Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms

Rhizosphere microorganisms play an important role in soil carbon flow, through turnover of root exudates, but there is little information on which organisms are actively involved or on the influence of environmental conditions on active communities. In this study, a (CO2)-C-13 pulse labelling field experiment was performed in an upland grassland soil, followed by RNA-stable isotope probing (SIP) analysis, to determine the effect of liming on the structure of the rhizosphere microbial community metabolizing root exudates. The lower limit of detection for SIP was determined in soil samples inoculated with a range of concentrations of C-13-labelled Pseudomonas fluorescens and was found to lie between 10(5) and 10(6) cells per gram of soil. The technique was capable of detecting microbial communities actively assimilating root exudates derived from recent photo-assimilate in the field. Denaturing gradient gel electrophoresis (DGGE) profiles of bacteria, archaea and fungi derived from fractions obtained from caesium trifluoroacetate (CsTFA) density gradient ultracentrifugation indicated that active communities in limed soils were more complex than those in unlimed soils and were more active in utilization of recently exuded C-13 compounds. In limed soils, the majority of the community detected by standard RNA-DGGE analysis appeared to be utilizing root exudates. In unlimed soils, DGGE profiles from C-12 and C-13 RNA fractions differed, suggesting that a proportion of the active community was utilizing other sources of organic carbon. These differences may reflect differences in the amount of root exudation under the different conditions.

Loss of exudates from the roots of perennial ryegrass inoculated with a range of micro-organisms

To determine the effect of microbial metabolites on the release of root exudates from perennial ryegrass, seedlings were pulse labelled with [¹⁴C]-CO₂ in the presence of a range of soil micro-organisms. Microbial inoculants were spatially separated from roots by Millipore membranes so that root infection did not occur. Using this technique, only microbial metabolites affected root exudation. The effect of microbial metabolites on carbon assimilation and distribution and root exudation was determined for 15 microbial species. Assimilation of a pulse label varied by over 3.5 fold, dependent on inoculant. Distribution of the label between roots and shoots also varied with inoculant, but the carbon pool that was most sensitive to inoculation was root exudation. In the absence of a microbial inoculant only 1% of assimilated label was exuded. Inoculation of the microcosms always caused an increase in exudation but the percentage exuded varied greatly, within the range of 3-34%. © 1995 Kluwer Academic Publishers.

Characterization of LeMir, a Root-Knot Nematode-Induced Gene in Tomato with an Encoded Product Secreted from the Root1

A tomato gene that is induced early after infection of tomato (Lycopersicon esculentum Mill.) with root-knot nematodes (Meloidogyne javanica) encodes a protein with 54% amino acid identity to miraculin, a flavorless protein that causes sour substances to be perceived as sweet. This gene was therefore named LeMir (L. esculentum miraculin). Sequence similarity places the encoded protein in the soybean trypsin-inhibitor family (Kunitz). LeMir mRNA is found in root, hypocotyl, and flower tissues, with the highest expression in the root. Rapid induction of expression upon nematode infection is localized to root tips. In situ hybridization shows that LeMir is expressed constitutively in the root-cap and root-tip epidermis. The LeMir protein product (LeMir) was produced in the yeast Pichia pastoris for generation of antibodies. Western-blot analysis showed that LeMir expression is up-regulated by nematode infection and by wounding. LeMir is also expressed in tomato callus tissue. Immunoprint analysis revealed that LeMir is expressed throughout the seedling root, but that levels are highest at the root/shoot junction. Analysis of seedling root exudates revealed that LeMir is secreted from the root into the surrounding environment, suggesting that it may interact with soil-borne microorganisms.

若尔盖高原花湖湖滨湿地甲烷排放研究

若尔盖高原湿地位于青藏高原东北部地区，平均海拔3,400-3,600m，是长江和黄河的自然分水区，区内发育了大面积的草本沼泽以及高寒沼泽化草甸、高寒湖泊。由于它所处的位置海拔高、气候波动较大，并处于我国三大自然区的交错过渡带，因而被认为是我国最为典型的脆弱湿地生态系统之一。由于地处偏远、自然环境条件恶劣等多方面的原因，针对若尔盖湿地的科学研究资料一直以来还非常缺乏。本文对国内外近年来在湿地生态系统甲烷排放过程、研究方法，以及关于湿地生态系统甲烷排放的影响因素进行了综述，并采用静态箱－气相色谱法，从湿地环境格局、湿地甲烷排放等方面，对若尔盖高原典型高寒湖泊湖滨不同类型湿地甲烷排放特征进行了研究，并进一步探讨了影响若尔盖高原高寒湖泊湖滨带甲烷排放的因素。得到如下结果：1．若尔盖高原花湖湖滨湿地在植物生长季（6 至8 月），甲烷排放平均速率为0.315 mg·m-2·h-1；不同月份间甲烷排放速率存在差异，分别为：-0.054、0.471、0.493 mg·m-2·h-1。不同类型湿地甲烷排放速率亦表现出差异，两栖蓼（Polygonum amphibium）湿地、滩涂和藏嵩草（Kobresia tibetica）草甸甲烷排放速率分别为：0.464、0.477、0.005mg·m-2·h-1。2．若尔盖高原花湖湖滨湿地甲烷排放速率与土壤10cm 温度显著相关。土壤温度是影响若尔盖高原花湖湖滨不同类型湿地甲烷排放的重要因素之一。随着土壤温度的升高，土壤微生物活性增强，使土壤中的氧消耗加快，氧化还原电位下降，有利于产甲烷菌的生长，从而增加土壤的甲烷产生量。3．地表水位与若尔盖高原花湖湖滨湿地甲烷排放速率相关性不显著。地表水覆盖，使得湿地土壤缺氧状况得到加强，增强了土壤中产甲烷菌的活性，促进甲烷形成，再通过植物、气泡或扩散的形式释放出土壤。但水层的加深，也使土壤中已产生的甲烷在通过气泡或扩散形式穿越水层时，被氧化的量增加，从而减少了甲烷向大气中的排放。4．植被高度以及植被地上生物量与若尔盖高原花湖湖滨带甲烷排放速率的相关性不显著。植物主要通过凋落物以及根系分泌物的输入为产甲烷菌提供基质，并作为土壤与大气之间的甲烷气体交换的传输途径；与其他环境因素共同影响湿地生态系统甲烷排放。The Zoige wetland on the eastern fringe of Qinghai-Tibetan Plateau, with averagealtitude between 3,400 and 3,600m, is the watershed of Yangtze River and YellowRiver. There are large area of peatland, subalpine meadow and lakes in this region.Due to its high elevation, transitional topology and high fluctuation of climate, theZoige wetlands represent one of the most fragile wetland ecosystems in China. And asa result of remote location and harsh environment conditions, the researches on theZoige wetland are relatively rare, especially the researches on the methane emissionfrom littoral zone of alpine lakes. Variations of methane emission rates as measuredby the method of static chamber – gas chromatography (GC) were detected fromlittoral zone of alpine lake on the Zoige Plateau. Relationships between methaneemission rates and environmental factors were analyzed. It is concluded that:1．The average methane emission rate in the littoral zone of Huahu Lake, ZoigePlateau is 0.315 mg·m-2·h-1, with evident spatial and temporal variations. The littoralzone has different methane effluxes with -0.054, 0.471, and 0.493 mg·CH4·m-2·h-1in June, July and August respectively. Different types of wetland have differentmethane emission rates, with value of 0.464, 0.477, and 0.005 mg·CH4·m-2·h-1 forPolygonum amphibium wetland ( PA ), Shoal ( S ) and Kobresi tibetica meadow ( KT ), respectively.2． The soil temperature at 10cm is significantly correlated with the methane effluxesin littoral zone of Huahu Lake, Zoige Plateau, and which is one of the most important factors influencing the methane emission from this region. The activities of soilmicroorganisms rise under higher soil temperature and increases oxygen consumptionand decreases Eh, which is in favor of the methanogensis, and enhances theproduction of methane in soil.3． The correlation between the standing water and methane effluxes from littoralzone of Huahu Lake is not significant. Because of the standing water, the anaerobicconditions of wetland soil have been enhanced, and are favor to the decomposition oforganic matter. And the anaerobic conditions strengthen the methanogensis’ activities,thus the methane production, which release to the atmosphere by diffusion, ebullitionand aerenchymal plants. With the water level’s increase, more methane produced insoil which is transferred by ebullitions or diffusion are oxidated, thus reduce themethane release to the atmosphere.4． The height and aboveground biomass of vegetation are not significant related tothe methane effluxes from littoral zone of Huahu Lake, Zoige Plateau. The vegetationprovides substrates for methanogensis by litter and root exudates; act as thetransportation way of methane between soil and atmosphere; influence the methaneemission of wetland ecosystems with other environment factors.

根系分泌物生态学研究

The study of root exudates enriches the theories and methods of rhizospheric soil ecology, and offers theory warranty that it can be used in agriculture and forest. This paper discusses the types and components of root exudates, mechanism of exudation, and the relationship between root exudates and the biotic and environmental factors. The development tendency and study aspect of root exudates in the future was evaluated as well.

甘蓝(Brassica oleracea L. var. capitata L.)富集铊的环境地球化学研究

通过对甘蓝进行品种差异、亚细胞分析、根际分泌物提取污染土壤中的铊、营养元素添加以及野外甘蓝样品采集分析，结合地球化学理论。分析了甘蓝对铊吸收富集的机理，并得出以下几点结论： (1) 甘蓝叶、根及茎对铊的吸收存在着明显差异，表明在面临土壤铊胁迫时，叶是铊的主要储存部位，而根和茎主要起到了转运作用。甘蓝中铊含量的升高导致了对钙和镁吸收能力的提高。不同品种甘蓝之间的吸收能力差别不大，通过选择种植对铊吸收能力小的甘蓝来控制铊的食物链危害是不可行的。此外，还应该避免在高铊土壤地区种植甘蓝。 (2) 高达92%的铊存在于甘蓝叶细胞液组分中，表明细胞液组分是铊在甘蓝叶细胞中的一个重要储存部位。但是在不同品种甘蓝叶中，铊的亚细胞分布形态没有显著差异，在甘蓝面对铊胁迫时，其叶细胞器组分中铊含量始终维持很低的含量。甘蓝对铊的解毒机制很可能就是通过在细胞内的区隔化作用(compartmentalization)，把进入体内的铊结合到细胞液组分以及细胞壁上，从而减少了铊对重要细胞器官的损伤。铊在甘蓝叶各亚细胞组分中的分配与常量元素存在一定的关系。在甘蓝叶细胞内，Tl+往细胞液组分中的传输很有可能是通过Na+/K+/2Cl–联合传输机制、Ca2+活化的钾离子通道以及一些需Mg2+或Mn2+的K+活化酶完成的。需要Mn2+参与的K+活化酶可能对于铊往细胞器中的转移起到了主导作用。在细胞壁中，很可能Ca2+活化的K+通道或者是某些特定的需要Mn2+的K+活化酶对铊的迁移或固定起了影响作用。 (3) 随着氮、磷、钾营养元素的加入，甘蓝地上部的生物量有一定程度的上升。影响主次因素依次均为氮>磷>钾。随着氮、磷、钾营养元素的加入，甘蓝地上部和地下部的铊含量并没有上升，而是有一定程度的下降。甘蓝地上部中铊含量的影响主次因素依次为磷>氮>钾，甘蓝地下部中铊含量的影响主次因素依次为氮>磷>钾。氮、磷、钾营养元素的加入都提高了甘蓝对铊的吸收量。甘蓝对铊吸收量的影响主次因素依次均为氮>磷>钾。因此我们认为，氮，磷，钾的加入显著提高了甘蓝生物量和铊的吸收量，但是随之而来的生物稀释效应，导致了甘蓝地上部和地下部含量的降低。运用铊累积量来判断营养元素对甘蓝吸收铊的影响更为客观和可靠。 (4) 通过对比蒸馏水和根际分泌物提取液对污染土壤中铊的提取能力，发现甘蓝根际分泌物提取液(root exudates)对污染土壤中的铊具有明显的活化作用。提取液的pH和土壤铊的提取率存在一定的正相关(R2=0.1659)，也就是说提取液的pH与其对污染土壤中铊的提取能力成正比。但是甘蓝体内各部分铊含量与其根际分泌物提取液对土壤铊的提取率没有任何关系，表明大量的植物非必需元素铊进入甘蓝后，并没有对其根际分泌物的产生任何影响。土壤pH越高，生长的甘蓝的根际分泌物提取液对土壤提取率就越高，甘蓝分泌物提取液对铊的提取率升高可以补偿由于土壤pH升高而造成的水溶态存在的铊减少。 (5) 铊在甘蓝叶片和叶柄中的分布状况为老叶叶片>新叶叶片>老叶叶柄>新叶叶柄，表明叶柄也是运输铊的一个重要器官。但是叶柄对铊的转运能力并没有茎那么强烈，而叶片才是甘蓝中最主要的铊储存部位。铊在根、茎、老叶和新叶中亚细胞的分布均为细胞液>>细胞壁>细胞器，这和前期室内温室培养甘蓝叶片中的分布结果是一致的。根据植物采矿经济理论的计算结果，很显然甘蓝可以成为土壤铊污染的植物修复和采矿的备选对象。

Flux and turnover of fixed carbon in soil microbial biomass of limed and unlimed plots of an upland grassland ecosystem

The influence of liming on rhizosphere microbial biomass C and incorporation of root exudates was studied in the field by in situ pulse labelling of temperate grassland vegetation with (13)CO(2) for a 3-day period. In plots that had been limed (CaCO(3) amended) annually for 3 years, incorporation into shoots and roots was, respectively, greater and lower than in unlimed plots. Analysis of chloroform-labile C demonstrated lower levels of (13)C incorporation into microbial biomass in limed soils compared to unlimed soils. The turnover of the recently assimilated (13)C compounds was faster in microbial biomass from limed than that from unlimed soils, suggesting that liming increases incorporation by microbial communities of root exudates. An exponential decay model of (13)C in total microbial biomass in limed soils indicated that the half-life of the tracer within this carbon pool was 4.7 days. Results are presented and discussed in relation to the absolute values of (13)C fixed and allocated within the plant-soil system.

Starvation Induces Expression of the Plant-Adhesin Gene, Mad2, of the Entomopathogenic Fungus Metarhizium robertsii.

Metarhizium robertsii is an entomopathogenic fungus that is additionally plant rhizosphere competent. Two adhesin-encoding gens, Mad1 and Mad2, are involved in insect pathogenesis or plant root colonization, respectively. This study examined differential expression of the Mad genes for M robertsii grown on a variety of insectand plant-related substrates. Mad1 was up regulated in response to insect cuticles and up regulation of Mad2 resulted from root exudates, tomato stems and non-preferred carbohydrates. A time course analysis that compared water, minimal media, and nutrient rich broth revealed Mad2 gene expression increased as nutrient availability decreased. The regulation of Mad2 compared to known stress-related genes (Hsp30, Hsp70 and ssgA) under various stresses (nutrient, pH, osmotic, oxidative, temperature) revealed Mad2 to be generally up regulated by nutrient starvation only. Examination of the Mad2 promoter region revealed two copies of a stress-response element (S TRE) known to be regulated under the general stress response pathway.

Diversité des champignons endophytes mycorhiziens et de classe II chez le pois chiche, et influence du génotype de la plante

réalisé en cotutelle avec la Faculté des Sciences de Tunis, Université Tunis El Manar.

Development and Integration of Biocontrol Products in Branched Broomrape (Phelipanche ramosa) management in Tomato

Parasitic weeds of the genera Striga, Orobanche, and Phelipanche pose a severe problem for agriculture because they are difficult to control and are highly destructive to several crops. The present work was carried out during the period October, 2009 to February, 2012 to evaluate the potential of arbuscular mycorrhizal fungi (AMF) to suppress P. ramosa on tomatoes and to investigate the effects of air-dried powder and aqueous extracts from Euphorbia hirta on germination and haustorium initiation in Phelipanche ramosa. The work was divided into three parts: a survey of the indigenous mycorrhizal flora in Sudan, second, laboratory and greenhouse experiments (conducted in Germany and Sudan) to construct a base for the third part, which was a field trial in Sudan. A survey was performed in 2009 in the White Nile state, Sudan to assess AMF spore densities and root colonization in nine fields planted with 13 different important agricultural crops. In addition, an attempt was made to study the relationship between soil physico-chemical properties and AMF spore density, colonization rate, species richness and other diversity indices. The mean percentage of AMF colonization was 34%, ranging from 19-50%. The spore densities (expressed as per 100 g dry soil) retrieved from the rhizosphere of different crops were relatively high, varying from 344 to 1222 with a mean of 798. There was no correlation between spore densities in soil and root colonization percentage. A total of 45 morphologically classifiable species representing ten genera of AMF were detected with no correlation between the number of species found in a soil sample and the spore density. The most abundant genus was Glomus (20 species). The AMF diversity expressed by the Shannon–Weaver index was highest in sorghum (H\= 2.27) and Jews mallow (H\= 2.13) and lowest in alfalfa (H\= 1.4). With respect to crop species, the genera Glomus and Entrophospora were encountered in almost all crops, except for Entrophospora in alfalfa. Kuklospora was found only in sugarcane and sorghum. The genus Ambispora was recovered only in mint and okra, while mint and onion were the only species on which no Acaulospora was found. The hierarchical cluster analysis based on the similarity among AMF communities with respect to crop species overall showed that species compositions were relatively similar with the highest dissimilarity of about 25% separating three of the mango samples and the four sorghum samples from all other samples. Laboratory experiments studied the influence of root and stem exudates of three tomato varieties infected by three different Glomus species on germination of P. ramosa. Root exudates were collected 21or 42 days after transplanting (DAT) and stem exudates 42 DAT and tested for their effects on germination of P. ramosa seeds in vitro. The tomato varieties studied did not have an effect on either mycorrhizal colonization or Phelipanche germination. Germination in response to exudates from 42 day old mycorrhizal plants was significantly reduced in comparison to non-mycorrhizal controls. Germination of P. ramosa in response to root exudates from 21 day old plants was consistently higher than for 42 day-old plants (F=121.6; P<.0001). Stem diffusates from non-mycorrhizal plants invariably elicited higher germination than diffusates from the corresponding mycorrhizal ones and differences were mostly statistically significant. A series of laboratory experiments was undertaken to investigate the effects of aqueous extracts from Euphorbia hirta on germination, radicle elongation, and haustorium initiation in P. ramosa. P. ramosa seeds conditioned in water and subsequently treated with diluted E. hirta extract (10-25% v/v) displayed considerable germination (47-62%). Increasing extract concentration to 50% or more reduced germination in response to the synthetic germination stimulants GR24 and Nijmegen-1 in a concentration dependent manner. P. ramosa germlings treated with diluted Euphorbia extract (10-75 % v/v) displayed haustorium initiation comparable to 2, 5-Dimethoxy-p-benzoquinon (DMBQ) at 20 µM. Euphorbia extract applied during conditioning reduced haustorium initiation in a concentration dependent manner. E. hirta extract or air-dried powder, applied to soil, induced considerable P. ramosa germination. Pot experiments were undertaken in a glasshouse at the University of Kassel, Germany, to investigate the effects of P. ramosa seed bank on tomato growth parameters. Different Phelipanche seed banks were established by mixing the parasite seeds (0 - 32 mg) with the potting medium in each pot. P. ramosa reduced all tomato growth parameters measured and the reduction progressively increased with seed bank. Root and total dry matter accumulation per tomato plant were most affected. P. ramosa emergence, number of tubercles, and tubercle dry weight increased with the seed bank and were, invariably, maximal with the highest seed bank. Another objective was to determine if different AM fungi differ in their effects on the colonization of tomatoes with P. ramosa and the performance of P. ramosa after colonization. Three AMF species viz. GIomus intraradices, Glomus mosseae and Glomus Sprint® were used in this study. For the infection, P. ramosa seeds (8 mg) were mixed with the top 5 cm soil in each pot. No mycorrhizal colonization was detected in un-inoculated control plants. P. ramosa infested, mycorrhiza inoculated tomato plants had significantly lower AMF colonization compared to plants not infested with P. ramosa. Inoculation with G. intraradices, G. mosseae and Glomus Sprint® reduced the number of emerged P. ramosa plants by 29.3, 45.3 and 62.7% and the number of tubercles by 22.2, 42 and 56.8%, respectively. Mycorrhizal root colonization was positively correlated with number of branches and total dry matter of tomatoes. Field experiments on tomato undertaken in 2010/12 were only partially successful because of insect infestations which resulted in the complete destruction of the second run of the experiment. The effects of the inoculation with AMF, the addition of 10 t ha-1 filter mud (FM), an organic residues from sugar processing and 36 or 72 kg N ha-1 on the infestation of tomatoes with P. ramosa were assessed. In un-inoculated control plants, AMF colonization ranged between 13.4 to 22.1% with no significant differences among FM and N treatments. Adding AMF or FM resulted in a significant increase of branching in the tomato plants with no additive effects. Dry weights were slightly increased through FM application when no N was applied and significantly at 36 kg N ha-1. There was no effect of FM on the time until the first Phelipanche emerged while AMF and N application interacted. Especially AMF inoculation resulted in a tendency to delayed P. ramosa emergence. The marketable yield was extremely low due to the strong fruit infestation with insects mainly whitefly Bemisia tabaci and tomato leaf miner (Tuta absoluta). Tomatoes inoculated with varied mycorrhiza species displayed different response to the insect infestation, as G. intraradices significantly reduced the infestation, while G. mosseae elicited higher insect infestation. The results of the present thesis indicate that there may be a potential of developing management strategies for P. ramosa targeting the pre-attachment stage namely germination and haustorial initiation using plant extracts. However, ways of practical use need to be developed. If such treatments can be combined with AMF inoculation also needs to be investigated. Overall, it will require a systematic approach to develop management tools that are easily applicable and affordable to Sudanese farmers. It is well-known that proper agronomical practices such as the design of an optimum crop rotation in cropping systems, reduced tillage, promotion of cover crops, the introduction of multi-microbial inoculants, and maintenance of proper phosphorus levels are advantageous if the mycorrhiza protection method is exploited against Phelipanche ramosa infestation. Without the knowledge about the biology of the parasitic weeds by the farmers and basic preventive measures such as hygiene and seed quality control no control strategy will be successful, however.

Exudation of alcohol and aldehyde sugars from roots of defoliated Lolium perenne L. grown under sterile conditions

Root exudates were collected over a 27 day period from defoliated and non-defoliated Lolium perenne L. plants grown under sterile conditions in microlysimeters. Eleven individual sugars, including both aldehyde and alcohol sugars, were identified and quantified with a gas chromatograph-mass spectrometer (GC-MS). There was no change in the number of sugars present between 7 and 27 days, but the exudation of alcohol sugars decreased rapidly at about day 12. Xylose and glucose were present in the largest amounts. Defoliation initially increased the total amount of sugars in the exudates, but continuous defoliation reduced total sugar exudation by 16% and induced changes in the exudation patterns of individual sugars. Defoliation enhanced exudation of erythritol, threitol, and xylitol, reduced exudation of glucose and arabitol, but had little effect on the amounts of other sugars exuded. The more complex 6 C, 5 OH aldehyde sugars, especially glucose, showed changes earlier and to a greater extent (17 days), than the 5 C, 4 OH (xylose and ribose) and 6 C 4 OH (fucose) aldehyde groups. These findings confirm the general finding that repeated defoliation reduces the quantity of total sugars exuded, but the pattern of release of individual sugars is complex and variable.