Widespread yet persistent low abundance of TIM5-like cyanophages in the oceans.

Ocean ecosystems are inhabited by a diverse set of viruses that impact microbial mortality and evolution. However, the distribution and abundances of specific viral lineages, particularly those from the large bank of rare viruses, remains largely unknown. Here, we assessed the diversity and abundance of the TIM5-like cyanophages. The sequencing of three new TIM5-like cyanophage genomes and environmental amplicons of a signature gene from the Red Sea revealed highly conserved gene content and sequence similarity. We adapted the polony method, a solid-phase polymerase chain reaction assay, to quantify TIM5-like cyanophages during three 2000 km expeditions in the Pacific Ocean and four annual cycles in the Red Sea. TIM5-like cyanophages were widespread, detected at all latitudes and seasons surveyed throughout the photic zone. Yet they were generally rare, ranging between <100 and 4000 viruses·ml-1 . Occasional peaks in abundance of 10- to 100-fold were observed, reaching 71,000 viruses·ml-1 . These peaks were ephemeral and seasonally variable in the Red Sea. Infection levels, quantified during one such peak, were very low. These characteristics of low diversity and abundance, as well as variable outbreaks, distinguishes the TIM5-like lineage from other major cyanophage lineages and illuminates that rare virus lineages can be persistent and widespread in the oceans.

Host-dependent differences in abundance, composition and host range of cyanophages from the Red Sea.

Cyanobacteria coexist in the oceans with a wealth of phages that infect them. While numerous studies have investigated Synechococcus phages, much less data are available for Prochlorococcus phages. Furthermore, little is known about cyanophage composition. Here, we examined the abundance and relative composition of cyanophages on six cyanobacterial hosts in samples collected during spring and summer from the Red Sea. Maximal abundances found on Synechococcus of 35 000 phages/ml are within ranges found previously, whereas the 24 000 phages/ml found on Prochlorococcus are approximately 10-fold higher than previous findings. T7-like, T4-like and 'unknown' phages were isolated on all hosts, including many T4-like phages on high-light adapted Prochlorococcus strains, whereas TIM5-like phages were found only on Synechococcus. Large differences in cyanophage abundance and composition were found for different hosts on the same sampling date, as well as for the same host on different dates, with few predictable patterns discerned. Host range analyses showed that T7-like and TIM5-like phages were quite host-specific, whereas the breadth of hosts for T4-like phages was related to host type: those isolated on high-light adapted Prochlorococcus were considerably more host-specific than those on low-light adapted Prochlorococcus or Synechococcus. These host-related differences likely contribute to the complexity of host-phage interactions in the oceans.

A novel lineage of myoviruses infecting cyanobacteria is widespread in the oceans.

Viruses infecting bacteria (phages) are thought to greatly impact microbial population dynamics as well as the genome diversity and evolution of their hosts. Here we report on the discovery of a novel lineage of tailed dsDNA phages belonging to the family Myoviridae and describe its first representative, S-TIM5, that infects the ubiquitous marine cyanobacterium, Synechococcus. The genome of this phage encodes an entirely unique set of structural proteins not found in any currently known phage, indicating that it uses lineage-specific genes for virion morphogenesis and represents a previously unknown lineage of myoviruses. Furthermore, among its distinctive collection of replication and DNA metabolism genes, it carries a mitochondrial-like DNA polymerase gene, providing strong evidence for the bacteriophage origin of the mitochondrial DNA polymerase. S-TIM5 also encodes an array of bacterial-like metabolism genes commonly found in phages infecting cyanobacteria including photosynthesis, carbon metabolism and phosphorus acquisition genes. This suggests a common gene pool and gene swapping of cyanophage-specific genes among different phage lineages despite distinct sets of structural and replication genes. All cytosines following purine nucleotides are methylated in the S-TIM5 genome, constituting a unique methylation pattern that likely protects the genome from nuclease degradation. This phage is abundant in the Red Sea and S-TIM5 gene homologs are widespread in the oceans. This unusual phage type is thus likely to be an important player in the oceans, impacting the population dynamics and evolution of their primary producing cyanobacterial hosts.

Diversity and evolutionary relationships of T7-like podoviruses infecting marine cyanobacteria.

Phages are extremely abundant in the oceans, influencing the population dynamics, diversity and evolution of their hosts. Here we assessed the diversity and phylogenetic relationships among T7-like cyanophages using DNA polymerase (replication), major capsid (structural) and photosynthesis psbA (host-derived) genes from isolated phages. DNA polymerase and major capsid phylogeny divided them into two discrete clades with no evidence for gene exchange between clades. Clade A phages primarily infect Synechococcus while clade B phages infect either Synechococcus or Prochlorococcus. The major capsid gene of one of the phages from clade B carries a putative intron. Nearly all clade B phages encode psbA whereas clade A phages do not. This suggests an ancient separation between cyanophages from these two clades, with the acquisition or loss of psbA occurring around the time of their divergence. A mix and match of clustering patterns was found for the replication and structural genes within each major clade, even among phages infecting different host genera. This is suggestive of numerous gene exchanges within each major clade and indicates that core phage functions have not coevolved with specific hosts. In contrast, clustering of phage psbA broadly tracks that of the host genus. These findings suggest that T7-like cyanophages evolve through clade-limited gene exchanges and that different genes are subjected to vastly different selection pressures.

Genetic engineering of marine cyanophages reveals integration but not lysogeny in T7-like cyanophages.

Marine cyanobacteria of the genera Synechococcus and Prochlorococcus are the most abundant photosynthetic organisms on earth, spanning vast regions of the oceans and contributing significantly to global primary production. Their viruses (cyanophages) greatly influence cyanobacterial ecology and evolution. Although many cyanophage genomes have been sequenced, insight into the functional role of cyanophage genes is limited by the lack of a cyanophage genetic engineering system. Here, we describe a simple, generalizable method for genetic engineering of cyanophages from multiple families, that we named REEP for REcombination, Enrichment and PCR screening. This method enables direct investigation of key cyanophage genes, and its simplicity makes it adaptable to other ecologically relevant host-virus systems. T7-like cyanophages often carry integrase genes and attachment sites, yet exhibit lytic infection dynamics. Here, using REEP, we investigated their ability to integrate and maintain a lysogenic life cycle. We found that these cyanophages integrate into the host genome and that the integrase and attachment site are required for integration. However, stable lysogens did not form. The frequency of integration was found to be low in both lab cultures and the oceans. These findings suggest that T7-like cyanophage integration is transient and is not part of a classical lysogenic cycle.

Comparative analyses of actinobacterial genomic fragments from Lake Kinneret.

The high genomic G+C group of Actinobacteria possesses a variety of physiological and metabolic properties, and exhibits diverse lifestyles and ecological distribution. In recent years, Actinobacteria have been found to frequently dominate samples obtained from freshwater samples. Furthermore, phylogenetic analyses have shown that 16S rRNA genes from uncultured actinobacterial freshwater samples cluster in four distinct lineages. While these lineages are abundant, little is known about them and currently no pure-culture representatives or genomic fragments of them are available. In a screen of a genomic library from the moderately eutrophic freshwater Lake Kinneret, five fosmid clones containing actinobacterial genomic fragments were found. Three approximately 40 kb genomic fragments were chosen for sequencing. Fosmids K003 and K005 showed high similarity and were affiliated with the acIV actinobacterial freshwater lineage. Fosmid K004 was affiliated with the highly abundant acI lineage. A comparative genomic analysis revealed high synteny between the two freshwater clones K003 and K005 but a lower synteny between these two and the K004 fosmid. Fosmids K003 and K005 share an identical arrangement of arginine biosynthesis gene while K004 showed a slightly different arrangement by lacking the argF gene. Fosmid Ant4E12, an Antarctic actinobacterial clone, showed a higher synteny with K003/5 than K004 and a similar arginine operon, but in a different genomic context. The Clusters of Orthologous Groups categories assignment of the three fosmids yielded genes that were mostly involved in amino acid and nucleotide metabolism, as well as transport and ribosomal RNA translation, structure and biogenesis. These genomic fragments represent the first sequences to be published from these lineages, providing a cornerstone for future work on this environmentally dominant group.

New insights into metabolic properties of marine bacteria encoding proteorhodopsins.

Proteorhodopsin phototrophy was recently discovered in oceanic surface waters. In an effort to characterize uncultured proteorhodopsin-exploiting bacteria, large-insert bacterial artificial chromosome (BAC) libraries from the Mediterranean Sea and Red Sea were analyzed. Fifty-five BACs carried diverse proteorhodopsin genes, and we confirmed the function of five. We calculate that proteorhodopsin-exploiting bacteria account for 13% of microorganisms in the photic zone. We further show that some proteorhodopsin-containing bacteria possess a retinal biosynthetic pathway and a reverse sulfite reductase operon, employed by prokaryotes oxidizing sulfur compounds. Thus, these novel phototrophs are an unexpectedly large and metabolically diverse component of the marine microbial surface water.

Transcriptome dynamics of a broad host-range cyanophage and its hosts.

Cyanobacteria are highly abundant in the oceans and are constantly exposed to lytic viruses. The T4-like cyanomyoviruses are abundant in the marine environment and have broad host-ranges relative to other cyanophages. It is currently unknown whether broad host-range phages specifically tailor their infection program for each host, or employ the same program irrespective of the host infected. Also unknown is how different hosts respond to infection by the same phage. Here we used microarray and RNA-seq analyses to investigate the interaction between the Syn9 T4-like cyanophage and three phylogenetically, ecologically and genomically distinct marine Synechococcus strains: WH7803, WH8102 and WH8109. Strikingly, Syn9 led a nearly identical infection and transcriptional program in all three hosts. Different to previous assumptions for T4-like cyanophages, three temporally regulated gene expression classes were observed. Furthermore, a novel regulatory element controlled early-gene transcription, and host-like promoters drove middle gene transcription, different to the regulatory paradigm for T4. Similar results were found for the P-TIM40 phage during infection of Prochlorococcus NATL2A. Moreover, genomic and metagenomic analyses indicate that these regulatory elements are abundant and conserved among T4-like cyanophages. In contrast to the near-identical transcriptional program employed by Syn9, host responses to infection involved host-specific genes primarily located in hypervariable genomic islands, substantiating islands as a major axis of phage-cyanobacteria interactions. Our findings suggest that the ability of broad host-range phages to infect multiple hosts is more likely dependent on the effectiveness of host defense strategies than on differential tailoring of the infection process by the phage.

Preparation of BAC libraries from marine microbial populations.

A protocol is presented here for the construction of BAC (bacterial artificial chromosome) libraries from planktonic microbial communities collected in marine environments. The protocol describes the collection and preparation of the planktonic microbial cells, high molecular weight DNA purification from those cells, the preparation of the BAC vector, and the special ligation and electrotransformation procedures required for successful library preparation. With small modifications, this protocol can be applied to microbes collected from other environments.

The P-SSP7 cyanophage has a linear genome with direct terminal repeats.

P-SSP7 is a T7-like phage that infects the cyanobacterium Prochlorococcus MED4. MED4 is a member of the high-light-adapted Prochlorococcus ecotypes that are abundant in the surface oceans and contribute significantly to primary production. P-SSP7 has become a model system for the investigation of T7-like phages that infect Prochlorococcus. It was classified as T7-like based on genome content and organization. However, because its genome assembled as a circular molecule, it was thought to be circularly permuted and to lack the direct terminal repeats found in other T7-like phages. Here we sequenced the ends of the P-SSP7 genome and found that the genome map is linear and contains a 206 bp repeat at both genome ends. Furthermore, we found that a 728 bp region of the genome originally placed downstream of the last ORF is actually located upstream of the first ORF on the genome map. These findings suggest that P-SSP7 is likely to use the direct terminal repeats for genome replication and packaging in a similar manner to other T7-like phages. Moreover, these results highlight the importance of experimentally verifying the ends of phage genomes, and will facilitate the use of P-SSP7 as a model for the correct assembly and end determination of the many T7-like phages isolated from the marine environment that are currently being sequenced.

Microbial community genomics in eastern Mediterranean Sea surface waters.

Offshore waters of the eastern Mediterranean Sea are one of the most oligotrophic regions on Earth in which the primary productivity is phosphorus limited. To study the unexplored function and physiology of microbes inhabiting this system, we have analyzed a genomic library from the eastern Mediterranean Sea surface waters by sequencing both termini of nearly 5000 clones. Genome recruitment strategies showed that the majority of high-scoring pairs corresponded to genomes from the Alphaproteobacteria (SAR11-like and Rhodobacterales), Cyanobacteria (Synechococcus and high-light adapted Prochlorococcus) and diverse uncultured Gammaproteobacteria. The community structure observed, as evaluated by both protein similarity scores or metabolic potential, was similar to that found in the euphotic zone of the ALOHA station off Hawaii but very different from that of deep aphotic zones in both the Mediterranean Sea and the Pacific Ocean. In addition, a strong enrichment toward phosphate and phosphonate uptake and utilization metabolism was also observed.

Widespread distribution of proteorhodopsins in freshwater and brackish ecosystems.

Proteorhodopsins (PRs) are light-driven proton pumps that have been found in a variety of marine environments. The goal of this study was to search for PR presence in different freshwater and brackish environments and to explore the diversity of non-marine PR protein. Here, we show that PRs exist in distinctly different aquatic environments, ranging from clear water lakes to peat lakes and in the Baltic Sea. Some of the PRs observed in this study formed unique clades that were not previously observed in marine environments, whereas others were similar to PRs found in non-marine samples of the Global Ocean Sampling (GOS) expedition. Furthermore, the similarity of several PRs isolated from lakes in different parts of the world suggests that these genes are dispersed globally and that they may encode unique functional capabilities enabling successful competition in a wide range of freshwater environments. Phylogenomic analysis of genes found on these GOS scaffolds suggests that some of the freshwater PRs are found in freshwater Flavobacteria and freshwater SAR11-like bacteria.

Adaptation and spectral tuning in divergent marine proteorhodopsins from the eastern Mediterranean and the Sargasso Seas.

Proteorhodopsins (PRs) phototrophy was recently discovered in oceanic surface waters. PRs have been observed in different marine environments and in diverse taxa, including the ubiquitous marine alphaproteobacterial SAR11 group and the uncultured gammaproteobacterial SAR86 group. Previously, two SAR86 PR subgroups, discovered in the Pacific Ocean, were shown to absorb light with different maxima, lambda max 527 nm (green) and lambda max 490 nm (blue) and their distribution was explained by prevailing light conditions - green pigments at the surface and blue in deeper waters. Here, we show that PRs display high diversity in geographically distinct patterns despite similar physical water column properties such as mixing and light penetration. We compared summer and winter samples representing stratified and mixed conditions from both the Mediterranean and Sargasso Sea. As expected, in the Mediterranean Sea, green pigments were mainly confined to the surface and the percentage of blue pigments increased toward deeper samples; in the Sargasso Sea, unexpectedly, all PRs were of the blue type. As an additional result, both locations show seasonal dependence in the distribution of different PR families. Finally, spectral tuning was not restricted to a single PR family as previously reported but occurs across the sampled PR families from various microbial taxa. The distribution of tunable PRs across the PR tree suggests that ready adaptability has been distributed widely among microorganisms, and may be a reason that PRs are abundant and taxonomically widely dispersed.

Potential photosynthesis gene recombination between Prochlorococcus and Synechococcus via viral intermediates.

Genes (psbA and psbD) encoding for photosynthetically important proteins were recently found in a number of cultured cyanophage genomes. This phenomenon may be a beneficial trait to the viruses or their photosynthetic cyanobacterial hosts, or may represent an untapped pool of genes involved in the formation of the photosynthetic apparatus that are prone to lateral gene transfer. Here we show analyses of psbA genes from uncultured environmental viruses and prophage populations. We observe a statistically significant separation between viral genes and their potential Synechococcus hosts' genes, and statistical analyses under models of codon evolution indicate that the psbA genes of viruses are evolving under levels of purifying selection that are virtually indistinguishable from their hosts. Furthermore, our data also indicate the possible exchange and reshuffling of psbA genes between Synechococcus and Prochlorococcus via phage intermediates. Overall, these observations raise the possibility that marine viruses serve as a potential genetic pool in shaping the evolution of cyanobacterial photosynthesis.

Roseobacter-like bacteria in red and mediterranean sea aerobic anoxygenic photosynthetic populations.

Bacteriochlorophyll a-containing aerobic anoxygenic phototrophs (AAnP) have been proposed to account for up to 11% of the total surface water microbial community and to potentially have great ecological importance in the world's oceans. Recently, environmental and genomic data based on analysis of the pufM gene identified the existence of alpha-proteobacteria as well as possible gamma-like proteobacteria among AAnP in the Pacific Ocean. Here we report on analyses of environmental samples from the Red and Mediterranean Seas by using pufM as well as the bchX and bchL genes as molecular markers. The majority of photosynthesis genes retrieved from these seas were related to Roseobacter-like AAnP sequences. Furthermore, the sequence of a novel photosynthetic operon organization from an uncultured Roseobacter-like bacterial artificial chromosome retrieved from the Red Sea is described. The data show the presence of Roseobacter-like bacteria in Red and Mediterranean Sea AAnP populations in the seasons analyzed.

Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment.

Proteorhodopsin, a retinal-binding protein, represents a potentially significant source of light-driven energy production in the world's oceans. The distribution of photochemically divergent proteorhodopsins is stratified according to depth. Here, we present evidence that such photochemical diversity was tuned by Darwinian selection. By using a Bayesian method, we identified sites targeted by Darwinian selection and mapped them to three-dimensional models of proteorhodopsins. We suggest that spectral fine-tuning results from the combined effect of amino acids that directly interact with retinal and those that influence the confirmation of the retinal-binding pocket.

Novel Proteorhodopsin variants from the Mediterranean and Red Seas.

Proteorhodopsins, ubiquitous retinylidene photoactive proton pumps, were recently found in the widespread uncultured SAR86 bacterial group in oceanic surface waters. To survey proteorhodopsin diversity, new degenerate sets of proteorhodopsin primers were designed based on a genomic proteorhodopsin gene sequence originating from an Antarctic fosmid library. New proteorhodopsin variants were identified in Red Sea samples that were most similar to the original green-light absorbing proteorhodopsins found in Monterey Bay California. Unlike green-absorbing proteorhodopsins however, these new variants contained a glutamine residue at position 105, the same site recently shown to control spectral tuning in naturally occurring proteorhodopsins. Different proteorhodopsin variants were also found in the Mediterranean Sea. These proteorhodopsins formed new and distinctive proteorhodopsin groups. Phylogenetic analyses show that some of the new variants were very different from previously characterized proteorhodopsins, and formed the deepest branching groups found so far among marine proteorhodopsins. The existence of these varied proteorhodopsin sequences suggests that this class of proteins has undergone substantial evolution. These variants could represent functionally divergent paralogous genes, derived from the same or similar species, or orthologous proteorhodopsins that are distributed amongst divergent planktonic microbial taxa.

Different SAR86 subgroups harbour divergent proteorhodopsins.

Proteorhodopsins (PRs), bacterial photoactive proton pumps, were originally detected in the uncultured marine gamma-proteobacterial SAR86 group. PRs are now known to occur in both the gamma and alpha marine proteobacterial lineages. Recent environmental shotgun sequence analysis in the Sargasso Sea has added yet more diversity, and a potentially broader taxonomic distribution, to the PR family. Much remains to be learned, however, about within-taxon PR variability and the broader organismal distribution of different PR types. We report here genomic analyses of large genome fragments from different subgroups of the SAR86 lineage, recovered from naturally occurring bacterioplankton populations in coastal Red Sea and open ocean Pacific waters. Sequence comparisons were performed on large bacterial artificial chromosomes (BACs) bearing both rRNA and PR genes, derived from different SAR86 subgroups. Our analyses indicated the presence of different PR sequence types within the same SAR86 rRNA subgroup. The data suggested that the distribution of particular PR types does not necessarily parallel the phylogenetic relationship inferred from highly conserved genes such as rRNA. Further analyses of the genomic regions flanking PR also revealed a potential pathway for the biosynthesis of retinal, the PR chromophore that is required to generate the functionally active photoprotein. Finally, comparison of our results with recently reported Sargasso Sea environmental shotgun sequence assemblies demonstrated the utility of BAC clones for interpreting environmental shotgun sequence data, much of which is represented in short contigs that have an overall low depth of coverage.

Characterization of RS29, a blue-green proteorhodopsin variant from the Red Sea.

Using structural modeling comparisons and mutagenesis, amino acid residue 105 was found to function as a spectral tuning switch in marine proteorhodopsins (PR). Changes at this position account for most of the spectral difference between blue-absorbing PRs (B-PRs), and green-absorbing PRs (G-PRs). Here we analyzed a Red Sea variant (RS29) from a new family of PRs that is composed of G-PR type variants that possess glutamine instead of leucine at position 105 like in B-PRs. The absorption spectrum as well as photocycle of RS29 variant were measured and compared to point-mutated 'position 105' PRs. Unexpectedly, the absorption maximum of RS29 was 515 nm, a smaller blue shift compared to the 498 nm maximum of G-PR_L105Q. We found that two additional residues at positions 65 and 70 each contribute a small red shift to the absorption spectrum of G-PR and therefore appear to account for the intermediate absorption maximum of RS29 by their opposing influences on the spectrum. Our results show that in addition to the retinal pocket position 105 determinant, other residues predicted to be outside the retinal pocket fine-tune the absorption spectra of marine PRs. The RS29 photochemical reaction cycle was found to be 2 orders of magnitude slower than that of G-PR with a t(1/2) of >600 ms. This result raises the possibility of regulatory (i.e. sensory) rather than energy harvesting functions for some members of the PR family.

Diversification and spectral tuning in marine proteorhodopsins.

Proteorhodopsins, ubiquitous retinylidene photoactive proton pumps, were recently discovered in the cosmopolitan uncultured SAR86 bacterial group in oceanic surface waters. Two related proteorhodopsin families were found that absorb light with different absorption maxima, 525 nm (green) and 490 nm (blue), and their distribution was shown to be stratified with depth. Using structural modeling comparisons and mutagenesis, we report here on a single amino acid residue at position 105 that functions as a spectral tuning switch and accounts for most of the spectral difference between the two pigment families. Furthermore, looking at natural environments, we found novel proteorhodopsin gene clusters spanning the range of 540-505 nm and containing changes in the same identified key switch residue leading to changes in their absorption maxima. The results suggest a simultaneous diversification of green proteorhodopsin and the new key switch variant pigments. Our observations demonstrate that this single-residue switch mechanism is the major determinant of proteorhodopsin wavelength regulation in natural marine environments.