Effects of Elevated CO 2 on Communities of Denitrifying Bacteria and Methanogens in a Temperate Marsh Microcosm

Microbial Ecology

Volumn 64, Issue 2, 2012, Pages 485-498

  Lee, Seung Hoon ^a   Kim, Seon Young ^b   Kang, Hojeong ^a  

^a Yonsei University   (South Korea)

^b National Institute of Environmental Research   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); JUNCUS EFFUSUS; SCIRPUS; TYPHA LATIFOLIA;

CARBON DIOXIDE; METHANE; METHYL COENZYME M REDUCTASE; NITRITE REDUCTASE; OXIDOREDUCTASE;

ARTICLE; BACTERIUM; CHEMISTRY; DENITRIFICATION; DNA SEQUENCE; DRUG EFFECT; ECOSYSTEM; ENZYMOLOGY; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; SOIL; TYPHACEAE; WETLAND;

BACTERIA; CARBON DIOXIDE; DENITRIFICATION; ECOSYSTEM; METHANE; MOLECULAR SEQUENCE DATA; NITRITE REDUCTASES; OXIDOREDUCTASES; SEQUENCE ANALYSIS, DNA; SOIL; SOIL MICROBIOLOGY; TYPHACEAE; WETLANDS;

EID: 84864366932     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-012-0036-8     Document Type: Article

References (66)

1. 2O release and on the community structure of ammonia oxidizers and denitrifiers. Appl Environ Microbiol 68: 5685-5692.
2. 2. Soil Biol Biochem 35: 729-732.
3. Barnard R, Leadley PW, Hungate BA (2005) Global change, nitrification, and denitrification: a review. Glob Giogeochem Cyles 19.
4. 2. Global Change Biol 11: 203-212.
5. Braker G, Fesefeldt A, Witzel K-P (1998) Development of PCR primer system for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl Environ Microbiol 64: 3796-3775.
6. Brussaarda L, de Ruiterb PC, Brown GG (2007) Soil biodiversity for agricultural sustainability. Agric Ecosyst Environ 121: 233-244.
7. Castro HF, Classen AT, Austin EE, Norby RJ, Schadt CW (2010) Soil microbial community response to multiple experimental climate change drivers. Appl Environ Microbiol 76: 999-1007.
8. Cavigelli M, Robertson GP (2000) The functional significance of denitrifier community composition in terrestrial ecosystem. Ecology 81: 1402-1414.
9. Cavigelli M, Robertson GP (2001) Role of denitrifier diversity in rates of nitrous oxide consumption in a terrestrial ecosystem. Soil Biol Biochem 33: 297-310.
10. Conrad R (2006) Microbial ecology of methanogens and methanotrophs. Adv Agron 96: 1-63.
11. 2 on fine root length and distribution in an oak-palmetto scrub ecosystem in central Florida. Global Change Biol 2: 143-148.
12. 2. FEMS Microb Ecol 49: 445-454.
13. Dilly O, Bloem J, Vos A, Munch JC (2004) Bacterial diversity in agricultural soils during litter decomposition. Appl Environ Microbiol 70: 468-474.
14. 2. The ISME Journal 3: 1204-1217.
15. 2 enrichment on microbial community structure in calcareous grassland. Plant Soil 264: 313-323.
16. 2 effects on peatland plant community carbon dynamics and DOC production. Ecosystems 10: 635-647.
17. Fraser LH, Catry SM, Steer D (2004) A test of four plant species to reduce total nitrogen and total phosphorus from soil leachate in subsurface wetland microcosm. Bioresource Tech 94: 185-192.
18. Freeman C, Fenner N, Ostle NJ, Kang H, Dowrick DJ, Reynolds B, Lock MA, Sleep D, Hughes S, Hudson J (2004) Dissolved organic carbon export from peatlands under elevated carbon dioxide levels. Nature 430: 195-198.
19. 2 (Swiss FACE). Soil Biol Biochem 37: 1962-1965.
20. Gersberg RM, Elkins BV, Lyons SR, Goldman CR (1986) Role of aquatic plants in wastewater treatment by artificial wetlands. Water Res 20: 363-368.
21. Grayston SJ, Griffith GS, Mawdsley JL, Campbell CD, Bardgett RD (2001) Accounting for variability in soil microbial communities of temperate upland grassland ecosystems. Soil Biol Biochem 33: 533-551.
22. Groner E, Novoplansky A (2003) Reconsidering diversity-productivity relationships: directness of productivity estimates matters. Ecol Lett 6: 695-699.
23. Gutknecht JLM, Goodman RM, Balser TC (2006) Linking soil process and microbial ecology in freshwater wetland ecosystems. Plant Soil 289: 17-34.
24. 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.
25. Henry S, Bru D, Stres B, Hallet S, Philippot L (2006) Quantitative detection of the nosZ gene, encoding nitrous oxide reductase, and comparison of the abundances of 16S rRNA, narG, nirK, and nosZ genes in soils. Appl Environ Microbiol 72: 5181-5189.
26. Hunt PG, Matheny TA, Szogi AA (2003) Denitrification in constructed wetlands used for treatment of swine wastewater. J Environ Qual 32: 727-735.
27. 2: the Swiss free air carbon dioxide enrichment experiment. Plant Soil 198: 89-95.
28. Intergovernmental Panel on Climate Change (IPCC) (2007) Climate change 2007. Cambridge University Press, Cambridge.
29. 2 alters soil microbial communities associated with trembling aspen (Populus tremuloides) roots. Microb Ecol 50: 102-109.
30. Jossi M, Fromin N, Tarnawski S, Kohler F, Gillet F, Aragno N, Hemelin J (2006) How elevated pCO2 modifies total and metabolically active bacterial communities in the rhizosphere of two perennial grasses grown under field conditions. FEMS Microb Ecol 55: 339-350.
31. Kemnitz D, Chin K-J, Bodelier P, Conrad R (2004) Community analysis of methanogenic archaea within a riparian flooding gradient. Environ Microbiol 6: 449-461.
32. 4 fluxes and biomass production of Phleum pratense on farmed peat soil. Soil Biol Biochem 37: 739-750.
33. Kim S-Y, Lee S-H, Freeman C, Fenner N, Kang H (2008) Comparative analysis of soil microbial community structures and their responses to drought in bog, fen, and riparian wetland. Soil Biol Biochem 40: 2874-2880.
34. 2 enrichment: a synthesis. Acta Oecol 18: 165-176.
35. Lipson DA, Blair M, Barron-Gafford G, Grieve K, Murthy R (2006) Relationship between microbial community structure and soil processes under elevated atmosphere carbon dioxide. Microb Ecol 51: 302-314.
36. Liu X, Tiquia SM, Holguin G, Wu L, Nold SC, Devol AH, Luo K, Palumbo AV, Tiedje JM, Zhou J (2003) Molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the Pacific Coast of Mexico. Appl Environ Microbiol 69: 3549-3560.
37. Long SP, Ainsworth EA, Rogers A, Ort DR (2004) Rising atmospheric carbon dioxide: plants FACE the future. Annu Rev Plant Biol 55: 591-628.
38. Luton PE, Wayne JM, Sharp RJ, Riley PW (2002) The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 148: 3521-3530.
39. Ma K, Conrad R, Lu Y (2012) Response of methanogen mcrA genes and their transcripts to an alternate dry/wet cycle of paddy field soil. Appl Environ Microbiol 78: 445-454.
40. Marschner P, Yang CH, Lieberei R, Crowley DE (2001) Soil and plant species effects on bacterial community composition in the rhizosphere. Soil Biol Biochem 33: 1437-1445.
41. McCann KS (2000) The diversity-stability debate. Nature 405: 228-233.
42. Miethling R, Wieland G, Backhaus H, Tebbe CC (2000) Variation of microbial rhizosphere communities in response to crop species, soil origin, and inoculation with Sinorhizobium meliloti L33. Microb Ecol 40: 43-56.
43. Mitsch WJ, Gosselink JG (1993) Wetlands. Wiley, New York.
44. Mounier E, Hallet S, Cheneby D, Benizri E, Gruet Y, Nguyen C, Piutti S, Robin C, Slezack-Deschaumes S, Martin-Laurent F, Germon JC, Philippot L (2004) Influence of maize mucilage on the diversity and activity of the denitrifying community. Environ Microbiol 6: 301-312.
45. 2 and temperature: a discussion of observations, measurement methods, and models. New Phytologist 162: 311-322.
46. Priemé A, Braker G, Tiedje JM (2002) Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils. Appl Environ Microbiol 68: 1893-1900.
47. Rajaniemi TK (2003) Explaining productivity-diversity relationships in plants. Oikos 101: 449-457.
48. Schimel JP, Gulledge J (1998) Microbial community structure and global trace gases. Global Change Biol 4: 745-758.
49. Sheik CS, Beasley WH, Elshahed MS, Zhou X, Luo Y, Krumholz LR (2011) Effect of warming and drought on grassland microbial communities. ISME J 5: 1692-1700.
50. Šimek 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.
51. Smalla K, Wieland G, Buchner A, Zock A, Parzy J, Kaiser S, Roskot N, Heuer H, Berg G (2001) Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol 67: 4742-4751.
52. Song K, Lee S-H, Mitsch WJ, Kang H (2010) Different responses of denitrification rates and denitrifying bacterial communities to hydrologic pulsing in created wetlands. Soil Biol Biochem 42: 1721-1727.
53. Song K, Lee S-H, Kang H (2011) Denitrification rates and community structure of denitrifying bacteria in newly constructed wetland. Eur J Soil Biol 47: 24-29.
54. 2: comparisons of mass loss of litter with soil respiration and soil microbial biomass. Soil Biol Biochem 32: 1359-1366.
55. 2 in the rhizosphere of perennial grasses. Soil Biol Biochem 38: 1193-1201.
56. Urbanová Z, Picek T, Bárta J (2011) Effect of peat re-wetting on carbon and nutrient fluxes, greenhouse gas production and diversity of methanogenic archaeal community. Ecol Eng 37: 1017-1026.
57. Vale M, Nguyen C, Dambrine E, Dupouey JL (2005) Microbial activity in the rhizosphere soil of six herbaceous species cultivated in a greenhouse is correlated with shoot biomass and root C concentrations. Soil Biol Biochem 37: 2329-2333.
58. 2 levels. Ecol Appl 1: 175-181.
59. Waldrop MP, Zak DP, Blackwood CB, Curtis CD, Tilman D (2006) Resource availability controls fungal diversity across a plant diversity gradient. Ecol Lett 9: 1127-1135.
60. Whitman WB, Jeanthon C (2006) Methanococcales. Prokaryotes 3: 257-273.
61. Wolsing M, Priemé A (2004) Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments. FEMS Microb Ecol 48: 261-71.
62. Yan T, Fields MW, Wu L, Zu Y, Tiedje JM, Zhou J (2003) Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater. Environ Microbiol 5: 13-24.
63. Yang H-S, Kim C (2007) The riparian vegetation of close-to-nature river and streams in Korea. Korean J Plant Resources 20: 234-241.
64. Yin B, Crowley D, Sparovek G, Jose de Melo W, Borneman J (2000) Bacterial functional redundancy along a soil reclamation gradient. Appl Environ Microbiol 66: 4361-4365.
65. Zhou J, Xia B, Treves DA, Wu L-Y, Marsh TL, O'Neill RV, Palumbo AV, Tiedje JM (2002) Spatial and resource factors influencing high microbial diversity in soil. Appl Environ Microbiol 68: 326-334.
66. Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 61: 533-616.