Resource availability effects on nitrate-reducing microbial communities in a freshwater wetland

Wetlands

Volumn 33, Issue 2, 2013, Pages 301-310

  Morrissey, Ember M ^a   Jenkins, Amy S ^a   Brown, Bonnie L ^a   Franklin, Rima B ^a  

^a VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

Author keywords

Carbon lability; Denitrification; Dissimilatory nitrate reduction to ammonium; Microbial community structure; Nitrate reduction; Soil organic matter

Indexed keywords

ABUNDANCE; AMMONIUM; COMMUNITY STRUCTURE; DENITRIFICATION; FRESHWATER ENVIRONMENT; MICROBIAL COMMUNITY; NITRATE; RESOURCE AVAILABILITY; SOIL MICROORGANISM; SOIL ORGANIC MATTER; WETLAND;

EID: 84902477159     PISSN: 02775212     EISSN: 19436246     Source Type: Journal    
DOI: 10.1007/s13157-013-0384-2     Document Type: Article

References (58)

1. Allison SD, Martiny JBH (2008) Resistance, resilience, and redundancy in microbial communities. Proceedings of the National Academy of Sciences USA 105:11512-11519
2. An S, Gardner W (2002) Dissimilatory nitrate reduction to ammonium (DNRA) as a nitrogen link, versus denitrification as a sink in a shallow estuary (Laguna Madre/Baffin Bay, Texas). Marine Ecology Progress Series 237:41-50
3. Antil RS, Bar Tal A, Fine P, Hadas A (2011) Predicting nitrogen and carbon mineralization of composted manure and sewage sludge in soil. Compost Science Utilization 19:33-43
4. Attard E, Recous S, Chabbi A, De Berranger C, Guillaumaud N, Labreuche J, Philippot L, Schmid B, Roux L (2011) Soil environmental conditions rather than denitrifier abundance and diversity drive potential denitrification after changes in land uses. Global Change Biology 17:1975-1989
5. Baxter A, Johnson L, Edgerton J, Royer T, Leff L (2012) Structure and function of denitrifying bacterial assemblages in low-order Indiana streams. Freshwater Science 31:304-317
6. Bruland GL, Richardson CJ, Daniels WL (2009) Microbial and geochemical responses to organic matter amendments in a created wetland. Wetlands 29:1153-1165
7. Burchell MR II, Skaggs RW, Lee CR, Broome S, Chescheir GM, Osborne J (2007) Substrate organic matter to improve nitrate removal in surface-flow constructed wetlands. Journal of Environmental Quality 36:194-207
8. Burgin A, Hamilton S (2007) Have we overemphasized the role of denitrification in aquatic ecosystems? A review of nitrate removal pathways. Frontiers in Ecology and the Environment 5:89-96
9. Button D (1993) Nutrient-limited microbial growth kinetics: overview and recent advances. Anton Van Leeuwenhoek 63:225-235
10. Canfield D, Glazer A, Falkowski P (2010) The evolution and future of Earth's nitrogen cycle. Science 330:192-196
11. Conrad R (1996) Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO). Microbiology Reviews 60:609-640
12. Dang H, Wang C, Li J, Li T, Tian F, Jin W, Ding Y, Zhang Z (2009) Diversity and distribution of sediment nirS-encoding bacterial assemblages in response to environmental gradients in the eutrophiedJiaozhou Bay, China. Microbial Ecology 58:161-169
13. Davis L (1995) A handbook of constructed wetlands: A guide to creating wetlands for-agricultural wastewater, domestic wastewater, coal mine drainage, stormwater in the Mid-Atlantic Region. USDA-Natural Resources Conservation Service and the US Environmental Protection Agency, 55 pp
14. Dimitriu P, Lee D, Grayston S (2010) An evaluation of the functional significance of peat microorganisms using a reciprocal transplant approach. Soil Biology and Biochemistry 42:65-71
15. Dodla S, Wang J, DeLaune R, Cook R (2008) Denitrification potential and its relation to organic carbon quality in three coastal wetland soils. Science of the Total Environment 407:471-480
16. Doutereol I, Goulder R, Lillie M (2010) Soil microbial community response to land-management and depth, related to the degradation of organic matter in English wetlands: Implications for the in situ preservation of archaeological remains. Applied Soil Ecology 44:219-227
17. Erler DV, Eyre BD, Davison L (2008) The contribution of anammox and denitrification to sediment N2 production in a surface flow constructed wetland. Environmental Science and Technology 42:9144-9150
18. Fierer N, Bradford M, Jackson R (2007) Toward an ecological classification of soil bacteria. Ecology 88:1354-1364
19. Fisher J, Acreman M (2004) Wetland nutrient removal: a review of the evidence. Hydrology and Earth System Science 8:673-685
20. Fleming-Singer MS, Horne AJ (2002) Enhanced nitrate removal efficiency in wetland microcosms using an episediment layer for denitrification. Environmental Science and Technology 36:1231-1237
21. Fuhrman J (2009) Microbial community structure and its functional implications. Nature 459:193-199
22. Hammer O. (2001) PAST: Paleontological statistics software package for education and data analysis. Palaeontol Electron 4:1-9
23. Hill A, Cardaci M (2004) Denitrification and organic carbon availability in riparian wetland soils and subsurface sediments. Soil Science Society of America Journal 68:320-325
24. Jones C, Hallin S (2010) Ecological and evolutionary factors underlying global and local assembly of denitrifier communities. ISME Journal 4:633-642
25. Jones C, 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. Molecular Biology and Evolution 25:1955-1966
26. Kadlec R (2012) Constructed marshes for nitrate removal. Critical Reviews in Environmental Science and Technology 42:934-1005
27. Kiesel B, Balcke G, Dietrich J, Vogt C, Geyer R (2008) Microbial community shifts as a response to efficient degradation of chlorobenzene under hypoxic conditions. Biodegradation 19:435-446
28. Koop-Jakobsen K, Giblin A (2009) Anammox in tidal marsh sediments: the role of salinity, nitrogen loading, and marsh vegetation. Estuaries and Coasts 32:238-245
29. Koop-Jakobsen K, Giblin A (2010) The effect of increased nitrate loading on nitrate reduction via denitrification and DNRA in salt marsh sediments. Limnology and Oceanography 55:789-802
30. Kovárová-Kovar K, Egli T (1998) Growth kinetics of suspended microbial cells: From single-substrate-controlled growth to mixed-substrate kinetics. Microbiology and Molecular Biology Reviews 62:646-666
31. Krishnani K (2010) Detection and diversity of nitrifying and denitrifying functional genes in coastal aquaculture. Aquaculture 302:57-70
32. Lam P, Lavik G, Jensen MM, van deVossenberg J, Schmid M,WoebkenD, Gutierrez D, Amann R, JettenMS, KuypersMM(2009) Revising the nitrogen cycle in the Peruvian oxygen minimum zone. Proceedings of the National Academy of Sciences USA 106:4752-4757
33. Lou Y, Ren L, Li Z, Zhang T, Inubushi K (2007) Effect of rice residues on carbon dioxide and nitrous oxide emissions from a paddy soil of subtropical China. Water Air and Soil Pollution 178:157-168
34. Ma H, Aelion C (2005) Ammonium production during microbial nitrate removal in soil microcosms from a developing marsh estuary. Soil Biology and Biochemistry 37:1869-1878
35. Magalhaes C, Bano N, Wiebe W, Bordalo A, Hollibaugh J (2008) Dynamics of nitrous oxide reductase genes (nosZ) in intertidal rocky biofilms and sediments of the Douro River Estuary (Portugal), and their relation to N-biogeochemistry. Microbial Ecology 55:259-269
36. Mohan S, Schmid M, Jetten M, Cole J (2004) Detection and widespread distribution of the nrfAgene encoding nitrite reduction to ammonia, a short circuit in the biological nitrogen cycle that competes with denitrification. FEMS Microbiology Ecology 49:433-443
37. Moore T, Trofymow J, Siltanen M, Prescott C (2005) Patterns of decomposition and carbon, nitrogen, and phosphorus dynamics of litter in upland forest and peatland sites in central Canada. Canadian Journal of Forest Research 35:133-142
38. Nizzoli D, Carraro E, Nigro V, Viaroli P (2010) Effect of organic enrichment and thermal regime on denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in hypolimnetic sediments of two lowland lakes. Water Research 44:2715-2724
39. Oksanen JF, Blanchet G, Kindt R, Legendre P, Minchin PR, O'Hara RB, Simpson GL, Solymos PM, Stevens HH, Wagner H (2012) vegan: Community Ecology Package. R package version 2.0-3
40. Peralta A, Matthews J, Kent A (2010) Microbial community structure and denitrification in a wetland mitigation bank. Applied and Environmental Microbiology 76:4207-4215
41. Philippot L, Hallin S (2005) Finding the missing link between diversity and activity using denitrifying bacteria as a model functional community. Current Opinions in Microbiology 8:234-239
42. Reddy R, DeLaune R (2008) Biogeochemistry of wetlands: science and applications. CRC Press Taylor and Francis Group, Boca.
43. Raton Reed H, Martiny J (2007) Testing the functional significance of microbial composition in natural communities. FEMS Microbiology Ecology 62:161-170
44. Sall J (2005) JMP start statistics: a guide to statistics and data analysis using JMP and JMP IN software. SAS Institute Inc, Cary.
45. Scott J, McCarthy M, Gardner W, Doyle R (2008) Denitrification, dissimilatory nitrate reduction to ammonium, and nitrogen fixation along a nitrate concentration gradient in a created freshwater wetland. Biogeochemistry 87:99-111.
46. Smith C, Nedwell D, Dong L, Osborn AM (2007) Diversity and abundance of nitrate reductase genes (narGand napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments. Applied and Environmental Microbiology 73:3612-3622
47. Song K, Lee S, Kang H (2011) Denitrification rates and community structure of denitrifying bacteria in newly constructed wetland. European Journal of Soil Biology 47:24-29
48. Sutton-Grier A, Ho M, Richardson C (2009) Organic amendments improve soil conditions and denitrification in a restored riparian wetland. Wetlands 29:343-352
49. Takeuchi J (2006) Habitat segregation of a functional gene encoding nitrate ammonification in estuarine sediments. Geomicrobiology Journal 23:75-87
50. Tang H, Yan K, Zhang L, Chi F, Li Q, Lian S, Wei D (2010) Diversity analysis of nitrite reductase genes (nirS) in black soil under different long-term fertilization conditions. Annals of Microbiology 60:97-104
51. Throback I, Enwall K, Jarvis A, Hallin S (2004) Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiology Ecology 49:401-417
52. Thullner M, Regnier P, Van Cappellen P (2007) Modeling microbiallyinduced carbon degradation in redox-stratified subsurface environments: Concepts and open questions. Geomicrobiology Journal 24:139-155
53. Tiedje JM (1988) Ecology of denitrification and dissimilatory nitrate reduction to ammonium. In: Zehnder A (ed) Biology of anaerobic microorganisms. John Wiley and Sons, New York, pp 179-244
54. Tuomela M, Vikman M, Hatakka A, Itävaara M (2000) Biodegradation of lignin in a compost environment: a review. Bioresource Technology 72:169-183
55. Ullah S, Faulkner S (2006) Use of cotton gin trash to enhance denitrification in restored forested wetlands. Forest Ecology and Management 237:557-563
56. Warneke S, Schipper L, Matiasek M, Scow K, Cameron S, Bruesewitz D, McDonald I (2011) Nitrate removal, communities of denitrifiers and adverse effects in different carbon substrates for use in denitrification beds. Water Research 45:5463-5475
57. Wolsing M, Prieme 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 Microbiology Ecology 48:261-271
58. Yadav S, Kaushik R, Saxena A, Arora D (2011) Diversity and phylogeny of plant growth-promoting bacilli from moderately acidic soil. Journal of Basic Microbiology 51:98-106