鄂尔多斯高原景观要素空间格局及植物与环境关系的定量解析

鄂尔多斯高原是一个多层次、复杂的生态过渡带，具有复杂多样的环境条件、生态特点，因此也就具有复杂多样的植物与环境关系。本文从群落和景观两个尺度水平上研究鄂尔多斯高原植物或植被与环境关系及景观空间格局。利用鄂尔多斯高原野外植物群落样方调坦数据、微生境环境数据、气候数据，以典范对应分析（Canonical Correspondence Analysis, CCA）的方法分析了鄂尔多斯高原植物分布空间格局与环境要素的关系并对秋类环境要素对鄂尔多斯高原植物空间分布格局的贡献进行了定量分解;利用1:500 000 鄂尔多斯高原植被、土壤、土地利用、土地沙漠化类型等专题地图在GIS支持下分析了鄂尔多斯高原景观空间格局、并利用上述专题图数据加上鄂尔多斯高原气候数据库分析了土壤、土地利用、土地利用、土地沙漠化和气候等对鄂尔多斯高原植被空间分布格局的作用。通过分析，得到了以下主要结论： 1 在分析方法上、利用典范对应分析的方法，把植物分布的空间因素与环境因素分离的方法发展为植物分布空间格局不同类型影响因素作用的定量分离，提出了相应的概念模型和实现方法。 2 影响鄂尔多斯高原植物分布空间格局的主要微生境环境要素是基质类型、地下水位、覆沙厚度等，而影响鄂尔多斯高原分布空间格局的主要气候要素中，降水和干湿指标的作用大于温度和热量指标的作用。 3 通过对鄂尔多斯高原植物分布空间格局与环境关系的研究，以植物对微生境环境要素的反应为根据，把鄂尔多斯高原主要植物划分为4个大类群：梁地植物、沙地植物、草甸植物和耐盐植物。根据它们对气候要素的反应，把鄂尔多斯高原主要植物划分为典型草原植物、荒漠草原植物和草原化荒漠植物3大类。进一步，根据鄂尔多劳动保护高原植物与环境关系的研究，进行了鄂尔多斯高原植被功能型划分的尝试，得到了鄂尔多斯高原的12种主要植被功能型。 4 对鄂尔多斯高原植物分布的空间格局的影响环境因素的贡献作了定量地分解。分析结果显示：鄂尔多斯高原植物分布空间格局中有27.02％可由已知环境变量得到解释，其中21.56％与微生境环境要素相关，7.51％与气候要素的作用有关，而气候与微生境环境要素的耦合作用的份额为2.05％。根据植物生长是否直接受到地下水的影响，鄂尔多斯高原存在两大类型生态特点差异明显的生境类型：中性立地和隐域生境，对两大类型生境上影响植物空间分布格局的环境要素的作用也进行了定量分解。分析结果表明：对于植物生长不直接受地下水影响的中性立地，已知环境要素的作用可以解释植物空间分布格局总信息的29.36％，稍大于对总体上鄂尔多斯高原植物分布空间格局的解释，其中9.23％与气候要素相关，22.08％与微生境环境要素相关，而两种类型环境要素的耦合作用则占1.95％。对于植物生长直接受到地下水影响的隐域生境，所有已知环境要素对植物分布空间格局的贡献率为72.28％，其中气候要素的作用为30.31％，微生境环境要素的作用为49.08％，两类环境要素的耦合作用为7.11％。 5 描述景观空间格局的指数多种多样，这些能数在描述特定区域的景观空间格局时是有信息冗余的。本文对利用FRAGSTATS所获得的鄂尔多斯高原植被、土壤、土地利用、土地沙漠化等景观分量的20个景观指数实施了因子分析。通过因子分析，我们可以把描述鄂尔多斯高原景观空间格局的景观指数归并为以下8类：多样性指数、斑块多度指数、斑块类型丰富度指数、斑块面积指数、斑块形状指数、分形维数、空间配置指数和斑块面积变异指数。通过因子分析，还得到了这些景观指数对描述鄂尔多斯景观格局的共性特征：在描述鄂尔多斯高原景观空间格局时，作用最大的是多样性指数、斑块多度指数、面积加权平均斑块形状指数和面积加权平均分形维数，其次是斑块类型丰富度指数、平均分维指数、平均形状指数和斑块面积指数，而空间配置指数（扩散与毗连指数）和斑块面积变异指数的作用则比较微弱。 6 对鄂尔多斯高原景观指数的因子分析是非常有效和成功的。因子分析对鄂尔多斯高原植被、土壤、土地利用、土地沙漠化景观指数的分析分别得到了5-6个主要因子，可以表达原有20个景观指数所表达信息的91.1-96.0％，即可以反应鄂尔多斯高原景观空间格局的大部分信息。本文所进行的因子分析对因子进行了方差最大化(Varimax)正交旋转的处理，因子分析得到的每一个主要因子都有一个或几个与之相关性非常高的景观指数与之对应，因此，就可以用与因子分析所得主要因子相关性最高的景观指数代替该主要因子来表达鄂尔多斯高原的景观空间格局。另外还因为有些景观指数之间具有极高的相关系数，所以对因子分析所得到的景观指数可以进一步精减，最后利用因子分析成功地把原有20个景观指数减少到了11个。最后被选来描述鄂尔多斯高原景观格局的景观指数有下列11个：MSIEI（修正的Simpson均匀度指数）、AWMPFD（面积加权平均斑块分形维数）、AWMSI（面积加权平均形状指数）、NP（斑块数目）、PR（斑块类型丰富度）、MSI（平均形状指数）、MPFD（平均斑块分形维数）、MPS（平均斑块面积）、PSCV（斑块面积变异系数）、DLFD（双对数分形维数）和IJI（扩散与毗连指数）。 7 鄂尔多斯高原植被、土壤、土地利用在景观组成结构上具有一个共同特点，就是各种类型的面积差异极大，少数类型占有极大比重，而其余面积则很小。产生这一情形的原因主要与人为活动的强烈影响有关，表现在地带性的植被与土壤面积所占的比重不高，沙地、沙生植被与风沙土则占有很大比重。 8 以地带性植被和滩地隐域性植被表示的鄂尔多斯高原的原生植被仅占高原面积的不足30％，而以地带性土壤和滩地隐域性土壤表示的原生性土壤占鄂尔多斯高原总面积的近40％，说明土壤退化不如植被退化严重，或滞后于植被退化。 9 鄂尔多斯高原各景观指数的空间变化曲线，植被与土壤很相近，具有非常相似的格局;土地利用景观格局空间变化特征与植被、土壤等明显不同;土地沙漠化的景观格局空间变化曲线介植被曲线、土壤曲线与土地利用曲线之间，说明土地沙漠化不仅是一个受人为活动影响的过程，而且与自然过程密切相关。 10 鄂尔多斯高原景观格局的空间梯度变化表现出了东西向和南北向的梯度，但总体上以东西向的变化比较明显。 11 通过鄂尔多斯高原土壤类型、土地利用、土地沙漠化等景观要素、气候、空间要素与鄂尔多斯高原植被空间分布格局的CCA分析，探讨了它们之间的相互关系。以对鄂尔多斯高原植被组成数据的总方差解释的百分率为标准，土壤对鄂尔多斯植被分布的空间格局的作用最大，其方差贡献率可达44.28％，其次是土地利用与鄂尔多斯高原植被的关系也很密切，土地利用对鄂尔多斯高原植被空间分布格局的方差贡献率为22.45％，空间因素对鄂尔多斯高原植被空间分布格局的贡献率为17.51％，土地沙漠化对鄂尔多斯高原植被空间分布格局的贡献为15.65％，排在第四位;气候因素对鄂尔多斯高原植被空间格局的贡献率为11.95％，居第五位。 12 在气候要素对鄂尔多斯高原植被空间分布格局的作用中，降水与干湿指标的作用大于温度与热量指标的作用。这一点与利用野外调查样方的群落数据植物与气候关系的分析是完全一致的。CCA分析还表明鄂尔多斯高原植被空间格局的东西向变化大于南北向分异。 13 在群落和景观水平上，鄂尔多斯高原植物空间分布或植被格局的影响因素的作用具有相似的格局，即气候因子的作用明显地小于地质、土壤、水文等微生境环境要素（群落水平）或土壤（景观水平）的作用，并在这两个尺度上气候要素对植物空间分布或植被格局的定量解释份额上也是非常相近的，都仅有10％左右。气候因子对鄂尔多斯高原植物空间分布格局的这种弱的解释能力，从侧面说明了人为活动等非自然因素对鄂尔多斯高原植物空间分布格局的强烈作用。 14 在鄂尔多斯高原生态系统管理上，应协调人与自然的关系;加强鄂尔多斯高原的生物多样性保育，对于本区生态和经济对非常重要的滩地，应协调好对其开发利用与保护的关系;在鄂尔多斯高原土地沙漠化防治方面，应把调整人地关系与自然生态背景与条件相结合，如使用“三圈”模式等生态系统管理模式等。

油菜内源和外源蛋白的表达及环境因素的影响

植物与昆虫的互作关系是个长期进化的过程，虫害给农业生产带来巨大损失。本研究以甘蓝型油菜（Brassica napus）为例，研究了不同环境条件和遗传背景下外源基因的表达与效用，同时利用蛋白质组技术，研究了虫害损伤模拟条件下植物可能存在的内源抗性机制。甘蓝型油菜中转入了人工合成的Bt（Bacillus thuringiensis）杀虫基因，能使植物产生抗虫蛋白抵御虫害。我们在湖北湖南两个实验点进行了大田实验，按植株生长发育的4个不同时期从转基因植株的叶片上采样，研究抗虫蛋白在植物体内的表达动态。植株顶部第三片展开叶的Bt毒蛋白浓度在结荚期前随植物生长而不断增加，而在结荚期出现或增或减的现象。采样叶片的可溶性总蛋白浓度含量一直呈增加的趋势，直到结荚以后出现含量的明显降低。同时，收集了转基因油菜与湘油15号在田间自然杂交形成的杂交后代种子用于栽培，用GFP仪检测杂交后代的绿色荧光蛋白（green fluorescent protein），并用聚合酶链式反应（polymerase chain reaction, PCR）检测并确认带有转基因的杂交植株。为了检测带有转基因的杂交后代油菜中Bt毒蛋白的杀虫效率，用对Bt毒蛋白敏感的试虫品系——初孵棉铃虫幼虫（Helicoverpa armigera）进行杀虫活性检测实验。结果表明，携带Bt基因的杂交湘油及其转基因亲本对试虫的体重增长量均产生了负面影响，可以推断在调查取样的植株生长发育阶段，转基因杂交后代与其转基因亲本植株的杀虫效率没有显著差异。转基因植物及其杂交后代中抗虫蛋白的持续表达及田间带有转基因的自播植物的出现会使害虫产生耐受抗性的潜在可能性增加。 相对于人为增加的抗虫基因，植物在长期对抗昆虫的过程中也进化形成了自我防御机制，能够产生特异的抗性蛋白来应对昆虫的取食。本研究用机械损伤模拟害虫取食，对比了油菜受到物理损伤前后可溶性总蛋白的含量变化并试图通过蛋白质组学技术来检测可能发生变化的蛋白质。Bradford定量测定发现，同一植株同一叶片损伤前后可溶性总蛋白含量差异显著，损伤后蛋白表达量显著增高。蛋白质组双向凝胶电泳及其差异分析显示，损伤前后有8个蛋白质点发生明显的上调或下调。选择其中2个差异蛋白点经过MALDI-TOF质谱鉴定，它们分别是Rubisco小亚基前体以及果糖－1，6－二磷酸醛缩酶和粪卟啉－3－氧化酶的混合物，这些蛋白质在其他植物的抗逆研究中也有报道，它们可能在油菜叶片应答机械损伤过程中对维持植物的生理功能也有重要作用。

Do leaves of plants on phosphorus-impoverished soils contain high concentrations of phenolic defence compounds?

Prominent theories of plant defence have predicted that plants growing on nutrient-poor soils produce more phenolic defence compounds than those on richer soils. Only recently has the Protein Competition Model (PCM) of phenolic allocation suggested that N and P limitation could have different effects because the nutrients are involved in different cellular metabolic processes. 2. We extend the prediction of the PCM and hypothesize that N will have a greater influence on the production of phenolic defensive compounds than P availability, because N limitation reduces protein production and thus competition for phenylalanine, a precursor of many phenolic compounds. In contrast, P acts as a recyclable cofactor in these reactions, allowing protein and hence phenolic production to continue under low P conditions. 3. We test this hypothesis by comparing the foliar concentrations of phenolic compounds in (i) phenotypes of 21 species growing on P-rich alluvial terraces and P-depleted marine terraces in southern New Zealand, and (ii) 87 species growing under similar climates on comparatively P-rich soils in New Zealand vs. P-depleted soils in Tasmania. 4. Foliar P concentrations of plants from the marine terraces were about half those of plants from alluvial soils, and much lower in Tasmania than in New Zealand. However, foliar concentrations of N and phenolic compounds were similar across sites in both comparisons, supporting the hypothesis that N availability is a more important determinant of plant investment in phenolic defensive compounds than P availability. We found no indication that reduced soil P levels influenced plant concentrations of phenolic compounds. There was wide variation in the foliar N and P concentrations among species, and those with low foliar nutrient concentrations produced more phenolics (including condensed tannins). 5. Our study is the first trait comparison extending beyond standard leaf economics to include secondary metabolites related to defence in forest plants, and emphasizes that N and P have different influences on the production of phenolic defence compounds. © 2009 British Ecological Society.

Impacts of culling and exclusion of browsers on vegetation recovery across New Zealand forests

Introduced browsing animals negatively impact New Zealand's indigenous ecosystems. Eradicating introduced browsers is currently unfeasible at large scales, but culling since the 1960s has successfully reduced populations to a fraction of their earlier sizes. Here we ask whether culling of ungulates has allowed populations of woody plant species to recover across New Zealand forests. Using 73 pairs of permanent fenced exclosure and unfenced control plots, we found rapid increases in sapling densities within exclosures located in disturbed forests, particularly if a seedling bank was already present. Recovery was slower in thinning stands and hampered by dense fern cover. We inferred ungulate diet preference from species recovery rates inside exclosures to test whether culling increased abundance of preferred species across a national network of 574 unfenced permanent forest plots. Across this network, saplings were observed irrespective of their preference to ungulates in the 1970s, but preferred species were rarer within disturbed sites in the 1990s after long-term culling and despite nationwide increases in sapling densities. This indicates that preferred species are relatively heavily affected by browsing after culling, presumably because remaining animals will increase consumption of preferred species as competition is reduced. Our results clearly suggest that culling will not return preferred plants to the landscape immediately, even given suitable conditions for regeneration. Complete removal of ungulates rather than simply reducing their densities may be required for recovery in heavily browsed temperate forests, but since this is only feasible at small spatial scales, management efforts must target sites of high conservation value. © 2012 Elsevier Ltd.

Review of the genus Bursaphelenchus Fuchs, 1937 (Nematoda, Aphelenchida) with some conclusions on the host-parasite and vector-parasite evolution.

INTRODUCTION AND GOALS: Genus Bursaphelenchus includes several pests of the world importance for the rural economy, the most dangerous are the Bursaphelenchus xylophilus (the pinewood nematode caused decline of the pine trees in south Asia and in one spot area in Europe, Portugal, Peninsula de Setubal) and the Bursaphelenchus cocophilus, causing the decline of coco-palm plantations in Carribean and Latin American regions. The peculiarity of the host-parasite association of the genus that the nematode life cycle includes three trophic components: plant (mostly a tree), insect vector and a fungus. Goals of the presentation is to list all species of the world fauna and all efficient diagnostic characters, then create the identification tool and analyze the similarity of species and possible ways and causes of the host-parasite evolution of the group. RESULTS: Complete list of species with synonymy and a catalogue of all efficient diagnostic characters with their states, selected from papers of the most experienced taxonomists of the genus, are given for the genus Bursaphelenchus. List of known records of Bursaphelenchus species with names of natural vectors and plants and their families is given (for world pests the most important groups of trees and insects are listed). The tabular, traditional and computer-aided keys are presented. Dendrograms of species relationships (UPGMA, standard distance: mean character difference) based on all efficient taxonomic characters and separately on the spicule characters only, are given. Discussion whether the species groups are natural or purely diagnostic ones is based on the relationships dendrograms and the vector and associated plant ranges of Bursaphelenchus species; the xylophilus species group (B. xylophilus, B. abruptus, B. baujardi, B. conicaudatus, B. eroshenkii, B. fraudulentus, B. kolymensis, B. luxuriosae; B. mucronatus), the hunti group (B. hunti, B. seani, B. kevini and B. fungivorus) are probably the natural ones. CONCLUSIONS: The parasitic nematode association includes three trophic components: plant, insect vector and fungus. The initial insect-plant complex Scolytidae-Pinaceae is changeable and only in rare occasions the change of the preferred vector to Cerambycidae (the xylophilus group), Hymenoptera (the hunti group) led to formation of the natural species-groups. From the analysis it is clear that although the vector range is changeable it is comparatively more important for the evolution of the genus Bursaphelenchus than associations with plants at the family level. Data on the fungi species (3rd component in natural Bursaphelenchus associations) are insufficient for the detailed comparative analysis.

Microbe-mediated recovery of salt marshes contaminated with oil hydrocarbons

Salt marshes are highly productive intertidal habitats that serve as nursery grounds for many commercially and economically important species. Because of their location and physical and biological characteristics, salt marshes are considered to be particularly vulnerable to anthropogenic inputs of oil hydrocarbons. Sediment contamination with oil is especially dangerous for salt marsh vegetation, since low molecular weight aromatic hydrocarbons can affect plants at all stages of development. However, the use of vegetation for bioremediation (phytoremediation), by removal or sequestration of contaminants, has been intensively studied. Phytoremediation is an efficient, inexpensive and environmental friendly approach for the removal of aromatic hydrocarbons, through direct incorporation by the plant and by the intervention of degrading microbial populations in the rhizosphere (microbe-assisted phytoremediation). Rhizosphere microbial communities are enriched in important catabolic genotypes for degradation of oil hydrocarbons (OH) which may have a potential for detoxification of the sediment surrounding the roots. In addition, since rhizosphere bacterial populations may also internalize into plant tissues (endophytes), rhizocompetent AH degrading populations may be important for in planta AH degradation and detoxification. The present study involved field work and microcosms experiments aiming the characterization of relevant plant-microbe interactions in oilimpacted salt marshes and the understanding of the effect of rhizosphere and endosphere bacteria in the role of salt marsh plants as potential phytoremediation agents. In the field approach, molecular tools were used to assess how plant species- and OH pollution affect sediment bacterial composition [bulk sediment and sediment surrounding the roots (rhizosphere) of Halimione portulacoides and Sarcocornia perennis subsp. perennis] in a temperate estuary (Ria de Aveiro, Portugal) chronically exposed to OH pollution. In addition, the 16S rRNA gene sequences retrieved in this study were used to generate in silico metagenomes and to evaluate the distribution of potential bacterial traits in different microhabitats. Moreover, a combination of culture-dependent and -independent approaches was used to investigate the effect of oil hydrocarbons contamination on the structure and function of endophytic bacterial communities of salt marsh plants.Root systems of H. portulacoides and S. perennis subsp. perennis appear to be able to exert a strong influence on bacterial composition and in silico metagenome analysis showed enrichment of genes involved in the process of polycyclic aromatic hydrocarbon (PAH) degradation in the rhizosphere of halophyte plants. The culturable fraction of endophytic degraders was essentially closely related to known OH-degrading Pseudomonas species and endophytic communities revealed sitespecific effects related to the level of OH contamination in the sediment. In order to determine the effects of oil contamination on plant condition and on the responses in terms of structure and function of the bacterial community associated with plant roots (rhizosphere, endosphere), a microcosms approach was set up. The salt marsh plant Halimione portulacoides was inoculated with a previous isolated Pseudomonas sp. endophytic degrader and the 2-methylnaphthalene was used as model PAH contaminant. The results showed that H. portulacoides health and growth were not affected by the contamination with the tested concentration. Moreover, the decrease of 2-methylnaphthalene at the end of experiment, can suggest that H. portulacoides can be considered as a potential plant for future uses in phytoremedition approaches of contaminated salt marsh. The acceleration of hydrocarbon degradation by inoculation of the plants with the hydrocarbon-degrading Pseudomonas sp. could not, however, be demonstrated, although the effects of inoculation on the structure of the endophytic community observed at the end of the experiment indicate that the strain may be an efficient colonizer of H. portulacoides roots. The results obtained in this work suggest that H. portulacoides tolerates moderate concentrations of 2-methylnaphthalene and can be regarded as a promising agent for phytoremedition approaches in salt marshes contaminated with oil hydrocarbons. Plant/microbe interactions may have an important role in the degradation process, as plants support a diverse endophytic bacterial community, enriched in genetic factors (genes and plasmids) for hydrocarbon degradation.

The fate and toxicity of the flavonoids naringenin and formononetin in soil

The flavonoid class of plant secondary metabolites play a multifunctional role in below-ground plant-microbe interactions with their best known function as signals in the nitrogen fixing legume-rhizobia symbiosis. Flavonoids enter rhizosphere soil as a result of root exudation and senescence but little is known about their subsequent fate or impacts on microbial activity. Therefore, the present study examined the sorptive behaviour, biodegradation and impact on dehydrogenase activity (as determined by iodonitrotetrazolium chloride reduction) of the flavonoids naringenin and formononetin in soil. Organic carbon normalised partition coefficients, log K-oc, of 3.12 (formononetin) and 3.19 (naringenin) were estimated from sorption isotherms and, after comparison with literature log K-oc values for compounds whose soil behaviour is better characterised, the test flavonoids were deemed to be moderately sorbed. Naringenin (spiked at 50 mu g g(-1)) was biodegraded without a detectable lag phase with concentrations reduced to 0.13 +/- 0.01 mu g g(-1) at the end of the 96 h time course. Biodegradation of formononetin proceeded after a lag phase of similar to 24 with concentrations reduced to 4.5 +/- 1% of the sterile control after 72 h. Most probable number (MPN) analysis revealed that prior to the addition of flavonoids, the soil contained 5.4 x 10(6) MPNg(-1) (naringenin) and 7.9 x 10(5) MPNg(-1) (formononetin) catabolic microbes. Formononetin concentration had no significant (p > 0.05) effect on soil dehydrogenase activity, whereas naringenin concentration had an overall but non-systematic impact (p = 0.045). These results are discussed with reference to likely total and bioavailable concentrations of flavonoids experienced by microbes in the rhizosphere. (c) 2007 Elsevier Ltd. All rights reserved.

Role of polyhydroxybutyrate and glycogen as carbon storage compounds in pea and bean bacteroids

Rhizobium leguminosarum synthesizes polyhydroxybutyrate and glycogen as its main carbon storage compounds. To examine the role of these compounds in bacteroid development and in symbiotic efficiency, single and double mutants of R. legumosarum bv. viciae were made which lack polyhydroxybutyrate synthase (phaC), glycogen synthase (glgA), or both. For comparison, a single phaC mutant also was isolated in a bean-nodulating strain of R. leguminosarum bv. phaseoli. In one large glasshouse trial, the growth of pea plants inoculated with the R. leguminosarum bv. viciae phaC mutant were significantly reduced compared with wild-type-inoculated plants. However, in subsequent glasshouse and growth-room studies, the growth of pea plants inoculated with the mutant were similar to wildtype-inoculated plants. Bean plants were unaffected by the loss of polyhydroxybutyrate biosynthesis in bacteroids. Pea plants nodulated by a glycogen synthase mutants or the glgA/phaC double mutant, grew as well as the wild type in growth-room experiments. Light and electron micrographs revealed that pea nodules infected with the glgA mutant accumulated large amounts of starch in the II/III interzone. This suggests that glycogen may be the dominant carbon storage compound in pea bacteroids. Polyhydroxybutyrate was present in bacteria in the infection thread of pea plants but was broken down during bacteroid formation. In nodules infected with a phaC mutant of R. leguminosarum bv. viciae, there was a drop in the amount of starch in the II/III interzone, where bacteroids form. Therefore, we propose a carbon burst hypothesis for bacteroid formation, where polyhydroxybutyrate accumulated by bacteria is degraded to fuel bacteroid differentiation.

Role of polyhydroxybutyrate and glycogen as carbon storage compounds in pea and bean bacteroids

Rhizobium leguminosarum synthesizes polyhydroxybutyrate and glycogen as its main carbon storage compounds. To examine the role of these compounds in bacteroid development and in symbiotic efficiency, single and double mutants of R. legumosarum bv. viciae were made which lack polyhydroxybutyrate synthase (phaC), glycogen synthase (glgA), or both. For comparison, a single phaC mutant also was isolated in a bean-nodulating strain of R. leguminosarum bv. phaseoli. In one large glasshouse trial, the growth of pea plants inoculated with the R. leguminosarum bv. viciae phaC mutant were significantly reduced compared with wild-type-inoculated plants. However, in subsequent glasshouse and growth-room studies, the growth of pea plants inoculated with the mutant were similar to wildtype-inoculated plants. Bean plants were unaffected by the loss of polyhydroxybutyrate biosynthesis in bacteroids. Pea plants nodulated by a glycogen synthase mutants or the glgA/phaC double mutant, grew as well as the wild type in growth-room experiments. Light and electron micrographs revealed that pea nodules infected with the glgA mutant accumulated large amounts of starch in the II/III interzone. This suggests that glycogen may be the dominant carbon storage compound in pea bacteroids. Polyhydroxybutyrate was present in bacteria in the infection thread of pea plants but was broken down during bacteroid formation. In nodules infected with a phaC mutant of R. leguminosarum bv. viciae, there was a drop in the amount of starch in the II/III interzone, where bacteroids form. Therefore, we propose a carbon burst hypothesis for bacteroid formation, where polyhydroxybutyrate accumulated by bacteria is degraded to fuel bacteroid differentiation.

Confocal imaging of pseudomonas syringae pv. phaseolicola colony development in bean reveals reduced multiplication of strains containing the genomic island PPHGI-1.

Pseudomonas syringae pv. phaseolicola is the seed borne causative agent of halo blight in the common bean Phaseolus vulgaris. Pseudomonas syringae pv. phaseolicola race 4 strain 1302A contains the avirulence gene hopAR1 (located on a 106-kb genomic island, PPHGI-1, and earlier named avrPphB), which matches resistance gene R3 in P. vulgaris cultivar Tendergreen (TG) and causes a rapid hypersensitive reaction (HR). Here, we have fluorescently labeled selected Pseudomonas syringae pv. phaseolicola 1302A and 1448A strains (with and without PPHGI-1) to enable confocal imaging of in-planta colony formation within the apoplast of resistant (TG) and susceptible (Canadian Wonder [CW]) P. vulgaris leaves. Temporal quantification of fluorescent Pseudomonas syringae pv. phaseolicola colony development correlated with in-planta bacterial multiplication (measured as CFU/ml) and is, therefore, an effective means of monitoring Pseudomonas syringae pv. phaseolicola endophytic colonization and survival in P. vulgaris. We present advances in the application of confocal microscopy for in-planta visualization of Pseudomonas syringae pv. phaseolicola colony development in the leaf mesophyll to show how the HR defense response greatly affects colony morphology and bacterial survival. Unexpectedly, the presence of PPHGI-1 was found to cause a reduction of colony development in susceptible P. vulgaris CW leaf tissue. We discuss the evolutionary consequences that the acquisition and retention of PPHGI-1 brings to Pseudomonas syringae pv. phaseolicola in planta.

Pseudomonas genomes: diverse and adaptable

Members of the genus Pseudomonas inhabit a wide variety of environments, which is reflected in their versatile metabolic capacity and broad potential for adaptation to fluctuating environmental conditions. Here, we examine and compare the genomes of a range of Pseudomonas spp. encompassing plant, insect and human pathogens, and environmental saprophytes. In addition to a large number of allelic differences of common genes that confer regulatory and metabolic flexibility, genome analysis suggests that many other factors contribute to the diversity and adaptability of Pseudomonas spp. Horizontal gene transfer has impacted the capability of pathogenic Pseudomonas spp. in terms of disease severity (Pseudomonas aeruginosa) and specificity (Pseudomonas syringae). Genome rearrangements likely contribute to adaptation, and a considerable complement of unique genes undoubtedly contributes to strain- and species-specific activities by as yet unknown mechanisms. Because of the lack of conserved phenotypic differences, the classification of the genus has long been contentious. DNA hybridization and genome-based analyses show close relationships among members of P. aeruginosa, but that isolates within the Pseudomonas fluorescens and P. syringae species are less closely related and may constitute different species. Collectively, genome sequences of Pseudomonas spp. have provided insights into pathogenesis and the genetic basis for diversity and adaptation.

Pseudomonas syringae pv. phaseolicola: from ‘has bean’ to supermodel

Pseudomonas syringae pv. phaseolicola causes halo blight of the common bean, Phaseolus vulgaris, worldwide and remains difficult to control. Races of the pathogen cause either disease symptoms or a resistant hypersensitive response on a series of differentially reacting bean cultivars. The molecular genetics of the interaction between P. syringae pv. phaseolicola and bean, and the evolution of bacterial virulence, have been investigated in depth and this research has led to important discoveries in the field of plant-microbe interactions. In this review, we discuss several of the areas of study that chart the rise of P. syringae pv. phaseolicola from a common pathogen of bean plants to a molecular plant-pathogen supermodel bacterium. Taxonomy: Bacteria; Proteobacteria, gamma subdivision; order Pseudomonadales; family Pseudomonadaceae; genus Pseudomonas; species Pseudomonas syringae; Genomospecies 2; pathogenic variety phaseolicola. Microbiological properties: Gram-negative, aerobic, motile, rod-shaped, 1.5 µm long, 0.7-1.2 µm in diameter, at least one polar flagellum, optimal temperatures for growth of 25-30 °C, oxidase negative, arginine dihydrolase negative, levan positive and elicits the hypersensitive response on tobacco. Host range: Major bacterial disease of common bean (Phaseolus vulgaris) in temperate regions and above medium altitudes in the tropics. Natural infections have been recorded on several other legume species, including all members of the tribe Phaseoleae with the exception of Desmodium spp. and Pisum sativum. Disease symptoms: Water-soaked lesions on leaves, pods, stems or petioles, that quickly develop greenish-yellow haloes on leaves at temperatures of less than 23 °C. Infected seeds may be symptomless, or have wrinkled or buttery-yellow patches on the seed coat. Seedling infection is recognized by general chlorosis, stunting and distortion of growth. Epidemiology: Seed borne and disseminated from exudation by water-splash and wind occurring during rainfall. Bacteria invade through wounds and natural openings (notably stomata). Weedy and cultivated alternative hosts may also harbour the bacterium. Disease control: Some measure of control is achieved with copper formulations and streptomycin. Pathogen-free seed and resistant cultivars are recommended. Useful websites: Pseudomonas-plant interaction http://www.pseudomonas-syringae.org/; PseudoDB http://xbase.bham.ac.uk/pseudodb/; Plant Associated and Environmental Microbes Database (PAMDB) http://genome.ppws.vt.edu/cgi-bin/MLST/home.pl; PseudoMLSA Database http://www.uib.es/microbiologiaBD/Welcome.html.

Marine Isotope Stage 9 environments of fluvial deposits at Hackney, north London, UK

Middle Pleistocene deposits at Hackney, north London comprise a thick unit of organic sands and silts occupying a channel near the confluence of the River Thames in south-eastern England and its left-bank tributary the River Lea. They represent a short time interval, perhaps no more than a few years, within a late Middle Pleistocene interglacial. The organic sediments are overlain by unfossiliferous sands and gravels indicating deposition on the floodplain of a braided river under cool or cold climatic conditions. The fossil plant, insect, mollusc and vertebrate remains from the interglacial deposits all indicate climatic conditions with summers warmer than the present in SE England, and winters with a similar thermal climate. The biostratigraphic evidence suggests that the time period represented by the organic unit is part of MIS 9, although the geochronological evidence for such an age is inconclusive. The palaeontological evidence strongly suggests that this temperate stage was warmer than the succeeding temperate stage MIS 7 or the Holocene, and approaching the Ipswichian (MISs 5e) in its warmth. The multidisciplinary description of the Hackney deposits is one of the first to reconstruct terrestrial conditions in Marine Isotope Stage 9 in Western Europe.

Global transcriptome analysis and identification of differentially expressed genes after infection of Fragaria vesca with powdery mildew (Podosphaera aphanis)

Background: Podosphaera aphanis, the causal agent of strawberry powdery mildew causes significant economic loss worldwide. Methods: We used the diploid strawberry species Fragaria vesca as a model to study plant pathogen interactions. RNA-seq was employed to generate a transcriptome dataset from two accessions, F. vesca ssp. vesca Hawaii 4 (HW) and F. vesca f. semperflorens Yellow Wonder 5AF7 (YW) at 1 d (1 DAI) and 8 d (8 DAI) after infection. Results: Of the total reads identified about 999 million (92%) mapped to the F. vesca genome. These transcripts were derived from a total of 23,470 and 23,464 genes in HW and YW, respectively from the three time points (control, 1 and 8 DAI). Analysis identified 1,567, 1,846 and 1,145 up-regulated genes between control and 1 DAI, control and 8 DAI, and 1 and 8 DAI, respectively in HW. Similarly, 1,336, 1,619 and 968 genes were up-regulated in YW. Also 646, 1,098 and 624 down-regulated genes were identified in HW, while 571, 754 and 627 genes were down-regulated in YW between all three time points, respectively. Conclusion: Investigation of differentially expressed genes (log2 fold changes �5) between control and 1 DAI in both HW and YW identified a large number of genes related to secondary metabolism, signal transduction; transcriptional regulation and disease resistance were highly expressed. These included flavonoid 3´-monooxygenase, peroxidase 15, glucan endo-1,3-β-glucosidase 2, receptor-like kinases, transcription factors, germin-like proteins, F-box proteins, NB-ARC and NBS-LRR proteins. This is the first application of RNA-seq to any pathogen interaction in strawberry