Supplementary Materials

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation

Maria G. Pachiadaki, Eva Sintes, Kristin Bergauer, Julia M. Brown, Nicholas R. Record, Brandon K. Swan, Mary Elizabeth Mathyer, Steven J. Hallam, Purificacion Lopez-Garcia, Yoshihiro Takaki, Takuro Nunoura, Tanja Woyke, Gerhard J. Herndl, Ramunas Stepanauskas

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Figs. S1 to S12
  • Captions for tables S1 to S8
  • References
Table S1
Relative abundance of the identified NOB by the 16S rRNA gene screening for each sorted sample.
Table S2
Assembly metrics and origin of each NOB SAG.
Table S3
Assembly metrics and origin of all SAGs.
Table S4
Location, metrics and accession information of the metagenomes used for this study.
Table S5
Glycolysis/glyconeogenesis genes of the NOB SAGs deposited in IMG.
Table S6
Expression values of NOB-affiliated proteins. Expression was calculated in a semi-quantitative manner, based on the NSAF (normalized spectral abundance factor) value.
Table S7
Relative expression of all ORFs of AG-538-K21 Nitrospinae SAG. Metatranscriptomic fragments that map in each ORF were normalized by ORF length and are presented as FPKM (Fragments per ORF Kilobase per Million Mapped fragments) values. For the analyses, we used a metatranscriptome from North Atlantic [50.86, -28.86; 2000m], and the publicly available metagenomes SRR1301208 (Eastern Mediterranean [36.51, 15.68; 2200m] in situ filtered and preserved), SRR3882725 (Gulf of Dulce [8.72, -83.42; 90m]), SRR3883063 (LineP transect, Subarctic Pacific Ocean, Station 20 [49.57, -138.67; 1000m]), SRR3883064 (LineP transect, Subarctic Pacific Ocean, Station 04 [48.65, -126.67; 500m]), SRR3883065 (LineP transect, Subarctic Pacific Ocean, Station 04 [48.65, -126.67; 1300m]), SRR3883066 (LineP transect, Subarctic Pacific Ocean, Station 20 [49.57, -138.67; 500m]) and SRR3883067 (LineP transect, Subarctic Pacific Ocean, Station 04 [48.65, -126.67; 1000m])
Table S8
Results of the incubation experiments. Mesopelagic samples for which complete data were recorded were used for the extrapolation (marked with an asterisk).