Next-Generation Sequencing of Functional Marker Genes for Anaerobic Degraders of Petroleum Hydrocarbons in Contaminated Environments

Netzer, Frederick von; Granitsiotis, Michael S.; Szalay, Anna R.; Lueders, Tillmann

doi:10.1007/978-3-319-33598-8_15-1

Cited by 5 publications

(4 citation statements)

References 81 publications

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“…Similar observations were made in a methanogenic consortium enriched from Shengli oilfield amended with heavy oil (Cheng et al 2019). Since there still remained uncertain with respect to the key active microorganisms and activation pathways in this work, more microbial and functional information are expected to be explored via omicsbased sequencings and other chemical techniques (Gieg and Toth 2016;von Netzer et al 2018). And also, there may exist novel pathway documented recently based on metagenomics analysis (Liu et al 2019).…”

Section: Putative Paraffin Degradation Pathway In Thermophilic Methansupporting

confidence: 55%

Long-chain n-alkane biodegradation coupling to methane production in an enriched culture from production water of a high-temperature oil reservoir

et al. 2020

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Paraffinic n-alkanes (C22-C30), crucial portions of residual oil, are generally considered to be difficult to be biodegraded owing to their general solidity at ambient temperatures and low water solubility, rendering relatively little known about metabolic processes in different methanogenic hydrocarbon-contaminated environments. Here, we established a methanogenic C22-C30 n-alkane-degrading enrichment culture derived from a high-temperature oil reservoir production water. During two-year incubation (736 days), unexpectedly significant methane production was observed. The measured maximum methane yield rate (164.40 μmol L −1 d −1) occurred during the incubation period from day 351 to 513. The nearly complete consumption (> 97%) of paraffinic n-alkanes and the detection of dicarboxylic acids in n-alkane-amended cultures indicated the biotransformation of paraffin to methane under anoxic condition. 16S rRNA gene analysis suggested that the dominant methanogen in n-alkane-degrading cultures shifted from Methanothermobacter on day 322 to Thermoplasmatales on day 736. Bacterial community analysis based on high-throughput sequencing revealed that members of Proteobacteria and Firmicutes exhibiting predominant in control cultures, while microorganisms affiliated with Actinobacteria turned into the most dominant phylum in n-alkanedependent cultures. Additionally, the relative abundance of mcrA gene based on genomic DNA significantly increased over the incubation time, suggesting an important role of methanogens in these consortia. This work extends our understanding of methanogenic paraffinic n-alkanes conversion and has biotechnological implications for microbial enhanced recovery of residual hydrocarbons and effective bioremediation of hydrocarbon-containing biospheres.

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Section: Putative Paraffin Degradation Pathway In Thermophilic Methansupporting

confidence: 55%

Long-chain n-alkane biodegradation coupling to methane production in an enriched culture from production water of a high-temperature oil reservoir

et al. 2020

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“…Omics, e.g., proteomics, transcriptomics, metabolomics and genomics, aid in the regulation of genes for bioremediation [249]). With the help of next-generation sequencing and high-throughput sequencing (HTS), genes responsible for bioremediation are resolved [250]. In gene editing, engineered nucleases or molecular scissors are used to manipulate DNA.…”

Section: Molecular Approaches For Bioremediationmentioning

confidence: 99%

Microbial Remediation: A Promising Tool for Reclamation of Contaminated Sites with Special Emphasis on Heavy Metal and Pesticide Pollution: A Review

et al. 2022

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Heavy metal and pesticide pollution have become an inevitable part of the modern industrialized environment that find their way into all ecosystems. Because of their persistent nature, recalcitrance, high toxicity and biological enrichment, metal and pesticide pollution has threatened the stability of the environment as well as the health of living beings. Due to the environmental persistence of heavy metals and pesticides, they get accumulated in the environs and consequently lead to food chain contamination. Therefore, remediation of heavy metals and pesticide contaminations needs to be addressed as a high priority. Various physico-chemical approaches have been employed for this purpose, but they have significant drawbacks such as high expenses, high labor, alteration in soil properties, disruption of native soil microflora and generation of toxic by-products. Researchers worldwide are focusing on bioremediation strategies to overcome this multifaceted problem, i.e., the removal, immobilization and detoxification of pesticides and heavy metals, in the most efficient and cost-effective ways. For a period of millions of evolutionary years, microorganisms have become resistant to intoxicants and have developed the capability to remediate heavy metal ions and pesticides, and as a result, they have helped in the restoration of the natural state of degraded environs with long term environmental benefits. Keeping in view the environmental and health concerns imposed by heavy metals and pesticides in our society, we aimed to present a generalized picture of the bioremediation capacity of microorganisms. We explore the use of bacteria, fungi, algae and genetically engineered microbes for the remediation of both metals and pesticides. This review summarizes the major detoxification pathways and bioremediation technologies; in addition to that, a brief account is given of molecular approaches such as systemic biology, gene editing and omics that have enhanced the bioremediation process and widened its microbiological techniques toward the remediation of heavy metals and pesticides.

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“…Enzymes that were functionally sourced from public databases are the foundation of a wide variety of technologies. The integration of several computational techniques in silico are applicable to studies, genomics, metagenomics, metabolomics, transcriptomics, proteomics and biodegradation network pave the way for heavy metal bioremediation (VON NETZER et al, 2018;PUROHIT et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Mining a bioremediation genetic toolbox in the novel environmental bacteria Enterobacter cloacae strain amazonensis

Carvalho,

Viana,

Astolfi

et al. 2024

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The rise of environmental pollution is a threat to planetary and human health. Microbes encode a wide range of enzymes with sophisticated catalytic properties to mitigate toxic chemicals from nature. Bioprospecting environmental bacteria can be a powerful resource for improved enzymes to optimize bioremediation processes. Here, we present a promising genetic toolbox sequenced from a novel multi-resistant bacterial strain isolated from industrial wastewater and sewage-contaminated stream in the city of Manaus, Amazonas, Brazil. We report Enterobacter cloacae amazonensis as a highly heavy-metal resistant and antibiotic multi-resistant strain. Functional and comparative genomics of the E. cloacae strain amazonensis draft genome revealed the annotation of 104 genes encoding proteins involved in the metabolism of copper, cobalt, zinc, cadmium, chromium, mercury and arsenic, as well as a plethora of broad-spectrum resistant genes. As a proof of concept, we characterized a plasmid mobile element from the amazonensis strain, pEN_Amazonensis, in the model biotechnological workhorse E. coli, leading to the robust acquisition of mercury and antibiotic resistance. Here, we highlighted the potential of bioprospecting genetic novelty from environmental bacteria through comparative genomics, paving the way for a genetic toolbox for bioremediation processes.

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Next-Generation Sequencing of Functional Marker Genes for Anaerobic Degraders of Petroleum Hydrocarbons in Contaminated Environments

Cited by 5 publications

References 81 publications

Long-chain n-alkane biodegradation coupling to methane production in an enriched culture from production water of a high-temperature oil reservoir

Long-chain n-alkane biodegradation coupling to methane production in an enriched culture from production water of a high-temperature oil reservoir

Microbial Remediation: A Promising Tool for Reclamation of Contaminated Sites with Special Emphasis on Heavy Metal and Pesticide Pollution: A Review

Mining a bioremediation genetic toolbox in the novel environmental bacteria Enterobacter cloacae strain amazonensis

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