Unravelling Plant-Microbe Synergy

Unravelling Plant-Microbe Synergy focuses on agriculturally important microorganisms (AIM’s) that are indigenous to soil and roots of the plant. These microbes contributing to nutrient balance, growth regulators, suppressing pathogens, alleviate stress response, orchestrating immune response and improving crop performance as they are offering sustainable and alternative solutions to the use of chemicals in agriculture. As plant microbe synergy is an enthralling subject, is multidisciplinary in nature, and concerns scientists involved in applied, and environmental microbiology and plant health and plant protection, Unravelling Plant-Microbe Synergy is an ideal resource that emphasizes the current trends of, and probable future of, microbes mediated amelioration of abiotic and biotic stress, agriculture sustainability, induced systemic tolerance and plant health protection. Unravelling Plant-Microbe Synergy discloses the microbial interaction for stress management and provides a better understanding to know the recent mechanisms to cope these environmental stresses. Unravelling Plant-Microbe Synergy bridges the gap in recent advances in the microbes interaction and rhizosphere engineering.

• Emphasizes the plant microbes interactions, induced systemic tolerance, stress responsive genes and diversity of microorganisms
• Illustrates the current impact of climate change on plant productivity along with mitigation strategies
• Provides a two-way interactive approach to both plants and microbes, and includes multi-omics approaches

• Language: English
• Publisher: Academic Press
• Release date: Oct 27, 2022
• ISBN: 9780323985321

Book preview

Chapter 1: Multiomics strategies for alleviation of abiotic stresses in plants

Dinesh Chandraa,b; Pankaj Bhattc    a Department of Biological Sciences, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India

b Govt. Inter Collge Chamtola, Almora, Uttarakhand, India

c Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN, United States

Abstract

To satisfy the food demands of the increasing global population, agricultural productivity needs to be enhanced. Earlier, crop production was improved by extensive application of chemical fertilizers and pesticides that led to severe environmental duress; however, these practices cannot be continued and we have to move toward the use of more environment-friendly practices. The main hurdle to increasing food production is abiotic stress. Among abiotic stresses, water-deficit conditions, salinity, heat waves, excessive water (flooding), heavy rains, and frost hamper agricultural productivity worldwide. Among the leading alternatives to chemical fertilizers are microbes that are already present in nature and act as growth stimulators for plant growth and also help in the easing of abiotic and biotic stresses. Microorganisms, through the production of exopolysaccharides and biofilm formation, influence the characteristics of soil. These attributes of microbes make a significant impact on sustainable agriculture. Using a variety of microbes, it is possible to manage the current world food deficit. Our aim is to provide a compilation of the advances made in understanding the mechanisms of stress alleviation in crop plants for their conversion to higher productivity. Strategies of multiomics depict that plant–microbe interactions generate a large amount of information that help in determining what is happening in real time within cells. In addition, we further demonstrate the future avenues of rhizospheric microbes in sustainable agricultural production.

Keywords

Plant–microbe interaction; Abiotic stresses; Crop productivity; Omics; Rhizosphere; Plant growth-promoting bacteria

Chapter outline

Introduction

Plant responses to abiotic stress

Abiotic stress alleviation by microbes

Drought stress

Salinity stress

Heavy metal stress

Heat stress

Microbe-mediated alleviation of abiotic stresses in plants: The omics approaches

Genomics

Transcriptomics

Metagenomics

Proteomics

Metabolomics

Induction of abiotic stress-responsive genes for stress relief by PGPB

Conclusions and future perspectives

Acknowledgments

References

Acknowledgments

The corresponding author of this chapter is extremely thankful to the staff members of GIC Chamtola, Almora, Uttarakhand, for providing a peaceful environment for writing this chapter and other necessary facilities.

Introduction

By 2050, it is predicted that there will be 9 billion people on this planet, and, to feed this spectacular number of people, food production needs to be augmented by almost 60% of its current status (FAO, 2009). If this feels like a humongous task, then we can only imagine doing this while keeping in mind that we need to achieve this using methods that are the least hazardous to our Mother Earth. Gone are the days when mindless application of chemicals and fertilizers was the answer. Time and again, debates about a sustainable approach to combat this food deficit have taken place and making use of plant–microbe interactions has come out as the most sought out solution. The main cause of diminishing agricultural productivity is abiotic stress that is a consequence of adverse climatic conditions (Grayson, 2013). A report by the FAO (2007) shows that the areas unaffected by any environmental constraint are only 3.5% of the global land area. Abiotic stresses that hamper plant growth and productivity include droughts, salinity, flooding, anaerobiosis, nutrient starvation, light intensity, low/high temperatures, and submergence (Glick, 2012; Chandra et al., 2019a, b, 2020). About 64% of the global land area is affected by droughts (water deficit), followed by cold (57%), acidic soils (15%), floods (13%), mineral deficiency (9%), and salinity (6%) (Mittler, 2006; Cramer et al., 2011). The area under dryland agriculture in the world is 5.2 billion hectares, out of which 3.6 billion hectares of land is affected by problems such as salinity, soil degradation, and erosion (Riadh et al., 2010). These problems ultimately impact the total irrigated land and consequently diminish crop yield through loss of crops (Ruan et al., 2010: Flowers et al., 2010; Qadir et al., 2014). It is extremely difficult to precisely measure agricultural loss with respect to the loss of crop production (qualitative and quantitative) and soil health by abiotic stresses (Cramer et al., 2011).

Plants have intrinsic mechanisms to sustain environmental conditions (Simontacchi et al., 2015). Alterations in external environmental conditions cause plant metabolism out of maintaining homeostasis and necessitate that plants harbor some advanced molecular mechanisms within their cellular system to lessen the negative effects of abiotic stresses (Foyer and Noctor, 2005; Gill and Tuteja, 2010). During the course of evolution, plants have gained protective mechanisms to combat adverse environmental situations and these mechanisms cause metabolic reprogramming in the cell and enable routine biophysicochemical processes, regardless of external environmental conditions (Massad et al., 2012; Yolcu et al., 2016).

Plant responses to abiotic stress

Plants have several ways to sense the changing environmental conditions and maintain their homeostasis by tolerance, avoidance, recovery, and escape mechanisms. Their responses to environmental stimuli encompass changes at the cellular, physiological, transcriptomic, genetic, and metabolic levels (Atkinson and Urwin, 2012). Plant growth and development is severely impacted by abiotic stress, thereby leading to heavy loss of global agriculture (Verma and Deepti, 2016). Drought, salinity, frost, and heat result in decreased water content within cells, followed by the simultaneous development of phenotypic, biochemical, and molecular responses to stresses (Xu and Zhou, 2006). The most important parameter in sensing abiotic stimuli is the root architecture that is supposed to be subtler and act accordingly in soils (Khan et al., 2016). At the same time, in the environment, a plant may face multiple stresses but its complexity of responses is different for each stress. These responses lead to the expression of several genes, followed by metabolic programming in cells. The abiotic stress-mitigating mechanism contains multiple stages of plant development (Meena et al., 2017). The chief mechanisms in the tolerance of abiotic stresses are defense, repair, acclimation, and adaptation. Plants are sensitive to water stress. Under drought stress conditions, peroxidation leads to negative consequences in antioxidant metabolism (Xu et al., 2014). The activity of enzymatic antioxidants (SOD, CAT, APX, GPX) varies from plant to plant under drought stress (Xu et al., 2015; Chandra et al., 2018a, 2019a, b).

After drought, salinity is another factor that causes distresses to modern agricultural practices. Nearly 33% of irrigated land and 20% of arable land are affected by salinity worldwide (Machado and Serralheiro, 2017). There are two ways that salinity exerts its effects: the first is through a higher concentration of salts that makes the soil harder, hence making the roots unable to extract water, and the second is through a higher concentration of salts that is toxic to plant cells. Plant health is affected by a higher concentration of salts in soils; therefore, cells in tissues respond differently to salinity stress (Voesenek and Pierik, 2008). McCue and Hanson (1990) observed that an increased level of salt decreases the osmotic potential of cells, which leads to iron toxicity and affects the vitality of plants by hampering plant growth and development and finally causing death. Salinity stress decreases aromatic amino acid levels and increases proline accumulation, polyols, and glycine betaine in cells. In addition, salinity stress increases antioxidant enzymes, modulation of hormones, and generation of nitric oxide (Gupta and Huang, 2014). A stressed condition changes the gene expression pattern of cells (Dinneny et al., 2008). SOS1, SOS2, and SOS3 proteins participate in the signaling pathway of SOS (Hasegawa et al., 2000).

Heat stress also affects crop productivity. Due to climate change, the global temperature is increasing, and this has a negative impact on the morphological, biochemical, and physiological properties of plants. A higher temperature reduces the seed germination rate, respiration, and photosynthesis and decreases membrane permeability (Xu et al., 2014). Heat stress also denatures the protein and causes inactivation of enzymes, loss of membrane integrity, and inhibition of protein synthesis (Mitra et al., 2021). Plants respond to heat stress by altering their primary and secondary metabolites and enhanced expressions of HSP and ROS (Iba, 2002). Plants sustain the impact of heat stress by the mechanisms of ROS scavenging, antioxidant metabolites, compatible solute accumulation, transcriptional modulation, and chaperone signaling (Wahid et al., 2007). Similarly, cod stress (freezing and chilling) retards the growth and productivity of crops and sometime even cause their death (Miura and Furumoto, 2013).

The occurrence of heavy metals is prevalent in agricultural soils. The main sources of contamination of agricultural lands are pesticides, untreated household and industrial wastewater, and organic and chemical fertilizers (Dhaliwal et al., 2020; Shah et al., 2020a, b; Zhang and Wang, 2020). In many countries, industrial units like textile, oil, tanneries, marbles, mining, sugar industry, paper, aluminum, and metal plating release a huge amount of unprocessed wastewater rich in heavy metals such as (arsenic), Ni (nickel), Pb (lead), Cr (chromium), and Cd (cadmium); eventually all these metals are transported to the soils through irrigation, and these exert destructive effects on crop growth and productivity, quality and safety of crops, and human and soil health (Gill et al., 2016). It has been observed that at a normal concentration, many metals have a nutritional requirement for all living organisms because of their involvement in homeostasis and protein synthesis and their roles as stimulator and enzymatic cofactors.

Plant morphological, physiological, and biochemical functions are impaired by a higher concentration of heavy metals. For example, accumulation of Pb causes phytotoxicity and reduced plant growth and inhibits seed germination, root elongation, seedling development, transpiration rate, chlorophyll synthesis, and protein and water content (Opeolu et al., 2010). Similarly, Ni is toxic to plants at a higher concentration and retards growth, metabolism, seed germination, and shoot and root growth and induces leaf spotting of plants. Cu is also essential for the normal functioning of plants, and its higher concentration is harmful to plant growth and impairs root growth and morphology (Sheldon and Menzies, 2005). In addition, Hg is lethal to plants and diminishes the transpiration rate, photosynthesis, chlorophyll synthesis, and water uptake (Singh et al., 2019). Among heavy metals, Cd is extremely lethal to plants and has overwhelming impacts on seed germination, nitrogen assimilation, plant height, leaf chlorosis, necrosis, antioxidative enzymes, and yield of crops (Ali et al., 2015; Javed et al., 2019; Wang et al., 2019). Because of its longer half-life, nonbiodegradable nature, and a higher retention rate, Cd is toxic to the metabolic process even at a low concentration (Tanwir et al., 2021).

A higher concentration of Cd in a soil–plant system diminishes Zn, Ca, Fe, Mg, Mn, and K uptake and translocation due to cationic competition at root uptake sites, and, as a result, oxidative stress is triggered, which leads to higher electrolyte leakage and production of hydrogen peroxide and malondialdehyde, whereas antioxidant activities are diminished (Rehman et al., 2017; Tao et al., 2020). Metal toxicity results in proline accumulation that provides stress tolerance to plants. Under metal stress, the role of proline in resisting ROS accumulation, osmotic adjustment, cytosolic pH buffer, peroxidation of cellular lipids to maintain cell membrane integrity and also act as a signaling molecule (Hossain et al., 2014). To a certain extent, plants are capable of coping with the negative impacts of oxidative damage caused by metal stress, but, beyond a threshold level, a higher concentration of Cd leads to a diminutive growth of plants (Bukhari et al., 2016). The removal of heavy metals from the environment requires a cost-effective and sustainable approach. At present, the techniques that are currently being used in remediation are extremely costly and toxic to the soil structure (Glick, 2010).

In addition to the abovementioned stresses, temperature and nutrient stress also hamper crop growth and productivity. A higher temperature distresses plant growth and damages cellular proteins, leading to cell death. Similarly, a low temperature lessens the metabolism due to inhibition of enzyme reactions and the interaction among macromolecules, thus modulating the membrane’s properties and changes in the protein structure (Andreas et al., 2012). Compared to plants that are exposed to individual stress, those exposed to multiple stresses have more beneficial impacts because a blend of stresses decreases the detrimental effects of each other, thereby enhancing the survivability of plants. In multiple stress situations that occur concurrently with field conditions, complicated mechanisms occur in plants to help them deal with promptly changing adverse conditions.

Abiotic stress alleviation by microbes

Abiotic stress as well as biotic communities restrict plant growth and development. Plants show tolerance mechanisms to abiotic stresses by two ways: (a) avoidance of the negative impacts of stress by activation of the response system and (b) use of antistress agents (biochemical compounds) produced by microbes (Schulze, 2005; Meena et al., 2017). Abiotic stress conditions exert adverse effects on plant growth and development, and these negative impacts are alleviated by plant growth-promoting bacteria (PGPB), as shown in Fig. 1.1.

Fig. 1.1

Fig. 1.1 Effects of abiotic stresses on plants and the possible role of PGPB in mitigating abiotic stresses.

Drought stress

Droughts exert a negative effect on the productivity of crops. Enhancing food security under droughts is a crucial task for crop breeders. Therefore, utilization of microbes to combat drought-induced damage in plants is the need of the hour at present. A drought is an influential cause of constraining crop growth and yield. It is anticipated that by 2050, 50% of the world’s land area will suffer from water shortage (Gupta et al., 2020). Hence, in order to ensure food security, cultivation of drought-tolerant crops is an urgent need. Several studies have demonstrated that an exogenous application of rhizobacteria and their growth-promoting traits boosts the drought tolerance of crops (Hassan et al., 2020; Huan et al., 2020).

A drought exerts its negative effects on plants by several means such as a reduced rate of photosynthesis, a low germination rate, loss of membrane integrity, and an increased production of ROS (Delshadi et al., 2017; Chandra et al., 2019a, b). PGPB improve plant growth by enhancing osmolyte production, accumulation of antioxidant photosynthetic capacity, gas exchange, relative water content, etc. under drought stress (Xiao et al., 2017; Zhang et al., 2021a, b). The previous findings of many researchers have also revealed that rhizobacteria are associated with drought tolerance (Zhang et al., 2019; Chandra et al., 2020; Goswami and Suresh, 2020). The role of PGPB in relieving drought stress and augmenting plant growth and development is summarized in Table 1.1

Table 1.1

A phytohormone such as ABA, which is produced by bacteria, is helpful in the easing of drought stress (Forni et al., 2017). Increased levels of ABA in Arabidopsis have been observed following inoculation of Phyllobacterium brassicacearum STM196, thereby decreasing the rate of transpiration in leaves (Bresson et al., 2013). Treatment of wheat seedling with Azospirillum showed a significant increase in osmotic stress tolerance because of morphological changes in the xylem structure (Pereyra et al., 2012). The reason for enhanced tolerance is upregulation of the inodole-3-pyruvate decarboxylase gene, which results in increased synthesis of IAA in inoculant cells. Similarly, Bacillus sp. is also involved in imparting drought tolerance in plants. Rhizobacteria such as Bacillus thuringiensis are stated to increase drought resistance in French lavender plants by increasing IAA production that could enhance the metabolic activities of plants and improve the physiological and nutritional status of plants (Armada et al., 2014). Under well-watered and drought-stressed conditions, rhizobacterial strains (BN-5 and MD-23) producing EPS, IAA, and ACC deaminase increase the productivity and quality of maize.

The ACC deaminase-producing strains of bacteria play a significant role in the alleviation of drought stress impact on plants. Ethylene regulates the metabolic activities of plants, and its synthesis is regulated by both abiotic and biotic environmental conditions. The phytohormone ethylene controls the homeostasis, resulting in restricted growth of the shoot and root in a stressful environment (Glick et al., 2007). Treatment of pepper and tomato with ARV8 (Achromobacter piechaudii) exhibiting ACC deaminase activity enhanced the plants’ fresh/dry weight (Mayak et al., 2004). Similarly, 5C-2 (Variovorax paradoxus)-treated plants showed enhanced plant growth and yield contributing parameters (Belimov et al., 2009). In addition, Belimov et al. (2015) also reported that in both water-deficit and well-watered conditions, ACC deaminase and auxin-producing rhizobacteria improved the growth and yield of potatoes. Hence, it is believed that execution of rhizobacteria in drought-impacted soils offers a cost-effective strategy for viable crop health as well as yield of crops.

Our study also demonstrated that treatment with Variovorax paradoxus RAA3 and a consortium of four strains of Pseudomonas spp. (DPC12, DPB13, DPB15, and DPB16) producing ACC deaminase significantly augmented wheat growth under rain-fed conditions via increased nutrient concentration and antioxidant potential (Chandra et al., 2019a). In another study, we also noticed that when wheat drought and sensitive variety treated with ACC deaminase producing strain of Pseudomonas palleroniana DPB16, Pseudomonas sp. UW4, and Variovorax paradoxus RAA3 enhanced the growth, yield and nutritional content under drought and rainfed conditions (Chandra et al., 2019b). Microorganisms secrete salicylic acid (SA) that is involved in the regulation of plant growth and development as well as in plant drought response. SA also acts as a signaling molecule and induces the expression of several genes that are involved in the synthesis of antioxidants, chaperones, HSPs, enzymes, and secondary metabolites under stress conditions (Kumar et al., 2019).

Salinity stress

Various PGPR genera including Acetobacter, Achromobacter, Aeromonas, Azospirillum, Bacillus, Bradyrhizobium, Chryseobacterium, Flavobacterium, Pseudomonas, Sinorhizobium, etc. have been demonstrated to increase the productivity of different crops in salt-affected soils. The chemotactic, ACC deaminase, and IAA attributes of bacteria can battle with different stresses including salinity stress (Glick, 1995). Rhizobacteria can induce induced systemic tolerance (IST) to fight against the changes in plants and to develop tolerance mechanisms in plants against salinity stress (Yang et al., 2009). Beneficial microorganisms are extremely helpful in solving the problem of salinity. Several PGPB have been described to inhabit plant roots and diminish the impact of salinity and salt stress by different mechanisms as summarized in Tables 1.2 and 1.3.

Table 1.2

Table 1.3