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

Soil bacteria are very important in biogeochemical cycles and have been used for crop production for decades. Plant–bacterial interactions in the rhizosphere are the determinants of plant health and soil fertility. Free-living soil bacteria beneficial to plant growth, usually referred to as plant growth promoting rhizobacteria (PGPR), are capable of promoting plant growth by colonizing the plant root. PGPR are also termed plant health promoting rhizobacteria (PHPR) or nodule promoting rhizobacteria (NPR). These are associated with the rhizosphere, which is an important soil ecological environment for plant–microbe interactions. Symbiotic nitrogen-fixing bacteria include the cyanobacteria of the genera Rhizobium, Bradyrhizobium, Azorhizobium, Allorhizobium, Sinorhizobium and Mesorhizobium. Free-living nitrogen-fixing bacteria or associative nitrogen fixers, for example bacteria belonging to the species Azospirillum, Enterobacter, Klebsiella and Pseudomonas, have been shown to attach to the root and efficiently colonize root surfaces. PGPR have the potential to contribute to sustainable plant growth promotion. Generally, PGPR function in three different ways: synthesizing particular compounds for the plants, facilitating the uptake of certain nutrients from the soil, and lessening or preventing the plants from diseases. Plant growth promotion and development can be facilitated both directly and indirectly. Indirect plant growth promotion includes the prevention of the deleterious effects of phytopathogenic organisms. This can be achieved by the production of siderophores, i.e. small metal-binding molecules. Biological control of soil-borne plant pathogens and the synthesis of antibiotics have also been reported in several bacterial species. Another mechanism by which PGPR can inhibit phytopathogens is the production of hydrogen cyanide (HCN) and/or fungal cell wall degrading enzymes, e.g., chitinase and s-1,3-glucanase. Direct plant growth promotion includes symbiotic and non-symbiotic PGPR which function through production of plant hormones such as auxins, cytokinins, gibberellins, ethylene and abscisic acid. Production of indole-3-ethanol or indole-3-acetic acid (IAA), the compounds belonging to auxins, have been reported for several bacterial genera. Some PGPR function as a sink for 1-aminocyclopropane-1-carboxylate (ACC), the immediate precursor of ethylene in higher plants, by hydrolyzing it into α-ketobutyrate and ammonia, and in this way promote root growth by lowering indigenous ethylene levels in the micro-rhizo environment. PGPR also help in solubilization of mineral phosphates and other nutrients, enhance resistance to stress, stabilize soil aggregates, and improve soil structure and organic matter content. PGPR retain more soil organic N, and other nutrients in the plant–soil system, thus reducing the need for fertilizer N and P and enhancing release of the nutrients.

Soil beneficial bacteria and their role in plant growth promotion: a review

Phosphorus is the second important key element after nitrogen as a mineral nutrient in terms of quantitative plant requirement. Although abundant in soils, in both organic and inorganic forms, its availability is restricted as it occurs mostly in insoluble forms. The P content in average soil is about 0.05% (w/w) but only 0.1% of the total P is available to plant because of poor solubility and its fixation in soil (Illmer and Schinner, Soil Biol Biochem 27:257-263, 1995). An adequate supply of phosphorus during early phases of plant development is important for laying down the primordia of plant reproductive parts. It plays significant role in increasing root ramification and strength thereby imparting vitality and disease resistance capacity to plant. It also helps in seed formation and in early maturation of crops like cereals and legumes. Poor availability or deficiency of phosphorus (P) markedly reduces plant size and growth. Phosphorus accounts about 0.2 - 0.8% of the plant dry weight. To satisfy crop nutritional requirements, P is usually added to soil as chemical P fertilizer, however synthesis of chemical P fertilizer is highly energy intensive processes, and has long term impacts on the environment in terms of eutrophication, soil fertilility depletion, carbon footprint. Moreover, plants can use only a small amount of this P since 75–90% of added P is precipitated by metal–cation complexes, and rapidly becomes fixed in soils. Such environmental concerns have led to the search for sustainable way of P nutrition of crops. In this regards phosphate-solubilizing microorganisms (PSM) have been seen as best eco-friendly means for P nutrition of crop. Although, several bacterial (pseudomonads and bacilli) and fungal strains (Aspergilli and Penicillium) have been identified as PSM their performance under in situ conditions is not reliable and therefore needs to be improved by using either genetically modified strains or co-inoculation techniques. This review focuses on the diversity of PSM, mechanism of P solubilization, role of various phosphatases, impact of various factors on P solubilization, the present and future scenario of their use and potential for application of this knowledge in managing a sustainable environmental system.

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Phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils

With increasing demand of agricultural production and as the peak in global production will occur in the next decades, phosphorus (P) is receiving more attention as a nonrenewable resource ([Cordell et al., 2009][1]; [Gilbert, 2009][2]). One unique characteristic of P is its low availability due to

/pdf/phosphorus-dynamics-from-soil-to-plant-1ziaqrbh4d.pdf

Phosphorus Dynamics: From Soil to Plant

Phosphate solubilizing bacteria from subtropical soil and their tricalcium phosphate solubilizing abilities

The key to achieving successful, reproducible results following the introduction of beneficial microbes into soil relies on the survival rate of the inoculated bacteria in a heterogeneous soil environment and hence an improved encapsulation method was developed. Owing to the constraints associated with the inoculum formulation, in this study, encapsulation of a plant growth promoting bacteria (PGPB) isolate Bacillus subtilis CC-pg104 was attempted with alginate by enriching the bead microenvironment with humic acid. High viability of the encapsulated bacteria was observed with minimum cell loss upon storage for 5 months. Steady and constant cell release from the bead was observed for 1 week at different pH. Encapsulated cells remained active as evidenced by their ability to solubilize calcium phosphate in vitro. Successful plant growth promotion of lettuce by the encapsulated bacteria under gnotobiotic and sterile environment was also achieved. Feasibility of this improved encapsulation technique is mainly due to the dual benefits of humic acid to microbe and plant and its chemical properties allowing an easy mixing with alginate without interfering in the formation of the alginate gel beads by cross-linking with Ca2+ ions. Thus, the encapsulation method described in this study can be effectively used to protect the PGPB inoculum from adverse conditions of the soil for their successful establishment in the rhizosphere.

Encapsulation of plant growth-promoting bacteria in alginate beads enriched with humic acid.

A yellow-pigmented bacterial strain (CC-H3-2T), isolated from the rhizosphere of Lactuca sativa L. (garden lettuce) in Taiwan, was investigated using a polyphasic taxonomic approach. The cells were Gram-negative, rod-shaped and non-spore-forming. Phylogenetic analyses using the 16S rRNA gene sequence of the isolate indicated that the organism belongs to the genus Chryseobacterium, with the highest sequence similarity to the type strains of Chryseobacterium indoltheticum (97.7 %), Chryseobacterium scophthalmum (97.5 %), Chryseobacterium joostei (97.2 %) and Chryseobacterium defluvii (97.2 %). The major whole-cell fatty acids were iso-C(15 : 0) (52.2 %) and iso-C(17 : 0) 3-OH. DNA-DNA hybridization experiments revealed levels of only 27.4 % to C. scophthalmum, 27.1 % to C. indoltheticum, 14.1 % to C. joostei and 7.8 % to C. defluvii. DNA-DNA relatedness and biochemical and chemotaxonomic properties demonstrate that strain CC-H3-2T represents a novel species, for which the name Chryseobacterium formosense sp. nov. is proposed. The type strain is CC-H3-2T (=CCUG 49271T=CIP 108367T).

Chryseobacterium formosense sp. nov., isolated from the rhizosphere of Lactuca sativa L. (garden lettuce).

Analysis of the 16S rRNA gene sequences of species currently assigned to the genus Flexibacter has shown extensive intrageneric phylogenetic heterogeneity. It has been shown in previous studies that the species [Flexibacter] sancti, [Flexibacter] filiformis and [Flexibacter] japonensis were most closely related to Chitinophaga pinensis. In addition, [Cytophaga] arvensicola and species of the genus Terrimonas also clustered into this phylogenetic group. Although the similarities of 16S rRNA gene sequences were low (88.5-96.4 %), there is no evidence for clear phenotypic differences between these organisms that justify assignment to different genera. A proposal is made to transfer these species to the genus Chitinophaga as Chitinophaga sancti comb. nov., Chitinophaga filiformis comb. nov., Chitinophaga japonenis comb. nov. and Chitinophaga arvensicola comb. nov. on the basis of phylogenetic and phenotypic data. Furthermore, a novel species is described within this genus, Chitinophaga skermanii sp. nov., with strain CC-SG1B(T) (=CCUG 52510(T)=CIP 109140(T)) as the type strain.

Transfer of [Flexibacter] sancti, [Flexibacter] filiformis, [Flexibacter] japonensis and [Cytophaga] arvensicola to the genus Chitinophaga and description of Chitinophaga skermanii sp. nov.

A pale-pink strain (CC-FR2-10T) from the rhizosphere of the sacred tree Ficus religiosa L. in Taiwan was investigated by using a polyphasic taxonomic approach. The cells were Gram-positive, rod-shaped and non-spore-forming. Phylogenetic analyses using the 16S rRNA gene sequence of the isolate indicated that the organism belongs to the genus Deinococcus, the highest sequence similarities being found with Deinococcus grandis (96.1 %), Deinococcus radiodurans (94.3 %), Deinococcus radiopugnans (93.2 %), Deinococcus indicus (93.0 %), Deinococcus proteolyticus (92.5 %), Deinococcus murrayi (92.4 %) and Deinococcus geothermalis (90.7 %). The DNA-DNA relatedness with respect to D. grandis DSM 3963T was 17.9 %. Chemotaxonomic data revealed that strain CC-FR2-10T contains only menaquinone MK-8 as the respiratory quinone, unknown phosphoglycolipids as the predominant polar lipids and 16 : 1omega7c, 17 : 1omega8c and 17 : 1omega9c iso as the predominant fatty acids. The biochemical and chemotaxonomic properties demonstrate that strain CC-FR2-10T represents a novel species, for which the name Deinococcus ficus sp. nov. is proposed. The type strain is CC-FR2-10T (=CCUG 51391T [corrected] = CIP 108832T).

Wei-An Lai

Papers

Phosphate solubilizing bacteria from subtropical soil and their tricalcium phosphate solubilizing abilities

Encapsulation of plant growth-promoting bacteria in alginate beads enriched with humic acid.

Chryseobacterium formosense sp. nov., isolated from the rhizosphere of Lactuca sativa L. (garden lettuce).

Transfer of [Flexibacter] sancti, [Flexibacter] filiformis, [Flexibacter] japonensis and [Cytophaga] arvensicola to the genus Chitinophaga and description of Chitinophaga skermanii sp. nov.

Deinococcus ficus sp. nov., isolated from the rhizosphere of Ficus religiosa L.