Widespread yet persistent low abundance of <scp>TIM5</scp>‐like cyanophages in the oceans

Baran, Nava; Carlson, Michael C. G.; Sabehi, Gazalah; Peleg, Margalit; Kondratyeva, Kira; Pekarski, Irena; Lindell, Debbie

doi:10.1111/1462-2920.16210

Cited by 3 publications

(1 citation statement)

References 90 publications

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“…There are clearly multiple additional factors not measured here that contribute to this unexplained variation, such as organic nutrients (bottom-up controls) [ 71 , 72 , 73 ], interactions with cellular predators (i.e., grazers) (top-down controls) [ 74 , 75 , 76 ], allopathic interactions between cyanobacteria (‘lateral’ controls) [ 77 ], and predation by non-T4 cyanophages such as T7 cyanophages [ 65 ]. Indeed S-TIM5-like cyanophages, a lineage of non-T4 cyanomyoviruses, exhibit variation over time [ 78 ]. However, there are fewer genomes available for non-T4 cyanophages, which makes it difficult to determine relevant ANI levels (and corresponding marker gene divergence) at which species-like populations are delineated, and this is, in part, why we have focused on T4-like cyanophage populations here.…”

Section: Discussionmentioning

confidence: 99%

Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics

Dart

Fuhrman

Ahlgren

2023

Viruses

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Cyanophages exert important top-down controls on their cyanobacteria hosts; however, concurrent analysis of both phage and host populations is needed to better assess phage–host interaction models. We analyzed picocyanobacteria Prochlorococcus and Synechococcus and T4-like cyanophage communities in Pacific Ocean surface waters using five years of monthly viral and cellular fraction metagenomes. Cyanophage communities contained thousands of mostly low-abundance (<2% relative abundance) species with varying temporal dynamics, categorized as seasonally recurring or non-seasonal and occurring persistently, occasionally, or sporadically (detected in ≥85%, 15-85%, or <15% of samples, respectively). Viromes contained mostly seasonal and persistent phages (~40% each), while cellular fraction metagenomes had mostly sporadic species (~50%), reflecting that these sample sets capture different steps of the infection cycle—virions from prior infections or within currently infected cells, respectively. Two groups of seasonal phages correlated to Synechococcus or Prochlorococcus were abundant in spring/summer or fall/winter, respectively. Cyanophages likely have a strong influence on the host community structure, as their communities explained up to 32% of host community variation. These results support how both seasonally recurrent and apparent stochastic processes, likely determined by host availability and different host-range strategies among phages, are critical to phage–host interactions and dynamics, consistent with both the Kill-the-Winner and the Bank models.

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Section: Discussionmentioning

confidence: 99%

Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics

Dart

Fuhrman

Ahlgren

2023

Viruses

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Spatio-temporal variability of airborne viruses over sub-Antarctic South Georgia: Effects of sampling device and proximity of the ocean

Das,

Malard,

Pearce

et al. 2024

Preprint

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Studying airborne viral diversity in pristine, remote environments like the sub-Antarctic island South Georgia provides crucial insights into viral ecology and their role in sustaining unique ecosystems. Viruses influence microbial dynamics and nutrient cycles, which are vital for ecological balance and long-term ecosystem sustainability. We explored the community composition of airborne viral operational taxonomic units (vOTUs) of two sites in South Georgia, using various sampling devices and viral metagenomics. The Coriolis µ device (wet collection) was the most effective, yielding 30 viral scaffolds. Two-thirds of the scaffolds were from sea-level samples, indicating that location impacts viral diversity. Protein-based clustering of 39 vOTUs revealed similarities of 15 with known marine viruses, suggesting oceanic influence on the island's airborne viral community. Genes related to UV damage protection and photosynthesis from two airborne vOTUs were widely distributed in the major oceans, emphasizing the potential resilience in changing climates. Host predictions indicated associations with bacterial genera likeRickettsia,Myroides, and Bacteroidota. Some vOTUs matched viruses from extremophiles, indicating adaptations to harsh environments. This study provides a baseline for understanding the complexity and sustainability of airborne viral communities in remote ecosystems, underscoring the need for continued monitoring in the face of environmental change.

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

Baran

Carlson

Sabehi

et al. 2022

Environmental Microbiology

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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 virusesÁml À1 . Occasional peaks in abundance of 10-to 100-fold were observed, reaching 71,000 virusesÁml À1 . 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.

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

Cited by 3 publications

References 90 publications

Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics

Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics

Spatio-temporal variability of airborne viruses over sub-Antarctic South Georgia: Effects of sampling device and proximity of the ocean

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

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