Methanogen diversity and community composition in peatlands of the central to northern Appalachian Mountain region, North America

Biogeochemistry

Volumn 109, Issue 1-3, 2012, Pages 117-131

  Yavitt, Joseph B ^a   Yashiro, Erika ^a,b   Cadillo Quiroz, Hinsby ^a,c   Zinder, Stephen H ^a  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c ARIZONA STATE UNIVERSITY   (United States)

Author keywords

16S ribosomal RNA; Beta diversity; Environmental gradient; Microbial communities; Peatland; Spatial turnover

Indexed keywords

CLIMATE CHANGE; COMMUNITY COMPOSITION; DIVERSITY INDEX; ENVIRONMENTAL GRADIENT; METHANE; METHANOGENIC BACTERIUM; MICROBIAL COMMUNITY; MOSS; PEAT SOIL; PEATLAND; PH; SHRUB; SOIL MICROORGANISM; SPATIAL ANALYSIS; TAXONOMY; TURNOVER;

APPALACHIANS; CANADA; ONTARIO [CANADA]; UNITED STATES; WEST VIRGINIA;

ARCHAEA; BRYOPHYTA; OTUS; SPHAGNUM;

EID: 84860113191     PISSN: 01682563     EISSN: 1573515X     Source Type: Journal    
DOI: 10.1007/s10533-011-9644-5     Document Type: Article

References (86)

1. Allison SD, Martiny JBH (2008) Resistance, resilience, and redundancy in microbial communities. Proc Natl Acad Sci USA 105: 11512-11519.
2. Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
3. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2006) New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72: 5734-5741.
4. Basiliko N, Dees PM, Merkel SM, Yavitt JB (2003) Methane biogeochemistry and methanogen communities in two northern peatland ecosystems, New York State. Geomicrobiol J 20: 563-577.
5. Beer J, Lee K, Whiticar M, Blodau C (2008) Geochemical control on organic matter decomposition in a northern peatland. Limnol Oceanogr 53: 1393-1407.
6. Begak DA (1926) Microbiological study of the high-moor peatland: quantitative assessment of bacteria in the high-moor peat. Pochvovedenie 2: 64-75.
7. Bell T (2010) Experimental tests of the bacterial distance-decay relationship. ISME J 4: 1357-1365.
8. Bennett AF, Lenski RE (1993) Evolutionary adaptation to temperature II. Thermal niches of experimental lines of E. coli. Evolution 47: 1-12.
9. Bernard JM, MacDonald JG Jr (1974) Primary production and life history of Carex lacustris. Can J Bot 52: 117-123.
10. Boyd ES, Hamilton TL, Spear JR, Lavin M, Peters JW (2010) [FeFe]-hydrogenase in Yellowstone National Park: evidence for dispersal limitation and phylogenetic niche conservatism. ISME J 4: 1485-1495.
11. 2-utilizing methanogenic enrichment cultures from an acidic peat bog in New York State. FEMS Microbiol Ecol 57: 206-216.
12. 2O fluxes. Biogeochemistry. doi: 10. 1007/s10533-011-9655-2.
13. Bryant JA, Lamanna C, Morlon H, Kerkhoff AJ, Enquist BJ, Green JL (2008) Microbes on mountainsides: contrasting elevational patterns of bacteria and plant diversity. Proc Natl Acad Sci USA 105: 11505-11511.
14. Cadillo-Quiroz H, Bräuer S, Yashiro E, Sun C, Yavitt J, Zinder S (2006) Vertical profiles of methanogenesis and methanogens in two contrasting acidic peatlands in central New York State, USA. Environ Microbiol 8: 1428-1440.
15. Cadillo-Quiroz H, Yashiro E, Yavitt JB, Zinder SH (2008) Characterization of the archaeal community in a minerotrophic fen and terminal restriction fragment length polymorphism-directed isolation of a novel hydrogenotrophic methanogen. Appl Environ Microbiol 74: 2059-2068.
16. Clark JM, Chapman PJ, Adamson JK, Lane SN (2005) Influence of drought-induced acidification on the mobility of dissolved organic carbon in peat soils. Glob Change Biol 11: 791-809.
17. Cohan F, Perry L (2007) A systematics for discovering the fundamental units of bacterial diversity. Curr Biol 17: R373-R386.
18. Colwell R (2005) EstimateS: statistical estimation of species richness and shard species from samples. Version 7. 5. User's guide and application. http://viceroy. eeb. uconn. edu/EstimateS.
19. 2O, and NO). Microbiol Rev 60: 609-640.
20. Conrad R, Erkel C, Liesack W (2006) Rice Cluster I methanogens, an important group of Archaea producing greenhouse gas in soil. Curr Opin Biotechnol 17: 262-267.
21. Davidar P, Rajagopal B, Mohandass D, Puyravaud J-P, Condit R, Wright SJ, Leigh EG (2007) The effect of climatic gradients, topographic variation and species traits on the beta diversity of rain forest trees. Global Ecol Biogeogr 16: 510-518.
22. Dettling MD, Yavitt JB, Zinder SH (2006) Control of carbon mineralization by alternative electron acceptors in four peatlands, central New York State, USA. Wetlands 26: 917-927.
23. Dlugokencky EJ, Nisbet EG, Fisher R, Lowry D (2011) Global atmospheric methane: budget, changes and dangers. Philos Trans R Soc A 369: 2058-2072.
24. Dobrovol'skaya TG, Golovchenko AV, Pankratov TA, Lysak LV, Zvyagintsev DG (2009) Assessment of the bacterial diversity in soils: evolution of approaches and methods. Eurasian Soil Sci 42: 1138.
25. Docherty KM, Balser TC, Bohannan BJM, Gutknecht JLM (2011) Soil microbial responses to fire andinteracting global change factors in a California annual grassland. Biogeochemistry. doi: 10. 1007/s10533-011-9654-3.
26. Duivenvoorden JF, Svenning J-C, Wright SJ (2002) Beta diversity in tropical forests. Science 295: 636-637.
27. Dumbrell AJ, Nelson M, Helgason T, Dytham C, Fitter AH (2010) Relative roles of niche and neutral processes in structuring a soil microbial community. ISME J 4: 337-345.
28. Fierer N (2008) Microbial biogeography: patterns in microbial diversity across space and time. In: Zengler K (ed) Accessing uncultivated microorganisms: from the environment to organisms and genomes and back. ASM Press, Washington, DC, pp 95-115.
29. Fuhrman JA (2009) Microbial community structure and its functional implications. Nature 459: 193-199.
30. Galand PE, Fritxe H, Conrad R, Yrjala K (2005) Pathways for methanogenesis and diversity of methanogenic archaea in three boreal peatland ecosystems. Appl Environ Microbiol 71: 2195-2198.
31. Garcia Jl, Patel BKC, Ollivier B (2000) Taxonomic, phylogenetic and ecological diversity on methanogenic Archaea. Anaerobe 6: 205-226.
32. Good I (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40: 237-264.
33. Grosskopf R, Janssen PH, Liesack W (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.
34. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
35. Hales BA, Edwards C, Ritchie DA, Hall G, Pickup RW, Saunders JR (1996) Isolation and identification of methanogen-specific DNA from blanket bog peat by PCR amplification and sequence analysis. Appl Environ Microbiol 62: 668-675.
36. Hillebrand H, Bennett DM, Cadotte MC (2008) The consequences of dominance: review of evenness effects on local and regional ecosystem processes. Ecology 89: 1510-1520.
37. Horn MA, Matthies C, Kusel K, Schramm A, Drake HL (2003) Hydrogenotrophic methanogenesis by moderately acid-tolerant methanogens of a methane-emitting acidic peat. Appl Environ Microbiol 69: 74-83.
38. Hubbell SP (2001) The unified neutral theory of biodiversity and biogeography. Princeton University Press, Princeton, NJ.
39. Jaccard P (1912) The distribution of the flora in the alpine zone. New Phytol 11: 37-50.
40. Jones MM, Tuomisto H, Clark DB, Olivas P (2006) Effects of mesoscale environmental heterogeneity and dispersal limitation on floristic variation in rain forest ferns. J Ecol 94: 181-195.
41. 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.
42. Kotsyurbenko OR, Chin KJ, Glagolev MV, Stubner S, Simankova MV, Nozhevnikova AN, Conrad R (2004) Acetoclastic and hydrogenotrophic methane production and methanogenic populations in an acidic West-Siberian peat bog. Environ Microbiol 6: 1159-1173.
43. Kurczewski FE (1999) Historic and prehistoric changes in the Rome, New York pine barrens. Northeast Nat 6: 327-340.
44. Lauber CL, Knight R, Hamady M, Fierer N (2009) Soil pH as a predictor of soil bacterial community structure at the continental scale: a pyrosequencing-based assessment. Appl Environ Microbiol 75: 5111-5120.
45. Le Roux PC, McGeoch MA (2008) Rapid range expansion and community reorganization in response to warming. Glob Change Biol 14: 2950-2962.
46. Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
47. Ludwig W, Strunk O, Westram R et al (2004) ARB: a software environment for sequence data. Nucl Acids Res 32: 1363-1371.
48. Lyons KG, Brigham CA, Traut B, Schwartz MW (2005) Rare species and ecosystem functioning. Conserv Biol 19: 1019-1024.
49. Magurran AE (2004) Measuring biological diversity. Blackwell, Oxford.
50. Martiny JBH, Eisen JA, Penn K, Allison SD, Horner-Devine MC (2011) Drivers of bacterial beta-diversity depend on spatial scale. Proc Natl Acad Sci USA 108: 7850-7854.
51. Maxwell JA, Davis MB (1972) Pollen evidence of Pleistocene and Holocene vegetation on the Allegheny Plateau, Maryland. Quatern Res 2: 506-530.
52. McBride MB, Richards BK, Steenhuis T, Russo J, Sauve S (1997) Mobility and solubility of toxic metals and nutrients in soil fifteen years after sludge application. Soil Sci 162: 487-500.
53. Meng L, Hess PGM, Mahowald NM et al (2011) Sensitivity of wetland methane emissions to model assumptions: application and model testing against site observations. Biogeosci Discuss 8: 6095-6160.
54. Moldan F, Wright RF, Lofgren S et al (2001) Long-term changes in acidification and recovery at nine calibrated catchments in Norway, Sweden and Finland. Hydrol Earth Syst Sci 5: 339-350.
55. Moore TR, Basiliko N (2006) Decomposition. Boreal peatland ecosystems. In: Wieder RK, Vitt DH (eds) Ecological studies, vol 188. Springer-Verlag, Berlin.
56. 2 exchange in an ombrotrophic bog. J Ecol 90: 25-36.
57. Morlon H, Chuyong G, Condit R, Hubbell S, Kenfack D, Thomas D, Valencia R, Green JL (2008) A general framework for the distance-decay of similarity in ecological communities. Ecol Lett 11: 94-917.
58. O'Brien EM, Field R, Whittaker RJ (2000) Climatic gradients in woody plant (tree and shrub) diversity: water-energy dynamics, residual variation, and topography. Oikos 89: 588-600.
59. Page SE (2010) Diversity and complexity. Princeton University Press, Princeton, NJ.
60. Posada D (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25: 1253-1256.
61. Prinn R, Jacoby H, Sokolov A et al (1999) Integrated global system model for climate policy assessment: feedbacks and sensitivity studies. Clim Change 41: 469-546.
62. Raghoebarsing AA, Pol A, van de Pas-Schoonen KT et al (2006) A microbial consortium couples anaerobic methane oxidation to denitrification. Nature 440: 918-921.
63. Rosenfeld JS (2002) Functional redundancy in ecology and conservation. Oikos 98: 156-162.
64. Rydin H, Jeglum JK (2006) The biology of peatlands. Oxford University Press, Oxford.
65. Sakai S, Imachi H, Sekiguchi Y, Ohashi A, Harada H, Kamagata Y (2007) Isolation of key methanogens for global methane emission from rice paddy fields: a novel isolate affiliated with the clone cluster Rice Cluster I. Appl Environ Microbiol 73: 4326-4331.
66. Schimel JP, Gulledge J (1998) Microbial community structure and global trace gases. Glob Change Biol 4: 745-758.
67. Schloss PD, Westcott SL, Ryabin T et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
68. Shotyk W (1996) Peat bog archives of atmospheric metal deposition: geochemical evaluation of peat profiles, natural variations in metal concentrations, and metal enrichment factors. Environ Rev 4: 149-183.
69. 4 cycling in a shallow peat fen in Central New York State, USA. Wetlands 26: 20-29.
70. Smemo KA, Yavitt JB (2011) Anaerobic oxidation of methane: an underappreciated aspect of methane cycling in peatland ecosystems? Biogeosciences 8: 779-793.
71. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR et al (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci USA 103: 12115-12120.
72. Soininen J, McDonald R, Hillebrand H (2007) The distance decay of similarity in ecological communities. Ecography 30: 3-12.
73. Steinberg LM, Regan JM (2008) Phylogenetic comparison of the methanogenic communities from an acidic, oligotrophic fen and an anaerobic digester treating municipal wastewater sludge. Appl Environ Microbiol 74: 6663-6671.
74. Todd-Brown KEO, Hopkins FM, Kivlin SM, Talbot JM, Allison SD (2011) A framework for representing microbial decomposition in coupled climate models. Biogeochemistry. doi: 10. 1007/s10533-011-9635-6.
75. Utsumi M, Belova SE, King GM, Uchiyama H (2003) Phylogenetic comparison of methanogen diversity in different wetland soils. J Gen Appl Microbiol 49: 75-83.
76. Verry ES, Brooks KN, Nichols DS, Ferris DR, Sebestyen SD (2011) Watershed hydrology. In: Kolka RK, Sebestyen SD, Verry ES, Brooks KN (eds) Peatland biogeochemistry and watershed hydrology at the Marcell Experimental Forest. CRC Press, Boca Raton, FL, pp 193-212.
77. Waksman SA, Purvis ER (1932) The microbiological population of peat. Soil Sci 34: 95-109.
78. Wallenstein MD, Hall EK (2011) A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning. Biogeochemistry. doi: 10. 1007/s10533-011-9641-8.
79. Walther G-R (2010) Community and ecosystem responses to recent climate change. Philos Trans R Soc B 365: 2019-2024.
80. Whittaker RH (1972) Evolution and measurement of species diversity. Taxon 21: 213-251.
81. Wieder RK (1985) Peat and water chemistry at Big Run Bog, a peatland in the Appalachian Mountains of West Virginia. Biogeochemistry 1: 277-302.
82. Wieder RK, Yavitt JB (1994) Peatlands and global climate change: insights from comparative studies situated along a latitudinal gradient. Wetlands 14: 233-242.
83. Williams CJ, Yavitt JB (2003) Botanical composition of peat and degree of peat decomposition in three temperate peatlands. Ecoscience 10: 85-95.
84. Woodcock S, Curtis TP, Head IM, Lunn M, Sloan WT (2006) Taxa-area relationships for microbes: the undersampled and the unseen. Ecol Lett 9: 805-812.
85. 2 in northern peatlands. Eur J Soil Sci 56: 169-178.
86. Yue JC, Clayton MK (2005) A similarity measure based on species proportions. Commun Stat Theory Methods 34: 2123-2131.