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Background: Arsenic (As) metabolism pathways and their coupling to nitrogen (N) and carbon (C) cycling contribute to elemental biogeochemical cycling. However, how whole-microbial communities respond to As stress and which taxa are the predominant As-transforming bacteria or archaea in situ remains unclear. Hence, by constructing and applying ROCker profiles to precisely detect and quantify As oxidation (aioA, arxA) and reduction (arrA, arsC1, arsC2) genes in short-read metagenomic and metatranscriptomic datasets, we investigated the dominant microbial communities involved in arsenite (As(III)) oxidation and arsenate (As(V)) reduction and revealed their potential pathways for coupling As with N and C in situ in rice paddies. Results: Five ROCker models were constructed to quantify the abundance and transcriptional activity of short-read sequences encoding As oxidation (aioA and arxA) and reduction (arrA, arsC1, arsC2) genes in paddy soils. Our results revealed that the sub-communities carrying the aioA and arsC2 genes were predominantly responsible for As(III) oxidation and As(V) reduction, respectively. Moreover, a newly identified As(III) oxidation gene, arxA, was detected in genomes assigned to various phyla and showed significantly increased transcriptional activity with increasing soil pH, indicating its important role in As(III) oxidation in alkaline soils. The significant correlation of the transcriptional activities of aioA with the narG and nirK denitrification genes, of arxA with the napA and nirS denitrification genes and of arrA/arsC2 with the pmoA and mcrA genes implied the coupling of As(III) oxidation with denitrification and As(V) reduction with methane oxidation. Various microbial taxa including Burkholderiales, Desulfatiglandales, and Hyphomicrobiales (formerly Rhizobiales) are involved in the coupling of As with N and C metabolism processes. Moreover, these correlated As and N/C genes often co-occur in the same genome and exhibit greater transcriptional activity in paddy soils with As contamination than in those without contamination. Conclusions: Our results revealed the comprehensive detection and typing of short-read sequences associated with As oxidation and reduction genes via custom-built ROCker models, and shed light on the various microbial taxa involved in the coupling of As and N and C metabolism in situ in paddy soils. The contribution of the arxA sub-communities to the coupling of As(III) oxidation with nitrate reduction and the arsC sub-communities to the coupling of As(V) reduction with methane oxidation expands our knowledge of the interrelationships among As, N, and C cycling in paddy soils. 5-kbCdqq-d7KqfyvRVSSUf Video Abstract [ABSTRACT FROM AUTHOR]

The study focused on the photodegradation of profoxydim, a low-toxicity cyclohexanedione herbicide commonly used in rice crops, under simulated sunlight conditions. Profoxydim's behavior in paddy field conditions is not well understood, and this research aimed to fill that gap, particularly examining the effect of commonly utilized organic amendments such as biochar (BC) on its degradation. Results indicated that profoxydim degrades rapidly, with a half-life of 2.4 ± 0.3 h in paddy water and 1.03 ± 0.1 h in paddy soil. However, when BC was introduced, the degradation slowed significantly, extending the half-lives to 3.1 ± 0.2 h in water and 3.07 ± 0.5 h in soil. The study identified five degradation products (DPs) using TOF mass accuracy measurements and MS/MS spectra fragmentation. Two of these DPs were found to be more stable than profoxydim itself. Additionally, the research proposed a novel photodegradation pathway, highlighting processes such as homolytic C-N bond cleavage, photoisomerization, and photoinduced oxidation. The study's findings contribute new insights into the environmental fate of profoxydim, offering a deeper understanding of its transformation in rice paddy fields and aiding in the assessment of potential risks associated with its residues in agricultural environments. [ABSTRACT FROM AUTHOR]

Bioavailability, enrichment, and risk of phosphorus (P) and its fraction composition were monitored in the paddy soils of Kunnukara during the pre-cultivation and post-harvest periods in the years 2020 and 2021. Iron-bound P (≥ 105.56 ± 0.05 mg/kg) was found highest among the P fractions. The bioavailability of P was recorded at peak value during the post-harvest period, contributed by organic P, Iron bound P, and loosely bound P. Principal component analysis inferred that loosely bound P was pH-dependent and significantly influenced by cation exchange, particle density, soil aggregate stability, and total organic carbon (TOC) in the post-harvest soil, whereas TOC, aluminium-bound P, and calcium-bound P in the pre-cultivation soils. Additionally, physico-chemical parameters like electrical conductivity, bulk density, specific gravity, TOC, and soil aggregate stability have a significant impact on the composition of P fractions in the soil. Bioavailable phosphorus (BAP) ranged from 642.78 ± 0.49 to 594.20 ± 1.23 mg/kg during the post-harvest period. Moreover, the contribution of BAP to total P ranged from 99.45 to 99.54%, indicating the fact that soil is sufficient in BAP. Pollution indices revealed that the paddy soils are at risk of eutrophication. Phosphorus Pollution Index (PPI) > 1 exhibited moderate pollution (1.06 to 1.07) at the topsoil (0–15 cm) and PPI < 1, mild pollution (0.92 to 0.99) at 15–30 cm depths. The organic nitrogen index ≥ 0.133 indicates severe soil pollution in the study site. An extended fertilizer application in the field contributes to nutrient enrichment and warrants the risk of contamination in nearby riverine systems (River Periyar and River Chalakkudy). [ABSTRACT FROM AUTHOR]

A nitrogen-fixing strain designated SG130T was isolated from paddy soil in Fujian Province, China. Strain SG130T was Gram-staining-negative, rod-shaped, and strictly anaerobic. Strain SG130T showed the highest 16S rRNA gene sequence similarities with the type strains Dendrosporobacter quercicolus DSM 1736T (91.7%), Anaeroarcus burkinensis DSM 6283T (91.0%) and Anaerospora hongkongensis HKU 15T (90.9%). Furthermore, the phylogenetic and phylogenomic analysis also suggested strain SG130T clustered with members of the family Sporomusaceae and was distinguished from other genera within this family. Growth of strain SG130T was observed at 25–45 °C (optimum 30 °C), pH 6.0–9.5 (optimum 7.0) and 0–1% (w/v) NaCl (optimum 0.1%). The quinones were Q-8 and Q-9. The polar lipids were phosphatidylserine (PS), phosphatidylethanolamine (PE), glycolipid (GL), phospholipid (PL) and an unidentified lipid (UL). The major fatty acids (> 10%) were iso-C13:0 3OH (26.6%), iso-C17:1 (15.6%) and iso-C15:1 F (11.4%). The genomic DNA G + C content was 50.7%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG130T and the most closely related type strain D. quercicolus DSM 1736T (ANI 68.0% and dDDH 20.3%) were both below the cut-off level for species delineation. The average amino acid identity (AAI) between strain SG130T and the most closely related type strain D. quercicolus DSM 1736T was 63.2%, which was below the cut-off value for bacterial genus delineation (65%). Strain SG130T possessed core genes (nifHDK) involved in nitrogen fixation, and nitrogenase activity (106.38 μmol C2H4 g−1 protein h−1) was examined using the acetylene reduction assay. Based on the above results, strain SG130T is confirmed to represent a novel genus of the family Sporomusaceae, for which the name Azotosporobacter soli gen. nov., sp. nov. is proposed. The type strain is SG130T (= GDMCC 1.3312T = JCM 35641T). [ABSTRACT FROM AUTHOR]

In this research, two novel Fe(III)-reducing bacteria, SG10T and SG198T of genus Geothrix, were isolated from the rice field of Fujian Agriculture and Forestry University in Fuzhou, Fujian Province, China. Strains SG10T and SG198T were strictly anaerobic, rod-shaped and Gram-stain-negative. The two novel strains exhibited iron reduction ability, utilizing various single organic acid as the elector donor and Fe(III) as a terminal electron acceptor. Strains SG10T and SG198T showed the highest 16S rRNA sequences similarities to the type strains of Geothrix oryzisoli SG189T (99.0–99.5%) and Geothrix paludis SG195T (99.0–99.7%), respectively. The phylogenetic trees based on the 16S rRNA gene and genome 120 conserved core genes showed that strains SG10T and SG198T belong to the genus Geothrix. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the phylogenetic neighbors and the two isolated strains were 86.1–94.3% and 30.7–59.5%, respectively. The major fatty acids were iso-C15:0, anteiso-C15:0, C16:0 and iso-C13:0 3OH, and MK-8 was the main respiratory quinone. According to above results, the two strains were assigned to the genus Geothrix with the names Geothrix campi sp. nov. and Geothrix mesophila sp. nov. Type strains are SG10T (= GDMCC 1.3406 T = JCM 39331 T) and SG198T (= GDMCC 62910 T = KCTC 25635 T), respectively. [ABSTRACT FROM AUTHOR]

Background: Arsenic (As) metabolism by soil microorganisms has an impact on As geochemical cycling in paddy soils, which in turn affects As uptake in rice. However, little is known about the key microorganisms involved in this process in Japanese paddy soil. Results: Total RNA was extracted from Japanese paddy soils with different levels of dissolved As under flooded conditions, and the transcription of As metabolic genes (arrA, ttrA and arsM) was analyzed via a metatranscriptomic approach. The results showed that ttrA was the predominant respiratory arsenate reductase gene transcribed in these soils rather than arrA, suggesting that ttrA contributes to the reductive dissolution of As. The predominant taxa expressing ttrA differed among soils but were mostly associated with genera known for their iron- and/or sulfate-reduction activity. In addition, a wide variety of microorganisms expressed and upregulated arsM approximately 5.0- to 13.2-fold at 9 d compared with 3 d of incubation under flooded conditions in flasks. Conclusions: Our results support the involvement of microbial activity in the geochemical cycling of As in Japanese paddy soils and suggest that ttrA may be one of the key genes involved in the formation of arsenite, an inorganic species taken up by rice. [ABSTRACT FROM AUTHOR]

Aims: The application of cover crop residue is an important means in managing paddy soil. This study was to investigate the influences of minerals on the mineralization of organic matter and the community and necromass of microbes in paddy soils amended with cover crop residue. Methods: 13C-labelled cover crop residue (Astragalus sinicus L.) was prepared using a pulse labeling method. The mineralization of cover crop residue and native soil organic matter and the community and necromass of microbes in two flooded paddy soils amended with or without illite, goethite and ferrihydrite was investigated by incubation experiments. The released CO2/CH4 was analyzed by gas chromatography. Amino sugar was used as the biomarker of microbial residue carbon. Soil microbial communities were analyzed by high-throughput sequencing and quantitative polymerase chain reaction. Results: Illite, goethite and ferrihydrite significantly decreased the amounts of both CO2 and CH4 emissions from native soil organic carbon in both paddy soils. Moreover, the inhibition efficiency followed the same sequence of ferrihydrite > goethite > illite for both CO2 and CH4 emissions. However, ferrihydrite significantly stimulated the mineralization of cover crop residue in both paddy soils. The examined minerals, especially ferrihydrite, also tended to decrease bacterial and fungal abundance and diversity in both paddy soils. Moreover, the contents of both bacterial and fungal residue carbon were significantly decreased by the examined minerals in alkaline paddy soil. Conclusion: Examined minerals tended to decrease total mineralization of cover crop residue and native organic matter, the microbial abundance, diversity, and necromass in flooded paddy soils. [ABSTRACT FROM AUTHOR]

Agricultural soil is the main source of greenhouse gas emissions, among which carbon dioxide (CO2) is an important greenhouse gas, impacting the global climate. In China, as a large rice-producing country, carbon sequestration and CO2 mitigation in paddy soil are crucial for the mitigation of global climate change. While biochar has been widely used in the mitigation of soil greenhouse gas emissions, the application site of biochar, i.e., whether or not it is the same as its feedstocks, may generate different effects on soil CO2 emissions due to the differences in the element and nutrient concentrations in its feedstocks, especially when applied in fertilized soil. In order to explore the effects of biochar application with different feedstocks on the mitigation of CO2 emissions from paddy soil, this experiment took paddy soil in a red soil area as the research object, using rice straw and Camellia oleifera fruit shell as raw materials to produce biochar (adding an amount of 40 g kg−1 soil) and urea as an external nitrogen source (adding an amount of 200 mg kg−1 soil). The effects of two different types of biochar derived from feedstocks with different producing origins on the CO2 emissions from paddy soil were studied via laboratory control incubation studies. The results showed that (1) the effects of rice straw biochar addition on the soil pH, NO3−-N and total available nitrogen (AN) content were significantly higher than those of Camellia oleifera fruit shell biochar (the scale of the increase was higher by 6.40%, 579.7% and 180.1%, respectively). (2) The CO2 emission rate and cumulative emissions of soil supplemented with rice straw biochar were significantly lower than in that supplemented with Camellia oleifera fruit shell biochar (decreases of 28.0% and 27.5%, respectively). Our findings suggest that the efficiency of emission mitigation of rice straw biochar is better than that of Camellia oleifera fruit shell applied to paddy soil. While future studies considering more types of greenhouse gases will be necessary to expand these findings, this study indicates that biochar prepared from in situ feedstock can be used to reduce greenhouse gas emissions in rice fields, so as to ensure sustainable development and achieve energy conservation and emission reduction goals. This study will benefit future agricultural practices when choosing biochar as a greenhouse gas mitigation strategy in the context of global warming, as well as other global changes following global warming, caused by elevated atmospheric greenhouse gases. [ABSTRACT FROM AUTHOR]

BACKGROUND: Flusulfinam, a novel chiral herbicide, effectively controls Echinochloa crusgalli and Digitaria sanguinalis in paddy fields, indicating significant potential for practical agricultural applications. However, limited information is available on flusulfinam from a chiral perspective. A comprehensive evaluation of the enantiomeric levels of flusulfinam was performed. RESULTS: Two enantiomers, R‐(+)‐ and S‐(−)‐flusulfinam, were separately eluted using a Chiralcel OX‐RH column. The bioactivity of R‐flusulfinam against the two was 1.4–3.1 fold that of Rac‐flusulfinam against two weed species. R‐flusulfinam toxicity to Danio rerio larvae and Selenastrum capricornutumwere was 0.8‐ and 3.0‐fold higher than Rac‐flusulfinam, respectively. Degradation experiments were conducted using soil samples from four Chinese provinces. The findings indicated that S‐flusulfinam (half‐life T1/2 = 40.8 days) exhibits preferential degradation than R‐flusulfinam (T1/2 = 46.2–57.8 days) in the soils of three provinces. Under anaerobic conditions, soil from Anhui exhibited preferential degradation of R‐flusulfinam (T1/2 = 46.2 days) over S‐flusulfinam (T1/2 = 63 days). Furthermore, two hydrolysis products of flusulfinam (M299 and M100) are proposed for the first time. CONCLUSION: The enantioselective bioactivity, toxicity and degradation of flusulfinam were investigated. Our findings indicate that R‐flusulfinam is an extremely effective and low‐toxicity enantiomer for the tested species. The soil degradation test indicated that the degradation of flusulfinam was accelerated by higher organic matter content and lower soil pH. Furthermore, microbial communities may play a crucial role in driving the enantioselective degradation processes. This study lays the groundwork for the systematic evaluation of flusulfinam from an enantiomeric perspective. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

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Background: Paddy soil is a typical soil type affected by anthropogenic management and factors related to natural soil formation. The evolution from mudflats to typical paddy soils can significantly affect the soil microecology. Previous studies have reported the evolution of soil physicochemical properties, microbes, and related soil environmental factors in a millennium paddy soil chronosequence. However, the potential biological mechanisms of changes in metabolites and microbes–metabolites interaction are poorly understood. Therefore, a combination of high-throughput sequencing and environmental pseudotargeted metabolomics techniques was adopted to explore the effects of the millennium paddy soil chronosequence on microbial communities, metabolites, and their functions and interactions. Results: The soil ecology changed greatly in the first 60 years of the transition from mudflat to paddy planting. Among the microbial communities, the response of the bacteria to the chronosequence was more sensitive than that of fungi. Among them, the bacterial communities of Proteobacteria, Bacteroidetes, Acidobacteria, and Nitrospirae exhibited regular succession over the chronosequence, but the fungal communities did not show regular changes. Bacterial function prediction revealed that the beginning of the critical stage of the evolution from mudflat to paddy soil involved the organic matter cycle and energy flow. In contrast, fungi were characterized mainly by pathogenic and saprophytic functions. The results of the principal component analysis of the metabolites revealed a similar pattern of change as that of the microbes. Seventy-five characteristic metabolites exhibited three trends of change during the development of the paddy soil chronosequence. Twenty-five differentially active metabolic pathways, including glyoxylate and dicarboxylate metabolism, starch and sucrose metabolism, and galactose metabolism, were enriched. In addition, correlation analysis revealed that long-chain fatty acids, short-chain fatty acids, phenolic acids, carbohydrates, and polyalcohols significantly regulate the microbial communities in paddy soil. Conclusions: Combining metabolome and microbiome has expanded the overall understanding of the development of paddy soil under anthropogenic management. During the development of a paddy soil chronosequence, the synergistic regulation of soil physicochemical properties and metabolites in the microbial community results in increased productivity. This study provides a new perspective on microbes and metabolites interaction. [ABSTRACT FROM AUTHOR]

Abstract Background Arsenic (As) metabolism pathways and their coupling to nitrogen (N) and carbon (C) cycling contribute to elemental biogeochemical cycling. However, how whole-microbial communities respond to As stress and which taxa are the predominant As-transforming bacteria or archaea in situ remains unclear. Hence, by constructing and applying ROCker profiles to precisely detect and quantify As oxidation (aioA, arxA) and reduction (arrA, arsC1, arsC2) genes in short-read metagenomic and metatranscriptomic datasets, we investigated the dominant microbial communities involved in arsenite (As(III)) oxidation and arsenate (As(V)) reduction and revealed their potential pathways for coupling As with N and C in situ in rice paddies. Results Five ROCker models were constructed to quantify the abundance and transcriptional activity of short-read sequences encoding As oxidation (aioA and arxA) and reduction (arrA, arsC1, arsC2) genes in paddy soils. Our results revealed that the sub-communities carrying the aioA and arsC2 genes were predominantly responsible for As(III) oxidation and As(V) reduction, respectively. Moreover, a newly identified As(III) oxidation gene, arxA, was detected in genomes assigned to various phyla and showed significantly increased transcriptional activity with increasing soil pH, indicating its important role in As(III) oxidation in alkaline soils. The significant correlation of the transcriptional activities of aioA with the narG and nirK denitrification genes, of arxA with the napA and nirS denitrification genes and of arrA/arsC2 with the pmoA and mcrA genes implied the coupling of As(III) oxidation with denitrification and As(V) reduction with methane oxidation. Various microbial taxa including Burkholderiales, Desulfatiglandales, and Hyphomicrobiales (formerly Rhizobiales) are involved in the coupling of As with N and C metabolism processes. Moreover, these correlated As and N/C genes often co-occur in the same genome and exhibit greater transcriptional activity in paddy soils with As contamination than in those without contamination. Conclusions Our results revealed the comprehensive detection and typing of short-read sequences associated with As oxidation and reduction genes via custom-built ROCker models, and shed light on the various microbial taxa involved in the coupling of As and N and C metabolism in situ in paddy soils. The contribution of the arxA sub-communities to the coupling of As(III) oxidation with nitrate reduction and the arsC sub-communities to the coupling of As(V) reduction with methane oxidation expands our knowledge of the interrelationships among As, N, and C cycling in paddy soils. Video Abstract

Abstract The study focused on the photodegradation of profoxydim, a low-toxicity cyclohexanedione herbicide commonly used in rice crops, under simulated sunlight conditions. Profoxydim’s behavior in paddy field conditions is not well understood, and this research aimed to fill that gap, particularly examining the effect of commonly utilized organic amendments such as biochar (BC) on its degradation. Results indicated that profoxydim degrades rapidly, with a half-life of 2.4 ± 0.3 h in paddy water and 1.03 ± 0.1 h in paddy soil. However, when BC was introduced, the degradation slowed significantly, extending the half-lives to 3.1 ± 0.2 h in water and 3.07 ± 0.5 h in soil. The study identified five degradation products (DPs) using TOF mass accuracy measurements and MS/MS spectra fragmentation. Two of these DPs were found to be more stable than profoxydim itself. Additionally, the research proposed a novel photodegradation pathway, highlighting processes such as homolytic C-N bond cleavage, photoisomerization, and photoinduced oxidation. The study’s findings contribute new insights into the environmental fate of profoxydim, offering a deeper understanding of its transformation in rice paddy fields and aiding in the assessment of potential risks associated with its residues in agricultural environments.

Abstract Background Arsenic (As) metabolism by soil microorganisms has an impact on As geochemical cycling in paddy soils, which in turn affects As uptake in rice. However, little is known about the key microorganisms involved in this process in Japanese paddy soil. Results Total RNA was extracted from Japanese paddy soils with different levels of dissolved As under flooded conditions, and the transcription of As metabolic genes (arrA, ttrA and arsM) was analyzed via a metatranscriptomic approach. The results showed that ttrA was the predominant respiratory arsenate reductase gene transcribed in these soils rather than arrA, suggesting that ttrA contributes to the reductive dissolution of As. The predominant taxa expressing ttrA differed among soils but were mostly associated with genera known for their iron- and/or sulfate-reduction activity. In addition, a wide variety of microorganisms expressed and upregulated arsM approximately 5.0- to 13.2-fold at 9 d compared with 3 d of incubation under flooded conditions in flasks. Conclusions Our results support the involvement of microbial activity in the geochemical cycling of As in Japanese paddy soils and suggest that ttrA may be one of the key genes involved in the formation of arsenite, an inorganic species taken up by rice.

Undisturbed soil columns were used to study the effect of sterile rice spikelets-derived biochar (SRSB) on NH4+-N, available P, and available K leaching and nutrients availability in a paddy soil under continuous standing water (CSW) condition. The experiment was conducted for two crop cycles and comprised of three treatments: recommended dose of sole chemical fertilizers (CF), CF+SRSB (2 t ha−1), and control. In both crop cycles, incorporation of SRSB reduced the leachate NH4+-N and available K concentrations, while increased the available P concentration compared to sole CF. The SRSB amendment reduced the cumulative losses of NH4+-N by 35–38% and available K by 23–25% than CF only. However, there was no significant variation in cumulative available P loss between SRSB and CF only. The reduced leaching loss of NH4+-N and available K could be attributed to the better nutrient adsorption capacity of SRSB. After completion of two crop cycles, the soil pH, soil organic carbon, soil total N, available P, and available K increased with SRSB amended soils than sole CF. This study showed positive effects of SRSB on retaining nutrients and increasing their availability in the soil which could benefit efficient fertilizer management in paddy soil under CSW.

Abstract Background Paddy soil is a typical soil type affected by anthropogenic management and factors related to natural soil formation. The evolution from mudflats to typical paddy soils can significantly affect the soil microecology. Previous studies have reported the evolution of soil physicochemical properties, microbes, and related soil environmental factors in a millennium paddy soil chronosequence. However, the potential biological mechanisms of changes in metabolites and microbes–metabolites interaction are poorly understood. Therefore, a combination of high-throughput sequencing and environmental pseudotargeted metabolomics techniques was adopted to explore the effects of the millennium paddy soil chronosequence on microbial communities, metabolites, and their functions and interactions. Results The soil ecology changed greatly in the first 60 years of the transition from mudflat to paddy planting. Among the microbial communities, the response of the bacteria to the chronosequence was more sensitive than that of fungi. Among them, the bacterial communities of Proteobacteria, Bacteroidetes, Acidobacteria, and Nitrospirae exhibited regular succession over the chronosequence, but the fungal communities did not show regular changes. Bacterial function prediction revealed that the beginning of the critical stage of the evolution from mudflat to paddy soil involved the organic matter cycle and energy flow. In contrast, fungi were characterized mainly by pathogenic and saprophytic functions. The results of the principal component analysis of the metabolites revealed a similar pattern of change as that of the microbes. Seventy-five characteristic metabolites exhibited three trends of change during the development of the paddy soil chronosequence. Twenty-five differentially active metabolic pathways, including glyoxylate and dicarboxylate metabolism, starch and sucrose metabolism, and galactose metabolism, were enriched. In addition, correlation analysis revealed that long-chain fatty acids, short-chain fatty acids, phenolic acids, carbohydrates, and polyalcohols significantly regulate the microbial communities in paddy soil. Conclusions Combining metabolome and microbiome has expanded the overall understanding of the development of paddy soil under anthropogenic management. During the development of a paddy soil chronosequence, the synergistic regulation of soil physicochemical properties and metabolites in the microbial community results in increased productivity. This study provides a new perspective on microbes and metabolites interaction. Graphical Abstract

Integrated rice–aquatic animal farming has become a vital strategy for enhancing food security. To assess the effects of integrated rice–giant river prawn (Macrobrachium rosenbergii) farming (IRPF) on agricultural ecosystems, we used 16S rRNA gene sequencing to analyze soil bacterial communities in comparison with traditional rice monoculture (RM). Our study revealed that the IRPF did not significantly affect the diversity of the soil bacterial community. However, during the initial culture stage, IRPF markedly increased the relative abundance of the phylum candidate division NC10 and the genus Candidatus Methylomirabilis, enhancing nitrogen-cycling-related functions within the bacterial community. Additionally, IRPF reduced the complexity and stability of these communities in the early to middle culture stages. While stochastic processes usually dominate the assembly of these communities, IRPF restricted bacterial migration and reduced the influence of these stochastic processes. Furthermore, IRPF had a significant impact on environmental factors within paddy soils, strongly correlating with shifts in bacterial communities, particularly through variations in soil nitrite concentration. In conclusion, the influence of IRPF on the bacterial community in paddy soils was primarily observed during the early and middle culture stages, and the impacts of IRPF on the soil bacterial community were primarily driven by environmental changes, especially soil nitrite concentration. These findings provide theoretical insights and a reference for understanding the microbiological impacts of different integrated rice–fish farming systems on agricultural ecosystems. [ABSTRACT FROM AUTHOR]

Periodic redox condition changes in acidic paddy soils substantially induce the biogeochemical redox cycling, and consequently affect Cd availability. However, the underlying biogeochemical mechanisms of the complicated redox processes in paddy soil remain poorly understood. Thus, we investigated the dynamics of Cd fractions under anoxic (0–40 days) and oxic (40–55 days) conditions. The available Cd content was evaluated using the diffusive gradients in thin film (DGT) technique, and the results show it decreased from 6.3 μg L–1 to below 0.1 μg L–1 under anoxic conditions, but rapidly increased to 13.5 μg L–1 under oxic conditions. Both sequential extraction procedures and X-ray absorption spectroscopy (XAS) analyses found that majority of available Cd transformed to organic matter complex and Fe-Mn oxides fractions, rather than bounded with sulfides. The soil chemical properties further evaluated, and the correlation analysis and principal component analysis results suggested that the key factors in soils for the available Cd was the SO 4 2–, pH, and surface site concentration. The reduction of SO 4 2– could generate sulfides which may precipitate with dissolved Cd. The biogeochemical redox cycling of Fe/N/S determined the changes of soil pH and consequently influenced adsorption behavior of Cd. The breakdown of the soil aggregations changed the surface site concentration, which may affect the immobilization of Cd. A process-based kinetic model was established, and it found that iron biogeochemical redox cycling dominated the changes of soil pH, and thereby contributed to majority Cd retention by Fe-Mn oxides (34.4 %) and organic matter (33.7 %). In addition, sulfur biogeochemical redox cycling only contributed to 13.6 % of the total Cd contents, because of relatively low Cd solubility in contaminated soils and the competition with other cations for limited sulfides. The findings provide robust targets for interpreting the iron and sulfur biogeochemical processes for Cd availability and would be helpful for developing the precise and effective remediation strategies in Cd-contaminated soils. [ABSTRACT FROM AUTHOR]

Taking fresh soil samples from a rice–wheat rotation field (RW), a permanently flooded rice field (PF), and a double-rice cropping field (DR: DRE for the early rice; DRL for the late rice), we measured the CH4 production potential (MPP), the relative contribution of acetate-dependent methanogenesis (ƒac), soil properties, and methanogenic archaeal communities mainly in order to reveal the temporal variation and corresponding influencing factors of methanogenic pathways in paddy soils. Consistent with the change in dissolved organic C (DOC) content, the MPP generally decreased with rice growth in RW and DRL while increasing in PF and DRE. Based on the measurements of stable carbon isotopes, the estimated ƒac-value in PF dropped sharply from 54%-61% at the tillering stage to 30%-35% at the booting stage and rose again at the ripening stage. This variation pattern was positively correlated with that of acetate content, perhaps resulting from the activation of acetoclastic Methanosarcina. In contrast, the ƒac-value in RW and DR rose from 20%-44% at the tillering stage to 49%-59% at the ripening stage, possibly owing to the increase in the relative abundance of acetoclastic Methanothrix. The relative abundance of Methanosarcina in PF was 3%-4% higher than those in RW and DR, whereas that of Methanothrix was 3%-7% lower (P < 0.05). Soil acetate, DOC, and moisture contents significantly affected the methanogenic community composition. Our results demonstrate that the temporal variation of methanogenic pathways was influenced by the relative abundance of acetoclastic methanogens depending on the acetate level. [ABSTRACT FROM AUTHOR]

Rice (Oryza sativa L.) residues (root and straw) are unique substrates for microbes in paddy soils. Microbial respiration (RH) of paddy soils is likely to be affected by substrate quality. However, no relevant study on the effects of changed rice residue chemistry by climate change on the temperature sensitivity (Q10) of the RH of soils amended with the residues is available. To fill this knowledge gap, we conducted an incubation experiment (at 15, 25, and 35 °C) with rice residues of which lignin, nonstructural carbohydrate (NSC), and carbon-to-nitrogen ratio (C/N) were modified by growing the rice plants under different CO2 and air temperature (Tair). Co-elevated CO2 and Tair decreased lignin and C/N but increased the NSC contents of the residues, leading to the greater RH in the soils amended with rice residues produced under co-elevated CO2 and Tair compared to other CO2 or Tair treatments. However, the Q10 values of the RH of soils amended with rice residues produced under different CO2 and Tair were marginally changed, probably due to other confounding factors such as soil enzyme activity and nutrient availability. Despite that, there was a negative relationship between NSC and Q10 for soils amended with straw of which C/N is lower than root, agreeing with the kinetic theory on "substrate quality–Q10 relationship". Our result suggests that residue chemistry may not affect the Q10 of soils with root residue, but for straw-amended soils, less-recalcitrant NSC rather than more-recalcitrant lignin of straw may be critical in determining the Q10 of the soils. [ABSTRACT FROM AUTHOR]

Irrigated and rain-fed rice fields are unique agroecosystems and anthropogenic wetlands whose main feature is seasonal flooding. Flooded soils are characterized by spatiotemporal shifts and oscillation of the oxygen status and redox potential, sustaining varieties of microbial metabolisms, where bacteria and methanogenic archaea play principal roles and thus have been the major research targets. In this review, we focus on the diversity and ecology of protists—often overlooked biological entities—in wetland rice field soils. Protists with different ecological functions, i.e., phagotrophs, phototrophs, saprotrophs, and parasites, inhabit a rice field soil with a community- and individual-level adaptation to the wide range of oxygen tensions and redox potential. Other agricultural managements like fertilization and char application also influence the protist community. They link to the material cycling in rice soil and affect the activities and community composition of the microorganisms involved in the biogeochemical cycles. Rice roots are the hot spot for protists, which control the rhizospheric bacterial community and could increase the plant productivity through enhancing nutrient release and altering bacterial activities. This review highlights the essential roles of protists in a wetland rice field soil and needs for further research to fill the gaps in knowledge regarding the diversity and functions of the protists in this unique agroecosystem. [ABSTRACT FROM AUTHOR]

Methanotrophs of the genus Methylocystis are frequently found in rice paddies. Although more than ten facultative methanotrophs have been reported since 2005, none of these strains was isolated from paddy soil. Here, a facultative methane-oxidizing bacterium, Methylocystis iwaonis SD4, was isolated and characterized from rhizosphere samples of rice plants in Nanjing, China. This strain grew well on methane or methanol but was able to grow slowly using acetate or ethanol. Moreover, strain SD4 showed sustained growth at low concentrations of methane (100 and 500 ppmv). M. iwaonis SD4 could utilize diverse nitrogen sources, including nitrate, urea, ammonium as well as dinitrogen. Strain SD4 possessed genes encoding both the particulate methane monooxygenase and the soluble methane monooxygenase. Simple and rapid genetic manipulation methods were established for this strain, enabling vector transformation and unmarked genetic manipulation. Fast growth rate and efficient genetic tools make M. iwaonis SD4 an ideal model to study facultative methanotrophs, and the ability to grow on low concentration of methane implies its potential in methane removal. [ABSTRACT FROM AUTHOR]

Plants acquire potassium (K) not only from exchangeable K fractions but also from non-exchangeable K fractions. However, factors affecting the amount of K supplied from the non-exchangeable K fraction have not been well understood. In this study, the effects of soils and exchangeable K on the amount of K supplied to rice from the non-exchangeable K fraction were investigated for six Japanese paddy soils diluted with different rates of quartz sand. The amounts of K supplied from the non-exchangeable K fractions (recharged K) ranged from 14.4 to 137 mg K2O kg−1, equivalent to 10 to 61% of the total K acquired by rice. The amounts of recharged K were affected by the exchangeable K levels in three out of six soils. Although the cultivation experiments were conducted under various K conditions including severe K deficiency, exchangeable K was detected after cultivation in all soils, and the contents of exchangeable K were almost identical for each soil regardless of the dilution ratio of soil with quartz sand. Accordingly, there would be at least three types of non-exchangeable K fractions which dissolve into soil solution to attain a specific level of exchangeable K: (i) a non-exchangeable K fraction that releases K regardless of the exchangeable K level; (ii) a non-exchangeable K fraction that easily releases K with the decrease in exchangeable K under sufficient K conditions without inducing K-deficient symptoms in rice; and (iii) a non-exchangeable K fraction that releases K with the decrease in exchangeable K only under severe K-deficient conditions with accompanying deficient symptoms in rice. The application of K fertilizer would reduce the amount of recharged K acquired by rice from fractions (ii) and (iii), whereas fraction (i) would remain unaffected by the fertilized K until the level of exchangeable K reaches a specific level for each soil. The release of K from a fraction (iii) only occurred under conditions of severe K deficiency; hence, farmers should not rely on this fraction for K supply. [ABSTRACT FROM AUTHOR]

Compared with 454 sequencing technology, short-read sequencing (e.g., Illumina) technology generates sequences of high accuracy, but limited length (<500 bp). Such a limitation can prove that studying a target gene using a large amplicon (>500 bp) is challenging. The ammonia monooxygenase subunit A (amoA) gene of ammonia-oxidizing archaea (AOA), which plays a crucial part in the nitrification process, is such a gene. By providing a full overview of the community of a functional microbial guild, 16S ribosomal ribonucleic acid (rRNA) gene sequencing could overcome this problem. However, it remains unclear how 16S rRNA primer selection influences the quantification of relative abundance and the identification of community composition of nitrifiers, especially AOA. In the present study, a comparison was made between the performance of primer pairs 338F-806R, 515F-806R, and 515F-907R to a shotgun metagenome approach. The structure of nitrifier communities subjected to different long-term organic matter amendment and water management protocols was assessed. Overall, we observed higher Chao1 richness diversity of soil total bacteria by using 515F-806R compared to 338F-806R and 515F-907R, while higher Pielou's evenness diversity was observed by using 515F-806R and 515F-907R compared to 338F-806R. The studied primer pairs revealed different performances on the relative abundance of Thaumarchaeota, AOB, and NOB. The Thaumarchaeota 16S rRNA sequence was rarely detected using 338F-806R, while the relative abundances of Thaumarchaeota detected using 515F-806R were higher than those detected by using 515F-907R. AOB showed higher proportions in the 338F-806R and 515F-907R data, than in 515F-806R data. Different primers pairs showed significant change in relative proportion of NOB. Nonetheless, we found consistent patterns of the phylotype distribution of nitrifiers in different treatments. Nitrosopumilales (NP) and Nitrososphaerales (NS) clades were the dominant members of the AOA community in soils subject to controlled irrigation, whereas Ca. Nitrosotaleales (NT) and NS clades dominated the AOA community in soils subject to flooding irrigation. Nitrospira lineage II was the dominant NOB phylotype in all samples. Overall, ideal 16S rRNA primer pairs were identified for the analysis of nitrifier communities. Moreover, NP and NT clades of AOA might have distinct environmental adaptation strategies under different irrigation treatments. [ABSTRACT FROM AUTHOR]

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Purpose: To clarify the geographical distribution pattern of asymbiotic nitrogen activity and diazotrophic community in paddy soils, and to understand the primary environmental driving factors driving asymbiotic nitrogen fixation rate (ANFR) and community diversity. Materials and methods: The ANFR and the environmental driving factors of diazotrophic community diversity were investigated in 76 paddy soils across 6 major rice-growing regions in China by 15N2 labeling and nifH gene high-throughput sequencing. Results and discussions: Among all the sample sites, the northeast region had relatively higher ANFR (p < 0.05) compared to other regions. There was no significant correlation between soil ANFR and nifH abundance. The ANFR was significantly affected by Mo, total N and total P, while C:N ratio, exchangeable Ca and pH had a significant influence on nifH abundance. Proteobacteria, Thermodesulfobacteriota and Cyanobacteria dominated within the diazotrophic community across the paddy soils. Furthermore, 50.7% of the variance in community compositions could be attributed to different environmental variables. These multifactorial drivers, including Ca, C:N ratio, Mg, Na, Mn, N:P ratio, Mo and pH, significantly influence formation of specific diazotrophic microbial groups. Conclusions: (1) No significant correlation between the rate of asymbiotic nitrogen fixation in paddy soil and the abundance of the nifH gene. (2) The ANFR was significantly positively correlated with the molybdenum, phosphorus, potassium, nitrogen and organic carbon contents. (3) The abundance of the nifH gene was primarily correlated with Ca content and the soil C:N ratio. (4) Distinct diazotrophic communities are influenced by different environmental drivers. (5) Alphaproteobacteria and Spirochaetota are more abundant in soils with high elevated nitrogen and molybdenum content, indicating their significant contributions to nitrogen fixation in paddy soil. [ABSTRACT FROM AUTHOR]

In previous studies, iron-based nanomaterials, especially biochar (BC)-supported sulfidized nanoscale zero-valent iron (S-nZVI/BC), have been widely used for the remediation of soil contaminants. However, its potential risks to the soil ecological environment are still unknown. This study aims to explore the effects of 3% added S-nZVI/BC on soil environment and microorganisms during the remediation of Cd contaminated yellow–brown soil of paddy field. The results showed that after 49 d of incubation, S-nZVI/BC significantly reduced physiologically based extraction test (PBET) extractable Cd concentration (P < 0.05), and increased the immobilization efficiency of Cd by 16.51% and 17.43% compared with S-nZVI and nZVI/BC alone, respectively. Meanwhile, the application of S-nZVI/BC significantly increased soil urease and sucrase activities by 0.153 and 0.446 times, respectively (P < 0.05), improving the soil environmental quality and promoting the soil nitrogen cycle and carbon cycle. The results from the analysis of the 16S rRNA genes indicated that S-nZVI/BC treatment had a minimal effect on the bacterial community and did not appreciably alter the species of the original dominant bacterial phylum. Importantly, compared to other iron-based nanomaterials, incorporating S-nZVI/BC significantly increased the soil organic carbon (OC) content and decreased the excessive release of iron (P < 0.05). This study also found a significant negative correlation between OC content and Fe(II) content (P < 0.05). It might originate from the reducing effect of Fe-reducing bacteria, which consumed OC to promote the reduction of Fe(III). Accompanying this process, the redistribution of Cd and Fe mineral phases in the soil as well as the generation of secondary Fe(II) minerals facilitated Cd immobilization. Overall, S-nZVI/BC could effectively reduce the bioavailability of Cd, increase soil nutrients and enzyme activities, with less toxic impacts on the soil microorganisms. [ABSTRACT FROM AUTHOR]

Soil texture affects rice nutrient uptake and yield formation by influencing soil structure, microbial activity, and soil nutrient supply capacity. Analyzing the relationship between soil texture, nutrient content, and rice agronomic traits is of great significance for precise and efficient fertilizer application. The tillage layer (0–20 cm) of 31 paddy fields in China's main rice-producing areas was collected to perform rice pot experiments, and soil texture characteristics, physicochemical properties, microbial-related indicators, and rice agronomic traits were measured and analyzed. The results showed that these soils could be classified into four types of soil texture: loamy sandy soil, sandy loam soil, silty loam soil, and silty soil. Analysis of variance showed that the available nitrogen (AN), available potassium (AK), and available phosphorus (AP) contents were the highest in silty loam, silty, and sandy loam soils, respectively, and silt loamy soil had the highest CEC. Principal component analysis (PCA) also showed that soil physicochemical properties can be distinguished to a certain extent according to soil texture types. For the relationship of soil texture parameters and soil physicochemical properties, soil organic matter (OM), total nitrogen (TN), AN, ammonium nitrogen (NH4+-N), and microbial carbon (MBC) contents were positively correlated with soil clay content, AK was positively correlated with silt content, and soil phosphorus status was significantly related to pH. Mantel's test revealed significant correlations between rice N, P, and K nutrient status, dry matter accumulation, and yield, and soil available nutrient content, MBC, pH, and soil texture parameters. Structural equation modeling (SEM) indicated that sand affected soil available nutrients by regulating pH, while clay can positively influence soil available nutrients by affecting soil organic matter mineralization and microbial activity, thus influencing nutrient absorption and yield formation in rice. Overall, in rice production, the silty and silty loam paddy soil with fine texture and higher clay content facilitates the mineralization of soil organic matter and the activity of soil microbes, resulting in more available soil nutrients, which benefits the rice absorption and accumulation of nutrients. Furthermore, a higher content of clay also promotes the distribution of dry matter to the panicle, thereby promoting rice yield formation. [ABSTRACT FROM AUTHOR]

Pymetrozine is an insecticide that is widely used, causing severe environmental problems. This study determined the pymetrozine degradation by an enrichment culture of microorganisms from paddy soil. The results showed that the enrichment culture utilized 67.3 ± 10.1% of the pure substrate as the sole carbon and nitrogen source in liquid media after 36 h. However, the utilization rates of pymetrozine in herbicide were lower than those of the pure substrate. The maximum utilization rates of pure pymetrozine and pymetrozine in herbicide were 0.051 ± 0.006 and 0.039 ± 0.004 mmol/h, respectively. During the degradation, the metabolites 4-amino-6-methyl-4,5-dihydro-2H-[1,2,4]triazine-3-one and nicotinic acid were produced and then further degraded. In addition, the inoculation of a fungal strain, Phanerochaete sp. Th1, which degraded rice straw components, increased pymetrozine degradation in rice straw and soil. The study provides essential information on pymetrozine degradation in liquid media, rice straw during solid-state fermentation, and soil. [ABSTRACT FROM AUTHOR]

Purpose: Soil colloids significantly influence the transfer of phosphorus (P) from agricultural lands to aquatic ecosystems. Nevertheless, the impact of soil amendments, such as biochar, on colloidal P release and mobilization is not fully understood. This study aimed to explore how biochar amendments affect the dynamics of soil colloidal P in paddy soils, particularly focusing on the interaction between soil aggregation and colloidal P mobilization. Materials and methods: We conducted a soil incubation experiment to investigate the effects of rape straw-derived biochar (SBC) and chicken manure-derived biochar (MBC) on soil aggregate stability, P distribution, and colloidal P content in paddy soils with different fertility levels. Soil aggregates were fractionated using wet sieving and sedimentation methods, whereas colloidal P was determined through ultracentrifugation. Results and discussion: Our findings demonstrated that both MBC and SBC addition increased soil aggregation by promoting the formation of larger aggregates (> 250 μm and 53–250 μm), while reducing the proportion of smaller soil aggregates (< 2 μm, 2–20 μm, and 20–53 μm). Biochar addition led to an increased allocation of P in soil aggregates of > 250 μm and 53–250 μm, with the observed rise in total P content primarily attributed to the inherent P within the added biochar. MBC exhibited a more pronounced impact on soil P dynamics than SBC. Despite enhanced soil aggregation, MBC addition substantially increased soil colloidal P and dissolved P, suggesting potential environmental risks associated with P loss. The elevated degree of P saturation resulting from MBC addition appeared to play a more critical role in regulating soil colloidal P release and mobilization. Conclusion: Our study highlights the importance of carefully considering the long-term application of P-enriched biochar in paddy soils, as this practice may lead to P loss even in the presence of increased soil aggregate stability. [ABSTRACT FROM AUTHOR]

Farmland soil shows strong heterogeneity due to crop rotations and fertilizer inputs, and characterization of soil heterogeneity will benefit understanding soil management. In this study, the technique of laser induced breakdown spectroscopy (LIBS) was used to investigate the heterogeneity of paddy soil in-situ at mesoscale (20 μm ∼ 2 mm) under long term input of controlled release nitrogen. Principal component analysis (PCA) of LIBS spectra interpreted elements distribution in the first three PCs. PC1 contained higher proportions of K, O, Al, Si, Na, Ca and Mg information (more than 50 %), PC2 contained more proportions of Li, Ti, Fe, K, Mg and Si information (40 %), and PC3 contained more proportions of Ca, Mg, Mo, Ti and Pb information (35–40 %). The Red-Green-Blue composite using PC1, PC2 and PC3 as color codes was constructed. Soil heterogeneity was in-situ visualized by color blending maps at mesoscale and the hierarchical cluster analysis showed that increasing input of controlled released nitrogen altered soil heterogeneity. Therefore, LIBS provided a method to achieve a digital description of soil heterogeneity at mesoscale, which could be an alternative option to capture spatio-temporal soil information for evaluating the effects of agricultural management on soil quality.

Global warming can accelerate soil organic matter (SOM) decomposition resulting in faster carbon (C) loss and positive climate-C feedback. Previous studies on response of SOM decomposition to climate change mainly focus on plow soil layer. However, the effects of elevated CO2 and soil warming on soil organic carbon (SOC) and total nitrogen (TN) contents and mineralization are rarely studied in subsoil layer. In this study, soil samples were collected from the 0–50-cm paddy soil layer of the Tsukuba free-air CO2 enrichment experimental site with elevated CO2 (+200 ppm) and soil warming (+2 °C), Japan, after 5-year rice growth season. The amounts of SOC, TN, δ13C, and δ15N were analyzed. A 4-week anaerobic incubation experiment was conducted to measure C decomposition and N mineralization potentials. Due to the intrinsic variation in SOC and TN contents in soil layers and fields, the effects of elevated CO2 and soil warming on C decomposition and N mineralization potentials could not be determined here. However, the effect of elevated CO2 on δ13C was only found in 0‒10-cm soil layer. In the 0–50-cm soil profiles, significant correlations were observed among SOC and TN, δ13C and δ15N, decomposed C and mineralized N, and δ13C of decomposed C. The variables associated with soil C and N pools, and dynamics showed large spatial heterogeneity within paddy field, due to variation in the original land use history. Therefore, great caution should be exercised when evaluating the effects of elevated CO2 and temperature on SOM decomposition and sequestration in paddy soil profiles.

Carbon (C) sequestration in soil plays a crucial role in increasing soil quality through recommended management practices including applying organic amendments, following cropping patterns, fallow periods etc. This study aimed to assess the influence of rice-based cropping patterns on soil C and nutrient status in surface (0-15 cm) and sub-surface soil (15-30 cm). Soils of five rice-based cropping patterns [Boro (winter rice)-Fallow-Fallow, Boro-Fallow-Aman (monsoon rice), Boro-Fallow-Aman-Mustard, Boro-Aus (summer rice)-Aman, Vegetables-short Fallow-Aman] from farmers' fields of Mymensingh district in Bangladesh were collected. Bulk soils were physically fractionated into particulate organic matter (POM: >53 µm) and mineral associated OM (MOM: < 53 µm) to assess the organic C (OC) distribution. Bulk soils were analyzed for soil pH, electrical conductivity, soil texture, nutrients (OC, nitrogen (N), phosphorus (P), potassium (K) and sulphur (S)) contents. The results showed that all studied parameters varied significantly among the cropping patterns and soil depths. Surface soils contain higher amount of OC, N, P, K and S than sub-surface soils under all rice-based cropping patterns. Overall, relatively higher macronutrients (P, K, S) concentration was found in the cropping patterns with a greater number of crops compared to the patterns including fallow period. In contrast, OC and N were the highest in Boro-Fallow-Fallow field followed by Vegetables-short Fallow-Aman and the rest three patterns, which might correspond to less disturbance of soil. All the rice-based cropping patterns had noticeable proportion of MOM (presumably stable OC) than labile POM which indicates the capacity of paddy soils in sequestering OC in soils. However, this capacity can be influenced by the pattern and probably also by the management systems, e.g., tillage and nutrient managements. These findings revealed the necessity of paying more attention to the selection of cropping pattern and proper land/or crop management for higher C sequestration in arable soil. [Fundam Appl Agric 2024; 9(3.000): 186-194]

Abstract Arsenic (As) detoxification in polluted soils by iron-based materials can be mediated by the endogenous soil organic matter (SOM), nevertheless the mechanisms remain unclear. Herein, endogenous SOM in a paddy soil was substantially removed to understand its roles on As immobilization by biochar-supported zero-valent iron (ZVI/BC). The results demonstrated that ZVI/BC application significantly decreased As bioavailability by 64.2% compared with the control soil under the anaerobic condition. XPS and HR-TEM suggested As immobilization by ZVI/BC mainly invoked the formation of ternary complexes (i.e., As-Fe-SOM). However, SOM depletion compromised the efficacy of ZVI/BC for As immobilization by 289.8%. This is likely because SOM depletion increased the fulvic acid and OH− contents in soils. Besides, ZVI/BC increased the proportion of As(III) in available As fraction, but SOM depletion altered the mechanisms associated with As(V) reduction. That is, As(V) reduction resulted from the reductive capacity of ZVI in the pristine soil, but the As(V)-reducing bacteria contributed greater to As(V) reduction in the SOM-depleted soil. Additionally, SOM depletion boosted the abundances of Fe(III)- and As(V)-reducing bacteria such as Bacillus and Ammoniphilus in soils, which enhanced the dissimilatory arsenate reduction. Thus, this work highlighted the importance of SOM in the remediation of As-contaminated soils by ZVI/BC. Graphical Abstract

This study explored the mechanisms underlying the release and transformation of potassium from potassium‐rich minerals in paddy soils derived from purple soils. While potassium is abundant in these minerals, it is typically insoluble and inaccessible to plants. The agricultural practices employed in paddy soils may activate insoluble mineral potassium, potentially reducing potassium fertilizer applications. The activation of mineral potassium not only helps alleviate the dependence on soluble potassium fertilizers in rice cultivation, but also contributes to enhancing food security and sustainable agricultural development. Despite these potential benefits, the transformation pathways of mineral potassium in paddy soils remain unclear, posing an important science question that requires further investigation. This study collected data from a long‐term fertilizer experiment of paddy soils derived from purple soils with abundant potassium‐rich minerals (1982–2019, rice‐wheat rotation). The results revealed that paddy management could drive the transformation of potassium in illite minerals in paddy soils and meet the long‐term growth needs of crops. Submergence reduction significantly increased the concentration of positive ions such as Fe2+ and Ca2+ and provided a pathway for the free movement of ions, promoting the substitution of these ions with interlayer potassium of minerals. This substitution and alternating reduction and oxidation conditions played an important role in the transformation of potassium in illite minerals. The study indicates the promising potential for using crushed illite rocks in rice paddies as a substitute for traditional potassium fertilizers. [ABSTRACT FROM AUTHOR]

Heavy metal pollution in agricultural soils is one of the main problems in agricultural production worldwide, which threatens human health and the environment. To evaluate the pollution levels of heavy metals and the ecological risks in an agricultural area from Sánchez Ramírez Province, Dominican Republic, the concentration levels of heavy metals (Fe, Mn, Cr, Ni, Cu, Zn, Pb, and As) were measured using energy-dispersive X-ray fluorescence spectroscopy (EDXRF). Several pollution indices, including the geo-accumulation index (Igeo), enrichment factor (EF), and single pollution index (PI), were used to investigate the pollution status. The spatial distribution of different heavy metals in the studied soils was also determined. The mean concentrations of Fe, Mn, Cr, Ni, Cu, Zn, Pb, and As were 73735, 1616, 426; 34; 20; 200; 43; and 5 mg kg−1, respectively. These results indicated that the mean concentration of Cr, Cu, Zn, and Pb exceeded FAO-recommended levels for healthy agricultural soils. However, the potential ecological risks assessment indicated a low-risk status. The results obtained could help improve soil–rice–environment management practices and prevent heavy metal pollution in this type of production system, protecting the health of the local population and the environment. [ABSTRACT FROM AUTHOR]

The current study explored the contamination of heavy metals in the paddy fields of Kashmore district treated with synthetic fertilizer and mixed fertilizer, based on the route of input (irrigation water, fertilization, atmospheric precipitation) and output fluxes (surface runoff, water leaching, and crop biomass). The soil and irrigation water quality of selected paddy fields treated with synthetic fertilizer and mixed fertilizer was also examined according to the standard protocol. Moreover, the measurement of heavy metals in soil, input and output was done by atomic absorption spectrometry. The principal component analysis data indicated that the paddy field-5 and paddy field-6 soils treated with synthetic fertilizer and paddy field-5 soils treated with mixed fertilizer showed high distribution scores for physicochemical parameters and heavy metals. The bioaccumulation and translocation of heavy metals in the studied paddy field indicated that the soils and irrigation water of paddy fields treated with synthetic fertilizer and mixed fertilizer are suitable for rice cultivation. The elevated levels of heavy metals in soils treated with mixed fertilizer might be due to heavy metals contamination in irrigation water, synthetic fertilizers, and livestock manures. The experimental data showed an insignificant difference in heavy metal contents in different parts of all paddy fields (p < 0.05). The atmospheric deposition is a significant input contributor of heavy metals in contamination in paddy fields. The rice straw uptake is a prime source of heavy metals in paddy fields, but their removal may efficiently decrease the intake of heavy metals from studied paddy fields. [ABSTRACT FROM AUTHOR]

• More Cd was immobilized in the flooding period than that in the drainage period. • ZVI reduced the release of Cd and promoted Cd immobilization during drainage process. • Adding ZVI was more conducive to Cd immobilization than directly increasing soil pH. • Adding ZVI in the flooding stage immobilized more Cd than that in the drainage stage. Zero-valent iron (ZVI) is a promising material for the remediation of Cd-contaminated paddy soils. However, the effects of ZVI added during flooding or drainage processes on cadmium (Cd) retention remain unclear. Herein, Cd-contaminated paddy soil was incubated for 40 days of flooding and then for 15 days of drainage, and the underlying mechanisms of Cd immobilization coupled with Fe/S/N redox processes were investigated. The addition of ZVI to the flooding process was more conducive to Cd immobilization. Less potential available Cd was detected by adding ZVI before flooding, which may be due to the increase in paddy soil pH and newly formed secondary Fe minerals. Moreover, the reductive dissolution of Fe minerals promoted the release of soil colloids, thereby increasing significantly the surface sites and causing Cd immobilization. Additionally, the addition of ZVI before flooding played a vital role in Cd retention after soil drainage. In contrast, the addition of ZVI in the drainage phase was not conducive to Cd retention, which might be due to the rapid decrease in soil pH that inhibited Cd adsorption and further immobilization on soil surfaces. The findings of this study demonstrated that Cd availability in paddy soil was largely reduced by adding ZVI during the flooding period and provide a novel insight into the mechanisms of ZVI remediation in Cd-contaminated paddy soils. [Display omitted] [ABSTRACT FROM AUTHOR]

Background: Cricket feces is a potential high-quality soil amendment, but there is currently no established optimum rate for its application in paddy soils with varying moisture contents. This study therefore aimed to evaluate the effects of varied rates of cricket feces on soil properties, rice growth and yield in paddy soils with differing moisture contents. Methods: Two study factors were evaluated: (i) the maximum water-holding capacity (WHCmax) and flooded soils and (ii) cricket feces applied at rates of 0 (unamended), 3.13 (low), 6.25 (medium) and 12.50 (high) t/ha. Result: The total grain weight of rice in soil with WHCmax was 2.60, 4.33, 6.91 and 7.49 g/hill under the cricket feces from unamended to high rates, respectively, with no significant difference between the medium and high rates. Meanwhile, the total grain weight in flooded soil was 1.85, 4.02, 4.70 and 5.72 g/hill, respectively. Cricket feces increased the content of essential elements and decreased the acidity and toxicity of Al, Ca and Na in the soil, thereby promoting rice growth and yield. The optimal application rates of cricket feces for rice in the WHCmax soil were determined to be the medium rate, while that in flooded soil was the high rate. [ABSTRACT FROM AUTHOR]

Rice is one of the staple foods in Asian countries, and rice paddies are significant sources of greenhouse gas (GHG) emissions in agricultural sectors. In addition, drainage practice has been recognized as a key factor influencing both rice production and GHG emissions. In this field pot study, the effect of drainage method (e.g., intermittent drainage (ID) and continuous flooding (CF)) on GHG (CO2 and CH4) emissions was determined from three Korean paddies (BG, MG, and JS series), varying soil properties such as soil texture, labile carbon, and mineral types. The emission of GHGs was evidently influenced by the drainage, depending on the paddy's redox (Eh) shift upon flooding events. The Eh decline upon flooding was slower in JS pot, where pore-water concentration of ferric and sulfate ions is the highest (~up to 3-fold) among three paddies. MG pot was 2- to 3-fold more percolative than the others and the Eh drop during the flooding period was the smallest (staying above −50 mV). In ID treatment, CH4 emission (t CO2-eq ha−1 y−1) was reduced in a wide range by 5.6 for JS pot, 2.08 for BG pot, and 0.29 for MG pot relative to CF, whereas CO2 emissions (t CO2-eq ha−1 y−1) were increased by 1.25 for JS pot, 1.07 for BG pot, and 0.48 for MG pot due to the enhanced oxidation of labile carbon. Grain yield and aboveground biomass production from ID were no less than those from CF (p < 0.05). Consequently, the increase in global warming potential (Σ GWP) by ID varied as the order of JS (37%) > BG (14%) > MG (~0%) pots, and the negligible effect observed for MG pot is due to the equivalent trade-off between CO2 and CH4. The different benefits of drainage practices among paddy pots is due to the redox response of paddy systems. The findings will be helpful to promote the efficacy of drainage practice on mitigating GHG emissions for the sustainable agronomic management of rice paddies in response to climate change. [ABSTRACT FROM AUTHOR]

Arsenic (As) detoxification in polluted soils by iron-based materials can be mediated by the endogenous soil organic matter (SOM), nevertheless the mechanisms remain unclear. Herein, endogenous SOM in a paddy soil was substantially removed to understand its roles on As immobilization by biochar-supported zero-valent iron (ZVI/BC). The results demonstrated that ZVI/BC application significantly decreased As bioavailability by 64.2% compared with the control soil under the anaerobic condition. XPS and HR-TEM suggested As immobilization by ZVI/BC mainly invoked the formation of ternary complexes (i.e., As-Fe-SOM). However, SOM depletion compromised the efficacy of ZVI/BC for As immobilization by 289.8%. This is likely because SOM depletion increased the fulvic acid and OH− contents in soils. Besides, ZVI/BC increased the proportion of As(III) in available As fraction, but SOM depletion altered the mechanisms associated with As(V) reduction. That is, As(V) reduction resulted from the reductive capacity of ZVI in the pristine soil, but the As(V)-reducing bacteria contributed greater to As(V) reduction in the SOM-depleted soil. Additionally, SOM depletion boosted the abundances of Fe(III)- and As(V)-reducing bacteria such as Bacillus and Ammoniphilus in soils, which enhanced the dissimilatory arsenate reduction. Thus, this work highlighted the importance of SOM in the remediation of As-contaminated soils by ZVI/BC. Highlights: Endogenous soil organic matter (SOM) was removed to understand its roles in arsenic (As) immobilization by ZVI/BC. SOM depletion compromised the efficacy of ZVI/BC for As immobilization. As(V)-reducing bacteria contributed greater to As reduction in the SOM-depleted soil. [ABSTRACT FROM AUTHOR]

One of the most concerning global environmental issues is the pollution of agricultural soils by heavy metals (HMs), especially cadmium, which not only affects human health through Cd-containing foods but also impacts the quality of rice. The soil's nitrification and denitrification processes, coupled with the release of volatile organic compounds by plants, raise substantial concerns. In this review, we summarize the recent literature related to the deleterious effects of Cd on both soil processes related to the N cycle and rice quality, particularly aroma, in different water management practices. Under both continuous flooding (CF) and alternate wetting and drying (AWD) conditions, cadmium has been observed to reduce both the nitrification and denitrification processes. The adverse effects are more pronounced in alternate wetting and drying (AWD) as compared to continuous flooding (CF). Similarly, the alteration in rice aroma is more significant in AWD than in CF. The precise modulation of volatile organic compounds (VOCs) by Cd remains unclear based on the available literature. Nevertheless, HM accumulation is higher in AWD conditions compared to CF, leading to a detrimental impact on volatile organic compounds (VOCs). The literature concludes that AWD practices should be avoided in Cd-contaminated fields to decrease accumulation and maintain the quality of the rice. In the future, rhizospheric engineering and plant biotechnology can be used to decrease the transport of HMs from the soil to the plant's edible parts. [ABSTRACT FROM AUTHOR]

Introduction: Crop straw, a major by-product of agricultural production, is pivotal in maintaining soil health and preserving the ecological environment. While straw incorporation is widely recognized as a sustainable practice, the incomplete decomposition of crop residues poses challenges to plant growth, increasing the risk of pests and diseases. This necessitates a comprehensive investigation. Methods: The current study employs a 28-day pot experiment to simulate the degradation of rice straw in paddy soils. The impacts of bioaugmentation and biostimulation on lignocellulose degradation are systematically evaluated. Results: Results indicate a high lignocellulose degradation ability in paddy soil, with over 80% straw weight loss within 28 days. Bioaugmentation with a lignocellulolytic microbial consortium enhances straw degradation during the initial stage (0-14 days). In contrast, biostimulation with readily available nutrients leads to soil acidification, hindering straw degradation and reducing microbial diversity. Furthermore, pH emerges as a critical factor influencing microbial community stability and function during lignocellulose degradation. Microbial co-occurrence network analysis reveals thatmicroorganisms occupy ecological niches associated with different cellulose components. Notably, Module M2, comprising Proteobacteria, Firmicutes, Gemmatimonadota, Actinobacteriota, Bacteroidota, Myxococcota, Halobacterota, and Acidobacteriota, positively correlates with pH and weight loss. Discussion: This study significantly advances our understanding of microbial mechanisms in soil decomposition, emphasizing the pivotal role of pH in community stability and function in paddy soil. These findings can inform future strategies for managing rice straw while safeguarding soil ecosystem health. [ABSTRACT FROM AUTHOR]

Landfills have the potential to contribute to mercury (Hg) pollution, due to the burial of waste containing mercury. Mercury from domestic waste can enter the soil surrounding landfills through surface runoff and leachate. In this study, we assessed the levels of Hg in the paddy soil around the Nam Son landfill, the largest landfill in the North of Vietnam, during both rainy (September 2021) and dry (January 2022) seasons. The concentration of Hg was in the range of 20.5 to 79.7 μg/kg dry w.t. in Bac Son and Nam Son, and 16.6 μg/kg dry w.t. at a higher reference site. In most of the samples, the rainy season showed higher Hg concentrations than the dry season. Soil samples taken closer to the landfill exhibited higher levels of Hg contamination compared to those in more distant paddy areas, suggesting a decreasing trend of Hg concentration as one moves away from the pollution source. Additionally, Hg concentration was found to decrease vertically from the surface, with the higher value observed in the surface layer (0–5 cm), and the lower in the bottom layer (20–25 cm). The geo-accumulation index showed that all the sampling points were moderately to heavily polluted, indicating that Hg was lost from the waste source in the landfill. This study provides valuable insights into the spatial and vertical distribution of Hg pollution in the topsoil and highlights the importance of managing and assessing the risks of Hg-containing waste. [ABSTRACT FROM AUTHOR]

The freezing winter temperatures in Northeast China hinder the breakdown speed of straw, making it challenging to implement widespread straw return in rice fields, meaning that crop remnants are not efficiently utilised. This study involved a pot experiment conducted on rice plants that were treated with varying quantities of biochar: CK (no biochar); BC1 (5 t ha−1); BC2 (10 t ha−1); and BC3 (20 t ha−1). An investigation was conducted to examine the impact of biochar on the soil organic carbon (SOC), humus (HS) composition, humic acid (HA) structure, and rice yield of paddy fields. The findings demonstrated that the use of biochar led to a substantial rise in SOC and HA-C concentrations in the soil layer between 20 and 40 cm. Additionally, biochar's application enhanced soil humification. Notably, the treatment with BC3 (20 t ha−1) had the most pronounced impact. The O/C ratio in the HA and the relative strength of the peaks at 1620 cm−1 on the infrared spectra showed a more pronounced response to the BC3 treatment compared to the other biochar treatments. However, the application of the BC1 treatment at a rate of 5 t ha−1 and the BC2 treatment at a rate of 10 t ha−1 had a minimal impact on the fluorescence intensity of humic acid (HA). The application of the BC3 treatment increased the aromatic nature of the humic acid (HA) in paddy soil, leading to the formation of an intricate and enduring HA structure. Furthermore, the use of the BC3 treatment resulted in a notable enhancement in the quantity of spikes, spike weight, and number of grains per spike. Additionally, it positively impacted the accumulation of dry matter in the spike, leading to a substantial 13.7% increase in the rice yield. Applying biochar at a rate of 20 t ha−1 is a sensible and effective approach to enhance the soil organic carbon (SOC) content, enhance the stability of the humic acid (HA)'s structure, and raise the rice yield in the rice-growing area of Northeast China. This study's findings will establish a theoretical foundation for utilising soil biochar in the rice fields located in Northeast China. [ABSTRACT FROM AUTHOR]

In agricultural ecosystems, incorporation of crop residues has been practiced as a recycling approach for sustaining soil organic matter (SOM) and soil fertility. However, how crop residue amendments in different forms (direct straw return, converted as manure and pyrolyzed as biochar) affect soil organic carbon (SOC) pools and SOM composition is not well known. In this study, a short-term (2015–2019) field experiment in paddy soil was conducted with a one-time maize residue amendment, consistently in a single doses of 10 Mg ha−1 organic carbon (OC) equivalent, in three forms: air-dried straw (CS), cattle manure (CM) and biochar (CB). No residue amendment (CK) was used as control. Topsoil organic matter changes were analysed using 13C isotopic tracing, biomarker analysis, and solid-state 13C nuclear magnetic resonance spectroscopy in combination with soil aggregate density/size fractionation. After four cropping cycles following amendment, SOC content was unchanged under CS and CM but increased by 24% under CB; However, the OC pool ratio of particulate organic matter (POM) to mineral-associated organic matter (MAOM) significantly increased under all amendments compared to CK. The δ13C values indicated that maize-derived OC was preserved the most in the POM within the macroaggregates, particularly under CB. Regarding the molecular composition, all residue amendments increased the abundance ratio of plant- to microbe-derived lipids. Plant-derived lipids were primarily concentrated in macroaggregates, whereas microbial lipids were more prevalent in the silt–clay fractions. Lignin phenols were significantly enriched only in microaggregates under CS relative to CK. Overall, SOM changes in the paddy topsoil following crop residue amendment in different forms were depicted by OC pool redistribution and molecular composition alteration. The study highlighted that biochar amendment, instead of straw or manure, greatly enhanced SOC accumulation by promoting macro-aggregation, which in turn preserved plant-derived carbon through the direct input of the persistent char in a rice paddy.

Following ion-adsorption rare earth mining, the residual tailings experience considerable heavy metal contamination and gradually evolve into a pollution source. Therefore, the leaching characteristics and environmental impact of heavy metals in ion-adsorption rare earth tailings require immediate and thorough investigation. This study adopted batch and column experiments to investigate the leaching behaviour of heavy metals in tailings and assess the impact of tailings on paddy soil, thereby providing a scientific basis for environmental protection in mining areas. The results showed that Mn, Zn, and Pb contents were 431.67, 155.05, and 264.33 mg·kg−1, respectively, which were several times higher than their respective background values, thereby indicating significant heavy metal contamination in the tailings. The batch leaching experiment indicated that Mn and Pb were priority control heavy metals. Heavy metals were divided into fast and slow leaching stages. The Mn and Pb leaching concentrations far exceeded environmental limits. The DoseResp model perfectly fitted the leaching of all heavy metals from the tailings (R2 > 0.99). In conjunction with the findings of the column experiment and correlation analysis, the chemical form, rainfall pH, ammonia nitrogen, and mineral properties were identified as the primary factors controlling heavy metal release from tailings. Rainfall primarily caused heavy metal migration in the acid-extraction form from the tailings. The tailing leachate not only introduced heavy metals into the paddy soil but also caused the transformation of the chemical form of heavy metals in the paddy soil, further exacerbating the environmental risk posed by heavy metals. The study findings are significant for environmental conservation in mining areas and implementing environmentally friendly practices in rare earth mining.