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.
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.
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