Bacterial Bioremediation Research Articles

Gordonia sp. BSTG01 isolated from Hevea brasiliensis plantation efficiently degrades polyisoprene (rubber).

The online version contains supplementary material available at 10.1007/s13205-021-03063-5.

Factors Influencing the Bacterial Bioremediation of Hydrocarbon Contaminants in the Soil: Mechanisms and Impacts

The discharge of hydrocarbons and their derivatives to environments due to human and/or natural activities cause environmental pollution (soil, water, and air) and affect the natural functioning of an ecosystem. To minimize or eradicate environmental pollution by hydrocarbon contaminants, studies showed strategies including physical, chemical, and biological approaches. Among those strategies, the use of biological techniques (especially bacterial biodegradation) is critically important to remove hydrocarbon contaminants. The current review discusses the insights of major factors that enhance or hinder the bacterial bioremediation of hydrocarbon contaminants (aliphatic, aromatic, and polyaromatic hydrocarbons) in the soil. The key factors limiting the overall hydrocarbon biodegradation are generally categorized as biotic factors and abiotic factors. Among various environmental factors, temperature range from 30 to 40°C, pH range from 5 to 8, moisture availability range from 30 to 90%, carbon/nitrogen/phosphorous (C/N/P; 100:20:1) ratio, and 10–40% of oxygen for aerobic degradation are the key factors that show positive correlation for greatest hydrocarbon biodegradation rate by altering the activities of the microbial and degradative enzymes in soil. In addition, the formation of biofilm and production of biosurfactants in hydrocarbon-polluted soil environments increase microbial adaptation to low bioavailability of hydrophobic compounds, and genes that encode for hydrocarbon degradative enzymes are critical for the potential of microbes to bioremediate soils contaminated with hydrocarbon pollutants. Therefore, this review works on the identification of factors for effective hydrocarbon biodegradation, understanding, and optimization of those factors that are essential and critical.

Bacterial bioremediation: Strategies adopted by microbial-community to remediate lead from the environment

Bacterial bioremediation: Strategies adopted by microbial-community to remediate lead from the environment

Lead pollution and bacterial bioremediation: a review

Lead pollution and bacterial bioremediation: a review

Degradation and Detoxification of Congo Red azo dye by Immobilized Laccase of Streptomyces sviceus

The discharge of textile effluents enriched with reactive azo dyes is of critical importance owing to inability of the dyes to degrade in waste water and their carcinogenic, mutagenic effects to various organisms. This study initiated based on the need to gaze into molecular mechanism of marine bacterial bioremediation process to develop strategies for the decolorization and detoxification of the synthetic azo dyes. The experimental work carried out to explore decolorization and degradation efficacy of laccase derived from marine actinobacteria, Streptomyces sviceus by choosing Congo red-21 as model azo dye. The extracellular production of laccase was confirmed with plate assay in medium supplemented with ABTS as substrate. Laccase was purified to homogeneity from 72hrs culture of Streptomyces sviceus by Fast performance liquid chromatography and the molecular size of laccase was noticed as 60 kDa. The purified laccase was immobilized with an efficiency of 82% by Calcium alginate method. The crude, purified and immobilized forms of the laccase enzyme was used to decolorize the Congo red-21. Crude laccase enzyme showed 69% of decolorization of Congo red-21 after 48h where as purified and immobilized laccase represented 78% and 92% of colour removal after 24 h respectively. Fourier-transform infrared spectroscopy, High Performance Liquid Chromatography and Gas chromatography–mass spectrometry were used to unravel the molecular mechanism of dye detoxification and also identify nontoxic products released from Congo Red-21 upon administration with immobilized laccase. Based on GC-MS data, it may deduce that immobilized laccase of Streptomyces sviceus cleaves the Congo red-21 dye followed by oxidative cleavage, desulfonation, deamination, demethylation process.

Dye degradation potential of Acinetobacter baumannii strain VITVB against commercial azo dyes

The textile industry is an age-old industry in human civilization and to date, it contributes to a major portion of the economy in several nations. However, the generation of a huge volume of toxic colored effluent is a major environmental concern. Azo dyes are extensively used for textile dyeing and are thus found in the wastewater. In this article, bacterial bioremediation of azo dyes was studied. Acinetobacter baumannii strain VITVB, a gram-negative bacterium aerobically decolorized 500 mg L−1 of two textile azo dyes Reactive Blue 221 (RB-221) and Reactive Black 5 (RB-5) with 90% and 87% efficiency after 48 h under static condition. Dye degradation was further maximized by optimization studies. A. baumanii VITVB exerted maximum dye degradation within 24 h under optimized conditions of pH 9, temperature at 45 °C, 5% NaCl concentration, and supplementation of 1% starch (Carbon source) and 1% peptone (Nitrogen source) in growth media. Dye Degradation was then analyzed. Fourier transform infrared spectra of pure and degraded dyes revealed that the potential bacterial strain targeted the characteristic chromophore group (N = N) during the break down of dyes. High-performance liquid chromatography of pure and degraded dyes presented the emergence of different peaks at altered retention times, which also indicates the degradation of dyes. Gas Chromatography–Mass Spectrometry chromatogram revealed probable end products as diphenylmethane from RB-221 degradation and benzene,1,1'-Pentylidenebis from RB-5 degradation. Finally, phytotoxicity and biotoxicity assays implied the nontoxicity of the degraded metabolites of RB-221 and RB-5. Pure dyes inhibited seed germination, showed marked phenotypic changes and cellular damages in plants (Cicer arietinum and Tagetes erecta) while the degraded metabolites promoted a healthy seed germination rate and no marked cellular damages or phenotypic changes in plants. Artemia salina cysts also showed a similar pattern as major hatchability inhibition occurred with pure dyes compared to degraded dye metabolites.

A novel bioreactor system to purify contaminated runoff water

Water scarcity has become a global crisis and an economic burden. Environmental challenges in climate change, population growth, and urbanization have raised serious concerns for safe drinking water, food security, social stability, and public health. Current physicochemical purification techniques are costly, chemically-invasive, or ineffective. The aim of this study was to engineer an eco-friendly and cost-effective water purification system using an ex-situ bioremediation approach. The main objective was to use limestone, denitrifying bacteria, and sulfate-reducing bacteria present in the soil as natural resources. Organic compost was added as a carbon source to enhance activities of intrinsic soil bacteria. All samples were collected from mining and industrial sites in Eastern Pennsylvania. We evaluated and verified the feasibility of a novel modular bioreactor system for the effective removal of nitrate, sulfate, and heavy metals from runoff water while increasing its alkalinity. The impacts of pH and temperature on the bioremediation efficiency were evaluated, revealing ideal temperatures to be above 16°C and pH above 7. Nitrate levels dropped from 80 ppm to 0 ppm, and pH increased from 4 to above 7 consistently. Combining neutralization with bacterial bioremediation proved to have synergistic benefits within 30 minutes of treatment. Results showed a successful removal of nitrate (NO3-), sulfate (SO42-), sulfite (SO32-), Zinc (Zn), Copper (Cu), Aluminum (Al), and Lead (Pb) from contaminated wastewater. This system is a cost-effective, energy-efficient, and practical tool that opens numerous avenues for generating sustainable, portable, and fast water purification options for low-income communities. A large-scale system could be adapted for commercial or industrial purposes.

Efficiency of pyoverdines in iron removal from flocking asbestos waste: An innovative bacterial bioremediation strategy

The use of asbestos-containing products has been banned in many countries since the beginning of the 80′s due to its carcinogenic properties. However, asbestos is widely present in private and public buildings, resulting in the need to process a vast amount of asbestos-containing waste. Among the current technologies for the destruction of asbestos fibers, biodegradation by fungi, lichens, and, more recently, bacteria has been described. We previously reported the involvement of the bacterial siderophore pyoverdine in the release of iron from the two asbestos groups, serpentines and amphiboles. Among the large diversity encountered in the pyoverdine family, we examined whether these siderophores can alter flocking asbestos waste as well. All the tested pyoverdines were efficient in chrysotile-gypsum and amosite-gypsum weathering, although some exhibited higher iron dissolution. Iron was solubilized by pyoverdines from Pseudomonas aeruginosa and mandelii in a time-dependent manner from chrysotile-gypsum within 24 h. Renewal of pyoverdine-containing supernatant every 24 or 96 h allowed iron removal from chrysotile-gypsum at each cycle, until a limit was reached after 42 days of total incubation. Moreover, the dissolution was concentration-dependent, as demonstrated for the pyoverdine of P. mandelii. Pyoverdine-asbestos weathering could therefore become an innovative method to reduce anthropogenic waste.

Amelioration of heavy metal stress by endophytic Bacillus amyloliquefaciens RWL-1 in rice by regulating metabolic changes: potential for bacterial bioremediation.

This study aimed to investigate the bioremediation efficiency of phytohormone-producing endophytic Bacillus amyloliquefaciens RWL-1 isolated from rice seeds. In this study, we tested RWL-1 against various heavy metals (Cu, Cr, Pb, and Cd). Among the tested heavy metals, RWL-1 showed the highest tolerance for Cu stress and we observed alterations in growth kinetics with various Cu concentrations (1, 2.5, and 5 mM). We confirmed the biosorption potential of RWL-1 by scanning electron microscopy coupled with energy-dispersive X-ray spectrometry showing that Cu ions were adsorbed on RWL-1 cell surfaces. We further tested RWL-1 for its plant growth promoting and stress reliance efficiency in response to a dose-dependent increase in soil Cu (1, 2.5, and 5 mM). The RWL-1 inoculation significantly increased seedling biomass and growth attributes compared with non-inoculated control seedlings with and without Cu stress. Moreover, RWL-1 inoculation significantly promoted a physiochemical response in seedlings with and without Cu stress by reducing Cu uptake, improving carbohydrate levels (glucose, sucrose, fructose, and raffinose), enhancing amino acids regulation, and augmenting antioxidant levels (POD, PPO, and GHS). Levels of stress-responsive phytohormones such as abscisic acid (ABA) and jasmonic acid were significantly reduced in RWL-1-inoculated seedlings as compared with non-inoculated control seedlings under normal condition and same levels of Cu stress. In conclusion, the inoculation of B. amyloliquefaciens RWL-1 can significantly improve plant growth in Cu-contaminated soil and reduce metal accumulation, thus making plants safer for consumption. This approach could be tremendously helpful for safe and sustainable agriculture in heavy metal-contaminated areas.

The use of bacterial bioremediation of metals in aquatic environments in the twenty-first century: a systematic review.

Metal pollution is a current environmental issue as a consequence of unregulated anthropic activiy. A wide range of bioremediation strategies have been successfully implemented to recover contaminated areas. Among them, bacterial bioremediation stands out as a promising tool to confront these types of concerns. This study aimed to compare and discuss worldwide scientific evolution of bacterial potential for metal bioremediation in aquatic ecosystems. The study consisted of a systematic review, elaborated through a conceptual hypothesis model, during the period from 2000 to 2016, using PubMed, MEDLINE, and SciELO databases as data resources. The countries with the largest number of reports included in this work were India and the USA. Industrial wastewater discharge was the main subject associated to metal contamination/pollution and where bacterial bioremediations have mostly been applied. Biosorption is the main bioremediation mechanism described. Bacterial adaptation to metal presence was discussed in all the selected studies, and chromium was the most researched bioremedied substrate. Gram-negative Pseudomonas aeruginosas and the Gram-positive Bacillus subtilis bacteria were microorganisms with the greatest applicability for metal bioremediation. Most reports involved the study of genes and/or proteins related to metal metabolism and/or resistence, and Chromobacterium violaceum was the most studied. The present work shows the relevance of metal bacterial bioremediation through the high number of studies aimed at understanding the microbiological mechanisms involved. Moreover, the developed processes applied in removal and/or reducing the resulting environmental metal contaminant/pollutant load have become a current and increasingly biotechnological issue for recovering impacted areas.

Copper-resistant bacteria reduces oxidative stress and uptake of copper in lentil plants: potential for bacterial bioremediation.

For effective microbe-assisted bioremediation, metal-resistant plant growth-promoting bacteria (PGPB) must facilitate plant growth by restricting excess metal uptake in plants, leading to prevent its bio-amplification in the ecosystem. The aims of our study were to isolate and characterize copper (Cu)-resistant PGPB from waste water receiving contaminated soil. In addition, we investigated the phytotoxic effect of copper on the lentil plants inoculated with copper-resistant bacteria Providencia vermicola, grown in copper-contaminated soil. Copper-resistant P. vermicola showed multiple plant growth promoting characteristics, when used as a seed inoculant. It protected the lentil plants from copper toxicity with a considerable increase in root and shoot length, plant dry weight and leaf area. A notable increase in different gas exchange characteristics such as A, E, C i , g s , and A/E, as well as increase in N and P accumulation were also recorded in inoculated plants as compared to un-inoculated copper stressed plants. In addition, leaf chlorophyll content, root nodulation, number of pods, 1,000 seed weight were also higher in inoculated plants as compared with non-inoculated ones. Anti-oxidative defense mechanism improved significantly via elevated expression of reactive oxygen species -scavenging enzymes including ascorbate peroxidase, superoxide dismutase, catalase, and guaiacol peroxidase with alternate decrease in malondialdehyde and H2O2 contents, reduced electrolyte leakage, proline, and total phenolic contents suggesting that inoculation of P. vermicola triggered heavy metals stress-related defense pathways under copper stress. Overall, the results demonstrated that the P. vermicola seed inoculation confer heavy metal stress tolerance in lentil plant which can be used as a potent biotechnological tool to cope with the problems of copper pollution in crop plants for better yield.

Escherichia coli NemA Is an Efficient Chromate Reductase That Can Be Biologically Immobilized to Provide a Cell Free System for Remediation of Hexavalent Chromium

Hexavalent chromium is a serious and widespread environmental pollutant. Although many bacteria have been identified that can transform highly water-soluble and toxic Cr(VI) to insoluble and relatively non-toxic Cr(III), bacterial bioremediation of Cr(VI) pollution is limited by a number of issues, in particular chromium toxicity to the remediating cells. To address this we sought to develop an immobilized enzymatic system for Cr(VI) remediation. To identify novel Cr(VI) reductase enzymes we first screened cell extracts from an Escherichia coli library of soluble oxidoreductases derived from a range of bacteria, but found that a number of these enzymes can reduce Cr(VI) indirectly, via redox intermediates present in the crude extracts. Instead, activity assays for 15 candidate enzymes purified as His6-tagged proteins identified E. coli NemA as a highly efficient Cr(VI) reductase (kcat/KM = 1.1×105 M−1s−1 with NADH as cofactor). Fusion of nemA to the polyhydroxyalkanoate synthase gene phaC from Ralstonia eutropha enabled high-level biosynthesis of functionalized polyhydroxyalkanoate granules displaying stable and active NemA on their surface. When these granules were combined with either Bacillus subtilis glucose dehydrogenase or Candida boidinii formate dehydrogenase as a cofactor regenerating partner, high levels of chromate transformation were observed with only low initial concentrations of expensive NADH cofactor being required, the overall reaction being powered by consumption of the cheap sacrificial substrates glucose or formic acid, respectively. This system therefore offers promise as an economic solution for ex situ Cr(VI) remediation.

Recovery of mitosporic fungi actively growing in soils after bacterial bioremediation of oily sludge and their potential for removing recalcitrant hydrocarbons

Bacterial bioremediation is a widely used technique to remove or neutralize contaminants. However, the enzymatic capabilities of bacteria are limited and, consequently, recalcitrant compounds remain in the soil. Fungi can help to overcome this drawback, since their enzymatic repertoire is extensive. In this study, the diversity of viable, actively growing, filamentous fungi was explored in soils previously subjected to bioremediation with bacterial consortia from three petroleum exploitation fields. Diversity was estimated using both morphological traits and ITS rDNA sequencing. We recovered a highly diverse group of morphotypes from each field, most of them previously reported genera of fungi associated with bioremediation ( Aspergillus, Paecilomyces, and Penicillium), but a high proportion (40%) of the fungal species detected have never previously been reported as being involved in degradation of hydrocarbons. To build evidence of the isolates as potential bioremediation agents, their laccase and peroxidase activities were measured in vitro; peroxidase activity was a common trend in these fungi. The detection of peroxidase activity suggests adaptation of these fungi to the residual contaminants after bacterial action. Bioaugmentation of the fungal isolates in microcosms contaminated with oily sludge resulted in higher removal of the asphaltenic fraction compared to no bioaugmented microcosms. Our method allowed us to screen for and isolate viable mycelia within a contaminated environment, a strategy efficient for our environmental protection goals.

An Emphasis on Xenobiotic Degradation in Environmental Clean up

Setting up of new industries or expansion of existing industrial establishments resulted in the disposal of industrial effluents, which discharge untreated effluents causing air, water, soil and soil solid waste pollution. These disposed materials have high persistence capacities and also can change in to toxic recalcitrant up on combining with other eco-materials or manmade products. Remediation is the only way to tackle these so called xenobiotic compounds and to reduce the hazards caused by them. Even though, several practices have been implemented for degrading these recalcitrants, bioremediation step is proved to show the significa t impact on them. Giving a brief note on types of xenobionts and their impact on the environment, this study attempts to highlight on different xenobiotic degradation methods like bacterial bioremediation, phycoremediation, phytoremediation, photoremediation etc.

Surfactants and Bacterial Bioremediation of Polycyclic Aromatic Hydrocarbon Contaminated Soil—Unlocking the Targets

The activities of man produce significant levels of toxic polycyclic aromatic hydrocarbon compounds (PAHs), which have been identified as excellent candidates for biodegradative removal from contaminated sites. PAHs strongly sorb to soil particles and can also partition into a nonaqueous phase, often limiting bioavailability. In this context, synthetic surfactants and biosurfactants will be discussed as a means to mobilize and solubilize PAHs, potentially increasing bioavailability and subsequent microbial degradation. The fundamentals of bioremediation will be discussed as an important tool that can be used to reduce, remove, or attenuate pollutants at PAH-contaminated sites.

Use of Genetically Engineered Microorganisms (GEMs) for the Bioremediation of Contaminants

ABSTRACTThis paper presents a critical review of the literature on the application of genetically engineered microorganisms (GEMs) in bioremediation. The important aspects of using GEMs in bioremediation, such as development of novel strains with desirable properties through pathway construction and the modification of enzyme specificity and affinity, are discussed in detail. Particular attention is given to the genetic engineering of bacteria using bacterial hemoglobin (VHb) for the treatment of aromatic organic compounds under hypoxic conditions. The application of VHb technology may advance treatment of contaminated sites, where oxygen availability limits the growth of aerobic bioremediating bacteria, as well as the functioning of oxygenases required for mineralization of many organic pollutants. Despite the many advantages of GEMs, there are still concerns that their introduction into polluted sites to enhance bioremediation may have adverse environmental effects, such as gene transfer. The extent of horizontal gene transfer from GEMs in the environment, compared to that of native organisms including benefits regarding bacterial bioremediation that may occur as a result of such transfer, is discussed. Recent advances in tracking methods and containment strategies for GEMs, including several biological systems that have been developed to detect the fate of GEMs in the environment, are also summarized in this review. Critical research questions pertaining to the development and implementation of GEMs for enhanced bioremediation have been identified and posed for possible future research.

Mechanism of chromate reduction by the Escherichia coli protein, NfsA, and the role of different chromate reductases in minimizing oxidative stress during chromate reduction.

Chromate [Cr(VI)] is a serious environmental pollutant, which is amenable to bacterial bioremediation. NfsA, the major oxygen-insensitive nitroreductase of Escherichia coli, is a flavoprotein that is able to reduce chromate to less soluble and less toxic Cr(III). We show that this process involves single-electron transfer, giving rise to a flavin semiquinone form of NfsA and Cr(V) as intermediates, which redox cycle, generating more reactive oxygen species (ROS) than a divalent chromate reducer, YieF. However, NfsA generates less ROS than a known one-electron chromate reducer, lipoyl dehydrogenase (LpDH), suggesting that NfsA employs a mixture of uni- and di-valent electron transfer steps. The presence of YieF, ChrR (another chromate reductase we previously characterized), or NfsA in an LpDH-catalysed chromate reduction reaction decreased ROS generation by c. 65, 40, or 20%, respectively, suggesting that these enzymes can pre-empt ROS generation by LpDH. We previously showed that ChrR protects Pseudomonas putida against chromate toxicity; here we show that NfsA or YieF overproduction can also increase the tolerance of E. coli to this compound.

Chromate-reducing properties of soluble flavoproteins from Pseudomonas putida and Escherichia coli.

Cr(VI) (chromate) is a toxic, soluble environmental contaminant. Bacteria can reduce chromate to the insoluble and less toxic Cr(III), and thus chromate bioremediation is of interest. Genetic and protein engineering of suitable enzymes can improve bacterial bioremediation. Many bacterial enzymes catalyze one-electron reduction of chromate, generating Cr(V), which redox cycles, generating excessive reactive oxygen species (ROS). Such enzymes are not appropriate for bioremediation, as they harm the bacteria and their primary end product is not Cr(III). In this work, the chromate reductase activities of two electrophoretically pure soluble bacterial flavoproteins--ChrR (from Pseudomonas putida) and YieF (from Escherichia coli)-were examined. Both are dimers and reduce chromate efficiently to Cr(III) (kcat/Km = approximately 2 x 10(4) M(-1) x s(-1)). The ChrR dimer generated a flavin semiquinone during chromate reduction and transferred >25% of the NADH electrons to ROS. However, the semiquinone was formed transiently and ROS diminished with time. Thus, ChrR probably generates Cr(V), but only transiently. Studies with mutants showed that ChrR protects against chromate toxicity; this is possibly because it preempts chromate reduction by the cellular one-electron reducers, thereby minimizing ROS generation. ChrR is thus a suitable enzyme for further studies. During chromate reduction by YieF, no flavin semiquinone was generated and only 25% of the NADH electrons were transferred to ROS. The YieF dimer may therefore be an obligatory four-electron chromate reducer which in one step transfers three electrons to chromate and one to molecular oxygen. As a mutant lacking this enzyme could not be obtained, the role of YieF in chromate protection could not be directly explored. The results nevertheless suggest that YieF may be an even more suitable candidate for further studies than ChrR.

Characteristics of dam sediments with heavy metals at the Jinzu River, Toyama, Japan, and the experiment of bacterial bioremediation

Characteristics of dam sediments with heavy metals at the Jinzu River, Toyama, Japan, and the experiment of bacterial bioremediation

Limited Roles for Salicylate and Phthalate in Bacterial PAH Bioremediation

We have isolated and identified 12 previously unreported strains of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria. Three of these isolates belong to the genus Burkholderia, with the remainder comprised of two Pseudomonas species, and seven strains from the genus Sphingomonas. These isolates were examined for their ability to utilize a variety of three- to five-ring PAHs as sole sources of carbon and energy. All were also checked for the ability to grow on salicylic acid and phthalic acid, two compounds that are key intermediates in almost all published PAH degradative pathways. Only 3 of the 12 strains were able to grow on both of these monoaromatic acids, while three others (all Sphingomonas) could not grow on either. The implications of these findings on the universal applicability of known PAH catabolic pathways, and on possible induction of PAH degradation by pathway intermediates, are discussed.