PCR-DGGE技术分析浸矿体系细菌群落结构的实验优化

为了研究低品位黄铜矿细菌搅拌浸出的浸矿菌液中的细菌群落结构,对 PCR-DGGE(变性梯度凝胶电泳)技术相关的实验方法进行了优化,主要涉及低丰度基因组 DNA提取方法优化、16SrRNA基因的 PCR扩增条件优化以及变性梯度凝胶电泳条件的优化.结果表明,采用分级离心多次浓缩的方法收集矿浆样品中的菌体,再用试剂盒提取基因组 DNA,有较好效果;使用含特定“GC夹板”的引物5′-CGCCCGCCGCGCCCCGCGCCCGTCCCGCCGCCCCCGCCCG-3′进行热启动降落 PCR,能显著提高目的条带的 PCR扩增效率;当 DGGE电泳设置温度为60℃左右,胶浓度为6%,尿素变性梯度为30%~50%,恒定电压为100V,时间为9h时,可以获得效果较好的 DGGE电泳图谱,该优化方案提高了对浸矿体系中细菌群落结构的检测效果     

Spatial and temporal changes in Actinobacterial dominance in experimental artificial groundwater recharge

Artificial groundwater recharge (AGR) is used in the drinking water industry to supplement groundwater resources and to minimise the use of chemicals in water treatment. This study analysed the spatial and temporal changes of microbial communities in AGR using two test systems: a nutrient-amended fluidized-bed reactor (FBR) and a sand column. Structural changes in the feed lake water (Lake Roine), FBR, and sand column bacterial communities were determined by denaturing gradient gel electrophoresis (DGGE) and the length heterogeneity analysis of amplified 16S rRNA genes (LH-PCR). Two clone libraries were created to link the LH-PCR results to the dominant bacterial groups. The lake water bacterial community was relatively stable, with three bands dominating in all LH-PCR products. The most dominant fragment accounted for up to 72% and was derived from Actinobacteria. Based on the clone libraries and LH-PCR data, Actinobacteria also dominated in the unattached bacterial community of the FBR, whereas several Proteobacterial groups were more abundant on the FBR carrier particles. In the stabilised AGR system a major change in the community structure of the lake water bacteria took place during passage within the first 0.6 m in the sand column as the community composition shifted from Actinobacteria-dominated populations to a diverse, mainly Proteobacterial communities. Concurrently, most of the dissolved organic carbon (DOC) was removed at this stage. In summary, the study showed that the make-up of microbial communities in experimental AGR systems responded to changes in their environment. LH-PCR showed potential as a method to determine microbial community dynamics in long-term studies at real-scale AGR sites. This is the first step to provide data on microbial community dynamics in AGR for drinking water production.     

Characterization of nitrifying granules produced in an aerobic upflow fluidized bed reactor

Since nitrification is the rate-determining step in the biological nitrogen removal from wastewater, many research studies have been conducted on the immobilization of nitrifying bacteria. In this research, granulation of nitrifying bacteria in an aerobic upflow fluidized bed (AUFB) reactor in a nitrification process for inorganic wastewater containing 500 g/m³ of NH₄⁺-N was investigated. It was observed that spherical, pseudocubic and elliptical granules with a diameter of 346 μm were produced at the bottom of the reactor after 300 days. Denaturing gradient gel electrophoresis analysis revealed that Nitrosomonas-like bacteria were the dominant ammonia-oxidizing species in the granules. Many colonies of Nitrosomonas-like bacteria were found in the outer part of the granules based on the spatial distribution analysis by fluorescence in situ hybridization. By stepwise reduction of the hydraulic retention time, the ammonia removal rate of the AUFB reactor containing these nitrifying granules finally reached 1.5 kg-N/m³/day. Results suggested that the use of granules realizes the retention of a large amount of nitrifying bacteria in the reactor, which guarantees a highly efficient nitrification.     

Exploiting olive oil mill effluents as a renewable resource for production of biodegradable polymers through a combined anaerobic–aerobic process

BACKGROUND: The performance of a three‐stage process for polyhydroxyalkanoate (PHA) bioproduction from olive oil mill effluents (OME) has been investigated. In the first anaerobic stage OME were fermented in a packed bed biofilm reactor into volatile fatty acids (VFAs). This VFA‐rich effluent was fed to the second stage, operated in an aerobic sequencing batch reactor (SBR), to enrich mixed cultures able to store PHAs. Finally, the storage response of the selected consortia was exploited in the third aerobic stage, operated in batch conditions. RESULTS: The anaerobic stage increased the VFA percentage in the OME from 18% to ～32% of the overall chemical oxygen demand (COD). A biomass with high storage response was successfully enriched in the SBR fed with the fermented OME at an organic load rate of 8.5 gCOD L^?1 d^?1, with maximum storage rate and yield (146 mgCOD gCOD^?1 h^?1 and 0.36 COD COD^?1, respectively) very similar to those obtained with a synthetic VFA mixture. By means of denaturing gradient gel electrophoresis (DGGE) analysis, different bacterial strains were identified during the two SBR runs: Lampropedia hyalina and Candidatus Meganema perideroedes, with the synthetic feed or the fermented OMEs, respectively. In the third stage, operated at increasing loads, the maximum concentration of the PHA produced increased linearly with the substrate fed. Moreover, about half of the stored PHAs were produced from substrates other than VFAs, mostly alcohols. CONCLUSION: The results obtained indicate that the process is effective for simultaneous treatment of OME and their valorization as a renewable resource for PHA production. Copyright © 2009 Society of Chemical Industry     

Removal of polychlorinated dioxins by semi-aerobic fed-batch composting with biostimulation of “Dehalococcoides”

A semi-aerobic, mesophilic, fed-batch composting (FBC) reactor loaded with household garbage was used to remove polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs). The reactor was packed with woodchips as the solid matrix and PCDD/F-contaminated soil or flyash and then operated at a waste-loading rate of 0.5 kg (wet wt) day^- 1. All congeners of PCDD/Fs (initial concentration, 200–830 pmol g^- 1 [dry wt]) were totally reduced during the over period of operation, with a half reduction time of 4 months. Direct cell counting and respiratory quinone profiling showed that the reactors at the fully acclimated stage harbored a high population density of bacteria (10¹¹ g^- 1 [dry wt]) with members of the Actinobacteria predominating. Real-time quantitative PCR showed that the population of “Dehalococcoides” and its phylogenetic relatives of Chloroflexi as the possible dechlorinators varied between at the order of 10⁷ to 10⁸ g^- 1 (dry wt). A “Dehalococcoides”-containing dechlorinating culture from the soil-treating reactor was successfully enriched with a model PCDD/F compound, fthalide. 16S rRNA gene-targeted PCR-denaturated gradient gel electrophoresis and clone library analyses showed that this culture comprised at least three major phylogenetic groups of bacteria, Acidaminobacter, “Dehalococcoides,” and Rhizobium. These results suggest that the semi-aerobic FBC process is applicable for the bioremediation of PCDD/Fs and possibly other haloorganic compounds with the biostimulation of “Dehalococcoides” and its relatives as the potent dechlorinators.     

Application of the denaturing gradient gel electrophoresis (DGGE) technique as an efficient diagnostic tool for ciliate communities in soil

Ciliates (or Ciliophora) are ubiquitous organisms which can be widely used as bioindicators in ecosystems exposed to anthropogenic and industrial influences. The evaluation of the environmental impact on soil ciliate communities with methods relying on morphology-based identification may be hampered by the large number of samples usually required for a statistically supported, reliable conclusion. Cultivation-independent molecular-biological diagnostic tools are a promising alternative to greatly simplify and accelerate such studies. In this present work a ciliate-specific fingerprint method based on the amplification of a phylogenetic marker gene (i.e. the 18S ribosomal RNA gene) with subsequent analysis by denaturing gradient gel electrophoresis (DGGE) was developed and used to monitor community shifts in a polycyclic aromatic hydrocarbon (PAH) polluted soil. The semi-nested approach generated ciliate-specific amplification products from all soil samples and allowed to distinguish community profiles from a PAH-polluted and a non-polluted control soil. Subsequent sequence analysis of excised bands provided evidence that polluted soil samples are dominated by organisms belonging to the class Colpodea. The general DGGE approach presented in this study might thus in principle serve as a fast and reproducible diagnostic tool, complementing and facilitating future ecological and ecotoxicological monitoring of ciliates in polluted habitats.     

Evaluation of microbial dynamics during the ripening of a traditional Taiwanese naturally fermented ham

Isolation and identification of the autochthonous starter from a naturally fermented meat allows control of the fermentation process and promises microbiological safety for this specialty. Thus the purpose of this study was to identify the lactic acid bacteria and coagulase-negative cocci present in a traditional Taiwanese naturally fermented ham (TNFH) and to study the microbial dynamics at different ripening stages; the approach was a combination of conventional microbiological cultivation, polymerase chain reaction-denaturing gradient gel electrophoresis and DNA sequencing. In total, twelve different strains of lactic acid bacteria and three Staphylococcus strains were identified in the TNFH samples, whereas only 5 dominant strains were observed in the TNFH samples when the DGGE as a culture-independent method was applied. The bacterial ecology on the surface of the samples was mainly characterized by the stable presence of Lactobacillus sakei and Staphylococcus saprophyticus; nonetheless Leuconostoc mesenteroides and Carnobacterium divergens were the most abundant bacteria found in the final product. These results are also agreed with the findings of the culture-independent method. In addition, Microbacterium spp., Carnobacterium spp., Enterobacter spp., Brochothrix spp., Enterococcus spp., and Bacillus spp. were also present at the beginning of the ripening, but few bacteria were found at the center of the TNFH samples during the early ripening stages. However, after 30 days of ripening, the microbial ecology at the center of the TNFH samples paralleled that of the surface. Finally, as far as we have been able to determine, our report is the first to investigate the microbiological dynamics in fermented meat products using combination of cultivation, the Harrison disc method, DGGE and DNA sequencing as the culture-dependent method. Our report is also the first to show the presence of Staphylococcus arlettae in a fermented sausage and ham product.