Pelagic Bacteria, Archaea, and Viruses

McMahon, Katherine D.; Newton, Ryan J.

doi:10.1016/b978-0-12-822701-5.00023-9

Cited by 3 publications

(2 citation statements)

References 369 publications

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“…Globally, freshwater lakes are undergoing rapid change due to landscape and climate alterations. Microbial communities are foundational players in freshwater ecology 4 , and characterizing the diversity, function, ecology, and evolution of their viruses will improve our understanding of a major top-down control of microbial communities.…”

Section: Mainmentioning

confidence: 99%

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A 20-year time-series of a freshwater lake reveals seasonal dynamics and environmental drivers of viral diversity, ecology, and evolution

Anantharaman,

Zhou,

Tran

et al. 2024

Preprint

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Long-term ecological studies are powerful tools to investigate microbiomes and ecosystem change but have mostly ignored viruses. Here, we leveraged a 20-year time-series of a freshwater lake to characterize 1.3 million viral genomes over time, seasonality, and environmental factors. We identified 578 auxiliary metabolic gene (AMG) clusters representing over 150,000 AMGs, the most abundant of which, including psbA for photosynthesis, pmoC for methane oxidation, and katG for hydrogen peroxide decomposition, were consistently represented in viruses across decades and seasons. We observed positive associations and niche differentiation between virus-host pairs during seasonal change including in keystone taxa, Cyanobacteria, methanotrophs, and Nanopelagicales. Environmental constraints, specifically inorganic carbon and ammonium influenced viral abundances over time, and highlighted roles of viruses in both “top-down” and “bottom-up” interactions. Key evolutionary processes shaping gene and genome-wide selection included favored fitness genes, reduced genomic heterogeneity, and dominant sub-populations carrying specific genes. Overall, our study advances understanding of diversity, ecological dynamics, and evolutionary trajectories of viruses in Earth’s microbiomes and ecosystems.

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Section: Mainmentioning

confidence: 99%

“…grazing by protists, viral lysis) and bottomup (e.g. water temperature, nutrient concentrations) drivers 4 . We expect these dynamics to also manifest in measured viral abundances and potential viral roles.…”

Section: Environmental Constraints Indirectly Influence Viral Abundan...mentioning

confidence: 99%

A 20-year time-series of a freshwater lake reveals seasonal dynamics and environmental drivers of viral diversity, ecology, and evolution

Anantharaman,

Zhou,

Tran

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

Unravelling viral ecology and evolution over 20 years in a freshwater lake

Zhou,

Tran,

Martin

et al. 2025

Nat Microbiol

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A 20-year time-series of a freshwater lake reveals seasonal dynamics and environmental drivers of viral diversity, ecology, and evolution

Zhou,

Tran,

Martin

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

Long-term ecological studies are powerful tools to investigate microbiomes and ecosystem change but have mostly ignored viruses. Here, we leveraged a 20-year time-series of a freshwater lake to characterize 1.3 million viral genomes over time, seasonality, and environmental factors. We identified 578 auxiliary metabolic gene (AMG) clusters representing over 150,000 AMGs, the most abundant of which, includingpsbAfor photosynthesis,pmoCfor methane oxidation, andkatGfor hydrogen peroxide decomposition, were consistently represented in viruses across decades and seasons. We observed positive associations and niche differentiation between virus-host pairs during seasonal change including in keystone taxa, Cyanobacteria, methanotrophs, and Nanopelagicales. Environmental constraints, specifically inorganic carbon and ammonium influenced viral abundances over time, and highlighted roles of viruses in both “top-down” and “bottom-up” interactions. Key evolutionary processes shaping gene and genome-wide selection included favored fitness genes, reduced genomic heterogeneity, and dominant sub-populations carrying specific genes. Overall, our study advances understanding of diversity, ecological dynamics, and evolutionary trajectories of viruses in Earth’s microbiomes and ecosystems.

show abstract

Pelagic Bacteria, Archaea, and Viruses

Cited by 3 publications

References 369 publications

A 20-year time-series of a freshwater lake reveals seasonal dynamics and environmental drivers of viral diversity, ecology, and evolution

A 20-year time-series of a freshwater lake reveals seasonal dynamics and environmental drivers of viral diversity, ecology, and evolution

Unravelling viral ecology and evolution over 20 years in a freshwater lake

A 20-year time-series of a freshwater lake reveals seasonal dynamics and environmental drivers of viral diversity, ecology, and evolution

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