Probing potential microbial coupling of carbon and nitrogen cycling during decomposition of maize residue by 13C-DNA-SIP

Soil Biology and Biochemistry

Volumn 70, Issue , 2014, Pages 12-21

  Fan, Fenliang ^a   Yin, Chang ^a   Tang, Yongjun ^b   Li, Zhaojun ^a   Song, Alin ^a   Wakelin, Steven A ^c   Zou, Jun ^b   Liang, Yongchao ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b HUNAN INSTITUTE OF ENGINEERING   (China)

^c AGRESEARCH LTD   (New Zealand)

Author keywords

13C; Decomposition; Denitrification; Maize; NifH; NirS; Nitrogen fixation; Stable isotope probing

Indexed keywords

13C; MAIZE; NIFH; NIRS; STABLE-ISOTOPE PROBING;

BACTERIA; BACTERIOLOGY; CARBON; DENITRIFICATION; ISOTOPES; NITROGEN; NITROGEN FIXATION; RNA;

DECOMPOSITION;

BACTERIUM; CARBON CYCLE; CARBON ISOTOPE; CROP RESIDUE; DECOMPOSITION; DENITRIFICATION; ISOTOPIC ANALYSIS; MAIZE; NITROGEN CYCLE; NITROGEN FIXATION; SOIL MICROORGANISM; STABLE ISOTOPE;

CHINA;

EID: 84890914288     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2013.12.002     Document Type: Article

References (47)

1. Aerts R. Climate, leaf litter chemistry and leaf litter decomposition in terrestrial ecosystems: a triangular relationship. Oikos 1997, 79:439-449.
2. 13C-labelled wheat residue as estimated by DNA- and RNA-SIP techniques. Environ. Microbiol. 2007, 9:752-764.
3. Cole J.R., Wang Q., Cardenas E., Fish J., Chai B., Farris R.J., Kulam-Syed-Mohideen A.S., McGarrell D.M., Marsh T., Garrity G.M. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009, 37:D141-D145.
4. 2 as the sole nitrogen source. Appl. Environ. Microbiol. 1983, 45:711-713.
5. Eichorst S.A., Kuske C.R. Identification of cellulose-responsive bacterial and fungal communities in geographically and edaphically different soils by using stable isotope probing. Appl. Environ. Microbiol. 2012, 78:2316-2327.
6. 15N-DNA stable isotope probing. Pedobiologia 2011, 54:187-193.
7. 15N-DNA stable isotope probing. Fungal Ecol. 2011, 4:115-119.
8. Fan F.L., Yang Q.B., Li Z.J., Wei D., Cui X.A., Liang Y.C. Impacts of organic and inorganic fertilizers on nitrification in a cold climate soil are linked to the bacterial ammonia oxidizer community. Microb. Ecol. 2011, 62:982-990.
9. Fan F.L., Li Z.J., Wakelin S.A., Yu W.T., Liang Y.C. Mineral fertilizer alters cellulolytic community structure and suppresses soil cellobiohydrolase activity in a long term fertilization experiment. Soil Biol. Biochem. 2012, 55:70-77.
10. Fierer N., Bradford M.A., Jackson R.B. Toward an ecological classification of soil bacteria. Ecology 2007, 88:1354-1364.
11. Gan Y., Qiu Q., Liu P., Rui J., Lu Y. Syntrophic oxidation of propionate in rice field soil at 15 and 30°C under methanogenic conditions. Appl. Environ. Microbiol. 2012, 78:4923-4932.
12. Ginige M.P., Keller J., Blackall L.L. Investigation of an acetate-fed denitrifying microbial community by stable isotope probing, full-cycle rRNA analysis, and fluorescent in situ hybridization-microautoradiography. Appl. Environ. Microbiol. 2005, 71:8683-8691.
13. Ginige M.P., Hugenholtz P., Daims H., Wagner M., Keller J., Blackall L.L. Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community. Appl. Environ. Microbiol. 2004, 70:588-596.
14. Gledhill W.E., Casida L.E. Predominant catalase-negative soil bacteria. III. Agromyces, gen. n., microorganisms intermediary to Actinomyces and Nocardia. Appl. Microbiol. 1969, 18:340-349.
15. Hansel C.M., Fendorf S., Jardine P.M., Francis C.A. Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Appl. Environ. Microbiol. 2008, 74:1620-1633.
16. Hattori S., Kamagata Y., Hanada S., Shoun H. Thermacetogenium phaeum gen. nov., sp. nov., a strictly anaerobic, thermophilic, syntrophic acetate-oxidizing bacterium. Int. J. Syst. Evol. Microbiol. 2000, 50:1601-1609.
17. He R., Wooller M.J., Pohlman J.W., Catranis C., Quensen J., Tiedje J.M., Leigh M.B. Identification of functionally active aerobic methanotrophs in sediments from an arctic lake using stable isotope probing. Environ. Microbiol. 2012, 14:1403-1419.
18. Huber T., Faulkner G., Hugenholtz P. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 2004, 20:2317-2319.
19. Kim M.K., Na J.-R., Lee T.-H., Im W.-T., Soung N.-K., Yang D.-C. Solirubrobacter soli sp. nov., isolated from soil of a ginseng field. Int. J. Syst. Evol. Microbiol. 2007, 57:1453-1455.
20. Lam S.K., Lin E., Norton R., Chen D. The effect of increased atmospheric carbon dioxide concentration on emissions of nitrous oxide, carbon dioxide and methane from a wheat field in a semi-arid environment in northern China. Soil Biol. Biochem. 2011, 43:458-461.
21. Lane D.J. 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics 1991, 177-203. John Wiley & Son Ltd, Chichester, United Kingdom. E. Stackebrandt, M. Goodfellow (Eds.).
22. 13C-labeled plant residue in soil: analysis by a DNA-SIP approach. Soil Biol. Biochem. 2011, 43:814-822.
23. Li L.-J., Han X.-Z., You M.-Y., Horwath W.R. Nitrous oxide emissions from Mollisols as affected by long-term applications of organic amendments and chemical fertilizers. Sci. Total Environ. 2013, 452:302-308.
24. Li Y., Watanabe T., Asakawa S., Kimura M. Bacterial communities that decompose root cap cells in an anaerobic soil: estimation by DNA-SIP method using rice plant callus cells. Soil Sci. Plant Nutr. 2012, 58:297-308.
25. Liu P., Qiu Q., Lu Y. Syntrophomonadaceae-affiliated species as active butyrate-utilizing syntrophs in paddy field soil. Appl. Environ. Microbiol. 2011, 77:3884-3887.
26. Lu F., Wang X., Han B., Ouyang Z., Duan X., Zheng H.U.A., Miao H. Soil carbon sequestrations by nitrogen fertilizer application, straw return and non-tillage in China's cropland. Glob. Change Biol. 2009, 15:281-305.
27. Marschner P., Umar S., Baumann K. The microbial community composition changes rapidly in the early stages of decomposition of wheat residue. Soil Biol. Biochem. 2011, 43:445-451.
28. McComb J.A., Elliott J., Dilworth M.J. Acetylene reduction by Rhizobium in pure culture. Nature 1975, 256:409-410.
29. Melillo J.M., Aber J.D., Muratore J.F. Nitrogen and lignin control of hardwood leaf litter decomposition dynamics. Ecology 1982, 63:621-626.
30. Mohagheghi A., Grohmann K., Himmel M., Leighton L., Updegraff D.M. Isolation and characterization of Acidothermus cellulolyticus gen. nov., sp. nov., a new genus of thermophilic, acidophilic, cellulolytic bacteria. Int. J. Syst. Bacteriol. 1986, 36:435-443.
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. Appl. Environ. Microbiol. 1993, 59:695-700.
32. Nakamura K., Hiraishi A., Yoshimi Y., Kawaharasaki M., Masuda K., Kamagata Y. Microlunatus phosphovorus gen. nov., sp. nov., a new gram-positive polyphosphate-accumulating bacterium isolated from activated sludge. Int. J. Syst. Bacteriol. 1995, 45:17-22.
33. Pascault N., Ranjard L., Kaisermann A., Bachar D., Christen R., Terrat S., Mathieu O., Lévêque J., Mougel C., Henault C. Stimulation of different functional groups of bacteria by various plant residues as a driver of soil priming effect. Ecosystems 2013, 1-13. 10.1007/s10021-013-9650-7.
34. Poly F., Monrozier L.J., Bally R. Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. Res. Microbiol. 2001, 152:95-103.
35. Rui J., Peng J., Lu Y. Succession of bacterial populations during plant residue decomposition in rice field soil. Appl. Environ. Microbiol. 2009, 75:4879-4886.
36. Schellenberger S., Kolb S., Drake H.L. Metabolic responses of novel cellulolytic and saccharolytic agricultural soil bacteria to oxygen. Environ. Microbiol. 2010, 12:845-861.
37. 13C potato tissues on the bacterial and fungal community composition of soil. Soil Biol. Biochem. 2012, 49:88-95.
38. 13C-labelled straw in the rice rhizosphere. Environ. Microbiol. Rep. 2011, 3:587-596.
39. Smil V. Crop residues: agriculture's largest harvest. BioScience 1999, 49:299-308.
40. Tamura K., Dudley J., Nei M., Kumar S. MEGA 4: molecular evolutionary genetics analysis (MEGA) software version 4. 0. Mol. Biol. Evol. 2007, 24:1596-1599.
41. Throbäck I.N., Enwall K., Jarvis Å., Hallin S. Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiol. Ecol. 2004, 49:401-417.
42. Urzì C., Salamone P., Schumann P., Rohde M., Stackebrandt E. Blastococcus saxobsidens sp. nov., and emended descriptions of the genus Blastococcus Ahrens and Moll 1970 and Blastococcus aggregatus Ahrens and Moll 1970. Int. J. Syst. Evol. Microbiol. 2004, 54:253-259.
43. van der Zaan B.M., Saia F.T., Stams A.J.M., Plugge C.M., de Vos W.M., Smidt H., Langenhoff A.A.M., Gerritse J. Anaerobic benzene degradation under denitrifying conditions: peptococcaceae as dominant benzene degraders and evidence for a syntrophic process. Environ. Microbiol. 2012, 14:1171-1181.
44. van Kessel C., Hartley C. Agricultural management of grain legumes: has it led to an increase in nitrogen fixation?. Field Crops Res. 2000, 65:165-181.
45. Wang G., Skipper H.D. Identification of denitrifying rhizobacteria from bentgrass and bermudagrass golf greens. J.Appl. Microbiol. 2004, 97:827-837.
46. Xu Y., Yu W., Ma Q., Zhou H. Responses of bacterial and archaeal ammonia oxidisers of an acidic luvisols soil to different nitrogen fertilization rates after 9 years. Biol. Fertil. Soils 2012, 48:827-837.
47. Yin C., Fan F.L., Li Z.J., Song A.l., Zhu P., Peng C., Liang Y.C. The influence of long-term application of organic and inorganic fertilizer on the composition and abundance of nirS-harboring denitrifiers in black soil. Environ. Sci. 2012, 33:3967-3975. (in Chinese).