油气田土壤甲烷氧化菌实时荧光定量PCR检测技术的 建立与应用

【目的】建立快速检测甲烷氧化菌含量的SYBR GreenⅠ实时荧光定量PCR技术,用于油气微生物勘探。【方法】以含有甲烷氧化菌功能基因pmoA片段的重组质粒为标准品,优化实验条件,建立标准曲线,进行敏感性、重复性和特异性评价,并将该技术用于实际样品的检测。【结果】该技术标准曲线的相关系数R2为0.999 9,扩增效率为99.976%,检测范围为3.897×101-3.897×109 copies/μL,检出限约为40 copies/μL,重复性实验中CT值的变异系数优于3%,对12种非甲烷氧化菌均没有扩增,显示该技术具有很好的敏感性、重复性和特异性。利用该技术对气田、油田和非油气田土样进行了检测,发现气田具有明显的异常高值。【结论】为油气田的勘探建立了一种高效、特异、灵敏、准确的甲烷氧化菌荧光定量PCR检测技术,同时为其它指示菌检测技术的建立提供了参考。     

Quantitative detection of Helicobacter pylori in water samples by real-time PCR amplification of the cag pathogenicity island gene, cagE

Aims:  A new real-time PCR assay that simultaneously amplifies a 102-bp fragment of the cagE gene from Helicobacter pylori and a new internal positive control containing a specific sequence of the gyrB gene from Aeromonas hydrophila , was developed and validated for the detection of H. pylori in environmental samples.
Methods and Results:  The specificity, limits of detection and quantification, repeatability, reproducibility, and accuracy of the method were calculated. The resulting values confirmed the applicability of the method for the quantitative detection of H. pylori . The feasibility of the method was also evaluated by testing 13 pyloric antrum-positive biopsies and 69 water samples, including potable (10), surface (19) and wastewater (40) matrices. The results showed that all the biopsies and 3 of the 40 wastewater samples analysed were positive.
Conclusions:  This real-time PCR method provides a sensitive, specific, and accurate method for the rapid quantification of H. pylori in environmental samples.
Significance and Impact of the Study:  The PCR diagnostic system proposed in this work, provides a suitable tool for the quantitative detection of H. pylori in environmental samples and can be useful for verifying the role of water as a potential route of its transmission.     

Specific and sensitive detection of Ralstonia solanacearum in soil with quantitative, real-time PCR assays

Aims:  The aim of this study was to develop a sensitive and an effective method suitable for large-scale detection and quantification of Ralstonia solanacearum in soil.
Methods and Results:  Based on the specific sequence of R. solanacearum strain G1000, the primer pair R.sol1-R.sol2 and the TaqMan probe Rs-pro were designed, and specific and sensitive PCR detection methods were successfully established. The detection limit was 100 fg μl⁻¹ DNA in conventional PCR and 1·2 fg μl⁻¹ in real-time PCR. By combining real-time PCR with the modified protocols to extract DNA from soil, it was possible to achieve real-time detection of R. solanacearum in soil, and the degree of sensitivity was 100 fg μl⁻¹. To detect inhibition in soil samples, an exogenous internal positive control (IPC) was included preventing false negative results, and IPC was successfully amplified from all samples tested. The methodology developed was used to detect the presence of R. solanacearum in tobacco fields in China.
Conclusions:  The real-time PCR combined with the protocol to extract DNA from soil led to the development of a specific, sensitive and rapid detection method for R. solanacearum in soil.
Significance and Impact of the Study:  The real-time PCR improves the detection sensitivity and specificity and provides an important tool for routine detection of R. solanacearum in soil samples and for epidemiological and ecological studies.     

A single-run, real-time PCR for detection and identification of Borrelia burgdorferi sensu lato species, based on the hbb gene sequence

Lyme borreliosis is the most important vector-borne disease caused by spirochetes within the Borrelia burgdorferi sensu lato (B. burgdorferi sl) complex. There is strong evidence that different species of this group of genetically diverse spirochetes are involved in distinct clinical manifestations of the disease. In order to differentiate species within this bacterial complex, we developed a real-time-PCR protocol, which targets the hbb gene. We designed a fluorescein-labeled probe specific of a region of this gene harboring a polymorphism linked to species. An internally Red640 labeled primer allowed a fluorescence resonance energy transfer to occur. The sensitivity of this method was in the range of 10 bacteria per assay. After amplification, a melting curve was generated for genotyping. Analysis of these melting curves clearly allowed the distinction between the main European species of B. burgdorferi sl. One hundred seventy tick extracts were analysed by this hbb-based method and in parallel by amplification of the 5S-23S intergenic spacer and RFLP analyses. There was a good correlation between these two methods. We conclude that this hbb-based real-time-PCR is suitable for epidemiological studies on field-collected ticks, although rare mutations in the genomic sequence spanned by the probe could lead to misidentification.     

Calibration of quantitative real-time TaqMan PCR by correlation with hyphal biomass and ITS copies in mycelia of Piloderma croceum

DNA-based quantification methods such as real-time TaqMan PCR allow a rapid and highly sensitive species-specific quantification of isolated fungal DNA material, but most quantification systems are only able to measure relative amounts of biomass or biomass changes during different treatments. In this experiment, an already established DNA quantification system for the ectomycorrhizal fungus Piloderma croceum, based on the ITS region of ribosomal DNA, was calibrated to absolute biomass to obtain a direct correlation between mycelial biomass and isolated ITS copies. Thin layers of sterile mycelia were cultured on slides. The mycelial biomass was calculated from measurements of the total hyphal length using image analysis, followed by determination of the mycelial volume, and multiplied by the specific weight of hyphae obtained from literature data. Using the very same mycelium, the number of ITS copies was quantified by TaqMan PCR. The mean value of 1047 (+/- 185) copies per mm hypha results in possible data for a direct conversion: one billion (10 (9)) ITS copies corresponded to 0.79 mg hyphal dry weight. For the ribosomal ITS multi-copy genes, the number of ITS copies could be calculated to approx. 152 (+/- 26) copies per dikaryotic cell. These conversion data now allow determination of the mycelial biomass of Piloderma croceum using real-time TaqMan PCR, a prerequisite for competition experiments with Piloderma croceum.     

Quantification of conidial density of Aspergillus flavus and A. parasiticus in soil from almond orchards using real-time PCR

Aims:  To design the Aspergillus flavus and Aspergillus parasiticus -specific primers and a real-time PCR assay for quantification of the conidial density in soil.
Methods and Results:  Aspergillus flavus and A. parasiticus -specific DNA primers were designed based on internal transcribed spacer sequences to distinguish these two species and from other Aspergillus and other fungal species. A method of pathogen DNA extraction directly from soil samples was developed. Using the designed primers, a real-time PCR assay was developed to quantitatively determine the conidial density of each A. flavus and A. parasiticus in soil, after generating corresponding standard curves. Known conidial densities of each A. flavus or A. parasiticus in soil significantly correlated with those tested with the real-time PCR.
Conclusions:  This study demonstrated the applicability of the real-time PCR assay in studies of quantifying A. flavus and A. parasiticus in soil as inoculum sources.
Significance and Impact of the Study:  The A. flacus and A. parasitic -specific primers can be widely used in aflatoxin research. The real-time PCR assay developed in this study provides a potential approach to quantify the plant pathogen density from not only soil but also other sources in relation to aflatoxin contamination from environment, food and feed commodities.     

Potentiality of the cox1 gene in the taxonomic resolution of soil fungi

We explored the potential of the cox1 gene in the species resolution of soil fungi and compared it with the nuclear internal transcribed spacer (ITS) and small subunit (SSU)-rDNA. Conserved primers allowing the amplification of the fungal cox1 gene were designed, and a total of 47 isolates of Zygomycota and Ascomycota were investigated. The analysis revealed a lack of introns in >90% of the isolates. Comparison of the species of each of the six studied genera showed high interspecific sequence polymorphisms. Indeed, the average of nucleotide variations (4.2–11%) according to the genus, due mainly to the nucleotide substitutions, led to the taxonomic resolution of all the species studied regarding both ITS and SSU-rDNA, in which <88% were discriminated. The phylogenetic analysis performed after alignment of the cox1 gene across distant fungal species was in accordance with the well-known taxonomic position of the species studied and no overlap was observed between intra- and interspecific variations. These results clearly demonstrated that the cox1 sequences could provide good molecular markers for the determination of the species composition of environmental samples and constitute an important advance to study soil fungal biodiversity.     

土壤灭菌-生物有机肥联用对连作马铃薯及土壤真菌群落结构的影响

甘肃省中部沿黄灌区是全国重要的加工型马铃薯生产基地,然而因集约化生产带来的连作障碍问题已经严重影响到当地马铃薯种植业的健康发展。结合田间试验和相关的室内分析,从马铃薯块茎产量和品质、植株生理特征和土壤真菌群落结构等角度,初步评估土壤灭菌和生物有机肥联用(Ammonia Disinfection plus Bio-organic Fertilizer Regulation,ABR)对马铃薯连作障碍的防控效果。同对照相比,ABR处理的块茎产量和商品薯率分别显著增加约71.1%—152.1%和39.2%—53.3%,但块茎化学品质变化不大。ABR处理叶绿素含量和根系活力较CK均显著增加,而叶片和根系丙二醛含量显著下降。PCR-DGGE分析发现,ABR处理显著影响了马铃薯连作土壤的真菌群落结构,表现为真菌群落的多样性指数较CK相比显著下降。ABR处理还有效抑制了土传病害的滋生,植株发病率和收获后的病薯率较CK分别显著下降约67.2%—82.2%和69.1%—70.5%。采用Real-time PCR评估连作土壤中3种优势致病真菌的数量变化,显示ABR处理下立枯丝核菌、茄病镰刀菌和接骨木镰刀菌的数量在生育期内较CK均有不同程度的下降。综合来看,土壤灭菌和生物有机肥联用技术在防控甘肃省中部沿黄灌区马铃薯连作障碍上具有较大的应用潜力,而对土传病害的抑制和微生物群落结构的改善是其主要的作用机理。     

Detection and quantification of Paenibacillus polymyxa in the rhizosphere of wild barley (Hordeum spontaneum) with real-time PCR

Aim:  To detect and quantify the plant drought tolerance enhancing bacterium Paenibacillus polymyxa in a collection of 160 Hordeum spontaneum rhizosphere samples at the 'Evolution Canyon' ('EC'), Israel.
Methods and Results:  PCR primers and a FAM-TAMRA probe (6-carboxyfluorescein, 6-carboxy-tetramethyl-rhodamine) targeting 16S rRNA genes were designed and used to detect and quantify the target strain. Two commercial kits, Bio101 Fast Spin and Mo Bio Ultra Clean Soil DNA, were tested for DNA isolation from the rhizosphere and surrounding soil. Population densities of P. polymyxa were studied in the rhizosphere of wild barley and surrounding soil from the contrasting climatic slopes at the 'EC' using the real-time PCR and culture based methods.
Conclusion:  Paenibacillus polymyxa is one of the best established species in wild barley rhizosphere at the 'EC' slopes. With the real-time PCR assay we are able to detect 1 pg of DNA per PCR corresponding to 100 cells per ml. The results at the 'EC' correlate well to bacterial estimations by culture based methods.
Significance and Impact of the Study:  Significantly higher P. polymyxa cell number was detected in the rhizosphere of arid 'African' microclimate indicating possible role of adaptive co-evolution with plants.     

Validation of a cotton-specific gene, Sad1, used as an endogenous reference gene in qualitative and real-time quantitative PCR detection of transgenic cottons

Genetically modified (GM) cotton lines have been approved for commercialization and widely cultivated in many countries, especially in China. As a step towards the development of reliable qualitative and quantitative PCR methods for detecting GM cottons, we report here the validation of the cotton (Gossypium hirsutum) endogenous reference control gene, Sad1, using conventional and real-time (RT)-PCR methods. Both methods were tested on 15 different G. hirsutum cultivars, and identical amplicons were obtained with all of them. No amplicons were observed when DNA samples from three species of genus Gossypium, Arabidopsis thaliana, maize, and soybean and others were used as amplified templates, demonstrating that these two systems are specific for the identification and quantification of G. hirsutum. The results of Southern blot analysis also showed that the Sad1 gene was two copies in these 15 different G. hirsutum cultivars. Furthermore, one multiplex RT-quantitative PCR employing this gene as an endogenous reference gene was designed to quantify the Cry1A(c) gene modified from Bacillus thuringiensis (Bt) in the insect-resistant cottons, such as Mon531 and GK19. The quantification detection limit of the Cry1A(c) and Sad1 genes was as low as 10 pg of genomic DNA. These results indicat that the Sad1 gene can be used as an endogenous reference gene for both qualitative and quantitative PCR detection of GM cottons.     

辽宁老秃顶子北坡植物群落物种多样性及其与土壤特性的相关性分析

通过沿海拔梯度的系统样方调查,利用物种丰富度、α多样性和β多样性等指标,对辽宁老秃顶子北坡植物群落木本层和草本层物种多样性随海拔梯度的变化趋势进行了研究,并对植物群落物种多样性与土壤特性之间的相关关系进行了初步探索。结果表明:木本植物物种多样性随海拔梯度的升高呈波动式降低的趋势;草本植物物种多样性随海拔梯度的变化趋势为先降低后升高;群落类型间的过渡带是植物物种替换速率较高的地区;老秃顶子北坡土壤类型以棕色森林土和暗棕色森林土为主,土壤有机质含量较高;群落物种多样性与土壤特性之间存在着一定的负相关性。     

Estimation of the influence of selected products on co-infection with N. apis/N. ceranae in Apis mellifera using real-time PCR

To protect the world’s honey bee population many scientific centres are searching for products and methods that control nosemosis. Real-time PCR was used to assess infection level in worker bees infected with Nosema spp. in bee colonies co-infected with Nosema apis and Nosema ceranae after the administration of three products (Nozevit, ApiHerb and ApiX) and sugar syrup. The study was conducted in the field condition therefore there was no possibility to affect the number of spores in the selected material. The study demonstrated considerable differences in the number of spores of individual Nosema spp. in the analysed samples of bees. HSD Tukey’s test showed that the statistically significant effect on limiting the N. apis invasion had ApiX (p – 0.049). Nozevit, Apiherb and syrup showed no statistically significant effect on reducing the amount of N. apis spores. The same test showed that the statistically significant effect on limiting the N. ceranae invasion had: Nozevit (p – 0.014), Apiherb (p – 0.032), ApiX (p – 0.034) and syrup (p – 0.033). There was no statistically significant decrease in the N. ceranae spores in the control group.     

香菇锰过氧化物酶基因（LeMnP1）生物信息学分析及高温胁迫下的表达

本研究对香菇锰过氧化物酶基因（manganese peroxidase 1,MnP1）进行了生物信息学分析,选用香菇出发菌株18和诱变菌株18N44作为实验材料,经测定高温胁迫后菌丝恢复生长速度,分析了高温胁迫过程中香菇锰过氧化物酶基因（LeMnP1）的表达水平及酶活性。结果表明：LeMnP1定位于细胞外,该蛋白属于过氧化物酶超家族,与其他担子菌具有较高的同源性。18N44在高温胁迫后其恢复能力明显强于18;在高温胁迫过程中,18N44中LeMnP1的基因表达水平均高于18,呈现先上升后下降的趋势;在未处理时,18N44的MnP活性显著高于18,随着高温胁迫时间延长,其酶活性显著下降,18的LeMnP1基因表达量及酶活性在整个高温胁迫过程中基本维持稳定。据此推测锰过氧化物酶基因的相对高表达,可能是18N44高温胁迫后恢复生长快的原因之一。     

Detection of Laribacter hongkongensis using species-specific duplex PCR assays targeting the 16S rRNA gene and the 16S-23S rRNA intergenic spacer region (ISR)

Aims: For the rapid detection of Laribacter hongkongensis, which is associated with human community‐acquired gastroenteritis and traveller’s diarrhoea, we developed a duplex species‐specific PCR assay. Methods and Results: Full‐length of the 16S–23S rRNA intergenic spacer region (ISR) sequences of 52 L. hongkongensis isolates were obtained by PCR‐based sequencing. Two species‐specific primer pairs targeting 16S rRNA gene and ISR were designed for duplex PCR detection of L. hongkongensis. The L. hongkongensis species‐specific duplex PCR assay showed 100% specificity, and the minimum detectable level was 2·1 × 10^?2 ng μl^?1 genomic DNA which corresponds to 5000 CFU ml^?1. Conclusions: The high specificity and sensitivity of the assay make it suitable for rapid detection of L. hongkongensis. Significance and Impact of the Study: This species‐specific duplex PCR method provides a rapid, simple, and reliable alternative to conventional methods to identify L. hongkongensis and may have applications in both clinical and environmental microbiology.     

Survival of a novel endophytic fungus Phomopsis liquidambari B3 in the indole-contaminated soil detected by real-time PCR and its effects on the indigenous microbial community

The recently isolated fungal strain Phomopsis liquidambari B3 can degrade high concentrations of indole, indicating its potential for the bioremediation of indole-contaminated soil. In this study, a specific real-time PCR was developed to detect the survival of P. liquidambari B3 in soil. Subsequently, degradation activity of strain B3 and its effects on indigenous microbial community were analyzed. Results showed the amount of P. liquidambari B3 genomic DNA increased to a maximum 5.67 log (pg g⁻¹ dry soil) 10 days after inoculation of 5.04 log (pg g⁻¹ dry soil), and then gradually decreased with time and after 40 days it was below the detection limit. By the end of the experiment (day 40), bioaugmented microsoms showed a 93.7% decrease in indole, while the values for biostimulated and control microcosms were much lower. Higher microbial biomass and enzyme activities were observed in bioaugmented soil. Denaturing gradient gel electrophoresis analysis showed bioaugmentation increased richness of resident microbial community. These results indicate that P. liquidambari B3 is effective for the remediation of indole-contaminated soil and also provides valuable information about the behavior of the inoculant population during bioremediation, which could be directly used in the risk assessment of inoculant population and optimization of bioremediation process.     

宁南旱区耕作覆盖对马铃薯产量及土壤水热特征的影响

为探究耕作覆盖对土壤水热及旱作马铃薯产量的影响,连续2年在宁南旱区不同耕作深度结合覆盖模式下开展了研究工作。结果表明: 耕作深度、覆盖材料对马铃薯播种期0～100 cm土层土壤贮水量有极显著影响,而二者交互作用无显著影响;2019年土壤贮水量以深松30 cm覆盖地膜处理最高,2020年以深松40 cm覆盖秸秆处理较高,分别较翻耕15 cm不覆盖处理(对照)显著提高16.9%和33.4%;耕作深度、覆盖材料可显著影响马铃薯关键生育期土壤贮水量;同一耕作深度下土壤贮水量以秸秆、地膜覆盖处理效果较好,同一覆盖材料下以深松30～40 cm处理最佳。覆盖材料、耕作深度与覆盖材料二者交互作用对播种-现蕾期0～25 cm土层土壤有效积温影响显著;同一耕作深度下覆盖地膜处理土壤有效积温平均较不覆盖处理显著增加9.3%,而覆盖秸秆处理较不覆盖处理显著降低18.7%;2019和2020年各处理全生育期土壤有效积温分别以深松30 cm和深松40 cm覆盖地膜处理最高。2019年马铃薯总产量和经济效益以深松30 cm覆盖秸秆处理较高,分别较对照显著提高84.6%和107.9%;2020年以深松40 cm覆盖秸秆处理最佳,分别较对照显著提高81.7%和105.7%。耕作深度、覆盖材料对作物水热利用效率均有显著影响,水分利用效率以深松30～40 cm覆盖秸秆处理较高,而积温利用效率不同耕作深度结合秸秆覆盖各处理均较翻对照显著提高。相关分析表明,块茎形成期的土壤水分和有效积温对马铃薯总产量的形成至关重要,而全生育期土壤水分对总产量的影响高于土壤有效积温。可见,深松30～40 cm覆盖秸秆处理可改善土壤水热状况,实现马铃薯增产增收和水热资源的高效利用,在宁南半干旱区马铃薯生产中有一定的应用推广价值。     

Detection of Microsporum canis in the skin scrapings and hairs of dogs with dermatophytosis based on sequences of the chitin synthase 1 gene

In the present study, to confirm Microsporum canis infection rapidly, we detected the chitin synthase gene 1 (CHS1) gene of M. canis in the hair and skin samples of four dogs with dermatophytosis. Amplification of the DNAs in the four samples with CHS1 primers yielded fragments of about 620-bp. Nucleotide sequence analysis of the CHS1 gene fragments from samples and a reference strain of M. canis gene showed more than 99% similarity. The method presented in this study can rapidly detect the DNA of M. canis in skin scrapings, and we anticipate that it will be a useful microbiological tool for the diagnosis of M. canis infections in animals and humans.