High-resolution metagenomic reconstruction of the freshwater spring bloom

作者：Vinicius Kavagutti, Paul‐Adrian Bulzu, Maria‐Cecilia Chiriac, Michaela M. Salcher, Indranil Mukherjee, Tanja Shabarova, Vesna Grujčić, Maliheh Mehrshad, Vojtěch Kasalický, Adrian‐Ștefan Andrei, Jitka Jezberová, Jaromír Seďa, Pavel Rychtecký, Petr Znachor, Karel Šimek, Rohit Ghai · 发表于：Microbiome · 年份：2023 · DOI：10.1186/s40168-022-01451-4 · 被引用次数：90 · 研究领域：Bacteriophages and microbial interactions、Protist diversity and phylogeny、Genomics and Phylogenetic Studies

BACKGROUND: The phytoplankton spring bloom in freshwater habitats is a complex, recurring, and dynamic ecological spectacle that unfolds at multiple biological scales. Although enormous taxonomic shifts in microbial assemblages during and after the bloom have been reported, genomic information on the microbial community of the spring bloom remains scarce. RESULTS: We performed a high-resolution spatio-temporal sampling of the spring bloom in a freshwater reservoir and describe a multitude of previously unknown taxa using metagenome-assembled genomes of eukaryotes, prokaryotes, and viruses in combination with a broad array of methodologies. The recovered genomes reveal multiple distributional dynamics for several bacterial groups with progressively increasing stratification. Analyses of abundances of metagenome-assembled genomes in concert with CARD-FISH revealed remarkably similar in situ doubling time estimates for dominant genome-streamlined microbial lineages. Discordance between quantitations of cryptophytes arising from sequence data and microscopic identification suggested the presence of hidden, yet extremely abundant aplastidic cryptophytes that were confirmed by CARD-FISH analyses. Aplastidic cryptophytes are prevalent throughout the water column but have never been considered in prior models of plankton dynamics. We also recovered the first metagenomic-assembled genomes of freshwater protists (a diatom and a haptophyte) along with thousands of giant viral genomic co...