Phylogenetic analysis of tnpR. genes in mercury resistant soil bacteria: the relationship between DNA sequencing and RFLP typing approaches

Abstract The diversity of resolvase ( tnpR ) genes carried by a number of mercury resistant soil bacteria has been investigated by DNA sequencing. The resulting DNA sequence information was compared to previously published tnp R. DNA sequences and to previously published restriction fragment length polymorphism (RFLP) data, permitting the relationships between DNA sequencing and RFLP approaches to be studied by the use of phylogenetic trees. DNA maximum likelihood and DNA parsimony were used to construct a variety of phylogenetic trees. DNA sequencing confirmed the validity of RFLP analysis and highlighted the importance of restriction endonuclease choice upon the resulting RFLP patterns and dendrogram topology. The tnp R genes of two previously uncharacterised mercury resistant bacteria, T2–7 and T2–12 were also studied. DNA sequence data placed T2–7 in a previously described gene class, tnp R-D and T2–12 in a new gene class, tnp R-F. The significance of this data with respect to the recombination and evolution events occurring within bacterial populations are discussed.     

Microbial retention of mercury from waste streams in a laboratory column containing merA gene bacteria

Abstract: The microorganisms used for the mercury retention experiments were natural isolates and genetically engineered bacteria. All mercury-resistant strains contained the merA gene. Column experiments with these strains were carried out by immobilizing them on different support materials. To obtain kinetic data of the reductase activity for whole cells and the crude extract, batch experiments were carried out under different conditions.     

Genetic diversity within mer genes directly amplified from communities of noncultivated soil and sediment bacteria

Individual merRTΔP regions were amplified from DNA directly isolated from soil and sediment samples using consensus primers derived from the conserved mer sequences of Tn501, Tn21 and pMER419. Soil and sediment samples were taken from four sites in the British Isles; one ‘pristine’ (SB) and three polluted (SO, SE, T2) with respect to mercury. The sizes of the PCR products amplified (= 1 kb) were consistent with their generation from mer determinants related to the archetypal elements found in Gram negative bacteria. Forty-five individual clones of sequences obtained from these four sites were isolated which hybridized (> 70% homology) to a merRTΔP probe from Tn501. The diversity of these amplified mer genes was analysed using Restriction Fragment Length Polymorphism (RFLP) profiling. Fourteen RFLP classes were distinguished, 12 of which proved to be novel and only two of which had been identified in an earlier study of 40 Gram negative mercury resistant bacteria cultured from the same four sites. UPGMA analysis was used to examine the relationships between the 22 classes of determinant identified. The T2 site, which has the longest history of mercury exposure, was found to have the greatest level of diversity in terms of numbers of classes of determinant, while the SO site, which had the highest mercury levels showed relatively low variation. Variation of mer genes within and between the sequences from cultivated bacteria and from total bacterial DNA shows clearly that analysing only sequences from cultivated organisms results in a gross underestimation of genetic variation.     

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     

油菜内生细菌16S核糖体DNA的RFLP分析

植物内生细菌定殖在植物组织内部但不引起明显的病害症状。从健康油菜植株的不同器官中分离到大量内生细菌,这些细菌菌落形态存在明显的差异,表明油菜组织中存在大量内生细菌,且类群丰富。分离到的122株内生细菌根据菌落形态可以划分为35类;利用细菌通用引物对16S核糖体DNA进行扩增, 获得约15 kb片段,分别用内切酶HaeⅢ和MspⅠ对扩增产物进行限制性酶切,产生不同的酶切图谱,根据酶切图谱聚类分析结果,所有供试菌株被归为39类,这一结果从遗传上显示油菜内生细菌类群的多样性。两种方法归类结果比较发现菌落特征所反映的信息量有限,只能作为初步的参考指标,核糖体DNA的限制性片段长度多态性分析快速、准确,可以作为油菜内生细菌多样性分析的一种有效方法     

Diversity of mercury resistance determinants among Bacillus strains isolated from sediment of Minamata Bay

Thirty mercury-resistant (Hg R) Bacillus strains were isolated from mercury-polluted sediment of Minamata Bay, Japan. Mercury resistance phenotypes were classified into broad-spectrum (resistant to inorganic Hg(2+) and organomercurials) and narrow-spectrum (resistant to inorganic Hg(2+) and sensitive to organomercurials) groups. Polymerase chain reaction (PCR) product sizes and the restriction nuclease site maps of mer operon regions from all broad-spectrum Hg R Bacillus were identical to that of Bacillus megaterium MB1. On the other hand, the PCR products of the targeted merP (extracellular mercury-binding protein gene) and merA (intracellular mercury reductase protein gene) regions from the narrow-spectrum Hg R Bacillus were generally smaller than those of the B. megaterium MB1 mer determinant. Diversity of gene structure configurations was also observed by restriction fragment length polymorphism (RFLP) profiles of the merA PCR products from the narrow-spectrum Hg R Bacillus. The genetic diversity of narrow-spectrum mer operons was greater than that of broad-spectrum ones.     

利用扩增片段长度多态性分析鉴别炭疽和蜡样芽孢杆菌

目的:利用扩增片段长度多态性(AFLP)分析建立鉴别炭疽芽孢杆菌和蜡样芽孢杆菌的分子生物学方法。方法:3株炭疽芽孢杆菌和3株蜡样芽孢杆菌基因组经限制性内切酶EcoRⅠ和MseⅠ酶切后与对应接头连接,通过预扩增和选择性扩增获得特异性DNA片段,将片段进行毛细管电泳,并利用GeneScan和BioNumerics软件对电泳数据进行分析。结果:选择性扩增最佳引物组合为EcoRⅠ-G/MseⅠ-A,其扩增片段在100~500 bp范围内的有效数量为40~50条;比较炭疽芽孢杆菌和蜡样芽孢杆菌的AFLP特征峰值图和DNA指纹图谱,确定了5个有明显差异的片段区。结论:利用AFLP分析可对芽孢杆菌属中相近的炭疽芽孢杆菌和蜡样芽孢杆菌进行鉴别,该方法可作为炭疽芽孢杆菌传统鉴定方法的补充。     

Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen-suppressive soil

Soil that is suppressive to disease caused by fungal pathogens is an interesting source to target for novel chitinases that might be contributing towards disease suppression. In this study, we screened for chitinase genes, in a phytopathogen-suppressive soil in three ways: (1) from a metagenomic library constructed from microbial cells extracted from soil, (2) from directly extracted DNA and (3) from bacterial isolates with antifungal and chitinase activities. Terminal restriction fragment length polymorphism (T-RFLP) of chitinase genes revealed differences in amplified chitinase genes from the metagenomic library and the directly extracted DNA, but approximately 40% of the identified chitinase terminal restriction fragments (TRFs) were found in both sources. All of the chitinase TRFs from the isolates were matched to TRFs in the directly extracted DNA and the metagenomic library. The most abundant chitinase TRF in the soil DNA and the metagenomic library corresponded to the TRF¹⁰³ of the isolate Streptomyces mutomycini and/or Streptomyces clavifer . There were good matches between T-RFLP profiles of chitinase gene fragments obtained from different sources of DNA. However, there were also differences in both the chitinase and the 16S rRNA gene T-RFLP patterns depending on the source of DNA, emphasizing the lack of complete coverage of the gene diversity by any of the approaches used.     

Generation-means analysis and quantitative trait locus mapping of anthracnose stalk rot genes in maize

A generation-means analysis was performed on two maize populations, each segregating for genes conferring resistance to anthracnose stalk rot (ASR). The populations were derived from a cross of DE811ASR x DE811 and of DE811ASR x LH132. The resistant parent, DE811ASR, was obtained through introgression with MP305 as the donor and DE811 as the recurrent parent. The analysis revealed significant additive effects in both populations and a significant additive x dominant effect in the DES11ASR x DES11 population. Quantitative trait locus (QTL) mapping, using restriction fragment length polymorphism (RFLP)-based molecular markers, indicated a significant QTL on linkage group 4 in both populations. The QTL analysis confirmed additive inheritance in both populations. This work demonstrates a close correspondence between generation-means analysis and discrete observations using molecular markers. Linkage of a genetic marker to genes conferring resistance to ASR will be useful for the introgression of resistance into elite germplasm.This research was part of a thesis submitted by the first author in partial fulfillment of the requirements for a MS degree. Published as Miscellaneous Paper number 1491 of the Delaware Agricultural Experiment Station     

西藏土壤中耐辐射阿氏芽胞杆菌T61的分离和鉴定

【目的】对分离自西藏土样的菌株T61进行分离、鉴定和UV辐射抗性分析。【方法】对菌株T61进行形态和生理生化鉴定;对16S r RNA基因进行克隆和测序,构建系统进化树;测定脂肪酸成分和GC含量,将T61与最相近种进行DNA-DNA杂交;测定T61的UV辐射抗性曲线。【结果】T61细胞杆状,长度约为2μm,直径约为1μm,革兰氏阳性,可产生内生孢子。G+C含量为38.02%。脂肪酸主要成分是C14:0 iso、C15:0 iso和C15:0 anteiso。16S r RNA基因与阿氏芽胞杆菌B8W22T和巨大芽胞杆菌IAM13418T相似度最高,分别达到99.93%和99.53%。DNA-DNA杂交分析表明,T61与阿氏芽胞杆菌B8W22T的相似度为81.4%,而与巨大芽胞杆菌IAM13418T的相似度只有50.3%。UV辐射抗性分析显示,T61 D10为100 J/m2,远高于辐射敏感的大肠杆菌K12和枯草芽孢杆菌等菌株。【结论】菌株T61是一株阿氏芽胞杆菌,命名为Bacillus aryabhattai T61,其对UV辐射具有较强的抗性。     

Genetic and physical mapping of the patatin genes in potato and tomato

Summary Genes for the major storage protein of potato, patatin, have been mapped genetically and physically in both the potato and tomato genomes. In potato, all patatin genes detected by the cDNA clone pGM01 map to a single locus at the end of the long arm of chromosome 8. By means of pulsed field gel electrophoresis (PFGE) it was possible further to delimit this locus, containing 10–15 copies of the gene, to a maximum size of 1.4 million base pairs. Hybridizations with class-specific clones suggest that the locus is at least partially divided into domains containing the two major types of patatin genes, class I and II. In tomato, patatin-homologous sequences were found to reside at the orthologous locus at the end of chromosome 8. The approximately three copies in tomato were localized by PFGE to a single fragment of 300 kilobases. Whereas the class II-specific 5 promoter sequences reside in tomato at the same locus as the coding sequences, the single class I-specific copy of the 5 promoter sequences was localized on chromosome 3 with no coding sequence attached to it. A clone from this chromosome 3 locus of tomato was isolated and by restriction fragment length polymorphism mapping it could be further shown that a similar class I-specific sequence also exists on chromosome 3 of potato. As in tomato, this copy on chromosome 3 is not linked to a coding sequence for patatin. The results are discussed with respect to genome evolution and PFGE analysis of complex gene families.     

PCR-based restriction fragment length polymorphism (RFLP) analysis and serotyping of Campylobacter jejuni isolates from diarrheic patients in China and Japan

Abstract A molecular typing approach for Campylobacter jejuni was applied with restriction fragment length polymorphism (RFLP) analysis of a 702-bp PCR-amplified portion of the flagellin-A ( flaA ) gene. We analyzed a total of 179 strains, including 69 independent clinical isolates from diarrheic patients in Japan, 85 isolates in China, and 25 heat-stable (HS) serotype strains by Penner and Hennessy ((1980) J. Clin. Microbiol. 12, 732–737). Six Afa I, seven Mbo I, and five Hae III RFLPs were found in the 702-bp flaA segment from the 179 strains. Using a combination of these three enzymes, 25 separate RFLP groups were recognized. While 59 of 154 (38.3%) strains obtained in Japan and China were nontypeable by the HS antigenic scheme, all but two of 154 (98.7%) could be typed by RFLP typing. All 11 isolates of HS-19 strains, which are frequently isolated from Guillain-Barré syndrome (GBS) patients, showed an identical RFLP pattern (Cj-1), and Cj-1 consisted only of HS-19 strains. This suggests that the HS-19:Cj-l strain is distinct among C. jejuni strains. This molecular typing method provides a rapid and reliable typing scheme for epidemiological studies of C. jejuni , and may also be useful for the analysis of C. jejuni subtypes from GBS patients.     

苏云金芽胞杆菌4.0718菌株中杀虫晶体蛋白基因的定位及鉴定

[目的]对苏云金芽胞杆菌(Bacillus thuringiensis,简称Bt)4.0718菌株中的杀虫晶体蛋白基因(insecticidal crystal protein gene,简称cry基因)进行定位和鉴定,系统分析高毒力Bt4.0718菌株的杀虫基因背景.[方法]采用脉冲电泳(PFGE)分离Bt 4.0718菌株的基因组DNA,确定该菌株的PFGE图谱和质粒图谱;采用Southern杂交分析该菌株中cry基因的定位,并使用PCR及PCR产物限制性片段长度多态性分析(PCR-RFLP)方法鉴定该菌株染色体和质粒上含有的cry基因类型.[结果]确定了Bt 4.0718菌株的PFGE图谱和质粒图潜,鉴定到Bt4.0718菌株的染色体和质粒上均定位有cry基因,且分别包含crylAa、crylAc、cry2Aa和cry2Ab 4种基因成分.但染色体上含有的cry基因可能不如质粒上含有的cry基因具有完整的开放阅渎框.[结论]首次在Bt 4.0718菌株的染色体上发现有丰富的cry基因,且与质粒上含有的cry基因类型一致.     

In vitro propagation, restriction fragment length polymorphism, and random amplified polymorphic DNA analyses of Angelica plants

Angelica acutiloba, a medicinal plant used as a natural medicine Touki, was clonally propagated through axillary buds in vitro. No substantial differences were found in the random amplified polymorphic DNA (RAPD) pattern between the original A. acutiloba and the plant propagated in vitro, suggesting no changes in the DNA sequences and structure during in vitro propagation. The genetic similarities of several Angelica plants were investigated by restriction fragment length polymorphism (RFLP) and RAPD analyses. The RFLP and RAPD patterns of A. sinensis Diels were substantially different from those of A. acutiloba. Using ten different restriction enzymes, no RFLP was observed in the varieties of A. acutiloba. By RAPD analysis, A. acutiloba varieties can be classified into two major subgroups, i.e., A. acutiloba Kitagawa and A. acutiloba Kitagawa var. sugiyamae Hikino. The varieties of A. acutiloba Kitagawa in Japan and Angelica spp. in northeast China exhibited a very close genetic relationship. Received: 13 March 1998 / Revision received: 28 July 1998 / Accepted: 21 August 1998     

Biochemical and molecular identification of Enterococcus spp. from red pitaya

Red pitaya is a popular fruit worldwide due to its unique appearance and high nutrient contents. Many studies about the nutritional content and the physico-chemical characteristics of red pitaya have been performed but microorganisms that occurred naturally in the fruit remained unknown. Therefore, this study was conducted to characterize the enterococci present in red pitaya. Enterococci were isolated from red pitaya fruit and characterized with biochemical tests, randomly amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) of the 16S rDNA region. A total of 30 bacteria were isolated from red pitaya, of which 20 isolates were confirmed as enterococci, genus Enterococcus. 13 isolates were further confirmed as Enterococcus casseliflavus and 7 were identified as Enterococcus gallinarum.     

Ribotyping of Pseudomonas aeruginosa isolates from patients and water springs and genome fingerprinting of variants concerning mucoidy

Abstract Thirty-one strains of Pseudomonas aeruginosa , isolated from water springs, clinical isolates (some of which were from cystic fibrosis (CF) patients), and two type cultures, were characterized by ribotyping. After restriction of chromosomal DNA of the different isolates with Eco RI and hybridization of Southern transfer blots with 2-acetylaminofluorene labelled Escherichia coli 16S + 23S rRNA probe, eleven different ribopatterns were obtained, representing variations of a dominant profile. This largely predominant pattern included both type cultures, all six isolates from water springs, 33% of the nine CF isolates and 43% of fourteen other clinical isolates most of them from nosocomial infections. When the genomic macrorestriction fingerprints of three mucoid CF isolates, with Ase I, Dra I or Bfr I were compared with those of their spontaneous variants, concerning mucoidy, no differences were detected.