Rice (Oryza sativa L.) is the world’s second most important cereal crop and a staple food for approximately 50% of the global population. Furthermore, the carbon (C) rhizodeposited from rice roots into paddy soil plays an important role in C sequestration (Huang et al. 2010; Tian et al. 2013; Wei et al. 2019), as this fraction represents an appreciable proportion (up to 0.52 Gt of CO2 equivalents) of biosphere CO2 (Ge et al. 2012, 2015). Recent studies on rice have characterized the distribution of rhizodeposited C in different soil organic matter pools, as well as the interactions between soil physicochemical and microbial properties in the plant–soil–atmosphere continuum. Moreover, given the current trends in global climate, these studies have also examined how such properties are affected by agricultural practices, such as water management, fertilizer application, and cropping system, under global environmental change scenarios based on factors such elevated CO2 and temperature (Li et al., 2019).

This Special Issue S79 (Rice & paddy soils) was conceived with the aim of bringing together a range of studies that can provide quantitative and mechanistic insights into the key processes involved in rhizodeposited C stabilization and primed organic matter mineralization in paddy soils, as well as the uptake and turnover of elements, particularly those of C, nitrogen (N), and phosphorus (P), in these soils. These studies serve to illustrate how cutting-edge techniques, including isotopic (13CO2 and 15N) labeling and biomarker (DNA-based stable isotope probing, DNA-SIP) and molecular biological (Illumina-based high-throughput sequencing) analyses have been applied to examine the effects of agricultural practices and global environmental change on source and sink relationships in the rice–paddy system.

From among the original 30 manuscripts that were submitted from groups around the world, 12 have been accepted for publication in this issue, and although all of these studies were performed China, each involved collaboration with international colleagues. The new findings presented in these papers will serve to enhance our current understanding of soil C, N, and P utilization and their associated biogeochemical processes, as well as providing insights into rice performance, particularly that linked with the emission of greenhouse gases such as nitrous oxide (N2O) and C sequestration via rhizodeposition in the rice–paddy system.

The two papers by Guo et al. (2019) and Lu et al. (2019), for example, respectively focus on N-use efficiency (NUE) and rice yield in response to agricultural practices, including N fertilization as N-free control, farmers’ fertilization practice, and optimal N management, and the external application of 1,2-benzenediol, catechin (a root-secreted phytotoxin), and a crystalline flavonoid compound (C15H14O6). Guo et al. (2019) found that compared with the fertilization practices of farmers, optimal N management can enhance the N nutrient index, leaf area index, net photosynthetic rate, and grain weight of rice, as well as shortening the length of the grain-filling period, thereby promoting higher NUE and yield. Lu et al. (2019) demonstrate that under a rice–rice–rape rotation, compared with a 2.0 μmol L−1 or higher application of 1,2-benzenediol, the external application of 0.20 μmol L−1 1,2-benzenediol significantly enhanced root N uptake, nitrate reductase and glutamine synthetase activities, and physiological NUE, and hence rice growth and yield.

In a further four papers, the authors examine nitrification activity in response to fertilization and temperature. Liu et al. (2018) show that in response to the addition of N and organic C (glucose) to two paddy soils (pH 4.9 and 6.2), heterotrophic nitrification and denitrification were the predominant processes contributing to N2O production, whereas a comparatively low soil pH was found to inhibit soil nitrification and the activity of ammonia oxidizers. However, on the basis of 15N-labeled callus and acetylene inhabitation analyses, Liu et al. (2019a) showed autotrophic nitrification to be the primary determinant of NH3 release from rice callus and stimulated the growth of ammonia-oxidizing archaea (AOA) in a pH 6.9 paddy soil. Furthermore 13CO2-DNA-SIP analysis indicated that the activity of AOA in soil was significantly greater than that of ammonia-oxidizing bacteria (AOB) in response to callus amendment. Zhang et al. (2019) also used 13CO2-DNA SIP and high-throughput sequencing to examine the activities of paddy soil microbiota, and accordingly found that the autotrophic nitrification and growth of AOB were significantly stimulated at an elevated temperature of 20 °C compared with 15 °C, and that there were shifts in active ammonia oxidizers from AOA to AOB and among nitrite-oxidizing bacteria from Nitrospira moscoviensis to Nitrospira japonica at 20 °C. In a further study, Liu et al. (2019b) demonstrated that fertilization resulted in significantly higher methane (CH4) emission from a paddy soil, which could be attributed to a decrease in redox potential in the vicinity of roots and reduced concentrations of dissolved oxygen at the soil–water interface. As a consequence of the altered soil oxygen status, the activity of bacteria in the genera of Methanoregula (methanogens) and Methylococcus (type I methanotrophs) was stimulated, whereas that of bacteria in the genus Methylocystis (type II methanotrophs) was inhibited, thereby leading to an increase in CH4 emission.

The allocation of assimilated C in rice–paddy soil systems in response to fertilization and rice growth stage is a subject addressed in a further five papers published in this issue. In their study of the distribution and fates of photosynthesized C in rice, Xiao et al. (2019) demonstrated that N fertilization during the elongation stage enhanced the allocation of photosynthesized C, whereas allocation was inhibited by fertilization during the heading stage. Examining the effects of two fertilization regimes (N fertilization and no-N fertilization), Zang et al. (2019) found that 13C rhizodeposition and its turnover rate were promoted to a greater extent by N fertilization, although both fertilization regimes resulted in a similar net accumulation of C in paddy soil. Furthermore, on the basis of 6-h 13CO2 pulse labeling analyses during the tillering, elongation, heading, and filling growth stages, these authors observed marked decreases in both the C allocated to roots and C input into soil with a progression in rice growth. These finding were found to be consistent with previous observations, as confirmed by a literature survey covering 94 published studies. In their study on C allocation, Zang et al. (2019) observed no immediate effects on C allocation following C assimilation but found that all administered C remained below ground. They also found that during a single season of rice cultivation, the total belowground net C input in paddy soil reached between 630 and 1080 kg C ha−1, of which 160–330 kg C ha−1 was rhizodeposited C. In addition, Luo et al. (2018) found that N fertilization promoted the incorporation of photosynthetically derived C into soil organic C in 0.25–2.0 mm large aggregates and the humic acid fraction These results thus indicate that N fertilization can influence the distribution of rhizodeposited C within soil organic C pools, and thereby determine the C sequestration potential of rice plants. In a further study, Zhao et al. (2018) demonstrated that the combined application of organic C (carboxymethyl cellulose) and mineral N ((NH4)2SO4) altered the composition of the soil microbial community, including reductions in the populations of gram-positive bacteria and fungi, whereas sole N fertilization was found to stimulate the growth of gram-negative bacteria and actinomycetes. Furthermore, Atere et al. (2018) found that combined C and N fertilization promoted a decrease in the distribution of rhizodeposited C within soil organic C and microbial organisms by 0.68- and 0.53-fold, respectively. These authors also showed that with continuous rice growth after 6, 14, and 22 days of 13CO2 labeling, smaller amounts of 13C were incorporated into soil at the 6th and 14th days, regardless of whether the rice had been under an alternative wetting–drying (AWD) cycle or under continuous flooding (CF). In the AWD treatment (6–8 days), potted rice plants were initially irrigated, and then subsequently dried until the moisture content was between ~70% and 75% of the water-holding capacity, after which the plants were re-flooded, and the procedure repeated for three complete wetting–drying cycles. In contrast, compared with a no-P fertilization treatment, after 22 days of 13CO2 labeling with P fertilization at a rate of 80 mg P kg−1, new assimilation of C into >250 μm macroaggregates increased by 32% under AWD and 42% under CF. The authors found that the observed effects of P fertilization on the allocation of newly assimilated C into 250–53 μm microaggregates and < 53 μm silt + clay, which were respectively increased by 97% and 83% after 22 days of 13CO2 labeling, was largely independent of water management. Furthermore, they demonstrated that P fertilization led to a higher incorporation of 13C into the light fraction of rhizospheric soil (75% at AWD and 90% at CF). The authors accordingly concluded that, compared with no P-fertilization, the application of P fertilizer in conjunction with the water-saving management of wetting and drying could enhance C sequestration in paddy soil.

In the final paper, Wei et al. (2018) describe their study of the enzymatic expansion of the rice rhizosphere using soil zymography (Fig. 1). They found that P fertilization narrowed the enzymatic rhizosphere, whereas the effects of cellulose addition and timing tended to be enzyme specific. During rice growth from 35 to 45 days after transplanting, there was an increase in the rhizospheric range of β-glucosidase (β-Glu) from 1.0–2.6 to 1.4–3.5 mm, and a decrease in that of both acid and alkaline phosphatases (ACP and ALP), from 1.3 to 3.5 mm, and cellobiohydrolase (CBH), from 1.5 to 4.5 mm. In most cases, the rhizospheric ranges of ACP and ALP were found to be similar, and showed increases of 0.7–1.3 mm and 0.9–1.3 mm, respectively, after 35 and 45 days of rice growth in response to the application of mineral P + cellulose. Compared with no-P fertilization, P fertilization decreased the rhizospheric ranges of β-Glu, CBH, and phosphatases by ~1.0, 1.7–2.6, and ~0.6 mm, respectively. The authors accordingly concluded that the combined effect of P and C plays an important role in determining a broadening of the “rhizosphere effect” with respect to enzyme activity.

Fig. 1
figure 1

A conceptional diagram showing the expansion of the enzymatic rhizosphere of rice as affected by carbon and phosphorus application and number of rice growth days (Modified from Figs. 3 and 7 of Wei et al. 2018). Abbreviations: β-Glu, β-glucosidase; ACP, acid phosphatase; ALP, alkaline phosphatase; CBH, cellobiohydrolase; and PO4, NaH2PO4

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Finally, as guest editors, we would like to express our sincere thanks to all the authors who submitted their manuscripts, irrespective of whether or not these were eventually accepted for publication in this special issue. We also wish to express are gratitude to all the reviewers, responsible editors, the Editor-in-Chief Hans Lambert, and Lieve Bultynck and Archie Miras from Plant and Soil for their continuous assistance in making this special issue a success.