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Snapshot of the Eukaryotic Gene Expression in Muskoxen Rumen—A Metatranscriptomic Approach

Title:

Snapshot of the Eukaryotic Gene Expression in Muskoxen Rumen—A Metatranscriptomic Approach

Kelso, Janet, Qi, Meng, Wang, Pan, O'Toole, Nicholas, Barboza, Perry S., Ungerfeld, Emilio, Leigh, Mary Beth, Selinger, L. Brent, Butler, Greg, Tsang, Adrian, McAllister, Tim A. and Forster, Robert J. (2011) Snapshot of the Eukaryotic Gene Expression in Muskoxen Rumen—A Metatranscriptomic Approach. PLoS ONE, 6 (5). e20521. ISSN 1932-6203

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Official URL: http://dx.doi.org/10.1371/journal.pone.0020521

Abstract

Background
Herbivores rely on digestive tract lignocellulolytic microorganisms, including bacteria, fungi and protozoa, to derive energy and carbon from plant cell wall polysaccharides. Culture independent metagenomic studies have been used to reveal the genetic content of the bacterial species within gut microbiomes. However, the nature of the genes encoded by eukaryotic protozoa and fungi within these environments has not been explored using metagenomic or metatranscriptomic approaches.

Methodology/Principal Findings
In this study, a metatranscriptomic approach was used to investigate the functional diversity of the eukaryotic microorganisms within the rumen of muskoxen (Ovibos moschatus), with a focus on plant cell wall degrading enzymes. Polyadenylated RNA (mRNA) was sequenced on the Illumina Genome Analyzer II system and 2.8 gigabases of sequences were obtained and 59129 contigs assembled. Plant cell wall degrading enzyme modules including glycoside hydrolases, carbohydrate esterases and polysaccharide lyases were identified from over 2500 contigs. These included a number of glycoside hydrolase family 6 (GH6), GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies.

Conclusions/Significance
The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes. This study provides a snapshot of eukaryotic gene expression in the muskoxen rumen, and identifies a number of candidate genes coding for potentially valuable lignocellulolytic enzymes.

Divisions:Concordia University > Faculty of Arts and Science > Biology
Item Type:Article
Refereed:Yes
Authors:Kelso, Janet and Qi, Meng and Wang, Pan and O'Toole, Nicholas and Barboza, Perry S. and Ungerfeld, Emilio and Leigh, Mary Beth and Selinger, L. Brent and Butler, Greg and Tsang, Adrian and McAllister, Tim A. and Forster, Robert J.
Journal or Publication:PLoS ONE
Date:31 May 2011
Digital Object Identifier (DOI):10.1371/journal.pone.0020521
ID Code:7714
Deposited By: Danielle Dennie
Deposited On:11 Jul 2011 14:24
Last Modified:18 Jan 2018 17:31

References:

1.Flint HJ (1997) The rumen microbial ecosystem–some recent developments. Trends Microbiol 5: 483–488.

2.Russell JB, Rychlik JL (2001) Factors that alter rumen microbial ecology. Science 292: 1119–1122.

3.Krause DO, Denman SE, Mackie RI, Morrison M, Rae AL, et al. (2003) Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics. FEMS Microbiol Rev 27: 663–693.

4.Flint HJ, Bayer EA, Rincon MT, Lamed R, White BA (2008) Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat Rev Microbiol 6: 121–131.

5.Berg Miller ME, Antonopoulos DA, Rincon MT, Band M, Bari A, et al. (2009) Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1. PLoS ONE 4: e6650.

6.Morrison M, Daugherty SC, Nelson WC, Davidsen T, Nelson KE (2010) The FibRumBa database: a resource for biologists with interests in gastrointestinal microbial ecology, plant biomass degradation, and anaerobic microbiology. Microb Ecol 59: 212–213.

7.Cai S, Li J, Hu FZ, Zhang K, Luo Y, et al. (2010) Cellulosilyticum ruminicola, a newly described rumen bacterium that possesses redundant fibrolytic-protein-encoding genes and degrades lignocellulose with multiple carbohydrate- borne fibrolytic enzymes. Appl Environ Microbiol 76: 3818–3824.

8.Purushe J, Fouts DE, Morrison M, White BA, Mackie RI, et al. (2010) Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche. Microb Ecol 60: 721–729.

9.Kelly WJ, Leahy SC, Altermann E, Yeoman CJ, Dunne JC, et al. (2010) The glycobiome of the rumen bacterium Butyrivibrio proteoclasticus B316(T) highlights adaptation to a polysaccharide-rich environment. PLoS ONE 5: e11942.

10.Brulc JM, Antonopoulos DA, Miller ME, Wilson MK, Yannarell AC, et al. (2009) Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci U S A 106: 1948–1953.

11.Pope PB, Denman SE, Jones M, Tringe SG, Barry K, et al. (2010) Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proc Natl Acad Sci U S A 107: 14793–14798.

12.Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, et al. (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331: 463–467.

13.Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, et al. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450: 560–565.

14.Orpin CG, Joblin KN (1997) The rumen anaerobic fungi. In: Hobson PN, Stewart CS, editors. The rumen microbial ecosystem. Second edition ed: Blackie Academic and Professional. pp. 140–195.

15.Williams AG, Coleman GS (1997) The rumen protozoa. In: Hobson PN, Stewart CS, editors. The rumen microbial ecosystem. London, United Kingdom: Blackie Academic and Professional Publishers. pp. 73–139.

16.Rezaeian M, Beakes GW, Parker DS (2004) Distribution and estimation of anaerobic zoosporic fungi along the digestive tracts of sheep. Mycol Res 108: 1227–1233.

17.Liggenstoffer AS, Youssef NH, Couger MB, Elshahed MS (2010) Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores. ISME J 4: 1225–1235.

18.Devillard E, Newbold CJ, Scott KP, Forano E, Wallace RJ, et al. (1999) A xylanase produced by the rumen anaerobic protozoan Polyplastron multivesiculatum shows close sequence similarity to family 11 xylanases from gram-positive bacteria. FEMS Microbiol Lett 181: 145–152.

19.Bera-Maillet C, Devillard E, Cezette M, Jouany JP, Forano E (2005) Xylanases and carboxymethylcellulases of the rumen protozoa Polyplastron multivesiculatum, Eudiplodinium maggii and Entodinium sp. FEMS Microbiol Lett 244: 149–156.

20.Tilman D, Socolow R, Foley JA, Hill J, Larson E, et al. (2009) Energy. Beneficial biofuels–the food, energy, and environment trilemma. Science 325: 270–271.

21.Zhang YH, Himmel ME, Mielenz JR (2006) Outlook for cellulase improvement: screening and selection strategies. Biotechnol Adv 24: 452–481.

22.Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57–63.

23.Barboza PS, Peltier TC, Forster RJ (2006) Ruminal fermentation and fill change with season in an arctic grazer: responses to hyperphagia and hypophagia in muskoxen (Ovibos moschatus). Physiol Biochem Zool 79: 497–513.

24.Crater AR, Barboza PS, Forster RJ (2007) Regulation of rumen fermentation during seasonal fluctuations in food intake of muskoxen. Comp Biochem Physiol A Mol Integr Physiol 146: 233–241.

25.Nicholson MJ, Theodorou MK, Brookman JL (2005) Molecular analysis of the anaerobic rumen fungus Orpinomyces - insights into an AT-rich genome. Microbiology 151: 121–133.

26.Neidhardt FC, Umbarger HE (1996) Chemical composition of Escherichia coli. In: Neidhardt FCea, editor. Escherichia coli and Salmonella: Cellular and Molecular Biology 2nd ed. Washington, D.C.: ASM Press. pp. 13–17.

27.Willner D, Thurber RV, Rohwer F (2009) Metagenomic signatures of 86 microbial and viral metagenomes. Environ Microbiol 11: 1752–1766.

28.Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, et al. (2007) A higher-level phylogenetic classification of the Fungi. Mycol Res 111: 509–547.

29.Williams AG (1986) Rumen holotrich ciliate protozoa. Microbiol Rev 50: 25–49.

30.Boxma B, de Graaf RM, van der Staay GW, van Alen TA, Ricard G, et al. (2005) An anaerobic mitochondrion that produces hydrogen. Nature 434: 74–79.

31.Saloheimo M, Paloheimo M, Hakola S, Pere J, Swanson B, et al. (2002) Swollenin, a Trichoderma reesei protein with sequence similarity to the plant expansins, exhibits disruption activity on cellulosic materials. Eur J Biochem 269: 4202–4211.

32.Steenbakkers PJM, Li X-L, Ximenes EA, Arts JG, Chen H, et al. (2001) Noncatalytic docking domains of cellulosomes of anaerobic fungi. J Bacteriol 183: 5325–5333.

33.Nagy T, Tunnicliffe RB, Higgins LD, Walters C, Gilbert HJ, et al. (2007) Characterization of a double dockerin from the cellulosome of the anaerobic fungus Piromyces equi. J Mol Biol 373: 612–622.

34.Allgaier M, Reddy A, Park JI, Ivanova N, D'Haeseleer P, et al. (2010) Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS ONE 5: e8812.

35.McAllister TA, Bae HD, Jones GA, Cheng KJ (1994) Microbial attachment and feed digestion in the rumen. J Anim Sci 72: 3004–3018.

36.Williams AG, Strachan NH (1984) Polysaccharide degrading enzymes in microbial populations from the liquid and solid fractions of bovine rumen digesta. Can J Anim Sci 64: 58–59(supplement).

37.Wang P, Qi M, Barboza PS, Leith MB, Ungerfeld E, et al. (2011) Isolation of high-quality total RNA from rumen anaerobic bacteria and fungi, and subsequent detection of glycoside hydrolases. Can J Microbiol. (In press).

38.Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, et al. (2008) Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci U S A 105: 3805–3810.

39.Poretsky RS, Hewson I, Sun S, Allen AE, Zehr JP, et al. (2009) Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre. Environ Microbiol 11: 1358–1375.

40.Gilbert JA, Field D, Huang Y, Edwards R, Li W, et al. (2008) Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE 3: e3042.

41.Gifford SM, Sharma S, Rinta-Kanto JM, Moran MA (2011) Quantitative analysis of a deeply sequenced marine microbial metatranscriptome. ISME J 5: 461–472.

42.Poroyko V, White JR, Wang M, Donovan S, Alverdy J, et al. (2010) Gut microbial gene expression in mother-fed and formula-fed piglets. PLoS ONE 5: e12459.

43.Kong Y, Teather R, Forster R (2010) Composition, spatial distribution, and diversity of the bacterial communities in the rumen of cows fed different forages. FEMS Microbiol Ecol 74: 612–622.

44.Stevenson DM, Weimer PJ (2007) Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR. Appl Microbiol Biotechnol 75: 165–174.

45.Orpin CG, Joblin KN (1988) The rumen anaerobic fungi. In: Hobson PN, editor. The rumen microbial ecosystem. London: Elsevier Appl Sci. pp. 129–150.

46.Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66: 506–577.

47.Gloster TM, Ibatullin FM, Macauley K, Eklof JM, Roberts S, et al. (2007) Characterization and three-dimensional structures of two distinct bacterial xyloglucanases from families GH5 and GH12. J Biol Chem 282: 19177–19189.

48.Yaoi K, Kondo H, Hiyoshi A, Noro N, Sugimoto H, et al. (2007) The structural basis for the exo-mode of action in GH74 oligoxyloglucan reducing end-specific cellobiohydrolase. J Mol Biol 370: 53–62.

49.Garcia-Vallve S, Romeu A, Palau J (2000) Horizontal gene transfer of glycosyl hydrolases of the rumen fungi. Mol Biol Evol 17: 352–361.

50.Ricard G, McEwan NR, Dutilh BE, Jouany JP, Macheboeuf D, et al. (2006) Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment. BMC Genomics 7: 22.

51.Hungate RE, Bryant MP, Mah RA (1964) The Rumen Bacteria and Protozoa. Annu Rev Microbiol 18: 131–166.

52.Orpin CG (1975) Studies on the rumen flagellate Neocallimastix frontalis. J Gen Microbiol 91: 249–262.

53.Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821–829.

54.Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9: 868–877. Find this article online
55.Li W (2009) Analysis and comparison of very large metagenomes with fast clustering and functional annotation. BMC Bioinformatics 10: 359.

56.Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188–7196.

57.Huang Y, Gilna P, Li W (2009) Identification of ribosomal RNA genes in metagenomic fragments. Bioinformatics 25: 1338–1340.

58.Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955–964.

59.Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome Res 17: 377–386.

60.Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, et al. (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 37: D233–238.

61.Eddy SR (2009) A new generation of homology search tools based on probabilistic inference. Genome Inform 23: 205–211.

62.Notredame C, Higgins DG, Heringa J (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205–217.

63.Qi M, Nelson KE, Daugherty SC, Nelson WC, Hance IR, et al. (2005) Novel molecular features of the fibrolytic intestinal bacterium Fibrobacter intestinalis not shared with Fibrobacter succinogenes as determined by suppressive subtractive hybridization. J Bacteriol 187: 3739–3751
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