Freshwaters ecosystems are critical but fragile environments directly affecting society and its welfare. However, our understanding of genuinely freshwater microbial communities, constrained by our capacity to manipulate its prokaryotic participants in axenic cultures, remains very rudimentary. Even the most abundant components, freshwater Actinobacteria, remain largely unknown. Here, applying deep metagenomic sequencing to the microbial community of a freshwater reservoir, we were able to circumvent this traditional bottleneck and reconstruct de novo seven distinct streamlined actinobacterial genomes. These genomes represent three new groups of photoheterotrophic, planktonic Actinobacteria. We describe for the first time genomes of two novel clades, acMicro (Micrococcineae, related to Luna2,) and acAMD (Actinomycetales, related to acTH1). Besides, an aggregate of contigs belonged to a new branch of the Acidimicrobiales. All are estimated to have small genomes (~1.2 Mb) and their GC content varied from 40-61%. One of the Micrococcineae genomes encodes a proteorhodopsin, a rhodopsin type reported for the first time in Actinobacteria.The remarkable potential capacity of some of these genomes to transform recalcitrant plant detrital material, particularly lignin derived compounds, suggests close linkages between the terrestrial and aquatic realms. Moreover, abundances of Actinobacteria correlate inversely to those of Cyanobacteria that are responsible for prolonged and frequently irretrievable damage to freshwater ecosystems. This suggests that they might serve as sentinels of impending ecological catastrophes.

CytometryThis readme file describes the raw data files for cytometry as performed in the above publication For any further queries please contact antonio.picazo-mozo@uv.esRAW_Actino_Amadorio_FISHThis readme file describes the data file for FISH as performed in the above publication For any further queries please contact antonio.picazo-mozo@uv.esphylogenetic-treesThis readme file describes the tree files for all phylogenetic analyses as performed in the above publication For any further queries please contact ghai.rohit@gmail.com16S-alignmentsThis readme file describes the 16S alignments as performed in the above publication For any further queries please contact ghai.rohit@gmail.com