Axial Differences in Community Structure of Crenarchaeota and Euryarchaeota in the Highly Compartmentalized Gut of the Soil-Feeding Termite Cubitermes orthognathus

Applied and Environmental Microbiology

Volumn 67, Issue 10, 2001, Pages 4880-4890

  Friedrich, Michael W ^a   Schmitt Wagner, Dirk ^b   Lueders, Tillmann ^a   Brune, Andreas ^b  

^a MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

^b UNIVERSITY OF KONSTANZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL DNA; RNA 16S;

ANIMAL; ARTICLE; CLASSIFICATION; CRENARCHAEOTA; DNA SEQUENCE; ECOSYSTEM; EURYARCHAEOTA; GENETICS; INTESTINE; ISOPTERA; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY; PHYSIOLOGY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RNA GENE; SOIL;

ANIMALS; CRENARCHAEOTA; DNA, ARCHAEAL; ECOSYSTEM; EURYARCHAEOTA; GENES, RRNA; INTESTINES; ISOPTERA; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL;

EID: 0035488974     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.67.10.4880-4890.2001     Document Type: Article

References (55)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Barns, S. M., C. F. Delwiche, J. D. Palmer, and N. R. Pace. 1996. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. USA 93:9188-9193.
3. Berthelet, M., L. G. Whyte, and C. W. Greer. 1996. Rapid, direct extraction of DNA from soils for PCR analysis using polyvinylpolypyrrolidone spin columns. FEMS Microbiol. Lett. 138:17-22.
4. Bignell, D. E., and P. Eggleton. 1995. On the elevated intestinal pH of higher termites (Isoptera: Termitidae). Insectes Sociaux 42:57-69.
5. Bignell, D. E., P. Eggleton, L. Nunes, and K. L. Thomas. 1997. Termites as mediators of carbon fluxes in tropical forests: budgets for carbon dioxide and methane emissions, p. 109-134. In A. B. Watt, N. E. Stork, and M. D. Hunter (ed.), Forests and insects. Chapman and Hall, London, United Kingdom.
6. Bintrim, S. B., T. J. Donohue, J. Handelsman, G. P. Roberts, and R. M. Goodman. 1997. Molecular phylogeny of Archaea from soil. Proc. Natl. Acad. Sci. USA 94:277-282.
7. Boone, D. R., W. B. Whitman, and P. E. Rouviere. 1993. Diversity and taxonomy of methanogens, p. 35-80. In J. G. Ferry (ed.), Methanogenesis. Chapman & Hall, New York, N.Y.
8. Brauman, A., M. D. Kane, M. Labat, and J. A. Breznak. 1992. Genesis of acetate and methane by gut bacteria of nutritionally diverse termites. Science 257:1384-1387.
9. Breznak, J. A. 1994. Acetogenesis from carbon dioxide in termite guts, p. 303-330. In H. L. Drake (ed.), Acetogenesis. Chapman & Hall, New York, N.Y.
10. Breznak, J. A. 2000. Ecology of prokaryotic microbes in the guts of wood-and litter-feeding termites, p. 209-231. In T. Abe, D. E. Bignell, and M. Higashi (ed.), Termites: evolution, sociality, symbiosis, ecology. Kluwer Academic Publishers, Dordrecht, The Netherlands.
11. Brosius, J., M. L. Palmer, P. J. Kennedy, and H. F. Noller. 1978. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc. Natl. Acad. Sci. USA 75:4801-4805.
12. Brune, A. 1998. Termite guts: the world's smallest bioreactors. Trends Biotechnol. 16:16-21.
13. Brune, A., and M. Friedrich. 2000. Microecology of the termite gut: structure and function on a microscale. Curr. Opin. Microbiol. 3:263-269.
14. Brune, A., and M. Kühl. 1996. pH profiles of the extremely alkaline hindguts of soil-feeding termites (Isoptera: Termitidae) determined with microelectrodes. J. Insect Physiol. 42:1121-1127.
15. Buckley, D. H., J. R. Graber, and T. M. Schmidt. 1998. Phylogenetic analysis of nonthermophilic members of the kingdom Crenarchaeota and their diversity and abundance in soils. Appl. Environ. Microbiol. 64:4333-4339.
16. Chin, K. J., T. Lukow, and R. Conrad. 1999. Effect of temperature on structure and function of the methanogenic archaeal community in an anoxic rice field soil. Appl. Environ. Microbiol. 65:2341-2349.
17. DeLong, E. F. 1998. Everything in moderation: Archaea as 'non-extremophiles'. Curr. Opin. Genet. Dev. 8:649-654.
18. Ebert, A., and A. Brune. 1997. Hydrogen concentration profiles at the oxic-anoxic interface: a microsensor study of the hindgut of the wood-feeding lower termite Reticulitermes flavipes (Kollar). Appl. Environ. Microbiol. 63: 4039-4046.
19. Godon, J. J., E. Zumstein, P. Dabert, F. Habouzit, and R. Moletta. 1997. Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl. Environ. Microbiol. 63:2802-2813.
20. Großkopf, R., S. Stubner, and W. Liesack. 1998. Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. Appl. Environ. Microbiol. 64:4983-4989.
21. Großkopf, R., P. H. Janssen, and W. Liesack. 1998. Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl. Environ. Microbiol. 64:960-969.
22. Heck, K. L., Jr., G. Van Belle, and D. Simberloff. 1975. Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecology 56:1459-1461.
23. Henckel, T., M. Friedrich, and R. Conrad. 1999. Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. Appl. Environ. Microbiol. 65:1980-1990.
24. Hurlbert, S. H. 1971. The nonconcept of species diversity: a critique and alternative parameters. Ecology 52:577-586.
25. Kappler, A., and A. Brune. 1999. Influence of gut alkalinity and oxygen status on mobilization and size-class distribution of humic acids in the hindgut of soil-feeding termites. Appl. Soil Ecol. 13:219-229.
26. Karner, M. B., E. F. DeLong, and D. M. Karl. 2001. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409:507-510.
27. Leadbetter, J. R., and J. A. Breznak. 1996. Physiological ecology of Methanobrevibacter cuticularis sp. nov. and Methanobrevibacter curvatus sp. nov., isolated from the hindgut of the termite Reticulitermes flavipes. Appl. Environ. Microbiol. 62:3620-3631.
28. Leadbetter, J. R., L. D. Crosby, and J. A. Breznak. 1998. Methanobrevibacter filiformis sp. nov., a filamentous methanogen from termite hindguts. Arch. Microbiol. 169:287-292.
29. Ludwig, W., S. H. Bauer, M. Bauer, I. Held, G. Kirchhof, R. Schulze, I. Huber, S. Spring, A. Hartmann, and K. H. Schleifer. 1997. Detection and in situ identification of representatives of a widely distributed new bacterial phylum. FEMS Microbiol. Lett. 153:181-190.
30. Ludwig, W., O. Strunk, S. Klugbauer, N. Klugbauer, M. Weizenegger, J. Neumaier, M. Bachleitner, and K. H. Schleifer. 1998. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19:554-568.
31. Lueders, T., and M. Friedrich. 2000. Archaeal population dynamics during sequential reduction processes in rice field soil. Appl. Environ. Microbiol. 66:2732-2742.
32. McInerney, J. O., M. Wilkinson, J. W. Patching, T. M. Embley, and R. Powell. 1995. Recovery and phylogenetic analysis of novel archaeal rRNA sequences from a deep-sea deposit feeder. Appl. Environ. Microbiol. 61: 1646-1648.
33. Moré, M. I, J. B. Herrick, M. C. Silva, W. C. Ghiorse, and E. L. Madsen. 1994. Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Appl. Environ. Microbiol. 60:1572-1580.
34. 33a. Ohkuma, M., and T. Kudo. 1998. Phylogenetic analysis of the symbiotic intestinal microflora of the termite Cryptotermes domesticus. FEMS Microbiol. Lett. 164:389-395.
35. 33b. Ohkuma, M., S. Noda, K. Horikoshi, and T. Kudo. 1995. Phylogeny of symbiotic methanogens in the gut of the termite Reticulitermes speratus. FEMS Microbiol. Lett. 134:45-50.
36. Ohkuma, M., S. Noda, and T. Kudo. 1999. Phylogenetic relationships of symbiotic methanogens in diverse termites. FEMS Microbiol. Lett. 171:147-153.
37. Osborn, A. M., E. R. B. Moore, and K. N. Timmis. 2000. An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ. Microbiol. 2:39-50.
38. Ramakrishnan, B., T. Lueders, R. Conrad, and M. Friedrich. 2000. Effect of soil aggregate size on methanogenesis and archaeal community structure in anoxic rice field soil. FEMS Microbiol. Ecol. 32:261-270.
39. Rotthauwe, J. H., K. P. Witzel, and W. Liesack. 1997. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 63:4704-4712.
40. Rouland, C., A. Brauman, M. Labat, and M. Lepage. 1993. Nutritional factors affecting methane emission from termites. Chemosphere 26:617-622.
41. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
42. Sanderson, M. G. 1996. Biomass of termites and their emissions of methane and carbon dioxide: a global database. Glob. Biogeochem. Cycles 10:543-557.
43. Schmitt-Wagner, D., and A. Brune. 1999. Hydrogen profiles and localization of methanogenic activities in the highly compartmentalized hindgut of soil-feeding higher termites (Cubitermes spp.). Appl. Environ. Microbiol. 65: 4490-4496.
44. Shinzato, N., T. Matsumoto, I. Yamaoka, T. Oshima, and A. Yamagishi. 1999. Phylogenetic diversity of symbiotic methanogens living in the hindgut of the lower termite Reticulitermes speratus analyzed by PCR and in situ hybridization. Appl. Environ. Microbiol. 65:837-840.
45. Sprenger, W. W., M. C. van Belzen, J. Rosenberg, J. H. Hackstein, and J. T. Keltjens. 2000. Methanomicrococcus blatticola gen. nov., sp. nov., a methanol- and methylamine-reducing methanogen from the hindgut of the cockroach Periplaneta americana. Int. J. Syst. Evol. Microbiol. 50:1989-1999.
46. Stackebrandt, E., and B. M. Goebel. 1994. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44:846-849.
47. Suzuki, M. T., M. S. Rappe, and S. J. Giovannoni. 1998. Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Appl. Environ. Microbiol. 64:4522-4529.
48. Tholen, A., and A. Brune. 1999. Localization and in situ activities of homoacetogenic bacteria in the highly compartmentalized hindgut of soil-feeding higher termites (Cubitermes spp.). Appl. Environ. Microbiol. 65: 4497-4505.
49. Tholen, A., and A. Brune. 2000. Impact of oxygen on metabolic fluxes and in situ rates of reductive acetogenesis in the hindgut of the wood-feeding termite Reticulitermes flavipes. Environ. Microbiol. 2:436-449.
50. Tholen, A., B. Schink, and A. Brune. 1997. The gut microflora of Reticulitermes flavipes, its relation to oxygen, and evidence for oxygen-dependent acetogenesis by the most abundant Enterococcus sp. FEMS Microbiol. Ecol. 24:137-149.
51. Tokura, M., M. Ohkuma, and T. Kudo. 2000. Molecular phylogeny of methanogens associated with flagellated protists in the gut and with the gut epithelium of termites. FEMS Microbiol. Ecol. 33:233-240.
52. Van Der Maarel, M. J. E. C., R. R. E. Artz, R. Haanstra, and L. J. Forney. 1998. Association of marine archaea with the digestive tracts of two marine fish species. Appl. Environ. Microbiol. 64:2894-2898.
53. von Wintzingerode, F., U. B. Goebel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229.
54. Weisburg, W. G., S. M. Barns, D. A. Pelletier, and D. J. Lane. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173:697-703.
55. Woese, C. R., O. Kandler, and M. L. Wheelis. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87:4576-4579.