Plant-Microbe Interactions: A Comprehensive Review

The co-evolution of plants and their associated diverse microorganisms has been a field of wide scientific research since the past. However, the ecological relevance of such co-evolution has recently been realized. According to the theories of evolution, ‘survival of the fittest’ has been an age-old fundamental concept, where every organism modifies itself to adapt to its changing environment while sustaining its vital processes. Understanding the interactions at the molecular level between the stationary plants and their diverse interacting partners has not only helped in deciphering the basis of evolution but also provided a better outlook towards the multidimensional interactions between the organisms of the plant microbiome. Ideally plant ‘holobiont’ comprises the host and all microbial partners of its different locations such as the rhizosphere, endosphere, and phyllosphere. The behavioral patterns of the microbes with their hosts located at different zones designate them as symbionts, commensals, and/or pathogens. Each type of relationship has its basis of establishment and evolution. The present study aims to explain the basis of the evolution of plantmicrobe interaction ranging from symbiosis to parasitism and understanding its evolutionary dynamics from an ecological perspective. Besides, the study shall also explain the role of microbiome in plant-microbe interaction and its ecological significance when subjected to climatic undulations. Overall, the study aims to put forth a comprehensive outlook on the understanding of ecology-driven evolutionary changes of plant-microbe interaction and its relevance in the present age of climate change.

Biotic stress imposes several detrimental effects such as nutritional and physiological imbalance that subsequently leads to a huge yield loss of crop plants. Climate change and rapid urbanization also act as positive catalysts for the prevalence of biotic stressors. Acquiring the knowledge of dynamic rhizosphere and phyllosphere microbes has opened a new horizon of eco-friendly, economical biotic stress management of plants that can also overcome the drawbacks of traditional agricultural practices. Plant growth-promoting rhizobacteria (PGPR) are potent biocontrol agents that can mitigate biotic stress by several mechanisms such as by modulating plant growth regulators, producing extracellular polysaccharides (EPS), up-regulating defence responsive genes, and stimulating Induced Systemic Resistance (ISR), which subsequently increase plant productivity and stress tolerance. Moreover, with respect to above-ground plant-microbe interaction i.e. Phyllosphere microbial communities (PMC) have immense potential to ameliorate biotic stress by modulating phytohormone and changing existing microbial communities. Even though, our knowledge about these hyper-diverse beneficial plant-microbe interactions is still illusive. In this chapter, we have critically analyzed the role of PGPR and PMC in biotic stress management, in light of promoting this agricultural practice on a large scale.

Plants are the most important constituents of our environment. Despite their function in producing energy by capturing photons from sunlight, they are the only source of atmospheric oxygen by the process of photosynthesis. Since the last 100 years, a huge amount of agrobiodiversity has been lost and many are at risk of extinction. The existing crop plants are also at the constant threat of different biotic and abiotic stress factors. Every year yield of the agricultural crops is curtailed dramatically by changing environmental pressure and associated pathogenic ingression. Many works are carried out in this field to demonstrate defense signaling in plants in response to either biotic or abiotic interactors. Artificial neural networking (ANN) system is a revolutionizing bioinformatic technology that can predict any problem with maximum logic depending on the weights given in different situations. The application of this ANN in predicting biological networks will be capable of changing the scenario of plant infection biology completely. In such context, the present article intends to demonstrate basic ANN and their probable application in future plant-microbe interactions to develop a sustainable agrosystem.

Rice is one of the highest consumed food gains in the world and is a key commercial product in the world economy. However, recurring outbreaks of viral diseases in rice lead to a significant loss of yield and economy in several Asian, African, and Latin American countries. Mixed virus infections are common in field conditions. They often lead to synergistic enhancement of the pathogenicity of one or both infecting viruses. However, in certain cases, antagonistic interaction between the viruses leading to the suppression of infectivity of one by the other virus has also been reported. Out of all rice-infecting viruses, 4 pairs of viruses are known for being involved in mixed infection, where symptom development and pathogenicity of the diseases get synergistically enhanced. Rice tungro disease is one of the most wellknown diseases in this category that occurs due to simultaneous infection by the Rice tungro spherical virus and Rice tungro bacilliform virus and is responsible for major economic losses in South and Southeast Asia. On the other hand, mixed infection by Southern rice black-streaked dwarf virus and Rice ragged stunt virus came into the picture rather recently. Interestingly, all the mixed virus infections in rice are transmitted by insect vectors. Therefore, elucidating the complex interactions between the host-virus-vector pathosystems is pivotal for finding ways to control both single and mixed virus infections in rice.

This book chapter explores the complex landscape of pathogens affecting legumes and the biotechnological strategies employed for their mitigation. Focusing on diverse biotic stresses, including fungi, bacteria, and nematodes, the chapter underscores the complex interactions between legumes and microbial pathogens. The application of advanced biotechnological tools such as marker-assisted selection (MAS), quantitative trait loci (QTLs) mapping, and transgenic techniques has shown promising outcomes in bolstering resistance against these threats. Despite the considerable progress in understanding and managing legume pathogens through biotechnological interventions, crucial research gaps persist. The identified areas for future exploration include a deeper understanding of molecular mechanisms governing plant-pathogen interactions, continuous efforts to identify emerging or less-studied pathogens, ensuring long-term durability of resistance, integrating multi-omics approaches for a holistic understanding, and bridging the gap between laboratory findings and practical field applications. Addressing these research gaps will not only contribute to more effective and sustainable strategies for mitigating legume diseases but also play a pivotal role in ensuring global food security and agricultural sustainability.

Pigeonpea (Cajanus cajan (L.) Millspaugh) is the seventh most economically important legume crop in the world, cultivated on 6.09 million hectares of land across the world with 5.01 million tonnes of global productivity. Fusarium udum Butler is responsible for vascular wilt, the most devastating pigeon pea disease throughout the world. Management of Fusarium-wilt through cultural practices is not effective enough, and chemical control methods cause the killing of non-target beneficial soil microorganisms. Biological practices using various antagonistic fungi or microorganisms are found to be more effective than other practices. Expression analysis and molecular characterization of various biotic and abiotic stress-related molecular factors have been established in order to understand the host defense response mechanism. Development of disease-resistant cultivars through markerassisted breeding programs is restricted due to insufficient genome resources, pathogenic variability, and location-specific occurrence and behavior of pathogenic isolates. Marker-assisted breeding through the introgression of resistance (R) genes is difficult to achieve in pigeon pea, as mapping of R genes was not completed in the recent past. Therefore, understanding molecular factors and signaling pathways associated with disease resistance or susceptibility is supposed to be helpful in finding out future directions for wilt management. Whole genome sequencing, transcriptome profiling through cDNA, AFLP and NGS, etc., are convenient methods to recognize the mechanism of host defense and defense regulatory pathways during Fusarium-wilt. The recent availability of pigeonpea whole genome sequence and transcriptome-wide marker resources and molecular characterization of disease-responsive molecular factors can efficiently be utilized for accelerating resistant breeding programs.

Tomato is a nutrient-rich vegetable crop plant consumed worldwide. Tomato is a fruit-bearing crop plant of the Solanaceae family. This plant harbors diverse microbes in its rhizosphere, phyllosphere, and endosphere, of which, beneficial microbes can promote their growth, and harmful pathogens can cause various diseases and play a crucial role in determining their overall growth, development, and fitness. Since the plant is being colonized by both beneficial and harmful microbes, the tomato has become an excellent model system for the study of plant-microbe interactions. Besides, their yield is limited due to several pathogen attacks. Therefore, it is crucial to understand both the disease biology and the interaction of beneficial microbes with the tomato plant to obtain extensive knowledge which would ultimately help to find out the possible mechanisms for controlling diseases in tomatoes as well as other Solanaceae crops like potatoes, eggplant, etc. for sustainable agriculture. Here in this chapter, we will discuss the details of the biology of the interaction of both the beneficial and harmful microbes with the tomato plant.

Nitrogen is one of the most abundantly available elements in the atmosphere, but it is not available in a biologically utilizable form. In nature, lightning storms and biological nitrogen fixation (BNF) by prokaryotes are responsible for converting the inorganic atmospheric nitrogen into forms that can be utilized by biological systems. The process of BNF occurs only in prokaryotes expressing the enzyme nitrogenase. Some plants, like legumes and a few non-legumes, can form symbiotic relationships with specific nitrogen-fixing bacteria, forming a specialized organ called nodules. Low oxygen content inside the nodules and easy access to sugars from the host plant help the bacteria in expressing nitrogenase. The host plant in turn benefits by utilizing the fixed nitrogen. Most of the staple food crops do not have the capacity to form nodules for harbouring nitrogen-fixing microbes; further, the increase in population has compounded the intensity of cultivation across agroecosystems. Hence, nitrogen becomes limiting for crop plants and it becomes imperative to encourage sustainable methods like BNF for providing N. Synthetic fertilizers used presently by the farmers, are a major cause of pollution. In such a scenario, the associative, endophytic, and free-living nitrogen fixers or biotechnological interventions hold the key to providing pollution-free nitrogen to these crop plants. In this chapter, we will discuss the diversity of nitrogen-fixing systems and the methods of assessing and utilizing these microbes for crop benefit.

In natural ecosystems, macronutrients and micronutrients are present as complexes with organic or inorganic molecules in soil, and hence bio-availability of both is low. Plants depend on microbes to improve the availability of nutrients. Microorganisms increase nutrient uptake by plants through siderophore production or mineralization or solubilization activity. Microbes depolymerize and mineralize complexes using their metabolic pathways. Subsequently, these minerals are released into the soil in soluble form. Mycorrhizal fungi, bacteria, fungi present in the rhizosphere soil, and bacterial and fungal endophytes contribute to plant nutrient acquisition and are referred to as plant microbiomes. Research on plant-microbe interactions has shown that plant-associated microbes are recruited by plants and are influenced by soil type and plant genome. Conversely, microorganisms show adaptations to survive in the rhizosphere of a particular plant. This chapter focuses on plant-microbe interactions and mechanisms underlying the nutritional benefits that plants receive from the rhizosphere microbiome.

Soil salinization results in the continuous reduction of agricultural land worldwide. Salinity, a major abiotic stressor, adversely affects plant growth and development by interfering with various physiological, biochemical, and molecular processes. These processes include nutrient imbalance, osmotic stress, ionic stress, oxidative stress, membrane destabilization, reduced photosynthetic capacity, protein synthesis, energy and lipid metabolism, DNA replication, protein metabolism, and cell division. Despite the rapid increase in the global population, food production is not sufficient to meet the challenges posed by such growth. In this context, salt-tolerant plant growth-promoting rhizobacteria (ST-PGPR) may play a crucial role in sustainable agriculture to meet the ever-increasing demand for food. ST-PGPR can enhance plant growth, development, and productivity by producing phytohormones, 1- aminocyclopropane-1-carboxylate deaminase (ACC) activity, phosphate solubilization, exopolysaccharide (EPS) production, siderophore production, biological nitrogen fixation, and the synthesis of compatible solutes, among other mechanisms. The generation of reactive oxygen species (ROS) at low concentrations is a natural phenomenon, but at elevated levels, they can cause oxidative damage. Salinity-induced osmotic stress and ionic stress lead to the overproduction of ROS, which, at severe levels, can result in cell and plant death. ST-PGPR can mitigate the overproduction of ROS under saline stress, thereby protecting the plant from oxidative damage. In this discussion, we shed some light on salt stress sensitivity, the impact of salinity, the role of salt-tolerant PGPR, and their mechanisms in promoting plant growth, antioxidant defense, osmotolerance, and ion homeostasis under saline conditions, enabling plants to mitigate salt stress.