多能硫杆菌RubisCO基因同源性分析

以氧化亚铁硫杆菌1,5—二磷酸核酮糖羧化酶/加氧酶(RubisCO)基因为探针,与氧化硫硫杆菌和多能硫杆菌的染色体DNA杂交。结果表明,氧化硫硫杆菌的染色体DNA能够与氧化亚铁硫杆菌RubisCO基因探针杂交。而多能硫杆菌不能与其杂交,然而却能够与球形红杆菌RubisCO基因探针杂交,同源性高。由于RubisCO在进化上的高度保守性,因此认为它们在RubisCO进化关系上应属于不同的类群。     

脱氮硫杆菌的脱硫特性及其处理恶臭物质硫化氢的应用

污水和污泥的处理过程中会产生大量的恶臭气体硫化氢(H2S)。脱氮硫杆菌是氧化H2S和其他硫化物的重要的脱硫工程菌。本文阐述了脱氮硫杆菌的生物学特性和氧化H2S的两种途径。分析了反应体系中的硫化物负荷、硝酸盐和亚硝酸盐的浓度、氧含量以及pH值等因素对氧化效果、反应速率、氧化途径及产物形式的影响。介绍了脱氮硫杆菌在恶臭污染治理中的应用及其在同步处理含氮含硫恶臭物质方面的发展趋势。     

一株异养脱硫反硝化菌株的筛选及其生物脱硫脱氮特性研究

【目的】从生物脱硫脱氮EGSB-DSR反应器的污泥中分离筛选出具有生物脱硫脱氮特性的细菌,并对其生物脱硫脱氮的性能进行研究。【方法】采用Hungate厌氧滚管技术筛选功能微生物,从稳定运行的生物脱硫脱氮EGSB-DSR反应器的污泥中分离筛选出一株高效的生物脱硫脱氮细菌A2。【结果】经过16S rRNA基因序列鉴定,菌株A2为固氮弧菌属(Azoarcus sp.)。其典型特征为能够以有机碳作为电子供体,将亚硝酸盐或者硝酸盐转化为氮气的同时还能将硫化物氧化为硫单质。因此具备了高效同步代谢有机碳、NO3–和S2–的特征。这是首次关于固氮弧菌属能够进行反硝化脱硫的相关报道。对菌株A2的生物脱硫脱氮能力的分析表明,在硫化物S2–浓度200 mg/L,NO3?浓度87.5 mg/L,乙酸根离子浓度200 mg/L的条件下,菌株A2在20 h内完成对碳、氮、硫的脱除。菌株对于碳、氮去除率均达到99%,对于硫的去除率达到95%。【结论】结果表明固氮弧菌属A2具有高效的生物脱硫脱氮功能,将有望成为强化生物脱硫脱氮工艺的潜在微生物资源。     

脱氮除硫菌株的分离鉴定和功能确认

从长期稳定运行的脱氮除硫反应器污泥中,分离获得两株具有脱氮除硫功能的芽孢杆菌。经形态观察、生理试验和16SrDNA序列比对,将两菌株归入芽孢杆菌属,菌株CB归类于Bacillus pseudofirmus,菌株CS则与Bacillus hemicellulosilytus和Bacillus halodurans最为接近。以Biolog板检测,菌株CB的基质多样性不明显,菌株CS则可利用Biolog板中多种碳源。菌株CB和菌株CS都能以硝酸盐氧化硫化物,其中菌株CB对硝酸盐、硫化物的转化能力大于CS,菌株CB对硝酸盐的亲和力也大于菌株CS。     

脱氮硫杆菌对硫酸盐还原菌生长的抑制作用

为了研究脱氮硫杆菌(Thiobacillus denitrificans,TDN)对硫酸盐还原菌(sulfate-reducing bacteria,SRB)生长的影响,将从污水中分离到的硫酸盐还原菌和从pH为2~3的酸性土壤中分离到的脱氮硫杆菌(TDN)用于含适当浓度硫酸盐和硝酸盐的模拟污水的处理,并测定单菌或混菌培养后系统中硫酸盐、硝酸盐浓度的变化以及硫化氢的产量。结果表明,在仅接种硫酸盐还原菌的培养系统中,硫酸盐和硝酸盐的含量分别降低4.8%和1.0%;而在同时接种脱氮硫杆菌和硫酸盐还原菌的系统中硫酸盐的含量升高了4.7%,但硝酸盐氮含量降低了25%,这一作用随着培养基中硝酸盐起始浓度的提高而得到加强。另外,混菌培养系统的硫化氢浓度比单一硫酸盐还原菌培养系统降低了65.93%。由此推断,在混菌培养系统中,脱氮硫杆菌通过其反硝化过程产生的代谢产物使硫酸盐还原菌的生长环境条件发生改变,从而抑制其生长并减少了硫化氢的产生。这对预防硫酸盐还原菌带来的不利影响提供了有效的措施。     

废水中的脱氮除硫研究

随着氮、硫污染物对江河湖泊污染的扩大,同步脱氮除硫已成为净化水体的一个重要课题。试验中采用UASB反应器,接种含有厌氧氨氧化菌的污泥处理含有氮硫的废水。通过硫酸盐取代亚硝酸作为电子受体,驯化同步脱氮除硫。进水浓氨氮和硫酸盐浓度分别控制在50～60mg·L^-1和210～240mg·L^-1的情况下,60天后得到一定的稳定处理效果,出水氨氮和硫酸盐浓度为30mg·L和160mg·L^-1。这种新型的脱氮除硫现象有助于为氮硫循环开辟新的途径。     

荧光原位杂交技术对土壤石油降解菌的检测

从辽河油田样品中筛选出一株高效石油降解菌,经鉴定为地衣芽孢杆菌。针对其16S rRNA设计寡核苷酸探针。荧光原位杂交(FISH)技术利用寡核苷酸探针检测特定细胞内的互补核苷酸序列。通过对纯菌和泥浆中地衣芽孢杆菌的FISH进行优化,得到泥浆中地衣芽孢杆菌的荧光原位杂交实验条件：样品固定时间17 h,杂交温度46 ℃,杂交时间3 h,杂交液中去离子甲酰胺浓度35%,冲洗缓冲液中与去离子甲酰胺对应的NaCl的浓度88 mmol·L^-1。运用上述FISH技术监测生物泥浆反应器中地衣芽孢杆菌量的变化,并与泥浆中含油率的变化进行比较,二者的变化情况符合微生物降解石油的趋势,为监测含油污泥中微生物的变化提供了一种可行的技术。     

用反向斑点杂交方法检测猪常见致病菌

目的:建立检测猪常见致病菌的反向斑点杂交方法。方法:将23S rRNA基因芯片用的针对12种细菌的25～30 mer探针加长到30～38 mer,2对通用引物序列不变。用地高辛标记下游引物,以尼龙膜为载体制备膜芯片,检验探针/膜杂交的特异性和敏感性;另外设计1条大肠杆菌K88基因探针、一段带K88探针的报告基因和1对报告基因的反向PCR引物,在PCR体系中增加封口的K88报告基因和反向引物对,被检样品扩增后进行膜杂交。结果:修改的13条探针与参考目标菌株在膜上成特异性杂交,对52个参考菌株和野外分离株的检测准确率为92%;膜杂交的敏感性与玻片芯片接近,最小检出量为100 fg DNA;在尼龙膜上增加K88探针,与3重PCR产物杂交,可以检测到大肠杆菌K88毒力基因。结论:建立的反向斑点杂交方法简便快速,检测成本低,可用于仪器设备不足的实验室,同时可以加入检测如大肠杆菌K88等致病基因,提高基于保守基因的芯片的诊断能力。     

Anammox反应器启动前后微生物群落结构差异性

接种A^2/O回流污泥启动Anammox-UASB反应器,研究了上升流速对系统脱氮性能影响,利用高通量测序对反应器中微生物群落结构变化进行了研究。结果表明,历时35 d成功启动Anammox反应器。上升流速升高可以明显促进脱氮效果,在最佳上升流速为1.14 m/h时TN去除率达84.74%,去除速率高达0.766 gTN/(L·d)。高通量分析表明,Anammox污泥群落Alpha多样性较接种污泥明显减少,Anammox污泥中的Anammox菌主要为Candidatus Jettenia和Candidatus Brocadia两个属,同时检测到大量的其他脱氮微生物菌属,系统中这些脱氮微生物的大量增值使系统脱氮能力逐步提高。     

磁珠富集法分离小黄李基因组微卫星DNA片段

将微卫星探针5′端生物素化后与链亲和素磁珠特异结合,用磁珠和探针的结合物与两端连接已知序列人工接头的中国李品种小黄李(Prunus salicinacv.Xiaohuangli)基因组DNA酶切片段杂交,以此杂交片段为模板用人工接头序列为引物进行PCR扩增,根据PCR产物测序结果设计引物作为微卫星DNA的标记引物.结果在随机挑选的36个克隆进行菌落PCR检测时,从31个阳性克隆中挑选18个克隆进行测序后获得了12条特异序列,设计的8对SSR引物均在5个中国李受试品种上获得了预期的扩增产物,其中4对引物在受试品种上表现出多态性.     

Quantification of Hyphomicrobium populations in activated sludge from an industrial wastewater treatment system as determined by 16S rRNA analysis

The bacterial community structure of the activated sludge from a 25 million-gal-per-day industrial wastewater treatment plant was investigated using rRNA analysis. 16S ribosomal DNA (rDNA) libraries were created from three sludge samples taken on different dates. Partial rRNA gene sequences were obtained for 46 rDNA clones, and nearly complete 16S rRNA sequences were obtained for 18 clones. Seventeen of these clones were members of the beta subdivision, and their sequences showed high homology to sequences of known bacterial species as well as published 16S rDNA sequences from other activated sludge sources. Sixteen clones belonged to the alpha subdivision, 7 of which showed similarity to Hyphomicrobium species. This cluster was chosen for further studies due to earlier work on Hyphomicrobium sp. strain M3 isolated from this treatment plant. A nearly full-length 16S rDNA sequence was obtained from Hyphomicrobium sp. strain M3. Phylogenetic analysis revealed that Hyphomicrobium sp. strain M3 was 99% similar to Hyphomicrobium denitrificans DSM 1869(T) in Hyphomicrobium cluster II. Three of the cloned sequences from the activated sludge samples also grouped with those of Hyphomicrobium cluster II, with a 96% sequence similarity to that of Hyphomicrobium sp. strain M3. The other four cloned sequences from the activated sludge sample were more closely related to those of the Hyphomicrobium cluster I organisms (95 to 97% similarity). Whole-cell fluorescence hybridization of microorganisms in the activated sludge with genus-specific Hyphomicrobium probe S-G-Hypho-1241-a-A-19 enhanced the visualization of Hyphomicrobium and revealed that Hyphomicrobium appears to be abundant both on the outside of flocs and within the floc structure. Dot blot hybridization of activated sludge samples from 1995 with probes designed for Hyphomicrobium cluster I and Hyphomicrobium cluster II indicated that Hyphomicrobium cluster II-positive 16S rRNA dominated over Hyphomicrobium cluster I-positive 16S rRNA by 3- to 12-fold. Hyphomicrobium 16S rRNA comprised approximately 5% of the 16S rRNA in the activated sludge.     

Anaerobic mineralization of quaternary carbon atoms: isolation of denitrifying bacteria on dimethylmalonate.

The microbial capacity to degrade simple organic compounds with quaternary carbon atoms was demonstrated by enrichment and isolation of five denitrifying strains on dimethylmalonate as the sole electron donor and carbon source. Quantitative growth experiments showed a complete mineralization of dimethylmalonate. According to phylogenetic analysis of the complete 16S rRNA genes, two strains isolated from activated sewage sludge were related to the genus Paracoccus within the alpha-Proteobacteria (98.0 and 98.2% 16S rRNA gene similarity to Paracoccus denitrificans(T)), and three strains isolated from freshwater ditches were affiliated with the beta-Proteobacteria (97.4 and 98.3% 16S rRNA gene similarity to Herbaspirillum seropedicae(T) and Acidovorax facilis(T), respectively). Most-probable-number determinations for denitrifying populations in sewage sludge yielded 4.6 x 10(4) dimethylmalonate-utilizing cells ml(-1), representing up to 0.4% of the total culturable nitrate-reducing population.     

Combined Molecular and Conventional Analyses of Nitrifying Bacterium Diversity in Activated Sludge: Nitrosococcus mobilis and Nitrospira-Like Bacteria as Dominant Populations

The ammonia-oxidizing and nitrite-oxidizing bacterial populations occurring in the nitrifying activated sludge of an industrial wastewater treatment plant receiving sewage with high ammonia concentrations were studied by use of a polyphasic approach. In situ hybridization with a set of hierarchical 16S rRNA-targeted probes for ammonia-oxidizing bacteria revealed the dominance of Nitrosococcus mobilis-like bacteria. The phylogenetic affiliation suggested by fluorescent in situ hybridization (FISH) was confirmed by isolation of N. mobilis as the numerically dominant ammonia oxidizer and subsequent comparative 16S rRNA gene (rDNA) sequence and DNA-DNA hybridization analyses. For molecular fine-scale analysis of the ammonia-oxidizing population, a partial stretch of the gene encoding the active-site polypeptide of ammonia monooxygenase (amoA) was amplified from total DNA extracted from ammonia oxidizer isolates and from activated sludge. However, comparative sequence analysis of 13 amoA clone sequences from activated sludge demonstrated that these sequences were highly similar to each other and to the corresponding amoA gene fragments of Nitrosomonas europaea Nm50 and the N. mobilis isolate. The unexpected high sequence similarity between the amoA gene fragments of the N. mobilis isolate and N. europaea indicates a possible lateral gene transfer event. Although a Nitrobacter strain was isolated, members of the nitrite-oxidizing genus Nitrobacter were not detectable in the activated sludge by in situ hybridization. Therefore, we used the rRNA approach to investigate the abundance of other well-known nitrite-oxidizing bacterial genera. Three different methods were used for DNA extraction from the activated sludge. For each DNA preparation, almost full-length genes encoding small-subunit rRNA were separately amplified and used to generate three 16S rDNA libraries. By comparative sequence analysis, 2 of 60 randomly selected clones could be assigned to the nitrite-oxidizing bacteria of the genus Nitrospira. Based on these clone sequences, a specific 16S rRNA-targeted probe was developed. FISH of the activated sludge with this probe demonstrated that Nitrospira-like bacteria were present in significant numbers (9% of the total bacterial counts) and frequently occurred in coaggregated microcolonies with N. mobilis.     

Quantification of Hyphomicrobium Populations in Activated Sludge from an Industrial Wastewater Treatment System as Determined by 16S rRNA Analysis

The bacterial community structure of the activated sludge from a 25 million-gal-per-day industrial wastewater treatment plant was investigated using rRNA analysis. 16S ribosomal DNA (rDNA) libraries were created from three sludge samples taken on different dates. Partial rRNA gene sequences were obtained for 46 rDNA clones, and nearly complete 16S rRNA sequences were obtained for 18 clones. Seventeen of these clones were members of the beta subdivision, and their sequences showed high homology to sequences of known bacterial species as well as published 16S rDNA sequences from other activated sludge sources. Sixteen clones belonged to the alpha subdivision, 7 of which showed similarity to Hyphomicrobium species. This cluster was chosen for further studies due to earlier work on Hyphomicrobium sp. strain M3 isolated from this treatment plant. A nearly full-length 16S rDNA sequence was obtained from Hyphomicrobium sp. strain M3. Phylogenetic analysis revealed that Hyphomicrobium sp. strain M3 was 99% similar to Hyphomicrobium denitrificans DSM 1869^T in Hyphomicrobium cluster II. Three of the cloned sequences from the activated sludge samples also grouped with those of Hyphomicrobium cluster II, with a 96% sequence similarity to that of Hyphomicrobium sp. strain M3. The other four cloned sequences from the activated sludge sample were more closely related to those of the Hyphomicrobium cluster I organisms (95 to 97% similarity). Whole-cell fluorescence hybridization of microorganisms in the activated sludge with genus-specific Hyphomicrobium probe S-G-Hypho-1241-a-A-19 enhanced the visualization of Hyphomicrobium and revealed that Hyphomicrobium appears to be abundant both on the outside of flocs and within the floc structure. Dot blot hybridization of activated sludge samples from 1995 with probes designed for Hyphomicrobium cluster I and Hyphomicrobium cluster II indicated that Hyphomicrobium cluster II-positive 16S rRNA dominated over Hyphomicrobium cluster I-positive 16S rRNA by 3- to 12-fold. Hyphomicrobium 16S rRNA comprised approximately 5% of the 16S rRNA in the activated sludge.     

Overexpression in Escherichia coli of the AT-rich trpA and trpB genes from the hyperthermophilic archaeon Pyrococcus furiosus

Micromanipulation was used to obtain an isolate (BEN 52) of Eikelboom Type 1851 from a bulking activated sludge plant. Its 16S rDNA sequence reveals its closest relative is 'Roseiflexus castenholzii', a member of the phylum 'Chloroflexi', class 'Chloroflexi', previously called the green non-sulfur bacteria. The 16S rRNA targeted oligonucleotide probe designed for fluorescence in situ hybridisation against this sequence successfully identified filamentous bacteria with the morphological features of Type 1851 in activated sludge samples from plants in several countries and different operational configurations.     

Isolation and characterization of halophilic bacteria from Urmia Lake in Iran

Urmia Lake is one of the most permanent hypersaline lakes in the world which is threatened by hypersalinity and serious dryness. In spite of its importance no paper has been published regarding bacterial community of this lake. Accordingly, the present study aimed to investigate the halophilic bacteria in the aforementioned lake. In so doing, thirty seven strains were isolated on six different culture media. The isolated strains were characterized using phenotypic and genotypic methods. Growth of the strains occurred at 2535 degrees C, pH 6-9 and 7 to 20% (w/v) NaCl indicating that most of the isolates were moderately halophiles. Catalase, oxidase and urease activities were found to be positive for the majority of the isolates. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolated bacteria belonged to two major taxa: Gammaproteobacteria (92%, including Salicola [46%], Pseudomonas [13.5%], Marinobacter [ 11%], Idiomarina [11%], and Halomonas [8%]) and Firmicutes (8%, including Bacillus [5%] and Halobacillus [3%]). In addition, a novel bacterium whose 16S rRNA gene sequence showed almost 98% sequence identity with the taxonomically troubled DSM 3050T, Halovibrio denitrificans HGD 3T and Halospina denitrificans HGD 1-3T, each, was isolated. 16S rRNA gene similarity levels along with phenotypic characteristics suggest that some of the isolated strains could be regarded as potential type strain for novel species, on which further studies are recommended.     

16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales"

For simultaneous identification of members of the betaproteobacterial order "Rhodocyclales" in environmental samples, a 16S rRNA gene-targeted oligonucleotide microarray (RHC-PhyloChip) consisting of 79 probes was developed. Probe design was based on phylogenetic analysis of available 16S rRNA sequences from all cultured and as yet uncultured members of the "Rhodocyclales." The multiple nested probe set was evaluated for microarray hybridization with 16S rRNA gene PCR amplicons from 29 reference organisms. Subsequently, the RHC-PhyloChip was successfully used for cultivation-independent "Rhodocyclales" diversity analysis in activated sludge from an industrial wastewater treatment plant. The implementation of a newly designed "Rhodocyclales"-selective PCR amplification system prior to microarray hybridization greatly enhanced the sensitivity of the RHC-PhyloChip and thus enabled the detection of "Rhodocyclales" populations with relative abundances of less than 1% of all bacteria (as determined by fluorescence in situ hybridization) in the activated sludge. The presence of as yet uncultured Zoogloea-, Ferribacterium/Dechloromonas-, and Sterolibacterium-related bacteria in the industrial activated sludge, as indicated by the RHC-PhyloChip analysis, was confirmed by retrieval of their 16S rRNA gene sequences and subsequent phylogenetic analysis, demonstrating the suitability of the RHC-PhyloChip as a novel monitoring tool for environmental microbiology.     

Characterization and molecular methods for detection of a novel spiroplasma pathogenic to Penaeus vannamei

Traditionally, Spiroplasma spp. have only been isolated from the surfaces of flowers and other plant parts, from the guts and hemolymph of various insects, and from vascular plant fluids (phloem sap) and insects that feed on these fluids. In this article, we report the first pathogenic spiroplasma to be discovered in shrimp and the results of its characterization through histological evaluation, in situ hybridization assays, transmission electron microscopy, 16S rRNA sequence homology, and injection infectivity studies. In addition, molecular methods are described that were developed for the detection of this microorganism, which was determined to be the causative disease agent in Colombian farm-raised Penaeus vannamei suffering from high mortalities. Using standard histological methods and in situ hybridization assays, it was confirmed that P. vannamei was infected with this pathogenic spiroplasma. Histological analysis revealed systemic inflammatory reactions in affected organs/tissues. In an attempt to identify the bacteria, frozen infected P. vannamei samples, from the initial epizootic, were used to sequence the 16S rRNA gene and develop molecular detection methods. The 16S rRNA gene was amplified by PCR and then sequenced. The sequence data were analyzed using the GenBank BLAST search and the results revealed a 98% homology with Spiroplasma citri, a pathogen of citrus trees. The 16S rRNA sequence data were evaluated for development of unique PCR primers to the putative spiroplasma. Using PCR primers developed for the spiralin gene of Spiroplasma spp., a digoxigenin-labeled probe was developed and tested. This probe was species-specific, with no positive reactions or cross-reactivity occurring with other bacterial samples tested in this format.     

Determination of 16S ribosomal RNA gene copy number in Streptococcus uberis, S. agalactiae, S. dysgalactiae and S. parauberis

Abstract Species-specific oligonucleotide probes and a universal oligonucleotide probe derived from sequences of 16S rRNA were hybridised to chromosomal DNA from Streptococcus agalactiae, S. dysgalactiae, S. parauberis and S. uberis following digestion with Eco RI. Due to the presence of a unique Eco RI site in each 16S rRNA gene, the number of hybridised fragments was indicative of the number of 16S rRNA genes. Southern hybridisation indicated six 16S rRNA genes in ten isolates of S. agalactiae , five genes in ten isolates of S. uberis , five genes in six isolates and six in another isolate of S. dysgalactiae , and six genes in four isolates of S. parauberis . For a fifth isolate of S. parauberis , six 16S rRNA genes were indicated by the universal probe but only five when hybridised to the species-specific probe, indicating sequence variation (microheterogeneity) within the probe target region.     

Isolation,characterization, and abundance of filamentous members of <Emphasis Type="Italic">Caldilineae</Emphasis> in activated sludge

Chloroflexi are currently believed to serve as backbone forming agents in the activated sludge of wastewater treatment plants (WWTPs). In this study, we isolated and characterized filamentous bacteria in the class Caldilineae of the phylum Chloroflexi in municipal WWTPs. Diversity analysis using Chloroflexi-specific 16S rRNA gene clone libraries showed that 97% of the clones belonged to the subdivision Anaerolineae comprising the two classes Anaerolineae (95%) and Caldilineae (2%). Clones of Caldilineae were related to a thermophilic filament Caldilinea aerophila with 93% 16S rRNA gene sequence similarity. We obtained filamentous isolates classified into the class Caldilineae showing the best match to C. aerophila with 89% 16S rRNA gene sequence similarity. Isolates showed no ability to assimilate glucose or N-acetylglucosamine or to degrade biopolymers which were observed in filamentous Chloroflexi of WWTPs. The assessment of relative abundance based on quantitative PCR of the 16S rRNA gene indicated that members of the class Caldilineae comprised 12–19% of the Chloroflexi in the activated sludge. Additionally, fluorescence in situ hybridization experiments showed that diverse filamentous Caldilineae inhabit the activated sludge of municipal WWTPs. These findings yield insight into the role of filamentous mesophilic Caldilinea in stabilizing flocs of activated sludge in a wide range of WWTPs.