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

Yiqiang Chen,Tong Zhang,Yulin Wang,Martin F Polz,David Paez-Espino

doi:10.1038/s41467-021-25678-1

Abstract

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.

Highlights

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
We show that viruses may impact functional microorganisms in biological nutrient removal and the carbon cycle in WWTPs, linking viruses with aerobic/anaerobic heterotrophs, and other functional microorganisms controlling N/P removal
CRISPR spacers represent a collection of memories regarding past virus invasions, whereas High throughput chromosome conformation capture (Hi-C) data provide a snapshot of ongoing virus–host interactions

Summary

Introduction

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. Viruses are an important but poorly explored component of this system, reaching 10–1000-fold higher concentrations than their counterparts in other aquatic systems[3,4] Through specific interactions such as host lysis or lysogeny, viruses can directly impact prokaryotic communities and have been implicated in causing 41% of the variation in community composition in anaerobic digesters (AD), considerably >15% estimated due to abiotic factors[5]. Considering this potential importance of viruses in AS systems, we asked what the diversity and variation are among different WWTPs and how viruses may impact prokaryotic taxa, especially those that contribute to the removal of organic matter and inorganic nutrients. This work provides a genomic reference for the potential future design of the phage treatment to tackle sludge foaming problems

Methods

Results

Conclusion