Degradability of commercial mixtures of polychlorobiphenyls by three Rhodococcus strains
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Cited by 3 publications
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(Pan)genomic analysis of two Rhodococcus isolates and their role in phenolic compound degradation
The genus Rhodococcus is recognized for its potential to degrade a large range of aromatic substances, including plant-derived phenolic compounds. We used comparative genomics in the context of the broader Rhodococcus pan-genome to study genomic traits of two newly described Rhodococcus strains (type-strain Rhodococcus pseudokoreensis R79 T and Rhodococcus koreensis R85) isolated from apple rhizosphere. Of particular interest was their ability to degrade phenolic compounds as part of an integrated approach to treat apple replant disease (ARD) syndrome. The pan-genome of the genus Rhodococcus based on 109 high-quality genomes was open with a small core (1.3%) consisting of genes assigned to basic cell functioning. The range of genome sizes in Rhodococcus was high, from 3.7 to 10.9 Mbp. Genomes from host-associated strains were generally smaller compared to environmental isolates which were characterized by exceptionally large genome sizes. Due to large genomic differences, we propose the reclassification of distinct groups of rhodococci like the Rhodococcus equi cluster to new genera. Taxonomic species affiliation was the most important factor in predicting genetic content and clustering of the genomes. Additionally, we found genes that discriminated between the strains based on habitat. All members of the genus Rhodococcus had at least one gene involved in the pathway for the degradation of benzoate, while biphenyl degradation was mainly restricted to strains in close phylogenetic relationships with our isolates. The ~40% of genes still unclassified in larger Rhodococcus genomes, particularly those of environmental isolates, need more research to explore the metabolic potential of this genus. IMPORTANCE Rhodococcus is a diverse, metabolically powerful genus, with high potential to adapt to different habitats due to the linear plasmids and large genome sizes. The analysis of its pan-genome allowed us to separate host-associated from environmental strains, supporting taxonomic reclassification. It was shown which genes contribute to the differentiation of the genomes based on habitat, which can possibly be used for targeted isolation and screening for desired traits. With respect to apple replant disease (ARD), our isolates showed genome traits that suggest potential for application in reducing plant-derived phenolic substances in soil, which makes them good candidates for further testing against ARD.
(Pan)genomic analysis of two Rhodococcus isolates and their role in phenolic compound degradation
The genus Rhodococcus is recognized for its potential to degrade a large range of aromatic substances, including plant-derived phenolic compounds. We used comparative genomics in the context of the broader Rhodococcus pan-genome to study genomic traits of two newly described Rhodococcus strains (type-strain Rhodococcus pseudokoreensis R79 T and Rhodococcus koreensis R85) isolated from apple rhizosphere. Of particular interest was their ability to degrade phenolic compounds as part of an integrated approach to treat apple replant disease (ARD) syndrome. The pan-genome of the genus Rhodococcus based on 109 high-quality genomes was open with a small core (1.3%) consisting of genes assigned to basic cell functioning. The range of genome sizes in Rhodococcus was high, from 3.7 to 10.9 Mbp. Genomes from host-associated strains were generally smaller compared to environmental isolates which were characterized by exceptionally large genome sizes. Due to large genomic differences, we propose the reclassification of distinct groups of rhodococci like the Rhodococcus equi cluster to new genera. Taxonomic species affiliation was the most important factor in predicting genetic content and clustering of the genomes. Additionally, we found genes that discriminated between the strains based on habitat. All members of the genus Rhodococcus had at least one gene involved in the pathway for the degradation of benzoate, while biphenyl degradation was mainly restricted to strains in close phylogenetic relationships with our isolates. The ~40% of genes still unclassified in larger Rhodococcus genomes, particularly those of environmental isolates, need more research to explore the metabolic potential of this genus. IMPORTANCE Rhodococcus is a diverse, metabolically powerful genus, with high potential to adapt to different habitats due to the linear plasmids and large genome sizes. The analysis of its pan-genome allowed us to separate host-associated from environmental strains, supporting taxonomic reclassification. It was shown which genes contribute to the differentiation of the genomes based on habitat, which can possibly be used for targeted isolation and screening for desired traits. With respect to apple replant disease (ARD), our isolates showed genome traits that suggest potential for application in reducing plant-derived phenolic substances in soil, which makes them good candidates for further testing against ARD.
Environmental Implications of Energy Sources: A Review on Technologies for Cleaning Oil-Contaminated Ecosystems
This review analyzes the main methods for cleaning up oil pollution in natural ecosystems, with a particular focus on the synergy between chemical and microbiological techniques for environmental remediation. While biological methods are a green and inexpensive soil remediation technique, they have a major limitation in their inability to clean up high concentrations of toxic contaminants. The poor performance of chemical methods stems from the high cost of chemicals and concerns over their negative and toxic effects on the environment. Physical methods also have high costs due to energy consumption and the need for additional treatment of gases generated during decontamination, making them ineffective for soil remediation. The main principle of bioremediation is based on microorganisms’ ability to degrade complex organic compounds, such as petroleum. This process is described in this review. This combination of methods allows for a higher level of decontamination of soil and water ecosystems, even against pollutants that are usually resistant to degradation, such as oil derivatives. While existing methods for cleaning oil-contaminated ecosystems are highly effective, they require significant material costs to implement. Additionally, the review discusses how the joint use of current and future biotechnology techniques can lead to the development of an effective set of strategies to protect soil and water systems from oil pollution. The reviewed studies show that a hybrid biotechnological approach is the most effective remediation method. When biological decontamination methods are adopted, the optimized combination of different remediation strategies can overcome the limitations of each technique, allowing efficiencies of even more than 70% to be achieved, given that the choice still depends on the type of contaminant, its concentration, and the properties of the receiving substrate.
Aerobic bacterial degradation of polychlorinated biphenyls and their hydroxy and methoxy derivatives
Polychlorinated biphenyls are persistent organic pollutants hazardous to humans and to the environment. The products of biotransformation of these compounds can exist in natural objects as hydroxy and methoxy derivatives. This review summarizes the biodegradation pathways of polychlorinated biphenyls under the action of aerobic bacterial strains. The possibility of complete biodegradation of polychlorinated biphenyls and their derivatives under laboratory conditions is demonstrated. This information is valuable for researchers specializing in the biotransformations and toxicity of polychloroarene derivatives and would be useful for the development of remediation processes of natural objects contaminated with polychlorinated biphenyls.<br> The bibliography includes 253 references.
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