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Microbial Ecology

Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree

Omri M. Finkel, Tom O. Delmont, Anton F. Post, Shimshon Belkin
P. D. Schloss, Editor
Omri M. Finkel
aInstitute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
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Tom O. Delmont
bJosephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biology Laboratory, Woods Hole, Massachusetts, USA
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Anton F. Post
bJosephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biology Laboratory, Woods Hole, Massachusetts, USA
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Shimshon Belkin
aInstitute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
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P. D. Schloss
University of Michigan
Roles: Editor
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DOI: 10.1128/AEM.00483-16
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ABSTRACT

The leaves of Tamarix aphylla, a globally distributed, salt-secreting desert tree, are dotted with alkaline droplets of high salinity. To successfully inhabit these organic carbon-rich droplets, bacteria need to be adapted to multiple stress factors, including high salinity, high alkalinity, high UV radiation, and periodic desiccation. To identify genes that are important for survival in this harsh habitat, microbial community DNA was extracted from the leaf surfaces of 10 Tamarix aphylla trees along a 350-km longitudinal gradient. Shotgun metagenomic sequencing, contig assembly, and binning yielded 17 genome bins, six of which were >80% complete. These genomic bins, representing three phyla (Proteobacteria, Bacteroidetes, and Firmicutes), were closely related to halophilic and alkaliphilic taxa isolated from aquatic and soil environments. Comparison of these genomic bins to the genomes of their closest relatives revealed functional traits characteristic of bacterial populations inhabiting the Tamarix phyllosphere, independent of their taxonomic affiliation. These functions, most notably light-sensing genes, are postulated to represent important adaptations toward colonization of this habitat.

IMPORTANCE Plant leaves are an extensive and diverse microbial habitat, forming the main interface between solar energy and the terrestrial biosphere. There are hundreds of thousands of plant species in the world, exhibiting a wide range of morphologies, leaf surface chemistries, and ecological ranges. In order to understand the core adaptations of microorganisms to this habitat, it is important to diversify the type of leaves that are studied. This study provides an analysis of the genomic content of the most abundant bacterial inhabitants of the globally distributed, salt-secreting desert tree Tamarix aphylla. Draft genomes of these bacteria were assembled, using the culture-independent technique of assembly and binning of metagenomic data. Analysis of the genomes reveals traits that are important for survival in this habitat, most notably, light-sensing and light utilization genes.

FOOTNOTES

    • Received 16 February 2016.
    • Accepted 29 February 2016.
    • Accepted manuscript posted online 4 March 2016.
  • Supplemental material for this article may be found at http://dx.doi.org/10.1128/AEM.00483-16.

  • Copyright © 2016, American Society for Microbiology. All Rights Reserved.
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Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree
Omri M. Finkel, Tom O. Delmont, Anton F. Post, Shimshon Belkin
Applied and Environmental Microbiology Apr 2016, 82 (9) 2854-2861; DOI: 10.1128/AEM.00483-16

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Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree
Omri M. Finkel, Tom O. Delmont, Anton F. Post, Shimshon Belkin
Applied and Environmental Microbiology Apr 2016, 82 (9) 2854-2861; DOI: 10.1128/AEM.00483-16
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