Keywords

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11.1 Introduction

Soil is a complex and heterogeneous system consisting of both living and nonliving components . The nonliving components of soil include soil texture (sand, salt, and clay) and organic matter, while soil living components are composed of soil flora (algae, fungi, and bacteria) and fauna (nematodes, arthropods, earthworm, and mollusks). Soils have a large number of bacteria, fungi, and animal species. It is reported that one cm3 of fertile soil may have up to 1010 bacteria belonging to an estimated 104 species (Anderson and Weigel 2003). Soil microbes are important biological components of soil and perform functions in soil fertility through nutrient cycling and organic matter degradation (Tejada et al. 2014). Plant species get nutritional benefits from association with soil microbial mutualism and often provide sugars to these microbes, e.g., legumes and ectomycorrhizal tree species respond positively to rhizobia and fungi, respectively, compared to nonlegumes and non-ectomycorrhizal plants (Abbott et al. 2015). Soil microbes have a critical role in the functioning of terrestrial ecosystems and act as drivers of plant diversity (Van Der Heijden et al. 2008). Free-living soil microbes promote plant diversity by increasing the nutrient pool and alter the plant dominance due to symbiotic and pathogenic interactions (Prober et al. 2015). Similarly, plant diversity promotes soil microbes by providing food resources (exudates and litter), physical microhabitats, and environmental conditions (Millard and Singh 2010; Prober et al. 2015). Ecologists are well aware of the significance of microbes in soil functions, but it is due to advancements in the technology that enabled scientists to extract and characterize microbial communities to assess their functions in the soil (Bardgett et al. 2005).

The interactions between plant and microbe in the rhizospheric soil determine many processes including plant growth, pollutant degradation, and nutrient mobilization through atmospheric nitrogen fixation, solubilization of nutrients and control movements, and availability of pollutants to plants by the production of chelating agents, biosurfactants, acidification, redox changes, and phosphate solubilization (Glick 2010; Rajkumar et al. 2013). Bacteria and fungi transform and degrade different types of pollutants including pollutants from agriculture origin. The term degradation describes a variety of processes undertaken by the microbe: for example, the pollutant substances may either be completely mineralized, or it may undergo the partial transformation before a nontoxic metabolite excreted in the soil and become immobilized by bonding to matrix component like humic acid (Kiel and Engesser 2015; Murphy 2016).

Agrochemical is a generic term for the chemical products used in agriculture which may include pesticides (herbicides, insecticides, and fungicides), synthetic fertilizers, growth agents, and raw manures. Balanced application of fertilizers can promote soil organic matter and soil microbial diversity and hence improve soil functions and ultimately increases the soil resistance against environmental stresses. The use of these agrochemicals may increase the yield of crops , but their excessive use poses a great threat to environment, especially soil biology. Long-term and excessive uses of synthetic fertilizers (N, P, and K) along with organic fertilizers (manures) were reported to seriously affect soil microbial and soil enzymatic activities (Zhang et al. 2015b). Pesticides when entering into soil can cause environmental hazards and greatly alter the soil biochemical and microbial aspects. Soil microbes on the other hand overcome the toxic effects of these chemicals by performing different functions in the soils and make them less toxic for the environment.

The soil enzymatic activities are used as indicator for soil fertility and quality. These activities are important to predict microbiological and biochemical processes involved in organic matter synthesis and decomposition, nutrient cycling and availability, and biodegradation of toxic organic pollutants especially pesticide utilization in agriculture (Raiesi and Beheshti 2014). Enzymes are also important to monitor sudden changes in the soil environment because of their rapid response to any change within the soil. Studies showed that long-term supply of P and N can affect the soil microbial activities, and absolute and specific acid phosphate activities decreased as mineral P application rates and ratios increase (Zhang et al. 2015b). Apart from the degradation of agrochemicals, soil enzymatic activities also inhibited due to exposure to external pollutants like heavy metals, pesticides, and certain antibiotics used in agriculture. Soil enzymes like urease, alkaline phosphatase, and invertase are considered to be the indicators of soil disruption under stress (Jin et al. 2015). Certain microbial enzymes (urease and protease) are involved in the organic matter decomposition and N dynamics by participating in the hydrolysis of peptide bonds and release of NH+4 (Wang et al. 2008).

11.2 Agrochemical and Soil Microbes

Soil microbes perform crucial functions for the restoration of polluted soils and therefore are considered important component of ecosystem restoration (Harris-Hellal et al. 2009; Liu et al. 2016). Soil microorganisms are closely associated with plant roots, contributing to nutrient cycling, and show resistance and tolerance to pests, diseases, drought, and heavy metals and improve the soil structure. In this regard, soil microbial diversity and community composition are important indicators of soil health (Liu et al. 2016). The biodiversity and composition of soil microbes are influenced by many factors like pH, organic matter, and the additives such as pesticides and fertilizers. Actinobacteria and Proteobacteria were reported to be most abundant phyla in relation to soil containing agrochemicals and had a positive relationship with atrazine in soil (Liu et al. 2016). Similarly, Arthrobacter communities found in contaminated soils showed atrazine-degrading capabilities by having trzN, atzB, and atzC genes (Zhang et al. 2015b). Soil management practices such as type of rotation, proportion of organic material, and intensity of tillage can alter the physicochemical characteristics of the soil. These practices can manage the biogeochemical cycles and the dynamics of the microbiota, including colonization of arbuscular mycorrhizal fungi. The conventional tillage practices where crop residues are removed along with the synthetic inputs of herbicides exaggerate the negative effect of herbicides on the microbial population. Synthetic fertilizers and herbicides along with the type of organic material had greatly affected the enzymatic activities and mycorrhizal colonization in the soil (Mariela et al. 2016). Addition of soil organic matter in the form of compost provides several microorganisms and nutrients to indigenous degraders. Pentachlorophenol (PCP) is used in the wood treatment and persists in the environment and classified as priority contaminant. Many fungi such as Phanerochaete chrysosporium, Antracophyllum discolor, Trametes versicolor, Ganoderma lucidum, Armillaria mellea, and Gloeophyllum striatum showed potential to degrade and mineralize PCP (Bosso et al. 2015a, b). Bosso et al. (2015a) also found that compost and fungal strains had a synergistic effect on the reduction of more than 95 % of the extractable PCP. The use of organic fertilizers can enhance the microbial diversity and soil health. Long-term use of organic fertilizer contributed to the improvement of soil C and N contents and most enzyme activities (Zhang et al. 2015a) (Table 11.1).

Table 11.1 Relationship of agrochemical/manures and soil microbes on the health of soil
Full size table

11.3 Effect of Agrochemicals on Soil Biological Process in Soil

Agrochemicals are used to enhance or protect the agricultural crops, vegetables, and livestock through the world. Agrochemicals include all chemical products which are manufactured or processed for use in the agriculture sector and allied industries . According to The American Heritage Science Dictionary, “agrochemicals” are defined as a chemical, such as a hormone, a fungicide, or an insecticide, that improves the production of crops. Pesticides are used to protect the crops from insects and diseases, and fertilizers are used to fulfill the deficiency of nutrients.

Agrochemical (fertilizer, pesticides, and insecticide) application is considerably increased in the developing world. Agrochemicals perform an important role in intensive agriculture . The use of these agrochemicals is a low-cost method of increasing production and gives the farmer a high economic return for his labor and investment. In our agricultural systems, pesticides and insecticides are introduced to protect crops against insects, pests, and weeds to minimize harmful effects and to get maximum yield (Yang et al. 2007). The ultimate objective of using fertilizer and pesticides is to enhance the crop yield for maximum benefit. Agrochemicals are very important component of an agricultural industry for increasing crop yield from viewpoint of economic; therefore, their continued use is essential (Yang et al. 2007). Insecticides and pesticides are part of insect and pest control strategies which help in improving public health .

No doubt, agrochemicals (fertilizer, pesticide, and insecticides) have tremendous role in the increase of crop production (Blain 1989; Hashmi et al. 2004); on the other hand, these agrochemicals have generated many environmental and health issues. Agrochemicals directly affect the soil microbes which ultimately deteriorate the soil health. Pesticides may drastically affect the proliferation of beneficial soil microorganisms and their associated biotransformation in the soil. The best pesticide is the one, which only toxic to targeted organism and degrade it and not contaminate the soil environment. When nontarget organism is exposed to the applied pesticide, the pesticide may have harmful effects on that nontarget organism . (Odenkirchen and Eisler 1988; Bretaud et al. 2000; Galloway and Handy 2003).

Total amount of applied pesticide which reaches to targeted organism is about 0.1%, while remaining 99.9% contaminates soil environment. (Pimentel 1995; Ardley 1999; Chenseng et al. 2006; Carriger et al. 2006). Hence, these harmful compounds enter the food chain through food crops and soil and cause toxicity to the biodiversity (Araújo et al. 2003; CFTRI 2003). The use of pesticides is increasing day by day in agriculture sector; toxic chemicals in agrochemical directly affect the soil microorganisms (Baxter and Cummings 2008). A pesticide (Simethoate) applied to the agriculture crops also has negative effects on the microbial diversity and the soil enzyme activity in soil (Begum and Rajesh 2015). The indigenous microorganisms are affected by the application of an herbicide Bromoxynil (Baxter and Cummings 2008).

Pesticide application caused reduction in microorganisms present in the soil (Ubuoh et al. 2012). Some pesticides disturbed molecular interactions between plants and nitrogen-fixing rhizobia and consequently reduced the vital process of biological nitrogen fixation . Inactivation of phosphorus-solubilizing and nitrogen-fixing microorganisms is observed in pesticide-contaminated soils (Hussain et al. 2009a, b). A great difference has been observed between microbial population in pesticide-treated and nontreated soil confirming the effects of microbial deduction and extinction due to indiscriminate ways of applying pesticide in the soil (Ubuoh et al. 2012). Pesticides also influence soil biochemical processes driven by microbial and enzymatic reactions (Demanou et al. 2004). Nitrogenous fertilizers decrease the mycorrhizal fungus spore number and root colonization. Application of fertilizer adversely affects soil microorganisms. Negative effect of pesticide on the symbiotic efficiency and nitrogenase activities was observed on Rhizobium leguminosarum bv, Trifolii KGL, Sinorhizobium meliloti Bp, Bradyrhizobium sp., and Ornithopus B bacteria (Demanou et al. 2004). Pesticides have adversely affected the microbial mineralization of organic compounds and related biotransformation like nutrient dynamics and their bioavailability to plants.

In general, fungi, actinomycetes, and the phosphorus-solubilizing microbes were more affected by the agrochemicals (fertilizers, pesticides, insecticide, etc.) with reductions in their abundance. Microorganisms presented varying behavior depending on the agrochemical and the nitrogen fixers were stimulated. Chemicals may affect in different ways the microorganisms that are responsible for the decomposition of organic matter in the rhizospheric soil.

11.4 Effect of Agrochemicals on Soil Enzymes

The living microbial fractions of soil are the governing bodies of a soil ecosystem, and their diversity dictates the potential of a soil to support life. These soil microbes exudate several enzymes performing many fundamental processes in soils. The activities of these enzymes in soil are keenly important for sustainable use of a soil as natural resource . These enzymes are involved in geochemical cycling of all chemical elements, which continue the flow of nutrients in ecosyste m not only in soil but, in fact, of the whole planet Earth. However, the emergence of industrial era and the use of chemicals in crop production severely deteriorated the soil health, especially the biological conditions (Trasar-Cepeda et al. 2000; Chu et al. 2003).

In a modern agriculture system, a huge amount of agrochemicals are being incorporated in soil as amendments, fertilizers, and pesticides during the production of a crop. The residual and hazardous effect of these chemicals on living beings is well documented. From a soil microbiologist’s point of view, these chemicals are also equally harmful for the microbial populations of the soil resulting in severe destruction of soil enzymatic activity (Dong et al. 2005; Qiu et al. 2006). These chemicals eradicate the beneficial soil microbes which ultimately remove important enzymatic components from a chain of reactions that play vital role in synchronizing important chemical processes in soil (Hernandez-Rodriguez et al. 2006).

There are numerous enzymes that are present in a soil ecosystem. The most important microbial enzymes are dehydrogenase, fluorescein diacetate hydrolase, and enzymes involved in biochemical cycles of nutrients, i.e., enzymes involved in C cycle, P cycle, N cycle, and S cycle (Ronhede et al. 2007). These microbial enzymes are the indicators of soil biological health, fertility, as well as the chemical status of the soil (Trasar-Cepeda et al. 2000; Chu et al. 2003). Consequently, the assessment of a particular enzyme activity plays an important part in understanding the biogeochemical cycles of nutrients. The effect of agrochemicals on soil microbes is assessed by determining several functional attributes that mainly includes the monitoring of enzymes related to the mineralization of nutrients (N, P, S, etc.). These parameters are important as the biogeochemical cycling and transformation of nutrients require microbial enzymes (Antonious 2003; Bending et al. 2004). Agrochemicals incorporated in the soil interrupt the metabolism or enzymatic activities (Hussain et al. 2009a, b). Adverse influences of agrochemicals on soil microbial enzymatic, e.g., hydrolases, oxidoreductases, and dehydrogenase, activities have been reported in the literature (Gianfreda and Bollag 1994; Kalam et al. 2004; Menon et al. 2005; Gil-Sotres et al. 2005; Hussain et al. 2009a, b).

Dehydrogenases are important enzymes synthesized by almost all living cells. These are involved in the respiration reactions in organisms. In soil, its presence regulates the decomposition of organic matter. This microbial enzyme is the indicator of inclusive activity of soil microbial population. The literature showed that agrochemicals significantly reduce the activity of dehydrogenase enzyme (Sebiomo et al. 2012). Several insecticides, fungicides, and herbicides are reported to suppress the activity of this enzyme (Burrows and Edwards 2004; Bending et al. 2007; Rasool and Reshi 2010; Sebiomo et al. 2012). However, the impact of these chemicals on soil microbes is regulated by the physiochemical properties of agrochemicals as well as by the nature of the soil and prevalent environmental circumstances (Monkiedje and Spiteller 2002). In general, the activity of dehydrogenase is severely affected by fungicides that are formulated to act on metabolic machinery of pathogen (Dick et al. 2000; Bello et al. 2008).

The fluorescein diacetate hydrolase (FDH ) is also an important functional enzyme in soil ecosystem. It is an important enzymatic parameter to measure the activity of microbial enzymatic activities. These enzymes are related to hydrolyze fluorescein diacetate compounds present in soil and take part in nutrient cycling. Measuring the FDH activity has the potential to roughly denote soil enzymatic activities and collected biological impacts (Janvier et al. 2007; Bishnu et al. 2012). Fluorescein diacetate compounds are hydrolyzed by several FDH enzymes including protease, esterase, amylase, etc. The studies showed that FDH activity is stimulated by the application of imidazolines, organophosphate, and organochlorines (Kalyani et al. 2010; Riah et al. 2014).

The literature showed that microbes involved in the cycling of C, P, N, and S had a variety of response toward pesticide application. The enzymes involved in C cycling, i.e., cellulase and b-glucosidase, are not widely reported to be affected by agrochemicals. Most of the pesticides have neutral effect on their activity (Deng and Tabatabai 1994; Niemi et al. 2009). Omar and Abdel-Sater (2001) reported that even ten times higher doses of herbicides have no pronounced effect on cellulase and b-glucosidase activities . However, some fungicides from amide group are reported to have inhibitory effect on cellulase and b-glucosidase activities (Monkiedje and Spiteller 2002; Niemi and Vepsalainen 2005). Phosphorus cycle enzymes are grouped into five major classes, i.e., the phosphomonoesterases (PME), the phosphodiesterases (PDE), the phosphotriesterases (PTE), the pyrophosphatases (PP), and the phosphoamidases (Riah et al. 2014). Acid phosphatase and alkaline phosphatase function in low and high pH, respectively, are key enzymes involved in P cycling in soil, and are included in PME. These are diverse enzymes adapted to catalyze hydrolysis organic phosphoric acid (Monkiedje and Spiteller 2002; Riah et al. 2014). The activity of phosphatase enzymes are negatively affected by the higher concentrations of pesticides which hamper the velocity of P cycle in the ecosystem (Schneider et al. 2001). Studies showed that this decrease in phosphatases directly related to P stress and plant growth (Dick et al. 2000; Sharma et al. 2010; Monkiedje and Spiteller 2002). Urease is an important enzyme involved in N cycling by catalyzing the hydrolysis of organic urea. This enzyme is integral N transformation in soil, and it is mainly derived from plant and soil microbes (Riah et al. 2014). It is reported that agrochemicals have negative impact on urease activity (Sukul 2006; Caceres et al. 2009; Tejada 2009). On the other hand, the activities of enzymes involved in S cycling are positively affected by most of the agrochemicals, and literature shows that the enzymes show accelerated activities under high concentration of pesticides (Ganeshamurthy and Takkar 1997; Kertesz and Mirleau 2004; Riah et al. 2014).

The incorporation of high concentrations of chemicals in soil severely disturbs the natural equilibrium of soil enzymes that affect the natural cycles otherwise going on a constant speed. The literature showed that these chemicals, in most cases, may speed up or inhibit the activities of soil enzymes that alter the nature of soil processes. However, there is a huge gap present in literature for understanding the chemical, physical, and biological nature of effected processes and enzymatic activities.

11.5 Role of Soil Microbes for Detoxification of Agrochemicals

The use of living organisms for the removal of agrochemical pollutant from the soil is a common process for the remediation of soil because of its low cost and environment-friendly approach (Mackay and Frasar 2000). Biotic degradation is the use of microorganisms, plants, or their enzymes to detoxify contaminants in the soil and water environments (Lu et al. 2006). Most living organisms are capable of directly degrading the agrochemical pollutants, and some of the microbes have the ability of metabolizing even very complex compounds. Biotic degradation is divided in to two different types: microbes and plants.

Microorganisms present in the soil also degrade the agrochemicals. Degradation of a persistent organochlorine pesticide like endosulfan by the soil microbes is an effective approach. Three bacterial strains, Pseudomonas spinosa, P. aeruginosa, and Burkholderia cepacia, were reported as efficient degraders of endosulfan (Hussain et al. 2007). Microbial technology (using plant growth-promoting bacteria) has received increasing attention to detoxify the hazardous waste from the environment (Radhika et al. 2006).

Different bacterial species , including members of the genera Flavobacterium, Alcaligenes, Rhodococcus, and Pseudomonas, metabolize toxic compound which is found in pesticide and insecticides (Aislabie and Lloyd-Jones 1995; Richins et al. 1997; Mulchandani et al. 1999). Soil microorganisms have the ability to degrade the toxic compounds of pesticides in the soil (Hussain et al. 2007). The use of bacteria for the degradation and detoxification of toxic chemicals released from agrochemicals (pesticides and fertilizers) is an effective and environment-friendly tool to decontaminate the polluted areas. Indigenous bacteria are capable of metabolizing toxic compounds of pesticides and provide environmentally friendly means of on-site detoxification. Environmental factors such as temperature, pH, water potential, nutrient, amount of pesticides and fertilizer directly influence the rate of biodegradations. Presences of inductive enzyme are also necessary for the degradation of toxic compounds (Singh et al. 2009).

Best suitable pathway of degradation is the most important factor for the remediation of the agrochemical-contaminated soil. Degradation of toxic agrochemical compounds affected by different physical, chemical, and biological factors to a variable extent in the soil environment is a highly complex process (Lu et al. 2006).

Remaining products of pesticides after fully degradation by soil microbial assimilation result to enhance soil microorganisms population and their activities (Das and Mukherjee 2000). Different insecticides with different doses affected the chemical and microbiological properties of rhizospheric soil in rice field. Carbofuran strongly stimulated the mineralization of organic carbon. Microorganisms have similar herbicide-degraded processes and an intrinsic nature for rapid genetic adaptation to chemicals in the environment. Pollutants of diverse chemical nature could be remediated from soil and water with the use of potential microorganisms in the soil.

11.6 Conclusions and Future Perspectives

The interaction of plants and microbes in rhizospheric soil controlled many process like plant growth, nutrient mobilization, nitrogen fixation, pollutant degradation, and control movement and availability of pollutants through chelating agents, biosurfactants, and acidification. Agrochemicals such as fertilizers, herbicides, and pesticides contributed a lot in the production of food and fiber but had profound effects on the soil fertility and health. Extensive use of these chemicals caused a stress over natural resources along with the increase in water and air pollution. Soil microbes are under great threat by the application of diverse nature of agrochemicals which interrupt large biochemical reactions performed by the soil microbes. Many functions like C, P, S, and N cycle, metabolism, and enzymatic activities performed by soil microbes are disrupted by the application of agrochemicals. The use of organic/natural resources should be promoted against agrochemicals which enhance the microbial activities in soil and hence can improve soil health. Moreover, soil microbes have the potential to remediate the agrochemical-contaminated soils thus improving soil fertility. Therefore, researchers and scientists should develop and follow technologies for sustainable use of natural resources.