Genomic and proteomic characterization of "Candidatus Nitrosopelagicus brevis": an ammonia-oxidizing archaeon from the open ocean

Abstract

Thaumarchaeota are among the most abundant microbial cells in the ocean, but difficulty in cultivating marine Thaumarchaeota has hindered investigation into the physiological and evolutionary basis of their success. We report here a closed genome assembled from a highly enriched culture of the ammonia-oxidizing pelagic thaumarchaeon CN25, originating from the open ocean. The CN25 genome exhibits strong evidence of genome streamlining, including a 1.23-Mbp genome, a high coding density, and a low number of paralogous genes. Proteomic analysis recovered nearly 70% of the predicted proteins encoded by the genome, demonstrating that a high fraction of the genome is translated. In contrast to other minimal marine microbes that acquire, rather than synthesize, cofactors, CN25 encodes and expresses near-complete biosynthetic pathways for multiple vitamins. Metagenomic fragment recruitment indicated the presence of DNA sequences >90% identical to the CN25 genome throughout the oligotrophic ocean. We propose the provisional name "Candidatus Nitrosopelagicus brevis" str. CN25 for this minimalist marine thaumarchaeon and suggest it as a potential model system for understanding archaeal adaptation to the open ocean.

Keywords: archaea; genome streamlining; marine metagenomics; nitrification.

Fig. 1.

The 1.23-Mbp genome and proteome of Ca. N. brevis str. CN25. The outermost ring is the position along the genome in thousands of nucleotide base pairs and annotations of the 15 most abundant proteins in the proteome, plus ammonia monooxygenase subunit a (amoA). The second ring (histogram) is the relative abundance of protein spectral counts detected in a global proteome. The third and fourth rings (blue and cyan) indicate predicted ORFs on the plus and minus strands, respectively. The fifth ring (red) indicates the location of putative genomic island regions (IR). The sixth or innermost ring (green) is GC anomaly based on a 2,000-bp moving average. Key to protein annotations: 1. conserved domain protein (T478_1299); 2. ATP synthase (T478_1372); 3. conserved domain protein (T478_1300); 4. translation elongation factor EF-1 (T478_0861); 5. AAA family ATPase (T478_0115); 6. RNA polymerase subunit A (rpoA, T478_0275); 7. RNA polymerase subunit B (rpoB, T478_0274); 8. alcohol dehydrogenase (T478_1333); 9. putative glutamate dehydrogenase (T478_1059); 10. putative malate dehydrogenase (T478_0268); 11. conserved hypothetical protein (T478_0572); 12. oxidoreductase, short chain dehydrogenase (T478_0869); 13. ATP synthase alpha/beta chain T478_1371); 14. flavodoxin (T478_0486); 15. putative acetyl-CoA carboxylase (T478_1175). Relative abundance of all proteins identified in the global proteome is provided as an SI Appendix, Dataset S1.

Fig. 2.

Sequences highly similar to Ca. N. brevis dominate marine metagenomes. Competitive metagenomic fragment recruitment between the Ca. N. brevis genome assembly (Left) and N. maritimus (Right) at >90% nucleotide identity in marine metagenomic datasets from the Hawai’i Ocean Time-series (ALOHA), Bermuda Atlantic Time-series Station (BATS), and the Global Ocean Sampling Expedition (GOS). Regions highlighted in red indicate genomic IR in Ca. N. brevis.

Fig. 3.

(A) Combined metagenomic fragment recruitment to the Ca. N. brevis and N. maritimus genomes at three different nucleotide identity cutoffs. Bins are exclusive; that is, once a read is recruited at 90% identity, it is removed from the analysis and is thus not counted twice. Recruitment to ribosomal RNA genes has been excluded. (B) Detailed results of competitive fragment recruitment to Ca. N. brevis and N. maritimus in the 70–89% identity band from A indicating the fraction of total reads recruited to each genome. Metagenomic dataset numbers refer to the following accession numbers (preceeded by CAM_) in the CAMERA database: 1, PROJ_AntarcticaAquatic; 2, PROJ_BATS; 3, PROJ_Bacterioplankton; 4, PROJ_BotanyBay; 5, PROJ_HOT; 6, PROJ_LineIsland; 7, PROJ_MontereyBay; 8, PROJ_PML; 9, PROJ_PeruMarginSediment; 10, PROJ_SapeloIsland; 11, PROJ_SargassoSea; 12, PROJ_WesternChannelOMM; 13, P0000712; 14, P0000715; 15, P0000719; 16, P0000828; and 17, P0001028. Details of each metagenomic dataset are provided in SI Appendix, Table S8.