Distribution And Evolution Of Auxiliary Metabolic Genes In Marine Roseobacter Viruses

As the most abundant life form in the ocean,marine viruses play an important role in marine ecosystems.Marine viruses are the major driver in the top-down control on marine microbial communities.Moreover,viruses play a vital role in the biogeochemical cycle of marine environments.Auxiliary metabolic genes(AMGs)are widely distributed in the genomes of marine viruses.AMGs are originally derived from host genomes,and reach viral genomes through horizontal gene transfer.Viral AMGs redirect energy and metabolism via hijacking the cellular machinery of their hosts,and they usually overcome metabolic bottlenecks during infection to maximize viral production.Both the viruses infecting marine autotrophs and heterotrophs have been widely ovserved to harbour AMGs.AMG content of viruses infecting marine autotrophs have been well studied,whereas AMGs of marine heterotrophic viruses have only been limited studied.Roseobacter is an ecologically important clade in the marine ecosystem.AMGs in roseophages which infect roseobacters have been reported,however,the content and context of AMGs in roseophage genomes have not been systematically studied yet.The aims of the thesis are to identify roseophage AMGs,revealing the AMG distribution pattern across roseophage genomes,and to reconstruct the acquisition history of roseophage AMGs through horizontal gene transfer and vertical gene transfer.First,we obtained the full-length genome sequence and the morphological informations of a roseophage isolated from the Xiamen coastal waters.We have classified the new roseophage and identified auxiliary metabolic genes in its genome.Then we use comparative genomics to analyze all genomes of isolated roseophage to uncover unreported AMGs,and to investigate the distribution pattern and evolutionary history of AMGs across roseophage genomes.Finally,we used metagenomic workflow developed for marine viral community research to identify viral contigs from cryoconite metagenomic datasets.We built a global scale cryoconite viral genome database to study the diversity and AMGs.The main progress is as follows:1.We used culture method to isolate a new roseophage from coastal waters of Xiamen and name it as vB_DshP-R13LH.The new roseophage represented a novel genus we proposed to name as Xianganvirus.Xianganvirus belongs to the subfamily,Schitoviridae family.The capsid size of vB_DshP-R13LH was 70nm,with a 40nm length non-contractile tail.SDS-PAGE and mass spectrometry of the particle revealed classical Rhodovirinae structure proteins.By comparing conserved genes of Rhodovirinae against IMG/VR environmental viral genomes,we found that all phages belonging to Rhodovirinae,including vB_DshP-R13 LH,were distributed in estuaries and bays.We identified six AMGs in vB_DshP-R13LH genome,including the ribosome protein encoding gene(RP).AMGs in vB_DshP-R13LH have the potential ability to promote de novo DNA synthesis during infection,and RP gene may promote host protein expression.We also found that vB_DshP-R13LH tRNA pool favors the expression of its own RP coding gene.2.We identified 180 AMGs in 50 isolated roseophage genomes.Comparative genomic study showed that AMGs were more conserved comparing to the average level of all roseophage genes.The frequency of roseophage AMGs is approximately one-fifth of that in cyanophages.High frequency roseophage AMGs were involved in the nucleotide biosynthesis pathway and their possible function is to overcome metabolic bottlenecks in nucleotide biosynthesis during infection.Roseophage AMGs may facilitate host de novo DNA synthesis,thus converting a greater proportion of Roseobacter cell lysate into viral particles.This will promotes the efficiency of viral shunts in the oceans.We found that the content of roseophage AMGs was most affected by phage lifestyle(lysis or lysogenic)and host range,while weakly correlated with environmental factors.3.We reconstructed the evolutionary histories of roseophage AMGs,and found that AMGs in Rhodovirinae clustered separately in phylogenetic trees.Thus,vB_DshP-R13LH has acquired its AMGs through different horizontal gene transfer(HGT)events.Previous comparative genomic study of Schitoviridae genomes found that HGT events rarely occurred in Rhodovirinae.However,we found that phages belonging to Rhodovirinae has preserved AMGs acquired by historical HGT events,and previous study underestimate HGT events happened in Rhodovirinae subfamily.In phylogenetic trees,roseophage AMGs tend to cluster with homologs from hosts and other roseophages,rather than homologs from previously reported cyanophages.We reconstructed the evolutionary history of roseophage AMGs by analyzing their distribution in genomic islands across the roseophage genomes defined by locally co-linear blocks(LCBs).Roseopodoviruses show relatively stable genomic islands containing high-frequency AMGs,and these genes are likely maintained through vertical inheritance.By contrast,high-frequency AMGs in roseosiphoviruses are located in variable genomic islands and thus appear to have multiple evolutionary origins.4.We applied metagenomic workflow to all 66 reported cryoconite metagenomic datasets to create a global cryoconite viral genomes database.Our database expanded the number of known cryoconite viral genomes by 4 times.We found that the cryoconite viral community has relatively high diversity,with an average Shannon index similar to marine viral communites and soil viral communites.Cryoconite viral community is unique and consists mainly of viral genomes that never been reported previously.Many viral clusters distributed in spatially distant cryoconites,suggesting that these viral clades were restricted to the cryoconite environment and distributed globally.The comparison of cryconite viral community structures showed that viral communities in polar cryoconites also differ from the alpine viral community.AMGs are widely distributed in cryoconite viral genomes,including genes related to energy metabolism,carbon fixation and sulfur metabolic pathways,suggesting that viruses may play an important role in the geochemical cycle of cryoconites.We have identified multiple genes in cryoconite viral genomes that may promote cold adaptation of their hosts.Cold adaptation genes in cryoconite viral genomes have the potential to enhance cell membrane fluidity,alter the ratio of amino acid residues of host proteins and increase molecular chaperone expression to aid protein folding.The worldwide distribution of cold-adaptation AMGs in cryoconites suggested that cryoconite viruses might help microbial communites to adapt cold environment.