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Since toxic element pollution is widespread in soils near gold mines due to increasing mining activities, the adverse effects of potentially toxic elements (PTEs) in the soils on ecological systems and human health cannot be ignored. However, assessments of PTE pollution in soils and their ecological-health risks on a national scale are still limited. Here, the concentrations of eight PTEs in soils near gold mines throughout China were obtained from published articles. Based on these data, the pollution levels and ecological-health risks of the eight PTEs in soils were comprehensively estimated. The results showed that the average contents of As, Cr, Cd, Pb, Hg, Cu, Ni, and Zn were 81.62, 79.82, 1.04, 206.03, 2.05, 40.82, 71.82, and 130.42 mg kg

Variation in soil microbial metabolism remains highly uncertain in predicting soil carbon (C) sequestration, and is particularly and poorly understood in agroecosystem with high soil phosphorus (P) variability. This study quantified metabolic limitation of microbes and their association with carbon use efficiency (CUE) via extracellular enzymatic stoichiometry and biogeochemical equilibrium models in field experiment employing five inorganic P gradients (0, 75, 150, 225, and 300 kg P ha−1) in farmland used to grow peas. Results showed P fertilization significantly increased soil Olsen-P and NO3−-N contents, and enzyme activities (β-1,4-glucosidase and β-D-cellobiosidase) were significantly affected by P fertilization. It indicated that P fertilization significantly decreased microbial P limitation due to the increase of soil available P. Interestingly, P application also significantly decreased microbial nitrogen (N) limitation, a phenomenon primarily attributable to increasing NO3−-N content via increasing biological N fixation within the pea field. Furthermore, P fertilization increased microbial CUE because the reduction in microbial N and P limitation leads to higher C allocation to microbial growth. Partial least squares path modeling (PLS-PM) further revealed that the reduction of microbial metabolic limitation is conducive to soil C sequestration. Our study revealed that P application in agroecosystem can alleviate not only microbial P limitation but also N limitation, which further reduces soil C loss via increasing microbial CUE. This study provides important insight into better understanding the mechanisms whereby fertilization mediates soil C cycling driven by microbial metabolism in agricultural ecosystems.

Soil enzyme activities have been suggested as suitable indicators for the evaluation of metal contamination because they are susceptible to microbial changes caused by heavy metal stress and are strictly related to soil nutrient cycles. However, there is a growing lack of recognition and summary of the historic advancements that use soil enzymology as the proposal of evaluation methods. Here, we review the most common methods of heavy metal pollution evaluation based on enzyme activities, which include single enzyme index, combined enzyme index, enzyme-based functional diversity index, microbiological stress index, and ecoenzymatic stoichiometry models. This review critically examines the advantages and disadvantages of these methods based on their execution complexity, performance, and ecological implications and gets a glimpse of avenues to come to improved future evaluation systems. Indices based on a single enzyme are variable and have no consistent response to soil heavy metals, and the following three composite indices are characterized by the loss of many critical microbial processes, which thus not conducive to reflect the effects of heavy metals on soil ecosystems. Considering the dexterity of ecoenzymatic stoichiometry methods in reflecting changes in soil functions under heavy metal stress, we propose that microbial metabolic limitations quantified by ecoenzymatic stoichiometry models could be promising indicators for enhancing the reality and acceptance of results and further improving the potential for actual utility in environmental decision-making.

Heavy metals can exist in soil for a long time and seriously affect soil quality. The coexistence of various heavy metal pollutants leads to biotoxicity and alters the activity of microorganisms. Soil microbial metabolism plays an important role in nutrient cycling and biochemical processes of soil ecosystem. However, the effects of heavy metal contamination on microbial metabolism in soil are still unclear. This study aims to reveal the responses of microbial metabolic limitation to heavy metals using extracellular enzyme stoichiometry, and further to evaluate the potential impacts of heavy metal pollution on soil nutrient cycle. The results showed that soil microbial metabolism reflected by the ecoenzymatic activities had a significant response to soil heavy metals pollution. The metabolism was limited by soil carbon (C) and phosphorus (P) under varied heavy metal levels, and the increase of heavy metal concentration significantly increased the microbial C limitation, while had no effect on microbial P limitation. Microorganisms may increase the energy investment in metabolism to resist heavy metal stress and thus induce C release. The results suggest that energy metabolism selected by microorganisms in response to long-term heavy metal stress could increase soil C release, which is not conducive to the soil C sequestration. Our study emphasizes that ecoenzymatic stoichiometry could be a promising methodology for evaluating the toxicity of heavy metal pollution and its ecological effects on nutrient cycling.

Tea gardens, being a key agroecosystem type, are an important source of nitrous oxide (N2O) emissions. However, main factors that regulate N2O emissions following urea and organic matter amendments have yet to be clarified. To investigate the influence of different fertilization management measures on N2O emissions in tea garden soil, a 50-day laboratory incubation experiment was conducted. Five treatments were designed for this experiment: control (CK), urea (U), rapeseed cake (R), urea + rapeseed cake (2:1, UR1), and urea + rapeseed cake (1:2, UR2). N2O emission flux in the R treatment peaked at 14.12 μg kg−1 h−1 on day 19, which occurred later than the UR1, UR2, and U treatments. Cumulative N2O emissions from the R and UR2 treatments were 6073 and 4296 μg kg−1, respectively, which were greater by a factor of 11.2 and 7.9, respectively, compared to the U treatment. Moreover, N2O emissions of the UR1 and UR2 treatments were significantly lower than the R treatment. Additionally, N2O emissions were also significantly positively correlated to pH levels and microbial biomass carbon (MBC) content. MBC content had the most direct and greatest influence on soil N2O emissions, indicating that MBC could be the key limiting factor for N2O emissions in this experiment. A single application of rapeseed cake caused an increase in N2O emissions, whereas the combined application of rapeseed cake and a synthetic N fertilizer (urea) caused a decrease in N2O emissions. Results from this study offer potential strategies to mitigate soil N2O emissions from tea garden agroecosystems through improved field fertilization management.

High plant diversity is usually linked with high soil microbial diversity, which is hypothesized to be attributed to a high diversity of components in the soil leachate, but experimental evidence is scarce. The aim of this study was to determine if the variation in soil leachate caused by plant diversity could affect the soil microbial community. A microcosm experiment was conducted to determine the effect of plant diversity on the soil microbial community by measuring soil leachate in a gradient of plant richness from levels 1 (one species) to 3 (three species). Plant richness significantly affected the diversity of soil leachate and microbial communities. The amount and diversity of soil leachate, microbial biomass carbon (C), basal respiration, β-1,4-glucosidase activity, β-1,4-N-acetylglucosaminidase activity, bacterial biomass, fungal biomass, total microorganism biomass, and microbial diversity (Shannon diversity index and evenness) were highest at richness level 3. Changes in the microbial community were best explained by variation in the amount and diversity of leachate. Linear regression and correlation analyses indicated that leachate diversity had a close association with microbial Shannon diversity and evenness, whereas leachate amount had a close association with microbial biomass C, total microbial biomass, bacterial biomass, enzyme activities, and abundance of microbial groups. An ordinary least squares multiple regression and the structural equation model demonstrated that leachate amount had a greater effect on microbial biomass than leachate diversity, which had a greater impact on microbial Shannon diversity and evenness. Our results indicate that plant diversity drives changes in soil microbial communities by altering the amount and diversity of leachate in the soil. The diversity of soil leachate determined the diversity of the microbial community to some extent.

Soil microbial communities play critical function during nutrient cycling. However, with the increasing nutrient input into terrestrial ecosystems from human activities, the responses of soil microorganisms to the aboveground vegetation across agricultural-to-natural succession stages are still poorly understand. The aim of this study was to evaluate the changes of soil microbial communities in three typical succession stages (the cropland, the grassland, and the brushland, respectively). A field experiment was carried out in an ecological restoration region. Soil samples were collected from three succession stages (the cropland, the grassland, and the brushland) based on their well-dated successional chronosequence in July 2016. Illumina MiSeq sequencing was used to identify the bacterial community structures. The responses of soil bacterial communities and its relationships with soil physicochemical properties and enzyme activities were assessed. The results showed that soil nutrients (soil organic carbon (SOC), total N, and NH4+) and enzyme activities (β-1,4-glucosidase and phosphatase) were significantly increased across the conversion from agricultural to natural ecosystem, and the enzyme activities were significantly affected by SOC and total N. It indicated that vegetation restoration greatly improved soil quality and nutrient cycling rates mediated by microbial metabolisms. Furthermore, there were no changes in soil bacterial community structures during the three vegetation succession stages, which implied the stability and adaption of microbial communities under the vegetation succession in semiarid climate. It should be noted that Firmicutes taxa were more sensitive than other taxa during natural vegetation recovery. Structural equation model (SEM) revealed that soil nutrients (soil organic matter (SOM) and total P), element stoichiometry (SOC:total P), and extracellular enzyme activities (urease and alkaline phosphatase) were dominant factors to shape the relative abundance of Firmicutes. Firmicutes can be considered as bio-indicators to monitor soil quality and nutrient turnover during natural vegetation recovery. This study presents better understanding about the connections among soil nutrient cycling, enzyme activities, and soil bacterial communities during vegetation natural restoration, especially in typical ecological critical zone.

Enzymes in the soil are useful for assessing heavy metal soil pollution. We analyzed the activity of a number of enzymes, including urease, protease, catalase, and alkaline phosphatase, in three types of land (farmland, woodland, and grassland) to evaluate soil pollution by heavy metals (Pb, Zn, and Cd). Our results showed that the tested soil was polluted by a combination of Pb, Zn, and Cd, but the primary pollutant was Cd. An ecological dose analysis demonstrated that urease was the most sensitive enzyme to Pb and Cd in the farmland, and catalase and phosphatase were the most sensitive enzymes to Pb, Zn, and Cd in the woodland and grassland. The ecological risk of Cd (E Cd ) was the smallest in all three types of land, suggesting that Cd was the major metal inhibiting enzyme activity. Electrical conductivity (EC) was shown to be a negative regulator, while nitrogen, phosphorus, and clay contents were positive regulators of soil enzyme activity. The total enzyme index (TEI) inhibition rates in the woodland were 22.2 and 38.6% under moderate and heavy pollution, respectively, which were lower than those of the other two types of land. Therefore, woodlands might be the optimum land use choice in relieving heavy metal pollution. Taken together, this study identified the key metal pollutant inhibiting soil enzyme activity and suitable land use patterns around typical metal mine. These results provide possible improvement strategies to the phytomanagement of metal-contaminated land around world.

Biodegradable chelant-enhanced phytoremediation offers an alternative treatment technique for metal contaminated soils, but most studies to date have addressed on phytoextraction efficiency rather than comprehensive understanding of the interactions among plant, soil microbes, and biodegradable chelants. In the present study, we investigated the impacts of biodegradable chelants, including nitrilotriacetate, S,S-ethylenediaminedisuccinic acid (EDDS), and citric acid on soil microbes, nitrogen transformation, and metal removal from contaminated soils. The EDDS addition to soil showed the strongest ability to promote the nitrogen cycling in soil, ryegrass tissue, and microbial metabolism in comparison with other chelants. Both bacterial community-level physiological profiles and soil mass specific heat rates demonstrated that soil microbial activity was inhibited after the EDDS application (between day 2 and 10), but this effect completely vanished on day 30, indicating the revitalization of microbial activity and community structure in the soil system. The results of quantitative real-time PCR revealed that the EDDS application stimulated denitrification in soil by increasing nitrite reductase genes, especially nirS. These new findings demonstrated that the nitrogen release capacity of biodegradable chelants plays an important role in accelerating nitrogen transformation, enhancing soil microbial structure and activity, and improving phytoextraction efficiency in contaminated soil.

VaPAT1 functions as a stress-inducible GRAS gene and enhanced cold, drought and salt tolerance in transgenic Arabidopsis via modulation of the expression of a series of stress-related genes. The plant-specific GRAS transcription factor family regulates diverse processes involved in plant growth, development and stress responses. In this study, VaPAT1, a GRAS gene from Vitis amurensis was isolated and functionally characterized. Sequence alignment and phylogenetic analysis showed that VaPAT1 has a high sequence identity to CmsGRAS and OsCIGR1, which belong to PAT1 branch of GRAS family and function in stress resistance. The transcription of VaPAT1 was markedly induced by stress-related phytohormone abscisic acid (ABA) and various abiotic stress treatments such as cold, drought and high salinity, however, it was repressed by exogenous gibberellic acid (GA) application. Overexpression of VaPAT1 increased the cold, drought and high salinity tolerance in transgenic Arabidopsis. When compared with wild type (WT) seedlings, the VaPAT1-overexpression lines accumulated higher levels of proline and soluble sugar under these stress treatments. Moreover, stress-related genes such as AtSIZ1, AtCBF1, AtATR1/MYB34, AtMYC2, AtCOR15A, AtRD29A and AtRD29B showed higher expression levels in VaPAT1 transgenic lines than in WT Arabidopsis under normal growth conditions. Together, our results indicated that VaPAT1 functions as a positive transcriptional regulator involved in grapevine abiotic stress responses.

The sorption mechanism of nickel (Ni) at the illite/water interface was investigated using batch, sorption modelling, extended X-ray absorption fine structure (EXAFS), and extraction approaches. The results showed that Ni(II) sorption on illite was strongly dependent on pH, contact time, temperature, and initial Ni(II) concentration. At a low initial Ni(II) concentration, the ion exchange species of ≡X2Ni° and the inner-sphere complexes including ≡SsONi+, ≡SwONi+ and ≡SwONiOH° species are observed on the sorption edges of Ni(II) on illite. As the initial Ni(II) concentration increased to 1.7 × 10−3 mol/L, precipitates including surface-induced precipitation of s-Ni(OH)2 and amorphous Ni(OH)2 became more significant, especially under neutral to alkaline conditions. EXAFS analysis confirmed that Ni-Al layered double hydroxide (LDH) can gradually form with an increase in the contact time. At pH 7.0, α-Ni(OH)2 was produced in the initial stage and then transformed to the more stable form of Ni-Al LDH with increasing contact time because of the increased Al3+ dissolution. With an increase in temperatures, α-Ni(OH)2 phase on illite transformed to Ni-Al LDH phase, indicating a lower thermodynamic stability compared to Ni-Al LDH phase. These results are important to understand the geochemical behaviors to effectively remediate soil contaminated with Ni(II).

Long non-coding RNAs (lncRNAs) were found to widely exist in eukaryotes and play important roles in most biological processes. Trees belonging to Populus spp. are economically important because of their fast-growing characteristics and wide use for wood, pulp, paper, and fuel. However, the prevalence of leaf rust disease caused by Melampsora spp. on some species of Populus severely affects their growth and decreases wood production. Therefore, the identification and characterization of lncRNAs involved in the defense of Melampsora spp. would not only help us to understand plant-pathogen interactions but also provide genetic elements for producing disease-resistant poplars. In the present study, an RNA-Seq transcriptome analysis was performed for poplar leaves in response to early infection by M. larici-populina. The hybrid variety “NL895” (P. × euramericana) was used as plant material. A total of 3994 lncRNAs were identified by mining the RNA-Seq data. The identified lncRNAs had lower abundance, fewer exons, and shorter lengths when compared to protein-coding genes. In addition, 53 lncRNAs were differentially expressed between treatments and controls. Two of these 53 lncRNAs were predicted to compete to be the target of miRNAs. Moreover, the differentially expressed lncRNAs were found to be preferentially located in close proximity to the protein-coding genes they co-expressed. In this study, we were able to show that lncRNAs may play important roles in plant-pathogen interactions in the poplar. This study also improves our understanding of how plants deploy their defense system when encountering biotic stresses.

Grapevine is an important fruit crop that has undergone a long history of evolution. Analysis of the whole genome sequence of grapevine has revealed presence of an early palaeo-hexaploid along with three complements. Thus, gene duplication and genome expansion are common in this genome. In this study, we identified 17,922 duplicated genes in the whole grapevine genome. Among these, 2,039; 628; 1,428; 722; and 2,942 were identified respectively as produced by genome-wide, tandem, proximal, retrotransposed, and DNA-based transposed duplications. Analyses of the evolutionary patterns for different types of duplication using non-synonymous and synonymous substitution rates uncovered a series of underlying rules. Thereafter, all the grapevine genes were classified into families, and the contributions of different types of duplication to the expansion of large families were revealed. No duplication type was solely responsible for the formation of any large gene family, but some families showed enrichment of a special type of duplication. On the basis of this study, we believe that uncovering the underlying rules for gene duplications, expansions of gene families, and their evolutionary styles will contribute significantly to a comprehensive understanding of the features of the grapevine genome.