Figures (4)  Tables (2)

    • Figure 1. 

      Analytical diagram of the metagenomic virome data from raw data to binning.

    • Figure 2. 

      Overview of virus distribution. (a) Relative abundance (log10 [RPKM + 1]) of identified viruses based on contigs along three full-scale WWTPs; (b) Shannon index of viruses across all samples. (c) Density curve of virus prevalence across samples (default bandwidth = 0.12), viruses denoted in red are persistent across full-scale with 100% prevalence. (d) Shannon diversity index among three WWTPs.

    • Figure 3. 

      (a) PCA analysis of viruses among three WWTPs. Composition and abundance of the top 20 most abundant (average abundance) viruses along the three full-scale WWTPs. (b) AAO WWTP. (c) AAO-MBR WWTP. (d) MBR. (e) A total of 88 viruses were detected in the influent and effluent of three WWTPs, and the abundance heatmap. Viruses with relative abundance > 10% were highlighted with ***, and ** refers to relative abundance between 5% and 10%. The risk family on the WHO 2024 PHEIC list was marked in red (high risk), and orange (medium/low risk). (f)–(j) Linear regression analyses between representative pathogen and virus with highest prevalence and abundance—(f)–(h) P. aeruginosa; (i), (j) A. caviae.

    • Figure 4. 

      Occurrence of AMGs and their full-scale regulation in three WWTPs. (a), (b) Detected 12 metabolism AMGs value across all samples and their distribution along the full-scale process, respectively. (c) Bray-Curtis similarity heatmap of AMGs across all the samples, ** refers to that similarity < 0.2. (d), (e) MDS analyses of AMGs in bioreactor sections among three WWTPs (ns. p > 0.05), and between wastewater and sludge (** p < 0.01), respectively. (f) The left bar plot represents the number of detected metabolism-related genes, while the numbers in parentheses indicate the number of corresponding AMGs identified in each WWTP.

    • Ranking AAO-IFW AAO-DEW AAO-MBR-IFW AAO-MBR-DEW MBR-IFW MBR-EFW
      1 Schitoviridae *Weiservirinae *Straboviridae Straboviridae **Peduoviridae Kyanoviridae
      2 Autographiviridae *Gracegardnervirinae Adenoviridae **Peduoviridae *Kyanoviridae Obolenskvirus
      3 Triavirus *Hendrixvirinae **Peduoviridae *Gracegardnervirinae Deejayvirinae **Peduoviridae
      4 *Steigviridae **Peduoviridae **Casjensviridae **Casjensviridae **Casjensviridae *Hendrixvirinae
      5 **Peduoviridae Mesyanzhinovviridae Gracegardnervirinae Adenoviridae Casadabanvirus **Casjensviridae
      6 Demerecviridae Kyanoviridae *Suoliviridae *Guernseyvirinae Bronfenbrennervirinae *Autographiviridae
      7 Guernseyvirinae *Guernseyvirinae Iridoviridae Zobellviridae *Suoliviridae *Gracegardnervirinae
      8 Obolenskvirus Sepvirinae Hendrixvirinae Suoliviridae Arquatrovirinae *Weiservirinae
      9 Queuovirinae *Autographiviridae Autographiviridae *Weiservirinae *Steigviridae Sepvirinae
      10 Deejayvirinae Ceeclamvirinae *Steigviridae Iridoviridae Weiservirinae *Mesyanzhinovviridae
      11 *Straboviridae Zobellviridae Guernseyvirinae Steigviridae *Tybeckvirinae Steigviridae
      12 *Tybeckvirinae **Casjensviridae *Kyanoviridae Schitoviridae Kostyavirus Herelleviridae
      13 Intestiviridae Wizardvirus Zobellviridae Queuovirinae *Straboviridae Schitoviridae
      14 Ackermannviridae Triavirus Obolenskvirus *Dolichocephalovirinae Herelleviridae *Guernseyvirinae
      15 **Casjensviridae Ounavirinae Mesyanzhinovviridae Metaviridae Aliusviridae *Dolichocephalovirinae
      16 *Kyanoviridae Herelleviridae *Tybeckvirinae *Mesyanzhinovviridae Queuovirinae Boydwoodruffvirinae
      17 Vequintavirinae Queuovirinae Weiservirinae Vilmaviridae Stephanstirmvirinae Korravirus
      18 *Suoliviridae *Dolichocephalovirinae Schitoviridae Boydwoodruffvirinae Parvoviridae Suoliviridae
      19 Drexlerviridae Marthavirus Fernvirus *Hendrixvirinae Triavirus Tybeckvirinae
      20 Arquatrovirinae Pclasvirinae Tectiviridae *Autographiviridae Boydwoodruffvirinae Vilmaviridae
      ** Peduoviridae, ** Casjensviridae are two of the top 20 viruses that persistently exist in six treatment units with the highest prevalence, marked in pink. Species marked in green and * are the viruses that persistently exist in influent sections, and species marked in grey and * are persistent in effluent.

      Table 1. 

      The top 20 relatively abundant viruses of influent and effluent in three WWTPs

    • AAO WWTP Contigs predicted AAO-MBR WWTP Contigs predicted MBR WWTP Contigs predicted
      *Acidobacteriota 18 *Acidobacteriota 14 *Acidobacteriota 9
      *Actinomycetota 560 Actinomycetota 254 Actinomycetota 159
      Aenigmatarchaeota 4 − − − −
      − − Armatimonadota 2 Armatimonadota 1
      Asgardarchaeota 3 Asgardarchaeota 1 Asgardarchaeota 7
      Atribacterota 4 Atribacterota 0 Atribacterota 0
      *Bacillota 137 Bacillota 54 Bacillota 118
      *Bacteroidota 356 *Bacteroidota 503 *Bacteroidota 297
      − − − − Bipolaricaulota 1
      Caldisericota 1 − − Caldisericota 3
      *Campylobacterota 10 *Campylobacterota 2 *Campylobacterota 16
      *Chloroflexota 88 *Chloroflexota 20 *Chloroflexota 24
      *Cyanobacteriota 34 Cyanobacteriota 41 Cyanobacteriota 27
      − − − − Deinococcota 2
      *Dependentiae 3 *Dependentiae 6 Dependentiae 1
      − − Desulfobacterota 2 *Desulfobacterota 5
      Elusimicrobiota 5 − − − −
      Fibrobacterota 1 − − − −
      *Gemmatimonadota 20 Gemmatimonadota 1 Gemmatimonadota 11
      − − Goldbacteria 0 Goldbacteria 1
      *Halobacteriota 1 Halobacteriota 1 Halobacteriota 4
      Hydrogenedentota 4 − − − −
      Iainarchaeota 1 − − − −
      Krumholzibacteriota 32 − − Krumholzibacteriota 3
      Methanobacteriota 2 Methanobacteriota 16 Methanobacteriota 8
      − − Methylomirabilota 1 − −
      − − − − Muirbacteria 2
      *Myxococcota 93 *Myxococcota 56 Myxococcota 26
      Nanoarchaeota 6 − − Nanoarchaeota 2
      *Nitrospirota 26 Nitrospirota 22 Nitrospirota 12
      Omnitrophota 15 − − Omnitrophota 4
      *Patescibacteria 47 *Patescibacteria 35 *Patescibacteria 33
      *Planctomycetota 67 Planctomycetota 23 Planctomycetota 26
      *Pseudomonadota 1,675 Pseudomonadota 855 Pseudomonadota 637
      Spirochaetota 4 − − *Spirochaetota 2
      Sumerlaeota 1 − − Sumerlaeota 2
      − − Thermoplasmatota 1 Thermoplasmatota 10
      − − Thermoproteota 1 Thermoproteota 4
      *Verrucomicrobiota 28 *Verrucomicrobiota 29 Verrucomicrobiota 17
      Taxonomies identified from recovered MAGs are highlighted in red.

      Table 2. 

      The quantity of predicted host contigs across all sampling sites of three WWTPs