Aerobic Respiration
This term describes the metabolic processes that  generate ATP in association with a chemiosmotic process driven by a respiratory chain that depends on the use of oxygen as the ultimate electron acceptor. Water is the ultimate reduced end product and in animal cells these processes occur in mitochondria where ATP is made by oxidative phosphorylation. In mitochondria tricarboxylic acid cycle activity and fatty acid oxidation provide most of the reducing equivalents that fuel this process but reducing equivalents released by metabolite oxidation reactions in the cytosol can be shuttled into mitochondria to supply a small proportion of ATP needs. [See graphical overview]

Anaerobic
Organisms that do not take up molecular oxygen from the growth environment are described as living anaerobically.  Some species of microorganisms that live anaerobic lifestyles are only able to thrive under conditions where the oxygen tension of the growth environment is extremely low; they are killed by the intermediate reactive oxygen species generated when oxygen is partially reduced.  ATP production in anaerobic organisms is achieved either by fermentation or anaerobic respiration.

Anaerobic respiration
This term describes the metabolic processes in anaerobic life forms that generate ATP by a process that depends on a chemiosmotic mechanism where the ultimate electron acceptor is not oxygen.  The reduced product of the electron transport chain is therefore not water.  Methanogens in the reticulo-rumen use part of the carbon dioxide that they take up from the growth environment for this purpose; the product of its reduction is methane.  Other organisms can use fumarate reductase for ATP production by anaerobic respiration.  Fumarate is reduced by NADH to succinate in a redox cycle which achieves charge separation across a membrane and ATP synthesis is driven by dissipation of the energy inherent in the electrochemical ion gradient.

Autotrophy
Life forms that use carbon dioxide as the sole or principal carbon source for growth are described as autotrophs, and the use of carbon dioxide is called autotrophic carbon dioxide fixation.  In the reticulo-rumen the autotrophs are the methanogens and the homoacetogens and both of these groups of microorganisms use the acetyl CoA pathway of CO2 fixation. These, and other autotrophs that live in the dark, (and who do not carry out photosynthesis) may also be called chemoautotrophs just to make that point (organisms that carry out photosynthesis are phototrophs and most are autotrophic, hence the descriptor photoautotrohic). The term chemolithoautotrophy can also be applied to the methanogens and the homoacetogens. The "litho" component of the name conveys the idea that they derive reducing equivalents (for reductive biosynthesis and for ATP generation) from the oxidation of hydrogen which is an inorganic compound.

Cellulolytic
Many microorganisms produce cellulases which hydrolyse the glucose polymer cellulose, releasing glucose, obtaining thereby a substrate for chemoheterotrophic growth.  Some species secrete these enzymes into the extracellular medium and glucose released from the polymer can also be used as a growth substrate by species that do not make cellulases.  The cellulase producers are therefore of primary importance in the metabolic economy of the reticulo-rumen because they provide the growth substrate for other species that would not otherwise grow here.

Fermentation
This is used as a catch all term to describe anaerobic mechanisms in heterotrophic organisms in which reduced carbon substrates are oxidized to generate high phosphoryl group transfer substrates where ATP synthesis occurs by phosphoryl group transfer.  Kinases catalyse ATP production.  The yield of ATP per mole of reduced carbon substrate utilized is low because of the way redox balance is maintained in the organism.

Efficiency of food conversion
In this CAL the important issue in regard to food conversion efficiency relates to the production of propionate in the reticulo-rumen, the factors that affect it, and the utilization of propionate in the liver of the host ruminant. First you must remember that methanogens alter the pattern of fermentation of some organisms with which they live in syntrophic relationships so as to reduce succinate production. Succinate is a substrate for production of propionate in some other microorganisms. Propionate is an important gluconeogenic substrate in the liver of the host.  This means that a reduction in propionate production places increased demands on the use of amino acids for gluconeogenesis in the host liver and kidney cortex. This reduces the availability of amino acids for protein production in host tissues such as muscle.  From this it is clear that abundant growth of methanogens in the reticulo-rumen causes reduced food conversion efficiency in the host.  The effect can be clearly demonstrated in controlled feeding trials and is one of the reasons for Agribusiness interest in Methanogenesis.
 
Gram staining
Christian Gram invented a staining system for visualisation of bacteria using light microscopy  based on the differential retention of a crystal violet-iodine complex within the cell membrane. Gram positive bacteria retain the stain when washed with alcohol or acetone whereas Gram negative bacteria lose the stain as a result of the washing process. Gram negative bacteria are however able to be visualised with a pink counter stain called safranin.  The Gram staining characteristics of different bacterial species is still used by microbiologists but  the information obtained is merely descriptive; it can not be used to identify cell wall structure or composition nor can it be used to classify organisms by their metabolic characteristics.  For example some methanogens are gram positive and others are gram negative.
 
Heterotrophy
Heterotrophic organisms are contrasted with autotrophic life forms in that their carbon needs derive from organic nutrients which they take up from the growth environment.  These organic nutrients are also used as the source of reducing equivalents for reductive biosyntheses and, in addition, their oxidation provides the free energy needed to support a chemiosmotic mechanism which powers ATP synthesis.  Animals are heterotrophs, and most microorganisms are hetertrophs.

Homoacetogen
Acetate is the predominant end product of the chemoheterotrophic lifestyles of the mixed population of microorganisms that live in the reticulo-rumen.  Many species produce acetate but one group; the homoacetogens are particularly important because they can live both as chemoautotrophs (like methanogens) generating ATP in association with a chemiosmotic mechanism, and as chemoheterotrophs deriving ATP also by phosphoryl group transfer in a fermentation pathway.  They have only recently been identified in the reticulo-rumen and since they produce mainly acetate as the end product of their metabolism they are undoubtedly partly responsible for the predominance of acetate as an end product of microbial metabolism.

Methanogenesis
Methane production in the reticulo-rumen is due to the presence of methanogens which are in a group of microorganisms known as archaea. They used to be known as archebacteria but recent phylogenetic analysis has put them in a class separate from other prokaryotes. They are strict anaerobes and generate ATP by anaerobic respiration.  The methane they produce can not be used by the host ruminant, nor by other microorganisms, and it is lost from the reticulo-rumen by eructation. This represents loss of feed carbon and reduction of methanogenesis is a high priority agribusiness objective.  Methane is a greenhouse gas and this is another basis for interest in metabolism in the rumen.

Methanotrophic
Methanotrophic organisms use methane as a carbon source for growth and they use aerobic respiration to make ATP using reducing equivalents released by methane oxidation. Since all of the well characterised methanotrophs are aerobic organisms it is not surprising that they don't occur in association with methanogens and their presence in the reticulo-rumen has not been recorded. Just recently however evidence has been obtained strongly suggesting the co-existence of methanogens and methanotrophs in anaerobic submarine sediments 500 meters below the surface of the sea offshore from northern California (Hinrichs et al., 1999, Nature 398, 802-805). The metabolism of these methanotrophic organisms has not been characterised but, as the authors note, the finding "represents a substantial reassessement of archaeal metabolic capabilities".

Redox-balance
In anaerobic chemoheterotrophic organisms where ATP production occurs in fermentation pathways by phosphoryl group transfer, production of the necessary high phosphoryl group transfer metabolites involves intermediary oxidation reactions where NAD or NADP are used as the oxidizing agents. Since oxygen is not available as the ultimate electron acceptor for regeneration of the oxidized forms of these intermediary electron carriers a metabolite of the original organic growth substrate has to be used for this purpose.  Examples are the reduction of pyruvate to produce lactate or the reduction of acetaldehyde to produce ethanol.  Rumen microorganisms utilize a diverse array of these and other such redox couples to achieve redox balance.

Syntrophy
Syntrophy is the name given to the association between two species of microorganisms, growing in the same culture environment, where each exhibits growth characteristics that depend on the presence of the other organism. The monograph by Fenchel and Finlay describes a number of examples.  In the reticulo-rumen there are cases where methanogens grow in syntrophic relations with other species of microorganisms. The methanogens depend on the hydrogen and carbon dioxide produced by other species and some of these other species (such as Ruminococcus) grow better in the presence of the methanogens because of the altered patterns of redox balance associated with reduced partial pressure of hydrogen in the growth environment (due to interspecies hydrogen transfer).