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

Abstract

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.

Temporal turnover of viral biodiversity and functional potential in intertidal wetlands

“…To investigate the functional potential of intertidal viruses, 82,648 protein-coding genes carried by 3238 mVCs were initially clustered at 80% coverage and 60% identity 12 , 21 , resulting in 41,363 viral protein clusters (vPCs), representing the functional gene composition of viral communities. A total of 10,328 vPCs were assigned to known orthologous groups by searching against the eggNOG database, of which ~41.1% were functionally unknown (Supplementary Table 5 ).…”

“…A central goal in viral ecology is to resolve the patterns and ecological mechanisms that how the viral biodiversity is generated and maintained in complex natural ecosystems across space and through time 11 . Over the past years, the employment of multi-omics approaches has demonstrated that even the tiny viral particles also followed typical spatial scaling patterns (e.g., DDR) in complex ecosystems 12 , 13 , 21 . However, how viral communities change over time in complex natural ecosystems remains less studied.…”

“…Spatial turnover is defined as the changes in species composition or biodiversity from place to place 19 , while temporal turnover represents the number of species eliminated and replaced per unit time 20 . Leveraged by sampling over large scales 12 , 13 , 21 , typical biogeographic patterns, such as distance-decay relationship (DDR), followed by viral taxa and functional potentials, have been demonstrated. However, less attention has been received on the studies of viral temporal turnovers compared to their spatial turnovers, especially in complex natural ecosystems 11 .…”

Viral diversiy within marine biofilms and their potential roles in microbially influenced corrosion

“…AMG flgE may be associated with the formation of biofilms in the SRP. In activated sludge, AMGs were found to participate in dissimilatory sulfate reduction [47]. This finding implies that viruses have the potential to directly participate in the MIC process by SRP.…”