Induced plant responses to microbes and insects

Plants are members of complex communities and interact both with antagonists and beneficial organisms. An important question in plant defense-signaling research is how plants integrate signals induced by pathogens, insect herbivores and beneficial microbes into the most appropriate adaptive response. Molecular and genomic tools are now being used to uncover the complexity of the induced defense signaling networks that have evolved during the arms races between plants and the other organisms with which they intimately interact. To understand the functioning of the complex defense signaling network in nature, molecular biologists and ecologists have joined forces to place molecular mechanisms of induced plant defenses in an ecological perspective. In this Research Topic, we aim to provide an on-line, open-access snapshot of the current state of the art of the field of induced plant responses to microbes and insects, with a special focus on the translation of molecular mechanisms to ecology and vice versa. We will collect Original Research and Review papers on the topic, but also other article types, such as Methods and Opinions are welcome

Phenotypic analysis of Arabidopsis mutants: trypan blue stain for fungi, oomycetes, and dead plant cells

Trypan blue stains vasculature, dead plant cells, and fungal and oomycete hyphae. It is useful for assessing the extent of colonization of tissue, and for detecting microlesions present in certain lesion mimic mutants. Trypan blue staining requires chloral hydrate for destaining, which is inconvenient, because it is a controlled substance. The chloral hydrate can be replaced with 1:2 lactophenol:ethanol, but the background staining will be higher than it is when chloral hydrate is used

Phenotypic analysis of Arabidopsis mutants: trypan blue stain for fungi, oomycetes, and dead plant cells

Trypan blue stains vasculature, dead plant cells, and fungal and oomycete hyphae. It is useful for assessing the extent of colonization of tissue, and for detecting microlesions present in certain lesion mimic mutants. Trypan blue staining requires chloral hydrate for destaining, which is inconvenient, because it is a controlled substance. The chloral hydrate can be replaced with 1:2 lactophenol:ethanol, but the background staining will be higher than it is when chloral hydrate is used

Costs and benefits of hormone-regulated plant defenses

Plants activate defence responses to protect themselves against microbial pathogens and herbivorous insects. However, induction of defences comes at a price, as the associated allocation costs, autotoxicity costs and ecological costs form fitness penalties. Upon pathogen or insect attack, resources are allocated to defences instead of to plant growth and reproduction, while above- and below-ground interactions with beneficial organisms may also be disturbed. The phytohormones salicylic acid and jasmonic acid are major players in the regulation of induced defences and their associated fitness costs. Hormone-controlled signalling pathways cross-communicate, providing the plant with a finely tuned defence regulatory system that can contribute to a reduction of fitness costs by repressing ineffective defences. However, this sophisticated regulatory system causes ecological costs, because activated resistance to one organism can suppress resistance to another. Moreover, the system can be hijacked by invading organisms that manipulate it for their own benefit. Priming for enhanced defence emerged as a defence mechanism with limited fitness costs. Because priming results in a faster and stronger activation of defence only after pathogen or insect attack, the limited costs of the primed state are often outweighed by the benefits in environments with pathogen or herbivore pressure. The balance between protection and fitness is crucial for a plant’s success and is therefore of great interest for plant breeders and farmers. By combining molecular knowledge and ecological relevance of defence mechanisms, one can gain fundamental insight into how and why plants integrate different immune signals to cope with their natural multitrophic environment in a cost-effective manne

Costs and benefits of hormone-regulated plant defences

Plants activate defence responses to protect themselves against microbial pathogens and herbivorous insects. However, induction of defences comes at a price, as the associated allocation costs, auto-toxicity costs and ecological costs form fitness penalties. Upon pathogen or insect attack, resources are allocated to defences instead of to plant growth and reproduction, while above-belowground interactions with beneficial organisms may also be disturbed. The phytohormones salicylic acid and jasmonic acid are major players in the regulation of induced defences and their associated fitness costs. Hormone-controlled signalling pathways cross-communicate, providing the plant with a finely-tuned defence regulatory system that can contribute to a reduction of fitness costs by repressing ineffective defences. However, this sophisticated regulatory system causes ecological costs, because activated resistance to one organism can suppress resistance to another. Moreover, the system can be hijacked by invading organisms that manipulate it for their own benefit. Priming for enhanced defence emerged as a defence mechanism with limited fitness costs. Because, priming results in a faster and stronger activation of defence only after pathogen or insect attack, the limited costs of the primed state are often outweighed by the benefits in environments with pathogen or herbivore pressure. The balance between protection and fitness is crucial for a plant’s success and is therefore of high interest for plant breeders and farmers. By combining molecular knowledge and ecological relevance of defence mechanisms we can gain fundamental insight into how and why plants integrate different immune signals to cope with their natural multitrophic environment in a cost-effective manner

Jasmonate signaling in plant interactions with resistance-inducing beneficial microbes.

Beneficial soil-borne microorganisms can induce an enhanced defensive capacity in above-ground plant parts that provides protection against a broad spectrum of microbial pathogens and even insect herbivores. The phytohormones jasmonic acid (JA) and ethylene emerged as important regulators of this induced systemic resistance (ISR). ISR triggered by plant growth-promoting rhizobacteria and fungi is often not associated with enhanced biosynthesis of these hormones, nor with massive changes in defense-related gene expression. Instead, ISR-expressing plants are primed for enhanced defense. Priming is characterized by a faster and stronger expression of cellular defense responses that become activated only upon pathogen or insect attack, resulting in an enhanced level of resistance to the invader encountered. Recent advances in induced defense signaling research revealed regulators of ISR and suggest a model in which (JA)-related transcription factors play a central role in establishing the primed state

Plant immune responses triggered by beneficial microbes.

Beneficial soil-borne microorganisms, such as plant growth promoting rhizobacteria and mycorrhizal fungi, can improve plant performance by inducing systemic defense responses that confer broad-spectrum resistance to plant pathogens and even insect herbivores. Different beneficial microbe-associated molecular patterns (MAMPs) are recognized by the plant, which results in a mild, but effective activation of the plant immune responses in systemic tissues. Evidence is accumulating that systemic resistance induced by different beneficials is regulated by similar jasmonate-dependent and ethylene-dependent signaling pathways and is associated with priming for enhanced defense

RNA-Seq: revelation of the messengers

Next-generation RNA-sequencing (RNA-Seq) is rapidly outcompeting microarrays as the technology of choice for whole-transcriptome studies. However, the bioinformatics skills required for RNA-Seq data analysis often pose a significant hurdle for many biologists. Here, we put forward the concepts and considerations that are critical for RNA-Seq data analysis and provide a generic tutorial with example data that outlines the whole pipeline from next-generation sequencing output to quantification of differential gene expression