Ecological success in freshwater lakes: insights from novel cultivated lineages of the abundant Nanopelagicales order

作者：Maria‐Cecilia Chiriac, Paul Layoun, Clafy Fernandes, Tiberiu Szöke‐Nagy, Vojtěch Kasalický, Yusuke Okazaki, Jason Woodhouse, Hans‐Peter Grossart, Kasia Piwosz, Petr Znachor, Bettina Sonntag, Cristiana Callieri, Sandi Orlić, Rubén Sommaruga, Cécile Lepère, Corinne Biderre‐Petit, Helen Tammert, Daniel P. R. Herlemann, Mirosław Ślusarczyk, Anna Bednarska, Horia Leonard Banciu, Mariusz Zalewski, Adam Woźniczka, Rohit Ghai, Michaela M. Salcher, Markus Haber · 发表于：Microbiome · 年份：2025 · DOI：10.1186/s40168-025-02272-x · 被引用次数：1 · 研究领域：Aquatic Ecosystems and Phytoplankton Dynamics、Diatoms and Algae Research、Marine and coastal ecosystems

BACKGROUND: ), reduced genome sizes (<1.5 Mbp), and low GC content. These characteristics reflect adaptations to a free-living life strategy in oligotrophic environments. While many Nanopelagicales metagenome-assembled genomes and single-amplified genomes are available in public databases, strain-level microdiversity within this lineage remains poorly understood. This is mainly attributed to the incomplete nature of these genomes and the difficulty in isolating and maintaining pure cultures, with only 20 genome-sequenced cultures available to date. RESULTS: Here, we report the isolation and genome analysis of 72 new Nanopelagicales strains, including members of Planktophila and a novel, previously uncultured genus, Aquilimus. High interspecific diversity and microdiversity were observed in the genus Planktophila, which likely facilitates the coexistence of closely related species within the same habitats by allowing fine-scale niche partitioning. The unusually high diversity of transporters for small organic compounds, along with carbohydrate-active enzymes, suggests that Planktophila members can degrade plant and algal polymers and import the resulting products to support growth. A notable finding is the repeated, independent loss of the oxidative phase of the pentose phosphate pathway in abundant Nanopelagicales species, which may represent an energy-saving adaptation in oligotrophic waters. Two species (Planktophila vernalis and Nanopelagicus abundans) seem to be equally a...