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)

Host-microbe interactions: Shaping the evolution of the plant immune response

Plants are engaged in a continuous co-evolutionary struggle for dominance with their pathogens. The outcomes of these interactions are of particular importance to human activities, as they can have dramatic effects on agricultural systems. The recent convergence of molecular studies of plant immunity and pathogen infection strategies is revealing an integrated picture of the plant-pathogen interaction from the perspective of both organisms. Plants have an amazing capacity to recognize pathogens through strategies involving both conserved and variable pathogen elicitors, and pathogens manipulate the defence response through secretion of virulence effector molecules. These insights suggest novel biotechnological approaches to crop protection.

/pdf/plant-immunity-towards-an-integrated-view-of-plant-pathogen-3835470zf1.pdf

Plant immunity: towards an integrated view of plant―pathogen interactions

Plant hormones have pivotal roles in the regulation of plant growth, development, and reproduction. Additionally, they emerged as cellular signal molecules with key functions in the regulation of immune responses to microbial pathogens, insect herbivores, and beneficial microbes. Their signaling pathways are interconnected in a complex network, which provides plants with an enormous regulatory potential to rapidly adapt to their biotic environment and to utilize their limited resources for growth and survival in a cost-efficient manner. Plants activate their immune system to counteract attack by pathogens or herbivorous insects. Intriguingly, successful plant enemies evolved ingenious mechanisms to rewire the plant’s hormone signaling circuitry to suppress or evade host immunity. Evidence is emerging that beneficial root-inhabiting microbes also hijack the hormone-regulated immune signaling network to establish a prolonged mutualistic association, highlighting the central role of plant hormones in the regulation of plant growth and survival.

/pdf/hormonal-modulation-of-plant-immunity-na0dumzzdp.pdf

Hormonal Modulation of Plant Immunity

Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth–promoting bacteria and fungi in the rhizosphere prime the whole plant body for enhanced defense against a broad range of pathogens and insect herbivores. A wide variety of root-associated mutualists, including Pseudomonas, Bacillus, Trichoderma, and mycorrhiza species sensitize the plant immune system for enhanced defense without directly activating costly defenses. This review focuses on molecular processes at the interface between plant roots and ISR-eliciting mutualists, and on the progress in our understanding of ISR signaling and systemic defense priming. The central role of the root-specific transcription factor MYB72 in the onset of ISR and the role of phytohormones and defense regulatory proteins in the expression of ISR in aboveground plant parts are highlighted. Finally, the ecological function of ISR-inducing microbes in the root microbiome is discussed.

/pdf/induced-systemic-resistance-by-beneficial-microbes-9uemo31ql5.pdf

Induced systemic resistance by beneficial microbes

Effectors in Plant–Insect Interactions

Plant parasites must colonise and reproduce on plants to survive In most cases, active immune responses, triggered by (conserved) microbe-encoded molecules keep invaders at bay Post-translational modifications (PTMs) of proteins are vital for contextual regulation and integration of plant immune responses Pathogens and pests secrete proteins (effectors) to interfere with plant immunity through modification of host target functions and disruption of immune signalling networks Importantly, molecular virulence strategies of distinct pathogens converge on a small set of regulators with central roles in plant immunity The extent of convergence between pathogen and herbivorous insect virulence strategies is largely unexplored Here we report that effectors from the oomycete pathogen, Phytophthora capsici, and the major aphid pest, Myzus persicae target the host immune regulator SIZ1, an E3 SUMO ligase SIZ1-regulated immunity in Arabidopsis against bacterial pathogens is known to require the resistance protein SNC1, and signalling components PAD4 and EDS1 We show that SIZ1 functions as a negative regulator of plant immunity to aphids and an oomycete pathogen However, this immune regulation is independent of SNC1, PAD4 and EDS1-signalling pointing to the presence of a novel SIZ1-mediated immune signalling route Our results suggest convergence of distinct pathogen and pest virulence strategies on an E3 SUMO ligase that negatively regulates plant immunity

/pdf/virulence-strategies-of-an-insect-herbivore-and-oomycete-2zr4biaatl.pdf

Virulence strategies of an insect herbivore and oomycete plant pathogen converge on host E3 SUMO ligase SIZ1 to suppress plant immunity

Crops are exposed to myriad abiotic and biotic stressors with negative consequences. Two stressors that are expected to increase under climate change are drought and infestation with herbivorous insects, including important aphid species. Expanding our understanding of the impact drought has on the plant-aphid relationship will become increasingly important under future climate scenarios. Here we use a previously characterised plant-aphid system comprising a susceptible variety of barley, a wild relative of barley with partial-aphid resistance, and the bird cherry-oat aphid to examine the drought-plant-aphid relationship. We show that drought has a negative effect on plant physiology and aphid fitness and provide evidence to suggest that plant resistance influences aphid responses to drought stress. Furthermore, we show that the expression of thionin genes, plant defensive compounds that contribute to aphid resistance, increase in susceptible plants exposed to drought stress but remain at constant levels in the partially-resistant plant, suggesting they play an important role in determining the success of aphid populations. This study highlights the role of plant defensive processes in mediating the interactions between the environment, plants, and herbivorous insects.

/pdf/drought-stress-increases-the-expression-of-barley-defence-60lgc1zw.pdf

Drought stress increases the expression of barley defence genes with negative consequences for infesting cereal aphids.

Aphids frequently associate with facultative endosymbiotic bacteria which influence aphid physiology in myriad ways. Endosymbiont infection can increase aphid resistance against parasitoids and pathogens, modulate plant responses to aphid feeding, and promote aphid virulence. These endosymbiotic relationships can also decrease aphid fitness in the absence of natural enemies or when feeding on less suitable plant types. Here, we use the Electrical Penetration Graph (EPG) technique to monitor feeding behaviour of four genetically-similar clonal lines of a cereal-feeding aphid, Rhopalosiphum padi, differentially infected (+/−) with the facultative protective endosymbiont, Hamiltonella defensa, to understand how physiological processes at the aphid-plant interface are affected by endosymbiont infection. Endosymbiont-infected aphids exhibited altered probing and feeding patterns compared with uninfected aphids, characterised by a two-fold increase in the number of plant cell punctures, a 50% reduction in the duration of each cellular puncture, and a greater probability of achieving sustained ingestion of plant phloem. Feeding behaviour was altered further by host plant identity: endosymbiont-infected aphids spent less time probing into plant tissue, required twice as many probes into plant tissue to reach plant phloem, and showed a 44% reduction in phloem ingestion when feeding on the partially-resistant wild relative of barley, Hordeum spontaneum 5, compared with a commercial barley cultivar. These observations might explain reduced growth of H. defensa-infected aphids on the former host plant. This study is the first to demonstrate a physiological mechanism at the aphid-plant interface contributing to endosymbiont effects on aphid fitness on different quality plants through altered aphid feeding behaviour. Summary Reduced performance of aphids infected with a common facultative endosymbiont on poor quality plants may be explained by changes in aphid probing behaviour and decreased phloem sap ingestion.

https://www.biorxiv.org/content/biorxiv/early/2019/05/30/652974.full.pdf

A fitness cost resulting from Hamiltonella defensa infection is associated with altered probing and feeding behaviour in Rhopalosiphum padi

Aphids, including the bird cherry-oat aphid (Rhopalosiphum padi), are significant agricultural pests. Aphid populations are typically controlled using insecticides, but there is increasing demand for more sustainable pest management practices. The wild relative of barley, Hordeum spontaneum 5 (Hsp5) has been described as partially-resistant to R. padi. Partial-resistance is proposed to involve higher thionin and lipoxygenase gene expression. However, the underlying mechanistic processes are unknown. In this study we compared Hsp5 with a susceptible cultivar of barley (Concerto) to test the extent to which partial-resistance affects aphid fitness. We used the electrical penetration graph technique to monitor R. padi feeding patterns to elucidate the tissue location of partial-resistance factors alongside molecular and biochemical analyses to identify potential mechanisms. We show that partial-resistance in Hsp5 extends to three aphid species and is mediated by phloem/mesophyll-based factors, leading to a three-fold increase in the time aphids take to establish sustained phloem ingestion. Partial-resistance likely involves elevated expression of defence and phytohormone genes alongside altered phloem amino acid composition. Further work is required to establish the function of these traits, however this study highlights plant tissues which are important in conferring broad-spectrum partial-resistance against aphids in barley. Highlight Partial-resistance against aphids in wild barley is based in the mesophyll and vascular tissue and is potentially associated with higher basal defence gene expression and altered phloem amino acid composition.

/pdf/partial-resistance-against-aphids-in-wild-barley-involves-qgfsbglkvw.pdf

Jorunn I. B. Bos

Papers

Effectors in Plant–Insect Interactions

Virulence strategies of an insect herbivore and oomycete plant pathogen converge on host E3 SUMO ligase SIZ1 to suppress plant immunity

Drought stress increases the expression of barley defence genes with negative consequences for infesting cereal aphids.

A fitness cost resulting from Hamiltonella defensa infection is associated with altered probing and feeding behaviour in Rhopalosiphum padi

Partial-resistance against aphids in wild barley involves phloem and mesophyll-based defences