不同土壤类型下甘蔗根系AM真菌多样性及与土壤因子关系

甘蔗是广西重要的糖料作物,本研究通过建立克隆文库、土壤养分分析和根样染色等方法测定了33个采样点3种土壤类型(赤红壤,红壤,砖红壤)下甘蔗根系AM真菌多样性及其与土壤因子的关系。结果表明,3种土壤类型的甘蔗根系共鉴定出6科6属11种AM真菌,AM真菌各属频度存在明显差异,其中球囊霉属的频度值最高,在33个根系样品中有32个存在该属,为广西甘蔗根系AM真菌的优势属,而类球囊霉属、无梗囊霉属、近明球囊霉属、多样孢囊霉属和盾巨孢囊霉属5个属为稀有属。3种土壤类型的甘蔗根系均发现有球囊霉属和盾巨孢囊霉属;近明球囊霉属、无梗囊霉属和类球囊霉属仅在赤红壤的甘蔗根系中出现;而多样孢囊霉属仅在在赤红壤和砖红壤的甘蔗根系中出现。土壤的pH与AM菌根侵染率呈显著正相关,而有机质、总N、有效P、交换性Mg2+与AM菌根侵染率均呈负相关。本研究表明,自然条件下甘蔗根系具有相对丰富的AM真菌类群,这些AM真菌可能在甘蔗生长过程中发挥着重要的生态功能。     

Electrotropism of Maize Roots : Role of the Root Cap and Relationship to Gravitropism

We examined the kinetics of electrotropic curvature in solutions of low electrolyte concentration using primary roots of maize (Zea mays L., variety Merit). When submerged in oxygenated solution across which an electric field was applied, the roots curved rapidly and strongly toward the positive electrode (anode). The strength of the electrotropic response increased and the latent period decreased with increasing field strength. At a field strength of 7.5 volts per centimeter the latent period was 6.6 minutes and curvature reached 60 degrees in about 1 hour. For electric fields greater than 10 volts per centimeter the latent period was less than 1 minute. There was no response to electric fields less than 2.8 volts per centimeter. Both electrotropism and growth were inhibited when indoleacetic acid (10 micromolar) was included in the medium. The auxin transport inhibitor pyrenoylbenzoic acid strongly inhibited electrotropism without inhibiting growth. Electrotropism was enhanced by treatments that interfere with gravitropism, e.g. decapping the roots or pretreating them with ethyleneglycol-bis-[β-ethylether]-N,N,N′,N′-tetraacetic acid. Similarly, roots of agravitropic pea (Pisum sativum, variety Ageotropum) seedlings were more responsive to electrotropic stimulation than roots of normal (variety Alaska) seedlings. The data indicate that the early steps of gravitropism and electrotropism occur by independent mechanisms. However, the motor mechanisms of the two responses may have features in common since auxin and auxin transport inhibitors reduced both gravitropism and electrotropism.     

Cluster Roots: A Curiosity in Context

Cluster roots are an adaptation for nutrient acquisition from nutrient-poor soils. They develop on root systems of a range of species belonging to a number of different families (e.g., Proteaceae, Casuarinaceae, Fabaceae and Myricaceae) and are also found on root systems of some crop species (e.g., albus, Macadamia integrifoliaandCucurbita pepo). Their morphology is variable but typically, large numbers of determinate branch roots develop over very short distances of main root axes. Root clusters are ephemeral, and continually replaced by extension of the main root axes. Carboxylates are released from cluster roots at very fast rates for only a few days during a brief developmental window termed an ‘exudative burst’. Most of the studies of cluster-root metabolism have been carried out using the crop plant L. albus, but results on native plants have provided important additional information on carbon metabolism and exudate composition. Cluster-root forming species are generally non-mycorrhizal, and rely upon their specialised roots for the acquisition of phosphorus and other scarcely available nutrients. Phosphorus is a key plant nutrient for altering cluster-root formation, but their formation is also influenced by N and Fe. The initiation and growth of cluster roots is enhanced when plants are grown at a very low phosphate supply (viz. ≤1 μM P), and cluster-root suppression occurs at relatively higher P supplies. An important feature of some Proteaceae is storage of phosphorus in stem tissues which is associated with the seasonality of cluster-root development and P uptake (winter) and shoot growth (summer), and also maintains low leaf [P]. Some species of Proteaceae develop symptoms of P toxicity at relatively low external P supply. Our findings with Hakea prostrata (Proteaceae) indicate that P-toxicity symptoms result after the capacity of tissues to store P is exceeded. P accumulation in H. prostrata is due to its strongly decreased capacity to down-regulate P uptake when the external P supply is supra-optimal. The present review investigates cluster-root functioning in (1) L.albus (white lupin), the model crop plant for cluster-root studies, and (2) native Proteaceae that have evolved in phosphate-impoverished environments.     

Focus Issue on Roots: Root Nutrient Foraging

During a plant''s lifecycle, the availability of nutrients in the soil is mostly heterogeneous in space and time. Plants are able to adapt to nutrient shortage or localized nutrient availability by altering their root system architecture to efficiently explore soil zones containing the limited nutrient. It has been shown that the deficiency of different nutrients induces root architectural and morphological changes that are, at least to some extent, nutrient specific. Here, we highlight what is known about the importance of individual root system components for nutrient acquisition and how developmental and physiological responses can be coupled to increase nutrient foraging by roots. In addition, we review prominent molecular mechanisms involved in altering the root system in response to local nutrient availability or to the plant''s nutritional status.In natural and agricultural soils, the ability of plants to quickly and efficiently acquire nutrients may determine their competitive success and productivity. Because mineral elements interact differently with themselves and other soil constituents or are carried by water out of the rooted soil volume, their availability to plants may decrease and lead to nutrient deficiency. Under these conditions, plants activate foraging responses that include morphological changes, such as the modulation of root system architecture (RSA) or root hair formation, and physiological changes, such as the release of nutrient-mobilizing root exudates or the expression of nutrient transporters (Gojon et al., 2009; Hinsinger et al., 2009; Gruber et al., 2013). These responses are often spatially coupled to increase the root-soil interaction zone and improve the ability of the plant to intercept immobile nutrients. Noteworthy, although not discussed herein, symbiosis or associative rhizosphere microorganisms can also alter the RSA and enhance the foraging capacity of the plant (Gutjahr and Paszkowski, 2013). Here, we provide an update on the morphological responses induced by plants to forage sparingly available nutrients and some of the underlying molecular mechanisms known to date to be involved in RSA adaptations to nutrient availabilities.     

Pattern Formation in Cluster Roots: Some Developmental and Evolutionary Considerations

Cluster roots, also known as proteoid roots, are one of themajor adaptations for nutrient acquisition in terrestrial vascularsporophytes, occurring in many important plant families, inkey areas of biodiversity, and in significant ecological niches.Their development and function are closely linked and presentan ideal experimental system with which to investigate the basisof pattern and its morphogenetic amplification. Both meristemfunction and root initiation are controlled within a spatialand temporal framework, resulting in predictive phenotypic expression.In this paper, these patterns of development are described withinthe context of our knowledge of lateral root initiation anddevelopment. Recent work is summarized in an attempt to highlightthe issues of most importance for future research. The caseof the genus Lupinus is taken as a means of exploring the phylogeneticrelationships of species with cluster roots. The first evidenceof cluster roots having arisen only once within the Lupinusgenus is presented. Copyright 2000 Annals of Botany Company Cluster root, development, lateral root, lupin evolution, nutrient acquisition, pattern, proteoid root     

郭岩山不同海拔丝栗栲细根功能性状及其与土壤因子的关系

为揭示丝栗栲(Castanopsis fargesii)细根功能性状对环境变化的适应机制,对郭岩山500、700、900 m海拔处丝栗栲细根功能性状及其与土壤因子的关系进行研究。结果表明,丝栗栲细根生物量与细根根长密度、表面积密度、组织密度及体积密度呈正相关,细根根长密度、体积密度、表面积密度和比根长4个性状间均呈极显著正相关关系,且均与细根组织密度呈显著负相关。根际土含水量、C和N含量与细根比根长、根长密度、体积密度、表面积密度均存在显著正相关关系,而土壤容重与细根组织密度呈正相关。海拔700 m的细根生物量、根长密度、表面积密度及体积密度显著大于海拔500和900 m的。500和900 m海拔的根长密度、表面积密度与土壤深度呈负相关,而500 m海拔细根的组织密度与土壤深度呈正相关。因此,郭岩山丝栗栲通过改变细根功能性状来适应海拔和土壤的变化。     

纽荷尔脐橙园土壤营养与果实品质相关性研究

本试验测定湖北省秭归县柑橘良种示范场、兴山县高阳镇宝坪村和巴东县东瀼口镇雷家坪村的纽荷尔脐橙园0~40cm土层的营养状况,分析了相应果园纽荷尔脐橙果实的主要品质,经多元线性逐步回归分析结果表明,在一定范围内,纽荷尔脐橙果实的可滴定酸含量与土壤有机质含量呈线性负相关,固酸比与土壤速效钾含量呈线性正相关,VitC含量与土壤有效磷含量呈线性正相关。     

三裂叶野葛毛状根的生长及其培养基营养物质的消耗变化

研究了发根农杆菌（Agrobacterium rhizogenes）ATCC15834遗传转化产生的三裂叶野葛（Pueraria phaseoloides）毛状根在液体培养过程中生长及其部分营养物质消耗的关系．结果表明：三裂叶野葛毛状根液体培养0～4d内处于生长迟滞期、8～16d为快速生长期、16d后进入生长平台期．培养基的PO4^2-、硝态氮和铵态氮在毛状根液体培养过程中被逐渐吸收和消耗,培养16d时培养基中的PO4^3-被消耗殆尽,其浓度仅为培养基起始PO4^3-浓度的0．26％;培养基的铵态氮和硝态氮则在培养20d时才消耗殆尽;而培养基中的Ca^2＋浓度在培养过程中逐渐降低．但在培养20d时仍未被完全消耗,其浓度约为起始浓度的30．5％．培养基的pH值随培养时间的延长而不断降低,培养20d后pH值由5．62降低到4．09;而毛状根的颜色也随培养基pH值的降低和培养时间的延长逐渐由白色变成浅黄色和浅褐色．该结果为今后设计合适的培养基以开展野葛毛状根的大规模液体培养来生产葛根素提供了可能性．     

荒漠草原典型群落土壤粒径和养分的分布特征及其关系研究

为了明确荒漠草原区土壤机械组成与养分的关系,以宁夏盐池荒漠草原4种典型群落为研究对象,通过对不同群落(柠条、沙蒿、蒙古冰草、短花针茅)表层(0~5cm)、亚表层(5~10cm)和深层(10~15cm)土壤粒径分布分形(PSD)、养分含量的动态变化分析,揭示荒漠草原区土壤结构与土壤养分的相关性。结果表明:(1)4种典型群落土壤PSD均呈正态分布,不同群落间的土壤PSD差异显著,粒径100~500μm颗粒含量对PSD影响最大,不同群落间的差异大于不同生境间或不同土层间。(2)4种典型群落除全磷(TP)外,其余土壤全肥均随土壤深度增加呈降低趋势,且冠下大于丛间,表现出荒漠草原区特殊的"肥岛"聚集效应,不同群落间分布特征均表现为:柠条短花针茅蒙古冰草沙蒿,速效养分含量相对较高,各群落均达到适宜水平。(3)土壤养分与土壤PSD显著相关,除速效磷(AP)外,其余土壤养分与土壤分形维数(D)均呈正相关关系,粒径100~250μm、250~500μm颗粒与土壤养分呈显著或极显著负相关关系,土壤中的黏粒、粉粒在有机无机胶结过程及土壤良好的结构维持中起主要作用。     

Influence of Environmental Factors on Antagonism of Fungi by Bacteria in Soil: Nutrient Levels

The addition of 0.25, 0.5, or 1.0% glucose to a soil (K) amended with either 6% kaolinite (K6K) or montmorillonite (K6M) or the adjustment of the C/N ratio of the soils from 23/1 to 10/1 with NH₄NO₃ eliminated the inhibition of Aspergillus niger by Serratia marcescens, regardless of whether the fungus and bacterium were inoculated into the same or separate sites in the soils. The adjustment of the C/N ratio to 15/1 or of the C/P ratio from 1,000/1 to 100/1 with KH₂PO₄ did not eliminate the antagonism. However, with the higher glucose and NH₄NO₃ amendments, S. marcescens died out in the K and K6K (but not in the K6M) soils, apparently due to reductions in pH that resulted from the increased metabolism induced by added nutrients. In soils amended with CaCO₃, S. marcescens did not die out, but the inhibition of A. niger by S. marcescens or Agrobacterium radiobacter was eliminated or reduced by the addition of glucose, but not of NH₄NO₃, and was influenced by the clay mineralogy and pH of the soils. When NH₄NO₃ was added to the soils adjusted with CaCO₃ to pH values above 6.0, growth of A. niger was inhibited, regardless of whether bacteria were present or not, as a result of the volatilization of NH₃. Bacillus cereus and another species of Bacillus did not inhibit A. niger under any of the environmental conditions. There was a direct correlation between the degree of inhibition and the rate of glucose utilization by the various bacteria, indicating that the antagonism of A. niger by some bacteria in soil was the result primarily of a competition for carbon and that this competition was influenced by other environmental factors, such as pH and clay mineralogy.     

Focus Issue on Roots: Natural Variation of Root Traits: From Development to Nutrient Uptake

The root system has a crucial role for plant growth and productivity. Due to the challenges of heterogeneous soil environments, diverse environmental signals are integrated into root developmental decisions. While root growth and growth responses are genetically determined, there is substantial natural variation for these traits. Studying the genetic basis of the natural variation of root growth traits can not only shed light on their evolution and ecological relevance but also can be used to map the genes and their alleles responsible for the regulation of these traits. Analysis of root phenotypes has revealed growth strategies and root growth responses to a variety of environmental stimuli, as well as the extent of natural variation of a variety of root traits including ion content, cellular properties, and root system architectures. Linkage and association mapping approaches have uncovered causal genes underlying the variation of these traits.Since their advent more than 400 million years ago, vascular plants have drastically transformed the land surface of our planet and facilitated the dense colonization of its land masses (Algeo and Scheckler, 1998; Gibling and Davies, 2012). Key to this was the evolution of root systems that enable plants to forage their environment for nutrients and water and anchor themselves tightly in the soil substrate. Soils are very heterogeneous environments, and because of the constant need to optimize root distribution in the soil according to sometimes conflicting parameters, root growth and development are some of the most plastic traits in plants. This plasticity is guided by environmental information that is integrated into decisions regarding how fast and in which direction to grow and where and when to place new lateral roots (LRs; Malamy and Ryan, 2001; Malamy, 2005). The distribution and function of roots are of crucial importance for plants. In fact, they are considered the most limiting factors for plant growth in almost all natural ecosystems (Den Herder et al., 2010). Not surprisingly, the plant root system plays a major role in yield and overall plant productivity (Lynch, 1995; Den Herder et al., 2010).The extent of plasticity is determined by genetic components (Pigliucci, 2005). For instance, one ecotype of a plant species may be able to increase root growth rate on a certain stimulus, whereas another ecotype lacks this characteristic (Gifford et al., 2013). The genetic components that govern traits in different ecotypes represent the outcome of adaptation arising from the selection of those traits that allow better adapted populations to reproduce more successfully (higher fitness) than less well-adapted populations (Trontin et al., 2011; Savolainen, 2013). Although local adaptation is common in plants and animals, its genetic basis is still poorly understood (Savolainen et al., 2013). Traits that drive local adaptation are often quantitative traits shaped by multiple genes. Therefore, phenotypic differences are often caused by allelic variation at several loci, each of them making small contributions to the trait (Weigel and Nordborg, 2005; Rockman, 2012). Studying the genetic basis of the natural variation of traits cannot only shed light on the evolution of these traits and their ecological relevance but also, can be used to map the genes responsible for the regulation of these traits.Most efforts to study intraspecies genetic variation to find trait-governing genes or identify useful traits have been conducted in crop species and the model plant Arabidopsis (Arabidopsis thaliana). Whereas in crop species, traits that are used have been subjected to human-directed selection during domestication, often with the aim of increasing productivity, in Arabidopsis, it is mostly natural selection that is examined. Arabidopsis is widely distributed around the world, inhabiting diverse environments that include beaches, rocky slopes, riverbanks, roadsides, and areas surrounding agriculture fields (Horton et al., 2012). A large number of accessions has been collected over the past decades from locations all over the world and made available to the scientific community. Importantly, these accessions of Arabidopsis exhibit a striking diversity of phenotypic variation of morphology and physiology (Koornneef et al., 2004) and can be used to understand the genetic and molecular bases of traits using quantitative genetics. Variations of traits are measured in a panel of genetically distinct plant strains and then correlated with the occurrence of genetic markers in these plants. Linked or associated genome regions can eventually be identified, and additional analysis can be conducted to find the causal genes. Self-fertilizing species, such as Arabidopsis, are particularly suited for such approaches, because they can be maintained as inbred lines and therefore, need to be genotyped only one time, after which they can be phenotyped multiple times. In the past, natural variation has been used to map causal genes mainly by using recombinant inbred lines (RILs) approaches; these are very powerful but lack a high mapping resolution, and they can only capture a very small subset of the allelic diversity (Korte and Farlow, 2013). However, the advent of new and cheap large-scale genotyping and sequencing technologies has enabled large-scale, high-resolution genotyping (Horton et al., 2012) and even the complete sequencing of a large number of plant strains (http://1001genomes.org; 3,000 Rice Genomes Project, 2014). With these data, genome-wide association studies (GWASs) for identification of alleles responsible for many different quantitative traits have become feasible (Weigel, 2012). In these studies, traits of a large number of accessions are measured and subsequently associated with genotyped markers, most frequently single-nucleotide polymorphism. Although GWASs are a very powerful tool and in principle, allow for a high mapping accuracy, a notable disadvantage is that the complexity of the population structure can confound these studies. However, there has been remarkable progress addressing this issue (Atwell et al., 2010; Segura et al., 2012).In this review, we highlight recent progress in understanding the genetic bases of natural variation of growth, development, and physiology of the root system. After briefly explaining how root growth and development give rise to the root system architecture (RSA), we highlight natural variation and what has been learned from it for fundamental processes in root growth and development, root growth responses to nutrient availability, and ion uptake and homeostasis.     

Nutrient Uptake Changes in Ascorbate Free Radical-Stimulated Onion Roots

Long-term treatments with ascorbate free radical-stimulated glucose, fucose, sucrose, and nitrate uptake in Allium cepa roots. Glucose and fucose showed saturation kinetics in untreated roots, but after treatment with the ascorbate free radical, uptake was linear with time. Although the rates of nitrate and sucrose uptake increased after treatment with ascorbate free radical, the kinetics were similar to those observed in the controls. Ascorbate and dehydroascorbate inhibited nutrient uptake. The uptake rates for all nutrients increased throughout the 48-h period of pretreatment with ascorbate free radical. During the treatment an increase in the vacuole volume and tonoplast surface area also occurred. These results show the relationship between an increase in vacuolar volume and stimulated nutrient uptake from ascorbate-free radical, resulting in enhanced root elongation. These results suggest that activation of a transplasma membrane redox system by ascorbate-free radical is involved in these responses.     

小麦残茬落叶的分解与土壤因子间动态关系的研究

东北高寒地区的黑钙土土质优良肥沃 ,适合小麦、大豆和玉米等种植。近年来 ,由于人们只重视无机化肥的使用 ,忽视了地力培育 ,大量秸秆被移出田外 ,造成土壤有机质含量降低 ,土壤板结 ,使原本高产的农田逐渐变成中低产田 ,甚至有的已成为撂荒地。因此 ,研究当前农田土壤对枯枝落叶的分解现状 ,对于认识现有耕种条件下 ,农田土壤亚系统的物质转化和能量流动具有实际意义。1　研究地区和研究方法1 .1　自然概况该研究是在黑龙江省克山师专农场进行的。地理位置位于东经 1 2 5°8′～ 1 2 6°8′,北纬 47°50′～ 48°33′。年均气温 1 .3℃ ,1…     

Late Maturation of Large Metaxylem Vessels in Soybean Roots: Significance for Water and Nutrient Supply to the Shoot

The large, late metaxylem (LMX) in the roots of soybean beginsdevelopment in the centre of the stele after lignification ofthe early metaxylem poles. Subsequent maturation of the firstappearing LMX elements is gradual. They were never mature inthe 8-d-old seedlings examined. In 10 to 15-d-old plants thefirst LMX matured to open vessels at a mean of 17 cm proximalto the root tip. Additional LMX vessels developed in more proximalregions of the roots and these also matured gradually. Based on calculations from relative vessel diameters, the potentialflow of xylem sap in a single central LMX vessel is 50 timesthat in the total of all the early metaxylem (EMX) vessels ofa typical primary root of soybean. There was a marked dependence of relative leaf area on the lengthof primary root with open LMX vessels. This may result fromthe predicted increased water and nutrient flow to the shoot,facilitated by the opening of the large vessels. It is suggestedthat, as in maize, the living LMX elements may function in ionaccumulation. Dicotyledonous roots, soybean, Glycine max, xylem vessels, xylem maturation, water conduction     

Nutrient Distribution in the Potato Tuber in Relation to Soil pH

Potato tubers grown in experimental plots maintained at nominalpH values ranging from 4.5 to 7.5 were sampled by striking coresections from heel to rose ends. These were divided into consecutivepieces and analyzed for cations and anions and also the traceelements iron, manganese and copper. Linear regression equationswere fitted to each set of data thus giving the gradient ofeach constituent from heel to rose ends of the tubers. The gradientof each constituent within the tuber could then be comparedin relation to soil pH. Only the calcium content of the tuberincreased markedly with increased pH but the ratios of potassiumplus sodium to calcium plus magnesium and of phosphorus to ironboth showed maxima at pH 6 and decreased towards either endof the pH range. Solanum tuberosum, potato, tuber, calcium availability, soil pH     

土壤—作物系统的养分转化及其对土壤养分平衡的影响

土壤作为一个开放系统,与作物间通过物质转化与能量流动组成相互依存和影响的体系。近几年来我们对我国太湖地区稻田土壤生态系统中氮、磷、钾养分的转化及其可能产生的影响作过为期3年的田间定位试验研究,本文谨将其中的部分结果整理成文,以供共同探讨。     

Endogenous Ammonium Generation in Maize Roots and its Relationship to other Ammonium Fluxes

An investigation to determine the magnitude of the back reactionswhich occur during net ammonium uptake by roots and during netammonium assimilation within roots was undertaken with maize(Zea mays L.). Ten-day-old seedlings, which had been grown on250 mmol m^–3 ammonium at pH 4 or 6, were pretreated for3 h in the absence or presence of 500 mmol m ^–3 MSX (methionine-DL-sulphoximine),an inhibitor of the glutamine synthetase-catalysed pathway ofammonium assimilation. They were then exposed for 2 h to 99A% ¹⁵N-ammonium ± MSX. Substantial ammonium cycling occurredduring net ammonium uptake. Efflux was enhanced by MSX treatment,reflecting a 2- to 3-fold accumulation of ammonium in the roottissue. Influx of ammonium was also increased by treatment withMSX, indicating that influx was enhanced when products of ammoniumassimilation were dissipated. The decline in root ¹⁴N-ammoniumaccounted for only a small fraction of the ¹⁴N-ammonium recoveredin the ambient ¹⁵N-ammonium solution, revealing a substantialgeneration of endogenous ¹⁴N-ammonium during the 2 h exposure.The net quantity of ammonium generated was increased appreciablywhen assimilation of ammonium was restricted by MSX and it wasestimated to occur at least 50% faster than net ammonium uptake.Presence of MSX severely decreased translocation of ¹⁵N to shootsbut had a smaller influence on incorporation of ¹⁵N into macromoleculesof the root tissue. The various ammonium flux rates were notgreatly affected by growth at pH 4.0, implying a considerableresistance of ammonium assimilation processes in these maizeroots to the high ambient acidity commonly induced by exposureto ammonium Key words: Ammonium generation, uptake, assimilation     

Focus Issue on Roots: Functional Soil Microbiome: Belowground Solutions to an Aboveground Problem

There is considerable evidence in the literature that beneficial rhizospheric microbes can alter plant morphology, enhance plant growth, and increase mineral content. Of late, there is a surge to understand the impact of the microbiome on plant health. Recent research shows the utilization of novel sequencing techniques to identify the microbiome in model systems such as Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). However, it is not known how the community of microbes identified may play a role to improve plant health and fitness. There are very few detailed studies with isolated beneficial microbes showing the importance of the functional microbiome in plant fitness and disease protection. Some recent work on the cultivated microbiome in rice (Oryza sativa) shows that a wide diversity of bacterial species is associated with the roots of field-grown rice plants. However, the biological significance and potential effects of the microbiome on the host plants are completely unknown. Work performed with isolated strains showed various genetic pathways that are involved in the recognition of host-specific factors that play roles in beneficial host-microbe interactions. The composition of the microbiome in plants is dynamic and controlled by multiple factors. In the case of the rhizosphere, temperature, pH, and the presence of chemical signals from bacteria, plants, and nematodes all shape the environment and influence which organisms will flourish. This provides a basis for plants and their microbiomes to selectively associate with one another. This Update addresses the importance of the functional microbiome to identify phenotypes that may provide a sustainable and effective strategy to increase crop yield and food security.In recent years, the term plant microbiome has received substantial attention, since it influences both plant health and productivity. The plant microbiome encompasses the diverse functional gene pool, originating from viruses, prokaryotes, and eukaryotes, associated with various habitats of a plant host. Such plant habitats range from the whole organism (individual plants) to specific organs (e.g. roots, leaves, shoots, flowers, and seeds, including zones of interaction between roots and the surrounding soil, the rhizosphere; Rout and Southworth, 2013). The rhizosphere is the region of the soil being continuously influenced by plant roots through the rhizodeposition of exudates, mucilages, and sloughed cells (Uren, 2001; Bais et al., 2006; Moe, 2013). Thus, plant roots can influence the surrounding soil and inhabiting organisms. Mutually, the rhizosphere organisms can influence the plant by producing regulatory compounds. Thus, the rhizospheric microbiome acts as a highly evolved external functional milieu for plants (for review, see Bais et al., 2006; Badri et al., 2009b; Pineda et al., 2010; Shi et al., 2011; Philippot et al., 2013; Spence and Bais, 2013; Turner et al., 2013a; Spence et al., 2014). In another sense, it is considered as a second genome to a plant (Berendsen et al., 2012). Plant rhizospheric microbiomes have positive or negative influence on plant growth and fitness. It is influenced directly by beneficial mutualistic microbes or pathogens and indirectly through decomposition, nutrient solubilization, nutrient cycling (Glick 1995), secretion of plant growth hormones (Narula et al., 2006; Ortíz-Castro et al., 2008; Ali et al., 2009; Mishra et al., 2009), antagonism of pathogens (Kloepper et al., 2004), and induction of the plant immune system (Pieterse et al., 2001; Ramamoorthy et al., 2001; Vessey, 2003; Rudrappa et al., 2008, 2010). The establishment of plant and rhizospheric microbiome interaction is a highly coordinated event influenced by the plant host and soil. Recent studies show that plant host and developmental stage has a significant influence on shaping the rhizospheric microbiome (Peiffer et al., 2013; Chaparro et al., 2014).There are various factors involved in the establishment of the rhizospheric and endophytic microbiome. They are greatly affected by soil and host type (Bulgarelli et al., 2012; Lundberg et al., 2012). Apart from these factors, other external factors such as biotic/abiotic stress, climatic conditions, and anthropogenic effects also can impact the microbial population dynamics in particular plant species. Plant host species differences can mainly be perceived from the secretory exudates by microbes. The root exudates act as a crucial driving force for multitrophic interactions in the rhizosphere involving microbes, neighboring plants, and nematodes (Bais et al., 2006). Thus, it is important to understand root exudate-shaped microbial community profiling in establishing phenotypes involved in plant health. Microbial components associated with plant hosts have to respond to these exudates along with utilizing them in order to grow competitively in a complex interactive root environment. Commonly, there are three groups of microbes present in the rhizosphere, commensal, beneficial, and pathogenic microbes, and their competition for plant nutrition and interactions confer the overall soil suppressiveness against pathogens and insects (Berendsen et al., 2012).Traditionally, the components of the plant microbiome were characterized by isolating and culturing microbes on different media and growth conditions. These culture-based techniques missed the vast majority of microbial diversity in an environment or in plant-associated habitats, which is now detectable by modern culture-independent molecular techniques for analyzing whole environmental metagenomes (comprising all organisms’ genomes). Over the last 5 years, these culture-independent techniques have dramatically changed our view of the microbial diversity in a particular environment, from which only less than 1% are culturable (Hugenholtz et al., 1998). After discovering the importance of the conserved 16S ribosomal RNA (rRNA) sequence (Woese and Fox, 1977) and the first use of denaturing gradient gel electrophoresis (DGGE) of the amplified 16S rRNA gene in the analysis of a microbial community (Muyzer et al., 1993), there was a sudden explosion of research toward microbial ecology using various molecular fingerprinting techniques. Apart from DGGE, thermal gradient gel electrophoresis, and fluorescence in situ hybridization, clone library construction of microbial community-amplified products and sequencing emerged as other supporting techniques for better understanding of microbial ecology (Muyzer, 1999). Furthermore, there are many newer techniques used to understand the microbiome, from metagenomics to metaproteomics (Friedrich, 2006; Mendes et al., 2011; Knief et al., 2012; Rincon-Florez et al., 2013; Schlaeppi et al., 2014; Yergeau et al., 2014). These techniques cover the whole microbiome, instead of selecting particular species, unlike conventional microbial analysis. However, their presence was not yet correlated well with the phenotypic manifestation (phenome) they establish in the host plant.As a consequence of population growth, food consumption is also increasing. On the other hand, cultivable agricultural land and productivity are significantly reduced due to global industrialization, drought, salinity, and global warming (Gamalero et al., 2009). This problem is only addressed by practicing the sustainable agriculture that protects the health of the ecosystem. The basic principle of sustainable agriculture is to significantly reduce the chemical input, such as fertilizers, insecticides, and herbicides, while reducing the emission of greenhouse gas. Manipulation of the plant microbiome has great potential in reducing the incidence of pests and diseases (van Loon et al., 1998; Kloepper et al., 2004; Van Oosten et al., 2008), promoting plant growth and plant fitness, and increasing productivity (Kloepper and Schroth 1978; Lugtenberg and Kamilova, 2009; Vessey, 2003). Single strains or mixed inoculum treatments induced resistance to multiple plant diseases (Jetiyanon and Kloepper, 2002). In recent years, several microbial biofertilizers and inoculants were formulated, produced, marketed, and successfully used by farmers worldwide (Bhardwaj et al., 2014). Although plants are being considered as a metaorganism (East, 2013), our understanding of the exact manifestation of this microbiome on plant health in terms of phenotypes is insufficient. Of late, there is a surge to understand and explore the genomic wealth of rhizosphere microbes. Hence, this Update will focus mainly on existing knowledge based on the root microbiome, its functional importance, and its potential relationship to the establishment of a host phenome, toward achieving sustainable agriculture.