黄瓜连作土壤微生物区系变化研究

研究了黄瓜根部土壤主要微生物类群随连作茬次的反应,并着重用变性梯度凝胶电泳(DGGE)监测黄瓜根际未培养优势菌群的动态变化。结果表明:随着连作茬次增加,土壤可培养微生物数量减少,其中细菌数量降低更为明显,对连作表现出较高的敏感性,放线菌对黄瓜连作反应稍滞后,至第三茬时开始呈现降低趋势。黄瓜连作致使少数真菌种群富集,同时多种真菌类群数量减少,种群变化呈现单一化趋势,多样性水平降低。DGGE分析结果表明黄瓜连作引起根际Bacillus sp.、Pseudom onas sp.和另一未培养细菌种群数量减少,而同时引起Sphingom onas sp.类群数量增加。实验结果暗示,黄瓜连作破坏根部微生物种群生态平衡,使其多样性水平降低。     

金霉素对畜禽养殖废水厌氧生物处理及细菌多样性的影响

该文研究了不同金霉素浓度下畜禽养殖废水厌氧生物处理系统的COD去除率和产甲烷量,运用PCR—DGGE及差异DNA片段回收克隆测序的方法分析了金霉素对该厌氧生物处理系统细菌多样性的影响。结果表明随着金霉素浓度的增加,畜禽养殖废水的COD去除率和产甲烷量均会受到抑制,产甲烷量差值从6．9％扩大到29．2％,COD去除率从90．89％降至86．96％,而对照组COD去除率达到94．46％。PCR—DGGE分析表明金霉素胁迫能够显著降低畜禽养殖废水厌氧生物处理系统中的细菌多样性,细菌群落丰富度值从0．913降至0．652,而对照组的丰富度值为1。     

Effects of transient temperature conditions on the divergence of activated sludge bacterial community structure and function

The effect of temperature fluctuations on bacterial community structure and function in lab-scale sequencing batch reactors treating bleached kraft mill effluent was investigated. An increase in temperature from 30 to 45 degrees C caused shifts in both bacterial community structure and function. Triplicate reactors were highly similar for 40 days following startup. After the temperature shift, their community structure and function started to diverge from each other and from the control. A multi-response permutation procedure confirmed that the variability in community structure between transient and control reactors were greater than that among the triplicate transient reactors. The fact that these disturbances manifest themselves in different ways in apparently identical reactors suggests a high degree of variability between replicate systems.     

Systematic study of the effect of operating variables on reactor performance and microbial diversity in laboratory-scale activated sludge reactors

Biological treatment processes are “complex systems” where many different kinds of microbes grow and interact in a dynamic manner. Understanding the relationship between microbial diversity and bioreactor performance could facilitate the optimisation of bioreactor design and enable the solution of bioreactor-related problems. However, systematic studies of the effects of operating variables on microbial diversity and reactor performance are rare. In this study, we determined the effects of different operating conditions and system configurations on the performance of laboratory-scale activated sludge reactors and microbial diversity, based on experiments designed using the factorial design approach. We found that the overall system performance and the diversity of the microbial communities in the reactors were affected by changes in the operating parameters. However, the relationship between diversity and performance was sometimes counterintuitive, as increases in system performance were not always associated with increased community diversity. Reactor configuration and addition of soil had the biggest effects on reactor performance, while the effects of organic loading rates and feed composition were less marked. Of all these parameters, reactor configuration was the only one that had a consistent effect on reactor community diversity.     

Common key acidogen populations in anaerobic reactors treating different wastewaters: molecular identification and quantitative monitoring

Bacterial population dynamics during the start-up of three lab-scale anaerobic reactors treating different wastewaters, i.e., synthetic glucose wastewater, whey permeate, and liquefied sewage sludge, were assessed using a combination of denaturing gradient gel electrophoresis (DGGE) and real-time PCR techniques. The DGGE results showed that bacterial populations related to Aeromonas spp. and Clostridium sticklandii emerged as common and prominent acidogens in all reactors. Two real-time PCR primer/probe sets targeting Aeromonas or C. sticklandii were developed, and successfully applied to quantitatively investigate their dynamics in relation to changes in reactor performance. Quantitative analysis demonstrated that both Aeromonas- and C. sticklandii-related populations were highly abundant for acidogenic period in all reactors. Aeromonas populations accounted for up to 86.6-95.3% of total bacterial 16S rRNA genes during start-up, suggesting that, given its capability of utilizing carbohydrate, Aeromonas is likely the major acidogen group responsible for the rapid initial fermentation of carbohydrate. C. sticklandii, able to utilize specific amino acids only, occupied up to 8.5-55.2% of total bacterial 16S rRNA genes in the reactors tested. Growth of this population is inferred to be supported, at least in part, by non-substrate amino acid sources like cell debris or extracellular excretions, particularly in the reactor fed on synthetic glucose wastewater with no amino acid source. The quantitative dynamics of the two acidogen groups of interest, together with their putative functions, suggest that Aeromonas and C. sticklandii populations were numerically as well as functionally important in all reactors tested, regardless of the differences in substrate composition. Particularly, the members of Aeromonas supposedly play vital roles in anaerobic digesters treating various substrates under acidogenic, fermentative start-up conditions.     

Cider Apple Native Microbiota Characterization by PCR‐DGGE

The surface microbiota of different recognized apple varieties used to elaborate a Protected Designation of Origin cider was studied to analyse the microbial diversity and its potential link to the microorganisms involved in the cider fermentation process. The V3 region of the bacterial 16S gene and the D1 domain of the eukaryotic 26S gene were amplified by polymerase chain reaction (PCR) and analysed by denaturing gradient gel electrophoresis (DGGE). The most intense bands found in the DGGE profiles were sequenced and compared with those in the GenBank database. The profiles showed a high microbial diversity, but little variation was found among the varieties. Identification of the bands showed that the usual species associated with an apple juice fermentation were not found, suggesting that the microorganisms responsible for spontaneous fermentation come from the equipment and the production environment. Copyright © 2015 The Institute of Brewing & Distilling     

Analysis of bacterial communities of traditional fermented West African cereal foods using culture independent methods

In this study, the microbial composition of kunu-zaki and ogi, two popular foods in Nigeria produced after natural, uncontrolled fermentation of cereals, was assessed by culture-independent molecular profiling methods. In particular, PCR-denaturing gradient gel electrophoresis and construction of 16S rRNA gene clone libraries revealed the presence of diverse bacterial communities. DNA sequencing of the highly variable V3 region of the 16S rRNA genes obtained from PCR-DGGE fingerprints identified species related to Weissella confusa, Lactobacillus fermentum, Lactobacillus amylolyticus, Lactobacillus delbrueckii subsp. bulgaricus, Bacillus spp. and Lactococcus lactis spp lactis from food samples obtained from northern and southern geographical locations. A more comprehensive analysis of 272 full-length 16S rRNA gene inserts revealed that 70% of them were assigned to the Lactobacillaceae family and 19% to the Streptococcaceae family. Interestingly, sequences associated with a particular food type were also identified. For example, L. plantarum, L. pantheris and L. vaccinostercus were found in ogi but not in kunu-zaki while W. confusa, Streptococcus lutetiensis and Streptococcus gallolyticus subsp. macedonicus were found in kunu-zaki but not in ogi. Phylotypes corresponding to potentially pathogenic bacteria, such as Clostridium perfringens and Bacillus cereus were also detected highlighting the need for controlled fermentation processes.     

Microbial populations on brewery filling hall surfaces – Progress towards functional coatings

Microbial populations on equipment surfaces of beverage filling lines were investigated as a function of surface coating type, location and time. Photocatalytic metal-ion doped (Ag or Mo) and non-doped TiO₂ coatings deposited using reactive magnetron sputtering and spray coating methods were studied as means to reduce microbial numbers accumulating on the surfaces. The coatings were applied to stainless steel coupons, which were mounted to one canning and one glass bottle filling line for 3–5 months. After exposure microbial numbers on the coupons were evaluated by culturing, and bacterial community profiles were characterised with PCR-DGGE (denaturing gradient gel electrophoresis). The results showed that the longer the run time after washes the higher microbial numbers were detected, and that the two filling lines each had their characteristic bacterial community. The major species identified were members of Acinetobacter sp., lactic acid bacteria and enterobacteria. No clear effect of the different coating materials on the microbial numbers or bacterial community composition on the surfaces was shown. In conclusion, functional coatings with sufficient mechanical and chemical durability for industrial surfaces have been developed. Although these coatings have been previously reported to reduce the number of microorganisms on the surfaces in vitro, their efficacy in the challenging beverage process conditions was not proven.     

Culture independent methods to assess the diversity and dynamics of microbiota during food fermentation

Culture independent methods first appeared in the food microbiology field at the end of the 90s and since then they have been applied extensively. These methods do not rely on cultivation and target nucleic acids (DNA and RNA) to identify and follow the changes that occur in the main populations present in a specific ecosystem. The method that has most often been used as a culture independent method in food microbiology is denaturing gradient gel electrophoresis (DGGE). The number of papers dealing with DGGE grew exponentially in the late nineties and, by analysing the studies available in the literature, it is possible to describe a trend in the subjects that have been investigated. DGGE was first used as a tool to monitor the ecology of fermented food, such as fermented sausage, cheese and sourdough, and later it also showed its potential in microbial spoilage process. In the last few years, the main application of DGGE has been to study fermented food from Asia, Africa and South America.