Detection of Horizontal Transfer of Housekeeping and Hydrocarbons Catabolism Genes in Bacterial Genus with Potential to Application in Bioremediation Process

Rodrigues, Edmo Montes; Freitas, Fernanda; Siqueira, Tatiane de Paula

doi:10.4236/oalib.1104454

Cited by 4 publications

(4 citation statements)

References 50 publications

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“…3 and 4 some branches contained alkB/M and ladA genes originating from genomes belonging to distantly related phyla. The placement of phylogenetically diverse groups in one branch hint at horizontal transfer of these genes between microbial taxa [ 16 ]. Additionally, apart from the chromosomal type, both alkB/M and ladA genes have previously been reported to be also located on plasmids (OCT and pLW1071), corroborating their potential for horizontal transfer.…”

Section: Resultsmentioning

confidence: 99%

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Somee

Amoozegar

Dastgheib³

et al. 2022

BMC Genomics

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Background Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. Results Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria. Conclusion Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.

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Section: Resultsmentioning

confidence: 99%

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Somee

Amoozegar

Dastgheib³

et al. 2022

BMC Genomics

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show abstract

“…The branching pattern of these clades partially followed the taxonomic signal of the genomes they were retrieved from, specifically for most dominant phyla; however, some branches also contained alkB/M and ladA genes originating from different and distantly related phyla. The placement of phylogenetically diverse groups in one branch is likely to result from the horizontal transfer of these genes between microbial taxa [16]. Additionally, apart from the chromosomal type, both alkB/M and ladA genes have previously been reported to be located on plasmids (OCT and pLW1071), corroborating their potential for horizontal transfer.…”

Section: Resultsmentioning

confidence: 85%

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Somee

Amoozegar

Dastgheib³

et al. 2022

Preprint

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Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen. They mainly accumulate in oil reservoirs, but aromatic HCs can also have other sources and are widely distributed in the biosphere. Our perception of pathways for biotic degradation of major HCs and genetic information of key enzymes in these bioconversion processes have mainly been based on cultured microbes and are biased by uneven taxonomic representation. Here we use Annotree to provide a gene-centric view of aerobic degradation of aliphatic and aromatic HCs in a total of 23446 genomes from 123 bacterial and 14 archaeal phyla. Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. While genomes containing full pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota, other lineages capable of mediating such key steps could partner with representatives with truncated HC degradation pathways and collaboratively drive the process. Phylogeny reconstruction shows that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.

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“…Moreover, the homology of DNA sequences and organization of degrading genes carried by conjugative plasmids may be indicators that horizontal gene transfers can occur between HC-degrading bacteria during microbial adaptation to xenobiotics (Abbasian et al 2016). This is supported by in silico analysis, which demonstrated that HC-degrading genes alkB and catA can be subjected to horizontal transfer events among bacterial communities spreading the potential to degrade HCs (Rodrigues et al 2018). In an interesting study, Taghavi et al (2005) reported for the first time in planta horizontal gene transfer among plant-associated endophytic bacteria.…”

Section: Uptake and Degradation Of Hydrocarbons By Bacteriamentioning

confidence: 93%

Plant-Microbiome Interactions in Hydrocarbon-Contaminated Soils

Agnello

Morelli

Panno

2020

Plant Microbe Symbiosis

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The use of green remediation technologies (i.e., phytoremediation, bioremediation, mycoremediation) for the restoration of hydrocarbon-contaminated sites is one of the keys for sustainable development. These technologies rely on the joint action of biotic components of the ecosystem, namely, plants, bacteria, and fungi. Despite the fact that previous studies showed that the clean-up of hydrocarbons could be achieved individually by plants or microorganisms, present investigations suggest that the interaction of plants with their surrounding microbiome determines the outcomes of green remediation technologies. This book chapter reviews the state of the art to explain the two-way relationship established between plants and their associated microbiome in hydrocarbon-polluted soils. Special focus is put on stressing the results obtained in recent studies that employ omics approaches.

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Detection of Horizontal Transfer of Housekeeping and Hydrocarbons Catabolism Genes in Bacterial Genus with Potential to Application in Bioremediation Process

Cited by 4 publications

References 50 publications

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Plant-Microbiome Interactions in Hydrocarbon-Contaminated Soils

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