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Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics

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Science  23 Oct 2015:
Vol. 350, Issue 6259, pp. 434-438
DOI: 10.1126/science.aac7745
  • Fig. 1 Phylogenetic trees showing the placement of the BA1, BA2, and E09 genomes in the archaeal phylum Bathyarchaeota.

    (A) Maximum-likelihood tree of 295 archaea, inferred from a concatenated alignment of 144 proteins and rooted with the DPANN (Diapherotrites Parvarchaeota Aenigmarchaeota Nanoarchaeota Nanohaloarchaeota) superphyla (27). Support values are shown with white (≥80%) and black (≥90%) circles and indicate the minimum support under nonparametric bootstrapping, gene jackknifing, and taxon jackknifing (supplementary materials). (B) Maximum-likelihood 16S rRNA gene tree showing the placement of bathyarchaeotal representatives relative to environmental sequences, including genes recovered from Coal Oil Point. Thaumarchaeota and Aigarchaeota 16S rRNA sequences from reference genomes were used as an outgroup. Bathyarchaeota (formerly MCG) groups are based on the classification in (9). Nonparametric support values are shown with white (≥80%) and black (≥90%) circles. Environmental context and genomes or National Center for Biotechnology Information accession numbers are given. Scale bars indicate expected number of substitutions per site.

  • Fig. 2 Key metabolic pathways in the BA1 and BA2 genomes.

    Genes and pathways found in both BA1 and BA2 (black), only found in BA1 (blue), only found in BA2 (orange), or missing from both genomes (gray) are indicated. Genes associated with the pathways highlighted in this figure are presented in tables S9 (BA1) and S10 (BA2). In the BA1 genome, +mtrH genes are adjacent to corrinoid proteins. A bathyarchaeotal contig containing mcrCD genes was identified in the metagenome, which probably belongs to the BA1 genome (supplementary text). EMP/ED, Embden-Meyerhof-Parnas/Entner–Doudoroff pathway; TCA, tricarboxcylic acid.

  • Fig. 3 Maximum-likelihood trees of McrA.

    (A) Placement of nearly full-length McrA protein sequences (≥400 amino acids) identified within the Surat Basin and Coal Oil Point metagenomes, in relation to 153 proteins obtained from GenBank. Lineages were collapsed (depicted as wedges) and labeled according to the lowest common ancestor of all taxa in the lineage. (B) Maximum-likelihood tree of nearly full-length and partial McrA sequences identified within the Surat Basin and Coal Oil Point metagenomes. Nonparametric support values are shown with white (≥80%) and black (≥90%) circles. Information about the Surat Basin wells is given in fig. S1. SBC, Santa Barbara Channel.

  • Table 1 Summary statistics of Bathyarchaeota genomes.
    BA1 (this study)BA2 (this study)E09 [from (13)
    Completeness*91.6%93.8%21.5%
    Contamination*2.8%3.7%0.0%
    Total length (base pairs)1,931,7141,455,689529,171
    GC content47.1%44.2%43.3%
    Number of scaffolds895787
    Number of contigs965887
    N50 of contigs32,67743,51913,721
    Number of coding sequences†24031761603
    Coding density80.8%83.6%81.7%
    Average coverage35.849.8no data
    Relative abundance‡0.92%1.03%no data

    *Based on lineage-specific marker sets determined with CheckM (28). †Inferred with Prodigal (29). ‡Estimated from the proportion of reads mapped to the genome.

    Supplementary Materials

    • Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics

      Paul N. Evans, Donovan H. Parks, Grayson L. Chadwick, Steven J. Robbins, Victoria J. Orphan, Suzanne D. Golding, Gene W. Tyson

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

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      • Materials and Methods
      • Supplementary Text
      • Figs. S1 to S14
      • Tables S1 to S13
      • Full Reference List

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