Table of Contents Author Guidelines Submit a Manuscript
International Journal of Genomics
Volume 2015, Article ID 572121, 11 pages
http://dx.doi.org/10.1155/2015/572121
Research Article

Response of Spatial Patterns of Denitrifying Bacteria Communities to Water Properties in the Stream Inlets at Dianchi Lake, China

1Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
2Key Lab of Food Quality and Safety of Jiangsu Province, State Key Laboratory Breeding Base, 50 Zhongling Street, Nanjing 210014, China

Received 3 July 2015; Accepted 16 August 2015

Academic Editor: Marián Brestič

Copyright © 2015 Neng Yi et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. P. J. Mulholland, A. M. Helton, G. C. Poole et al., “Stream denitrification across biomes and its response to anthropogenic nitrate loading,” Nature, vol. 452, no. 7184, pp. 202–205, 2008. View at Publisher · View at Google Scholar · View at Scopus
  2. S. Seitzinger, J. A. Harrison, J. K. Böhlke et al., “Denitrification across landscapes and waterscapes: a synthesis,” Ecological Applications, vol. 16, no. 6, pp. 2064–2090, 2006. View at Publisher · View at Google Scholar · View at Scopus
  3. F. Azam and A. Z. Worden, “Microbes, molecules, and marine ecosystems,” Science, vol. 303, no. 5664, pp. 1622–1624, 2004. View at Publisher · View at Google Scholar · View at Scopus
  4. K. Song, H. Kang, L. Zhang, and W. J. Mitsch, “Seasonal and spatial variations of denitrification and denitrifying bacterial community structure in created riverine wetlands,” Ecological Engineering, vol. 38, no. 1, pp. 130–134, 2012. View at Publisher · View at Google Scholar · View at Scopus
  5. J. Vymazal, “Removal of nutrients in various types of constructed wetlands,” Science of the Total Environment, vol. 380, no. 1–3, pp. 48–65, 2007. View at Publisher · View at Google Scholar · View at Scopus
  6. D. Chèneby, A. Hartmann, C. Hénault, E. Topp, and J. C. Germon, “Diversity of denitrifying microflora and ability to reduce N2O in two soils,” Biology and Fertility of Soils, vol. 28, no. 1, pp. 19–26, 1998. View at Publisher · View at Google Scholar · View at Scopus
  7. E. Kandeler, T. Brune, E. Enowashu et al., “Response of total and nitrate-dissimilating bacteria to reduced N deposition in a spruce forest soil profile,” FEMS Microbiology Ecology, vol. 67, no. 3, pp. 444–454, 2009. View at Publisher · View at Google Scholar · View at Scopus
  8. S. E. Morales, T. Cosart, and W. E. Holben, “Bacterial gene abundances as indicators of greenhouse gas emission in soils,” The ISME Journal, vol. 4, no. 6, pp. 799–808, 2010. View at Publisher · View at Google Scholar · View at Scopus
  9. D. L. Kirchman, A. I. Dittel, S. E. G. Findlay, and D. Fischer, “Changes in bacterial activity and community structure in response to dissolved organic matter in the Hudson River, New York,” Aquatic Microbial Ecology, vol. 35, no. 3, pp. 243–257, 2004. View at Publisher · View at Google Scholar · View at Scopus
  10. A. Cébron, T. Berthe, and J. Garnier, “Nitrification and nitrifying bacteria in the lower Seine River and estuary (France),” Applied and Environmental Microbiology, vol. 69, no. 12, pp. 7091–7100, 2003. View at Publisher · View at Google Scholar · View at Scopus
  11. A. Cébron, M. Coci, J. Garnier, and H. J. Laanbroek, “Denaturing gradient gel electrophoretic analysis of ammonia-oxidizing bacterial community structure in the lower seine river: impact of paris wastewater effluents,” Applied and Environmental Microbiology, vol. 70, no. 11, pp. 6726–6737, 2004. View at Publisher · View at Google Scholar · View at Scopus
  12. Z. Liu, S. Huang, G. Sun, Z. Xu, and M. Xu, “Phylogenetic diversity, composition and distribution of bacterioplankton community in the Dongjiang River, China,” FEMS Microbiology Ecology, vol. 80, no. 1, pp. 30–44, 2012. View at Publisher · View at Google Scholar · View at Scopus
  13. B. C. Crump and J. E. Hobbie, “Synchrony and seasonality in bacterioplankton communities of two temperate rivers,” Limnology and Oceanography, vol. 50, no. 6, pp. 1718–1729, 2005. View at Publisher · View at Google Scholar · View at Scopus
  14. K. Enwall, L. Philippot, and S. Hallin, “Activity and composition of the denitrifying bacterial community respond differently to long-term fertilization,” Applied and Environmental Microbiology, vol. 71, no. 12, pp. 8335–8343, 2005. View at Publisher · View at Google Scholar · View at Scopus
  15. S. Hallin, C. M. Jones, M. Schloter, and L. Philippot, “Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment,” The ISME Journal, vol. 3, no. 5, pp. 597–605, 2009. View at Publisher · View at Google Scholar · View at Scopus
  16. M. Wolsing and A. Priemé, “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, vol. 48, no. 2, pp. 261–271, 2004. View at Publisher · View at Google Scholar · View at Scopus
  17. K. Enwall, I. N. Throbäck, M. Stenberg, M. Söderström, and S. Hallin, “Soil resources influence spatial patterns of denitrifying communities at scales compatible with land management,” Applied and Environmental Microbiology, vol. 76, no. 7, pp. 2243–2250, 2010. View at Publisher · View at Google Scholar · View at Scopus
  18. L. Philippot, J. Andert, C. M. Jones, D. Bru, and S. Hallin, “Importance of denitrifiers lacking the genes encoding the nitrous oxide reductase for N2O emissions from soil,” Global Change Biology, vol. 17, no. 3, pp. 1497–1504, 2011. View at Publisher · View at Google Scholar · View at Scopus
  19. J. Čuhel, M. Šimek, R. J. Laughlin et al., “Insights into the effect of soil pH on N2O and N2 emissions and denitrifier community size and activity,” Applied and Environmental Microbiology, vol. 76, no. 6, pp. 1870–1878, 2010. View at Publisher · View at Google Scholar · View at Scopus
  20. J. K. M. Walker, K. N. Egger, and G. H. R. Henry, “Long-term experimental warming alters nitrogen-cycling communities but site factors remain the primary drivers of community structure in high arctic tundra soils,” The ISME Journal, vol. 2, no. 9, pp. 982–995, 2008. View at Publisher · View at Google Scholar · View at Scopus
  21. T. Yan, M. W. Fields, L. Wu, Y. Zu, J. M. Tiedje, and J. Zhou, “Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate-and uranium-contaminated groundwater,” Environmental Microbiology, vol. 5, no. 1, pp. 13–24, 2003. View at Publisher · View at Google Scholar · View at Scopus
  22. K. Hamonts, T. J. Clough, A. Stewart et al., “Effect of nitrogen and waterlogging on denitrifier gene abundance, community structure and activity in the rhizosphere of wheat,” FEMS Microbiology Ecology, vol. 83, no. 3, pp. 568–584, 2013. View at Publisher · View at Google Scholar · View at Scopus
  23. J.-Z. He, Y. Zheng, C.-R. Chen, Y.-Q. He, and L.-M. Zhang, “Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and culture-independent approaches,” Journal of Soils and Sediments, vol. 8, no. 5, pp. 349–358, 2008. View at Publisher · View at Google Scholar · View at Scopus
  24. Y. Huang, H. Wen, J. Cai, M. Cai, and J. Sun, “Key aquatic environmental factors affecting ecosystem health of streams in the Dianchi Lake Watershed, China,” Procedia Environmental Sciences, vol. 2, no. 10, pp. 868–880, 2010. View at Publisher · View at Google Scholar
  25. Y. J. Yu, J. Guan, Y. W. Ma, S. Yu, H. Guo, and L. Bao, “Aquatic environmental quality variation in Lake Dianchi watershed,” Procedia Environmental Sciences, vol. 2, no. 10, pp. 76–81, 2010. View at Publisher · View at Google Scholar
  26. State Environmental Protection Administration, The National Standard of The People's Republic of China-Surface Water Environmental Quality Standards, China Environmental Science Press, 2002.
  27. Ncdenr, Basin Wide Assessment Report: Cape Fear River Basin, Division of Water Quality, Department of Environment and Natural Resources, Raleigh, NC, USA, 2004.
  28. C. Féray and B. Montuelle, “Chemical and microbial hypotheses explaining the effect of wastewater treatment plant discharges on the nitrifying communities in freshwater sediment,” Chemosphere, vol. 50, no. 7, pp. 919–928, 2003. View at Publisher · View at Google Scholar · View at Scopus
  29. K. Kloos, A. Mergel, C. Rösch, and H. Bothe, “Denitrification within the genus azospirillum and other associative bacteria,” Australian Journal of Plant Physiology, vol. 28, no. 9, pp. 991–998, 2001. View at Google Scholar · View at Scopus
  30. I. N. Throbäck, K. Enwall, Å. Jarvis, and S. Hallin, “Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE,” FEMS Microbiology Ecology, vol. 49, no. 3, pp. 401–417, 2004. View at Publisher · View at Google Scholar · View at Scopus
  31. V. Michotey, V. Méjean, and P. Bonin, “Comparison of methods for quantification of cytochrome cd1-denitrifying bacteria in environmental marine samples,” Applied and Environmental Microbiology, vol. 66, no. 4, pp. 1564–1571, 2000. View at Publisher · View at Google Scholar · View at Scopus
  32. G. Braker and J. M. Tiedje, “Nitric oxide reductase (norB) genes from pure cultures and environmental samples,” Applied and Environmental Microbiology, vol. 69, no. 6, pp. 3476–3483, 2003. View at Publisher · View at Google Scholar · View at Scopus
  33. S. Hallin and P.-E. Lindgren, “PCR detection of genes encoding nitrite reductase in denitrifying bacteria,” Applied and Environmental Microbiology, vol. 65, no. 4, pp. 1652–1657, 1999. View at Google Scholar · View at Scopus
  34. S. Henry, D. Bru, B. Stres, S. Hallet, and L. Philippot, “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,” Applied and Environmental Microbiology, vol. 72, no. 8, pp. 5181–5189, 2006. View at Publisher · View at Google Scholar · View at Scopus
  35. D. Radojkovic and J. Kusic, “Silver staining of denaturing gradient gel electrophoresis gels,” Clinical Chemistry, vol. 46, no. 6, pp. 883–884, 2000. View at Google Scholar · View at Scopus
  36. D. Roesti, R. Gaur, B. N. Johri et al., “Plant growth stage, fertiliser management and bio-inoculation of arbuscular mycorrhizal fungi and plant growth promoting rhizobacteria affect the rhizobacterial community structure in rain-fed wheat fields,” Soil Biology and Biochemistry, vol. 38, no. 5, pp. 1111–1120, 2006. View at Publisher · View at Google Scholar · View at Scopus
  37. J. Lepš and P. Šmilauer, Multivariate Analysis of Ecological Data using CANOCO, Cambridge University Press, Cambridge, UK, 2003. View at Publisher · View at Google Scholar
  38. J. Zhang, G. Zeng, Y. Chen et al., “Effects of physico-chemical parameters on the bacterial and fungal communities during agricultural waste composting,” Bioresource Technology, vol. 102, no. 3, pp. 2950–2956, 2011. View at Publisher · View at Google Scholar · View at Scopus
  39. J. L. Faulwetter, V. Gagnon, C. Sundberg et al., “Microbial processes influencing performance of treatment wetlands: a review,” Ecological Engineering, vol. 35, no. 6, pp. 987–1004, 2009. View at Publisher · View at Google Scholar · View at Scopus
  40. Z.-F. Zhou, Y.-M. Zheng, J.-P. Shen, L.-M. Zhang, and J.-Z. He, “Response of denitrification genes nirS, nirK, and nosZ to irrigation water quality in a Chinese agricultural soil,” Environmental Science and Pollution Research, vol. 18, no. 9, pp. 1644–1652, 2011. View at Publisher · View at Google Scholar · View at Scopus
  41. Z. Jin, F.-Y. Ji, X. Xu, X.-Y. Xu, Q.-K. Chen, and Q. Li, “Microbial and metabolic characterization of a denitrifying phosphorus-uptake/side stream phosphorus removal system for treating domestic sewage,” Biodegradation, vol. 25, no. 6, pp. 777–786, 2014. View at Publisher · View at Google Scholar · View at Scopus
  42. B. Wang, B. Huang, W. Jin et al., “Occurrence, distribution, and sources of six phenolic endocrine disrupting chemicals in the 22 river estuaries around Dianchi Lake in China,” Environmental Science and Pollution Research, vol. 20, no. 5, pp. 3185–3194, 2013. View at Publisher · View at Google Scholar · View at Scopus
  43. J. Xiong, Z. He, J. D. Van Nostrand et al., “Assessing the microbial community and functional genes in a vertical soil profile with long-term arsenic contamination,” PLoS ONE, vol. 7, no. 11, Article ID e50507, 2012. View at Publisher · View at Google Scholar · View at Scopus
  44. H. M. A. Mahmoud, R. Goulder, and G. R. Carvalho, “The response of epilithic bacteria to different metals regime in two upland streams: assessed by conventional microbiological methods and PCR-DGGE,” Archiv für Hydrobiologie, vol. 163, no. 3, pp. 405–427, 2005. View at Publisher · View at Google Scholar · View at Scopus
  45. J. K. Böhlke, R. C. Antweiler, J. W. Harvey et al., “Multi-scale measurements and modeling of denitrification in streams with varying flow and nitrate concentration in the upper Mississippi River basin, USA,” Biogeochemistry, vol. 93, no. 1-2, pp. 117–141, 2009. View at Publisher · View at Google Scholar · View at Scopus
  46. C. Yin, F. L. Fan, A. Song, Z. Li, W. Yu, and Y. Liang, “Different denitrification potential of aquic brown soil in Northeast China under inorganic and organic fertilization accompanied by distinct changes of nirS- and nirK-denitrifying bacterial community,” European Journal of Soil Biology, vol. 65, pp. 47–56, 2014. View at Publisher · View at Google Scholar · View at Scopus
  47. B. J. Peterson, W. M. Wollheim, P. J. Mulholland et al., “Control of nitrogen export from watersheds by headwater streams,” Science, vol. 292, no. 5514, pp. 86–90, 2001. View at Publisher · View at Google Scholar · View at Scopus
  48. Y. Gao, N. Yi, Z. Zhang, H. Liu, and S. Yan, “Fate of 15NO3 and 15NH4+ in the treatment of eutrophic water using the floating macrophyte, Eichhornia crassipes,” Journal of Environmental Quality, vol. 41, no. 5, pp. 1653–1660, 2012. View at Publisher · View at Google Scholar · View at Scopus
  49. N. Yi, Y. Gao, X.-H. Long et al., “Eichhornia crassipes cleans wetlands by enhancing the nitrogen removal and modulating denitrifying bacteria community,” CLEAN—Soil, Air, Water, vol. 42, no. 5, pp. 664–673, 2014. View at Publisher · View at Google Scholar · View at Scopus
  50. B. Wei, X. Yu, S. Zhang, and L. Gu, “Comparison of the community structures of ammonia-oxidizing bacteria and archaea in rhizoplanes of floating aquatic macrophytes,” Microbiological Research, vol. 166, no. 6, pp. 468–474, 2011. View at Publisher · View at Google Scholar · View at Scopus
  51. T. J. Battin, L. A. Kaplan, J. D. Newbold, and C. M. E. Hansen, “Contributions of microbial biofilms to ecosystem processes in stream mesocosms,” Nature, vol. 426, no. 6965, pp. 439–442, 2003. View at Publisher · View at Google Scholar · View at Scopus
  52. P. M. Groffman, A. M. Dorsey, and P. M. Mayer, “N processing within geomorphic structures in urban streams,” Journal of the North American Benthological Society, vol. 24, no. 3, pp. 613–625, 2005. View at Publisher · View at Google Scholar · View at Scopus
  53. C. W. Knapp, W. K. Dodds, K. C. Wilson, J. M. O'Brien, and D. W. Graham, “Spatial heterogeneity of denitrification genes in a highly homogenous urban stream,” Environmental Science & Technology, vol. 43, no. 12, pp. 4273–4279, 2009. View at Publisher · View at Google Scholar · View at Scopus
  54. S. Hallin, I. N. Throbäck, J. Dicksved, and M. Pell, “Metabolic profiles and genetic diversity of denitrifying communities in activated sludge after addition of methanol or ethanol,” Applied and Environmental Microbiology, vol. 72, no. 8, pp. 5445–5452, 2006. View at Publisher · View at Google Scholar · View at Scopus
  55. B. B. Oakley, C. A. Francis, K. J. Roberts, C. A. Fuchsman, S. Srinivasan, and J. T. Staley, “Analysis of nitrite reductase (nirK and nirS) genes and cultivation reveal depauperate community of denitrifying bacteria in the Black Sea suboxic zone,” Environmental Microbiology, vol. 9, no. 1, pp. 118–130, 2007. View at Publisher · View at Google Scholar · View at Scopus
  56. J. M. Smith and A. Ogram, “Genetic and functional variation in denitrifier populations along a short-term restoration chronosequence,” Applied and Environmental Microbiology, vol. 74, no. 18, pp. 5615–5620, 2008. View at Publisher · View at Google Scholar · View at Scopus
  57. A. García-Lledó, A. Vilar-Sanz, R. Trias, S. Hallin, and L. Bañeras, “Genetic potential for N2O emissions from the sediment of a free water surface constructed wetland,” Water Research, vol. 45, no. 17, pp. 5621–5632, 2011. View at Publisher · View at Google Scholar · View at Scopus
  58. D. W. Graham, C. Trippett, W. K. Dodds et al., “Correlations between in situ denitrification activity and nir-gene abundances in pristine and impacted prairie streams,” Environmental Pollution, vol. 158, no. 10, pp. 3225–3229, 2010. View at Publisher · View at Google Scholar · View at Scopus
  59. C. M. Jones and S. Hallin, “Ecological and evolutionary factors underlying global and local assembly of denitrifier communities,” The ISME Journal, vol. 4, no. 5, pp. 633–641, 2010. View at Publisher · View at Google Scholar · View at Scopus
  60. L. Philippot, J. Čuhel, N. P. A. Saby et al., “Mapping field-scale spatial patterns of size and activity of the denitrifier community,” Environmental Microbiology, vol. 11, no. 6, pp. 1518–1526, 2009. View at Publisher · View at Google Scholar · View at Scopus
  61. C. M. Jones, B. Stres, M. Rosenquist, and S. Hallin, “Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification,” Molecular Biology and Evolution, vol. 25, no. 9, pp. 1955–1966, 2008. View at Publisher · View at Google Scholar · View at Scopus
  62. W. G. Zumft, “Cell biology and molecular basis of denitrification,” Microbiology and Molecular Biology Reviews, vol. 61, no. 4, pp. 533–616, 1997. View at Google Scholar · View at Scopus
  63. A. B. Glockner, A. Jüngst, and W. G. Zumft, “Copper-containing nitrite reductase from Pseudomonas aureofaciens is functional in a mutationally cytochrome cd1-free background (NirS-) of Pseudomonas stutzeri,” Archives of Microbiology, vol. 160, no. 1, pp. 18–26, 1993. View at Publisher · View at Google Scholar · View at Scopus
  64. J. C. Finlay, G. E. Small, and R. W. Sterner, “Human influences on nitrogen removal in lakes,” Science, vol. 342, no. 6155, pp. 247–250, 2013. View at Publisher · View at Google Scholar · View at Scopus
  65. E. S. Bernhardt, “Cleaner lakes are dirtier lakes,” Science, vol. 342, no. 6155, pp. 205–206, 2013. View at Publisher · View at Google Scholar · View at Scopus
  66. J. J. Rich, R. S. Heichen, P. J. Bottomley, K. Cromack Jr., and D. D. Myrold, “Community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils,” Applied and Environmental Microbiology, vol. 69, no. 10, pp. 5974–5982, 2003. View at Publisher · View at Google Scholar · View at Scopus
  67. M. Castro-González, G. Braker, L. Farías, and O. Ulloa, “Communities of nirS-type denitrifiers in the water column of the oxygen minimum zone in the eastern South Pacific,” Environmental Microbiology, vol. 7, no. 9, pp. 1298–1306, 2005. View at Publisher · View at Google Scholar · View at Scopus
  68. J. P. Schimel and J. Gulledge, “Microbial community structure and global trace gases,” Global Change Biology, vol. 4, no. 7, pp. 745–758, 1998. View at Publisher · View at Google Scholar · View at Scopus
  69. G. Braker, J. Schwarz, and R. Conrad, “Influence of temperature on the composition and activity of denitrifying soil communities,” FEMS Microbiology Ecology, vol. 73, no. 1, pp. 134–148, 2010. View at Publisher · View at Google Scholar · View at Scopus
  70. L. Holtan-Hartwig, P. Dörsch, and L. R. Bakken, “Low temperature control of soil denitrifying communities: kinetics of N2O production and reduction,” Soil Biology and Biochemistry, vol. 34, no. 11, pp. 1797–1806, 2002. View at Publisher · View at Google Scholar · View at Scopus
  71. L. Zhang, G. Zeng, J. Zhang et al., “Response of denitrifying genes coding for nitrite (nirK or nirS) and nitrous oxide (nosZ) reductases to different physico-chemical parameters during agricultural waste composting,” Applied Microbiology and Biotechnology, vol. 99, no. 9, pp. 4059–4070, 2015. View at Publisher · View at Google Scholar · View at Scopus