biostudies-literatureKrinos AIU.S. Department of EnergyU.S. National Science FoundationU.S. Department of AgricultureNational Science Foundation133https://www.ebi.ac.uk/biostudies/studies/S-EPMC11265017biostudies-literatureUnknown12(1)<h4>Background</h4>Protists, single-celled eukaryotic organisms, are critical to food web ecology, contributing to primary productivity and connecting small bacteria and archaea to higher trophic levels. Lake Mendota is a large, eutrophic natural lake that is a Long-Term Ecological Research site and among the world's best-studied freshwater systems. Metagenomic samples have been collected and shotgun sequenced from Lake Mendota for the last 20 years. Here, we analyze this comprehensive time series to infer changes to the structure and function of the protistan community and to hypothesize about their interactions with bacteria.<h4>Results</h4>Based on small subunit rRNA genes extracted from the metagenomes and metagenome-assembled genomes of microeukaryotes, we identify shifts in the eukarMicrobiomeTime-series metagenomics reveals changing protistan ecology of a temperate dimictic lake.PMC11265017SC0020347WIS01516DE-AC02-05CH112312011002DEB-9632853McMahon KDSchulz FWoyke TRohwer RRKrinos AIBowers RMfalseTime-series metagenomics reveals changing protistan ecology of a temperate dimictic lake.<h4>Background</h4>Protists, single-celled eukaryotic organisms, are critical to food web ecology, contributing to primary productivity and connecting small bacteria and archaea to higher trophic levels. Lake Mendota is a large, eutrophic natural lake that is a Long-Term Ecological Research site and among the world's best-studied freshwater systems. Metagenomic samples have been collected and shotgun sequenced from Lake Mendota for the last 20 years. Here, we analyze this comprehensive time series to infer changes to the structure and function of the protistan community and to hypothesize about their interactions with bacteria.<h4>Results</h4>Based on small subunit rRNA genes extracted from the metagenomes and metagenome-assembled genomes of microeukaryotes, we identify shifts in the eukar2024-01-01T00:00:00Z2024 Jul2026-05-22T03:20:51.699Z2025-06-01T01:16:06.383ZS-EPMC112650173903063210.1186/s40168-024-01831-y