Tree bark and soil ammonia oxidizers: A molecular study on a historical forest of Central Italy

Fresenius Environmental Bulletin

Volumn 17, Issue 7 B, 2008, Pages 882-889

  Ceccherini, Maria Teresa ^a   Ascher, Judith ^a   Agnelli, Alessandro ^b   Certini, Giacomo ^a   Pietramellara, Giacomo ^a   Piovanelli, Carlo ^b   Nannipieri, Paolo ^a  

^a UNIVERSITY OF FLORENCE   (Italy)

^b Istituto Sperimentale per lo Studio e la Difesa del Suolo   (Italy)

Author keywords

16s rDNA fingerprinting; AOB population; Pine; Potential ammonia oxidizing activity; Soil and bark DNA; Soil ecology

Indexed keywords

AMMONIA; BACTERIUM; BARK; COMMUNITY STRUCTURE; CONIFEROUS FOREST; CONIFEROUS TREE; DNA FINGERPRINTING; ENVIRONMENTAL FACTOR; FOREST SOIL; MICROBIAL COMMUNITY; OXIDATION; PH; SOIL MICROORGANISM;

EURASIA; EUROPE; ITALY; SOUTHERN EUROPE;

BACTERIA (MICROORGANISMS); NITROSOMONADALES;

EID: 52749090787     PISSN: 10184619     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (42)

1. Compton, J.E., Watrud, L.S., Porteous, L.A. and DeGrood, S. (2004) Response of soil microbial biomass and community composition to chronic nitrogen additions at Harvard forest. Forest Ecology and Management 196, 143-158.
2. Stephen, J.R., McCaig, A.E., Smith, Z., Prosser, J.I. and Embley, T.M. (1996) Molecular diversity of soil and marine 16S rRNA gene sequences related to β-subgroup ammonia- oxidizing bacteria. Appl. Environ. Microbiol. 62, 4147-4154.
3. Phillips, C.J., Harris, D., Dollhopf, S.L., Gross, K.L., Prosser, J.I. and Paul, E.A. (2000) Effects of agronomic treatments on structure and function of ammonia-oxidizing communities. Appl. Environ. Microbiol. 66, 5410-5418.
4. Purkhold, U., Pommerening-Röser, A., Juretschko, S., Schid, M.C., Koops, H.-P. and Wagner, M. (2000) Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl. Environ. Microbiol. 66, 5368-5382.
5. Hayatsu, M. (1993) The lowest limit of pH for nitrification in tea soil and isolation of an acidophilic ammonia oxidizing bacterium. Soil Sci. Plant Nutrition 39, 219-226.
6. Hastings, R.C., Butler, C., Singleton, I., Saunders, J.R. and McCarthy, A.J. (2000) Analysis of ammonia-oxidizing bacteria populations in acid forest soil during conditions of moisture limitation. Lett. Appl. Microbiol. 30, 14-18.
7. De Boer, W. and Kowalchuk, G.A. (2001) Nitrification in acid soils: micro-organisms and mechanisms. Soil Biol. Biochem. 33, 853-866.
8. Jordan, F.L., Cantera, J.J.L., Fenn, M.E. and Stein, L.Y. (2005) Autotrophic ammonia-oxidizing bacteria contribute minimally to nitrification in a nitrogen-impacted forested ecosystem. Applied and Environmental Micrbiology 71, 197-206.
9. Hastings, R.C., Saunders, J.R., Hall, G.H., Pickup, R.W. and and McCarthy, A.J. (1998) Application of molecular biological techniques to a seasonal study of ammonia oxidation in a eutrophic freshwater lake. Appl. Environ. Microbiol. 64, 3674-3682.
10. Kowalchuk, G.A., Stephen, J.R., DeBoer, W., Prosser, J.I., Embley, T.M. and and Woldendorp, J.W. (1997) Analysis of ammonia-oxidizing bacteria of the β subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl. Environ. Microbiol. 63, 1489-1497.
11. McCaig, A.E., Embley, T.M. and and Prosser, J.I. (1994) Molecular analysis of enrichment cultures of marine ammonia-oxidizers. FEMS Microbiology Letters 120, 363-368.
12. Phillips, C.J., Smith, Z., Embley, T.M. and and Prosser, J.I. (1999) Phylogenetic differences between particle-associated and planktonic ammonia-oxidising bacteria of the b subdivision of the class Proteobacteria in the Northwestern Mediterranean Sea. Appl. Environ. Microbiol. 65, 779-786.
13. Pommerening-Roser, A., Rath, G. and and Koops, H.-P. (1996) Phylogenetic diversity within the genus Nitrosomonas. Systematic and Applied Microbiology 19, 344-351.
14. Rotthauwe, J.-H., Witzel, K.-P. and and Liesack, W. (1997) The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 63, 4704-4712.
15. Utaker, J.B., Bakken, L., Jiang, Q.Q. and and Nes, I.F. (1995) Phylogenetic analysis of seven new isolates of ammonia-oxidizing bacteria based on 16S rRNA gene sequences. Systematic and Applied Microbiology 18, 549-559.
16. Voytek, M.A. and and Ward, B.B. (1995) Detection of ammonia-oxidizing bacteria of the beta-subclass of the class Proteobacteria in aquatic samples with the PCR. Appl. Environ. Microbiol. 61, 1444-1450.
17. Hastings, R.C., Ceccherini, M.T., Miclaus, N., Saunders, J.R., Bazzicalupo, M. and and McCarthy, A.J. (1997) Direct molecular biological analysis of ammonia oxidising bacteria population in cultivated soil plots treated with swine manure. FEMS Microbiology Ecology.
18. McCaig, A.E., Phillips, C.J., Stephen, J.R., Kowalchuk, G.A., Harvey, S.M., Herbert, R.A., Embley, T.M. and and Prosser, J.I. (1999) Nitrogen cycling and community structure of proteobacterial β-subgroup ammonia-oxidising bacteria within polluted marine fish farm sediments. Appl. Environ. Microbiol. 65, 213-220.
19. Stehr, G., Bottcher, B., Dittberner, P., Rath, G. and Koops, H.-P. (1995) The ammonia-oxidizing nitrifying populations of the River Elbe estuary. FEMS Microbiol. Ecol. 17, 177-186.
20. Castaldini, M., Ceccherini, M., Papini, R. and Miclaus, N. (1997) Molecular and biochemical study of autotrophic ammonia oxidizers in a vertic soil of Tuscany. Fresenius Environmental Bulletin 6, 622-626.
21. Ceccherini, M.T., Castaldini, M., Azzini, A., Fancelli, S., Bazzicalupo, M. and Miclaus, N. (2001) Occurrence of Azospirillum brasilense in soils amended with swine manure. Annals of Microbiology 51, 29-38.
22. Gersper, P.L. and Holowaychuk, N. (1970) Effects of stem-flow water on a Miami soil under a beech tree. Soil Sci. Soc. Am. Proc. 34, 779-794.
23. Hornung, M. (1985) Acidification of soils by trees and forest. Soil Use Managem. 1, 24-28.
24. Lodhi, M.A.K. (1977) The influence and comparison of individual forest trees on soil properties and possible inhibition of nitrification due to intact vegetation. Am. J. Bot. 64, 260-264.
25. Zinke, P.J. (1962) The pattern of individual forest trees on soil properties. Ecology 43, 130-133.
26. Andersson, T. (1991) Influence of stemflow and throughfall from common oak (Quercus-Robur) on soil chemistry and vegetation patterns. Can. J. Forest Res. 21, 917-924.
27. Certini, G., Ugolini, F.C., Corti, G. and Agnelli, A. (1998) Early stages of podzolization under Corsican pine (Pinus nigra Arn. ssp. laricio). Geoderma 83, 103-125.
28. Scheu, S. and and Poser, G. (1996) The soil macrofauna (Diplopoda, Isopoda, Lumbricidae and Chilopoda) near tree trunks in a beechwood on limestone: Indications for stem-flow induced changes in community structure. Appl. Soil Ecol. 3, 115-125.
29. Ceccherini, M.T., Castaldini, M., Piovanelli, C., Hastings, R.C., McCarthy, A.J., Bazzicalupo, M. and Miclaus, N. (1998) Effects of swine manure fertilization on autotrophic ammonia oxidising bacteria. Appl. Soil Ecol. 7, 149-157.
30. Ugolini, F.C., Corti, G., Agnelli, A. and Piccardi, F. (1996) Mineralogical, physical, and chemical properties of rock fragments in soil. Soil Sci. 161, 521-542.
31. Soil Survey Staff (1996) Keys to soil taxonomy. 7th ed. U.S.D.A., N.R.C.S., U.S. Govt. Printing Office, Washington, DC, USA 644.
32. Fani, R., Bandi, C., Bazzicalupo, M., Ceccherini, M.T., Fancelli, A., Gallori, E., Gerace, L., Grifoni, A., Miclaus, N and Damiani, G. (1995) Phylogeny of the genus Azospirillum based on 16S rDNA sequence. FEMS Microbiology Letters 129, 195-200.
33. Smit, E., Leeflang, P. and Wernars, D. (1997) Detection of shifts in microbial community structure and diversity in soil caused by copper contamination using amplified ribosomal DNA restriction analysis. FEMS Microbiol. Ecol. 23, 249-261.
34. Rochelle, P.A., Will, J.A.K., Fry, J.C., Jenkins, G.J.S., Parkes, R.J., Turley C.M. and Weightman, A.J. (1995) Extraction and amplification of 16S rRNA genes from deep marine sediments and seawaterto assess bacterial community diversity. Nucleic acids in the environment, Trevors, J.T., van Elsas, J.D. (Eds) cap. 11, 219-239.
35. Belser, L.W., and Mays, E. L. (1982) Use of nitrifier activity measurements to estimate the efficiency of viable nitrifier counts in soils and sediments. Appl. Environ. Microbiol. 43, 945-948.
36. Nei, M. and Li, W.H. (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. 76, 5269-5273.
37. Lescuyer, P., Picot, S., Bracchi, V., Burnod, J., Austin, J., Pérard, A. and and Ambroise-Thomas, P. (1997) Detection of RAPD Markers Correlated with Chloroquine Resistance in Plasmodium falciparum. Genome Res. 7, 747-753.
38. R Development, Core and Team (2006) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.
39. Bej, A.K., and Mahbubani, M.H. (1994) PCR technology: current innovations. CRC Press, Boca Raton.
40. Marstorp, H. and Witter, E. (1999) Extractable dsDNA and product formation as measures of microbial growth in soil upon substrate addition. Soil Biology and Biochemistry 31, 1443-1453.
41. Renella, G., Landi, L., Ascher, J., Ceccherini, M.T., Pietramellara, G. and Nannipieri, P. (2006) Phosphomonoesterase production and persistence and composition of bacterial communities during plant material decomposition in soils with different pH values. Soil Biol. Biochem. 38, 795-802.
42. De Boer, W., Tietema, A., Klein Gunnewiek, P.J.A. and and Laanbroek, H.J. (1992) The chemolithotrophic ammonium-oxidizing community in a nitrogen-saturated acid forest soil in relation to pH-dependent nitrifying activity. Soil Biol. Biochem. 24, 229-234.