Biology subjects

Tahan, R.

Publications and source records attributed to Tahan, R..

5 recordsLinked to original sources

bioRxiv2026

Virus-grazer interplay enhances virus production, particle aggregation, and trophic efficiency during infection of Prochlorococcus

Viruses and grazers are fundamental agents of mortality in the oceans, impacting phytoplankton populations and organic matter cycling. Although viruses and grazers co-occur in nature, they are typically studied in isolation in laboratory experiments, limiting our understanding of their combined ecosystem impacts. Here, using a simplified ecosystem approach, we investigated individual and combined effects of the T7-like cyanopodovirus, P-SSP7, and the protistan grazer, Paraphysomonas bandaiensis, on the abundant marine cyanobacterium, Prochlorococcus MED4, and co-occurring non-photosynthetic heterotrophic bacteria (bacteria from here on). We observed that, individually, viruses and grazers caused substantial Prochlorococcus mortality. Viral lysis also triggered increases in damaged Prochlorococcus cells, dissolved organic matter release, and bacterial growth, while grazing reduced bacterial abundances. When grazers and viruses were combined, Prochlorococcus mortality was lower than expected from the sum of their individual effects. Contrary to expectations, this reduced Prochlorococcus mortality did not result in fewer viruses or grazers. Instead, virus-grazer-Prochlorococcus interplay resulted in greater virus production, maintenance of grazer growth, and a dramatic increase in particle aggregation. Our results reveal trophic cooperation and efficiency in which competition between viruses and grazers was likely mitigated, with virus progeny production enhanced by grazers, and grazer growth sustained through a shift to alternative food sources (bacteria, damaged cells, aggregates) secondarily derived from Prochlorococcus following viral lysis. The synergistic enhancement of particle aggregation via grazer-virus-phytoplankton interplay observed with the small buoyant Prochlorococcus phytoplankter underscores the importance of food web interactions for the flow of phytoplankton-fixed carbon within, and export from, the photic zone. SignificanceViruses and grazers both use phytoplankton as a resource for reproduction. In a simplified experimental system with Prochlorococcus, an important primary producer in the oceans, we found that the interplay between viruses and grazers led to reduced mortality of Prochlorococcus. Despite this reduced mortality, virus-grazer interactions resulted in elevated virus production and a dramatic increase in organic matter aggregation. Furthermore, grazer abundance was not affected by this interplay, likely due to the transfer of organic matter from Prochlorococcus to bacteria and aggregates, which the grazers could consume as alternative food sources. These findings provide insights into the complexity of ecosystem interactions and how they impact the fate of organic matter fixed by phytoplankton in the oceans.

microbiology↗

bioRxiv2025

A functional cyanophage thioredoxin increases competitive phage fitness

Viruses carry many homologs of cellular genes as well as small genes of unknown function, often called viral dark matter. One cellular-like gene present in viruses is the redox protein thioredoxin, found in all domains of cellular life. However, the functional relevance and evolutionary benefit of viral-encoded thioredoxins, and small genes of unknown function, remain unclear. Both types of genes are present in marine cyanophages, viruses that infect the globally important marine cyanobacteria. In the T7-like cyanophage, Syn5, the phage thioredoxin overlaps with a small gene of unknown function that we named cve for cyanophage virulence enhancer. While thioredoxin genes are common across a wide variety of viruses infecting diverse host types, we found that cve is restricted to cyanophages. Genetic inactivation of thioredoxin and cve in the Syn5 cyanophage revealed that thioredoxin enhanced phage fitness, increasing phage genome replication and progeny production. Furthermore, redox active Syn5 thioredoxin negatively impacted host growth, indicating that its activity is detrimental to host metabolism. The cve gene increased phage virulence yet reduced phage burst size, and is thus a double-edged sword. Despite this trade-off, cve significantly enhanced overall phage fitness emphasizing the importance of virulence for viral fitness. Our findings indicate that viral-encoded thioredoxin and cve genes differentially alter infection properties to provide an evolutionary advantage to the Syn5 phage. They further reveal the function of a small, cyanophage-specific gene of unknown function, unveiling the first known host-type-specific virulence enhancer in viruses.

microbiology↗

bioRxiv2025

Inferring single-cell heterogeneity of bacteriophage life-history traits from population-scale dynamics

Phage-induced lysis of bacteria transforms population dynamics, community structure, and ecosystem functioning. Scaling up infected cell fate to quantify population- and ecosystem-scale impacts requires estimates of viral life history traits, including underlying heterogeneity in the timing, efficiency, and outcome of lytic infections. However, the variability of lysis-associated phage traits remains poorly characterized. Here, we infer single-cell heterogeneity in lysis-associated traits for an ecologically relevant system: Syn9, a T4-like cyanophage infecting Synechococcus strain WH8109, a representative of globally abundant marine cyanobacteria. We estimate the heterogeneous distribution of latent period and burst size using a nonlinear model of infection dynamics applied to population-scale time series data. We then validate our inference approach using a single-cell assay - demonstrating the feasibility of inferring phage trait heterogeneity from population data even in the absence of single-cell experiments. The variation in Syn9s latent period exceeds that previously found in coliphages and reinforces the limitations of representing viral traits with a single value. Moreover, by partitioning lytic events via the inferred heterogeneous latent period distribution, we show that realized burst size variability is largely explained by differences in latent period, providing a path forward to measure and integrate trait (co)variation into population and ecosystem models.

microbiology↗

bioRxiv2024

Oceanic photosynthesis is directly affected by cyanophage NblA proteins

Marine picocyanobacteria are abundant photosynthetic organisms of global importance. They coexist in the ocean with cyanophages, viruses that infect cyanobacteria. Cyanophages carry many auxiliary metabolic genes acquired from their hosts that are thought to redirect host metabolism for the phages benefit1-5. One such gene is nblA which is present in multiple cyanophage families2,6-8. Under nutrient deprivation the cyanobacterial NblA is responsible for inducing proteolytic degradation of the phycobilisome9-11, the large cyanobacterial photosynthetic light harvesting complex. This increases the pool of amino acids available for essential tasks11, serving as a survival mechanism12. Ectopic expression of different cyanophage nblA genes results in host pigment protein degradation9,6. However, the benefit of the cyanophage-encoded NblA for the cyanophage and the broader impact on the host are unknown. Here, using a recently developed genetic manipulation system for marine cyanophages14, we reveal that cyanophage NblA significantly accelerates the cyanophage infection cycle, directs degradation of the host phycobilisome and other proteins and reduces host photosynthetic light harvesting efficiency. Metagenomic analysis revealed that cyanophages carrying nblA are widespread in the oceans and compose 35% and 65% of oceanic T7-like cyanophages in the surface and deep photic zones, respectively. Our results show a large benefit of the nblA gene to the cyanophage while exerting a negative effect on the host photosynthetic apparatus and host photosynthesis. These findings suggest that cyanophage nblA has an adverse global impact on light harvesting by oceanic picocyanobacteria.

microbiology↗

bioRxiv2021

Characterization of heliorhodopsins detected via functional metagenomics in freshwater Actinobacteria, Chloroflexi and Archaea

Rhodopsins are widespread in microbes residing in diverse aquatic environments across the globe. Recently, a new unusual rhodopsin family, the heliorhodopsins (HeRs), was discovered, distributed among diverse bacteria, archaea, eukarya and even viruses. Here, using functional metagenomics on samples from Lake HaHula and Ein Afek reserve, we found and characterized ten HeRs representing divergent members of the family. The expressed HeRs absorb light in the green and yellow wavelengths and originate from Actinobacteria, Chloroflexi and Archaea. The photocycle of the HeR from Chloroflexi revealed a low accumulation of the M-intermediate that we connect to the lack of two conserved histidine residues in transmembrane helices 1 and 2 in this protein. Another of HeR, from Actinobacteria, exhibited an unusually fast photocycle (166 ms, 5 times faster than HeR-48C12). To further explore the still unresolved question of the HeR function, we performed an analysis of protein families among genes neighboring HeRs, in our clones and thousands of other microbes. This analysis revealed a putative connection between HeRs and genes involved in oxidative stress. At the same time, very few protein families were found to distinguish genes surrounding prokaryotic HeRs from those surrounding rhodopsin pumps. The strongest association was found with the DegV family involved in activation of fatty acids and uncharacterized family DUF2177, which allowed us to hypothesize that HeRs are involved in membrane lipid remodeling. This work further establishes functional metagenomics as a simple and fruitful method of screening for new rhodopsins. SignificanceThe recently discovered divergent rhodopsin family of heliorhodopsins is abundant in freshwater environments. In this study, we sampled a habitat rich in dissolved organic matter to increase our chances of finding spectrally shifted rhodopsins. Using functional metagenomics, diverse heliorhodopsins absorbing green and yellow light were discovered. The metagenomic clones originated from diverse prokaryotic groups: Actinobacteria, Chloroflexi and even Archaea, emphasizing the versatility of the E. coli expression system used. Photocycles of representative heliorhodopsins were measured and exhibited diverse kinetic characteristics. Analysis of genes neighboring heliorhodopsins in diverse prokaryotes revealed their putative connection to membrane lipid re-modeling and oxidative stress. Our findings suggest that functional metagenomics is a productive method for the discovery of new and diverse rhodopsins.

microbiology↗