Supplementary Figure 1. Covariation between the relative abundances (% of total sequences) of OTUs categorized as lognormal or logistic. Due to their very similar dynamics, the two groups were considered together as ‘logistic’ for subsequent analyses (see Methods and Results).

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*# Supplementary Figure 2. OTU accumulation curve of the 108 surface stations sampled

"# Supplementary Figure 3. Non-metric multidimensional scaling (NMDS) plots based on Bray–Curtis distances of 16S-rDNA based taxonomic composition of the 108 surface free-living prokaryotic communities sampled during the Malaspina expedition. Samples are color-coded by ocean (a), cruise leg (b), in situ water temperature (c) and dissolved oxygen concentration (d).

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9# Supplementary Figure 4. Variation in the environmental breadth of OTUs within each of the three SPAD categories. Environmental breadth was calculated as the maximum range in (a) temperature, (b) salinity, (c) dissolved oxygen or (d) chlorophyll concentration occupied by each individual OTU, independently of its abundance. The dotted line indicates the maximum variation shown by each particular variable considering the whole surface dataset. Note that normal-like OTUs are present across the whole environmental gradients, whereas most logistic OTUs appear at more restricted conditions.

:# Supplementary Figure 5. 16S-rDNA based taxonomic composition of the OTUs within each SpAD category across the seven legs sampled during the Malaspina Expedition. See map in Figure 1 for location of each transect. The classification was performed at the phylum level in most cases, but the Phyla Proteobacteria (Prot), Bacteroidetes (Bact) and Planctomycetes (Planct) were split into classes or order level, and Cyanobacteria (Cya) into genus level.

Normal-like OTUs Bimodal OTUs Logis6c OTUs

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[# Supplementary Figure 6. Changes in the taxonomic composition and abundance (number of reads) of logistic (rare) taxa that became abundant (>1% of the local relative abundance) at least in one occasion (see Results for details) for legs 2, 4 and 5, which showed the highest proportions of logistic taxa (see Figure 3d). Note that very few OTUs (7, 19 and 12, respectively) were responsible for the observed increases in the contribution of logistic OTUs to total sequences. The classification was performed at the phylum level in some cases, but the Phyla Proteobacteria (Prot), Bacteroidetes (Bact) and Planctomycetes (Planct) were split into classes or order level, and Cyanobacteria (Cya) into genus level.

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s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 Supplementary Figure 9. Number of available NCBI genomes with 16S rRNA gene sequences ≥ 99% similar to individual normal-like OTU sequences. Each bar refers to an individual OTU whose taxonomic affiliation is indicated in the below the X axis. Note that of the 68 normal-like OTUs, only 24 matched publicly available genomes.

Cyanobacterial Non-cyanobacterial

AEGEAN-169_marine_group Prochl Syn SAR11 Sulfitobacter Erythrobacter

'# Supplementary Table 1. Taxonomic identity of the bacterial OTUs that were categorized as ‘normal -like’ after each of the analyses shown in Figure 6 using datasets differing in potential niche heterogeneity. The last column indicates the figure panel (i.e., the particular analysis) where each normal -like OTU was identified . Shaded values indicate those OTUs that were categorized as ‘normal -like’ in more than one case.

Phylum Class Order Family Genus Normal -like in: OTU_49 Bacteroidetes Cytophagia Cytophagales Flammeovirgaceae Marinoscillum Fig 6b OTU_68 Bacteroidetes Flavobacteriia Flavobacteriales Flavobacteriaceae NS4_marine_group Fig 6b,c OTU_29 Bacteroidetes Flavobacteriia Flavobacteriales Flavobacteriaceae NS5_marine_group Fig 6b OTU_52 Bacteroidetes Flavobacteriia Flavobacteriales NS9_marine_group uncultured_bacterium Fig 6b OTU_1 Cyanobacteria Cyanobacteria SubsectionI FamilyI Prochlorococcus Fig 6b OTU_3 Cyanobacteria Cyanobacteria SubsectionI FamilyI Prochlorococcus Fig 6b,c OTU_82 Cyanobacteria Cyanobacteria SubsectionI FamilyI Prochlorococcus Fig 6b,c OTU_17300 Cyanobacteria Cyanobacteria SubsectionI FamilyI Synechococcus Fig 6b,c OTU_23 Proteobacteria Alphaproteobacteria Rhodobacterales Rhodobacteraceae uncultured Fig 6b,c OTU_24 Proteobacteria Alphaproteobacteria Rhodobacterales Rhodobacteraceae uncultured Fig 6b,c OTU_33 Proteobacteria Alphaproteobacteria Rhodobacterales Rhodobacteraceae uncultured Fig 6b OTU_26 Proteobacteria Alphaproteobacteria Rickettsiales SAR116_clade uncultured_marine_bacterium Fig 6b,c OTU_5 Proteobacteria Alphaproteobacteria SAR11_clade Surface_1 marine_metagenome Fig 6c OTU_6669 Proteobacteria Alphaproteobacteria SAR11_clade Surface_1 marine_metagenome Fig 6b,c OTU_17367 Proteobacteria Alphaproteobacteria SAR11_clade Surface_1 uncultured_marine_bacterium Fig. 6c OTU_112 Proteobacteria Alphaproteobacteria SAR11_clade Surface_1 uncultured_SAR11_cluster_alpha_proteobacterium Fig. 6c OTU_13131 Proteobacteria Alphaproteobacteria SAR11_clade Surface_1 unidentified_marine_bacterioplankton Fig. 6c OTU_19 Proteobacteria Alphaproteobacteria SAR11_clade Surface_1 unidentified_marine_bacterioplankton Fig 6b,c OTU_21730 Proteobacteria Alphaproteobacteria SAR11_clade Surface_1 unidentified_marine_bacterioplankton Fig. 6c OTU_89 Proteobacteria Alphaproteobacteria SAR11_clade Surface_1 unidentified_marine_bacterioplankton Fig 6b,c OTU_21 Proteobacteria Alphaproteobacteria SAR11_clade Surface_2 unidentified _marine_bacterioplankton Fig 6b,c OTU_55 Proteobacteria Alphaproteobacteria SAR11_clade Surface_4 uncultured_bacterium Fig. 6c OTU_13 Proteobacteria Alphaproteobacteria Sphingomonadales Erythrobacteraceae Erythrobacter Fig 6b,d OTU_14 Proteobacteria Alphaproteobacteria Sphingomonadales Erythrobacteraceae Erythrobacter Fig. 6d OTU_56 Proteobacteria Gammaproteobacteria Oceanospirillales SAR86_clade marine_metagenome Fig 6b,c OTU_67 Proteobacteria Gammaproteobacteria Oceanospirillales SAR86_clade unidentified_marine_bacterioplankton Fig 6b,c Supplementary Table 1. Taxonomic identity of the bacterial OTUs that were categorized as ‘normal -like’ after each of the analyses shown in Figure 6 using datasets differing in potential niche heterogeneity. The last column indicates the figure panel (i.e., the particular analysis) where each normal -like OTU was identified . Shaded values indicate those OTUs that were categorized as ‘normal -like’ in more than one case.

Phylum Class Order Family Genus Normal -like in: OTU_49 Bacteroidetes Cytophagia Cytophagales Flammeovirgaceae Marinoscillum Fig 6b OTU_68 Bacteroidetes Flavobacteriia Flavobacteriales Flavobacteriaceae NS4_marine_group Fig 6b,c OTU_29 Bacteroidetes Flavobacteriia Flavobacteriales Flavobacteriaceae NS5_marine_group Fig 6b OTU_52 Bacteroidetes Flavobacteriia Flavobacteriales NS9_marine_group uncultured_bacterium Fig 6b OTU_1 Cyanobacteria Cyanobacteria SubsectionI FamilyI Prochlorococcus Fig 6b OTU_3 Cyanobacteria Cyanobacteria SubsectionI FamilyI Prochlorococcus Fig 6b,c OTU_82 Cyanobacteria Cyanobacteria SubsectionI FamilyI Prochlorococcus Fig 6b,c OTU_17300 Cyanobacteria Cyanobacteria SubsectionI FamilyI Synechococcus Fig 6b,c OTU_23 Proteobacteria Alphaproteobacteria Rhodobacterales Rhodobacteraceae uncultured Fig 6b,c OTU_24 Proteobacteria Alphaproteobacteria Rhodobacterales Rhodobacteraceae uncultured Fig 6b,c OTU_33 Proteobacteria Alphaproteobacteria Rhodobacterales Rhodobacteraceae uncultured Fig 6b OTU_26 Proteobacteria Alphaproteobacteria Rickettsiales SAR116_clade uncultured_marine_bacterium Fig 6b,c OTU_5 Proteobacteria Alphaproteobacteria SAR11_clade Surface_1 marine_metagenome Fig 6c OTU_6669 Proteobacteria Alphaproteobacteria SAR11_clade Surface_1 marine_metagenome Fig 6b,c OTU_17367 Proteobacteria Alphaproteobacteria SAR11_clade Surface_1 uncultured_marine_bacterium Fig. 6c OTU_112 Proteobacteria Alphaproteobacteria SAR11_clade Surface_1 uncultured_SAR11_cluster_alpha_proteobacterium Fig. 6c OTU_13131 Proteobacteria Alphaproteobacteria SAR11_clade Surface_1 unidentified_marine_bacterioplankton Fig. 6c OTU_19 Proteobacteria Alphaproteobacteria SAR11_clade Surface_1 unidentified_marine_bacterioplankton Fig 6b,c OTU_21730 Proteobacteria Alphaproteobacteria SAR11_clade Surface_1 unidentified_marine_bacterioplankton Fig. 6c OTU_89 Proteobacteria Alphaproteobacteria SAR11_clade Surface_1 unidentified_marine_bacterioplankton Fig 6b,c OTU_21 Proteobacteria Alphaproteobacteria SAR11_clade Surface_2 unidentified _marine_bacterioplankton Fig 6b,c OTU_55 Proteobacteria Alphaproteobacteria SAR11_clade Surface_4 uncultured_bacterium Fig. 6c OTU_13 Proteobacteria Alphaproteobacteria Sphingomonadales Erythrobacteraceae Erythrobacter Fig 6b,d OTU_14 Proteobacteria Alphaproteobacteria Sphingomonadales Erythrobacteraceae Erythrobacter Fig. 6d OTU_56 Proteobacteria Gammaproteobacteria Oceanospirillales SAR86_clade marine_metagenome Fig 6b,c OTU_67 Proteobacteria Gammaproteobacteria Oceanospirillales SAR86_clade unidentified_marine_bacterioplankton Fig 6b,c