences,Hefei 230041,China

Abstract:

With the implementation of China's zero-growth policy for chemical fertilizer application, increasing attention has been directed toward exploring organic fertilizers as partial substitutes for chemical fertilizers. This study investigated rice cultivation under four fertilization regimes: conventional chemical fertilization (CK) and organic fertilizer substitution at 10% (T1), 20% (T2), and 30% (T3) of total chemical fertilizer equivalents. Key findings include: (1) Comparised with CK, the T1, T2, and T3 treatments increased rice yields by 6.22%, 9.06%, and 4.68%, respectively. Organic fertilizer substitution significantly improved grain quality through reduced chalkiness (8.78%-19.49%), decreased amylose content (9.56%12.95%), and increased protein levels (10.06%-17.29%), collectively enhancing palatability. (2) Seasonal greenhouse gas (GHG) emission patterns showed treatment-independent consistency, but cumulative emissions varied with substitution ratios. Notably, T2 and T3 achieved 10.84% and 25.92% reductions in GHG intensity (GHGI) respectively compared to CK, indicating effective emission mitigation. (3) Organic amendments significantly altered soil microbial community structure. Dominant phyla across treatments included Proteobacteria (8.85%-10.51%), Acidobacteria (10.16%-33.82%), Bacteroidetes (10.82%-71.38%), Chloroflexi (17.05%-22.70%), and Patescibacteria (212.15%-308.41%), The precise mechanisms underlying these microbial-mediated emission processes require further investigation. These findings demonstrate that 20% organic substitution (T2) optimally balances yield enhancement (9.06%) with environmental sustainability (11.00%), providing an effective strategy for green agricultural development in rice production systems.

Page(s): 1243-1254

DOI: 10.30848/PJB2025-4(36)

Published: Journal: Pakistan Journal of Botany, Volume: 57, Issue: 4, Year: 2025

Keywords:

Rice , microorganisms , Greenhouse gas emissions , Rice quality

References:

[1] Allen M.R.,Fuglestvedt J.S.,Shine K.P.,Reisinger A.,Pierrehumbert R.T.,Forster P.M. .2016 .New use of global warming potentials to compare cumulative and short-lived climate pollutants. Nat. Clim, 6(8) : 773-776.

[2] Anas M.,Liao F.,Verma K.K.,Sarwar M.A.,Mahmood A.,Chen Z.L.,Li Q.,Zeng X.P.,Liu Y.,Li Y.R. .2020 .Fate of nitrogen, in agriculture and environment: agronomic, ecophysiological and molecular approaches to improve nitrogen use efficiency. Biol. Res., 53 : 1-20.

[3] Baruah A.,Baruah K.K. .2015 .Organic Manures and Crop Residues as Fertilizer Substitutes: Impact on Nitrous Oxide Emission, Plant Growth and Grain Yield in Pre-Monsoon Rice Cropping System. J. Environ. Prot. Ecol., 06 : 755-770.

[4] Black H. I. J.,Parekh N.R.,Chaplow J.S.,Monson F.,Watkins J.,Creamer R.,Potter E.D.,Poskitt J.M.,Rowland P.,Ainsworth G.,Hornung M. .2003 .Assessing soil biodiversity across Great Britain: national trends in the occurrence of heterotrophic bacteria and invertebrates in soil. JEM., 67(3) : 255-266.

[5] Cao Y.,Tian Y.,Yin B.,Zhu Z. .2013 .Assessment of ammonia volatilization from paddy fields under crop management practices aimed to increase grain yield and N efficiency. Field. Crop. Res., 147 : 23-31.

[6] Case S. D. C.,M. Oelofse Y.,Hou O.,Oenema L.S.,Jensen L.S. .2017 .Farmer perceptions and use of organic waste products as fertilizers - A survey study of potential benefits and barriers. , 151 : 84-95.

[7] Cui X.,Zhang Y.,Gao J.,Peng F.,Gao P. .2018 .Long-term combined application of manure and chemical fertilizer sustained higher nutrient status and rhizospheric bacterial diversity in reddish paddy soil of Central South China. Sci. Rep, 8(1) : 16554.

[8] Dan Y.,Zhu-Hong Y.,Xun X.,Ying Y.,Ming-Da L.,GuiXian X. .2018 .Effects of chemical fertilizer reduction and organic fertilizer use on the greenhouse gas emissions of early rice fields. J. Agro-Environ. Sci., 37(11) : 2443-2450.

[9] Dang P.,Li C.,Lu C.,Zhang M.,Wan C.,Wang H.,Chen Y.,Qin X.,Liao and K.H.M. Siddique Y. .2022 .Effect of fertilizer management on the soil bacterial community in agroecosystems across the globe. Agr. Ecosyst. Environ., 326 : 107795.

[10] Ding L.J.,Su J.Q.,Sun G.X.,Wu J.S.,Wei W.X. .2018 .Increased microbial functional diversity under long-term organic and integrated fertilization in a paddy soil. AMB., 102(4) : 1969-1982.

[11] Dobrovol'skaya D.G.,Zvyagintsev I.Y.,Chernov A.V.,Golovchenko G.M.,Zenova L. V.,Lysak N.A.,Manucharova O.E.,Marfenina L.M.,Polyanskaya A.L.,Stepanov and M.M. Umarov A.L. .2015 .The role of microorganisms in the ecological functions of soils. EurAsian, 48(9) : 959-967.

[12] Elkholy M. M.,Mahrous S. E.,El-Tohamy S.A. .2010 .Integrated effect of mineral, compost and biofertilizers on soil fertility and tested crops productivity. Res. J. Agric. Biol. Sci., 6(4) : 453-465.

[13] Gao N.,Shen W.,Camargo E.,Shiratori Y.,Nishizawa T.,Isobe K.,He X.,Senoo K. .2017 .Nitrous oxide (N2O)- reducing denitrifier-inoculated organic fertilizer mitigates N2O emissions from agricultural soils. Biol. Fert. Soils, 53(8) : 885-898.

[14] Henry S.,Bru D.,Stres B.,Hallet S.,Philippot L. .2006 .nosZ genes in soils. Appl. Environ. Microb., 72(8) : 5181-5189.

[15] Hong C. O.,Kang J.S.,Shin H.M.,Cho J.H.,Suh J.M. .2013 .Effect of compost and tillage on soil carbon sequestration and stability in paddy soil. Int. J. Environ. Sci., 22(11) : 1509-1517.

[16] Hou H.Q.,X.M. Liu J. J,Lv Z.Z.,Lan X.J.,Liu Y.Z. .2020 .Effects of different proportions of organic fertilizer instead of chemical fertilizer on rice yield and nitrogen use efficiency. Soil, 52(04) : 758-765.

[17] Huang L.,Yu J.,Yang J.,Zhang R.,Bai Y.,Sun C.,Zhuang H. .2016 .Relationships Between yield, quality and nitrogen uptake and utilization of organically grown rice varieties. Pedosphere, 26(1) : 85-97.

[18] Ike I. A,Karanfil T.,Cho J.,Hur J. .2019 .Oxidation byproducts from the degradation of dissolved organic matter by advanced oxidation processes - A critical review. Water. Res., 164 : 114929.

[19] Iqbal A.,He L.,Ali I.,Ullah S.,Khan A.,Akhtar K.,Wei S.,Fahad S.,Khan R.,Jiang L. .2021 .Co-incorporation of manure and inorganic fertilizer improves leaf physiological traits, rice production and soil functionality in a paddy field. Sci. Rep, 11(1) : 10048.

[20] Iqbal J.,Hu R.,Lin S.,Hatano R.,Feng M.,Lu L.,Ahamadou B.,Du L. .2009 .CO2 emission in a subtropical red paddy soil (Ultisol) as affected by straw and N-fertilizer applications: A case study in Southern China. , 131(3) : 292-302.

[21] Kim S. I.,Park B. H.,Song Y. K.,Shin Y. K. .2002 .Emission characteristics of methane and nitrous oxide by management of water and nutrient in a rice paddy soil. Korean. J. Environ. Agric., 21(2) : H71-H79.

[22] Kimura M. .1997 .Sources of methane emitted from paddy fields. Nutr, 49(1) : 153-161.

[23] Lanning ,T. ,Siebenmorgen P.A.,Counce A.A.,Ambardekar A.,Mauromoustakos A. .2011 .Extreme nighttime air temperatures in 2010 impact rice chalkiness and milling quality. Field. Crop. Res., 124(1) : 132-136.

[24] Lauber C. L.,Strickland M.S.,Bradford M.A.,Fierer N. .2008 .The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil, 40(9) : 2407-2415.

[25] Mer Le,Roger J. and P. .2001 .Production, oxidation, emission and consumption of methane by soils: A review. Eur. J. Soil. Biol, 37(1) : 25-50.

[26] Limpiyakorn T.,Kurisu F.,Yagi O. .2006 .Quantification of ammonia-oxidizing bacteria populations in full-scale sewage activated sludge systems and assessment of system variables affecting their performance. Water. Sci. Technol, 54(1) : 91-99.

[27] Lin M.,Yang S.,Chen H.,Letuma P.,Khan M.U.,Huang J.,Shen L.,Lin W. .2023 .Optimally combined application of organic and chemical fertilizers increases grain yield and improves rhizosphere microecological properties in rice ratooning. Crop. Sci., 63(2) : 764-783.

[28] Lin W.,Lin M.,Zhou H.,Wu H.,Li Z.,Lin W. .2019 .The effects of chemical and organic fertilizer usage on rhizosphere soil in tea orchards. PloS, 14(5) : e0217018.

[29] Liu L.,Zheng X.,Wei X.,Kai Z.,Xu Y. .2021 .Excessive application of chemical fertilizer and organophosphorus pesticides induced total phosphorus loss from planting causing surface water eutrophication. Sci. Rep, 11(1) : 23015.

[30] López-Mondéjar R.,Voříšková J.,Větrovský T.,Baldrian P. .2015 .The bacterial community inhabiting temperate deciduous forests is vertically stratified and undergoes seasonal dynamics. Soil. Biol, 87 : 43-50.

[31] Moe K.,Moh S.M.,Htwe A.Z.,Kajihara Y.,Yamakawa T. .2019 .Effects of integrated organic and inorganic fertilizers on yield and growth parameters of rice varieties. Rice. Sci., 26(5) : 309-318.

[32] Noguchi M.,Kurisu F.,Furumai H. .2014 .Timeresolved DNA stable isotope probing links Desulfobacteralesand Coriobacteriaceae-related bacteria to anaerobic degradation of benzene under methanogenic conditions. Microbes. Environ., 29(2) : 191-9.

[33] Sadet-Bourgeteau S.,Houot S.,Dequiedt V.,Nowak V.,Tardy S.,Terrat D.,Montenach V.,Mercier B.,Karimi N.Chemidlin,Prévost-Bouré P.A.,Maron P.A. .2018 .Lasting effect of repeated application of organic waste products on microbial communities in arable soils. Appl, 125 : 278-287.

[34] Sánchez-Osuna M.,Barbé J.,Erill I. .2017 .Comparative genomics of the DNA damage-inducible network in the Patescibacteria. , 19(9) : 3465-3474.

[35] Sander B.O.,Samson M.,Buresh R.J. .2014 .Methane and nitrous oxide emissions from flooded rice fields as affected by water and straw management between rice crops. , 235 : 355-362.

[36] Schütz H.,Holzapfel-Pschorn A.,Conrad R.,Rennenberg H.,Seiler W. .1989 .A 3-year continuous record on the influence of daytime, season, and fertilizer treatment on methane emission rates from an Italian rice paddy. J Geophys. ResAtmos., 94(D13) : 16405-16416.

[37] Shan J.,Yan X. .2013 .Effects of crop residue returning on nitrous oxide emissions in agricultural soils. Atmos. Environ., 71 : 170-175.

[38] Shi X.R.,Ren B.B.,Jiang L.L.,Fan S.X.,Cao Y.L.,Ma D.R. .2021 .Effects of organic manure partial substitution for chemical fertilizer on the photosynthetic rate, nitrogen use efficiency and yield of rice. J. Appl. Ecol., 32(1) : 154-162.

[39] Tao S. A.,Wakelin Y.,Liang B.,Hu G.,Chu G. .2018 .Nitrous oxide emission and denitrifier communities in drip-irrigated calcareous soil as affected by chemical and organic fertilizers. Sci. Total, 612 : 739-749.

[40] Wei W.,Isobe K.,Shiratori Y.,Nishizawa T.,Ohte N.,Otsuka S.,Senoo K. .2014 .N2O emission from cropland field soil through fungal denitrification after surface applications of organic fertilizer. Soil, 69 : 157-167.

[41] Wei W.,Yan Y.,Cao J.,Christie P.,Zhang F.,Fan M. .2016 .Effects of combined application of organic amendments and fertilizers on crop yield and soil organic matter: An integrated analysis of long-term experiments. Agr. Ecosyst. Environ., 225 : 86-92.

[42] Wu J. J.,Peng H.,Xie Y.H.,Guan D.,Tian F.X.,Zhu J.,Huo L.J. .2018 .Effects of different organic fertilizers on greenhouse gas emissions and yield in paddy soils. Trans. CSAE, 34 : 162-169.

[43] Xiong Z.Q.,Xing G.X.,Zhu Z.L. .2007 .Nitrous oxide and methane emissions as affected by water, soil and nitrogen Project supported by the National Natural Science Foundation of China. , 17(2) : 146-155.

[44] Yang S.,Xiao Y.N.,Xu J. .2018 .Organic fertilizer application increases the soil respiration and net ecosystem carbon dioxide absorption of paddy fields under watersaving irrigation. Environ. Sci. Pollut, 25(10) : 9958-9968.

[45] Zhai L. M.,Liu H.B.,Zhang J.Z.,Huang J.,Wang B.R. .2011 .Long-term application of organic manure and mineral fertilizer on N2O and CO2 emissions in a red soil from cultivated maize-wheat rotation in China. Agricultural. Sciences in China, 10(11) : 1748-1757.

[46] Zu-Cong C.,Guo-Ding K.,Tsuruta H.,Mosier A.J.P. .2005 .Estimate of CH4 emissions from year-round flooded rice fields during rice growing season in China. , 15(001) : 66-71.

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