Bioinformatics analysis identifies potential ferroptosis key genes in the pathogenesis of diabetic peripheral neuropathy.

Background: Diabetic peripheral neuropathy (DPN) is a serious complication in Diabetes Mellitus (DM) patients and the underlying mechanism is yet unclear. Ferroptosis has been recently intensively researched as a key process in the pathogenesis of diabetes but there yet has been no related bioinformatics-based studies in the context of DPN. Methods: We used data mining and data analysis techniques to screen differentially expressed genes (DEGs) and immune cell content in patients with DPN, DM patients and healthy participants (dataset GSE95849). These DEGs were then intersected with the ferroptosis dataset (FerrDb) to obtain ferroptosis DEGs and the associated key molecules and miRNAs interactions were predicted. Results: A total of 33 ferroptosis DEGs were obtained. Functional pathway enrichment analysis revealed 127 significantly related biological processes, 10 cellular components, 3 molecular functions and 30 KEGG signal pathways. The biological processes that were significantly enriched were in response to extracellular stimulus and oxidative stress. Key modules constructed by the protein-protein interaction network analysis led to the confirmation of the following genes of interest: DCAF7, GABARAPL1, ACSL4, SESN2 and RB1. Further miRNA interaction prediction revealed the possible involvement of miRNAs such as miR108b-8p, miR34a-5p, mir15b-5p, miR-5838-5p, miR-192-5p, miR-222-3p and miR-23c. Immune-environment content of samples between DM and DPN patients revealed significant difference in the levels of endothelial cells and fibroblasts, which further speculates their possible involvement in the pathogenesis of DPN. Conclusion: Our findings could provide insight for investigations about the role of ferroptosis in the development of DPN.

[Effect of Organic Matter Promotion on Nitrogen-Cycling Genes and Functional Microorganisms in Acidic Red Soils].

The application of exogenous organic matter is considered the main method of increasing the organic matter content of acidic red soils. Nitrogen is an important limiting factor for soil fertility. Changes to the soil ecosystem under organic matter promotion can affect soil nitrogen cycling and related functional microorganisms; however, there have been no studies on this aspect. Acidic upland red soils, with or without long-term organic fertilizer application, were chosen as the research materials in this study. Based on metagenomic sequencing and alignment in the nitrogen-cycling gene database, the present study aimed to investigate the effect of organic matter promotion on nitrogen-cycling genes and functional microorganisms in acidic red soils, which had been amended with exogenous organic matter for 32 years. The results showed that organic matter promotion in acidic soils increased the total organic carbon and total nitrogen content, and alleviated soil acidification. Organic matter promotion increased the soil net nitrification activity and potential for ammoxidation. Organic matter promotion increased the abundance of amoA genes (encoding ammonia monooxygenase) and nar, nap, nir, nor, and nos genes (encoding denitrification reductase); decreased the abundance of hao genes (encoding hydroxylamine oxidase) and nrf genes related to the dissimilatory nitrate reduction to ammonia; increased the abundance of glnA, gdh, glsA, ansB, and nao genes related to organic nitrogen metabolism; altered the abundance of functional genes related to assimilatory nitrate reduction; and changed the community composition of nitrogen-cycling microorganisms. After organic matter promotion, alleviation of soil acidification and enhancement of total organic carbon were the most important factors that affected the abundance of nitrogen-cycling genes and the community composition of functional microorganisms. Our results comprehensively investigated the inorganic and organic nitrogen-cycling genes, and correlated the functional genes, microbial populations, and functional activities in the ammonia oxidizing process, which provided supporting data to understand the nitrogen-cycling characteristics of acidic red soils and provided ideas for acidic soil improvement.

The voltage signals of microbial fuel cell-based sensors positively correlated with methane emission flux in paddy fields of China.

Previous studies showed that exoelectrogenic bacteria in paddy soil could suppress methanogens and methanogenesis after they were enriched by application of Fe3+ or running microbial fuel cells (MFCs). However, the relationship between exoelectrogenic bacteria and methanogens without the enrichment process is unknown. Our study was conducted in three paddy fields in China and over three seasons. We explored novel MFC-based sensors to in situ detect voltage signals that were generated from paddy soil within 10 min. The voltage and methane emission flux were determined as an indicator of the exoelectrogenic activity and methanogenic activity, respectively. The abundance of exoelectrogenic bacteria was assessed by quantifying five exoelectrogenic bacterial-associated genera including Geobacter, Shewanella, Anaeromyxobacter, Desulfovibrio and Clostridium, while the methanogens were studied by quantifying and sequencing the mcrA gene. The results showed that the abundance of exoelectrogenic bacteria and the voltage signals were positively correlated to the abundance of mcrA gene and methane emission flux, respectively. Moreover, non-metric dimensional scaling reveals that the abundance of Geobacter, Desulfovibrio and Clostridium significantly correlated with that of Methanomassiliicoccus, Methanoregula and Methanolinea. The present study suggests that the voltage signals might act as a novel indicator of methane emission flux in paddy fields.

[Effects of glyphosate-resistant transgenic soybean on soil rhizospheric bacteria and rhizobia.] / æŠ—è‰ç”˜è†¦è½¬åŸºå› å¤§è±†å¯¹æ ¹é™ åœŸå£¤ç»†èŒåŠæ ¹ç˜¤èŒçš„å½±å“.

Transgenic soybean is the most widely grown genetically modified crop in the world, with herbicide resistance being the major modified trait. Microbial community is one of the most important indicators for soil quality. The effects of glyphosate-resistant transgenic soybean and glyphosate application on rhizospheric bacteria and rhizobia still remained unknown. In this study, with the non-transgenic parent Zhongdou 32 as control (CK), we investigated the effects of the G10-epsps transgenic glyphosate-resistance soybean SHZD32-01 without or with glyphosate application (abbreviated as GR and GR+G, respectively) on rhizospheric bacteria and rhizobia at different growth stages of soybean in field. Compared with CK, GR and GR+G had effects on soil pH, total organic carbon, total nitrogen and ammonium contents at the seedling and mature stages. GR significantly increased the abundance and diversity of soil rhizospheric bacterial community at the podding stage. GR+G significantly increased the abundance of soil rhizospheric bacterial community at the podding stage but decreased its diversity at the seeding and podding stages. GR and GR+G changed the relative abundance of dominant bacteria populations. Proteobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Actinobacteria were generally the dominant ones among the three treatments across all growth stages. Furthermore, GR and GR+G changed the relative abundance of rhizobia but did not change that of soybean-nodulating rhizobia, Bradyrhizobium and Sinorhizobium. The relative abundance of rhizobia in GR+G was decreased significantly at the podding stage. The abundance of actinobacteria and rhizobia was mainly affected by soil pH. Glyphosate-resistant transgenic soybean without or with glyphosate application altered soil rhizospheric bacteria and rhizobia at the podding stage, but the effects disappeared along with the growth of soybean.

Bacterial Bioreporter-Based Mercury and Phenanthrene Assessment in Yangtze River Delta Soils of China.

Genetically engineered bacterial whole-cell bioreporters were deployed to investigate bioavailable mercury (b-Hg) and phenanthrene (b-PHE). Characterized by high sensitivity and specificity in aqueous solutions, the bioreporter system could detect in amended soils the concentrations of b-Hg and b-PHE in the ranges of 19.6 to 111.6 and 21.5 to 110.9 µg kg, respectively. The sensitivity of the system allowed for the combined analysis of b-Hg and b-PHE from real environmental samples. Therefore, soil samples from three large refinery facilities were tested, and the results from the instrumental analysis strongly correlated with the ones obtained with the bioreporter method. Large-scale and fast screening of soil contamination across the Yangtze River Delta in Eastern China was conducted. More than 36% of the samples contained b-Hg, whereas the fractions of b-PHE were below the detection limit for all the samples. These results indicated a higher toxicity and more hazardous condition for Hg contamination than for PHE. Population densities and airborne 10-µm particulate matter (PM10) concentrations were used as parameters for comparison with the spatial distribution of the b-Hg and b-PHE fractions. The results revealed that the bioreporters could offer a rapid and cost-efficient method to test soil samples from contaminated areas and provide a screening tool for environmental risk assessment.

[Nitrification Activity and Autotrophic Nitrifiers in Long-term Fertilized Acidic Upland Soils].

Soil microcosm incubation, molecular ecology techniques including denaturing gradient gel electrophoresis and Illumina MiSeq high-throughput sequencing, and bioinformatics analysis were carried out to investigate the effect of long-term fertilization with chemical fertilizers (NPK) and organic manure (OM) on soil nitrification activity and the autotrophic nitrifying communities in acidic upland soils. No fertilization soil (CK) was the control. Relationships between soil nitrification activities, autotrophic nitrifying communities, and soil characteristics were further evaluated. Long-term fertilization significantly increased the soil organic carbon and inorganic nitrogen contents. Fertilization with organic manure significantly increased soil pH and total nitrogen contents, but decreased soil C/N. Autotrophic nitrification dominated soil nitrification, and accounted for 73.60%-85.32% of total nitrification. Fertilization significantly increased soil autotrophic nitrification activity and the highest value was observed in the OM soil. During the microcosm incubation, the absolute abundances of amoA genes and the relative abundances of 16S rRNA genes of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the OM soil significantly increased. The relative abundances of 16S rRNA genes of the AOA greatly increased in both CK and NPK soils. These results suggested the remarkable activity of AOA in the three soils (the predominant population was Nitrososphaera,>99.30%) and implied that AOB was active in the OM soil (the predominant population was Nitrosospira,>99.99%). We also found the activity of nitrite-oxidizing bacteria (NOB) in the OM soil, and the predominant population was Nitrospira (>96.69%). Stepwise regression analysis demonstrated that soil autotrophic nitrification activity was significantly affected by soil total nitrogen content, whereas the abundances of archaeal and bacterial amoA genes were significantly affected by soil organic carbon content and soil pH, respectively. We also found significant positive correlation between the relative abundance of Nitrososphaera and soil nitrate content and a negative correlation between the relative abundance of Nitrosospira and Nitrospira with soil C/N. Overall, our results showed that long-term fertilization greatly increased soil nitrification activity and altered the autotrophic nitrifying communities in acidic upland soils. Soil autotrophic nitrification activity was significantly stimulated by soil total nitrogen content. The Nitrososphaera group played a critical role in nitrification of acidic upland soils. The increased soil pH and decreased soil C/N stimulated the growth of Nitrosospira.

Characterization of Electricity Generated by Soil in Microbial Fuel Cells and the Isolation of Soil Source Exoelectrogenic Bacteria.

Soil has been used to generate electrical power in microbial fuel cells (MFCs) and exhibited several potential applications. This study aimed to reveal the effect of soil properties on the generated electricity and the diversity of soil source exoelectrogenic bacteria. Seven soil samples were collected across China and packed into air-cathode MFCs to generate electricity over a 270 days period. The Fe(III)-reducing bacteria in soil were enriched and sequenced by Illumina pyrosequencing. Culturable strains of Fe(III)-reducing bacteria were isolated and identified phylogenetically. Their exoelectrogenic ability was evaluated by polarization measurement. The results showed that soils with higher organic carbon (OC) content but lower soil pH generated higher peak voltage and charge. The sequencing of Fe(III)-reducing bacteria showed that Clostridia were dominant in all soil samples. At the family level, Clostridiales Family XI incertae sedis were dominant in soils with lower OC content but higher pH (>8), while Clostridiaceae, Lachnospiraceae, and Planococcaceae were dominant in soils with higher OC content but lower pH. The isolated culturable strains were allied phylogenetically to 15 different species, of which 11 were Clostridium. The others were Robinsoniella peoriensis, Hydrogenoanaerobacterium saccharovorans, Eubacterium contortum, and Oscillibacter ruminantium. The maximum power density generated by the isolates in the MFCs ranged from 16.4 to 28.6 mW m-2. We concluded that soil OC content had the most important effect on power generation and that the Clostridiaceae were the dominant exoelectrogenic bacterial group in soil. This study might lead to the discovery of more soil source exoelectrogenic bacteria species.

[Application of Microbial Fuel Cells in Reducing Methane Emission from Rice Paddy].

We aimed to study whether the methane emission from rice paddy with straw return can be alleviated in microbial fuel cells (MFCs). In our study, the soil mixed with 0. 5% ( mass fraction) rice straw was packed into MFCs reactors, then flooded with excess of sterilized water and transplanted with rice seedlings followed by the operation of MFCs. The MFCs were operated for 98 days covering five stages of seeding, tillering, mid-season aeration, rice filling, and ripening. The voltage data were recorded continuously and in real time during the MFCs operation and the methane emitted was collected once a week using the static chamber method and the methane emission flux was determined by gas chromatography. The results showed that the MFCs current increased and reached the peak value in the seeding and tillering stages and the operation of MFCs significantly reduced the accumulative methane emission in these two stages. The possible reason could be that the electrogens competed with methanogens for organic substrates. The height, the above and below ground biomass, and the productivity of rice plants were not significantly affected by the 98-day operation of MFCs. Our study provides a potential green and sustainable technology for the reduction of CH, emission from rice paddy fields.

Application of genetically engineered microbial whole-cell biosensors for combined chemosensing.

The progress of genetically engineered microbial whole-cell biosensors for chemosensing and monitoring has been developed in the last 20 years. Those biosensors respond to target chemicals and produce output signals, which offer a simple and alternative way of assessment approaches. As actual pollution caused by human activities usually contains a combination of different chemical substances, how to employ those biosensors to accurately detect real contaminant samples and evaluate biological effects of the combined chemicals has become a realistic object of environmental researches. In this review, we outlined different types of the recent method of genetically engineered microbial whole-cell biosensors for combined chemical evaluation, epitomized their detection performance, threshold, specificity, and application progress that have been achieved up to now. We also discussed the applicability and limitations of this biosensor technology and analyzed the optimum conditions for their environmental assessment in a combined way.

[Research Progress in Technology of Using Soil Micro-organisms to Generate Electricity and Its Potential Applications].

Microbial fuel cells ( microbial fuel cells, MFCs) are devices in which micro-organisms convert chemical energy into electrical power. Soil has electrogenic bacteria and organic substrates, thus can generate electrical current in MFCs. Soil MFCs can be operated and applied to real-time and continuously monitor soil pollution, remove soil pollutants and to reduce methane emitted from flooded rice paddy, without energy consumption and the application of chemical reagents to the soil. Instead, the operation of soil MFCs generates small amount of electrical power. Therefore, soil MFCs are useful in the development of environment-friendly technology for monitoring and remediating soil pollution, which have potential value for applications in the domain of environmental science and engineering. However, much of advanced technology hasn't been applied into soil MFCs since the studies on soil MFCs was not started until recently. This paper summarized the research progress in related to soil MFCs combining with the frontier of MFCs technology, and brought forward the possible direction in studies on soil MFCs.

[Construction of Hg(2+)-induced luminescent reporter gene system and its application to detect mercury in red soil].

A luminescent reporter gene system was constructed by fusing the mercury-inducible promoter, P(merT), and its regulatory gene, merR with a promoterless reporter gene EGFP. A stable whole-cell reporter was created by mini-Tn5 and introducing the merR-egfp system cassette into the chromosome of Pseudomonas putida strain, then applied it for mercury detection in the red soil of Jiangxi province, the fluorescence density of the sensor strain was confirmed in soil extraction and fluorescence intensity was quantified by flow cytometry. The results showed positive correlation with the mercury pollutant in the concentration range of 0.04-50 mg x kg(-1). The background heavy metal irons such as Cr2+, Zn2+, Co2+, Cu2+, Pb2+, Ag+ at certain level did not interfere with the measurement. The key factor for detecting the fluorescence density was the induction time and the optimal temperature for EGFP expression was 30-35 degrees C. Spiked with 0.1 mg x kg(-1) Hg2+ and after 15 and 30 days incubation, red soil samples were extracted and evaluated water soluble, bioavailable, organic matter bound and residual fractions of mercury by both sensor strain and analytical way. The sensor strain appeared to have a detection range similar to that of atomic absorption spectroscopy (AAS) method and the effective detection ratio was 35%-64%.

[Effects of long-term fertilization on phospholipid fatty acids and enzyme activities in paddy red soil].

Soil samples were collected from the paddy fields at the Ecological Experimental Station of Red Soil, Chinese Academy of Sciences under different treatments of long-term fertilization, and their phospholipid fatty acids (PLFAs) and enzyme activities were determined. The results showed that soil enzyme activities, nutrient contents, microbial biomass, and PLFAs varied greatly with different fertilizations. Fertilization increased the kinds and amount of soil PLFAs. Compared with fertilized soil, unfertilized soil had more fungal PLFAs but less bacterial PLFAs, indicating that fungus was more adaptable to infertile soils than bacteria. Soils applied with NPK and organic fertilizer had higher amount of total PLFAs, which was 3.22 and 1.79 times higher than that under N fertilization and no fertilization. It was indicated that balanced fertilization with NPK or applying organic fertilizer was more beneficial to the growth of plants. Fertilization could also increase soil enzyme activities, and soil urease and phosphatase activities could be used as the indicators of soil fertility.

[Research advances in aerobic denitrifiers].

This paper reviewed the varieties and characteristics of aerobic denitrifiers, their action mechanisms, and the factors affecting aerobic denitrification. Aerobic denitrifiers mainly include Pseudomonas, Alcaligenes, Paracoccus and Bacillus, which are either aerobic or facultative aerobic, and heterotrophic. They can denitrify under aerobic conditions, with the main product being N2O. They can also convert NH4+ -N to gas product. The nitrate reductase which catalyzes the denitrification is periplasmic nitrate reductase rather than membrane-bound nitrate reductase. Dissolved oxygen concentration and C/N ratio are the main factors affecting aerobic denitrification. The main methods for screening aerobic denitrifiers, such as intermittent aeration and selected culture, were also introduced. The research advances in the application of aerobic denitrifiers in aquaculture, waste water processing, and bio-degradation of organic pollutants, as well as the contributions of aerobic denitrifiers to soil nitrogen emission were summarized.

[Isolation of 2,4-dichlorophenol degrading bacterium strain and cloning and expression of its 2,4-dichlorophenol hydroxylase gene].

2,4-Dichlorophenol is toxic and biorefratory organic pollutant. A 2,4-dichlorophenol degrading bacterial strain GT241-1, identified as Pseudomonas sp., was isolated from soil samples which was collected from drainage area of several 2,4-dichlorophenol producing factories. Strain GT241-1 had strong 2,4-dichlorophenol degrading ability, it could decompose 91% 2, 4-dichlorophenol of 90 mg/L within 48 hours at 25 - 30 degrees C, and could utilize 2,4-dichlorophenol, 2,4-dichlorophenoxyacetic acid (2,4-D), benzoate and catechol as sole carbon and energy source. Southern blot showed that 2,4-dichlorophenol hydroxylase gene (dcpA) of strain GT241-1 locates on the about 10kb EcoR I/Xba I fragment. This fragment was recovered, linked to the vecter pUC19 and transformed into the E. coli DH5alpha. A aim transformant, Z539, was obtained by dot blotting from about 1200 transformants. PCR and the sequencing results shew that the whole dcpA gene is contained within the 10kb EcoR I /Xba I fragment of pZ539. This fragment was shortened to about 2.4kb by HindmIII. The shorted fragment was subcloned to vecter pRSET-B to get a transformant BS1-12. The subcloned fragment was sequenced. Sequencing results showed that the whole length of the subcloned fragment containing dcpA is 2389bp and the nucleotide span of coding region is from number 276 to number 2072 (1797 bp), with ATG and TAA as start and stop codon respectively. The sequence analysis of dcpA and the deduced amino acid encoded by dcpA showed that they are different from the relative sequences registered in the GenBank. The subcloned fragment carry the promoter of dcpA, this can deduce from the fact that the upflow length of dcpA coding region is 275bp, and further confirmed by the 2,4-dichlorophenol hydroxylase activity measurement results. The 2,4-dichlorophenol hydroxylase activity of transformant Z539 and BS1-12 were detected, the results showed these transformants have 2,4-dichlorophenol hydroxylase activity. By comparison, the activity of these transformants were lower than that of the strain GT241-1.