Effect of chemical and physical parameters on a pulp mill biotreatment bacterial community

The bacterial community composition in an activated sludge plant treatment from a bleached kraft pulp mill was monitored over a period of 209 days. Using DGGE and terminal-Restriction Fragment Length Polymorphism (t-RFLP) analysis we generated community DNA fingerprints over the time period. Both methods produce fingerprints that can be used to monitor stability in the system and generate fragments that can be associated with bacterial taxa. Chemical and physical parameters were also collected during that same time frame. We found a number of significant correlations with influent variables such as temperature, chemical oxygen demand (COD), Biochemical oxygen demand (BOD) and chloroform concentrations suggesting that these were the most likely parameters to influence the bacterial community structure. In addition several taxa correlated to important performance indicators such as COD/BOD removals and SVI. Multivariate analysis also confirmed the strong links between taxa variation and temperature, nutrient loads, chloroform and also one class of filaments. Establishing the identity of these taxa and their ecological preferences will greatly enhance our understanding and management of biological treatment systems.     

香蕉抗性淀粉对C57BL/6J肥胖小鼠肠道放线菌群的调控作用

目的:研究不同剂量香蕉抗性淀粉(resistant starch,RS)对高脂饮食诱导的C57BL/6J肥胖小鼠肠道放线菌群多样性的影响。方法:将40只C57BL/6J小鼠随机分为5组,分别采用普通饲料(CONV)、高脂饲料(HF)以及添加5%、10%、15%香蕉抗性淀粉的高脂饲料(5%RS+HF、10%RS+HF、15%RS+HF)进行饮食干预,8周后采用变性梯度凝胶电泳(denaturing gradient gel electrophoresis,DGGE)技术对小鼠粪便样本放线菌菌群组成进行分析,采用实时荧光定量聚合酶链式反应技术对小鼠粪便样本双歧杆菌数量进行比较。结果:DGGE图谱分析显示,HF组聚类与其余4组彻底分离,抗性淀粉各组趋于成簇但无明显界限。5%RS+HF组与15%RS+HF组放线菌多样性和丰富度方面均显著低于CONV组与HF组(P0.05),10%RS+HF组多样性和丰富度较另外2组RS+HF组有所上升。高脂饲料能够极显著降低肠道中双歧杆菌数量(P0.01),而10%和15%香蕉抗性淀粉的加入均高度显著增加双歧杆菌数量(P0.001)。结论:香蕉抗性淀粉可恢复肥胖小鼠肠道放线菌群多样性,显著促进双歧杆菌生长,且具有剂量依赖关系。     

不同区域污水处理厂活性污泥中微生物菌落结构分析

结合纯种分离纯化和变性梯度凝胶电泳法（DGGE）分析了中国不同区域污水处理厂的曝气池中活性污泥的微生物群落结构及差异性。其中,可培养微生物经纯化后对16s rDNA片段进行PCR扩增并测序,在Blast中分析后构建系统发育树。分离培养得到的89种细菌大部分属于β-变形菌门（Bataproteobacteria）、γ-变形菌门（Gamaproteobacteria）和厚壁菌门（Firmicutes）。DGGE分析表明所有活性污泥样品中的菌种丰富度都很高,不同的样品中存在很多相同的条带,是属于所有活性污泥中共有的优势菌群,说明不同的活性污泥系统具有高度的生物相似性;每个地区的样品中也都含有自己的特异条带。并且同一地区活性污泥的相似性大于不同地区活性污泥的相似性,主要与各地区不同的自然经济环境和人们的生活习惯相关。     

Assessment of commercial probiotic products in China for labelling accuracy and probiotic characterisation of selected isolates

Microbial populations in probiotic supplements in China were investigated using the plate count method and PCR–DGGE technique. Our results indicated that total viable cells in most probiotic products could meet the minimum requirement of the Chinese National Standards (10⁶ CFU/mL); however, total viable cell counts of the species detected in the probiotic products did not correspond with the cell number given in the label.     

Xanthohumol does not affect the composition of rat intestinal microbiota

Xanthohumol (XN), a prenylated chalcone, has been proposed to have beneficial effects on human health, including antimicrobial activity. To clarify whether the exposure to XN has an impact on the composition of the intestinal microbiota, 100 mg XN/kg body weight was given daily to rats for 4 wk. Diversity of the fecal microbial community was analyzed using PCR-DGGE. Although intact XN was detected in the feces of the rats at a concentration of up to 2.3 mg/g fecal dry weight, major shifts in the PCR-DGGE patterns in response to this flavonoid were not observed. The similarity index decreased slightly from 70 to 62% for the XN-treated rats and from 71 to 63% for the untreated animals. Thus, changes in the rat fecal microbiota observed in the course of the XN application are most likely due to intraindividual variability. However, the water content of the feces increased significantly during the XN treatment period.     

Yeast dynamics during the fermentation of brined green olives treated in the field with kaolin and Bordeaux mixture to control the olive fruit fly

The yeast microbiota associated with naturally fermented and inoculated green table olives, differently treated in the field with non-conventional repellent and antiovipositional products in the control of Bactrocera oleae, was analysed using a combination of culture-dependent and -independent molecular fingerprinting. The routine yeast isolation gave rise to 118 strains, whose identification was performed by PCR-RFLP of the internal transcribed spacer (ITS) regions. Total DNA was extracted directly from the brine throughout fermentation by means of an experimental protocol that included the removal of Taq polymerase inhibitors. Denaturing Gradient Gel Electrophoresis (DGGE) of 26S rRNA gene PCR amplicons highlighted the yeast community. Comparison of both culture-dependent and independent methods indicated that the yeast species Saccharomyces cerevisiae, Wickerhamomyces anomalus, Candida diddensiae and Issatchenkia orientalis were dominant during fermentation despite the addition of the Lactobacillus plantarum starter used in brining. The resultant isolated species were unaffected by treatments in field, except for C. diddensiae whose growth was delayed by kaolin.     

Evaluation and optimisation of bacterial genomic DNA extraction for no-culture techniques applied to vinegars

Direct genomic DNA extraction from vinegars was set up and suitability for PCR assays performed by PCR/DGGE and sequencing of 16S rRNA gene. The method was tested on 12 intermediary products of special vinegars, fruit vinegars and condiments produced from different raw materials and procedures. DNAs extraction was performed on pellets by chemical, enzymatic, resin mediated methods and their modifications. Suitable yield and DNA purity were obtained by modification of a method based on the use of PVP/CTAB to remove polyphenolic components and esopolysaccharides. By sequencing of bands from DGGE gel, Gluconacetobacter europaeus, Acetobacter malorum/cerevisiae and Acetobacter orleanensis were detected as main species in samples having more than 4% of acetic acid content. From samples having no acetic acid content, sequences retrieved from excised bands revealed high similarity with prokaryotes with no function on vinegar fermentation: Burkholderia spp., Cupriavidus spp., Lactococcus lactis and Leuconostoc mesenteroides. The method was suitable to be applied for no-culture study of vinegars containing polyphenols and esopolysaccharides allowing a more complete assessment of vinegar bacteria.     

A DGGE Marker‐Mediated Fast Monitoring of Bacterial Diversity and Comprehensive Identification of High‐Temperature Daqu Starter

Bacteria play an essential role in Daqu starter (Daqu) fermentation. The identification of Daqu bacteria was investigated by polymerase chain reaction (PCR) based denaturing gradient gel electrophoresis (DGGE) analysis of the highly variable V3 region of the 16S rRNA gene. Here, we define a novel DGGE marker for the quick identification of Daqu bacteria. A dynamic alteration of the bacterial populations at different stages of fermentation was determined through a 2‐y continuous monitoring. The physicochemical parameters of Daqu at different fermentation stages were investigated by weighing, NaOH titration, and HCl hydrolysis together with Fehling reagent methods. Furthermore, infrared spectral analysis using Fourier Transformed Infrared Spectroscopy was performed to determine physicochemical changes of Daqu. Therefore, our studies provide key insight for a comprehensive quality control of Daqu at different fermentation stages using the PCR‐DGGE analysis combined with the physicochemical measurement.     

Dynamics of the functional gene copy number and overall bacterial community during microcystin-LR degradation by a biological treatment facility in a drinking water treatment plant

Information is limited on the potential for microcystins (MCs) degradation by carrier-attached biofilms obtained in winter that were not exposed to detectable levels of MCs in the preceding months. Under controlled laboratory conditions, we confirmed that microcystin-LR (MCLR) was effectively biodegraded within 5.5 days in cultures of the biofilm sampled in winter. Quantitative polymerase chain reaction (qPCR) assays revealed that seasonal variations in the MCLR-degradation potential of the biofilm were closely related to the initial MCLR-degrader population in the biofilm. Indigenous MCLR-degraders in the biofilm could accumulate by exposure to natural MCLR in the water column, accelerating MCLR-degradation. The qPCR assay suggested that MCLR may be a primary substrate for the degraders in the presence of another labile organic carbon associated with the biofilm under the present study conditions. qPCR and PCR-denaturing gradient gel electrophoresis (DGGE) for 16S rDNA demonstrated that the overall bacterial population from the winter biofilm rapidly increased with the MCLR-degrader population and remained stable after day 3.5, while the overall bacterial community structure shifted throughout the entire biodegradation period. This study is important to the in-depth understanding of microbial degradation of MCs and could facilitate the bioremediation of MCs in polluted habitats.     

Spatial Distribution of Bacterial Communities and Related Biochemical Properties in Luzhou‐Flavor Liquor‐Fermented Grains

Grain fermenting with separate layers in a fermentation pit is the typical and experiential brewing technology for Chinese Luzhou‐flavor liquor. However, it is still unclear to what extent the bacterial communities in the different layers of fermented grains (FG) effects the liquor's quality. In this study, the spatial distributions of bacterial communities in Luzhou‐flavor liquor FG (top, middle, and bottom layers) from 2 distinctive factories (Jiannanchun and Fenggu) were investigated using culture‐independent approaches (phospholipid fatty acid [PLFA] and polymerase chain reaction–denaturing gel electrophoresis [DGGE]). The relationship between bacterial community and biochemical properties was also assessed by Canonical correspondence analysis (CCA). No significant variation in moisture was observed in spatial samples, and the highest content of acidity and total ester was detected in the bottom layer (P < 0.05). A high level of ethanol was observed in the top and middle layers of Fenggu and Jiannanchun, respectively. Significant spatial distribution of the total PLFA was only shown in the 50‐y‐old pits (P < 0.05), and Gram negative bacteria was the prominent community. Bacterial 16S rDNA DGGE analysis revealed that the most abundant bacterial community was in the top layers of the FG both from Fenggu and Jiannanchun, with Lactobacillaceae accounting for 30% of the total DGGE bands and Lactobacillus acetotolerans was the dominant species. FG samples from the same pit had a highly similar bacterial community structure according to the hierarchal cluster tree. CCA suggested that the moisture, acidity, ethanol, and reducing sugar were the main factors affecting the distribution of L. acetotolerans. Our results will facilitate the knowledge about the spatial distribution of bacterial communities and the relationship with their living environment.