Vol.:(0123456789)1 3

Environmental Sustainability (2020) 3:91–103 https://doi.org/10.1007/s42398-020-00099-w

REVIEW

Bioremediation: an emerging effective approach towards environment restoration

Veni Pande1,2 · Satish Chandra Pandey1,2 · Diksha Sati1 · Veena Pande2 · Mukesh Samant1

Received: 5 May 2019 / Revised: 2 February 2020 / Accepted: 4 February 2020 / Published online: 28 February 2020 © Society for Environmental Sustainability 2020

AbstractEnvironmental pollution and its remediation are one of the major problems around the globe. Broad varieties of pollutants viz. pesticides, hydrocarbons, heavy metals, and dyes, etc. are the key players, which are mainly responsible for environmen-tal pollution. Residual contaminants are also difficult to eliminate. Bioremediation is one of the most efficient technologies for the reduction of environmental pollutants that recovers the contaminated site back to its actual form. So far only a small number of microbes (culturable microbes) have been exploited and a huge microbial diversity is still unexplored. To enhance the metabolic potential of the microbes, ecological restoration and degradation of recalcitrant pollutants, various bioremedia-tion approaches like chemotaxis, biostimulation, bioaugmentation, biofilm formation, application of genetically engineered microorganisms, advanced omics, have been widely used. In the last few years, the metabolic potential of microbes has tremendously improved the realization of degradation and remediation of environmental pollution. Microorganisms help in the restoration of contaminated habitats by cleaning up waste in a environmentally safe manner along with the production of safe end products. This review discusses the important processes involved in enhancing bioremediation and recent advances in microbes and plants associated bioremediation.

Keywords Pesticides · Bioremediation · Chemotaxis · Biostimulation · Bioaugmentation

Introduction

Over the past few decades due to rapid industrialization and modern agricultural practices environment has been polluted severely, which has resulted in pollution of air, water, soil and even the food consumed by animals and humans. The problem is worldwide and possibly can cause a threat to both the environment and human health (Samant et al. 2018). The use of pesticides and herbicides helps to increase agri-cultural productivity; however unremitting the application of these chemicals causes a huge loss of biodiversity and

contamination of agricultural land. Based on the half-life, pollutants remain in the environment for a different period, few of them fade away within a short period by microbial transformation into less or non-toxic by-products, while some pollutants such as dichlorodiphenyltrichloroethane (DDT), hexachlorocyclohexane (HCH), polychlorinated dibenzodioxyfurans (PCDDF/Fs), dioxins and chlordane may remain in the surroundings over a longer period and enter the food web, where they get biomagnified (Chiuchi-olo 2004; Pandey et al. 2019a). This uncontrolled release of lethal pollutants into the surroundings is a serious issue. Conventional approaches such as pyrolysis, land-filling, and recycling for the removal of contaminants are not that efficient and end with the production of toxic compounds. Thus, the use of microorganisms is more preferable over the conventional methods for the remediation of toxic envi-ronmental pollutants. In other words, bioremediation is a tool that causes restoration of the natural surroundings by removing pollutants from the environment and thereby pre-venting further pollution. Compared to alternative methods of remediation i.e. chemical and physical, bioremediation is environment-friendly and cost-effective as well. Through

Veni Pande and Satish Chandra Pandey contributed equally to this study.

* Mukesh Samant mukeshsamant@gmail.com

1 Cell and Molecular Biology Laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora, Uttarakhand 263601, India

2 Department of Biotechnology, Kumaun University, Bhimtal Campus, Bhimtal, Nainital 263136, Uttarakhand, India

92 Environmental Sustainability (2020) 3:91–103

1 3

bioremediation, the toxicity of the pollutants can be reduced by utilizing the metabolic potential of microorganisms that transforms, mineralizes and immobilizes the highly toxic pollutants into lesser non-toxic forms. Some of the xenobi-otic compounds, such as highly halogenated, nitrated aro-matic compounds and few pesticides are still not reported to be degraded by microorganisms (Gangola et al. 2019). However, the efficiency of microorganisms relies on diverse factors i.e. concentration, chemical nature of pollutants, availability and physiological features of the environment. So the components that affect the degradation potential of microorganisms are either concerned with nutritional requirements or environmental factors. Further, based on the elimination of toxic compounds and their shipping methods, bioremediation is of the following two types: in situ and ex situ. Moreover, recent practices incorporate the application of genetically engineered microorganisms (GEMs) for the efficient degradation of pollutants. For the remediation of different pollutants under specific conditions, GEMs have been demonstrated successfully as they have better genetic makeup to deal with pollutants. Because of the inefficient degradation by culturable microorganisms, the removal of various poisonous and refractory pollutants remains a prob-lem for the environmental biotechnologists. However, the main hurdles for the use of GEMs under the field conditions are ecological concerns and regulatory restrictions. Despite having high efficiency for bioremediation, there is restricted application of GEMs into the environment because of the uncontrolled propagation and horizontal gene transfer. To minimize the propagation of GEMs and their effects on the native population of organisms, there is a requirement of constructing their life cycle in a controlled manner. Allow-ing the death of biocatalyst as soon as the pollutant has been minimized, helps to reduce the risks in the development of these technologies for effective bioremediation. The present review aims to endow comprehensive details of combined approaches that have been executed or can be executed for efficient evaluation of bioremediation processes.

Techniques in bioremediation

Based upon transportation and removal of toxic compounds, bioremediation has been characterized into in situ and ex situ.

In situ

In situ techniques involve the treatment of pollutants at their respective place with minimal disturbances. It not only saves the cost of transport but also makes use of risk-free microorganisms to remove chemical contami-nants. Also, it avoids disturbances as it causes treatment

at the polluted site and does not involve any excavation. This is also a safer mode for the remediation of harmful compounds. For the treatment of dyes, chlorinated sol-vents, hydrocarbon and heavy metal polluted sites, vari-ous in situ bioremediation methods have been effectively implemented (Pande et al. 2019; Roy et al. 2015). Some-times the in situ bioremediation techniques are improved i.e. engineered in situ bioremediation; while others are implemented as such without any enhancement and are known as intrinsic bioremediation or natural attenuation. Most commonly used in situ processes are bioventing, bio-sparging and bioaugmentation.

Bioventing is one of the most commonly used in situ treatment techniques that require aeration and nutrient supply into the infected soil to enhance the growth and activity of the native microbial population. In this pro-cess, the low airflow rate is required, and enough oxygen for biodegradation is supplied that reduces the volatiliza-tion and discharge of pollutants into the environment. It is more efficient when the water table (contamination) is deep under the soil surface and is usually applicable for the removal of simple hydrocarbons. Due to the varia-tions in the soil texture and structure of the hydrocarbon, the rate of removal of the pollutants may vary from one site to another. Whereas in biosparging, the concentra-tion of groundwater oxygen is amplified by introducing pressurized air underneath the water table resulting in enhanced biodegradation rate of the pollutants by indig-enous microbes. It enhances aerobic degradation as well as volatilization (Lambert et al. 2009). During the injec-tion of oxygen at the polluted site, control of pressure is required to avoid the movement of volatile matter into the atmosphere. The two important factors that contribute to the efficiency of biosparging are soil permeability and pol-lutant biodegradability. Usually, the application of bio-sparging is found to be more at the sites containing petro-leum products with medium weight just like jet fuel or diesel. Biodegradation of heavier products like lubricating oil, normally takes a longer time than that of lighter prod-ucts like gasoline. However, biosparging can be applied at these sites too (Garima and Singh 2016). In some cases, the biodegradation rate can be enhanced through the addi-tion of efficient pollutant degrading strain(s) that causes degradation at high rates or are specifically well adapted to thrive under existing conditions, and this is known as bioaugmentation. For an effective approach, the introduced organism(s) must compete with native microbial popula-tion and also should be widespread all through the matrix otherwise the outcome will be limited and treatment will not persist for long (http://dx.doi.org/10.4172/2155-6199.10002 48). Bioaugmentation in a natural environment is known for isolation, characterization, and standardiza-tion of microorganisms to degrade pollutants.

93Environmental Sustainability (2020) 3:91–103

1 3

Ex‑situ

Ex-situ treatment is not given at the sites but somewhere else. It requires excavating pollutants from the contaminated sites and shipping of polluted soil or propelling groundwater to the treatment site. This process is independent of the envi-ronmental factors as carried out in the absence of a natural environment, and therefore, the treatment method of target pollutants can be altered using physico-chemical methods before and/or during the degradation. Depending upon the physical condition of the pollutant during bioremediation, ex situ bioremediation can be characterized as solid and slurry phase treatment.

Solid and slurry phase treatment

This system includes landfarming, composting and soil piles. It is effective in the treatment of organic wastes, prob-lematic household and industrial wastes, municipal solid and sewage wastes (Pandey et al. 2019b). In landfarming, the impure soil is collected and disseminated above a pre-pared bed which is then tilled from time to time until the soil becomes deprived of contaminants. This enhances the aerobic degradation process by supporting the growth and movement of naturally occurring biodegradative microor-ganisms. Usually, this method applies to handle peripheral soil (10–35 cm) (Shinde 2013). As a dumping substitute, land farming has gained much focus because of its capability to minimize monitoring and maintenance costs, and cleanup liabilities as well. Composting necessitates the collection of the impure soil and then mixing it with non-hazardous organic materials like vegetative wastes or manure. This facilitates efficient microbial growth and also raises the temperature required during the process (Shinde 2013). It is effective in the elimination of PAH, RDX and TNT (Van Deuren et al. 2002). Biopiles involve both landfarming and composting. Here, engineered cells are developed as aer-ated composted piles and the process is maintained by the supplementing compost to the contaminated soil. Applica-tion of biopiles is generally in the removal of petroleum hydrocarbons and it also regulates the physical losses of the pollutants through volatilization and leaching, thus it is a refined form of landfarming. Biopiles maintain a suitable condition for native microorganisms (aerobic and anaerobic) (Shinde 2013). Slurry phase treatment comprises a mixture of solid–liquid in the bioreactors. It is comparatively faster than other treatment techniques. A bioreactor is a huge res-ervoir that involves the blending of contaminated soil along with water and several other supplements to make a stable interaction between soil contaminants and native microor-ganisms. Furthermore, the optimum environment for the contaminant degradation by the microbes is maintained by

supplementing oxygen and nutrients and by regulating the environment inside the bioreactor. After the completion of treatment process, water is eliminated from the solid wastes which are either dumped or processed further to decontami-nate, if they still contain pollutants.

Approaches towards enhancement of bioremediation

The process of bioremediation can be enhanced through several means. Some of the important processes involved are as follows:

Chemotaxis

A wide spectrum of behavioral adaptations are shown by microorganisms that enhances the in situ treatment of biore-mediation. Among them, chemotaxis is well known, with these chemotactic abilities potent microorganisms can easily migrate towards pollutants. Therefore, chemotaxis is consid-ered important for in situ bioremediation because it increases the bioavailability of pollutants significantly and hence enhances the performance. In a varied aqueous arrangement a wild- type bacterial strain has shown to degrade naphtha-lene more rapidly as compared to its unmovable (non-chem-otactic) mutant (Law and Aitken 2003). It is reported that the factors like the pace of mass transport and degeneration of hydrophobic contaminants concerned with the non-aqueous phase liquid have been found to increase considerably by chemotaxis (Law and Aitken 2003). In contaminated soil, bacteria are easily accessed to hydrophobic organic pol-lutants associated with non- aqueous phase liquids and develop biofilms on the attached surfaces to gain nourish-ment. Therefore, chemotaxis supports biofilm formation and encourages bacteria to adsorb nutrients (contaminants) by helping in the attachment to the abiotic surface. Chemotaxis of various pollutants like nitroaromatic compounds (NACs), polycyclic aromatic hydrocarbons (PAHs), explosives, petroleum coupled hydrocarbons and their relevant meta-bolic intermediates have been exhibited by a few bacterial strains that belong to diverse taxonomic groups (Gordillo et al. 2007). Initially, bacterial chemotaxis was classified based on chemoattractant involved during the process. Later on, chemotaxis was classified based on metabolism, which further bifurcates chemotactic responses into (1) metabo-lism-dependent and (2) metabolism-independent. Moreover, the movement of bacteria towards electron acceptor/donors is possibly included in the metabolism-dependent chemo-taxis. Enhancement of chemotactic behavior and develop-ment of bioremediation processes can be improved further by the research and understanding of mechanisms (Olson et al. 2004). Enhancing the in situ bioremediation further

94 Environmental Sustainability (2020) 3:91–103

1 3

requires improvement in qualitative and quantitative exper-iments. The molecular mechanisms behind the regulation of chemotactic responses is also very important to be ana-lyzed. The whole-genome sequencing and transcriptomic investigations have manifested an enormous quantity of genetic elements associated with chemotaxis than the prior assumptions (Lange et al. 2007). Studies have displayed sig-nificant utility of phosphorylation and dephosphorylation in facilitating bacterial chemotaxis. Thus providing mobility to non-chemotactic strains through genetic modification may help to study further the regulatory mechanism involved in chemotaxis and therefore, enhance the in situ bioremedia-tion process.

Biosurfactants/biofilm formation

For the enhancement of in situ bioremediation, adaptations like the formation of biofilm and/or biosurfactants can be successfully implemented. The application of a surfactant can overcome the bioaccessibility of hydrophobic organic pollutants to potential biodegrading bacteria and improve the communication between microbes and contaminants. It has been reported that biosurfactants obtained from Bacillus subtilis MTCC1427 increases the biodegradation of chlorin-ated pesticide endosulfan. This elevated the slow pace of microbial degradation for recalcitrant endosulfan by up to 30–45% (Odukkathil and Vasudevan 2013). The application of biosurfactant has also enhanced the bioremediation of various other pollutants like n-alkanes and PAHs (Garcia-Junco et al. 2003). Generally, under natural environmental conditions microorganisms form a slimy layer which is gen-erated by the action of diverse bacteria, while adhering to a substrate or matrix. This slimy layer has been described as a microbial film and is found to be a valuable feature of micro-organisms existing in the environment. The utility of micro-bial biofilm in pathogenesis has been indicated in earlier studies, where their major role in bacterial survival against the host immune response has been clearly described (Kariy-ama and Kumon 2003). Though earlier studies reveal the role of biofilm in the enhancement of in situ bioremediation but the biodegradation kinetics of polychlorinated hydro-carbons and chlorinated aliphatic compounds were acceler-ated by the use of biofilm reactors (Arora et al. 2012). More studies on the effect of biofilm in microbial degradation are required to improve the in situ bioremediation process.

Genetically engineered microorganisms (GEMs)

The development of bacteria with amplified degradation capability by combining genetic constituents from various organisms in one recipient strain can be a better option for carrying out bioremediation. To achieve this, various aspects for designing compatible GEMs should be optimized, e.g.

developing new metabolic pathways, amplifying the spec-trum of established pathways, avoiding diversion of sub-strates into toxic intermediates or unproductive routes, enhancing the substrate flux through pathways to circumvent the build-up of obstructing intermediates, elevating the bio-availability of hydrophobic pollutants, improving strength of catabolic activities and enhancing the requisite proper-ties of microbes concerning to the process. Availability of whole-genome of microbes and different catabolic operon facilitates the development of GEMs through the mixing of genes and promoters thereby increasing  their in situ poten-tial. So far several GEMs have been effectively developed which efficiently manifested bioremediation under in vitro condition. However, in situ application of these GEMs is not much impactful as these are associated with the risk of horizontal gene transfer, which causes unrestrained propaga-tion (of the GEMs) in the environment (Naik and Duraphe 2012). Therefore, GEMs can be a matter of concern. For the past decades, researchers have made various attempts to prevent the survival of the GEMs in the atmosphere and introduced the restricted suicidal arrangement called ‘bacterial containment systems’ depicted by different cata-bolic regulatory genes and killer genes (Torres et al. 2003). These types of gene pairs of killer and ‘killer–anti-killer’ are related to numerous bacterial plasmids, chromosomes, and bacteriophages. Expression of two dissimilar genes–the toxin, and a particular antidote plays a major role in kill-ing–anti-killing mechanism. The killer toxin is consistent for some time while the counterpart of anti-killing is highly unstable. Similarly, the antidotes (either an antisense RNA or a protein) either prevent their synthesis or neutralize their cognate toxins (protein) (Petersen 2011). In cells, without plasmid, the molecular mechanism of toxin inactivation is regulated by differential decomposition rates of the toxin and the antidote. A few lethal genes like sac, Relf, hok, colE3, and nuc have been reported, which have been associ-ated with the construction of various containment systems (Petersen 2011). The first containment system was forthput by Molin (Molin et al. 1987). Later on, the investigators customized the theory of the suicidal system as a ‘fail-safe’ structure for delivering GEMs into the atmosphere towards effective bioremediation. Besides this, the use of GEMs in the ex situ bioremediation process in bioreactors is consid-ered to be more efficient, as there is no competition with indigenous microorganisms and also they are maintained with controlled temperature and growth conditions (Urgun-Demirtas et al. 2006). Further, field studies are mandatory to check the efficiency and associated risk factors of GEM after incorporating into the natural ecosystems. Before using such strategies for bioremediation biotechnologists should always be concerned about ethical issues. The modified genetic con-stitution of the organism should be understood as whole and the organism should only be confined to the site of action.

95Environmental Sustainability (2020) 3:91–103

1 3

Omics approaches in bioremediation

To clear out the environmental pollutants, the microbes based bioremediation methods exploit the native microbial population and this biodegradation rate relies upon various environmental factors and amount of pollutant (Chakraborty et al. 2012). Consequently, a successful bioremediation pro-cess necessitates the blending of diverse multifaceted vari-ables that will provide us a better understanding and pre-diction of pollutant’s fate. Metagenomics, transcriptomics, proteomics, etc. are such diverse molecular strategies that are persistently discovering their pertinence in the field of the in situ bioremediation process (Fig. 1) and thus mak-ing us aware of the precise mechanisms. These approaches help us to assemble information on biodegrading genes, proteins, and metabolites. Also, the arrival of NGS (next-generation sequencing) and in silico techniques have ren-dered a pathway for thorough metagenomic, proteomic and bioinformatic studies of diverse eco-friendly microbes which renders an exceptional understanding of major pathways for biodegradation.

Metagenomics is the study of microbial populations at a genomic level in a planned manner. More than 99% of the microbes (inhabiting different natural environments) either are uncultivable or are not easy to culture thereby rendering a big limitation to the culture-dependent systems (Bursle and Robson 2016; Dickson et al. 2014). This technique allows investigation of the complete genome sequence of a sample (genomics) and large samples of genomes directly from the environment (metagenomics) that help in facilitating the process of bioremediation.

Various studies have been conducted that explain how proteomics helps to enhance bioremediation (Duarte et al. 2017; Techtmann and Hazen 2016; Tripathi et al. 2018). Further, diversity of unculturable microbes can also be uti-lized which results in the identification of desired degrada-tive genes and their properties by developing metagenomics libraries, which can be further transferred to culturable bac-teria (Jaiswal et al. 2019; Malla et al. 2018). In the metagen-omics, recognition and selection of metagenomes from the contaminated environments play a vital role. In contrast to other bioremediation methods, the metagenomic study pro-vides us more promising outcomes with an improved ratio of degradation.

Despite being an extremely effective tool in understand-ing the genetic makeup of the microorganisms that inhabit the different environments, metagenomics provides a partial role in manifesting the expression and activity of the genes. Predicting the practical performance of microbial consor-tia is made feasible by the advanced metatranscriptomics and metaproteomics approaches (Verberkmoes et al. 2009). There is a huge significance of metatranscriptomics stud-ies in the investigations associated with the environmental restoration, as these verify the gene activity within a speci-fied environmental condition. While combined effects of other omic based practices along with environmental pro-teomics can help to provide much better results. Proteom-ics is employed in the investigations that contribute to the understanding of adaptation mechanisms which predomi-nantly focus on the extremophilic surroundings. Some of the studies related to proteomics have shown its potential in increasing the rate of bioremediation to a large extent

Fig. 1 Different approaches used for the estimation of the environmental sustainability of the in situ bioremediation pro-cess (FISH fluorescent in situ hybridization, ARDRA ampli-fied ribosomal DNA restriction analysis, RFLP restriction frag-ment length polymorphism, D/TGGE denaturation/temperature gradient gel electrophoresis, RT-PCR real time polymerase chain reaction, CFU colony-forming unit)

96 Environmental Sustainability (2020) 3:91–103

1 3

(Kim et al. 2007; Zhao et al. 2005). Likewise an integrative approach of proteomic and transcriptomic in JS666 strain of Polaromonas sp. have manifested gene upregulation by a suspected carcinogen cisdichloroethene (cDCE) (Jen-nings et al. 2009). On the other hand microarray evalua-tion of the whole genome disclosed the transcriptome of Geobacter uraniireducens strain which was developing on subsurface sediments polluted with uranium (Holmes et al. 2009). Moreover, various other studies have also explored the significance and success of metatranscriptomics and pro-teomics for microbial-mediated bioremediation (Niu et al. 2018).To study the variation in the physiology of microbes all through bioremediation, proteomics is considered ben-eficial therefore, usually it is used to enhance the knowledge about the physiology of microbial reaction towards xenobi-otics, varying temperatures and several other stress-causing agents (Lacerda and Reardon 2009). Metagenomics has now strengthened its worth by exhibiting a significant role in analyzing the functional range of the microbial consortia. For the environmental samples, building up of the models to predict microbial behavior can be achieved by utilizing metabolome dependent strategies. Metabolomics is recent among various approaches that are utilized in the omics studies, and includes analysis of metabolite profiles of a cell under controlled circumstances. Exposure of microbial cells under various environmental stresses causes the discharge of different low molecular weight metabolites (primary and secondary) which can be functionally estimated by metabo-lomic studies. Our knowledge of the physiological potential of the microbes has been enhanced significantly through metagenomic strategies. Researchers (Bargiela et al. 2015; Dong et al. 2019; Malla et al. 2018) have used metabolomics for the bioremediation of different sites which were severely contaminated with petroleum hydrocarbons and uncovered the importance of general aerobic processes in the biodegra-dation revealing the existence of > 4776 metabolites involved in the process. This depicts the high metabolic heterogeneity within the contaminated site. Various other reports have also manifested the utilization of metabolomics in analyzing bio-degradation of environmental pollutants (Brune and Bayer 2012; Keum et al. 2008; Tang et al. 2009).

Still, comprehensive analysis is obligatory that can dem-onstrate the results of numerous separate reactions taking place concurrently in a microbial system. This will help to envisage the performance of microbes within a given envi-ronmental condition. The progress in the advancement of in silico studies is making these descriptions feasible. Thus, bioinformatics may also help to unbox microbial communi-ties that have not yet been detected. With the help of omics studies novel genes, transcripts or enzymes which can help in xenobiotic bioremediation can be identified. Further, some of these shortlisted genes/transcripts, enzymes can be evaluated by in vitro experiments to obtain their optimum

efficacy which can be further used for enhancing the poten-tial of in situ bioremediation methods.

Ecological factors and their role in bioremediation

Biotic factors

Biotic factors that greatly influence the microbial degra-dation processes comprise of the various native biologi-cal forms nearby the polluted site. These factors affect the bioremediation process by decreasing the survival activity and microbial movement associated with the degradation. Such changes are the consequences of competition between microorganisms for limited carbon sources, ‘protozoan grazing’ and ‘other eukaryotic interfaces. The amount of the pollutant and degradative microbes and subsequently the amount of enzyme(s) formed by each cell (catalyst) deter-mines the degradation rate. For effective and successful bioremediation, it is extremely important to maintain the microbial growth and this essentially requires an adequate amount of nutrients and oxygen in a usable form. Some stud-ies have favorably shown the application of processes like repetitive bioaugmentation’ (Lima et al. 2009), pre-induction and repeated inoculation (Singer et al. 2000) to avoid the reduction in effective microbial growth.

Abiotic factors

Several other physical factors like aeration, temperature, and resistance of environmental pH by changing the elec-tro-kinetic and redox state of the contaminated sample may also regulate the pace of pollutant degradation (Luo et al. 2005). In situ bioremediation is largely influenced by vari-ous abiotic factors of the site. Microbial treatment requires a very constricted variety of physicochemical frameworks for efficient degradation of pollutants and hence variations in these optimal parameters mostly lead to reduced efficiency of degradation. Temperature has a great influence on the microbial activity and in turn, affects the biodegradation rate by regulating the rate of enzyme-catalyzed reactions. With the decreasing temperature, the rate of biodegrada-tion gets slow and at very low temperatures  biodegradation rate is exceedingly low. Conversely, there is an increase in microbial metabolic activity that leads to improvement in the rate of biodegrdation with an increase in soil temperature even up to a maximum of about 65 °C. However, a very high temperature can be harmful to some microorganisms (https ://www.mdeq.ms.gov/wp-conte nt/uploa ds/2017/06/Biore media tion). Besides, a great range of pH also favors biodegradation but in aquatic and terrestrial systems mostly pH of 6.5–8.5 range is considered to be best for the process

97Environmental Sustainability (2020) 3:91–103

1 3

to occur efficiently. It has a great impact on solubility and nutrient availability, therefore, influences the biological activity. For example, the optimum value of pH, for the solu-bility of phosphorus is 6.5 and hence below and above this, the solubility declines (https ://www.mdeq.ms.gov/wp-conte nt/uploa ds/2017/06/Biore media tion). Furthermore, a wide range of nutrients like nitrogen, calcium, sulfur, magnesium, potassium, phosphorus, copper, manganese, zinc, iron and certain other trace elements are required for cell growth. For efficient microbial degradation, there should be sufficiency of the nutrients. Mostly nitrogen and phosphorous become deficient in the contaminated environment and are added in a useable form (ammonia for nitrogen, phosphate for phos-phorous) to the bioremediation system (Malik 2006). Water not only helps to transport nutrients and organic components across the microbial system but also helps in the ejection of metabolic waste of the cell. There is also a great influence of the quantity of water present in the soil pores as it is associated with oxygen exchange. Excessive water content can also have a negative impact as it clogs the soil and pre-vents the oxygen exchange across the soil (unless anaerobic condition is needed) thus reducing the biodegradation rate (Malik 2006). Studies have implied that these factors have the potential to control the ability of in situ bioremediation by various mechanisms.

Biological systems involved in bioremediation

Role of microbes in bioremediation

Bioremediation involves living organisms mainly the micro-organisms that have the potential to degrade hazardous envi-ronmental contaminants or to transfer them to less toxic form. Depending upon the use of various organisms, some specific terms such as phytoremediation and mycoremedia-tion are used to specify bioremediation. Different microor-ganisms can degrade diverse contaminants depending upon their concentration and also upon the metabolic require-ments. Microorganisms are said to play a significant role and show the greatest potential in bioremediation across the globe. Microbes degrade the pollutants through enzymatic action by consuming organic substrates as carbon and energy sources and obtain raw material and energy for their duplica-tion and maintenance.

Organisms used in bioremediation should meet certain requirements (Alexander 1994):

(a) The organism must have the  potential to survive and demonstrate its biological activity in polluted environment; (b) the organism should have the potential to get access to the contaminant that is generally adsorbed to solid surfaces or not soluble in aqueous environments; (c) the organisms

must have effective enzymes responsible for bio-remedi-ation; (d) the active site of the enzymes concerned with bioremediation must be accessible to the substrate; (e) there must be a close intra or extracellular contact in enzymatic and contaminant system, (f) have capability to survive and fluorish in the harsh polluted eecosystems. Most of the widely detected microbes in the contaminated sites are Pseu-domonas species. In 1974, the first patent to be registered for petroleum degradation as a bioremediation agent was Pseu-domonas putida (Prescott et al. 2002). Further, petroleum and oil slicks can also be biodegraded using Corynebacteria, Mycobacteria, Pseudomonads, and yeasts as a (Sardrood et al. 2013). A number of the aerobic bacteria that are known as pesticide and hydrocarbon (both alkanes and polyaro-matic) degraders most often include Pseudomonas, Alca-ligens, Sphingomonas, Rhodococcus, and Mycobacterium (Table 1). Aerobic bacteria are more frequently used for the process in comparison to  anaerobic bacteria. Anaerobic bacteria are known to degrade polychlorinated biphenyls (PCBs), chloroform, dechlorinate and trichloroethylene (TCE) in sediments (such as lake and river beds). Among the fungi, ligninolytic ones such as Phanaerochaete chrys-osporium have been found to be useful in the bioremediation of a variety of recalcitrant poisonous environmental pollut-ants namely plastics, TNT, DDT, and several high molecu-lar weight polynuclear aromatics. Moreover, methylotrophs are also known to be involved with the bioremediation of a wide range of contaminants including 1,2-dichloroethane, chlorinated aliphatic trichloroethylene, and various other. Geobacter metallireducens has the potential to reduce met-als and convert them into non-toxic forms. It helps in the removal of uranium from mining operations, water draining systems and the polluted groundwater (Kumar et al. 2011). Most of the hazardous compounds that cannot be mineral-ized individually by a microorganism can be degraded by microbial consortium. Among them, 2, 4, 6-trinitrotoluene (TNT), polychlorinated biphenyls, polyaromatic hydrocar-bons, aliphatic and aromatic halogenated organics, etc. are known to be degraded by microbial consortia. Microbial consortium degrades these pollutants in a stepwise manner and involves synergy and co-metabolism (Table 2).

Role of plants in bioremediation

Plants and their associated microorganisms play a signifi-cant role in the bioremediation of different toxic compounds (toxic PHC’s, PAHs, dyes, and pesticides) present in water, soil, sediments, etc. The process of phytoremediation involves different steps i.e. phytoextraction, phytostabiliza-tion phytovolatilization, phytodegradation and phytofiltra-tion (Alkorta et al. 2004) (Fig. 2).

Phytoaccumulation which is also known as phytoex-traction is a process in which plants accumulate or extract

98 Environmental Sustainability (2020) 3:91–103

1 3

the contaminants directly into their shoots and roots, after which these plants can be collected and incinerated. Usu-ally, by this method, contamination of heavy metals such as Ni, Hg, and Cd are remediated. In another process known as phytostabilization (or phytoimmobilization), plants trim down the movement, availability, erosion, leaching, of soil contaminants, thereby blocking their route towards ground-water or into the food system. In soil system plants also help in immobilizing heavy metals through precipitation, sorption via roots, reducing metal valance and, complex formation in the root rhizosphere. Remediation of several volatile heavy metals such as Hg and Se is also associated with plants through a process known as phytovolatilization (Karami and Shamsuddin 2010). In this process, the plant

takes up the soluble pollutants from the water via the roots, transfers them to the foliage and later volatilizes them into the atmosphere with the help of stomata. A limitation to this process is that it does not leads to the complete elimination of pollutants but instead causes their movement from one medium to other from where they can again enter the soil and water. Another important process of pollutant reme-diation by plants is known as phytodegradation, in which there is breakdown or transformation of metals into less toxic forms by the help of intrinsic or secreted enzymes. It is also known as phytotransformation. This helps in the elimination of polar organic contaminants like atrazine and also non-polar organic pollutants such as phenanthrene. Similar to phytodegradation is rhizosphere degradation or

Table 1 Potential microbes associated with the bioremediation of toxic pollutants

Pollutant Microorganism (s) References

Atrazine Acinetobacter species Singh et al. (2004b)Enterobacter spp., Bacillus spp., Providencia sp,

and Pseudomonas spp.El-Bestawy et al. (2014)

Methyl tert-butyl ether Hydrogenophaga flava ENV735 Streger et al. (2002)β-Proteobacterium strain PM1 Smith et al. (2005)

Carbon tetrachloride Pseudomonas stutzeri KC Dybas et al. (2002)Orange3,4-(4nitrophenylazo) aniline Pleurotus ostreatus Zaho (2006)2,4-Dichlorophenoxyacetic acid Ralstonia eutropha (pJP4) Daane and Häggblom (1999)

Ralstonia eutropha JMP134 Roane et al. (2001)Chlorpyrifos Bacterium strain B-14 Singh et al. (2004a)Benzene, toluene, and o-xylene (BTX). Pseudomonas putida MHF 7109 Singh and Fulekar (2010)Benzene, anthracene, hydrocarbons PCB’s Pseudomonas spp. Cybulski et al. (2003)Halogenated hydrocarbons, phenoxyacetates Bacillus spp. Cybulski et al. (2003)Hydrocarbons aromatics Rhodococcus spp. Dean-Ross et al. (2002)Organochlorine (lindane) Streptomyces spp. Fuentes et al. (2010)Glyphosate Pseudomonas puteda, P. aeruginosa and Acine-

tobacter faecalisOlawale and Akintobi (2011)

Organophosphorous pesticide-malathion Staohylococcus aureua Akilandeswari and Sona (2013)

Table 2 Microbial consortium involved in the biodegradation of recalcitrant compounds

Compound Organism References

Atrazine Consortia degrading atrazine Goux et al. (2003)1,1,1-Trichloroethane Butane-utilizing enrichment culture Jitnuyanont et al. (2001)Chloroethenes Consortium that contains Dehalococcoides Adamson et al. (2003)

Consortium that contains Dehalococcoides Major et al. (2002)Chlorobenzenes P. putidaGJ31, P. aeruginosaRHO1 and P. putidaF1ΔCC Wenderoth et al. (2003)BTEX Methanogenic consortia Da Silva and Alvarez (2004)Polychlorinated biphenyl (soil) Arthrobacter sp. B1B and Ralstoniaeutrophus H850 Singer et al. (2000)Toluene Nitrate-reducing genera Azoarcus and Thauera, iron- reducing Geo-

bacter metallireducensHarwood and Gibson (1997)

Tolune Pseudomonas Putida strain mt-2 Thauera aromatic strain K172, Geobacter metallireducens

Meckenstock et al. (1999)

99Environmental Sustainability (2020) 3:91–103

1 3

rhizodegradation that reduces the toxicity of contaminants through the enzymatic action of rhizospheric microorgan-isms. Rhizoremediation helps in improving the plant growth and development and in turn microbes receive nutrients from the plant. It generally helps in the remediation of organic pollutants such as PHCs and PAHs from soil. For elimi-nating contaminants from water and other aqueous streams plants perform phytofiltration. This process involves the absorption or adsorption of the metals thus reducing their mobility in underground water. Depending upon the part of the plant involved in the process, it can be defined as blasto-filtration (when seedlings are used), rhizofiltration (when roots of plants are used) or caulofiltration (when excised plant shoots are used) (Mesjasz-Przybylowicz et al. 2004).

For the phytoremediation of PHC-polluted soil, some of the efficiently involved plants are Italian ryehrass (Lolium perenne), sorghum (Sorghum bicolour), maize (Zea mays), tall fescue (Festuca arundinacea), alfalfa (Medicago sativa var. Harpe), elephant grass (Pennisetum purpureum), Ber-muda grass (Cynodon dactylon), birdsfoot trefoil (Lotus cor-niculatus var. Leo), sunflower (Helianthus annuus), south-ern crabgrass (Digitaria sanguinalis), red clover (Trifolium

pratense), beggar ticks (Bidens cernua) and sedge species (Cyperus rotundus) (Ayotamuno et al. 2010; Basumatary et al. 2012, 2013; Hall et al. 2011; Tang et al. 2010; Yousaf et al. 2010).

Both microbial and phyto remediation processes are very viable approaches for the treatment of PHCs polluted sites. The use of plant-associated bacteria is considered to be very impactful to restore PHC polluted sites. Besides all the nutrients and factors necessary for microbial growth and multiplication are available in the rhizosphere as root exudates which enhances rate of bioremediation rate and PHC- degradation ability of bacteria is associated with the presence of catabolic genes and enzymes, which are responsible for the utilization of complex chemicals pre-sent in the mixture of petroleum for carbon and energy (Gupta et al. 2018, 2019). Also, the presence of bacteria can positively affect the plant directly or indirectly by pro-ducing phytohormones and inhibiting ethylene production. The concentration of pollutants is reduced by inoculating phytoremediators with the appropriate microorganisms. Also, the growth of the plant is increased by the inocu-lated microorganisms. Furthermore, some rhizobacteria

Fig. 2 Various processes associ-ated with phytoremediation of pollutants

100 Environmental Sustainability (2020) 3:91–103

1 3

(Azospirillum spp.) and endophytic bacteria (Pseudomonas spp.) have also been used for the remediation of PHC pol-luted soils (Cybulski et al. 2003).

Additional microbial processes for biodegradation: exploring microbial diversity

Still, a huge population of prokaryotes is unexplored hence tapping the potential of these bacteria can offer a better bioremediation along with understanding the interrelation-ship of bacteria in contaminated sites. In 1 g of soil there can be around 10,000 unknown prokaryotic species, and within each species there is diversity of bacteria (Torsvik and Ovreas 2002). However, these unculturable microor-ganisms are associated phylogenetically with the culturable minority (Zhou et al. 2003). Due to inefficient cultivation techniques, a large proportion of unculturable microbes have not been utilized as yet. So, to harness and use them first there is need to characterize the unculturable microbes phy-logenetically. A thorough study of contaminated sites has provided information on significant diversity about unknown and uncultured bacteria which are associated with biodeg-radation. Recently, several techniques have been generated for the characterization and monitoring of the functional diversity of microbes in different environments. 16S rDNA sequencing is a technique that can provide a better phyloge-netic relationship of particular microbes to the other micro-organisms (Zhou et al. 2003). The efficiency of molecular techniques can overcome the problem of accessing the microbial diversity of unexplored and unculturable bacteria of different surroundings including contaminated sites. Vari-ous studies (MacNaughton et al. 1999) reveal that culture-dependent methods are not sufficient enough to characterize the microbial population in an ecosystem; thus to overcome this, metagenomics can play an important role. Biological diversity of microorganisms can be accessed by recogniz-ing genes engaged in the production of commercially valu-able compounds like amylase, cellulase, chitinase, esterase, lipase etc (Daniel 2004; Rondon et al. 2000; Schloss and Handelsman 2003; Voget et al. 2003). Furthermore, the genome of unculturable microorganisms has also been rec-reated by recognizing overlapping fragments in the metagen-omics library and by ‘walking’ clone to clone, to put each chromosome together (Venter et al. 2004). Metagenomics can identify novel pathways and enzymes that can efficiently biodegrade pollutants which are otherwise poorly biodegrad-able. Further, the range of metagenomics can be enhanced by allowing desirable genes into hosts such as Pseudomonas sp., which have potential to degrade other pollutants (Daniel 2004; Martinez et al. 2004). Thus, the development of com-petent ‘designer biocatalysts’ can contribute to the improve-ment of bioremediation process.

Future prospects

Bioremediation is emerging as a necessity to clean up the planet of dangerous pollutants introduced due to anthro-pogenic activities. Though bioremediation is eco-friendly and economical for restoring the biological and physic-ochemical properties of the degraded soil (Arora 2018; Guang-Guo 2018), but still these in-situ techniques need to be improvised and more research and ethical issues need to be tackled for the use of improvised and efficient GEM’s. Moreover, the development of pollutant degrading micro-bial consortium requires more studies to determine the catabolic potential degrading microbes both individualy and in combination (Arora and Panosyan 2019). This will strengthen our understanding of microbial consortia-medi-ated remediation of contaminated sites. Various conserva-tive processes of bioremediation involve a considerable amount of volatile hydrocarbons which remain undegraded and can be transferred to the atmosphere through volatili-zation. Therefore, conventional methods require hydrocar-bon and waste remediation, which destroys the volatile organic fraction as well. For utilizing the full potential of known as well as novel species, it is very essential to expand our knowledge to know the interaction among microbial communities and the polluted environment. Aim of the forthcoming investigations should be in consolidat-ing all the omics-based studies along with computational approaches that will allow the researchers to build an obvi-ous and absolute knowledge of microbial mediated biore-mediation pathways. Undoubtedly, the methodical applica-tion of microbial consortia with back up and knowledge of well defined molecular and biochemical mechanisms will allow the successful implementation of bioremedia-tion techniques. The operations of these strategies are still in nascent stage; however with development of omics approches huge data is coming up that should be structured properly in a database. Application of omics strategies in the investigation of microbial molecular action leading to the conversion of hazardous pollutants would assist in trailing the desired organism and also effectively eradicat-ing the pollutants.

Conclusion

The knowledge regarding the perilous impacts of various chemical pollutants has directed towards enhancement in the research work to construct the methods of remedia-tion that could be useful to eliminate pollutants. Biore-mediation is one such method that is considered safe, inexpensive, environmentally amiable and removes the

101Environmental Sustainability (2020) 3:91–103

1 3

pollutants by speeding up the natural process of biodeg-radation. Therefore, to widen the knowledge of microbial communities and their reaction towards the environmental pollutants there is an urgent need for better understand-ing the microbial genetics to enhance pollutant degrading potential of the effective organisms. Undoubtedly, biore-mediation is rendering a pathway for a better pollution free planet leading to its sustainability.

Acknowledgements Authors are thankful to the Department of Zool-ogy, Kumaun University, SSJ Campus, Almora (Uttarakhand), India and for providing facility and space for this research work.

Compliance with ethical standards

Conflict of interest On behalf of all authors, the corresponding author states that there is no conflict of interest.

References

Adamson DT, McDade JM, Hughes JB (2003) Inoculation of a DNAPL source zone to initiate reductive dechlorination of PCE. Environ Sci Technol 37:2525–2533

Akilandeswari K, Sona V (2013) Efficiency of Staphylococcus aureu-sin the degradation an organo phosphorous pesticide Malathion. J Pharm Sci Innov 2:15

Alexander M (1994) Biodegradation and bioremediation. Academic Press, New York

Alkorta I, Hernández-Allica J, Becerril JM, Amezaga I, Albizu I, Garbisu C (2004) Recent findings on the phytoremediation of soils contaminated with environmentally toxic heavy metals and metalloids such as zinc, cadmium, lead, and arsenic. Rev Environ Sci Biotechnol 3:71–90

Arora NK (2018) Bioremediation: a green approach for restoration of polluted ecosystems. Env Sustain 1:305–307

Arora NK, Panosyan H (2019) Extremophiles: applications and roles in environmental sustainability. Env Sustain 2:217–218

Arora PK, Sasikala C, Ramana CV (2012) Degradation of chlorin-ated nitroaromatic compounds. Appl Microbiol Biotechnol 93:2265–2277

Ayotamuno JM, Kogbara RB, Agele EA, Agoro OS (2010) Compost-ing and phytoremediation treatment of petroleum sludge. Soil Sediment Contam 19:686–695

Bargiela R, Herbst FA, Martínez-Martínez M, Seifert J, Rojo D, Cap-pello S (2015) Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation. Pro-teomics 15:3508–3520

Basumatary B, Bordoloi S, Sarma HP (2012) Crude oil-contaminated soil phytoremediation by using Cyperus brevifolius (Rottb.) Hassk Water. Air Soil Pollut 223:3373–3383

Basumatary B, Saikia R, Chandra Das H, Bordoloi S (2013) Field note: phytoremediation of petroleum sludge contaminated field using sedge species, Cyperus rotundus (Linn.) and Cyperus brevifolius (Rottb.) Hassk. Int J Phytoremediation 15:877–888

Brune KD, Bayer TS (2012) Engineering microbial consortia to enhance biomining and bioremediation. Front Microbiol 2:203

Bursle E, Robson J (2016) Non-culture methods for detecting infection. Aust Prescr 39:171

Chakraborty R, Wu CH, Hazen TC (2012) Systems biology approach to bioremediation. Curr Opin Biotechnol 23:483–490

Chiuchiolo AL (2004) Persistent organic pollutants at the base of the Antarctic marine food web. Environ Sci Technol 38:3551–3557

Cybulski Z, Dzuirla E, Kaczorek E, Olszanowski A (2003) The influ-ence of emulsifiers on hydrocarbon biodegradation by Pseu-domonadacea and Bacillacea strains. Spill Sci Technol Bull 8:503–507

Da Silva ML, Alvarez PJ (2004) Enhanced anaerobic biodegrada-tion of benzene-toluene-ethylbenzene-xylene-ethanol mixtures in bioaugmented aquifer columns. Appl Environ Microbiol 70:4720–4726

Daane L, Häggblom M (1999) Earthworm egg capsules as vectors for the environmental introduction of biodegradative bacteria. Appl Environ Microbiol 65:2376–2381

Daniel R (2004) The soil metagenome—a rich resource for the discov-ery of novel natural products. Curr Opin Biotechnol 15:199–204

Dean-Ross D, Moody J, Cerniglia CE (2002) Utilization of mixtures of polycyclic aromatic hydrocarbons by bacteria isolated from contaminated sediment. FEMS Microbiol Ecol 41:1–7

Dickson RP, Erb-Downward JR, Prescott HC, Martinez FJ, Curtis JL, Lama VN, Huffnagle GB (2014) Analysis of culture-dependent versus culture-independent techniques for identification of bac-teria in clinically obtained bronchoalveolar lavage fluid. J Clin Microbiol 52:3605–3613

Dong X et al (2019) Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sedi-ments. Nat Commun 10:1816

Duarte M, Nielsen A, Camarinha-Silva A, Vilchez-Vargas R, Bruls T, Wos-Oxley ML (2017) Functional soil metagenomics: elucida-tion of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation. Environ Microbiol 19:2992–3011

Dybas MJ et al (2002) Development, operation, and long-term per-formance of a full-scale biocurtain utilizing bioaugmentation. Environ Sci Technol 36:3635–3644

El-Bestawy E, Sabir J, Mansy A, Zabermawi N (2014) Comparison among the efficiency of different bioremediation technologies of Atrazine-contaminated soils. J Bioremed Biodeg 5:237

Fuentes MS, Benimeli CS, Cuozzo SA, Saez JM, Amoroso MJ (2010) Microorganisms capable to degrade organochlorine pesticides. Curr Res Technol Educ Top Appl Microbiol Microb Biotechnol 2(2):1255–1264

Gangola S, Joshi S, Kumar S, Pandey SC (2019) Comparative analysis of fungal and bacterial enzymes in biodegradation of xenobi-otic compounds. Smart bioremediation technologies: microbial enzymes. Academic Press, Cambridge, MA, pp 169–189

Garcia-Junco M, Gomez-Lahoz C, Niqui-Arroyo J-L, Ortega-Calvo J-J (2003) Biosurfactant-and biodegradation-enhanced partitioning of polycyclic aromatic hydrocarbons from nonaqueous-phase liquids. Environ Sci Technol 37:2988–2996

Gordillo F, Chavez FP, Jerez CA (2007) Motility and chemotaxis of Pseudomonas sp. B4 towards polychlorobiphenyls and chlo-robenzoates. FEMS Microbiol Ecol 60:322–328

Goux S, Shapir N, El Fantroussi S, Lelong S, Agathos SN, Pussemier L (2003) Long-term maintenance of rapid atrazine degradation in soils inoculated with atrazine degraders. Water Air Soil Pollut Focus 3:131–142

Guang-Guo Y (2018) Remediation and mitigation strategies. Inte-grated analytical approaches for pesticide management. Elsevier, Amsterdam

Gupta G, Chandra A, Varjani SJ, Banerjee C, Kumar V (2018) Role of biosurfactants in enhancing the microbial degradation of pyrene. In: Bioremediation: applications for environmental protection and management. Springer, Singapore

Gupta G, Kumar V, Pal AK (2019) Microbial degradation of high molecular weight polycyclic aromatic hydrocarbons with empha-sis on pyrene. Polycycl Aromat Compd 39:124–138

102 Environmental Sustainability (2020) 3:91–103

1 3

Hall J, Soole K, Bentham R (2011) Hydrocarbon phytoremedia-tion in the family Fabacea—a review. Int J Phytoremediation 13:317–332

Harwood CS, Gibson J (1997) Shedding light on anaerobic benzene ring degradation: a process unique to prokaryotes? J Bacteriol 179:301–309

Holmes DE, O’Neil RA, Chavan MA, N’Guessan LA, Vrionis HA, Perpetua LA (2009) Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments. ISME J 3:216–230

http://dx.doi.org/10.4172/2155-6199.10002 48https ://www.mdeq.ms.gov/wp-conte nt/uploa ds/2017/06/Biore media

tionJaiswal S, Singh DK, Shukla P (2019) Gene editing and systems biol-

ogy tools for pesticide bioremediation: a review. Front Microbiol 10:87

Jennings LK, Chartrand MMG, Lacrampe-Couloume G, Lollar BS, Spain JC, Gossett JM (2009) Proteomic and transcriptomic analyses reveal genes upregulated by cis-dichloroethene in Pola-romonas sp. strain JS666. Appl Environ Microbiol 75:3733–3744

Jitnuyanont P, Sayavedra-Soto LA, Semprini L (2001) Bioaugmenta-tion of butane-utilizing microorganisms to promote cometabo-lism of 1,1,1-trichloroethane in groundwater microcosms. Bio-degradation 12:11–22

Karami A, Shamsuddin ZH (2010) Phytoremediation of heavy met-als with several efficiency enhancer methods. Afr J Biotechnol 9:3689–3698

Kariyama R, Kumon H (2003) Biofilm infections. Nihon rinsho Jpn J Clin Med 61:266

Keum YS, Seo JS, Li QX, Kim JH (2008) Comparative metabolomic analysis of Sinorhizobium sp. C4 during the degradation of phen-anthrene. Appl Microbiol Biotechnol 80:863–872

Kim S-J, Kweon O, Jones RC, Freeman JP, Edmondson RD, Cerniglia CE (2007) Complete and integrated pyrene degradation pathway in Mycobacterium vanbaalenii PYR-1 based on systems biology. J Bacteriol 189:464–472

Kumar A, Bisht B, Joshi V, Dhewa T (2011) Review on bioremedia-tion of polluted environment: a management tool. Int J Environ Sci 1:1079

Lacerda CM, Reardon KF (2009) Environmental proteomics: applica-tions of proteome profiling in environmental microbiology and biotechnology. Brief Funct Genom Proteom 8:75–87

Lambert JM, Yang T, Thomson NR, Barker JF (2009) Pulsed biosparg-ing of a residual fuel source emplaced at CFB borden. Int J Soil Sediment Water 2:6

Lange C et al (2007) Genome-wide analysis of growth phase-dependent translational and transcriptional regulation in halophilic archaea. BMC Genom 8:415

Law AM, Aitken MD (2003) Bacterial chemotaxis to naphthalene desorbing from a nonaqueous liquid. Appl Environ Microbiol 69:5968–5973

Lima D et al (2009) Evaluating a bioremediation tool for atrazine con-taminated soils in open soil microcosms: the effectiveness of bioaugmentation and biostimulation approaches. Chemosphere 74:187–192

Luo Q, Zhang X, Wang H, Qian Y (2005) The use of non-uniform electrokinetics to enhance in situ bioremediation of phenol-con-taminated soil. J Hazard Mater 121:187–194

MacNaughton SJ, Stephen JR, Venosa AD, Davis GA, Chang YJ, White DC (1999) Microbial population changes during biore-mediation of an experimental oil spill. Appl Environ Microbiol 65:3566–3574

Major DW et al (2002) Field demonstration of successful bioaugmen-tation to achieve dechlorination of tetrachloroethene to ethene. Environ Sci Technol 36:5106–5116

Malik A (2006) Bioremediation. In: Environmental Microbiology. national science digital library, (xth five year plan network pro-ject of NISCAIR (CSIR), UGC, MHRD, New Delhi)

Malla MA, Dubey A, Yadav S, Kumar A, Hashem A, Abd Allah EF (2018) Understanding and designing the strategies for the microbe-mediated remediation of environmental contaminants using omics approaches. Front Microbiol 9:1132

Martinez A, Kolvek SJ, Yip CL, Hopke J, Brown KA, MacNeil IA, Osburne MS (2004) Genetically modified bacterial strains and novel bacterial artificial chromosome shuttle vectors for con-structing environmental libraries and detecting heterologous natural products in multiple expression hosts. Appl Environ Microbiol 70:2452–2463

Meckenstock RU, Morasch B, Warthmann R, Schink B, Annweiler E, Michaelis W, Richnow HH (1999) 13C/12C isotope fractionation of aromatic hydrocarbons during microbial degradation. Environ Microbiol 1:409–414

Mesjasz-Przybylowicz J et al (2004) Uptake of cadmium, lead, nickel and zinc from soil and water solutions by the nickel hyperaccu-mulator Berkheya coddii. Acta Biol Cracov Bot 46:75–85

Molin S, Klemm P, Poulsen L, Biehl H, Gerdes K, Andersson P (1987) Conditional suicide system for containment of bacteria and plas-mids. Nat Biotechnol 5:1315

Naik M, Duraphe M (2012) Review paper on–parameters affecting bioremediation. Int J Life Sci Pharma Res 2:L77–L80

Niu H, Wang J, Zhuang W, Liu D, Chen Y, Zhu C (2018) Compara-tive transcriptomic and proteomic analysis of Arthrobacter sp. CGMCC 3584 responding to dissolved oxygen for cAMP pro-duction. Sci Rep 8:1–13

Odukkathil G, Vasudevan N (2013) Enhanced biodegradation of endo-sulfan and its major metabolite endosulfate by a biosurfactant producing bacterium. J Environ Sci Health Part B 48:462–469

Olawale A, Akintobi O (2011) Biodegradation of glyphosate pesticide by bacteria isolated from agricultural soil Report and Opinion 3:124–128

Olson MS, Ford RM, Smith JA, Fernandez EJ (2004) Quantification of bacterial chemotaxis in porous media using magnetic resonance imaging. Environ Sci Technol 38:3864–3870

Pande V, Pandey SC, Joshi T, Sati D, Gangola S, Kumar S, Samant M (2019) Biodegradation of toxic dyes: a comparative study of enzyme action in a microbial system. In: Smart bioremediation technologies: microbial enzymes. pp 255

Pandey SC, Pande V, Sati D, Gangola S, Kumar S, Pandey A, Samant M (2019) Microbial keratinase: a tool for bioremediation of feather waste. In: Smart bioremediation technologies: microbial enzyme. pp 217

Pandey SC, Pandey A, Joshi T, Pande V, Sati D, Samant M (2019) Microbiological monitoring in the biodegradation of food waste. in: global initiatives for waste reduction and cutting food loss. In: IGI Global. pp 116–140

Petersen J (2011) Phylogeny and compatibility: plasmid classification in the genomics era. Arch Microbiol 193:313–321

Prescott LM, Harley JP, Klein DA (2002) Microbiology, 5th edn. McGrawHill, New York

Roane TM, Josephson KL, Pepper IL (2001) Dual-bioaugmentation strategy to enhance remediation of cocontaminated soil. Appl Environ Microbiol 67:3208–3215

Rondon MR et al (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547

Roy M, Giri AK, Dutta S, Mukherjee P (2015) Integrated phytobial remediation for sustainable management of arsenic in soil and water. Environ Int 75:180–198

Samant M, Pandey SC, Pandey A (2018) Impact of hazardous waste material on environment and their management strategies. In:

103Environmental Sustainability (2020) 3:91–103

1 3

Microbial biotechnology in environmental monitoring and cleanup. pp 175–192

Sardrood BP, Goltapeh EM, Varma A (2013) An introduction to biore-mediation. Fungi as bioremediators. Springer, Berlin, Heidel-berg, pp 3–27

Schloss PD, Handelsman J (2003) Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14:303–310

Shinde S (2013) Bioremediation. Overview Recent Res Sci Technol 5:67–72

Singer A, Gilbert E, Luepromchai E, Crowley D (2000) Bioremedia-tion of polychlorinated biphenyl-contaminated soil using carvone and surfactant-grown bacteria. Appl Microbiol Biotechnol 54:838–843

Garima T, Singh, SP (2016) Application of bioremediation on solid waste management: a review. Solid Waste Manag Policy Plan Sustain Soc 143

Singh D, Fulekar MH (2010) Biodegradation of petroleum hydrocar-bons by Pseudomonas putida strain MHF 7109 CLEAN–soil. Air Water 38:781–786

Singh BK, Walker A, Morgan JA, Wright DJ (2004a) Biodegrada-tion of chlorpyrifos by enterobacter strain B-14 and its use in bioremediation of contaminated soils. Appl Environ Microbiol 70:4855–4863

Singh P, Suri CR, Cameotra SS (2004b) Isolation of a member of Aci-netobacter species involved in atrazine degradation. Biochem Biophys Res Commun 317:697–702

Smith AE, Hristova K, Wood I, Mackay DM, Lory E, Lorenzana D, Scow KM (2005) Comparison of biostimulation versus bioaug-mentation with bacterial strain PM1 for treatment of groundwater contaminated with methyl tertiary butyl ether (MTBE). Environ Health Perspect 113:317–322

Streger SH, Vainberg S, Dong H, Hatzinger PB (2002) Enhancing transport of hydrogenophaga flava ENV735 for bioaugmenta-tion of aquifers contaminated with methyl tert-butyl ether. Appl Environ Microbiol 68:5571–5579

Tang YJ, Martin HG, Dehal PS, Deutschbauer A, Llora X, Meadows A (2009) Metabolic flux analysis of Shewanella spp. reveals evo-lutionary robustness in central carbon metabolism. Biotechnol Bioeng 102:1161–1169

Tang J, Wang R, Niu X, Zhou Q (2010) Enhancement of soil petroleum remediation by using a combination of ryegrass (Lolium perenne) and different microorganisms. Soil Tillage Res 110:87–93

Techtmann SM, Hazen TC (2016) Metagenomic applications in envi-ronmental monitoring and bioremediation. J Ind Microbiol Bio-technol 43:1345–1354

Torres B, Jaenecke S, Timmis KN, García JL, Díaz E (2003) A dual lethal system to enhance containment of recombinant micro-organisms. Microbiology 149:3595–3601

Torsvik V, Ovreas L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245

Tripathi M, Singh D, Vikram S, Singh V, Kumar S (2018) Metagen-omic approach towards bioprospection of novel biomolecule(s) and environmental bioremediation. Annu Res Rev Biol 22:1–12

Urgun-Demirtas M, Stark B, Pagilla K (2006) Use of genetically engi-neered microorganisms (GEMs) for the bioremediation of con-taminants. Crit Rev Biotechnol 26:145–164

Van Deuren J, Lloyd T, Chhetry S, Raycharn L, Peck J (2002) Reme-diation technologies screening matrix and reference guide, vol 4. Federal Remediation Technologies Roundtable

Venter JC et al (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74

Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, Halfvarson J, Lefsrud MG, Apajalahti J, Tysk C, Hettich RL, Jansson JK (2009) Shotgun metaproteomics of the human distal gut microbiota. ISME J 3:179

Voget S, Leggewie C, Uesbeck A, Raasch C, Jaeger KE, Streit WR (2003) Prospecting for novel biocatalysts in a soil metagenome. Appl Environ Microbiol 69:6235–6242

Wenderoth D, Rosenbrock P, Abraham W-R, Pieper D, Höfle M (2003) Bacterial community dynamics during biostimulation and bio-augmentation experiments aiming at chlorobenzene degradation in groundwater. Microb Ecol 46:161–176

Yousaf S, Ripka K, Reichenauer T, Andria V, Afzal M, Sessitsch A (2010) Hydrocarbon degradation and plant colonization by selected bacterial strains isolated from Italian ryegrass and birds-foot trefoil. J Appl Microbiol 109:1389–1401

Zhao B, Yeo CC, Poh CL (2005) Proteome investigation of the global regulatory role of s54 in response to gentisate induction in Pseu-domonas alcaligenes NCIMB 9867. Proteomic 5:1868–1876

Zhao X, Hardin IR, Hwang HM (2006) Biodegradation of a model azo disperse dye by the white rot fungus Pleurotus ostreatus. Int Biodeterior Biodegrad 57:1–6

Zhou J et al (2003) Bacterial phylogenetic diversity and a novel candi-date division of two humid region, sandy surface soils. Soil Biol Biochem 35:915–924

Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.