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)

Manuscript in preparation

Declines in bumble bee species in the past 60 years are well documented in Europe, where they are driven primarily by habitat loss and declines in floral abundance and diversity resulting from agricultural intensification. Impacts of habitat degradation and fragmentation are likely to be compounded by the social nature of bumble bees and their largely monogamous breeding system, which renders their effective population size low. Hence, populations are susceptible to stochastic extinction events and inbreeding. In North America, catastrophic declines of some bumble bee species since the 1990s are probably attributable to the accidental introduction of a nonnative parasite from Europe, a result of global trade in domesticated bumble bee colonies used for pollination of greenhouse crops. Given the importance of bumble bees as pollinators of crops and wildflowers, steps must be taken to prevent further declines. Suggested measures include tight regulation of commercial bumble bee use and targeted use of environmentally comparable schemes to enhance floristic diversity in agricultural landscapes.

/pdf/decline-and-conservation-of-bumble-bees-1thgzzqlml.pdf

Decline and conservation of bumble bees

Insect pathogens as biological control agents: Back to the future.

Over the past 50 years, crop protection has relied heavily on synthetic chemical pesticides, but their availability is now declining as a result of new legislation and the evolution of resistance in pest populations. Therefore, alternative pest management tactics are needed. Biopesticides are pest management agents based on living micro-organisms or natural products. They have proven potential for pest management and they are being used across the world. However, they are regulated by systems designed originally for chemical pesticides that have created market entry barriers by imposing burdensome costs on the biopesticide industry. There are also significant technical barriers to making biopesticides more effective. In the European Union, a greater emphasis on Integrated Pest Management (IPM) as part of agricultural policy may lead to innovations in the way that biopesticides are regulated. There are also new opportunities for developing biopesticides in IPM by combining ecological science with post-genomics technologies. The new biopesticide products that will result from this research will bring with them new regulatory and economic challenges that must be addressed through joint working between social and natural scientists, policy makers and industry.

/pdf/the-development-regulation-and-use-of-biopesticides-for-13tfzivkej.pdf

The development, regulation and use of biopesticides for integrated pest management.

PART I NEMATODE MORPHOLOGY AND TAXONOMY Morphology and Taxonomy of Nematodes Used in Biocontrol - S P Stock, University of Arizona, USA, and D J Hunt, CABI Bioscience, Surrey, UK PART II ENTOMOPATHOGENIC NEMATODES Biology and Behavior - C Griffin, National University of Ireland, UK, N Boemare, Universite Montpellier II, France, and E E Lewis, Virginia Technology Institute, USA Mass Production - R-U Ehlers and D I Shapiro-Ilan Formulation and Quality - P S Grewal, and A Peters, e-nema GmbH, Germany Application Technology - D J Wright, Imperial College London, UK, A Peters, S Schroer, Christian-Albrechts University Kiel, Germany, and J Patterson Fife, Battelle Memorial Institute, USA Forum on Safety and Regulation - R-U Ehlers Lawn, Turfgrass and Pasture Applications, P S Grewal, A M Koppenhofer, Rutgers University, USA, and H Y Choo, Gyeongsang National University, Republic of Korea Glasshouse Applications, M Tomalak, Institute of Plant Protection, Poland - S Piggot, Littlehampton, UK and G B Jagdale, Ohio State University, USA Nursery and Tree Application - R W H M van Tol, Wageningen-UR, Wageningen, The Netherlands and M J Raupp, University of Maryland, USA Mushroom Applications - S Jess, Department of Agriculture and Rural Development for Northern Ireland, H Schweizer, Queen's University of Belfast, and M Kirkpatrick, NIHPBS Loughgall, County Armagh, UK Orchard Applications - D I Shapiro-Ilan, L W Duncan, University of Florida, Lake Alfred, USA, L A Lacey, USDA-ARS, Washington, USA and R Han, Guangdong Entomological Institute, Guangzhou, China Soft Fruit Applications - R S Cowles, Connecticut Agricultural Experiment Station, USA, S Polavarapu, (Deceased), R N Williams, Ohio State University, USA, A Thies, e-nema, France, and R-U Ehlers Vegetable and Tuber Crop Applications - G Belair, Agriculture and Agrifood Canada, Canada, D J Wright, and G Curto, Servizio Fitosanitario Regione emilia-Romagna, Italy Cereal, Fiber, Medicinal, and Oilseed Crop Applications - H E Cabanillas, USDA ARS, USA, R J Wright, University of Nebraska-Lincoln, USA and R V Vyas, Gujarat Agricultural University, India Forestry Applications - P Torr and M J Wilson, University of Aberdeen, UK and S Heritage, Forestry Research, Northern Research Station, Roslin, UK Applications for the Control of Pests of Humans and Animals - I Glazer, Volcani Center, Israel, M Samish, Kimron Veterinary Institute, Bet-Dagan, Israel, and F G del Pino, Universitat Autonoma de Barcelona, Spain Application for Social Insect Control - D H Gouge, University of Arizona, USA A Systems Approach to Conservation of Entomopathogenic Nematodes, M Barbercheck, Pennsylvania State University, USA, and C W Hoy, Ohio State University, USA Interactions with Plant-parasitic Nematodes - E E Lewis and P S Grewal Compatibility and Interactions with Agrochemicals and Other Biocontrol Agents - A M Koppenhofer and P S Grewal PART 3 ENTOMOPHILIC NEMATODES Application of Beddingia siricidicola for Sirex Wood Wasp Control - R A Bedding, CSIRO, Australia and E T Iede, EMBRAPA Florestas, Brazil The Entomophilic Thripinema - J E Funderburk and K Sims Latsha, University of Florida, USA Mermithid Nematodes - E G Platzer, B A Mullens, University of California, Riverside, USA and M M Shamseldean, Cairo University, Egypt PART 4 SLUG-PARASITIC NEMATODES Biology, Production, and Formulation of Slug-parasitic Nematodes - M J Wilson and P S Grewal Field Application of Slug-parasitic Nematodes - A Ester, Applied Plant Research Ltd, The Netherlands and M J Wilson PART 5 PREDATORY NEMATODES Potential of Predatory Nematodes to Control Plant-parasitic Nematodes - A L Bilgrami and C Brey, Rutgers University, USA PART 6 FUNGAL FEEDING NEMATODES Potential of Fungal Feeding Nematodes for the Control of Soilborne Plant Pathogens - N Ishibashi, Saga University, Japan PART 7 CONCLUSIONS AND FUTURE DIRECTIONS Critical Issues and Research Needs for Expanding the Use of Nematodes in Biocontrol - P S Grewal, R-U Ehlers and D I Shapiro-Ilan

Nematodes as biocontrol agents

https://www.crec.ifas.ufl.edu/extension/diaprepes/bibliography/PDF/2BioCont381.pdf

Application technology and environmental considerations for use of entomopathogenic nematodes in biological control

Factors affecting commercial success: case studies in cotton, turf and citrus.

Production and application technology is critical for the success of entomopathogenic nematodes (EPNs) in biological control. Production approaches include in vivo, and in vitro methods (solid or liquid fermentation). For laboratory use and small scale field experiments, in vivo production of EPNs appears to be the appropriate method. In vivo production is also appropriate for niche markets and small growers where a lack of capital, scientific expertise or infrastructure cannot justify large investments into in vitro culture technology. In vitro technology is used when large scale production is needed at reasonable quality and cost. Infective juveniles of entomopathogenic nematodes are usually applied using various spray equipment and standard irrigation systems. Enhanced efficacy in EPN applications can be facilitated through improved delivery mechanisms (e.g., cadaver application) or optimization of spray equipment. Substantial progress has been made in recent years in developing EPN formulations, particularly for above ground applications, e.g., mixing EPNs with surfactants or polymers or with sprayable gels. Bait formulations and insect host cadavers can enhance EPN persistence and reduce the quantity of nematodes required per unit area. This review provides a summary and analysis of factors that affect production and application of EPNs and offers insights for their future in biological insect suppression.

/pdf/entomopathogenic-nematode-production-and-application-1hnp5iaro8.pdf

David I. Shapiro-Ilan

Papers

Insect pathogens as biological control agents: Back to the future.

Nematodes as biocontrol agents

Application technology and environmental considerations for use of entomopathogenic nematodes in biological control

Factors affecting commercial success: case studies in cotton, turf and citrus.

Entomopathogenic nematode production and application technology