Fig. 1
From: Diverse hydrogen production and consumption pathways influence methane production in ruminants
Heatmap showing distribution of enzymes mediating H2 production and H2 consumption in orders of rumen microorganisms. Results are shown based on screens of the 501 genomes of cultured rumen bacteria and archaea (410 from the Hungate collection plus 91 other genomes). Partial hydrogenase sequences were also retrieved and classified from four rumen ciliates and two rumen fungi. The left-hand side of the heatmap shows the distribution of the catalytic subunits of enzymes that catalyse H2 oxidation and production. These are divided into fermentative hydrogenases (H2-producing; group A1, A2, B FeFe-hydrogenases), bifurcating hydrogenases (bidirectional; group A3, A4 FeFe-hydrogenases), respiratory hydrogenases (H2-uptake; group 1b, 1c, 1d, 1f, 1i, 2d NiFe-hydrogenases), methanogenic hydrogenases (H2-uptake; group 1k, 3a, 3c, 4h, 4i NiFe-hydrogenases, Fe-hydrogenases), energy-converting hydrogenases (bidirectional; group 4a, 4c, 4e, 4f, 4g NiFe-hydrogenases), sensory hydrogenases (group C FeFe-hydrogenases) and nitrogenases (H2-producing; NifH). The right-hand side shows the distribution of the catalytic subunits of key reductases in H2 consumption pathways. They are genes for methanogenesis (McrA, methyl-CoM reductase), acetogenesis (AcsB, acetyl-CoA synthase), sulfate reduction (DsrA, dissimilatory sulfite reductase; AprA, adenylylsulfate reductase; AsrA, alternative sulfite reductase), fumarate reduction (FrdA, fumarate reductase), nitrate ammonification (NarG, dissimilatory nitrate reductase; NapA, periplasmic nitrate reductase; NrfA, ammonia-forming nitrite reductase), dimethyl sulfoxide and trimethylamine N-oxide reduction (DmsA, DMSO and TMAO reductase) and aerobic respiration (CydA, cytochrome bd oxidase). Only hydrogenase-encoding orders are shown. Table S2 shows the distribution of these enzymes by genome, Figure S1 depicts hydrogenase subgroup distribution by class, and Table S1 lists the FASTA sequences of the retrieved reads
