research paper about bioremediation

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Bioremediation articles from across Nature Portfolio

Bioremediation is a process that uses living organisms, mostly microorganisms and plants, to degrade and reduce or detoxify waste products and pollutants.

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EDITORIAL article

Editorial: recent advances in bioremediation/biodegradation by extreme microorganisms.

• 1 Facultad de Ciencias Exactas, CINDEFI (CCT, La Plata-CONICET, UNLP), Universidad Nacional de la Plata, La Plata, Argentina
• 2 Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
• 3 Faculty of Sciences, Universiti Teknologi Malaysia, Skudai, Malaysia
• 4 Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
• 5 International Genome Centre, Jiangsu University, Zhenjiang, China

Editorial on the Research Topic Recent Advances in Bioremediation/Biodegradation by Extreme Microorganisms

To remediate polluted sites, biological processes have many advantages from economic, environmental, and practical aspects. Adsorption and biodegradation of organic contaminants and the immobilization, mobilization, and/or transformation of metal(loid)s are the main remediation processes that can be mediated by the action of several microorganisms especially those extremophiles surviving in hostile environments with high concentrations of pollutants. The aim of this Research Topic of Frontiers in Microbiology is to provide an appropriate platform to publish the latest results on the bioremediation of various pollutants by extremophilic pure cultures or microbial consortia. This Research Topic consists of 4 reviews and 7 original articles.

Marques reviewed the theme of extremophiles as microfactories which are able to provide genetic or metabolic mechanisms as controlled services to the clean-up of environmental pollution. The review focuses on metal and radionuclides pollution, and includes a discussion about the use of synthetic biology to improve the bioremediation processes.

Two articles in this Research Topic are focused on heavy metal(loid)s contaminants. Figueroa et al. described that several microorganisms exhibited high resistance to 19 metal(loid)s. Most of those strains displayed metal or metalloid reducing activity, and have been successfully used for the biological synthesis of nanostructures containing metal(loid)s. Tellurium and gold nanostructures showed antibacterial properties, which inhibited E. coli and L. monocytogenes growth. Acid mine drainage (AMD) is considered a severe environmental problem provoked by the microbial oxidation of sulfidic minerals. Gupta et al. explored the abundance and role of indigenous microorganisms displaying sulfate- and metal(loid)- reducing activity in the natural attenuation of an AMD impacted soil (AIS). The addition of nutrients (e.g., cysteine and lactate) to AIS increased the activity of such microorganisms achieving an increase in pH from 3.5 to 6.6, and reduction of sulfate (95%), iron (50%), and other heavy metals. In this way, Gupta et al. demonstrated that addition of nutrients could biostimulated the growth of some members of phylum Firmicutes (e.g., sulfate- and iron- reducing microorganisms) and bioremediate AMD impacted sites.

Orellana et al. reviewed extensively the most recent research on polyextremophilic microorganisms isolated from a wide range of extreme environments including salars, geothermal springs, deserts, ice fields, and diverse zones in Chile such as Altiplano, Atacama Desert, Central Chile, Patagonia, and Antarctica. This review also discussed the molecular and physiological capabilities of many of these isolates which were beneficial for bioremediation processes.

Diverse anthropogenic activities, particularly the emission due to the burning of fossil fuels, have triggered an alarming rise of CO 2 in the environment. A description of the measures of greenhouse gases emission is reviewed by Bose and Satyanarayana. In this review, authors discussed the merits and demerits of various approaches with extensive bibliographical material. Finally, a deep description of the use of carbonic anhydrases (CA) for biomineralization of CO 2 was included. This methodology was proposed as one of the most economical methods to mitigate global warming.

The other six articles in this Research Topic are related to the bioremediation of organic pollutants. Park and Park described the strategies for alkane degradation under extreme conditions (e.g., low and high temperatures, high salt, and acidic and anaerobic conditions). Alkane degraders seem to possess exclusive metabolic pathways and survival strategies. The thermophilic sulfate-reducing archaeon Archaeoglobus fulgidus uses a novel alkylsuccinate synthase for long-chain alkane degradation, and the thermophilic Candidatus Syntrophoarchaeum butanivorans anaerobically oxidizes butane via alkyl-coenzyme M formation. In addition to alkane degradation, extremophiles produce energy via the glyoxylate shunt and the Pta-AckA pathway when grown on a diverse range of alkanes under stress conditions.

Blázquez et al. focused on the bioremediation of aromatic compounds such as toluene and xylenes. The degradation of such pollutants is relevant due to their carcinogenic and neurotoxic effects to humans. This article provided evidences that the bss and bbs genes are not only essential for anaerobic degradation of toluene but also for m-xylene oxidation in the beta-proteobacterium Azoarcus sp. The peripheral pathway for the anaerobic oxidation of toluene would consist of an initial activation catalyzed by a benzylsuccinate synthase and a subsequent modified oxidation of benzylsuccinate to benzoyl-CoA and succinyl-CoA (both pathways encoded by bbs genes). Su et al. determined the crystal structure of the dibenzothiophene (DBT) sulfone monooxygenase ( BdsA ) from Bacillus subtilis at the resolution of 2.2 Å. This is one of the key enzymes in the 4S desulfurization pathway catalyzing the oxidation of DBT sulfone to 2′-hydroxybiphenyl 2-sulfonic acid. The structure of the BdsA-FMN complex at 2.4 Å was also determined. Finally, Su et al. showed that mutations in the residues involved in catalysis or flavin substrate-binding, resulted in a significant loss of enzymatic activity.

Meier et al. studies the catabolism of hydroxylated aromatic acids in A. adeninivorans and showed that the genes encoding enzymes involved catabolic pathway of gallic acid are induced using aromatic acid substrates as inducers. Through the construction of gallic acid decarboxylase disruption mutants, the authors showed that gallic acid decarboxylase Agdc1p was the only enzyme responsible for the transformation of gallic acid. They suggest that this enzyme might have useful industrial applications not only in bioremediation processes but also in synthesis of chemicals.

Chandra et al. detected that effluents discharged from the pulp and paper industry contain various refractory and androgenic compounds, even after secondary treatment by activated processes. Most of these compounds are classified as endocrine-disrupting chemicals and are environmental toxicants. This study also assessed the degradability of such compounds by biostimulation. The results suggested that pulp and paper mill wastewater, after this secondary detoxification process, could be safe for disposal.

Lastly, Kirtzel et al. investigated the ability of Schizophyllum commune to degrade black slates (e.g., metamorphic rocks rich in sulfides, heavy metals and organic matters). S. commune is a filamentous basidiomycete possesses a broad range of enzymes including multicopper oxidases such as laccases and laccase-like oxidases. Both life forms (haploid monokaryotic and mated dikaryotic strains) were able to degrade the slate releasing metals at the same time.

This Research Topic of Frontiers in Microbiology shows how bioremediation by means of extremophiles is an active research theme.

Author Contributions

All authors listed have made a substantial, direct and intellectual contribution to the work, and approved it for publication.

ED is Superior Researcher at CINDEFI (CONICET, Argentina) and acknowledges the financial support from ANPCYT (PICT 2015 0463 and PICT 2016 2535). This project was co-financially supported by Universiti Teknologi Malaysia RU grant (Grant number: 16H89) and (UK-SEA-NUOF) with project number 4B297. K-GC thanked University of Malaya for financial support (PPP grants: PG136-2016A, PG133-2016A, HIR grant: H50001-A-000027). RS acknowledges the support from National Science Foundation in the form of BuG ReMeDEE initiative (Award # 1736255).

Conflict of Interest Statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Keywords: pollutants, bioremediation, biodegradation, biomineralization, extremophiles

Citation: Donati ER, Sani RK, Goh KM and Chan K-G (2019) Editorial: Recent Advances in Bioremediation/Biodegradation by Extreme Microorganisms. Front. Microbiol. 10:1851. doi: 10.3389/fmicb.2019.01851

Received: 26 June 2019; Accepted: 26 July 2019; Published: 14 August 2019.

Reviewed by:

Copyright © 2019 Donati, Sani, Goh and Chan. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) . The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: Edgardo Rubén Donati, donati@quimica.unlp.edu.ar

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

Bioremediation: a green approach for restoration of polluted ecosystems

• Published: 23 November 2018
• Volume 1 , pages 305–307, ( 2018 )

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• Naveen Kumar Arora 1  

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Anthropogenic activities have resulted in deterioration of ecosystems throughout the globe making them unfit for survival of indigenous biological forms. This has also put a huge pressure on the fast receding natural resources. Environmental pollution has been a major concern over the past few decades influencing the quality of life. Rampant industrialization, improper agricultural methods, unchecked discharge of pollutants into land and water bodies has severely contaminated the ecosystems on earth. This has resulted in inadequate use of natural resources, increase in barren fields, loss of biodiversity, problem of potable water and huge economic losses which are very difficult to even estimate. Manmade chemicals are increasing by the day and many of them are recalcitrant and most being xenobiotic. As per estimates every year 10 million tons of toxic chemicals are released into the environment around the globe. Due to the addition of dangerous toxic chemicals such as polycyclic aromatic hydrocarbons (PAH), polychlorinated biphenyls (PCBs), soil and water systems have become contaminated. These pollutants are carcinogenic and are persistent, causing great harm to the ecosystems harming the health of the environment and causing damage to all life forms. Heavy metal pollution is another baleful influence of human activity on environment. Industrial processes including refineries, metal processing units, waste incineration, fossil fuel burning, nuclear power plants, lead based paints, plastics, electronic wastes, agrochemicals, pharmaceutical chemicals, vehicle exhausts, leather industries are the major sources of heavy metal contamination in the environment. Heavy metals degrade the quality of soil and water, rendering them unsustainable and of little or no use, also negatively impacting the biological health of ecosystems. The green revolution in 1950s or 60s although helped in increasing food productivity but caused acute toxification of the environment due to the injudicious use of chemical pesticides and fertilizers. Recalcitrant nature, particularly of the pesticides has resulted in their long term accumulation in soil, water and food chains. As per the report of Food and Agriculture Organization (FAO) production of pesticides has increased from 0.2 million tons in 1950 to 5 million tons in 2000 resulting in deterioration of fertile land, killing non-targeted microbes, birds, animals and proving fatal for human health. World Health Organization (WHO) estimates that pesticides cause quarter of a million premature deaths and over 3 million people are being hospitalized each year due to poisoning. Oil spills in oceans and on land have also played havoc with the respective ecosystems endangering the life and quality of natural systems to a great extent. In last 5 years 40,000 tonnes of oil was estimated to be spilled in the marine ecosystems through offshore mining, accidents, damaged tankers etc. The insoluble oil strata cuts off the oxygen supply and sunlight from entering the water body causing the death of flora and fauna, extinction of species and reduced microbial population. On land spilled oil forms a layer, impacting the oxygen levels and releasing toxic components, rendering the system non-fertile.

Apart from these, climate change caused by ever-increasing emission of green house gases (GHGs), has resulted in degradation of ecosystems due to rising temperature, droughts, floods etc. Incidences of heavy or very low rains have become common now throughout the globe causing flash floods or drought. Very recent floods in Kerala, India, one of the biggest in last 100 years in the region, have completely devastated the agricultural fields and yields due to accumulation of silt and washing off of the top soil. Similarly, wild fires in California have resulted in great loss to the forest, ecosystem of the region and also to human life, rendering the soil and the region greatly impacted. Incidences of heat waves in Europe and other parts of the world are now much more common. The impact of climate change and addition of chemicals has resulted in desertification and salinization of land resulting in lower productivity and lesser availability of biological resources. Approximately one billion hectares of land is suffering from the problem of salinity around the globe and this menace is increasing by the day. Water bodies including rivers, lakes or oceans have been impacted, causing great loss to their biodiversity or utility. With increasing human population we need more and more resources, productive fields, clean water bodies so as to get the maximum out of the natural resources. For this we have to clean-up the mess and remove toxic pollutants from the ecosystems, reclaim waste and marginal lands, saline soils, rejuvenate fresh water bodies and make oceans free of contaminants.

Over the years, various conventional methods like physical, chemical and thermal processes have been used to clean and remediate the ecosystems. But there have been several and some serious drawbacks associated with these processes, such as production of toxic intermediates, transport of contaminated soil/ water for treatment, high costs of treatment and inefficient revival of natural flora and fauna. However, use of biodegradation and bioremediation techniques involving biological systems such as microorganisms or their products and plants, are sustainable, cost effective options abating and rendering the pollutants harmless by natural biological activities. In bioremediation biological systems are applied for reclamation of the contaminated soil/ water by transformation of toxic pollutants into less hazardous or completely non-hazardous forms. The bioremediation technology includes extensive use of microorganisms or their enzymatic machineries, phytoremediation (plants) and rhizoremediation (plant and microbe interactions) techniques. Bioremediation is of two types depending on their site of application including cheaper and much effective in situ remediation where pollutants are treated on the site of contamination and the ex situ remediation where the contaminated samples are brought to laboratory and industries and are treated; used more for treatment of highly polluted but for smaller area or for systems such as ground water, where it is not advisable to add microbes or their enzymes. Technical aspects of bioremediation involve various mechanisms such as biosequestration, biodegradation, phytohydraulics, biological extraction, and volatilization by which microbes or plants immobilize or transform the complex moieties of the pollutants remediating the land and water. These biological systems have successfully been applied in cleaning up of ground water, lagoons, sludge, water streams, agricultural lands, oil spills, petroleum and hydrocarbon contaminated sites. Bioremediation through microorganisms generally involves the application of aerobic bacteria reported to degrade pesticides and hydrocarbons, both alkanes and polyaromatic compounds and several other pollutants. Anaerobic bacteria are used for bioremediation of PCBs in river sediments and dechlorination of trichloroethylene (TCE), and chloroform; lignolytic fungi for degradation of toxic and persistent pollutants; methylotrophs for remediation of chlorinated aliphatics trichloroethylene and 1, 2-dichloroethane and so on. Large scale treatment of petroleum hydrocarbon contamination in oceans, waste water treatment in polar regions, removal of toxic pollutants from agro-industrial wastes, treatment of polluted shorelines have been reported to be successfully done through microbial based bioremediation. Heavy metal contamination from soil is being effectively removed by microbial or phytoremediation techniques. Rhizoremediation is a cheap and efficient technique useful for remediation of contaminated soils by the combined action of plant and their symbiotic rhizosphere microbes. Plant growth promoting microbes have been used for reclamation of saline or non-fertile marginal lands by enhancing crop productivity. After repeated use year after year, these microbes with symbiotic partners i.e. plants help to reclaim the barren and saline soils making them fertile. This results in bioremediation of such wastelands and also control of climate change due to increased carbon sequestration by the remediated ecosystems. Many success stories of highly and vastly contaminated sites are now known, including long shore lines, as in Alaska oil spill, or decontamination of polluted soils or agriculture fields. Genetic engineering has very important role to play in the area of bioremediation. Capable microorganisms are engineered to improve their cell membrane transportation or their enzymatic attributes supporting the enhanced and wide spectral degradation of pollutants. “Superbugs” are the most popular examples of genetically engineered biological tools, significant in remediating oil spills and other toxic pollutants. Microbes are being engineered to have genes for degradation of multiple components of the complex crude oil and there are success stories in this area. Pyrosequencing, a next-generation molecular approach, is contributing to study pollutant-microbe interactions. With the help of pyrosequencing, environmental responses of microbes to contaminants, microbiome resistance against pollutants, diversity of fungal degrading genes in soil, can be known and used much more efficiently in bioremediation of contaminated sites. Quorum sensing properties of microbes have also been implemented for bioremediation as stimulation of signaling molecules like acylated homoserine lactone (AHL) also regulate gene expression for exopolysaccharides (EPS) and biofilm formation helping in degradation. Microbial fuel cells, microbial electrolysis cells and microbial desalination cells, bioelectrical wells and biofiltration are other advanced biotechnological approaches used for removal of various toxicants from the environment. Exploitation of effective genes from non-culturable microbes in a contaminated ecosystem can be used for degradation and remediation of complex or multiple polluted sites. Metagenomics, transcriptomics, metabolomics and fluxomics can play very important roles in future to identify the important genes involved in biodegradation, their expression, release of important enzymes and rates of metabolic reaction even in highly contaminated ecosystems. This can go a long way in improving the quality of stressed ecosystems, because most of them have huge populations of non-culturable microbes with great genetic pool and abilities to survive and flourish in such habitats. Need is to exploit them by the process of bioaugmentation of nutrients or through co-metabolism. Hence, although we have already achieved a bit in the area of bioremediation but a lot is yet to be explored and future of this green technology in cleaning up the environment is very bright.

Bioremediation has a great potential with notable achievements already reported from around the globe. But still this excellent and eco-friendly low input biotechnology has been underutilized. The global market scenario of bioremediation technology and services is showing an elevation with compound annual growth rate of 8.3% from 2017 to 2025. This can be much higher if exploited and developed properly. Bioremediation and biodegradation are the key focus areas of the journal “Environmental Sustainability”. We need to clean the mess created by anthropogenic activities through green technologies so as to provide a healthy and sustainable planet to the future generations.

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Arora, N.K. Bioremediation: a green approach for restoration of polluted ecosystems. Environmental Sustainability 1 , 305–307 (2018). https://doi.org/10.1007/s42398-018-00036-y

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Published : 23 November 2018

Issue Date : 01 December 2018

DOI : https://doi.org/10.1007/s42398-018-00036-y

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