Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

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Science  28 Sep 2012:
Vol. 337, Issue 6102, pp. 1661-1665
DOI: 10.1126/science.1224041

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  1. Fig. 1

    Maximum likelihood 16S rRNA gene phylogenetic tree showing the placement of the uncultivated phyla recovered by EMIRGE (bold text). The closest representative to each EMIRGE sequence is denoted in parentheses (clone library or Silva accession number). The bar chart indicates the relative abundance of each sequence in the A, C, and D samples (maximum is 11%), with bootstrap support >80 noted. The 16S rRNA tree from all organisms and details are provided in fig. S2 and (7).

  2. Fig. 2

    Detection of alternative coding. (A) Histogram of average open reading frame (ORF) length achieved with ORF predictions using the standard bacterial genetic code. The peak with unusually small gene lengths is associated with ORFs that should have been predicted using code 4. (B) Peptides identified by proteomics were mapped onto proteins with code 4 predictions to verify that UGA codes for tryptophan (W).

  3. Fig. 3

    Metabolic models with detected genes (white box), genes with proteins confirmed by proteomics (green box), and genes missing from pathways (red box). For full gene information for box numbers see table S4. (A) OD1-i may produce acetate, ethanol, lactate, and hydrogen as fermentation end products. Hydrogen could be generated via NiFe type 4 membrane-bound hydrogenases (red outline) and cytoplasmic type 3b sulfhydrogenase (yellow outline). The expanded view shows type 4 hydrogenase-generated PMF and ATP synthesis (red line) and possible hydrogen cycling to type 3b hydrogenases (black dashed line). FDH, formate dehydrogenase; Fdox and Fdred, oxidized and reduced ferredoxin, respectively; G3P, glyceraldehyde-3-phosphate; MHC, multiheme c-type cytochrome; NADP+, nicotinamide adenine dinucleotide phosphate; Q/QH, ubiquinone–reduced ubiquinone; rhodobacter nitrogen-fixing (RNF) complex. (B) PERs produce acetate and formate from pyruvate (no formate dehydrogenases or hydrogenases were identified). PER genomes lack detectable mechanisms for recovering additional energy via membrane-potential coupled to ATP synthase but may use RuBisCO, analogous to Archaea, for salvaging ATP by shunting nucleotides through central-carbon metabolism. PEP, phosphoenolpyruvate.

  4. Fig. 4

    Maximum likelihood phylogenetic tree constructed for the RuBisCO large subunit. Together, the new sequences resolve a novel intermediate II/III RuBisCO lineage (black). Bootstrap values >80 are shown. The position of the node for the II/III hybrid clade is strongly supported, as it is present in >92% of all trees examined during bootstrap analysis in this and prior analyses (>100%) (23).