Diversity of Bacterial Communities in a Profile of a Winter Wheat Field: Known and Unknown Members
详细信息 查看全文
- 作者：Aurore Stroobants (1)
Florine Degrune (1)
Claire Olivier (2)
Céline Muys (3)
Christian Roisin (2)
Gilles Colinet (4)
Bernard Bodson (5)
Daniel Portetelle (1)
Micheline Vandenbol (1) - 刊名：Microbial Ecology
- 出版年：2014
- 出版时间：November 2014
- 年：2014
- 卷：68
- 期：4
- 页码：822-833
- 全文大小：1,277 KB
- 参考文献：1. Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci U S A 99(16):10494-0499 CrossRef
2. Gans J, Wolinsky M, Dunbar J (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309(5739):1387-390 CrossRef
3. Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72(3):1719-728 CrossRef
4. Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180(18):4765-774
5. Rappé MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369-94 CrossRef
6. Hartmann M, Lee S, Hallam SJ, Mohn WW (2009) Bacterial, archaeal and eukaryal community structures throughout soil horizons of harvested and naturally disturbed forest stands. Environ Microbiol 11(12):3045-062 CrossRef
7. Nemergut DR, Cleveland CC, Wieder WR, Washenberger CL, Townsend AR (2010) Plot-scale manipulations of organic matter inputs to soils correlate with shifts in microbial community composition in a lowland tropical rain forest. Soil Biol Biochem 42(12):2153-160 CrossRef
8. Eilers KG, Debenport S, Anderson S, Fierer N (2012) Digging deeper to find unique microbial communities: the strong effect of depth on the structure of bacterial and archaeal communities in soil. Soil Biol Biochem 50:58-5 CrossRef
9. Thomson BC, Ostle N, McNamara N, Bailey MJ, Whiteley AS, Griffiths RI (2010) Vegetation affects the relative abundances of dominant soil bacterial taxa and soil respiration rates in an upland grassland soil. Microb Ecol 59(2):335-43 CrossRef
10. Will C, Thürmer A, Wollherr A, Nacke H, Herold N, Schrumpf M et al (2010) Horizon-specific bacterial community composition of German grassland soils, as revealed by pyrosequencing-based analysis of 16S rRNA genes. Appl Environ Microbiol 76(20):6751-759 CrossRef
11. Preem JK, Truu J, Truu M, Mander ü, Oopkaup K, L?hmus K et al (2012) Bacterial community structure and its relationship to soil physico-chemical characteristics in alder stands with different management histories. Ecol Eng 49:10-7 CrossRef
12. Rohini-Kumar M, Osborne JW, Saravanan VS (2013) Comparison of soil bacterial communities of / Pinus patula of Nilgiris, western ghats with other biogeographically distant pine forest clone libraries. Microb Ecol 66(1):132-44 CrossRef
13. Navarrete AA, Cannavan FS, Taketani RG, Tsai SM (2010) A molecular survey of the diversity of microbial communities in different Amazonian agricultural model systems. Diversity 2:787-09 CrossRef
14. Orr CH, James A, Leifert C, Cooper JM, Cummings SP (2011) Diversity and activity of free-living nitrogen-fixing bacteria and total bacteria in organic and conventionally managed soils. Appl Environ Microbiol 77(3):911-19 CrossRef
15. Ding GC, Piceno YM, Heuer H, Weinert N, Dohrmann AB, Carrillo A et al (2013) Changes of soil bacterial diversity as a consequence of agricultural land use in a semi-arid ecosystem. PLoS ONE 8(3):e59497. doi:10.1371/journal.pone.0059497 CrossRef
1 - 作者单位：Aurore Stroobants (1)
Florine Degrune (1)
Claire Olivier (2)
Céline Muys (3)
Christian Roisin (2)
Gilles Colinet (4)
Bernard Bodson (5)
Daniel Portetelle (1)
Micheline Vandenbol (1)
1. Unité de Microbiologie et Génomique, Université de Liège, Gembloux Agro-Bio Tech, Avenue Maréchal Juin 6, 5030, Gembloux, Belgium
2. Unité Fertilité des sols et Protection des eaux (U9), Centre wallon de Recherches agronomiques, Rue du Bordia 4, 5030, Gembloux, Belgium
3. Bioinformatics, Progenus SA, Rue des Praules 2, 5030, Gembloux, Belgium
4. Sciences et technologie de l’environnement, Gembloux Agro-Bio Tech, Université de Liège, Passage des Déportés 2, 5030, Gembloux, Belgium
5. Unité de Phytotechnie des Régions tempérées, Université de Liège, Gembloux Agro-Bio Tech, Passage des Déportés 2, 5030, Gembloux, Belgium - ISSN：1432-184X
文摘
In soils, bacteria are very abundant and diverse. They are involved in various agro-ecosystem processes such as the nitrogen cycle, organic matter degradation, and soil formation. Yet, little is known about the distribution and composition of bacterial communities through the soil profile, particularly in agricultural soils, as most studies have focused only on topsoils or forest and grassland soils. In the present work, we have used bar-coded pyrosequencing analysis of the V3 region of the 16S rRNA gene to analyze bacterial diversity in a profile (depths 10, 25, and 45?cm) of a well-characterized field of winter wheat. Taxonomic assignment was carried out with the Ribosomal Database Project (RDP) Classifier program with three bootstrap scores: a main run at 0.80, a confirmation run at 0.99, and a run at 0 to gain information on the unknown bacteria. Our results show that biomass and bacterial quantity and diversity decreased greatly with depth. Depth also had an impact, in terms of relative sequence abundance, on 81?% of the most represented taxonomic ranks, notably the ranks Proteobacteria, Bacteroidetes, Actinobacteridae, and Acidobacteria. Bacterial community composition differed more strongly between the topsoil (10 and 25?cm) and subsoil (45?cm) than between levels in the topsoil, mainly because of shifts in the carbon, nitrogen, and potassium contents. The subsoil also contained more unknown bacteria, 53.96?% on the average, than did the topsoil, with 42.06?% at 10?cm and 45.59?% at 25?cm. Most of these unknown bacteria seem to belong to Deltaproteobacteria, Actinobacteria, Rhizobiales, and Acidobacteria.