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substrates for methane production, but some
methanogens (e.g. Methanosarcina barkeri ) are
also able to produce methane from acetate, meth-
ylamines and methanol (Stewart et al ., 1997).
Until recently, our understanding of the
diversity and microbial interactions between
methanogens and other rumen microorgan-
isms has been very limited. However, knowl-
edge of this ecosystem is rapidly accumulating,
particularly with the advances of molecular
biology (e.g. bar-coded pyrosequencing) and
culture independent technologies. Molecular-
based studies from Australia, New Zealand and
the USA have made significant contributions to
our knowledge of methanogen ecology and
diversity in the rumen (Miller and Wolin, 1986;
Lin et al ., 1997; Sharp et al ., 1998; Tokura et al .,
1999; Jarvis et al ., 2000; Yanagita et al ., 2000;
Tajima et al ., 2001; Whitford et al ., 2001; Irbis
and Ushida, 2004; Shin et al ., 2004; Skillman
et al ., 2004, 2006; Wright et al ., 2004b, 2006,
2007, 2008; Janssen and Kirs, 2008;
Ouwerkerk et al ., 2008; Brulc et al ., 2009; Hook
et al ., 2009, 2011; Sundset et al ., 2009a, b;
Williams et al ., 2009; Zhou et al ., 2009, 2010;
Leahy et al ., 2010; Pei et al ., 2010; King et al .,
2011; Franzolin et al ., 2012; Lee et al ., 2012).
Many of these studies have indicated that gut
methanogens tend to differ depending on diet
and geographical location, and that Methano-
brevibacter phylotypes are the dominant metha-
nogens in ruminant livestock worldwide
(Wright et al ., 2008).
Fig. 16.1. A photomicrograph of a mixed
population of rumen protozoa.
major sources of hydrogen in the rumen, and
methanogens living on (extracellular) and
within (intracellular) the rumen ciliates may
generate up to 37% of the methane emissions
from ruminant animals (Finlay et al ., 1994;
Hegarty, 1999a, b). Accordingly, when rumi-
nants were defaunated (i.e. made protozoa-free),
they produced on average 13% less methane
than faunated ruminants (Kreuzer, 1986;
Hegarty, 1999a). Commonly observed protozoa
in the bovine rumen that have this unique asso-
ciation with the methanogens are from the gen-
era Entodinium, Epidinium, Ophryoscolex and
Polyplastron , while, the methanogens most often
associated with the protozoa are from the orders
(Sharp et al ., 1998).
Rumen protozoa have been estimated to
account for half of the microbial biomass in the
rumen, and contribute to up to one-third of
fibre digestion (Hungate, 1966; Williams and
Coleman, 1997). The rumen ciliates Isotricha
and Dasytricha (Fig. 16.2) are very important in
utilizing soluble sugars and controlling the rate
of carbohydrate fermentation, especially when
large quantities of soluble carbohydrates are
present in the diet, whereas some entodiniomor-
phid ciliates are responsible for controlling
starch digestion by engulfing whole starch gran-
ules. However, some rumen ciliates can also
have a negative impact on ruminant protein
metabolism. Microbial protein accounts for as
much as 90% of the amino acids reaching the
small intestine of the animal. The rumen cili-
ates, also a source of microbial protein, do not
Rumen protozoa
Rumen ciliates (Fig. 16.1) are involved in host
metabolism and digestion of plant material in
the rumen. Young ruminants isolated at birth
do not contain rumen protozoa (Eadie, 1962;
Dehority, 1978; Fonty et al ., 1988), but become
faunated as a result of adults regurgitating food
and rumen contents back into the mouth during
rumination and salivating on feed, which is then
consumed by the young animal, or the protozoa
are passed directly by the mother to its offspring
during grooming (Dehority, 1993).
There is a complex relationship between the
ciliated protozoa (e.g. ciliates) and methanogens
in the rumen. Rumen protozoa are one of the
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