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SRX008324: 454 Sequencing of phyllosphere microbiota
2 LS454 (454 GS FLX) runs: 1.1M spots, 283.9M bases, 558Mb downloads

Design: Cells were washed from the leaf material by 3 min of alternate shaking, vortexing, and sonication. The cell suspen sion was separated from the leaf material by filtration through a nylon mesh (pore size 200 m; Spectrum Europe BV, Breda, Th e Netherlands). 6 mL of 80% Percoll (Sigma-Aldrich) was pipetted below the cell suspension, and the 50-mL tubes were centrif uged for 5 min at 800 g. The bacterial cell suspension above the Percoll layer was transferred into a fresh 50-mL tube and c ells were pelleted at 3,150 g for 15 min. Cell pellets from multiple tubes were pooled into 1.5 mL reaction tubes and washed twice with TE-buffer plus Pefabloc SC. Cell pellets were immediately frozen at -20C.
Submitted by: Institute of Molecular Biology University of Zurich (IMB-UZH)
Study: Metagenome isolated from the soybean phyllosphere
show Abstracthide Abstract
For terrestrial plants, the phyllosphere represents the interface between the above-ground parts of plants and the air. Conservative estimates indicate that the roughly one billion square kilometers of world-wide leaf surfaces host more than 10e26 bacteria, which are the most abundant colonizers of this habitat. The overall microbiota in this ecosystem is thus sufficiently large to have an impact on the global carbon and nitrogen cycles. Additionally, the phyllosphere inhabitants influence their hosts at the level of the individual plants. To a large extent, interest in phyllosphere microbiology has been driven by investigations on plant pathogens. Their spread, colonization, survival, and pathogenicity mechanisms have been subject of numerous studies. Much less understood are non-pathogenic microorganisms that inhabit the phyllosphere. The composition of the phyllosphere microbiota has been analyzed in only a few studies by cultivation-independent methods. However, such methods are essential in light of the yet uncultivated majority of bacteria existing in nature. Not only their identity, but in particular the physiological properties of phyllosphere bacteria, their adaptations to the habitat, and their potential role, e.g. with respect to modulating population sizes of pathogens, remain largely unknown. Current knowledge on the traits important in the phyllosphere is derived from relatively few studies on gene expression, and stems mostly from model bacteria cultivated on host plants under controlled conditions. However, under natural conditions, plants and their residing microorganisms are exposed to a host of diverse, highly variable environmental factors including UV light, temperature, and water availability; moreover, individual microbes are subjected to competition with other microorganisms over resources such as nutrients and space. Towards a deeper understanding of phyllosphere microbiology, and in particular to learn more about the commensal majority of plant leaf colonizing bacteria, which may be of relevance for plant health and development, integrated approaches are needed. Metagenomic and metaproteomic approaches (community proteogenomics) were combined in our study to analyze bacterial phyllosphere communities in situ (the phyllosphere is defined here as the environment comprising both the surface and the apoplast of leaves). This strategy provided insight into the physiology of bacteria and revealed common adaptation mechanisms among the phyllosphere populations. In this study, genomic DNA was isolated from the microbial phyllosphere community of leaves from agriculturally grown soybean (Glycine max). <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&db=Nucleotide&cmd=search&term=FN421717:FN421842[accn]">FN421717-FN421842 </a> are ribosomal RNA sequences associated with this project.
Sample: Generic sample from phyllosphere metagenome
SAMN00003121 • SRS004919 • All experiments • All runs
Name: Soybean 2
Instrument: 454 GS FLX
Strategy: WGS
Selection: RANDOM
Layout: SINGLE
Spot descriptor:

Runs: 2 runs, 1.1M spots, 283.9M bases, 558Mb
Run# of Spots# of BasesSizePublished


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