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Microbial communities of soil aggregate-size fractions were explored with molecular and networking assays for topsoil samples from a clayey rice paddy under long-term fertilization treatments. The treatments included no fertilizer (NF) as control, chemical fertilizer only (CF), chemical fertilizer with swine manure (CFM), and chemical fertilizer with rice straw return (CFS). Following a wet-sieving protocol, water-stable aggregates were separated into size fractions of large macroaggregates (L-MacA, >2,000 μm), macroaggregates (MacA, 2,000–250 μm), microaggregates (MicA, 250–53 μm), fine microaggregates (F-MicA, 53–2 μm), and fine clay (F-Clay, <2 μm). Mass proportion was 32.3–38.2% for F-MicA, 23.0–31.5% for MacA, 19.0–23.1% for MicA, 9.1–12.0% for L-MacA, and 4.9–7.5% for F-Clay, respectively. The proportion of MacA was increased, but F-Clay was reduced by fertilization, whereas the mean weight diameter was increased by 8.0–16.2% from 534.8 μm under NF to 621.5 μm under CFM. Fertilization affected bacterial 16S rRNA and fungal 18S rRNA gene abundance in F-MicA and F-Clay but not in aggregates in size larger than 53 μm. However, bacterial and fungal community α-diversities and community structures were quite more divergent among the fertilization treatments in all size fractions. Organic carbon and gene abundance of bacteria and fungi were enriched in both L-MacA and MacA but depleted in F-Clay, whereas microbial Shannon diversity was rarely changed by fraction size under the four treatments. L-MacA and MacA contained more bacteria of r-strategists and copiotrophs, whereas F-MicA and F-Clay were demonstrated with a higher abundance of K-strategists and oligotrophs. Guilds of parasitic and litter saprotrophic fungi were enriched in F-MicA but depleted in L-MacA. Furthermore, most of bacterial and fungal operational taxonomic units were strongly interacted in L-MacA and MacA rather than in MicA and F-Clay. Thus, MacA acted as micro-hotspots enriched with functional and networked microbial communities, which were enhanced with organic/inorganic fertilization in the rice paddy. [ABSTRACT FROM AUTHOR]

A field experiment was conducted in a Cd-contaminated rice paddy field to evaluate the effect of inorganic and organic metal stabilizers on Cd mobility and rice uptake. A dose of inorganic stabilizer of calcium hydroxide (CH), silicon slag (SS), and wheat straw biochar (BC) was amended respectively to topsoil before rice transplanting. Rice production was managed with the same water regime and fertilization practices consistently between treatments including a control without amendment. Samples of topsoil and rice plant were collected at rice harvest to analyze the Cd mobility and uptake by rice. Without affecting rice grain yield, the stabilizers significantly decreased CaCl-extractable Cd in a range of 44 to 75 % compared to the control, corresponding to soil pH changes under the different treatments. Accordingly, Cd concentrations both in rice tissue and in rice grain were very significantly decreased under these treatments. The decrease in rice Cd uptake was correlated to the decrease in extractable Cd, which was again correlated to soil pH change under the different treatments, indicating a prevalent role of liming effect by the amendments. While applied at a large amount in a single year, organic stabilizer of BC decreased Cd extractability by up to 43 % and Cd rice uptake by up to 61 %, being the most effective on Cd immobilization. However, the long-term effect on soil health and potential tradeoff effects with different stabilizers deserve further field monitoring studies. [ABSTRACT FROM AUTHOR]

Purpose: Rice paddy soils undergo pedogenesis driven by periodic flooding and drainage cycles that lead to accumulation of organic matter and the stratification of nutrients and oxygen in the soil profile. Here, we examined the effects of continuous rice cultivation on microbial community structures, enzyme activities, and chemical properties for paddy soils along a chronosequence representing 0-700 years of rice cropping in China. Materials and methods: Changes in the abundance and composition of bacterial and fungal communities were characterized at three depths (0-5, 5-10, and 10-20 cm) in relation to organic carbon, total nitrogen, dissolved organic carbon, microbial biomass carbon/nitrogen, and activities of acid phosphatase, invertase, and urease. Results and discussion: Both soil organic carbon and total nitrogen increased over time at all three depths, while pH generally decreased. Microbial abundance (bacteria and fungi) and invertase and urease activity significantly increased with the duration of rice cultivation, especially in the surface layer. Fungal abundance and acid phosphatase activity declined with depth, whereas bacterial abundance was highest at the 5-10-cm soil depth. Profiles of the microbial community based on PCR-DGGE of 16S rRNA indicated that the composition of fungal communities was strongly influenced by soil depth, whereas soil bacterial community structures were similar throughout the profile. Conclusions: Soil bioactivity (microbial abundance and soil enzymes) gradually increased with organic carbon and total nitrogen accumulation under prolonged rice cultivation. Microbial activity decreased with depth, and soil microbial communities were stratified with soil depth. The fungal community was more sensitive than the bacterial community to cultivation age and soil depth. However, the mechanism of fungal community succession with rice cultivation needs further research. [ABSTRACT FROM AUTHOR]

While microbial nitrogen transformations in soils had been known to be affected by heavy metal pollution, changes in abundance and community structure of the mediating microbial populations had been not yet well characterized in polluted rice soils. Here, by using the prevailing molecular fingerprinting and enzyme activity assays and comparisons to adjacent non-polluted soils, we examined changes in the abundance and activity of ammonia oxidizing and denitrifying communities of rice paddies in two sites with different metal accumulation situation under long-term pollution from metal mining and smelter activities. Potential nitrifying activity was significantly reduced in polluted paddies in both sites while potential denitrifying activity reduced only in the soils with high Cu accumulation up to 1300 mg kg−1. Copy numbers of amoA (AOA and AOB genes) were lower in both polluted paddies, following the trend with the enzyme assays, whereas that of nirK was not significantly affected. Analysis of the DGGE profiles revealed a shift in the community structure of AOA, and to a lesser extent, differences in the community structure of AOB and denitrifier between soils from the two sites with different pollution intensity and metal composition. All of the retrieved AOB sequences belonged to the genus Nitrosospira, among which species Cluster 4 appeared more sensitive to metal pollution. In contrast, nirK genes were widely distributed among different bacterial genera that were represented differentially between the polluted and unpolluted paddies. This could suggest either a possible non-specific target of the primers conventionally used in soil study or complex interactions between soil properties and metal contents on the observed community and activity changes, and thus on the N transformation in the polluted rice soils. [ABSTRACT FROM AUTHOR]

Chemical and microbial characterisations of particle-size fractions ( PSFs) from a rice paddy soil subjected to long-term heavy metal pollution ( P) and nonpolluted ( NP) soil were performed to investigate whether the distribution of heavy metals ( Cd, Cu, Pb and Zn) regulates microbial community activity, abundance and diversity at the microenvironment scale. The soils were physically fractionated into coarse sand, fine sand, silt and clay fractions. Long-term heavy metal pollution notably decreased soil basal respiration (a measurement of the total activity of the soil microbial community) and microbial biomass carbon ( MBC) across the fractions by 3-45% and 21-53%, respectively. The coarse sand fraction was more affected by pollution than the clay fraction and displayed a significantly lower MBC content and respiration and dehydrogenase activity compared with the nonpolluted soils. The abundances and diversities of bacteria were less affected within the PSFs under pollution. However, significant decreases in the abundances and diversities of fungi were noted, which may have strongly contributed to the decrease in MBC. Sequencing of denaturing gradient gel electrophoresis bands revealed that the groups Acidobacteria, Ascomycota and Chytridiomycota were clearly inhibited under pollution. Our findings suggest that long-term heavy metal pollution decreased the microbial biomass, activity and diversity in PSFs, particularly in the large-size fractions. [ABSTRACT FROM AUTHOR]

Biochar soil amendment has been increasingly recommended for enhancing soil fertility and crop productivity while reducing greenhouse gas emissions in agricultural soils. However, a clear understanding of the cost benefits and longevity of the positive effects over long term would be a prerequisite for large scale biochar production and application in agriculture. In this study, the long-term effects of a single biochar amendment on soil fertility, crop yield and greenhouse gas emissions were assessed in a six-year field experiment of a fertile rice paddy from Southwest China. The field trial was established in 2010 and was managed under a rice-winter wheat rotation system throughout six years until 2016. The experiment employed a nested design with biochar soil amendment at application rates of 0, 20 and 40 t ha−1 without N fertilization, and 150 kg ha−1 with N fertilization, respectively. Soil properties and crop yields were measured and the emissions of CH 4 and N 2 O were monitored during the rice cultivation period in the 1st, 2nd and 5th year since 2010. Soil pH, organic carbon, total N and available potassium content were all increased under biochar amendment and persisted throughout the six years. However, grain yields across the years were generally not affected by biochar amendment except a yield increase in 2015. This grain yield increase (18.3%) was reported in the wheat season of 2015, when biochar had been applied at 40 t ha−1 in plots along with N fertilizer. Biochar amendment reduced N 2 O emissions from the rice paddies only for the first two seasons following the single amendment. In conclusion, a single but high rate of biochar amendment provided limited and temporary benefits for improving grain yields and reduction of greenhouse gases in the fertile paddy soil. • Long-term lasting effects of a single biochar amendment were investigated; • Biochar provided limited and temporary benefits for grain production; • Biochar addition improved soil fertility and this effect could last at least for 6 years. • Soil fertility improvement with biochar addition did not lead to rice yield increase. • Reduction effect of N 2 O emission with biochar only lasted two rice seasons. [ABSTRACT FROM AUTHOR]

Abstract Abundance and allocation of organic matter, microbial community and their extracellular enzyme activities in soil aggregates had been increasingly concerned for mediating biogeochemical cycle and biodiversity provided by soil. In this study, the variations of soil organic carbon (SOC) accumulation and extracellular enzyme activities in aggregate size fractions of a rice paddy with long-term fertilization treatments were analyzed. These treatments included no fertilizer application (NF) as a control, chemical fertilizer only (CF), chemical fertilizer combined with swine manure (CFM), and with straw residue return (CFS). Hereby, size fractions of soil aggregates respectively of >2000 μm (large macroaggregates), 250–2000 μm (macroaggregates), 53–250 μm (microaggregates), 2–53 μm (fine aggregates), and <2 μm (fine clay) were obtained from undisturbed soil cores following water-dispersion and subsequent wet-sieving using a low energy separation protocol. Of these aggregate fractions, SOC and total nitrogen (N) contents were determined with wet digestion and soil enzyme activities were analyzed with substrate-induction incubation assays. Contents of SOC and total N were both highest in macroaggregates, followed by large macroaggregates and microaggregates, but depleted in fine microaggregates. Activities of carbon-degrading enzymes and N -acetyl-glucosaminidase were markedly enriched in soil aggregate fractions in size >53 μm. Whereas, activity of phenol oxidase was generally concentrated in soil aggregate fractions in size between 2 and 2000 μm while that of peroxidase in size between 53 and 2000 μm. Activity of β -glucosidase and cellobiohydrolase was both significantly elevated under CFS and that of peroxidase under CF, CFM and CFS treatments, but phenol oxidase activity was suppressed under CFS treatment. The enzyme activities of β -xylosidase, β -glucosidase, cellobiohydrolase and N -acetyl-glucosaminidase varied greatly (CVs up to 50%), rather with size fractions than with treatments, while those of α-Glucosidase and phenol oxidase varied moderately (CVs up to 35%), rather with treatments than with size fractions. However, those of acid phosphatase and peroxidase changed slightly (CVs up to 20%), regardless of both size fractions and fertilization treatments. Thus, abundance and enrichment of all the soil enzyme activities analyzed depended not on SOC although the overall extracellular enzyme activity was generally well correlated to SOC abundance, among aggregate size fractions. Only activities of carbon-degrading enzymes were greatly enriched in macroaggregates, which were seen reduced under combined organo/mineral fertilization. This study highlighted macroaggregates as biochemically active micro- hotspots and lower activities of carbon-degrading enzymes with SOC accumulation under long-term rational fertilization in the rice paddy. Graphical abstract Unlabelled Image Highlights • Water stable aggregates separated from a rice paddy under fertilization treatment • Enzyme activities changed inconsistently with C and N levels among size fractions. • Aggregate enzyme activities varied rather with size classes than with fertilization. • Much increased carbon degrading enzyme activities in macro-aggregates • Macroaggregates as biochemical hotpots, sensitive to fertilization practice [ABSTRACT FROM AUTHOR]

While microbial nitrogen transformations in terrestrial ecosystems are known to be affected by global climate change, changes in abundance and composition of mediating microorganisms in agricultural soils under climate change have not yet been well characterized. Here, using well-established molecular fingerprinting techniques and biochemical assays, we tried to analyze changes in nitrifier abundance, composition and activity in the rhizosphere under simultaneously elevated atmospheric CO 2 and temperature conditions in a Chinese paddy field. Abundance, rather than community composition of ammonia oxidizing archaea and bacteria (AOA and AOB) responded to the climate change treatments, and the effect was greater on the heading and ripening stages (36–52%) than on the tillering stage (8–26%). Elevated atmospheric CO 2 significantly increased AOA and AOB abundance at the heading and ripening stages. Treatment of WA (warming of canopy air) alone did not affect the abundance or community structure of AOA or AOB in the rice rhizosphere at any growth stage. The simultaneous application of CO 2 enrichment and warming affected ammonia oxidizer communities differently than independent application of CO 2 enrichment or warming, with warming negating the stimulating effect of CO 2 enrichment. Phylogenic analysis indicated that all AOA clones fell within the soil and sediment lineage while all AOB clones were classified as Nitrosospira . Although no changes to soil NH 4 + or NO 3 − contents were found, potential nitrification rate generally increased under the treatments with elevated CO 2 at all rice growth stages. This could imply a complexity of the joint effect by elevated CO 2 on soil properties, plant N uptake and microbial growth. These results suggest that impacts of climate change on N transformation in the rice paddy occur through interactions between effects of climate change on ammonia oxidizer communities and soil properties. Further studies would be required on multiple effects by simulated climate changes on soil properties, N transformations and microbial communities, for a sound understanding of potential changes in N cycling and rice productivity under global climate change. [ABSTRACT FROM AUTHOR]

Highlights: [•] Biochar treatment at 20–40tha−1 reduced rice Cd by 20%–90% from metal polluted rice fields. [•] Grain Cd under biochar treatment fell in a safe level by 0.4mgkg−1 in soils with Cd in range 0.16–4.83mgkg−1. [•] Biochar amendment caused Cd immobilization primarily due to the liming effect by biochar. [Copyright &y& Elsevier]

Highlights: [•] We reported changes in microbial community under biochar amendment in a field study. [•] Biochar soil amendment (BSA) increased bacterial but decreased fungal gene abundance. [•] Both bacterial and fungal community structure were clearly affected by BSA. [•] Changes in soil enzyme activities could partially support the above findings. [•] BSA could potentially affect the soil C and N cycling of the rice soil ecosystem. [Copyright &y& Elsevier]

While biochar enhanced carbon sequestration and stability of soil organic matter (SOM), changes in organic molecular composition in biochar-amended soils had been poorly addressed. In this study, molecular composition changes of a paddy topsoil 2 years following amendments at 10 t ha−1 OC equivalent with untreated (CS), manured (CM) and charred (CB) maize straw were compared to no amendment (CK). Topsoil SOM was sequentially extracted with ultrapure water (UWE), solvent (TSE), base hydrolysis (BHY) and CuO oxidation (CUO) and molecular compounds in these extracted fractions were detected quantitatively by GC/MS. Compared to CK, SOC content was increased respectively by 12% under CS and CM, and by 36% under CB. Fraction abundance both of UWE and CUO was increased but that of TSE unchanged under CS and CM, while that of BHY unchanged under CS but increased by > 60% under CM and CB, respectively. Under CB relative to CS and CM, abundance of TSE and BHY fractions was greatly increased but that of UWE and CUO unchanged. Specifically, abundances of water-soluble monosaccharides, low molecular weight organic acids and lignin-derived phenols, especially cinnamyl-based monomers, were all enhanced under CS, but abundances of n-alkanols, fatty acids in free lipids and di-acids and hydroxyl fatty acids in bound lipids were decreased under both CS and CM. In contrast, CB amendment increased abundances of n-alkanols, alkanes and sterols in free lipids while enhanced molecular and functional group diversity of UWE and TSE fractions. Overall, short-term crop residue amendment altered the abundance and molecular diversity of OM mainly associated with short-lived UWE and labile TSE fractions and biochar enhanced preservation of plant derived molecules mainly in lipids. Thus, returning crop residue as biochar could be a sustainable approach to enhance not only SOM pool but molecular diversity also in agricultural soils. [Display omitted] • Amendment of untreated, manured and charred maize straw to a rice paddy at carbon equivalent compared in a field experiment. • Molecular changes of topsoil organic matter following amendment explored using sequential extraction - GC/MS detection. • Positive changes in diversity of both single molecules and functional groups of labile organic matter with charred straw. • Relative abundance of labile fraction and its composition indicative of OC dynamics with straw treatments. • Plant-derived biomarkers decreased under fresh straw but preserved under charred straw. [ABSTRACT FROM AUTHOR]