Biology and Fertility of Soils

, Volume 50, Issue 1, pp 25–35 | Cite as

Bacterial diversity of a wooded riparian strip soil specifically designed for enhancing the denitrification process

  • Md. Mizanur Rahman
  • Marina Basaglia
  • Elena Vendramin
  • Bruno Boz
  • Federico Fontana
  • Bruna Gumiero
  • Sergio Casella
Original Paper

Abstract

This research is part of a project aimed at verifying the potential of a specifically assessed wooded riparian zone in removing the excess of combined nitrogen from the Zero River so as to reduce nutrient inputs into the Venice Lagoon. Among the specific objectives of the project, there was the determination of change in the composition of the microbial populations of soil of the wooded riparian strip. The composition of the bacterial communities collected at different depths inside and outside the riparian strip was determined by combined approaches involving cultivation (CFU), microscopic approaches (CTC test), and DNA-based techniques (ARDRA and DGGE). The size of the living population was the same inside and outside the experimental strip, with a minor percentage of culturable bacteria. Higher numbers of metabolically active bacteria and higher bacterial diversity were detected in the internal soil, with deeper soil layers showing reduced diversity, thus indicating that soil management within the riparian strip effectively supports the viability of bacterial communities. Total operational taxonomic units (OTUs) and percentage of single OTUs were also found to be always higher in the internal soil samples for all soil layers, with the percentage of Firmicutes increasing and Actinobacteria decreasing with depth. The increasing soil organic carbon inputs due to the contribution of the growing plants were found to support bacterial diversity in all soil layers. DNA-based analysis also indicated a clear effect of the applied treatments on soil bacterial diversity and a well-defined separation of the bacterial communities related to the different soil layers of the riparian strip.

Keywords

Phytoremediation Riparian wooded strip Denitrification Soil microbial population dynamic Soil microbial communities DGGE 

Notes

Acknowledgments

This work was supported by Consorzio Acque Risorgive and Veneto Region. Md. M. R. was a recipient of a Ph.D. fellowship of the University of Padua.

Supplementary material

374_2013_828_Fig6_ESM.jpg (642 kb)
ESM 1

(JPEG 642 kb)

374_2013_828_MOESM1_ESM.eps (841 kb)
High resolution image (EPS 840 kb)
374_2013_828_MOESM2_ESM.docx (326 kb)
ESM 2(DOCX 326 kb)
374_2013_828_MOESM3_ESM.docx (76 kb)
ESM 3(DOCX 75 kb)

References

  1. Agnelli A, Ascher J, Corti G, Ceccherini MT, Nannipieri P, Pietramellara G (2004) Distribution of microbial communities in a forest soil profile investigated by microbial biomass, soil respiration and DGGE of total and extracellular DNA. Soil Biol Biochem 36:859–868CrossRefGoogle Scholar
  2. APHA, AWWA, WEF (2005) Standard methods for the examination of water and wastewater, 21st edn. American Public Health Association, Washington, DCGoogle Scholar
  3. Basaglia M, Casella S, Peruch U, Poggiolini S, Vamerali T, Mosca G, Vanderleyden J, De Troch P, Nuti MP (2003) Field release of genetically marked Azospirillum brasilense in association with Sorghum bicolor L. Plant Soil 256:281–290CrossRefGoogle Scholar
  4. Bothe H, Ferguson SJ, Newton WE (2006) Biology of the nitrogen cycle. Elsevier, AmsterdamGoogle Scholar
  5. Boz B, MdM R, Bottegal M, Basaglia M, Squartini A, Gumiero B, Casella S (2013) Vegetation, soil and hydrology management influence denitrification activity and the composition of nirK-type denitrifier communities in a newly afforested riparian buffer. N Biotechnol. doi:10.1016/j.nbt.2013.03.009 PubMedGoogle Scholar
  6. Brandt KK, Petersen A, Holm PE, Nybroe O (2006) Decreased abundance and diversity of culturable Pseudomonas spp. populations with increasing copper exposure in the sugar beet rhizosphere. FEMS Microbiol Ecol 56:281–291PubMedCrossRefGoogle Scholar
  7. Braun B, Böckelmann U, Grohmann E, Szewzyk U (2006) Polyphasic characterization of the bacterial community in an urban soil profile with in situ and culture dependent methods. Appl Soil Ecol 31:267–279CrossRefGoogle Scholar
  8. Brookes PC, Landman A, Pruden G, Jenkinson DS (1985) Chloroform fumigation and the release of soil nitrogen: a rapid direct extraction method to measure microbial biomass nitrogen in soil. Soil Biol Biochem 17:837–842CrossRefGoogle Scholar
  9. Fierer N, Schimmel JP, Holden PA (2003) Influence of drying–rewetting frequency on soil bacterial community structure. Microb Ecol 45:63–71PubMedCrossRefGoogle Scholar
  10. Garbeva P, van Elsas JD, van Veen JA (2008) Rhizosphere microbial community and its response to plant species and soil history. Plant Soil 302:19–32CrossRefGoogle Scholar
  11. Gomes NCM, Kosheleva IA, Abraham WR, Smalla K (2005) Effects of the inoculant strain Pseudomonas putida KT2442 (pNF142) and of naphthalene contamination on the soil bacterial community. FEMS Microbiol Ecol 54:21–33PubMedCrossRefGoogle Scholar
  12. Grayston SJ, Wang S, Campbell CD, Edwards AC (1998) Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biol Biochem 30:369–378CrossRefGoogle Scholar
  13. Griffiths RI, Whiteley AS, O'Donnell AG, Bailey MJ (2000) Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl Environ Microbiol 66:5488–5491PubMedCentralPubMedCrossRefGoogle Scholar
  14. Gumiero B, Boz B, Cornelio P, Casella S (2011) Shallow groundwater nitrogen and denitrification in a newly afforested, subirrigated riparian buffer. J Appl Ecol 48:1135–1144CrossRefGoogle Scholar
  15. Haycock NE, Pinay G (1993) Groundwater nitrate dynamics in grass and poplar vegetated riparian buffer strips during the winter. J Environ Quality 22:273–278CrossRefGoogle Scholar
  16. Hefting MM, de Klein JJM (1998) Nitrogen removal in buffer strips along a lowland stream in the Netherlands: a pilot study. Environ Pollution 102:521–526CrossRefGoogle Scholar
  17. Heuer H, Kroppenstedt RM, Berg G, Smalla K (2002) Effects of T4 lysozyme release from transgenic potato roots on bacterial rhizosphere communities are negligible relative to natural factors. Appl Environ Microbiol 68:1325–1335PubMedCentralPubMedCrossRefGoogle Scholar
  18. Heuer H, Krsek M, Baker P, Smalla K, Wellington EMH (1997) Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 63:3233–3241PubMedCentralPubMedGoogle Scholar
  19. Heylen K, Vanparys B, Wittebolle L, Verstraete W, Boon N, De Vos P (2006) Cultivation of denitrifying bacteria: optimization of isolation conditions and diversity study. Appl Environ Microbiol 72:2637–2643PubMedCentralPubMedCrossRefGoogle Scholar
  20. Hoffmann CC, Berg P, Dahl M, Larsen SE, Andersen HE, Andersen B (2006) Groundwater flow and transport of nutrients through a riparian meadow-field data and modeling. J Hydrol 331:315–335CrossRefGoogle Scholar
  21. Ibekwe AM, Poss JA, Grattan SR, Grieve CM, Suarez D (2010) Bacterial diversity in cucumber (Cucumis sativus) rhizosphere in response to salinity, soil pH, and boron. Soil Biol Biochem 42:567–575CrossRefGoogle Scholar
  22. Ishii S, Yamamoto M, Kikuchi M, Oshima K, Hattori M, Otsuka S, Senoo K (2009) Microbial populations responsive to denitrification-inducing conditions in rice paddy soil, as revealed by comparative 16S rRNA gene analysis. Appl Environ Microbiol 75:7070–7078PubMedCentralPubMedCrossRefGoogle Scholar
  23. James JB, Sherman TD, Devereux R (2006) Analysis of bacterial communities in sea grass bed sediments by double-gradient denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA genes. Microb Ecol 52:655–661PubMedCrossRefGoogle Scholar
  24. Kapley A, Baere TD, Purohit HJ (2007) Eubacterial diversity of activated biomass from a common effluent treatment plant. Res Microbiol 158:494–500PubMedCrossRefGoogle Scholar
  25. Kent AD, Triplett EW (2002) Microbial communities and their interactions in soil and rhizosphere ecosystems. Ann Rev Microbiol 56:211–236CrossRefGoogle Scholar
  26. Kirk JL, Beaudette LA, Hart M, Moutoglis P, Klironomos JN, Lee H, Trevors JT (2004) Methods of studying soil microbial diversity. J Microbiol Meth 58:169–188CrossRefGoogle Scholar
  27. Lee CG, Fletcher TD, Sun G (2009) Nitrogen removal in constructed wetland systems. Eng Life Sci 9:11–22CrossRefGoogle Scholar
  28. Li Z, Xu J, Tang C, Wu J, Muhammad A, Wang H (2006) Application of 16S r DNA-PCR amplification and DGGE fingerprinting for detection of shift in microbial community diversity in Cu-, Zn-, and Cd-contaminated paddy soils. Chemosphere 62:1374–1380PubMedCrossRefGoogle Scholar
  29. Lowrance RR, Todd RL, Fail J Jr, Hendrickson O Jr, Leonard R, Asmussen LE (1984) Riparian forest as nutrient filters in agricultural watersheds. Bioscience 34:374–377CrossRefGoogle Scholar
  30. Lynch JM, Benedetti A, Insam H, Nuti MP, Smalla K, Torsvik V, Nannipieri P (2004) Microbial diversity in soil: ecological theories, the contribution of molecular techniques and the impact of transgenic plants and transgenic microorganisms. Biol Fertil Soils 40:363–385CrossRefGoogle Scholar
  31. Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ, Wade WG (1998) Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64:795–799PubMedCentralPubMedGoogle Scholar
  32. Mocali S, Paffetti D, Emiliani G, Benedetti A, Fani R (2008) Diversity of heterotrophic aerobic cultivable microbial communities of soils treated with fumigants and dynamics of metabolic, microbial, and mineralization quotients. Biol Fertil Soils 44:557–569CrossRefGoogle Scholar
  33. Mühling M, Woolven-Allen J, Murrell C, Joint I (2008) Improved group-specific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities. ISME J 2:379–392PubMedCrossRefGoogle Scholar
  34. 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 59:695–700PubMedCentralPubMedGoogle Scholar
  35. Nannipieri P, Paul E (2009) The chemical and functional characterization of soil N and its biotic components. Soil Biol Biochem 41:2357–2369CrossRefGoogle Scholar
  36. Navarro-Noya YE, Jan-Roblero J, González-Chávez MC, Hernández-Gama R, Hernández-Rodríguez C (2010) Bacterial communities associated with the rhizosphere of pioneer plants (Bahia xylopoda and Viguiera linearis) growing on heavy metals-contaminated soils. Antonie van Leeuwenhoek 97:335–349PubMedCrossRefGoogle Scholar
  37. Osborn AM, Moore ERB, Timmis KN (2000) An evaluation of terminal restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ Microbiol 2:39–50PubMedCrossRefGoogle Scholar
  38. Shannon CE, Weaver W (1963) The mathematical theory of communication. University of Illinois Press, UrbanaGoogle Scholar
  39. Spruill TB (2004) Effectiveness of riparian buffers in controlling ground-water discharge of nitrate to streams in selected hydrogeologic settings of the North Carolina Coastal Plain. Water Sci Techol 49:63–70Google Scholar
  40. Tan G-L, Shu WS, Zhou WH, Li XL, Yu Lan C, Huang LN (2009) Seasonal and spatial variations in microbial community structure and diversity in the acid stream draining across an ongoing surface mining site. FEMS Microbiol Ecol 70:277–285CrossRefGoogle Scholar
  41. Tilak KVBR, Ranganayaki N, Pal KK, De R, Saxena AK, Nautiyal CS, Mittal S, Tripathi AK, Johri BN (2005) Diversity of plant growth and soil health supporting bacteria. Curr Sci 89:136–150Google Scholar
  42. Toffanin A, Basaglia M, Ciardi C, Vian P, Povolo S, Casella S (2000) Energy content decrease and viable-not-culturable status induced by oxygen limitation coupled to the presence of nitrogen oxides in Rhizobiumhedysari”. Biol Fertil Soils 31:484–488CrossRefGoogle Scholar
  43. USDA-SCS (US Department of Agriculture, Soil Conservation Service) (1984) User’s guide for the CREAMS computer model—Washington Computer Center version. USDA-SCS TR-72, Washington, DCGoogle Scholar
  44. Verhoeven JTA, Arheimer B, Yin C, Hefting MM (2006) Regional and global concerns over wetlands and water quality. Trends Ecol Evolut 21:96–103CrossRefGoogle Scholar
  45. Vidon PGF, Hill AR (2004) Landscape controls on nitrate removal in stream riparian zones. Water Resour Res 40:1–14. doi:10.1029/2003WR002473 (article number W03201)CrossRefGoogle Scholar
  46. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) A naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267PubMedCentralPubMedCrossRefGoogle Scholar
  47. Wani AA, Surakasi VP, Siddharth J, Raghavan RG, Patole MS, Ranade D, Shouche YS (2006) Molecular analyses of microbial diversity associated with the Lonar soda lake in India: an impact crater in a basalt area. Res Microbiol 157:928–937PubMedCrossRefGoogle Scholar
  48. Wenhui Z, Zucong C, Lichu Y, He Z (2007) Effects of the long-term application of inorganic fertilizers on microbial community diversity in rice-planting red soil as studied by using PCR-DGGE. Acta Ecol Sin 27:4011–4018CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Md. Mizanur Rahman
    • 1
    • 3
  • Marina Basaglia
    • 1
  • Elena Vendramin
    • 1
  • Bruno Boz
    • 1
  • Federico Fontana
    • 1
  • Bruna Gumiero
    • 2
  • Sergio Casella
    • 1
  1. 1.Department of Agriculture Food Natural Resources Animals and Environment (DAFNAE)Università degli Studi di PadovaLegnaroItaly
  2. 2.Department of Evolutionary and Experimental BiologyBologna UniversityBolognaItaly
  3. 3.Department of Biotechnology and Genetic EngineeringIslamic UniversityKushtiaBangladesh

Personalised recommendations