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In-situ Bioremediation: An Eco-sustainable Approach for the Decontamination of Polluted Sites

Shamsul Haq1, Asma Absar Bhatti1, Suhail Ahmad Bhat2, Shafat Ahmad Mir1, and Ansar ul Haq3

1?Division of Environmental Sciences, Sher-e-Kashmir University of Agricultural Science and Technology, Srinagar, Jammu and Kashmir, India

2?Department of Biochemistry, Pondicherry University, Puducherry, India

3?Department of Chemistry, University of Kashmir, Srinagar, Jammu and Kashmir, India

1.1 Introduction

The environment has been severely polluted with chemicals that are poisonous both to the environment and to human beings [1-3]. A polyphasic approach has been adapted to overcome the effect of these toxic pollutants that includes (i) stringent regulations for the production and usage of complex chemicals, (ii) the treatment and safe disposal of harmful chemicals, and (iii) the reclamation of polluted sites [4, 5]. The first two are defensive in nature and minimize damage to environment, while the latter is a restorative mechanism [6, 7]. The methods of bioremediation are used for (i) the conversion of highly toxic to less-toxic substances, (ii) the mineralization of contaminants, and (iii) pollutant immobilization [8-12]. Microorganisms in general, and bacteria in particular, harbor enormous metabolic diversity, allowing them to utilize the complex chemicals as energy sources [11, 13]. Further, due to genetic evolution they attain a new metabolic potential to degrade newly added xenobiotic substances [13-15]. The other major focus area of bioremediation studies has been the characterization of metabolic pathways and their respective molecular regulations [16-18]. The advent of whole genome sequencing and related genomics methods has also given rise to new avenues for genome-wide screening of degradative genetic elements and regulatory sequences among the pollutant-degrading strains [19-22]. The main concerns for using isolated microorganisms are: (i) the portion of microorganisms may have substantial potential of degrading pollutants and (ii) true degradation of pollutants is not often a true reflection of the in-situ bioremediation [23, 24]. The perfect bioremediation techniques need to be executed in such a manner that microorganisms counter a variety of biotic and abiotic factors [23-26]. These factors greatly affect the efficiency of bioremediation process through various mechanisms [27]. Numerous studies also suggest that these are not only the environmental factors but also the technological advances, which affect the process of bioremediation. From the above studies, a major area of environmental research has emerged that assess the eco-sustainability of in-situ bioremediation process. Furthermore, various programs are required to monitor and address the following uncertainties: the expected remediation of hazardous substances, the potential of microorganisms, and the adverse impact of remediation processes on various environmental factors [28]. Previously, only the kinetics of degradation was determined but, with the advancement of ecological techniques, community behavior has also been made mandatory for in-situ bioremediation studies [29, 30].

The key target of a bioremediation technique is to improve the effectiveness of the restoration of contaminated sites in a cost-effective and environmental-friendly manner. There is no single technique for restoring contaminated sites but research on the basis of nature and type of pollutants has led to the development of new techniques. Autochthonous microorganisms present in polluted environments hold the key to solving most of the challenges associated with biodegradation and bioremediation of polluting substances [31] provided that environmental conditions are suitable for their growth and metabolism. Bioremediation is ecofriendly and cost effective, which offers major advantages of this process over conventional physical and chemical methods. The bioremediation process mainly depends upon the nature of the pollutant, which include: agrochemicals, chlorinated compounds, dyes, greenhouse gases, heavy metals, hydrocarbons, nuclear waste, sewage, and plastics. The nature, depth, and degree of contamination, location, and cost are considered in any bioremediation technique [32, 33]. Furthermore, O2 concentration, nutrient content, temperature, pH, and other factors also are very important in considering the bioremediation technique.

1.2 Ex-situ Versus In-situ Bioremediation

In-situ bioremediation is the removal of pollutants under natural conditions by using microbial potential without excavating for polluted samples [34-36], whereas ex-situ bioremediation is the degradation of pollutants in excavated samples [37, 38]. There is a noteworthy difference between the two methods of bioremediation, both in terms of experimental control and the end result. While considering the performance of these two methods of bioremediation, it was found that the degradation process in situ is more variable than ex situ [37]. The other significant advantage of the application of an ex-situ bioremediation method is its independence from environmental factors that could adversely affect the efficacy of the process. Further, "because ex situ bioremediation is carried out in nonnatural environments, the process can be manipulated easily by physico-chemical treatments of the target pollutant before and/or during the degradation" [39]. In spite of the selective advantages of ex-situ bioremediation techniques, the in-situ bioremediation technique constitutes the most widely used technological treatment for the restoration of polluted environments [36, 37, 40, 41]. One-fourth of all remediation projects make use of in-situ bioremediation strategies [36]. In-situ bioremediation technology is less expensive because it does not need evacuation and it also releases fewer pollutants. The other important aspect of in-situ bioremediation process is its applicability to diverse environmental niches for example, industrial sites, aquifers [42], soil subsurface [43], and groundwater [35, 44]. The significance of in-situ bioremediation is increased by abundant presence and activity of microorganisms, thereby enhancing the efficiency of the decontamination process even in non-accessible environments. Ex-situ bioremediation is carried out by several methods, which are non-related, e.g., slurry phase bioremediation and solid-phase bioremediation, which are driven by the physico-chemical properties of contaminants [45, 46]. In-situ bioremediation techniques can be categorized as (i) biostimulation or (ii) bioaugmentation [36, 40, 41, 47] and focus mainly on speeding up the removal of toxic pollutants. The choice between the two techniques is determined by: the physico-chemical characteristics of the polluted area, the presence of co-contaminants, and the type and concentration of the pollutant, for example. It is suggested that ex-situ bioremediation methods are useful for the remediation of (i) soils polluted with recalcitrant pollutants in higher concentrations, (ii) soils rich in clay where the permeability of pollutants is low, (iii) sites where conditions are not favorable for biological activities, and (iv) where microorganisms are not released for a range of reasons [48]. The selection of a bioremediation technique based on the expected outcome is very important. The enhanced degradation by in-situ bioremediation can result in increased contamination of lesser hydrophobic metabolites in the water sources in the vicinity of the source contamination [49, 50].

1.3 In-situ Bioremediation Techniques

1.3.1 Bioaugmentation

Successful bioremediation processes require the use of various strategies for the specific environmental conditions of polluted sites. The most frequently used bioaugmentation strategy is the addition of a pure bacterial strain that is preadapted or the addition of a preadapted consortium that has been genetically engineered through adding biodegradation relevant genes to them [51]. Feasibility studies are a prerequisite for any planned intervention. They usually revolve around screening, followed by tailoring of a competent microbial formula for a particular site. The screening must be based on the ability of the microbes and also on the factors that enable the cells to be activated and persistent under the particular environmental conditions. In order to select the competent microbe it is crucial to have prior knowledge of microbes [23, 52]. Once the contamination is of both high metal concentrations and organic pollutants, the degradation of organic compounds may be constrained by co-contaminants [53]. The use of a multicomponent system such as a microbial consortium gives a better performance in the environment than single component systems [54]. It is...