Potato cultivar type affects the structure of ammonia oxidizer communities in field soil under potato beyond the rhizosphere

Soil Biology and Biochemistry

Volumn 50, Issue , 2012, Pages 85-95

  Dias, Armando Cavalcante Franco ^a   Hoogwout, Eelco Frans ^a   Pereira e Silva, Michele de Cassia ^a   Salles, Joana Falcão ^a   van Overbeek, Leonard Simon ^b   van Elsas, Jan Dirk ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

Ammonia oxidizers; Cultivar; Plant growth stage; Rhizosphere; Soil type

Indexed keywords

AMMONIA OXIDIZERS; CULTIVAR; PLANT GROWTH STAGES; RHIZOSPHERE; SOIL TYPES;

AMMONIA; GENES; POLYMERASE CHAIN REACTION; POPULATION STATISTICS; SOCIAL SCIENCES;

SOILS;

ABUNDANCE; AMMONIA; BACTERIUM; COMMUNITY STRUCTURE; CULTIVAR; FIELD SURVEY; POPULATION SIZE; POTATO; PROKARYOTE; RHIZOSPHERE; SOIL TYPE;

ARCHAEA; BACTERIA (MICROORGANISMS); SOLANUM TUBEROSUM;

EID: 84859514263     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2012.03.006     Document Type: Article

References (50)

1. Adair K.L., Schwartz E. Evidence that ammonia-oxidizing archaea are more abundant than ammonia-oxidizing bacteria in semi-arid soils of Northern Arizona, USA. Microbial Ecology 2008, 56:420-426.
2. Avrahami S., Conrad R. Patterns of community change among ammonia oxidizers in meadow soils upon long-term incubation at different temperatures. Applied and Environmental Microbiology 2003, 69:6152-6164.
3. Avrahami S., Conrad R. Cold-temperate climate: a factor for selection of ammonia oxidizers in upland soil?. Canadian Journal of Microbiology 2005, 51:709-714.
4. 2O release and on the community structure of ammonia oxidizers and denitrifiers. Applied and Environmental Microbiology 2002, 68:5685-5692.
5. Avrahami S., Liesack W., Conrad R. Effects of temperature and fertilizer on activity and community structure of soil ammonia oxidizers. Environmental Microbiology 2003, 5:691-705.
6. Beman J.M., Popp B.N., Francis C.A. Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California. ISME Journal 2008, 2:429-441.
7. Bruinsma M., Kowalchuk G.A., van Veen J.A. Effects of genetically modified plants on microbial communities and processes in soil. Biology and Fertility of Soils 2003, 37:329-377.
8. Chen X.P., Zhu Y.G., Xia Y., Shen J.P., He J.Z. Ammonia oxidizing archaea: important players in paddy rhizosphere soil?. Environmental Microbiology 2008, 10:1978-1987.
9. Clarke K.R., Green R.H. Statistical design and analysis for a biological effects study. Marine Ecology Progress Series 1988, 46:213-226.
10. De Boer W., Kowalchuk G.A. Nitrification in acid soils: micro-organisms and mechanisms. Soil Biology & Biochemistry 2001, 33:853-866.
11. De Boer W., Gunnewiek P.A., Laanbroek H.J. Ammonium-oxidation at low pH by a chemolithotrophic bacterium belonging to the genus Nitrosospira. Soil Biology & Biochemistry 1995, 27:127-132.
12. Di H.J., Cameron K.C., Shen J.-P., Winefield C.S., O'Callaghan M., Bowatte S., He J.-Z. Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions. FEMS Microbiology Ecology 2010, 72:386-394.
13. Dias A.C.F., Dini-Andreote F., Taketani R.G., Tsai S.M., Azevedo J.L., Melo I.S., Andreote F.D. Archaeal communities in three contrasting mangrove sediments. Journal of Soils and Sediments 2011, e-pub ahead of print 14 September 2011. 10.1007/s11368-011-0423-7.
14. Erguder T.H., Boon N., Wittebolle L., Marzorati M., Verstraete W. Environmental factors shaping the ecological niches of ammonia oxidizing archaea. FEMS Microbiology Review 2009, 33:855-869.
15. Glaser K., Hackl E., Inselsbacher E., Strauss J., Wanek W., Zechmeister-Boltenstern S., Sessitsch A. Dynamics of ammonia-oxidizing communities in barley-planted bulk soil and rhizosphere following nitrate and ammonium fertilizer amendment. FEMS Microbiology Ecology 2010, 74:575-591.
16. Hack H., Gall H., Klemke Th., Klose R., Meier U., Stauss R., Witzenberger A. Phänologische Entwicklungsstadien der Kartoffel (Solanumtuberosum L.). Codierung und Beschreibung nach der erweiterten BBCH-Skala mit Abbildungen. Nachrichtenbl. Deut. Pflanzenschutzd 1993, 45:11-19.
17. Hallin S., Jones C.M., Schloter M., Philippot L. Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment. ISME Journal 2009, 3:597-605.
18. He J.Z., Shen J.P., Zhang L.M., Zhu Y.G., Zheng Y.M., Xu M.G., Di H. Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammoniaoxidizingarchaea of a Chinese upland red soil under longterm fertilization practices. Environmental Microbiology 2007, 9:2364-2374.
19. Höfferle S., Nicol G.W., Levin P., Hacin J., Prosser J.I., Mandic-Mulec I. Ammonium supply rate influences archaeal and bacterial ammonia oxidizers in a wetland soil vertical profile. FEMS Microbiology Ecology 2010, 74:302-315.
20. Huber T., Faulkner G., Hugenholtz P. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 2004, 20:2317-2319.
21. Inceoglu ö., Salles J.F., van Overbeek L., van Elsas J.D. Effects of plant genotype and growth stage on the betaproteobacterial communities associated with different potato cultivars in two fields. Applied and Environmental Microbiology 2010, 11:3675-3684.
22. Inceoglu ö., Al-Soud W.A., Salles J.F., Semenov A.V., van Elsas J.D. Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing. Plos One 2011, 6(8):e23321. 10.1371/journal.pone.0023321.
23. Jia Z., Conrad R. Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environmental Microbiology 2009, 11:1658-1671.
24. + activity, and net nitrification in an acid soil. Soil Biology & Biochemistry 2011, 43:2215-2221.
25. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide-sequences. Journal of Molecular Evolution 1980, 16:111-120.
26. Koops H.P., Purkhold U., Pommerening-Roser A., Timmermann G., Wagner M. The Lithoautotrophic Ammonia Oxidizers. The Prokaryotes: an Evolving Electronic Resource for the Microbiological Community 2003, 778-811. Springer Verlag, New York. M. Dworkin (Ed.).
27. Kowalchuk G.A., Stephen J.R. Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annual Review Microbiology 2001, 55:485-529.
28. Kowalchuk G.A., Stephen J.R., De Boer W., Prosser J., Embley T.M., Woldendorp J.W. Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR amplified 16S ribosomal DNA fragments. Applied and Environmental Microbiology 1997, 63:1489-1497.
29. Lehtovirta-Morley L., Stoecker K., Vilcinskas A., Prosser J.I., Nicol G.W. Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proceedings of the National Academy of Sciences of the United States of America 2011, 108:15892-15897.
30. Leininger S., Urich T., Schloter M., et al. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 2006, 442:806-809.
31. Muyzer G., de Waal E.C., Uitterlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology 1993, 59:695-700.
32. Nicol G.W., Schleper C. Ammonia oxidizing Crenarchaeota: important players in the nitrogen cycle?. Trends Microbiology 2006, 14:207-212.
33. Nicol G.W., Leininger S., Schleper C., Prosser J.I. The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environmental Microbiology 2008, 10:2966-2978.
34. Pereira e Silva M.C., Semenov A.V., van Elsas J.D., Salles J.F. Seasonal variations in diversity and abundance of diazotrophic communities across soils. FEMS Microbiology Ecology 2011, 77:57-68.
35. Philippot L., Hallin S., Borjesson G., Baggs E.M. Biochemical cycling in the rhizosphere having an impact on global change. Plant Soil 2009, 321:61-81.
36. Prosser J.I., Nicol G.W. Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environmental Microbiology 2008, 10:2931-2941.
37. Rasch F., Knapp D., Kaiser C., Koranda M., Kitzler B., Zechmeister-Boltenstern S., Richter A., Sessitsch A. Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest. ISME Journal 2011, 5:389-402.
38. Roux X.L., Poly F., Currey P., Commeaux C., Hai B., Nicol G.W., Prosser J.I., Schloter M., Attard E., Klumpp K. Effects of aboveground grazing on coupling among nitrifier activity, abundance and community structure. ISME Journal 2008, 2:221-232.
39. Saitou N., Nei M. The Neighbor-Joining Method - A new method for reconstructing phylogenetic trees. Molecular Biology Evolution 1987, 4:406-425.
40. Schauss K., Focks A., Leininger S., Kotzerke A., Heuer H., Thiele-Bruhn S., Sharma S., Wilke B.-M., Matthies M., Smalla K., Munch J.C., Amelung W., Kaupenjohann M., Schloter M., Schleper C. Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils. Environmental Microbiology 2009, 11:446-456.
41. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B. Introducing MOTHUR: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 2009, 75:7537-7541.
42. Shen J.P., Zhang L.M., Zhu Y.G., Zhang J.B., He J.Z. Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environmental Microbiology 2008, 10:1601-1611.
43. Stephen J.R., McCaig A.E., Smith Z., Prosser J.I., Embley T.M. Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria. Applied and Environmental Microbiology 1996, 62:4147-4154.
44. Tourna M., Freitag T.E., Nicol G.W., Prosser J.I. Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environmental Microbiology 2008, 10:1357-1364.
45. Töwe S., Albert A., Kleineidam K., Brankatschk R., Dümig A., Welzl G., Munch J.C., Zeyer J., Schloter M. Abundance of microbes involved in nitrogen transformation in the rhizosphere of Leucanthemopsisalpina (L.) Heywood grown in soils from different sites of the Damma Glacier Forefield. Microbial Ecology 2010, 60:762-770.
46. Treusch A.H.S., Leininger A., Kletzin S.C., Schuster H., Klenk P., Schleper C. Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophiliccrenarchaeota in nitrogen cycling. Environmental Microbiology 2005, 7:1985-1995.
47. Wessén E., Söderström M., Stenberg M., Bru D., Hellman M., Welsh A., Thomsen F., et al. Spatial distribution of ammonia-oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning. The ISME Journal 2011, 5:1213-1225.
48. Wuchter C., Abbas B., Coolen M.J., Herfort L., van Bleijswijk J., Timmers P., Strous M., Teira E., Herndl G.J., Middelburg J.J., Schouten S., Sinninghe Damste J.S. Archaeal nitrification in the ocean. Proceedings of the National Academy of Sciences of the United States of America 2006, 103(33):12317-12322.
49. Yao H., Gao Y., Nicol G.W., Campbell C.D., Prosser J.I., Zhang L., Han W., Singh B.K. Links between ammonia oxidizer community structure, abundance and nitrification potential in acidic soils. Applied and Environmental Microbiology 2011, 77:4618-4625.
50. Zhang L.M., Wang M., Prosser J.I., Zheng Y.M., He J.Z. Altitude ammonia-oxidizing bacteria and archaea in soils of Mount Everest. FEMS Microbiology Ecology 2009, 70:52-61.