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  • RESEARCH ARTICLE
    Qirui An, Yunyang Li, Na Zheng, Jincai Ma, Shengnan Hou, Siyu Sun, Sujing Wang, Pengyang Li, Xiaoqian Li, Chunmei Zhao

    • The relative abundance of rhizosphere soil bacteria has significantly positive correlation with BCF of Cd and Cu.

    • Obvious variations of predominant species of bacterial communities in rhizosphere soil would emerge in the additions with different concentrations of Cd-Cu mixtures.

    • In the additions with Cd and Cu, the mean of rhizosphere soil bacterial community diversity index was ranked as: Cu alone>Cd-Cu mixtures>Cd pollution.

    • The PCA and PERMANOVA analysis showed that Cu may be the main factor changing the composition of rhizosphere soil bacteria.

    To study the effects of combined Cd and Cu pollution on rhizosphere bacterial community. High-throughput sequencing was used to examine the response of rhizosphere bacterial communities to heavy-metal stress under single and mixed pollution of cadmium (Cd) and copper (Cu). With additions of Cd and Cu, the mean diversity index of rhizosphere bacterial community was in the order Cu alone>Cd-Cu mixtures>Cd alone. In all Cd and Cu treatments, the dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi and Acidobacteria. In the additions with different concentrations of Cd-Cu mixtures, LEfSe indicated that there were differences in the predominant species of rhizosphere bacterial communities. Some genera such as Streptomyces and Microbacterium belonging to Actinobacteria as biomarkers were significantly enriched in both control and treatments, while some genera such as Pseudoxanthomonas and Rhodopseudomonas belonging to Proteobacteria as biomarkers were observed to be enriched in the additions with single and mixture of Cd and Cu. According to the Nonmetric multidimensional scaling (NMDS) analysis, the structure of rhizosphere bacterial community was different between treatments and the CK. Principal Component Analysis (PCA) and permutational multivariate analysis of variance (PERMANOVA) showed that there were significant differences among treatments (p<0.01), and that the addition of Cu might be the primary factor affecting the composition of rhizosphere bacterial communities.

  • RESEARCH ARTICLE
    Juan Xue, Xue Wei, Haiyan Guo, Changting Wang, Pengfei Wu

    The alpine wetlands in the Qinghai-Tibetan Plateau have degraded in recent decades. However, the response of the soil food web to the degradation is still unclear. Four habitats including a wet meadow (WM), a grassland meadow (GM), a moderately degraded meadow (MDM) and a severely degraded meadow (SDM) (sandy meadows) were selected along the degrees of degradation. The soil macrofaunal biomass and the environmental factors of vegetation and soil were investigated. The soil macrofaunal community biomass increased significantly from WM to MDM and decreased to a very small amount in SDM, with most taxa disappearing. The biomass of the trophic groups of detritivores, herbivores and predators exhibited similar responses to soil macrofaunal communities. The relative biomass of detritivores increased from WM to MDM, but herbivores responded in an opposite manner, resulting in the dominant trophic group and trophic structure varying progressively from WM to GM to MDM. Soil properties but not vegetation determined the changes in trophic groups and trophic structure. The results implied that the higher trophic levels (carnivores or omnivores) responded more sensitively than the lower trophic levels (herbivores) to alpine wetland degradation. Our results also suggested that soil macrofauna have a habitat-specific characteristic trophic structure and can be used as indicators of soil health conditions.

  • RESEARCH ARTICLE
    Lin Mei, Yihong Yue, Yong Qin, Xueping Chen, Fushun Wang

    • A calibration models for the rapid determination of TOC and TN contents using FTIRS.

    • Ÿ A rapid analytical method for quantitatively calculating TOC and TN.

    Ÿ• A general model for TOC and TN quantitative analysis in reservoir sediments in the southwest China.

    This study aims to quantitatively assess the total organic carbon (TOC) and total nitrogen (TN) content of reservoir sediments in southwest China using Fourier transform infrared spectroscopy (FTIRS). FTIRS measurements were performed on 187 sediment samples from four reservoirs to develop calibration models that relate FTIR spectral information with conventional property concentrations using partial least squares regression (PLSR). Robust calibration models were established for TOC and TN content. The external validation of these models yielded a significant correlation between FTIR-inferred and conventionally measured concentrations of R2 = 0.88 for TOC, R2 = 0.90 for TN. This method can be performed with a small sample size and is non-destructive throughout the simple measurement process. The TOC and TN content in the sediment can be determined with high effectiveness without being overly expensive, making it an advantageous method when measuring a large number of samples.

  • RESEARCH ARTICLE
    Yali Wang, Yinsheng Li, Hongpei Geng, Qian Zuo, Michelle Thunders, Jiangping Qiu

    Ÿ 24 differentially expressed proteins (DEPs) were identified by proteomic method.

    Ÿ DEPs function as metabolism, signal transduction, stress-related and transport etc.

    Ÿ Proteomics of As exposure help to explore its toxicity mechanism in earthworm.

    Arsenic (As) is broadly distributed due to natural and anthropogenic sources, and it is toxic to organisms. This study aimed to investigate the proteomic response in earthworm exposed to As3+ . Earthworms were exposed to As3+ in soil at 5–80 mg kg–1, and samples were collected after 60 days exposure. Two-dimensional electrophoresis (2-DE) was used to separate the proteins in earthworm homogenate, then differentially expressed proteins (DEPs) were identified using MALDI-TOF/TOF-MS analysis. After 2-DE, 36 DEPs were found and 24 of them were successfully identified. 79.2% of DEPs were upregulated compared to the control group. The maximum fold change reached 53.8 in spot 3108 in the 80 mg kg–1 As group. Two proteins were not found in the control group but found in the As treated groups. Proteins were grouped into metabolism, signal transduction, stress-related, transport, regulation, and predicted/hypothetical protein categories based on their function. The protein–protein interaction between the DEPs indicated that serum albumin (ALB) is very important, related to 6 other proteins. Proteins were then verified by western blot, the results were in agreement with the proteomic analyses. The identification of induced or repressed proteins because of As3+ in earthworms is helpful to explore the underlying mechanisms of soil arsenic ecotoxicity.

  • RESEARCH ARTICLE
    Xiaojing Hu, Haidong Gu, Junjie Liu, Baoku Zhou, Dan Wei, Xueli Chen, Guanghua Wang

    • Fungal communities were more sensitive to N fertilizers than P, K fertilizers.

    • More harmonious and stable fungal network induced by P, K fertilizers.

    • N fertilizers induced lower fungal community resistance with detriments on crop yields.

    Nitrogen (N), phosphate (P), and potassium (K) are the three most important nutrients applied into agricultural soils, but the impacts of their single or combined application on soil fungal community structure and stability are still open questions. Using qPCR and Illumina Miseq sequencing, the variation of soil fungal communities in response to long-term addition of N, P, or K fertilization alone and their combinations in a Mollisol field was investigated in this study. In addition, the fungal community resistance indices and network structure were studied. Results showed that N fertilizations (N, NK, NP and NPK treatments) rather than P, K fertilizations (P, K and PK treatments) significantly increased fungal abundance, but decreased fungal diversity and shifted fungal community structures when compared to non-fertilization (NoF). Additionally, N fertilization treatments presented lower resistance of fungal communities to environment disturbances than those of P, K fertilization treatments. More numbers and higher abundances of changed fungal taxa at the genus and OTU levels were induced by N fertilizations rather than by addition of P, K fertilizers. In addition, N fertilizations induced a more changeable fungal network and complex pathogenic subnetwork with many positive interactions among responding plant pathogens (RP, the changeable plant pathogens induced by fertilizers addition compared to NoF) when compared to P, K fertilizations. These RP directly and negatively influenced fungal community resistance examined by structural equation modeling (SEM), which were indirectly detrimental to soybean yields. Our findings revealed that addition of N fertilizers significantly disturbed fungal communities and promoted pathogenic interactions, and provided insights into the optimization of fertilization strategies toward agricultural sustainability.

  • RESEARCH ARTICLE
    Haojie Feng, Hong Pan, Chengliang Li, Yuping Zhuge

    • Both organic and inorganic fertilizations stimulate soil aggregation.

    • Organic and inorganic fertilizers enhance organic carbon storage at aggregate scale.

    • Aggregate-associated bacterial communities were more sensitive to organic fertilizers than to chemical ones.

    • The complexity of bacterial network structures decreased with decreasing of aggregate size.

    • The competitive interactions among bacterial communities were intensified with decreasing of aggregate size.

    Differently sized soil aggregates, with non-uniform distribution of space and nutrients, provide spatially heterogeneous microenvironments for microorganisms and are important for controlling microbial community ecology and biogeochemistry in soils. Here, we investigated the prokaryotic communities within different aggregate-size fractions: macroaggregate (>0.25 mm), microaggregate (0.053–0.25 mm) and silt+ clay (<0.053 mm). These were isolated from fluvo-aquic soils under 39-year fertilization strategies: no fertilizer (CK), chemical fertilizer (NPK), manure fertilizer (M), and combination of manure and chemical fertilizers (MNPK). The results showed that the proportion of macroaggregate, soil aggregate-associated organic carbon (SOC) content and aggregate stability were all significantly increased by both manure and chemical fertilizations. Organic fertilizations (M and MNPK) more effectively boosted formation and stability of macroaggregates and enhanced SOC concentration than NPK. The distribution patterns of microorganisms in aggregates were primarily shaped by fertilization and aggregate size. They explained 76.9% of the variance in bacterial community compositions. Fertilizations, especially with organic fertilizers primarily transitioned bacterial communities from slow-growing oligotrophic groups (e.g., Chloroflexi) dominance to fast-growing copiotrophic groups (e.g., Proteobacteria and Bacteroidetes) dominance across all aggregate sizes. Macroaggregates possessed a more stable bacterial community and efficiency of resource transfer, while smaller aggregates increased antagonism and weakened mutualism among bacterial communities. Overall, combination of manure and chemical fertilizers was crucial for increasing SOC content and aggregation, leading to a clear shift in bacterial community structures at aggregate scale.

  • RESEARCH ARTICLE
    Yuanze Li, Huakun Zhou, Wenjing Chen, Yang Wu, LeiLei Qiao, ZiRan Yan, GuoBin Liu, Sha Xue

    •No notable effect from long-term warming on activity of nutrient-acquiring enzymes.

    •Long-term warming does not notably affect enzymatic stoichiometry.

    •Significant, positive correlation between ecoenzyme activity and soil nutrients, microbial biomass.

    •Phosphorus limitation found for all soil microbes at different depths.

    Microbes play an important role in the carbon cycle and nutrient flow of the soil ecosystem. However, the response of microbial activities to long-term warming over decades is poorly understood. To determine how warming changes ecoenzyme activity and microbial nutrient limitation, we conducted a long-term, 21 years, experiment, on the Qinghai–Tibet Plateau. We selected typical grass- and shrub-covered plots, used fiberglass open-top chambers (OTCs) to raise the temperature, conducted soil sampling at different depths, studied the response of nutrient-acquiring enzyme activity and stoichiometry, and conducted vector analysis of stoichiometry. Our results showed that long-term warming did not have a notable effect on the activity of nutrient-acquiring enzymes or enzymatic stoichiometry. However, Spearman correlation analysis indicated a significant and positive correlation between ecoenzyme activity and the available nutrients and microbial biomass in soil. Vector analysis of stoichiometry showed phosphorus limitation for all soil microbes at different depths, regardless of whether the soil experienced warming. These changes in enzymatic stoichiometry and vector analysis suggested that microbial nutrient limitation was not alleviated substantially by long-term warming, and warming did not considerably affect the stratification of microbial nutrient limitation. Our research has also shown that long-term warming does not significantly change soil ecoenzyme activity and original microbial nutrient limitation at different soil depths within the OTUsʼ impact range. These results could help improve understanding of microbial thermal acclimation and response to future long-term global warming.

  • RESEARCH ARTICLE
    Pengshuai Shao, Tian Li, Kaikai Dong, Hongjun Yang, Jingkuan Sun

    • SIC was higher at a low salinity of<6‰, and declined with increased salinity.

    • SOC and microbial residues exponentially decreased during increasing salinity.

    • Microbial residues and SOC was tightly related to the variations in SIC.

    • Microbial residues act as the proxy converting SIC to SOC in saline lands.

    Soil inorganic carbon (SIC), including mainly carbonate, is a key component of terrestrial soil C pool. Autotrophic microorganisms can assimilate carbonate as the main or unique C source, how microorganisms convert SIC to soil organic carbon (SOC) remains unclear. A systematic field survey (n = 94) was performed to evaluate the shift in soil C components (i.e., SIC, SOC, and microbial residues) along a natural salinity gradient (ranging from 0.5‰ to 19‰), and further to explore how microbial necromass as an indicator converting SIC into SOC in the Yellow River delta. We observed that SIC levels linearly decreased with increasing salinity, ranging from ~12 g kg−1 (salinity<6‰) to ~10 g kg−1 (salinity >6‰). Additionally, the concentrations of SOC and microbial residues exponentially decreased from salinity<6‰ to salinity >6‰, with the decline of 39% and 70%, respectively. Microbial residues and SOC was tightly related to the variations in SIC. The structural equation model showed the causality on explanation of SOC variations with SIC through microbial residues, which can contribute 89% of the variance in SOC storage combined with SIC. Taken together, these two statistical analyses can support that microbial residues can serve as an indicator of SIC transition to SOC. This study highlights the regulation of microbial residues in SIC cycling, enhancing the role of SIC playing in C biogeochemical cycles and enriching organic C reservoirs in coastal saline soils.

  • RESEARCH ARTICLE
    Zhijie Li, Rüdiger Reichel, Zimin Li, Kaijun Yang, Li Zhang, Bo Tan, Rui Yin, Kerui Zhao, Zhenfeng Xu

    • Snow absence increased soil N availabilities within soil aggregates.

    • Snow absence did not change net N mineralization rate within soil aggregates.

    • Soil enzyme activities affected by snow were different within soil aggregates.

    Winter climate change has great potential to affect the functioning of terrestrial ecosystems. In particular, increased soil frost associated with reduced insulating snow cover may impact the soil nitrogen (N) dynamics in cold ecosystems, but little is known about the variability of these effects among the soil aggregates. A snow manipulation experiment was conducted to investigate the effects of snow absence on N cycling within soil aggregates in a spruce forest on the eastern Tibetan Plateau of China. The extractable soil available N (ammonium and nitrate), net N mineralization rate, and N cycling-related enzyme activities (urease, nitrate reductase, and nitrite reductase) were measured in large macroaggregate (>2 mm), small macroaggregate (0.25–2 mm), and microaggregate (<0.25 mm) during the early thawing period in the years of 2016 and 2017. Snow absence increased soil N availabilities and nitrite reductase activity in microaggregate, but did not affect net N mineralization rate, urease or nitrate reductase activities in any of the aggregate fractions. Regardless of snow manipulations, both soil inorganic N and nitrate reductase were higher in small macroaggregate than in the other two fractions. The effect of aggregate size and sampling year was significant on soil mineral N, net N mineralization rate, and nitrite reductase activity. Our results indicated that snow cover change exerts the largest impact on soil N cycling within microaggregate, and its effect is dependent on winter conditions (e.g., snow cover and temperature). Such findings have important implications for soil N cycling in snow-covered subalpine forests experiencing pronounced winter climate change.

  • RESEARCH ARTICLE
    Jie Zhao, Kelin Wang

    • Soil nematode samples can be quite turbid, which are not satisfactory for microscopy.

    • Three methods were designed for cleaning turbid nematode suspensions.

    • Nematode abundance did not significantly differ among control and the three methods.

    • Repeated centrifugation had slightly higher recovery rate of nematodes than the other methods.

    Soil nematodes are useful ecological indicators and can be extracted from soil by a variety of techniques. Because the extracted nematode samples (suspensions) can be quite turbid (i.e., they contain soil particles and organic particles in addition to nematodes), quantitative and taxonomic analyses of the nematodes by microscopy can be difficult. In this study, the following three methods for cleaning turbid suspensions obtained from Baermann funnels were assessed: repeated centrifugation at 692.5 ´g for 1 min, repeated settling at low-temperature (4°C) for 24 h, and a combination of low-temperature settling and centrifugation. Nematodes were extracted with Baermann funnels from soil samples collected from four land-use types (since land-use type can affect the turbidity of nematode suspensions), and the resulting suspensions were cleaned by the three methods before nematode abundance was assessed. As a control, samples (i.e., suspensions) were simply diluted with water, and nematodes were counted in the entire volume. The results showed that, within each land-use type, nematode abundance did not significantly differ between the control and the three cleaning methods. Averaged across all land-use types, however, the nematode recovery rate was slightly higher with repeated centrifugation than with the other two cleaning methods. Therefore, the proposed methods are sound for cleaning turbid nematode suspensions, and repeated centrifugation is the most efficient method.