High-Resolution Temporal and Spatial Patterns of Virome in Wastewater Treatment Systems

Significant impact of bleaching treatment on phage-host interaction dynamics in a full-scale wastewater treatment plant

The temporal dynamics of phage-host interactions within full-scale biological wastewater treatment (BWT) plants remain inadequately characterized. Here, we provide an in-depth investigation of viral and bacterial dynamics over a nine-year period in an activated sludge BWT plant, where bleach addition was applied to control sludge foaming. By conducting bioinformatic analyses on 98 metagenomic time-series samples, we reconstructed 3,486 bacterial genomes and 2,435 complete or near-complete viral genomes, which were classified into 361 bacterial and 889 viral clusters, respectively. Our results demonstrate that the primary bleaching event induced significant shifts in both bacterial and viral communities, as well as in virus-host interactions, as evidenced by alterations in bacteria-virus interaction networks and virus-to-host ratio dynamics. Following bleaching, the bacteria-virus network became less interconnected but more compartmentalized. Viral communities mirrored bacterial dynamics, indicating a strong coupling in phage-host interactions. Among the identified virus-host pairs, many exhibited a decelerating rise in viral abundance relative to host abundance, with virus-to-host ratios generally displaying a negative correlation with host abundance. This trend was particularly pronounced in virus-host pairs where viruses harbored integrase genes, indicative of temperate dynamics resembling a "Piggyback-the-Winner" model. Notably, the bleaching intervention appeared to induce a transition from lysogeny to lysis in viruses associated with some foaming-related bacterial species, suggesting a potential virus-involved indirect mechanism by which bleaching mitigates sludge foaming.

Quantification of Particle-Associated Viruses in Secondary Treated Wastewater Effluent

Viruses can interact with a broad range of inorganic and organic particles in water and wastewater. These associations can protect viruses from inactivation by quenching chemical disinfectants or blocking ultraviolet light transmission, and a much higher dosage of disinfectants is required to inactivate particle-associated viruses than free viruses. There have been only few studies of the association of viruses with particles in wastewater, particularly in secondary treated effluent. As secondary effluent is the source water to the reclaimed water treatment system, this study quantified indigenous enteric viruses, and viral indicators associated with particles in secondary effluents collected from five full-scale water reclamation facilities in the United States. Particle-associated viruses were enumerated using a sequential filtration followed by microfluidic digital PCR. This study showed that enteric viruses and viral indicators (crAssphage and pepper mild mottle virus, PMMoV) were attached to particles of different sizes in secondary effluent. Significantly higher concentrations of RNA viruses including PMMoV, norovirus, and enterovirus were detected in filtrate of the sequential filtration, which contained particles < 0.45 µm. DNA viruses including adenovirus and crAssphage were found to be more associated with larger particles in secondary effluent. Overall, high correlations were observed between viral indicators and enteric viruses, supporting the use of crAssphage and PMMoV to evaluate virus removal efficiency in water and wastewater treatment processes. The association of viruses with particles in wastewater has significant implications on wastewater treatment and disinfection processes as well as virus enumeration in wastewater.

Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities

Bacteria have evolved various antiviral defense systems (DSs) to protect themselves, but how DSs respond to the variation of bacteriophages in complex bacterial communities and whether DSs function effectively in maintaining the stability of bacterial community structure and function remain unknown. Here, we conducted a long-term metagenomic investigation on the composition of bacterial and phage communities of monthly collected activated sludge (AS) samples from two full-scale wastewater treatment plants over 6 years and found that DSs were widespread in AS, with 91.1% of metagenome-assembled genomes (MAGs) having more than one complete DS. The stability of the bacterial community was maintained under the fluctuations of the phage community, and DS abundance and phage abundance were strongly positively correlated; there was a 0-3-month time lag in the responses of DSs to phage fluctuations. The rapid turnover of clustered regularly interspaced short palindromic repeat spacer repertoires further highlighted the dynamic nature of bacterial defense mechanisms. A pan-immunity phenomenon was also observed, with nearly identical MAGs showing significant differences in DS composition, which contributed to community stability at the species level. This study provides novel insights into the complexity of phage-bacteria interactions in complex bacterial communities and reveals the key roles of DSs in stabilizing bacterial community structure and function.

Longitudinal dynamics and cross-domain interactions of eukaryotic populations in wastewater treatment plants

Activated sludge is a large reservoir of novel microorganisms and microbial genetic diversity. While much attention has been given to the profile and functions of prokaryotes, the eukaryotic diversity remains largely unexplored. In this study, we analysed longitudinal activated sludge samples spanning 13 years from the largest secondary wastewater treatment plants in Hong Kong, unveiling a wealth of eukaryotic taxa and 681 856 non-redundant protein-coding genes, the majority (416 044) of which appeared novel. Ciliophora was the most dominant phylum with a significant increase after a transient intervention (bleaching event). Our metagenomic analysis reveals close linkage and covariation of eukaryotes, prokaryotes, and prokaryotic viruses (phages), indicating common responses to environmental changes such as transient intervention and intermittent fluctuations. Furthermore, high-resolution cross-domain relationships were interpreted by S-map, demonstrating a predatory role of Arthropoda, Ascomycota, Mucoromycota, and Rotifera. This high-resolution profile of microbial dynamics expands our knowledge on yet-to-be-cultured populations and their cross-domain interactions and highlights the ecological importance of eukaryotes in the activated sludge ecosystem.

Making waves: Intelligent phage cocktail design, a pathway to precise microbial control in water systems

Current practices in water and wastewater treatment to control unwanted microbes have led to new problems, including health effects from disinfection byproducts, growth of opportunistic pathogens resistant to residual disinfectants (e.g., chlorine), and antibiotic resistance. These challenges are spurring interest in rethinking our practices of microbial control. Simultaneously, advances in molecular biology and computation power are driving renewed interest in using phages (viruses that infect bacteria) to precisely control microbial growth (aka, phage biocontrol). In this Making Waves article, I begin by reviewing the current state of research into phage cocktail design, emphasizing our limited understanding of the features of successful phage cocktails (combinations of multiple types of phages). I describe the state of modeling phage-bacteria interactions and underscore the need for increasing research efforts to predict phage cocktail success, a key gap slowing the application of phage biocontrol. I also detail how research must also focus on techniques for engineering more effective phages to offer a more rapid alternative to phage discovery from natural environments. In this way, phage cocktails comprised of phages with complementary infection strategies may be designed. The final area for increased research effort that I highlight is the need for phage cocktail design to account for possible unintended environmental effects, a risk that is increasingly acknowledged in phage ecology studies but mostly ignored by those developing phage biocontrol technologies. By focusing more research effort towards the areas necessary for intelligent phage cocktail design, we can accelerate the development of phage-based biocontrol in water systems and improve public health.

Method evaluation for viruses in activated sludge: Concentration, sequencing, and identification

Activated sludge (AS) in wastewater treatment plants is one of the largest artificial microbial ecosystems on earth and it makes enormous contributions to human societies. Viruses are an important component in AS with a high abundance. However, their communities and functionalities have not been as widely explored as those of other microorganisms, such as bacteria. This gap is mainly due to technical challenges in effective viral concentration, extraction, and sequencing. In this study, we compared four kinds of concentration methods, two sequencing approaches, and four identification bioinformatic tools to evaluate the whole analysis workflow for viruses in AS. Results showed flocculation, filtration, and resuspension (FFR) could get the longest DNA lengths and ultracentrifugation obtained the highest DNA yields for viruses in AS. Based on the results of present study, FFR and tangential flow filtration with the membrane pore size of 100 kDa were most recommended to concentrate viruses in AS samples with huge volumes. Besides, different concentration methods could get different viral catalogs and thus multiple methods should be combined to get the whole picture of viruses in the system. In addition, geNomad was the most recommended identification tool for viruses in the present study and the long-read sequencing could improve the assembly statistics of viruses when compared with the short-read sequencing. For the 8192 viral operational taxonomic units in this study, 95.1 % of them were phages and belonged to the same lineage at the order level of Caudovirales. Virulent phages dominated the AS system and Pseudomonadota were the main host. Taken together, this study provides new insights into methods selection for virus research of AS.

Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system

BACKGROUND

Understanding the interactions and dynamics of microbiotas within biological wastewater treatment systems is essential for ensuring their stability and long-term sustainability. In this study, we developed a systematic framework employing multi-omics and Hi-C sequencing to extensively investigate prokaryotic and phage communities within a hybrid biofilm and activated sludge system.

RESULTS

We uncovered distinct distribution patterns, metabolic capabilities, and activities of functional prokaryotes through the analysis of 454 reconstructed prokaryotic genomes. Additionally, we reconstructed a phage catalog comprising 18,645 viral operational taxonomic units (vOTUs) with high length and contiguity using hybrid assembly, and a distinct distribution of phages was depicted between activated sludge (AS) and biofilm. Importantly, 1340 host-phage pairs were established using Hi-C and conventional in silico methods, unveiling the host-determined phage prevalence. The majority of predicted hosts were found to be involved in various crucial metabolic processes, highlighting the potential vital roles of phages in influencing substance metabolism within this system. Moreover, auxiliary metabolic genes (AMGs) related to various categories (e.g., carbohydrate degradation, sulfur metabolism, transporter) were predicted. Subsequent activity analysis emphasized their potential ability to mediate host metabolism during infection. We also profiled the temporal dynamics of phages and their associated hosts using 13-month time-series metagenomic data, further demonstrating their tight interactions. Notably, we observed lineage-specific infection patterns, such as potentially host abundance- or phage/host ratio-driven phage population changes.

CONCLUSIONS

The insights gained from this research contribute to the growing body of knowledge surrounding interactions and dynamics of host-phage and pave the way for further exploration and potential applications in the field of microbial ecology. Video Abstract.

Symbiotic virus-bacteria interactions in biological treatment of coking wastewater manipulating bacterial physiological activities

Biological treatment is commonly used in coking wastewater (CWW) treatment. Prokaryotic microbial communities in CWW treatment have been comprehensively studied. However, viruses, as the critical microorganisms affecting microbial processes and thus engineering parameters, still remain poorly understood in CWW treatment context. Employing viromics sequencing, the composition and function of the viral community in CWW treatment were discovered, revealing novel viral communities and key auxiliary metabolic functions. Caudovirales appeared to be the predominant viral order in the oxic-hydrolytic-oxic (OHO) CWW treatment combination, showing relative abundances of 62.47 %, 56.64 % and 92.20 % in bioreactors O1, H and O2, respectively. At the family level, Myoviridae, Podoviridae and Siphoviridae mainly prevailed in bioreactors O1 and H while Phycodnaviridae dominated in O2. A total of 56.23-92.24% of novel viral contigs defied family-level characterization in this distinct CWW habitat. The virus-host prediction results revealed most viruses infecting the specific functional taxa Pseudomonas, Acidovorax and Thauera in the entire OHO combination, demonstrating the viruses affecting bacterial physiology and pollutants removal from CWW. Viral auxiliary metabolic genes (AMGs) were screened, revealing their involvement in the metabolism of contaminants and toxicity tolerance. In the bioreactor O1, AMGs were enriched in detoxification and phosphorus ingestion, where glutathione S-transferase (GSTs) and beta-ketoadipyl CoA thiolase (fadA) participated in biodegradation of polycyclic aromatic hydrocarbons and phenols, respectively. In the bioreactors H and O2, the AMGs focused on cell division and epicyte formation of the hosts, where GDPmannose 4,6-dehydratase (gmd) related to lipopolysaccharides biosynthesis was considered to play an important role in the growth of nitrifiers. The diversities of viruses and AMGs decreased along the CWW treatment process, pointing to a reinforced virus-host adaptive strategy in stressful operation environments. In this study, the symbiotic virus-bacteria interaction patterns were proposed with a theoretical basis for promoting CWW biological treatment efficiency. The findings filled the gaps in the virus-bacteria interactions at the full-scale CWW treatment and provided great value for understanding the mechanism of biological toxicity and sludge activity in industrial wastewater treatment.

A panoramic view of the virosphere in three wastewater treatment plants by integrating viral-like particle-concentrated and traditional non-concentrated metagenomic approaches

Wastewater biotreatment systems harbor a rich diversity of microorganisms, and the effectiveness of biotreatment systems largely depends on the activity of these microorganisms. Specifically, viruses play a crucial role in altering microbial behavior and metabolic processes throughout their infection phases, an aspect that has recently attracted considerable interest. Two metagenomic approaches, viral-like particle-concentrated (VPC, representing free viral-like particles) and non-concentrated (NC, representing the cellular fraction), were employed to assess their efficacy in revealing virome characteristics, including taxonomy, diversity, host interactions, lifestyle, dynamics, and functional genes across processing units of three wastewater treatment plants (WWTPs). Our findings indicate that each approach offers unique insights into the viral community and functional composition. Their combined use proved effective in elucidating WWTP viromes. We identified nearly 50,000 viral contigs, with Cressdnaviricota and Uroviricota being the predominant phyla in the VPC and NC fractions, respectively. Notably, two pathogenic viral families, Asfarviridae and Adenoviridae, were commonly found in these WWTPs. We also observed significant differences in the viromes of WWTPs processing different types of wastewater. Additionally, various phage-derived auxiliary metabolic genes (AMGs) were active at the RNA level, contributing to the metabolism of the microbial community, particularly in carbon, sulfur, and phosphorus cycling. Moreover, we identified 29 virus-carried antibiotic resistance genes (ARGs) with potential for host transfer, highlighting the role of viruses in spreading ARGs in the environment. Overall, this study provides a detailed and integrated view of the virosphere in three WWTPs through the application of VPC and NC metagenomic approaches. Our findings enhance the understanding of viral communities, offering valuable insights for optimizing the operation and regulation of wastewater treatment systems.

Temporal Dynamics and Contribution of Phage Community to the Prevalence of Antibiotic Resistance Genes in a Full-Scale Sludge Anaerobic Digestion Plant

Anaerobic digestion (AD) is an important biological resource recovery process, where microorganisms play key roles for material transformation. There has been some knowledge about the prokaryotic community and antibiotic resistance genes (ARGs) in AD, but there has been very limited knowledge of phages. In this study, samples from a full-scale AD plant were collected over 13 months, sequenced, and analyzed for viral and prokaryotic metagenomes. Totally, 3015 viral operational taxonomic units (vOTUs) were detected, mostly assigned to Caudoviricetes. The phage community had faster temporal variation than the prokaryotic community. Warm seasons harbored a higher abundance of both temperate phages and broad host-range phages. Seven ARGs of 6 subtypes were carried by 20 vOTUs, a representative ermT gene was synthesized and expressed, and the resistance activity in the host was examined, confirming the real activity of virus-carried ARGs in the AD process. Some of the ARGs were horizontally transferred between the phage and prokaryotic genomes. However, phage infection was not found to contribute to ARG transfer. This study provided an insight into the ecological patterns of the phage community, confirmed the antibiotic resistance activity of virus-carried ARGs, evaluated the contribution of phages on the ARG prevalence, and laid the foundation for the control strategies of the community and antibiotic resistance in the AD process.

Metagenome sequencing reveals shifts in phage-associated antibiotic resistance genes from influent to effluent in wastewater treatment plants

Antibiotic resistance poses a significant threat to global health, and the microbe-rich activated sludge environment may contribute to the dissemination of antibiotic resistance genes (ARGs). ARGs spread across various bacterial populations via multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages (phages). However, the potential role of phages in spreading ARGs in wastewater treatment systems remains unclear. This study characterized the core resistome, mobile genetic elements (MGEs), and virus-associated ARGs (vir_ARGs) in influents (Inf) and effluents (Eff) samples from nine WWTPs in eastern China. The abundance of ARGs in the Inf samples was higher than that in the Eff samples. A total of 21 core ARGs were identified, accounting for 38.70 %-83.70 % of the different samples. There was an increase in MGEs associated with phage-related processes from influents to effluents (from 12.68 % to 21.10 %). These MGEs showed strong correlations in relative abundance and composition with the core ARGs in the Eff samples. Across the Inf and Eff samples, 58 unique vir_ARGs were detected, with the Eff samples exhibiting higher diversity of vir_ARGs than the Inf samples. Statistical analyses indicated a robust relationship between core ARG profile, MGEs associated with phage-related processes, and vir_ARG composition in the Eff samples. Additionally, the co-occurrence of MGEs and ARGs in viral genomes was observed, ranging from 22.73 % to 68.75 %. This co-occurrence may exacerbate the persistence and spread of ARGs within WWTPs. The findings present new information on the changes in core ARGs, MGEs, and phage-associated ARGs from influents to effluents in WWTPs and provide new insights into the role of phage-associated ARGs in these systems.

Bacteriophages: Vectors of or weapons against the transmission of antibiotic resistance genes in hospital wastewater systems?

Antimicrobial resistance poses a serious threat to human health and is responsible for the death of millions of people annually. Hospital wastewater is an important hotspot for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). However, little is known about the relationship between phages and ARGs in hospital wastewater systems (HWS). In the present study, the viral diversity of 12 HWSs using data from public metagenomic databases was investigated. Viruses were widely found in both the influent and effluent of each HWS. A total of 45 unique ARGs were carried by 85 viral contigs, which accounted for only 0.14% of the total viral populations, implying that ARGs were not commonly present in phages. Three efflux pump genes were identified as shared between phages and bacterial genomes. However, the predominant types of ARGs in HWS such as aminoglycoside- and beta-lactam-resistance genes were rarely found in phages. Based on CRISPR spacer and tRNA matches, interactions between 171 viral contigs and 60 antibiotic-resistant genomes were predicted, including interactions involving phages and vancomycin-resistant Enterococcus_B faecium or beta-lactam-resistant Klebsiella pneumoniae. More than half (56.1%) of these viral contigs indicated lytic and none of them carried ARGs. As the vOTUs in this study had few ARGs and were primarily lytic, HWS may be a valuable source for phage discovery. Future studies will be able to experimentally validate these sequence-based results to confirm the suitability of HWS phages for pathogen control measures in wastewater.

Global diversity and biogeography of DNA viral communities in activated sludge systems

BACKGROUND

Activated sludge (AS) systems in wastewater treatment plants (WWTPs) harbor enormous viruses that regulate microbial metabolism and nutrient cycling, significantly influencing the stability of AS systems. However, our knowledge about the diversity of viral taxonomic groups and functional traits in global AS systems is still limited. To address this gap, we investigated the global diversity and biogeography of DNA viral communities in AS systems using 85,114 viral operational taxonomic units (vOTUs) recovered from 144 AS samples collected across 54 WWTPs from 13 different countries.

RESULTS

AS viral communities and their functional traits exhibited distance-decay relationship (DDR) at the global scale and latitudinal diversity gradient (LDG) from equator to mid-latitude. Furthermore, it was observed that AS viral community and functional gene structures were largely driven by the geographic factors and wastewater types, of which the geographic factors were more important. Carrying and disseminating auxiliary metabolic genes (AMGs) associated with the degradation of polysaccharides, sulfate reduction, denitrification, and organic phosphoester hydrolysis, as well as the lysis of crucial functional microbes that govern biogeochemical cycles were two major ways by which viruses could regulate AS functions. It was worth noting that our study revealed a high abundance of antibiotic resistance genes (ARGs) in viral genomes, suggesting that viruses were key reservoirs of ARGs in AS systems.

CONCLUSIONS

Our results demonstrated the highly diverse taxonomic groups and functional traits of viruses in AS systems. Viral lysis of host microbes and virus-mediated HGT can regulate the biogeochemical and nutrient cycles, thus affecting the performance of AS systems. These findings provide important insights into the viral diversity, function, and ecology in AS systems on a global scale. Video Abstract.

Sample and library preparation approaches for the analysis of the virome of irrigation water

BACKGROUND

The virome (i.e. community of mainly RNA and DNA eukaryotic viruses and bacteriophages) of waters is yet to be extensively explored. In particular, the virome of waters used for irrigation could therefore potentially carry viral pathogens that can contaminate fresh produce. One problem in obtaining viral sequences from irrigation waters is the relatively low amount of virus particles, as well as the presence of human, bacterial and protozoan cells. The present aimed study was to compare different processing, amplification, and sequencing approaches for virome characterization in irrigation waters.

RESULTS

Our analyses considered percentages of viral reads, values for diversity indices and number of families found in sequencing results. The results obtained suggest that enrichment protocols using two (bezonase and microccocal nuclease) or four enzymes at once (bezonase, microccocal nuclease, DNAse and RNase), regardless of an Amicon filtration step, are more appropriate than separated enzymatic treatments for virome characterization in irrigation water. The NetoVIR protocol combined with the ScriptSeq v2 RNA-Seq Library (P0-L20 protocol) showed the highest percentages of RNA viruses and identified the higher number of families.

CONCLUSION

Although virome characterization applied in irrigation waters is an important tool for protecting public health by informing on circulating human and zoonotic infections, optimized and standardized procedures should be followed to reduce the variability of results related to either the sample itself and the downstream bioinformatics analyses. Our results show that virome characterization can be an important tool in the discovery of pathogenic viruses in the environment and can be used to inform and optimize reference-based detection methods provided that appropriate and rigorous controls are included. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Virus impacted community adaptation in oligotrophic groundwater environment revealed by Hi-C coupled metagenomic and viromic study

Viruses play a crucial role in microbial mortality, diversity and biogeochemical cycles. Groundwater is the largest global freshwater and one of the most oligotrophic aquatic systems on Earth, but how microbial and viral communities are shaped in this special habitat is largely unexplored. In this study, we collected groundwater samples from 23 to 60 m aquifers at Yinchuan Plain, China. In total, 1920 non-reductant viral contigs were retrieved from metagenomes and viromes constructed by Illumina and Nanopore hybrid sequencing. Only 3% of them could be clustered with known viruses, most of which were Caudoviricetes. Coupling 1.2 Tb Hi-C sequencing with CRISPR matching and homology search, we connected 469 viruses with their hosts while some viral clusters presented a broad-host-range trait. Meanwhile, a large proportion of biosynthesis related auxiliary metabolism genes were identified. Those characteristics might benefit viruses for a better survival in this special oligotrophic environment. Additionally, the groundwater virome showed genomic features distinct from those of the open ocean and wastewater treatment facilities in GC distribution and unannotated gene compositions. This paper expands the current knowledge of the global viromic records and serves as a foundation for a more thorough understanding of viruses in groundwater.

Potential Auxiliary Metabolic Capabilities and Activities Reveal Biochemical Impacts of Viruses in Municipal Wastewater Treatment Plants

Viruses influence biogeochemical cycles in oceans, freshwater, soil, and human gut through infection and by modulating virocell metabolism through virus-encoded auxiliary metabolic genes (vAMGs). However, the geographical distribution, potential metabolic function, and engineering significance of vAMGs in wastewater treatment plants (WWTPs) remain to be explored. Here, 752 single-contig viral genomes with high confidence, 510 of which belonged to Caudovirales, were recovered from the activated sludge metagenomes of 32 geographically distributed WWTPs. A total of 101 vAMGs involved in various metabolic pathways were identified, the most common of which were the queuosine biosynthesis genes folE, queD, and queE and the sulfur metabolism gene cysH. Phylogenetic analysis and virus-host relationship prediction revealed the probable evolutionary histories of vAMGs involved in carbon (acpP and prsA), nitrogen (amoC), sulfur (cysH), and phosphate (phoH) metabolism, which potentially mediate microbial carbon and nutrient cycling. Notably, 11 of the 38 (28.3%) vAMGs identified in the metagenomes with corresponding metatranscriptomes were transcriptionally expressed, implying an active functional state. This meta-analysis provides the first broad catalog of vAMGs in municipal WWTPs and how they may assist in the basic physiological reactions of their microbial hosts or nutrient cycling in the WWTPs, and therefore, may have important effects on the engineering of wastewater treatment processes.

Microbial density-dependent viral dynamics and low activity of temperate phages in the activated sludge process

The ecological behavior of bacteriophages (phages), the most abundant biological entity in wastewater treatment systems, is poorly understood, especially that of temperate phages. Here, the temporal dynamics of lytic and temperate phages in a laboratory-scale activated sludge reactor with a sludge bulking issue was investigated using coupled sludge metagenomic and viromic analyses. The lysogenic fragments (prophages) identified were widely distributed in the reconstructed metagenome-assembled genomes (61.7%, n = 227). However, only 12.3% of the identified prophages experienced lysogenic-lytic switching, and the abundance contribution of prophages to free virus communities was only 0.02-0.3%, indicating low activity of temperate phages. Although the sludge community changed dramatically during reactor operation, no massive prophage induction events were detected. Statistical analyses showed strong correlations between sludge concentration and free virus and temperate phage communities, suggesting microbial density-dependent virus dynamics in the sludge microbiota.

Diversity and potential functional characteristics of phage communities colonizing microplastic biofilms

The multiple ecological influences and potential microbial degradation of microplastics are generally attributed to the microbial communities colonized on microplastics. Phages play an important role in the composition and function of their bacterial hosts, yet the occurrence and the potential functional characteristics of phages in the biofilms of microplastics have not been known. This study, for the first time, explored the diversity, composition, and potential function characteristics of phage communities living in the biofilms of PP, PE, and PET microplastics and stones, cultured in the same site, via the metagenome method. The results showed that a total of 240 non-redundant virus OTUs (vOTUs), distributed in at least four orders and seven families, were detected from biofilm metagenomes of microplastics. Compared to stones, some phages were selectively enriched by microplastic biofilms, with 13 vOTUs uniquely colonized on three microplastics, and these vOTUs mainly belong to the family Autographiviridae and Podoviridae. Except for the evenness of PP, the richness index, Chao 1 index, and abundance of phage communities of three microplastics were much higher than that of stone. At least 8 bacterial phyla and 72 genera were possibly infected by phages. Compared to the stones, both composition and abundance of the phages and hosts presented significant and strong correlations for three microplastics. Some of the bacterial hosts on microplastics were likely involved in the microplastic degradation, fermenters, nitrogen transformation processes, and so on. A total of 124 encoding auxiliary metabolic genes (AMGs) were detected from viral contigs. The abundance of AMGs in microplastics was much higher than that of stones, which may provide more direct or indirect support for the bacterial degradation of microplastics. This study provides a new perspective on the occurrence and potential functions of phages on microplastic biofilms, thus expanding our understanding of microbial communities on microplastic biofilms.

Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming

The rise of global temperature causes the degradation of the substantial reserves of carbon (C) stored in tundra soils, in which microbial processes play critical roles. Viruses are known to influence the soil C cycle by encoding auxiliary metabolic genes and infecting key microorganisms, but their regulation of microbial communities under climate warming remains unexplored. In this study, we evaluated the responses of viral communities for about 5 years of experimental warming at two depths (15 to 25 cm and 45 to 55 cm) in the Alaskan permafrost region. Our results showed that the viral community and functional gene composition and abundances (including viral functional genes related to replication, structure, infection, and lysis) were significantly influenced by environmental conditions such as total nitrogen (N), total C, and soil thawing duration. Although long-term warming did not impact the viral community composition at the two depths, some glycoside hydrolases encoded by viruses were more abundant at both depths of the warmed plots. With the continuous reduction of total C, viruses may alleviate methane release by altering infection strategies on methanogens. Importantly, viruses can adopt lysogenic and lytic lifestyles to manipulate microbial communities at different soil depths, respectively, which could be one of the major factors causing the differences in microbial responses to warming. This study provides a new ecological perspective on how viruses regulate the responses of microbes to warming at community and functional scales. IMPORTANCE Permafrost thawing causes microbial release of greenhouse gases, exacerbating climate warming. Some previous studies examined the responses of the microbial communities and functions to warming in permafrost region, but the roles of viruses in mediating the responses of microbial communities to warming are poorly understood. This study revealed that warming induced changes in some viral functional classes and in the virus/microbe ratios for specific lineages, which might influence the entire microbial community. Furthermore, differences in viral communities and functions, along with soil depths, are important factors influencing microbial responses to warming. Collectively, our study revealed the regulation of microbial communities by viruses and demonstrated the importance of viruses in the microbial ecology research.

Phage-host interactions: The neglected part of biological wastewater treatment

In wastewater treatment plants (WWTPs), the stable operation of biological wastewater treatment is strongly dependent on the stability of associated microbiota. Bacteriophages (phages), viruses that specifically infect bacteria and archaea, are highly abundant and diverse in WWTPs. Although phages do not have known metabolic functions for themselves, they can shape functional microbiota via various phage-host interactions to impact biological wastewater treatment. However, the developments of phage-host interaction in WWTPs and their impact on biological wastewater treatment are overlooked. Here, we review the current knowledge regarding the phage-host interactions in biological wastewater treatment, mainly focusing on the characteristics of different phage populations, the phage-driven changes in functional microbiota, and the potential driving factors of phage-host interactions. We also discuss the efforts required further to understand and manipulate the phage-host interactions in biological wastewater treatment. Overall, this review advocates more attention to the phage dynamics in WWTPs.

Viral Community and Virus-Associated Antibiotic Resistance Genes in Soils Amended with Organic Fertilizers

Antibiotic resistance is a global health concern. Long-term organic fertilization can influence the antibiotic resistome of agricultural soils, posing potential risks to human health. However, little is known about the contribution of viruses to the dissemination of antibiotic resistance genes (ARGs) in this context. Here, we profiled the viral communities and virus-associated ARGs in a long-term (over 10 years) organic fertilized field by viral metagenomic analysis. A total of 61,520 viral populations (viral operational taxonomic units, vOTUs) were retrieved, of which 21,308 were assigned at the family level. The viral community structures were significantly correlated with the bacterial community structures (P < 0.001) and the dosage of applied sewage sludge (r² = 0.782). A total of 16 unique ARGs were detected in soil viromes, and the number of virus-associated ARG subtypes was higher in sewage sludge treatments (except for 1 SS) than others. The network analysis showed that the application of the organic fertilizer increased the bacteria-virus interactions, suggesting that the chances of ARG exchange between viruses and their hosts may increase. Overall, our results provide a novel understanding about virus-associated ARGs and factors affecting the profile of viral community in fertilized soil.

Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy

BACKGROUND

Long-read sequencing has shown its tremendous potential to address genome assembly challenges, e.g., achieving the first telomere-to-telomere assembly of a gapless human chromosome. However, many issues remain unresolved when leveraging error-prone long reads to characterize high-complexity metagenomes, for instance, complete/high-quality genome reconstruction from highly complex systems.

RESULTS

Here, we developed an iterative haplotype-resolved hierarchical clustering-based hybrid assembly (HCBHA) approach that capitalizes on a hybrid (error-prone long reads and high-accuracy short reads) sequencing strategy to reconstruct (near-) complete genomes from highly complex metagenomes. Using the HCBHA approach, we first phase short and long reads from the highly complex metagenomic dataset into different candidate bacterial haplotypes, then perform hybrid assembly of each bacterial genome individually. We reconstructed 557 metagenome-assembled genomes (MAGs) with an average N50 of 574 Kb from a deeply sequenced, highly complex activated sludge (AS) metagenome. These high-contiguity MAGs contained 14 closed genomes and 111 high-quality (HQ) MAGs including full-length rRNA operons, which accounted for 61.1% of the microbial community. Leveraging the near-complete genomes, we also profiled the metabolic potential of the AS microbiome and identified 2153 biosynthetic gene clusters (BGCs) encoded within the recovered AS MAGs.

CONCLUSION

Our results established the feasibility of an iterative haplotype-resolved HCBHA approach to reconstruct (near-) complete genomes from highly complex ecosystems, providing new insights into "complete metagenomics". The retrieved high-contiguity MAGs illustrated that various biosynthetic gene clusters (BGCs) were harbored in the AS microbiome. The high diversity of BGCs highlights the potential to discover new natural products biosynthesized by the AS microbial community, aside from the traditional function (e.g., organic carbon and nitrogen removal) in wastewater treatment. Video Abstract.

Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years

BACKGROUND

Microbial communities in both natural and applied settings reliably carry out myriads of functions, yet how stable these taxonomically diverse assemblages can be and what causes them to transition between states remains poorly understood. We studied monthly activated sludge (AS) samples collected over 9 years from a full-scale wastewater treatment plant to answer how complex AS communities evolve in the long term and how the community functions change when there is a disturbance in operational parameters.

RESULTS

Here, we show that a microbial community in activated sludge (AS) system fluctuated around a stable average for 3 years but was then abruptly pushed into an alternative stable state by a simple transient disturbance (bleaching). While the taxonomic composition rapidly turned into a new state following the disturbance, the metabolic profile of the community and system performance remained remarkably stable. A total of 920 metagenome-assembled genomes (MAGs), representing approximately 70% of the community in the studied AS ecosystem, were recovered from the 97 monthly AS metagenomes. Comparative genomic analysis revealed an increased ability to aggregate in the cohorts of MAGs with correlated dynamics that are dominant after the bleaching event. Fine-scale analysis of dynamics also revealed cohorts that dominated during different periods and showed successional dynamics on seasonal and longer time scales due to temperature fluctuation and gradual changes in mean residence time in the reactor, respectively.

CONCLUSIONS

Our work highlights that communities can assume different stable states under highly similar environmental conditions and that a specific disturbance threshold may lead to a rapid shift in community composition. Video Abstract.

Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants

As one of the largest biotechnological applications, activated sludge (AS) systems in wastewater treatment plants (WWTPs) harbor enormous viruses, with 10-1,000-fold higher concentrations than in natural environments. However, the compositional variation and host-connections of AS viruses remain poorly explored. Here, we report a catalogue of ~50,000 prokaryotic viruses from six WWTPs, increasing the number of described viral species of AS by 23-fold, and showing the very high viral diversity which is largely unknown (98.4-99.6% of total viral contigs). Most viral genera are represented in more than one AS system with 53 identified across all. Viral infection widely spans 8 archaeal and 58 bacterial phyla, linking viruses with aerobic/anaerobic heterotrophs, and other functional microorganisms controlling nitrogen/phosphorous removal. Notably, Mycobacterium, notorious for causing AS foaming, is associated with 402 viral genera. Our findings expand the current AS virus catalogue and provide reference for the phage treatment to control undesired microorganisms in WWTPs.

Metagenomic and viromic data mining reveals viral threats in biologically treated domestic wastewater

Activated sludge (AS), a common biological secondary treatment process in wastewater treatment plants (WWTPs), is known to remove a large spectrum of microorganisms. Yet little is known about its effect on the entire viral community. After compiling 3 Tbp of next-generation sequencing (NGS) metagenomic/viromic datasets consisted of 119 sub-datasets of influent, effluent, and AS samples from 27 WWTPs, viral removal efficacy is evaluated through data mining. The normalized abundance of viruses suggests effluents exhibit the highest viral prevalence (3.21 ± 3.26%, n = 13) followed by the AS (0.48 ± 0.25%, n = 57) and influents (0.23 ± 0.17%, n = 17). In contrast, plasmids, representing genetic element of bacteria, show higher average prevalence (0.73 ± 0.82%, n = 17) in influents than those of the AS (0.63 ± 0.26%, n = 57) and effluents (0.35 ± 0.42%, n = 13). Furthermore, the abundance-occupancy analysis identifies 142 core phage viruses and 17 non-phages core viruses, including several pathogenic viruses in the AS virome. The persistent occurrence of pathogenic viruses, coupled with non-favorable virus removal by the AS treatment, reveals the hidden virus threats in biologically treated domestic wastewater. The mechanisms for why viruses persist and the possibility that WWTPs are potential hotspots for viral survival deserve attention.

Enhanced mutualistic symbiosis between soil phages and bacteria with elevated chromium-induced environmental stress

BACKGROUND

Microbe-virus interactions have broad implications on the composition, function, and evolution of microbiomes. Elucidating the effects of environmental stresses on these interactions is critical to identify the ecological function of viral communities and understand microbiome environmental adaptation. Heavy metal-contaminated soils represent a relevant ecosystem to study the interplay between microbes, viruses, and environmental stressors.

RESULTS

Metagenomic analysis revealed that Cr pollution adversely altered the abundance, diversity, and composition of viral and bacterial communities. Host-phage linkage based on CRISPR indicated that, in soils with high Cr contamination, the abundance of phages associated with heavy metal-tolerant hosts increased, as did the relative abundance of phages with broad host ranges (identified as host-phage linkages across genera), which would facilitate transfection and broader distribution of heavy metal resistance genes in the bacterial community. Examining variations along the pollutant gradient, enhanced mutualistic phage-bacterium interactions were observed in the face of greater environmental stresses. Specifically, the fractions of lysogens in bacterial communities (identified by integrase genes within bacterial genomes and prophage induction assay by mitomycin-C) were positively correlated with Cr contamination levels. Furthermore, viral genomic analysis demonstrated that lysogenic phages under higher Cr-induced stresses carried more auxiliary metabolic genes regulating microbial heavy metal detoxification.

CONCLUSION

With the intensification of Cr-induced environmental stresses, the composition, replication strategy, and ecological function of the phage community all evolve alongside the bacterial community to adapt to extreme habitats. These result in a transformation of the phage-bacterium interaction from parasitism to mutualism in extreme environments and underscore the influential role of phages in bacterial adaptation to pollution-related stress and in related biogeochemical processes. Video Abstract.

Bias of library preparation for virome characterization in untreated and treated wastewaters

The use of metagenomics for virome characterization and its implementation for wastewater analyses, including wastewater-based epidemiology, has increased in the last years. However, the lack of standardized methods can led to highly different results. The aim of this work was to analyze virome profiles in upstream and downstream wastewater samples collected from four wastewater treatment plants (WWTPs) using two different library preparation kits. Viral particles were enriched from wastewater concentrates using a filtration and nuclease digestion procedure prior to total nucleic acid (NA) extraction. Sequencing was performed using the ScriptSeq v2 RNA-Seq (LS) and the NEBNext Ultra II RNA (NB) library preparation kits. Cleaned reads and contigs were annotated using a curated in-house database composed by reads assigned to viruses at NCBI. Significant differences in viral families and in the ratio of detection were shown between the two library kits used. The use of LS library showed Virgaviridae, Microviridae and Siphoviridae as the most abundant families; while Ackermannviridae and Helleviridae were highly represented within the NB library. Additionally, the two sequencing libraries produced outcomes that differed in the detection of viral indicators. These results highlighted the importance of library selection for studying viruses in untreated and treated wastewater. Our results underline the need for further studies to elucidate the influence of sequencing procedures in virome profiles in wastewater matrices in order to improve the knowledge of the virome in the water environment.

The novel SARS-CoV-2 pandemic: Possible environmental transmission, detection, persistence and fate during wastewater and water treatment

The contagious SARS-CoV-2 virus, responsible for COVID-19 disease, has infected over 27 million people across the globe within a few months. While literature on SARS-CoV-2 indicates that its transmission may occur predominantly via aerosolization of virus-laden droplets, the possibility of alternate routes of transmission and/or reinfection via the environment requires considerable scientific attention. This review aims to collate information on possible transmission routes of this virus, to ascertain its fate in the environment. Concomitant with the presence of SARS-CoV-2 viral RNA in faeces and saliva of infected patients, studies also indicated its occurrence in raw wastewater, primary sludge and river water. Therefore sewerage system could be a possible route of virus outbreak, a possible tool to assess viral community spread and future surveillance technique. Hence, this review looked into detection, occurrence and fate of SARS-CoV-2 during primary, secondary, and tertiary wastewater and water treatment processes based on published literature on SARS-CoV and other enveloped viruses. The review also highlights the need for focused research on occurrence and fate of SARS-CoV-2 in various environmental matrices. Utilization of this information in environmental transmission models developed for other enveloped and enteric viruses can facilitate risk assessment studies. Preliminary research efforts with SARS-CoV-2 and established scientific reports on other coronaviruses indicate that the threat of virus transmission from the aquatic environment may be currently non-existent. However, the presence of viral RNA in wastewater provides an early warning that highlights the need for effective sewage treatment to prevent a future outbreak of SARS-CoV-2.

Seasonal Prevalence of Ammonia-Oxidizing Archaea in a Full-Scale Municipal Wastewater Treatment Plant Treating Saline Wastewater Revealed by a 6-Year Time-Series Analysis

Although several molecular-based studies have demonstrated the involvement of ammonia-oxidizing archaea (AOA) in ammonia oxidation in wastewater treatment plants (WWTPs), factors affecting the persistence and growth of AOA in these engineered systems have not been resolved. Here, we show a seasonal prevalence of AOA in a full-scale WWTP (Shatin, Hong Kong SAR) over a 6-year period of observation, even outnumbering ammonia-oxidizing bacteria in the seasonal peaks in 3 years, which may be due to the high bioavailable copper concentrations. Comparative analysis of three metagenome-assembled genomes of group I.1a AOA obtained from the activated sludge and 16S rRNA gene sequences recovered from marine sediments suggested that the seawater used for toilet flushing was the primary source of the WWTP AOA. A rare AOA population in the estuarine source water became transiently abundant in the WWTP with a metagenome-based relative abundance of up to 1.3% over three seasons of observation. Correlation-based network analysis revealed a robust co-occurrence relationship between these AOA and organisms potentially active in nitrite oxidation. Moreover, a strong correlation between the dominant AOA and an abundant proteobacterial organism suggested that capacity for extracellular polymeric substance production by the proteobacterium could provide a niche for AOA within bioaggregates. Together, the study highlights the importance of long-term observation in identifying biotic and abiotic factors governing population dynamics in open systems such as full-scale WWTPs.

Revealing antimicrobial resistance in stormwater with MinION

Discharge of urban stormwater containing organic matter, heavy metals and sometime human feces, to the natural aquatic reservoirs without any treatment is not only an environmental problem. It can lead to prevalence of antibiotic resistant bacteria in stormwater systems and transmission of antibiotic resistance genes to the environment. We performed antibiotic resistome identification and virus detection in stormwater samples from Stockholm, using publicly available metagenomic sequencing MinION data. A MinION platform offers low-cost, precise environmental metagenomics analysis. 37 groups of antibiotic resistant bacteria (ARB), 11 resistance types with 26 resistance mechanisms - antibiotic resistance genes (ARGs) giving tolerance to the aminoglycoside, beta-lactams, fosmidomycin, MLS, multidrug and vancomycin were identified using ARGpore pipeline. The majority of the identified bacteria species were related to the natural environment such as soil and were not dangerous to human. Alarmingly, human pathogenic bacteria carrying resistance to antibiotics currently used against them (Bordetella resistant to macrolides and multidrug resistant Propionibacterium avidum) were also found in the samples. Most abundant viruses identified belonged to Caudovirales and Herpesvirales and they were not carrying ARGs. Unlike the virome, resistome and ARB were not unique for stormwater sampling points. This results underline the need for extensive monitoring of the microbial community structure in the urban stormwater systems to assess antimicrobial resistance spread.

Profile of the Spatial Distribution Patterns of the Human and Bacteriophage Virome in a Wastewater Treatment Plant Located in the South of Spain

In wastewater treatment plants, most microbial characterization has focused on bacterial, archaeal, and fungal populations. Due to the difficult isolation, quantification, and identification of viruses, only a limited number of virome studies associated with wastewater treatment plants have been carried out. However, the virus populations play an important role in the microbial dynamics in wastewater treatment systems and the biosafety of effluents. In this work, the viral members present in influent wastewater, mixed liquor (aerobic bioreactor), excess sludge, and effluent water of a conventional activated sludge system for the treatment of urban wastewater were identified. Viral members were observed by transmission electron microscopy and studied through next-generation sequencing studies. The results showed the dominance of bacteriophages in the viral community in all samples, with the dominant viral phylotype classified as Escherichia coli O157 typing phage 7. Moreover, different human viruses, such as Cynomolgus cytomegalovirus and Gammaherpesvirus, were also detected.

Exploration of the antibiotic resistome in a wastewater treatment plant by a nine-year longitudinal metagenomic study

The spread of antibiotic resistance genes (ARGs) is a growing global problem. Activated sludge (AS) in wastewater treatment plants (WWTPs) has been proposed as a hotspot for ARGs. However, few studies have been conducted to uncover the temporal dynamics of the resistome of AS in WWTPs by long-term longitudinal sampling. In this study, we quantified ARGs and identified their host microbiome in a Hong Kong WWTP in 97 monthly AS samples spanning 9 years. Throughout this analysis, we demonstrated that both the abundance and structures of the resistome changed significantly every two to three years, implying that there was a successive selection of resistomes in the AS system over the study period. The detection of genes of antibiotic-resistant pathogens that are emerging major threats to public health in the AS samples, including mcr, CRE (carbapenem-resistant Enterobacteriaceae) and MRSA (methicillin-resistant Staphylococcus aureus)-related genes, highlight the role of WWTPs as reservoirs of ARGs. In addition, the core resistome (abundant and persistent genes) in AS were found to overlap with those in other ecosystems such as urban sewage, livestock feces, and fishpond sediments, revealing the broad dissemination of ARGs in WWTPs and other environments. Annual variation of resistomes were explained via structural equation modeling (SEM), which deciphered the structural linkages of determining factors such as the operational parameters, microbial community composition and horizontal gene transfer (HGT). Specifically, potentially relevant antibiotic resistance bacteria (ARBs) were explored and discussed based on assembly-based analyses and network correlations. Moreover, consistent with the clear relationship between resistomes and mobile genetic elements (MGEs), it was found that there was a relatively high potential for gene exchange in AS in comparison with soil genomes, which could be explained by the engineering features of WWTPs. Based on these findings, longitudinal monitoring of WWTPs is warranted for risk assessment to reveal emerging ARGs, resistome evolution, correlations with ARBs, and the potential for spread in downstream environments and concomitant exposure risks for humans.

Bacteriophages in Natural and Artificial Environments

Bacteriophages (phages) are biological entities that have attracted a great deal of attention in recent years. They have been reported as the most abundant biological entities on the planet and their ability to impact the composition of bacterial communities is of great interest. In this review, we aim to explore where phages exist in natural and artificial environments and how they impact communities. The natural environment in this review will focus on the human body, soils, and the marine environment. In these naturally occurring environments there is an abundance of phages suggesting a role in the maintenance of bacterial community homeostasis. The artificial environment focuses on wastewater treatment plants, industrial processes, followed by pharmaceutical formulations. As in natural environments, the existence of bacteria in manmade wastewater treatment plants and industrial processes inevitably attracts phages. The presence of phages in these environments can inhibit the bacteria required for efficient water treatment or food production. Alternatively, they can have a positive impact by eliminating recalcitrant organisms. Finally, we conclude by describing how phages can be manipulated or formulated into pharmaceutical products in the laboratory for use in natural or artificial environments.

Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing

BACKGROUND

Wastewater treatment plants (WWTPs) are recognized as hotspots for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Despite our understanding of the composition and distribution of ARGs in WWTPs, the genetic location, host, and fate of ARGs remain largely unknown.

RESULTS

In this study, we combined Oxford Nanopore and Illumina metagenomics sequencing to comprehensively uncover the resistome context of influent, activated sludge, and effluent of three WWTPs and simultaneously track the hosts of the ARGs. The results showed that most of the ARGs detected in all compartments of the WWTPs were carried by plasmids. Transposons and integrons also showed higher prevalence on plasmids than on the ARG-carrying chromosome. Notably, integrative and conjugative elements (ICEs) carrying five types of ARGs were detected, and they may play an important role in facilitating the transfer of ARGs, particularly for tetracycline and macrolide-lincosamide-streptogramin (MLS). A broad spectrum of ARGs carried by plasmids (29 subtypes) and ICEs (4 subtypes) was persistent across the WWTPs. Host tracking showed a variety of antibiotic-resistant bacteria in the effluent, suggesting the high potential for their dissemination into receiving environments. Importantly, phenotype-genotype analysis confirmed the significant role of conjugative plasmids in facilitating the survival and persistence of multidrug-resistant bacteria in the WWTPs. At last, the consistency in the quantitative results for major ARGs types revealed by Nanopore and Illumina sequencing platforms demonstrated the feasibility of Nanopore sequencing for resistome quantification.

CONCLUSION

Overall, these findings substantially expand our current knowledge of resistome in WWTPs, and help establish a baseline analysis framework to study ARGs in the environment.