Few highly abundant operational taxonomic units dominate within rumen methanogenic archaeal species in New Zealand sheep and cattle

Applied and Environmental Microbiology

Volumn 81, Issue 3, 2015, Pages 986-995

  Seedorf, Henning ^a   Kittelmann, Sandra ^a   Janssen, Peter H ^a  

^a AGRESEARCH GRASSLANDS   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

MAMMALS; RNA; STATISTICS;

16S RRNA GENE; COMMUNITY STRUCTURES; OPERATIONAL TAXONOMIC UNITS; RELATIVE ABUNDANCE; RESEARCH CENTRES; SEQUENCE IDENTITY; STANDARD DEVIATION; TREATMENT GROUP;

METHANOGENS;

ABUNDANCE; CLADISTICS; COMMUNITY STRUCTURE; GENE EXPRESSION; LIVESTOCK; METHANOGENIC BACTERIUM; RNA; SPECIES DIVERSITY; TAXONOMY;

NEW ZEALAND;

ANIMALIA; ARCHAEA; BOS; METHANOBACTERIALES; METHANOBREVIBACTER GOTTSCHALKII; METHANOBREVIBACTER RUMINANTIUM; METHANOSPHAERA; OTUS; OVIS ARIES;

ARCHAEAL DNA; METHANE; RIBOSOME DNA; RNA 16S;

ANIMAL; ANIMAL FOOD; ARCHAEON; BIOTA; BOVINE; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; METABOLISM; MICROBIOLOGY; NEW ZEALAND; PHYLOGENY; RUMEN; SHEEP;

ANIMAL FEED; ANIMALS; ARCHAEA; BIOTA; CATTLE; CLUSTER ANALYSIS; DNA, ARCHAEAL; DNA, RIBOSOMAL; METHANE; NEW ZEALAND; PHYLOGENY; RNA, RIBOSOMAL, 16S; RUMEN; SEQUENCE ANALYSIS, DNA; SHEEP;

EID: 84921395812     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.03018-14     Document Type: Article

References (46)

1. Yusuf RO, Noor ZZ, Abba AH, Hassan MAA, Din MFM. 2012. Methane emission by sectors: a comprehensive review of emission sources and mitigation methods. Renew Sustain Energy Rev 16:5059-5070. http://dx.doi.org/10.1016/j.rser.2012.04.008.
2. Clark H, Kelliher F, Pinares-Patino C. 2011. Reducing CH4 emissions from grazing ruminants in New Zealand: challenges and opportunities. Asian Australas J Anim Sci 24:295-302. http://dx.doi.org/10.5713/ajas.2011.r.04.
3. Joblin KN. 2005. Methanogenic archaea, p 47-53. In Makkar HPS, Mc-Sweeney CS (ed), Methods in gut microbial ecology for ruminants. Springer, Dordrecht, The Netherlands.
4. Janssen PH, Kirs M. 2008. Structure of the archaeal community of the rumen. Appl Environ Microbiol 74:3619-3625. http://dx.doi.org/10.1128/AEM.02812-07.
5. Iino T, Tamaki H, Tamazawa S, Ueno Y, Ohkuma M, Suzuki K, Igarashi Y, Haruta S. 2013. Candidatus Methanogranum caenicola: a novel methanogen from the anaerobic digested sludge, and proposal of Methanomassiliicoccaceae fam. nov. and Methanomassiliicoccales ord. nov., for a methanogenic lineage of the class Thermoplasmata. Microbes Environ 28:244-250. http://dx.doi.org/10.1264/jsme2.ME12189.
6. Tajima K, Nagamine T, Matsui H, Nakamura M, Aminov RI. 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. http://dx.doi.org/10.1111/j.1574-6968.2001.tb10694.x.
7. Kemnitz D, Kolb S, Conrad R. 2005. Phenotypic characterization of rice cluster III archaea without prior isolation by applying quantitative polymerase chain reaction to an enrichment culture. Environ Microbiol 7:553-565. http://dx.doi.org/10.1111/j.1462-2920.2005.00723.x.
8. Paul K, Nonoh JO, Mikulski L, Brune A. 2012. "Methanoplasmatales," Thermoplasmatales-related archaea in termite guts and other environments, are the seventh order of methanogens. Appl Environ Microbiol 78:8245-8253. http://dx.doi.org/10.1128/AEM.02193-12.
9. Fricke WF, Seedorf H, Henne A, Krüer M, Liesegang H, Hedderich R, Gottschalk G, Thauer RK. 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. http://dx.doi.org/10.1128/JB.188.2.642-658.2006.
10. Miller TL, Wolin MJ. 1985. Methanosphaera stadtmaniae gen. nov., sp. nov.: a species that forms methane by reducing methanol with hydrogen. Arch Microbiol 141:116-122. http://dx.doi.org/10.1007/BF00423270.
11. Borrel G, Harris HM, Parisot N, Gaci N, Tottey W, Mihajlovski A, Deane J, Gribaldo S, Bardot O, Peyretaillade E, Peyret P, O'Toole PW, Brugere JF. 2013. Genome sequence of "Candidatus Methanomassiliicoccus intestinalis" Issoire-Mx1, a third Thermoplasmatales-related methanogenic archaeon from human feces. Genome Announc 1:e00453-13. http://dx.doi.org/10.1128/genomeA.00453-13.
12. Dridi B, Fardeau ML, Ollivier B, Raoult D, Drancourt M. 2012. Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. Int J Syst Evol Microbiol 62:1902-1907. http://dx.doi.org/10.1099/ijs.0.033712-0.
13. Poulsen M, Schwab C, Jensen BB, Engberg RM, Spang A, Canibe N, Højberg O, Milinovich G, Fragner L, Schleper C. 2013. Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen. Nat Commun 4:1428. http://dx.doi.org/10.1038/ncomms2432.
14. Seedorf H, Kittelmann S, Henderson G, Janssen PH. 2014. RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments. PeerJ 2:e494. http://dx.doi.org/10.7717/peerj.494.
15. Leahy S, Kelly W, Ronimus R, Wedlock N, Altermann E, Attwood G. 2013. Genome sequencing of rumen bacteria and archaea and its application to methane mitigation strategies. Animal 7:235-243. http://dx.doi.org/10.1017/S1751731113000700.
16. Henderson G, Cox F, Kittelmann S, Miri VH, Zethof M, Noel SJ, Waghorn GC, Janssen PH. 2013. Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities. PLoS One 8:e74787. http://dx.doi.org/10.1371/journal.pone.0074787.
17. Rius A, Kittelmann S, Macdonald K, Waghorn G, Janssen P, Sikkema E. 2012. Nitrogen metabolism and rumen microbial enumeration in lactating cows with divergent residual feed intake fed high-digestibility pasture. J Dairy Sci 95:5024-5034. http://dx.doi.org/10.3168/jds.2012-5392.
18. Kittelmann S, Seedorf H, Walters WA, Clemente JC, Knight R, Gordon JI, Janssen PH. 2013. Simultaneous amplicon sequencing to explore cooccurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities. PLoS One 8:e47879. http://dx.doi.org/10.1371/journal.pone.0047879.
19. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335-336. http://dx.doi.org/10.1038/nmeth.f.303.
20. Bragg L, Stone G, Imelfort M, Hugenholtz P, Tyson GW. 2012. Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nat Methods 9:425-426. http://dx.doi.org/10.1038/nmeth.1990.
21. Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460 -2461. http://dx.doi.org/10.1093/bioinformatics/btq461.
22. Shannon CE. 1948. A mathematical theory of communication. Bell Syst Tech J 27:379 -423. http://dx.doi.org/10.1002/j.1538-7305.1948.tb01338.x.
23. Pielou E. 1966. The measurement of diversity in different types of biological collections. J Theor Biol 13:131-144. http://dx.doi.org/10.1016/0022-5193(66)90013-0.
24. R Development Core Team. 2011. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
25. Suzuki R, Shimodaira H. 2006. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22:1540-1542. http://dx.doi.org/10.1093/bioinformatics/btl117.
26. Pruesse E, Peplies J, Glöckner FO. 2012. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28: 1823-1829. http://dx.doi.org/10.1093/bioinformatics/bts252.
27. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Buchner A, Lai T, Steppi S, Jobb G, Förster W. 2004. ARB: a software environment for sequence data. Nucleic Acids Res 32:1363-1371. http://dx.doi.org/10.1093/nar/gkh293.
28. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690. http://dx.doi.org/10.1093/bioinformatics/btl446.
29. Gilbert RA, Ouwerkerk D, Zhang LH, Klieve AV. 2010. In vitro detection and primary cultivation of bacteria producing materials inhibitory to ruminal methanogens. J Microbiol Methods 80:217-218. http://dx.doi.org/10.1016/j.mimet.2009.12.004.
30. Borrel G, Harris HM, Tottey W, Mihajlovski A, Parisot N, Peyretaillade E, Peyret P, Gribaldo S, O'Toole PW, Brugère J-F. 2012. Genome sequence of "Candidatus Methanomethylophilus alvus" Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens. J Bacteriol 194:6944-6945. http://dx.doi.org/10.1128/JB.01867-12.
31. Jeyanathan J, Kirs M, Ronimus RS, Hoskin SO, Janssen PH. 2011. Methanogen community structure in the rumens of farmed sheep, cattle and red deer fed different diets. FEMS Microbiol Ecol 76:311-326. http://dx.doi.org/10.1111/j.1574-6941.2011.01056.x.
32. Shin EC, Choi BR, Lim WJ, Hong SY, An CL, Cho KM, Kim YK, An JM, Kang JM, Lee SS. 2004. Phylogenetic analysis of archaea in three fractions of cow rumen based on the 16S rDNA sequence. Anaerobe 10:313-319. http://dx.doi.org/10.1016/j.anaerobe.2004.08.002.
33. Chaudhary P, Sirohi S. 2009. Dominance of Methanomicrobium phylotype in methanogen population present in Murrah buffaloes (Bubalus bubalis). Lett Appl Microbiol 49:274-277. http://dx.doi.org/10.1111/j.1472-765X.2009.02654.x.
34. Kim M, Morrison M, Yu Z. 2011. Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes. J Microbiol Methods 84:81-87. http://dx.doi.org/10.1016/j.mimet.2010.10.020.
35. Tymensen LD, McAllister TA. 2012. Community structure analysis of methanogens associated with rumen protozoa reveals bias in universal archaeal primers. Appl Environ Microbiol 78:4051-4056. http://dx.doi.org/10.1128/AEM.07994-11.
36. Jin W, Cheng Y-F, Mao S-Y, Zhu W-Y. 2011. Isolation of natural cultures of anaerobic fungi and indigenously associated methanogens from herbivores and their bioconversion of lignocellulosic materials to methane. Bioresour Technol 102:7925-7931. http://dx.doi.org/10.1016/j.biortech.2011.06.026.
37. Leahy SC, Kelly WJ, Altermann E, Ronimus RS, Yeoman CJ, Pacheco DM, Li D, Kong Z, McTavish S, Sang C, Lambie SC, Janssen PH, Dey D, Attwood GT. 2010. The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PLoS One 5:e8926. http://dx.doi.org/10.1371/journal.pone.0008926.
38. Leahy SC, Kelly WJ, Li D, Li Y, Altermann E, Cox F, Attwood GT. 2013. The complete genome sequence of Methanobrevibacter sp. AbM4. Stand Genomic Sci 8:215-227. http://dx.doi.org/10.4056/sigs.3977691.
39. Lee J-H, Rhee M-S, Kumar S, Lee G-H, Chang D-H, Kim D-S, Choi S-H, Lee D-W, Yoon M-H, Kim B-C. 2013. Genome sequence of Methanobrevibacter sp. strain JH1, isolated from rumen of Korean native cattle. Genome Announc 1:e00002-13. http://dx.doi.org/10.1128/genomeA.00002-13.
40. Dridi B, Henry M, El Khéchine A, Raoult D, Drancourt M. 2009. High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS One 4:e7063. http://dx.doi.org/10.1371/journal.pone.0007063.
41. Hansen EE, Lozupone CA, Rey FE, Wu M, Guruge JL, Narra A, Goodfellow J, Zaneveld JR, McDonald DT, Goodrich JA, Heath AC, Knight R, Gordon JI. 2011. Pan-genome of the dominant human gutassociated archaeon, Methanobrevibacter smithii, studied in twins. Proc Natl Acad Sci U S A 108:4599-4606. http://dx.doi.org/10.1073/pnas.1000071108.
42. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499: 431-437. http://dx.doi.org/10.1038/nature12352.
43. King EE, Smith RP, St-Pierre B, Wright A-DG. 2011. Differences in the rumen methanogen populations of lactating Jersey and Holstein dairy cows under the same diet regimen. Appl Environ Microbiol 77:5682-5687. http://dx.doi.org/10.1128/AEM.05130-11.
44. Kittelmann S, Pinares-Patiño CS, Seedorf H, Kirk MR, Ganesh S, McEwan JC, Janssen PH. 2014. Two different bacterial community types are linked with the low-methane emission trait in sheep. PLoS One 9:e103171. http://dx.doi.org/10.1371/journal.pone.0103171.
45. Wolin MJ. 1980. The rumen fermentation: a model for microbial interactions in anaerobic ecosystems. Adv Microb Ecol 3:49-77.
46. Zhou M, Hernandez-Sanabria E, Guan LL. 2010. Characterization of variation in rumen methanogenic communities under different dietary and host feed efficiency conditions, as determined by PCR-denaturing gradient gel electrophoresis analysis. Appl Environ Microbiol 76:3776-3786. http://dx.doi.org/10.1128/AEM.00010-10.