Figure 1. Summary diagram describing interrelationships between the ruminant forestomach, its resident microbial population and the host animal. After Hungate RE (1985) Anaerobic biotransformations of organic matter. In: Leadbetter ER and Poindexter JJ (eds) Bacteria in Nature, vol. 1, pp.39–95. New York: Plenum.

Figure 2. Phylogenetic placement of 16S rDNA sequences of rumen bacteria. An Aquifex pyrophilus sequence is used as the outgroup for rooting the tree. Numbers by each node are confidence levels generated from 1000 bootstrap trees. The scale bar is in fixed nucleotide substitutions per sequence position. Sequences retrieved from 16S rDNA clone libraries from uncultivated bacteria have the prefix RF or RC. Sequences of nonruminal bacteria (nonitalicized) are inserted into the tree to improve resolution.

Figure 3. Phylogenetic placement of 16S rDNA sequences from the rumen archaea. The sequence of the Crenarchaeota representative, Pyrolobus fumarius, is used as the outgroup for rooting the tree. Numbers by each node are confidence levels generated from 1000 bootstrap trees. The scale bar is in fixed nucleotide substitutions per sequence position. All rumen archaeal sequences available in databases are included in the tree to infer their phylogenetic positions. Other taxonomic groups of Euryarchaeota are represented by a single sequence from each order.

Figure 4. Phylogenetic placement of 18S rDNA sequences from the rumen ciliate protozoa. The Blepharisma americanum sequence is used as the outgroup for rooting the tree. Numbers above each node are confidence levels generated from 1000 bootstrap trees. The scale bar is in fixed nucleotide substitutions per sequence position. All rumen protozoan sequences available in databases are included in the tree to infer their positions in the ciliate phylogenetic tree. Also, the tree includes the three sequences of the free-living haptorian ciliates, close relatives of the rumen ciliates. All other classes are represented by a single sequence.

Figure 5. Phylogenetic placement of 18S rDNA sequences from the rumen fungi. The Dermocystidium sp. sequence which represents a protistan clade near the animal–fungal divergence is used as the outgroup for rooting the tree. Numbers by each node are confidence levels generated from 1000 bootstrap trees. The scale bar is in fixed nucleotide substitutions per sequence position. All rumen fungal sequences available in databases are included into the tree to infer their positions in the fungal phylogenetic tree. Other fungal sequences include the closest relatives, namely the Zygomycetes (Basidiobolus ranarum and Endogone pisiformis) and Chytridiomycetes (Spizellomyces acuminatus and Chytridium confervae).

Figure 6. Biochemical pathway of hydrogen-dependent reduction of carbon dioxide to methane. The  C₁ unit is sequentially modified, reduced and transferred bound to novel coenzymes which participate in the reaction cycle. The chemical structures of the unusual methanogenic coenzymes are located adjacent to the reaction steps in which they participate.