Prokaryotic virus

Only identifiable prophages were found in our study and future work will need to focus on the recovery of phages from the cellular portion to obtain a comprehensive picture of virus diversity in AS systems. Nonetheless, our study suggests that it may be possible in the future to define a virome specific for AS systems within WWTPs.

A high proportion of common viral genera as well as many others could be linked to functional microorganisms in WWTPs. Although the exact contribution of viral predation to the mortality of functional microorganisms remains to be investigated, viruses could potentially influence important metabolic functions through top—down control.

By encoding various groups of AMGs, viruses could additionally alter carbon recycling and nutrients acquisition in their hosts. Also, recombination events among viruses could evade CRISPR-Cas immune system by increasing genetic diversity 31 , making it more challenging for us to track possible hosts.

It has to be noted that Hi-C method also has its limitations, for example, the spurious links owing to shared sequence fragments between closely related bacteria or viruses.

Overall, a combination of three sets of data in this study, namely targeted metagenomics, direct metagenomics, and Hi-C metagenomics, provided a holistic view of the virus—host interactions in complex ecosystems. In our study, viral genera were shown to infect Mycobacterium, which is a genus containing foaming bacteria abundant in WWTPs. This finding opens the possibility to isolate and apply related viruses to eliminate foaming bacteria in situ. Conventionally, disinfectants are applied to curb pathogens and control sludge bulking and foaming However, due to their non-specificity, benign microorganisms are also killed.

In order to control microorganisms in a more targeted and sustainable way, phage treatment might be a means to selectively kill undesired microorganisms. For instance, two recent studies have reported the use of phages to curb foaming-associated filamentous bacteria effectively 33 , Moreover, from a clinical perspective, WWTP samples have already proven useful for isolating phages to kill the lethal superbug Acinetobacter baumannii A recent study also reported a simple and efficient technology to generate new phage genomes artificially and accelerate the process of phage treatment By isolating or synthesizing phages and applying them to remove other undesired microorganisms e.

In detail, supernatants were filtered through 0. The filtrate was iron-chloride flocculated, collected on 0. Polyethylene glycol was subsequently added to precipitate viruses.

The samples were supplemented with ethylenediaminetetraacetic acid to inactivate nucleases. The assembled contigs were processed for downstream bioinformatics analysis. Two different methods 38 , i. The results were subsequently screened using three different criteria The first one is that total no. The second one is that no. MEGAN6 45 was then applied to analyze taxonomy and those contigs assigned to viruses were identified as metagenomic viral contigs.

Metagenomic viral contigs identified by the above-mentioned two pipelines were added together for further analyses. Trimmed and filtered reads were pooled with each sample with a ratio ranging from to For pooled-sample de-novo assembly, results showed that our recovered mock phage genomes had an average of At the amino-acid level, our recovered phage genomes shared an average of Gene-sharing networks were used for viral clustering Predicted proteins from all the data sets in the present study were uploaded to CyVerse Discovery Environment and vContact2 version 0.

Those viral contigs that cannot be assigned to any VCs were classified as singletons. Results were visualized by Cytoscape version 3. The number of sequences in each habitat was 2. To make it comparable with the number of sequences of this study 50k , only 50k sequences were randomly picked for data sets of marine and freshwater ecosystems for viral clustering. The mapping results were used for the calculation of the average coverage of viral contigs bases of the aligned part of all the reads divided by the length of viral contigs.

The average coverage was divided by data set size for normalization, denoted as the average normalized coverage, to determine the relative abundance against the sum of the coverages in all viral contigs.

Of , genomes, 90, BLASTn-short was performed between reference viral genomes and spacers. Different coverage, identity, and e-value were tested to achieve a balance between recall percentage and precision percentage.

These parameters were applied for all the data sets in our study. Only the best hits were retained for further analysis. Then we used the same criteria to select the best hit. Results showed that on average 0. However, none of them could link spacers from different domains of life. All predicted proteins of viral contigs were compared with eggNOG database 5. Results were further categorized according to COG function class.

The pellets were split into two parts. Formaldehyde-crosslinking was further quenched by glycine. After spinning down pellets, crosslinked AS sample was ground into a fine powder in a liquid nitrogen-chilled mortar. Two strategies have been applied for downstream bioinformatics analysis. Further information on research design is available in the Nature Research Reporting Summary linked to this article.

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Ok Cookie options. E-mail newsletter. It appears that you are currently using Ad Blocking software. What are the consequences? The little existing ecological data on phage populations indicate a large variety of environmental niches and survival strategies.

The host cell is the main resource for phages and the resource quality, i. Virus-induced mortality of prokaryotes varies strongly on a temporal and spatial scale and shows that phages can be important predators of bacterioplankton. This mortality and the release of cell lysis products into the environment can strongly influence microbial food web processes and biogeochemical cycles. Phages can also affect host diversity, e.