Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits
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Akibode, 2011, Global and regional trends in production, trade and consumption of food legume crops
Badri, 2013, Application of natural blends of phytochemicals derived from the root exudates of Arabidopsis to the soil reveal that phenolic related compounds predominantly modulate the soil microbiome, J Biol Chem, 288, 4502, 10.1074/jbc.M112.433300
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
Bitocchi, 2012, Mesoamerican origin of the common bean (Phaseolus vulgaris L.) is revealed by sequence data, Proc Natl Acad Sci USA, 109, E788, 10.1073/pnas.1108973109
Blair, 2012, Diversification and population structure in common beans (Phaseolus vulgaris L.), PLoS One, 7, e49488, 10.1371/journal.pone.0049488
Broughton, 2003, Beans (Phaseolus spp.)—model food legumes, Plant Soil, 252, 55, 10.1023/A:1024146710611
Brown, 2012, Diet-induced dysbiosis of the intestinal microbiota and the effects on immunity and disease, Nutrients, 4, 1095, 10.3390/nu4081095
Bulgarelli, 2015, Structure and function of the bacterial root microbiota in wild and domesticated barley, Cell Host Microbe, 17, 392, 10.1016/j.chom.2015.01.011
Bulgarelli, 2012, Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota, Nature, 488, 91, 10.1038/nature11336
Bulgarelli, 2013, Structure and functions of the bacterial microbiota of plants, Annu Rev Plant Biol, 64, 807, 10.1146/annurev-arplant-050312-120106
Carvalhais, 2013, Activation of the jasmonic acid plant defence pathway alters the composition of rhizosphere bacterial communities, PLoS One, 8, e56457, 10.1371/journal.pone.0056457
Chang, 2015, Second-generation PLINK: rising to the challenge of larger and richer datasets, GigaScience, 4, 7, 10.1186/s13742-015-0047-8
Chapelle, 2016, Fungal invasion of the rhizosphere microbiome, ISME J, 10, 265, 10.1038/ismej.2015.82
Cole, 2014, Ribosomal Database Project: data and tools for high throughput rRNA analysis, Nucleic Acids Res, 42, D633, 10.1093/nar/gkt1244
Comas, 2013, Root traits contributing to plant productivity under drought, Front Plant Sci, 4, 442, 10.3389/fpls.2013.00442
De Filippo, 2010, Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa, Proc Natl Acad Sci USA, 107, 14691, 10.1073/pnas.1005963107
Desiderio, 2013, Chloroplast microsatellite diversity in Phaseolus vulgaris, Front Plant Sci, 3, 1, 10.3389/fpls.2012.00312
Dodt, 2012, FLEXBAR—flexible barcode and adapter processing for next-generation sequencing platforms, Biology, 1, 895, 10.3390/biology1030895
Doebley, 2006, The molecular genetics of crop domestication, Cell, 127, 1309, 10.1016/j.cell.2006.12.006
Dumbrell, 2010, Relative roles of niche and neutral process in structuring a soil microbial community, ISME J, 4, 337, 10.1038/ismej.2009.122
Earl, 2012, STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method, Conserv Genet Resour, 4, 359, 10.1007/s12686-011-9548-7
Edgar, 2010, Search and clustering hundreds of times faster than BLAST, Bioinformatics, 26, 2460, 10.1093/bioinformatics/btq461
Edgar, 2011, UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, 27, 2194, 10.1093/bioinformatics/btr381
Etienne, 2005, A new sampling formula for neutral biodiversity, Ecol Lett, 8, 253, 10.1111/j.1461-0248.2004.00717.x
Evanno, 2005, Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study, Mol Ecol, 14, 2611, 10.1111/j.1365-294X.2005.02553.x
Gepts, 1998, Origin and evolution of common bean: past events and recent trends, HortScience, 33, 1124, 10.21273/HORTSCI.33.7.1124
Gepts, 1985, F1 hybrid weakness in the common bean, J Hered, 76, 447, 10.1093/oxfordjournals.jhered.a110142
Gepts, 1986, Phaseolin variability among wild and cultivated common beans (Phaseolus vulgaris from Colombia, Econ Bot, 40, 469, 10.1007/BF02859660
González, 2012, CCA: Canonical correlation analysis
Gotelli, 2001, Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness, Ecol Lett, 4, 379, 10.1046/j.1461-0248.2001.00230.x
Illumina, 2013, 16S Metagenomic sequencing library preparation
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
Jaccoud, 2001, Diversity arrays: a solid state technology for sequence information independent genotyping, Nucleic Acids Res, 29, e25, 10.1093/nar/29.4.e25
Jones, 2009, Carbon flow in the rhizosphere: carbon trading at the soil–root interface, Plant Soil, 321, 5, 10.1007/s11104-009-9925-0
Köster, 2012, Snakemake-a scalable bioinformatics workflow engine, Bioinformatics, 28, 2520, 10.1093/bioinformatics/bts480
Kuczynski, 2012, Using QIIME to analyze 16S rRNA gene sequences from microbial communities, Curr Protoc Chem Biol, 1E, 1
Lakshmanan, 2012, Microbe-associated molecular patterns-triggered root responses mediate beneficial rhizobacterial recruitment in Arabidopsis, Plant Physiol, 160, 1642, 10.1104/pp.112.200386
Lebeis, 2015, Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa, Science, 349, 860, 10.1126/science.aaa8764
Leff, 2016, Plant domestication and the assembly of bacterial and fungal communities associated with strains of the common sunflower, Helianthus annuus, New Phytol, 214, 412, 10.1111/nph.14323
Ley, 2006, Ecological and evolutionary forces shaping microbial diversity in the human intestine, Cell, 124, 837, 10.1016/j.cell.2006.02.017
Lundberg, 2012, Defining the core Arabidopsis thaliana root microbiome, Nature, 488, 86, 10.1038/nature11237
Marschner, 2002, Spatial and temporal dynamics of the microbial community structure in the rhizosphere of cluster roots of white lupin (Lupinus albus L.), Plant Soil, 246, 167, 10.1023/A:1020663909890
Martín-Robles, 2015, Libro de resúmenes de comunicaciones del 4° Congreso Ibérico de Ecología, 10.7818/4IberianEcologicalCongress.2015
McMurdie, 2013, phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data, PLoS One, 8, e61217, 10.1371/journal.pone.0061217
McDonald, 2012, The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome, Gigascience, 1, 7, 10.1186/2047-217X-1-7
Masella, 2012, PANDAseq: paired-end assembler for illumina sequences, BMC Bioinform, 13, 31, 10.1186/1471-2105-13-31
Mendes, 2014, Taxonomical and functional microbial community selection in soybean rhizosphere, ISME J, 8, 1577, 10.1038/ismej.2014.17
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
Mendes, 2011, Deciphering the rhizosphere microbiome for disease-suppressive bacteria, Science, 332, 1097, 10.1126/science.1203980
Ofek, 2014, Host signature effect on plant root-associated microbiomes revealed through analyses of resident vs. active communities, Environ Microbiol, 16, 2157, 10.1111/1462-2920.12228
Oksanen, 2016, vegan: Community Ecology Package
Paulson, 2013, Differential abundance analysis for microbial marker-gene surveys, Nat Methods, 10, 1200, 10.1038/nmeth.2658
Paulson, 2016, metagenomeSeq: Statistical analysis for sparse high-throughput sequencing. Bioconductor package
Peiffer, 2013, Diversity and heritability of the maize rhizosphere microbiome under field conditions, Proc Natl Acad Sci USA, 110, 6548, 10.1073/pnas.1302837110
Pérez-Jaramillo, 2016, Impact of plant domestication on rhizosphere microbiome assembly and functions, Plant Mol Biol, 90, 635, 10.1007/s11103-015-0337-7
Philippot, 2013, Going back to the roots: the microbial ecology of the rhizosphere, Nature Rev Microbiol, 11, 789, 10.1038/nrmicro3109
Pritchard, 2000, Inference of population structure using multilocus genotype data, Genetics, 155, 945, 10.1093/genetics/155.2.945
R Core Team, 2015, R: a language and environment for statistical computing
Ritchie, 2015, limma powers differential expression analyses for RNA-sequencing and microarray studies, Nucleic Acids Res, 43, e47, 10.1093/nar/gkv007
Rognes, 2015, VSEARCH
Schlaeppi, 2014, Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives, Proc Natl Acad Sci USA, 111, 585, 10.1073/pnas.1321597111
Thomas, 2011, Environmental and gut bacteroidetes: the food connection, Front Microbiol, 2, 93, 10.3389/fmicb.2011.00093
Toro, 1990, Wild bean (Phaseolus vulgaris L.): description and distribution (International Board for Plant Genetics Resources (IBGPR) and Centro Internacional de Agricultura Tropical (CIAT), Cali, Colombia)
Turnbaugh, 2006, An obesity-associated gut microbiome with increased capacity for energy harvest, Nature, 444, 1027, 10.1038/nature05414
Turner, 2013, Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants, ISME J, 7, 2248, 10.1038/ismej.2013.119
Yin, 2013, Role of bacterial communities in the natural suppression of Rhizoctonia solani Bare Patch Disease of Wheat (Triticum aestivum L.), Appl Environ Microbiol, 79, 7428, 10.1128/AEM.01610-13
Zachow, 2014, Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima - ancestor of all beet crops - and modern sugar beets, Front Microbiol, 5, 415, 10.3389/fmicb.2014.00415