The effects of pH change and NO-3 pulse on microbial community structure and function: A vernal pool microcosm study

FEMS Microbiology Ecology

Volumn 81, Issue 3, 2012, Pages 660-672

  Carrino Kyker, Sarah R ^a,b   Smemo, Kurt A ^b,c   Burke, David J ^a,b  

^a CASE WESTERN RESERVE UNIVERSITY   (United States)

^b Holden Arboretum   (United States)

^c KENT STATE UNIVERSITY   (United States)

Author keywords

Bacteria; Denitrification; Denitrifiers; Fungi; Respiration

Indexed keywords

FRESH WATER; NITRATE;

BACTERIUM; COMMUNITY STRUCTURE; DENITRIFICATION; EPHEMERAL POOL; FUNGUS; MICROBIAL COMMUNITY; MICROCOSM; PH; RESPIRATION;

ARTICLE; BACTERIUM; CHEMISTRY; CLASSIFICATION; DENITRIFICATION; ECOSYSTEM; FUNGUS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; PH; PLANT LEAF; SEASON; SOIL; TREE;

BACTERIA; DENITRIFICATION; ECOSYSTEM; FRESH WATER; FUNGI; HYDROGEN-ION CONCENTRATION; NITRATES; PLANT LEAVES; SEASONS; SOIL; SOIL MICROBIOLOGY; TREES;

BACTERIA (MICROORGANISMS); FUNGI;

EID: 84864616864     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2012.01397.x     Document Type: Article

References (67)

1. Attard E, Recous S, Chabb A, De Berranger C, Guillaumaud N, Labreuches J, Philippot L, Schmid B & Le Roux X (2011) Soil environmental conditions rather than denitrifier abundance and diversity drive potential denitrification after changes in land uses. Glob Change Biol 17: 1975-1989.
2. Balser TC & Firestone MK (2005) Linking microbial community composition and soil processes in a California annual grassland and mixed-conifer forest. Biogeochemistry 73: 395-415.
3. Balser TC, Kinzig AP & Firestone MK (2001) Linking soil microbial communities and ecosystem functioning. The Functional Consequences of Biodiversity (Kinzig AP, Pacala SW & Tilman D, eds), pp. 265-293. Princeton University Press, Princeton, NJ.
4. Bell T, Newman JA, Silverman BW, Turner SL & Lilley AK (2005) The contribution of species richness and composition to bacterial services. Nat Lett 436: 1157-1160.
5. Bell CW, Acosta-Martinez V, McIntyre NE, Cox S, Tissue DT & Zak JC (2009) Linking microbial community structure and function to seasonal differences in soil moisture and temperature in a chihuahuan desert grassland. Microb Ecol 58: 827-842.
6. 2 of microbial communities in forest soils. Soil Biol Biochem 30: 1269-1274.
7. Booth IR (1985) Regulation of cytoplasmic pH in bacteria. Microbiol Rev 49: 359-378.
8. Brooks RT (2000) Annual and seasonal variation and the effects of hydroperiod on benthic macroinvertebrates of seasonal forest ("vernal") ponds in central Massachusetts, USA. Wetlands 20: 707-715.
9. Burke DJ, Martin KJ, Rygiewicz PT & Topa MA (2005) Ectomycorrhizal fungi identification in single and pooled root samples: terminal restriction fragment length polymorphism (TRFLP) and morphotyping compared. Soil Biol Biochem 37: 1683-1694.
10. Burke DJ, Kretzer AM, Rygiewicz PT & Topa MA (2006) Soil bacterial diversity in a loblolly pine plantation: influence of ectomycorrhizas and fertilization. FEMS Microbiol Ecol 57: 409-419.
11. Burke DJ, Dunham SM & Kretzer AM (2008) Molecular analysis of bacterial communities associated with the roots of Douglas fir (Pseudotsuga menziesii) colonized by different ectomycorrhizal fungi. FEMS Microbiol Ecol 65: 299-309.
12. Carrino-Kyker SR & Swanson AK (2007) Seasonal physicochemical characteristics of thirty Northern Ohio temporary pools along gradients of GIS-delineated human land-use. Wetlands 27: 749-760.
13. Carrino-Kyker SR & Swanson AK (2008) Temporal and spatial patterns of eukaryotic and bacterial communities found in Ohio vernal pools as determined by denaturing gradient gel electrophoresis. Appl Environ Microbiol 74: 2554-2557.
14. Carrino-Kyker SR, Swanson AK & Burke DJ (2011) Changes in eukaryotic microbial communities of vernal pools along an urban-rural land use gradient. Aquat Microb Ecol 62: 13-24.
15. Cavigelli MA & Robertson GP (2000) The functional significance of denitrifier community composition in a terrestrial ecosystem. Ecology 81: 1402-1414.
16. Chu Z, Jin X, Iwami N & Inamori Y (2007) The effect of temperature on growth characteristics and competitions of Microcystis aeruginosa and Oscillatoria mougeotii in a shallow, eutrophic lake simulator system. Hydrobiologia 581: 217-223.
17. Colburn EA (2004) Vernal Pools: Natural History and Conservation. The McDonald and Woodward Publishing Company, Blacksburg, VA.
18. Dandie CE, Wertz S, Leclair CL, Goyer C, Burton DL, Patten CL, Zebarth BJ & Trevors JT (2011) Abundance, diversity and functional gene expression of denitrifier communities in adjacent riparian agricultural zones. FEMS Microbiol Ecol 72: 69-82.
19. Dangles O, Gessner MO, Geurold F & Chauvet E (2004) Impacts of stream acidification on litter breakdown: implications for assessing ecosystem functioning. J Appl Ecol 41: 365-378.
20. Deiglmayr K, Philippot L & Kandeler E (2006) Functional stability of the nitrate-reducing community in grassland soils towards high nitrate supply. Soil Biol Biochem 38: 2980-2984.
21. Demoling F, Nilsson LO & Bååth E (2008) Bacteria and fungal response to nitrogen fertilization in three coniferous forest soils. Soil Biol Biochem 40: 370-379.
22. Dong L, Smith CJ, Papaspyrou S, Stott A, Osborn AM & Nedwell DB (2009) Changes in benthic denitrification, nitrate ammonification, and annamox process rates and nitrate and nitrite reductase gene abundances along an estuarine gradient (the Colne estuary, United Kingdom). Appl Environ Microbiol 75: 3171-3179.
23. Dorea CC & Clarke BA (2008) Effect of aluminium on microbial respiration. Water Air Soil Pollut 89: 353-358.
24. Edwards IP, Zak DR, Kellner H, Eisenlord SD & Pregitzer KS (2011) Simulated atmospheric N deposition alters fungal community composition and suppresses ligninolytic gene expression in a northern hardwood forest. PLoS ONE 6: e20421.
25. Enwall K, Philippot L & Hallin S (2005) Activity and composition of the denitrifying bacterial community respond differently to long-term fertilization. Appl Environ Microbiol 71: 8335-8343.
26. Fierer N & Jackson RB (2006) The diversity and biogeography of soil bacterial communities. P Natl Acad Sci USA 103: 626-631.
27. Graham DW, Trippett C, Dodds WK, O'Brien JM, Banner EBK, Head IM, Smith MS, Yang RK & Knapp CW (2010) Correlations between in situ denitrification activity and nir-gene abundances in pristine and impacted prairie streams. Environ Pollut 158: 3225-3229.
28. Groffman PM, Holland EA, Myrold DD, Robertson GP & Zou X (1999) Denitrification. Standard Soil Methods for Long-Term Ecological Research (Robertson GP, Coleman DC, Bledsoe CS & Sollins P, eds), pp. 272-288. Oxford University Press, New York, NY.
29. Gutknecht JLM, Goodman RM & Balser TC (2006) Linking soil process and microbial ecology in freshwater wetland ecosystems. Plant Soil 289: 17-34.
30. Hallin S, Jones CM, Schloter M & Philippot L (2009) Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment. ISME J 3: 597-605.
31. - deposition in a northern hardwood forest? Microb Ecol 57: 728-739.
32. 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.
33. Kandeler E, Deiglmayr K, Tscherko D, Bru D & Philippot L (2006) Abundance of narG, nirS, nirK, and nosZ genes of denitrifying bacteria during primary successions of a glacier foreland. Appl Environ Microbiol 72: 5957-5962.
34. Kandeler E, Brune T, Enowashu E, Dörr N, Guggenberger G, Lamersdorf N & Philippot L (2009) Response of total and nitrate-dissimilating bacteria to reduced N deposition in a spruce forest soil profile. FEMS Microbiol Ecol 67: 444-454.
35. Knowles R (1982) Denitrification. Microbiol Rev 46: 46-70.
36. Kutner MH, Nachtsheim CJ, Neter J & Li W (2005) Applied Linear Statistical Models. The McGraw-Hill Companies, New York, NY.
37. Laposata MM & Dunson WA (1998) Effects of boron and nitrate on hatching success of amphibian eggs. Arch Environ Contam Toxicol 35: 615-619.
38. Lauber CL, Hamady M, Knight R & Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75: 5111-5120.
39. Ma WK, Bedard-Haughn A, Siciliano SD & Farrell RE (2008) Relationship between nitrifier and denitrifier community composition and abundance in predicting nitrous oxide emissions from ephemeral wetland soils. Soil Biol Biochem 40: 1114-1123.
40. Madigan MT, Martinko JM & Parker J, eds (2003) Brock Biology of Microorganisms. Pearson Education Inc., Upper Saddle River, NJ.
41. Martin KJ & Rygiewicz PT (2005) Fungal specific primers developed for analysis of the ITS region of environmental DNA extracts. BMC Microbiol 5: 28.
42. McArthur JV (2006) Microbial Ecology: An Evolutionary Approach. Elsevier Inc., Burlington, MA.
43. McCune B & Grace JB (2002) Analysis of Ecological Eommunities. MjM Software Design, Gleneden Beach, OR.
44. McGrady-Steed J, Harris PM & Morin PJ (1997) Biodiversity regulates ecosystem predictability. Nature 390: 162-165.
45. 4 oxidation without altering community composition of soil methanotrophs. Soil Biol Biochem 42: 101-107.
46. Moldan B & Černý J, eds (1994) Biogeochemistry of Small Catchments. John Wiley & Sons Ltd, Chichester.
47. Morales SE, Cosart T & Holben WE (2010) Bacterial gene abundances as indicators of greenhouse gas emissions in soils. ISME J 4: 799-808.
48. Muyzer G, de Waal EC & Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695-700.
49. Muyzer G, Teske A & Wirsen CP (1995) Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol 164: 165-172.
50. Nielsen UN, Ayres E, Wall DH & Bardgett RD (2011) Soil biodiversity and carbon cycling: a review and synthesis of studies examining diversity-function relationships. Eur J Soil Sci 62: 105-116.
51. Parkin TB, Sexstone AJ & Tiedje JM (1985) Adaptation of denitrifying populations to low soil pH. Appl Environ Microbiol 49: 1053-1056.
52. Philippot L & Hallin S (2006) Molecular analyses of soil denitrifying bacteria. Molecular Techniques for Soil, Rhizosphere and Plant Microorganisms (Cooper JE & Rao JR, eds), pp. 146-165. CAB International Pub, Cambridge, MA.
53. Rao SS, Paolini D & Leppard GG (1984) Effects of low-pH stress on morphology and activity of bacteria from lakes receiving acid precipitation. Hydrobiologia 114: 115-121.
54. Rich JJ & Myrold DD (2004) Community composition and activities of denitrifying bacteria from adjacent agricultural soil, riparian soil, and creek sediment in Oregon, USA. Soil Biol Biochem 36: 1431-1441.
55. Rich JJ, Heichen RS, Bottomley PJ, Cromack K & Myrold DD (2003) Community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils. Appl Environ Microbiol 69: 5974-5982.
56. 2-fixing, and total-community bacteria by terminal restriction fragment length polymorphism analysis using multiple restriction enzymes. Appl Environ Microbiol 71: 2026-2035.
57. Rösch C, Mergel A & Bothe H (2002) Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil. Appl Environ Microbiol 68: 3818-3829.
58. Rousk J, Bååth E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, Knight R & Fierer N (2010) Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J 4: 1340-1351.
59. Šimek M, Jíŝová L & Hopkins DW (2002) What is the so-called optimum pH for denitrification in soil? Soil Biol Biochem 34: 1227-1234.
60. Smucker NJ & Vis ML (2011) Acid mine drainage affects the development and function of epilithic biofilms in streams. J N Am Benthol Soc 30: 728-738.
61. Stumm W & Morgan JJ (1996) Aquatic Chemistry, Chemical Equilibria and Rates in Natural Waters, 3rd edn. John Wiley & Sons, Inc., New York, NY.
62. 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.
63. van der Valk AG (2006) The Biology of Freshwater Wetlands. Oxford University Press, Oxford, UK.
64. Wallenstein MD, Myrold DD, Firestone M & Voytek M (2006) Environmental controls on denitrifying communities and denitrification rates: insights from molecular methods. Ecol Appl 16: 2143-2152.
65. Wetzel RG (2001) Limnology: Lake and River Ecosystems, 3rd edn. Academic Press, San Diego, CA.
66. Williams DD (2006) The Biology of Temporary Waters. Oxford University Press, Oxford, UK.
67. Yoshinari T & Knowles R (1976) Acetylene inhibition of nitrous oxide reduction by denitrifying bacteria. Biochem Biophys Res Commun 69: 705-710.