Article Figures & Data
Figures
- FIG 1
Median relative abundance of phyla/proteobacterial classes in freshwater and marine samples collected from surface (a) and deep (b) waters. The deepest hypolimnion (below thermocline) sample collected from stratified lakes and marine samples collected at depths >75m were classified as “deep” samples. Diagonal lines indicate a 1:1 relationship.
- FIG 2
Species accumulation curves for taxonomic groups that contain shared marine and freshwater MED nodes as the number of freshwater sites included in the analysis increases (a) and as the number of marine sites included in the analysis increases (b). The percentage of sequences shared between habitats with all sites analyzed is included to the right of each curve; the total number of MED nodes within each group in freshwater and marine habitats, respectively, is indicated in parentheses.
- FIG 3
Maximum sequence identity threshold (i.e., finest-scale resolution) at which pairs of marine and freshwater samples share common taxa. Box plots indicate the median, quartiles, and range of values observed for all marine-freshwater sample pairs. Colored boxes indicate phyla/proteobacterial classes that contain 5 or more shared MED nodes while gray boxes indicate groups that contain 1 to 3 shared MED nodes. The heatmap to the right illustrates the number of freshwater (F) and marine (M) samples containing representatives of each phylum/proteobacterial class. *, Actinobacteria cutoff values were calculated with a preclustered data set (see Fig. S5 for comparison of all groups using a preclustered data set).
- FIG 4
Observations of non-LD12 SAR11. (a) 16S rRNA V4 region gene tree constructed using representative sequences from each SAR11 node. The first ring indicates whether nodes were found only in marine (blue) or freshwater samples (green) while the second ring indicates nodes that are shared across habitat types (orange). (b) Number of non-LD12 SAR11 clade sequences detected at four stations (MI18M, MI27M, MI41M, ON33M) and three depths (SRF, surface; DCL, deep chlorophyll maximum layer; BOT, near-bottom) on Lakes Michigan and Ontario.
- FIG 5
Metagenomic evidence for non-LD12 SAR11 in the Laurentian Great Lakes. (a) Percentage of classified reads identified as LD12 (green) in an open ocean sample (Marine), compared to marine (i.e., non-LD12) SAR11 (blue) in each of the five Laurentian Great Lakes (SU, Superior; MI, Michigan; HU, Huron; ER, Erie; ON, Ontario). Ridge plots present the distribution of identified reads across all protein clusters with greater than 100 reads classified as SAR11 or LD12 at a likelihood value of 0.95. (b) Neighbor-joining consensus tree of 1.2-kb nucleotide sequences from the protein cluster identified as COG2609 (pyruvate dehydrogenase complex, dehydrogenase E1 component). Strain names are colored based on phylogenetic classification within the SAR11 clade: green, LD12 sequences from group IIIb; light blue, group IIIa, sister group to IIIb; medium blue, all other marine SAR11 clades included in the analysis (Ia, II); black, a contig assembled from the Lake Erie metagenome. Consensus support values (%) are indicated on branches.
Tables
- TABLE 1
Genera containing at least two shared MED nodes
Phylum/class Order Family Genusb No. of
shared
nodesActinobacteria Acidimicrobiales OM1_clade “Ca. Actinomarina” 2 Actinobacteria Acidimicrobiales Sva0996a Sva0996a 2 Actinobacteria Corynebacteriales Mycobacteriaceae Mycobacterium 2 Actinobacteria Micrococcales Microbacteriaceae “Ca. Aquiluna” 4 Actinobacteria PeM15 PeM15 PeM15 4 Bacteroidetes Flavobacteriales Cryomorphaceae Fluviicola 5 Bacteroidetes Sphingobacteriales Chitinophagaceae Sediminibacterium 2 Bacteroidetes Sphingobacteriales NS11-12a NS11-12a 3 Cyanobacteria Subsection I Family I Synechococcus 3 Marinimicrobia SAR406 clade SAR406 clade SAR406 clade 4 Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas 4 Alphaproteobacteria Rhizobiales Methylobacteriaceae Methylobacterium 3 Alphaproteobacteria Sphingomonadales Sphingomonadaceae Novosphingobium 2 Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingobium 3 Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas 3 Betaproteobacteria Burkholderiales Burkholderiaceae Ralstonia 2 Betaproteobacteria Burkholderiales Comamonadaceae Aquabacterium 2 Deltaproteobacteria SAR324 clade SAR324 clade SAR324 clade 3 Gammaproteobacteria Alteromonadales Alteromonadaceae Marinobacter 2 Gammaproteobacteria E01-9C-26a E01-9C-26a E01-9C-26a 2 Gammaproteobacteria Oceanospirillales Oceanospirillaceae Pseudohongiella 4 Gammaproteobacteria Oceanospirillales OM182 clade OM182 clade 2 Gammaproteobacteria Oceanospirillales SAR86 clade SAR86 clade 2 Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter 5 Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas 3 Gammaproteobacteria Vibrionales Vibrionaceae Vibrio 2 Euryarchaeota Thermoplasmatales Marine group II Marine group II 2 Thaumarchaeota Unknown order Unknown family “Ca. Nitrosopumilus” 2 - TABLE 2
16S rRNA v4 region sequencing data sets included in the meta-analysis
No. of samples Study system Depth(s) sampleda BioProject accession no.
(reference)Freshwater samples (45 total) 11 Four Laurentian Great Lakes Surface, DCL, deep This study 2 Glacier Lake, NY 6 m, 14 m PRJEB12903 1 JBL_J07_HES, Sweden Integrated PRJNA244610 (79) 1 Lake Keluke, China Surface PRJNA294836 (80) 1 Faselfad lakes, Austria Integrated PRJNA297573 (81) 14 Seven high-nutrient lakes, MI Surface, deep PRJNA304344 (82) 9 Five low-nutrient lakes, MI Surface, deep PRJNA304344 (82) 6 Three humic lakes, WI Integrated epi, integrated hypo PRJEB15148 (83) Marine samples (32 total) 1 Caribbean Sea Surface PRJEB10633 (28) 2 Coastal Red Sea (2 sites) Surface PRJNA279146 (54) 1 Drake Passage Surface PRJEB10633 (28) 12 Gulf of Mexico (3 sites) Surface, multiple depths PRJNA327040 (84) 1 Helgoland North Sea Surface PRJNA266669 (85) 1 Long Island Sound Surface PRJEB10633 (28) 2 North Pacific Surface, 100 m PRJEB10633 (28) 8 San Pedro Ocean Time Series (2 dates: April,
July 2013)Surface, multiple depths PRJEB10633 (28) 2 Sargasso Sea (2 sites) Surface, 200 m PRJEB10633 (28) 1 Tropical Western Atlantic Ocean 40 m PRJEB10633 (28) 1 Weddell Sea Surface PRJEB10633 (28) ↵a Abbreviations: DCL, deep chlorophyll layer; epi, epilimnion; hypo, hypolimnion.
- TABLE 3
SAR11 and LD12 genomes included in pangenomic analysis
Genome name SAR11 clade Classification GenBank accession no. Alphaproteobacterium HIMB114 IIIa SAR11 NZ_ADAC02000001 Alphaproteobacterium HIMB59 V SAR11 NC_018644 “Candidatus Pelagibacter” sp. HTCC7211 Ia.2 SAR11 ABVS00000000 “Candidatus Pelagibacter” sp. IMCC9063 IIIa SAR11 NC_015380 “Candidatus Pelagibacter ubique” HIMB058 II SAR11 ATTF01000000 “Candidatus Pelagibacter ubique” HIMB083 Ia.2 SAR11 AZAL00000000 “Candidatus Pelagibacter ubique” HTCC1062 Ia.1 SAR11 NC_007205 “Candidatus Pelagibacter ubique” HTCC8051 Ia.2 SAR11 AWZY00000000 SCGC AAA280-B11 IIIb LD12 AQUH00000000 SCGC AAA027-C06 IIIb LD12 AQPD00000000 SCGC AAA028-C07 IIIb LD12 ATTB01000000 SCGC AAA028-D10 IIIb LD12 AZOF00000000 SCGC AAA280-P20 IIIb LD12 AQUE00000000 SCGC AAA023-L09 IIIb LD12 ATTD01000000 SCGC AAA027-L15 IIIb LD12 AQUG00000000 SCGC AAA487-M09 IIIb LD12 ATTC00000000 SCGC AAA024-N17 IIIb LD12 AQZA00000000 SCGC AAA280-P20 IIIb LD12 AQUE00000000 “Candidatus Fonsibacter ubiquis” LSUCC0530 IIIb LD12 NZ_CP024034 Lake_Baikal_MAG Unknown SAR11 NSIJ01000001
FIG S1
Log10 fold change as a function of log10-transformed median relative abundances in each habitat plotted for orders (a, b) and families (c, d) in freshwater (a, c) and marine (b, d) systems. A solid gray line is plotted at a log10 fold change of 0, indicating that marine and freshwater median relative abundances are equal. Dotted gray lines are plotted at log10 fold changes of 1 and −1, which correspond to median abundance in one habitat being 10× higher than the median abundance in the other habitat. Download FIG S1, EPS file, 0.5 MB.
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FIG S2
Principal coordinate analysis of unweighted UniFrac distances between marine and freshwater assemblages characterized by 16S rRNA V4 gene sequences (a). The same ordination color coded by nutrient classification and labeling a group of outlier freshwater samples as those collected from dystrophic bog lakes (b). Download FIG S2, EPS file, 0.5 MB.
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FIG S3
Median unweighted UniFrac distances (bars indicate range) between pairs of freshwater and marine samples compared to unweighted UniFrac distance between combined freshwater and combined marine samples for each phylum and proteobacterial class (a). Unweighted UniFrac distances between combined freshwater and combined marine samples for orders (b) and families (c) within each phylum/class. Phyla, classes, orders, and families are included in the analysis if they occurred in at least 3 freshwater and 3 marine samples and contained at least 5 nodes. Download FIG S3, EPS file, 0.3 MB.
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TABLE S1
UniFrac distance calculated between marine and freshwater sequences for each family. Download Table S1, PDF file, 0.04 MB.
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FIG S4
Phylogenetic trees of select phyla and proteobacterial classes: (A) Alphaproteobacteria, (B) Actinobacteria, (C) Betaproteobacteria, (D) Chloroflexi. External ring colors indicate the habitats where MED nodes were detected in the data set: freshwater (green), marine (blue), both (orange). Notable clades are indicated by colored wedges. Download FIG S4, EPS file, 1.6 MB.
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FIG S5
Fraction of freshwater nodes shared with marine systems as a function of freshwater sites sampled (a) and fraction of marine nodes shared with freshwater systems as a function of marine sites sampled (b). Download FIG S5, EPS file, 0.4 MB.
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FIG S6
As sequence identity cutoff value increases, more taxa are shared between marine-freshwater sample pairs. Decrease in Jaccard index between marine-freshwater sample pairs (unshared taxa)/(shared taxa) with increasing sequence similarity cutoff values for Alphaproteobacteria and Verrucomicrobia (a). Example phylogenetic trees are shown for groups with high sequence similarity (b) and low sequence similarity (c) between marine (blue) and freshwater (green) samples. Download FIG S6, EPS file, 0.9 MB.
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FIG S7
Minimum sequence identity threshold (i.e., finest-scale resolution) at which pairs of marine and freshwater samples share common taxa. In contrast to Fig. 2, this analysis used a data set where sequences were preclustered to allow up to 2 base pair differences within a sequence group. Box plots indicate the median, quartiles, and range of values observed for all marine-freshwater sample pairs. A heat map illustrates the number of freshwater (F) and marine (M) samples containing representatives of each phylum/proteobacterial class. Download FIG S7, EPS file, 0.4 MB.
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FIG S8
Neighbor-joining consensus tree of nucleotide sequences (a) and nucleotide and protein alignment (b) of partial genes from the protein cluster identified as COG2609 (pyruvate dehydrogenase complex, dehydrogenase E1 component). Strain names are colored based on phylogenetic classification within the SAR11 clade: green, LD12 sequences from group IIIb; light blue, group IIIa, sister group to IIIb; blue, all other marine SAR11 clades included in the analysis (Ia, II); black, a sequence read from the Lake Erie metagenome identified by pplacer as marine SAR11. Consensus support values (%) are indicated on tree branches (a). Vertical boxes have been added to the alignment to indicate amino acids where the Great Lakes sequence contains shared characters with a subset of included strains. Download FIG S8, JPG file, 0.8 MB.
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TABLE S2
Additional information on 16S rRNA tag sequencing data sets compiled for the meta-analysis. Download Table S2, PDF file, 0.1 MB.
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