1
Plant Microbiome : Past, Present and Future

Akhilendra Pratap Bharati1, Ashutosh Kumar2, Sunita Kumari2, Anjney Sharma1, Prem Lal Kashyap3, Sudheer Kumar3, Madhumita Srivastava4, and Alok Kumar Srivastava1

1 ICAR-National Bureau of Agriculturally Important Microorgansims, Mau, Uttar Pradesh, India

2 ICAR-Indian Institute of Seed Science, Mau, Uttar Pradesh, India

3 ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, Haryana, India

4 Sunbeam College for Women, Varanasi, Uttar Pradesh, India

1.1 Introduction

The evolution on earth have revealed the association of microbes to a plant and its specific tissue or organs (Compant et al. 2019; Hardoim et al. 2015; Reinhold-Hurek et al. 2015; Spinler et al. 2019; Uroz et al. 2019; Vorholt 2012). Plant microbiome encloses all associated plant microbes, whether phyllospheric, rhizospheric, or endospheric (all microbial genomes) (Brader et al. 2017; Lemanceau et al. 2017). Revealing of plant microbiome functionality has led to knowledge about plant microbe interactions, which are advantageous for plant growth and its production. The demographic, environmental, climatic, and man-made conditions have made crop production very challenging (Asl 2017; Kanianska 2016; Templeton and Scherr 1999). Microorganisms have been shown very advantageous in sustainable crop production. They have shown potential as biofertilizers, biopesticides, and growth enhancers (Bhardwaj et al. 2014; Cheng et al. 2017; Gopalakrishnan et al. 2015; Goswami et al. 2019; Kashyap et al. 2017b; Kushwaha et al. 2019a; Marrone 2019; Mendes et al. 2013; Mitter et al. 2016; Singh et al. 2019b). They have proven good alternatives compared with chemical products as excessive use of these can affect the harmony and microbiota of plant, which may lead to disintegration of soil fertility and quality (Lemaire et al. 2014; Marenya and Barrett 2009; Vorholt et al. 2017). There are number of inoculants proposed by the researchers, but with limited success in the field (Müller et al. 2016; Souza et al. 2015). Manipulation of the plant microbiome has the potential to improve crop production, reduce plant diseases (Andrews 1992; Bloemberg and Lugtenberg 2001; Hegazi et al. 2019; Singh et al. 2019a) and greenhouse gas emission and chemical inputs (Adesemoye et al. 2009; Cheng et al. 2017; Marrone 2019; Singh et al. 2010). In addition to this, it is important for nutrient cycling (the global biogeochemical cycle) also (Philippot et al. 2009).

Almost all the plants host a microbial community, including bacteria, archaea, fungi, and blue green algae. The rhizospheric microbiome includes microbes associated with the roots along with the soil. The phyllospheric microbiome includes the plant arial surface microbes, whereas the endospheric microbiome include all microbes associated with the internal tissue termed endophytes. The rhizosphere is very rich in a soil-derived microbial community influenced by plant mucilage and root exudates (Kent and Triplett 2002). The phyllosphere is nutrient poor and subject to extreme temperature, radiation, and moisture (Kushwaha et al. 2019b; Vorholt 2012). The rhizospheric and phyllospheric microbes are closely associated with the plant surface and termed epiphytes, whereas the microbes associated with the internal organs and tissues are termed endophytes. The enrichment of microorganisms in the plant is not random, but a targeted process (Berg et al. 2017). The attraction of microbes to the root by the nutrients and the secondary metabolites has been studied. Chemoattractants and repellants have also been studied in the past few years (Feng et al. 2018; Oku et al. 2014; Pinedo et al. 2015). Although the structure of plant microbiomes is well studied, there are many knowledge gaps because of the plant species-specific components; targeted studies have been performed on crops and model plants such as Arabidopsis. The gaps are especially related to plants in natural ecosystems and their relationship to plant health.

So much application and the increasing complexity of the microbiomes have led to the development of many techniques in the field of identification, as well as taxonomy. For the identification of microbes, several classical methods had been used previously which included phenotypical as well as biochemical methods. These methods were only effective with the culturable microbes, so it was mandatory to develop the technology (Jesumirhewe et al. 2016). Nowadays, there are many more sequencing technologies which have been further improved. Besides 16S ribosomal RNA and internal transcribed spacer (ITS) sequencing, the use of MALDI-TOF-MS (matrix assisted laser desorption ionization-time of flight-mass spectroscopy) have proven to be useful in microbe identification (Adekambi and Drancourt 2004; Chen et al. 2000; Kashyap et al. 2016; Nouwens et al. 2000; Peng et al. 2005; Pieper et al. 2006; Rai et al. 2016; Sharma et al. 2015). Several polymerase chain reaction (PCR) based technologies such as repetitive PCR, amplified fragment length polymorphism (AFLP), random amplification of polymorphic DNA (RAPD), and multiplex PCR have been improved (Kashyap et al. 2016; Rai et al. 2015, 2016; Srivastava et al. 2014). The NGS (next generation sequencing) and multi-omics (genomics, metagenomics, transcriptomics, and proteomics) technologies allow much deeper insight into the structure of plant-associated microbial communities and its interaction with the ecosystem which support and often extends the current body of knowledge (Berg et al. 2015; Jansson and Baker 2016). In addition to this, these tools also reveal the functional dynamics and plant-microbe interaction as well as new PGP (plant growth promoting) traits.

In brief this chapter includes several approaches for studying the plant microbiome, the past and present tools for the identification of the microbiome and their advancement. In addition to these we have discussed the different microbes present in different plant parts. This chapter gives an overview of the application of the microbes in agriculture and the allied sectors. Figure 1.1 describes the pictorial representation of the structure of the plant microbiome, its biotic (plant microbe interaction) and abiotic factors which govern the structure and composition, its study using classical and modern tools and its application in the field of agriculture and other allied sectors.

Figure 1.1 Plant microbiome structure, function, application, and their study using modern tools. The abiotic factors affect the microbiome which includes mainly bacteria, fungi, blue-green algae and several other microbes. They interact with the plant environment by means of different methods. Because of the interaction, they develop some characteristics which benefit each other. There are several tools to study all these components. The figure depicts the basics of plant microbiome components and their study. MS: mass-spectroscopy; NGS: next generation sequencing; GMO: genetically modified organism; PGPR: plant growth-promoting rhizobacteria.

1.2 Plant Microbiome

Microbes evolved on Earth approximately 3.5 billion years ago and eventually occupied every habitable environment in the planet's biosphere (Margulis 1981). Although microorganisms are known to be responsible for key functions on Earth, such as nutrient and biogeochemical cycling, and determining the health and disease state of the planet's plant and animal inhabitants, more than millions of microbes thought to exist have yet to be discovered. The plant microbiome includes only a fraction of the existing microbiome, which can be further divided on the basis of the localization and association to the plant part (Sanchez-Canizares et al. 2017). On the basis of localization, the microbiome may be divided into rhizospheric, phyllospheric, and endospheric. Figure 1.2 explains the components of the plant microbiome, and their interaction.

Figure 1.2 Components of the plant microbiome and its interrelations. SAR: systemic acquired resistance; ISR: Induced systemic resistance

1.2.1 Rhizospheric Microbiome

The rhizospheric microbiome is generally influenced by the deposition of mucilage secreted by root exudates and sloughed cells. The root exudates contain a number of organic acids, sugar, amino acids, fatty acids, vitamins, growth factors, hormones, and secondary metabolites. These compounds particularly decide the fate of the rhizospheric microbiome. The rhizospheric microbiome is of particular interest because of the plant growth promoting characteristics (Cai et al. 2017; Goswami et al. 2019; Guo et al. 2019; Pereira et al. 2019; Sharma et al. 2019; Singh et al. 2014; Solanki et al. 2012; Srivastava et al. 2013). They are generally described as plant growth promoting rhizobacteria (PGPR) and they act through a...