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      Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest.

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          Abstract

          The phyllosphere--the aerial surfaces of plants, including leaves--is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density-growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant-microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function.

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          Most cited references 67

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          QIIME allows analysis of high-throughput community sequencing data.

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            Search and clustering orders of magnitude faster than BLAST.

             Robert Edgar (2010)
            Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets. Binaries are available at no charge for non-commercial use at http://www.drive5.com/usearch.
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              APE: Analyses of Phylogenetics and Evolution in R language.

              Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.
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                Author and article information

                Journal
                Proc. Natl. Acad. Sci. U.S.A.
                Proceedings of the National Academy of Sciences of the United States of America
                1091-6490
                0027-8424
                Sep 23 2014
                : 111
                : 38
                Affiliations
                [1 ] Département des sciences biologiques, Université du Québec à Montréal, Montreal, Quebec, Canada H3C 3P8; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403; kembel.steven_w@uqam.ca.
                [2 ] Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721;
                [3 ] Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403;
                [4 ] Smithsonian Tropical Research Institute, Panama 0843-03092, Panama; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095; and.
                [5 ] Smithsonian Tropical Research Institute, Panama 0843-03092, Panama;
                [6 ] Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403; Santa Fe Institute, Santa Fe, NM 87501.
                Article
                1216057111
                10.1073/pnas.1216057111
                25225376

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