Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs

Abstract

Freshwater picocyanobacteria including Synechococcus remain poorly studied at the genomic level, compared to their marine representatives. Here, using a metagenomic assembly approach we discovered two novel Synechococcus sp. genomes from two freshwater reservoirs Tous and Lake Lanier, both sharing 96% average nucleotide identity and displaying high abundance levels in these two lakes located at similar altitudes and temperate latitudes. These new genomes have the smallest estimated size (2.2 Mb) and average intergenic spacer length (20 bp) of any previously sequenced freshwater Synechococcus, which may contribute to their success in oligotrophic freshwater systems. Fluorescent in situ hybridization confirmed that Synechococcus sp. Tous comprises small cells (0.987 ± 0.139 μm length, 0.723 ± 0.119 μm width) that amount to 90% of the picocyanobacteria in Tous. They appear together in a phylogenomic tree with Synechococcus sp. RCC307 strain, the main representative of sub-cluster 5.3 that has itself one of the smallest marine Synechococcus genomes. We detected a type II phycobilisome (PBS) gene cluster in both genomes, which suggests that they belong to a phycoerythrin-rich pink low-light ecotype. The decrease of acidic proteins and the higher content of basic transporters and membrane proteins in the novel Synechococcus genomes, compared to marine representatives, support their freshwater specialization. A sulfate Cys transporter which is absent in marine but has been identified in many freshwater cyanobacteria was also detected in Synechococcus sp. Tous. The RuBisCo subunits from this microbe are phylogenetically close to the freshwater amoeba Paulinella chromatophora symbiont, hinting to a freshwater origin of the carboxysome operon of this protist. The novel genomes enlarge the known diversity of freshwater Synechococcus and improve the overall knowledge of the relationships among members of this genus at large.

Ecological and genomic features of two widespread freshwater picocyanobacteria

“…The pattern observed by the metagenomic fragment recruitment in other temperate lakes and reservoirs (Figs and ) points toward a high abundance of S. lacustris in temperate freshwater ecosystems, especially in the Lanier and Tous reservoirs, as previously described (Cabello‐Yeves et al ., ). The datasets from the Sparkling Lake, Dexter and Amadorio reservoirs also showed the presence of this microbe (from 5 to 20 RPKG).…”

“…The limnological features of Tous reservoir during sampling are given in Cabello‐Yeves et al . (). Strains were cultured in BG11 medium (Rippka et al ., ) diluted two‐fold, at 14°C with an irradiance of 10–20 μmol photons m −2 s −1 supplied by Gro‐Lux lamps under light/dark cycles of 14:10 h. We followed the dilution to the extinction methodology.…”

“…A threshold value of greater than 95% of identity and greater than 50 bp of alignment length was used to count a hit. The metagenomic data sets that gave positive hits for the presence of our strains are publicly available:, including for the Amadorio (Ghai et al ., ) and Tous reservoirs (Cabello‐Yeves et al ., ), Lake Lanier (Oh et al ., ), Dexter Reservoir (PRJNA312985), Sparkling Lake (SRR6476262, SRR6476264), Amazonian Lakes (Toyama et al ., ), Lake Erie (SRR6201979, SRR6201526 and PRJNA288501), Lake Baikal (Cabello‐Yeves et al ., ) and the Baltic Sea (Hugerth et al ., ). Additional features of the datasets used are described in Supporting Information Datasheet 1.…”

“…Here, we present the ecological and genomic characterization of two picocyanobacterial strains both isolated from Tous reservoir (Spain), an oligotrophic freshwater system. The strains were characterized as Synechococcus lacustris Tous (Cabello‐Yeves et al ., ), previously described as an MAG from the same habitat, and the other strain is proposed here as a member of the Synechococcaceae family but from a separate genus: Cyanobium usitatum Tous. Both picocyanobacteria have a coccoid morphology and a similar genome size, but are affiliated with different sub‐clusters within the genera Synechococcus/Cyanobium.…”

“…Genetic studies based on the 16S rRNA and cytochrome b6 (petB) genes have revealed the presence of two major marine sub-clusters 5.1A/B (Scanlan et al, 2009;Mazard et al, 2012), whilst approximately 13 nonmarine sub-clusters of freshwater, brackish and euryhaline origin have been detected (Callieri et al, 2013). While sub-clusters 5.1A/B are restricted to marine representatives (except for the halotolerant clade VIII), subclusters 5.2 and 5.3 encompass marine, euryhaline and freshwater species (Cabello-Yeves et al, 2017), which widens the previously known polyphyletic nature of picocyanobacteria from the Synechococcus/Cyanobium genus (Shih et al, 2013). Evolutionary reconstruction models based on phylogenomics, Bayesian relaxed molecular clocks or Bayesian stochastic character mapping analysis revealed a possible transition of Synechococcus species from freshwater to brackish and marine environments, which is also consistent with the greater diversity of freshwater species compared with their marine representatives (Blank and Sanchez-Baracaldo, 2010;Sánchez-Baracaldo, 2015).…”