Paddy Soil Ecosystem Research Articles

Investigating drivers of N2 loss and N2O reducers in paddy soils across China

Denitrification plays a pivotal role in nitrogen (N) cycling in rice paddies, significantly impacting N loss and greenhouse gas emissions. Accurate quantification of net N2 emissions from paddy fields is therefore essential for improving fertilizer N use efficiency. However, challenges in directly measuring gaseous N2 hinder our understanding of microbially-mediated N loss in paddy soils at large scales. In this study, we investigated net N2 loss and its influencing factors in 45 paddy soils across China using membrane inlet mass spectrometry and N2/Ar technique, complemented by microbial community analysis via metagenomics. Potential N2 loss rates varied from 0.41 to 3.58 nmol N g−1 h−1, with no significant regional differences. However, soils from rice-upland rotation (1.72 ± 0.64 nmol N g−1 h−1) and mono-rice cropping systems (1.41 ± 0.53 nmol N g−1 h−1) exhibited higher N2 loss rates compared to double-rice cropping soils (1.13 ± 0.62 nmol N g−1 h−1). Our results revealed a unimodal relationship between soil N2 loss rates and soil pH, with N2O reducers and soil properties primarily regulating regional variations in N2 loss. Significant ecological differentiation was observed within both nosZ Clade I and Clade II, with soil pH emerging as the key factor shaping their community composition. Specifically, in rice-upland rotations, soil moisture and pH significantly influenced nosZ Clade I, while in double-rice cropping systems, soil texture and pH were the main factors affecting nosZ Clade II, thereby driving N2 loss. These findings enhance our understanding of N2 loss dynamics in paddy soil ecosystems, underscoring the critical role of N2O reducers on microbial-derived N2 loss and highlighting the importance of developing strategies to mitigate N2O emissions by balancing N2 loss through the manipulation of N2O-reducing and N2O-producing microbes.

Partitioning denitrification pathways in N2O emissions from re-flooded dry paddy soils

In flooded paddy fields, peak greenhouse gas nitrous oxide (N2O) emission after rewetting the dry soils is widely recognised. However, the relative contribution of biotic and abiotic factors to this emission remains uncertain. In this study, we used the isotope technique (δ18O and δ15NSP) and molecular-based microbial analysis in an anoxic incubation experiment to evaluate the contributions of bacterial, fungal, and chemical denitrification to N2O emissions. We collected eight representative paddy soils across southern China for an incubation experiment. Results show that during the 10-day incubation period, the net N2O emissions were mainly produced by fungal denitrification, which accounted for 58–77% in six of the eight investigated flooded paddy soils. In contrast, bacterial denitrification contributed 6–15% of the net N2O emissions. Moreover, around 11–35% of the total N2O emissions were derived from chemical denitrification in all soil types. Variation partitioning analysis (VPA) and principal component analysis (PCA) demonstrated that initial soil organic carbon (OC) concentrations were the primary regulator of N2O source patterns. Soils with relatively lower OC concentration (7–15 mg g−1) tend to be dominated by fungal denitrification, which accounted for the net N2O production at the end of the incubation period. Overall, these findings highlight the dominance of the fungal denitrification pathway for N2O production in flooded paddy soils, which predominates in soils with relatively lower OC content. This suggests that fungal contribution should be considered when optimizing agricultural management system timing to control N2O emissions in flooded paddy soil ecosystems, and for the relevant establishment of predictive numerical models in the future.

Niche differentiation and biogeography of Bathyarchaeia in paddy soil ecosystems: a case study in eastern China

Bathyarchaeia (formerly Bathyarchaeota) is a group of highly abundant archaeal communities that play important roles in global biogeochemical cycling. Bathyarchaeia is predominantly found in sediments and hot springs. However, their presence in arable soils is relatively limited. In this study, we aimed to investigate the spatial distributions and diversity of Bathyarchaeia in paddy soils across eastern China, which is a major rice production region. The relative abundance of Bathyarchaeia among total archaea ranged from 3 to 68% in paddy soils, and Bathy-6 was the dominant subgroup among the Bathyarchaeia (70–80% of all sequences). Bathyarchaeia showed higher migration ability and wider niche width based on the neutral and null model simulations. Bathy-6 was primarily assembled by deterministic processes. Soil pH and C/N ratio were identified as key factors influencing the Bathyarchaeia composition, whereas C/N ratio and mean annual temperature influenced the relative abundance of Bathyarchaeia. Network analysis showed that specific Bathyarchaeia taxa occupied keystone positions in the archaeal community and co-occurred with some methanogenic archaea, including Methanosarcina and Methanobacteria, and ammonia-oxidizing archaea belonging to Nitrososphaeria. This study provides important insights into the biogeography and niche differentiation of Bathyarchaeia particularly in paddy soil ecosystems.

Nitrogen fixation and transcriptome of a new diazotrophic Geomonas from paddy soils.

The ability of Geomonas species to fix nitrogen gas (N2) is an important metabolic feature for its application as a plant growth-promoting rhizobacterium. This research is of great importance as it provides the first comprehensive direct experimental evidence of nitrogen fixation by the genus Geomonas in pure culture. We isolated a number of Geomonas strains from paddy soils and determined that nifH was present in these strains. This study demonstrated that these Geomonas species harbored genes encoding nitrogenase, as do Geobacter and Anaeromyxobacter in the same class of Deltaproteobacteria. We demonstrated N2-dependent growth of Geomonas and determined regulation of gene expression associated with nitrogen fixation. The research establishes and advances our understanding of nitrogen fixation in Geomonas.

Compost-derived humic acid impacts on the biodechlorination of pentachlorophenol in high organic matter paddy soil

The long-term accumulation of pentachlorophenol (PCP) has adversely affected the paddy soil ecosystem. PCP reductive dechlorination under anaerobic conditions is an efficient pathway for PCP degradation. This process is affected by the content of organic matter and the iron mineral composition of the soil. Our previous study analyzed the effects of compost-derived Humic acids (HAs) on reductive dechlorination of PCP in a paddy soil system under Fe-reducing conditions. The effects and mechanisms of high organic matter and compost-derived HAs in promoting PCP dechlorination need further investigation. This study examined paddy soils with high organic matter content in Heilongjiang Province. PCP reductive dechlorination in this system was studied using HAs from three stages of municipal solid waste compost as soil supplements. The results showed that natural HA and microorganisms could promote the dechlorination and transformation of PCP in the paddy soil system. After removing humic acid, the detected concentrations of PCP in paddy soil and solid-liquid interface were 1.84 and 9.67 times of those in the original soil experiment, respectively. The concentration of low chlorine products decreased significantly in the sterilized group. Compost-derived HAs from different stage were also presented various effect on PCP reductive dichlorination. Furthermore, the synergistic effect between natural HA and compost-derived HAs would limit the electron donating capacity of compost-derived HAs in the paddy soil with high organic matter. Organic matter in soil has an important influence on pollutant fate. Late-stage HA were more effective in promoting PCP degradation than early-and middle-stage HAs. The research provided a comprehensive and meticulous analyses of the effects of compost-derived HAs on PCP bio-dechlorination in paddy soil with high organic matter.

Environmental pseudotargeted metabolomics: A high throughput and wide coverage method for metabolic profiling of 1000-year paddy soil chronosequences

Pseudotargeted metabolomics is achieved by introducing an algorithm designed to choose ions for selected ion monitoring from identified metabolites. This method integrates the advantages of both untargeted and targeted metabolomics. In this study, environmental pseudotargeted metabolomics was established to analyze the soil metabolites, based on microwave assisted derivatization followed by gas chromatography–mass spectrometry analysis. The method development included the optimization of extraction factors and derivatization conditions, evaluation of silylation reagent types and matrix-dependent behaviors. Under the optimal conditions, the microwave oximation and silylation were completed in 5 min and 9 min. A total of 184 metabolites from 26 chemical classifications were identified in soil matrices. The method validation demonstrated excellent performance in terms of linearity (correlation coefficient > 0.99), repeatability (relative standard deviation (RSD) < 20 %), reproducibility (RSD < 25 %), stability (relative difference < 10 % within 18 h), and sensitivity (16–110 times higher signal-to-noise ratio). This developed method was applied to characterize the metabolite compositions and metabolic profiling in a 1000-year paddy soil chronosequence. The relative abundance of trehalose was highest in 6-(40.3 %), 60-(55.8 %), 300-(67.7 %)and 1000-(61.7 %)years paddy soil, respectively, but long-chain fatty acids were most abundant in marine sediment (57.4 %). Forty-two characteristic metabolites were considered as primarily responsible for discriminating and characterizing the paddy soil chronosequences development and seven major metabolic pathways were altered. In addition, GC–MS metabolite profile presented better discriminating power in paddy soil ecosystem changes than phospholipid fatty acids (PLFAs). Overall, environmental pseudotargeted metabolomics can provide a high throughout and wide coverage approach for performing metabolic profiling in the soil research.

Soil Microbial Diversity and Community Composition in Rice-Fish Co-Culture and Rice Monoculture Farming System.

Simple SummaryThe integration of fish in rice fields can influence the diversity and structural composition of soil microbial communities. Therefore, soil microorganisms between rice–fish co-culture (RF) and rice monoculture (MC) were compared. The key findings revealed that Actinobacteria, Chloroflexi, Proteobacteria, Acidobacteria, and Planctomycetes were the most dominant taxa across both paddy fields. The most abundant genus in MC belonged to Anaeromyxobacter, whereas that in RF was Bacillus. Nitrogen fixation, aromatic compound degradation, and hydrocarbon degradation were more abundant in RF. Phosphatase, β-glucosidase, cellulase, and urease enzymes were detected in both paddy fields. However, a 2-year conversion from organic rice to rice–fish co-culture may not be long enough to significantly alter alpha diversity indices.Soil microorganisms play an important role in determining nutrient cycling. The integration of fish into rice fields can influence the diversity and structural composition of soil microbial communities. However, regarding the rice–fish co-culture (RF) farming system in Thailand, the study of the diversity and composition of soil microbes is still limited. Here, we aim to compare the microbial diversity, community composition, and functional structure of the bacterial communities between RF and rice monoculture (MC) farming systems and identify the environmental factors shaping bacterial community composition. Bacterial taxonomy was observed using 16s rRNA gene amplicon sequencing, and the functional structures of the bacterial communities were predicted based on their taxonomy and sequences. The results showed that soil organic carbon, total nitrogen (TN), organic matter, available phosphorous, and clay content were significantly higher in RF than in MC. The most dominant taxa across both paddy rice fields belonged to Actinobacteria, Chloroflexi, Proteobacteria, Acidobacteria, and Planctomycetes. The taxa Nitrosporae, Rokubacteria, GAL15, and Elusimicrobia were significantly different between both rice fields. At the genus level, Bacillus, Anaeromyxobacter, and HSB OF53-F07 were the predominant genera in both rice fields. The most abundant genus in MC was Anaeromyxobacter, whereas RF belonged to Bacillus. The community composition in MC was positively correlated with magnesium and sand content, while in RF was positively correlated with pH, TN, and clay content. Nitrogen fixation, aromatic compound degradation, and hydrocarbon degradation were more abundant in RF, while cellulolysis, nitrification, ureolysis, and phototrophy functional groups were more abundant in MC. The enzymes involved in paddy soil ecosystems included phosphatase, β-glucosidase, cellulase, and urease. These results provide novel insights into integrated fish in the paddy field as an efficient agricultural development strategy for enhancing soil microorganisms that increase soil fertility.

Effects of organic fertilization on functional microbial communities associated with greenhouse gas emissions in paddy soils

Soil microbial communities play a key role in the biochemical processes and nutrient cycles of the soil ecosystem and their byproducts, including greenhouse gases (GHGs). Organic fertilization influences bacterial soil biodiversity and is an essential emission source of GHGs in paddy soil ecosystems. However, the impact of organic fertilization on the functional microorganisms associated with the GHGs methane and nitrous oxide remains unknown. We conducted paddy soil field experiments under three different treatments (no fertilization, base fertilization, and organic fertilization) to investigate the contribution of organic fertilization to soil nutrients and the functional microorganisms associated with GHG emissions. We found that organic fertilization effectively increased the soil organic matter (P < 0.001), soil organic carbon (P < 0.001), and total nitrogen (P < 0.05) as well as the richness (operational taxonomic units and abundance-based coverage estimators) of the methanogenic communities. Correlation analyses showed that methanogenic communities that were present in abundance were more vulnerable to perturbations in soil properties compared to nitrifying bacterial communities. Partial least squares path model analyses elucidated that organic fertilization directly affected both methanogenic communities and nitrifying bacterial communities (P < 0.05), thereby accelerating methane emissions. Strong co-occurrence networks were observed within the soil-dominant phyla Acidobacteria, Bacteroidetes, and Proteobacteria. Our findings highlight the impact of organic fertilization on soil nutrients and functional microorganisms and guide mitigating GHG emissions from paddy soil agroecosystems.

Comparative Analysis of Paddy Soil Denitrifying Bacteria with Soil Phospholipid Fatty Acid Profile

To characterize the metabolic versatility of denitrifying bacterial communities residing in the paddy soil, phospholipid fatty acid (PLFA) analyses were done along with nosZ encoding nitrous oxide reductase gene-based PCR-DGGE and real-time Q-PCR analysis. In this study, we have analyzed the abundance of nitrous oxide reductase (nosZ) genes and DGGE-based denitrifier community assessment was found to be correlated with soil PLFA profile in terms of their pattern analysis. Among all detected denitrifying bacteria, Ochrobactrum sp. represented a major fraction following Cupriavidus and uncultured bacteria. The data related to nosZ gene abundance were found to show similar pattern with PLFA-based lipid profile. Greater amount of lipid content (C18-C20) and denitrifiers diversity was apparently visible at Chandauli of Eastern UP, India and thus positively impact each other in the soil. Our study suggests that the nosZ-based DGGE and gene abundance data were increased in response to soil PLFA profiles. Subsequently, the presence of an increased lipid content of soil samples with increased abundance and diversity of denitrifying bacteria could be helpful in managing nutrient dynamics as well as microbial dynamics of paddy soil ecosystem.

Nitrogen Addition Decreases Dissimilatory Nitrate Reduction to Ammonium in Rice Paddies.

Dissimilatory nitrate reduction to ammonium (DNRA), denitrification, anaerobic ammonium oxidation (anammox), and biological N2 fixation (BNF) can influence the nitrogen (N) use efficiency of rice production. While the effect of N application on BNF is known, little is known about its effect on NO3- partitioning between DNRA, denitrification, and anammox. Here, we investigated the effect of N application on DNRA, denitrification, anammox, and BNF and on the abundance of relevant genes in three paddy soils in Australia. Rice was grown in a glasshouse with N fertilizer (150 kg N ha-1) and without N fertilizer for 75 days, and the rhizosphere and bulk soils were collected separately for laboratory incubation and quantitative PCR analysis. Nitrogen application reduced DNRA rates by >16% in all the soils regardless of the rhizospheric zone, but it did not affect the nrfA gene abundance. Without N, the amount and proportion of NO3- reduced by DNRA (0.42 to 0.52 μg g-1 soil day-1 and 45 to 55%, respectively) were similar to or higher than the amount and proportion reduced by denitrification. However, with N the amount of NO3- reduced by DNRA (0.32 to 0.40 μg g-1 soil day-1) was 40 to 50% lower than the amount of NO3- reduced by denitrification. Denitrification loss increased by >20% with N addition and was affected by the rhizospheric zones. Nitrogen loss was minimal through anammox, while BNF added 0.02 to 0.25 μg N g-1 soil day-1 We found that DNRA plays a significant positive role in paddy soil N retention, as it accounts for up to 55% of the total NO3- reduction, but this is reduced by N application.IMPORTANCE This study provides evidence that nitrogen addition reduces nitrogen retention through DNRA and increases nitrogen loss via denitrification in a paddy soil ecosystem. DNRA is one of the major NO3- reduction processes, and it can outcompete denitrification in NO3- consumption when rice paddies are low in nitrogen. A significant level of DNRA activity in paddy soils indicates that DNRA plays an important role in retaining nitrogen by reducing NO3- availability for denitrification and leaching. Our study shows that by reducing N addition to rice paddies, there is a positive effect from reduced nitrogen loss but, more importantly, from the conversion of NO3- to NH4+, which is the favored form of mineral nitrogen for plant uptake.

Adsorption and Desorption of Cry1Ab Proteins on Differently Textured Paddy Soils

In recent years, selected cry genes from Bacillus thuringiensis (Bt) encoding the production of Cry proteins (Bt toxins) have been engineered into crop plants (Bt-crops). Through the cultivation of Bt crops and the application of Bt pesticides, Cry proteins could be introduced into arable soils. The interaction between the proteins and soils was analyzed in this study to investigate the affinity of Cry proteins in paddy soil ecosystems. Four Paddy soils were selected to represent different soil textures. Cry proteins were spiked in soils, and the amount of protein adsorbed was measured over 24 h. Desorption of Cry1Ab proteins from paddy soils was performed by washing with sterile Milli-Q water (H2OMQ), and subsequently extracted with an extraction buffer. The paddy soils had a strong affinity for Cry1Ab proteins. Most of the Cry1Ab proteins added (> 98%) were rapidly adsorbed on the paddy soils tested. More Cry1Ab proteins were adsorbed on non-sterile soils than on sterile soils. Less than 2% of the adsorbed Cry1Ab proteins were desorbed using H2OMQ, while a considerable proportion of the adsorbed proteins could be desorbed with the buffer, ranging from 20% to 40%. The amount of proteins desorbed increased with the increases in the initial amount of Cry1Ab proteins added to the paddy soils. The concentration of Cry1Ab proteins desorbed from the paddy soils was higher for sterile soils than non-sterile ones. Our results indicate that Bt toxins released via the cultivation of Bt crops, the application of Bt pesticides can be adsorbed on paddy soils, and soil texture could impose an impact on the adsorption capability.

Molecular Chemodiversity of Dissolved Organic Matter in Paddy Soils.

Organic matter (OM), and dissolved organic matter (DOM), have a major influence upon biogeochemical processes; most significantly, the carbon cycle. To date, very few studies have examined the spatial heterogeneity of DOM in paddy soils. Thus, very little is known about the DOM molecular profiles and the key environmental factors that underpin DOM molecular chemodiversity in paddy soils. Here, Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry was applied to unambiguously resolve 11 361 molecular formulas in 16 paddy soils; thereby elucidating the molecular characteristics of paddy soil DOM. Soil pH, iron complexing index (Fep/FeR) and C/N ratio were established to be key factors controlling DOM profiles. Polycyclic aromatics (derived from combustion) and polyphenols (derived from plants) increased with increasing pH, while polyphenols molecules, pyrogenic aromatics, and carboxylic compounds decreased with increasing iron complexing index. Patterns in molecular profiles indicated DOM in paddy soils to become more recalcitrant at higher soil C/N ratio and higher pH. Furthermore, plant-derived polyphenols and pyrogenic DOM were retained favorably by iron and the chemodiversity of DOM in paddy soil increased with increasing soil C/N ratios. This study provides critical information about DOM characteristics at a molecular level and will inform better global management of soil carbon in paddy soil ecosystems.

Dynamics of Rice Photosynthesized Carbon Input and Its Response to Nitrogen Fertilization at the Jointing Stage:13 C-CO2 Pulse-labeling

Photosynthesized carbon (C) is an important source of soil organic C in paddy fields, and its input and distribution are affected by rice growth and soil fertility. Fertilizer application plays an important role in rice growth. The 13C pulse-labeling method was used to quantify the dynamics and distribution of input photosynthesized C in the rice-(rhizosphere-and bulk-) soil system and its response to nitrogen fertilizer (N) application. The results suggested that N fertilization significantly increased the rice aboveground and the root biomass and decreased the rice biomass root/shoot ratio. The amount of assimilated 13C gradually decreased in the rice plants but gradually decreased over 0-6 days and increased over 6-26 days in the rhizosphere and bulk soil during rice growth. N fertilization significantly increased the amount of assimilated 13C in the rhizosphere soil by 9.5%-32.6% compared with the control. In comparison to the unfertilized treatment, the application of N fertilization resulted in higher photosynthetic13C in rice aboveground and in the root by 24.5%-134.7% and 9.1%-106%, respectively. With the N fertilized and unfertilized treatments, 85.5%-93.2% and 91.3%-95.7%, respectively, of input photosynthetic 13C was distributed in the rice plants. The results suggested that N fertilization significantly affected the distribution of photosynthesized C in the rice-soil system (P<0.01). After 26 days of pulse labeling, the distribution of photosynthetic 13C into rice aboveground was increased by 13.4%, while the distribution into the rhizosphere and bulk soil were decreased by 21.9% and 52.2%, respectively, in the N fertilized treatments compared with the unfertilized treatments. Therefore, the N application increased the distribution of photosynthesized carbon in the soil-rice system but decreased the accumulation in the rhizosphere and bulk soil. The findings of this study provided a theoretical basis for our understanding of the dynamic of photosynthetic C in the plant-soil system and the assimilation of the soil organic matter pool in the paddy soil ecosystem.

Effect of oxidizing and reducing agents in soil on methane production in Southeast Asian paddies

ABSTRACTMethane is one of the greenhouse gases emitted from paddy soil ecosystems and may induce global warming and climate change; therefore, mitigation options are urgently required to establish mitigation technology to reduce methane emission without affecting rice production. Methane is produced by a balance between oxidizing agents (such as iron) and reducing agents (easily decomposable soil organic matter), according to the so-called Takai theory. To evaluate options for mitigating methane production potential and to examine the applicability of the Takai theory in Southeast Asian paddy soils, 23 soil samples were collected from Thailand, Indonesia, Philippines, and Vietnam. These soil samples were anaerobically incubated to measure their methane production potential and examined to see whether their chemical properties, such as the ferrous, total iron, and organic matter contents, were correlated. We found a significant negative correlation between the methane production potential and the total iron content, and a positive correlation between the methane production potential and the hexose content, as an index for a soil’s easily decomposable organic matter content. The methane–C/CO2–C production ratio was also positively correlated with the mineralizable nitrogen/ferrous contents ratio, which indicated that the Takai theory, established for Japanese paddy soils, is also useful in Southeast Asian paddy soils and that the soil’s iron content is important to estimate the methane production potential.

Bacterial, archaeal, and fungal community responses to acid mine drainage-laden pollution in a rice paddy soil ecosystem

Lacking sufficient clean water, the paddy soils along the Hengshi River have suffered from long-term acid mine drainage (AMD) contamination. The impacted cropland is too heavily contaminated to grow food safely. The microbial communities inhabiting the environment play pivotal roles in the crop growth, health, and ecological services. In this study, the bacterial, archaeal, and fungal communities in the impacted paddy soil were examined using high-throughput Illumina MiSeq sequencing. The results showed that AMD irrigation considerably enriched the bacterial phylum Acidobacteria and the archaeal phylum Crenarchaeota, while the fungal community was more stable. The abundances of Acidobacteria and Crenarchaeota were significantly positively correlated with the AMD-related environmental factors of pH and heavy metals (Cu, Pb, and Zn). In the most contaminated samples, communities were dominated by the bacteria Candidatus Solibacter and Candidatus Koribacter from the Acidobacteria family. Functional gene profile analysis demonstrated that the energy metabolic processes of the microbial communities, especially C/N related pathways, have adjusted and are well-adapted to tolerating AMD contamination. The present study described the structural and functional differentiation of microbial communities in the rice paddy soil under AMD irrigation. The results are useful for the development of bioremediation strategies using native microbes in the cleanup and biorestoration of AMD-contaminated agriculture soil.

Microaerobic iron oxidation and carbon assimilation and associated microbial community in paddy soil

Iron oxidation is a prevalent and important biogeochemical process in paddy soil, but little is known about whether and how microbially mediated iron oxidation is coupled with carbon assimilation, particularly under microaerobic conditions. Here, we investigated kinetics of CO2 assimilation and Fe(II) oxidation in an incubation experiment with paddy soil under suboxic conditions, and profiled the associated microbial community using DNA-stable isotope probing and 16S rRNA gene-based sequencing. The results showed that CO2 assimilation and Fe(II) oxidation in the gradient tubes were predominantly mediated by the microbes enriched in the paddy soil, primarily Azospirillum and Magnetospirillum, as their relative abundances were higher in the 13C heavy fractions compared to 12C heavy fractions. This study provided direct evidence of chemoautotrophic microaerophiles linking iron oxidation and carbon assimilation at the oxic–anoxic interface in the paddy soil ecosystem.

Effect of Straw Application on the Dynamics of Exogenous Nitrogen and Microbial Activity in Paddy Soil

Returning straw to the field provides an important source of fertilizer that can increase soil fertility. However, the rate of straw carbon utilization is low and large amounts of greenhouse gases are emitted due to the high carbon to nitrogen ratio of the straw mass. In this regard, the application of inorganic nitrogen and phosphate fertilizers can control the ratio of elements in the soil, increase the activity of microorganisms and their utilization of elements, and promote the improvement of soil fertility. In this study, straw application conditions were simulated, and inorganic nitrogen fertilizer labeled with 15N was added to examine the effects of different nutrient fertilizer additions on the transformation and distribution of exogenous nitrogen in the soil, and also the characteristics of the microbial response. The results showed that application of straw increased the contents of ammonia nitrogen and total nitrogen in the soil and soil solution. When both straw and inorganic nitrogen fertilizer were applied, the 15N-TN in the soil remained at 28 to 33 μg during the 100-day culture phase. In contrast, 15N-NH4+ increased gradually during the initial 30 days of the culture phase, but subsequently decreased gradually. Application of phosphate increased the contents of 15N-TN and 15N-NH4+ in the soil, but decreased the content of 15N in the soil solution by 28%. The distribution of inorganic nitrogen in the soil showed that the proportion of 15N in the soil remained at 52%-61%. Addition of phosphate fertilizer increased the distribution ratio of 15N in the soil by up to 16.5%, whereas the proportion of 15N in the soil solution decreased from 36% on the fifth day to 30% on the 100th day, thereby the loss amount of 15N reduced by 1.2-fold. Addition of straw promoted microbial activity and significantly increased the microbial biomass nitrogen (MBN) content of the soil. Addition of inorganic fertilizer further promoted the microbial activity of the soil. After the 100-day culture experiment, the addition of straw, inorganic nitrogen, and phosphate fertilizer increased MBN to between 2.0-fold and 2.2-fold that of the control treatments. Addition of phosphate fertilizer increased the utilization of 15N by microorganisms, so that the amount of 15N-MBN was 1.5-fold higher than that of treatments where only straw and nitrogen fertilizer were added. Examination of soil enzyme activity showed that nitrogen fertilizer reduced soil enzyme activity and substrate affinity. When both nitrogen and phosphate fertilizers were added, the enzyme activity was 48.1% higher than that when only straw was added. The findings of this study thus provide a theoretical basis for furthering our understanding on the nitrogen cycle of the paddy soil ecosystem, the improvement of soil fertility, and the reduction of greenhouse gas emissions.

Microprofiling of nitrogen patches in paddy soil: Analysis of spatiotemporal nutrient heterogeneity at the microscale.

Flooded paddy soil ecosystems in the tropics support the cultivation of the majority of the world’s leading crop, rice, and nitrogen (N) availability in the paddy-soil rooting zone limits rice production more than any other nutritional factor. Yet, little is known about the dynamic response of paddy soil to N-fertiliser application, in terms of horizontal and vertical patchiness in N distribution and transformation. Here, we present a microscale analysis of the profile of ammonium (NH4+) and nitrate (NO3−), nitrification, oxygen (O2water and O2soil), and pH (pHwater and pHsoil) in paddy soils, collected from two representative rice-production areas in subtropical China. NH4+ and NO3− exhibited dramatic spatiotemporal profiles within N patches on the microscale. We show that pHsoil became constant at 1.0–3.5 mm depth, and O2soil became undetectable at 1.7–4.0 mm. Fertiliser application significantly increased pH, and decreased O2, within N patches. Path analysis showed that the factors governing nitrification scaled in the order: pHwater > pHsoil > NH4+ > O2water > NO3− > O2soil. We discuss the soil properties that decide the degree of nutrient patchiness within them and argue that such knowledge is critical to intelligent appraisals of nutrient-use efficiencies in the field.

Long-term fertilization of P coupled with N greatly improved microbial activities in a paddy soil ecosystem derived from infertile land

Microcalorimetry was used to study the effects of long-term (20 years) fertilization regimes on microbial activities in a paddy soil in southern China derived from infertile land. Managements of phosphorus fertilizer coupled with nitrogen fertilizer significantly promoted the contents of total and available P, mineral N and microbial biomass C (MBC) (P < 0.05). Both principal component analysis (PCA) of calorimetric indices and metabolic quotient of heat (QT/MBC) showed that fertilization of P coupled with N, P-deficient fertilization and non-fertilized control significantly separated from each other. Redundancy analysis plot showed that rate of heat output (QT/t), peak power (Pmax) and constant of growth rate (k) were significantly correlated with soil total and available P, total and mineral N, which were greatly increased by the P fertilizer coupled with N fertilizer. In contrast, QT/MBC and peak time (tmax) were greatly increased by the P-deficient treatments. In addition, QT/t as a new introduced parameter was negatively correlated well with QT/MBC (R2 = 0.93, P < 0.01). Accordingly, integrating microcalorimetric result analyzed by PCA as well as sensitive indicators of QT/MBC, QT/t and tmax are useful to assess soil microbial activity. The higher QT/t, lower QT/MBC and tmax indicate higher microbial activity and soil quality. In conclusion, long-term fertilization of P coupled with N, especially combined organic fertilizer greatly improved soil fertility and microbial activity; in contrast, deficiency of soil P had lower microbial activity in the paddy soil derived from infertile land.

Community structure and soil pH determine chemoautotrophic carbon dioxide fixation in drained paddy soils.

Previous studies suggested that microbial photosynthesis plays a potential role in paddy fields, but little is known about chemoautotrophic carbon fixers in drained paddy soils. We conducted a microcosm study using soil samples from five paddy fields to determine the environmental factors and quantify key functional microbial taxa involved in chemoautotrophic carbon fixation. We used stable isotope probing in combination with phospholipid fatty acid (PLFA) and molecular approaches. The amount of microbial (13)CO2 fixation was determined by quantification of (13)C-enriched fatty acid methyl esters and ranged from 21.28 to 72.48 ng of (13)C (g of dry soil)(-1), and the corresponding ratio (labeled PLFA-C:total PLFA-C) ranged from 0.06 to 0.49%. The amount of incorporationof (13)CO2 into PLFAs significantly increased with soil pH except at pH 7.8. PLFA and high-throughput sequencing results indicated a dominant role of Gram-negative bacteria or proteobacteria in (13)CO2 fixation. Correlation analysis indicated a significant association between microbial community structure and carbon fixation. We provide direct evidence of chemoautotrophic C fixation in soils with statistical evidence of microbial community structure regulation of inorganic carbon fixation in the paddy soil ecosystem.