The Effects of Heavy Metals Pollution on Nitrogen Transformation and Volatile Organic Compounds in Paddy Soil under Different Water Management Practices

2. Different Water Management Practices for Rice Cultivation

Globally, about 4 billion people are suffering from water scarcity [35]. Furthermore, for sustainable rice production, a shortage of water is a major threat. In order to ensure food security, alternative ways such as less water for rice cultivation are very important. Therefore, in modern agriculture practices water-saving irrigation for rice cultivation must be the point of concentration in future research. Various approaches and technologies can be taken into account, such as alternate wetting and drying (AWD), reducing the outflow of unproductive water, adopting direct seeding, implementing the rice intensification system, employing the rice aerobic system, embracing the ground cover rice production system, and utilizing tensiometers for scheduled irrigation. These technologies can improve water use efficiency and significantly decrease the demand for water for the production of rice.

2.1. Continuous Flooding (CF)

Warm and waterlogged soil is used for rice cultivation. Continuous flooding (CF) is a traditional rice-growing practice in which the rice paddies are flooded by the farmers throughout the rice-growing season. Globally, 70% of the rice cultivation is carried out under CF. CF based rice cultivation is highly productive but some problems related to soil health and environment have been reported. Soil degradation, elevated methane emissions, and the substantial accumulation of harmful substances like arsenic and mercury are primarily associated with rice cultivation using chemical fertilizer-based practices [36].

Lowland rice irrigation covers about 79 million hectares worldwide, with an estimated 75% world’s rice production. The global crop irrigation area covered in Asia is approximately 56%, where 40-46% is rice cultivation [37]. About 64-83% of the irrigated area in the Southeast, 46-52% in the East, and 30-35% in the South Asia are occupied by rice cultivation. In comparison to other irrigated crops in the field, rice needs 2-3 times more water [38]. From developed 70% freshwater resources worldwide, rice irrigated receives 24-30% share.

Several factors, such as global warming, rice competition with other seasonal crops, industries, and civic requirements for water, may cause economic or physical water shortages for rice cultivation [39]. In the future, several million hectares of lowland rice irrigated systems will face water shortage by 2050 [5]. In account of all the issues related to the CF rice irrigation system, the development of water-saving irrigation system is compulsory for sustainable rice cultivation [5]. The International Rice Research Institute (IRRI) introduced alternate wetting and drying (AWD) water management technology, among other water-saving rice irrigation systems, to deal with expected water shortages in the future. AWD has got worldwide attention and several research studies are available that are becoming increasingly widespread [40].

2.2. Alternate Wetting and Drying

Developing agronomic practices that minimize water usage for irrigation while sustaining high yields is essential to support the increasing global population. To address the issue of water scarcity in rice agricultural production, alternate wetting and drying (AWD) water management practices are being adopted [36,41]. Under AWD conditions, rice fields are drained out for a certain period in which the field obtains a certain level of moisture and is then re-flooded. It has been reported that using AWD water technology saves about 23% of the water used for rice irrigation when compared to CF practices [6,38]. AWD technology has the potential to reduce greenhouse gas (GHG) emissions, particularly methane (CH₄) gas [36,42]. Alternate wetting and drying conditions decreased by about 45-90% global warming potential (GWP − CH₄ + N₂O) compared to CF. Human activities generate about 48Gt CO₂ annually, which can increase global warming. Therefore, to reduce GHG emissions from paddy fields, it is critical to promote AWD adaptation globally [43]. In the USA, for example, farmers received carbon credits under the project “Voluntary Emission Reductions in Rice Management Systems” involves farmers adopting practices aimed at minimizing greenhouse gas (GHG) emissions, with AWD being one practice [44]. On the other hand, AWD also reduced arsenic (As) accumulation in rice grains [41,45] and methylmercury concentration in soils, and lowered the consumption of energy/fuel where pumping is in practice for irrigation [36,46,47]. Many efforts have been made to promote AWD in Asia because to its benefits [48]. In China, the “mid-season” drain is widely adopted which is somewhat similar to AWD [49]. However, global AWD technology adoption is limited due to a variety of factors limiting rice productivity [36,46,50].

Since the 1990s, China has embraced water-saving irrigation methods such as thin-shallow-wet-dry irrigation [51] and alternate drying-wetting [52,53]. Soil water management strategies influence oxygen transfer, nitrogen transformation, and soil redox potential [9,10,54]. Soil microbial biomass carbon (MCB) and nitrogen (MBN) have been significantly affected by irrigation practices [55,56]. In paddy soils, MBC and MBN decreased in continuous flooding irrigation as compared to intermitted irrigation [57]. Other studies have reported high N₂O emissions from paddy fields with intermittent irrigation and midseason drainage [58,59].

Soil moisture is very important during the rice grain filling stage. Grain quality and yield are both impacted by water levels during rice reproduction and the filling stage [60,61]. Both CF and AWD effectively enhanced the quality of rice grains [62]. For example, AWD improved grain head recovery, grain weight, and protein contents [63,64]. Similarly, rice kernel opaqueness, abortiveness, and chalkiness were reduced significantly in AWD [60,64]. In addition, AWD significantly increased the nutritional value of the rice grain such as high antioxidants, total tocopherols, γ-oryzanol, flavonoids, zinc and iron [65]. Furthermore, AWD significantly decreased arsenic in the rice grain [66].

2.3. Popular Methods around the Globe

Globally, rice production and greenhouse gas production are under the influence of two important factors i.e., water management and application of nitrogen fertilizer. China is one of the largest rice-producing countries; water shortage threatens rice cultivation. The most popular rice cultivation method is CF. However, due to water shortage and greenhouse gas emissions, nowadays different water-saving irrigation systems are in practice around the globe (Table 1). Among different water-saving irrigation, AWD is the most practiced technology for rice production.

However, different studies reported AWD decreased CH₄ and increased N₂O emissions. Moreover, while applying medium nitrogen (N), the optimal rice grain yield has been observed in the case of AWD in contrast to the conventional flooding-midseason drainage-flooding irrigation (PFD) approach. Different studies from Bangladesh, the Philippines, China, and Pakistan reported a 4.52% average increase in rice yield (t/ha) under AWD than CF. Similarly, water use efficiency (WUE) was also increased in AWD as compared to CF.

Another rice production system termed as [46] applied in different regions of the world. In ARS, rice is grown under non-saturated, non-flooded, and non-puddled soil conditions [67]. The yield obtained from ARS was higher than in upland conditions but lower than in flooded conditions. In cool temperate regions, ARS is a successful system for rice production. However, a partial aerobic rice system (PARS) is more suitable alternative for ARS in warm humid regions. There have been reports that ARS reduces rice yield over time, and it has been proposed that this technique may not be ideal for long-term rice agriculture [68]. Several factors among them are Zn, Fe, K, N, and P deficiencies, root-knot nematodes and weeds are responsible for the yield reduction in ARS [69]. However, it save about 50% of irrigation water compared to CF.

Table 1. Different strategies used for Water-Saving irrigation of Rice Production.

S. No	Technologies for Conserving Water in Rice Cultivation.	Reference
1	Surface Irrigation Techniques in Rice Cultivation.	[70,71,72]
	2. Drip Irrigation Methodology in Rice Cultivation.	[68]
	3. Sprinkler Irrigation Approach for Rice Cultivation.	[73]
2	1. Alternate wetting and drying (AWD)	[10,74]
	2. Soil water potential (SWP)	[36,75]
	3. Mulching Cultivation without Flooding	[76,77]
	4. Aerobic rice system [46]
	5. Optimal Irrigation Regimen (OIR)	[73]
	6. Saturated soil culture (SSC)	[78]
	7. Field water level (FWL)	[73]
	8. Intermittent drainage (ID)	[79]
	9. Leaching and flushing methods (LFM)	[73]
	10. Conventional flooding-midseason drainage-flooding irrigation (FDF)	[1]

Table 1. Different strategies used for Water-Saving irrigation of Rice Production.

S. No	Technologies for Conserving Water in Rice Cultivation.	Reference
1	Surface Irrigation Techniques in Rice Cultivation.	[70,71,72]
	2. Drip Irrigation Methodology in Rice Cultivation.	[68]
	3. Sprinkler Irrigation Approach for Rice Cultivation.	[73]
2	1. Alternate wetting and drying (AWD)	[10,74]
	2. Soil water potential (SWP)	[36,75]
	3. Mulching Cultivation without Flooding	[76,77]
	4. Aerobic rice system [46]
	5. Optimal Irrigation Regimen (OIR)	[73]
	6. Saturated soil culture (SSC)	[78]
	7. Field water level (FWL)	[73]
	8. Intermittent drainage (ID)	[79]
	9. Leaching and flushing methods (LFM)	[73]
	10. Conventional flooding-midseason drainage-flooding irrigation (FDF)	[1]

2.4. Heavy Metal Pollution in Paddy Soil

Cadmium [1] is considered one of the hazardous heavy metals that permeates the soil through various sources [9]. Its pollution is a severe global issue since it can build in agricultural soil and edible sections of crops, and eating those contaminated components can cause cancer in humans [10]. Various natural and anthropogenic sources like rock weathering, atmospheric deposition, urbanization, and wastewater irrigation, sewage sludge application, overuse of phosphate fertilization, mining, and smelting originate Cd contamination in the soil [80]. Geological parent material decides the background of Cd level. However, generally it has been reported a range from (0.06-1.1 mg kg^-1) with a 0.01 mg kg^-1 lower and 2.7 mg kg^-1 higher value [80]. However, due to human activities, the Cd level (up to 14 mg kg^-1) has been reported in several regions of the world. Several factors such as cultivars, crop species, and soil properties contribute to the accumulation of Cd in plants.

2.5. Sources

2.5.1. Natural Ways of Cd Origination (Geogenic)

Naturally, Cd is existing in all rocks in entire soils. Among the top 20 priority hazardous metals, Cd ranked 7th [81]. Different rocks have different Cd concentrations. For example sedimentary deposits rocks have higher Cd than igneous and metamorphic rocks [82]. Thus, the soils originating from sedimentary phosphatic rocks have more Cd due to high Cd concentration [83,84]. Where the soils develop on phosphorites, shales or carbonates then the geogenic soil Cd concentration range from 0.01-10 or 100 mg kg^-1 [85,86]. Cd exhibits weak sorption to the surfaces of both organic matter and minerals in the soil. Cadmium from mineral lattices releases slowly by weathering of high-Cd parent rocks [87].

Soil Cd is hard to distinguish either via geogenic or anthropogenic origin. Generally, Cd enriched topsoil is assumed to occur via farm and atmosphere inputs. Nevertheless, this is not the case, as Cd is transported to subsoils through the biological cycle [88]. Furthermore, via vegetation, Cd in agricultural brings from subsoils to topsoil [89]. At a continental scale, the concentration of Cd in European soil is primarily influenced by geological factors rather than anthropogenic inputs, despite the widespread use of intensive fertilizers, urban wastes, and manures in agriculture [90].

2.5.2. Anthropogenic Sources of Cd Input

Human activities are the leading cause of worldwide Cd deposition in the environment, accounting for 13, 000 tons of the 30, 000 tons of Cd inclined to the environment each year [10,91]. In the agriculture soils, Cd had been introduced by various sources and its concentration is generally lower than 0.2 mg kg^-1. The level of Cd in the agriculture soils increased due to long-term phosphate fertilizer application along with sewage water used for irrigation purposes [92]. Discharged wastewater, mining activities (exhaust and solid waste), the smelting sector, and atmospheric deposition, on the other hand, all contribute to Cd contamination of agricultural soil. Blast furnaces sludge and flue dust contain a relatively high content of Cd [93]. The oxidizable and residual fraction of textile dyeing plants, sludge, has been reported to consist of an average 3.72 mg kg^-1 Cd [94]. In Changsha City which is the capital of Hunan Province of China, dust analysis showed that 50% Cd was insoluble and reducible fractions in PM 2.5 from re-suspension of dust, fuel combustion, vehicular emissions, and other pollution sources, speciation analysis during spring [95]. Nevertheless, the predominant source of Cd input into the soil arises from agricultural activities, such as the irrigation of wastewater. Unnecessary phosphate and organic fertilizer applications, and random disposal of untreated urban sewage sludge and garbage [96]. The issue of Cd input via phosphate fertilizer application in agriculture soils of China is controllable because naturally phosphate and Cd contents are low in the native phosphate rocks of China, which lead to import high-quality phosphate fertilizers which contain a high level of Cd [97]. The Cd content was about 7.5-156 mg kg^-1, 84-144 mg kg^-1, 9.5 mg kg^-1, and 24.5 mg kg^-1 in imported ammonium phosphate, single superphosphate, normal superphosphate, and triple-superphosphate, respectively, which exceeded the standards [97]. Atmospheric deposition of Cd in paddy soil have been reported about 65-70% [98]. Similarly, fertilizers, particularly phosphate fertilizers and biosolid contribute 10-50% each to Cd accumulation in paddy field [99]. However, in China, animal manure about 55% contributed to total soil Cd inputs [100].

2.6. Chinese Paddy Fields and Heavy Metal (HM)

In china, paddy soil Cd contamination is a widespread problem. The Cd paddy soil issue is more sever in some mining and industrial regions of China. The range of paddy soil Cd contamination range from 0.01-5.50 mg kg^-1, with an average value of 0.23 mg kg^-1 [101]. Hunan was reported with highest Cd (0.73 mg kg^-1), whereas Guangxi and Sichuan provinces were recorded 0.70 and 0.46 mg kg-1 paddy soil Cd. However, in 1990s, the background value of Cd in Chinese paddy soil was 0.1 mg kg^-1 [98]. Paddy Cd contamination across China following the trend like Northwest > South central > East > Northeast > North [98]. In China, paddy fields are mostly contaminated by Cd due to the smelting of the ores of Cu, Pb, and zinc [91,102]. Cd contents of rice grains are greatly varying. Rice grains sampled from the field and market were reported to have raised levels of Cd, up to 7.0 and 1.24 mg kg^-1, respectively [102]. A study containing 100 rice grain samples in Hunan, one of the large nonferrous metals production zones, reported only 15% of rice grains meet the standard level of As, Cd and Pb [103]. Another study randomly collected 63 rice grain samples from the open markets of Jiangxi and Anhui, along with 7 samples from Guangdong., Hunan, and Jiangxi, and Cd level in about 70% of grain samples was found to be higher than the standard 0.2 mg kg^-1 [104].

3. HM and Soil N Transformation

Rice plants prefer ammonium to nitrate. When both ammonium and nitrate are present, rice seedlings exhibit a faster uptake of NH₄⁺ compared to NO₃⁻ [105]. From last half-century, due to the NH₄⁺ preference of the rice, farmers used to cultivate rice in paddy fields, ammonium-based fertilizers like ammonium sulfate and urea are applied [105]. In addition, organic fertilizers for rice cultivation are also commonly applied in the fields, in which the organic N is converted to ammonium through a biological process called ammonification (mineralization of N). Due to the low level of oxygen or depletion in paddy soils, the rate of ammonification is slower compared with upland soils [106]. Depletion of O₂ in soils not only slow down the ammonification but also limits the process of ammonium oxidation (NH₄⁺ to NO₃^-) and immobilization of N (microbial assimilation of NH₄⁺ i.e., the conversion of inorganic N to organic N), which lead to the accumulation of NH₄⁺ in soils [107].

3.1. The Significance of Nitrification and Denitrification Processes in Paddy Soils

The most limiting nutrient for rice production is generally known as N. Denitrification in paddy soils was initially studied in order to make the efficient use of fertilizers and link the gaseous products such as NO, N₂O, and N₂ with the microbial process involved in the reduction of nitrate [108]. The thin oxidized layer of paddy soils is the region where nitrification occurs while denitrification takes place below the oxidized layer [109]. The loss of N from paddy soils included ammonia volatilization, nitrate leaching and nitrification [110]. The denitrification occurred just following nitrification in paddy soils. It is proposed that ammonium fertilizers should be deeply applied before waterlogging (4-5 days) in paddy fields to overcome the N loss from the paddies [111]. N transformation on a microscale in the flooded soil surface layer reported a high number of nitrifiers and denitrifiers bacteria in the above 2 cm layer than the below-reduced layer of paddy soil [11,112]. After one to two weeks of waterlogging low-molecular-weight organic molecules (acetate) accumulated in the top layer which increased the denitrifiers bacteria. The correlation of organic carbon and denitrifiers bacteria in another environment along with lake sediments and river waters also have been reported [113]. The most important factor for the controlling of denitrification is the availability of organic C since it provides electrons donor for the denitrifiers. Rice plant roots release O₂ in the rhizosphere, therefore nitrification and denitrification activities were also reported for rice rhizosphere [114,115] and green algae which grown in rice fields [116], as well as in the bulk soil between the oxidized and reduced layers. The process of nitrification-denitrification in rice paddy soil may cause the loss of N from the applied fertilizer. Globally, 40% of the total greenhouse gas emission recorded from paddy soils. Different studies have been reported the little emission of N₂O from the paddy soil under control condition than the upland field crops [117,118]. Denitrification is a strong activity of rice paddy soils, as a result, little emission of N₂O occurred by conversion of N₂O into N₂ [119]. Furthermore, several studies on dissolved N₂O in the rice surface and groundwater have been conducted [120]. These findings suggested that little emission of N₂O gas from rice paddy soil occurred due to the N₂O reducers, present in the rice paddy fields [121]. However, recent findings suggested that iron plague in the rhizosphere contribute largely to N₂O emission that was previously ignored [122].

3.2. Nitrification

Nitrification is a totally microbial mediated process in which nitrate (NO₃⁻) formation takes place by ammonium (NH₄⁺) oxidation via nitrite (NO₂⁻) [9,123,124] (Figure 1). This is the energy acquiring process for autotrophic nitrifiers. The process in which NO₃^- or NO₂^- formation takes place from inorganic N (NH₄⁺) and organic N without energy acquired by microbes is known as heterotrophic nitrification and the microbes termed as heterotrophs [123].

Nitrification has been divided into two steps: the oxidation of ammonia (NH₄⁺→NO₂⁻) and nitrite oxidation (NO₂⁻→NO₃⁻). Nitrosospira spp. and Nitrosomonas spp. of Betaproteobacteria and Nitrosococcus spp. of Gamma proteobacteria, these bacteria are known as ammonia-oxidizing bacteria [11] can carry out the oxidation of ammonia. Archaea, along with bacteria can also take place in ammonia oxidation which is termed as ammonia-oxidizing archaea [12] [125,126]. Different studies have been reported a higher number of AOA than AOB in the ocean [127]. A positive correlation of AOB abundance was observed with rice paddy nitrification activity soil which indicates that AOB could be the major players of nitrification than AOA [128]. However, with the application of urea fertilization increased the abundances of both AOA and AOB in the rice rhizosphere [129,130]. Recent reports showed, comammox relative contribution to nitrification is higher than AOA and AOB in the rice paddy soil [128].

The diversity of ammonia-oxidizing bacteria [11] communities has been investigated in rice paddy soils [131]. The rice genotypes can also influence the diversity of AOB [132]. In China, rice paddy soil the Nitrosospira spp. are the most dominated AOB [133,134,135], while biochar amended rice paddy soil favored amoA gene containing AOB just related to Nitrosomonas spp., [136]. Among the other factors, fertilizer practices may change the AOB community in the soil because of the environments with high ammonia concentration (like wastewater) Nitrosomonas spp. predominates while in the soil Nitrosospira spp. is the major AOB [137]. Nitrite-oxidizing-bacteria (NOB) form the genera of Nitrobacter, Nitrospina, Nitrococcus, and Nitrospira perform the nitrite oxidation which is the second step of nitrification [138,139].

3.3. Denitrification

Denitrification is a process in which gaseous form of N (NO, N₂O and N₂) forms via the stepwise reduction of (NO₃^- and NO₂^-) by microbial respiration (Figure 1). Microbes utilize nitrogen oxides as electron acceptors in lieu of oxygen when operating under anaerobic conditions for respiration.

Nitrous oxide also acts as an electron acceptor but non-denitrifiers reduce N₂O [140]. Two types of nitrite reductases are responsible for denitrification i.e copper-containing NirK encoded by gene nirK, and NirS cytochrome cd1-containing enzyme encoded by nirS gene [12]. These enzymes transform oxidized ammonia to NO, and N₂O. Finally nitrous oxide reductase enzymes encoded by nosZ, reduces N₂O into N₂. Nitrite reductases (nirK and nirS) gene related community has been studied in detail [12,141]. In the rice paddy soil, the average gene copy number of nirK, nirS, and nosZ were 7.65×10^-7, 3×10^-7, and 8.71×10^-7, respectively [9] 16S sequencing approaches in paddy soil, revealed that denitrifiers community genes are distributed in Betaprotobacteria. The phylum was further divided in to Azospira and Burkholderiales, belonging to the genus Herbaspirillum, and Rhodocyclales in the rice paddy soil under denitrifying conditions [142].

The soil type, plant genome, pH, Eh, organic matter, temperature, substrate, and fertilizers affects the response of microbes towards denitrification. For example, with increasing temperature, increases the denitrification rate in paddy soil [143,144]. Similarly, high moisture also increased denitrification [144]. However, opposite is true for N fertilizer. N fertilizers increased the nirK gene abundances and decreased nirS in paddy field [141].

3.4. Production of N₂O

Nitrous oxides production occurs through different sources in the soil, incomplete denitrification can lead to the production of N₂O (NO₃⁻→NO₂⁻ →NO →N₂O →N₂). The lack of N₂O reducing enzymes in the denitrifiers can also lead to the production of N₂O [145], one such example is the denitrification activities of fungus, in which N₂O is the major end product. Not only denitrifiers are the only source of N₂O, but some ammonia oxidizers are also the source of N₂O production either through hydroxylamine oxidation or nitrifier denitrification [146]. Both AOA and AOB have been reported for the nitrifier denitrification because they are positive for nitrite reductase gene (nirK). These microbes first perform the activity of ammonium oxidation then oxygen-depleted environment converts the product into N₂O and N₂ which is termed as nitrifier denitrification or the reduction of nitrite [147]. One of the intermediate products of ammonia oxidation is hydroxylamine, during the oxidation of hydroxylamine, N₂O produced as a byproduct. A study reported both AOA and AOB for the N₂O is production via the hydroxylamine oxidation pathway. In addition, dissimilatory nitrate reduction to ammonium (DNRA) bacteria has been reported for N₂O [148]. Non-denitrifiers can also produce N₂O by the reduction of nitric oxide as detoxification of toxic NO molecule. In this process, quinol-type nitric oxide reductase (qNor) has been reported instead of denitrifiers containing cytochrome c-type nitric oxide reductase (cNor) [140,149]. Chemodenitrification has also been reported in which nitrite is reduced to NO and N₂O [150].

3.5. Reduction of N₂O

Though different way N₂O produced in the soil can be used as electron acceptors by different N₂O reducer’s microbes for respiration which contains the N₂O reductase (nosZ) [151,152]. The ability of N₂O reduction into N₂ had been reported in a phylogenetically diverse group of bacteria and archaea. This reduction of N₂O is the part of denitrification but some denitrifiers lack the enzymes to reduce it into N₂ gas. In addition, the reduction of N₂O can also be done by some DNRA bacteria in the rice paddy soil [153]. Both culture-dependent (FSC) and culture-independent [90] analyses were used for the detection of N₂O reducers in the rice paddy soil [154,155]. Herbaspirillum sp. strains were grown under the conditions which exist during rice paddy soil denitrification and were reported as the active player of N₂O reduction step of the denitrification [156]. Herbaspirillum and Azospirillumcan had been reported as denitrifiers recently, depending on the environmental condition these bacteria may be acting like N fixers or N losers from the soil just like legume symbiont Bradyrhizobium which perform both processes (N fixation and denitrification) [157,158].

3.6. Effect of Cd on N Cycle in Paddy Soils

For bioavailability, different definitions exist but it can be defined as the chemical availability to the living receptors either directly or through uptake (Figure 1). The main concern during metal contamination in the soil is the bio-available portion of metal not the total metal concentration because only the bio-available portion uptake is possible for plants from the soil [159]. The most important factors which control the availability of the metals in the soil are pH and organic matter [160,161]. In the rhizosphere of the plant, heavy metals bioavailability depends on soil type, plant genotype, metals speciation, and the change in biological and physicochemical of the soil induced by roots [162,163]. Spatially and temporally rhizosphere varies which acts as a dynamic habitat [164]. The rhizosphere is the most complex hot spot which is comprised of a diverse plant-associated microbial community, responsible for the metal mobilization and immobilization in the soil either directly or indirectly [165,166]. The mobilization of metals occurs through the release of chelators or redox changes done by the microbial processes in the rhizosphere such as chelation, chemical transformation, and soil pH reduction via protonation, while the immobilization of metals occurs in the rhizosphere by biosorption or bioprecipitation via microbes [167,168]. In a recent study reported higher metals-tolerant bacteria in the rhizosphere microbial communities [169].

3.6.1. Nitrification

Soil physical and chemical properties of soil influence the microbial-mediated processes rates in the field environments [170,171,172]. Nitrification and denitrification processes are not only affected by the soil pH but a recent study reported that soil NH₄⁺-N and C/N also responsible while changing the abundances of soil microbial communities [173]. The effect of metals on ammonia oxidation depends upon the specific metal or combination of metals in the environments like no change in the abundance of AOA was reported in mercury-spiked soil used for vegetable cultivation while Cu spiked up to 1000 mg kg^-1 changed the AOA community in the grassland and arable soils [174,175]. A study has reported that Cu was more toxic to the ammonia oxidizer community as compared to Ni. For example, Cu strongly affects the AOB community in the sludge-amended soil and adaptability was more common to Zn and Ni [176]. However, general microbial community was shown more vulnerable to Cu and Cr contamination as compared to Zn and Ni as well [177]. Heavy metals pollution had a negative effect on the abundance, diversity, activity, and composition of AOA and AOB in the natural soil [10]. Another study reported a higher copy number of AOA than AOB in the rice paddy field, contaminated with heavy metals and the ratio of AOA to AOB copy number was in the range of 2.5 to 59 [175].

3.6.2. Denitrification

Denitrification is a heavy metal sensitive process and the heavy metals concentration in the soil directly proportional to its inhibition [178]. Heavy metals change the denitrifiers in the soil which reflect the inhibition of denitrification (Figure 1). A recent study reported a significant change in the composition of the denitrifiers in the metals polluted paddy soil via denaturing gradient gel electrophoresis (DGGE) [179]. In addition, in the rice paddy soil, the microbial community has been reported to adopt the metal stress by changing the abundances of certain microbial taxa. Not only the abundance but also the functional potential has been reported altered in the metals polluted paddy soil. The replacement process is the main factor for the adaptability of heavy metals of the microorganisms while soil pH variation is totally responsible for the community richness[180]. The negative effect of metals on the abundance of denitrifiers was also varied with the elements. The copy of nirK and nosZ genes sharply decreased with the spiked Cu in a 6 days lab incubation experiments but a recovery in copy number of the denitrifiers genes has been reported for long time incubation [181]. The heavy metals pollution especially the Cd decreased the abundance, diversity, and structure of both nitrifiers and denitrifiers in the rice paddy soil [182].

3.6.3. Greenhouse Gases from Paddy Fields under Metals Contamination

The application of N fertilizers is essential for rice production with high yield. However, due to the overuse of N fertilizers, the production of GHG such as nitrous oxide (N₂O) is one of the major concerns [183,184]. Different studies have addressed these problems by specifying which soil types are more prone to N losses by describing many environmental and management factors linking to biological nitrogen transformation [185,186]. However, the question, how heavy metals pollution could affect the biological transformation in the soil is still on the list to answer, especially, the introduction of heavy metals through atmospheric deposition versus spiked metals into the soil which suddenly increases the heavy metals concentration in the soil [176,187]. Another issue is the linking between changes in N transformation genes abundances and heavy metals contamination in soils. It will become more difficult to address this issue in rice paddy soils where significant changes occur in the redox potential due to wet/dry cycles which affect the heavy metals bioavailability, structures of microbial community and rate of biological transformations of N [180,188].

Among all the green GHG, N₂O is the most radiative GHG increasing 0.26% in the atmosphere per year [180]. Incomplete denitrification results in the production of nitrous oxide in which the last reduction step fails to reduce the N₂O into N₂ in the soil. It had been reported that about 60% of the total N₂O globally is produced by anthropogenic sources with the major players is known as paddy fields [189,190]. China’s paddy fields produced up to 29.0 Gg of N₂O emissions which are about 7-11% of total GHG emission from China’s croplands [51,191]. Recent studies have shown that in metal-polluted paddy soils, microbial biomass and fungal to bacterial ratio are declined with an increase in the concentration of heavy metals, which could lead to changes in carbon (C) cycling. Heavy-metal contamination in soil could affect the rates of microbial-mediated biogeochemical processes. For example, soil nitrification rates were suppressed by metal salts such as CdCl₂ and ZnCl₂, both in spiked soil samples in short-term studies and in polluted fields where metals typically accumulated at a slower rate [192,193,194]. In a study using surface wetland sediments spiked with multiple metals, total denitrification activity was inhibited by Cd (30.9%), Zn (24.9%) and Cu (18.9%) over a period of 7 days of incubation, with Cd being the strongest inhibitor[195]. Heavy-metal pollution was found to affect the activities of denitrifying bacteria and ammonia oxidizers in soil [196].

3.7. Different Forms of Cd and Its Mineralization under the Change in Redox Conditions of the Soil

Various forms of heavy metals are consistently found in the soil, each exhibiting distinct levels of toxicity, bioavailability, and solubility such as 1) insolubly precipitated with other soil, 2) The structural elements of the lattices within clay minerals, 3) Substitutable in both organic and inorganic components, and, 4) dissolved (in soil solution) [197]. The properties of soil such as pH, soil redox potentials (Eh), cation exchange capacity, and organic matter contents, Mn and Fe oxides, clay minerals, and calcium carbonate [9]. Changes in soil Eh impact the bioavailability of Cd due to alterations in redox status and variations in electron acceptors. In aerobic, oxidizing conditions, Cd commonly exists as a soluble salt and cationic form, specifically Cd^2+. However, in anaerobic situations with a low redox potential, Cd tends to exist as precipitated species like CdS and CdCO₃ [198]. Conversely, alterations in redox potential influence both the organic matter and mineral components of the soil [100]. Furthermore, soil redox conditions regulate the microbial community characteristics and functions [199,200].

The soil moisture regime regulates both soil Eh and biological activity. Paddy soil typically experiences saturated conditions. Heavy metals are found in solid-phase components, and the introduction of heavy metals to paddy soil leads to their transition from more labile fractions to less labile fractions [201,202]. At field capacity moisture, Cd exhibited lower stability when compared to saturated conditions [203]. The saturated regime resulted in more complete transformation of metals toward the stable fractions than the field capacity regime [203]. Soil kept dry exhibited significantly higher soluble concentrations of Cd, Cu, and Zn than the field capacity and the saturated treatment [204].

Management practices such as air drying cycles are pertinent to soil moisture conditions, influencing the exchangeable fraction of heavy metals in the soil. Air drying enhanced Cd desorption in soil and the leachability of metals from dredged canal sediment increased during drying and oxidation processes [205,206]. Drying the soil in an oven resulted in notable rises in the concentrations of dissolved copper (Cu) and nickel (Ni). This outcome can be attributed to the complexation of these metals with increased levels of humic acid and fulvic acid in the soil [207]. Air drying enhances the extractability of manganese [118], iron (Fe), copper (Cu), and zinc [91] at low-incubation moisture levels, while reducing the extractability of metals at high-incubation moisture levels [208]. In paddy soil incubated under three distinct moisture regimes, the exchangeable fraction of copper (Cu), lead (Pb), and cadmium [1] exhibited the following order: 75% field capacity > wetting–drying cycle > flooding. Conversely, the reducible fraction followed the reverse order [209,210]. Eh stands as a crucial factor influencing the mobility of metals in soil or sediment, and is closely tied to soil moisture regulation [211]. Under oxidizing conditions, there is a discernible likelihood of significant heavy metal release [212].

4. Toxic Effects of Cd on Rice

Elevated cadmium [1] concentrations have the potential to impede plant growth, reduce grain yield and quality [212]. This can result in modifications to plant tissues, and disrupt the process of photosynthesis [212], and regulating expressions of at least 36 proteins in rice [213]. Accumulation and transport of Cd occur in various organs and cell organelles, once it enters into the rice [214]. Different researchers have reported the toxic effects of Cd on plant growth [215,216]. Stunted growth and chlorosis are the most typical Cd toxicity symptoms [217]. Due to the direct and indirect interaction of the high level of Cd in the leaves, chlorosis (chlorophyll loss) takes place. The change in physiological activities of plant-like respiration, cell proliferation, and photosynthesis indirectly [217], nitrogen metabolism, plant water relationship, and mineral nutrition under direct Cd stress had been reported, which resulted in poor growth and low biomass of plants [218]. Sensitivity to drought, enzymes inactivation, and damages to membranes of plants have been well-establishing facts of Cd toxicity [219]. It stops indirectly the photosynthesis of the plant by closing the stomata due to water conductance which reduces the access of CO₂ to the plant [220]. Directly, Cd prevents the photosynthesis by affecting electron transport, chloroplast organization, chlorophyll biosynthesis, and activity of Calvin Benson Bassham cycle enzymes [221,222].

The general symptoms of Cd toxicity in rice plants include growth inhibition, chlorosis of leaves and sheaths, brown root system, and wilted leaves [203,223]. Different metals-sulfide complexes make brown pigment which deposits on the surface of rice roots [224]. The production of lipid peroxides is a response to Cd toxicity in rice plants. In addition, the uptake of plant essential elements such as Fe, Zn, Mn, and Cu has also been reported to be affected by Cd toxicity in rice plants [225,226]. In addition, the light-harvesting center and photosystem II along with chlorophyll metabolism in rice leaves are affected by Cd [227].

5. HM and VOCs in Paddy Soil under DWMP

Various water management practices influence the Cd uptake in rice (Figure 2). Volatile organic compounds (VOCs) emitted by vegetation encompass a wide array of chemical molecules, predominantly comprised of isoprene, monoterpenes, and methanol [15,228]. In any case, the variety of plant-emitted VOCs depends on the plant species, the distinctive parts of the plants, or the growth conditions [229]. Plants can emit higher quantities of these molecules by directing a greater amount of carbon into stress-triggered volatile organic compounds (VOCs) when subjected to attacks by pathogens or herbivores. Additionally, exposure to various abiotic stresses such as UV radiation, ozone, drought, eutrophication, warming, and overall oxidative stress can also contribute to the increased release of these compounds [230,231,232,233]. Actually, many VOCs of the family of terpenes, such as isoprene and monoterpenes, are antioxidants and can protect cells from oxidative stress[233,234].

Under aerobic irrigation of rice, Cd uptake and isoprene emission decreased [235,236]. Isoprene (2-methyl-1, 3-butadiene) is an important plant VOC known for its plant protection role against numerous abiotic stimuli, including heat [237] and drought stress [238]. Cd decreases the activity of isoprene synthase, an enzyme responsible for conversion of dimethylallyl diphosphate (DMAPP) to isoprene [239,240]. Similarly, One class of VOCs, that Cd amplified was green leaf volatile (GLVs), which play a part in plant defense [239,241]. Furthermore, Cd contamination modulating the emission of terpenoids and expression of genes encoding terpene synthases (TPSs). TPSs is responsible for different terpenoids formation utilizing isopentenyl diphosphate (IPP) and DMAPP [239].

5.1. Volatile Terpenoids

The most abundant (more than 40,000 individual compounds) and structurally diverse group of floral volatiles are called terpenoids [242]. Terpenoids are essential for the growth and development of plants. Terpenoids are the components of abscisic acid (C15), membrane structures (sterols C30), photosynthetic pigments (carotenoids C40), involves in mitochondrial electron transport chain, and gibberellins (C20). Several plant secondary metabolites are terpenoids, such as mono-, sesqui- and diterpenes play important role in plant-plant interactions and plant-environment interaction [243].

Sesquiterpenes, Isoprenes and monoterpenes are known as volatile terpenoids and the largest class of plant volatile compounds (PVCs). They exist in almost every part of the plants including seeds, fruits, leaves, and roots. However, the predominantly PVCs are floral volatiles called lipophilic liquids. Floral volatiles are low molecular weight and high vapor pressure at ambient temperatures [243,244]. There is a link between the PVCs and plants pollinators [244,245]. They attract pollinators such as bats, birds, mammals, insects, and other animals as vectors for pollens transfer [246]. For Long range communication and evolutions of flowering plant, floral scent is an important source of communication [247]. Floral volatiles changes the behavioral response in respective pollinators. Floral volatiles upon emission guiding the pollinators towards the flowers. For example, more volatile terpenoids emitting by latifolia and Petunia axillaris, moths pollinated than the same genus Petunia integrifolia and Silene dioica a day-emitting bee-pollinated [243,248]. Cd inhibit terpenoids by interfering with enzymes responsible for terpenoid production production, such as geranylgeranyl diphosphate synthase (GGPPS), 1-deoxy-D-xylulose-5-phosphate synthase (DXS), and 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR). In rice, Cd reported to induce oxidative stress and damage the cellular membranes. Cellular membranes are mostly composed of sterols and carotenoids i.e., terpenoids. Furthermore, Cd in rice disrupting the hormonal balance and signaling pathways responsible for terpenoids metabolism [249].

5.2. Effects of Heavy Metals on Rice Fragrance

Aromatic 2-acetyl-1-pyrroline is the main ingredient in rice fragrance (2AP). Two genes, betaine aldehyde dehydrogenase (BADH1) and BADH2, functioned in the 2AP biosynthetic pathway. The exact mechanism of Cd affecting these genes is not well studied. However, studies reported that Cd may interfere with the expression and functions of BADH1 and BADH2, limiting rice yield and quality. For example, upon exposure to Cd, the expression of BADH1 and BADH2 in rice seedlings. Similar Cd lowered the activity of enzymes encoded by these genes BADH and betaine aldehyde synthase (Figure 3) [26,250]. These enzymes are in responsible for converting the aldehyde betaine into glycine, a precursor of 2AP. Glycine is a compatible solute which protect plants from stress. The decreased activity of these enzymes lower the levels of glycine betaine and higher levels of betaine aldehyde leads to plant toxicity. Furthermore, the accumulation of 2PA accumulation due to Cd in the grain also affected the rice fragrance [250].

The duplication of the BADH2 gene in rice decreased Cd accumulation in rice root and shoots under salt and Cd stress. Duplication increased the expression and activity of BADH2, which uptake more manganese, a micronutrient and competitor with Cd for transport in rice cell [251]. Furthermore, the introduction of the BADH2 gene duplication into various rice cultivars reduced Cd accumulation without impacting yield or grain quality [251]. Similarly, 96 rice accessions were found to have 12 single nucleotide polymorphisms (SNPs) in six cadmium-related genes, comprising BADH1 and BADH2 [99]. SNPs are linked with the Cd accretion in rice grains. In rice breeding practices, SNPs might be used as molecular markers for low-Cd accumulating rice cultivars.

6. Conclusions and Future Directions

Cadmium contamination poses serious threats to rice agriculture and paddy soil N transformation. The N transformation is severely affected in AWD practices than CF. Similarly, Cd interferes with the signaling and synthesis of plant cells that are responsible for VOC production and aroma. High Cd deposition in rice cells inhibits VOC formation; nevertheless, the precise mechanism by which VOC synthesis is modulated by DWMP remains unknown. This may compromise plant defense, induced by VOCs and rice aroma as well. The issue of rice aroma, quality, and yield can be mitigated in future breeding procedures by introducing low-Cd absorption rice cultivars and utilizing water-saving technology.

Currently, Cd accumulation in grains is reduced via agronomic parameters (soil improvement, water, fertilizer, tillage management) and applying silicon and abscisic acid externally. Another strategy is microbial and phytoremediation. However, these processes are cost-effective and laborious with low efficiency. Therefore, screening and breeding low Cd accumulation rice varieties is the only choice considered economical and effective. Crossbreeding is very effective in transferring low Cd gene pool to offspring. However, molecular marker assistant breeding can reduce the screening process in breeding and save time. In addition, mutation breeding also helps to develop low Cd accumulating variety quickly. However, molecular marker assistant breeding can reduce the screening process in breeding and save time. CRISPR and hybridization technologies can also be used to develop new low-Cd accumulator rice verities. Adaptations of such techniques by the breeders may develop rice variety that can be grown in Cd-polluted paddies but will maintain the aroma and grain quality.