Yongchao Liang

Denitrification potential under different fertilization regimes is closely coupled with changes in the denitrifying community in a black soil

Preferable inorganic fertilization over the last decades has led to fertility degradation of black soil in Northeast China. However, how fertilization regimes impact denitrification and its related bacterial community in this soil type is still unclear. Here, taking advantage of a suit of molecular ecological tools in combination of assaying the potential denitrification (DP), we explored the variation of activity, community structure, and abundance of nirS and nirK denitrifiers under four different fertilization regimes, namely no fertilization control (N0M0), organic pig manure (N0M1), inorganic fertilization (N1M0), and combination of inorganic fertilizer and pig manure (N1M1). The results indicated that organic fertilization increased DP, but inorganic fertilization had no impacts. The increase of DP was mirrored by the shift of nirS denitrifiers’ community structure but not by that of nirK denitrifiers’. Furthermore, the change of DP coincided with the variation of abundances of both denitrifiers. Shifts of community structure and abundance of nirS and nirK denitrifiers were correlated with the change of soil pH, total nitrogen (TN), organic matter (OM), C:P, total phosphorus (TP), and available phosphorus (Olsen P). Our results suggest that the change of DP under these four fertilization regimes was closely related to the shift of denitrifying bacteria communities resulting from the variation of properties in the black soil tested.

Root cell wall polysaccharides are involved in cadmium hyperaccumulation in Sedum alfredii

Background and aimsThe role of polysaccharide modification in metal accumulation in hyperaccumulators is still unknown. Our aim was to compare the differences in the role of root cell-wall polysaccharides in cadmium (Cd) accumulation between hyperaccumulating (HE) and non-hyperaccumulating ecotype (NHE) of Sedm alfredii.MethodsHydroponic experiments were performed to characterize root-to-shoot Cd translocation, cadmium species and polysaccharide modification in root cell-wall of S. alfredii using stable isotope tracing, X-ray absorption near edge structure and immunofluorescence localization techniques.ResultsCd absorbed was more readily available for transport to the shoots by the HE roots than by the NHE roots, which is confirmed by a 6-fold higher 113Cd concentration in xylem sap. Root Cd efflux originated mainly from the cell walls. The concentration of cell-wall polysaccharides and activity of pectin methylesterase were higher in the NHE than in the HE in the absence of Cd, and even higher in the presence of Cd. More pectins were methylated in the HE than in the NHE, indicating more free pectic acid residues in the NHE. The cell-wall-bound Cd was retained more tightly in the NHE than in the HE.ConclusionsCadmium hyperaccumulation by HE of S. alfredii is associated with its enhanced Cd flux into the xylem, which is partly regulated by cell-wall polysaccharide modification in roots.

Phosphorus and magnesium interactively modulate the elongation and directional growth of primary roots in Arabidopsis thaliana (L.) Heynh

Highlight Phosphorus and magnesium interactively affect root elongation and skewing by a pathway that is largely dependent upon the signalling function of auxin, which leads to accelerated cell expansion and division.

The apoplasmic pathway via the root apex and lateral roots contributes to Cd hyperaccumulation in the hyperaccumulator Sedum alfredii.

Highlight A portion of the cadmium taken up by the hyperaccumulator Sedum alfredii can be apoplasmically transported to the xylem via root apexes and lateral roots, where the suberin lamellae are not well developed.Although the significance of apoplasmic barriers in roots with regards to the uptake of toxic elements is generally known, the contribution of apoplasmic bypasses (ABs) to cadmium (Cd) hyperaccumulation is little understood. Here, we employed a combination of stable isotopic tracer techniques, an ABs tracer, hydraulic measurements, suberin lamellae staining, metabolic inhibitors, and antitranspirants to investigate and quantify the impact of the ABs on translocation of Cd to the xylem in roots of a hyperaccumulating (H) ecotype and a non-hyperaccumulating (NH) ecotype of Sedum alfredii In the H ecotype, the Cd content in the xylem sap was proportional to hydrostatic pressure, which was attributed to pressure-driven flow via the ABs. The contribution of the ABs to Cd transportation to the xylem was dependent on the Cd concentration applied to the H ecotype (up to 37% at the highest concentration used). Cd-treated H ecotype roots showed significantly higher hydraulic conductance compared with the NH ecotype (76 vs 52 × 10-8 m s-1MPa-1), which is in accordance with less extensive suberization due to reduced expression of suberin-related genes. The main entry sites of apoplasmically transported Cd were localized in the root apexes and lateral roots of the H ecotype, where suberin lamellae were not well developed. These findings highlight the significance of the apoplasmic bypass in Cd hyperaccumulation in hyperaccumulating ecotypes of S. alfredii.

Nitrous oxide emission and denitrifier communities in drip-irrigated calcareous soil as affected by chemical and organic fertilizers

The effects of consecutive application of chemical fertilizer with or without organic fertilizer on soil N2O emissions and denitrifying community structure in a drip-irrigated field were determined. The four fertilizer treatments were (i) unfertilized, (ii) chemical fertilizer, (iii) 60% chemical fertilizer plus cattle manure, and (iv) 60% chemical fertilizer plus biofertilizer. The treatments with organic amendments (i.e. cattle manure and biofertilizer) reduced cumulative N2O emissions by 4.9-9.9%, reduced the N2O emission factor by 1.3-42%, and increased denitrifying enzyme activities by 14.3-56.2%. The nirK gene copy numbers were greatest in soil which received only chemical fertilizer. In contrast, nirS- and nosZ-copy numbers were greatest in soil amended with chemical fertilizer plus biofertilizer. Chemical fertilizer application with or without organic fertilizer significantly changed the community structure of nirK-type denitrifiers relative to the unfertilized soil. In comparison, the nirS- and nosZ-type denitrifier genotypes varied in treatments receiving organic fertilizer but not chemical fertilizer alone. The changes in the denitrifier communities were closely associated with soil organic carbon (SOC), NO3-, NH4+, water holding capacity, and soil pH. Modeling indicated that N2O emissions in this soil were primarily associated with the abundance of nirS type denitrifying bacteria, SOC, and NO3-. Overall, our findings indicate that (i) the organic fertilizers increased denitrifying enzyme activity, increased denitrifying-bacteria gene copy numbers, but reduced N2O emissions, and (ii) nirS- and nosZ-type denitrifiers were more sensitive than nirK-type denitrifiers to the organic fertilizers.

Structural and functional variability in root-associated bacterial microbiomes of Cd/Zn hyperaccumulator Sedum alfredii

Interactions between roots and microbes affect plant’s resistance to abiotic stress. However, the structural and functional variation of root-associated microbiomes and their effects on metal accumulation in hyperaccumulators remain poorly understood. Here, we characterize the root-associated microbiota of a hyperaccumulating (HP) and a non-hyperaccumulating (NHP) genotype of Sedum alfredii by 16S ribosomal RNA gene profiling. We show that distinct microbiomes are observed in four spatially separable compartments: the bulk soil, rhizosphere, rhizoplane, and endosphere. Both the rhizosphere and rhizoplane were preferentially colonized by Proteobacteria, and the endosphere by Actinobacteria. The rhizosphere and endophytic microbiomes were dominated by the family of Sphingomonadaceae and Streptomycetaceae, respectively, which benefited for their survival and adaptation. The bacterial α-diversity decreases along the spatial gradient from the rhizosphere to the endosphere. Soil type and compartment were strongest determinants of root-associated community variation, and host genotype explained a small, but significant amount of variation. The enrichment of Bacteroidetes and depletion of Firmicutes and Planctomycetes in the HP endosphere compared with that of the NHP genotype may affect metal hyperaccumulation. Program PICRUSt predicted moderate functional differences in bacterial consortia across rhizocompartments and soil types. The functional categories involved in membrane transporters (specifically ATP-binding cassette transporters) and energy metabolism were overrepresented in endosphere of HP in comparison with NHP genotypes. Taken together, our study reveals substantial variation in structure and function of microbiomes colonizing different compartments, with the endophytic microbiota potentially playing an important role in heavy metal hyperaccumulation.

The contrasting effects of N -( n -butyl) thiophosphoric triamide (NBPT) on N 2 O emissions in arable soils differing in pH are underlain by complex microbial mechanisms

The urease inhibitor, N-(n-butyl) thiophosphoric triamide (NBPT), has been proposed to reduce synthetic fertilizer-N losses, including nitrous oxide (N2O) emissions from agricultural soils. However, the response of N2O emission to NBPT amendment is inconsistent across soils and associated microbial mechanisms remain largely unknown. Here we performed a meta-analysis of the effects of NBPT on N2O emissions and found NBPT significantly reduced N2O emissions in alkaline soils whereas no obvious effects exhibited in acid soils. Based on the finding of meta-analysis that pH was a key modifier in regulating the effect of NBPT on N2O emissions, we selected two arable soils differing in pH and conducted a microcosm study. In conjunction with measurement of N2O emission, community structure and abundance of functional guilds were assessed using T-RFLP and qPCR. Our results showed NBPT retarded urea hydrolysis and inhibited nitrification, but stimulated N2O emission in alkaline soil, whereas it exhibited no remarkable effects in acid soil, thereby only partly confirming the results of meta-analysis. Abundances of AOB and ureC-containing bacteria decreased, while abundance of AOA increased in both soils with NBPT addition. For acid soil, N2O emissions were significantly correlated with both abundances and community structures of AOA and ureC-containing bacteria, as well as abundance of AOB; for alkaline soil, abundances and community structures of AOB were correlated with N2O emission, as well as community structures of ureC-containing bacteria and archaea, indicating an inconsistent response pattern of community traits of N2O emissions-related functional guilds to NBPT between alkaline soil and acid soil. Our findings suggest that (i) efficacy of NBPT in N2O emission was mainly influenced by soil pH and (ii) variable effects of NBPT on N2O emission might originate not only from the direct effect of NBPT on community traits of urease-positive microbes, but from the indirect effect on ammonia oxidizers.

Effects of urease and nitrification inhibitors on the soil mineral nitrogen dynamics and nitrous oxide (N 2 O) emissions on calcareous soil

Urease inhibitors and nitrification inhibitors can reduce nitrogen (N) loss in agriculture soil. However, the effect of inhibitors on soil N2O emissions under the drip irrigation system remains unclear. A pot and a field experiment with two inhibitors were conducted to explore how inhibitors regulate soil nitrogen transformation and N2O emissions. In the pot experiment, three treatments included control, urea, and urea + N-(n-butyl)thiophosphoric triamide (NBPT, urease inhibitor). In the field experiment, three treatments included control, urea, and urea + NBPT + 2-chloro-6-(trichloromethyl)pyridine (nitrapyrin, nitrification inhibitor). The urease inhibition rate in the treatment of urea + NBPT was 27.5% at the 14th day of incubation (pot experiment), and NH4+-N was significantly decreased by 37–64% compared with urea alone treatment. In the field experiment, the nitrification inhibition rate in the treatment of urea + NBPT + nitrapyrin was 47.7 and 63.9% on the 3rd day after fertilization at the wheat heading and filling stages, respectively. Compared to urea treatment, NO3−-N concentration in the double-inhibitor-added treatment was significantly decreased by 32 and 20% on the 5th day after fertilization at the heading and filling stages, respectively; N2O fluxes were also decreased by 30.9 and 33.3% at the two stages of wheat, respectively. In total, adding an inhibitor reduced N loss by 7.39 and 7.44% at the 14th and 35th day in the pot experiment and by 10.53 and 6.65% at the two growing stages of wheat in the field experiment, respectively. Path and correlation analysis showed that N2O emissions were significantly correlated with soil NO3− in both pot and field experiments.

Endophytic bacterium Buttiauxella sp. SaSR13 improves plant growth and cadmium accumulation of hyperaccumulator Sedum alfredii

Inoculation with endophytic bacterium has been considered as a prospective application to improve the efficiency of phytoextraction. In this study, the effect of Buttiauxella sp. SaSR13 (SaSR13), a novel endophytic bacterium isolated from the root of hyperaccumulator Sedum alfredii, on plant growth and cadmium (Cd) accumulation in S. alfredii was investigated. Laser scanning confocal microscopic (LSCM) images showed that SaSR13 was mainly colonized in the root elongation and mature zones. The inoculation with SaSR13 to Cd-treated plants significantly enhanced plant growth (by 39 and 42% for shoot and root biomass, respectively), chlorophyll contents (by 38%), and Cd concentration in the shoot and root (by 32 and 22%, respectively). SaSR13 stimulated the development of roots (increased root length, surface area, and root tips number) due to an increase in the indole-3-acid (IAA) concentrations and a decrease in the concentrations of superoxide anion (O2.−) in plants grown under Cd stress. Furthermore, inoculation with SaSR13 enhanced the release of root exudates, especially malic acid and oxalic acid, which might have facilitated the uptake of Cd by S. alfredii. It is suggested that inoculation with endophytic bacterium SaSR13 is a promising bioaugmentation method to enhance the Cd phytoextraction efficiency by S. alfredii.