Root microbiota dynamics of perennial Arabis alpina are dependent on soil residence time but independent of flowering time

ISME Journal

Volumn 11, Issue 1, 2017, Pages 43-55

  Dombrowski, Nina ^a   Schlaeppi, Klaus ^b   Agler, Matthew T ^a   Hacquard, Stéphane ^a   Kemen, Eric ^a   Garrido Oter, Ruben ^a,c   Wunder, Jörg ^a   Coupland, George ^a   Schulze Lefert, Paul ^a  

^a MAX PLANCK INSTITUTE FOR PLANT BREEDING RESEARCH   (Germany)

^b AGROSCOPE RECKENHOLZ TÄNIKON RESEARCH STATION ART   (Switzerland)

^c HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMMUNITY DYNAMICS; FLOWERING; GENETIC ANALYSIS; GENOTYPE; HERB; MICROBIAL COMMUNITY; PERENNIAL PLANT; RESIDENCE TIME; ROOT SYSTEM; SOIL MICROORGANISM; SOIL TYPE;

ARABIDOPSIS THALIANA; ARABIS ALPINA; BACTERIA (MICROORGANISMS); BOECHERA STRICTA; CARDAMINE HIRSUTA;

SOIL;

ARABIS; ARCTIC; BACTERIUM; CHEMISTRY; CLASSIFICATION; FLOWER; GENETICS; GENOTYPE; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; MICROBIOLOGY; MICROFLORA; PLANT ROOT; SOIL;

ARABIS; ARCTIC REGIONS; BACTERIA; FLOWERS; GENOTYPE; MICROBIOTA; PLANT ROOTS; SOIL; SOIL MICROBIOLOGY;

EID: 84980367707     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2016.109     Document Type: Article

References (32)

1. Albani MC, Castaings L, Wötzel S, Mateos JL, Wunder J, Wang R et al. (2012). PEP1 of Arabis alpina is encoded by two overlapping genes that contribute to natural genetic variation in perennial flowering. PLoS Genet 8: e1003130.
2. Bai Y, Müller DB, Srinivas G, Garrido-Oter R, Potthoff E, Rott M et al. (2015). Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528: 364-369.
3. Beilstein MA, Nagalingum NS, Clements MD, Manchester SR, Mathews S. (2010). Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc Natl Acad Sci USA 107: 18724-18728.
4. Bernier G. (1988). The control of floral evocation and morphogenesis. Annu Rev Plant Physiol Plant Mol Biol 39: 175-219.
5. Billings WD, Mooney HA. (1968). The ecology of arctic and alpine plants. Biol Rev 43: 481-529.
6. Bodenhausen N, Horton MW, Bergelson J. (2013). Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana. PLoS One 8: e56329.
7. Bulgarelli D, Garrido-Oter R, Münch PC, Weiman A, Dröge J, Pan Y et al. (2015). Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17: 392-403.
8. Bulgarelli D, Rott M, Schlaeppi K, Themaat EVL, van, Ahmadinejad N, Assenza F et al. (2012). Revealing structure and assembly cues for Arabidop-sis root-inhabiting bacterial microbiota. Nature 488: 91-95.
9. Bulgarelli D, Schlaeppi K, Spaepen S, van Themaat EVL, Schulze-Lefert P. (2013). Structure and functions of the bacterial microbiota of Plants. Annu Rev Plant Biol 64: 807-838.
10. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
11. Chaparro JM, Badri DV, Vivanco JM. (2014). Rhizosphere microbiome assemblage is affected by plant development. ISME J 8: 790-803.
12. Chapin FS. (1983). Direct and indirect effects of temperature on arctic plants. Polar Biol 2: 47-52.
13. Chapin FS, Shaver GR. (1989). Differences in growth and nutrient use among arctic plant growth forms. Funct Ecol 3: 73.
14. Chelius MK, Triplett EW. (2001). The diversity of Archaea and Bacteria in association with the roots of Zea mays L. Microb Ecol 41: 252-263.
15. De-la-Peña C, Badri DV, Lei Z, Watson BS, Brandão MM, Silva-Filho MC et al. (2010). Root secretion of defense-related proteins is development-dependent and correlated with flowering time. J Biol Chem 285: 30654-30665.
16. Edgar RC. (2013). UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Meth-ods 10: 996-998.
17. Edwards J, Johnson C, Santos-Medellín C, Lurie E, Podishetty NK, Bhatnagar S et al. (2015). Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci USA 112: E911-E920.
18. Fierer N, Jackson RB. (2006). The diversity and biogeo-graphy of soil bacterial communities. Proc Natl Acad Sci USA 103: 626-631.
19. Hacquard S, Garrido-Oter R, González A, Spaepen S, Ackermann G, Lebeis S et al. (2015). Microbiota and host nutrition across plant and animal kingdoms. Cell Host Microbe 17: 603-616.
20. Lauber CL, Hamady M, Knight R, Fierer N. (2009). Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75: 5111-5120.
21. Lozupone C, Knight R. (2005). UniFrac: a new phyloge-netic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
22. Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S et al. (2012). Defining the core Arabidopsis thaliana root microbiome. Nature 488: 86-90.
23. Maignien L, DeForce EA, Chafee ME, Eren AM, Simmons SL. (2014). Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities. mBio 5: e00682-13.
24. Margesin R, Miteva V. (2011). Diversity and ecology of psychrophilic microorganisms. Res Microbiol 162: 346-361.
25. Nissinen RM, Männistö MK, van Elsas JD. (2012). Endophytic bacterial communities in three arctic plants from low arctic fell tundra are cold-adapted and host-plant specific. FEMS Microbiol Ecol 82: 510-522.
26. Panke-Buisse K, Poole AC, Goodrich JK, Ley RE, Kao-Kniffin J. (2015). Selection on soil microbiomes reveals reproducible impacts on plant function. ISME J 9: 980-989.
27. Peiffer JA, Spor A, Koren O, Jin Z, Tringe SG, Dangl JL et al. (2013). Diversity and heritability of the maize rhizo-sphere microbiome under field conditions. Proc Natl Acad Sci USA 110: 6548-6553.
28. Richardson AE, Barea J-M, McNeill AM, Prigent-Combaret C. (2009). Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms. Plant Soil 321: 305-339.
29. Schlaeppi K, Dombrowski N, Oter RG, Themaat EVL, van, Schulze-Lefert P. (2014). Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. Proc Natl Acad Sci USA 111: 585-592.
30. Vorholt JA. (2012). Microbial life in the phyllosphere. Nat Rev Microbiol 10: 828-840.
31. Wagner MR, Lundberg DS, Coleman-Derr D, Tringe SG, Dangl JL, Mitchell-Olds T. (2014). Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol Lett 17: 717-726.
32. Wang R, Farrona S, Vincent C, Joecker A, Schoof H, Turck F et al. (2009). PEP1 regulates perennial flowering in Arabis alpina. Nature 459: 423-427.