Seasonal Patterns in Microbial Community Composition in Denitrifying Bioreactors Treating Subsurface Agricultural Drainage

Microbial Ecology

Volumn 70, Issue 3, 2015, Pages 710-723

  Porter, Matthew D ^b,c   Andrus, J Malia ^a,d   Bartolerio, Nicholas A ^b,e   Rodriguez, Luis F ^a   Zhang, Yuanhui ^a   Zilles, Julie L ^b   Kent, Angela D ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b University of Illinois at Urbana Champaign   (United States)

^c ENVIRONMENTAL RESOURCES MANAGEMENT   (United States)

^d Waterborne Environmental Inc   (United States)

^e Strand Associates Inc   (United States)

Author keywords

Denitrification; Geostatistics; Nitrate removal; Seasonal variation; Subsurface drainage

Indexed keywords

WATER POLLUTANT;

AGRICULTURE; BACTERIAL PHENOMENA AND FUNCTIONS; BIOREACTOR; DENITRIFICATION; FUNGUS; ILLINOIS; METABOLISM; MICROBIOLOGY; MICROFLORA; PHYSIOLOGY; SEASON; WATER POLLUTANT;

AGRICULTURE; BACTERIAL PHYSIOLOGICAL PHENOMENA; BIOREACTORS; DENITRIFICATION; FUNGI; ILLINOIS; MICROBIOTA; SEASONS; WATER POLLUTANTS, CHEMICAL;

EID: 84942553089     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-015-0605-8     Document Type: Article

References (56)

1. Schipper LA, Robertson WD, Gold AJ, Jaynes DB, Cameron SC (2010) Denitrifying bioreactors—an approach for reducing nitrate loads to receiving waters. Ecol Eng 36:1532–1543. doi:10.1016/J.Ecoleng.2010.04.008
2. Blann KL, Anderson JL, Sands GR, Vondracek B (2009) Effects of agricultural drainage on aquatic ecosystems: a review. Crit Rev Environ Sci Technol 39:909–1001. doi:10.1080/10643380801977966
3. Dinnes DL, Karlen DL, Jaynes DB, Kaspar TC, Hatfield JL, Colvin TS, Cambardella CA (2002) Nitrogen management strategies to reduce nitrate leaching in tile-drained Midwestern soils. Agron J 94:153–171
4. Cameron SG, Schipper LA (2010) Nitrate removal and hydraulic performance of organic carbon for use in denitrification beds. Ecol Eng 36:1588–1595. doi:10.1016/J.Ecoleng.2010.03.010
5. Greenan CM, Moorman TB, Kaspar TC, Parkin TB, Jaynes DB (2006) Comparing carbon substrates for denitrification of subsurface drainage water. J Environ Qual 35:824–829. doi:10.2134/Jeq2005.0247
6. Chun JA, Cooke RA, Eheart JW, Cho J (2010) Estimation of flow and transport parameters for woodchip-based bioreactors: II. Field-scale bioreactor. Biosyst Eng 105:95–102. doi:10.1016/J.Biosystemseng.2009.09.018
7. Christianson L, Helmers M, Bhandari A, Moorman T (2013) Internal hydraulics of an agricultural drainage denitrification bioreactor. Ecol Eng 52:298–307. doi:10.1016/J.Ecoleng.2012.11.001
8. Long LM, Schipper LA, Bruesewitz DA (2011) Long-term nitrate removal in a denitrification wall. Agric Ecosyst Environ 140:514–520. doi:10.1016/J.Agee.2011.02.005
9. Moorman TB, Parkin TB, Kaspar TC, Jaynes DB (2010) Denitrification activity, wood loss, and N2O emissions over 9 years from a wood chip bioreactor. Ecol Eng 36:1567–1574. doi:10.1016/J.Ecoleng.2010.03.012
10. Robertson WD, Ptacek CJ, Brown SJ (2009) Rates of nitrate and perchlorate removal in a 5-year-old wood particle reactor treating agricultural drainage. Ground Water Monit Remediat 29:87–94. doi:10.1111/J.1745-6592.2009.01231.X
11. Warneke S, Schipper LA, Bruesewitz DA, McDonald I, Cameron S (2011) Rates, controls and potential adverse effects of nitrate removal in a denitrification bed. Ecol Eng 37:511–522. doi:10.1016/j.ecoleng.2010.12.006
12. Warneke S, Schipper LA, Matiasek MG, Scow KM, Cameron S, Bruesewitz DA, McDonald IR (2011) Nitrate removal, communities of denitrifiers and adverse effects in different carbon substrates for use in denitrification beds. Water Res 45:5463–5475. doi:10.1016/J.Watres.2011.08.007
13. Andrus JM, Porter MD, Rodríguez LF, Kuehlhorn T, Cooke RAC, Zhang Y, Kent AD, Zilles JL (2014) Spatial variation in the bacterial and denitrifying bacterial community in a biofilter treating subsurface agricultural drainage. Microb Ecol 67:265–272
14. Cooke R, Verma S (2012) Performance of drainage water management systems in Illinois, United States. J Soil Water Conserv 67:453–464. doi:10.2489/Jswc.67.6.453
15. Woli KP, David MB, Cooke RA, McIsaac GF, Mitchell CA (2010) Nitrogen balance in and export from agricultural fields associated with controlled drainage systems and denitrifying bioreactors. Ecol Eng 36:1558–1566. doi:10.1016/J.Ecoleng.2010.04.024
16. Seitzinger S, Harrison JA, Bohlke JK, Bouwman AF, Lowrance R, Peterson B, Tobias C, Van Drecht G (2006) Denitrification across landscapes and waterscapes: a synthesis. Ecol Appl 16:2064–2090. doi:10.1890/1051-0761(2006)016[2064:Dalawa]2.0.Co;2
17. 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. doi:10.1890/1051-0761(2006)016[2143:Ecodca]2.0.Co;2
18. Smith J, Wagner-Riddle C, Dunfield K (2010) Season and management related changes in the diversity of nitrifying and denitrifying bacteria over winter and spring. Appl Soil Ecol 44:138–146. doi:10.1016/J.Apsoil.2009.11.004
19. Laughlin RJ, Stevens RJ (2002) Evidence for fungal dominance of denitrification and codenitrification in a grassland soil. Soil Sci Soc Am J 66:1540–1548
20. Long A, Heitman J, Tobias C, Philips R, Song B (2013) Co-occuring anammox, denitrification, and codenitrification in agricultural soils. Appl Environ Microbiol 79:168–176. doi:10.1128/AEM. 02520-12
21. Sanford RA, Wagner DD, Wu Q, Chee-Sanford JC, Thomas SH, Cruz-Garcia C, Rodriguez G, Massol-Deya A, Krishnani KK, Ritalahti KM, Nissen S, Konstantinidis KT, Loffler FE (2012) Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils. Proc Natl Acad Sci U S A 109:19709–19714. doi:10.1073/pnas.1211238109
22. Jones CM, Graf DR, Bru D, Philippot L, Hallin S (2013) The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink. ISME J 7:417–426. doi:10.1038/ismej.2012.125
23. Appleford JM, Rodriguez LF, Cooke RAC, Zhang Y, Kent AD, Zilles J (2008) Characterization of microorganisms contributing to denitrification in tile train biofilters in Illinois. Proceedings of the 2008 ASABE Annual International Meeting, Providence, RI, paper no. 084583, pp 5605-5614
24. Crump BC, Hobbie JE (2005) Synchrony and seasonality in bacterioplankton communities of two temperate rivers. Limnol Oceanogr 50:1718–1729
25. Fuhrman JA, Hewson I, Schwalbach MS, Steele JA, Brown MV, Naeem S (2006) Annually reoccurring bacterial communities are predictable from ocean conditions. Proc Natl Acad Sci U S A 103:13104–13109. doi:10.1073/Pnas.0602399103
26. Jones SE, Shade AL, McMahon KD, Kent AD (2007) Comparison of primer sets for use in automated ribosomal intergenic spacer analysis of aquatic bacterial communities: an ecological perspective. Appl Environ Microbiol 73:659–662. doi:10.1128/Aem. 02130-06
27. Kent AD, Jones SE, Yannarell AC, Graham JM, Lauster GH, Kratz TK, Triplett EW (2004) Annual patterns in bacterioplankton community variability in a humic lake. Microb Ecol 48:550–560. doi:10.1007/s00248-004-0244-y
28. Nelson CE (2009) Phenology of high-elevation pelagic bacteria: the roles of meteorologic variability, catchment inputs and thermal stratification in structuring communities. ISME J 3:13–30. doi:10.1038/Ismej.2008.81
29. Shade A, Kent AD, Jones SE, Newton RJ, Triplett EW, McMahon KD (2007) Interannual dynamics and phenology of bacterial communities in a eutrophic lake. Limnol Oceanogr 52:487–494
30. Lauber CL, Ramirez KS, Aanderud Z, Lennon J, Fierer N (2013) Temporal variability in soil microbial communities across land-use types. ISME J 7:1641–1650. doi:10.1038/Ismej.2013.50
31. Boer SI, Hedtkamp SIC, van Beusekom JEE, Fuhrman JA, Boetius A, Ramette A (2009) Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands. ISME J 3:780–791. doi:10.1038/Ismej.2009.29
32. Song K, Lee SH, Kong H (2011) Denitrification rates and community structure of denitrifying bacteria in newly constructed wetland. Eur J Soil Biol 47:24–29. doi:10.1016/J.Ejsobi.2010.10.003
33. Gobet A, Boetius A, Ramette A (2014) Ecological coherence of diversity patterns derived from classical fingerprinting and Next Generation Sequencing techniques. Environ Microbiol 16:2672–2681. doi:10.1111/1462-2920.12308
34. van Dorst J, Bissett A, Palmer AS, Brown M, Snape I, Stark JS, Raymond B, McKinlay J, Ji M, Winsley T, Ferrari BC (2014) Community fingerprinting in a sequencing world. FEMS Microbiol Ecol 89:316–330. doi:10.1111/1574-6941.12308
35. Andrus JM (2011) Microbial community analysis for denitrifying biofilters. PhD dissertation, University of Illinois at Urbana-Champagin. http://hdl.handle.net/2142/24094
36. Peralta AL, Matthews JW, Kent AD (2010) Microbial community structure and denitrification in a wetland mitigation bank. Appl Environ Microbiol 76:4207–4215. doi:10.1128/Aem. 02977-09
37. Kent AD, Yannarell AC, Rusak JA, Triplett EW, McMahon KD (2007) Synchrony in aquatic microbial community dynamics. ISME J 1:38–47. doi:10.1038/Ismej.2007.6
38. Ranjard L, Poly F, Lata JC, Mougel C, Thioulouse J, Nazaret S (2001) Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability. Appl Environ Microbiol 67:4479–4487
39. 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. doi:10.1128/Aem. 69.10.5974-5982.2003
40. Yannarell AC, Triplett EW (2005) Geographic and environmental sources of variation in lake bacterial community composition. Appl Environ Microbiol 71:227–239. doi:10.1128/Aem. 71.1.227-239.2005
41. Rees G, Baldwin D, Watson G, Perryman S, Nielsen D (2004) Ordination and significance testing of microbial community composition derived from terminal restriction fragment length polymorphisms: application of multivariate statistics. Anton Leeuw Int J G 86:339–347. doi:10.1007/s10482-004-0498-x
42. terBraak CJF, Smilauer P (2002) CANOCO reference manual and CanoDraw for Windows user’s guide: software for canonical community ordination (version 4.5). Wageningen University and Research Center Publications, City, p 500
43. Clarke KR (1993) Nonparametric multivariate analyses of changes in community structure. Aust J Ecol 18:117–143
44. Clarke KR, Green RH (1988) Statistical design and analysis for a biological effects study. Mar Ecol Prog Ser 46:213–226
45. Legendre P, Legendre L (1998) Numerical ecology. Elsevier Science, Amsterdam
46. Bray JR, Curtis JT (1957) An ordination of the upland forest communities of southern Wisconsin. Ecol Monogr 27:326–349
47. Oden NL, Sokal RR (1986) Directional autocorrelation—an extension of spatial correlograms to 2 dimensions. Syst Zool 35:608–617
48. Legendre P (1993) Spatial autocorrelation: trouble or new paradigm? Ecology 74:1659–1673. doi:10.2307/1939924
49. Sexstone AJ, Parkin TB, Tiedje JM (1985) Temporal response of soil dentrification rates to rainfall and irrigation. Soil Sci Soc Am J 49:99–103
50. Shade A, Jones SE, McMahon KD (2008) The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics. Environ Microbiol 10:1057–1067. doi:10.1111/J.1462-2920.2007.01527.X
51. Peralta AL, Matthews JW, Kent AD (2014) Habitat specialization along a wetland moisture gradient differs between ammonia-oxidizing and denitrifying microorganisms. Microb Ecol 68:339–350. doi:10.1007/s00248-014-0407-4
52. Krave AS, Lin B, Braster M, Laverman AM, van Straalen NM, Roling WFM, van Verseveld HW (2002) Stratification and seasonal stability of diverse bacterial communities in a Pinus merkusii (pine) forest soil in central Java, Indonesia. Environ Microbiol 4:361–373
53. Lejon DPH, Chaussod R, Ranger J, Ranjard L (2005) Microbial community structure and density under different tree species in an acid forest soil (Morvan, France). Microb Ecol 50:614–625. doi:10.1007/S00248-005-5130-8
54. Goberna M, Insam H, Klammer S, Pascual JA, Sanchez J (2005) Microbial community structure at different depths in disturbed and undisturbed semiarid Mediterranean forest soils. Microb Ecol 50:315–326
55. Drenovsky RE, Vo D, Graham KJ, Scow KM (2004) Soil water content and organic carbon availability are major determinants of soil microbial community composition. Microb Ecol 48:424–430. doi:10.1007/S00248-003-1063-2
56. Kent AD, Jones SE, Yannarell AC, Graham JM, Lauster GH, Kratz TK, Triplett EW (2004) Annual patterns in bacterioplankton community variability in a humic lake. Microb Ecol 48:550–560