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Figure S1-2

Additional file 2: Supplementary Figure S1. Geographic location of the 17 freshwater lakes sampled in this study. Trophic state of each lake is marked by a different color. Supplementary Figure S2. Randomized Axelerated Maximum Likelihood (RAxML) tree of 16S rRNA genes of different classes of Patescibacteria. The tree was split in two subtrees with collapsed branches for better visibility. The 16S rRNA gene sequences recovered from MAGs generated in this study are shown in bold. Targets for eight newly designed oligonucleotide probes for CARD-FISH are indicated with different colors. Bootstrap values (100 bootstraps) are indicated as differently sized circles, the tree scale is given on top. Asterisks indicate sequences not targeted by probes pgri-99 and ABY1b-1343, # indicate one outgroup hit of probe adl2-134. Supplementary Figure S3. Abundance (%) of 16S rRNA gene sequences affiliated to different classes in CPR. Samples that had < 1% of total abundance in any CPR class were not added to the plot. Supplementary Figure S4. Epifluorescence microscopy images of ABY1 class members using the ABY1a-193 probe. Panels labeled with a. are the overlap of the probe (green), DAPI (blue) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S5. Epifluorescence microscopy images of ABY1 class members using the ABY1b-1343 probe. Panels labeled with a. are the overlap of the probe (green), DAPI (blue) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S6. Epifluorescence microscopy images of Paceibacteria class members using the Adl1-132 probe. Panels labeled with a. are the overlap of the probe (green), DAPI (blue) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S7A. Epifluorescence microscopy images of Paceibacteria class members using the Adl1-134 probe. Panels labeled with a. are the overlap of the probe (green), DAPI (blue) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S7B. Epifluorescence microscopy images of Paceibacteria class members using the Adl1-134 probe. Panels labeled with a. are the overlap of the probe (green), DAPI (blue) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S8. Epifluorescence microscopy images of Gracilibacteria class members using the Pgri-99 probe. Panels labeled with a. are the overlap of the probe (green), DAPI (blue) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S9. Epifluorescence microscopy images of Gracilibacteria class members using the Pgri-124 probe. Panels labeled with a. are the overlap of the probe (green), DAPI (blue) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S10. Epifluorescence microscopy images of Saccharimonadia class members using the SacA-77 probe. Panels labeled with a. are the overlap of the probe (green), DAPI (blue) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S11. Epifluorescence microscopy images of Paceibacteria class members using the ZE-1429 probe. Panels labeled with a. are the overlap of the probe (green), DAPI (blue) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S12. Positive control for the Saccharibacteria class members performed using the SacA-77 and EUB I-III probes. Panels labeled with a. are the overlap of DAPI (blue), the Sac-77 probe (green), the EUB I-III probe (orange) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S13. Positive control for the Gracilibacteria class members performed using the Pgri-124 and EUB I-III probes. Panels labeled with a. are the overlap of DAPI (blue), the Pgri-124 probe (green), the EUB I-III probe (orange) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S14a. Negative controls for filters used for FISH from different lakes. Panels labeled with a. are the overlap of DAPI (blue), the NON338 probe (green) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S14b. Negative controls for filters used for FISH from different lakes. Panels labeled with a. are the overlap of DAPI (blue), the NON338 probe (green) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S15a. Negative controls for filters used for FISH from different lakes. Panels labeled with a. are the overlap of DAPI (blue), CARD amplification (green) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S15b. Negative controls for filters used for FISH from different lakes. Panels labeled with a. are the overlap of DAPI (blue), CARD amplification (green) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S16. Boxplots for the length and width of individual CPR cells observed with the 8 FISH probed designed and tested in this study. L – Length, W – Width. Supplementary Figure S17. Percentage of genes in each KEGG module encoded by CPRs, free-living freshwater bacteria and symbionts. All representative CPR genomes from GTDB (>40% completeness

A combinatorial Gray code for a set of combinatorial objects is a sequence of all combinatorial objects in the set so that each object is derived from the preceding object by changing a small part. In this paper we design a Gray code for ordered trees with n vertices such that each ordered tree is derived from the preceding ordered tree by removing a leaf then appending a leaf elsewhere. Thus the change is just remove-and-append a leaf, which is the minimum., Comment: 14 pages

Additional file 1. Identification of phage defense mechanisms in CPRs.

A random geometric graph (RGG) is defined by placing n points uniformly at random in [0,n 1/d ] d , and joining two points by an edge whenever their Euclidean distance is at most some fixed r. We assume that r is larger than the critical value for the emergence of a connected component with Ω(n) nodes. We show that, with high probability (w.h.p.), for any two connected nodes with a Euclidean distance of $\omega (\frac{\log n}{r^{d-1}} )$ , their graph distance is only a constant factor larger than their Euclidean distance. This implies that the diameter of the largest connected component is Θ(n 1/d /r) w.h.p. We also prove that the condition on the Euclidean distance above is essentially tight. We also analyze the following randomized broadcast algorithm on RGGs. At the beginning, only one node from the largest connected component of the RGG is informed. Then, in each round, each informed node chooses a neighbor independently and uniformly at random and informs it. We prove that w.h.p. this algorithm informs every node in the largest connected component of an RGG within Θ(n 1/d /r+logn) rounds.