Table S1. Metagenomic library statistics
Table S2. Bacterial SSU rRNA amplicon library statistics
Table S3. Environmental measurements used for 25 m analyses
Table S4. Environmental measurements used for 500 m analyses
Table S5. Comparison of 25 m and 500 m shared and unique OTUs.
To calculate relative abundances all amplicon reads from samples within the same
depth were combined. * also in previous category.
Table S6. Number of reads in each 25 m metagenomic dataset assigned to each
taxonomic group
Table S7. Number of reads in each 500 m metagenomic dataset assigned to each
taxonomic group
Table S8a. Correlations between microbial community alpha diversity and
environmental properties at 25 m.
Legend. All diversity indices were resampled using rarefaction. Read depths as
follows: All SSU rRNA reads from metagenomic data: 892 Amplicon reads: 9661
Protein-coding reads from metagenomic data: 476661. Symbols: § averaged over
previous 4 days ¶ averaged over previous 30 days *significant below P< 0.1 after
applying the Benjamini-Hochberg procedure to account for multiple tests (n=24
hours of day light not included due to similarity with shortwave radiation).
Table S8b. Correlations between microbial community alpha diversity and pigments
(organism containing pigments) at 25 m.
Legend. All diversity indices were resampled using rarefaction. Read depths as
follows: All SSU rRNA reads from metagenomic data: 892 Amplicon reads: 9661
Protein-coding reads from metagenomic data: 476661. Symbols: *significant below
P< 0.1 after applying the Benjamini-Hochberg Procedure to account for multiple
tests (n=6).
Table S9. Mantel tests comparing microbial community beta diversity and
environmental properties at 25 m.
Legend. All diversity indices were resampled using rarefaction. Read depths as
follows: All SSU rRNA reads from metagenomic data: 892 Amplicon reads: 9661
Protein-coding reads from metagenomic data: 476661. The Spearman correlation
coefficient was used for mantel tests. Symbols: § averaged over previous 4 days ¶
averaged over previous 30 days *significant below P< 0.1 after applying the
Benjamini-Hochberg Procedure to account for multiple tests (n=24 hours of day
light not included due to similarity with shortwave radiation).
Table S10. Correlations between microbial community alpha diversity and
environmental properties at 500 m.
Legend. All diversity indices were resampled using rarefaction. Read depths as
follows: All SSU rRNA reads from metagenomic data: 1475^ Amplicon reads: 6909
Protein-coding reads from metagenomic data: 930072^. Symbols: ^HOT194_500m
excluded due to low sequencing depth § averaged over previous 4 days ¶ averaged
over previous 30 days *significant below P< 0.1 after applying the BenjaminiHochberg procedure to account for multiple tests (n=12).
Table S11. Mantel tests comparing microbial community beta diversity and
environmental properties at 500 m.
Legend. All diversity indices were resampled using rarefaction. Read depths as
follows: All SSU rRNA reads from metagenomic data: 1475^ Amplicon reads: 6909
Protein-coding reads from metagenomic data: 930072^. The Spearman correlation
coefficient was used for mantel tests. Symbols: ^HOT194_500m excluded due to
low sequencing depth § averaged over previous 4 days ¶ averaged over previous 30
days *significant below P< 0.1 after applying the Benjamini-Hochberg procedure to
account for multiple tests (n=12).
Table S12. Correlations between OTU module eigengenes and the most strongly
correlated environmental measurements at 25 m.
Legend. Modules were calculated using the 193 most abundant OTUs in the
amplicon datasets (see methods). Both positively and negatively correlated OTUs
were included in the same module. All environmental parameters that significantly
correlated with ME1 and ME2 are shown. For modules 3-6 only the environmental
parameter with the strongest correlation is shown as no environmental parameters
significantly correlated with these modules. P-values were adjusted using the
Benjamini-Hochberg procedure to account for multiple tests (n=144 24
environmental measurements (as in table S8a) x 6 modules.) Symbols: §averaged
over previous 4 days ¶ averaged over previous 30 days.
Table S13. Correlations between protein ortholog module eigengenes and the most
strongly correlated environmental measurements at 25 m.
Legend. Modules were calculated for protein orthologs from abundant taxonomic
groups in the metagenomic datasets (see methods). Both positively and negatively
correlated OTUs were included in the same module. All environmental parameters
that significantly correlated with modules are shown plus the environmental
parameter with the strongest correlation if no parameter significantly correlated. Pvalues were adjusted using the Benjamini-Hochberg procedure to account for
multiple tests (n=576 24 environmental measurements (as in table S8a) x 24
modules.) Symbols: ¶ averaged over previous 30 days.
Table S14. Correlations between module eigengenes and the most strongly
correlated environmental measurements at 500 m.
Modules were calculated using the 330 most abundant OTUs in the amplicon
datasets (see methods). Both positively and negatively correlated OTUs were
included in the same module. P-values were adjusted using the BenjaminiHochberg procedure to account for multiple tests (n=408 12 environmental
measurements (as in table S10) x 34 modules. Symbols: § as measured at ocean
surface and averaged over previous 4 days ¶ as measured at ocean surface and
averaged over previous 30 days.