| With the development of industry, human activities are making more and more important effects on global environmental changes. Till now, there are mainly three global environment problems, including an increase in CO2 concentration in the air, and nitrogen (N) deposition, and a decrease in biodiversity, which are all closely related to human activities. In the paper, the problem of nitrogen deposition was firstly studied by environmental microorganisms, with the cooperation of Dr. Zhou Jizhong in Oklahoma University in USA. And the microbial organisms in AMD (acid mine drainage) samples were still be studied. More and more new methods and techniques are being used to study microbial organisms in the environmental samples since the microbial organisms are various and complicated in them. In this paper, two molecular ecology techniques, which are Functional Gene Arrays (FGAs) and restriction fragment length polymorphism (RFLP), are used to study the microbial community structure and functional genes in aquatic and soil samples.(1) Nitrogenous fertilizer was added to simulate the effect of increasing nitrogen deposition in 24 soil samples, which were obtained from the BioCON (Biodiversity, CO2, and Nitrogen) ecological experiment site at the University of Minnesota's Cedar Creek Ecosystem Science Reserve in USA. Twelve samples were collected from the plots in which nitrogenous fertilizer was added and the rest 12 samples were collected from the plots without adding nitrogenous fertilizer. Soil microbial genomic DNA in 24 samples were extracted and analyzed with FGAs. The results showed that adding nitrogenous fertilizer would influence the structures of microbial community and plants in the samples. Adding nitrogenous fertilizer made aboveground plant biomass increase in the sampling points, at the same time it decreased the plant biomass of underground roots. After Adding nitrogenous fertilizer, microbial community diversity decreased in the soil samples in our study.(2) In terms of percentage, functional genes of eight categories involved in carbon cycling, nitrogen cycling, sulfur cycling, phosphorus cycling, antibiotics, metal resistance, energy process and organic remedation in the fertilized and non-fertilized samples are similar, and no significant difference was detected. In terms of gene number, eight functional gene categories involved in carbon cycling, nitrogen cycling, sulfur cycling, phosphorus cycling, antibiotics, metal resistance, energy process and other effects in the fertilized samples were less than that in the non-fertilized samples. According to the results of functional genes involved in carbon cycling, nitrogen cycling, sulfur cycling and phosphorus cycling, it indicated that in the fertilized samples the abundance of functional genes mostly declined, and the contrast was significant. In addition, the key functional genes participating in the nitrogen cycling were studied in details.(3) Relationship between13 external factors and microbial community structures in 24 samples was studied. The results showed that seven of the thirteen factors may play a key role, which were Belowground Nitrogen (%), Belowground C/N Ratio, Aboveground C/N Ratio, Belowground N (total) (g/m2), Aboveground N (total) (g/m2), pH, and moisture (0-20cm). In addition, Variation portioning analysis (VPA) was used to analyze the 13 external factors and functional gene data of 24 samples. The results showed that part "Environmental factors" could be able to independently explain 44.37% of the variation observed; part "Plant biomass" could be able to independently explain 8.21% of the variation observed; Interaction between "Plant biomass" and "Environmental factors" could explain 0.05% of the variation. There is 47.37% of the variation unexplained.(4) Through analysis of the four samples in 2005 and the four samples in 2009, the effect of adding nitrogenous fertilizer's time to microbial community structures and functional genes was determined. The result of DCA analysis showed that time of adding nitrogenous fertilizer would influence the microbial community structures in the eight samples. And samples in 2005 were separated well from samples in 2009. Based on results of the Shannon diversity index, Simpson diversity index, and number of functional genes in eight samples, results showed that diversity of microbial community structures in samples would increase with extending the time of adding nitrogenous fertilizer.(5) According to the results on the functional genes involved in carbon cycling, nitrogen cycling, sulfur cycling and phosphorus cycling in eight samples of 2005 and 2008, results indicated the abundance of most functional genes in the four samples of 2009 is higher than that in the four samples of 2005. But the contrast was not remarkable since P values of t-test were normally bigger than 0.1.(6) The bacterial communities in two acid mine drainage (AMD) samples from Yunfu sulfide mine in Guangdong province were determined by restriction fragment length polymorphism. The results showed that the bacterial communities in samples G1 and G2 were significantly different. And diversity of bacterial community in sample G2 was bigger than that in sample G1. There were totally 15 kinds of bacteria detected, which were divided into four divisions according to the phylogenetic analysis. The four divisions were Nitrospira, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. Microorganisms of genera Acidithiobacillus of the division Gammaproteobacteria, and microorganisms of the divison Betaproteobacteria were the dominant bacteria in the two AMD samples.(7) Through the clone sequencing in the two AMD samples and comparing with the gene data existed online, results showed that there are two new bacterial 16S rDNA detected in sample G1; and there were eight new bacterial 16S rDNA detected in sample G2. These new bacterial 16S rDNA sequence maybe mean new bacteria in the AMD samples. In addition, based on the results of bacterial communities and 29 element concentrations in the two AMD samples, it suggested that the concentrations of elements As, S and Fe maybe the key factors causing the difference in the two AMD samples.
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