Greater than the sum of their parts: Characterizing plant microbiomes at the community-level

Current Opinion in Plant Biology

Volumn 24, Issue , 2015, Pages 82-86

  Lebeis, Sarah L ^a  

^a UNIVERSITY OF TENNESSEE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENETICS; MICROBIOLOGY; MICROFLORA; PLANT; PLANT PHYSIOLOGY;

MICROBIOTA; PLANT PHYSIOLOGICAL PHENOMENA; PLANTS;

EID: 84923088032     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2015.02.004     Document Type: Review

References (44)

1. Bulgarelli D., et al. Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 2013, 64:807-838.
2. Guttman D., McHardy A.C., Schulze-Lefert P. Microbial genome-enabled insights into plant-microorganism interactions. Nat Rev Genet 2014, 15:797-813.
3. Arabidopsis Genome I. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815.
4. Michael T.P., Jackson S. The first 50 plant genomes. Plant Gen 2013, 6.
5. Wang W., et al. The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nat Commun 2014, 5:3311.
6. Nystedt B., et al. The Norway spruce genome sequence and conifer genome evolution. Nature 2013, 497:579-584.
7. Flusberg B.A., et al. Direct detection of DNA methylation during single-molecule: real-time sequencing. Nat Methods 2010, 7:461-465.
8. Badri D.V., et al. 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 2013, 288:4502-4512.
9. Bulgarelli D., et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 2012, 488:91-95.
10. Lundberg D.S., et al. Defining the core Arabidopsis thaliana root microbiome. Nature 2012, 488:86-90.
11. Knief C., et al. Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J 2012, 6:1378-1390.
12. Peiffer J.A., et al. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci USA 2013, 110:6548-6553.
13. Mendes R., et al. Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 2011, 332:1097-1100.
14. Gottel N.R., et al. Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types. Appl Environ Microbiol 2011, 77:5934-5944.
15. Redford A.J., et al. The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol 2010, 12:2885-2893.
16. Uroz S., et al. Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ Microbiol Rep 2010, 2:281-288.
17. Tringe S.G., et al. Comparative metagenomics of microbial communities. Science 2005, 308:554-557.
18. Bodenhausen N., Horton M.W., Bergelson J. Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana. PLoS One 2013, 8:e56329.
19. Redford A.J., Fierer N. Bacterial succession on the leaf surface: a novel system for studying successional dynamics. Microb Ecol 2009, 58:189-198.
20. Lennon J.T., Jones S.E. Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat Rev Microbiol 2011, 9:119-130.
21. Faith J.J., et al. The long-term stability of the human gut microbiota. Science 2013, 341:1237439.
22. Lundberg D.S., et al. Practical innovations for high-throughput amplicon sequencing. Nat Methods 2013, 10:999-1002.
23. Wrighton K.C., et al. Fermentation: hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science 2012, 337:1661-1665.
24. Albertsen M., et al. Genome sequences of rare: uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 2013, 31:533-538.
25. Imelfort M., et al. GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ 2014, 2:pe603.
26. Brown S.D., et al. Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides. J Bacteriol 2012, 194:5991-5993.
27. Ishoey T., et al. Genomic sequencing of single microbial cells from environmental samples. Curr Opin Microbiol 2008, 11:198-204.
28. Dumbrell A.J., et al. Distinct seasonal assemblages of arbuscular mycorrhizal fungi revealed by massively parallel pyrosequencing. New Phytol 2011, 190:794-804.
29. Bodenhausen N., et al. A synthetic community approach reveals plant genotypes affecting the phyllosphere microbiota. PLoS Genet 2014, 10:e1004283.
30. Delmotte N., et al. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci USA 2009, 106:16428-16433.
31. Knief C., et al. Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere. ISME J 2010, 4:719-728.
32. Maignien L., et al. Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities. MBio 2014, 5. e00682-13.
33. Mendes L.W., et al. Taxonomical and functional microbial community selection in soybean rhizosphere. ISME J 2014, 8:1577-1587.
34. Chaparro J.M., et al. Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions. PLoS One 2013, 8:e55731.
35. Chaparro J.M., Badri D.V., Vivanco J.M. Rhizosphere microbiome assemblage is affected by plant development. ISME J 2014, 8:790-803.
36. Schlaeppi K., et al. Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. Proc Natl Acad Sci USA 2013, 111:585-592.
37. Bakker M.G., et al. Diffuse symbioses: roles of plant-plant, plant-microbe and microbe-microbe interactions in structuring the soil microbiome. Mol Ecol 2014, 23:1571-1583.
38. Zuppinger-Dingley D., et al. Selection for niche differentiation in plant communities increases biodiversity effects. Nature 2014, 515:108-111.
39. Weyens N., et al. Exploiting plant-microbe partnerships to improve biomass production and remediation. Trends Biotechnol 2009, 27:591-598.
40. Berendsen R.L., Pieterse C.M., Bakker P.A. The rhizosphere microbiome and plant health. Trends Plant Sci 2012, 17:478-486.
41. Zapalski M.K. Is absence of proof a proof of absence? Comments on commensalism. Palaeogeogr Palaeoclimatol Palaeoecol 2011, 302:484-488.
42. Ofek-Lalzar M., et al. Niche and host-associated functional signatures of the root surface microbiome. Nat Commun 2014, 5:4950.
43. Sessitsch A., et al. Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol Plant Microbe Interact 2012, 25:28-36.
44. Turner T.R., et al. Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants. ISME J 2013, 7:2248-2258.