植物内生菌资源

植物内生菌是一类重要的微生物资源,近年来成为微生物资源研究的热点之一。对内生菌的多样性和开发利用的研究进展以及值得研究的问题等方面进行评述。     

植物内生菌增强植物对生物胁迫抗性的研究进展

植物在生长发育过程中因遭遇多种逆境的威胁而出现营养流失、产量大幅下降等问题，而使用传统的化学农药调控植物抗逆作用会对环境造成严重污染甚至危及人类健康，因此需要从天然成分中寻找合适的农药代替品。生活在每种植物体内的内生菌几乎都是植物微生态系统中的天然成分，因其特殊的生态位而可能对植物具有更加积极和直接的影响。然而目前，关于内生菌在提高宿主生物胁迫抗性等方面的作用机制还知之甚少。该文就植物内生菌的来源、多样性和对生物胁迫的抗性展开叙述。首先，总结了植物内生菌传播的主要方式，即水平传播和垂直传播；其次对内生菌种类的多样性以及在植物中的分布多样性进行了归纳与分析；最后，详细阐述了植物内生菌增强植物对生物胁迫应激耐受性(抗致病菌病害、抗虫害)的基本特点与作用机制，即植物内生菌可利用生态位竞争或营养位竞争产生的诱导抗性遏制病原菌感染，或合成抗生素类、生物碱类、几丁质类等次生代谢产物抑制病原菌或线虫的生长，从而防治病虫害。此外，基于内生菌增强植物生物胁迫抗性的研究现状进行了展望，为更加环保的生物防治制剂的开发与利用提供了参考。     

植物修复重金属污染及内生细菌效应

土壤和水体的重金属污染已严重危害人类生存环境与健康。由于受重金属污染的环境分布广泛,迫切需要开发经济的清除环境重金属的技术。植物修复是通过绿色植物降解或移除环境污染物,有望成为重金属污染环境的原位修复技术。植物内生菌是指定殖于健康植物的各种组织和器官内部的细菌,被感染的宿主植物不表现出外在病症,耐重金属的内生菌在多种超富集植物中存在。在植物修复过程中,野生型内生菌或基因工程内生菌的抗性系统能降低重金属植物毒性,促进其迁移金属。耐重金属内生菌还可以通过固氮、溶解矿物元素及产生类植物激素、铁载体和ACC脱氨酶等产物促进植物的生长。主要综述目前植物-内生菌相互作用及其潜在的促进植物修复重金属污染的研究进展。     

植物内生菌在生物防治中的应用

从植物内生菌的抗病虫机理及生防作用方面综述了植物内生菌在生物防治中的研究进展,对植物内生菌的抗病虫机理进行了探讨,并展望了植物内生菌在植物保护中的应用前景.     

银沙槐内生放线菌抗菌活性及其与内生细菌的拮抗关系

从荒漠濒危植物银沙槐根部分离到内生放线菌12株和内生细菌31株.以大肠杆菌、金黄色葡萄球菌和枯草芽孢杆菌为指示菌对内生放线菌进行了抗菌活性筛选.结果表明：3株放线菌对3种指示菌均有抑制作用,2株完全无抑菌作用.采用菌块抑制法分析内生放线菌对来自同一植物内生细菌的抑制效果,44.9%的组合出现抑制现象,最大抑菌圈直径为28.5mm,最小者仅8.25 mm,主要抑制对象是革兰氏阴性菌和芽孢菌;55.1%的组合无抑制现象.说明内生菌的相互作用具有多样性.     

内生真菌研究进展*

１内生真菌研究历史 内生菌（Ｅｎｄｏｐｈｙｔｅ）一词由 Ｄｅ Ｂａｒｙ（１８６６）首先提出,是指生活在植物组织内的微生物用以区分完那些生活在植物表面的表生菌（Ｅｐｉｐｈｙｔｅ）。按此定义植物的致病菌、菌根菌也归属于内生菌的概念范畴。Ｃａｒｒｏｌｌ（１９８６）将内生菌定义为生活在地上部分、活的植物组织内并不引起明显病害症状的真菌,突出强调内生菌与植物的互惠共生关系,因此,在这个内生菌概念的范畴内不包含植物致病菌和菌根菌。Ｐｅｔｒｉｎｉ（１９９１）把Ｃａｒｒｏｌｌ的概念范畴进一步扩展,将内生菌定义为那…     

植物内生菌群落组成及其功能研究进展

植物内生菌是栖居在植物组织内部、以宿主植物代谢物为营养物质的一类微生物。植物内生菌种类丰富,并通过不同的方式定殖在植物体内,与宿主植物互利共生。植物内生菌促进植物的生长发育,通过增强营养物质吸收、与病原菌竞争生态位、在代谢过程中产生抗菌物质以及诱导宿主植物产生抗性等机制,提高宿主植物的抗逆性,并且其群落的组成因生态环境、寄主植物不同部位、生长周期的不同发育阶段而显著不同。人们利用传统组织分离法、高通量测序法以及人工重组生物群落等研究方法对植物与内生菌相互作用进行了深入的研究。本文对植物内生菌群落的组成、内生菌对宿主植物影响的功能研究以及人工内生菌群的构建进行重点阐述,以期为植物内生菌的开发和利用奠定坚实基础。     

植物内生菌定殖检测技术及其应用

自然环境中内生菌定殖于植物体内,对宿主植物产生多种有益效应,但是内生菌定殖情况难以检测,相关研究不够深入系统。目前在该领域使用较为广泛的检测技术包括：荧光标记、抗生素标记、荧光定量PCR和高通量测序等。内生菌通过孔隙伤口和降解细胞壁等方式侵染植物,通过种子垂直传递核心内生菌。对植物内生菌定殖的侵染方式、定殖方法和检测技术进行了归纳和整理,介绍了内生菌多种侵染和迁移途径,总结了目前内生菌定殖在生物防治、促进植物生长和污染修复等方面的功能,综述了多种检测方式在应用中的特点,以期为内生菌定殖植物的相关研究及其应用提供参考依据。     

贵州马比木内生真菌的多样性研究

为了解贵州省马比木内生真菌的多样性,通过采集贵阳修文、遵义播州、铜仁万山3个县区的不同季节的健康马比木植物不同组织部位样本进行内生真菌的分离,分析分离菌ITS rDNA序列,采用分子系统学方法,对3个地区的不同季节马比木植物不同组织部位的内生真菌进行鉴定、归类,并进行多样性评价。结果表明,从1 444个马比木组织块中分离出1 037株内生真菌,分别隶属于30个属,其中间壳座属Diaporthe为优势属,分离率与分离频率分别为40.24%与57.58%;夏季内生真菌的多样性指数最高,4个季节的相似度在0.40-0.71之间,贵阳的相似性指数最高,三地的相似性指数在0.42-0.55之间,果实的多样性指数最高,各个组织部位的相似性指数在0.00-0.54之间。表面植株生长环境及部位对内生真菌的组成和多样性均有影响。     

植物内生菌研究进展

植物内生菌是指生活史中某一阶段生活在植物组织内,对植物没有明显病害症状的一类微生物,研究发现其主要包括内生细菌、内生真菌和内生放线菌。内生菌能够产生与宿主植物相同或相似的活性物质,从而拓宽了药用资源并且具有巨大的应用价值。从植物内生菌的分布规律及其生长特点,与宿主植物的关系,研究领域以及发展现状与存在问题等方面进行了综述,并对植物内生菌在药用资源开发中的前景进行了展望。     

Correcting for Sample Contamination in Genotype Calling of DNA Sequence Data

DNA sample contamination is a frequent problem in DNA sequencing studies and can result in genotyping errors and reduced power for association testing. We recently described methods to identify within-species DNA sample contamination based on sequencing read data, showed that our methods can reliably detect and estimate contamination levels as low as 1%, and suggested strategies to identify and remove contaminated samples from sequencing studies. Here we propose methods to model contamination during genotype calling as an alternative to removal of contaminated samples from further analyses. We compare our contamination-adjusted calls to calls that ignore contamination and to calls based on uncontaminated data. We demonstrate that, for moderate contamination levels (5%–20%), contamination-adjusted calls eliminate 48%–77% of the genotyping errors. For lower levels of contamination, our contamination correction methods produce genotypes nearly as accurate as those based on uncontaminated data. Our contamination correction methods are useful generally, but are particularly helpful for sample contamination levels from 2% to 20%.     

Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data

DNA sample contamination is a serious problem in DNA sequencing studies and may result in systematic genotype misclassification and false positive associations. Although methods exist to detect and filter out cross-species contamination, few methods to detect within-species sample contamination are available. In this paper, we describe methods to identify within-species DNA sample contamination based on (1) a combination of sequencing reads and array-based genotype data, (2) sequence reads alone, and (3) array-based genotype data alone. Analysis of sequencing reads allows contamination detection after sequence data is generated but prior to variant calling; analysis of array-based genotype data allows contamination detection prior to generation of costly sequence data. Through a combination of analysis of in silico and experimentally contaminated samples, we show that our methods can reliably detect and estimate levels of contamination as low as 1%. We evaluate the impact of DNA contamination on genotype accuracy and propose effective strategies to screen for and prevent DNA contamination in sequencing studies.     

Chronic contamination decreases disease spread: a Daphnia-fungus-copper case study

Chemical contamination and disease outbreaks have increased in many ecosystems. However, connecting pollution to disease spread remains difficult, in part, because contaminants can simultaneously exert direct and multi-generational effects on several host and parasite traits. To address these challenges, we parametrized a model using a zooplankton-fungus-copper system. In individual-level assays, we considered three sublethal contamination scenarios: no contamination, single-generation contamination (hosts and parasites exposed only during the assays) and multi-generational contamination (hosts and parasites exposed for several generations prior to and during the assays). Contamination boosted transmission by increasing contact of hosts with parasites. However, it diminished parasite reproduction by reducing the size and lifespan of infected hosts. Multi-generational contamination further reduced parasite reproduction. The parametrized model predicted that a single generation of contamination would enhance disease spread (via enhanced transmission), whereas multi-generational contamination would inhibit epidemics relative to unpolluted conditions (through greatly depressed parasite reproduction). In a population-level experiment, multi-generational contamination reduced the size of experimental epidemics but did not affect Daphnia populations without disease. This result highlights the importance of multi-generational effects for disease dynamics. Such integration of models with experiments can provide predictive power for disease problems in contaminated environments.     

An Assessment of Air As a Source of DNA Contamination Encountered When Performing PCR

Sensitive molecular methods, such as the PCR, can detect low-level contamination, and careful technique is required to reduce the impact of contaminants. Yet, some assays that are designed to detect high copy-number target sequences appear to be impossible to perform without contamination, and frequently, personnel or laboratory environment are held responsible as the source. This complicates diagnostic and research analysis when using molecular methods. To investigate the air specifically as a source of contamination, which might occur during PCR setup, we exposed tubes of water to the air of a laboratory and clean hood for up to 24 h. To increase the chances of contamination, we also investigated a busy open-plan office in the same way. All of the experiments showed the presence of human and rodent DNA contamination. However, there was no accumulation of the contamination in any of the environments investigated, suggesting that the air was not the source of contamination. Even the air from a busy open-plan office was a poor source of contamination for all of the DNA sequences investigated (human, bacterial, fungal, and rodent). This demonstrates that the personnel and immediate laboratory environment are not necessarily to blame for the observed contamination.     

Contamination and bacterial retention capacity of beef carcasses at the abattoir

The contamination of beef carcasses was studied together with the capacity of meat surfaces to retain bacteria along the processing line in the slaughter hall. The results showed that the contamination varied along the processing line, but that this pattern was essentially dependent on the contamination at the dressing station. It decreased or remained unchanged during the first 12 min and then increased, even without additional contamination. The contamination varied according to carcasses and micro-organisms studied and was not greatly affected by spray cleaning. The number of bacteria retained changed at a rate similar to that of the contaminants. The attachment was instantaneous. The results are discussed and compared with the various hypotheses about contamination and bacterial attachment processes.     

Sperm contamination in archived and contemporary herring samples

Studies using archived scales and otoliths to examine ancient fish populations have become increasingly common, despite many methodological challenges in ancient DNA research. Here, we describe a case of DNA contamination in both modern and historical samples of Pacific herring (Clupea pallasii), where the source of the contamination is likely from milt spillage during collection. We describe a series of experiments to remove contamination using pre-extraction wash treatments. Though contamination was easily removed from contemporary fin clippings, no method was successful at removing contamination from historical scales. We discuss the implications of our findings to the genetic analysis of archived samples.     

林木种子园花粉污染与防治措施

林木种子园花粉污染是影响种子园种子遗传品质的重要因子,由于野生同种花粉进入种子园而增加遗传损失。本文综述了国内外林木种子园花粉污染研究的概况、污染水平、影响污染水平的因子和减少污染的措施。研究表明：DNA分子标记在分析种子园交配动态和种子园管理效果方面非常有效（例如,cpDNA、RAPD和SSR）;种子园污染水平比预期的更高;花粉产量好像对污染水平没有影响;空间和生殖隔离也没有产生预期的效果。目前,人工辅助授粉和疏伐是减少花粉污染的两种有效措施。为了改善种子园林木的亲本平衡,人工处理技术的使用,例如：赤霉素A4/7处理技术和无性繁殖技术在种子园很受欢迎。污染程度其他方面的研究工作仍在继续,本文提到的基因流的研究。并对我国种子园花粉污染研究和花粉管理提出建议：当分析种子园花粉污染时,涉及到花粉基因型自然的（花粉扩散）、生理（开花时间）和花粉生活力等因素都应该被考虑。     

Analysis of predisposing factors for contamination of bone and tendon allografts

Bone and tissue allografts are widely used in transplantation. The increasing demand for safe allografts must be met, while minimizing disease transmission. We analysed the incidence and potential risk factors of allograft contamination and the effectiveness of disinfection, by reviewing 22 years of tissue bank activity and 474 donor procurements. We also compared different disinfection procedures used over the 22 years. The overall contamination rate was 10.1%. Risk factors were related to the donor or procurement method. Immediate culture at the tissue recovery site diminished the rate of false positives by reducing later sample manipulation. High-virulence allograft contamination was mainly related to donor factors, while low-virulence contamination was related to procurement methods. Analysis of donor-related risk factors showed no statistical differences for age, sex, or cause of death. An intensive care unit stay was associated with less contamination with high-virulence microbes. Procurement in a setting other than an operating theatre was associated with higher contamination rate. Team experience reduced contamination. Pelvic and tendon allografts were most frequently contaminated. Proper disinfection considerably reduced the contamination rate to 3.6%. We conclude that procurement must be performed under aseptic conditions, with short delays, and by trained personnel. Grafts should be disinfected and packed as soon as possible.     

Prevention of Salmonella cross-contamination in an oilmeal manufacturing plant

AIMS: The mechanisms of Salmonella contamination in an oilmeal plant were investigated and the basic data were collected in order to achieve control of Salmonella in oilmeal. METHODS AND RESULTS: Salmonella was detected in all contamination vectors and environmental factors investigated, namely: operators, processing floor, dust in the air and rodents. In particular, high concentrations of Salmonella were detected on the processing floor of the manufacturing area, which has high oil content. Steam was the most effective disinfection method used for the processing floor, as the effects of heat sterilization and disinfection may work in tandem. In addition, restricting the movement of operators of the production chain remarkably reduced Salmonella contamination, even in areas of otherwise high contamination. CONCLUSIONS: Within the oilmeal plant, high Salmonella contamination rates for the processing floor represent the greatest risk of contamination of oilmeal via operators, dust in the air and rodents. Therefore, control of the processing floor is the most important means for reducing the oilmeal contamination rate. SIGNIFICANCE AND IMPACT OF THE STUDY: Specific Salmonella control methods for oilmeal plants have been established.     

Capillary electrophoresis-single strand conformation polymorphism for the detection of multiple mutations leading to tuberculosis drug resistance

For rate determinations of anaerobic metabolism it is essential to maintain strictly anoxic conditions throughout the experiment. However, even if oxygen contamination can be avoided while preparing the incubation containers, it is still possible that the incubation containers themselves contaminate the samples by oxygen diffusing from or through their plastic or rubber components. In this study, we investigated the sources and extent of oxygen contamination during anoxic incubations, and present solutions to minimize oxygen contamination. In particular, we investigated oxygen contamination in Labco® Exetainers, glass vials with a butyl rubber septum in the screw cap, which are frequently used in microbiological experiments. Our results show that significant oxygen contamination occurred at different stages during the incubation. Contamination occurred when Exetainers were either filled or incubated for more than 16 h under oxic atmosphere, but also under an oxygen-free atmosphere due to diffusion of oxygen out of the butyl rubber septum. Therefore, to avoid oxygen contamination during incubations, we suggest (1) filling and incubating the incubation containers under anoxic atmosphere (glove bag) and (2) deoxygenating all elastomers in sample processing and incubation equipment. If initial oxygen contamination cannot be avoided, introduction of an anoxic headspace might help extract oxygen from the incubated sample and present a buffer against oxygen diffusing out of the septum. We modeled the amount of oxygen diffusing out of butyl rubber septa under different conditions, and results fitted well with the observed oxygen contamination. Thus, the model can be used to predict oxygen contamination under varying conditions and for differently sized septa.