Comparative genomic analysis of five freshwater cyanophages and reference-guided metagenomic data mining

Abstract

Background As important producers using photosynthesis on Earth, cyanobacteria contribute to the oxygenation of atmosphere and the primary production of biosphere. However, due to the eutrophication of urban waterbodies and global warming, uncontrollable growth of cyanobacteria usually leads to the seasonal outbreak of cyanobacterial blooms. Cyanophages, a group of viruses that specifically infect and lyse cyanobacteria, are considered as potential environment-friendly agents to control the harmful blooms. Compared to the marine counterparts, only a few freshwater cyanophages have been isolated and genome sequenced to date, largely limiting their characterizations and applications. Results Here, we isolated five freshwater cyanophages varying in tail morphology, termed Pam1~Pam5, all of which infect the cyanobacterium Pseudanabaena mucicola Chao 1806 that was isolated from the bloom-suffering Lake Chaohu in Anhui, China. The whole-genome sequencing showed that cyanophages Pam1~Pam5 all contain a dsDNA genome, varying in size from 36 to 142 Kb. Phylogenetic analyses suggested that Pam1~Pam5 possess different DNA packaging mechanisms and are evolutionarily distinct from each other. Notably, Pam1 and Pam5 have lysogeny-associated gene clusters, whereas Pam2 possesses 9 punctuated DNA segments identical to the CRISPR spacers in the host genome. Metagenomic data-based calculation of the relative abundance of Pam1~Pam5 at the Nanfei estuary towards the Lake Chaohu revealed that the short-tailed Pam1 and Pam5 account for the majority of the five cyanophages. Moreover, comparative analyses of the reference genomes of Pam1~Pam5 and previously reported cyanophages enabled us to identify three circular and seven linear contigs of virtual freshwater cyanophages from the metagenomic data of the Lake Chaohu. Conclusions We propose a high-throughput strategy to systematically identify cyanophages based on the currently available metagenomic data and the very limited reference genomes of experimentally isolated cyanophages. This strategy could be applied to mine the complete or partial genomes of unculturable bacteriophages and viruses. Transformation of the synthesized whole genomes of these virtual phages/viruses to proper hosts will enable the rescue of bona fide viral particles and eventually enrich the library of microorganisms that exist on Earth.

Fine structure and assembly pattern of a minimal myophage Pam3

“…Recently, we isolated a Myoviridae cyanophage termed Pam3 from Lake Chaohu in China, which specifically infects the host cyanobacteria Pseudanabaena mucicola ( 12 ). Genomic annotation indicated that, compared with phage T4, Pam3 harbors a much simpler baseplate composed of only six components gp19–gp24 encoded by the putative open reading frames ( Fig.…”

Characterization of a novel genus of jumbo phages and their application in wastewater treatment

“…The morphological characteristics of isolated phages were determined as previously described. 44 High titer phage sample (10 8 PFU/mL) was prepared after purification, placed on carbon-coated copper grids for 15 minutes for adsorption. After further drying, samples were stained with 2% uranyl acetate and examined in Tecnai G2 Spirit BioTWIN 120-kV transmission electron microscope (FEI Company, Hillsboro, USA) with magnification of 12000-16000 ×.…”

Tychonema sp. BBK16 Characterisation: Lifestyle, Phylogeny and Related Phages

“…These genes can alter the physiology of an infected cyanobacterium, increasing the production of progeny phage [ 22 ]. At the beginning of 2022, the NCBI Genome database contained about 500 sequences of complete genomes of cyanophages, most of which were isolated from marine Synechococcus and Prochlorococcus (order Synechococcales), but there are only a few examples of isolated and published cyanophages infecting Oscillatoriales cyanobacteria [ 23 , 24 , 25 , 26 , 27 , 28 , 29 ], and no Tychonema phages are described to date. However, some information about phage–host interactions can be recovered using the analysis of genomic CRISPR arrays [ 30 , 31 , 32 ].…”