Plant—Microbe Interaction under Climate Change

Introduction to a Virtual Special Issue on cell biology at the plant-microbe interface.

Summary Plants have a complex immune system that defends them against attackers (e.g. herbivores and microbial pathogens) but that also regulates the interactions with mutualistic organisms (e.g. mycorrhizal fungi and plant growth‐promoting rhizobacteria). Plants have to respond to multiple environmental challenges, so they need to integrate both signals associated with biotic and abiotic stresses in the most appropriate response to survive. Beneficial microbes such as rhizobacteria and mycorrhizal fungi can help plants to ‘deal’ with pathogens and herbivorous insects as well as to tolerate abiotic stress. Therefore, beneficial microbes may play an important role in a changing environment, where abiotic and biotic stresses on plants are expected to increase. The effects of beneficial microbes on herbivores are highly context‐dependent, but little is known on what is driving such dependency. Recent evidence shows that abiotic stresses such as changes in soil nutrients, drought and salt stress, as well as ozone can modify the outcome of plant–microbe–insect interactions. Here, we review how abiotic stress can affect plant–microbe, plant–insect and plant–microbe–insect interactions, and the role of the network of plant signal‐transduction pathways in regulating such interactions. Most of the studies on the effects of abiotic stress on plant–microbe–insect interactions show that the effects of microbes on herbivores (positive or negative) are strengthened under stressful conditions. We propose that, at least in part, this is due to the crosstalk of the different plant signalling pathways triggered by each stress individually. By understanding the cross‐regulation mechanisms we may be able to predict the possible outcomes of plant‐microbe–insect interactions under particular abiotic stress conditions. We also propose that microbes can help plants to deal with insects mainly under conditions that compromise efficient activation of plant defences. In the context of global change, it is crucial to understand how abiotic stresses will affect species interactions, especially those interactions that are beneficial for plants. The final aim of this review is to stimulate studies unravelling when these ‘beneficial’ microbes really benefit a plant.

Plants in their natural environment are facing large numbers of pathogenic microorganisms, mainly fungi and bacteria.[…].

Abiotic stresses are important limiting factors that limit the yields of crops. Plants need to develop such mechanisms that help in dealing with the harsh environment and soil health. Medicinal plants are important due to their medicinal, aesthetic, and bioactive phytochemical characteristics. Microorganisms display metabolic abilities to reduce stress in diverse environments. The beneficial microbes reside outside or inside plant tissues and perform numerous activities that control phytopathogens. They also include plant growth-promoting bacteria, such as endophytes present in the rhizosphere and phyllosphere. As microbes are the natural partners of plants, they ameliorate the effect of a harsh environment. Plant–microbe interaction is essential for the ecosystem. Plant–microbe interaction encompasses the complex mechanism inside the cell. Physiological, biochemical, and molecular studies help understand the complicated and integrated processes of plant–microbe interaction. Due to environmental changes and incessant stress, it is very important to distinguish and access information on plant–microbe interaction concerning defense against abiotic stresses. Multi-omics studies about plant–microbe interaction and their environment provide a deeper insight and provide multi-layered information that has a substantial chance for practical execution. In this chapter, we review the structure and function of microbiota, the physiological and molecular response of plant and microbiota against stress, and microbe-mediated mitigation of abiotic stresses. Additionally, how plant root exudates attract microbes that play a role in biological control has also been reviewed.

Plant mutualistic association with various beneficial microbes is referred to as the plant enhancer microbiome. These microbes are found either in episphere or endosphere of the plant tissues. Several pieces of evidence have highlighted that plant microbiomes and soil play a pivotal role in making soil nutrient balance which is readily available to plants and provide strength under various stresses. Recently different technologies relevant to plant microbiome and diversity such as sequencing technologies, metagenomics, and bioinformatics have been utilized. Knowledge about factors that shape the composition of plant microbes is still less explored. Here, current insights into the issues driving the above/below plant microbial diversities are explored. Primarily, we address the distribution of microbial communities above and below ground across plant habitats that has benefitted plants. Microbial communities are efficient regulators of biogeochemical cycle which is a better approach to mitigate changing climatic patterns aids in proper utilization of greenhouse gases for their metabolic mechanisms. The present review is thereby significant for assessing microbiome mitigation toward climate change and multiple avenues of plant- microbe interaction under commuting climatic scenario. Finally, we summarize factors that promote the structure and composition of the plant microbiome.

Chapter 20 - Plant-microbe interactions in photosynthesis, nutrient acquisition, and plant growth

Soil constitutes a wide range of microorganisms, both beneficial and harmful. Although the plant and microbial community have distinct differences with regard to their characteristics, their interaction may hold benefits for the agro-ecological system. This chapter's topic of discussion sheds light on the various plant-microbe interactions in the rhizosphere and phyllosphere, as well as in the soil environment. This mayenhance crop production in an indirect manner by inducing or enhancing various factors of crop production. Despite the fact that plant-microbe interaction may lead to both beneficial and harmful effects, still this interaction contributeshugely to a healthy and sustainable agroecosystem. The role of plant-microbe interaction in the fixation of nutrients, nutrient dynamics, and crop growth, as well as resistance to biotic and abiotic stresses are inevitable to have detailed research and study on their different aspects. This chapter will help the reader to have a brief and compiled idea on the interaction between plants and microbes.

Not a peripheral issue: secretion in plant–microbe interactions

In silico encounters: harnessing metabolic modelling to understand plant–microbe interactions

The process of plant immune response is orchestrated by intracellular signaling molecules. Since plants are devoid of a humoral system, they develop extensive mechanism of pathogen recognition, signal perception, and intricate cell signaling for their protection from biotic and abiotic stresses. The pathogenic attack induces calcium ion accumulation in the plant cells, resulting in calcium signatures that regulate the synthesis of proteins of defense system. These calcium signatures induct different calcium dependent proteins such as calmodulins (CaMs), calcineurin B-like proteins (CBLs), calcium-dependent protein kinases (CDPKs) and other signaling molecules to orchestrate the complex defense signaling. Using advanced biotechnological tools, the role of Ca2+ signaling during plant-microbe interactions and the role of CaM/CMLs and CDPKs in plant defense mechanism has been revealed to some extent. The Emerging perspectives on calcium signaling in plant-microbe interactions suggest that this complex interplay could be harnessed to improve plant resistance against pathogenic microbes. We present here an overview of current understanding in calcium signatures during plant-microbe interaction so as to imbibe a future direction of research.

SummaryPlant microbiomes have the potential to mitigate the impacts of climate change, yet both the complexity of climate change and the complexity of plant–microbe interactions make applications and future predictions challenging. Here, we embrace this complexity, reviewing how different aspects of climate change influence beneficial plant–microbe interactions and how advances in theory, tools, and applications may improve understanding and predictability of climate change effects on plants, microbiomes, and their roles within ecosystems. New advances include consideration of (1) interactions among climate stressors, such as more variable precipitation regimes combined with warmer mean temperature; (2) mechanisms that promote the stability of microbiome functions; (3) legacies of stress affecting the functionality of microbial communities under future stress; and (4) temporally repeated plant–microbe interactions or feedbacks. We also identify key gaps in each of these areas and spotlight the need for more research bridging molecular biology and ecology to develop a more mechanistic understanding of how climate change shapes beneficial microbe–plant interactions.

Optimistic contributions of plant growth-promoting bacteria for sustainable agriculture and climate stress alleviation

Chapter 7 - Emerging approaches to manipulate the plant microbiome and implications

Plants constantly monitor and cope with the fluctuating environment while hosting a diversity of plant-inhabiting microbes. The mode and outcome of plant-microbe interactions, including plant disease epidemics, are dynamically and profoundly influenced by abiotic factors, such as light, temperature, water and nutrients. Plants also utilize associations with beneficial microbes during adaptation to adverse conditions. Elucidation of the molecular bases for the plant-microbe-environment interactions is therefore of fundamental importance in the plant sciences. Following advances into individual stress signaling pathways, recent studies are beginning to reveal molecular intersections between biotic and abiotic stress responses and regulatory principles in combined stress responses. We outline mechanisms underlying environmental modulation of plant immunity and emerging roles for immune regulators in abiotic stress tolerance. Furthermore, we discuss how plants coordinate conflicting demands when exposed to combinations of different stresses, with attention to a possible determinant that links initial stress response to broad-spectrum stress tolerance or prioritization of specific stress tolerance.

The use of organic and inorganic fertilizers excessively to enhance soil fertility and crop productivity in the quest towards food security achievement has resulted in detrimental environmental effects, water and soil pollution and ecosystem imbalance. Exploitation of eco-friendly beneficial microbes, emerging microbial bioengineering technologies and the identification of novel microbial gene resources which can be used in transgenic and designer plant technologies for efficient nutrient management have been touted to be the next transformational revolution in food security and mitigation of agro-environmental degradation. Research studies in this direction have demonstrated that these plant–microbe interaction technologies can enhance plant uptake of nutrients, increase the use efficiency of organic and inorganic fertilizers and a decrease in farming cost. The focus of this chapter is on recent findings in areas of plant–microbe interaction for nutrient management, major beneficial microbes, their mechanism of action and plant–microbe interactions using transgenic technologies for efficient nutrient use.