The role of mobile genetic elements in organic micropollutant degradation during biological wastewater treatment

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Abstract

Wastewater treatment plants (WWTPs) are crucial for producing clean effluents from polluting sources such as hospitals, industries, and municipalities. In recent decades, many new organic compounds have ended up in surface waters in concentrations that, while very low, cause (chronic) toxicity to countless organisms. These organic micropollutants (OMPs) are usually quite recalcitrant and not sufficiently removed during wastewater treatment. Microbial degradation plays a pivotal role in OMP conversion. Microorganisms can adapt their metabolism to the use of novel molecules via mutations and rearrangements of existing genes in new clusters. Many catabolic genes have been found adjacent to mobile genetic elements (MGEs), which provide a stable scaffold to host new catabolic pathways and spread these genes in the microbial community. These mobile systems could be engineered to enhance OMP degradation in WWTPs, and this review aims to summarize and better understand the role that MGEs might play in the degradation and wastewater treatment process. Available data about the presence of catabolic MGEs in WWTPs are reviewed, and current methods used to identify and measure MGEs in environmental samples are critically evaluated. Finally, examples of how these MGEs could be used to improve micropollutant degradation in WWTPs are outlined. In the near future, advances in the use of MGEs will hopefully enable us to apply selective augmentation strategies to improve OMP conversion in WWTPs.

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Highlights

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Organic Micropollutants (OMPs) are not fully removed by wastewater treatment plants (WWTPs).
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OMP-degrading genes tend to be linked to mobile genetic elements (MGEs).
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Most catabolic MGEs in WWTPs were found with culture-based methods.
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Culture-independent methods for MGE analysis are critically reviewed.
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Limitations of MGE-mediated bioaugmentation strategies in WWTPs are discussed.

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Most cited references 144

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Opportunities and challenges in long-read sequencing data analysis

Shanika Amarasinghe, Shian Su, Xueyi Dong … (2020)

Long-read technologies are overcoming early limitations in accuracy and throughput, broadening their application domains in genomics. Dedicated analysis tools that take into account the characteristics of long-read data are thus required, but the fast pace of development of such tools can be overwhelming. To assist in the design and analysis of long-read sequencing projects, we review the current landscape of available tools and present an online interactive database, long-read-tools.org, to facilitate their browsing. We further focus on the principles of error correction, base modification detection, and long-read transcriptomics analysis and highlight the challenges that remain.

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A review on emerging contaminants in wastewaters and the environment: current knowledge, understudied areas and recommendations for future monitoring.

Bruce Petrie, Ruth Barden, Barbara Kasprzyk-Hordern (2015)

This review identifies understudied areas of emerging contaminant (EC) research in wastewaters and the environment, and recommends direction for future monitoring. Non-regulated trace organic ECs including pharmaceuticals, illicit drugs and personal care products are focused on due to ongoing policy initiatives and the expectant broadening of environmental legislation. These ECs are ubiquitous in the aquatic environment, mainly derived from the discharge of municipal wastewater effluents. Their presence is of concern due to the possible ecological impact (e.g., endocrine disruption) to biota within the environment. To better understand their fate in wastewaters and in the environment, a standardised approach to sampling is needed. This ensures representative data is attained and facilitates a better understanding of spatial and temporal trends of EC occurrence. During wastewater treatment, there is a lack of suspended particulate matter analysis due to further preparation requirements and a lack of good analytical approaches. This results in the under-reporting of several ECs entering wastewater treatment works (WwTWs) and the aquatic environment. Also, sludge can act as a concentrating medium for some chemicals during wastewater treatment. The majority of treated sludge is applied directly to agricultural land without analysis for ECs. As a result there is a paucity of information on the fate of ECs in soils and consequently, there has been no driver to investigate the toxicity to exposed terrestrial organisms. Therefore a more holistic approach to environmental monitoring is required, such that the fate and impact of ECs in all exposed environmental compartments are studied. The traditional analytical approach of applying targeted screening with low resolution mass spectrometry (e.g., triple quadrupoles) results in numerous chemicals such as transformation products going undetected. These can exhibit similar toxicity to the parent EC, demonstrating the necessity of using an integrated analytical approach which compliments targeted and non-targeted screening with biological assays to measure ecological impact. With respect to current toxicity testing protocols, failure to consider the enantiomeric distribution of chiral compounds found in the environment, and the possible toxicological differences between enantiomers is concerning. Such information is essential for the development of more accurate environmental risk assessment.

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Mobility of plasmids.

Chris Smillie, Fernando de la Cruz, Eduardo P. C. Rocha … (2010)

Plasmids are key vectors of horizontal gene transfer and essential genetic engineering tools. They code for genes involved in many aspects of microbial biology, including detoxication, virulence, ecological interactions, and antibiotic resistance. While many studies have decorticated the mechanisms of mobility in model plasmids, the identification and characterization of plasmid mobility from genome data are unexplored. By reviewing the available data and literature, we established a computational protocol to identify and classify conjugation and mobilization genetic modules in 1,730 plasmids. This allowed the accurate classification of proteobacterial conjugative or mobilizable systems in a combination of four mating pair formation and six relaxase families. The available evidence suggests that half of the plasmids are nonmobilizable and that half of the remaining plasmids are conjugative. Some conjugative systems are much more abundant than others and preferably associated with some clades or plasmid sizes. Most very large plasmids are nonmobilizable, with evidence of ongoing domestication into secondary chromosomes. The evolution of conjugation elements shows ancient divergence between mobility systems, with relaxases and type IV coupling proteins (T4CPs) often following separate paths from type IV secretion systems. Phylogenetic patterns of mobility proteins are consistent with the phylogeny of the host prokaryotes, suggesting that plasmid mobility is in general circumscribed within large clades. Our survey suggests the existence of unsuspected new relaxases in archaea and new conjugation systems in cyanobacteria and actinobacteria. Few genes, e.g., T4CPs, relaxases, and VirB4, are at the core of plasmid conjugation, and together with accessory genes, they have evolved into specific systems adapted to specific physiological and ecological contexts.

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Author and article information

Contributors

Cornelia U. Welte

Journal

Journal ID (nlm-ta): Water Res X

Journal ID (iso-abbrev): Water Res X

Title: Water Research X

Publisher: Elsevier

ISSN (Electronic): 2589-9147

Publication date PMC-release: 29 August 2020

Publication date Collection: 01 December 2020

Publication date (Electronic): 29 August 2020

Volume: 9

Electronic Location Identifier: 100065

Affiliations

[a ]Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, the Netherlands

[b ]Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, the Netherlands

Author notes

[∗ ]Corresponding author. Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, the Netherlands. c.welte@ 123456science.ru.nl

Article

Publisher ID: S2589-9147(20)30025-6 Publisher ID: 100065

DOI: 10.1016/j.wroa.2020.100065

PMC ID: 7494797

PubMed ID: 32984801

SO-VID: a6125184-79e9-4b69-823d-9149334d52e7

License:

This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

History

Date received : 29 June 2020

Date revision received : 19 August 2020

Date accepted : 28 August 2020

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The role of mobile genetic elements in organic micropollutant degradation during biological wastewater treatment

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Abstract

Graphical abstract

Highlights

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Trace Elements and Electrolytes

Most cited references 144

Opportunities and challenges in long-read sequencing data analysis

A review on emerging contaminants in wastewaters and the environment: current knowledge, understudied areas and recommendations for future monitoring.

Mobility of plasmids.

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Cited by 15

Most referenced authors 1,539