Previous Article | Next Article 
Applied and Environmental Microbiology, April 2009, p. 2598-2602, Vol. 75, No. 8
0099-2240/09/$08.00+0 doi:10.1128/AEM.02436-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
Community Composition and Density of Methanogens in the Foregut of the Tammar Wallaby (Macropus eugenii)
Paul N. Evans,1*
Lyn A. Hinds,2
Lindsay I. Sly,3
Christopher S. McSweeney,1
Mark Morrison,1 and
André-Denis G. Wright1
CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Brisbane, Queensland 4067, Australia,1
CSIRO Entomology, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia,2
School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Brisbane, Queensland 4067, Australia3
Received 23 October 2008/
Accepted 2 February 2009

ABSTRACT
The composition of the methanogenic archaeal community in the
foregut contents of Tammar wallabies (
Macropus eugenii) was
studied using 16S rRNA and methyl coenzyme reductase subunit
A (
mcrA) gene clone libraries. Methanogens belonging to the
Methanobacteriales and a well-supported cluster of uncultivated
archaeon sequences previously observed in the ovine and bovine
rumens were found. Methanogen densities ranged from 7.0
x 10
5 and 3.9
x 10
6 cells per gram of wet weight.

INTRODUCTION
Kangaroos and wallabies belong to the marsupial family Macropodidae
and are native to Australia. Because of their geographical isolation,
macropod marsupials have evolved separately from other herbivorous
animals, such as ruminants, but like ruminants, macropods have
a complex gut microbiome that includes fungi, archaea, bacteria,
and protozoa to coordinate plant biomass breakdown (
11). The
macropod foregut is functionally analogous to the rumen, yet
for reasons unknown, macropod species produce relatively low
levels of methane compared to ruminants (
5,
13,
30).
New species of bacteria (21) and protozoa (2-4) have been indentified in the macropod foregut, and the presence of fungi has also been reported (5). Preliminary studies have shown that methanogens are present in the kangaroo foregut (1) but can be absent or at levels below detection limits (22). This study represents the first attempt to describe the diversity of methanogens residing in the macropod foregut by using 16S rRNA and methyl coenzyme reductase A (mcrA) clone libraries in combination with quantitative real-time PCR.

Sample preparation and library construction.
Foregut contents were collected from a captive colony of female
Tammar wallabies (
Macropus eugenii). Eight wallabies, aged between
1.5 and 4 years, were euthanized at two different sampling dates,
November 2006 (five wallabies) and May 2007 (three wallabies),
and stomach contents collected. DNA from foregut contents was
pooled by sampling date and was extracted using the cetyltrimethylammonium
bromide method of Wright et al. (
32). Archaeal 16S rRNA genes
were PCR amplified using the gene primer set and protocol of
Wright and Pimm (
33), whereas the methanogen-specific methyl
coenzyme reductase A (
mcrA) gene was PCR amplified using the
primer set and protocol of Luton et al. (
18). PCR products were
cloned using a TOPO TA cloning kit according to the manufacturer's
instructions (Invitrogen Corporation, San Diego, CA).
In total, 191 16S rRNA clone inserts were sequenced using the primers Met448F (33), Met1027F (33), and Met780R (5'-TTCGTCCCTCACCGTC-3'). The 95 mcrA genes obtained were sequenced using the mcrA primer set of Luton et al. (18). All products were sequenced using a BigDye Terminator cycle sequencing kit (version 3.1) with an ABI 3730 genetic analyzer (Applied Biosystems). Pooled samples were used only for clone library analysis, but real-time PCR analysis was performed on DNA extractions from individual animals.

Phylogeny and real-time PCR.
All DNA sequence reads were edited manually and assembled into
contiguous sequences by using SEQMAN (DNASTAR) and checked for
chimeras using the program Bellerophon (
10). Sequences were
imported into the ARB software package (
16), release 07.07.11,
and aligned, and similarity matrices were constructed using
the Kimura-2 parameter correction method (
14). Neighbor-joining
dendrograms (
25) for both
mcrA and 16S rRNA gene sequences were
constructed using PHYLIP (
7) with 1,000 bootstrap resamplings.
Methanogen cell densities were estimated from foregut contents
of individual wallabies with the real-time PCR primers and calculation
methods of Denman et al. (
6).

Methanogen isolation.
A single methanogen isolate, WBY1, was purified from May 2007
wallaby foregut contents by using the modified RF30 medium and
anaerobic dilution techniques of Skillman et al. (
26). The 16S
rRNA and
mcrA genes from the methanogen isolate were PCR amplified
and resulting PCR products sequenced.

Clone library analysis.
From the first sampling date, both 16S rRNA (96 sequences) and
mcrA (35 sequences) gene libraries revealed the same three species,
Methanobrevibacter gottschalkii (
20),
Methanosphaera stadtmanae (
19), and an uncultivated archaeon, ON-CAN.17, from bovine rumen
contents (
35). The 16S rRNA gene sequences for the unknown archaeon
were dominant at the November sampling (91.7% of the 96 sequences),
compared to those for the
Methanobrevibacter sp. (6.2%). However,
with only 35 sequences from the November
mcrA library, the unknown
archaeon was as prevalent (48.6%) as the
Methanobrevibacter sp. (45.7%). Analysis of the 16S rRNA (95 sequences) and
mcrA (60 sequences) genelibraries from the May sampling revealed
the same three species. However,
Methanobrevibacter gottschalkii was now dominant (91.6%), with the unknown archaeon representing
only 6.3% of the sequences. The proportions of these three species
in the May
mcrA gene library were similar to those in the May
16S rRNA gene library, with the
Methanobrevibacter sp. and the
unknown archaeon accounting for 66.7% and 20.0% of sequences,
respectively.
Methanosphaera sequences were the minority in
each of the four clone libraries. These data imply a likely
difference in community proportion between the two sampling
dates, as
Methanobrevibacter gottschalkii was predominant at
the May (autumn) sampling while the novel archaeon phylotype
was predominant at the November (spring) sampling.
Overall, TW-MAY.02 represented 94 of the 191 sequences (99.4 to 100% identity) (Fig. 1) and had 98.9% identity to Methanobrevibacter gottschalkii, a methanogen isolated from the feces of a pig (20). Also, 56 of 95 mcrA sequences were 100% identical to each other, represented by TWM-MAY.01 (Fig. 2), and were 97.6% similar to Methanobrevibacter smithii PST, a near neighbor of Methanobrevibacter gottschalkii PGT. The reason for the dominance of a single Methanobrevibacter phylotype in the wallaby foregut is unknown, but environmental conditions and ecological pressures in the foregut likely favor this species over all others. Similarly, 420 methanogen clone sequences from chicken gut contents were found to be almost identical to each other (24). In contrast, Methanobrevibacter species from the rumen appear to form a continuum of species rather than discreet groups (12). The 16S rRNA gene of an isolate, WBY1, had 100% sequence identity to the Methanobrevibacter sp. clone library sequences (Fig. 1). Also, the mcrA sequence of WBY1 was 100% identical to those from the mcrA clone library (Fig. 2).
In addition, TW-NOV.03 represented 93 of the 191 16S rRNA gene
sequences (99.5 to 100% identity) (Fig.
1) and had 97.2% identity
to ON-CAN.17 (
35), an uncultured archaeon from bovine rumen
contents. The validly described species closest to TW-NOV.03
was
Thermoplasma acidophilum, with 73.8% identity. The 29
mcrA sequences that formed a grouping represented by TWM-NOV.04 (96.9
to 100% identity) (Fig.
2) had 99.8% identity to the bovine
rumen clone CLI40 (
6) and only 74.5% similarity to the nearest
known methanogen,
Methanosaeta concilii GP6
T. These
mcrA sequences
formed a monophyletic clade distantly related to
mcrA-like sequences
from a mixed culture containing archaea that oxidized methane
(
9). Given that the uncultivated archaeon sequences have genuine
mcrA genes, which are known only to exist in methanogenic archaea,
it is likely that these archaea are indeed methanogens, although
further evidence to support this notion is required.
Four 16S rRNA genes, represented by TW-MAY.10 (99.4 to 100% identity) (Fig. 1), had 95.9% similarity to Methanosphaera stadtmanae MCB-3T, which was isolated from human fecal material (19). Other Methanosphaera spp. have previously been detected in bovine (29, 31) and ovine (34) rumen contents. Ten mrtA clone library sequences, represented by TWM-MAY.10 (95.8 to 100% identity) (Fig. 2), had 95.8% similarity to Methanosphaera stadtmanae MCB-3T. A search of the Methanosphaera stadtmanae MCB-3T genome sequence (8) revealed the absence of mcrA genes but the presence of the mrtA isoform (data not shown). Although the mcrA gene has been shown to be a possible alternative to the 16S rRNA gene phylogeny (15, 17, 18, 27), anomalies due to conserved mcrA primer sites (6, 18) in the mrtA genes of Methanosphaera, Methanobacterium, Methanococcales, and Methanothermobacter spp. exist (Fig. 2). Because the mrtA gene is expressed at greater levels, with increased hydrogen concentrations, than the mcrA gene (23), under increased hydrogen concentrations, like that found in wallaby and kangaroo foreguts (5), Methanosphaera stadtmanae methanogens could be more prevalent than methanogens only possessing the mcrA gene.

Real-time PCR analysis.
Because no estimates of archaeon cell density from macropod
foregut contents exist, densities from bovine rumen contents
were also estimated using the methods of Denman et al. (
6).
The estimate of 9.8
x 10
8 cells per gram of rumen contents (Table
1) compares favorably to the estimate made by Denman et al.
(
6) (1.3
x 10
9 cells per gram of rumen contents obtained using
the
mcrA gene) as well as estimates for sheep (
26) and reindeer
(
28). Densities at the November sampling were similar to those
at the May sampling (Table
1), but this difference was not significant,
because of low sample numbers and estimate variation between
wallabies (Table
1). Overall, estimates of archaeal cell densities
varied between 7.0
x 10
5 and 3.9
x 10
6 cells per gram of wet
weight (Table
1) and were between 400- and 1,400-fold less than
estimates from rumen contents from the present study (Table
1). The lower methanogen densities may be why methane emissions
in Tammar wallabies were only 1 to 2% of digestible energy (
30),
compared to the 10.5% of digestible energy in the sheep rumen
(
13).
View this table:
[in this window]
[in a new window]
|
TABLE 1. Quantitative real-time PCR estimates of methanogen cell densities of individual wallabies for first and second sampling times and bovine rumen contents
|
In conclusion, methanogens and the unknown archaeon sequences
were similar to those previously identified in gut environments
and based on 16S rRNA gene sequences.
Methanobrevibacter spp.
were predominant at the May sampling date, while sequences from
the unknown archaeon were most numerous at the November sampling.

Nucleotide sequence accession numbers.
Of the 191 16S rRNA gene sequences, 79 different sequences were
deposited in the GenBank database (under accession numbers EU831322
to EU831401). Of the 95
mcrA gene sequences, 14 different sequences
were deposited in the GenBank database (under accession numbers
EU831308 to EU831321). The deposited sequences were designated
TW for 16S rRNA and TWM
mcrA genes and either NOV or MAY for
the two sampling dates. Sequence data from the new methanogen
isolate, WBY1, for the 16S rRNA gene and the
mcrA gene were
deposited in the GenBank database under accession numbers EU919428
and EU919429, respectively.
mcrA gene sequences from
Methanobrevibacter millerae ZA-10 (accession number EU919430),
Methanobrevibacter gottschalkii PG (accession number EU919431), and
Methanobrevibacter woesei GS (accession number EU919432) were deposited in the
GenBank database.

FOOTNOTES
* Corresponding author. Mailing address: CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Brisbane, Queensland 4067, Australia. Phone: 61 7 3214 2200. Fax: 61 7 3214 2900. E-mail:
Paul.Evans{at}csiro.au 
Published ahead of print on 13 February 2009. 

REFERENCES
1 - Baker, S. K., T. Schoep, N. J. Edwards, and A.-D. G. Wright. 2002. Methanogens in kangaroos. Reprod. Nutr. Dev. 42:S77.
2 - Cameron, S. L., and P. J. O'Donoghue. 2002. Trichostome ciliates from Australian marsupials. I. Bandia gen. nov. (Litostomatea: Amylovoracidae). Eur. J. Protistol. 38:405-429.[CrossRef]
3 - Cameron, S. L., and P. J. O'Donoghue. 2003. Trichostome ciliates from Australian marsupials. II. Polycosta gen. nov. (Litostomatea: Polycostidae fam. nov.). Eur. J. Protistol. 39:83-100.[CrossRef]
4 - Cameron, S. L., and P. J. O'Donoghue. 2003. Trichostome ciliates from Australian marsupials. III. Megavestibulum gen. nov. (Litostomatea: Macropodiniidae). Eur. J. Protistol. 39:123-138.[CrossRef]
5 - Dellow, D. W., I. D. Hume, R. T. J. Clarke, and T. Bauchop. 1988. Microbial activity in the forestomach of free-living macropodid marsupials: comparisons with laboratory studies. Aust. J. Zool. 36:383-395.[CrossRef]
6 - Denman, S. E., N. W. Tomkins, and C. S. McSweeney. 2007. Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane. FEMS Microbiol. Ecol. 62:313-322.[CrossRef][Medline]
7 - Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Department of Genetics, University of Washington, Seattle.
8 - Fricke, W. F., H. Seedorf, A. Henne, M. Krüer, H. Liesegang, R. Hedderich, G. Gottschalk, and R. K. Thauer. 2006. The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. J. Bacteriol. 188:642-658.[Abstract/Free Full Text]
9 - Hallam, S. J., P. R. Girguis, C. M. Preston, P. M. Richardson, and E. F. DeLong. 2003. Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Appl. Environ. Microbiol. 69:5483-5491.[Abstract/Free Full Text]
10 - Huber, T., G. Faulkner, and P. Hugenholtz. 2004. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317-2319.[Abstract/Free Full Text]
11 - Hume, I. D. 1984. Microbial fermentation in herbivorous marsupials. BioScience 34:435-440.[CrossRef]
12 - Janssen, P. H., and M. Kirs. 2008. Structure of the archaeal community of the rumen. Appl. Environ. Microbiol. 74:3619-3625.[Free Full Text]
13 - Kempton, T. J., R. M. Murray, and R. A. Leng. 1976. Methane production and digestibility measurements in the grey kangaroo and sheep. Aust. J. Biol. Sci. 29:209-214.[Medline]
14 - Kimura, M. 1980. A simple method of estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.[CrossRef][Medline]
15 - Lehmacher, A., and H. P. Klenk. 1994. Characterization and phylogeny of mcrII, a gene cluster encoding an isozyme of methyl coenzyme M reductase from hyperthermophilic Methanothermus fervidus. Mol. Gen. Genet. 243:198-206.[Medline]
16 - Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Forster, I. Brettske, S. Gerber, A. W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. Konig, T. Liss, R. Lussmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K. H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371.[Abstract/Free Full Text]
17 - Lueders, T., K. J. Chin, R. Conrad, and M. Friedrich. 2001. Molecular analyses of methyl-coenzyme M reductase alpha-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage. Environ. Microbiol. 3:194-204.[CrossRef][Medline]
18 - Luton, P. E., J. M. Wayne, R. J. Sharp, and P. W. Riley. 2002. The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 148:3521-3530.[Abstract/Free Full Text]
19 - Miller, T. L., and M. J. Wolin. 1985. Methanosphaera stadtmaniae gen-nov, sp-nov: a species that forms methane by reducing methanol with hydrogen. Arch. Microbiol. 141:116-122.[CrossRef][Medline]
20 - Miller, T. L., and C. Lin. 2002. Description of Methanobrevibacter gottschalkii sp. nov., Methanobrevibacter thaueri sp. nov., Methanobrevibacter woesei sp. nov. and Methanobrevibacter wolinii sp. nov. Int. J. Syst. Evol. Microbiol. 52:819-822.[Abstract]
21 - Ouwerkerk, D., A. V. Klieve, R. J. Forster, J. M. Templeton, and A. J. Maguire. 2005. Characterization of culturable anaerobic bacteria from the forestomach of an eastern grey kangaroo, Macropus giganteus. Lett. Appl. Microbiol. 41:327-333.[CrossRef][Medline]
22 - Ouwerkerk, D., A. J. Maguire, and A. V. Klieve. 2005. Reductive acetogenesis in the foregut of macropod marsupials in Australia, p. 98-101. In C. R. Soliva, J. Takahashi, and M. Kreuzer (ed.), Publication series, vol. 27. Institute of Animal Science, ETH, Zurich, Switzerland.
23 - Pennings, J. L., P. Vermeij, L. M. de Poorter, J. T. Keltjens, and G. D. Vogels. 2000. Adaptation of methane formation and enzyme contents during growth of Methanobacterium thermoautotrophicum (strain
H) in a fed-batch fermentor. Antonie van Leeuwenhoek 77:281-291.[CrossRef][Medline] 24 - Saengkerdsub, S., R. C. Anderson, H. H. Wilkinson, W.-K. Kim, D. J. Nisbet, and R. C. Ricke. 2007. Identification and quantification of methanogenic archaea in adult chicken ceca. Appl. Environ. Microbiol. 73:353-356.[Abstract/Free Full Text]
25 - Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for constructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.[Abstract]
26 - Skillman, L. C., P. N. Evans, G. E. Naylor, B. Morvan, G. N. Jarvis, and K. N. Joblin. 2004. 16S ribosomal DNA-directed PCR primers for ruminal methanogens and identification of methanogens colonising young lambs. Anaerobe 10:277-285.[CrossRef][Medline]
27 - Springer, E., M. S. Sachs, C. R. Woese, and D. R. Boone. 1995. Partial gene sequences for the A subunit of methyl-coenzyme M reductase (mcrI) as a phylogenetic tool for the family Methanosarcinaceae. Int. J. Syst. Bacteriol. 45:554-559.[Abstract/Free Full Text]
28 - Sundset, M. A., J. E. Edwards, Y. F. Cheng, R. S. Senosiain, M. N. Fraile, K. N. Northwood, K. E. Præsteng, T. Glad, S. D. Mathiesen, and A.-D. G. Wright. 2009. Molecular diversity of the rumen microbiome of Norwegian reindeer on natural summer pasture. Microb. Ecol. 57:335-348.[CrossRef][Medline]
29 - Tajima, K., T. Nagamine, H. Matsui, M. Nakamura, and R. I. Aminov. 2001. Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens. FEMS Microbiol. Lett. 200:67-72.[CrossRef][Medline]
30 - von Engelhardt, W., S. Wolter, H. Lawrenz, and J. A. Hemsley. 1978. Production of methane in two non-ruminant herbivores. Comp. Biochem. Physiol. A 60:309-311.
31 - Whitford, M. F., R. M. Teather, and R. J. Forster. 2001. Phylogenetic analysis of methanogens from the bovine rumen. BMC Microbiol. 1:5.[CrossRef][Medline]
32 - Wright, A.-D. G., B. A. Dehority, and D. H. Lynn. 1997. Phylogeny of the rumen ciliates Entodinium, Epidinium and Polyplastron (Litostomatea: Entodiniomorphida) inferred from small subunit ribosomal RNA sequences. J. Eukaryot. Microbiol. 44:61-67.[Medline]
33 - Wright, A.-D. G., and C. Pimm. 2003. Improved strategy for presumptive identification of methanogens using 16S riboprinting. J. Microbiol. Methods 55:337-349.[CrossRef][Medline]
34 - Wright, A.-D. G., A. J. Williams, B. Winder, C. T. Christophersen, S. L. Rodgers, and K. D. Smith. 2004. Molecular diversity of rumen methanogens from sheep in Western Australia. Appl. Environ. Microbiol. 70:1263-1270.[Abstract/Free Full Text]
35 - Wright, A.-D. G., C. H. Auckland, and D. H. Lynn. 2007. Molecular diversity of methanogens in feedlot cattle from Ontario and Prince Edward Island, Canada. Appl. Environ. Microbiol. 73:4206-4210.[Abstract/Free Full Text]
Applied and Environmental Microbiology, April 2009, p. 2598-2602, Vol. 75, No. 8
0099-2240/09/$08.00+0 doi:10.1128/AEM.02436-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.