Hongjie Di

Influence of black carbon addition on phenanthrene dissipation and microbial community structure in soil

Biodegradation processes and changes in microbial community structure were investigated in black carbon (BC) amended soils in a laboratory experiment using two soils (black soil and red soil). We applied different percentages of charcoal as BC (0%, 0.5% and 1% by weight) with 100 mg kg(-1) of phenanthrene. Soil samples were collected at different incubation times (0, 7, 15, 30, 60, 120 d). The amendment with BC caused a marked decrease in the dissipation (ascribed to mainly degradation and/or sequestration) of phenanthrene residues from soil. Extracted phenanthrene in black soil with 1% BC were higher, oppositely in red soil, 0.5% BC amendments were higher. There were significant changes in the PLFA pattern in phenanthrene-spiked soils with time but BC had little effect on the microbial community structure of phenanthrene-spiked soils, as indicated by principal component analysis (PCA) of the PLFA signatures.

Legacy effects of simulated short-term climate change on ammonia oxidisers, denitrifiers, and nitrous oxide emissions in an acid soil

Although the effect of simulated climate change on nitrous oxide (N2O) emissions and on associated microbial communities has been reported, it is not well understood if these effects are short-lived or long-lasting. Here, we conducted a field study to determine the interactive effects of simulated warmer and drier conditions on nitrifier and denitrifier communities and N2O emissions in an acidic soil and the longevity of the effects. A warmer (+2.3xa0°C) and drier climate (−7.4% soil moisture content) was created with greenhouses. The variation of microbial population abundance and community structure of ammonia-oxidizing archaea (AOA), bacteria (AOB), and denitrifiers (nirK/S, nosZ) were determined using real-time PCR and high-throughput sequencing. The results showed that the simulated warmer and drier conditions under the greenhouse following urea application significantly increased N2O emissions. There was also a moderate legacy effect on the N2O emissions when the greenhouses were removed in the urea treatment, although this effect only lasted a short period of time (about 60xa0days). The simulated climate change conditions changed the composition of AOA with the species affiliated to marine group 1.1a-associated lineage increasing significantly. The abundance of all the functional denitrifier genes decreased significantly under the simulated climate change conditions and the legacy effect, after the removal of greenhouses, significantly increased the abundance of AOB, AOA (mainly the species affiliated to marine group 1.1a-associated lineage), and nirK and nosZ genes in the urea-treated soil. In general, the effect of the simulated climate change was short-lived, with the denitrifier communities being able to return to ambient levels after a period of adaptation to ambient conditions. Therefore, the legacy effect of simulated short-time climate change conditions on the ammonia oxidizer and denitrifier communities and N2O emissions were temporary and once the conditions were removed, the microbial communities were able to adapt to the ambient conditions.

Ammonia oxidizers and nitrite-oxidizing bacteria respond differently to long-term manure application in four paddy soils of south of China

Nitrification plays an important role in the soil nitrogen (N) cycle, and fertilizer application may influence soil nitrifiers abundance and composition. However, the effect of long-term manure application in paddy soils on nitrifying populations is poorly understood. We chose four long-term manure experimental fields in the south of China to study how the abundance and community structure of nitrifiers would change in response to long-term manure application using quantitative PCR and Miseq sequencing analyses. Our results showed that manure application significantly increased ammonia oxidizing archaea (AOA) abundance at the ChangSha (CS) and NanChang (NC) sites, while the abundance of ammonia oxidizing bacteria (AOB) represented 4.8- and 12.8- fold increases at the JiaXing (JX) and YingTan (YT) sites, respectively. Miseq sequencing of 16S rRNA genes indicated that manure application altered the community structure of nitrifying populations, especially at the NC and YT sites. The application of manure significantly changed AOA and nitrite oxidizing bacteria (NOB) community structures but not those of AOB, suggesting that AOA and NOB may be more sensitive to manures. Variation partitioning analysis (VPA) and redundancy analysis (RDA) indicated that soil pH, TN, NO3--N and water content were the main factors in shaping nitrifying communities. These findings suggest that nitrifiers respond diversely to manure application, and soil physiochemical properties play an important role in determining nitrifiers abundance and communities with long-term manure addition.

Microbial pathways for nitrous oxide emissions from sheep urine and dung in a typical steppe grassland

The aim of this study was to determine the responses of nitrifiers and denitrifiers to understand microbial pathways of nitrous oxide (N2O) emissions in grassland soils that received inputs of sheep excreta. Sheep dung and synthetic sheep urine were applied at three different rates, simulating a single, double, or triple overlapping of urine or dung depositions in the field. Quantitative PCR and high-throughput sequencing were combined with process-based modeling to understand effects of sheep excreta on microbial populations and on pathways for N2O production. Results showed that emissions of N2O from urine were significantly higher than from dung, ranging from 0.12 to 0.78xa0kgxa0N2O-Nxa0ha−1 during the 3xa0months. The N2O emissions were significantly related to the bacterial amoA (ru2009=u20090.373, Pu2009<u20090.001) and nirK (ru2009=u20090.614, Pu2009<u20090.001) gene abundances. It was autotrophic nitrification that dominated N2O production in the low urine-N rate soils, whereas it was denitrification (including nitrifier denitrification and heterotrophic denitrification) that dominated N2O production in the high urine-N rate soils. Nitrifier denitrification was responsible for most of the N2O emissions in the dung-treated soils. This study suggests that nitrifier denitrification is indeed an important pathway for N2O emissions in these low fertility and dry grazed grassland ecosystems.

Impacts of long-term lack of potassium fertilization on different forms of soil potassium and crop yields on the North China Plains

PurposeThis study assessed changes in soil potassium (K) pools, soil K-bearing minerals, and crop yields without K-fertilizer application for 25xa0years on the North China Plains.Materials and methodsTwo long-term field experiments (over 25xa0years) in a wheat-maize rotation system were conducted: Experiment 1 was a randomized complete block experiment of three rates of fertilizer nitrogen (N: 0, 270, 540xa0kgxa0ha−1xa0year−1) and phosphorus (P: 0, 36, 72xa0kgxa0ha−1xa0year−1). Experiment 2 had an orthogonal treatment structure with three rates of N and P fertilizers and straw (0, 112.5, 187.5xa0kgxa0Nxa0ha−1xa0year−1; 0, 40, 80xa0kgxa0Pxa0ha−1xa0year−1; and 0, 2250, 4500xa0kgxa0strawxa0ha−1xa0year−1). The three different tillage methods were as follows: T1, conventional tillage with straw incorporation; T2, conventional tillage with straw cover on soil surface; and M, minimum tillage. Three replicates were designed for each treatment in both experiments. Different forms of K, including total K, mineral K (MK), slowly available K (SK), and rapidly available K (RK), were quantified by standard methods. Crop yield was calculated based on random quadrants’ data.Results and discussionThe results from both experiments indicated that the depletion of RK promoted the conversion of MK to SK by K release from hydromica. Crop yields in all the treatments with P fertilizer were significantly higher than those in N alone and CK treatments in both long-term experiments, suggesting that P fertilizer had a greater contribution in improving crop yield than N fertilizer after long-term lack of K fertilization. The average values of different forms of K and crop yield in exp. 2 were clearly higher than those in exp. 1. After 11xa0years of high rates of straw without chemical K fertilization, the average soil RK peaked. However, 5xa0years later, it showed a negative K budget and crop yield began to decline.ConclusionsFor over 25xa0years, fertilization and tillage managements had little impact on soil TK and MK contents because of the high feldspar and hydromica contents in the soil. The weathering of K-bearing minerals and fertilization significantly changed soil SK and RK contents, and hydromica was the main source of SK. P fertilizer was more important in increasing crop yield than N fertilizer and straw with long-term zero K inputs. To maintain high crop yield (12.02–13.82xa0txa0ha−1xa0year−1, the total yield of summer maize and winter wheat) and improve the fertilizer utilization efficiency, 150–228xa0kgxa0Kxa0ha−1 should be applied alongside 187.5xa0kgxa0Nxa0ha−1xa0year−1, 80xa0kgxa0Pxa0ha−1xa0year−1, and 4500xa0kgxa0strawxa0ha−1xa0year−1 every 16xa0years in this production system.

Impact of mowing management on nitrogen mineralization rate and fungal and bacterial communities in a semiarid grassland ecosystem

PurposeMicrobes play a key role in soil nutrient cycling and supply in the extensive semiarid grassland ecosystem, where no fertilizers are applied. However, the role of fungi vs bacteria in nitrogen (N) mineralization in such ecosystem is poorly understood. The objective of this study was to determine the impacts of different mowing practices on fungal and bacterial communities and the relationships between the two microbial communities and net N mineralization rate (Rm).Materials and methodsThis study was based on a 13-year mowing experiment in Inner Mongolia. The treatments included mowing once every second year (M1/2), mowing twice every 3xa0years (M2/3), mowing once a year (M1), mowing twice a year (M2), and the unmown (control, CK). Soil basic chemical properties, Rm, microbial biomass, bacterial and fungal community abundance, and diversity were determined, and fungal phylogeny and the relationship between microbial community and Rm were analyzed.Results and discussionModerate mowing (M1/2, M2/3, and M1) enhanced soil carbon and nitrogen stocks, Rm, fungal community abundance and diversity which might mainly because of the increased decomposer fungi species, but the higher frequency mowing (M2) significantly decreased the above. There was a significant correlation between fungal community abundance and Rm (rxa0=xa00.688, Pxa0=xa00.005) in this study. However, different mowing practices had little effect on the bacterial community, which might due to human disturbance (mowing practices) and poor environmental conditions (drought, limited available nitrogen and phosphorus).ConclusionsOverall, fungi may play a more important role than bacteria in N mineralization under mowing management in such a grassland ecosystem. Moderate-frequency mowing, e.g., M1, is more appropriate for maintaining soil microbial communities and soil fertility, whereas the high-frequency mowing, e.g., M2, is not sustainable for maintaining soil nutrients and microbial community in such a semiarid grassland ecosystem in a long term.

Alteration of gaseous nitrogen losses via anaerobic ammonium oxidation coupled with ferric reduction from paddy soils in Southern China

The bacteria-mediated anaerobic ammonium oxidation under iron reducing conditions, termed feammox, represents a process for alleviating N accumulation in anoxic soils. Fertilization, as an important agricultural strategy, needs to be investigated in order to determine its effects on nitrogen (N) removal via the feammox process in paddy soils. In this study, a slurry incubation experiment was conducted in fertilized paddy soils with a gradient of microbial reducible Fe(III) levels obtained from Southern China using 15N-isotope tracing techniques. Four fertilizer treatments were examined: an un-fertilized control (NF), chemical fertilizers (CF), chemical fertilizers plus manure (CMF) and chemical fertilizers plus crop straw (CSF). It was estimated that the potential N losses linked with feammox were 3.6-24.9u202fkgu202fNu202fha-1u202fy-1 in all the examined soils. Compared to the unfertilized soil (NF), fertilization stimulated feammox and led to higher (3.4-5.8 times) N losses. We postulate that the variations in the extent and rate of feammox between the unfertilized and fertilized soils were most likely due to differences in the abundance of the Acidimicrobiaceae bacterium A6 and the amounts of microbial reducible Fe(III). Further, the variations between soil treated with fertilizer (CF) only and soils coupled organic-chemical fertilizer (CMF and CSF) were due to the differences in the electron transfer mechanism mediated by electron shuttles from bacteria to Fe(III) minerals arising from the organic carbon applied. Overall, this study clearly illustrated the stimulatory effects of fertilization on feammox that resulted in higher N losses and suggested that feammox could be a crucial N removal pathway in paddy soils.

Understanding the relationships between grazing intensity and the distribution of nitrifying communities in grassland soils

Nitrifying microbes are of critical importance in regulating efficient nitrogen (N) cycling, which plays a crucial role in plant productivity and maintaining soil sustainability. Long-term different intensities of grazing can strongly influence the microbial communities, while our understanding of the complex nitrifying community in the grazed grassland soil environment is still limited. To investigate whether and how long-term grazing with different intensities influence soil nitrifying communities, high-throughput sequencing and quantitative PCR analyses were performed on soil samples from permanent grassland soils under four grazing intensities: 0 (G0), 1.5 (G1), 6 (G2) and 9 (G3) sheepha-1. Results showed that the G3 treatment significantly reduced the soil nutrient content and increased the soil bulk density, changes that are not sustainable in the long run. The G1 treatment, on the other hand, significantly increased the soil nutrient content and would improve soil fertility. Some functional microbes were specifically enriched after long term grazing, like Nitrospirae (phylum) to Nitrospira (class) in the G2 samples and Chromatiales (order) to Nitrosococcus (genus) in the G3 soils. The numerically dominant Nitrosococcus watsonii lineage of ammonia oxidizing bacteria (AOB) was observed in this grassland soil. The redundancy analysis (RDA) together with the structural equation modeling (SEM) analysis showed that grazing intensity was important in mediating the distribution of soil microorganisms and affected nitrifying communities by impacting soil physicochemical characteristics (e.g., bulk density, NH4+-N). These results showed the shifts of nitrifying communities across different grazing intensities, and could aid in the determination of an optimal grazing intensity for these grazed grassland soils.

Heterotrophic nitrification and denitrification are the main sources of nitrous oxide in two paddy soils

AimsPaddy soil is one of the main sources of global nitrous oxide (N2O) emissions via multiple pathways regulated by different microbes. However, the relative contributions of N2O production pathways with the addition of organic carbon (C) in different paddy soils are poorly understood.Methods15N-stable isotope and acetylene (C2H2) inhibition were used to differentiate the relative contributions of autotrophic and heterotrophic nitrification (ANF and HNF) and denitrification (DNF) to N2O emissions in two paddy soils (acid vs. neutral soil) with glucose addition.ResultsHNF and DNF were the main N2O pathways which contributed between 85% to 100% of the total N2O production at 70% water filled pore space. Low soil pH inhibited soil nitrification and the activity of ammonia oxidizers compared with neutral paddy soil. Glucose reduced nitrification rate and stimulated N2O production significantly, mainly via DNF in the two paddy soils. Moreover, glucose increased the relative contribution of DNF to total N2O production in the first 7xa0days and total N2O amounts from HNF over the 14-day incubation.ConclusionsHNF and DNF rather than ANF dominated the N2O emissions regardless of soil pH. Glucose had a positive effect on N2O emissions by influencing HNF and DNF.

Effects of different fertilization regimes on nitrogen and phosphorus losses by surface runoff and bacterial community in a vegetable soil

PurposeVegetables are major economic crops in China. Their cultivation usually involves high fertilizer application rates leading to significant losses of N and P to the wider environment, resulting in water contamination and low nutrient use efficiency. Hence, it is a matter of urgency to understand the mechanisms and factors that affect N and P losses in vegetable production systems in order to develop optimum fertilization regimes.Materials and methodsDifferent fertilization regimes were applied in a long-term chili (Capsicum spp. L.) production soil to study the effects on nitrogen (N) and phosphorus (P) runoff losses, microbial biomass, microbial community, and crop yields. Three fertilization regimes were implemented: control (no fertilizer; CK), farmer’s fertilization practice (FFP), and site-specific nutrient management (SSNM). A fixed collection device was used to quantify the total volume of water output after each precipitation event. All water samples were analyzed for total nitrogen, ammonium nitrogen (NH4+-N), nitrate nitrogen (NO3−-N), total phosphorus (TP), and available phosphorus (AP). Soil samples were collected for analysis of the physicochemical properties and for DNA extraction after chili harvest. High-throughput sequencing was used to further investigate the relationship between the microbial community and nutrient losses.Results and discussionThe SSNM fertilizer regime resulted in a 23.3% yield increase and enhanced agronomic N use efficiency from 11.87 to 15.67% compared with the FFP treatment. Soil available nutrients (i.e., AN and AP) and ATP content increased significantly after SSNM implementation. Under the SSNM regime, N losses decreased by 25.8% compared with FFP but did not lead to significantly different P losses. High-throughput sequencing results showed that each treatment formed a unique microbial community structure. VPA results revealed that the microbial community structure was mainly (50.56%) affected by the interactions between N and P. Mantel results indicated that the soil properties that significantly affected soil microbial community structure followed the order: AP, AK, and salinity.ConclusionsOur study has demonstrated that SSNM not only generates lower N losses but also provides higher contents of soil available nutrients and plant yield, which were mainly attributed to the multiple top dressings and meeting of the plants’ demand with adequate nutrient supplies. The combined data showed that the microbial community differentiation between the different fertilizer regimes was mainly linked to the interactions between N and P in the soil.