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.