Diversity and transcription of genes involved in respiratory As(V) reduction and As(III) methylation in Japanese paddy soils.

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.

Effects of warming and fertilization on nirK-, nirS- and nosZ-type denitrifier communities in paddy soil.

The effects of fertilization on soil denitrifying microorganisms are well-documented. However, the impact of global warming on these microorganisms, particularly regarding the interaction with fertilization, remains poorly understood. Here, a 4-year field warming experiment that included experimental warming (ET) and ambient temperature control (AC), with nitrogen (N) fertilizer applied (CF) or without N fertilizer (CK), was employed to assess the response of the abundance and community of nirK-, nirS- and nosZ- type denitrifiers to warming and fertilization in paddies, and to understand their relationship with potential denitrification rate (PDR). The results showed that warming amplified the positive effect of fertilization on abundance of nirK and nirS genes, while the abundance of nosZ remained unaffected. The copies of nirK and nirS under the ET-CF treatment were notably higher than in the other treatments. In the terms of biodiversity, warming diminished the effect of fertilization on the α-diversity of nirK and nirS, but it did not influence the α-diversity of nosZ. Besides, warming intensified the effect of fertilization on the ß-diversity of nirK, while the ß-diversity of nirS and nosZ remained unchanged in response to fertilization. Additionally, the community structure of denitrifiers varied with warming and/or fertilization. Specifically, Mesorhizobium (nirK), Proteobacteria (nirS) and Rhizobiales (nosZ) were dominant in AC-CK treatment. In the AC-CF treatment, Proteobacteria (nirK/S), Rhizobiales (nosZ) were the main taxa. For the ET treatments (ET-CF, ET-CK), Bradyrhizobiaceae (nirK), Proteobacteria (nirS) and Alphaproteobacteria (nosZ) were predominant. Correlation analysis revealed that soil pH, carbon and N content were the primary factors influencing nirK-, nirS-and nosZ- type denitrifiers. Moreover, PDR showed a positive relationship with nirK abundance, α-diversity of nosZ, and SOC. Overall, the results demonstrate that warming can modify the response of denitrifiers to fertilization, subsequently affecting denitrification rates, a phenomenon that merits attention.

Fe(III) reduction mediates vanadium release and reduction in vanadium contaminated paddy soil under different organic amendments.

Vanadium(V) contaminated soil is abundant in iron(Fe) oxides due to co-occurrence of V and Fe bearing minerals. However, biogeochemical transformation of redox-active V and Fe in soil, and the bacteria involved, has remained less investigated. This study explored the extent to which microbial mediated organic decomposition coupled to Fe(III) reduction contributed to V(V) release/reduction in V-contaminated paddy soil under different organic amendments. Soil flooding decreased toxic reducible V while increased less toxic oxidizable V. Glucose and straw promoted V(V) release with temporarily increasing V(V) concentration by 73.59-106.34 mg/kg compared to the control treatment and subsequently promoted V(V) reduction with decreasing V(V) to concentrations eventually similar to the control treatment. Biochar incorporation under glucose and straw amendments moderately alleviated V(V) release. The significantly positive correlation between Fe(II) and V(V) concentrations during the V solubilization process indicated a temporal coupling of Fe(III) reduction and V(V) release. Clostridium and Massilia mediated Fe(III) reductive dissolution and V(V) release, while Anaeromyxobacter, Sphingomonas, Bryobacter, Acidobacteriaceae and Anaerolineaceae contributed to V(V) reduction. This study provides a deeper understanding of V biotransformation coupled to Fe and C cycling and suggests a remediation strategy for V-contaminated soils via regulating Fe(III) reduction to weaken V(V) release or to promote V(V) reduction.

[Diversity and Functional Characteristics of Fungal Communities and Influencing Factors in Typical Paddy Fields of China].

To investigate the structure, diversity, and function of different paddy soil fungal communities and the factors affecting them in typical paddy cropping areas in China, five typical Chinese paddy soils were selected in this study, and the composition and diversity of soil fungal communities were comparatively analyzed using high-throughput sequencing technology and functionally predicted using the FUNGuild microecological tool. The results showed that： ① The fungal community diversity of soil samples from Heilongjiang （HLJ） was significantly lower than that of the other four regions （P<0.05）； the highest fungal community richness was found in paddy soils from Yunnan （YN）, which was significantly higher than that of the other regions （P<0.05）； and the soil samples from Hainan （HN）, Jiangxi （JX）, and Shandong （SD） were relatively close to each other. The highest average relative abundance at the level of the five typical paddy phyla was Ascomycota, and the genus with the highest average relative abundance was Tausonia. ② Fungi had the largest proportion of saprophytic trophic types, and their corresponding environmental functions were stronger. ③ The species abundance of soil fungi was highly significantly correlated with soil TP, EC, and BD （P<0.01）, and redundancy analyses also showed that soil TP was the main driver of the fungal community as well as the saprophytic functional taxa. The above results showed that the soil fungal community diversity and structure varied greatly among samples, and the relative abundance of fungal genera was affected by soil physical and chemical properties and altered the fungal community structure in paddy fields. The development of this study will provide theoretical references for the sustainable management based on fungal diversity and function of paddy fields.

Physicochemically protected organic carbon release is the rate-limiting step of rhizosphere priming in paddy soils.

Iron oxides affect the stability of soil organic matter (SOM), which in turn affects greenhouse gas emissions in paddy soils. They also regulate the direction and magnitude of the rhizosphere priming effect (RPE) by restricting SOM accessibility and microbial activity. However, the controlling steps and key factors that regulate the RPE magnitude under anoxic conditions are unknown. In this study, we investigated the mechanisms through which Fe(III) reduction affects the RPE using humic acid as an electron shuttle in paddy soils and conducting continuous 13CO2 labeling of rice plants. The RPE, measured via CO2 emission, was approximately 25 % greater in soils with humic acid than in soils without. A rapid increase in the RPE of CH4 emissions after 41 days was attenuated in soils containing humic acid. Root growth and Fe(III) reduction stimulated the total primed CO2 emissions from the rhizosphere independent of the microbial biomass and enzyme activities. Humic acid accelerated Fe(III) reduction, leading to a decrease in Fe-bound organic carbon and an increase in RPE (CO2 emissions). The rhizosphere-primed CO2 emissions decreased with increasing amounts of reactive Fe(III) (oxyhydr)oxides, which protected the SOM from microbial and enzymatic attacks. Biochemical Fe(III) reduction and physical aggregate destruction controlled the abiotic transformation of inaccessible SOM into bioavailable organic carbon, thereby regulating the RPE. The results suggest that the reduction of reactive Fe(III) minerals is the rate-limiting step in the release of the physicochemically protected SOM, which in turn determines the magnitude of rhizosphere priming in paddy soils.

Mobility, Bioavailability, and Enrichment of Soil-Bound Phosphorus in Flood-Prone Paddy Fields: A Case Study of Kunnukara, South India.

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).

Contrasting responses of gross N transformation to oxalic acid and glucose supplement in paddy soil.

Labile organic carbon (C) substrates could accelerate microbial transformation of soil N pool by stimulating the decomposition of large molecule organic N. However, it remains unclear how gross N transformation processes (protein depolymerization, amino acid uptake, microbial N mineralization and NH4+-N uptake rates) in response to individual C substrates. Typical paddy soil was incubated with the supplement of oxalic acid or glucose under simulated field water conditions for 16 days to assess the gross N transformation rates by 15N pool dilution assays. A mixture of 15N labeled amino acid was applied to gross protein depolymerization and amino acid uptake rates measurement, and 15N-(NH4)2SO4 was used to gross microbial N mineralization and NH4+-N uptake rates analyses. Oxalic acid supplement promoted the gross protein depolymerization, gross microbial uptake of amino acid, and gross N mineralization rates at the early stage. It was attributed that oxalic acid supplement urged microbes to decompose large molecular organic N to acquire amino acid derived C and excluded the superfluous N via mineralization as evidenced by the increase of NH4+-N. By contrast, glucose supplement diminished the gross N transformation processes, since microbes prefer to utilize the native NH4+-N to meet their N demand supported by the decreasing NH4+-N concentration in soil, and consequently inhibited the decomposition for the large molecule organic N. With the increase of microbial growth, especially for bacteria, glucose amendment stimulated the large molecular organic N depolymerization to acquire amino acid to maintain the microbial C/N stoichiometric balance. Compared to glucose treatment, oxalic acid supplement stimulated more N allocation into microbial growth but not for mineralization, and thus led to higher microbial N use efficiency, which was adverse for available inorganic N supply for rice growth in paddy ecosystem. Overall, this study emphasizes that low molecular organic C substrates of organic acid and glucose exerted contrasting influences on gross N transformation, and help to improve our understanding of the mechanism of the coupling biotransformation of C and N in paddy soil.

Influence of freeze-thaw process on As migration and microorganisms in aggregates of paddy soil.

A natural phenomenon known as the seasonal freeze-thaw (FT) cycle happens in cold temperature zone such as high latitude and high altitude regions where the soil frequently freezes and thaws in response to temperature variations. Global warming would increase the number of FT cycles in FT regions. However, the influence of FT process on arsenic (As) migration in paddy soil is seldom investigated. Herein, indoor simulation experiment was conducted to investigate the influence of FT process (60 cycles) on As migration from surface to deep soil and microorganisms in paddy soil column. Compared to non FT treatment groups, the concentrations of As in microaggregates of 8-10 cm depth and 18-20 cm depth in soil column of FT treatment group increased by 3.69 mg/kg and 4.16 mg/kg, respectively; the concentrations of As in macroaggregates of 8-10 cm depth and 18-20 cm depth in soil column of FT treatment group increased by 3.34 mg/kg and 3.94 mg/kg, respectively, indicating that FT process accelerated the As migration from surface to deep soil. FT process affected the microbial community structure by changing the physicochemical properties of the soil, which decreased the diversity and uniformity of bacterial community distribution in the soil. The relative abundance of two As-resistant bacteria, e.g., Sphingomonas and Lysobacter, increased by 8.2% and 11.35% after 60 cycles, respectively; moreover, total As in the soil was significantly (p < 0.05) negatively correlated with the alpha index of the soil microorganisms. This study would provide basic data for future study on determining environmental behavior and risk of metals in farm soils in seasonal FT aeras.

Aggravation of Cd availability in the plastisphere of paddy soil.

Soil plastisphere has attracted many concerns, however, its influence on cadmium (Cd) availability in paddy soil was still unclear. This study carried out batch microcosmic and bagging experiments to explore the influence of microplastic (MPs) on Cd availability in paddy soil under flooding conditions in the view of plastisphere. Results showed that the presence of MPs could act as plastisphere micro-environment. The bacterial community composition changed dramatically around the plastisphere compared with MPs-contaminated bulk soil and control soil. The relative abundance of Symbiobacteraceae, Rhodocyclaceae and Bryobacteraceae was improved in the plastisphere which contributed to the enhanced the reduction of Fe(III) and sulfate in flooding paddy soil. The higher content of Fe(II) and S content contributed to the enrichment of Cd in the plastisphere which aggravated Cd availability in paddy soil under flooding conditions. The partial least squares structure equation modeling results confirmed the presence of MPs in paddy soil could act as plastisphere which could change the bacterial community composition and improve the content Fe and S that was conductive to gather Cd in plastisphere. This study shed lights on the understanding of the role of plastisphere on Cd availability in paddy field ecosystem under flooding conditions.

Fulvic Acid Enhances Nitrogen Fixation and Retention in Paddy Soils through Microbial-Coupled Carbon and Nitrogen Cycling.

Fulvic acid, the most soluble and active humic substance, is widely used as an agent to remediate contaminated soils and improve soil fertility. However, the influence of fulvic acid (FA), as a microbial carbon source, on carbon and nitrogen cycles in paddy soils remains elusive. Therefore, to investigate it, an incubation experiment was conducted. Gas analyses indicated that the carbon dioxide and methane emissions were enhanced in FA treatment, which increased up to 94.08-fold and 5.06-fold, respectively. 15N-labeling experiments revealed that nitrogen fixation capability was promoted (1.2-fold) to reduce the carbon and nitrogen imbalance due to fulvic acid amendment. Metagenomic analysis further revealed that gene abundances of degradation of lignin-like compounds, gallate degradation, methanogenesis, nitrogen fixation, and urea hydrolysis increased, while the bacterial ammonia oxidation and anaerobic ammonium oxidation decreased, caused by FA application. Metabolic reconstruction of metagenome-assembled genomes revealed that Azospirillaceae, Methanosarcinaceae, and Bathyarchaeota, with higher abundance in FA treatment, were the key microorganisms to maintain the carbon and nitrogen balance. The metabolic pathways of fulvic acid degradation and coupled nitrogen fixation and retention were constructed. Collectively, our results provided novel insights into the theoretical basis of the use of humic substances for reducing nitrogen fertilization and climate change.

Iron­carbon complex types and bonding forms jointly control organic carbon mineralization in paddy soils.

The crucial role of iron (Fe) oxides in stabilizing soil organic carbon (SOC) is well recognized, but their effects on SOC mineralization remain poorly understood. To address this knowledge gap, we evaluated the effects of four typical Fe-bound OC (Fe-OC) complexes including adsorbed ferrihydrite (Fh)- and goethite (Goe)- 13C, coprecipitated Fh/Goe-13C and 13C-glucose as the control, on OC mineralization during an 80-day anaerobic incubation in a paddy soil. 13C-tracing indicated that Fe-13C complexes significantly stimulated CO2 emissions from both the input 13C and SOC compared with glucose alone. In contrast, the addition of Fh- and Goe-C complexes consistently inhibited CH4 emissions by 72-91 % and 21-61 % compared with glucose addition, respectively. Fe-OC complexes reduced the CO2 equivalent by 62-71 % and 17-41 % in soils with Fh-C and Goe-C complexes, respectively. We concluded that Fe crystallinity and its bonding forms with organic carbon jointly control SOC mineralization. The coprecipitated Goe-C complexes had the lowest OC mineralization rate and highest OC residence time among four Fe-OC complexes. These findings highlighted that promoting the formation of coprecipitated well-ordered minerals would increase SOC sequestration by reducing OC mineralization and mitigating the global warming effect in paddy management.

Mitigating soil nitrification and greenhouse gas emissions in non-paddy cropping systems by micro-molar hydrogen peroxide.

Non-paddy cropping systems play a significant role in food production. However, excessive nitrogen loss from non-paddy soils through nitrate leaching and ammonia volatilization poses a significant challenge to environmental sustainability. In this study, microcosm and field-scale experiments were conducted to explore the potential for using hydrogen peroxide (H2O2) to mitigate nitrogen loss and greenhouse gas emissions, aiming at filling gaps in knowledge regarding the underlying biochemical mechanisms. The results show that input of micromolar H2O2 from either artificial addition or natural rainwater into soils in the presence of magnetite (Fe3O4) could trigger Fenton-like reaction, which inhibited microbially mediated nitrification of soil-borne ammonium but did not affect the growth of the test crop plant (water spinach). In the absence of Fe3O4, input of rainwater-borne H2O2 into non-paddy soils caused reduction in the emissions of nitrous oxide (N2O) and carbon dioxide (CO2). There was a trend showing that the degree of reduction in N2O and CO2 fluxes increased with increasing concentration of rainwater-borne H2O2. It was likely that microbially mediated reduction of iron oxides took place during rainfall events, providing Fe(II) that is needed for reaction with rainwater-borne H2O2, triggering Fenton-like reaction to inhibit the soil microbes that mediate production of N2O and CO2 in the soils. The findings obtained from this study have implications for developing strategies to manage soil­nitrogen to minimize its environmental impacts.

Application of biochar and selenium together at low dose efficiently reduces mercury and methylmercury accumulation in rice grains.

Irrespective of cost and ecological risk, literatures have reported that both biochar and selenium (Se) alone at high application rate exhibited positive effects on decreasing rice mercury (Hg) uptake in high Hg contaminated paddy soil. In this study, we investigated whether biochar and Se together at low dose could efficiently reduce the rice grain Hg and MeHg accumulation in the slight Hg-contaminated soil. Compared with control (CK), the Hg concentration of grains in the BC3, Se0.5, and BC3 + Se0.5 treatments decreased by 5.4 %, 38.3 %, and 48.5 %, respectively. Co-application of biochar and Se also decreased the methylmercury (MeHg) concentration in rice grains by 29.1-91.6 %. The decrease of Hg and MeHg level in rice grains for biochar and Se treatments could be attributed to the following mechanisms: (1) high Hg (primarily inorganic Hg) adsorption on biochar through its high hydroxyl groups and large specific surface area; (2) Increased dissolved organic carbon and cysteine contents in pore water after biochar application, which reduced the availability of soil Hg through complexation; (3) Decreased bioavailability of Hg in soil due to the formation of HgSe precipitation which inhibited Hg uptake and translation by rice plant; (4) Both biochar and Se facilitated the reduction of MeHg in soil. Our results indicate that co-application of biochar and Se at low dose is a promising method to effectively mitigate Hg accumulation in rice grains from the slight Hg-contaminated soil.

[Effects of Long-term Biochar Addition on Denitrification N2O Emissions from Bacteria and Fungi in Paddy Soil].

Denitrification driven by bacteria and fungi is the main source of nitrous oxide （N2O） emissions from paddy soil. It is generally believed that biochar reduces N2O emissions by influencing the bacterial denitrification process, but the relevant mechanism of its impact on fungal denitrification is still unclear. In this study, the long-term straw carbonization returning experimental field in Changshu Agricultural Ecological Experimental Base of the Chinese Academy of Sciences was taken as the object. Through indoor anaerobic culture and molecular biology technology, the relative contributions of bacteria and fungi to denitrifying N2O production in paddy soil and the related microorganism mechanism were studied under different long-term biochar application amounts （blank, 2.25 t·hm-2, and 22.5 t·hm-2, respectively, expressed by BC0, BC1, and BC10）. The results showed that compared with that in BC0, biochar treatment significantly reduced N2O emission rate, denitrification potential, and cumulative N2O emissions, and the contribution of bacterial denitrification was greater than that of fungal denitrification in all three treatments. Among them, the relative contribution rate of bacterial denitrification in BC10 （62.9%） was significantly increased compared to BC0 （50.8%）, whereas the relative contribution rate of fungal denitrification in BC10 （37.1%） was significantly lower than that in BC0 （49.2%）. The application of biochar significantly increased the abundance of bacterial denitrification functional genes （nirK, nirS, and nosZ） but reduced the abundance of fungal nirK genes. The contribution rate of fungal denitrification was significantly positively correlated with the N2O emission rate and negatively correlated with soil pH, TN, SOM, and DOC. Biochar may have inhibited the growth of denitrifying fungi by increasing pH and carbon and nitrogen content, reducing the abundance of related functional genes, thereby weakening the reduction ability of NO to N2O during fungal denitrification process. This significantly reduces the contribution rate of N2O production during the fungal denitrification process and the denitrification N2O emissions from paddy soil. This study helps to broaden our understanding of the denitrification process in paddy soil and provides a theoretical basis for further regulating fungal denitrification N2O emissions.

Fe oxides simultaneously improve stability of Cd and carbon in paddy soil：The underlying influence at aggregate level.

Iron (Fe) oxides have a strong adsorption affinity for Cd and organic carbon (SOC). However, under alternate wet-dry (IF) condition,the influences of Fe oxides on the speciation and disrtribution of Cd and SOC in soil aggregates are unkown. In the present study, soils untreated (S), removed (S-Fe) or added (S+Fe) Fe oxide soils were blended with cadmium chloride solution and cultivated for 56 days under different moisture management practices. Compared with the S-Fe soil, the IF treatment increased the contents of Fe oxide-bound SOC (Fe-OC) and Fe/Mn oxide-bound Cd (Fe/Mn-Cd) by 18.5-29.8-fold and 1.45-2.45-fold, repectively, in the S and S+Fe soils, corresponding to a 36 %-42 % increase in the recalcitrant C pool (RCP) and a 53 %-87 % decrease in the exchangeable Cd content. These results could be attributed to soil particle aggregation and Fe redistribution. Fe addition promoted the transfer of Cd/SOC accumulated in microaggregates to macroaggregates and increased the variable negative charge content in macroaggregates and the adsorption capacity of macroaggregates for Cd/SOC. More Cd/SOC accumulated in macroaggregates in Fe oxide-bound form, which reduced the risk of Cd migration and Cd availability and increased the physical protection of SOC. Therefore, Fe oxide has great potential to simultaneously reduce carbon emissions and cadmium toxicity in paddy soil.

Evidence of Potential Anammox Activities from Rice Paddy Soils in Microaerobic and Anaerobic Conditions.

Anammox, a reaction in which microorganisms oxidize ammonia under anaerobic conditions, is used in the industry to remove ammonium from wastewater in an environmentally friendly manner. This process does not produce intermediate products such as nitrite or nitrate, which can act as secondary pollutants in soil and water environments. For industrial applications, anammox bacteria should be obtained from the environment and cultivated. Anammox bacteria generally exhibit a slow growth rate and may not produce a large number of cells due to their anaerobic metabolism. Additionally, their habitats appear to be limited to specific environments, such as oxidation-reduction transition zones. Consequently, most of the anammox bacteria that are used or studied originate from marine environments. In this study, anammox bacterial evidence was found in rice paddy soil and cultured under various conditions of aerobic, microaerobic, and anaerobic batch incubations to determine whether enrichment was possible. The anammox-specific gene (hzsA) and microbial community analyses were performed on the incubated soils. Although it was not easy to enrich anammox bacteria due to co-occurrence of denitrification and nitrification based on the chemistry data, potential existence of anammox bacteria was assumed in the terrestrial paddy soil environment. For potential industrial uses, anammox bacteria could be searched for in rice paddy soils by applying optimal enrichment conditions.

Long-term Application of Agricultural Amendments Regulate Hydroxyl Radicals Production during Oxygenation of Paddy Soils.

Hydroxyl radicals (•OH) play a significant role in contaminant transformation and element cycling during redox fluctuations in paddy soil. However, these important processes might be affected by widely used agricultural amendments, such as urea, pig manure, and biochar, which have rarely been explored, especially regarding their impact on soil aggregates and associated biogeochemical processes. Herein, based on five years of fertilization experiments in the field, we found that agricultural amendments, especially coapplication of fertilizers and biochar, significantly increased soil organic carbon contents and the abundances of iron (Fe)-reducing bacteria. They also substantially altered the fraction of soil aggregates, which consequently enhanced the electron-donating capacity and the formation of active Fe(II) species (i.e., 0.5 M HCl-Fe(II)) in soil aggregates (0-2 mm), especially in small aggregates (0-3 µm). The highest contents of active Fe(II) species in small aggregates were mainly responsible for the highest •OH production (increased by 1.7-2.4-fold) and naphthalene attenuation in paddy soil with coapplication of fertilizers and biochar. Overall, this study offers new insights into the effects of agricultural amendments on regulating •OH formation in paddy soil and proposes feasible strategies for soil remediation in agricultural fields, especially in soils with frequent occurrences of redox fluctuations.

Comparative evaluation of 16S rRNA primer pairs in identifying nitrifying guilds in soils under long-term organic fertilization and water management.

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.

Crenobacter oryzisoli sp. nov., a novel phosphate-solubilizing bacterium isolated from the paddy soil.

Two Gram-staining-negative, facultative anaerobic, rod-shaped and phosphate-solubilizing strains designated SG2303T and SG2305, were isolated from paddy soil in China. Phylogenetic analysis based on 16 S rRNA gene sequences indicated that SG2303T and SG2305 represented a member of the genus Crenobacter within the family Neisseriaceae of the phylum Pseudomonadota. Strain SG2303T displayed higher 16 S rRNA gene sequence similarities with members of the genus Crenobacter ranging from 93.5 to 94.0%. Strains C. luteus YIM 78141T and C. cavernae K1W11S-77T were closest related to the isolated strains and were considered as type strains. Growth of strain SG2303T occurred at 10-55 °C (optimum 37 °C), pH 5.0-9.0 (optimum pH 6.0-7.0) and 0-1% (w/v) NaCl (optimum 0%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG2303T and its closely related taxa were 76.1-78.2% and 20.5-22.1%, respectively. The genomic DNA G + C content was 62.2%. The quinone of strain SG2303T was Q-8. The major fatty acids (> 10%) of strain SG2303T were C16:0 (30.6%), summed feature 3 (C16:1ω7c and/or C16:1ω6c) (26.0%) and C12:0 3OH (12.1%). The polar lipids were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phospholipids (PL), glycolipid (GL) and unidentified lipids (UL). Based on the results of the phylogenetic, physiological, biochemical, and morphological analysis, strain SG2303T is recognized as a novel species of the genus Crenobacter, for which the name Crenobacter oryzisoli sp. nov. is proposed. The type strain is SG2303T (= GDMCC 1.3970T = JCM 36468T). In addition, SG2303T was also able of phosphorus solubilization and promoting the growth of rice seeds. Strain SG2303T exhibited a relatively high dissolvable phosphorus content of 2.52 µg·mL- 1.

A review of amendments for simultaneously reducing Cd and As availability in paddy soils and rice grain based on meta-analysis.

Arsenic (As) and cadmium (Cd) accumulation in rice grains is a global food safety issue, and various methods and materials have been used to remove or reduce As and Cd in agricultural soils and rice grains. Despite the availability of synthesized materials capable of simultaneous As and Cd reduction from soil and rice grains, the contributions, efficiency, and main ingredients of the materials for As and Cd immobilization remain unclear. The present study first summarized the biogeochemistry of As and Cd in paddy soils and their transfer in the soil-food-human continuum. We also reviewed a series of reported inorganic and organic materials for simultaneous immobilization of As and Cd in paddy soils, and their reduction efficiency of As and Cd bioavailability were listed and compared. Based on the abovementioned materials, the study conducted a meta-analysis of 38 articles with 2565 observations to quantify the impacts of materials on simultaneous As and Cd reduction from soil and rice grains. Meta-analysis results showed that combining organic and inorganic amendments corresponded to effect sizes of -62.3% and -67.8% on As and Cd accumulation in rice grains, while the effect sizes on As and Cd reduction in paddy soils were -44.2% and -46.2%, respectively. Application of Fe based materials significantly (P < 0.05) reduced As (-54.2%) and Cd (-74.9%), accounting for the highest immobilization efficiency of As and Cd in rice grain among all the reviewed materials, outweighing S, Mn, P, Si, and Ca based materials. Moreover, precipitation, surface complexation, ion exchange, and electrostatic attraction mechanisms were involved in the co-immobilization tactics. The present study underlines the application of combined organic and inorganic amendments in simultaneous As and Cd immobilization. It also highlighted that employing Fe-incorporated biochar material may be a potential strategy for co-mitigating As and Cd pollution in paddy soils and accumulation in rice grains.