Understanding the effects of external organic and inorganic components on soil fertility and quality is essential for improving low-yielding soils. We conducted a field study over two consecutive ...rice growing seasons to investigate the effect of applying chemical fertilizer (NPK), NPK plus green manure (NPKG), NPK plus pig manure (NPKM), and NPK plus straw (NPKS) on the soil nutrient status, enzyme activities involved in C, N, P, and S cycling, microbial community and rice yields of yellow clayey soil. Results showed that the fertilized treatments significantly improved rice yields over the first three experimental seasons. Compared with the NPK treatment, organic amendments produced more favorable effects on soil productivity. Notably, the NPKM treatment exhibited the highest levels of nutrient availability, microbial biomass carbon (MBC), activities of most enzymes and the microbial community. This resulted in the highest soil quality index (SQI) and rice yield, indicating better soil fertility and quality. Significant differences in enzyme activities and the microbial community were observed among the treatments, and redundancy analysis showed that MBC and available N were the key determinants affecting the soil enzyme activities and microbial community. The SQI score of the non-fertilized control (0.72) was comparable to that of the NPK (0.77), NPKG (0.81) and NPKS (0.79) treatments but significantly lower compared with NPKM (0.85). The significant correlation between rice yield and SQI suggests that SQI can be a useful to quantify soil quality changes caused by different agricultural management practices. The results indicate that application of NPK plus pig manure is the preferred option to enhance SOC accumulation, improve soil fertility and quality, and increase rice yield in yellow clayey soil.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The influence of inorganic or organic fertilization on soil microbial ecology has been emphasized recently, but less is known about rhizosphere effects on extracellular enzyme activities and ...microbial community structure. Eleven extracellular enzymes involved in C, N, P, and S cycling and microbial community structure in both the rhizosphere and bulk soil samples from a long-term (31-year) fertilizer experimental field at the wheat reproductive stage were investigated by microplate fluorometric assay and phospholipid fatty acid analysis (PLFA), respectively. The samples were taken from six treatments: control (CK, without fertilization), fertilizer N (N), fertilizer N and P (NP), fertilizer N, P and K (NPK), organic manure (M), and organic manure plus fertilizer N, P and K (MNPK). Responses to inorganic or organic fertilizers in the rhizosphere were significantly different from those in the bulk soil. Except for NO3−-N, thus, nutrient concentrations were generally higher in the rhizosphere than in the bulk soil. M and MNPK treatments greatly increased organic C, total N, NH4+-N and total S. Inorganic fertilizers (N, NP, and NPK) generally maintained or reduced most enzyme activities in the rhizosphere, but markedly increased these enzyme activities in the bulk soil. However, organic treatments (M and MNPK) enhanced most enzyme activities in both the rhizosphere and bulk soil. Higher total PLFA and lower ratios of bacteria to fungi and of actinomycetes to fungi were observed in the rhizosphere compared with the bulk soil. In the bulk soil, the ratios of bacteria to fungi and of actinomycetes to fungi were highest in the N treatment and lowest in the M treatment. However, in the rhizosphere there were no statistically significant differences in the abundance of bacteria, fungi and actinomycetes between the inorganic and organic treatments. Organic fertilization increased total PLFA and Gram+ to Gram− bacteria ratio in both the rhizosphere and bulk soil. Our results indicated that changes in fertilization regime had a greater impact on the bulk soil microbial community than in the rhizosphere.
► Positive effect of inorganic fertilizer on most enzyme activities in the bulk soil. ► Negative effect of inorganic fertilizer on most enzyme activities in the rhizosphere. ► Organic fertilizer enhanced enzyme activities in both the rhizosphere and bulk soil. ► Total PLFA was almost doubled in the rhizosphere by organic fertilization. ► The influence of fertilizer on soil microbes can be mediated by rhizosphere effects.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
•SOC and total N contents markedly increased with increasing biochar addition rate.•Exchangeable Ca and Mg contents decreased with increasing biochar addition rate.•Lower amounts of MC addition ...increased soil enzyme activities involved in C cycling.•Total N and exchangeable Ca were dominant factors affecting soil enzyme activities.•PLFA biomarkers were negatively related to SOC and total N contents.
Biochar addition to soil has been proposed as a strategy to enhance soil quality and crop productivity, which may also affect microbial activity. However, the response of soil enzymes and microbial community composition to biochar addition and the main factors that drive their consequent behavior have rarely been studied. Therefore, to investigate the combined effect of different amounts of biochar (0, 0.5, 1.0, 2.5 and 5.0% by mass) and urea application on soil nutrients, enzymatic activities and microbial community in a fluvo-aquic soil, we conducted a 90-day laboratory study. Increased maize biochar addition led to significantly increased soil organic carbon (SOC), total N, and exchangeable K and reduced soil exchangeable Ca. Soil total N and exchangeable Ca were dominant factors affecting soil enzyme activities. Activities of soil extracellular enzymes involved in C and S cycling (except β-xylosidase) suggested lower amounts of biochar addition (0.5% by mass) could increase soil enzyme activities, while higher amounts of biochar addition reduce soil enzyme activities. However, the activities of l-leucine aminopeptidase and urease, both of which are involved in N cycling, increased with the increase of biochar addition rate. Total phospholipid fatty acid content and the relative abundance of bacteria were significantly reduced with increasing biochar addition rate. The relative abundance of fungi in the urea-amended soil was significantly higher than that in the other treated soils, and abundance of actinomycetes did not show a clear response to biochar addition. The changes in the microbial community composition were mainly related to SOC and total N contents, with a significant negative correlation. We concluded that the effect of biochar addition on soil enzymes and microbial community composition was highly variable. There is an urgent need to further estimate both the positive and negative long-term effects of biochar on the soil quality and crop productivity in this region.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Organic substitution management (OSM) is a key technology employed to reduce the amount of chemical fertilizer used in agricultural operations with the goal of reducing environmental pollution and ...ensuring green and sustainable agricultural development in China. However, there is still limited information regarding the underlying interactions between soil nutrients, enzyme activities and microbial community structures after long-term partial substitution of inorganic N with organic amendments, and no suitable evaluation indicators of organic substitution effects have been identified. Here, distance-based redundancy analysis (dbRDA), principal component analysis (PCA), the partial least squares method (PLS) and the partial least squares path model (PLS-PM) were used to better understand the impact of substitution effects on soil biochemical indexes in a 34-year field experiment. We found that soil C/N significantly directly affected rice yield, and that a soil C/N ranging from 10.12 to 10.19 could sustain a rice yield between 7000 and 6800 kg ha−1. Moreover, the soil hydrolase activities of the carbon and fungi communities were significantly influenced by both C/N and pH, and the carbon-cycling enzyme activities were found to be more susceptible to C/N than nitrogen-cycling enzyme activities. The low soil C/N and high pH after OSM decreased the ratio of G+ to G− and fungi to bacteria, indicating OSM increased the nutrient availability and benefited growth of the bacterial community. Hence, we believe that soil C/N and pH together can be used as a comprehensive index for suitable evaluation of the effects of OSM.
•The soil C/N ratio is the main factor controlling rice yield.•Carbon-cycling enzyme activity is more susceptible to soil C/N and pH than nitrogen-cycling enzyme activity.•Soil fungi are more active than bacteria in response to soil C/N and pH.•OSM increased the nutrient availability and benefited growth of the bacterial community.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Ammonia oxidation is a critical step in the soil nitrogen (N) cycle and can be affected by the application of mineral fertilizers or organic manure. However, little is known about the rhizosphere ...effect on the function and structure of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities, the most important organisms responsible for ammonia oxidation in agricultural ecosystems. Here, the potential nitrification activity (PNA), population size and composition of AOB and AOA communities in both the rhizosphere and bulk soil from a long-term (31-year) fertilizer field experiment conducted during two seasons (wheat and maize) were investigated using the shaken slurry method, quantitative real-time polymerase chain reaction and denaturing gradient gel electrophoresis. N fertilization greatly enhanced PNA and AOB abundance, while manure application increased AOA abundance. The community structure of AOB exhibited more obvious shifts than that of AOA after long-term fertilization, resulting in more abundant AOB phylotypes similar to Nitrosospira clusters 3 and 4 in the N-fertilized treatments. Moreover, PNA was closely correlated with the abundance and community structure of AOB rather than that of AOA among soils during both seasons, indicating that AOB play an active role in ammonia oxidation. Conversely, the PNA and population sizes of AOB and AOA were typically higher in the rhizosphere than the bulk soil, implying a significant rhizosphere effect on ammonia oxidation. Cluster and redundancy analyses further showed that this rhizosphere effect played a more important role in shaping AOA community structure than long-term fertilization. Overall, the results indicate that AOB rather than AOA functionally dominate ammonia oxidation in the calcareous fluvo-aquic soil, and that rhizosphere effect and fertilization regime play different roles in the activity and community structures of AOB and AOA.
► N fertilizations increased PNA and AOB population size and diversity. ► Manure enhanced AOA population size in both bulk soil and the rhizosphere. ► PNA was correlated with the abundance and community structure of AOB rather than AOA. ► Rhizosphere effect, not fertilization, plays a key role in shaping the AOA community.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
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•Nitrogen (N) fertilizer increased microbial phosphorus (P) limitation.•Long-term application of organic fertilizers resulted in microbial N limitation.•Microbial P limitation drove ...shifts in bacterial community structure.•Microbial P limitation promoted the decomposition of labile organic matter.•Microbial P limitation directly affected soil N and P cycling.
Soil microbial growth and activity are generally limited by availability of resources such carbon (C), nitrogen (N), or phosphorus (P) in terrestrial ecosystems. However, how soil microbial response to resource limitation in intensive agricultural ecosystems is unclear. Four treatments, namely no fertiliser (CK), chemical fertiliser (NPK), only N fertiliser (N), and organic fertiliser with chemical fertiliser (MNPK), were selected to investigate the effects of different fertiliser practices on the pattern and degree of the limitation of soil microorganisms by elemental availability. The enzyme stoichiometry results indicated that under CK, NPK, and N fertiliser treatments, the soil microbial community as a whole was limited by the availability of C and P. N fertiliser application alone (N) considerably increased the limitation degree of P availability by soil microorganisms, which was caused by the increase in soil N/P. The increased microbial P limitation significantly increased the relative abundance of copiotrophic taxa (Actinobacteria and Sphingomonas) that use labile carbonaceous compounds (such as starch), whereas it significantly decreased the relative abundance of oligotrophic taxa (Acidobacteria and RB41) that use recalcitrant carbonaceous compounds (such as lignin, pectin, and hemicellulose) and important ratios of the microbial community structure (the ratio of fungi/bacteria and the ratio of gram-positive/negative bacteria). Changes in the microbial community structure may be unfavourable for the increase in soil organic matter originating from microorganisms (such as fungi). As per the partial least squares path modelling, N and P cycling was directly affected by microbial P limitation. Linear regression analysis further indicated that with an increase in P limitation, the abundance of functional genes related to N cycling (N fixation, nitrification, and denitrification), P capture (phosphatase and 3-phytase), and P retention (polyphosphate kinase) increased significantly. These results revealed that microorganisms in a P-limited environment adjust their abundance of functional genes to absorb and retain insufficient element (P) while accelerating the turnover of the excess element (N). This study revealed the status and extent of the resource limitation for soil microbial utilization under different long-term fertilisation regimes and indicated that soil bacterial communities respond to resource limitation by adjusting their community structure and element cycling.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Data related to the spatial variability of properties of paddy soil is critical for improving rice productivity and designing sustainable farming techniques. However, a systematic assessment focusing ...on the spatial variability of low-yield paddy soil has not been conducted in South China. In this context, 560 soil samples were collected across South China and analyzed for nine common chemical properties. Rice yield data was obtained by surveying farmers during soil sampling. Soil parameters and rice yield varied considerably throughout the study area and their coefficients of variation ranged from 17.3% to 74.2%. Experimental semivariograms were developed and a moderate spatial dependence was observed for all selected parameters. Distribution maps, derived by kriging interpolation, illustrated that these paddy fields were characterized by high concentrations of soil organic matter (SOM), total N (TN), available N (AN) and available Zn (AZn); pH values decreased widely comparing with the data reported by the National Soil Survey, especially in southeast China; the areas with low soil P concentrations (<10mgkg−1) were mainly located in southwest China; cation exchange capacity (CEC), available K (AK) and available Si (ASi) had similar trends in spatial distributions with high concentrations in southeast China and low concentrations in southwest. Notably, paddy fields in southeast China were typically deficient in AK due to their concentrations, all of which are almost less than 100mgkg−1. Correlation analysis revealed that rice yield was significantly positively correlated with pH, CEC, AK and ASi, while negatively correlated with AN and AZn. Low pH, AK, CEC and ASi levels may be the most important constraints limiting rice productivity and fertilizers with N and Zn may be over-used and must be applied appropriately. The soil quality index (SQI) was also calculated using the analyzed chemical properties and a significant correlation was observed between SQI and rice yield, supporting earlier findings that good soil chemical health is essential for optimum sustained crop production. The remarkable variations of SQI and rice yield indicated that the potential for increasing rice productivity is a real prospect. Therefore, regional planning fertilization should pay more attention to the spatial variability of soil chemical properties to avoid economic losses and environmental pollution, and especially to the limited nutrients.
•Geostatistics is a good method to characterize spatial variability of soil attributes.•Distribution maps of rice yield and nine soil chemical properties were produced.•Selected parameters varied considerably throughout the study area.•High levels of SOM, TN and AN were observed in paddy fields of Southern China.•Soil available K showed a serious deficiency in southeast China.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Kondo effect is an interesting phenomenon in quantum many-body physics. Niobium (Nb) is a conventional superconductor important for many superconducting device applications. It was long thought that ...the Kondo effect cannot be observed in Nb because the magnetic moment of a magnetic impurity, e.g. iron (Fe), would have been quenched in Nb. Here we report an observation of the Kondo effect in a Nb thin film structure. We found that by co-annealing Nb films with Fe in Argon gas at above 400 Formula: see textC for an hour, one can induce a Kondo effect in Nb. The Kondo effect is more pronounced at higher annealing temperature. The temperature dependence of the resistance suggests existence of remnant superconductivity at low temperatures even though the system never becomes superconducting. We find that the Hamann theory for the Kondo resistivity gives a satisfactory fitting to the result. The Hamann analysis gives a Kondo temperature for this Nb-Fe system at Formula: see text 16 K, well above the superconducting transition onset temperature 9 K of the starting Nb film, suggesting that the screening of the impurity spins is effective to allow Cooper pairs to form at low temperatures. We suggest that the mechanism by which the Fe impurities retain partially their magnetic moment is that they are located at the grain boundaries, not fully dissolved into the bcc lattice of Nb.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
The long non-coding RNAs (lncRNAs) are critical regulators of diverse biological processes. Nevertheless, a global view of its expression and function in the mouse retina, a crucial model for ...neurogenesis study, still needs to be made available.
Herein, by integrating the established gene models and the result from ab initio prediction using short- and long-read sequencing, we characterized 4,523 lncRNA genes (MRLGs) in developing mouse retinas (from the embryonic day of 12.5 to the neonatal day of P28), which was so far the most comprehensive collection of retinal lncRNAs. Next, derived from transcriptomics analyses of different tissues and developing retinas, we found that the MRLGs were highly spatiotemporal specific in expression and played essential roles in regulating the genesis and function of mouse retinas. In addition, we investigated the expression of MRLGs in some mouse mutants and revealed that 97 intergenic MRLGs might be involved in regulating differentiation and development of retinal neurons through Math5, Isl1, Brn3b, NRL, Onecut1, or Onecut2 mediated pathways.
In summary, this work significantly enhanced our knowledge of lncRNA genes in mouse retina development and provided valuable clues for future exploration of their biological roles.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Soil aggregates provide different ecological niches for microorganisms, and in turn, the microbial interactions affect soil aggregation process. The response of the microbial community in bulk soil ...to different fertilization regimes has been well studied; however, the co-occurrence patterns of bacteria and fungi in different aggregates under various fertilization regimes remain unclear. Based on the long-term field experiment, we found that fertilization regimes contributed more to fungal than to bacterial community composition. Long-term fertilization decreased microbial interactions in large macroaggregates (LM), macroaggregates (MA) and silt and clay (SC) fractions, but increased in microaggregates (MI). The application of manure with inorganic fertilizers (NPKM) significantly increased the intensive cooperation between bacteria and fungi in LM and MA. Microbial communities in LM and MA were well separated and showed strong competition against microbes in MI and SC; hence, we concluded that the microbial habitat could be divided into two groups, large fractions (LM and MA) and small fractions (MI and SC). The bacterial genera
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were keystone taxa in inorganic fertilization, and
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were keystone taxa in NPKM, which were all sensitive to soil aggregation. In this study, we demonstrated that the NPKM decreased the microbial interactions within and between kingdoms in LM, MA, and SC, but enhanced nutrient availability and microbial interactions in MI, leading to the formation of biofilms and the strengthening of stress tolerance, which finally stimulated the formation and stabilization of soil aggregates. Thus, this study revealed how soil microbial competition or cooperation responded to different fertilization regimes at aggregate scales, and provided evidence for the stimulation of soil stability.
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