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Microorganisms are the main drivers of MeHg production and degradation in the environment. However, little attention has been paid to the simultaneous investigation of the diversities of microbial MeHg producers and degraders in a given habitat.

Osteoarthritis (OA) is a multifactorial and chronic degenerative joint disease. Due to the adverse effects of currently used drugs, a safer and more effective therapy for treating OA is needed. Peroxisome proliferator-activated receptor-γ (PPARγ) is a key protein protecting cartilage. DNMT1-mediated hypermethylation of PPARγ promoter leads to its suppression. Therefore, DNMT1 might be an effective target for exerting cartilage protective effects by regulating the epigenetic expression of PPARγ. Dabushen decoction (DD) is a representative prescription of Dunhuang ancient medical prescription, which has a potential therapeutic effect on OA. So far, the research of the efficacy and material basis of DD in the treatment of OA remains unclear. In this study, Micro-CT, HE staining, S-O staining, and immunohistochemistry analysis were used to demonstrate that DD increased the expression of PPARγ and collagen synthesis in an OA rat model. Next, the structure of DNMT1 was used to screen the active constituents of DD by molecular docking method for treatment OA. Seven potential active constituents, including isoliquiritigenin, emodin, taxifolin, catalpol, alisol A, zingerone, and schisandrin C were hited. The protective effect of the potential active constituents to chondrocytes were evaluated by protein capillary electrophoresis, immunofluorescence assays, and ex vivo culture of rat knee cartilage. The five constituents, such as alisol A, emodin, taxifolin, isoliquiritigenin, and schisandrin C could promote the expression of PPARγ and ameliorate IL-1β-induced downregulation of collagen II and the production of MMP-13. Alisol A and Emodin could effectively mitigate cartilage damage. At last, molecular dynamics simulations with MM-GBSA method was applied to investigate the interaction pattern of the active constituents and DNMT1 complexes. The five constituents, such as alisol A, emodin, taxifolin, isoliquiritigenin, and schisandrin C achieved a stable binding pattern with DNMT1, in which alisol A has a relatively high binding free energy. In conclusion, this study elucidates that the active constituents of DD (alisol A, emodin, taxifolin, isoliquiritigenin, and schisandrin C) could ameliorate osteoarthritis via PPARγ preservation by targeting DNMT1.These findings facilitated clinical use of DD and provided a valuable strategy for developing natural epigenetic modulators from Chinese herbal formula.

Metalliferous mine tailings ponds are generally characterized by low levels of nutrient elements, sustained acidic conditions, and high contents of toxic metals. They represent one kind of extreme environments that are believed to resemble the Earth's early environmental conditions. There is increasing evidence that the diversity of fungi inhabiting mine tailings ponds is much higher than previously thought. However, little is known about functional guilds, community assembly, and co-occurrence patterns of fungi in such habitats. As a first attempt to address this critical knowledge gap, we employed high-throughput sequencing to characterize fungal communities in 33 mine tailings ponds distributed across 18 provinces of mainland China. A total of 5842 fungal phylotypes were identified, with saprotrophic fungi being the major functional guild. The predictors of fungal diversity in whole community and sub-communities differed considerably. Community assembly of the whole fungal community and individual functional guilds were primarily governed by stochastic processes. Total soil nitrogen and total phosphorus mediated the balance between stochastic and deterministic processes of the fungal community assembly. Co-occurrence network analysis uncovered a high modularity of the whole fungal community. The observed main modules largely consisted of saprotrophic fungi as well as various phylotypes that could not be assigned to known functional guilds. The richness of core fungal phylotypes, occupying vital positions in co-occurrence network, was positively correlated with edaphic properties such as soil enzyme activity. This indicates the important roles of core fungal phylotypes in soil organic matter decomposition and nutrient cycling. These findings improve our understanding of fungal ecology of extreme environments.

This study evaluated the effect of biochar and compost on physiochemical properties, heavy metal content, microbial biomass, enzyme activities, and plant growth in Pb-Zn mine tailings. In this study, a pot experiment was conducted to evaluate the effects of biochar, compost, and their combination on the availability of heavy metals, physicochemical features, and enzyme activities in mining soil. Compared to separate addition, the combined application of biochar and compost was more effective to improve soil pH, soil organic carbon (SOC), total nitrogen (TN), available phosphorus (AP), and potassium (AK). All amendments significantly decreased CaCl

The interaction between airway microbiome and host in chronic obstructive pulmonary disease (COPD) is poorly understood. Here we used a multi-omic meta-analysis approach to characterize the functional signature of airway microbiome in COPD. We retrieved all public COPD sputum microbiome datasets, totaling 1640 samples from 16S rRNA gene datasets and 26 samples from metagenomic datasets from across the world. We identified microbial taxonomic shifts using random effect meta-analysis and established a global classifier for COPD using 12 microbial genera. We inferred the metabolic potentials for the airway microbiome, established their molecular links to host targets, and explored their effects in a separate meta-analysis on 1340 public human airway transcriptome samples for COPD. 29.6% of differentially expressed human pathways were predicted to be targeted by microbiome metabolism. For inferred metabolite-host interactions, the flux of disease-modifying metabolites as predicted from host transcriptome was generally concordant with their predicted metabolic turnover in microbiome, suggesting a synergistic response between microbiome and host in COPD. The meta-analysis results were further validated by a pilot multi-omic study on 18 COPD patients and 10 controls, in which airway metagenome, metabolome, and host transcriptome were simultaneously characterized. 69.9% of the proposed "microbiome-metabolite-host" interaction links were validated in the independent multi-omic data. Butyrate, homocysteine, and palmitate were the microbial metabolites showing strongest interactions with COPD-associated host genes. Our meta-analysis uncovered functional properties of airway microbiome that interacted with COPD host gene signatures, and demonstrated the possibility of leveraging public multi-omic data to interrogate disease biology.

Mining is among the human activities with widest environmental impacts, and mining-impacted environments are characterized by high levels of metals that can co-select for antibiotic resistance genes (ARGs) in microorganisms. However, ARGs in mining-impacted environments are still poorly understood. Here, we conducted a comprehensive study of ARGs in such environments worldwide, taking advantage of 272 metagenomes generated from a global-scale data collection and two national sampling efforts in China. The average total abundance of the ARGs in globally distributed studied mine sites was 1572 times per gigabase, being rivaling that of urban sewage but much higher than that of freshwater sediments. Multidrug resistance genes accounted for 40% of the total ARG abundance, tended to co-occur with multimetal resistance genes, and were highly mobile (e.g. on average 16% occurring on plasmids). Among the 1848 high-quality metagenome-assembled genomes (MAGs), 85% carried at least one multidrug resistance gene plus one multimetal resistance gene. These high-quality ARG-carrying MAGs considerably expanded the phylogenetic diversity of ARG hosts, providing the first representatives of ARG-carrying MAGs for the Archaea domain and three bacterial phyla. Moreover, 54 high-quality ARG-carrying MAGs were identified as potential pathogens. Our findings suggest that mining-impacted environments worldwide are underexplored hotspots of multidrug resistance genes.

Mining-impacted environments are distributed globally and have become increasingly recognized as hotspots of antibiotic resistance genes (ARGs). However, there are currently no reports on treatment technologies to deal with such an important environmental problem. To narrow this knowledge gap, we implemented a phytostabilization project in an acidic copper mine tailings pond and employed metagenomics to explore ARG characteristics in the soil samples. Our results showed that phytostabilization decreased the total ARG abundance in 0-10 cm soil layer by 75 %, which was companied by a significant decrease in ARG mobility, and a significant increase in ARG diversity and microbial diversity. Phytostabilization was also found to drastically alter the ARG host composition and to significantly reduce the total abundance of virulence factor genes of ARG hosts. Soil nutrient status, heavy metal toxicity and SO

Low soil phosphorus (P) bioavailability causes the widespread occurrence of P-limited terrestrial ecosystems around the globe. Exploring the factors influencing soil P bioavailability at large spatial scales is critical for managing these ecosystems. However, previous studies have mostly focused on abiotic factors. In this study, we explored the effects of microbial factors on soil P bioavailability of terrestrial ecosystems using a country-scale sampling effort. Our results showed that soil microbial biomass carbon (MBC) and acid phosphatase were important predictors of soil P bioavailability of agro- and natural ecosystems across China although they appeared less important than total soil P. The two microbial factors had a positive effect on soil P bioavailability of both ecosystem types and were able to mediate the effects of several abiotic factors (e.g., mean annual temperature). Meanwhile, we revealed that soil phytase could affect soil P bioavailability at the country scale via ways similar to those of soil MBC and acid phosphatase, a pattern being more pronounced in agroecosystems than in natural ecosystems. Moreover, we obtained evidence for the positive effects of microbial genes encoding these enzymes on soil P bioavailability at the country scale although their effect sizes varied between the two ecosystem types. Taken together, this study demonstrated the remarkable effects of microbial factors on soil P bioavailability at a large spatial scale, highlighting the importance to consider microbial factors in managing the widespread P-limited terrestrial ecosystems.

Fungi in acid mine drainage (AMD) environments are of great concern due to their potentials of decomposing organic carbon, absorbing heavy metals and reducing AMD acidity. Based on morphological analysis and ITS/18S high-throughput sequencing technology, previous studies have provided deep insights into the diversity and community composition of fungi in AMD environments. However, knowledge about physiology, metabolic potential and transcriptome profiles of fungi inhabiting AMD environments is still scarce. Here, we reported the physiological, genomic, and transcriptomic characterization of Acidiella bohemica SYSU C17045 to improve our understanding of the physiological, genomic, and transcriptomic mechanisms underlying fungal adaptation to AMD environments. A. bohemica was isolated from an AMD environment, which has been proved to be an acidophilic fungus in this study. The surface of A. bohemica cultured in AMD solutions was covered with a large number of minerals such as jarosite. We thus inferred that the A. bohemica might have the potential of biologically induced mineralization. Taking advantage of PacBio single-molecule real-time sequencing, we obtained the high-quality genome sequences of A. bohemica (50 Mbp). To our knowledge, this was the first attempt to employ a third-generation sequencing technology to explore the genomic traits of fungi isolated from AMD environments. Moreover, our transcriptomic analysis revealed that a series of genes in the A. bohemica genome were related to its metabolic pathways of C, N, S, and Fe as well as its adaptation mechanisms, including the response to acid stress and the resistance to heavy metals. Overall, our physiological, genomic, and transcriptomic data provide a foundation for understanding the metabolic potential and adaptation mechanisms of fungi in AMD environments.

Phosphate-solubilizing microbes (PSMs) drive the biogeochemical cycling of phosphorus (P) and hold promise for sustainable agriculture. However, their global distribution, overall diversity and application potential remain unknown. Here, we present the first synthesis of their biogeography, diversity and utility, employing data from 399 papers published between 1981 and 2017, the results of a nationwide field survey in China consisting of 367 soil samples, and a genetic analysis of 12986 genome-sequenced prokaryotic strains. We show that at continental to global scales, the population density of PSMs in environmental samples is correlated with total P rather than pH. Remarkably, positive relationships exist between the population density of soil PSMs and available P, nitrate-nitrogen and dissolved organic carbon in soil, reflecting functional couplings between PSMs and microbes driving biogeochemical cycles of nitrogen and carbon. More than 2704 strains affiliated with at least nine archaeal, 88 fungal and 336 bacterial species were reported as PSMs. Only 2.59% of these strains have been tested for their efficiencies in improving crop growth or yield under field conditions, providing evidence that PSMs are more likely to exert positive effects on wheat growing in alkaline P-deficient soils. Our systematic genetic analysis reveals five promising PSM genera deserving much more attention.

Several abundant but yet uncultivated bacterial groups exist in extreme iron- and sulfur-rich environments, and the physiology, biodiversity, and ecological roles of these bacteria remain a mystery. Here we retrieved four metagenome-assembled genomes (MAGs) from an artificial acid mine drainage (AMD) system, and propose they belong to a new deltaproteobacterial order, Candidatus Acidulodesulfobacterales. The distribution pattern of Ca. Acidulodesulfobacterales in AMDs across Southeast China correlated strongly with ferrous iron. Reconstructed metabolic pathways and gene expression profiles showed that they were likely facultatively anaerobic autotrophs capable of nitrogen fixation. In addition to dissimilatory sulfate reduction, encoded by dsrAB, dsrD, dsrL, and dsrEFH genes, these microorganisms might also oxidize sulfide, depending on oxygen concentration and/or oxidation reduction potential. Several genes with homology to those involved in iron metabolism were also identified, suggesting their potential role in iron cycling. In addition, the expression of abundant resistance genes revealed the mechanisms of adaptation and response to the extreme environmental stresses endured by these organisms in the AMD environment. These findings shed light on the distribution, diversity, and potential ecological role of the new order Ca. Acidulodesulfobacterales in nature.

Objective To observe the effect of Qizhi Zhoufei granules on the expression of transforming growth factor-β1 (TGF-β1) and platelet-derived growth factor (PDGF) in lung tissue of rats with chronic obstructive pulmonary disease (COPD), and to explore the mechanism of the effect of Qizhi Zhoufei granules on airway inflammation and airway remodeling. Methods The COPD model was established in 60 SPF Wistar rats by intratracheal instillation of lipopolysaccharide (LPS) and smoking. Drug intervention began on the 29th day. The rats were randomly divided into blank group (N), model group (M), positive control group (D) and Qizhi Zhoufei granules high (HT), medium (MT) and low (LT) dose groups (10 rats in each group). On the 58th day, the changes of lung morphology were observed by hematoxylin eosin (HE) staining. The transcription level of TGF-β1, PDGF in rat lung tissue was detected by Q-PCR and the protein expression of TGF-β1, PDGF in rat lung tissue was detected by ELISA and Western blotting. Results Qizhi Zhoufei granules intervention group can improve the lung tissue pathological damage of COPD rats. Q-PCR showed that compared with control group, the expression of TGF-β1 mRNA (2.54±0.48), PDGF mRNA (2.07±0.39) in model group significantly higher than that in control group (P

Elevated arsenic (As) in soil is of public concern due to the carcinogenicity. Phosphorus (P) strongly influences the adsorption, absorption, transport, and transformation of As in the soil and in organisms due to the similarity of the chemical properties of P and As. In soil, P, particularly inorganic P, can release soil-retained As (mostly arsenate) by competing for adsorption sites. In plant and microbial systems, P usually reduces As (mainly arsenate) uptake and affects As biotransformation by competing for As transporters. The intensity and pattern of PAs interaction are highly dependent on the forms of As and P, and strongly influenced by various biotic and abiotic factors. An understanding of the PAs interaction in 'soil-plant-microbe' systems is of great value to prevent soil As from entering the human food chain. Here, we review PAs interactions and the main influential factors in soil, plant, and microbial subsystems and their effects on the As release, absorption, transformation, and transport in the 'soil-plant-microbe' system. We also analyze the application potential of P fertilization as a control for As pollution and suggest the research directions that need to be followed in the future.

Objective We proposed a modified triple incision technique (MTIT) for vulvar cancer patients with locally advanced disease and reported it in 2002. MTIT has gone through a series of modification and a modified MTIT (M-MTIT) came into being. The purpose of this study was to introduce M-MTIT and compare it with MTIT. Methods 57 vulvar cancer patients with clinical stage T2 (>4 cm) or T3 disease were included. Of them, 28 underwent MTIT and 29 underwent M-MTIT. Their data on surgery-related complications and survival outcomes were compared. Results The patients treated with M-MTIT developed significantly less surgery-related morbidities than patients treated with MTIT (24.1% vs. 60.7%, P = 0.005). Wound breakdown was the most common complication in our cohort, which occurred less frequently in the M-MTIT group than in the MTIT group (10.3% vs. 35.7%, P = 0.022). Multivariate logistic regression analysis identified M-MTIT as an independent predictor of reduced risk of wound breakdown. The incidence of other complications, including lymphedema, wound infection and cellulitis was lower in M-MTIT group than in MTIT group; however, the differences did not reach statistical significance. Median follow-up time of this study was 33 months. The Kaplan-Meier survival graphs did not show significant differences in recurrence-free survival and overall survival between the two groups. Conclusions M-MTIT correlates with lower morbidity rates and does not compromise oncological safety compared with MTIT. It could be considered as a safe and feasible option for vulvar cancer patients with locally advanced disease.

Objective To investigate whether CA125 normalization following neoadjuvant chemotherapy (NACT) can complement the chemotherapy response system (CRS) in the prognostication of patients with tubo-ovarian high-grade serous carcinoma (HGSC). Methods In total, 106 HGSC patients who received NACT followed by interval debulking surgery (IDS) for FIGO stage IIIC-IV disease were included, and their clinical data were retrospectively reviewed. The primary endpoint was progression-free survival (PFS). Cox regression analysis was performed to identify predictors of PFS. Results Following NACT, CRS3 was noted in 24 patients (22.6%), and CA125 normalization (≤ 35 U/ml) was noted in 54 patients (50.9%). Both CRS3 and CA125 normalization were identified as independent prognosticators of PFS. Combining these two factors, we stratified the 106 patients into three groups with different risks of recurrence: low-risk group (CRS3 + post-NACT CA125≤ 35 U/ml; n = 17, 16.0%), intermediate-risk group (CRS3 + post-NACT CA125 > 35 U/ml; n = 7, 6.6%) and high-risk group (CRS1-2; n= 82, 77.4%). The differences in PFS between the three groups were significant (log-rank test, P Conclusion Both the CRS system and the normalization of CA125 following NACT could reliably predict the risk of recurrence following primary treatment. The combination of the two factors refined the prognostic stratification of HGSC patients who were treated with NACT and IDS.

Esophageal squamous cell carcinoma (ESCC) is one of the deadliest cancer types with a poor prognosis due to the lack of symptoms in the early stages and a delayed diagnosis. The present study aimed to identify the risk factors significantly associated with prognosis and to search for novel effective diagnostic modalities for patients with early-stage ESCC. mRNA and methylation data of patients with ESCC and the corresponding clinical information were downloaded from The Cancer Genome Atlas (TCGA) database, and the representation features were screened using deep learning autoencoder. The univariate Cox regression model was used to select the prognosis-related features from the representation features. K-means clustering was used to cluster the TCGA samples. Support vector machine classifier was constructed based on the top 75 features mostly associated with the risk subgroups obtained from K-means clustering. Two ArrayExpress datasets were used to verify the reliability of the obtained risk subgroups. The differentially expressed genes and methylation genes (DEGs and DMGs) between the risk subgroups were analyzed, and pathway enrichment analysis was performed. A total of 500 representation features were produced. Using K-means clustering, the TCGA samples were clustered into two risk subgroups with significantly different overall survival rates. Joint multimodal representation strategy, which showed a good model fitness (C-index=0.760), outperformed early-fusion autoencoder strategy. The joint representation learning-based classification model had good robustness. A total of 1,107 DEGs and 199 DMGs were screened out between the two risk subgroups. The DEGs were involved in 70 pathways, the majority of which were correlated with metastasis and proliferation of various cancer types, including cytokine-cytokine receptor interaction, cell adhesion molecules PPAR signaling pathway, pathways in cancer, transcriptional misregulation in cancer and ECM-receptor interaction pathways. The two survival subgroups obtained via the joint representation learning-based model had good robustness, and had prognostic significance for patients with ESCC.

Owing to its sustainability and low cost, direct revegetation (DR) has been considered a promising alternative to capped revegetation (CR) for dealing with the serious environmental problem derived from various types of mine wastelands that are widespread in the world. However, a direct comparison of the performance of these two revegetation approaches for reclamation of extremely acidic mine wastelands and the underlying mechanisms is still lacking. To bridge this critical knowledge gap, we established 5000 m2 of vegetation on a highly acidified (pH

Background Autotrophic prokaryotes are crucial participants in the global carbon cycle, and autotrophic carbon fixation contributes approximately 50% of the global net primary production in aquatic ecosystems per year. Salinity is a prominent regulator structuring microbial communities in diverse aquatic ecosystems. However, little information is available regarding the compositional and physiological response of autotrophic microbial communities to salinity change. Here, we used genome-resolved metagenomics to study autotrophic microbial communities in 25 Tibetan lacustrine sediments with a salinity gradient (from 0.54‰ to 82.6‰). Results117 metagenome-assembled genomes (MAGs) with carbon fixation potential belonging to 12 phyla were retrieved, of which approximately 21% were not affiliated with the known orders, suggesting taxonomically diverse autotrophic assemblages in sediments. The total abundance of these putative autotrophs decreased significantly with increasing salinity, and the variation of sediment autotrophic communities was mainly driven by salinity, pH and TOC. Notably, a change in the predominant lineage from Betaproteobacteria to Deltaproteobacteria was observed along the salinity gradient, and the dominant pathway for carbon fixation shifted from the Calvin-Benson-Bassham (CBB) cycle to more energy efficient Wood-Lungdahl (WL) pathway with glycolysis from Entner-Doudoroff to more exergonic Embden-Meyerhof-Parnas, demonstrating that the physiological efficiency increases from freshwater to hypersaline autotrophic communities. Metabolic inference revealed major links for carbon fixation to the oxidation of reduced sulfur compounds, ferrous iron and carbon monoxide, denitrification and nitrogen fixation in these MAGs, as well as the occurrence of dissimilatory sulfate reduction and the WL pathway dominating hypersaline sediments, greatly extending the understanding of metabolic versatility and diverse ecological niches of autotrophic microorganisms. Conclusions This study provided a systematic attempt to characterize the response of carbon fixation pathways to salinity and the knowledge essential for revealing ecological roles of autotrophic prokaryotes in aquatic habitats. These findings suggest with increased salinity, physiological efficiency of the autotrophic community increases, which has important implications for understanding the carbon budget in aquatic ecosystems.

The clinical outcome after in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI) is diverse in infertility patients with polycystic ovary syndrome (PCOS). The aim of this study was to develop a nomogram based on an association of patients’ characteristics to predict the live birth rate in PCOS patients. All women in a public university hospital who attempted to conceive by IVF/ICSI for PCOS infertility from January 2014 to October 2018 were included. The nomogram was built from a training cohort of 178 consecutive patients and tested on an independent validation cohort of 81 patients. PCOS was confirmed in all participants. Three variates significantly associated with live birth rate of PCOS patients were BMI, total serum cholesterol (TC) and basal FSH. This predictive model built on the basis of BMI, TC, basal FSH, type of embryo transferred and age showed good calibration and discriminatory abilities, with an area under the curve (AUC) of 0.708 (95% CI 0.632–0.785) for the training cohort. The nomogram showed satisfactory goodness-of-fit and discrimination abilities in the independent validation cohort, with an AUC of 0.686 (95% CI 0.556–0.815). Our simple evidence-based nomogram presents graphically risk factors and prognostic models for IVF/ICSI outcomes in patients with PCOS, which can offer useful guidance to clinicians and patients for individual adjuvant therapy.

This study aims to identify a miRNAs signature for predicting overall survival (OS) in esophageal squamous cell carcinoma (ESCC) patients. MiRNA expression profiles and corresponding clinical information of 119 ESCC patients were obtained from NCBI GEO and used as the training set. Differentially expressed miRNAs (DEmiRNAs) were screened between early-stage and late-stage samples. Cox regression analysis, recursive feature elimination (RFE)-support vector machine (SVM) algorithm, and LASSO Cox regression model were used to identify prognostic miRNAs and consequently build a prognostic scoring model. Moreover, promising target genes of these prognostic miRNAs were predicted followed by construction of miRNA-target gene networks. Functional relevance of predicted target genes of these prognostic miRNAs in ESCC was analyzed by performing function enrichment analyses. There were 46 DEmiRNAs between early-stage and late-stage samples in the training set. A risk score model based on five miRNAs was built. The five-miRNA risk score could classify the training set into a high-risk group and a low-risk group with significantly different OS time. Risk stratification ability of the five-miRNA risk score was successfully validated on an independent set from the Cancer Genome Atlas (TCGA). Various biological processes and pathways were identified to be related to these miRNAs, such as Wnt signaling pathway, inflammatory mediator regulation of TRP channels pathway, and estrogen signaling pathway. The present study suggests a pathological stage-related five-miRNA signature that may have clinical implications in predicting prognosis of ESCC patients.

The application of anaerobic digestors to decentralized wastewater treatment systems (DWTS) has gained momentum worldwide due to their ease of operation, high efficiency, and ability to recycle wastewater. However, the microbial mechanisms responsible for the high efficiency and ability of DWTS to recycle wastewater are still unclear. In this study, the microbial community structure and function of two different anaerobic bioreactors (a primary sludge digestor, PSD, and anaerobic membrane bioreactor, AnMBR) of a DWTS located in Germany was investigated using 16S rRNA gene amplicon and metagenomic sequencing, respectively. The results showed that the microbial community structure was remarkably different in PSD and AnMBR. Methanobacteriaceae and Syntrophaceae were identified as the families that significantly differed in abundance between these two bioreactors. We also used genome-centered metagenomics to predict the microbial interactions and methane-generating pathway, which yielded 21 near-complete assembled genomes (MAGs) (average completeness of 93.0% and contamination of 2.9%). These MAGs together represented the majority of the microbial community. MAGs affiliated with methanogenic archaea, including Methanobacterium sp., Methanomicrobiales archaea, Methanomassiliicoccales archaea, and Methanosaeta concilii, were recruited, along with other syntrophic bacterial MAGs associated with anaerobic digestion. Key genes encoding enzymes involved in specific carbohydrate-active and methanogenic pathways in MAGs were identified to illustrate the microbial functions and interactions that occur during anaerobic digestion in the wastewater treatment. From the MAG information, it was predicted that bacteria affiliated with Bacteroidetes, Prolixibacteraceae, and Synergistaceae were the key bacteria involved in anaerobic digestion. In the methane production step, Methanobacterium sp. performed hydrogenotrophic methanogenesis, which reduced carbon dioxide to methane with hydrogen as the primary electron donor. Taken together, our findings provide a clear understanding of the methane-generating pathways and highlight the syntrophic interactions that occur during anaerobic digestion in DWTS.

Osteosarcoma is the most common primary malignancy of the bone, and macrophages play a promotional role during osteosarcoma development and progression. TIPE1 is known to function as a tumor suppressor in diverse cancers by inducing cell arrest and apoptosis. However, the biological function of TIPE1 in osteosarcoma is still unclear. The purpose of this study was to investigate the expression and function of TIPE1 in osteosarcoma. In the present study, TIPE1 expression in osteosarcoma cancer cells was determined by qPCR and western blotting. A subcutaneous tumor model was established to investigate the potential anti-tumor activity of TIPE1 in osteosarcoma. Further, flow cytometry, western blotting, immunofluorescence staining, and ELISA were performed to clarify the underlying mechanism by which TIPE1 regulates growth of osteosarcoma. Our results suggest that TIPE1 is downregulated in osteosarcoma cancer cells, and ectopic expression TIPE1 significantly inhibited osteosarcoma tumor growth in vivo. Furthermore, TIPE1 inhibits the infiltration of macrophages in osteosarcoma tumor by suppressing MCP-1 expression in osteosarcoma cells. Further in vivo study revealed that inhibition of MCP-1/CCR2 axis by Bindarit blocked the inhibitory effect of TIPE1 on osteosarcoma growth. Collectively, our results demonstrate the anti-tumor role of TIPE1 in osteosarcoma and reveal a novel therapy target for osteosarcoma.

Objective To explore the influence of Guiqiyiyuan Ointment on the expressions of caspase-3 and caspase-9 in the lung and kidney of the rats damaged by heavy ion (12C6+) radiation-induced bystander effect. Methods The Wistar male rats were equally and randomly divided into seven groups, normal control group (NCG), radiation alone group (RAG) and Chinese medicine group (CMG), with the latter two groups being redivided into 6, 12 and 24h groups according to the executing time. The Chinese medicine groups were given Guiqiyiyuan Ointment by gavage for two weeks in advance. The normal control group and the radiation alone groups were given the equal normal saline. Afterwards, the right lung of the rats in the radiation alone groups and Chinese medicine groups were radiated by 2Gy 12C6+ ion once. The rats in normal control group were not radiated. All groups of rats were executed 6, 12, and 24h after radiation. The protein and mRNA expressions of caspase-3 and caspase-9 in the right lung, left lung and left kidney were examined with immunohistochemistry and Q-PCR. Results Compared with the normal control group, the mRNA expressions of caspase-3 and caspase-9 in the right lung, left lung and left kidney in the radiation alone groups obviously increased 6 and 24h after radiation. While the protein expressions of caspase-3 and caspase-9 in the radiation alone group obviously increased only 24h after radiation (P

Objective To investigate the bystander effect injury to lung-heart-liver-spleen caused by 12C6+ beam radiation, and explore the prevention and treatment effect of Guiqiyiyuan ointment on the injury and its mechanism. Methods Ninety healthy male Wistar rats were randomly divided into 3 groups: NC group (normal control, normal saline 2ml/kg, n=30), SR group (simple radiation, 8Gy, 2ml/kg, n=30), GO group (Guiqiyiyuan ointment 11.83g/kg, radiation, 8Gy, n=30). All the rats received intragastric administration for 7 days. The right side of the lung was modeled by 12C6+ beam radiation. After modeling, the rats were killed at 48h. The heart, liver and spleen were taken. The malonaldehyde (MDA), glutathione (GSH), glutathione peroxidase (GSH-Px), superoxide dismutase (SOD) contents were measured by colorimetry, DNA methylation rate was assayed by ELISA, and the expressions of Dnmt1, Dnmt3a and Dnmt3b were detected by immunohistochemistry. Results Compared with NC group, the contents of SOD, GSH and GSH-Px decreased (P

Phytostabilization of an extremely acidic (pH < 3) mine tailings via direct revegetation remains a challenge, which can perhaps be attributed largely to a limited understanding of the responses of microbial communities in extremely acidic mine tailings to practical phytostabilization. In order to shed light on the mechanism by which amending materials used in phytostabilization practice help to improve the growth conditions in reconstructed root zones and thereby facilitate the initial establishment of vegetation in extremely acidic mine tailings, 4000 m2 of vegetation was established successfully within six months on an extremely acidic (pH 2.5) Cu mine tailings amended directly with ameliorants. Further, a comparative analysis of the microbial communities in amended layer of the reclaimed tailings (ALRT), unamended layer of the reclaimed tailings (ULRT) and the unreclaimed tailings (UT) was performed. The results revealed intriguing changes in microbial community composition following the phytostabilization. While UT communities were dominated by Euryarchaeota with relative abundances varying from 57% to 84%, Proteobacteria was the most predominant phylum in those of both ULRT and ALRT with relative abundances ranging from 29% to 53%. Ferroplasma and Aplasma, two archaeal genera involved in tailings acidification, existed in UT communities at high relative abundances (up to 52%), which were 14–913 times greater than those in ULRT and ALRT communities. The overall microbial community composition of ULRT was different greatly from that of UT, but tended to shift towards that of ALRT as the phytostabilization progressed. Redox potential was among the major determinants of microbial community composition of the tailings. These findings have implications for further development of effective phytostabilization schemes for extremely acidic mine tailings.

Objective To investigate the mechanism of Guiqiyiyuan Ointment (GO) for preventing and treating 12C6+ beam radiation induced lung and kidney bystander effect to provide a new strategy for prevention and treatment of clinical radiation injury. Methods Sixty healthy male Wistar rats were randomly and equally divided into 3 groups: NC group, SR group (simple radiation 2ml/kg), GO group(GO 2ml/kg intragastric administration for 7 days). The right side of the lung was modeled by 12C6+ beam radiation. After modeling, the rats were killed at 48h. The left lung, left and right kidney tissues were taken from the rats. The DNA methylation rate was detected by ELISA assay, pathological changes were observed by HE staining, and the expressions of Dnmt1, Dnmt3a and Dnmt3b were detected by immunohistochemistry. Results Compared with the NC group, the level of DNA methylation was decreased significantly (P

The initiation and progression of various types of tumors, such as lung neoplasms, are driven by a population of cells with stem cell properties and their microenvironment. Bone marrow mesenchymal stem cells (BM-MSCs) in long-term in vitro culture may exhibit spontaneous changes in stem cell biological properties, including malignant transformations; however, the molecular mechanisms of this have not been fully elucidated. In the present study, a BM-MSC and lung cancer A549 cell co-culture system was utilized to investigate how the tumor microenvironment may spontaneously change the proliferation, migration and differentiation of BM-MSCs. It was demonstrated that the lung cancer A549 microenvironment is able to induce changes in the cell morphology, proliferation, karyotype, cytoskeleton and migration ability of BM-MSCs in vitro. Compared with the control group BM-MSCs, the expression of Ras, phosphorylated-extracellular regulated protein kinases, nuclear factor-κB, P62 and B-cell lymphoma 2 (Bcl-2) proteins in groups of co-cultured BM-MSCs increased significantly (P

A major concern in developing microbially-assisted phytoextraction (MAP) is that the effects of introduced microbes on indigenous soil microbial community are profound and irreversible. To date, however, the microbial properties of soils subjected to MAP remain poorly understood. Therefore, we explored the effects of inoculation with a bacterial consortium enriched from acid mine drainage on not only the cadmium (Cd) phytoextraction efficiency of Averrhoa carambola but also the microbial properties of the Cd-contaminated soil. We conducted a field experiment and characterized the microbial community in the contaminated soil using next generation sequencing technology (Illumina MiSeq). The bacterial inoculation increased the Cd concentration in A. carambola shoot tissues by 20%–65%, leading to a relatively high Cd removal efficiency (4.63% annually). Meanwhile, there were no significant differences between the treatments in soil bacterial diversity and community composition one year after the initiation of the bacterial inoculation treatment. The most abundant genera of the introduced bacteria were found to either disappear from, or be present in similar relative abundance, in the soils of the different treatments, except Sulfobacillus. Collectively, our results provide evidence that MAP could be practiced with minor effects on indigenous soil microbial community.

Little is known about the changes in soil microbial phosphorus (P) cycling potential during terrestrial ecosystem management and restoration, although much research aims to enhance soil P cycling. Here, we used metagenomic sequencing to analyse 18 soil microbial communities at a P-deficient degraded mine site in southern China where ecological restoration was implemented using two soil ameliorants and eight plant species. Our results show that the relative abundances of key genes governing soil microbial P-cycling potential were higher at the restored site than at the unrestored site, indicating enhancement of soil P cycling following restoration. Thegcdgene, encoding an enzyme that mediates inorganic P solubilization, was predominant across soil samples and was a major determinant of bioavailable soil P. We reconstructed 39 near-complete bacterial genomes harboringgcd, which represented diverse novel phosphate-solubilizing microbial taxa. Strong correlations were found between the relative abundance of these genomes and bioavailable soil P, suggesting their contributions to the enhancement of soil P cycling. Moreover, 84 mobile genetic elements were detected in the scaffolds containinggcdin the 39 genomes, providing evidence for the role of phage-related horizontal gene transfer in assisting soil microbes to acquire new metabolic potential related to P cycling.

Current criteria for successful phytostabilization of metalliferous mine wastelands have paid much attention to soil physico-chemical properties and vegetation characteristics. However, it remains poorly understood as to how the soil microbial community responds to phytostabilization practices. To explore the effects of amendments on the microbial community after assisted phytostabilization of an extremely acidic metalliferous mine soil (pH &lt, 3), a pot experiment was performed in which different amendments and/or combinations including lime, nitrogen-phosphorus-potassium (NPK) compound fertilizer, phosphate fertilizer and river sediment were applied. Our results showed the following: (1) The amendments significantly increased soil microbial activity and biomass C, being 2.6&ndash, 4.9 and 1.9&ndash, 4.1 times higher than those in the controls, respectively. (2) The activities of dehydrogenase, cellulase and urease increased by 0.9&ndash, 7.5, 2.2&ndash, 6.8 and 6.7&ndash, 17.9 times while acid phosphatase activity decreased by 58.6%&ndash, 75.1% after the application of the amendments by comparison with the controls. (3) All the amendments enhanced the nutrient status of the mine soil, with organic matter, total nitrogen and total phosphorus increased by 5.7&ndash, 7.8, 3.1&ndash, 6.8 and 1.1&ndash, 1.9 times, relative to the mine soil. In addition, there were strong positive correlations between soil microbial community parameters and nutrient factors, suggesting that they were likely to be synergistic. From an economic view, the combination of lime (25 t ha&minus, 1) and sediment from the Pearl River (30%) was optimal for functional rehabilitation of the microbial community in the extremely acidic metalliferous mine soil studied.

Many Viola plants growing in mining areas exhibit high levels of cadmium (Cd) tolerance and accumulation, and thus are ideal organisms for comparative studies on molecular mechanisms of Cd hyperaccumulation. However, transcriptomic studies of hyperaccumulative plants in Violaceae are rare. Viola baoshanensis is an amazing Cd hyperaccumulator in metalliferous areas of China, whereas its relative V. inconspicua is a non-tolerant accumulator that resides at non-metalliferous sites. Here, comparative studies by transcriptome sequencing were performed to investigate the key pathways that are potentially responsible for the differential levels of Cd tolerance between these two Viola species. A cascade of genes involved in the ubiquitin proteosome system (UPS) pathway were observed to have constitutively higher transcription levels and more activation in response to Cd exposure in V. baoshanensis, implying that the enhanced degradation of misfolded proteins may lead to high resistance against Cd in this hyperaccumulator. Many genes related to sucrose metabolism, especially those involved in callose and trehalose biosynthesis, are among the most differentially expressed genes between the two Viola species, suggesting a crucial role of sucrose metabolism not only in cell wall modification through carbon supply but also in the antioxidant system as signaling molecules or antioxidants. A comparison among transcriptional patterns of some known transporters revealed that several tonoplast transporters are up-regulated in V. baoshanensis under Cd stress, suggesting more efficient compartmentalization of Cd in the vacuoles. Taken together, our findings provide valuable insight into Cd hypertolerance in V. baoshanensis, and the corresponding molecular mechanisms will be useful for future genetic engineering in phytoremediation.

To date, very few attempts have been made to systematically compare the effectiveness of agricultural and nonagricultural organic wastes for aided phytostabilization of mine tailings under field conditions. In this study, we performed a field trial to compare the effectiveness of three agricultural organic wastes: chicken manure (CM), crop straw (CS), and spent mushroom compost (SMC), with that of three nonagricultural organic wastes, municipal sludge (MS), medicinal herb residues (MHR), and sweet sorghum vinasse (SSV) for aided phytostabilization of a Pb-Zn mine tailings pond in Hunan Province, China. Eight plant species naturally established in the vicinity of the mine were selected and seeded onto trial plots. It was found that the CM-amended plots had the highest (p −2), compared to other treatments. CM was also one of the best amendments in terms of improving soil nutrient status, increasing activities of soil enzymes, and immobilizing soil Pb. In addition, CM-amended plots were characterized by their higher microbial diversity and distinct microbial community structure as compared to the control plots. MS was the second best amendment in promoting vegetation cover (71%) and biomass production (461 g m−2), and it performed as well as CM for improving nutrient status, immobilizing heavy metals, and increasing the activities of enzymes in the mine tailings. Suggestions for further lines of research are made in order to develop future investigations.

Acidification is a major constraint for revegetation of sulphidic metal-contaminated soils, as exemplified by the limited literature reporting the successful phytostabilization of mine soils associated with pH3 and high acidification potential. In this study, a combination of ameliorants (lime and chicken manure) and five acid-tolerant plant species has been employed in order to establish a self-sustaining vegetation cover on an extremely acid (pH3) polymetallic pyritic mine waste heap in southern China exhibiting high acidification potential. The results from the first two-year data showed that the addition of the amendments and the establishment of a plant cover were effective in preventing soil acidification. Net acid-generating potential of the mine soil decreased steadily, whilst pH and acid neutralization capacity increased over time. All the five acid-tolerant plants colonized successfully in the acidic metal-contaminated soil and developed a good vegetation cover within six months, and subsequent vegetation development enhanced organic matter accumulation and nutrient element status in the mine soil. The two-year remediation program performed on this extremely acid metalliferous soil indicated that aided phytostabilization can be a practical and effective restoration strategy for such extremely acid mine soils.