Among all the biotic and abiotic factors, the growth and variety of plant species is mainly dependent on the microbial communities of the soil ecosystem (Fierer 2017). The bioavailability of carbon, nitrogen and phosphorus can alter the traits of plant and is also interdependent on the microbiome of the soil (De Deyn et al. 2008). The soil which is contaminated with the anthropogenic activity such as heavy metals and ore mining land constitute an altered plant species diversity (Borymski et al. 2018). In mine tailing, the plant traits (life span, photosynthesis and morphological structures) are associated with the microbiome mediated process (Grigulis et al. 2013, Legay et al. 2017, Navarro et al. 2018). The plant microbe interaction is the driving component/system for the communities of plant; however, it is still not identified whether a plant-soil feedback mechanism is present. It is understood that the feedback mechanism can communicate the biotic and abiotic components in the ecosystem, availability of nutrients in the soil and the different plant species. Accessibility of nutrients for the plant depends on their physical structure and their chemical properties and the nutrient acquisition is believed to be an important driver of PSF (Guochen et al. 2018).

Soil Temperature

The temperature of the soil is the key determinant of physical, chemical and physiological reactions and, most importantly, for the activity of soil microbes present in the soil. The soil temperature directly affects the physiology of the microbes and indirectly exerts factors such as nutrient and substrate diffusion and water activity. The next factor is soil moisture about 80% of the net radiation is used to evaporate water, 5% for photosynthesis and 15% tends to warm the soil. The quality and the quantity of the rhizospliere also depends upon the temperature. The microbes present in the soil are classified according to the temperature in Table 5.

Table 5 Classification of bacteria based on temperature

Environmental class

Temperature range (°)

Optimum growth














Climate comprises two key features, temperature and rainfall, which indirectly affect the soil fertility and its productivity. The climate varies from region to region and thus the soil fertility, as the amount of moisture content in the soil also varies. Temperature also affects plant diversity as it also influences the microbiome of the soil and the organic matter content. The arid region usually lacks the topsoil, which provides mechanical support to the plant; hence, the arid region has sparse plant diversity (Sherchan et al. 2005). Apart from temperature and rainfall, greenhouse gases also alter the vegetation of the plant. Greenhouse gases are usually emitted during the combustion of fuel, industrialization, urbanization, and deforestation. These greenhouse gases get into the atmosphere, cause a drastic decrease in plant diversity and affect the temperature of the environment (Pathak et al. 2003).

Soil Texture

Soil texture refers to the various particles or granules present in the soil. It consists of various proportions of granule particles with varying size present in the soil. Based on the size, the granules are classified into different types (Rowell 1994). The different sizes of granules are listed in Table 6.

Table 6 Different particles with regard to their size




< 0,002mm





Clay, which is of diameter less than 0.002 mm, has the highest water holding and nutrient acquisition capacity. Soil with 30% of clay is a favourable condition for the plant growth, when other factors are also favourable.

Water Retention Capacity

The capacity of the soil to retain the water content and the capability of the plant for the uptake of water from the soil is called water retention capacity. The water accessibility for the plant is dependent on the depth of the root and the total water content between field capacity and wilting percentage of each layer invented by the root (Brady and Weil 1999). The water holding capacity of the soil depends on the organic matter, soil texture and structure and bulk density. These characters can affect the root depth.

Soil pH

Soil pH is an important and key property for the presence of microbial communities (Bohn 2001). Soil pH varies from acidity to alkalinity on a pH scale of 0 to 14, whereas pH 7 is neutral. The values above the neutral areas are alkaline and the value below the neutral pH is acidic pH. However, it has been experimented and proved that the plants can tolerate pH ranging from 5.5-6.5, which is the middle pH range (Blake and Goulding 2002). The availability of nutrients like calcium, magnesium, potassium, nitrogen, and sulphur, which are macronutrients, is generally found in strong acidic pH. On the other hand, ferrous, manganese, zinc, copper and cobalt are found in the soil which has low pH but higher concentration can be toxic to the plants (Bohn 2001).


An increase in anthropogenic activities leading to environmental contamination has gained awareness worldwide. Bioremediation is one of the safer methods which could create a cleaner environment. It is mainly chosen because it is cost-effective for the removal of contaminants from the contaminated sites which contain an extensive range of pollutants. Nature’s innate recycling mechanism involves certain types of microorganisms, which have the potential to bio transform high toxic metals into a less toxic form, which is utilized as their energy source. Removing the pollutants from the environment in a workable way is the main idea for choosing bioremediation; the role of microorganism in biodegradation of contaminants has intensified in recent years. Reduction of the pollutant toxicity present in the aquatic and land environment is carried out using biological organisms such as fungi and bacteria, which also play a key role in promoting the plant growth in the contaminated sites. Certain plant growth- promoting rhizomicrobes (PGPR) including bacillus, pseudomonas, mycobacterium, etc. help in augmented nutrient uptake, along with higher phosphate and nitrogen content of the plants. These rhizobacteria may also lead to metal mobilization and increase metal uptake by some plant species leading to microbe assisted phytoremediation of an environmentally polluted site. Microorganisms act as fairy-tale in the bioremediation of contaminated sites and for degradation purposes (Banerjee et al. 2018).

During pedogenesis, the weathered materials contain heavy metals which are considered as natural pollutants, thus causing risks to human health, plants, animals and the ecosystem. Heavy metal industries landfill and lead-based paints are the main source for heavy metal contamination. On the other hand, application of fertilizers, animal-based manures, biosolids (sewage sludge), different compost measures, pesticides, coal combustion residues in the form of fly ash, effluent discharge from petrochemical industries, etc. can lead to increase in the pollutants in the soil (Roychowdhury et al. 2019). The biological method is extensively used as it is cost-effective and environmentally friendly and it brings a sustainable way for the eradication of the contaminants (Banerjee et al. 2018).

Microorganism and Pollutants

Rhizopheric and endophytic microorganisms are found in rhizospheres and the stem, which effectively degrade anthropogenic compounds present in the contaminated soil. The most commonly and efficiently used methods are composting, bioremediation, biodegradation, and biotransformation. Microorganisms used in the degradation are Chorella vulgaris, Corynebacterium sps., Scenedesmus platydiscus, Streptococcocus., Bacillus sps., Staphylococcus sps., etc. Biodegradation of hydrocarbons takes place in the presence of oxygen (aerobic) as well as in the absence of oxygen (anaerobic) but effective degradation takes place in the absence of oxygen (anaerobic) (Mondal and Palit 2019). Plant growth-promoting rhizobacteria are found in the rhizospheres and they help in plant growth stimulation (Saharan and Nehra 2011). They also help in phytoremediation of heavy metals (Glick 2010). Rhizobacteria can uptake the contamination from the soil, especially heavy metals involving organic acid and biosurfactant production, which help to minimize the toxicity in the root region (Wu et al. 2006). Table 7 shows different bacterial strains which could degrade different pollutants.

Fungi also have the ability to degrade like bacteria and the organic matter (OM). Fungi can thrive at low pH and low moisture, which are suitable conditions for degradation of organic matter. Fungi are considered to degrade natural polymeric compounds, most efficiently with the production of multienzymes complexes by the extracellular membranes. Table 8 shows the different fungal strains which could degrade the different pollutants.

Table 7 Bacteria and the pollutants’ degradation




P. alcaligenes P. mendocina and P. putida, P. veronii, Achromobacter, Flavobacterium, Acinetobacter, Species of Staphylococcus, Shigella, Escherichia,

Klebsiella and Enterobacter.


Safiyanu et al. (2015)

Species of Bacillus,

Stenotrophomonas and Staphylococcus



Pseudomonas putida

Benzene and xylene

Safiyanu et al. (2015)

Bacillus coagulans, Pseudomonas cepacia, Serratia flcaria and Citrobacter koseri.

Crude oil

Kehinde and Isaac (2016)

Listeria denitrificans and Nocardia atlantica

Dyes from textile industries

Hassan et al. (2013)

Species of Rhodococcus

Polychlorinated biphenyl

Rajau (2005)

Pseudomonas sps., Micrococcus luteus and Proteus vulgaris


Priyanka and Archana (2011)

Table 8 Fungi and the pollutants’ degradation




Trichosporon cutaneum


Mortberg and Neujahr (1985)

Candida tropicalis, Candida lipolytica and Candida ernobii


De Cassia et al. (2007)

Candida methanosorbosa


Mucha et al. (2010)


PAH, biphenyl and pesticides

Fritsche and Hofrichter (2008)

Table 9 shows the different algal strains which could degrade the different pollutants.

Table 9 Algae and the Pollutant




Prototheca zopfi

Aromatic compounds

Walker et al. (1975)

Scenedesmus platydiscus,

S. quadricauda and Chlorella vulgaris


Wang and Chen (2006)

Certain plant growth promoting rhizobacteria PGPR) including Bacillus, Pseudomonas, Mycobacterium, etc. help in increased nutrient uptake, along with higher N and P content of the plants. These rhizomicrobes may also lead to mobilization of the metal and increase metal uptake by some plant species leading to microbe assisted phytoremediation of an environmentally polluted site (Roychowdhury et al. 2019).

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