封闭循环养殖系统中β变形菌亚纲氨氧化细菌的引物特异性

摘要:【目的】为探讨4 对不同的引物对封闭循环养殖系统生物膜中β 变形菌亚纲氨氧化细菌(β-AOB) 的特异性差异。【方法】采用16S rDNA 文库克隆技术对β-AOB 的多样性进行了分析。【结果】以引物CTO189f/CTO654r 扩增构建的文库中所含β-AOB 比例最高,可达67. 3%。不同封闭循环养殖系统的生物膜对引物的扩增效率有明显的影响,其中以养殖尼罗罗非鱼的封闭循环养殖系统生物膜为DNA 来源的,引物均有较高的扩增效率。【结论】针对封闭循环养殖系统生物膜中的β-AOB,特异性最高的是CTO189f /CTO654r 引物。     

Diversity of bacteria and mycobacteria in biofilms of two urban drinking water distribution systems

In this study, to give insight into the bacterial diversity of biofilms from full-scale drinking water distribution systems (DWDSs), the bacterial community compositions of biofilms from two urban DWDSs (Guangzhou and Beijing, China) were determined using a 16S rRNA gene library technique. Meanwhile, the occurrence and diversity of mycobacteria were also analyzed by a Mycobacterium -specific hsp gene assay. The biofilms from the full-scale DWDSs have complex bacterial populations. Proteobacteria was the common and predominant group in all biofilm samples, in agreement with previous reports. The community structures of bacteria at the three sites in Guangzhou DWDS were significantly different, despite the similar physicochemical properties of portable water. Some abundant and peculiar bacterial phylotypes were noteworthy, including Methylophilus , Massilia, and Planomicrobium , members of which are rarely found in DWDSs and their roles in DWDS biofilms are still unclear. The diversity of Mycobacterium species in biofilm samples was rather low. Mycobacterium arupense and Mycobacterium gordonae were the primary Mycobacterium species in Guangzhou and Beijing biofilms, respectively, indicating that M. arupense may be more resistant to chloride than M. gordonae.     

Diversity of ammonifying bacteria

The diversity of the micro-organisms, involved in the ammonification in natural waters was examined. The utilization of 41 organic compounds as the sole carbon and energy source was determined for 68 isolated strains. Within this group there was hardly any specificity for the substrate. A single linkage clustering demonstrated that the bacterial population which is able to take up amino acids in natural waters, is composed of a variety of micro-organisms which only slightly differ in their ability to utilize a variety of organic compounds.     

Diversity of cellulolytic bacteria in landfill

Nine of 37 cellulolytic bacterial isolates obtained from landfill waste could be easily differentiated on the basis of gross morphological characteristics. Four isolates were selected for further characterization and on the basis of initial results appear to be previously unidentified cellulolytic species of bacteria. An aerotolerant anaerobic, cellulolytic Clostridium and three obligately anaerobic cellulolytic Eubacterium isolates are described. The Clostridium has an unusually high pH optimum for growth of 7.7. The optimum temperature for growth is 50°C. The pH growth optimum of each of the Eubacterium isolates is around pH 7.0 while temperature optima are 37° 45° and 50°C for LFI, LF4 and LF5 respectively. Most isolates had growth optima in the thermophilic range. The ease with which apparently previously unidentified species could be isolated is a reflection of the unique and highly variable, heterogeneous environment within landfill waste.     

Diversity of culturable denitrifying bacteria

Sequence divergence in the ribosomal genes of known strains and isolates of aquatic denitrifying bacteria was investigated using restriction fragment length polymorphism (RFLP) analysis. The same cultures were characterized for their homology with antibody and gene probes for nitrite reductase (NiR), a key enzyme in the denitrification pathway, and for amplification with a set of polymerase chain reaction primers designed to amplify a portion of the NiR gene. The NiR probes were developed from Pseudomonas stutzeri (ATCC 14405) and several P. stutzeri strains were included in the analyses. The RFLP analysis clustered most of the P. stutzeri strains together, but detected considerable diversity within this group. Isolates from three aquatic environments exhibited within —and among — habitat diversity by RFLP. Hybridization with the NiR probes and amplification with the NiR primers were not correlated with the clustering of strains by rDNA RFLP analysis. The relationships among strains deduced from ribosomal DNA RFLP reflect heterogeneity within the P. stutzeri group and among other pseudomonads, and the patterns differ from those inferred from specificity of the NiR probes.Abbreviations NiR Nitrite reductase - PCR polymerase chain reaction - RFLP restriction fragment length polymorphism     

Diversity and host specificity of the Verminephrobacter-earthworm symbiosis

Symbiotic bacteria of the genus Verminephrobacter (Betaproteobacteria) were detected in the nephridia of 19 out of 23 investigated earthworm species (Oligochaeta: Lumbricidae) by 16S rRNA gene sequence analysis and fluorescence in situ hybridization (FISH). While all four Lumbricus species and three out of five Aporrectodea species were densely colonized by a mono-species culture of Verminephrobacter, other earthworm species contained mixed bacterial populations with varying proportions of Verminephrobacter; four species did not contain Verminephrobacter at all. The Verminephrobacter symbionts could be grouped into earthworm species-specific sequence clusters based on their 16S rRNA and RNA polymerase subunit B (rpoB) genes. Closely related host species harboured more closely related symbionts than did distantly related hosts. Co-diversification of the symbiotic partners could not be demonstrated unambiguously due to the poor resolution of the host phylogeny [based on histone H3 and cytochrome c oxidase subunit I (COI) gene sequence analyses]. However, there was a pattern of symbiont diversification within four groups of closely related hosts. The mean rate of symbiont 16S rRNA gene evolution was determined using a relaxed clock model, and the rate was calibrated with paleogeographical estimates of the time of origin of Lumbricid earthworms. The calibrated rates of symbiont 16S rRNA gene evolution are 0.012-0.026 substitutions per site per 50 million years and thus similar to rates reported from other symbiotic bacteria.     

Diversity of extremely halophilic bacteria

In this review, the history of the classification of the family Halobacteriaceae, the extremely halophilic aerobic Archaea, is reviewed with some emphasis on the recently described new genera Halobaculum, Halorubrum, Natrialba, Natronomonas, and "Haloterrigena." Speculation is made about the evolutionary relationship between members of the Halobacteriaceae and the extremely halophilic, anaerobic methanogens of the genera Methanohalobium and Methanohalophilus. Efforts to find missing links between the two groups are also reviewed. Received: January 22, 1998 / Accepted: February 16, 1998     

Diversity and specificity in location-based signaling outputs of neuronal GPCRs

The common mechanisms by which members of the G protein–coupled receptor (GPCR) family respond to neurotransmitters in the brain have been well studied. However, it is becoming increasingly clear that GPCRs show great diversity in their intracellular location, interacting partners and effectors, and signaling consequences. Here we will discuss recent studies on the diversity of location, effectors, and signaling of GPCRs, and how these could interact to generate specific spatiotemporal patterns of GPCR signaling in cells.     

郫县豆瓣细菌多样性及群落结构动态变化北大核心

【目的】通过检测郫县豆瓣在不同发酵阶段细菌的种类、丰度及数量,探究郫县豆瓣的不同发酵产品发酵过程中细菌的动态变化情况。【方法】采用16S rRNA基因测序对郫县豆瓣4个发酵阶段中细菌种类及丰度进行分析,利用荧光定量PCR(quantitative real-time PCR,qPCR)方法检测不同发酵阶段的细菌总数。【结果】郫县豆瓣在初期的发酵过程中细菌群落处于动态稳定,在不同发酵阶段细菌群落组成相对丰富,从郫县豆瓣整个初期的发酵过程来看,细菌群落多样性呈现升高的趋势,Shannon指数从1.25升高到3.50;在郫县豆瓣初期发酵过程中细菌群落的数量以及多样性与发酵环境息息相关,不同发酵阶段细菌群落的多样性也有所不同,其中在干辣椒发酵阶段中泛菌属(Pantoea)为最优势菌属,占比为20%;在蚕豆瓣发酵阶段中葡萄球菌属(Staphylococcus)的相对丰度最高,占比为38%;混合发酵后,在红油豆瓣发酵阶段的最优势菌属是乳酸杆菌属(Lactobacillus),占比达到27%,郫县豆瓣发酵阶段的最优势菌属是乳酸杆菌属(Lactobacillus),占比为62%。【结论】推断在郫县豆瓣不同发酵阶段初期相对丰度较大的菌属对郫县豆瓣的质量以及产量可能会产生重大影响。     

Broad substrate specificity of naphthalene- and biphenyl-utilizing bacteria

 Although aromatic compounds are most often present in the environment as components of complex mixtures, biodegradation studies commonly focus on the degradation of individual compounds. The present study was performed to investigate the range of aromatic substrates utilized by biphenyl- and naphthalene-degrading environmental isolates and to ascertain the effects of co-occurring substrates during the degradation of mono-aromatic compounds. Bacterial strains were isolated on the basis of their ability to utilize either biphenyl or naphthalene as a sole source of carbon. Growth and transformation assays were conducted on each isolate to determine the range of substrates degraded. One isolate, Pseudomonas putida BP18, was tested for the ability to biodegrade benzene, toluene, ethylbenzene and xylene isomers (BTEX) individually and as components of mixtures. Overall, the results indicate that organisms capable of growth on multi-ring aromatic compounds may be particularly versatile in terms of aromatic hydrocarbon biodegradation. Furthermore, growth and transformation assays performed with strain BP18 suggest that the biodegradation of BTEX and biphenyl by this strain is linked to a catabolic pathway with overlapping specificities. The broad substrate specificity of these environmental isolates has important implications for bioremediation efforts in the field. Received: 4 August 1999 / Received revision: 25 October 1999 / Accepted: 5 November 1999     

Substrate specificity of atrazine chlorohydrolase and atrazine-catabolizing bacteria

Bacterial atrazine catabolism is initiated by the enzyme atrazine chlorohydrolase (AtzA) in Pseudomonas sp. strain ADP. Other triazine herbicides are metabolized by bacteria, but the enzymological basis of this is unclear. Here we begin to address this by investigating the catalytic activity of AtzA by using substrate analogs. Purified AtzA from Pseudomonas sp. strain ADP catalyzed the hydrolysis of an atrazine analog that was substituted at the chlorine substituent by fluorine. AtzA did not catalyze the hydrolysis of atrazine analogs containing the pseudohalide azido, methoxy, and cyano groups or thiomethyl and amino groups. Atrazine analogs with a chlorine substituent at carbon 2 and N-alkyl groups, ranging in size from methyl to t-butyl, all underwent dechlorination by AtzA. AtzA catalyzed hydrolytic dechlorination when one nitrogen substituent was alkylated and the other was a free amino group. However, when both amino groups were unalkylated, no reaction occurred. Cell extracts were prepared from five strains capable of atrazine dechlorination and known to contain atzA or closely homologous gene sequences: Pseudomonas sp. strain ADP, Rhizobium strain PATR, Alcaligenes strain SG1, Agrobacterium radiobacter J14a, and Ralstonia picketti D. All showed identical substrate specificity to purified AtzA from Pseudomonas sp. strain ADP. Cell extracts from Clavibacter michiganensis ATZ1, which also contains a gene homologous to atzA, were able to transform atrazine analogs containing pseudohalide and thiomethyl groups, in addition to the substrates used by AtzA from Pseudomonas sp. strain ADP. This suggests that either (i) another enzyme(s) is present which confers the broader substrate range or (ii) the AtzA itself has a broader substrate range.     

Ribsome and messenger specificity in protein synthesis by bacteria

Ribosomes from Escherichia coli and Pseudomonas fluorescens, two Gram-negative bacteria, translated messenger RNA preparations from all bacteria tested (3 Gram-negative species, and 6 Gram-positive species) as well as f2 RNA and T4 early messenger RNA. Ribosomes from Clostridium pasteurianum, Streptococcus faecalis, and Bacillus subtilis, three Gram-positive organisms, did not translate messenger RNA preparations derived from any of the Gram-negative organisms, the f2 RNA, or the T4 early messenger RNA but did translate messenger preparations from all 6 Gram-positive bacterial species tested.     

土壤样品中细菌多样性的分析

微生物分子生态学的研究表明,自然界中只有很小部分的微生物得到了纯培养,绝大多数微生物是未被开发的和未知的,因此探索和培养那些未知的微生物物种可以发掘微生物新的菌种资源[1-2]。     

Diversity of bacteria contaminating paper machines

Formation of microbial biofilms and slimes is a general and serious problem in the operation of paper machines. Studies of microbial populations in paper machine-derived biofilms have been conducted using standard microbiological procedures; however, the bacterial genera present in this type of samples as well as their diversity are quite poorly known. Here, the bacterial diversity of 38 process water and 22 biofilm samples from four different Finnish paper machines were analyzed by length heterogeneity analysis of PCR-amplified 16S ribosomal DNA (LH-PCR). In addition, sequencing of the amplified 16S rRNA gene from 69 clones was conducted for characterization of the bacterial genera present in biofilm and slime samples. The LH-PCR profiles of both the free-living (process waters) and immobilized (biofilms) bacteria were diverse at all stages of the papermaking process. Out of the 69 sequenced clones, 44 belonged to alpha-Proteobacteria, most of which were close to the nitrogen-fixing root nodule genera Sinorhizobium, Rhizobium and Azorhizobium. Other clones were assigned to beta- and gamma-Proteobacteria and the phylum Bacteroidetes. In addition, eight of the clones were assigned to a yet uncultivated phylum, TM7. Finally, epifluorescence microscopy revealed that Gram-negative bacteria were predominant in both the biofilm (65%) and process water (54%) samples and a small coccoid cell morphology was most common in all samples. Together, our results show that the analysis of microbial samples from paper machines using modern molecular biology techniques adds valuable information and should, therefore, be useful as a more specific and sensitive microbiological method for the paper industry. This information could further be applied, e.g., in the development of more specific and environmental friendly antimicrobial agents for paper mills.     

Diversity of specificity and function of phosphate translocators in various plastids

This report gives a comparison of the specificity of phosphate translocators in various plastids. Whereas the phosphate translocator of the C₃ plant spinach mediates a counter exchange between inorganic phosphate, dihydroxyacetone phosphate, and 3-phosphoglycerate, the phosphate translocators in chloroplasts from C₄ and CAM plants transport phosphoenolpyruvate in addition to the above mentioned metabolites. In plastids from pea roots the phosphate translocator also transports glucose 6-phosphate. This diversity of phosphate translocators is discussed in view of the special functions of the various plastids.     

Carbohydrate specificity of lectins from luminous bacteria

The presence of lectins on a cell surface was demonstrated for 70 cultures of luminous bacteria using hemagglutination reactions. It was shown that hemagglutination of luminous bacteria is inhibited by glucose, maltose, fructose, mannose, and N-acetyl-D-glucosamine. The differences in the inhibition of hemagglutination of luminescent and nonluminescent (spontaneous mutants) symbiotic cultures by N-acetyl-D-galactosamine were revealed. The fact that N-acetyl-D-galactosamine inhibits hemagglutination of the luminescent symbiotic bacteria but does not inhibit hemagglutination of the symbiotic cultures lacking luminescence suggests that lectins with N-acetyl-D-galactosamine specificity are possibly involved in the formation and functioning of the symbiosis of luminous bacteria with marine animals possessing luminous organs.     

Diversity of L-methionine catabolism pathways in cheese-ripening bacteria

Enzymatic activities that could be involved in methanethiol generation in five cheese-ripening bacteria were assayed, and the major sulfur compounds produced were identified. L-Methionine and alpha-keto-gamma-methyl-thio-butyric acid demethiolating activities were detected in whole cells and cell extracts (CFEs) of all the bacteria tested. No L-methionine deaminase activity could be detected in any of the ripening bacteria and L-methionine aminotransferase was detected in CFEs of Brevibacterium linens, Micrococcus luteus, and Corynebacterium glutamicum. The results suggest that several pathways for L-methionine catabolism probably coexist in these ripening bacteria.     

Carbohydrate specificity of lectins from luminescent bacteria

The presence of lectins on a cell surface was demonstrated for 70 cultures of luminescent bacteria using hemagglutination reactions. It was shown that hemagglutination of luminescent bacteria is inhibited by glucose, maltose, fructose, mannose, and N-acetyl-D-glucosamine. The differences in the inhibition of hemagglutination of luminescent and nonluminescent (spontaneous mutants) symbiotic cultures by N-acetyl-D-galactosamine were revealed. The fact that N-acetyl-D-galactosamine inhibits hemagglutination of the luminescent symbiotic bacteria but does not inhibit hemagglutination of the symbiotic cultures lacking luminescence suggests that lectins with N-acetyl-D-galactosamine specificity are possibly involved in the formation and functioning of the symbiosis of luminescent bacteria with marine animals possessing luminous organs.     

Diversity and abundance of bacteria in an underground oil-storage cavity

Background  

Microorganisms inhabiting subterranean oil fields have recently attracted much attention. Since intact groundwater can easily be obtained from the bottom of underground oil-storage cavities without contamination by surface water, studies on such oil-storage cavities are expected to provide valuable information to understand microbial ecology of subterranean oil fields.