The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants

Evolution of Protein Molecules

Inducible defense-related proteins have been described in many plant species upon infection with oomycetes, fungi, bacteria, or viruses, or insect attack. Several types of proteins are common and have been classified into 17 families of pathogenesis-related proteins (PRs). Others have so far been found to occur more specifically in some plant species. Most PRs and related proteins are induced through the action of the signaling compounds salicylic acid, jasmonic acid, or ethylene, and possess antimicrobial activities in vitro through hydrolytic activities on cell walls, contact toxicity, and perhaps an involvement in defense signaling. However, when expressed in transgenic plants, they reduce only a limited number of diseases, depending on the nature of the protein, plant species, and pathogen involved. As exemplified by the PR-1 proteins in Arabidopsis and rice, many homologous proteins belonging to the same family are regulated developmentally and may serve different functions in specific organs or tissues. Several defense-related proteins are induced during senescence, wounding or cold stress, and some possess antifreeze activity. Many defense-related proteins are present constitutively in floral tissues and a substantial number of PR-like proteins in pollen, fruits, and vegetables can provoke allergy in humans. The evolutionary conservation of similar defense-related proteins in monocots and dicots, but also their divergent occurrence in other conditions, suggest that these proteins serve essential functions in plant life, whether in defense or not.

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Significance of Inducible Defense-related Proteins in Infected Plants

Plant growth-promoting rhizobacteria (PGPR) are naturally occurring soil bacteria that aggressively colonize plant roots and benefit plants by providing growth promotion. Inoculation of crop plants with certain strains of PGPR at an early stage of development improves biomass production through direct effects on root and shoots growth. Inoculation of ornamentals, forest trees, vegetables, and agricultural crops with PGPR may result in multiple effects on early-season plant growth, as seen in the enhancement of seedling germination, stand health, plant vigor, plant height, shoot weight, nutrient content of shoot tissues, early bloom, chlorophyll content, and increased nodulation in legumes. PGPR are reported to influence the growth, yield, and nutrient uptake by an array of mechanisms. They help in increasing nitrogen fixation in legumes, help in promoting free-living nitrogen-fixing bacteria, increase supply of other nutrients, such as phosphorus, sulphur, iron and copper, produce plant hormones, enhance other beneficial bacteria or fungi, control fungal and bacterial diseases and help in controlling insect pests. There has been much research interest in PGPR and there is now an increasing number of PGPR being commercialized for various crops. Several reviews have discussed specific aspects of growth promotion by PGPR. In this review, we have discussed various bacteria which act as PGPR, mechanisms and the desirable properties exhibited by them.

Plant Growth Promoting Rhizobacteria: A Critical Review

A pepper gene, CABPR1, which encodes basic pathogenesis-related protein 1, has been reported to be strongly induced after ethephon treatment, wounding, and tobacco mosaic virus infection. The potential role of CABPR1 in tolerance of biotic or abiotic stresses was examined in transgenic Nicotiana tabacum cv. xanthi plants. Overexpression of CABPR1 in tobacco plants enhanced tolerance not only to heavy metal stresses, but also to the oomycete pathogen Phytophthora nicotianae, and the bacterial pathogens Ralstonia solanacearum and Pseudomonas syringae pv. tabaci. RT-PCR revealed that the CABPR1 transgene increased expression of the PR-Q and glutathione S-transferase genes, but decreased expression of the PR-1a and thaumatin genes. Moreover, these transgenic lines exhibited significant decreases in total peroxidase activity and transcription level, suggesting that overexpression of CABPR1 in tobacco cells altered the balance of redox systems. Redox imbalance in transgenic lines may lead to H2O2 accumulation, triggering tolerance to biotic and abiotic stresses.

Overexpression of a pepper basic pathogenesis-related protein 1 gene in tobacco plants enhances resistance to heavy metal and pathogen stresses

Cereal grains are the most important food source for humans. As the global population continues to grow exponentially, the need for the enhanced yield and minimal loss of agricultural crops, mainly cereal grains, is increasing. In general, harvested grains are stored for specific time periods to guarantee their continuous supply throughout the year. During storage, economic losses due to reduction in quality and quantity of grains can become very significant. Grain loss is usually the result of its deterioration due to fungal contamination that can occur from preharvest to postharvest stages. The deleterious fungi can be classified based on predominance at different stages of crop growth and harvest that are affected by environmental factors such as water activity (aw) and eco-physiological requirements. These fungi include species such as those belonging to the genera Aspergillus and Penicillium that can produce mycotoxins harmful to animals and humans. The grain type and condition, environment, and biological factors can also influence the occurrence and predominance of mycotoxigenic fungi in stored grains. The main environmental factors influencing grain fungi and mycotoxins are temperature and aw. This review discusses the effects of temperature and aw on fungal growth and mycotoxin production in stored grains. The focus is on the occurrence and optimum and minimum growth requirements for grain fungi and mycotoxin production. The environmental influence on aflatoxin production and hypothesized mechanisms of its molecular suppression in response to environmental changes are also discussed. In addition, the use of controlled or modified atmosphere as an environmentally safe alternative to harmful agricultural chemicals is discussed and recommended future research issues are highlighted.

Influence of Temperature and Water Activity on Deleterious Fungi and Mycotoxin Production during Grain Storage.

Aims: Previously, we selected a bacterial strain (GSE09) antagonistic to Phytophthora capsici on pepper, which produced a volatile compound (2,4-di-tert-butylphenol), inhibiting the pathogen. In this study, we identified strain GSE09 and characterized some of the biological traits of this strain in relation to its antagonistic properties against P. capsici. In addition, we examined bacterial colonization on the root surface or in rhizosphere soil and the effect of various concentrations of the volatile compound and strain GSE09 on pathogen development and radicle infection as well as radicle growth.

Methods and Results:  Strain GSE09 was identified as Flavobacterium johnsoniae, which forms biofilms and produces indolic compounds and biosurfactant but not hydrogen cyanide (HCN) with little or low levels of antifungal activity and swimming and swarming activities. Fl. johnsoniae GSE09 effectively colonized on pepper root, rhizosphere, and bulk (pot) soil, which reduced the pathogen colonization in the roots and disease severity in the plants. Various concentrations of 2,4-di-tert-butylphenol or strain GSE09 inhibited pathogen development (mycelial growth, sporulation, and zoospore germination) in I-plate (a plastic plate containing a center partition). In addition, germinated seeds treated with the compound (1–100 μg ml−1) or the strain (102–1010 cells ml−1) significantly reduced radicle infection by P. capsici without radicle growth inhibition.

Conclusions:  These results indicate that colonization of pepper root and rhizosphere by the Fl. johnsoniae strain GSE09, which can form biofilms and produce indolic compounds, biosurfactant, and 2,4-di-tert-butylphenol, might provide effective biocontrol activity against P. capsici.

Significance and Impact of the Study:  To our knowledge, this is the first study demonstrating that the Fl. johnsoniae strain GSE09, as a potential biocontrol agent, can effectively protect pepper plants against P. capsici infection by colonizing the roots.

The volatile-producing Flavobacterium johnsoniae strain GSE09 shows biocontrol activity against Phytophthora capsici in pepper.

The lipid signal is essential for the activation of plant defense responses, but downstream components of the signaling pathway are still poorly defined. To investigate the biological functions of pepper lipid transfer protein (LTP), we carried out virus-induced gene silencing (VIGS) in pepper, constitutive expression of CALTPs and grafting experiments in the tobacco plant. Suppression of endogenous CALTPI and CALTPII by VIGS, respectively, resulted in enhanced susceptibility to Xanthomonas campestris pv. vescatoria and pepper mosaic mottle virus in pepper. On the other hand, the constitutive expression of CALTPI and CALTPII genes in tobacco plants showed enhanced resistance to oomycete pathogen, Phytophthora nicotianae and bacterial pathogen, Pseudomonas syringae pv. tabaci. Enhanced resistance is found to be associated with the enhanced CALTP transcript levels in the independent transgenic CALTPI or II tobacco lines. Induced resistance responses in grafted scion leaves revealed that LTP plays a role in long-distance systemic signaling in plants.

Overexpression of lipid transfer protein (LTP) genes enhances resistance to plant pathogens and LTP functions in long-distance systemic signaling in tobacco

The 5′ flanking region of the CALTPI gene, which encodes a basic lipid transfer protein, was isolated and characterized from the genomic DNA of Capsicum annuum. Four different regions of the promoter sequence of the CALTPI gene were fused to the β-glucuronidase (GUS) coding region. In an Agrobacterium-mediated transient expression assay, the transcriptional activations of the promoter deletions were examined in tobacco leaves after infection with Pseudomonas syringae pv. tabaci, and treatment with ethylene and salicylic acid. The −808 bp region of the CALTPI gene promoter sequence exhibited full promoter activity. The W-box and ERE-box elements, which are essential for induction by all signals, were localized in the region between −555 bp and −391 bp upstream of the translation initiation site. A CALTPI transgene was then introduced under the control of the 35S promoter into the Arabidopsis ecotype Col-0. Transgenic Arabidopsis lines expressing the CALTPI gene developed rapidly compared to the wild-type plants, indicating that CALTPI may be involved in plant development. Overexpression of the CALTPI gene enhanced the resistance against infection by P. syringae pv. tomato and Botrytis cinerea. The transgenic plants expressing the CALTPI gene also showed high levels of tolerance to NaCl and drought stresses at various vegetative growth stages. No transcription of the PR-1, PR-2, PR-5, thionin, and RD29A genes was observed in untreated leaf tissues of the transgenic plants. The enhanced resistance to pathogen and environmental stresses in transgenic Arabidopsis correlated with the enhanced expression of the CALTPI gene.

Identification of pathogen-responsive regions in the promoter of a pepper lipid transfer protein gene (CALTPI) and the enhanced resistance of the CALTPI transgenic Arabidopsis against pathogen and environmental stresses

Ki Deok Kim

Papers

Overexpression of a pepper basic pathogenesis-related protein 1 gene in tobacco plants enhances resistance to heavy metal and pathogen stresses

Influence of Temperature and Water Activity on Deleterious Fungi and Mycotoxin Production during Grain Storage.

The volatile-producing Flavobacterium johnsoniae strain GSE09 shows biocontrol activity against Phytophthora capsici in pepper.

Overexpression of lipid transfer protein (LTP) genes enhances resistance to plant pathogens and LTP functions in long-distance systemic signaling in tobacco

Identification of pathogen-responsive regions in the promoter of a pepper lipid transfer protein gene (CALTPI) and the enhanced resistance of the CALTPI transgenic Arabidopsis against pathogen and environmental stresses