Landscape‐scale spatial abundance distributions discriminate core from random components of boreal lake bacterioplankton

Aquatic bacterial communities harbour thousands of coexisting taxa. To meet the challenge of discriminating between a ‘core’ and a sporadically occurring ‘random’ component of these communities, we explored the spatial abundance distribution of individual bacterioplankton taxa across 198 boreal lakes and their associated fluvial networks (188 rivers). We found that all taxa could be grouped into four distinct categories based on model statistical distributions (normal like, bimodal, logistic and lognormal). The distribution patterns across lakes and their associated river networks showed that lake communities are composed of a core of taxa whose distribution appears to be linked to in‐lake environmental sorting (normal‐like and bimodal categories), and a large fraction of mostly rare bacteria (94% of all taxa) whose presence appears to be largely random and linked to downstream transport in aquatic networks (logistic and lognormal categories). These rare taxa are thus likely to reflect species sorting at upstream locations, providing a perspective of the conditions prevailing in entire aquatic networks rather than only in lakes.     

Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes

Hierarchical shotgun sequencing remains the method of choice for assembling high‐quality reference sequences of complex plant genomes. The efficient exploitation of current high‐throughput technologies and powerful computational facilities for large‐insert clone sequencing necessitates the sequencing and assembly of a large number of clones in parallel. We developed a multiplexed pipeline for shotgun sequencing and assembling individual bacterial artificial chromosomes (BACs) using the Illumina sequencing platform. We illustrate our approach by sequencing 668 barley BACs (Hordeum vulgare L.) in a single Illumina HiSeq 2000 lane. Using a newly designed parallelized computational pipeline, we obtained sequence assemblies of individual BACs that consist, on average, of eight sequence scaffolds and represent >98% of the genomic inserts. Our BAC assemblies are clearly superior to a whole‐genome shotgun assembly regarding contiguity, completeness and the representation of the gene space. Our methods may be employed to rapidly obtain high‐quality assemblies of a large number of clones to assemble map‐based reference sequences of plant and animal species with complex genomes by sequencing along a minimum tiling path.     

The Effect of Exposure to Decreasing Relative Humidity on the Viability of Phytophthora ramorum sporangia

Sporangia of three isolates of Phytophthora ramorum representing three different clonal lineages were subjected to relative humidity (RH) levels between 80 and 100% for exposure periods ranging from 1 to 24 h at 20°C in darkness. Plastic containers (21.5 × 14.5 × 5 cm) were used as humidity chambers with 130 ml of glycerine solution added to each container. Glycerine concentrations corresponded to 100, 95, 90, 85 and 80% RH based on refractive index measurements. Sporangia suspensions were pipeted onto nitrile mesh squares (1.5 × 1.5 cm, 15 micron pore size) which were placed in the humidity chambers and incubated at 20°C in darkness. Following exposure periods of 1, 2, 4, 8, 12 and 24 h, mesh squares were inverted onto Petri dishes of selective medium and sporangia germination assessed after 24 and 48 h. At 100% RH, we observed a mean value of 88% germination after 1 h exposure declining to 18% germination following 24 h incubation. At 95% RH, a steeper decline in germination was noted, with means ranging from 79% at 1 h to less than 1% at 24 h exposure. At 90% RH, no germination was noted after 8 or more h exposure, and values were 57%, 22% and 3% germination for the 1, 2 and 4 h exposures, respectively. Germination was only observed at 1 h exposure for both the 85% RH treatment (52% germination) and the 80% RH treatment (38% germination). The three isolates responded similarly over the range of RH values tested. The germination response of P. ramorum sporangia to RH values between 80% and 100% was comparable to that reported for other Phytophthora species. Knowledge of conditions that affect P. ramorum sporangia germination can shed light on pathogenesis and epidemic potential and lead to improved control recommendations.     

肉桂醛对增强辣椒疫霉病抗性的作用机制研究

该实验以辣椒疫霉菌(Phytophthora capsici)致病性菌株NJ01和‘苏椒5号’辣椒幼苗为研究对象,通过肉桂醛对辣椒疫霉菌的体外抑菌作用、室内侵染效果以及对辣椒幼苗防卫反应的调控作用,揭示肉桂醛对增强辣椒疫霉病抗性的作用机制。结果表明:(1)肉桂醛对实验所用致病性菌株NJ01的抑制中浓度(EC50)值为0.81mmol/L;肉桂醛处理可导致NJ01菌丝严重皱缩、畸形、断裂;PI染色显示NJ01菌丝出现明显的细胞死亡现象。(2)单独NJ01菌株接种的辣椒植株表现出明显病症(茎基部变黑褐色、干枯萎缩,植株倒伏,叶片脱落,生物量下降);而肉桂醛处理2h后接种NJ01菌株的辣椒植株长势良好,无明显病症,鲜重和叶绿素含量显著上升至对照水平。(3)与单独接种NJ01菌株处理相比,肉桂醛处理2h后接种NJ01菌株的辣椒植株体内抗氧化酶(CAT、SOD、POD)活性显著上升,抗氧化物质(GSH和ASA)含量显著增加。研究认为,肉桂醛可能通过抑制辣椒疫霉菌的生长及其对辣椒植株的侵染能力,同时调控辣椒植株防卫反应,进而提高辣椒对疫病抗性。     

婴儿与母亲皮肤细菌群落结构的比较分析

为探索母婴皮肤细菌群落特征,本研究对8对母婴7个不同皮肤部位的细菌群落进行焦磷酸测序分析。结果显示,皮肤细菌主要属于放线菌门(Actinobacteria)、厚壁菌门(Firmicutes)、变形菌门(Proteobacteria)和拟杆菌门(Bacteroidetes)。总体而言,母婴皮肤细菌群落的组成相似,但丰度存在差异。母亲皮肤表面的丙酸杆菌属(Propionibacterium)丰度显著高于婴儿(P<0.05)。在婴儿皮肤表面,链球菌属(Streptococcus)和葡萄球菌属(Staphylococcus)最丰富;剖宫产出生的婴儿额头表面葡萄球菌属的丰度显著高于自然分娩出生的婴儿(P<0.05)。婴儿皮肤表面特有的常驻菌属包括孪生球菌属(Gemella)、普雷沃菌属(Prevotella)、罗思菌属(Rothia)和韦荣球菌属(Veillonella)与成人常见的口腔细菌一致,表明母亲的口腔细菌对婴儿早期皮肤微生态有一定的塑造作用。婴儿皮肤表面的细菌种类与自己母亲相近,各细菌的含量则与其他婴儿相近。母亲皮脂溢出部位(额头和背部)的细菌多样性较其他部位低,且皮肤潮湿、干燥、脂溢部位之间细菌群落差异较大;而婴儿背部细菌群落与肘窝相似,额头与手背相似。     

水稻细菌性穗枯病的病原特性和抗性研究进展

水稻(Oryza sativa)细菌性穗枯病是世界性的重要病害之一, 严重威胁全球范围水稻的高产稳产。虽然该病目前仍被列为我国的检疫性病害, 但近几年的研究表明, 穗枯病随时有在内地蔓延的潜在危险, 因此除了加强检疫工作, 开展针对性的防控技术研发也十分必要。水稻细菌性穗枯病菌在侵染过程中涉及多种毒力因子, 同时, 水稻在与病原菌的长期互作过程中演化出了多种防卫机制, 抗性基因是主要的防卫机制之一。挖掘水稻基因组中抗细菌性穗枯病遗传位点并培育抗病品种是最安全且经济有效的防治途径。该文综述了水稻细菌性穗枯病的病原菌特性、发病特征、发病机制、病害循环和对水稻细菌性穗枯病的抗性研究现状, 以期为挖掘和分离水稻穗枯病抗性位点提供参考。     

QTL sequencing strategy to map genomic regions associated with resistance to ascochyta blight in chickpea

Whole‐genome sequencing‐based bulked segregant analysis (BSA) for mapping quantitative trait loci (QTL) provides an efficient alternative approach to conventional QTL analysis as it significantly reduces the scale and cost of analysis with comparable power to QTL detection using full mapping population. We tested the application of next‐generation sequencing (NGS)‐based BSA approach for mapping QTLs for ascochyta blight resistance in chickpea using two recombinant inbred line populations CPR‐01 and CPR‐02. Eleven QTLs in CPR‐01 and six QTLs in CPR‐02 populations were mapped on chromosomes Ca1, Ca2, Ca4, Ca6 and Ca7. The QTLs identified in CPR‐01 using conventional biparental mapping approach were used to compare the efficiency of NGS‐based BSA in detecting QTLs for ascochyta blight resistance. The QTLs on chromosomes Ca1, Ca4, Ca6 and Ca7 overlapped with the QTLs previously detected in CPR‐01 using conventional QTL mapping method. The QTLs on chromosome Ca4 were detected in both populations and overlapped with the previously reported QTLs indicating conserved region for ascochyta blight resistance across different chickpea genotypes. Six candidate genes in the QTL regions identified using NGS‐based BSA on chromosomes Ca2 and Ca4 were validated for their association with ascochyta blight resistance in the CPR‐02 population. This study demonstrated the efficiency of NGS‐based BSA as a rapid and cost‐effective method to identify QTLs associated with ascochyta blight in chickpea.