Different crop rotation systems as drivers of change in soil bacterial community structure and yield of rice, Oryza sativa

Biology and Fertility of Soils

Volumn 48, Issue 2, 2012, Pages 217-225

  Xuan, Do Thi ^a   Guong, Vo Thi ^b   Rosling, Anna ^a   Alström, Sadhna ^a   Chai, Benli ^c   Högberg, Nils ^a  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^b CAN THO UNIVERSITY   (Viet Nam)

^c MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

Bacterial communities; Crop rotation; Oryza sativa; Pyrosequencing; Yield

Indexed keywords

AGRICULTURAL SOIL; ALTERNATIVE AGRICULTURE; BACTERIUM; COMMUNITY RESPONSE; COMMUNITY STRUCTURE; CROP ROTATION; CROP YIELD; INTENSIVE AGRICULTURE; LEGUME; MAIZE; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; MONOCULTURE; PADDY FIELD; RICE; SOIL MICROORGANISM; SPECIES DIVERSITY;

BACTERIA (MICROORGANISMS); ORYZA SATIVA; VIGNA RADIATA VAR. RADIATA; ZEA MAYS;

EID: 84856078745     PISSN: 01782762     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00374-011-0618-5     Document Type: Article

References (37)

1. Acosta-Martínez V, Dowd S, Sun Y, Allen V (2008) Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem 40: 2762-2770.
2. Alvey S, Yang CH, Buerkert A, Crowley DE (2003) Cereal/legume rotation effects on rhizosphere bacterial community structure in West African soils. Biol Fertil Soils 37: 73-82.
3. Biswas JC, Ladha JK, Dazzo FB (2000) Rhizobia inoculation improves nutrient uptake and growth of lowland rice. Soil Sci Soc Am J 64: 1644-1650.
4. Cassman KG, De Datta SK, Olk DC, Alcantara JM, Samson MI, Descalsota JP, Dizon MA (1995) Yield decline and the nitrogen economy of long-term experiments on continuous, irrigated rice systems in the tropics. In: Lal R, Stewart BA (eds) Soil management: Experimental basis for sustainability and environmental quality. Lewis/CRC, Boca Raton, pp 181-222.
5. Claesson MJ, O'Sullivan O, Wang Q, Nikkilà J, Marchesi JR, Smidt H, de Vos WM, Ross R, O'Toole PW (2009) Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS ONE 4: e6669.
6. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucl Acids Res 37(1): D141-D145.
7. Costa R, Götz M, Mrotzek N, Lottmann J, Berg G, Smalla K (2006) Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds. FEMS Microbiol Ecol 56: 236-249.
8. da C Jesus E, Marsh TL, Tiedje JM, de S Moreira FM (2009) Changes in land use alter the structure of bacterial communities in Western Amazon soils. ISME J 3: 1004-1011.
9. da C. Jesus E, Susilawati E, Smith S, Wang Q, Chai B, Farris R, Rodrigues J, Thelen K, Tiedje J (2010) Bacterial communities in the rhizosphere of biofuel crops grown on marginal lands as evaluated by 16S rRNA gene pyrosequences. Bioenergy Res 3: 20-27.
10. De Datta SK, Gomez KA, Descalsota JP (1988) Changes in yield response to major nutrients and in soil fertility under intensive rice cropping. Soil Science 146: 350-358.
11. Dobermann A, Simbahan GC, Moya PF, Adviento MAA, Tiongco M, Witt C, Dawe D (2004) Methodology for socioeconomic and agronomic on-farm research in the RTDP project. In: Doberman A, Witt C, Dawe D (eds) Increasing productivity of intensive rice systems through site-specific nutrient management. Science Publishers/International Rice Research Institute, Enfield/Los Banos, pp 11-27.
12. Elbeltagy A, Nishioka K, Sato T, Suzuki H, Ye B, Hamada T, Isawa T, Mitsui H, Minamisawa K (2001) Endophytic colonization and in planta nitrogen fixation by a Herbaspirillum sp. isolated from wild rice species. Appl Environ Microbiol 67: 5285-5293.
13. Fantroussi SE, Mahillon J, Naveau H, Agathos SN (1997) Introduction and PCR detection of Desulfomonile tiedjei in soil slurry microcosms. Biodegradation 8: 125-133.
14. Fantroussi SE, Verschuere L, Verstraete W, Top EM (1999) Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles. Appl Environ Microbiol 65: 982-988.
15. Govindarajan M, Balandreau J, Kwon S, Weon H, Lakshminarasimhan C (2008) Effects of the inoculation of Burkholderia vietnamensis and related endophytic diazotrophic bacteria on grain yield of rice. Microb Ecol 55: 21-37.
16. Kim JS, Sparovek G, Longo RM, De Melo WJ, Crowley D (2007) Bacterial diversity of terra preta and pristine forest soil from the Western Amazon. Soil Biol Biochem 39: 684-690.
17. Ladygina N, Hedlund K (2010) Plant species influence microbial diversity and carbon allocation in the rhizosphere. Soil Biol Biochem 42: 162-168.
18. Larkin RP, Honeycutt CW (2006) Effects of different 3-year cropping systems on soil microbial communities and rhizoctonia diseases of potato. Phytopathology 96: 68-79.
19. Lee SH, Kim CG, Kang H (2011) Temporal dynamics of bacterial and fungal communities in a genetically modified (GM) rice ecosystem. Microb Ecol 61: 646-659.
20. Li QH, Wu FZ, Yang Y, Wang XZ (2009) Effects of rotation and interplanting on soil bacterial communities and cucumber yield. Acta Agriculturae Scandinavica Section B-Soil and Plant Science 59: 431-439.
21. Lozupone C, Hamady M, Knight R (2006) UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinforma 7: 371.
22. Marchner P, Yang CH, Lieberei R, Crowley DE (2001) Soil and plant specific effects on bacterial community composition in the rhizosphere. Soil Biol Biochem 33: 1437-1445.
23. Marenco RA, Santos AMB (1999) Crop rotation reduces weed competition and increases chlorophyll concentration and yield of rice. Pesqui Agropecu Bras 34: 1881-1887.
24. McCune B, Grace JB (2002) Analysis of ecological communities MjM software. Gleneden Beach, Oregon.
25. Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JHM, Piceno YM, DeSantis TZ, Andersen GL, Bakker PAHM, Raaijmakers JM (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332: 1097-1100.
26. Nandakumar R, Babu S, Viswanathan R, Raguchander T, Samiyappan R (2001) Induction of systemic resistance in rice against sheath blight disease by Pseudomonas fluorescens. Soil Biol Biochem 33: 603-612.
27. Oksanen J, Kindt R, Legendre P, O'Hara RB, Simpson GL, Solymos P, Stevens MHH, Wagner H (2009) Vegan: community ecology package version 1. 15-4 (2009-09-07). http://cran. r-project. org/.
28. Peterson TA, Varvel GE, USDA ARS (1989) Crop yield as affected by rotation and nitrogen rate. III. Corn. Agro J 81: 735-738.
29. Schutter M, Sandeno J, Dick R (2001) Seasonal, soil type, and alternative management influences on microbial communities of vegetable cropping systems. Biol Fertil Soils 34: 397-410.
30. Smalla K, Wieland G, Buchner A, Zock A, Parzy J, Kaiser S, Roskot N, Heuer H, Berg G (2001) Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol 67: 4742-4751.
31. Swofford DL (1998) PAUP* Phylogenetic analysis using parsimony (* and other methods). Version 4. Sinauer Associates, Sunderlands.
32. Vishwakarma P, Singh M, Dubey S (2010) Changes in methanotrophic community composition after rice crop harvest in tropical soils. Biol Fertil Soils 46: 471-479.
33. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
34. Wardle DA, Yeates GW, Williamson W, Bonner KI (2003) The response of a three trophic level soil food web to the identity and diversity of plant species and functional groups. Oikos 102: 45-56.
35. Warembourg FR, Roumet C, Lafont F (2003) Differences in rhizosphere carbon-partitioning among plant species of different families. Plant Soil 256: 347-357.
36. Wu M, Qin H, Chen Z, Wu J, Wei W (2011) Effect of long-term fertilization on bacterial composition in rice paddy soil. Biol Fertil Soils 47: 397-405.
37. Yanni YG, Rizk RY, Corich V, Squartini A, Ninke K, Philip-Hollingsworth S, Orgambide G, de Bruijn F, Stoltzfus J, Buckley D, Schmidt TM, Mateos PF, Ladha JK, Dazzo FB (1997) Natural endophytic association between Rhizobium leguminosarum bv. trifolii and rice roots and assessment of its potential to promote rice growth. Plant Soil 194: 99-114.