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)

Soil Chemical Analysis

B6nassy, C., 1955. R6marques sur deux Aphelinid6s: Aphelinus mytilaspidis Le Baron et Aphytis proclia Walker. Annls l~piphyt. 6: 11-17. Lord, F. T. & MacPhee, A. W., 1953. The influence of spray programs on the fauna of apple orchards in Nova Scotia II. Oyster shell scale. Can. Ent. 79: 196-209. Pickett, A. D., 1946. A progress report on long term spray programs. Rep. Nova Scotia Fruit Grow. Ass. 83 : 27-31. Pickett, A. D., 1967. The influence of spray programs on the fauna of apple orchards in Nova Scotia XIV. Can. Ent. 97: 816-821. Tothill, J. D., 1918. The predacious mite Hemisarcoptes malus Shimer and its relation to the natural control of the oyster shell scale Lepidosaphes ulmi L. Agric. Gaz. Can. 5 : 234-239.

http://link.springer.com/content/pdf/10.1007/BF01976688.pdf

Soil enzymes: Kuprevich, V. F. & Shcherbakova, T. A.: Translated from the Russian edition (1966), published by the Indian National Scientific Documentation Centre, New Delhi 1971. 392 pp., offset printing from type script, paper cover. Obtainable from U.S. Department of Commerce, National Technical Information Service, Springfield, Va. 22151

Climate Change 1995 is a scientific assessment that was generated by more than 1 000 contributors from over 50 nations. It was jointly co-ordinated through two international agencies; the World Meteorological Organization and the United Nations Environment Programme. The assessment was completed by the Intergovernmental Panel on Climate Change (IPCC) with a primary aim of reviewing the current state of knowledge concerning the impacts of climate change on physical and ecological systems, human health, and socioeconomic factors. The second aim was to review the available information on the technical and economic feasibility of the potential mitigation and adaptation strategies.

Climate Change 1995

Listeria monocytogenes is a Gram positive, aerobic, facultative anaerobic and nonacid fast bacterium, which can cause the disease listeriosis in both human and animals. It is widely distributed thoroughout the environment and has been isolated from various plant and animal food products associated with listeriosis outbreaks.

Contaminated ready-to-eat food products such as gravad and cold-smoked salmon and rainbow trout have been associated with human listeriosis in Sweden. The aim of this study was to analyse the occurrence and level of L. monocytogenes in
gravad and cold-smoked salmon (Salmo salar) products packed under vacuum or modified atmosphere from retail outlets in Sweden. Isolated strains were characterized by serotyping and the diversity of the strains within and between
producers were determined with PFGE (Pulsed-field gel electrophoresis). The characterized fish isolates were compared with previously characterized human strains.
L. monocytogenes was isolated from 11 (three manufacturers) of 56 products analysed. This included gravad salmon products from three manufacturers and cold-smoked salmon from one manufacturer. The highest level of L. monocytogenes found was 1500 cfu/g from a cold-smoked salmon product but the level was low (<100 cfu/g) in most of the products. Serovar 1/2a was predominant,
followed by 4b. Three products of gravad salmon harboured more than one serovar. PFGE typing of the 56 salmon isolates detected five Asc I types: four types were identical to human clinical strains with Asc I and one was identical and one was closely related to human clinical strains with Apa I. Isolation of identical or closely related L. monocytogenes strains from human clinical cases of listeriosis and gravad and cold-smoked salmon suggested that these kinds of products are possible sources of listeriosis in Sweden. Therefore, these products should be considered risk products for human listeriosis.

Listeria monocytogenes, a food-borne pathogen

Methane has profound impact on the physico-chemical properties in atmosphere leading to global climate change. Out of the various sources of CH4, rice fields are the most significant contributors. The processes involved in the emission of CH4 from rice fields to the atmosphere include CH4 production (methanogenesis) in the soil by methanogens, methane oxidation (methanotrophy) by methanotrophs and vertical transfer of CH4 via plant transport and diffusion or ebullition. In the overall methane dynamics rice plants act as : a) source of methanogenic substrate, b) conduit for CH4 through well developed system of inter cellular air space (aerenchyma), and c) potential methane oxidizing micro-habitat in the rhizosphere by diffusing oxygen which favour the growth and multiplication of methanotrophs. Apart from mechanistic uncertainties, there are several other uncertainties in the estimation of CH4 flux. Methane dynamics in the paddy field is controlled by a complex set of parameters linking the biological and physical characteristics of soil environment like temperature, carbon source, Eh, pH, soil microbes and properties of rice plants, etc. It has now become possible to isolate, detect and characterize the methanogens and methanotrophs by using molecular biological tools like PCR, FISH, etc. techniques. The apparent half saturation constant (Km) and maximum oxidation rate (Vmax) are distinctive parameters which determine the ability of bacteria to survive on atmospheric methane. Keywords. methane; methanotrophs; methanotrophy; methanogens; molecular tools

/pdf/microbial-ecology-of-methane-emission-in-rice-agroecosystem-4tcx106xse.pdf

Suresh Kumar Dubey

Papers

Microbial ecology of methane emission in rice agroecosystem: a review

Kinetic analysis reveals bacterial efficacy for biodegradation of chlorpyrifos and its hydrolyzing metabolite TCP

River Ganges water as reservoir of microbes with antibiotic and metal ion resistance genes: High throughput metagenomic approach.

Bio-methanol as a renewable fuel from waste biomass: Current trends and future perspective

Characterization of Listeria monocytogenes isolated from Ganges water, human clinical and milk samples at Varanasi, India