Genome-based discovery of polyketide-derived secondary metabolism pathways in the barley pathogen <i>Ramularia collo-cygni</i>

Ramularia collo-cygni causes Ramularia leaf spot (RLS) disease of barley. The fungus develops asymptomatically within its host until late in the growing season, when necrotic lesions become visible on upper leaves. Fungal secondary metabolites (SM) have been proposed as important factors in RLS lesion formation but the biosynthetic pathways involved remain largely unknown. Mining the R. collo-cygni genome revealed the presence of 10 polyketide synthases (PKS), 10 nonribosomal peptide synthetases (NRPS), and 3 hybrid PKS-NRPS (HPS) identified within clusters of genes with predicted functions associated with secondary metabolism. SM core genes along with their predicted transcriptional regulators exhibited transcriptional coexpression during infection of barley plants. Moreover, their expression peaked during early stages of host colonization and preceded or overlapped with the appearance of disease symptoms, suggesting that SM may manipulate the host to promote colonization or protect R. collo-cygni from competing organisms. Accordingly, R. collo-cygni inhibited the growth of several fungi in vitro, indicating that it synthesized and excreted antifungal agents. Taken together, these findings demonstrate that the R. collo-cygni genome contains the genetic architecture to synthesize a wide range of SM and suggests that coexpression of PKS and HPS is associated with competitive colonization of the host and early symptom development. [Formula: see text] Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY 4.0 International license . </jats:p

A DNA-barcode biodiversity standard analysis method (DNA-BSAM) reveals a large variance in the effect of a range of biological, chemical and physical soil management interventions at different sites, but location is one of the most important aspects determining the nature of agricultural soil microbiology

There are significant knowledge gaps in our understanding of how to sustainably manage agricultural soils to preserve soil biodiversity. Here we evaluate and quantify the effects of agricultural management and location on soil microbiology using nine field trials that have consistently applied different soil management practices in the United Kingdom using DNA barcode sequence data. We tested the basic hypothesis that various agricultural management interventions have a significant and greater effect on soil bacterial and fungal diversity than geographic location. The analyses of soil microbial DNA sequence data to date has lacked standardisation which prevents meaningful comparisons across sites and studies. Therefore, to analyse these data and crucially compare and quantify the size of any effects on soil bacterial and fungal biodiversity between sites, we developed and employed a post-sequencing DNA-barcode biodiversity standard analysis method (DNA-BSAM). The DNA-BSAM comprises a series of standardised bioinformatic steps for processing sequences but more importantly defines a standardised set of ecological indices and statistical tests. Use of the DNA-BSAM reveals the hypothesis was not strongly supported, and this was primarily because: 1) there was a large variance in the effects of various management interventions at different sites, and 2) that location had an equivalent or greater effect size than most management interventions for most metrics. Some dispersed sites imposed the same organic amendments interventions but showed different responses, and this combined with observations of strong differences in soil microbiomes by location tentatively suggests that any effect of management may be contingent on location. This means it could be unreliable to extrapolate the findings of individual trials to others. The widespread use of a standard approach will allow meaningful cross-comparisons between soil microbiome studies and thus a substantial evidence-base of the effects of land-use on soil microbiology to accumulate and inform soil management decisions.Agriculture and Horticulture Development Board (AHDB); British Beet Research Organisation (BBRO

The genome of the emerging barley pathogen Ramularia collo-cygni

Background Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive, necrotrophic pathogen that causes significant losses to green leaf area and hence grain yield and quality. Results The R. collo-cygni genome was sequenced using a combination of Illumina and Roche 454 technologies. The draft assembly of 30.3 Mb contained 11,617 predicted gene models. Our phylogenomic analysis confirmed the classification of this ascomycete fungus within the family Mycosphaerellaceae, order Capnodiales of the class Dothideomycetes. A predicted secretome comprising 1053 proteins included redox-related enzymes and carbohydrate-modifying enzymes and proteases. The relative paucity of plant cell wall degrading enzyme genes may be associated with the stealth pathogenesis characteristic of plant pathogens from the Mycosphaerellaceae. A large number of genes associated with secondary metabolite production, including homologs of toxin biosynthesis genes found in other Dothideomycete plant pathogens, were identified. Conclusions The genome sequence of R. collo-cygni provides a framework for understanding the genetic basis of pathogenesis in this important emerging pathogen. The reduced complement of carbohydrate-degrading enzyme genes is likely to reflect a strategy to avoid detection by host defences during its prolonged asymptomatic growth. Of particular interest will be the analysis of R. collo-cygni gene expression during interactions with the host barley, to understand what triggers this fungus to switch from being a benign endophyte to an aggressive necrotroph

Low damage cryogenic etching of low-K materials for advanced interconnects

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Cryogenic plasma-processed silicon microspikes as a high-performance anode material for lithium ion-batteries

International audienceMicro- or nano-structuring is essential in order to use Si as an anode material for lithium ion batteries. In the present study, we attempted to use Si wafers with a spiky microstructure (SMS), the so-called black-Si, prepared by a cryogenic reactive ion etching process with an SF6/O2 gas mixture, for Li half-cells. The SMS with various sizes of spikes from 2.0 μm (height) × 0.2 μm (width) to 21 μm × 1.0 μm was etched by varying the SF6/O2 gas flow ratio. An anode of SMS of 11 μm-height in average showed stable charge/discharge capacity and Coulombic efficiency higher than 99% for more than 300 cycles, causing no destruction to any part of the Si wafer. The spiky structure turned columnar after cycles, suggesting graded lithiation levels along the length. The present results suggest a strategy to utilize a wafer-based Si material for an anode of a lithium ion battery durable against repetitive lithiation/delithiation cycles

Plasma Cryogenic Etching: from 3D Integration to Low-k Materials

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Damage Free Cryogenic Etching of a Porous Organosilica Ultralow-k Film

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Low Damage Cryogenic Etching of Porous Organosilicate Low-k Materials Using SF6/O2/SiF4

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