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2 Plant Microbiome A Key to Managing Plant Diseases
Dipal B. Minipara1, Khushboo Pachhigar2, and Himanshu R. Barot3
1 Anand Agricultural University, Anand, Gujarat, India
2 Veer Narmad South Gujarat University, Surat, Gujarat, India
3 Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Banaskantha, Gujarat, India
2.1 Introduction
Microbes are fundamental for a balanced life on Earth, and understanding their function is crucial. Culture-based microbial techniques and next-generation sequencing have added benefits. Metagenomics studies have allowed studying the microbial genome and its function, which are not culturable but have an essential role in the ecosystem. Microbiome study enables the exploration of the genome of all microorganisms, including symbiont and pathogens. The microbial community varies with host health and environmental factors that shape the microbiome. The concept of association of microbiome with plant health and disease state received focus over the past decades. However, it is critical to identify prominent microbiota associated with biotic stress in variable environmental conditions on the field, as most studies were conducted under greenhouse conditions. Core microbiota, a host-associated persistence microbial community carrying functional genes, are critically important for plant health. Therefore, identifying host-associated core microbiota and their response toward biotic stress is essential to understanding disease management and improving productivity.
Plant microbiome can be categorized at the interface where plant and microbes can communicate, which include plant–microbe interaction at rhizosphere, phyllosphere, and endosphere (Figure 2.1) [1]. Plant microbiome alters as plant species or cultivar changes; it also depends on plant developmental stages, disease conditions, and geographical locations [2].
Figure 2.1 Plant–microbe interaction in rhizosphere, endosphere, and phyllosphere and biocontrol mechanism acquired by beneficial microorganism.
2.2 Plant–Microbe Interaction in the Rhizosphere
“Rhizosphere” is derived from “rhiza” or root and “sphere” or the field of influence in ancient Greek. The rhizosphere is the soil environment surrounding plant roots, and it is a crucial underground region for plant–microbe interaction. The rhizosphere comprises 10-fold microbes more than that in the surrounding soil, and the rhizosphere microbiome may consist of fungi, bacteria, archaea, actinomycetes, and viruses [3]. Roots utilize photosynthates to produce exudates used by rhizosphere microbiota to exchange nutrients and water [4]. Root exudates also function as signaling molecules, attractants, stimulants, or repellents to rhizosphere microbes. Bioactive compounds of exudates vary with plant species that define microbial community [5]. Root secretion influences soil pH, soil structure, oxygen obtainability, and influences plant–microbe interaction. A study on secondary metabolite benzoxazinoids showed it’s defensive role in cereals, alters rhizosphere fungal and bacterial microbiota, and influences plant growth [6]. Bacteria produce protein and polysaccharides, which allow them to attach with roots as biofilm aggregates [7]. Symbiotic association evolved millions of years ago, and most living plants form a symbiotic relationship with arbuscular mycorrhizal fungi (AMF) [8]. Upon sensation of strigolactone from plant roots, AMF initiates hyphal branching to colonize roots and releases lipochito oligosaccharides, promoting plant growth by increasing root surface area [1]. Almost all soilborne fungi are necrotrophic, and they do not require the living cell to acquire nutrients.
2.2.1 Microbial Population in the Rhizosphere
The most enriched microbiota in the rhizosphere are bacteria, which influence the plant rhizosphere significantly. Next-generation sequencing (NGS) has provided insight into microbial diversity and composition. Internal transcribed spacer (ITS), 16s rRNA sequencing of fungi and bacteria, respectively [9,10] and shotgun metagenomic sequencing [11] have unravelled root-associated microbiome. The relative abundance of taxonomic marker genes has provided more information on phyla Proteobacteria, Bacteroidetes, and Actinobacteria, which were augmented in the rhizosphere [12]. Predominant genera in the rhizosphere are Pseudomonas, Bacillus, Rhizobia, Azotobacter, Mycobacterium, Flavobacter, Cellulomonas, Agrobacterium, and Micrococcus [13]. So far, various gram-positive and aerobic spore-forming bacteria are inferior because of the low availability of oxygen [14]. For fungal communities, phyla Ascomycota, Basidiomycota followed by Zygomycota, Glomeromycota dominate in the rhizosphere of Arabidopsis thaliana. Plant-friendly microorganisms comprise nitrogen-fixing bacteria viz., Azotobacter, cyanobacteria, clostridium, plant growth-promoting rhizobacteria, fungi, and endo ectomycorrhizal fungi [13].
2.2.2 Biocontrol Mechanism in the Rhizosphere
To grow a healthy plant, it is necessary to examine soil niches surrounding the root area to detect pathogens and enhance advantageous microorganisms. The rhizosphere is the battlefield where phytopathogens acquire parasitic relations with the plant. Biocontrol agents have a mechanism that includes rivalry for space and nutrients, antagonistic activity, and hyperparasitism. The level of decomposition of organic matter influences microbial communities and biocontrol activities [14]. The introduction of beneficial microorganisms can also change microbial community structure in the rhizosphere.
2.2.2.1 Competition
Some strains of Pseudomonas fluorescens act as biocontrol by competing for nutrients and root surface colonization aggressively. Pseudomonas sp. RU47 colonizes the rhizosphere with sufficient density and compete with Rhizoctonia solani and minimizes the severity of black potato scurf and lettuce bottom rot in diluvial sand, alluvial loam, and loess loam soils [15]. The competition can also be for micro-nutrients, specifically iron, associated with high-affinity chelators called siderophores secreted by microorganisms. An experiment with transgenic tobacco overexpressing ferritin showed that fluorescent Pseudomonads could survive in a less iron-containing environment and have an antagonistic activity to the pathogen [16].
2.2.2.2 Parasitism
Parasitism as a biocontrol mechanism is mainly associated with fungal biocontrol agents. Biocontrol agents parasitize the pathogen by looping around fungal hyphae and derive nutrition from the pathogen. Some beneficial microorganism secretes hydrolytic enzymes such as chitinase and cellulase [17]. Trichoderma and Gliocladium parasitize on Rhizoctonia, Sclerotinia, Verticillium, and Gaeumannomyces and cause cell damage to the pathogen [18]. Firmicute bacteria Pasteuria penetrans also control Meloidogyne nematode, and its activity is stimulated by two beneficial rhizospheric bacteria [19].
2.2.2.3 Antagonism
Antagonism
