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

Aim: Aphids are abundant in natural and managed vegetation, supporting a diverse community of organisms and causing damage to agricultural crops. Using a meta-analysis approach, we aimed to advance understanding of how increased drought incidence will affect this ecologically and economically important insect group, and to characterise the underlying mechanisms. Location: Global. Time period: 1958-2020. Major taxa studied: Aphids. Methods: We used qualitative and quantitative synthesis techniques to determine whether drought stress has a negative, positive, or null effect on aphid fitness. We examined these effects in relation to 1) aphid biology, 2) the aphid-plant. species combination. We compiled two datasets: 1) a global dataset (n = 55 from 55 published studies) comprising one pooled effect size per study, and 2) an expanded dataset (n = 93) containing multiple datapoints per study, separated into different measures of aphid fitness but pooled across aphid-plant combinations. Where reported, we extracted data on the effect of drought on plant vigour, and plant tissue concentrations of nutrients and defensive compounds, to capture the potential causes of aphid responses. Results: Across all studies (global dataset), drought stress had a negative effect on aphid fitness: Hedges g = -0.57; 95% confidence interval (CI95) = ±0.31. The expanded dataset indicated that, on average, drought stress reduced aphid fecundity (g = -0.98; CI95 = ±0.50) and increased development time (g = 1.13; CI95 = ±1.02). Furthermore, drought stress had a negative impact on plant vigour (g = -7.06; CI95 = ±2.86) and increased plant concentrations of defensive chemicals (g = 3.14; CI95 = ±3.14). Main conclusions: Aphid fitness is typically reduced under drought, associated with reduced plant vigour and increased chemical defence in drought-stressed plants. We propose a conceptual model to predict drought effects on aphid fitness in relation to plant vigour and defence.

/pdf/stressful-times-in-a-climate-crisis-how-will-aphids-respond-4cxxkmownb.pdf

Stressful times in a climate crisis: how will aphids respond to more frequent drought?

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, with the expression of aphid detoxification genes increasing under drought when feeding on the susceptible plant but decreasing on the partially-resistant plant. Furthermore, we show that the expression of thionin genes, plant defensive compounds that contribute aphid resistance, increase ten-fold in susceptible plants exposed to drought stress but remain at constant levels in the partially-resistant plant, suggesting they play an important role in modulating 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-2v8ca2h7f7.pdf

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

Aphids secrete diverse repertoires of effectors into their hosts to promote the infestation process. While “omics”-approaches facilitated the identification and comparison of effector repertoires from a number of aphid species, the functional characterization of these proteins has been limited to dicot (model) plants. The bird cherry-oat aphid Rhopalosiphum padi is a pest of cereal crops, including barley. Here, we extended efforts to characterize aphid effectors with regards to their role in promoting susceptibility to the R. padi-barley interaction. We selected 3 R. padi effectors based on sequences similarity to previously characterized M. persicae effectors and assessed their subcellular localisation, expression, and role in promoting plant susceptibility. Expression of R. padi effectors RpC002 and Rp1 in transgenic barley lines enhanced plant susceptibility to R. padi but not M. persicae, for which barley is a poor host. Characterization of Rp1 transgenic barley lines revealed reduced gene expression of plant hormone signalling genes relevant to plant-aphid interactions, indicating this effector enhances susceptibility by suppressing plant defences in barley. Our data suggests that some aphid effectors specifically function when expressed in host species, and feature activities that benefit their corresponding aphid species.

https://www.biorxiv.org/content/biorxiv/early/2019/07/08/639476.full.pdf

An aphid effector promotes barley susceptibility through suppression of defence gene expression

The bird cherry aphid Rhopalosiphum padi and the green peach aphid Myzus persicae are devastating insect pests on agriculturally important crops. While the host range of R. padi consists mainly of cereal plants, M. persicae can infest thousands of plant species from across different plant families. However, despite a broad host range, which includes Nicotiana benthamiana, M. persicae performs poorly on barley. To gain insights into the role of aphid effectors in determining aphid host range, we undertook a comparative functional characterization approach for 3 predicted orthologous effector pairs from M. persicae and R. padi. We compared subcellular localisation and protein stability of these effectors in N. benthamiana and determined their contribution to host susceptibility. While subcellular localization of members of each effector pair was similar, we observed differences in proteins stability, especially in the case of RpC002 (R. padi C002)/MpC002 (M. persicae C002). For example, RpC002 was less expressed and/or stable than MpC002 in N. benthamiana and, in contrast to MpC002, did not enhance susceptibility in this plant species. However, expression of RpC002, as well as R. padi effector Rp1, in transgenic barley lines enhanced plant susceptibility to R. padi but not M. persicae. Our data suggests that some aphid effectors specifically function when expressed in host species, and feature activities that benefit their corresponding aphid species. Characterization of Rp1 transgenic barley lines revealed reduced gene expression of plant hormone signalling genes relevant to plant-aphid interactions, suggesting this effector enhances susceptibility by suppressing plant defences in barley.

https://www.biorxiv.org/content/biorxiv/early/2019/05/17/639476.full.pdf

Jorunn I. B. Bos

Papers

Stressful times in a climate crisis: how will aphids respond to more frequent drought?

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

An aphid effector promotes barley susceptibility through suppression of defence gene expression

A cereal aphid effector promotes barley susceptibility in a species-specific manner through suppression of defence gene expression.