Soil Microbiome for Plant Growth and Bioremediation

Soil Microbiome for Plant Growth and Bioremediation

Monika Yadav, Sonu Kumari, Junaid Ahmad Malik, Suphiya Khan
DOI: 10.4018/978-1-7998-7062-3.ch006
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Terrestrial soil is a complex part of the ecosystem hosting bacteria, fungi, protists, animals, and huge source of nutrients to plants. These soil-dwelling organisms exhibit an array of interactions with plants to span the full range of ecological possibilities. In the 19th century, many different bacterial strains were described as having plant growth favouring potential like Pseudomonas, Azospirillum, and even crop seeds were coated with bacterial cultures to improve growth and yield. The soil microbial community also recognized their considerable role to improve the soil health via energy transfer, catalyzing reactions, and nutrient mineralization. Thus, soil microorganisms and enzymatic process are generally regarded as rate-limiting steps in decomposition and nutrient cycling.
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The naturally prevalent sub-structure and shelter for plants, higher species, and diverse microorganisms such as bacteria, fungi, algae, annelids, and invertebrates is the soil ecosystem. The relationship between soil, plants and microorganisms is like an organization (Figure 1) that influences health and productivity rate of plants. The soil microbiome plays diverse role in transformation of nutrients via decomposition, mineralization, and preservation of available nutrients. The phyto-microbiome community might be divided into the rhizosphere, phyllosphere (phyllo-microbiome) and endosphere. Rhizosphere is situated in the region of the roots of the plants (Kembel et al. 2014). The phyllosphere consist of the microorganisms which are present in the plant aerial parts (Lundberg et al. 2012) and the endosphere refers to the microorganisms reside within the plant (Berg et al. 2014). The microbial community structure depends upon the interactions existing among soil biosphere, plant and microorganism. These relations are facilitated by compounds which are confined by plants or microorganisms as exudates (East 2013; Hardoim et al., 2015).

Figure 1.

Interaction between plant, microbiome and soil


Nowadays, the agricultural crop is experiencing numerous constraints such as soil health, climate variations and demographic development. As microorganisms possess the strong potential as biofertilizers or biopesticides which impart a curiosity to incorporate them as alternative to fertilizers in agricultural soils (Mendes et al., 2013).

Like microbial activity, enzymatic activities are also acting as a critical index of soil fertility (Rohrbacher and St-Arnaud 2016). These soil enzymes synthesized by microorganisms play a key role in catalyzing various metabolic and biochemical processes such as nutrient recycling, soil quality improvement, soil decontamination and degradation of organic matters (Dong et al. 2015). The enzymatic process is generally regarded as a rate-limiting step in the decomposition, mineralization and recycling of nutrients (Bing et al., 2012). Analysis of soil enzymes helps to establish correlation with soil physico-chemical characters, soil productivity, microbial activity, biochemical cycling of nutrients in soil and to evaluate the succession stage of an ecosystem (Jackson et al., 2012). Soil enzyme activities are sensitive to the change in soil environment caused by natural and anthropogenic factors. Hence, enzyme activities can be considered as effective indicators and biomarkers to assess the nature and quality of soil environment (Dong et al., 2015). The soil enzymes play an elementary role to facilitate the development of plants via establishing various biogeochemical cycles. As the study of soil microbiome/ enzyme functional diversity has been strengthened to boost the understanding of the linkages among the resource availability, microbial community structure, function and ecosystem processes. Study of soil microorganisms and enzymes gives information about the resource availability, release of nutrients in soil by degradation of organic matter and functioning of ecosystem. Nearly all soil functional processes, both chemical and biological processes, depend on enzymatic catalysis (Maron et al., 2007). Soil enzymes are mostly generated from the exudates of soil microorganisms, the decaying of plant and animal residues or even from dead cells (Peng, et al., 2003). For both kingdoms, environmental variables appear to be more important in determining community composition and function (Bahram et al., 2018).

In soil rhizosphere various bacteria, fungi, and algae are allied with plant roots and stimulate plant growth as a bio-fertilizer. The plant growth-promoting rhizobacteria (PGPR) has a potential to protect plants from pests, detoxify toxic metals, degrade xenobiotic compounds and accelerate nutrients adsorption (Ahemad and Khan 2012). For bacteria, pH is the predominant environmental variable that drives community composition, along with carbon and oxygen quality/quantity, soil moisture, nitrogen (N) and phosphorus (P) availability (Fierer, 2017). Bacterial functional diversity is strongly associated with mean annual precipitation whereas for fungi, C/N ratio is the strongest predictor of community composition and function, which may reflect higher energy requirements and niche specialization compared with bacteria (Bahram et al., 2018).

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