RESUMO
BACKGROUND: Symbioses between primary producers and bacteria are crucial for nutrient exchange that fosters host growth and niche adaptation. Yet, how viruses that infect bacteria (phages) influence these bacteria-eukaryote interactions is still largely unknown. Here, we investigate the role of viruses on the genomic diversity and functional adaptations of bacteria associated with pelagic sargassum. This brown alga has dramatically increased its distribution range in the Atlantic in the past decade and is predicted to continue expanding, imposing severe impacts on coastal ecosystems, economies, and human health. RESULTS: We reconstructed 73 bacterial and 3963 viral metagenome-assembled genomes (bMAGs and vMAGs, respectively) from coastal Sargassum natans VIII and surrounding seawater. S. natans VIII bMAGs were enriched in prophages compared to seawater (28% and 0.02%, respectively). Rhodobacterales and Synechococcus bMAGs, abundant members of the S. natans VIII microbiome, were shared between the algae and seawater but were associated with distinct phages in each environment. Genes related to biofilm formation and quorum sensing were enriched in S. natans VIII phages, indicating their potential to influence algal association in their bacterial hosts. In-vitro assays with a bacterial community harvested from sargassum surface biofilms and depleted of free viruses demonstrated that these bacteria are protected from lytic infection by seawater viruses but contain intact and inducible prophages. These bacteria form thicker biofilms when growing on sargassum-supplemented seawater compared to seawater controls, and phage induction using mitomycin C was associated with a significant decrease in biofilm formation. The induced metagenomes were enriched in genomic sequences classified as temperate viruses compared to uninduced controls. CONCLUSIONS: Our data shows that prophages contribute to the flexible genomes of S. natans VIII-associated bacteria. These prophages encode genes with symbiotic functions, and their induction decreases biofilm formation, an essential capacity for flexible symbioses between bacteria and the alga. These results indicate that prophage acquisition and induction contribute to genomic and functional diversification during sargassum-bacteria symbioses, with potential implications for algae growth. Video Abstract.
Assuntos
Bacteriófagos , Sargassum , Água do Mar , Simbiose , Sargassum/microbiologia , Bacteriófagos/genética , Bacteriófagos/fisiologia , Bacteriófagos/classificação , Bacteriófagos/isolamento & purificação , Água do Mar/microbiologia , Água do Mar/virologia , Genoma Viral , Metagenoma , Bactérias/virologia , Bactérias/genética , Bactérias/classificação , Genômica , Microbiota , Filogenia , Genoma Bacteriano , Synechococcus/virologia , Synechococcus/genéticaRESUMO
Antagonistic interactions between bacteriophage (phage) and its bacterial host drives the continual selection for resistance and counter-defence. To date, much remains unknown about the genomic evolution that occurs as part of the underlying mechanisms. Such is the case for the marine cyanobacteria Synechococcus and viruses (cyanophages) that infect them. Here, we monitored host and phage abundances, alongside genomic changes to the phage populations, in a 500-day (~55 bacterial generations) infection experiment between Synechococcus sp. WH7803 and the T4-type cyanophage S-PM2d, run parallel in three replicate chemostats (plus one control chemostat). Flow cytometric count of total abundances revealed relatively similar host-phage population dynamics across the chemostats, starting with a cycle of host population collapse and recovery that led to phases of host-phage coexistence. Whole-genome analysis of the S-PM2d populations detected an assemblage of strongly selected and repeatable genomic changes, and therefore parallel evolution in the phage populations, early in the experiment (sampled on day 39). These consisted mostly of non-synonymous single-nucleotide-polymorphisms and a few instances of indel, altogether affecting 18 open-reading-frames, the majority of which were predicted to encode virion structures including those involved in phage adsorption onto host (i.e., baseplate wedge, short tail fibre, adhesin component). Mutations that emerged later (sampled on day 500), on the other hand, were found at a larger range of frequencies, with many lacking repeatability across the chemostats. This is indicative of some degree of between-population divergence in the phage evolutionary trajectory over time. A few of the early and late mutations were detected within putative auxiliary metabolic genes, but these generally occurred in only one or two of the chemostats. Less repeatable mutations may have higher fitness costs, thus drawing our attention onto the role of trade-offs in modulating the trajectory of a host-phage coevolution.
Assuntos
Bacteriófagos , Synechococcus , Bacteriófagos/genética , Evolução Molecular , Mutação , Synechococcus/genética , Synechococcus/virologiaRESUMO
Cyanopodoviruses affect the mortality and population dynamics of the unicellular picocyanobacteria Prochlorococcus and Synechococcus, the dominant primary producers in the oceans. Known cyanopodoviruses all contain the DNA polymerase gene (DNA pol) that is important for phage DNA replication and widely used in field quantification and diversity studies. However, we isolated 18 cyanopodoviruses without identifiable DNA pol. They form a new MPP-C clade that was separated from the existing MPP-A, MPP-B, and P-RSP2 clades. The MPP-C phages have the smallest genomes (37.3-37.9 kb) among sequenced cyanophages, and show longer latent periods than the MPP-B phages. Metagenomic reads of both clades are highly abundant in surface waters, but the MPP-C phages show higher relative abundance in surface waters than in deeper waters, while MPP-B phages have higher relative abundance in deeper waters. Our study reveals that cyanophages with distinct genomic contents and infection kinetics can exhibit different depth profiles in the oceans.
Assuntos
Bacteriófagos , Synechococcus , DNA Polimerase Dirigida por DNA/genética , Oceanos e Mares , Filogenia , Synechococcus/virologiaRESUMO
Harmful algal blooms (HABs) are naturally occurring phenomena, and cyanobacteria are the most commonly occurring HABs in freshwater systems. Cyanobacteria HABs (cyanoHABs) negatively affect ecosystems and drinking water resources through the production of potent toxins. Furthermore, the frequency, duration, and distribution of cyanoHABs are increasing, and conditions that favor cyanobacteria growth are predicted to increase in the coming years. Current methods for mitigating cyanoHABs are generally short-lived and resource-intensive, and have negative impacts on non-target species. Cyanophages (viruses that specifically target cyanobacteria) have the potential to provide a highly specific control strategy with minimal impacts on non-target species and propagation in the environment. A detailed review (primarily up to 2020) of cyanophage lifecycle, diversity, and factors influencing infectivity is provided in this paper, along with a discussion of cyanophage and host cyanobacteria relationships for seven prominent cyanoHAB-forming genera in North America, including: Synechococcus, Microcystis, Dolichospermum, Aphanizomenon, Cylindrospermopsis, Planktothrix, and Lyngbya. Lastly, factors affecting the potential application of cyanophages as a cyanoHAB control strategy are discussed, including efficacy considerations, optimization, and scalability for large-scale applications.
Assuntos
Aphanizomenon , Bacteriófagos , Proliferação Nociva de Algas , Microcystis , Synechococcus , Aphanizomenon/virologia , Ecossistema , Interações Hospedeiro-Patógeno , Microcystis/virologia , Synechococcus/virologiaRESUMO
Cyanobacteria and cyanophages are present widely in both freshwater and marine environments. However, freshwater cyanophages remain unknown largely due to the small numbers of cyanophage isolates despite their ecological and environmental significance. In this study, we present the characterization of two novel lytic freshwater cyanophages isolated from a tropical inland lake in Singapore, namely, cyanopodovirus S-SRP01 and cyanomyovirus S-SRM01, infecting two different strains of Synechococcus spp. Functional annotation of S-SRP01 and S-SRM01 genomes revealed a high degree of homology with marine cyanophages. Phylogenetic trees of concatenated genes and whole-genome alignment provided further evidence that S-SRP01 is close evolutionarily to marine cyanopodoviruses, while S-SRM01 is evolutionarily close to marine cyanomyoviruses. Few genetic similarities between freshwater and marine cyanophages have been identified in previous studies. The isolation of S-SRP01 and S-SRM01 expand current knowledge on freshwater cyanophages infecting Synechococcus spp. Their high degree of gene sharing provides new insights into the evolutionary relationships between freshwater and marine cyanophages. This relatedness is further supported by the discovery of similar phenomenon from other freshwater viral metagenomes. IMPORTANCE This study expands the current knowledge on freshwater cyanophage isolates and cyanophage genetic diversity, indicating that freshwater and marine cyanophages infecting Synechococcus spp. may share close genetic similarity and evolutionary relationships.
Assuntos
Bacteriófagos , Evolução Biológica , Cianobactérias/virologia , Água Doce/virologia , Água do Mar/virologia , Bacteriófagos/classificação , Bacteriófagos/genética , Bacteriófagos/fisiologia , Especificidade de Hospedeiro , Filogenia , Alinhamento de Sequência , Synechococcus/virologiaRESUMO
Bacteriophages have long been known to use modified bases in their DNA to prevent cleavage by the host's restriction endonucleases. Among them, cyanophage S-2L is unique because its genome has all its adenines (A) systematically replaced by 2-aminoadenines (Z). Here, we identify a member of the PrimPol family as the sole possible polymerase of S-2L and we find it can incorporate both A and Z in front of a T. Its crystal structure at 1.5 Å resolution confirms that there is no structural element in the active site that could lead to the rejection of A in front of T. To resolve this contradiction, we show that a nearby gene is a triphosphohydolase specific of dATP (DatZ), that leaves intact all other dNTPs, including dZTP. This explains the absence of A in S-2L genome. Crystal structures of DatZ with various ligands, including one at sub-angstrom resolution, allow to describe its mechanism as a typical two-metal-ion mechanism and to set the stage for its engineering.
Assuntos
2-Aminopurina/análogos & derivados , Adenina/química , Bacteriófagos/genética , Cianobactérias/virologia , DNA Viral/química , Synechococcus/virologia , 2-Aminopurina/química , 2-Aminopurina/metabolismo , Adenina/metabolismo , Bacteriófagos/metabolismo , Sítios de Ligação/genética , Biocatálise , DNA Primase/química , DNA Primase/genética , DNA Primase/metabolismo , DNA Viral/genética , DNA Viral/metabolismo , DNA Polimerase Dirigida por DNA/química , DNA Polimerase Dirigida por DNA/genética , DNA Polimerase Dirigida por DNA/metabolismo , Ligação de Hidrogênio , Modelos Moleculares , Estrutura Molecular , Domínios Proteicos , Proteínas Virais/química , Proteínas Virais/genética , Proteínas Virais/metabolismoRESUMO
Marine picocyanobacteria belonging to genera Synechococcus and Prochlorococcus are genetically diverged and distributed into distinct biogeographical patterns, and both are infected by genetically closely related cyanopodoviruses. Previous studies have not fully explored whether the two virus-host systems share similar gene expression patterns during infection. Whole-genome expression dynamics of T7-like cyanopodovirus P-SSP7 and its host Prochlorococcus strain MED4 have already been reported. Here, we conducted genomic and transcriptomic analyses on T7-like cyanopodovirus S-SBP1 during its infection on Synechococcus strain WH7803. S-SBP1 has a latent period of 8 h and phage DNA production of 30 copies per cell. In terms of whole-genome phylogenetic relationships and average nucleotide identity, S-SBP1 was most similar to cyanopodovirus S-RIP2, which also infects Synechococcus WH7803. Three hypervariable genomic islands were identified when comparing the genomes of S-SBP1 and S-RIP2. Single nucleotide variants were also observed in three S-SBP1 genes, which were located within the island regions. Based on RNA-seq analysis, S-SBP1 genes clustered into three temporal expression classes, whose gene content was similar to that of P-SSP7. Thirty-two host genes were upregulated during phage infection, including those involved in carbon metabolism, ribosome components, and stress response. These upregulated genes were similar to those upregulated by Prochlorococcus MED4 in response to infection by P-SSP7. Our study demonstrates a programmed temporal expression pattern of cyanopodoviruses and hosts during infection.
Assuntos
Regulação Bacteriana da Expressão Gênica/genética , Regulação Viral da Expressão Gênica/genética , Myoviridae/genética , Synechococcus/genética , Synechococcus/virologia , Transcriptoma/genética , Expressão Gênica/genética , Perfilação da Expressão Gênica , Genoma Viral/genética , Ilhas Genômicas/genética , Filogenia , Prochlorococcus/genética , Prochlorococcus/virologia , Água do Mar/microbiologia , Synechococcus/classificaçãoRESUMO
The abundant and widespread unicellular cyanobacteria Synechococcus plays an important role in contributing to global phytoplankton primary production. In the present study, two novel cyanomyoviruses, S-N03 and S-H34 that infected Synechococcus MW02, were isolated from the coastal waters of the Yellow Sea. S-N03 contained a 167,069-bp genome comprising double-stranded DNA with a G + C content of 50.1%, 247 potential open reading frames and 1 tRNA; S-H34 contained a 167,040-bp genome with a G + C content of 50.1%, 246 potential open reading frames and 5 tRNAs. These two cyanophages contain fewer auxiliary metabolic genes (AMGs) than other previously isolated cyanophages. S-H34 in particular, is currently the only known cyanomyovirus that does not contain any AMGs related to photosynthesis. The absence of such common AMGs in S-N03 and S-H34, their distinct evolutionary history and ecological features imply that the energy for phage production might be obtained from other sources rather than being strictly dependent on the maintenance of photochemical ATP under high light. Phylogenetic analysis showed that the two isolated cyanophages clustered together and had a close relationship with two other cyanophages of low AMG content. Comparative genomic analysis, habitats and hosts across 81 representative cyanomyovirus showed that cyanomyovirus with less AMGs content all belonged to Synechococcus phages isolated from eutrophic waters. The relatively small genome size and high G + C content may also relate to the lower AMG content, as suggested by the significant correlation between the number of AMGs and G + C%. Therefore, the lower content of AMG in S-N03 and S-H34 might be a result of viral evolution that was likely shaped by habitat, host, and their genomic context. The genomic content of AMGs in cyanophages may have adaptive significance and provide clues to their evolution.
Assuntos
Bacteriófagos/genética , Cianobactérias/virologia , Genoma Viral , Synechococcus/virologia , Bacteriófagos/isolamento & purificação , Composição de Bases , Eutrofização , Evolução Molecular , Genômica , Redes e Vias Metabólicas , Filogenia , Água do Mar/virologiaRESUMO
A new cyanophage, S-B05, infecting a phycoerythrin-enriched (PE-type) Synechococcus strain was isolated by the liquid infection method, and its morphology and genetic features were examined. Phylogenetic analysis and morphological observation confirmed that S-B05 belongs to the family Myoviridae of the order Caudovirales. Its genome was fully sequenced, and found to be 208,857 bp in length with a G + C content of 39.9%. It contained 280 potential open reading frames and 123 conserved domains. Ninety-eight functional genes responsible for cyanophage structuring and packaging, DNA replication and regulation, and photosynthesis were identified, as well as genes encoding 172 hypothetical proteins. The genome of S-B05 is most similar to that of Prochlorococcus phage P-TIM68. Homologues of open reading frames of S-B05 can be found in various marine environments, as revealed by comparison of the S-B05 genome sequence to sequences in marine viral metagenomic databases. The presence of auxiliary metabolic genes (AMGs) related to photosynthesis, carbon metabolism, and phosphorus assimilation, as well as the phylogenetic relationships based on AMGs and the complete genome sequence, reflect the phage-host interaction mechanism or the specific adaptation strategy of the host to environmental conditions. The genome sequence information reported here will provide an important basis for further study of the adaptive evolution and ecological role of cyanophages and their hosts in the marine environment.
Assuntos
Genoma Viral , Myoviridae/classificação , Myoviridae/isolamento & purificação , Água do Mar/virologia , Synechococcus/virologia , Composição de Bases , Sequência de Bases , China , Especificidade de Hospedeiro , Metagenômica , Myoviridae/ultraestrutura , Fases de Leitura Aberta , Oceano Pacífico , Filogenia , Microbiologia da Água , Sequenciamento Completo do GenomaRESUMO
Cyanophages are characterized by vast genomic diversity and the formation of stable ecotypes over time. The evolution of phage diversity includes vertical processes, such as mutation, and horizontal processes, such as recombination and gene transfer. Here, we study the contribution of vertical and horizontal processes to short-term evolution of marine cyanophages. Analyzing time series data of Synechococcus-infecting Myoviridae ecotypes spanning up to 17 years, we found a high contribution of recombination relative to mutation (r/m) in all ecotypes. Additionally, we found a molecular clock of substitution and recombination in one ecotype, RIM8. The estimated RIM8 evolutionary rates are 2.2 genome-wide substitutions per year (1.275 × 10-5 substitutions/site/year) and 29 genome-wide nucleotide alterations due to recombination per year. We found 26 variable protein families, of which only two families have a predicted functional annotation, suggesting that they are auxiliary metabolic genes with bacterial homologs. A comparison of our rate estimates to other phage evolutionary rate estimates in the literature reveals a negative correlation of phage substitution rates with their genome size. A comparison to evolutionary rates in bacterial organisms further shows that phages have high rates of mutation and recombination compared to their bacterial hosts. We conclude that the increased recombination rate in phages likely contributes to their vast genomic diversity.
Assuntos
Taxa de Mutação , Myoviridae/genética , Água do Mar/virologia , Synechococcus/virologia , Ecótipo , Variação Genética , Genoma Viral/genética , Myoviridae/classificação , Myoviridae/isolamento & purificação , Filogenia , Recombinação Genética , Água do Mar/microbiologia , Proteínas Virais/genéticaRESUMO
Long-term coexistence between unicellular cyanobacteria and their lytic viruses (cyanophages) in the oceans is thought to be due to the presence of sensitive cells in which cyanophages reproduce, ultimately killing the cell, while other cyanobacteria survive due to resistance to infection. Here, we investigated resistance in marine cyanobacteria from the genera Synechococcus and Prochlorococcus and compared modes of resistance against specialist and generalist cyanophages belonging to the T7-like and T4-like cyanophage families. Resistance was extracellular in most interactions against specialist cyanophages irrespective of the phage family, preventing entry into the cell. In contrast, resistance was intracellular in practically all interactions against generalist T4-like cyanophages. The stage of intracellular arrest was interaction-specific, halting at various stages of the infection cycle. Incomplete infection cycles proceeded to various degrees of phage genome transcription and translation as well as phage genome replication in numerous interactions. In a particularly intriguing case, intracellular capsid assembly was observed, but the phage genome was not packaged. The cyanobacteria survived the encounter despite late-stage infection and partial genome degradation. We hypothesize that this is tolerated due to genome polyploidy, which we found for certain strains of both Synechococcus and Prochlorococcus Our findings unveil a heavy cost of promiscuous entry of generalist phages into nonhost cells that is rarely paid by specialist phages and suggests the presence of unknown mechanisms of intracellular resistance in the marine unicellular cyanobacteria. Furthermore, these findings indicate that the range for virus-mediated horizontal gene transfer extends beyond hosts to nonhost cyanobacterial cells.
Assuntos
Organismos Aquáticos , Bacteriófagos/fisiologia , Modelos Biológicos , Prochlorococcus , Synechococcus , Organismos Aquáticos/crescimento & desenvolvimento , Organismos Aquáticos/virologia , Prochlorococcus/crescimento & desenvolvimento , Prochlorococcus/virologia , Synechococcus/crescimento & desenvolvimento , Synechococcus/virologiaRESUMO
The building blocks of a virus derived from de novo biosynthesis during infection and/or catabolism of preexisting host cell biomass, and the relative contribution of these 2 sources has important consequences for understanding viral biogeochemistry. We determined the uptake of extracellular nitrogen (N) and its biosynthetic incorporation into both virus and host proteins using an isotope-labeling proteomics approach in a model marine cyanobacterium Synechococcus WH8102 infected by a lytic cyanophage S-SM1. By supplying dissolved N as 15N postinfection, we found that proteins in progeny phage particles were composed of up to 41% extracellularly derived N, while proteins of the infected host cell showed almost no isotope incorporation, demonstrating that de novo amino acid synthesis continues during infection and contributes specifically and substantially to phage replication. The source of N for phage protein synthesis shifted over the course of infection from mostly host derived in the early stages to more medium derived later on. We show that the photosystem II reaction center proteins D1 and D2, which are auxiliary metabolic genes (AMGs) in the S-SM1 genome, are made de novo during infection in an apparently light-dependent manner. We also identified a small set of host proteins that continue to be produced during infection; the majority are homologs of AMGs in S-SM1 or other viruses, suggesting selective continuation of host protein production during infection. The continued acquisition of nutrients by the infected cell and their utilization for phage replication are significant for both evolution and biogeochemical impact of viruses.
Assuntos
Organismos Aquáticos , Proteínas de Bactérias , Bacteriófagos , Nitrogênio/metabolismo , Complexo de Proteína do Fotossistema II , Synechococcus , Proteínas Virais , Organismos Aquáticos/genética , Organismos Aquáticos/metabolismo , Organismos Aquáticos/virologia , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Bacteriófagos/genética , Bacteriófagos/metabolismo , Complexo de Proteína do Fotossistema II/genética , Complexo de Proteína do Fotossistema II/metabolismo , Synechococcus/genética , Synechococcus/metabolismo , Synechococcus/virologia , Proteínas Virais/genética , Proteínas Virais/metabolismoRESUMO
As an adaptation to the daily light-dark (diel) cycle, cyanobacteria exhibit diurnal rhythms of gene expression and cell cycle. The light-dark cycle also affects the life cycle of viruses (cyanophages) that infect the unicellular picocyanobacteria Prochlorococcus and Synechococcus, which are the major primary producers in the oceans. For example, the adsorption of some cyanophages to the host cells depends on light, and the burst sizes of cyanophages are positively correlated to the length of light exposure during infection. Recent metatranscriptomic studies revealed transcriptional rhythms of field cyanophage populations. However, the underlying mechanism remains to be determined, as cyanophage laboratory cultures have not been shown to exhibit diurnal transcriptional rhythms. Here, we studied variation in infection patterns and gene expression of Prochlorococcus phages in laboratory culture conditions as a function of light. We found three distinct diel-dependent life history traits in dark conditions (diel traits): no adsorption (cyanophage P-HM2), adsorption but no replication (cyanophage P-SSM2), and replication (cyanophage P-SSP7). Under light-dark cycles, each cyanophage exhibited rhythmic transcript abundance, and cyanophages P-HM2 and P-SSM2 also exhibited rhythmic adsorption patterns. Finally, we show evidence to link the diurnal transcriptional rhythm of cyanophages to the photosynthetic activity of the host, thus providing a mechanistic explanation for the field observations of cyanophage transcriptional rhythms. Our study identifies that cultured viruses can exhibit diurnal rhythms during infection, which might impact cyanophage population-level dynamics in the oceans.
Assuntos
Bacteriófagos/genética , Ritmo Circadiano/genética , Viroses/genética , Replicação Viral/genética , Bacteriófagos/patogenicidade , Bacteriófagos/fisiologia , Ritmo Circadiano/fisiologia , Regulação Viral da Expressão Gênica/genética , Interações Hospedeiro-Patógeno/genética , Luz , Fotoperíodo , Fotossíntese/genética , Prochlorococcus/genética , Prochlorococcus/virologia , Synechococcus/genética , Synechococcus/virologiaRESUMO
Currently defined ecotypes in marine cyanobacteria Prochlorococcus and Synechococcus likely contain subpopulations that themselves are ecologically distinct. We developed and applied high-throughput sequencing for the 16S-23S rRNA internally transcribed spacer (ITS) to examine ecotype and fine-scale genotypic community dynamics for monthly surface water samples spanning 5 years at the San Pedro Ocean Time-series site. Ecotype-level structure displayed regular seasonal patterns including succession, consistent with strong forcing by seasonally varying abiotic parameters (e.g. temperature, nutrients, light). We identified tens to thousands of amplicon sequence variants (ASVs) within ecotypes, many of which exhibited distinct patterns over time, suggesting ecologically distinct populations within ecotypes. Community structure within some ecotypes exhibited regular, seasonal patterns, but not for others, indicating other more irregular processes such as phage interactions are important. Network analysis including T4-like phage genotypic data revealed distinct viral variants correlated with different groups of cyanobacterial ASVs including time-lagged predator-prey relationships. Variation partitioning analysis indicated that phage community structure more strongly explains cyanobacterial community structure at the ASV level than the abiotic environmental factors. These results support a hierarchical model whereby abiotic environmental factors more strongly shape niche partitioning at the broader ecotype level while phage interactions are more important in shaping community structure of fine-scale variants within ecotypes.
Assuntos
Bacteriófagos/fisiologia , Prochlorococcus/virologia , Água do Mar/microbiologia , Synechococcus/virologia , Bacteriófagos/genética , Ecossistema , Ecótipo , Filogenia , Prochlorococcus/genética , RNA Ribossômico 16S/genética , RNA Ribossômico 23S/genética , Synechococcus/genética , Microbiologia da ÁguaRESUMO
Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, a genome sequence of such temperate cyanophages remains unknown although genomic analysis indicate potential for lysogeny in certain marine cyanophages. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine cyanophage lineage, which contain, in addition to common cyanophage genes, a phycobilisome degradation protein NblA, an integrase and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a genomic island in Synechococcus WH8016. The island contains a relic prophage that does not resemble any previously reported cyanophage but shares several genes with the newly identified cyanophages reported here. Metagenomic recruitment indicates that the novel cyanophages are widespread, albeit at low abundance. Here, we describe a novel potentially lysogenic cyanophage family, their abundance and distribution in the marine environment.
Assuntos
Bacteriófagos/genética , Lisogenia/genética , Prófagos/genética , Água do Mar/virologia , Synechococcus/virologia , Bacteriófagos/classificação , Bacteriófagos/isolamento & purificação , Sequência de Bases , Genoma Viral , Ilhas Genômicas/genética , Metagenoma , Oceanos e Mares , Filogenia , Prófagos/classificação , Prófagos/isolamento & purificação , Synechococcus/genética , Proteínas Virais/genéticaRESUMO
A novel cyanophage, S-B64, which can infect marine Synechococcus WH8102, was isolated from the coastal waters of the Yellow Sea using the liquid serial dilution method. Morphological study by transmission electron microscopy revealed that the cyanophage belongs to Podovirus. It's genome, which was completely sequenced, contains a 151,867 bp DNA molecule with a G+C content of 41.78% and 186 potential open reading frames. The functions of the genes include cyanophage structure, cyanophage packaging, DNA replication and regulation. After primary characterization, it was found that the latent period is about 3 h, and it lysed after 8 h, the burst size is about 23 virions per cell. This information will provide an important benchmark for further research on the interaction between cyanophages and their hosts.
Assuntos
Bacteriófagos/genética , Bacteriófagos/isolamento & purificação , Genoma Viral , Podoviridae/genética , Podoviridae/isolamento & purificação , Água do Mar/virologia , Synechococcus/virologia , Bacteriófagos/classificação , Bacteriófagos/ultraestrutura , Composição de Bases , China , Genes Virais , Microscopia Eletrônica de Transmissão , Podoviridae/classificação , Podoviridae/ultraestrutura , Análise de Sequência de DNA , Vírion/ultraestruturaRESUMO
Bacteriophage possess a variety of auxiliary metabolic genes of bacterial origin. These proteins enable them to maximize infection efficiency, subverting bacterial metabolic processes for the purpose of viral genome replication and synthesis of the next generation of virion progeny. Here, we examined the enzymatic activity of a cyanophage MazG protein - a putative pyrophosphohydrolase previously implicated in regulation of the stringent response via reducing levels of the central alarmone molecule (p)ppGpp. We demonstrate, however, that the purified viral MazG shows no binding or hydrolysis activity against (p)ppGpp. Instead, dGTP and dCTP appear to be the preferred substrates of this protein, consistent with a role preferentially hydrolysing deoxyribonucleotides from the high GC content host Synechococcus genome. This showcases a new example of the fine-tuned nature of viral metabolic processes.
Assuntos
Bacteriófagos/enzimologia , Desoxirribonucleotídeos/metabolismo , Pirofosfatases/metabolismo , Proteínas Virais/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Bacteriófagos/classificação , Bacteriófagos/genética , Composição de Bases , Domínio Catalítico , Genoma Bacteriano/genética , Hidrólise , Filogenia , Pirofosfatases/química , Pirofosfatases/genética , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Especificidade por Substrato , Synechococcus/classificação , Synechococcus/enzimologia , Synechococcus/genética , Synechococcus/virologia , Proteínas Virais/química , Proteínas Virais/genéticaRESUMO
Dissolved organic matter (DOM) plays a central role in the microbial ecology and biogeochemistry of aquatic environments, yet little is known about how the mechanism of DOM release from its ultimate source, primary producer biomass, affects the molecular composition of the inputs to the dissolved pool. Here we used a model marine phytoplankton, the picocyanobacterium Synechococcus WH7803, to compare the composition of DOM released by three mechanisms: exudation, mechanical cell lysis and infection by the lytic phage S-SM1. A broad, untargeted analytical approach reveals the complexity of this freshly sourced DOM, and comparative analysis between DOM produced by the different mechanisms suggests that exudation and viral lysis are sources of unsaturated, oxygen-rich and possibly novel biomolecules. Furthermore, viral lysis of WH7803 by S-SM1 releases abundant peptides derived from specific proteolysis of the major light-harvesting protein phycoerythrin, raising the possibility that phage infection of these abundant cyanobacteria could be a significant source of high molecular weight dissolved organic nitrogen compounds.
Assuntos
Bacteriófagos/fisiologia , Compostos Orgânicos/química , Água do Mar/química , Synechococcus/química , Synechococcus/virologia , Biomassa , Peptídeos/química , Fitoplâncton/química , Fitoplâncton/crescimento & desenvolvimento , Fitoplâncton/virologia , Água do Mar/microbiologia , Água do Mar/virologia , Synechococcus/crescimento & desenvolvimentoRESUMO
Cyanophages are thought to affect the community structure, population dynamics, metabolic activity and evolution of picocyanobacteria and to impact the biogeochemical cycling in aquatic ecosystems. Here, we report an estuarine Synechococcus phage, S-CBWM1, which represents a novel viral lineage and exhibits interesting genetic features related to phage-host interactions and evolution. S-CBWM1 encapsidates four virion-associated proteins related to cellular metabolic regulation. Several novel auxiliary metabolic genes related to multidrug efflux, cell wall and capsule synthesis or modifications were also identified. In addition, the presence of the largest number of tRNA genes hitherto found in a phage genome may contribute to the translation efficiency of unique genes. These genomic and proteomic features of S-CBWM1 suggested phage-host interactions involved in adaptation to eutrophic estuarine environments. Phylogenetic and metagenomic analysis of the polγ gene in the S-CBWM1 genome provided new insights into the evolutionary path of mitochondrial DNA polymerase gamma. The S-CBWM1 psbA contains two group I introns, representing the first instance of multiple introns within psbA from phage. The isolation of S-CBWM1 reveals that estuarine ecosystems contain evolutionarily novel cyanophages that drive unique phage-host interactions.
Assuntos
Bacteriófagos/isolamento & purificação , Evolução Molecular , Synechococcus/virologia , Bacteriófagos/classificação , Bacteriófagos/genética , Bacteriófagos/fisiologia , Ecossistema , Estuários , Genoma Viral , Genômica , Interações Hospedeiro-Patógeno , Íntrons , Metagenômica , Filogenia , Proteômica , Synechococcus/genética , Synechococcus/fisiologia , Proteínas Virais/genética , Proteínas Virais/metabolismoRESUMO
Marine cyanobacteria are responsible for ~25% of the fixed carbon that enters the ocean biosphere. It is thought that abundant co-occurring viruses play an important role in regulating population dynamics of cyanobacteria and thus the cycling of carbon in the oceans. Despite this, little is known about how viral infections 'play-out' in the environment, particularly whether infections are resource or energy limited. Photoautotrophic organisms represent an ideal model to test this since available energy is modulated by the incoming light intensity through photophosphorylation. Therefore, we exploited phototrophy of the environmentally relevant marine cyanobacterium Synechococcus and monitored growth of a cyanobacterial virus (cyanophage). We found that light intensity has a marked effect on cyanophage infection dynamics, but that this is not manifest by a change in DNA synthesis. Instead, cyanophage development appears energy limited for the synthesis of proteins required during late infection. We posit that acquisition of auxiliary metabolic genes (AMGs) involved in light-dependent photosynthetic reactions acts to overcome this limitation. We show that cyanophages actively modulate expression of these AMGs in response to light intensity and provide evidence that such regulation may be facilitated by a novel mechanism involving light-dependent splicing of a group I intron in a photosynthetic AMG. Altogether, our data offers a mechanistic link between diurnal changes in irradiance and observed community level responses in metabolism, i.e., through an irradiance-dependent, viral-induced release of dissolved organic matter (DOM).