Wenxue Wei

Impact of Long-Term Fertilization on the Composition of Denitrifier Communities Based on Nitrite Reductase Analyses in a Paddy Soil

The effect of long-term fertilization on soil-denitrifying communities was determined by measuring the abundance and diversity of the nitrite reductase genes nirK and nirS. Soil samples were collected from plots of a long-term fertilization experiment started in 1990, located in Taoyuan (110°72″ E, 28°52″ N), China. The treatments were no fertilizer (NF), urea (UR), balanced mineral fertilizers (BM), and BM combined with rice straw (BMR). The abundance, diversity, and composition of the soil-denitrifying bacteria were determined by using real-time quantitative PCR, terminal restriction fragment length polymorphism (T-RFLP), and cloning and sequencing of nirK and nirS genes. There was a pronounced difference in the community composition and diversity of nirK-containing denitrifiers responding to the long-term fertilization regimes; however, less variation was observed in communities of nirS-containing denitrifiers, indicating that denitrifiers possessing nirK were more sensitive to the fertilization practices than those with nirS. In contrast, fertilization regimes had similar effects on the copy numbers of nirK and nirS genes. The BMR treatment had the highest copy numbers of nirK and nirS, followed by the two mineral fertilization regimes (UR and BM), and the lowest was in the NF treatment. Of the measured soil parameters, the differences in the community composition of nirK and the abundance of nir denitrifiers were highly correlated with the soil carbon content. Therefore, long-term fertilization resulted in a strong impact on the community structure of nirK populations only, and total organic carbon was the dominant factor in relation to the variations of nir community sizes.

Abundance and community structure of ammonia-oxidizing archaea and bacteria in an acid paddy soil

Nitrification is essential to the nitrogen cycle in paddy soils. However, it is still not clear which group of ammonia-oxidizing microorganisms plays more important roles in nitrification in the paddy soils. The changes in the abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated by real-time PCR, terminal restriction fragment length polymorphism, and clone library approaches in an acid red paddy soil subjected to long-term fertilization treatments, including treatment without fertilizers (CT); chemical fertilizer nitrogen (N); N and potassium (NK); N and phosphorus (NP); N, P, and K (NPK); and NPK plus recycled crop residues (NPK+C). The AOA population size in NPK+C was higher than those in CT, while minor changes in AOB population sizes were detected among the treatments. There were also some changes in AOA community composition responding to different fertilization treatments. Still few differences were detected in AOB community composition among the treatments. Phylogenetic analysis showed that the AOA sequences fell into two main clusters: cluster A and cluster soil/sediment. The AOB composition in this paddy soil was dominated by Nitrosospira cluster 12. These results suggested that the AOA were more sensitive than AOB to different fertilization treatments in the acid red paddy soil.

Effect of long-term fertilization on bacterial composition in rice paddy soil

We investigated the effect of long-term fertilization on bacterial abundance, composition, and diversity in paddy soil. The experiment started in 1990 in Taoyuan Agro-ecosystem Research Station in China (111°33′ E, 28°55′ N). The molecular approaches including real-time quantitative PCR, terminal restriction fragment length polymorphism, and clone library construction were employed using 16S rRNA gene as genetic marker. Application of inorganic fertilizers did not affect bacterial abundance, and rice straw incorporation combined with inorganic fertilizers significantly (P < 0.05) increased bacterial abundance with shifts in bacterial community composition. Among phylogenetic groups, γ-Proteobacteria was responsive to all fertilization regimes while Acidobacteria was relatively stable to fertilization practices. Inorganic fertilizer mainly affected γ-Proteobacteria and δ-Proteobacteria, while rice straw incorporation influenced β-Proteobacteria and Verrucomicrobia. Therefore, long-term fertilization can affect abundance and composition of bacterial communities in paddy soil.

Dissimilatory Nitrate Reduction Processes in Typical Chinese Paddy Soils: Rates, Relative Contributions, and Influencing Factors

Using soil slurry-based (15)N tracer combined with N2/Ar technique, the potential rates of denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA), and their respective contributions to total nitrate reduction were investigated in 11 typical paddy soils across China. The measured rates of denitrification, anammox, and DNRA varied from 2.37 to 8.31 nmol N g(-1) h(-1), 0.15 to 0.77 nmol N g(-1) h(-1) and 0.03 to 0.54 nmol N g(-1) h(-1), respectively. The denitrification and anammox rates were significantly correlated with the soil organic carbon content, nitrate concentration, and the abundance of nosZ genes. The DNRA rates were significantly correlated with the soil C/N, extractable organic carbon (EOC)/NO3(-) ratio, and sulfate concentration. Denitrification was the dominant pathway (76.75-92.47%), and anammox (4.48-9.23%) and DNRA (0.54-17.63%) also contributed substantially to total nitrate reduction. The N loss or N conservation attributed to anammox and DNRA was 4.06-21.24 and 0.89-15.01 g N m(-2) y(-1), respectively. This study reports the first simultaneous investigation of the dissimilatory nitrate reduction processes in paddy soils, highlighting that anammox and DNRA play important roles in removing nitrate and should be considered when evaluating N transformation processes in paddy fields.

Influence of fertilisation regimes on a nosZ-containing denitrifying community in a rice paddy soil

BACKGROUND Denitrification is a microbial process that has received considerable attention during the past decade since it can result in losses of added nitrogen fertilisers from agricultural soils. Paddy soil has been known to have strong denitrifying activity, but the denitrifying microorganisms responsible for fertilisers in paddy soil are not well known. The objective of this study was to explore the impacts of 17-year application of inorganic and organic fertiliser (rice straw) on the abundance and composition of a nosZ-denitrifier community in paddy soil. Soil samples were collected from CK plots (no fertiliser), N (nitrogen fertiliser), NPK (nitrogen, phosphorus and potassium fertilisers) and NPK + OM (NPK plus organic matter). The nitrous oxide reductase gene (nosZ) community composition was analysed using terminal restriction fragment length polymorphism, and the abundance was determined by quantitative PCR. RESULTS Both the largest abundance of nosZ-denitrifier and the highest potential denitrifying activity (PDA) occurred in the NPK + OM treatment with about four times higher than that in the CK and two times higher than that in the N and NPK treatments (no significant difference). Denitrifying community composition differed significantly among fertilisation treatments except for the comparison between CK and N treatments. Of the measured abiotic factors, total organic carbon was significantly correlated with the observed differences in community composition and abundance (P < 0.01 by Monte Carlo permutation). CONCLUSION This study shows that the addition of different fertilisers affects the size and composition of the nosZ-denitrifier community in paddy soil.

Phosphorus status and risk of phosphate leaching loss from vegetable soils of different planting years in suburbs of Changsha, China.

Abstract The aim of the study was to develop an index to assess the environmental risk of P loss potential in vegetable soils with chronic difference of plantation in the suburbs of Changsha, Hunan Province, China. Chemical methodology was used to study soil phosphorus status and the relationships between available P in soil and potential soil leaching P. The results showed that there was a significant linear relationship between Olsen P and CaCl 2 -P or P concentration in soil solution. Olsen P increased sharply when either CaCl 2 -P or P concentration in soil solution reached a certain level. It was confirmed that 80 mg kg −1 of Olsen P was the critical value of soil P leaching in the vegetable soils. P leaching probability over the critical was assessed by GIS and indicator Kriging and four secondary risks of phosphorus leaching loss were defined. In the area with vegetable cropping for over 30 yr (Chenjiadu) and 10–15 planting years (Huangxingzhen), the indices of phosphorus leaching loss risk were 3 and 2.93, respectively. These two areas belonged to strong secondary of risk of phosphate leaching loss. In the new vegetable planting field less than 2 yr (Ningxiang), the index was 0.06, which had almost no risk of phosphorus leaching. In vegetable soils in the suburban region of Changsha, the phosphorus leaching peotential is high and the phosphorus leaching loss is related to chronic length of vegetable cropping.

Effects of land utilization patterns on soil microbial communities in an acid red soil based on DNA and PLFA analyses

PurposeDisturbances such as cultivation, logging, and plantation occurred widely in acid red soil area of China, yet little is known about their effects on soil microbial community which is closely related to soil function. In this study, microbial community compositions were investigated in a red soil with different long-term land utilization patterns to understand the potential effects of cultivation and vegetation successions on relevant soil functions.Materials and methodsLand utilization patterns include restoration, degradation (logging), cropland, and pine plantation. Both DNA- and phospholipid fatty acid (PLFA)-based methods were used to measure the abundance and community structure of microorganisms.Results and discussionIn general, DNA- and PLFA-based methods showed similar results of microbial composition, but for some parameters, only one approach showed significant differences between different land utilization patterns. Land utilization patterns showed significant effects on abundance of total microbial community, bacteria, fungi, and actinomycetes which were all lowest in the cropland plot either by PLFA or DNA analyses. 17:0 cyclo/16:1 ω7c and 19:0 cyclo/18:1 ω7c which are possibly associated with environmental stresses also varied among different land utilization patterns. Both PLFA and T-RFLP analyses showed that each land utilization pattern possessed a specific microbial community structure.ConclusionsThese results revealed significant effects of different land utilization patterns especially cultivation and logging on soil microbial communities and suggested that we should be cautious in utilizing red soils to sustain soil properties and functions. Combination of DNA- and PLFA-based methods is effective to provide precise results of microbial composition.

Spatial variability of soil microbial biomass carbon, nitrogen and phosphorus in a hilly red soil landscape in subtropical China

Abstract Soil microbial biomass (SMB) is considered to be an important indicator of soil fertility and biological quality, and it presents strong spatial heterogeneity in relation to soil properties (e.g. soil texture, organic carbon, total nitrogen) and topography at various spatial and temporal scales. In the present study, geostatistics were used to analyze the spatial variability of soil microbial biomass carbon (MBC), nitrogen (MBN) and phosphorus (MBP) in a hilly red soil landscape (446 ha) in subtropical China. Five hundred and twenty-three soil samples at a soil depth of 0–20 cm were randomly collected from paddy fields, dry lands, orchards and wood lands in the study region. Significant negative correlations (r = −0.69 to −0.54) of MBC, MBN and MBP with elevation were observed. The Steins Matérn, Spherical and Gaussian models with effective ranges of 157, 252 and 213 m were best-fitted to the sample semivariograms of original MBC, MBN and MBP variables, respectively. All three SMB variables exhibited moderate spatial dependence. After detrending the elevation impact, the normal score transformed MBC and MBP still retained their moderate spatial autocorrelations with slightly decreased effective ranges, whereas the normal score transformed MBN demonstrated a very strong spatial dependence with a much shorter effective range of 70 m. Spatial distributions of the three SMB variables were estimated using both ordinary kriging (OK) and regression kriging (RK) with elevation as the predictor. The kriging predictions showed that soil MBC, MBN and MBP had overlapping spatial patterns, and furthermore the RK interpolations showed more details in space than the OK interpolations, with improved prediction accuracy. The spatial distribution of soil MBN demonstrated more hotspots than the other two SMB variables, implying that MBN might be more sensitive to environmental disturbances (such as fertilization, tillage and crop rotations).

Effects of top excision on the potassium accumulation and expression of potassium channel genes in tobacco

The effects of the removal of the shoot apex of tobacco on the relative transcript levels of potassium channel genes, determined by real-time PCR, and on the relationship between the expression of genes encoding potassium channels and potassium concentration, were studied. The results from the study indicated that comparatively more assimilates of photosynthesis were allocated to the apex in control plants than in both decapitated and IAA-treated decapitated plants. By contrast, dry matter in the upper leaves, roots, and stems in both decapitated and IAA-treated plants was significantly increased relative to control plants. The potassium level in whole plants decreased post-decapitation compared with control plants, and so did the potassium concentration in middle and upper leaves, stem, and roots. Expression of NKT1, NtKC1, NTORK1, and NKT2 was inhibited by decapitation in tobacco leaves with a gradual reduction after decapitation, but was induced in roots. The relative expression of NKT1, NTORK1, and NKT2 in tobacco leaves was higher than that in roots, whereas the expression of NtKC1 was higher in roots. The levels of inhibition and induction of NKT1, NtKC1, NTORK1, and NKT2 in leaves and roots, respectively, associated with decapitation were reduced by the application of IAA on the cut surface of the decapitated stem. Further results showed that the level of endogenous auxin IAA in decapitated plants, which dropped in leaves and increased in roots by 140.7% at 14 d compared with the control plant, might be attributed to the change in the expression of potassium channel genes. The results suggest that there is a reciprocal relationship among endogenous auxin IAA, expression of potassium channel genes and potassium accumulation. They further imply that the endogenous IAA probably plays a role in regulating the expression of potassium channel genes, and that variations in expression of these genes affected the accumulation and distribution of potassium in tobacco.

Differential Responses of Nitrifier and Denitrifier to Dicyandiamide in Short- and Long-Term Intensive Vegetable Cultivation Soils

Abstract Nitrification inhibitors, such as dicyandiamide (DCD), have been shown to decrease leaching from urea- and ammonium-based fertilizers in agricultural soils. The effect of nitrification inhibitors on nitrifier and denitrifier in short- and long-term intensive vegetable cultivation soils was poorly understood. In this study, the pot trial was conducted to investigate the differential responses of nitrifier ( amoA -containing bacteria) and denitrifier ( nirK -containing bacteria) to DCD in short-(soil S) and long-term (soil L) intensive vegetable cultivation soils. Quantitative polymerase chain reaction (qPCR) and terminal restriction fragment length polymorphism (T-RFLP) were employed to detect the abundance and composition of amoA- and nirK -containing communities. The results indicated that application of DCD led to a consistently higher NH 4 + -N concentration during the whole incubation in soil L, while it was quickly decreased in soil S after 21 days. Furthermore, DCD induced more severe decrease of the abundance of amoA -containing bacteria in soil L than in soil S. However, the abundance of the nirK- containing community was not significantly affected by DCD in both soils. Long-term vegetable cultivation resulted in a super-dominant amoA -containing bacteria group and less divergence in soil L compared with soil S, and DCD did not cause obvious shifts of the composition of ammonia-oxidising bacteria (AOB). On the contrary, both amoA- and nirK -containing bacterial compositions were influenced by DCD in soil S. The results suggested that long-term intensive vegetable cultivation with heavy nitrogen fertilization resulted in significant shifts of AOB community, and this community was sensitive to DCD, but denitrifiers were not clearly affected by DCD.