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)

The rhizosphere encompasses the millimeters of soil surrounding a plant root where complex biological and ecological processes occur. This review describes recent advances in elucidating the role of root exudates in interactions between plant roots and other plants, microbes, and nematodes present in the rhizosphere. Evidence indicating that root exudates may take part in the signaling events that initiate the execution of these interactions is also presented. Various positive and negative plant-plant and plant-microbe interactions are highlighted and described from the molecular to the ecosystem scale. Furthermore, methodologies to address these interactions under laboratory conditions are presented.

The Role of Root Exudates in Rhizosphere Interactions with Plants and Other Organisms

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

/pdf/fast-tree-computing-large-minimum-evolution-trees-with-4grq0gwfpy.pdf

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Contents
I. Introduction  424
II. The phosphorus conundrum 424
III. Adaptations to low P 424
IV. Uptake of P  424
V. P deficiency alters root development and function 426
VI. P deficiency modifies carbon metabolism 431
VII. Acid phosphatase 436
VIII. Genetic regulation of P responsive genes 437
IX. Improving P acquisition 439
X. Synopsis  440


Summary
Phosphorus (P) is limiting for crop yield on > 30% of the world's arable land and, by some estimates, world resources of inexpensive P may be depleted by 2050. Improvement of P acquisition and use by plants is critical for economic, humanitarian and environmental reasons. Plants have evolved a diverse array of strategies to obtain adequate P under limiting conditions, including modifications to root architecture, carbon metabolism and membrane structure, exudation of low molecular weight organic acids, protons and enzymes, and enhanced expression of the numerous genes involved in low-P adaptation. These adaptations may be less pronounced in mycorrhizal-associated plants. The formation of cluster roots under P-stress by the nonmycorrhizal species white lupin (Lupinus albus), and the accompanying biochemical changes exemplify many of the plant adaptations that enhance P acquisition and use. Physiological, biochemical, and molecular studies of white lupin and other species response to P-deficiency have identified targets that may be useful for plant improvement. Genomic approaches involving identification of expressed sequence tags (ESTs) found under low-P stress may also yield target sites for plant improvement. Interdisciplinary studies uniting plant breeding, biochemistry, soil science, and genetics under the large umbrella of genomics are prerequisite for rapid progress in improving nutrient acquisition and use in plants.

/pdf/phosphorus-acquisition-and-use-critical-adaptations-by-56im8qzi8m.pdf

Phosphorus acquisition and use: critical adaptations by plants for securing a nonrenewable resource

Priming effects are strong short-term changes in the turnover of soil organic matter caused by comparatively moderate treatments of the soil. In the course of priming effects large amounts of C, N and other nutrients can be released or immobilized in soil in a very short time. These effects have been measured in many field and laboratory experiments; however, only a few of the studies were aimed at an extended investigation of the mechanisms of such phenomena. The aim of this overview is to reveal possible causes and processes leading to priming actions using the references on agricultural ecosystems and model experiments. Multiple mechanisms and sources of released C and N are presented and summarized in Tables for positive and negative real and apparent priming effects induced after the addition of different organic and mineral substances to the soil. Soil microbial biomass plays the key role in the processes leading to the real priming effects. The most important mechanisms for the real priming effects are the acceleration or retardation of soil organic matter turnover due to increased activity or amount of microbial biomass. Isotopic exchange, pool substitution, and different uncontrolled losses of mineralized N from the soil are responsible for the apparent N priming effects. Other multiple mechanisms (predation, competition for nutrients between roots and microorganisms, preferred uptake, inhibition, etc.) in response to addition of different substances are also discussed. These mechanisms can be distinguished from each other by the simultaneous monitoring of C and N release dynamics; its comparison with the course of microbial activity; and by the labelling of different pools with 14 C or 13 C and 15 N. Quantitative methods for describing priming effects and their dynamics using 14 C and 15 N isotopes, as well as for non-isotopic studies are proposed.

Review of mechanisms and quantification of priming effects.

Organic acids, such as malate, citrate and oxalate, have been proposed to be involved in many processes operating in the rhizosphere, including nutrient acquisition and metal detoxification, alleviation of anaerobic stress in roots, mineral weathering and pathogen attraction. A full assessment of their role in these processes, however, cannot be determined unless the exact mechanisms of plant organic acid release and the fate of these compounds in the soil are more fully understood. This review therefore includes information on organic acid levels in plants (concentrations, compartmentalisation, spatial aspects, synthesis), plant efflux (passive versus active transport, theoretical versus experimental considerations), soil reactions (soil solution concentrations, sorption) and microbial considerations (mineralization). In summary, the release of organic acids from roots can operate by multiple mechanisms in response to a number of well-defined environmental stresses (e.g., Al, P and Fe stress, anoxia): These responses, however, are highly stress- and plant-species specific. In addition, this review indicates that the sorption of organic acids to the mineral phase and mineralisation by the soil's microbial biomass are critical to determining the effectiveness of organic acids in most rhizosphere processes.

Organic acids in the rhizosphere: a critical review

Optimisation of the anaerobic digestion of agricultural resources.

The loss of carbon from roots (rhizodeposition) and the consequent proliferation of microorganisms in the surrounding soil, coupled with the physical presence of a root and processes associated with nutrient uptake, gives rise to a unique zone of soil called the rhizosphere. In this review, we bring together evidence to show that roots can directly regulate most aspects of rhizosphere C flow either by regulating the exudation process itself or by directly regulating the recapture of exudates from soil. Root exudates have been hypothesized to be involved in the enhanced mobilization and acquisition of many nutrients from soil or the external detoxification of metals. With few exceptions, there is little mechanistic evidence from soil-based systems to support these propositions. We conclude that much more integrated work in realistic systems is required to quantify the functional significance of these processes in the field. We need to further unravel the complexities of the rhizosphere in order to fully engage with key scientific ideas such as the development of sustainable agricultural systems and the response of ecosystems to climate change. Contents I. Introduction 460 II. What is rhizodeposition? 460 III. Regulation of rhizodeposition 460 IV. How large is the root exudation C flux? 463 V. How responsive is the root exudation C flux? 463 VI. How responsive is the microbial community to root exudation? 464 VII. The role of root exudates in nutrient acquisition 464 VIII. Mycorrhizal fungi and rhizodeposition 471 IX. Future thoughts 474 Acknowledgements 474 References 474.

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/j.1469-8137.2004.01130.x

Plant and mycorrhizal regulation of rhizodeposition

Dissolved organic matter (DOM), typically quantified as dissolved organic carbon (DOC), has been hypothesized to play many roles in pedogenesis and soil biogeochemical cycles, however, most research to date concerning forest soils has focussed on the high molecular weight (HMW) components of this DOM. This review aims to assess the role of low molecular weight (LMW) DOM compounds in the C dynamics of temperate and boreal forest soils focussing in particular on organic acids, amino acids and sugars. The current knowledge of concentrations, mineralization kinetics and production rates and sources in soil are summarised. We conclude that although these LMW compounds are typically maintained at very low concentrations in the soil solution (

The carbon we do not see : The impact of low molecular weight compounds on carbon dynamics and respiration in forest soils - A review

Soil pH is often hypothesized to be a major factor regulating organic matter turnover and inorganic nitrogen production in agricultural soils. The aim of this study was to critically test the relationship between soil pH and rates of C and N cycling, and dissolved organic nitrogen (DON), in two long-term field experiments in which pH had been manipulated (Rothamsted silty clay loam, pH 3.5–6.8; Woburn sandy loam, pH 3.4–6.3). While alteration of pH for 37 years significantly affected crop production, it had no significant effect on total soil C and N or indigenous mineral N levels. This implies that at steady state, increased organic matter inputs to the soil are balanced by increased outputs of CO2. This is supported by the positive correlation between both plant productivity and intrinsic microbial respiration with soil pH. In addition, soil microbial biomass C and N, and nitrification were also significantly positively correlated with soil pH. Measurements of respiration following addition of urea and amino acids showed a significant decline in CO2 evolution with increasing soil acidity, whilst glucose mineralization showed no response to pH. In conclusion, it appears that changes in soil pH significantly affect soil microbial activity and the rate of soil C and N cycling. The evidence suggests that this response is partially indirect, being primarily linked to pH induced changes in net primary production and the availability of substrates. In addition, enhanced soil acidity may also act directly on the functioning of the microbial community itself.

David L. Jones

Papers

Organic acids in the rhizosphere: a critical review

Optimisation of the anaerobic digestion of agricultural resources.

Plant and mycorrhizal regulation of rhizodeposition

The carbon we do not see : The impact of low molecular weight compounds on carbon dynamics and respiration in forest soils - A review

PH regulation of carbon and nitrogen dynamics in two agricultural soils