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)

Evolution of Protein Molecules

High food demand for the world's teeming population necessitates the intensification of crop production in modern agriculture, which requires the extensive use of synthetic fertilizers for higher crop yield. The excessive use of chemical fertilizers, despite the high nutrients contents and ability to grow crops faster, discovered to be dangerous to the health and environment besides polluting the groundwater and atmosphere in the future. The alternative to these, biofertilizers arose today due to their attributes towards eco-friendly, cost-effective, and easy to apply in the agricultural field. Biofertilizers are a batch of diverse microorganisms, which can induce plant growth-promotion activities along with soil health, even under abiotic stress conditions. Biofertilizers maybe plant growth-promoting rhizobacteria, arbuscular mycorrhizal fungi, and as well as the consortia of other beneficial microbes. Biofertilizers can sustain plant growth performance, even in a challenging environment. The performance of perfect-candidate-biofertilizer in the agricultural field depends on crop type, properties of inoculants, technical background, and environmental condition. Biofertilizers can, directly or indirectly, help in attaining food security compared to the harmful effect of chemical fertilizers. A direct mechanism of Biofertilizers refers to phyto-stimulation and nutrient mobility, while an indirect mechanism poses bio-control activity. Direct mechanisms involve phytohormone production and phosphate, potassium, zinc, etc. solubilization. While, indirect-mechanism is HCN production, siderophore production, antibiotic production, etc. The present review elucidates the diversity of microbial inoculants (biofertilizers), their impacts on agricultural production through rising soil fertility, and overall crop yield. In line with related literature worked out by different researchers.

Biofertilizers: A Nexus between soil fertility and crop productivity under abiotic stress

Soil, the skin of the Earth is one of the fundamental natural resource and important component that contributes to the ecosystem. Soil performs a wide range of ecosystem services like food production, climate and water regulation, provision of energy and inhabiting various life forms. This fundamental natural resource of ecosystem is a home of diverse ranges of microbes (beneficial and pathogenic) known as soil microbiome, which are grouped into three domains i.e. archaea, bacteria, eukarya (fungi, algae and nematodes) of life. Diversity of soil microbiome varies with environment and their existence. They exist in bulk soil as well as root influenced soil. Soil microbes also show their existence in the different extreme environments. The microbial genera such as Achromobacter, Arthrobacter, Azospirillum, Azotobacter, Bacillus, Burkholderia, Exiguobacterium, Flavobacterium, Herbaspirillum, Methylobacterium, Paenibacillus, Pseudomonas, Rhizobium, Serratia and Staphylococcus have been reported as predominant in all the different conditions of soil. All the different groups of microbes present in the soil naturally plays a several significant roles like nutrients cycling, recycling of ground water, maintenance of soil fertility, decomposition of organic matter and formation of fossil fuels. As their role in environment these microbes may have several applications and can be used as in agriculture as plant protector and plant growth enhancer. Soil microbes can also be used in the environment for pollutants remediation and decomposition purposes. Present review deals with the biodiversity of beneficial soil microbiomes and their potential biotechnological contribution for nutrient cycling, plant growth improvement and nutrient uptake.

Biodiversity, and biotechnological contribution of beneficial soil microbiomes for nutrient cycling, plant growth improvement and nutrient uptake

Two PGPR strains from the rhizosphere of Haloxylon ammodendron promoted growth and enhanced drought tolerance of ryegrass

Chemical fertilizers can supply essential nutrients to crops increasing their yield, however, they can also cause serious environmental problems. Biofertilizer has received more and more attention because of its environmentally friendly and pollution-free characteristics. Haloxylon ammodendron, a desert succulent shrub, has become an important plant species for vegetation restoration in several deserts in China because of its strong drought tolerance. Its extensive root systems and unique rhizosphere bacterial community aid H. ammodendron adapt to this extreme environment. In this study, Bacillus sp. WM13-24 and Pseudomonas sp. M30-35 isolated from the rhizosphere of H. ammodendron in our previous study and Bacillus amyloliquefaciens GB03 and Sinorhizobium meliloti ACCC17578 as well-studied beneficial strains were used to prepare two types of biofertilizer, WM13-24 biofertilizer containing Bacillus sp. WM13-24 and integrated biofertilizer containing all the four strains. Results presented here showed that WM13-24 biofertilizer and the integrated biofertilizer improved chili plant growth, fruit yield and quality and the rhizosphere soil nitrogen content, enzyme activities, and the quantity and biodiversity of viable bacteria. Compared to the control, WM13-24 biofertilizer and a commercial biofertilizer, the integrated biofertilizer performed best in significantly increasing plant height, stem diameter, leaf length and width, chlorophyll content, fruit yield, soluble sugar content, ascorbic acid content, organic acid content, soil urease activity, catalase activity and the quantity and biodiversity of viable bacteria. This study provided a theoretical and practical basis for large scale development of integrated biofertilizers using beneficial rhizobacterial strains from the desert plant rhizosphere.

Biofertilizers with beneficial rhizobacteria improved plant growth and yield in chili (Capsicum annuum L.).

A Gram-negative aerobic bacterium, strain M30-35 T, was isolated from the rhizosphere of Haloxylon ammodendron in Tengger desert, Gansu province, northwest China. Our previous research indicated that strain M30-35 T can promote the growth of ryegrass (Lolium perenne L.). In this study, strain M30-35 T was subjected to a polyphasic taxonomic study. Phylogenetic analysis of the 16S rRNA gene and two other housekeeping genes (gyrB, rpoD) showed that strain M30-35 T is a member of Pseudomonas anguilliseptica group. The average nucleotide identity (ANI) scores for strains KMM 3042 T and FR1439T were 76.5% and 83.7%, respectively, and DNA-DNA hybridization (DDH) were 21.6% and 26.6%, respectively, and the rates were less than the threshold range for species determination. The dominant cellular fatty acids of strain M30-35 T were C16:0 (22.7%), summed feature 3 (C16:1ω7c and/or C16:1ω6c; 18.5%), summed feature 8 (C18:1ω7c and/or C18:1ω6c; 23.1%). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phospholipid and aminophospholipid and the predominant respiratory quinone was ubiquinone (Q9). On the basis of above data, it can be concluded that strain M30-35 T represents a novel species in the genus Pseudomonas, for which the name Pseudomonas rhizovicinus sp. nov. is proposed. The type strain is M30-35 T (= MCCC 1K03247T = KCTC 52664 T).

Taxonomic description of Pseudomonas rhizovicinus sp. nov., isolated from the rhizosphere of a desert shrub Haloxylon ammodendron.

A salt-tolerant, Gram-negative, rod-shaped and yellow-pigmented bacterium, designated strain AY-3RT, was isolated from rhizosphere soil of a desert xerophyte, Haloxylon ammodendron, sampled at Badain Jaran Desert, Alxa region, Inner Mongolia, PR China. Growth of this strain was observed at 20–42 °C (optimum, 28–30 °C), at pH 6.0–9.0 (optimum, pH 6.0–7.0) and at 0–8 % (w/v) NaCl (optimum, 3 %). Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain AY-3RT was a member of the genus Altererythrobacter , with the highest similarity to Altererythrobacter aerophilus Ery1T (97.6 %), followed by Altererythrobacter xinjiangensis S3-63T (96.9 %). The predominant fatty acids (>10.0 %) were C18 : 1ω7c, C17 : 1ω6c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid and one unknown polar lipid. The predominant respiratory quinone was ubiquinone-10. The G+C content of the genomic DNA of strain AY-3RT was 66.3 mol%. On the basis of the data from this polyphasic taxonomic study, strain AY-3RT represents a novel species of the genus Altererythrobacter , named Altererythrobacter rhizovicinus sp. nov. (=MCCC 1K03572T=KCTC 72280T).

Altererythrobacter rhizovicinus sp. nov., isolated from rhizosphere soil of Haloxylon ammodendron

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Biofertilizers with beneficial rhizobacteria improved plant growth and yield in chili (Capsicum annuum L.).

Taxonomic description of Pseudomonas rhizovicinus sp. nov., isolated from the rhizosphere of a desert shrub Haloxylon ammodendron.

Altererythrobacter rhizovicinus sp. nov., isolated from rhizosphere soil of Haloxylon ammodendron