Engineering bacteria for bioremediation

The treatment of environmental pollution by microorganisms is a promising technology. Various genetic approaches have been developed and used to optimize the enzymes, metabolic pathways and organisms relevant for biodegradation. New information on the metabolic routes and bottlenecks of degradation is still accumulating, enlarging the available toolbox. With molecular methods allowing the characterization of microbial community structure and activities, the performance of microorganisms under in situ conditions and in concert with the indigenous microflora will become predictable.     

Bioaugmentation and biostimulation strategies to improve the effectiveness of bioremediation processes

Bioremediation, involving bioaugmentation and/or biostimulation, being an economical and eco-friendly approach, has emerged as the most advantageous soil and water clean-up technique for contaminated sites containing heavy metals and/or organic pollutants. Addition of pre-grown microbial cultures to enhance the degradation of unwanted compounds (bioaugmentation) and/or injection of nutrients and other supplementary components to the native microbial population to induce propagation at a hastened rate (biostimulation), are the most common approaches for in situ bioremediation of accidental spills and chronically contaminated sites worldwide. However, many factors like strain selection, microbial ecology, type of contaminant, environmental constraints, as well as procedures of culture introduction, may lead to their failure. These drawbacks, along with fragmented literature, have opened a gap between laboratory trials and on-field application. The present review discusses the effectiveness as well as the limitations of bioaugmentation and biostimulation processes. A summary of experimental studies both in confined systems under controlled conditions and of real case studies in the field is presented. A comparative account between the two techniques and also the current scenario worldwide for in situ biotreatment using bioaugmentation and biostimulation, are addressed.     

Enhanced bioremediation efficiency of denim industrial effluent using bacterial biofilm onto polyurethane matrix (review)

This paper presents the review of the effects of bioremediation on the denim textile effluent using adapted bacterial cells immobilized on polyurethane foam. It further examines the various methods used in the biodecolorization of the industrial wastewater including the action of oxidative enzymes. Bacterial biofilms have great potential for the sustainable production of enzymes because of their high resistant, inherent characteristic of self immobilization and long term activity. It was also found that bacterial biofilm is widely used to treat textile wastewater because of the advantage derived from its ability to withstand under extreme conditions with their action of oxidoreductase enzymes.     

Cost-effective biostimulation strategy for wastewater decolorization using immobilized-cell systems

This study tended to evaluate threshold operation criteria of biostimulation for optimal biodecolorization in immobilized-cell systems (ICSs) using Porites corals as packing matrices. Indigenous Aeromonas hydrophila with high efficiency for decolorization isolated from Northeast Taiwan was used for study. As maximal treatment performance of ICS could only be achieved with maximal absorbed biomass with highest color removal capability. Maintaining optimal attached cells for cost-effective color removal efficiency inevitably required essential nutrients provided from rich media for biostimulation. With consideration of efficient cell attachment and maximal dye biodecolorization, our proposed method of “graphical reconstruction” quantitatively revealed the most economically-feasible strategy of medium stimulation for color removal. Our findings pointed out the maximal allowable inlet concentration and treatment capacity using our prediction of constant-slope isoclines of ICSs at cultures fed with different concentrations of nutrient sources. The method of isoclines upon transient dynamics of ICSs also provided a technically viable assessment for on-site professionals to quantitatively determine maximal biotreatment thresholds in biostimulation.     

Pilot plant for bioremediation of mercury-containing industrial wastewater

Mercury is an extremely toxic pollutant that is currently being emitted mainly by low level industrial sources. It is distributed globally through the atmosphere, from where it precipitates onto the surface of the Earth, enters aquatic organisms, accumulates in fish and finally affects the health of human populations. Microbes have evolved a mechanism for mercury detoxification [mercury resistance operon ( mer)] based on intracellular reduction of Hg(2+) to non-toxic Hg(0) by the mercuric reductase enzyme and subsequent diffusional loss of Hg(0) from the cell. It was shown that Hg(0) produced by microbial detoxification can be retained quantitatively in packed bed bioreactors, in which biofilms of mercury-resistant bacteria are grown on porous carrier material. This review describes operation of this system on a technical, fully automated, scale, and its operation at a chloralkali electrolysis factory. It was shown to work with high efficiency under fluctuating mercury concentrations and to be robust against transiently toxic conditions. The gradient of mercury concentration in the technical scale system exerted a strong selective pressure on the microbial community, which resulted in a succession of mercury-resistant strains at high mercury concentrations and an increase in phylogenetic and functional diversity at low mercury concentrations. Clean-up of mercury-containing wastewater by mercury-resistant microbes is a simple, environmentally friendly and cost-effective alternative to current treatment technologies.     

Bioprospection and selection of bacteria isolated from environments contaminated with petrochemical residues for application in bioremediation

The use of microorganisms with hydrocarbon degrading capability and biosurfactant producers have emerged as an alternative for sustainable treatment of environmental passives. In this study 45 bacteria were isolated from samples contaminated with petrochemical residues, from which 21 were obtained from Landfarming soil contaminated with oily sludge, 11 were obtained from petrochemical industry effluents and 13 were originated directly from oily sludge. The metabolization capability of different carbon sources, growth capacity and tolerance, biosurfactant production and enzymes detection were determined. A preliminary selection carried out through the analysis of capability for degrading hydrocarbons showed that 22% of the isolates were able to degrade all carbon sources employed. On the other hand, in 36% of the isolates, the degradation of the oily sludge started within 18–48 h. Those isolates were considered as the most efficient ones. Twenty isolates, identified based on partial sequencing of the 16S rRNA gene, were pre-selected. These isolates showed ability for growing in a medium containing 1% of oily sludge as the sole carbon source, tolerance in a medium containing up to 30% of oily sludge, ability for biosurfactant production, and expression of enzymes involved in degradation of aliphatic and aromatic compounds. Five bacteria, identified as Stenotrophomonas acidaminiphila BB5, Bacillus megaterium BB6, Bacillus cibi, Pseudomonas aeruginosa, and Bacillus cereus BS20 were shown to be promising for use as inoculum in bioremediation processes (bioaugmentation) of areas contaminated with petrochemical residues since they can use oily sludge as the sole carbon source and produce biosurfactants.     

Reductive dehalogenation of trichlorophenol in sediment from Rio-Bogotá, Colombia: the potential for intrinsic bioremediation and biostimulation

The domestic and industrial wastes from approximately 8 million residents are discharged to the Rio-Bogotá river. This study demonstrates the reductive dehalogenation of 2,4,6-trichlorophenol by Rio-Bogotá sediments and that the addition of an external carbon source can stimulate the process in microcosms.     

Glyphosate degradation by immobilized bacteria: field studies with industrial wastewater effluent.

Immobilized bacteria have been shown in the laboratory to effectively remove glyphosate from wastewater effluent discharged from an activated sludge treatment system. Bacterial consortia in lab columns maintained a 99% glyphosate-degrading activity (GDA) at a hydraulic residence time of less than 20 min. In this study, a pilot plant (capacity, 45 liters/min) was used for a field demonstration. Initially, activated sludge was enriched for microbes with GDA during a 3-week biocarrier activation period. Wastewater effluent was then spiked with glyphosate and NH4Cl and recycled through the pilot plant column during start-up. Microbes with GDA were enhanced by maintaining the pH at less than 8 and adding yeast extract (less than 10 mg/liter). Once the consortia were stabilized, the column capacity for glyphosate removal was determined in a 60-day continuous-flow study. Waste containing 50 mg of glyphosate per liter was pumped at increasing flow rates until a steady state was reached. A microbial GDA of greater than 90% was achieved at a 10-min hydraulic residence time (144 hydraulic turnovers per day). Additional studies showed that microbes with GDA were recoverable within (i) 5 days of an acid shock and (ii) 3 days after a 21-day dormancy (low-flow, low-maintenance) mode. These results suggest that full-scale use of immobilized bacteria can be a cost-effective and dependable technique for the biotreatment of industrial wastewater.     

Glyphosate degradation by immobilized bacteria: field studies with industrial wastewater effluent.

Immobilized bacteria have been shown in the laboratory to effectively remove glyphosate from wastewater effluent discharged from an activated sludge treatment system. Bacterial consortia in lab columns maintained a 99% glyphosate-degrading activity (GDA) at a hydraulic residence time of less than 20 min. In this study, a pilot plant (capacity, 45 liters/min) was used for a field demonstration. Initially, activated sludge was enriched for microbes with GDA during a 3-week biocarrier activation period. Wastewater effluent was then spiked with glyphosate and NH4Cl and recycled through the pilot plant column during start-up. Microbes with GDA were enhanced by maintaining the pH at less than 8 and adding yeast extract (less than 10 mg/liter). Once the consortia were stabilized, the column capacity for glyphosate removal was determined in a 60-day continuous-flow study. Waste containing 50 mg of glyphosate per liter was pumped at increasing flow rates until a steady state was reached. A microbial GDA of greater than 90% was achieved at a 10-min hydraulic residence time (144 hydraulic turnovers per day). Additional studies showed that microbes with GDA were recoverable within (i) 5 days of an acid shock and (ii) 3 days after a 21-day dormancy (low-flow, low-maintenance) mode. These results suggest that full-scale use of immobilized bacteria can be a cost-effective and dependable technique for the biotreatment of industrial wastewater.     

一株毒死蜱降解细菌的分离鉴定及其在土壤修复中的应用

从蔬菜大棚土壤中分离到一株能以毒死蜱为唯一碳源和能源生长的菌株DSP3,该菌在含毒死蜱（100mg/L）的酵母膏和蛋白胨与同样毒死蜱含量而无酵母膏蛋白胨的无机盐培养基中,18d对毒死蜱的降解率分别为986%和762%;在土壤实验中20d对毒死蜱（100mg/kg）的降解率接近100%,加入DSP3菌在蔬菜大棚新鲜土壤中能有效促进毒死蜱在土壤中的降解。根据生理生化特征、16S rDNA序列分析、（G+C）mol%测定和DNA同源性分析,将菌株DSP3鉴定为粪产碱杆菌（Alcaligenes faecalis）。     

Enhancing bioremediation of diesel-fuel-contaminated soil in a boreal climate: Comparison of biostimulation and bioaugmentation

Cold conditions delay bioremediation of oil hydrocarbons, but other bottlenecks also affect the outcome. Means to stimulate biodegradation of diesel oil hydrocarbons in contaminated soil were compared. Different combinations of nutrients, bulking agent, aeration, and microbial inocula were examined in lab simulations, and effective combinations were tested in field conditions. Bacterial communities were investigated by cloning and sequencing 16S-rRNA genes. Efficient degradation was attained when slow-release nutrients and aeration were used simultaneously. Bacterial inocula did not advance soil remediation, nor did they have any lasting effect on bacterial densities. Bacteria belonging to Proteobacteria were dominant in all cases. In the field test, a bulking agent promoting air passage through the soil ensured sufficient aeration, while forced air decreased the soil moisture excessively. We concluded that biostimulation via optimization of nitrogen and oxygen supply significantly improved bioremediation of oil-contaminated soil, while bioaugmentation had no additional effect.     

Uptake of lead by bacteria isolated from industrial effluents and their potential use in bioremediation of wastewater

Due to rising populations and human activities, heavy metals (HM) toxicity has become a serious problem for all life forms. The present study deals with isolating and identifying lead-resistant bacteria from contaminated wastewater of tanneries effluents. Two isolated strains were identified as Bacillus cereus (ID1), and Bacillus sp. (ID3), and both strains resisted a 25 mM concentration of Lead nitrate (Pb (NO₃)₂). After four days of treatment, Bacillus cereus (ID1) showed 80% lead uptake, and Bacillus sp. (ID3) showed 88%. Lead uptake was confirmed by Energy dispersive X-Ray (EDX) analysis. Fourier transform infrared spectroscopy (FTIR) showed that structural alterations had occurred in functional groups of the treated samples compared to the controls. Our research indicates that these Bacillus strains may be useful in bioremediating heavy metals from polluted environments. Further investigation into the processes involved in the uptake and homeostasis of heavy metals by these strains is required, as is the identification of the genes and enzymes responsible for Pb-bioremediation.     

Marine bacteria: potential candidates for enhanced bioremediation

Bacteria are widespread in nature as they can adapt to any extreme environmental conditions and perform various physiological activities. Marine environments are one of the most adverse environments owing to their varying nature of temperature, pH, salinity, sea surface temperature, currents, precipitation regimes and wind patterns. Due to the constant variation of environmental conditions, the microorganisms present in that environment are more suitably adapted to the adverse conditions, hence, possessing complex characteristic features of adaptation. Therefore, the bacteria isolated from the marine environments are supposed to be better utilized in bioremediation of heavy metals, hydrocarbon and many other recalcitrant compounds and xenobiotics through biofilm formation and production of extracellular polymeric substances. Many marine bacteria have been reported to have bioremediation potential. The advantage of using marine bacteria for bioremediation in situ is the direct use of organisms in any adverse conditions without any genetic manipulation. This review emphasizes the utilization of marine bacteria in the field of bioremediation and understanding the mechanism behind acquiring the characteristic feature of adaptive responses.     

Understanding the industrial application potential of lactic acid bacteria through genomics

Lactic acid bacteria (LAB) are a heterogeneous group of bacteria contributing to various industrial applications, ranging from food and beverage fermentation, bulk and fine chemicals production to pharmaceuticals manufacturing. Genome sequencing is booming; hitherto, 25 genomes of LAB have been published and many more are in progress. Based on genomic content of LAB, this review highlights some findings related to applications revealed by genomics and functional genomics analyses. Finally, this review summarizes mathematical modeling strategies of LAB in the context of genomics, to further our understanding of industrial related features.     

Comparative bioremediation of soils contaminated with diesel oil by natural attenuation, biostimulation and bioaugmentation

Bioremediation of diesel oil in soil can occur by natural attenuation, or treated by biostimulation or bioaugmentation. In this study we evaluated all three technologies on the degradation of total petroleum hydrocarbons (TPH) in soil. In addition, the number of diesel-degrading microorganisms present and microbial activity as indexed by the dehydrogenase assay were monitored. Soils contaminated with diesel oil in the field were collected from Long Beach, California, USA and Hong Kong, China. After 12 weeks of incubation, all three treatments showed differing effects on the degradation of light (C12-C23) and heavy (C23-C40) fractions of TPH in the soil samples. Bioaugmentation of the Long Beach soil showed the greatest degradation in the light (72.7%) and heavy (75.2%) fractions of TPH. Natural attenuation was more effective than biostimulation (addition of nutrients), most notably in the Hong Kong soil. The greatest microbial activity (dehydrogenase activity) was observed with bioaugmentation of the Long Beach soil (3.3-fold) and upon natural attenuation of the Hong Kong sample (4.0-fold). The number of diesel-degrading microorganisms and heterotrophic population was not influenced by the bioremediation treatments. Soil properties and the indigenous soil microbial population affect the degree of biodegradation; hence detailed site specific characterization studies are needed prior to deciding on the proper bioremediation method.     

Exploring threshold operation criteria of biostimulation for azo dye decolorization using immobilized cell systems

This follow-up study provided an evaluation on threshold operation criteria of biostimulation in immobilized cell systems (ICSs) with Aeromonas hydrophila onto packing materials Porites corals. Essential nutrients in appropriate flow rate for biostimulation were inevitably required to maintain maximum attached cell population for cost-effective biodecolorization. With the method of “graphical reconstruction”, the most economically feasible strategy of medium stimulation for color removal was quantitatively revealed. Our findings pointed out no matter what operation mode of reactor was (e.g., suspended batch cultures or ICS) color removal efficiency for A. hydrophila still strongly depended upon intrinsic kinetics and chemical reactivities of azo dyes. Mass transport effects in ICS might not play most significant roles to limit dye biodecolorization of A. hydrophila (except Reactive red 198, Reactive green 19), as relative rankings of color removal rates of various dyes were almost in parallel with those in suspended batch cultures.     

Intermittent aeration affects the bioremediation potential of two red algae cultured in finfish effluent

The high cost of aeration needed to tumble culture macroalgae is a limiting factor for integration with land-based finfish culture. Toward reducing this electricity cost, we compared intermittent aeration (16 h on:8 h off) with continuous aeration (24 h on) on the productivity of two strains of Chondrus crispus (Basin Head and Charlesville) and Palmaria palmata from Atlantic Canada between May and June 2011. Algal fronds were cultured under a 16:8-h light/dark photoperiod in 50-L tanks supplied with finfish effluent (49 μmol L^?1 of ammonium and 11 μmol L^?1 of phosphate) at a mean water flow rate of 0.4 L min^?1. Nitrogen (N) influx was 1.8 gN m^?2 day^?1, and phosphorus (P) influx was 0.9 gP m^?2 day^?1, with uptake rates ranging from 0.02 to 2.4 gN m^?2 day^?1 and ?0.2 to 0.4 gP m^?2 day^?1. On average, the macroalgae culture system (algae and biofilms) removed 1.0 gN m^?2 day^?1 (51.9 %). The growth of macroalgae (pooled across treatment and strain) ranged from 0.5 to 1.6 % day^?1, which accounted for a yield of 2.2 to 5.4 g DW m^?2 day^?1. Switching off aeration at night improved the growth rate of Basin Head Chondrus by 146 % and had no effect on growth rate or nitrogen and carbon removal by P. palmata and Charlesville Chondrus. Growth and yield of Basin Head Chondrus under intermittent aeration were over two times greater than both Charlesville Chondrus treatments.     

Arsenite oxidizing multiple metal resistant bacteria isolated from industrial effluent: their potential use in wastewater treatment

Arsenite oxidizing bacteria, isolated from industrial wastewater, showed high resistance against arsenite (40 mM) and other heavy metals (10 mM Pb; 8 mM Cd; 6 mM Cr; 10 mM Cu and 26.6 mM As⁵⁺). Bacterial isolates were characterized, on the basis of morphological, biochemical and 16S rRNA ribotyping, as Bacillus cereus (1.1S) and Acinetobacter junii (1.3S). The optimum temperature and pH for the growth of both strains were found to be 37 °C and 7. Both the strains showed maximum growth after 24 h of incubation. The predominant form of arsenite oxidase was extracellular in B. cereus while in A. junii both types of activities, intracellular and extracellular, were found_. The extracellular aresenite oxidase activity was found to be 730 and 750 µM/m for B. cereus and A. junii, respectively. The arsenite oxidase from both bacterial strains showed maximum activity at 37 °C, pH 7 and enhanced in the presence of Zn²⁺. The presence of two protein bands with molecular weight of approximately 70 and 14 kDa in the presence of arsenic points out a possible role in arsenite oxidation. Arsenite oxidation potential of B. cereus and A. junii was determined up to 92 and 88 % in industrial wastewater after 6 days of incubation. The bacterial treated wastewater improved the growth of Vigna radiata as compared to the untreated wastewater. It indicates that these bacterial strains may find some potential applications in wastewater treatment systems to transform toxic arsenite into less toxic form, arsenate.