Fig. 8: Genome-based ecophysiological inferences.
From: Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis
a The upper panel displays Growth Rate Index (GRiD) values of the obtained 30 species clusters ((A) Ilumatobacteraceae sp.11 n = 9; (A) Ilumatobacteraceae sp.4 n = 10; (A) Ilumatobacteraceae sp.7 n = 11; (A) Nanopelagicaceae sp.2 n = 10; (A) Nanopelagicaceae sp.3 n = 11; (A) Nanopelagicaceae sp.5 n = 12; (A) Nanopelagicaceae sp.8 n = 9; (A) Nanopelagicales sp.1 n = 9; (A) Planktophila sp.10 n = 9; (A) Planktophila sp.6 n = 14; (A) Planktophila sp.9 n = 11; (B) Bacteroidia sp.1 n = 17; (B) Chitinophagaceae sp.2 n = 13; (B) Chitinophagaceae sp.3 n = 13; (B) Chitinophagaceae sp.4 n = 11; (C) Chloroflexota sp.1 n = 11; (C) Chloroflexota sp.2 n = 14; (C) Chloroflexota sp.3 n = 10; (P) Alphaprot. sp.1 n = 11; (P) Burkholderiaceae sp.4 n = 9; (P) Limnohabitans sp.6 n = 10; (P) Polynucleobacter sp.3 n = 19; (P) Polynucleobacter sp.5 n = 9; (P) Rhodoferax sp.2 n = 10; (Pl) Phycisphaerales sp.1 n = 17; (V) Lacunisphaera sp.3 n = 11; (V) Opitutaceae sp.2 n = 12; (V) Opitutales sp.4 n = 9; (V) Opitutales sp.5 n = 12; (V) Opitutus sp.1 n = 9), where species with large and small genomes are represented with orange and light blue colors, respectively. The grey line serves as an indicator for GRiD values surpassing 2. b The bottom panel shows codon usage bias of highly expressed genes (CUBHE). As for the upper panel, species containing large genomes are depicted in orange, while species containing small genomes are in light blue ((A) Ilumatobacteraceae sp.11 n = 9; (A) Ilumatobacteraceae sp.4 n = 10; (A) Ilumatobacteraceae sp.7 n = 11; (A) Nanopelagicaceae sp.2 n = 10; (A) Nanopelagicaceae sp.3 n = 11; (A) Nanopelagicaceae sp.5 n = 12; (A) Nanopelagicaceae sp.8 n = 9; (A) Nanopelagicales sp.1 n = 9; (A) Planktophila sp.10 n = 9; (A) Planktophila sp.6 n = 14; (A) Planktophila sp.9 n = 11; (B) Bacteroidia sp.1 n = 17; (B) Chitinophagaceae sp.2 n = 13; (B) Chitinophagaceae sp.3 n = 13; (B) Chitinophagaceae sp.4 n = 11; (C) Chloroflexota sp.1 n = 11; (C) Chloroflexota sp.2 n = 14; (C) Chloroflexota sp.3 n = 10; (P) Alphaprot. sp.1 n = 11; (P) Burkholderiaceae sp.4 n = 9; (P) Limnohabitans sp.6 n = 10; (P) Polynucleobacter sp.3 n = 19; (P) Polynucleobacter sp.5 n = 9; (P) Rhodoferax sp.2 n = 10; (Pl) Phycisphaerales sp.1 n = 17; (V) Lacunisphaera sp.3 n = 11; (V) Opitutaceae sp.2 n = 12; (V) Opitutales sp.4 n = 9; (V) Opitutales sp.5 n = 12; (V) Opitutus sp.1 n = 9). The grey threshold line is positioned at a CUBHE value of 0.6. The central line across the boxplots identifies the median, marking the dataset’s midpoint. The box itself demarcates the interquartile range, extending from the first quartile to the third quartile, encapsulating the central 50% of the data. The whiskers project from the box to the furthest data points not categorized as outliers and show the spread of the main body of the dataset. Raw data is provided as a Source Data file.
