Biological control of problematic bacterial populations causing foaming in activated sludge wastewater treatment plants—phage therapy and beyond

Petrovski, Steve; Batinovic, Steven; Rose, Jim; Seviour, Robert J.

doi:10.1111/lam.13742

Cited by 8 publications

(2 citation statements)

References 73 publications

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“…While some genera are relatively well-studied, such as Streptomyces for antibiotic and natural product discovery, Corynebacterium as an established fermentation host, and Mycobacterium as a human and livestock pathogen (2)(3)(4)(5), most are poorly characterized (6)(7)(8). Among these, Rhodococcus, Nocardia, and Gordonia are three genera that contain numerous species with industrially relevant traits including natural product production, degradation of anthropogenic pollutants, and diverse carbon and nitrogen assimilation pathways that enable oligotrophic growth (8)(9)(10)(11)(12)(13)(14)(15). Members of the genus Rhodococcus, the best characterized of the three, display an especially broad range of phenotypes.…”

Section: Introductionmentioning

confidence: 99%

A modular toolkit for environmentalRhodococcus, Gordonia, andNocardiaenables complex metabolic manipulation

Jansen,

Alameri,

Wei

et al. 2024

Preprint

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Soil-dwelling Actinomycetes are a diverse and ubiquitous component of the global microbiome, but largely lack genetic tools comparable to those available in model species such asE. coliorPseudomonas putida, posing a fundamental barrier to their characterization and utilization as hosts for biotechnology. To address this, we have developed a modular plasmid assembly framework along with a series of genetic control elements for the previously genetically intractable Gram-positive environmental isolateRhodococcus ruberC208 and demonstrate conserved functionality in diverse environmental isolates ofRhodococcus, NocardiaandGordonia. This toolkit encompasses Mycobacteriale origins of replication, broad-host range antibiotic resistance markers, transcriptional and translational control elements, fluorescent reporters, a tetracycline-inducible system, and a counter-selectable marker. We use this toolkit to interrogate the carotenoid biosynthesis pathway inRhodococcus erythropolisN9T-4, a weakly carotenogenic environmental isolate and engineer higher pathway flux towards the keto-carotenoid canthaxanthin. This work establishes several new genetic tools for environmental Mycobacteriales and provides a synthetic biology framework to support the design of complex genetic circuits in these species.IMPORTANCESoil-dwelling Actinomycetes, particularly the Mycobacteriales, include both diverse new hosts for sustainable biomanufacturing and emerging opportunistic pathogens.Rhodococcus, GordoniaandNocardiaare three abundant genera with particularly flexible metabolisms and untapped potential for natural product discovery. Among these,Rhodococcus ruberC208 was shown to degrade polyethylene,Gordonia paraffinivoranscan assimilate carbon from solid hydrocarbons, andNocardia neocaledoniensis(and many otherNocardia) possesses dual isoprenoid biosynthesis pathways. Many species accumulate high levels of carotenoid pigments, indicative of highly active isoprenoid biosynthesis pathways which may be harnessed for fermentation of terpenes and other commodity isoprenoids. Modular genetic toolkits have proven valuable for both fundamental and applied research in model organisms, but such tools are lacking for most Actinomycetes. Our suite of genetic tools and DNA assembly framework were developed for broad functionality and to facilitate rapid prototyping of genetic constructs in these organisms.

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Section: Introductionmentioning

confidence: 99%

A modular toolkit for environmentalRhodococcus, Gordonia, andNocardiaenables complex metabolic manipulation

Jansen,

Alameri,

Wei

et al. 2024

Preprint

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show abstract

“…R. opacus phage Toil has been used as a bioextraction agent for biodiesel production, forcing the release of triacylglycerols from its host upon lytic infection [ 14 ]. Phage of Rhodococcus and other related Actinobacteria isolated from wastewater have been suggested for use as biocontrol agents to reduce foaming in activated sludge [ 15 , 16 ]. Phage YF1, which can infect R. equi , R. erythropolis , R. rhodochrous , and R. opacus , was used to identify potential new antimicrobial targets in its hosts, serving as a model for novel target discovery in other related organisms [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

Transcriptional dynamics during Rhodococcus erythropolis infection with phage WC1

Willner,

Paudel,

Halleran

et al. 2024

BMC Microbiol

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Background Belonging to the Actinobacteria phylum, members of the Rhodococcus genus thrive in soil, water, and even intracellularly. While most species are non-pathogenic, several cause respiratory disease in animals and, more rarely, in humans. Over 100 phages that infect Rhodococcus species have been isolated but despite their importance for Rhodococcus ecology and biotechnology applications, little is known regarding the molecular genetic interactions between phage and host during infection. To address this need, we report RNA-Seq analysis of a novel Rhodococcus erythopolis phage, WC1, analyzing both the phage and host transcriptome at various stages throughout the infection process. Results By five minutes post-infection WC1 showed upregulation of a CAS-4 family exonuclease, putative immunity repressor, an anti-restriction protein, while the host showed strong upregulation of DNA replication, SOS repair, and ribosomal protein genes. By 30 min post-infection, WC1 DNA synthesis genes were strongly upregulated while the host showed increased expression of transcriptional and translational machinery and downregulation of genes involved in carbon, energy, and lipid metabolism pathways. By 60 min WC1 strongly upregulated structural genes while the host showed a dramatic disruption of metal ion homeostasis. There was significant expression of both host and phage non-coding genes at all time points. While host gene expression declined over the course of infection, our results indicate that phage may exert more selective control, preserving the host’s regulatory mechanisms to create an environment conducive for virion production. Conclusions The Rhodococcus genus is well recognized for its ability to synthesize valuable compounds, particularly steroids, as well as its capacity to degrade a wide range of harmful environmental pollutants. A detailed understanding of these phage-host interactions and gene expression is not only essential for understanding the ecology of this important genus, but will also facilitate development of phage-mediated strategies for bioremediation as well as biocontrol in industrial processes and biomedical applications. Given the current lack of detailed global gene expression studies on any Rhodococcus species, our study addresses a pressing need to identify tools and genes, such as F6 and rpf, that can enhance the capacity of Rhodococcus species for bioremediation, biosynthesis and pathogen control.

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Potential use of bacteriophages as biocontrol agents against multidrug-resistant pathogens in wastewater treatment: a review

Ragab,

Mustafa,

Hassan

et al. 2024

Environmental Sustainability

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The conventional methods of wastewater treatment are essentially used to remove contaminants and pathogens from wastewater before it is released into the environment or used for other purposes. With the increasing number of Multidrug-Resistant (MDR) organisms in wastewater, the potential usefulness of conventional treatment methods has been re-evaluated. The conventional biological treatment and disinfection have been proven in many studies to increase the prevalence of Antibiotic Resistance Genes (ARG) in bacteria. More than 25 genes responsible for antibiotic resistance were found to be increased from influent to effluent in different Wastewater Treatment Plants (WWTPs). Additionally, many studies have discussed the high abundance of several Mobile Genetic Elements (MGEs) after disinfection by chlorination and ozonation. Bacteriophage-based therapy has emerged as an innovative method for effectively managing microorganisms in wastewater treatment and in various other applications. Bacteriophages can be utilized to kill pathogenic bacteria and eradicate the biofilms formed by the bacteria in wastewater treatment plants with low intrinsic toxicity. However, the use of bacteriophages has been associated with some limitations, including the narrow host range spectrum. This review provides a critical overview of the recent knowledge on the effect of biological treatment and disinfection on spreading antibiotic resistance. In addition, we highlight the interactions among bacteria and phages to sustain the water treatment process. We also emphasize the proposed improvement in wastewater treatment using bacteriophage-based therapy. Our focus is identifying gaps, opportunities, and critical concerns that should be addressed in further research.

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Biological control of problematic bacterial populations causing foaming in activated sludge wastewater treatment plants—phage therapy and beyond

Cited by 8 publications

References 73 publications

A modular toolkit for environmentalRhodococcus, Gordonia, andNocardiaenables complex metabolic manipulation

A modular toolkit for environmentalRhodococcus, Gordonia, andNocardiaenables complex metabolic manipulation

Transcriptional dynamics during Rhodococcus erythropolis infection with phage WC1

Potential use of bacteriophages as biocontrol agents against multidrug-resistant pathogens in wastewater treatment: a review

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