Functional bacterial and archaeal community structures of major trophic groups in a full-scale anaerobic sludge digester

Functional Bacteria and Archaea community structures of a full-scale anaerobic sludge digester were investigated by using a full-cycle 16S rRNA approach followed by microautoradiography (MAR)-fluorescent in situ hybridization (FISH) technique and micromanipulation. FISH analysis with a comprehensive set of 16S and 23S rRNA-targeted oligonucleotide probes based on 16S rRNA clone libraries revealed that the Gram-positive bacteria represented by probe HGC69A-hybridized Actinobacteria (8.5+/-1.4% of total 4', 6-diamidino-2-phenylindole (DAPI)-stained cells) and probe LGC354-hybridized Firmicutes (3.8+/-0.8%) were the major phylogenetic bacterial phyla, followed by Bacteroidetes (4.0+/-1.2%) and Chloroflexi (3.7+/-0.8%). The probe MX825-hybridized Methanosaeta (7.6+/-0.8%) was the most abundant archaeal group, followed by Methanomicrobiales (2.8+/-0.6%) and Methanobacteriaceae (2.7+/-0.4%). The functional community structures (diversity and relative abundance) of major trophic groups were quantitatively analyzed by MAR-FISH. The results revealed that glucose-degrading microbial community had higher abundance (ca. 10.6+/-4.9% of total DAPI-stained cells) and diversity (at least seven phylogenetic groups) as compared with fatty acid-utilizing microbial communities, which were more specialized to a few phylogenetic groups. Despite the dominance of Betaproteobacteria, members of Chloroflexi, Smithella, Syntrophomonas and Methanosaeta groups dominated the [(14)C]glucose-, [(14)C]propionate-, [(14)C]butyrate- and [(14)C]acetate-utilizing microorganism community, and accounted for 27.7+/-4.3%, 29.6+/-7.0%, 34.5+/-7.6% and 18.2+/-9.5%, respectively. In spite of low abundance (ca. 1%), the hitherto unknown metabolic functions of Spirochaeta and candidate phylum of TM7 as well as Synergistes were found to be glucose and acetate utilization, respectively.     

Natural organic matter (NOM) removal and structural changes in the bacterial community during artificial groundwater recharge with humic lake water

This study evaluated the removal of natural organic matter (NOM) and structural changes in the microbial community during infiltration of humic lake water at three artificial groundwater recharge (AGR) sites in Finland. The three sites were at waterworks in Hämeenlinna, Jyväskylä and Tuusula, sites A, B and C, respectively. Site A used groundwater recharge by both basin and sprinkling infiltration, site B used only sprinkling infiltration, and site C used only basin infiltration. Reductions of total organic carbon at sites A, B and C were 91%, 84% and 74%, respectively, in the winter, and 88%, 77% and 73%, respectively, in the summer. The Finnish national recommended value of 2 mg/l for TOC was achieved at all sites and the TOC of natural groundwater at site C was much lower, at 0.6 mg/l. Large molecular fractions of NOM were removed more efficiently than the smaller ones. Total amount of DAPI-stained cells decreased during infiltration at sites A, B and C in winter by 94%, 94% and 75% and in summer by 96%, 97% and 94%, respectively. Bacterial communities in raw waters and extracted groundwaters were diverse with changes occurring during infiltration, which was shown by DNA extraction followed by PCR of 16S rRNA genes and denaturing gradient gel electrophoresis (DGGE) fingerprinting. While the natural groundwater microbial community was diverse, it was different from that of the extracted groundwater in the AGR area. Simultaneous organic carbon removal and the decrease of bacterial counts during infiltration indicated biodegradation. In addition, the changing DGGE profiles during the process of infiltration, demonstrated that changing environmental conditions were reflected by changes in bacterial community composition.     

Effect of dilution rate on structure of a mesophilic acetate-degrading methanogenic community during continuous cultivation

The community structures of two mesophilic acetate-degrading methanogenic consortia enriched at dilution rates of 0.025 and 0.6 d(-1) were analyzed by fluorescence in situ hybridization (FISH) and phylogenetic analyses based on 16S rDNA clonal sequences and quantitative real-time polymerase chain reaction (PCR). FISH experiments with archaeal and bacterial domain-specific probes showed that archaeal cells were predominant and only a small number of bacterial cells were detected at both dilution rates. In the domain Archaea, the number of cells closely related to Methanosarcina barkeri was shown to be greater at the high dilution rate using FISH with species-specific probes. Taxonomic analyses based on rDNA clonal sequences obtained at the low and high dilution rates showed that 43% of 100 clones and 72% of 92 clones, respectively, were affiliated with the domain Archaea and the remainders at each dilution rate were affiliated with the domain Bacteria. Within the domain Archaea, all rDNA clones at both dilution rates were affiliated with the genera Methanosaeta or Methanosarcina of the aceticlastic methanogens. Within the domain Bacteria, the rDNA clones obtained at the low dilution rate were affiliated with four phyla, Firmicutes (36%), Bacteroidetes (9%), Chloroflexi (6%) and candidate division OP12 (5%). The rDNA clones obtained at the high dilution rate were affiliated with four phyla, Firmicutes (16%), Bacteroidetes (8%), Proteobacteria (1%) and candidate division OP12 (3%). Real-time quantitative PCR experiments showed that the number of rDNA sequences affiliated with the genus Methanosarcina was greater at the high dilution rate. In addition, a significant number of rDNA sequences affiliated with the genus Methanoculleus were detected only at the low dilution rate. Detection of a hydrogenotrophic methanogen at the low dilution rate suggests that the syntrophic acetate oxidation by hydrogenotrophic methanogens and acetate-oxidizing bacteria could occur at the low dilution rate.     

Runoff-related agricultural impact in relation to macroinvertebrate communities of the Lourens River, South Africa

A field study at the Lourens River, South Africa, was undertaken during the pesticide application period between November 2001 and January 2002 in order to investigate the potential relation of agricultural pollution to the aquatic macroinvertebrate fauna. The upper regions of the Lourens River were free of contamination (LR1), whereas subsequent stretches flowing through a 400-ha orchard area (LR2) received transient insecticide peaks. Continuously operating suspended-particle samplers as well as flood samplers operating during runoff events were used to measure pesticide contamination. In addition, various physicochemical and morphological parameters were examined. A survey of the macroinvertebrate communities associated with the rocky substrates was carried out every three weeks. Community indices were calculated using the South African Scoring System (SASS 5) for bioassessment of water quality in rivers. The two sites differed in pesticide pollution as well as in average turbidity levels (LR1 5.5 mg/L; LR2 64.3 mg/L), but were similar in bottom substrate composition and most other abiotic factors. At the downstream site (LR2), pesticide values of 0.05 microg/L azinphos-methyl in water as well as 49 microg/kg azinphos-methyl, 94 microg/kg chlorpyrifos and 122 microg/kg total endosulfan in suspended particles were found during runoff conditions. The macroinvertebrate communities of the two sampling sites were similar in terms of number of total individuals, but differed significantly (ANOVA) in average number of taxa (LR1 11.7, LR2 8.9). Seven out of 17 investigated taxa occurred in significantly reduced numbers or were even absent at the downstream site LR2. The community characteristics determined by SASS 5 showed a significantly less sensitive community structure at the downstream site (TS 41; ASPT 4.6), indicating continuously lower water quality compared to site LR1 (TS 80; ASPT 6.9). It is concluded that the Lourens River macroinvertebrate communities are affected by agricultural pollution, with pesticides and increased turbidity as the most important stressors.     

Bacterial community shifts in nonylphenol polyethoxylates-enriched activated sludge

A molecular approach was used to evaluate the effect of nonylphenol ethoxylate surfactants on the bacterial diversity in lab-scale activated sludge reactors. Separate bench-scale units were fed synthetic wastewater with and without addition of branched nonylphenol ethoxylates (NPnEO). The performance of the reactors, in terms of carbonaceous removal was largely unaffected by the presence of NP10EO in the feeding solution. However, addition of NP10EO exerted a pronounced shift in bacterial community composition. In situ hybridization analyzing larger phylogenetic groups of bacteria with ribosomal RNA-targeted oligonucleotide probes revealed the dominance of clusters composed of Betaproteobacteria, accounting for up to one-third of 4',6-diamidino-2-phenylindol-dihydrochloride (DAPI)-stained cells in NP10EO amended reactors and only 5% of DAPI-stained cells in the controls. These shifts in populations of larger phylogenetic groups were confirmed by dot-blot analysis of rRNA. Members of gamma subclass of Proteobacteria were present in low numbers in all activated sludge samples examined, suggesting that only bacteria affiliated with the beta subclass of Proteobacteria may have a specific role in NP10EO degradation.     

SSCP技术在微生物群落监测中的应用

综述了应用单链构象多态性技术(SSCP)对微生物群落进行分析的基本过程,以及在模式微生物群落、人工与自然群落结构和动态分析中的应用。并针对SSCP技术存在的问题提出了一些改进建议,指出在进行复杂微生物群落分析时,应采用含有甘油的高比率凝胶(丙烯酰胺∶双丙烯酰胺>49∶1)和低pH值(7.7)的TBE电泳缓冲液,并以λ核酸外切酶将PCR产物中的反意义链去掉以减少大量非特异带的出现,提高技术的分辨率。另外,该技术在SSCP条带的菌种唯一性和纯培养标记等方面还有待改进。     

基于网络社区模块结构的特征选择性能评价

利用网络社区模块结构作为特征选择的度量指标，给出了一种基于全局拓扑结构的特征选择性能评价方法。对一种基于免疫学原理的数据压缩和特征提取模型——人工免疫网络进行了验证，通过对数据特征提取前的抗原数据网络和特征提取后的记忆网络的网络社区模块结构的对比，达到对人工免疫网络(aiNET)的特征提取性能评价的目的。实验结果证实了人工免疫网络模型可以保持网络拓扑结构上的稳定性，验证了利用网络社区结构作为特征选择度量的合理性。     

Force-Based Incremental Algorithm for Mining Community Structure in Dynamic Network

Community structure is an important property of network. Being able to identify communities can provide invaluable help in exploiting and understanding both social and non-social networks. Several algorithms have been developed up till now. However, all these algorithms can work well only with small or moderate networks with vertexes of order 104. Besides, all the existing algorithms are off-line and cannot work well with highly dynamic networks such as web, in which web pages are updated frequently. When an already clustered network is updated, the entire network including original and incremental parts has to be recalculated, even though only slight changes are involved. To address this problem, an incremental algorithm is proposed, which allows for mining community structure in large-scale and dynamic networks. Based on the community structure detected previously, the algorithm takes little time to reclassify the entire network including both the original and incremental parts. Furthermore, the algorithm is faster than most of the existing algorithms such as Girvan and Newman＇s algorithm and its improved versions. Also, the algorithm can help to visualize these community structures in network and provide a new approach to research on the evolving process of dynamic networks.     

复杂网络的一种快速局部社团划分算法

为了快速准确地寻找大规模复杂网络的社团结构,文中基于节点度优先的思想,提出了一种新的寻找复杂网络中的局部社团结构的启发式算法.该算法的基本思想是从待求节点出发,基于节点的度有选择性的进行广度优先搜索,从而得到该节点所在的局部社团结构.由于该算法仅需要利用到节点的局部信息,因此时间复杂度很低,达到了线性的时间复杂度.将该算法应用于社会学中经典的Zachary网络,获得了满意的结果.最后,还分析了如何对该算法加以改进以进一步提高准确度.     

智能化指挥控制通讯系统设计

讨论了智能化指挥控制通讯系统的设计、系统的体系结构,以及研制设计中的一些问题。探讨了一些相应的设计方法和技术。