Feasibility of bioremediation of trichloroethylene contaminated sites by nitrifying bacteria through cometabolism with ammonia

Trichloroethylene inhibits nitrogen transformation and microbial community structure in Mollisol

Trichloroethylene (TCE) is the most ubiquitous halogenated organic pollutant in the environment, it is one of the 129 priority control pollutants. In order to clarify the influence of TCE on microorganisms and nitrogen transformation in Mollisol is the core purpose of this study. Results showed that 10 mg kg^-1 TCE is the concentration limit of ammonification in Mollisol. When the concentration of TCE reached 10 mg kg^-1 and the effect lasted for over 7 days, the process of ammonia oxidation to nitric acid in Mollisol will be affected. TCE affected the process of nitrate (NO₃^-) transformation into nitrite (NO₂^-) by affecting the activity of nitrate reductase, thereby affected the denitrification process in soil. When the concentration of TCE is more than 10 mg kg^-1 it reduced the ability of soil microorganisms to obtain nitrogen, thereby affecting soil nitrogen transformation. RDA (Redundancy analysis) showed that the activity of nitrate reductase and the number of nitrifying bacteria and denitrifying bacteria in soil was negatively correlated with the incubation of TCE. In addition, soil nitrate reductase, nitrite reductase, peroxidase activity, ammonifying bacteria, nitrifying bacteria and denitrifying bacteria were negatively correlated with TCE concentration. Beyond that PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) of functional gene structure depend on KEGG (Kyoto Encyclopedia of Genes and Genomes) showed that 20 mg kg^-1 TCE significantly inhibited the metabolism of energy and other substances in Mollisol. Based on the above, it is found that TCE significantly affected nitrification and denitrification in Mollisol, thus the nitrogen transformation in Mollisol was affected by TCE contamination.

Bioremediation of Hexanoic Acid and Phenanthrene in Oil Sands Tailings by the Microbial Consortium BioTiger™

Polycyclic aromatic hydrocarbons (PAHs) and naphthenic acids (NAs) are toxic contaminants of environmental concern found in process water and mature fine tailings, or tailings, from the oil sands industry. BioTiger™, a patented microbial consortium of twelve natural environmental isolates, was found to cometabolically biodegrade the NA hexanoic acid and the PAH phenanthrene in the presence of tailings. Hexanoamide was found to be produced and consumed during cometabolism of hexanoic acid. Mechanistic analysis demonstrated three of the BioTiger™ strains generated biosurfactants with the bacterial adhesion to hydrocarbons assay, seven with the methylene blue active substances assay, and nine with a hemolysis assay. Serial transfers of the BioTiger™ consortium demonstrated the stability of hexanoic acid degradation over several generations. The results demonstrate that BioTiger™ cometabolically biodegrades combinations of phenanthrene and hexanoic acid in tailings. This work reveals the potential for in situ bioremediation of tailings with this natural microbial consortium.

Roles of ammonia-oxidizing bacteria in improving metabolism and cometabolism of trace organic chemicals in biological wastewater treatment processes: A review

While there has been a significant recent improvement in the removal of pollutants in natural and engineered systems, trace organic chemicals (TrOCs) are posing a major threat to aquatic environments and human health. There is a critical need for developing potential strategies that aim at enhancing metabolism and/or cometabolism of these compounds. Recently, knowledge regarding biodegradation of TrOCs by ammonia-oxidizing bacteria (AOB) has been widely developed. This review aims to delineate an up-to-date version of the ecophysiology of AOB and outline current knowledge related to biodegradation efficiencies of the frequently reported TrOCs by AOB. The paper also provides an insight into biodegradation pathways by AOB and transformation products of these compounds and makes recommendations for future research of AOB. In brief, nitrifying WWTFs (wastewater treatment facilities) were superior in degrading most TrOCs than non-nitrifying WWTFs due to cometabolic biodegradation by the AOB. To fully understand and/or enhance the cometabolic biodegradation of TrOCs by AOB, recent molecular research has focused on numerous crucial factors including availability of the compounds to AOB, presence of growth substrate (NH₄-N), redox potentials, microorganism diversity (AOB and heterotrophs), physicochemical properties and operational parameters of the WWTFs, molecular structure of target TrOCs and membrane-based technologies, may all significantly impact the cometabolic biodegradation of TrOCs. Still, further exploration is required to elucidate the mechanisms involved in biodegradation of TrOCs by AOB and the toxicity levels of formed products.

Community composition of marine and brackish water ammonia-oxidizing consortia developed for aquaculture application

To mitigate the toxicity of ammonia in aquaculture systems, marine and brackish water ammonia-oxidizing bacterial consortia have been developed and are used for activation of nitrifying bioreactors integrated to recirculating aquaculture systems. To shed more light on to these biological entities, diversity of both the consortia were analyzed based on random cloning of 16S rRNA gene and ammonia-oxidizing bacterial specific amoA gene sequences. The dendrograms of representative clones on the basis of amplified ribosomal DNA restriction analysis generated 22 and 19 clusters for marine and brackish water nitrifying consortia, respectively. Phylogenetic analysis demonstrated the presence of various autotrophic nitrifiers belonging to α-, β- and γ-Proteobacteria, anaerobic ammonia oxidizers, heterotrophic denitrifiers, Bacteroidetes, and Actinobacteria. Distribution patterns of the organisms within the two consortia were determined using the software Geneious and diversity indices were investigated using Mega 5.0, VITCOMIC and Primer 7. The abundance of ammonia oxidizers was found in the order of 2.21 ± 0.25 × 10⁹ copies/g wet weight of marine consortium and 6.20 ± 0.23 × 10⁷ copies/g of brackish water consortium. Besides, marine ammonia-oxidizing consortium exhibited higher mean population diversity and Shannon Wiener diversity than the brackish water counterparts.

Natural attenuation potential of tricholoroethene in wetland plant roots: role of native ammonium-oxidizing microorganisms

Bench-scale microcosms with wetland plant roots were investigated to characterize the microbial contributions to contaminant degradation of trichloroethene (TCE) with ammonium. The batch system microcosms consisted of a known mass of wetland plant roots in aerobic growth media where the roots provided both an inoculum of root-associated ammonium-oxidizing microorganisms and a microbial habitat. Aqueous growth media, ammonium, and TCE were replaced weekly in batch microcosms while retaining roots and root-associated biomass. Molecular biology results indicated that ammonium-oxidizing bacteria (AOB) were enriched from wetland plant roots while analysis of contaminant and oxygen concentrations showed that those microorganisms can degrade TCE by aerobic cometabolism. Cometabolism of TCE, at 29 and 46 μg L(-1), was sustainable over the course of 9 weeks, with 20-30 mg L(-1) ammonium-N. However, at 69 μg L(-1) of TCE, ammonium oxidation and TCE cometabolism were completely deactivated in two weeks. This indicated that between 46 and 69 μg L(-1) TCE with 30 mg L(-1) ammonium-N there is a threshold [TCE] below which sustainable cometabolism can be maintained with ammonium as the primary substrate. However, cometabolism-induced microbial deactivation of ammonium oxidation and TCE degradation at 69 μg L(-1) TCE did not result in a lower abundance of the amoA gene in the microcosms, suggesting that the capacity to recover from TCE inhibition was still intact, given time and removal of stress. Our study indicates that microorganisms associated with wetland plant roots can assist in the natural attenuation of TCE in contaminated aquatic environments, such as urban or treatment wetlands, and wetlands impacted by industrial solvents.

Transcriptional responses of bacterial amoA gene to dimethyl sulfide inhibition in complex microbial communities

This study presented an approach by combining the real-time reverse transcription polymerase chain reaction with the terminal restriction fragment length polymorphism (T-RFLP) to investigate transcriptional responses of ammonia-oxidizing bacteria (AOB) to dimethyl sulfide (DMS) inhibition. Batch experiments with added ammonium and DMS were conducted using three activated sludges and Nitrosomonas europaea, and the transcriptional responses of the amo subunit A (amoA) mRNA were evaluated. It was found that DMS inhibited ammonium oxidation and amoA mRNA expression in all batch experiments but the inhibition degree observed was different for different sludges examined. It is likely that the different inhibitory effects of DMS on ammonium oxidation and amoA mRNA expression stemmed from different dominant AOB populations in the sludges. The T-RFLP results for amoA mRNA suggested that inhibition of ammonium oxidation by DMS to Nm. europaea-like AOB with T-RF 219/270 is relatively minor compared to other AOB populations in the examined sludges, such as Nm. europaea-like AOB with T-RF 491/491.

Nitrification and degradation of halogenated hydrocarbons--a tenuous balance for ammonia-oxidizing bacteria

The process of nitrification has the potential for the in situ bioremediation of halogenated compounds provided a number of challenges can be overcome. In nitrification, the microbial process where ammonia is oxidized to nitrate, ammonia-oxidizing bacteria (AOB) are key players and are capable of carrying out the biodegradation of recalcitrant halogenated compounds. Through industrial uses, halogenated compounds often find their way into wastewater, contaminating the environment and bodies of water that supply drinking water. In the reclamation of wastewater, halogenated compounds can be degraded by AOB but can also be detrimental to the process of nitrification. This minireview considers the ability of AOB to carry out cometabolism of halogenated compounds and the consequent inhibition of nitrification. Possible cometabolism monitoring methods that were derived from current information about AOB genomes are also discussed. AOB expression microarrays have detected mRNA of genes that are expressed at higher levels during stress and are deemed "sentinel" genes. Promoters of selected "sentinel" genes have been cloned and used to drive the expression of gene-reporter constructs. The latter are being tested as early warning biosensors of cometabolism-induced damage in Nitrosomonas europaea with promising results. These and other biosensors may help to preserve the tenuous balance that exists when nitrification occurs in waste streams containing alternative AOB substrates such as halogenated hydrocarbons.

Biological removal of the xenobiotic trichloroethylene (TCE) through cometabolism in nitrifying systems

In the present study, cometabolic TCE degradation was evaluated using NH(4)-N as the growth-substrate. At initial TCE concentrations up to 845 microg/L, TCE degradation followed first-order kinetics. The increase in ammonium utilization rate favored the degradation of TCE. This ensured that biological transformation of TCE in nitrifying systems is accomplished through a cometabolic pathway by the catalysis of non-specific ammonia oxygenase enzyme of nitrifiers. The transformation yield (T(y)) of TCE, the amount of TCE degraded per unit mass of NH(4)-N, strongly depended on the initial NH(4)-N and TCE concentrations. In order to allow a rough estimation of TCE removal and nitrification at different influent TCE and NH(4)-N concentrations, a linear relationship was developed between 1/T(y) and the initial NH(4)-N/TCE ratio. The estimated T(y) values lead to the conclusion that nitrifying systems are promising candidates for biological removal of TCE through cometabolism.

Kinetic analysis of the inhibitory effect of trichloroethylene (TCE) on nitrification in cometabolic degradation

In this study, the inhibitory effect of TCE on nitrification process was investigated with an enriched nitrifier culture. TCE was found to be a competitive inhibitor of ammonia oxidation and the inhibition constant (K(I)) was determined as 666-802 microg/l. The TCE affinity for the AMO enzyme was significantly higher than ammonium. The effect of TCE on ammonium utilization was evaluated with linearized plots of Monod equation (e.g., Lineweaver-Burk, Hanes-Woolf and Eadie-Hofstee plots) and non-linear least square regression (NLSR). No significant differences were found among these data evaluation methods in terms of kinetic parameters obtained.

Cometabolic degradation of TCE in enriched nitrifying batch systems

The aim of this study was to evaluate the effect of the trace pollutant trichloroethylene (TCE) on the nitrification process and to assess its cometabolic degradation. Nitrification was accomplished in batch suspended growth systems containing an enriched nitrifier culture. The presence of TCE resulted in both the inhibition of specific oxygen uptake rate (SOUR) and specific ammonium utilization rate (qNH(4)-N). In both SOUR and qNH(4)-N a 50% decrease was observed in a TCE concentration range of 1000-2000 ppb. TCE was cometabolically degraded by this enriched nitrifier culture. The cometabolic degradation of TCE was found to be dependent on initial TCE concentration. The results may be applicable in the treatment of TCE containing industrial wastewaters and contaminated groundwaters and soils.

Changes in soil microbial community composition induced by cometabolism of toluene and trichloroethylene

The effects of trichloroethylene (TCE) on microbial community composition were analyzed by reverse sample genome probing. Soil enrichments were incubated in dessicators containing an organic phase of either 1 or 10% (w/w) toluene in vacuum pump oil, delivering constant equilibrium aqueous concentrations of 16 and 143 mg/l, respectively. Increasing the equilibrium aqueous concentration of TCE from 0 to 10 mg/l led to shifts in community composition at 16, but not at 143 mg/l of toluene. In closed system co-degradation studies, TCE at an aqueous concentration of 1 mg/l was effectively degraded by toluene-degrading soil enrichments once the aqueous toluene concentration dropped below 25 mg/l. Little TCE degradation was observed at higher toluene concentrations (50-250 mg/l). The results indicate that TCE changes microbial community composition under conditions where it is being actively metabolized.

Identification and molecular characterization of a Bacillus subtilis IS13 strain involved in the biodegradation of 4,5,6-trichloroguaiacol

4,5,6-Trichloroguaiacol (4,5,6-TCG) is a recalcitrant organochlorine compound produced during pulp bleaching and a potential environmental hazard in paper mill effluents. We report here the identification by biochemical tests and molecular biological analysis, using 16S ribotyping, of a 4,5,6-TCG-degrading bacterium, identified as a strain of Bacillus subtilis that is most closely related according to the phylogenetic analysis to B. subtilis strain Lactipan (alignment score 99%). Biodegradation of 4,5,6-TCG by this organism in a mineral salts medium was shown to occur only when the inoculum was composed of cells in the stationary phase of growth and to be accelerated by an additional carbon source, such as glucose, sucrose, glycerol or molasses. An additional nitrogen source (as ammonium sulfate) did not affect the rate of 4,5,6-TGC removal. No plasmids were detected in the bacterial cells. This is the first strain of B. subtilis which degrades chlorophenols and shows that 4,5,6-TCG is not degraded by cometabolism and that the gene encoding this characteristic is probably located on the chromosome. The lack of requirement for additional nitrogen source, the ability to enhance biodegradation by adding cheap carbon sources such as molasses, and the fact the trait is likely to be stable since it is encoded on the cell chromosome, are all characteristics that make the organism an attractive possibility for treatment of wastes and environments polluted with organochlorine compounds.

Ammonia-oxidizing bacteria: a model for molecular microbial ecology

The eutrophication of many ecosystems in recent decades has led to an increased interest in the ecology of nitrogen transformation. Chemolitho-autotrophic ammonia-oxidizing bacteria are responsible for the rate-limiting step of nitrification in a wide variety of environments, making them important in the global cycling of nitrogen. These organisms are unique in their ability to use the conversion of ammonia to nitrite as their sole energy source. Because of the importance of this functional group of bacteria, understanding of their ecology and physiology has become a subject of intense research over recent years. The monophyletic nature of these bacteria in terrestrial environments has facilitated molecular biological approaches in studying their ecology, and progress in this field has been rapid. The ammonia-oxidizing bacteria of the beta-subclass Proteobacteria have become somewhat of a model system within molecular microbial ecology, and this chapter reviews recent progress in our knowledge of their distribution, diversity, and ecology.