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)

Half of all insect species are dependent on living plant tissues, consuming about 10% of plant annual production in natural habitats and an even greater percentage in agricultural systems, despite sophisticated control measures. Plants are generally remarkably well-protected against insect attack, with the result that most insects are highly specialized feeders. The mechanisms underlying plant resistance to invading herbivores on the one side, and insect food specialization on the other, are the main subjects of this book. For insects these include food-plant selection and the complex sensory processes involved, with their implications for learning and nutritional physiology, as well as the endocrinological spects of life cycle synchronization with host plant phenology. In the case of plants exposed to insect herbivores, they include the activation of defence systems in order to minimize damage, as well as the emission of chemical signals that may attract natural enemies of the invading herbivores and maybe exploited by neighbouring plants that mount defences as well.

Insect-plant biology

INTRODUCTION. Internal Organization of the Plant Body. Summary of Types of Cells and Tissues. General References. DEVELOPMENT OF THE SEED PLANT. The Embryo. From embryo to the Adult Plant. Apical Meristems and Their Derivatives. Differentiation, Specialization, and Morphogenesis. References. THE CELL. Cytoplasm. Nucleus. Plastids. Mitochondria. Microbodies. Vacuoles. Paramural Bodies. Ribosomes. Dictyosomes. Endoplasmic Reticulum. Lipid Globules. Microtubules. Ergastic Substances. References. CELL WALL. Macromolecular Components and Their Organization in the Wall. Cell Wall Layers. Intercellular Spaces. Pits, Primary Pit--Fields, and Plasmodesmata. Origin of Cell Wall During Cell Division. Growth of Cell Wall. References. PARENCHYMA AND COLLENCHYMA. Parenchyma. Collenchyma. References. SCLERENCHYMA. Sclereids. Fibers. Development of Sclereids and Fibers. References. EPIDERMIS. Composition. Developmental Aspects. Cell Wall. Stomata. Trichomes. References. XYLEM: GENERAL STRUCTURE AND CELL TYPES. Gross Structure of Secondary Xylem. Cell Types in the Secondary Xylem. Primary Xylem. Differentiation of Tracheary Elements. References. XYLEM: VARIATION IN WOOD STRUCTURE. Conifer Wood. Dicotyledon Wood. Some Factors in Development of Secondary Xylem. Identification of Wood. References. VASCULAR CAMBIUM. Organization of Cambium. Developmental Changes in the Initial Layer. Patterns and Causal Relations in Cambial Activity. References. PHLOEM. Cell Types. Primary Phloem. Secondary Phloem. References. PERIDERM. Structure of Periderm and Related Tissues. Development of Periderm. Outer Aspect of Bark in Relation to Structure. Lenticels. References. SECRETORY STRUCTURES. External Secretory Structures. Internal Secretory Structures. References. THE ROOT: PRIMARY STATE OF GROWTH. Types of Roots. Primary Structure. Development. References. THE ROOT: SECONDARY STATE OF GROWTH AND ADVENTITIOUS ROOTS. Common Types of Secondary Growth. Variations in Secondary Growths. Physiologic Aspects of Secondary Growth in Roots. Adventitious Roots. References. THE STEM: PRIMARY STATE OF GROWTH. External Morphology. Primary Structure. Development. References. THE STEM: SECONDARY GROWTH AND STRUCTURAL TYPES. Secondary Growth. Types of Stems. References. THE LEAF: BASIC STRUCTURE AND DEVELOPMENT. Morphology. Histology of Angiosperm Leaf. Development. Abscission. References. THE LEAF: VARIATIONS IN STRUCTURE. Leaf Structure and Environment. Dicotyledon Leaves. Monocotyledon Leaves. Gymnosperm Leaves. References. THE FLOWER: STRUCTURE AND DEVELOPMENT. Concept. Structure. Development. References. THE FLOWER: REPRODUCTIVE CYCLE. Microsporogenesis. Pollen. Male Gametophyte. Megasporogenesis. Female Gametophyte. Fertilization. References. THE FRUIT. Concept and Classification. The Fruit Wall. Fruit Types. Fruit Growths. Fruit Abscission. References. THE SEED. Concept and Morphology. Seed Development. Seed Coat. Nutrient Storage Tissues. References. EMBRYO AND SEEDLING. Mature Embryo. Development of Embryo. Classification of Embryos. Seedling. References. Glossary. Index.

Anatomy of Seed Plants

Biodiversity and Ecosystem Function

Managing metabolic resources is critical for insects during diapause when food sources are limited or unavailable. Insects accumulate reserves prior to diapause, and metabolic depression during diapause promotes reserve conservation. Sufficient reserves must be sequestered to both survive the diapause period and enable postdiapause development that may involve metabolically expensive functions such as metamorphosis or long-distance flight. Nutrient utilization during diapause is a dynamic process, and insects appear capable of sensing their energy reserves and using this information to regulate whether to enter diapause and how long to remain in diapause. Overwintering insects on a tight energy budget are likely to be especially vulnerable to increased temperatures associated with climate change. Molecular mechanisms involved in diapause nutrient regulation remain poorly known, but insulin signaling is likely a major player. We also discuss other possible candidates for diapause-associated nutrient regula...

Energetics of Insect Diapause

Seasonal accumulation of various mineral nutrients by galls of the chalcid Hemadas nubilipennis on lowbush blueberry were examined in various phases of gall development. Levels of copper, nickel, iron, and zinc were higher in tissues of galls in initiation phase compared to tips of ungalled shoots and in general were higher than galls in growth and maturation phases. Levels of manganese and magnesium in gall tissues decrease throughout the season compared to ungalled shoots. Levels of calcium are less in gall tissues in initiation phase compared to ungalled shoots, and elevated in maturation phase. Patterns of mineral concentration within galls at various phases of development are related to known physiological roles of minerals in plant nutrition; however, we conclude that patterns are variable and their significance in gall physiology requires further study.

Seasonal acquisition of mineral nutrients by a chalcid gall on lowbush blueberry

Normally, Urophora cardui (L.) induces galls on the stems of Cirsium arvense (L.) Scop. (Canada thistle). However, six galls were found in flowerheads when flies were cultured in growth chambers. All flowerhead galls developed from receptacle tissues of male thistle capitula and were structurally similar to those induced from stem tissues. The appearance of these atypical galls contributes to our understanding of organ specificity of gall-inducing insects.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0008347X00040931

Formation of flowerhead galls by the canada thistle gall-fly, urophora cardui (diptera: tephritidae), under cage conditions

Four 0·5 ha plots were established on freshly dried tailings of INCO Ltd. near Sudbury, Ontario, Canada and received the following treatments: 1) 125 t/ha Municipal Solid Waste (MSW) compost, 2) 250 t/ha MSW compost, 3) INCO's standard application of crushed limestone, fertilizer and hay mulch and 4) control - no application of compost. Application of compost at a rate of 250 t/ha yielded the same increase in tailings pH (from 2·80 to 4·65) as that achieved with the typical INCO application of 40 t lime/ha. The INCO treatment with lime and fertilizer resulted in no initial input of organic matter; whereas, a 250 t/ha application of compost increased organic content by 8·3%. Moisture retention in tailings at the two compost-treated plots was significantly higher (26%) than that of the INCO treated plots (<10%). Application of lime as part of the INCO treatment reduced levels of water soluble Cu and Ni from 22·8 pgCu/g to 0·4 pgCu/g and from 35·5 pgNi/g to 5·2 ngNi/g. Similar reductions in water so...

Evaluation of municipal solid waste (MSW) compost as a soil amendment for acidic, metalliferous mine tailings

Gall inducers are favoured as biocontrol agents of weeds because they tend to have a narrow host range. Six insect and one nematode gall inducer used in Canada are described in terms of their biology, gall morphology, gall physiology, and effectiveness in weed control. The species differ in plant organ attacked, requirement for moisture, whether the galls are induced by secretions or by severing xylem, and effectiveness, which in part relates to the ability of the gall to import nutrients. The most powerful galls divert assimilates from other sinks via a gall’s vascular system joined to that of their host. One of our examples also has mechanisms to compensate for reduction of turgor during drought. Two of the gall inducers enhance their nutrient supply by severing xylem in a plant nutrient sink. One, in the short-term sink of a thistle capitulum, obtains about a quarter of its assimilates at the expense of other capitula. The other, in the long-term sink of a rosette root, approximately halves seed production. Hypotheses are presented to explain various aspects of gall development and function.

Effectiveness of gall inducers in weed biological control

The industrially damaged lands around the smelters of Sudbury are inhabited by several species of plants that can tolerate high levels of toxic metals (Hogan and Rauser 1978; Cox and Hutchinson 1980). One of these plants, the sweet lowbush blueberry (Vaccinium angustifolium), has colonized large areas of the smelter-affected area. It is particularly abundant within the birch transition forest described in the previous chapter (Chapter 18). This chapter reviews the attributes of V. angustifolium that made it successful in the Sudbury industrially damaged lands. There are actually two species of blueberry near Sudbury, V. angustifolium and V. myrtilloides, of which V. angustifolium is the more common of the two. Although they are similar (see descriptions of each in Vander Kloet [1988]) and grow in the same habitats, care was taken to restrict our studies to V. angustifolium.

Joseph D. Shorthouse

Papers

Seasonal acquisition of mineral nutrients by a chalcid gall on lowbush blueberry

Formation of flowerhead galls by the canada thistle gall-fly, urophora cardui (diptera: tephritidae), under cage conditions

Evaluation of municipal solid waste (MSW) compost as a soil amendment for acidic, metalliferous mine tailings

Effectiveness of gall inducers in weed biological control

Potential Role of Lowbush Blueberry (Vaccinium angustifolium) in Colonizing Metal-Contaminated Ecosystems