植物根际微生物群落构建的研究进展

植物根际是指植物根系与土壤的交界面,是根系自身生命活动和代谢对土壤影响最直接、最强烈的区域,其物理、化学和生物性质不同于土体土壤。在这个区域里,与植物发生相互作用的大量微生物,被称为根际微生物。根际微生物在植物的生长发育和植物病虫害的生物防治等方面都具有十分重要的意义。本文总结了根际微生物群落构建的研究现状,介绍了根际微生物的经典和最新的研究方法,包括根箱法、同位素技术以及高通量测序、菌群定量分析、高通量分离培养等方法在根际微生物研究中的应用,讨论了植物根系分泌物(碳水化物、氨基酸、黄酮类、酚类、激素及其信号物质)和土壤物理化学性质对根际微生物群落的影响,概述了根际微生物-植物的互作机制,以及根际微生物群落对植物的促生作用、提高植物抗逆性和抑制作用,并对根际微生物群落研究中存在的问题和未来发展方向进行了展望。     

现代生物技术在根际微生物群落研究中的应用

根际微生物的定义为植物的根表及受根系直接影响的土壤区域中的微生物群落.根际微生物与植物根系相互作用,是植物生态系统物质交换的主要媒介.根际微生物群落的研究对于微生物生态学与植物生态学均具有重要意义.近年来现代生物学技术发展迅速,对根际自然群落中不可培养微生物的研究取得了突破.综述了目前已取得的研究进展,对现代生物技术在根际微生物群落研究中的应用做了讨论.     

根际微生物促进水稻氮利用的机制

根际微生物影响植物的生长及环境适应性。不同种属、不同种群的植物影响其环境微生物群落;反之,根际微生物也影响宿主植物生长发育与生态适应性。植物与根际微生物的互作现象及其机制,是生命科学研究关注的热点,也是农业微生物利用的关键问题。近期,中国科学家在该领域取得了突破性进展。通过对不同籼稻(Oryza sativa subsp. indica)和粳稻(O. sativa subsp. japonica)品种的根际微生物组进行研究,发现籼稻根际比粳稻根际富集更多参与氮代谢的微生物群落,且该现象与硝酸盐转运蛋白基因NRT1.1B在籼粳之间的自然变异相关联。通过对籼稻接种籼稻根际特异富集的微生物群体可以提高前者对有机氮的利用,促进其生长。该研究揭示了籼稻和粳稻根际微生物分化的分子基础,展示了利用根际微生物提高水稻营养高效吸收的应用前景。     

根际微生物促进水稻氮利用的机制

根际微生物影响植物的生长及环境适应性。不同种属、不同种群的植物影响其环境微生物群落; 反之, 根际微生物也影响宿主植物生长发育与生态适应性。植物与根际微生物的互作现象及其机制, 是生命科学研究关注的热点, 也是农业微生物利用的关键问题。近期, 中国科学家在该领域取得了突破性进展。通过对不同籼稻(Oryza sativa subsp. indica)和粳稻(O. sativa subsp. japonica)品种的根际微生物组进行研究, 发现籼稻根际比粳稻根际富集更多参与氮代谢的微生物群落, 且该现象与硝酸盐转运蛋白基因NRT1.1B在籼粳之间的自然变异相关联。通过对籼稻接种籼稻根际特异富集的微生物群体可以提高前者对有机氮的利用, 促进其生长。该研究揭示了籼稻和粳稻根际微生物分化的分子基础, 展示了利用根际微生物提高水稻营养高效吸收的应用前景。     

若干技术在根际微生物研究中的应用

根际微生物是指植物根表及近根土壤中的微生物。根际微生物的研究对于微生物生态学、植物生态学及工业生物技术开发均具有十分重要的意义。为了进行更全面的研究以应对根际微生物研究所面临的复杂挑战,需要将各种生物学研究方法结合起来使用。综述了目前国内外应用较广泛的基于分子生物学的根际微生物研究方法,并对若干主要方法进行了横向比较,重点论述了结合高通量测序技术和基因芯片技术的根际微生物研究方法的新进展,并对相关技术的应用现状及其未来应用前景进行了综述。     

绿色荧光蛋白在微生物根际定殖研究中的应用

农业有益微生物根际定殖能力的强弱决定着其应用效果的好坏,而作为荧光标记分子的GFP被认为是当前用于分子生态学研究中最理想的报告基因,成为近年来研究微生物根际定殖的热点方法.简要介绍GFP的一些特性及其在微生物根际定殖研究中的应用与前景展望.     

微生物肥料新型功能作用机理与根际定殖增强策略

微生物肥料是支撑农业绿色发展的重要投入品,根际益生菌是微生物肥料菌种的主要来源。我国农业发展对促进作物根系发育、增强作物耐盐胁迫能力等新型功能的微生物肥料提出了需求,然而目前对根际益生菌促进作物根系发育和增强耐盐胁迫的分子机理研究仍然薄弱,成为制约优异菌种选育的瓶颈。另一方面,微生物肥料的根际定殖能力低也是导致其田间应用效果差的重要因素。本文综述了根际益生菌调控根系发育、增强植物耐盐的活性物质和作用机理,分析其根际定殖的过程和菌植互作机制,提出了增强根际定殖的策略,以期为微生物肥料研究提供参考。     

薄荷根内生及根际细菌多样性探究

采用传统的培养方法和基于分子生物学技术的非培养方法对我国常用中药之一的薄荷植物的根内生及根际细菌进行研究,从而了解其中细菌群落的多样性。对分离得到的细菌菌株进行16S rDNA扩增和系统发育分析,结果表明,利用培养方法与非培养方法分离得到薄荷根内生细菌及根际细菌一些共有的细菌种类,但前者优势种群为g-变形杆菌,后者优势种群为芽孢杆菌,说明土壤细菌,特别是根际细菌是植物内生细菌的重要来源,但植物对其内生细菌具有选择压。首次报道了薄荷根内和根际具有丰富的微生物群落多样性,为进一步探索植物根系微生态环境中微生物群落的形成和生态功能提供了基础信息。在今后探讨植物与微生物相互作用关系时,有必要考虑土壤环境,特别是根际对其的影响的同时,更加重视植物与其相关联的细菌种类的选择作用。     

“根际微生物”专刊征稿函

自1904年德国科学家Lorenz Hiltner提出根际概念以来,其研究内容不断得以丰富和发展。根际是植物吸收的关键门户,是实现农业绿色发展的关键调控区域。根际微生物对植物的生长和健康发挥重要作用,被看作是植物的第二基因组,类似于肠道微生物对人体的功能。根际微生物中的益生菌具有活化根区养分、促进植物生长、增强植物抗逆、抑制土传病害等功能,是微生物肥料和微生物农药的主要菌种来源。随着国内外微生物组研究的开展,根际微生物组的整体功能更受关注,充分挖掘根际微生物组的功能促进作物增产是农业微生物的主要研究前沿之一。     

三七根际微生物群落组成及多样性研究

三七是驰名中外的名贵药材,具有多种药用功能,但由于三七连作障碍使三七的产量和品质受到极大的影响。通过对三七根际土壤(种植2年、种植3年、种植健康三七以及感病三七)微生物群落多态性的相关研究,揭示了土壤微生态组成与健康三七生长的相关性。基于微生物群落对不同碳氮源利用率的差异,在Biolog ECO生态培养板上培养三七根际土壤微生物,分别培养4 h、24 h、48 h、72 h、96 h、120 h、144 h、168 h来检测其代谢水平的变化;同时还针对不同年限和健康状况的三七根际土壤的酸碱度、有机质等土壤肥力属性进行了对比分析。研究结果显示:健康三七根际土与感病三七根际土的各项指标都具有很大的差异,其中健康三七根际土中的氮、磷、钾、镁含量和土壤微生物群落的生理活性均高于感病根际土;不同种植年限的土壤有机质等土壤肥力属性均有改变,主要表现为根际土壤微生物代谢功能降低和微生物结构组成简单。研究结果为三七种植克服其连作障碍提供了一定的土壤生态学信息和理论基础。     

Resilience of the rhizosphere to anthropogenic disturbance

The rhizosphere is a dominant site of microbial metabolism in soiland whereas it can be shown that anthropogenic disturbances can influence this metabolism,the impact of these disturbances on biodiversity is rather difficult to determineat the species level. This is in part because no more than 10% of the microbial species are culturable, and in part because there is very poor precision inplate counting, usually requiring a change of 300–500% to be significant. We have therefore used a functional approach. The `ecophysiological index' is based onr or K strategy of the organisms being counted. Also, enzyme families, microbial biomass,microbe/microbe and microbe/fauna interactions have been determined,along with nutrient uptake measurements. The techniques have been applied to determinethe effects of disturbances created by the introduction of GM plants and microorganismsto soil, these effects being small compared with those caused by time-honoured practices such as crop rotation and ploughing. Toxicity from industrial influences(e.g. cyanide) can be remediated by rhizosphere microorganisms.     

Temperature and soil microorganisms interact to affect <Emphasis Type="Italic">Dodonaea viscosa</Emphasis> growth on mountainsides

There is considerable interest in understanding the drivers of plant growth in the context of climate change. Soil microorganisms play an important role in affecting plant growth and functional traits. However, the role of interaction between soil microbes and temperature in affecting plant growth and functional traits remains unclear. The objective of this research was to investigate the effects of soil microbes, temperature, and their interaction on the growth and functional traits of Dodonaea viscosa in a mountain in Yuanmou county, southwest China. The experiment was conducted in climate chambers with a factorial design of three soil microbial communities (inoculated rhizosphere microbes from high elevation, inoculated rhizosphere microbes from low elevation, and autoclaved control) and two temperature conditions (colder and warmer). D. viscosa planted in inoculated rhizosphere microbes from both high and low elevations produced more total biomass with a lower root–shoot allometric exponent, and accumulated significantly more N and P nutrients than those in an autoclaved control, with no significant differences between the two microbial inoculations. Thus, rhizosphere soil microorganisms had positive effects on D. viscosa growth. However, the effect of the microbes on plant growth strongly depended on temperature. Warming had a positive effect on D. viscosa growth in inoculated rhizosphere microbe treatments, while the positive effect disappeared in the autoclaved control treatment. Our results indicate that temperature and soil microorganisms interact to affect D. viscosa growth. As the climate changes in the future in the studied region, the growth of D. viscosa may be greatly affected both directly and indirectly through the temperature–soil microbe interaction.     

Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere

The rhizosphere is of central importance not only for plant nutrition, health and quality but also for microorganism-driven carbon sequestration, ecosystem functioning and nutrient cycling in terrestrial ecosystems. A multitude of biotic and abiotic factors are assumed to influence the structural and functional diversity of microbial communities in the rhizosphere. In this review, recent studies on the influence of the two factors, plant species and soil type, on rhizosphere-associated microbial communities are discussed. Root exudates and the response of microorganisms to the latter as well as to root morphology were shown to shape rhizosphere microbial communities. All studies revealed that soil is the main reservoir for rhizosphere microorganisms. Many secrets of microbial life in the rhizosphere were recently uncovered due to the enormous progress in molecular and microscopic tools. Physiological and molecular data on the factors that drive selection processes in the rhizosphere are presented here. Furthermore, implications for agriculture, nature conservation and biotechnology will also be discussed.     

Dissecting the Rhizosphere complexity: The truffle-ground study case

The word Rhizosphere describes the part of the soil which is immediately adjacent to and affected by plant roots. This is a very dynamic environment where plants, soil and microorganisms interact. The plant releases, in addition to biologically active substances, nutritive substances (exudates), which create a privileged habitat for many microbial populations. The same microbes that live in the rhizosphere may be useful for the plant. Interest in this fascinating environment has increased over the years. However, our knowledge of the biology and diversity of microbial populations in the rhizosphere is still limited, because it has always been linked to traditional culture-based techniques. These methods, which only allow the study of cultured microorganisms, do not allow the majority of the organisms existing in nature to be characterized. Over the last few years, this limitation has been overcome through the introduction of methodologies that are independent of culture techniques. This different approach, which has revolutionized scientific research, is known as metagenomics. In this review, the rhizosphere environment is considered with particular attention to the fungal and symbiotic organisms, which populate it. The new environmental genomic techniques and how these have been applied to the study of the various environments and the rhizosphere are described. Finally, a specific rhizosphere, a truffle-ground, is described as our study case.      

异裂菊属根际微生物群落结构及功能多样性

异裂菊属是广西喀斯特石山区典型的特有属,根际微生物是其能否有效吸收、有效利用土壤养分和适应石山恶劣土壤环境的最直接表征之一。该研究采用DGGE和Biolog两种方法对异裂菊属植物根际和非根际微生物多样性进行了研究。结果表明:(1)异裂菊属5个种根际pH、碱解氮等9个养分含量都高于非根际。(2)5个种的根际、非根际存在2个共有细菌类群,但在数量上存在差异,3个种的根际条带小于非根际;5个种的根际、非根际微生物群落较为相似,较易聚在一起。(3)绢叶异裂菊根际微生物对碳源利用能力最强,凹脉异裂菊非根际最弱,其他对碳源的利用能力较接近;异裂菊属种根际微生物利用碳源的能力都高于非根际,根际微生物多样性指数均高于非根际,优势度指数与非根际基本相同或略高于非根际,丰富度和均匀度指数与优势度指数规律相似;异裂菊属根际、非根际微生物利用的碳源主要是糖类、羧酸类和氨基酸类化合物,4个种根际微生物利用碳源的能力高于非根际。(4)阳离子交换量、黏粒含量百分率和碱解氮是影响异裂菊属根际微生物碳源利用模式的最重要因子。总体来说,土壤理化性质对异裂菊属植物根际微生物群落多样性具有重要影响,异裂菊属通过分泌羧酸、糖等多类化合物提高了根际微生物的活性,进而有效地提高了根际肥力水平。     

艾比湖湿地盐节木土壤固氮微生物群落结构和丰度的环境异质性特点

【背景】新疆艾比湖湿地国家自然保护区作为国内最典型的温带干旱区湿地荒漠生态系统,对于富集生物多样性、平衡生态环境等方面存在着非凡的意义。目前关于艾比湖湿地根际与非根际土壤固氮微生物群落结构和丰度的相关研究还未见报道。【目的】通过分析新疆艾比湖湿地盐节木根际和非根际土壤固氮菌nifH基因的群落结构和丰度的环境异质性特点,及探讨微生物群落对国内极端干旱区脆弱敏感的艾比湖湿地生态系统循环过程中的作用,为改善荒漠化的艾比湖湿地环境提供理论依据。【方法】采用构建克隆文库和q-PCR的方法,并利用冗余分析法(Redundant analysis,RDA)探究土壤理化性质与固氮微生物群落结构及丰度的相关性。【结果】艾比湖湿地盐节木非根际土壤中nifH的多样性高于根际土壤,盐节木根际土壤的nifH序列优势种属主要为固氮根瘤菌属(Azorhizobium)和脱硫弧菌属(Desulfovibrio);非根际土壤的nifH序列优势种属主要是固氮弧菌属(Azoarcus)、太阳杆菌属(Heliobacteriummodesticaldum)和脱硫弧菌属(Desulfovibrio)。盐节木根际土壤nifH数量为4.08×104copies/g,盐节木非根际土壤中nifH的数量为5.52×103copies/g,根际土壤nifH的丰度高于非根际土壤。相关性分析显示,根际土壤的优势类群和丰度与硝态氮(NO3--N)、速效氮、总钾、含水量等因子显著相关,非根际土壤的优势类群和丰度与硝态氮(NO3--N)、速效氮、总磷、总钾、总氮呈显著相关。【结论】在盐节木根际土壤中nifH的丰度高于非根际土壤,而多样性则低于非根际土壤,而且硝态氮(NO3--N)、速效氮、总磷可能会影响固氮微生物的群落结构和丰度,这些特点为湖泊湿地的退化恢复提供理论和数据基础。     

Extracellular release of a heterologous phytase from roots of transgenic plants: does manipulation of rhizosphere biochemistry impact microbial community structure?

To maintain the sustainability of agriculture, it is imperative that the reliance of crops on inorganic phosphorus (P) fertilizers is reduced. One approach is to improve the ability of crop plants to acquire P from organic sources. Transgenic plants that produce microbial phytases have been suggested as a possible means to achieve this goal. However, neither the impact of heterologous expression of phytase on the ecology of microorganisms in the rhizosphere nor the impact of rhizosphere microorganisms on the efficacy of phytases in the rhizosphere of transgenic plants has been tested. In this paper, we demonstrate that the presence of rhizosphere microorganisms reduced the dependence of plants on extracellular secretion of phytase from roots when grown in a P-deficient soil. Despite this, the expression of phytase in transgenic plants had little or no impact on the microbial community structure as compared with control plant lines, whereas soil treatments, such as the addition of inorganic P, had large effects. The results demonstrate that soil microorganisms are explicitly involved in the availability of P to plants and that the microbial community in the rhizosphere appears to be resistant to the impacts of single-gene changes in plants designed to alter rhizosphere biochemistry and nutrient cycling.     

Effects of X-Ray Dose On Rhizosphere Studies Using X-Ray Computed Tomography

X-ray Computed Tomography (CT) is a non-destructive imaging technique originally designed for diagnostic medicine, which was adopted for rhizosphere and soil science applications in the early 1980s. X-ray CT enables researchers to simultaneously visualise and quantify the heterogeneous soil matrix of mineral grains, organic matter, air-filled pores and water-filled pores. Additionally, X-ray CT allows visualisation of plant roots in situ without the need for traditional invasive methods such as root washing. However, one routinely unreported aspect of X-ray CT is the potential effect of X-ray dose on the soil-borne microorganisms and plants in rhizosphere investigations. Here we aimed to i) highlight the need for more consistent reporting of X-ray CT parameters for dose to sample, ii) to provide an overview of previously reported impacts of X-rays on soil microorganisms and plant roots and iii) present new data investigating the response of plant roots and microbial communities to X-ray exposure. Fewer than 5% of the 126 publications included in the literature review contained sufficient information to calculate dose and only 2.4% of the publications explicitly state an estimate of dose received by each sample. We conducted a study involving rice roots growing in soil, observing no significant difference between the numbers of root tips, root volume and total root length in scanned versus unscanned samples. In parallel, a soil microbe experiment scanning samples over a total of 24 weeks observed no significant difference between the scanned and unscanned microbial biomass values. We conclude from the literature review and our own experiments that X-ray CT does not impact plant growth or soil microbial populations when employing a low level of dose (<30 Gy). However, the call for higher throughput X-ray CT means that doses that biological samples receive are likely to increase and thus should be closely monitored.     

Ecological Strategies of Soil Microbial Communities under Plants of Meadow Ecosystems

Dominant growth strategies of soil microbial communities of mown and unmown meadows were assessed with respect to the constants of saturation and maximal specific growth rate of microorganisms. The microbial community of mown-meadow soil was characterized by a greater biomass and activity due to prevalence of microorganisms with the r strategy, compared to the microbial community of unmown-meadow soil. In contrast to nonrhizosphere soil, rhizosphere soil was dominated by rapidly growing microorganisms with the r strategy. The dependence of the dominant ecological strategy of the rhizosphere microbial community on the vegetation stage of plants has been traced. Study of the effect of plant species on the growth strategies of rhizosphere microorganisms showed that the features of the K strategy are more pronounced in the following rhizosphere microbial communities of grasses at the same growth stage: r strategy–Bromopsis inermis L.–Poa pratensis L., P. compressa L.–Dactylis glomerata L.–Festuca pratensisL.–K strategy. In the absence of limitation by climatic factors, the growth strategies of rhizosphere microorganisms are determined by the competition between microorganisms and plants for nutrients.