Microbial Bioremediation of Petroleum Hydrocarbon– Contaminated Marine Environments

Petroleum pollution has become a serious environmental problem, which can cause harmful damage to the environment and human health. This pollutant is introduced into the environment from both natural and anthropogenic sources. Various physicochemical and biological treatments were developed for the cleanup of contaminated environments. However, bioremediation is based on the metabolic capabilities of microorganisms, and it is considered as the most basic and reliable way to eliminate contaminants, particularly petroleum and its recalcitrant compounds. It is more effective alternative comparing to classical remediation techniques. A high diversity of potential hydrocarbon degrader’s microorganisms was reported, and bacteria constitute the most abundant group, which has been well studied for hydrocarbon degradation. Several bioremediation approaches through bioaugmentation or/and biostimulation have been successfully applied. The interest on the optimizing of different parameters to achieve successful bioremediation technologies has been increased. In this chapter, we summarize the diversity and the hydrocarbon degradation potential of microorganism involved in the remediation of contaminated environments. We also present an overview of the efficient bioremediation strategies used for the decontamination of polluted marine environments

Genomic characterization of a polyvalent hydrocarbonoclastic bacterium Pseudomonas sp. strain BUN14

Bioremediation offers a viable alternative for the reduction of contaminants from the environment, particularly petroleum and its recalcitrant derivatives. In this study, the ability of a strain of Pseudomonas BUN14 to degrade crude oil, pristane and dioxin compounds, and to produce biosurfactants, was investigated. BUN14 is a halotolerant strain isolated from polluted sediment recovered from the refinery harbor on the Bizerte coast, north Tunisia and capable of producing surfactants. The strain BUN14 was assembled into 22 contigs of 4,898,053 bp with a mean GC content of 62.4%. Whole genome phylogeny and comparative genome analyses showed that strain BUN14 could be affiliated with two validly described Pseudomonas Type Strains, P. kunmingensis DSM 25974T and P. chloritidismutans AW-1T. The current study, however, revealed that the two Type Strains are probably conspecific and, given the priority of the latter, we proposed that P. kunmingensis DSM 25974 is a heteronym of P. chloritidismutans AW-1T. Using GC-FID analysis, we determined that BUN14 was able to use a range of hydrocarbons (crude oil, pristane, dibenzofuran, dibenzothiophene, naphthalene) as a sole carbon source. Genome analysis of BUN14 revealed the presence of a large repertoire of proteins (154) related to xenobiotic biodegradation and metabolism. Thus, 44 proteins were linked to the pathways for complete degradation of benzoate and naphthalene. The annotation of conserved functional domains led to the detection of putative genes encoding enzymes of the rhamnolipid biosynthesis pathway. Overall, the polyvalent hydrocarbon degradation capacity of BUN14 makes it a promising candidate for application in the bioremediation of polluted saline environments

The genome of Alcaligenes aquatilis strain BU33N: Insights into hydrocarbon degradation capacity

Environmental contamination with hydrocarbons though natural and anthropogenic activities is a serious threat to biodiversity and human health. Microbial bioremediation is considered as the effective means of treating such contamination. This study describes a biosurfactant producing bacterium capable of utilizing crude oil and various hydrocarbons as the sole carbon source. Strain BU33N was isolated from hydrocarbon polluted sediments from the Bizerte coast (northern Tunisia) and was identified as Alcaligenes aquatilis on the basis of 16S rRNA gene sequence analysis. When grown on crude oil and phenanthrene as sole carbon and energy sources, isolate BU33N was able to degrade ~86%, ~56% and 70% of TERHc, n-alkanes and phenanthrene, respectively. The draft genome sequence of the A. aquatilis strain BU33N was assembled into one scaffold of 3,838,299 bp (G+C content of 56.1%). Annotation of the BU33N genome resulted in 3,506 protein-coding genes and 56 rRNA genes. A large repertoire of genes related to the metabolism of aromatic compounds including genes encoding enzymes involved in the complete degradation of benzoate were identified. Also genes associated with resistance to heavy metals such as copper tolerance and cobalt-zinc-cadmium resistance were identified in BU33N. This work provides insight into the genomic basis of biodegradation capabilities and bioremediation/detoxification potential of A. aquatilis BU33N

Conversion of Uric Acid into Ammonium in Oil-Degrading Marine Microbial Communities: a Possible Role of Halomonads

Uric acid is a promising hydrophobic nitrogen source for biostimulation of microbial activities in oil-impacted marine environments. This study investigated metabolic processes and microbial community changes in a series of microcosms using sediment from the Mediterranean and the Red Sea amended with ammonium and uric acid. Respiration, emulsification, ammonium and protein concentration measurements suggested a rapid production of ammonium from uric acid accompanied by the development of microbial communities containing hydrocarbonoclastic bacteria after 3 weeks of incubation. About 80 % of uric acid was converted to ammonium within the first few days of the experiment. Microbial population dynamics were investigated by Ribosomal Intergenic Spacer Analysis and Illumina sequencing as well as by culture-based techniques. Resulting data indicated that strains related to Halomonas spp. converted uric acid into ammonium, which stimulated growth of microbial consortia dominated by Alcanivorax spp. and Pseudomonas spp. Several strains of Halomonas spp. were isolated on uric acid as the sole carbon source showed location specificity. These results point towards a possible role of halomonads in the conversion of uric acid to ammonium utilized by hydrocarbonoclastic bacteria.With exception of XH and JC, all authors were supported by the FP7 Project ULIXES (FP7-KBBE-2010-266473). This work was further funded by grant BIO2011-25012 from the Spanish Ministry of the Economy and Competitiveness. FM was supported by Università degli Studi di Milano, European Social Fund (FSE) and Regione Lombardia (contract BDote Ricerca^). DD acknowledges support of KAUST, King Abdullah University of Science and Technology. PG acknowledges the support of the European Commission through the project Kill-Spill (FP7, Contract Nr 312139).Peer Reviewe

Chapter Microbial Bioremediation of Petroleum Hydrocarbon – Contaminated Marine Environments

Petroleum pollution has become a serious environmental problem, which can cause harmful damage to the environment and human health. This pollutant is introduced into the environment from both natural and anthropogenic sources. Various physicochemical and biological treatments were developed for the cleanup of contaminated environments. However, bioremediation is based on the metabolic capabilities of microorganisms, and it is considered as the most basic and reliable way to eliminate contaminants, particularly petroleum and its recalcitrant compounds. It is more effective alternative comparing to classical remediation techniques. A high diversity of potential hydrocarbon degrader’s microorganisms was reported, and bacteria constitute the most abundant group, which has been well studied for hydrocarbon degradation. Several bioremediation approaches through bioaugmentation or/and biostimulation have been successfully applied. The interest on the optimizing of different parameters to achieve successful bioremediation technologies has been increased. In this chapter, we summarize the diversity and the hydrocarbon degradation potential of microorganism involved in the remediation of contaminated environments. We also present an overview of the efficient bioremediation strategies used for the decontamination of polluted marine environments

MADFORWATER. WP4 Field pilots for the adaptation and integration of technologies. Task4.3 Operation and optimization of the field pilots. Wastewater treatment performances and Irrigation/treated wastewater reuse performances. Municipal wastewater pilot. UMA-Tunisia

This dataset contains the data produced by UMA team in the framework of task 4.3 of MADFORWATER project. Two sets of data were generated during the first and the second periods of survey of the pilot to evaluate: (i) the Municipal Wastewater Treatment Pilot efficiency, and (ii) the impact of the Treated Municipal Wastewater (TMWW) reuse in agriculture. The first part of the data consists of quantitative survey results from monitoring the Pilot at different sampling points, including SP1: pilot plant inlet, sampling point after preliminary treatments in the main WWTP, SP2: outlet of the BOD oxidation section, SP3: outlet of the nitrification section and SP4: sample point after disinfection and secondary settler, constructed wetland (CW) inlet and SP5: sample after the constructed wetland. The monitored physicochemical parameters are: chemical oxygen demand (COD), Biochemical oxygen demand (BOD), Total Suspended Solids (TSS), the conductivity, the turbidity, Kjeldahl Nitrogen (NKj), nitrite (NO2), nitrate (NO3), ammonium (NH4), phosphate (PO4) and Total Phosphorous (TP), pH, Temperature and Dissolved Oxygen, E. coli. The second part of the data consist of the irrigation pilot reports on the performance of the Treated Municipal Wastewater (TMWW) reuse in agriculture. The supply of Plant Growth Promoting (PGP) bacteria through irrigation network was also investigated. A first-year corn field trial allowed the evaluation of the plant growth and crop production including roots and shoots fresh and dry weights, plant height, tassel length, plant and ear numbers, grain number, crop yield, crop biomass and 100-grain weight. The second-year field trial on wheat crop estimated the effect of TMWW and PGPB supply on shoot and spike lengths; root, shoot and spike weights; and wheat crop biomass. Data related to crop water productivity and soil microbiological quality are also reported for both crop types (Maize and Wheat)

MADFORWATER. WP2 Adaptation of wastewater treatment technologies for agricultural reuse. Task2.2 Municipal wastewater and drainage canal water treatment. UMA-Tunisia

This dataset contains the data produced by UMA team in the framework of task 2.2 of MADFORWATER project. This task deal with a set of data generated regarding the detection of antibiotic resistance genes and enterovirus, particularly Hepatitis A virus from Treated Municipal Wastewater. To monitor the prevalence of antibiotic resistant bacteria in MWW before and after treatment, the qualitative and quantitative PCR methods, allowing the detection of resistance genes in all microorganisms including the non-culturable species, were performed. PCR products of target antibiotic genes (tet(O), tet(Q), tet(W), tet(G), amp(C) and bla TEM) were loaded and visualized on agarose gels. For qPCR, the analysis was performed in order to detect and quantify the antibiotic resistance genes copy number. The investigation of the Hepatitis A virus prevalence in MTWW was performed using two different extraction methods (virus extraction, concentration and concentrate decontamination method according to US Environmental Protection Agency (1992) from Mud (M) and Supernatant (S) of the influent and from the effluent and virus concentration from water with adsorption/elution on glass wool (XP T 90-451. March 1996) (Rodier et al., 2009)) followed by qPCR. A specific attention was dedicated to the detection of SARS-CoV-2 in wastewaters using the same protocols developed and optimized under MADFORWATER (RNA extraction/concentration, cDNA synthesis, Q-RT-PCR) by using specific DNA primers approved in the RT-PCR test. This could contribute to better understanding and studying the emerged SARS-CoV-2 and its propagation routes and epidemiology in a given population (i.e. Tunis city). Regarding Microarray, the generated data were produced and elaborated basing on a list of targeted genes downloaded from accessible databases (NCBI, IMG, KEEG). The effectiveness of MWWTP cannot be approved without accepted microbiological quality. In the literature, there is a huge number of publications and standards related fecal or pathogen bacteria removal in wastewater treatment plant (WWTP), many publications show inefficiency of current MWWTP in removing virus but no standards dealing with virus detection from MWW in Tunisia. Generated data allowed the design of the WWchip, able to monitor catabolic genes markers of fecal indicators, pathogens indicators, virus and antibiotic resistant bacteria. A total of 3744 genes and 12832 probes were designated. In silico validation and verification of all probes was performed using the BLASTN algorithm and custom-made databases. Two set of data are proposed. The first one summarizes the gene type, number of genes and number of probes considered in the design of the WWchip. The list and sequences of all the probes of target genes is presented a second set of data. The data format produced by the microarray consists of a list of genes and corresponding values that represent relative DNA levels of each targeted gene. The developed WWChip will constitute a new rapid tool for pathogen monitoring of different types of treated wastewaters

The genome of Alcaligenes aquatilis strain BU33N: Insights into hydrocarbon degradation capacity.

Environmental contamination with hydrocarbons though natural and anthropogenic activities is a serious threat to biodiversity and human health. Microbial bioremediation is considered as the effective means of treating such contamination. This study describes a biosurfactant producing bacterium capable of utilizing crude oil and various hydrocarbons as the sole carbon source. Strain BU33N was isolated from hydrocarbon polluted sediments from the Bizerte coast (northern Tunisia) and was identified as Alcaligenes aquatilis on the basis of 16S rRNA gene sequence analysis. When grown on crude oil and phenanthrene as sole carbon and energy sources, isolate BU33N was able to degrade ~86%, ~56% and 70% of TERHc, n-alkanes and phenanthrene, respectively. The draft genome sequence of the A. aquatilis strain BU33N was assembled into one scaffold of 3,838,299 bp (G+C content of 56.1%). Annotation of the BU33N genome resulted in 3,506 protein-coding genes and 56 rRNA genes. A large repertoire of genes related to the metabolism of aromatic compounds including genes encoding enzymes involved in the complete degradation of benzoate were identified. Also genes associated with resistance to heavy metals such as copper tolerance and cobalt-zinc-cadmium resistance were identified in BU33N. This work provides insight into the genomic basis of biodegradation capabilities and bioremediation/detoxification potential of A. aquatilis BU33N

Assessment of biotechnological potentials of strains isolated from repasso olive pomace in Tunisia

International audienc

Genomic characterization of a polyvalent hydrocarbonoclastic bacterium Pseudomonas sp. strain BUN14

Bioremediation ofers a viable alternative for the reduction of contaminants from the environment, particularly petroleum and its recalcitrant derivatives. In this study, the ability of a strain of Pseudomonas BUN14 to degrade crude oil, pristane and dioxin compounds, and to produce biosurfactants, was investigated. BUN14 is a halotolerant strain isolated from polluted sediment recovered from the refnery harbor on the Bizerte coast, north Tunisia and capable of producing surfactants. The strain BUN14 was assembled into 22 contigs of 4,898,053 bp with a mean GC content of 62.4%. Whole genome phylogeny and comparative genome analyses showed that strain BUN14 could be afliated with two validly described Pseudomonas Type Strains, P. kunmingensis DSM 25974T and P. chloritidismutans AW-1T. The current study, however, revealed that the two Type Strains are probably conspecifc and, given the priority of the latter, we proposed that P. kunmingensis DSM 25974 is a heteronym of P. chloritidismutans AW-1T. Using GC-FID analysis, we determined that BUN14 was able to use a range of hydrocarbons (crude oil, pristane, dibenzofuran, dibenzothiophene, naphthalene) as a sole carbon source. Genome analysis of BUN14 revealed the presence of a large repertoire of proteins (154) related to xenobiotic biodegradation and metabolism. Thus, 44 proteins were linked to the pathways for complete degradation of benzoate and naphthalene. The annotation of conserved functional domains led to the detection of putative genes encoding enzymes of the rhamnolipid biosynthesis pathway. Overall, the polyvalent hydrocarbon degradation capacity of BUN14 makes it a promising candidate for application in the bioremediation of polluted saline environments.http://www.nature.com/srep/index.htmlpm2022Genetic