Integrating low levels of organic fertilizer improves soil fertility and rice yields in paddy fields by influencing microbial communities without increasing CH4 emissions (2023)


Rice is a staple for about half of the global population, and worldwide rice demand is expected to grow by 30% by 2050 (Zhu et al., 2018). Yet, growth in rice yields has stalled in 35% of rice-growing regions (Ray Deepak et al., 2012). Rice production growth has been constrained mostly due to depleted soil nutrients caused by prolonged conventional agriculture activities (Ray Deepak et al., 2012). Applying chemical fertilizers (CFs) in conventional agriculture has proven ineffectual as large amounts are lost or unavailable to crops; the loss of applied CFs can cause significant environmental problems such as soil acidification, water pollution, and a decline in soil microbial diversity, which can deteriorate the biological and physicochemical characteristics of soils (Cai et al., 2018; Lal, 2015). Moreover, excessive use of synthetic N fertilizers can increase greenhouse gases (GHGs) emissions, N leaching, and soil compaction, limiting plant development and productivity (Zhang et al., 2019; Yang et al., 2018). Thus, continued dependence on synthetic fertilizers for crop production could be more sustainable.

Alternatively, organic manure, such as animal manure and green manure, can fulfill all the agricultural requirements while also providing benefits that CFs do not, including the addition of organic matter along with greater amounts of nutrients, which increases crop production (Zhongqi et al., 2016; De Melo and Pereira, 2019). Fertilization with manure improves soil's physical, chemical, and biological qualities, primarily by decreasing soil bulk density and improving structure (Ullah et al., 2020; Du et al., 2020). Organic fertilizers are applied to soil in precise amounts to increase SOC and other vital plant nutrients, particularly N-P-K and micronutrients, in the soil (Akhtar et al., 2018; Iqbal et al., 2021). However, earlier studies have found that additions of organic manure can greatly increase methane emissions in flooded environments (Kim et al., 2014; Ho et al., 2015). Kim et al. (2014) observed that a farmyard manure treatment elevated methane emissions considerably due to increased C substrates for methanogenic bacteria and nutrient levels in the paddy field. Manure fertilization has commonly been observed to increase CH4 emission in paddy fields (Zhou et al., 2015), but co-treating rice farms with organic fertilizers and CFs has produced variable effects on CH4 emissions, including enhancing CH4 emissions, no effect, and reducing emissions (Das and Adhya, 2014; Ji et al., 2018b). Furthermore, a statistical model indicated that organic fertilizers are one of the most influential variables determining CH4 emissions (Yan et al., 2005). Thus, the environmental consequences of organic fertilizers in rice paddies should be assessed to understand better the trade-off between increased soil fertility/crop yields and increased GHG emissions.

Methane (CH4) is the second most abundant greenhouse gas in the atmosphere after carbon dioxide (CO2), but its relative contribution to GWP is more than twenty times that of CO2 (Stocker et al., 2013; Bridgham et al., 2013); thus, small changes in atmospheric CH4 can substantially influence global warming. Anthropogenic methane emissions have been responsible for approximately 16% of the overall rise in global solar irradiance, and environmental CH4 accumulation has been quickly growing (WMO, 2018). Paddy fields have been recognized as a primary biological source of anthropogenic CH4, accounting for approximately 10% of worldwide CH4 emissions, a number that is likely to increase in the future as the demand for rice increases along with the world's population (FAO, 2014; Nazaries et al., 2013). Additionally, rice paddies grew CH4 emissions from 14.4Tg in 1961 to 24.4Tg in 2016, with an average increase of 1.2Tg per decade (FAO, 2016). Thus, immediate action is required to reduce global GHGs emissions from paddy rice farming.

Methane is primarily generated in anaerobic environments (paddy field), where methanogenic archaea use plant or organic material inputs, such as organic fertilizer or plant residue, as organic substrates for methanogenesis (Ji et al., 2018a; Conrad et al., 2007). Meanwhile, to varying degrees, soil-produced CH4 is frequently absorbed by methanotrophs in soils before being released into the environment (Le Mer and Roger, 2001a; Bosse and Frenzel, 1997). As a result, soil methane flux to the atmosphere CH4 emissions depends on the cumulative activity of both methanogenic and methanotrophic populations. Rice paddies are a major source of environmental CH4 due to the severe anaerobic conditions that typically follow inundation with water (Zhao et al., 2011; Ma et al., 2013). The release of labile organic C compounds from decomposing soil organic matter could be a key determinant in influencing methanogenic activities and CH4 generation rates (Kim et al., 2012; Lu et al., 2000). Therefore, more attention has recently focused on assessing the responses of CH4 emissions and CH4-related microbial communities to organic manure application in rice farming (Wang et al., 2018).

To address the abovementioned concerns, field measurements for determining CH4 fluxes were made in two rice cropping seasons (early season: March–July; and late season: July–November) in 2020 and 2021 at two different locations, i.e., Nanning and Yulin City in Guangxi province, Southern China. Furthermore, this study aimed to identify a rational fertilization method using organic manure from rice production and methane mitigation perspectives and explore the related mechanisms. The main objectives were (i) to evaluate CH4 emissions released from fields treated with various combinations of organic and mineral fertilizers, (ii) to identify important biogeochemical parameters controlling CH4 emissions and the related microbial processes that drive them, and (iii) to evaluate the effects of integrated treatments on the biochemical attributes of soil and the rice grain yield.

Section snippets

Study site

Field studies were performed at the Guangxi University research stations in Nanning, China (2020 and 2021) and Yulin City (2021). These sites, i.e., Nanning and Yulin City, experience subtropical monsoon climates and have total annual precipitation amounts of 1356mm and 1280mm and average temperatures of 24.8°C and 23.5°C, respectively (Figs. S1 and S2). The soil physicochemical properties indicated that the soil in Nanning and Yulin City contained 15.7 and 16.3gkg−1 SOC and 1.4 and

Soil properties and grain yield

The integrated application of organic manure and CF (i.e., integrated fertilization management) substantially enhanced soil biochemical attributes, including pH, SOC, MBC, TN, and AN, compared with Pos-CF in both locations (i.e., Nanning and Yulin City) (Table 2). The fertilization effect was greatest for all measured variables when the manure input was high; however, no significant (P<0.05) differences between PM and CM were observed. Soil properties differed significantly, but the same

Soil properties and rice grain yield

In this study, continuous fertilization of manure and CF improved soil biochemical characteristics and rice grain yield. In contrast, grain yield and soil quality were reduced when only CF was applied. Soil biochemical parameters improved throughout the study period in the organic amendment treatments. Organic manure typically contains more organic matter and nutrients than synthetic fertilizer. The repeated application of organic fertilizer can enhance soil fertility and rice yield by


The current study showed that applying manure combined with synthetic fertilizer substantially affected soil quality, rice yield, and CH4 emissions. Applying low proportions of manure (30% organic manure and 70% CF) decreased CH4 emissions while sustaining soil health and higher rice yields. In contrast, high proportions of manure (60% organic manure and 40% CF) increased CH4 emissions while improving soil quality. However, the sole use of CF increased rice yields and CH4 emissions compared



    organic fertilizer


    chemical fertilizer


    poultry manure


    cattle manure


    available nitrogen


    total nitrogen


    soil organic carbon


    microbial biomass carbon


    greenhouse gases emission


    global warming potential

Declaration of competing interest

The all authors declare that they have no competing interests regarding the contents of this article.


This study was fiscally funded by China's National Key Research and Development Project (2016YFD030050902). We want to thank our collaborators at Guangxi University Agriculture Station for their research assistance.

© 2023 Elsevier B.V. All rights reserved.

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