Use of omic approaches for characterizing microbiota from suppressive compost to control soil-borne plant pathogens

Abstract

Microbiomes composition, diversity, and variability into a collection of suppressive composts were investigated for effective biological control of soil-borne phytopathogens. Pyrosequencing resulted be a reliable and faster method for characterizing fungal and bacterial microbiomes into composts derived from a varied feedstock of different composition, origin and provenience. Differences in taxonomic structure assessed by bioinformatics analyses were related to feedstock origin. Green composts derived from agro-waste and agroindustrial co/byproducts provided the most varied microbiomes either related to suppression of Rhizoctonia damping-off in bean and Verticillium wilt in eggplant, either to control of Phytium damping-off in cucumber and Phytophthora root rot in tomato. On the other hand, composted municipal solid wastes and co-composted cow manure with household waste prevalently given a most specific microbiota related to suppression of Fusarium wilt in melon.     

病毒诱导的基因沉默技术用于植物色素代谢机制的研究进展

色彩是评价园艺植物观赏性状的重要指标,而植物色素是影响植物色彩表型的关键因子。植物色素及其代谢产物在植物观赏器官颜色形成、植株生长发育调节及对逆境胁迫的响应等方面发挥着重要的作用,是植物研究领域长期关注的热点问题。病毒诱导基因沉默(virus-induced gene silencing,VIGS)是利用植物同源依赖性防御机制,特异性降低宿主内源性基因表达的一种重要基因组学工具,能够通过快速诱导植物基因沉默表型的产生,表征基因的功能,为缺乏遗传转化体系的植物的基因功能鉴定提供高效可行的替代方案。本文综述了VIGS技术在植物色素的生物合成、降解和调控机制上的应用现状,并探讨了VIGS技术在探究色素调控机制上的潜力和未来前景,以期进一步完善对不同植物色素的代谢过程和调控机制的理解,为改良植物色彩性状提供参考依据。     

Molecular analysis of genes encoding phenazine biosynthesis in the biological control bacterium Pseudomonas aureofaciens 30–84

Abstract The DNA sequence of five contiguous open reading frames encoding enzymes for phenazine biosynthesis in the biological control bacterium Pseudomonas aureofaciens 30–84 was determined. These open reading frames were named phzF, phzA, phzB, phzC and phzD . Protein PhzF is similar to 3-deoxy-D-arabino-heptulosonate-7-phosphate synthases of solanaceous plants. PhzA is similar to 2,3-dihydro-2,3-dihydroxybenzoate synthase (EntB) of Escherichia coli . PhzB shares similarity with both subunits of anthranilate synthase and the phzB open reading frame complemented an E. coli trpE mutant deficient in anthranilate synthase activity. Although phzC shares little similarity to known genes, its product is responsible for the conversion of phenazine-1-carboxylic acid to 2-hydroxy-phenazine-1-carboxylic acid. PhzD is similar to pyridoxamine phosphate oxidases. These results indicate that phenazine biosynthesis in P. aureofaciens shares similarities with the shikimic acid, enterochelin, and tryptophan biosynthetic pathways.     

Neuronal sub‐compartmentalization: a strategy to optimize neuronal function

Neurons are highly polarized cells that consist of three main structural and functional domains: a cell body or soma, an axon, and dendrites. These domains contain smaller compartments with essential roles for proper neuronal function, such as the axonal presynaptic boutons and the dendritic postsynaptic spines. The structure and function of these compartments have now been characterized in great detail. Intriguingly, however, in the last decade additional levels of compartmentalization within the axon and the dendrites have been identified, revealing that these structures are much more complex than previously thought. Herein we examine several types of structural and functional sub‐compartmentalization found in neurons of both vertebrates and invertebrates. For example, in mammalian neurons the axonal initial segment functions as a sub‐compartment to initiate the action potential, to select molecules passing into the axon, and to maintain neuronal polarization. Moreover, work in Drosophila melanogaster has shown that two distinct axonal guidance receptors are precisely clustered in adjacent segments of the commissural axons both in vivo and in vitro, suggesting a cell‐intrinsic mechanism underlying the compartmentalized receptor localization. In Caenorhabditis elegans, a subset of interneurons exhibits calcium dynamics that are localized to specific sections of the axon and control the gait of navigation, demonstrating a regulatory role of compartmentalized neuronal activity in behaviour. These findings have led to a number of new questions, which are important for our understanding of neuronal development and function. How are these sub‐compartments established and maintained? What molecular machinery and cellular events are involved? What is their functional significance for the neuron? Here, we reflect on these and other key questions that remain to be addressed in this expanding field of biology.     

报告基因技术及其在土壤质量监测中的应用

报告基因包括lux、gfp、lacZ、inaZ、luc、cat、xylE及uidA等,其中土壤质量监测中最常用的报告基因有lux、gfp、lacZ和inaZ 4种.从不同角度比较了土壤质量监测中最常用的上述4种报告基因,简要阐述了应用于土壤质量监测中的微生物监测报告基因的定义、类别、性质及特点,展示了报告基因表达系统的构建方式与检测方法,总结了报告基因技术在监测土壤重金属、污染物质、营养物质等化学物质以及在土壤微生物及其活动、土壤根际微生物与土壤中原生动物、植物间的相互作用等方面的应用.讨论了目前报告基因技术应用的局限性及未来研究方向和重点.     

Low-light image analysis of transgenic organisms using bacterial luciferase as a marker

Methods for measurement of a novel light-emitting reporter gene system in bacteria, yeast, plant cells, plant tissues and intact plant organs are described. The principle underlying the assay procedures is the bacterial luciferase catalysed oxidation of reduced flavin mononucleotide (FMNH₂) in the presence of the ten carbon aldehyde decanal, to yield FMN, decanoic acid, water and a photon of light at 490 nm which can be captured by X-ray film, a photomultiplier tube or, for in vivo measurements, an image-intensifier coupled to a video camera. This light measuring assay system is sensitive, easy to use, inexpensive, does not require radioactivity, and has been used successfully for rapid detection of bacterial transformants, the quantitative measurement of transient and stable gene expression in bacteria and yeast, and in vivo measurement of temporal and spatial gene expression throughout plant and animal development.     

一种适于家蚕细胞激素研究的双荧光素酶报告基因系统的内参质粒的构建

双荧光素酶报告基因系统能够提供灵敏的读数,但该系统需要依赖组成型表达的内参对读数进行归一化。然而,大多数内参并不是在所有条件下都组成型表达。为此,文中建立了一个有效的方法制备适于家蚕细胞双荧光素酶报告基因系统的内参质粒。首先,突变BmV gP78启动子上的激素应答相关元件,获得了在家蚕细胞中稳定表达的组成型启动子BmV gP78M;然后,用BmV gP78M替换pRL-SV40质粒上的SV40启动子和嵌合内含子序列,成功构建了pRL-V gP78M内参质粒;最后,通过细胞转染实验证实pRL-V gP78M内参在家蚕细胞系中稳定表达,并且pRL-V gP78M内参的表达活性不受蜕皮激素、保幼激素及激素相关转录因子的影响。最终,获得了在家蚕细胞中稳定表达且表达量适中的内参质粒pRL-V gP78M。该内参可以有效地作为双荧光素酶报告基因系统的内参质粒用于家蚕细胞系中激素的研究。同时,该内参质粒的构建方法也为构建适于其他物种细胞系的双荧光素酶报告基因系统的内参质粒提供了参考。     

Looking deeply into the nature of biological control

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The use of mutant and engineered microbial agents for biological control of plant diseases caused by Pythium: Achievements versus challenges

Pythium species are devasting pathogens causing major crop losses, e.g., damping-off in sugar beet caused by Pythium ultimum and root-rot of tomato caused by Pythium aphanidermatum. The use of natural antagonistic microorganisms is a promising environment-friendly approach to control Pythium-caused plant diseases. There are several examples of biocontrol of diseases caused by Pythium species but the application of bioeffectors (biological control agents) is limited for various reasons, including the restricted amount of gene-modification based biotechnological progress. The regulations in many countries prevent genetically modified bioeffectors from being routinely deployed in field conditions. Our two connected aims in this review are (1) to compile and assess achievements in genetic modification of bioeffectors which have been tested for parasitism or antagonism towards a Pythium plant pathogen or biocontrol of a plant disease caused by a Pythium species, and (2) discuss how a better performing bioeffector could be engineered to improve biocontrol of Pythium-caused plant diseases. We focus on the role of seven key mechanisms: cellulases, carbon catabolite de-repression, glycosylation, reactive oxygen species, chitin re-modelling, proteases, and toxic secondary metabolites. Genetic modifications of bioeffectors include gene deletion and overexpression, as well as the replacement of promoter elements to tune the gene expression to the presence of the pathogen. Gene-modifications are limited to fungal and bacterial bioeffectors due to the difficulty of gene modification in oomycete bioeffectors such as Pythium oligandrum. We assess how previous gene modifications could be combined and what other gene modification techniques could be introduced to make improved bioeffectors for Pythium-caused plant diseases. The broad host-range of Pythium spp. suggests engineering improved antagonistic traits of a bioeffector could be more effective than engineering plant-mediated traits i.e., engineer a bioeffector to antagonise a plant pathogen in common with multiple plant hosts rather than prime each unique plant host.     

稻鸭共作技术的生物防治效应

稻鸭共作是一项种养复合的、环境友好型的农业综合生产技术,起源于我国传统的稻田养鸭。鸭子与水稻共育于稻田中,二者存在共生互利关系,鸭子对稻田有害生物具有一定控制作用。文章综述了国内近年来利用稻鸭共作技术防治稻田病虫草害以及对稻田天敌的影响研究进展。从已有的研究中可以看出,稻鸭共作对草害和主要虫害有较好的控制效果,可在全生育期取代相应化学药剂的使用,对某些水稻病害具有一定的防治效果,对天敌种群也会产生一定的影响。但在鸭子对病虫草害防治的确切效应及其内在过程与机理方面,尚有待开展深入探究。     

基因编辑技术在大肠杆菌中的应用

利用基因编辑技术对大肠杆菌基因组进行改造可以研究基因功能,或改变其代谢途径大量生产原本成本较高的产物,从而获得可以生产特定产物的遗传稳定性工程菌株.目前可以对细菌基因组编辑的方法有Red同源重组、CRISPR/Cas9技术等.Red同源重组是比较传统的基因编辑技术,应用广泛,但编辑效率受整合片段大小的限制,基因编辑过程...     

Verticillium wilt of olive: a case study to implement an integrated strategy to control a soil-borne pathogen

Olive (Olea europaea L.) is one of the first domesticated and cultivated tree species and has historical, social and economical relevance. However, its future as a strategic commodity in Mediterranean agriculture is threatened by diverse biotic (traditional and new/emerging pests and diseases) and abiotic (erosion, climate change) menaces. These problems could also be of relevance for new geographical areas where olive cultivation is not traditional but is increasingly spreading (i.e., South America, Australia, etc). One of the major constraints for olive cultivation is Verticillium wilt, a vascular disease caused by the soil-borne fungus Verticillium dahliae Kleb. In this review we describe how Verticillium wilt of olive (VWO) has become a major problem for olive cultivation during the last two decades. Similar to other vascular diseases, VWO is difficult to manage and single control measure are mostly ineffective. Therefore, an integrated disease management strategy that fits modern sustainable agriculture criteria must be implemented. Multidisciplinary research efforts and advances to understand this pathosystem and to develop appropriate control measures are summarized. The main conclusion is that a holistic approach is the best strategy to effectively control VWO, integrating biological, chemical, physical, and cultural approaches.     

Is host‐specificity of weed biological control agents likely to evolve rapidly following establishment?

Over 352 herbivore species have now been intentionally introduced into new regions as weed biological control agents. Recent evidence shows that rapid and significant evolution in host-specificity can occur. The risk of non-target use by biological control agents increasing to unacceptable levels through rapid evolution therefore needs to be considered. In addition, weed biological control offers many as yet largely unexploited opportunities for improving our basic understanding of host-specificity and its evolution. We therefore evaluate the evidence that rapid evolution (1) alters the use of existing hosts, and (2) alters the fundamental host-range. Most cited examples of so-called host shifts from weed biological control were not the result of genetic change. There was only limited evidence of genetically altered performance on a non-target host and no evidence of altered fundamental host-range. We conclude, from both theory and the available data, that only altered use of existing hosts (through quantitative genetic changes) needs be considered when evaluating the risk of rapid evolution. Host-specificity testing methodologies can be improved and adapted to better assess the risk of occurrence of post-release evolution.     

Assessment of Boeremia exigua var. rhapontica,as a biological control agent of Russian knapweed (Rhaponticum repens)

Russian knapweed (Rhaponticum repens (L.) Hidalgo) is an herbaceous perennial weed that was introduced and has become invasive in the United States, particularly in the semi-arid west. It is characterized by its extensive root system, low seed production, and persistence. The weed has caused serious reductions in yields and crop value and may significantly devalue the land itself. Conventional control strategies have been inadequate because of the size of infestations and economic and environmental costs of control. Biological control has been a sought-after potential solution to this weed problem. In the summer of 2002, diseased R. repens plants were collected near Cankiri, Turkey, and the facultative saprophytic fungus Boeremia exigua isolate FDWSRU 02-059 was isolated from diseased plants. Bayesian analysis of the actin, beta-tubulin, calmodulin, elongation factor, and ITS genes, of 66 isolates, representing the ten species of Boeremia and the 11 varieties of B. exigua, including FDWSRU 02-059, showed that the isolate is a unique genetic entity and was named B. exigua var. rhapontica Berner, Woudenberg & Tunali, var. nov. MycoBank MB809363. Disease incidence and severity data from host-range determination tests conducted at 25 °C, the optimum temperature for growth and sporulation of B. ex. rhapontica, with adequate dew periods, were combined with a genetic distance matrix based on ITS sequences of 66 plant species related to R. repens. The combined disease and genetic data were analyzed by mixed model equations to produce best linear unbiased predictors (BLUPs), standard errors, and P > |t| values, in t-tests against zero, for disease incidence and severity for each species. BLUPs of disease incidence were significantly different from zero only for three Rhaponticum spp. while BLUPs of disease severity rankings were significantly different from zero only for R. repens, Rhaponticum carthamoides, Rhaponticum uniflorum, and Leuzea berardioides. Best linear unbiased predictors for differences in above-ground dry weights between control and inoculated plants of a subset of the species evaluated were not significant. However, above-ground damage by B. ex. rhapontica to R. repens was nearly twice that for any other species, except Rhaponticum species.     

桉树同安钮夜蛾生物学特性及防治的研究

同安钮夜蛾(Anua indiscriminata Moore)是近年来桉树产区出现的重要害虫之一。该虫在广东蕉岭1年发生4代,以蛹越冬,幼虫6-7龄。每年仅有1个发生高峰期,一般在9月出现。室内药效测定表明:高效氯氰菊酯、保尔、锐劲特、阿维菌素、印楝素、鱼藤氰和吡虫啉对同安钮夜蛾幼虫的毒杀效果均达100%;而Bt和灭幼脲Ⅲ号的杀虫效果分别为96.3%和92.6%。林间试验表明:高效氯氰菊酯、阿维烟剂和Bt对同安钮夜蛾幼虫的杀死率分别为100%、96.6%和89.7%;用烟雾机喷施阿维烟剂10倍柴油溶液,其杀虫率为82.2%。     

The potential of Isaria spp. as a bioinsecticide for the biological control of Nasutitermes corniger

The termite Nasutitermes corniger is a serious pest infesting urban areas of Brazil and many other countries. Control largely depends on synthetic pesticides whose indiscriminate use can impact the environment and the health of humans and other animals. Alternative strategies against insect pests, such as biological control by entomopathogenic fungi, could be effective while minimising these deleterious effects. We analysed the actions of the entomopathogenic fungi Isaria farinosa, Isaria fumosorosea, and Isaria javanica against the insect N. corniger. Our results indicated that the fungi examined were pathogenic against N. corniger, with I. farinosa ESALQ1355 being the most efficacious strain, resulting in the death of 95% of the workers (LC₅₀ 6.66?×?10⁴ conidia/mL) and 85% of the soldiers (LC₅₀ 6.81?×?10⁴ conidia/mL). This is the first report of the pathogenicity of Isaria spp. on N. corniger. These in vitro results suggest that I. farinosa ESALQ1355 demonstrates a significant biological potential for controlling N. corniger.     

Stable oscillations in mathematical models of biological control systems

Summary Oscillations in a class of piecewise linear (PL) equations which have been proposed to model biological control systems are considered. The flows in phase space determined by the PL equations can be classified by a directed graph, called a state transition diagram, on anN-cube. Each vertex of theN-cube corresponds to an orthant in phase space and each edge corresponds to an open boundary between neighboring orthants. If the state transition diagram contains a certain configuration called a cyclic attractor, then we prove that for the associated PL equation, all trajectories in the regions of phase space corresponding to the cyclic attractor either (i) approach a unique stable limit cycle attractor, or (ii) approach the origin, in the limitt→∞. An algebraic criterion is given to distinguish the two cases. Equations which can be used to model feedback inhibition are introduced to illustrate the techniques.     

新型基因表达调控元件——人工核糖开关的构建及筛选

核糖开关作为一种新发现的RNA元件,可以高效、准确、快速地执行基因调控任务,且免疫原性低,有可能在将来以顺式模块的方式应用于未来的基因治疗。近年来已经成功构建了多种人造核糖开关,构建方法主要是利用人工适体元件与基因表达调控元件组装,或者是在天然核糖开关基础上进行改造。文中全面综述了涉及人工核糖开关设计及筛选的技术,讨论了可以用于哺乳细胞、响应非天然配体信号、调控特征为热力学和动力学控制的核糖开关的设计新策略,并对核糖开关的筛选构建策略及其在基因治疗及新型药物开发领域的应用前景进行了展望。尽管目前将核糖开关设计成为功能强大的新型基因调控系统还面临很大的困难,但通过构效关系的研究、计算机辅助设计、体外筛选及细胞内筛选技术、高通量优化筛选等技术的综合应用,核糖开关一定可以成为有力的基因调控工具,如能成功应用则可大大促进基因治疗临床化的进程。     

AM真菌在植物病虫害生物防治中的作用机制

丛枝菌根(Arbuscular Mycorrhizae,AM)真菌是一类广泛分布于土壤生态系统中的有益微生物,能与大约80%的陆生高等植物形成共生体。由土传病原物侵染引起的土传病害被植物病理学界认定为最难防治的病害之一。研究表明,AM真菌能够拮抗由真菌、线虫、细菌等病原体引起的土传性植物病害,诱导宿主植物增强对病虫害的耐/抗病性。当前,利用AM真菌开展病虫害的生物防治已经引起生态学家和植物病理学家的广泛关注。基于此,围绕AM真菌在植物病虫害生物防治中的最新研究进展,从AM真菌改变植物根系形态结构、调节次生代谢产物的合成、改善植物根际微环境、与病原微生物直接竞争入侵位点和营养分配、诱导植株体内抗病防御体系的形成等角度,探究AM真菌在植物病虫害防治中的作用机理,以期为利用AM真菌开展植物病虫害的生物防治提供理论依据,并对本领域未来的发展方向和应用前景进行展望。     

均匀设计在候选内参基因RT—qPCR实验条件优化中的应用

目的探讨均匀设计在候选内参基因RT—qPCR实验条件优化中的应用,有助于后期实验筛选不同状态下THP～1细胞的稳定内参基因。方法以THP-1细胞cDNA为模板,eDNA模板量、引物浓度和退火温度3个因素为影响因素,应用均匀设计3因素8水平,探索影响候选内参基因RT-qPCR的扩增条件,检测不同实验条件下的扩增效果,在最优扩增条件下建立候选内参基因定量扩增的相对标准曲线,并检测扩增效率。结果通过均匀设计,完成对eDNA模板量、引物浓度和退火温度3因素8水平的实验条件优化,建立候选内参基因RT—qPCR检测的最佳组合为eDNA模板量0．5big、引物浓度200μmol／L、退火温度55℃。结论本实验选用均匀设计优化RT—qPCR实验条件,筛选出THP-1细胞候选内参基因RT—qPCR的最优实验条件。均匀设计适合于本实验研究多因素多水平试验条件的配比。