Taxonomical and functional microbial community selection in soybean rhizosphere
Tóm tắt
Từ khóa
Tài liệu tham khảo
Aziz, 2008, The RAST server: Rapid Annotation using Subsystems Technology, BMC Genomics, 9, 75, 10.1186/1471-2164-9-75
Bastian, 2009, Gephi: An Open Source Software for Exploring and Manipulating Networks
Benjamini, 1995, Controling the false discovery rate—a practical and powerful approach to multiple testing, J Roy Stat Soc, 57, 289, 10.1111/j.2517-6161.1995.tb02031.x
Berg, 2009, Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere, FEMS Microbiol Ecol, 68, 1, 10.1111/j.1574-6941.2009.00654.x
Brody, 2004, Sodium boric acid: Atriz-less, cooler conductive medium for DNA electrophoresis, Biotechniques, 36, 214, 10.2144/04362BM02
Bulgarelli, 2012, Revealing structure and assembly cues for Arabidopsis roo-inhabiting bacterial microbiota, Nature, 488, 91, 10.1038/nature11336
Burke, 2011, Bacterial community assembly based on functional genes rather than species, PNAS, 108, 14288, 10.1073/pnas.1101591108
Calvaruso, 2009, Rapid clay weathering in the rhizosphere of Norway spruce and oak in an acid forest ecosystem, SSSAJ, 73, 331, 10.2136/sssaj2007.0400
Caruso, 2011, Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale, ISME J, 5, 1406, 10.1038/ismej.2011.21
Chase, 2011, Disentangling the importance of ecological niches from stochastic processes across scales, Philos Trans R Soc Lond B Biol Sci, 366, 2351, 10.1098/rstb.2011.0063
Chave, 2004, Neutral theory and community ecology, Ecol Lett, 7, 241, 10.1111/j.1461-0248.2003.00566.x
Corpas, 2011, Nitric oxide imbalance provokes a nitrosative response in plants under abiotic stress, Plant Sci, 181, 604, 10.1016/j.plantsci.2011.04.005
DeAngelis, 2008, Selective progressive response of soil microbial community to wild oat roots, ISME J, 3, 168, 10.1038/ismej.2008.103
Dinsdale, 2008, Functional metagenomic profiling of nine biomes, Nature, 452, 629, 10.1038/nature06810
Dumbrell, 2010, Relative roles of niche and neutral process in structuring a soil microbial community, ISME J, 4, 337, 10.1038/ismej.2009.122
Feinstein, 2012, Taxa-area relationship and neutral dynamics influence the diversity of fungal communities on senesced tree leaves, Environ Microbiol, 14, 1488, 10.1111/j.1462-2920.2012.02737.x
Ferrenberg, 2013, Changes in assembly processes in soil bacterial communities following a wildfire disturbance, ISME J, 7, 1102, 10.1038/ismej.2013.11
Fisher, 1958, On grouping for maximum homogeneity, J Am Stat Assoc, 53, 789, 10.1080/01621459.1958.10501479
Haichar, 2008, Plant host habitat and root exudates shape soil bacterial community structure, ISME J, 2, 1221, 10.1038/ismej.2008.80
Hammer, 2001, PAST: paleontological statistics software package for education and data analysis, Palaeontologia Electronica, 4, 9
Hu, 2006, Two phosphate- and potassium-solubilizing bacteria isolated from Tianmu Mountain, Zhejiang, China, World J Microb Biotechnol, 22, 983, 10.1007/s11274-006-9144-2
Hubbell, 2001, Monographs in Population Biology 32
Jabot, 2008, Reconciling neutral community models and environmental filtering: theory and an empirical test, Oikos, 117, 1308, 10.1111/j.0030-1299.2008.16724.x
Knief, 2011, Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice, ISME J, 6, 1378, 10.1038/ismej.2011.192
Kowalchuk, 2002, Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms, Antonie Van Leeuwenhoek, 81, 509, 10.1023/A:1020565523615
Leibold, 2006, Coexistence of the niche and neutral perspectives in community ecology, Ecology, 87, 1399, 10.1890/0012-9658(2006)87[1399:COTNAN]2.0.CO;2
Lundberg, 2012, Defining the core Arabidopsis thaliana root microbiome, Nature, 488, 86, 10.1038/nature11237
MacArthur, 1957, On the relative abundance of bird species, Proc Natl Acad Sci USA, 43, 293, 10.1073/pnas.43.3.293
Marschner, 2001, Soil and plant specific effects on bacterial community composition in the rhizosphere, Soil Biol Biochem, 33, 1437, 10.1016/S0038-0717(01)00052-9
Marschner, 2011, Rhizosphere interactions between microorganisms and plants govern iron and phosphorus acquisition along the root axis—model and research methods, Soil Biol Biochem, 43, 883, 10.1016/j.soilbio.2011.01.005
McGill, 2007, Species abundance distribution: moving beyond single prediction theories to integration within an ecological framework, Ecol Lett, 10, 995, 10.1111/j.1461-0248.2007.01094.x
McGill, 2006, Empirical evaluation of neutral theory, Ecology, 87, 1411, 10.1890/0012-9658(2006)87[1411:EEONT]2.0.CO;2
Mendes, 2013, The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms, FEMS Microbiol Rev, 37, 634, 10.1111/1574-6976.12028
Meyer, 2008, The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes, BMC Bioinformatics, 9, 386, 10.1186/1471-2105-9-386
Motomura, 1932, On the statistical treatment of communities, Zool Mag, 44, 379
Navarrete, 2013, Acidobacterial community responses to agricultural management of soybean in Amazon forest soils, FEMS Microbiol Ecol, 83, 607, 10.1111/1574-6941.12018
Newcombe, 1998, Improved confidence intervals for the difference between binomial proportions based on paired data, Stat Med, 17, 2635, 10.1002/(SICI)1097-0258(19981130)17:22<2635::AID-SIM954>3.0.CO;2-C
Olden, 2003, Toward a mechanism understanding and prediction of biotic homogenization, Am Nat, 162, 442, 10.1086/378212
Parks, 2010, Identifying biologically relevant differences between metagenomic communities, Bioinformatics, 26, 715, 10.1093/bioinformatics/btq041
Philippot, 2013, Going back to the roots: the microbial ecology of the rhizosphere, Nat Rev Microbiol, 11, 789, 10.1038/nrmicro3109
R Development Core Team, 2007, R: A Language and Environment for Statistical Computing
Rasch, 2006, Rhizosphere bacteria affected by transgenic potatoes with antibacterial activities compared with the effects of soil, wild-type potatoes, vegetation stage and pathogen exposure, FEMS Microbiol Ecol, 56, 219, 10.1111/j.1574-6941.2005.00027.x
Robin, 2006, Effect of ferritin overexpression in tobacco on the structure of bacterial and pseudomonad communities associated with the roots, FEMS Microbiol Ecol, 58, 492, 10.1111/j.1574-6941.2006.00174.x
Rodrigues, 2013, Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities, PNAS, 110, 988, 10.1073/pnas.1220608110
Smith, 2012, Metagenomic comparison of microbial communities inhabiting confined and unconfined aquifer ecosystems, Environ Microbiol, 14, 240, 10.1111/j.1462-2920.2011.02614.x
Uroz, 2010, Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil, Environ Microbiol Rep, 2, 281, 10.1111/j.1758-2229.2009.00117.x