Molecular Aspects of Plant Beneficial Microbes in Agriculture

Vivek Sharma, Richa Salwan, Laith Khalil Tawfeeq Al-Ani

• Publisher: Academic Press
• Year: 2020
• Print ISBN: 9780128184691
• eBook ISBN: 9780128184707
• Topic: Technology & Engineering
• Subtopic: Agriculture
• Index: Technology & Engineering

Molecular Aspects of Plant Beneficial Microbes in Agriculture explores their diverse interactions, including the pathogenic and symbiotic relationship which leads to either a decrease or increase in crop productivity. Focusing on these environmentally-friendly approaches, the book explores their potential in changing climatic conditions. It presents the exploration and regulation of beneficial microbes in offering sustainable and alternative solutions to the use of chemicals in agriculture. The beneficial microbes presented here are capable of contributing to nutrient balance, growth regulators, suppressing pathogens, orchestrating immune response and improving crop performance.The book also offers insights into the advancements in DNA technology and bioinformatic approaches which have provided in-depth knowledge about the molecular arsenal involved in mineral uptake, nitrogen fixation, growth promotion and biocontrol attributes.- Covers the molecular attributes of biocontrol, PGPR and mycorrhizal associations involved in the three-way interaction between beneficial microbes-host-pathogen- Explores the role of technological interventions in exploring molecular mechanisms- Provides detailed and comprehensive insights about recent trends in the use of microbial genetic engineering for agricultural application

Chapter 1

Overview and challenges in the implementation of plant beneficial microbes

Vivek Sharma¹, Anu Sharma¹ and Richa Salwan², ¹University Centre for Research and Development, Chandigarh University, Sahibzada Ajit Singh Nagar, India, ²College of Horticulture and Forestry (Dr. Y. S. Parmar University of Horticulture & Forestry) Neri, Hamirpur, India

Abstract

The beneficial microbiome associated to plants have remarkable prospective to expand the plant resilience and crop yields in an agriculture system. Considerable evidences on the role of plant beneficial microbes on altering the morphology of plant, manage pests and enhancing growth and immunity of plants and positive impact on mineral acquisitions are available. In recent times, advancements in DNA sequencing and editing techniques, played vital role in understanding the influence of the microbiomes both at endosphere and rhizosphere level in model plants such as Arabidopsis thaliana as well as in agriculturally important crops. Different plant beneficial microorganisms, solubilize mineral and nutrients in the soil, mitigate resistance to environmental stresses, suppress pathogens, improve plant growth and yield, therefore can be a potential alternate to increase agricultural productivity. Understanding the microbiome beneficial behavior with associated plants can offer a viable solution to enhance the agricultural production, which can minimize fertilizers use and biofungicides in agricultural fields. Although the bioformulations of plant beneficial microorganisms and their products are extensively explored to facilitate their use for a sustainable and enhanced crop productivity. However, prior to extensive usage of these plant assisting microorganisms, their efficiency and reliability to perform under a wide range of environmental conditions, need to be evaluated. It need intensive efforts among researchers, industrial partners and agriculturalists, to understand and implement the plant beneficial microbes in modern agricultural systems need careful address of several issues. This book chapter, provides an overview of plant beneficial microorganisms including plant growth promoting rhizobacteria, biocontrol agents and mycorrhiza.

Keywords

Microbiome; Biocontrol; Plant probiotics; Plant growth Rhizobacteria; Challenges

Chapter outline

Outline

• 1.1. Introduction 1
• 1.2. Soil microbiome and its significance 2
• 1.3. Plant microbiome and its potential 4
• 1.4. Methods to investigate the composition of root exudate 5
• 1.5. Diversity of the inoculum 5
• 1.6. Role of omic technologies and modeling tools in plant microbiome 5
• 1.7. Functional aspects of plant beneficial microorganisms 6
• 1.8. Plant beneficial microbiome in soil 7
• 1.9. Plant beneficial microbiome in agricultural crops 7
• 1.10. Microbes mediated plant salt tolerance 7
• 1.11. Holistic view of plant, microbiome and environment interactions 8
• 1.12. Public interest and the future of plant beneficial microbiome 9
• 1.13. Conclusion 10
• References 11
• Further reading 18

1.1 Introduction

At present, agricultural farming uses 75% of total fresh water and that usage can be alarming in the coming days, if inclinations in population size and contemporary methods of farming continue (Molden et al., 2007). However, emphasis to enhance the food production to cope up with growing worldwide food requirements for perpetually growing human population generates severe ecological vulnerabilities, such as deficiency of water and salinity (Golldack et al., 2014) and extensive usage of chemicals in the form of fertilizers and pesticides. These parameters have intensified and impose main threats to our ecosystem and agricultural production (Trenberth et al., 2014; Lakshmanan et al., 2017). Plant beneficial microorganisms are an attractive alternative for sustainable and enhanced growth (Chaparro et al., 2013). The use of beneficial microbes in agriculture was largely underutilized in 18th century, however, U.S. Department of Agriculture endorsed the inoculation rhizobium for legume crops, after the experimental demonstration of their role in fixing nitrogen (Schneider, 1892). In last few years, a number of individual microbes have been explored for their role in plant growth promotion, N & P uptake (Afzal and Bano, 2008), and combating disease resistance (Harman et al., 2004; Sharma et al., 2017a,b; Sharma, et al., 2018a,b). Mostly, these efforts were limited to individual microbial strains (Sharma et al., 2012; Sharma et al., 2016a,b; Busby et al., 2017; Salwan et al., 2019).

Beneficial microorganisms can help in nutrient acquisitions such nitrogen from atmosphere, irons and from soil inhibit plant pathogens, and secrete metabolites which can augment the plant growth (Singh et al., 2011). These microorganisms represent comprehensive range of microorganisms including nitrogen-fixing bacteria both as symbiotic (Mendes et al., 2013) or free living, plant growth-promoting rhizobacteria (PGPR), and fungi involve in mycorrhizal associations (Mendes et al., 2013; Arora et al., 2016), as well as biocontrol agents (Sharma et al., 2012; Sharma et al., 2016a,b; Sharma et al., 2017a,b; Sharma et al., 2018a,b). Different members of bacteria including Azotobacter, Azospirillum, Bacillus spp, Pseudomonas fluorescence, Rhizobium, Frankia and other members of actinobacteria are termed as PGPR, due to their growth promoting effect the plants (Nadeem et al., 2014). The plant beneficial fungal counterpart such as Trichoderma strains (Sharma et al., 2012; Sharma et al., 2016a,b; Sharma et al., 2017a,b; Sharma et al., 2018a,b) also suppress the pathogens their antagonistic activity by producing lytic enzymes (Sharma et al., 2012; Sharma & Shanmugam, 2012, Sharma et al., 2016a,b, 2017a,b; Sharma et al., 2018a,b) and secondary metabolites, promotes the plant growth through growth regulator production (Bhattacharyya and Jha, 2012) and enhance the plant immunity. The other benefits of these plants beneficial microorganisms involves increase in the formation of secondary roots, roots elongation, assisting nutrient acquisition, and suppression of the plant pathogens (Ali et al., 2014; Bashan et al., 2014; Arora et al., 2016). The other benefits competition for space, antibiotic production, symbiotic association in soil (Kloepper et al., 1980; Kilian et al., 2000; Avis et al., 2008) or phylloplane (Araujo et al., 2005; Raaijmakers and Mazzola, 2016; Arora et al., 2016) and even alleviate salt stress tolerance in crops (Egamberdieva et al., 2013; Nadeem et al., 2014). The role of microbiomes to augment crop production is prehistoric and evidences can be found back to $300 BCE (Vessey, 2003). The first industrial bioinoculant. ‘nitrogin’, patented during the microbiology golden age in 1896 and past the Haber–Bosch method by 15 years (Sahoo et al., 2013). Currently, the Organic Materials Review Institute (OMRI) (https://www.omri.org/omri-lists) lists over 170 ‘microbial inoculants’ and more than 274 as ‘microbial products’, for crop fertilizers or crop management (Finkel et al., 2017)

Nearly 45 million hectares of worldwide irrigated area is saline which limit the plant growth and hence decreases crop production (Munns and Tester, 2008). The effect of plant beneficial microorganisms against salinity is well documented. For example, Bacillus amyloliquefaciens a plant growth promoting rhizobacteria, improve the plant growth in rice (Nautiyal et al., 2013). Similar to this, inoculation of Azotobacter chroococcum, enhance the plant biomass in maize under salt stress (Rojas-Tapias et al., 2012). The combination of rhizobia and Pseudomonas spp. improved negative effect of salt stress in Galega officinalis plants (Egamberdieva et al., 2013; Arora et al., 2016). On the other side, biocontrol agents are gaining attentions for plant diseases and pest managements and offers resilience to biotic and abiotic stresses (Mendes et al., 2013; Weller et al., 2002). Four categories of biocontrol systems; i- natural, ii-conservation, iii-classical, and iv-augmentative biological control are defined in the literature (Eilenberg et al., 2001; Cock et al., 2010). In natural biocontrol works without human involvement and here, pest/pathogens are managed using naturally prevailing beneficial organisms (Waage and Greathead, 1988). The second conservation based biocontrol system, involves human actions which defend and arouse the performance of prevailing natural enemy. In third category, natural enemies collected from one area are released ...

Table of contents

• Cover image
• Title page
• Table of Contents
• Copyright
• List of contributors
• Chapter 1. Overview and challenges in the implementation of plant beneficial microbes
• Chapter 2. Plant beneficial microbes: do they have a role as antiviral agents in agriculture?
• Chapter 3. Multilegume biofertilizer: a dream
• Chapter 4. The effect of incompatible plant pathogens on the host plant
• Chapter 5. Language of plant-microbe-microbe interactions in rhizospheric ecosystems
• Chapter 6. Application and biological impact of endophytic bacteria as IAA producers
• Chapter 7. Molecular aspects of biocontrol species of Streptomyces in agricultural crops
• Chapter 8. Root exudates, a key factor in the plant-bacteria interaction mechanisms
• Chapter 9. Insight into plant-bacteria-fungi interactions to improve plant performance via remediation of heavy metals: an overview
• Chapter 10. Signaling pathway of induced systemic resistance
• Chapter 11. Role of fungal elicitors in plant defense mechanism
• Chapter 12. Versatility of Trichoderma in plant disease management
• Chapter 13. Knock, knock-let the bacteria in: enzymatic potential of plant associated bacteria
• Chapter 14. Beneficial role of viruses in plants
• Chapter 15. Microbial phytases in plant minerals acquisition
• Chapter 16. PGPR secondary metabolites: an active syrup for improvement of plant health
• Chapter 17. Volatile organic compounds mediated plant-microbe interactions in soil
• Chapter 18. Molecular mechanisms in plant growth promoting bacteria (PGPR) to resist environmental stress in plants
• Chapter 19. Biogeographic distribution of chickpea rhizobia in the world
• Chapter 20. Arbuscular mycorrhiza, a fungal perspective
• Chapter 21. Engineering bacterial ACC deaminase for improving plant productivity under stressful conditions
• Chapter 22. Role of rhizobacteria in alleviating salt stress
• Chapter 23. Nematophagous and entomopathogenic fungi: new insights into the beneficial fungus-plant interaction
• Chapter 24. Secondary metabolites and lytic tool box of trichoderma and their role in plant health
• Chapter 25. Endophytic fungi: positive association with plants
• Chapter 26. Using molecular techniques applied to beneficial microorganisms as biotechnological tools for controlling agricultural plant pathogens and pest
• Chapter 27. CRISPR/Cas9 mediated genome engineering in microbes and its application in plant beneficial effects
• Chapter 28. Understanding the molecular basis of the tripartite interaction between host-pathogen-bioagent through proteomic approach
• Chapter 29. Frankia and the actinorhizal symbiosis
• Chapter 30. Advances in Frankia genome studies and molecular aspects of tolerance to environmental stresses
• Chapter 31. Tripartite interactions between plants, trichoderma and the pathogenic fungi
• Chapter 32. Applications of agriculturally important microorganisms for sustainable crop production
• Chapter 33. Beneficial microorganisms in the remediation of heavy metals
• Index