Recently, Professor Zhou Zhichao's research group at the Institute for Advanced Study, Shenzhen University, published a study titled"Unraveling viral ecology and evolution over twenty years in a freshwater lake"in the prestigious journalNature Microbiology(a Nature Index journal with a 2023 impact factor of 20.5, classified as a top-tier journal by the Chinese Academy of Sciences). Utilizing two decades of monitoring data from Lake Mendota collected by the Hasler Laboratory of Limnology at the University of Wisconsin, the study analyzed metagenomic and metatranscriptomic sequences to reveal patterns in over 1.3 million viral genomes across time, seasons, and environmental changes. Professor Zhou Zhichao is the first author, with the Institute for Advanced Study and the Synthetic Biology Research Center at Shenzhen University as the second and third contributing institutions.
The research identified over 140,000 auxiliary metabolic genes (AMGs) associated with carbon, nitrogen, and sulfur cycling, spanning a wide range of functional categories. High-abundance AMGs such aspsbA,pmoC, andkatGdisplayed stable distribution and two host association patterns: "broad host" and "narrow host." Broad host AMGs, with high abundance and frequency, were minimally affected by environmental changes and primarily involved in sulfur metabolism and folate synthesis. Narrow host AMGs supported specific host functions, such as the photosynthesis genepsbAin cyanophages andgndandzwfgenes linked to the pentose phosphate pathway.
The study also uncovered correlations and ecological niche differentiation between viruses and hosts during seasonal changes. It revealed that high-frequency viral populations undergo both single-gene positive selection and whole-genome evolution, including: (1) positive selection on adaptive genes, (2) reduced genomic SNP heterogeneity over time, and (3) dominance of subpopulations carrying specific advantageous genes. These adaptations enhance viral fitness by optimizing genome replication, host transcription regulation, and stress mitigation. In the "Kill-The-Winner" model, such viral subpopulations emerge as "royal family" viruses, maintaining ecological stability while undergoing genetic and physiological evolution.
Additionally, by linking time-series environmental data with viral abundance, the study demonstrated how factors like inorganic carbon and ammonium indirectly affect viral populations through virus-host interactions. It highlighted the intricate interplay between "bottom-up" nutrient supply and primary productivity with "top-down" predator-prey dynamics.
This research provides novel insights into viral diversity, ecological dynamics, and roles in biogeochemical processes in freshwater systems. It underscores the importance of studying viruses within broader contexts of biodiversity, virus-host interactions, and environmental constraints. The study was funded by the Synthetic Biology Research Center and the startup research grants at Shenzhen University.
Original article link:https://www.nature.com/articles/s41564-024-01876-7
