Identification of genes specifically required for the anaerobic metabolism of benzene in Geobacter metallireducens

Assessing the impacts of oil contamination on microbial communities in a Niger Delta soil

Oil spills are a global challenge, contaminating the environment with organics and metals known to elicit toxic effects. Ecosystems within Nigeria's Niger Delta have suffered from prolonged severe spills for many decades but the level of impact on the soil microbial community structure and the potential for contaminant bioremediation remains unclear. Here, we assessed the extent/impact of an oil spill in this area 6 months after the accident on both the soil microbial community/diversity and the distribution of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHDGNα) genes, responsible for encoding enzymes involved in the degradation of PAHs, across the impacted area. Analyses confirmed the presence of oil contamination, including metals such as Cr and Ni, across the whole impacted area and at depth. The contamination impacted on the microbial community composition, resulting in a lower diversity in all contaminated soils. Gamma-, Delta-, Alpha- proteobacteria and Acidobacteriia dominated 16S rRNA gene sequences across the contaminated area, while Ktedonobacteria dominated the non-contaminated soils. The PAH-RHDαGN genes were only detected in the contaminated area, highlighting a clear relationship with the oil contamination/hydrocarbon metabolism. Correlation analysis indicated significant positive relationships between the oil contaminants (organics, Cr and Ni), PAH-RHDαGN gene, and the presence of bacteria/archaea such as Anaerolinea, Spirochaetia Bacteroidia Thermoplasmata, Methanomicrobia, and Methanobacteria indicating that the oil contamination not only impacted the microbial community/diversity present, but that the microbes across the impacted area and at depth were potentially playing an important role in degrading the oil contamination present. These findings provide new insights on the level of oil contamination remaining 6 months after an oil spill, its impacts on indigenous soil microbial communities and their potential for in situ bioremediation within a Niger Delta's ecosystem. It highlights the strength of using a cross-disciplinary approach to assess the extent of oil pollution in a single study.

The role of predicted chemotactic and hydrocarbon degrading taxa in natural source zone depletion at a legacy petroleum hydrocarbon site

Petroleum hydrocarbon contamination is a global problem which can cause long-term environmental damage and impacts water security. Natural source zone depletion (NSZD) is the natural degradation of such contaminants. Chemotaxis is an aspect of NSZD which is not fully understood, but one that grants microorganisms the ability to alter their motion in response to a chemical concentration gradient potentially enhancing petroleum NSZD mass removal rates. This study investigates the distribution of potentially chemotactic and hydrocarbon degrading microbes (CD) across the water table of a legacy petroleum hydrocarbon site near Perth, Western Australia in areas impacted by crude oil, diesel and jet fuel. Core samples were recovered and analysed for hydrocarbon contamination using gas chromatography. Predictive metagenomic profiling was undertaken to infer functionality using a combination of 16 S rRNA sequencing and PICRUSt2 analysis. Naphthalene contamination was found to significantly increase the occurrence of potential CD microbes, including members of the Comamonadaceae and Geobacteraceae families, which may enhance NSZD. Further work to explore and define this link is important for reliable estimation of biodegradation of petroleum hydrocarbon fuels. Furthermore, the outcomes suggest that the chemotactic parameter within existing NSZD models should be reviewed to accommodate CD accumulation in areas of naphthalene contamination, thereby providing a more accurate quantification of risk from petroleum impacts in subsurface environments, and the scale of risk mitigation due to NSZD.

Geobacter benzoatilyticus sp. nov., a novel benzoate-oxidizing, iron-reducing bacterium isolated from petroleum contaminated soil

A strictly anaerobic bacterial strain, designated Jerry-YXT, was isolated from petroleum-contaminated soil sampled in China. Strain Jerry-YXT was a Gram-stain-negative bacterium forming reddish colonies. It grew optimally at 30 °C and pH 7.0, and tolerated 1.0 % (w/v) NaCl. Strain Jerry-YXT was able to use fumarate, ferric citrate and ferrihydrite as electron acceptors, and ethanol, acetate and benzoate as electron donors. The major fatty acids of this strain were C16 : 0 and C16 : 1  ω7c/C16 : 1  ω6c (summed feature 3). The 16S rRNA gene sequence-based phylogenetic analysis placed this strain in the genus Geobacter , being most closely related to Geobacter metallireducens (98.2 % similarity), Geobacter hydrogenophilus (98.1 %) and Geobacter grbiciae (98.0 %). The DNA G+C content was 57.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between the genomes of strain Jerry-YXT and G. metallireducens GS-15T were 81.8 and 35.4 %, respectively. The results of the polyphasic study allowed the genotypic and phenotypic differentiation of strain Jerry-YXT from its closest species, which suggested that strain Jerry-YXT represents a novel species of the genus Geobacter . The name for the proposed new species is Geobacter benzoatilyticus sp. nov. The type strain is Jerry-YXT (=MCCC 1K05659T=JCM 39190T).

Anaerobic phenanthrene biodegradation by a newly isolated sulfate-reducer, strain PheS1, and exploration of the biotransformation pathway

Phenanthrene is a widespread and harmful polycyclic aromatic hydrocarbon that is difficult to anaerobically biodegrade. Current challenges in anaerobic phenanthrene bioremediation are a lack of degrading cultures and limited knowledge of biotransformation pathways. Under sulfate-reducing conditions, pure-cultures and biotransformation processes for anaerobic phenanthrene biodegradation are poorly understood. In this study, strain PheS1, which is phylogenetically closely related to Desulfotomaculum, was found to be a sulfate-reducing phenanthrene-degrading bacterium. Anaerobic phenanthrene biodegradation using PheS1 was proposed based on metabolite and genome analyses, and the initial step was identified as carboxylation based on the detection of 2-phenanthroic acid, [¹³C]-2-phenanthroic acid, and [D9]-2- phenanthroic acid when phenanthrene+HCO₃^-, phenanthrene+H¹³CO₃^-, and [D10]-phenanthrene+HCO₃^- were used as the substrate, respectively. PheS1 genome ubiD gene encoding of carboxylase putatively involved in the biodegradation was performed. Next, benzene ring reduction and cleavage that produced benzene compounds and cyclohexane derivative were reported to occur in the downstream biotransformation processes. Additionally, benzene, naphthalene, benz[a]anthracene, and anthracene can be utilised by PheS1, whereas pyrene and benz[a]pyrene cannot. We discovered a new phenanthrene-degrading sulfate-reducer and provided the anaerobic phenanthrene biotransformation pathway under sulfate-reducing conditions, which can act as a reference for practical applications in bioremediation and for studying the molecular mechanisms of phenanthrene in anaerobic zones.

Investigation of anaerobic biodegradation of phenanthrene by a sulfate-dependent Geobacter sulfurreducens strain PheS2

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous and harmful contaminants, which can be degraded aerobically. However, the persistence of PAHs in anoxic environments indicates that anaerobic biodegradation of PAHs should also be investigated. Pure-culture and biotransformation processes for anaerobic phenanthrene biodegradation with sulfate as a terminal electron acceptor remains in its infancy. In this study, we investigated anaerobic biodegradation of PAHs by PheS2, an isolated phenanthrene-utilizing sulfate-reducer, using phenanthrene as a model compound. PheS2 was phylogenetically closely related to Geobacter sulfurreducens and reduced sulfate to sulfide during anaerobic phenanthrene biodegradation. Phenanthrene biodegradation processes were detected using gas chromatography-mass spectrometry, genome, and reverse transcription quantitative PCR analyses. Carboxylation was the initial step of anaerobic phenanthrene biodegradation based upon detection of 2- and 4-phenanthroic acid, its isotopically labeled analogs when using ¹³C-labeled bicarbonate and fully deuterated-phenanthrene (C14D10), and genes encoding enzymes putatively involved in the biodegradation. Further, ring-system reducing and cleavage occurred, and substituted benzene series and cyclohexane derivatives were detected in downstream biotransformation metabolites. Additionally, PheS2 can degrade benzene, naphthalene, anthracene, and benz[a]anthracene, but not pyrene and benz[a]pyrene. This study describes the isolation of an anaerobic phenanthrene-degrading sulfate-reducer, the first pure-culture evidence of phenanthrene biotransformation processes with sulfate as an electron acceptor.

Exploration of the biotransformation processes in the biodegradation of phenanthrene by a facultative anaerobe, strain PheF2, with Fe(III) or O2 as an electron acceptor

The study of biodegradation of polycyclic aromatic hydrocarbons (PAHs) with metal ions as electron acceptors is still in its infancy. Here, a pure culture of PheF2 sharing 99.79% 16S rRNA-sequence similarity with Trichococcus alkaliphilus, which was recently reported to degrade PAHs, was isolated and found to degrade PAHs with Fe (III) or O₂ reduction. Phenanthrene was selected as a model of PAH to study the biodegradation process by PheF2 with Fe (III) or O₂ as an electron acceptor. PheF2 exhibited nearly 100%, 37.1%, and 28.5% anaerobic biodegradation of phenanthrene at initial concentrations of 280.7 μM, 280.6 μM, and 281.3 μM, respectively, within 10 days under anaerobic conditions with XAD-7 as a carrier, heptamethylnonane (HMN) as a solution, and nothing, respectively. PheF2 could degrade nearly 100% of the initial phenanthrene concentration of 283.4 μM under aerobic conditions within three days. The initial step of phenanthrene biodegradation by PheF2 involved carboxylation and dioxygenation under anaerobic and aerobic conditions, respectively. The biotransformation processes of phenanthrene degradation by PheF2 with Fe(III) or O₂ as an electron acceptor were explored by metabolite and genome analysis. These findings provide an important theoretical support for evaluation of PAHs fate and for PAHs pollution control or remediation in anaerobic and aerobic environments.

Comparative proteomics of Geobacter sulfurreducens PCAT in response to acetate, formate and/or hydrogen as electron donor

Geobacter sulfurreducens is a model bacterium to study the degradation of organic compounds coupled to the reduction of Fe(III). The response of G. sulfurreducens to the electron donors acetate, formate, hydrogen and a mixture of all three with Fe(III) citrate as electron acceptor was studied using comparative physiological and proteomic approaches. Variations in the supplied electron donors resulted in differential abundance of proteins involved in the citric acid cycle (CAC), gluconeogenesis, electron transport, and hydrogenases and formate dehydrogenase. Our results provided new insights into the electron donor metabolism of G. sulfurreducens. Remarkably, formate was the preferred electron donor compared to acetate, hydrogen, or acetate plus hydrogen. When hydrogen was the electron donor, formate was formed, which was associated with a high abundance of formate dehydrogenase. Notably, abundant proteins of two CO₂ fixation pathways (acetyl-CoA pathway and the reversed oxidative CAC) corroborated chemolithoautotrophic growth of G. sulfurreducens with formate or hydrogen and CO₂ , and provided novel insight into chemolithoautotrophic growth of G. sulfurreducens.

Anaerobic biodegradation of phenanthrene by a newly isolated nitrate-dependent Achromobacter denitrificans strain PheN1 and exploration of the biotransformation processes by metabolite and genome analyses

Polycyclic aromatic hydrocarbons (PAHs) are widespread and harmful contaminants and are more persistent under anaerobic conditions. The bioremediation of PAHs in anaerobic zones has been enhanced by treating the contamination with nitrate, which is thermodynamically favourable, cost-effective, and highly soluble. However, anaerobic PAHs biotransformation processes that employ nitrate as an electron acceptor have not been fully explored. In this study, we investigated the anaerobic biotransformation of PAHs by strain PheN1, a newly isolated phenanthrene-degrading denitrifier, using phenanthrene as a model compound. PheN1 is phylogenetically closely related to Achromobacter denitrificans and reduces nitrate to nitrite (not N₂ ) during the anaerobic phenanthrene degradation process. Phenanthrene biotransformation processes were detected using gas chromatography-mass spectrometry and were further examined by reverse transcription-quantitative PCR and genome analyses. Carboxylation and methylation were both found to be the initial steps in the phenanthrene degradation process. Downstream biotransformation processed benzene compounds and cyclohexane derivatives. This study describes the isolation of an anaerobic phenanthrene-degrading bacterium along with the pure-culture evidence of phenanthrene biotransformation processes with nitrate as an electron acceptor. The findings in this study can improve our understanding of anaerobic PAHs biodegradation processes and guide PAHs bioremediation by adding nitrate to anaerobic environments.

Oxygenic denitrification for nitrogen removal with less greenhouse gas emissions: Microbiology and potential applications

Nitrogen pollution is a worldwide problem and has been extensively treated by canonical denitrification (CDN) process. However, the CDN process generates several issues such as intensive greenhouse gas (GHG) emissions. In the past years, a novel biological nitrogen removal (BNR) process of oxygenic denitrification (O2DN) has been proposed as a promising alternative to the CDN process. The classic denitrification four steps are simplified to three steps by O2DN bacteria without producing and releasing the intermediate nitrous oxide (N₂O), a potent GHG. In this article, we summarized the findings in previous literatures as well as our results, including involved microorganisms and metabolic mechanisms, functional genes and microbial detection, kinetics and influencing factors and their potential applications in wastewater treatment. Based on our knowledge and experience, the benefits and limitations of the current O2DN process were analyzed. Since O2DN is a new field in wastewater treatment, more research and application is required, especially the development of integrated processes and the quantitative assessment of the contribution of O2DN process in natural habitats and engineered systems.

A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (21-36% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.

Bacterial nitrogen fixation in sand bioreactors treating winery wastewater with a high carbon to nitrogen ratio

Heterotrophic bacteria proliferate in organic-rich environments and systems containing sufficient essential nutrients. Nitrogen, phosphorus and potassium are the nutrients required in the highest concentrations. The ratio of carbon to nitrogen is an important consideration for wastewater bioremediation because insufficient nitrogen may result in decreased treatment efficiency. It has been shown that during the treatment of effluent from the pulp and paper industry, bacterial nitrogen fixation can supplement the nitrogen requirements of suspended growth systems. This study was conducted using physicochemical analyses and culture-dependent and -independent techniques to ascertain whether nitrogen-fixing bacteria were selected in biological sand filters used to treat synthetic winery wastewater with a high carbon to nitrogen ratio (193:1). The systems performed well, with the influent COD of 1351 mg/L being reduced by 84-89%. It was shown that the nitrogen fixing bacterial population was influenced by the presence of synthetic winery effluent in the surface layers of the biological sand filters, but not in the deeper layers. It was hypothesised that this was due to the greater availability of atmospheric nitrogen at the surface. The numbers of culture-able nitrogen-fixing bacteria, including presumptive Azotobacter spp. exhibited 1-2 log increases at the surface. The results of this study confirm that nitrogen fixation is an important mechanism to be considered during treatment of high carbon to nitrogen wastewater. If biological treatment systems can be operated to stimulate this phenomenon, it may obviate the need for nitrogen addition.

Opportunities for groundwater microbial electro-remediation

Groundwater pollution is a serious worldwide concern. Aromatic compounds, chlorinated hydrocarbons, metals and nutrients among others can be widely found in different aquifers all over the world. However, there is a lack of sustainable technologies able to treat these kinds of compounds. Microbial electro‐remediation, by the means of microbial electrochemical technologies (MET), can become a promising alternative in the near future. MET can be applied for groundwater treatment in situ or ex situ, as well as for monitoring the chemical state or the microbiological activity. This document reviews the current knowledge achieved on microbial electro‐remediation of groundwater and its applications.

Genetic switches and related tools for controlling gene expression and electrical outputs of Geobacter sulfurreducens

Physiological studies and biotechnology applications of Geobacter species have been limited by a lack of genetic tools. Therefore, potential additional molecular strategies for controlling metabolism were explored. When the gene for citrate synthase, or acetyl-CoA transferase, was placed under the control of a LacI/IPTG regulator/inducer system, cells grew on acetate only in the presence of IPTG. The TetR/AT system could also be used to control citrate synthase gene expression and acetate metabolism. A strain that required IPTG for growth on D-lactate was constructed by placing the gene for D-lactate dehydrogenase under the control of the LacI/IPTG system. D-Lactate served as an inducer in a strain in which a D-lactate responsive promoter and transcription repressor were used to control citrate synthase expression. Iron- and potassium-responsive systems were successfully incorporated to regulate citrate synthase expression and growth on acetate. Linking the appropriate degradation tags on the citrate synthase protein made it possible to control acetate metabolism with either the endogenous ClpXP or exogenous Lon protease and tag system. The ability to control current output from Geobacter biofilms and the construction of an AND logic gate for acetate metabolism suggested that the tools developed may be applicable for biosensor and biocomputing applications.