Temporal changes in methane oxidizing and denitrifying communities and their activities in a drained peat soil

Wetlands

Volumn 32, Issue 6, 2012, Pages 1047-1055

  Andert, Janet ^a,b,c   Börjesson, Gunnar ^a   Hallin, Sara ^a  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^b MAX PLANCK INSTITUTE OF COLLOIDS AND INTERFACES   (Germany)

^c LEIBNIZ INSTITUTE FOR AGRICULTURAL ENGINEERING AND BIOECONOMY ATB   (Germany)

Author keywords

Denitrification; GHG emissions; Methane oxidation; Nitrous oxide; Organic soil

Indexed keywords

BACTERIUM; COMMUNITY COMPOSITION; DENITRIFICATION; GREENHOUSE GAS; METHANE; METHANOTROPHY; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; OXIDATION; PEAT SOIL; PH; SOIL DEPTH; SOIL MICROORGANISM; SOIL PROFILE; TEMPORAL VARIATION;

SWEDEN;

BACTERIA (MICROORGANISMS);

EID: 84871498983     PISSN: 02775212     EISSN: 19436246     Source Type: Journal    
DOI: 10.1007/s13157-012-0335-3     Document Type: Article

References (52)

1. Alm J, Saarnio S, Nykänen H, Silvola J, Martikainen PJ (1999) Winter CO2, CH4 and N2O fluxes on some natural and drained boreal peatlands. Biogeochemistry 44:163-186
2. Belova SE, Baani M, Suzina NE, Bodelier PLE, Liesack W, Dedysh SN (2011) Acetate utilization as a survival strategy of peatinhabiting Methylocystis spp. Environ Microbiol 3:36-46
3. Blume E, Bischoff M, Reichert JM, Moorman T, Konopka A, Turco RF (2002) Surface and subsurface microbial biomass, community structure and metabolic activity as a function of soil depth and season. Appl Soil Ecol 20:171-181
4. Bodelier PLE, Laanbroek HJ (2004) Nitrogen as a regulatory factor of methane oxidation in soils and sediments. FEMS Microbiol Ecol 47:265-277
5. Bodelier PLE, Roslev P, Henckel T, Frenzel P (2000) Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice roots. Nature 403:421-424
6. Bowman J (2006) The methylotrophs - The families Methylococcaceae and Methylocystaceae. In: Dworkin M et al (eds) The prokaryotes. Springer, New York, pp 266-289
7. Bull ID, Parekh NR, Hall GH, Ineson P, Evershed RP (2000) Detection and classification of atmospheric methane oxidizing bacteria in soil. Nature 405:175-178
8. Conrad R (1996) Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO). Microbiol Rev 60:609-640
9. Costello AM, Lidstrom ME (1999) Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments. Appl Environ Microbiol 65:5066-5074
10. Dannenmann M, Butterbach-Bahl K, Gasche R, Willibald G, Papen H (2008) Dinitrogen emissions and the N2:N2O emission ratio of a Rendzic Leptosol as influenced by pH and forest thinning. Soil Biol Biochem 40:2317-2323
11. Dedysh SN, Knief C, Dunfield PF (2005) Methylocella species are facultatively methanotrophic. J Bacteriol 187:4665-4670
12. Enwall K, Hallin S (2009) Comparison of T-RFLP and DGGE techniques to assess denitrifier community composition in soil. Lett Appl Microbiol 48:145-148
13. Enwall K, Philippot L, Hallin S (2005) Activity and composition of the denitrifying community respond differently to long-term fertilization. Appl Environ Microbiol 71:8335-8343
14. Ettwig KF, Butler MK et al (2010) Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 464:543-548
15. Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci U S A 103:626-631
16. Firestone MK, Firestone RB, Tiedje JM (1980) Nitrous oxide from soil denitrification: factors controlling its biological production. Science 208:749-751
17. Gorham E (1991) Northern Peatlands: role in the carbon cycle and probable responses to climatic warming. Ecol Appl 1:182-195
18. Gulledge J, Schimel JP (1998) Low-concentration kinetics of atmospheric CH4 oxidation in soil and mechanism of NH4 + inhibition. Appl Environ Microbiol 64:4291-4298
19. Hoffmann T, Horz H-P, Kemnitz D, Conrad R (2002) Diversity of the particulate methane monooxygenase gene in methanotrophic samples from different rice field soils in China and the Philippines. Syst Appl Microbiol 25:267-274
20. Holmes AJ, Costello A, Lidstrom ME, Murrell CJ (1995) Evidence that participate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol Lett 132:203-208
21. Holtan-Hartwig L, Dörsch P, Bakken LR (2002) Low temperature control of soil denitrifying communities: kinetics of N2O production and reduction. Soil Biol Biochem 34:1797-1806
22. Horz H-P, Yimga MT, Liesack W (2001) Detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoA, mmoX, mxaF and 16S rRNA and ribosomal DNA, including pmoA-based Terminal Restriction Length Polymorphism profiling. Appl Environ Microbiol 67:4177-4185
23. Horz H-P, Rich V, Avrahami S, Bohannan BJM (2005) Methaneoxidizing bacteria in a California upland soil: diversity and response to simulated global change. Appl Environ Microbiol 71:2642-2652
24. Im J, Lee S-W, Yoon S, DiSpirito AA, Semrau JD (2011) Characterization of a novel facultative Methylocystis species capable of growth on methane, acetate and ethanol. Environ Microbiol Rep 3:174-181
25. Jones CM, Stres B, Rosenquist M, Hallin S (2008) Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification. Mol Biol Evol 25:1955-1966
26. Jones CM, Welsh A, Throbäck IN, Dörsch P, Bakken LR, Hallin S (2011) Phenotypic and genotypic heterogeneity among closely related soil-borne N2-and N2O-producing Bacillus isolates harboring the nosZ gene. FEMS Microbiol Ecol 76:541-552
27. Kesik M, Blagodatsky S, Papen H, Butterbach-Bahl K (2006) Effect of pH, temperature and substrate on N2O, NO and CO2 production by Alcaligenes faecalis. J Appl Microbiol 101:655-667
28. Knittel K, Boetius A (2009) Anaerobic oxidation of methane: progress with an unknown process. Annu Rev Microbiol 63:311-334
29. Lai DYF (2009) Methane dynamics in northern peatlands: a review. Pedosphere 19:409-421
30. Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencingbased assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75:5111-5120
31. LeMer J, Roger P (2001) Production, oxidation and consumption of methane by soils: a review. Eur J Soil Biol 37:25-50
32. Maljanen M, Hytönen J, Martikainen PJ (2001) Fluxes of N2O, CH4 and CO2 on afforested boreal agricultural soils. Plant Soil 231:113-121
33. Martikainen PJ, Nykänen H, Alm J, Silvola J (1995) Change in fluxes of carbon dioxide, methane and nitrous oxide due to forest drainage of mire sites of different trophy. Plant Soil 168:571-577
34. Mohanty SR, Bodelier PLE, Floris V, Conrad R (2006) Differential effects of nitrogenous fertilizers on methane-consuming microbes in rice field and forest soils. Appl Environ Microbiol 72:1346-1354
35. Murrell JC, McDonald IR, Bourne DG (1998) Molecular methods for the study of methanotroph ecology. FEMS Microbiol Ecol 27:103-114
36. Naeem S (1998) Species redundancy and ecosystem reliability. Conserv Biol 12:39-45
37. Nedwell DB, Watson A (1995) CH4 production, oxidation and emission in a UK ombrotrophic peat bog: influence of SO4 2-from acid rain. Soil Biol Biochem 27:893-903
38. Nykanen H, Alm J, Lang K, Silvola J, Martikainen PJ (1995) Emissions of CH4, N2O and CO2 from a virgin fen and a fen drained for grassland in Finland. J Biogeogr 22:351-357
39. Palmer K, Drake HL, Horn MA (2010) Association of novel and highly diverse acid-tolerant denitrifiers with N2O fluxes of an acidic fen. Appl Environ Microbiol 76:1125-1134
40. Pell M, Stenberg B, Stenström J, Torstensson L (1996) Potential denitrification activity assay in soil - with or without chloramphenicol? Soil Biol Biochem 28:393-398
41. Philippot L, Hallin S, Schloter M (2007) Ecology of denitrifying prokaryotes in agricultural soil. Adv Agron 96:249-305
42. Ravishankara AR, Daniel JS, Portmann RW (2009) Nitrous oxide (N2O): the dominant ozone-depleting substance emitted in the 21st century. Science 326:123-125
43. Regina K, Nykänen H, Silvola J, Martikainen P (1996) Fluxes of nitrous oxide from boreal peatlands as affected by peatland type, water table level and nitrification capacity. Biogeochemistry 35:401-418
44. Regina K, Syväsalo E, Hannukkala A, Esala M (2004) Fluxes of N2O from farmed peat soils in Finland. Eur J Soil Sci 55:591-599
45. Robertson GP, Tiedje JM (1987) Nitrous oxide sources in aerobic soils: nitrification, denitrification and other biological processes. Soil Biol Biochem 19:187-193
46. Simek M, Cooper JE (2002) The influence of soil pH on denitrification: progress towards the understanding of this interaction over the last 50 years. Eur J Soil Sci 53:345-354
47. Smemo KA, Yavitt JB (2011) Anaerobic oxidation of methane: an underappreciated aspect of methane cycling in peatland ecosystems? Biogeosciences 8:779-793
48. Stralis-Pavese N, Sessitsch A, Weilharter A, Reichenauer T, Riesing J, Csontos J, Murrell CJ, Bodrossy L (2004) Optimization of diagnostic microarray for application in analyzing landfill methanotroph communities under different plant covers. Environ Microbiol 6:401-417
49. Thomsen J, Geest T, Cox R (1994) Mass-spectrometric studies of the effect of pH on the accumulation of intermediates in denitrification by Paracoccus denitrificans. Appl Environ Microbiol 60:536-541
50. Throbäck IN, Enwall K, Jarvis Å, Hallin S (2004) Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiol Ecol 49:401-417
51. Walker BH (1992) Biodiversity and ecological redundancy. Conserv Biol 6:18-23
52. Weslien P, Klemedtsson ÅK, Börjesson G, Klemedtsson L (2009) Strong pH influence on N2O and CH4 fluxes from forested organic soils. Eur J Soil Sci 60:311-320