Analysis of transduction in wastewater bacterial populations by targeting the phage-derived 16S rRNA gene sequences

Contribution of wastewater to antimicrobial resistance: A review article

OBJECTIVES

Antimicrobial resistance (AMR) is a global challenge that has raised concern globally, owing to its detrimental effects on the health and economy of countries. The ever-growing threat of AMR and sources of AMR are still being investigated. Wastewater plays an important role as a habitat for bacteria and an environment conducive to gene transfer. The primary aim of this review was to highlight the contribution of wastewater to AMR.

METHODS

Evidence of AMR in wastewater was drawn from literature published in the last 10 years, from 2012 to 2022.

RESULTS

Wastewater from agricultural practices, pharmaceutical manufacturing plants, and hospital effluents was established to promote AMR. Furthermore, stress factors such as the presence of antibiotics, heavy metals, pH, and temperature initiate and propagate AMR in bacteria living in wastewater. AMR in bacteria from wastewater was established to be either natural or acquired. Wastewater treatment techniques such as membrane filtration, coagulation, adsorption, and advanced oxidation processes have been used to remove resistant bacteria with varying success levels.

CONCLUSION

Wastewater is a major contributor to AMR, and an understanding of its role in AMR is necessary to find a lasting solution. In this regard, the spread of AMR in wastewater should be considered a threat that requires a strategy to stop further damage.

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

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.

Impact of Redox Conditions on Antibiotic Resistance Conjugative Gene Transfer Frequency and Plasmid Fate in Wastewater Ecosystems

Wastewater is a common pathway for the spread of antibiotic resistance (AR) genes and bacteria into the environment. Biological treatment can mitigate this path, but horizontal gene transfer (HGT) between bacteria also occurs in such processes, although the influence of bioreactor habitat and ecology on HGT frequency is not well understood. Here, we quantified how oxidation-reduction (redox) conditions impact the fate of a Green fluorescent protein (Gfp)-tagged AR plasmid (pRP4-gfp) within an E. coli host (EcoFJ1) in the liquid phase and biofilms in bioreactors. Replicate reactors treating domestic wastewater were operated under stable aerobic (+195 ± 25 mV), anoxic (-15 ± 50 mV), and anaerobic (-195 ± 15 mV) conditions, and flow cytometry and selective plating were used to quantify donor strain, EcoFJ1(pRP4-gfp), and putative transconjugants over time. Plasmid pRP4-gfp-bearing cells disappeared rapidly in aerobic ecosystems (∼2.0 log reduction after 72 h), especially in the liquid phase. In contrast, EcoFJ1(pRP4-gfp) and putative transconjugants persisted much longer in anaerobic biofilms (∼1.0 log reduction, after 72 h). Plasmid transfer frequencies were also higher under anaerobic conditions. In parallel, protozoan abundances were over 20 times higher in aerobic reactors relative to anaerobic reactors, and protozoa numbers significantly inversely correlated with pRP4-gfp signals across all reactors (p < 0.05). Taken together, observed HGT frequency and plasmid retention are impacted by habitat conditions and trophic effects, especially oxygen conditions and apparent predation. New aerobic bioreactor designs are needed, ideally employing passive aeration to save energy, to minimize resistance HGT in biological wastewater treatment processes.

Assessing the performance and microbial community of hybrid moving bed and conventional membrane bioreactors treating municipal wastewater

A conventional (SB-CMBR) and a hybrid moving-bed (SB-HMBR) sequencing batch membrane bioreactor treating municipal wastewater were compared during their start-up in terms of organic matter and nutrient removal, membrane fouling characteristics and microbial community. Both systems exhibited similar COD, ammonium, total nitrogen (TN) and phosphorus removal efficiency, amounting up to 96%, 99%, 70% and 85%, respectively. Results from cycle tests revealed that the contribution of attached biomass to the overall ammonium removal in the hybrid reactor was marginal. Moreover, higher despite the similar phosphorus removal efficiency attained in both reactors, nitrate-dosing activity batch assays specifically revealed that the anoxic phosphate uptake rate (PUR) in the SB-HMBR was 1.71 times higher than in the SB-CMBR. Moreover, a higher frequency of Candidatus Accumulibacter-related polyphosphate-accumulating organisms was observed in the biofilm carriers of the hybrid reactor. These findings may explain why the overall PUR was almost 50% higher in the SB-HMBR. By operating the reactors in sequencing batch mode, adhesion of particles on the membrane surface was reduced while fouling was mitigated as compared to continuous MBR systems. Better filterability conditions with lower fouling rate were found in the SB-HMBR, important features of the hybrid reactor for reducing membrane cleaning-related energy demand.

Identification of a bacteriophage from an environmental multidrug-resistant E. coli isolate and its function in horizontal transfer of ARGs

Horizontal transfer of ARGs was generally considered to be mediated by three methods - transformation, conjugation and transduction through phages - during which the contribution of bacteriophages to gene transfer in the environment is unclear or even questioned. In this study, a multiple-antibiotic-resistant Escherichia coli strain and its phage (YZ1) were isolated from a municipal wastewater treatment system. The results of the morphological and genomic analyses of phage YZ1 showed that it is a member of the T7 viral genus in the subfamily Autographivirinae. Its genome is similar to that of the E. coli phage K1F in both organization and sequence and does not encode ARGs. However, 28 paired reads in the raw sequencing data aligned to ARGs, including those promoting β-lactam, aminoglycoside, and fluoroquinolone resistance, among others. Quantitative PCR showed that ARGs were present in bacteriophage DNA (approximately 10³ copies/mL) and were also detected in the bacterial host DNA. The results suggested that while infrequent, some ARG-carrying transducing phages were presumably generated by erroneous packaging during infection of antibiotic-resistant bacteria, which may create the possibility of horizontal transfer of ARGs.

Insights of Phage-Host Interaction in Hypersaline Ecosystem through Metagenomics Analyses

Bacteriophages, as the most abundant biological entities on Earth, place significant predation pressure on their hosts. This pressure plays a critical role in the evolution, diversity, and abundance of bacteria. In addition, phages modulate the genetic diversity of prokaryotic communities through the transfer of auxiliary metabolic genes. Various studies have been conducted in diverse ecosystems to understand phage-host interactions and their effects on prokaryote metabolism and community composition. However, hypersaline environments remain among the least studied ecosystems and the interaction between the phages and prokaryotes in these habitats is poorly understood. This study begins to fill this knowledge gap by analyzing bacteriophage-host interactions in the Great Salt Lake, the largest prehistoric hypersaline lake in the Western Hemisphere. Our metagenomics analyses allowed us to comprehensively identify the bacterial and phage communities with Proteobacteria, Firmicutes, and Bacteroidetes as the most dominant bacterial species and Siphoviridae, Myoviridae, and Podoviridae as the most dominant viral families found in the metagenomic sequences. We also characterized interactions between the phage and prokaryotic communities of Great Salt Lake and determined how these interactions possibly influence the community diversity, structure, and biogeochemical cycles. In addition, presence of prophages and their interaction with the prokaryotic host was studied and showed the possibility of prophage induction and subsequent infection of prokaryotic community present in the Great Salt Lake environment under different environmental stress factors. We found that carbon cycle was the most susceptible nutrient cycling pathways to prophage induction in the presence of environmental stresses. This study gives an enhanced snapshot of phage and prokaryote abundance and diversity as well as their interactions in a hypersaline complex ecosystem, which can pave the way for further research studies.

Effect of operational strategies on activated sludge's acclimation to phenol, subsequent aerobic granulation, and accumulation of polyhydoxyalkanoates

Aerobic granules, a relative novel form of microbial aggregate, are capable of degrading many toxic organic pollutants. Appropriate strategy is needed to acclimate seed sludge to the toxic compounds for successful granulation. In this study, two distinct strategies, i.e. mixed or single carbon sources, were experimented to obtain phenol-acclimated sludge. Their effects on reactor performance, biomass characteristics, microbial population and the granulation process were analyzed. Sludge fed with phenol alone exhibited faster acclimation and earlier appearance of granules, but possibly lower microbial diversity and reactor stability. Using a mixture of acetate and phenol in the acclimation stage, on the other hand, led to a reactor with slower phenol degradation and granulation, but eventual formation of strong and stable aerobic granules. In addition, the content of intracellular polyhydoxyakanoates (PHA) was also monitored, and significant accumulation was observed during the pre-granulation stage, where PHA >50% of dry weight was observed in both reactors.

Microbiological mechanism of the improved nitrogen and phosphorus removal by embedding microbial fuel cell in Anaerobic-Anoxic-Oxic wastewater treatment process

Anaerobic-Anoxic-Oxic (AA/O) wastewater treatment process is a widely used wastewater treatment process for simultaneous nitrogen and phosphorus removal. Microbial fuel cell (MFC) can generate electricity and treat the organic wastewater simultaneously. Our previous research showed that embedding MFC in AA/O wastewater treatment process could enhance the pollutants removal efficiency. However, the mechanism was not clear. In this study, a lab-scale corridor-style AA/O reactor with MFC embedded was operated and both the total nitrogen and total phosphorus removal efficiencies were enhanced. DGGE and Illumina Miseq results demonstrated that both the microbial community structures on the surface of the cathode and in the suspensions of cathode chamber have been changed. The percentage of Thauera and Emticicia, identified as denitrifying bacteria, increased significantly in the suspension liquid when the MFC was embedded in the AA/O reactor. Moreover, the genus Rheinheimera were significantly enriched on the cathode surface, which might contribute to both the nitrogen removal enhancement and electricity generation.

Fake virus particles generated by fluorescence microscopy

Many laboratories are actively studying the abundance and roles of viruses in natural ecosystems. In these studies, the presence and number of viral particles is usually determined using fluorescent dyes. However, DNA associated with membrane-derived vesicles (MVs), gene transfer agents (GTAs), or cell debris can produce fluorescent dots that can be confused with viral particles. We suspect that fluorescence counting can lead to overestimation of virus numbers and even suggest the presence of viruses when there are none. Future studies in environmental virology should acknowledge this point and consider how to bypass this problem. Besides trying to improve discrimination between virions and MVs, we suggest adopting less holistic approaches, focusing on the detection of known virus groups and the isolation of new viruses from a broader range of hosts.

Evidence of bacteriophage-mediated horizontal transfer of bacterial 16S rRNA genes in the viral metagenome of the marine sponge Hymeniacidon perlevis

Marine sponges have never been directly examined with respect to the presence of viruses or their potential involvement in horizontal gene transfer. Here we demonstrate for the first time, to our knowledge, the presence of viruses in the marine sponge Hymeniacidon perlevis. Moreover, bacterial 16S rDNA was detected in DNA isolated from these viruses, indicating that phage-derived transduction appears to occur in H. perlevis. Phylogenetic analysis revealed that bacterial 16S rDNA isolated from sponge-derived viral and total DNA differed significantly, indicating that not all species are equally involved in transduction.

Gene transfer agents: phage-like elements of genetic exchange

Horizontal gene transfer is important in the evolution of bacterial and archaeal genomes. An interesting genetic exchange process is carried out by diverse phage-like gene transfer agents (GTAs) that are found in a wide range of prokaryotes. Although GTAs resemble phages, they lack the hallmark capabilities that define typical phages, and they package random pieces of the producing cell's genome. In this Review, we discuss the defining characteristics of the GTAs that have been identified to date, along with potential functions for these agents and the possible evolutionary forces that act on the genes involved in their production.

Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers

Biodegradation of anthropogenic pollutants in shallow aquifers is an important microbial ecosystem service which is mainly brought about by indigenous anaerobic microorganisms. For the management of contaminated sites, risk assessment and control of natural attenuation, the assessment of in situ biodegradation and the underlying microbial processes is essential. The development of novel molecular methods, "omics" approaches, and high-throughput techniques has revealed new insight into complex microbial communities and their functions in anoxic environmental systems. This review summarizes recent advances in the application of molecular methods to study anaerobic microbial communities in contaminated terrestrial subsurface ecosystems. We focus on current approaches to analyze composition, dynamics, and functional diversity of subsurface communities, to link identity to activity and metabolic function, and to identify the ecophysiological role of not yet cultured microbes and syntrophic consortia. We discuss recent molecular surveys of contaminated sites from an ecological viewpoint regarding degrader ecotypes, abiotic factors shaping anaerobic communities, and biotic interactions underpinning the importance of microbial cooperation for microbial ecosystem services such as contaminant degradation.

Extent and variation of phage-borne bacterial 16S rRNA gene sequences in wastewater environments

Phage metagenomes isolated from wastewater over a 12-month period were analyzed. The results suggested that various strains of Proteobacteria, Bacteroidetes, and other phyla are likely to participate in transduction. The patterns of 16S rRNA sequences found in phage metagenomes did not follow changes in the total bacterial community.

Bacteriophages and genetic mobilization in sewage and faecally polluted environments

Bacteriophages are one of the most abundant entities on the planet and are present in high concentrations within humans and animals, mostly in the gut. Phages that infect intestinal bacteria are released by defecation and remain free in extra‐intestinal environments, where they usually persist for longer than their bacterial hosts. Recent studies indicate that a large amount of the genetic information in bacterial genomes and in natural environments is of phage origin. In addition, metagenomic analysis reveals that a substantial number of bacterial genes are present in viral DNA in different environments. These facts support the belief that phages can play a significant role in horizontal gene transfer between bacteria. Bacteriophages are known to transfer genes by generalized and specialized transduction and indeed there are some examples of phages found in the environment carrying and transducing genes of bacterial origin. A successful transduction in the environment requires certain conditions, e.g. phage and bacterial numbers need to exceed certain threshold concentrations, the bacteria need to exist in an infection‐competent physiological state, and lastly, the physical conditions in the environment (pH, temperature, etc. of the supporting matrix) have to be suitable for phage infection. All three factors are reviewed here, and the available information suggests: (i) that the number of intestinal bacteria and phages in faecally contaminated environments guarantees bacteria–phage encounters, (ii) that transduction to intestinal bacteria in the environment is probable, and (iii) that transduction is more frequent than previously thought. Therefore, we suggest that phage‐mediated horizontal transfer between intestinal bacteria, or between intestinal and autochthonous bacteria in extra‐intestinal environments, might take place and that its relevance for the emergence of new bacterial strains and potential pathogens should not be ignored.