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      Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota

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          Abstract

          By changing soil properties, plants can modify their growth environment. Although the soil microbiota is known to play a key role in the resulting plant-soil feedbacks, the proximal mechanisms underlying this phenomenon remain unknown. We found that benzoxazinoids, a class of defensive secondary metabolites that are released by roots of cereals such as wheat and maize, alter root-associated fungal and bacterial communities, decrease plant growth, increase jasmonate signaling and plant defenses, and suppress herbivore performance in the next plant generation. Complementation experiments demonstrate that the benzoxazinoid breakdown product 6-methoxy-benzoxazolin-2-one (MBOA), which accumulates in the soil during the conditioning phase, is both sufficient and necessary to trigger the observed phenotypic changes. Sterilization, fungal and bacterial profiling and complementation experiments reveal that MBOA acts indirectly by altering root-associated microbiota. Our results reveal a mechanism by which plants determine the composition of rhizosphere microbiota, plant performance and plant-herbivore interactions of the next generation.

          Abstract

          Plants can modify soil microbiota through root exudation, but how this process influences plant health in turn is often unclear. Here, Hu et al. show that maize benzoxazinoids released into the soil modify root-associated microbiota and thereby increase leaf defenses of the next plant generation.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            FLASH: fast length adjustment of short reads to improve genome assemblies.

            Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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              Feed Your Friends: Do Plant Exudates Shape the Root Microbiome?

              Plant health in natural environments depends on interactions with complex and dynamic communities comprising macro- and microorganisms. While many studies have provided insights into the composition of rhizosphere microbiomes (rhizobiomes), little is known about whether plants shape their rhizobiomes. Here, we discuss physiological factors of plants that may govern plant-microbe interactions, focusing on root physiology and the role of root exudates. Given that only a few plant transport proteins are known to be involved in root metabolite export, we suggest novel families putatively involved in this process. Finally, building off of the features discussed in this review, and in analogy to well-known symbioses, we elaborate on a possible sequence of events governing rhizobiome assembly.
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                Author and article information

                Contributors
                klaus.schlaeppi@ips.unibe.ch
                matthias.erb@ips.unibe.ch
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                16 July 2018
                16 July 2018
                2018
                : 9
                : 2738
                Affiliations
                [1 ]ISNI 0000 0001 0726 5157, GRID grid.5734.5, Institute of Plant Sciences, , University of Bern, ; 3013 Bern, Switzerland
                [2 ]ISNI 0000 0004 4681 910X, GRID grid.417771.3, Division of Agroecology and Environment, , Agroscope, ; 8046 Zürich, Switzerland
                [3 ]ISNI 0000 0004 4681 910X, GRID grid.417771.3, Division of Plant Protection, , Agroscope, ; 1260 Nyon, Switzerland
                [4 ]ISNI 0000 0004 1937 0650, GRID grid.7400.3, Department of Evolutionary Biology and Environmental Studies, , University of Zürich, ; 8057 Zürich, Switzerland
                [5 ]ISNI 0000000120346234, GRID grid.5477.1, Institute of Environmental Biology, , Utrecht University, ; 3508 TC Utrecht, The Netherlands
                Author information
                http://orcid.org/0000-0002-7791-9440
                http://orcid.org/0000-0002-6785-0099
                http://orcid.org/0000-0003-3620-0875
                http://orcid.org/0000-0002-4446-9834
                Article
                5122
                10.1038/s41467-018-05122-7
                6048113
                30013066
                95cb2bff-380d-46e6-9f3e-b825ad99ea00
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 4 October 2017
                : 14 June 2018
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100001711, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation);
                Award ID: 160786
                Award ID: 136184
                Award ID: 164480
                Award ID: 165891
                Award Recipient :
                Funded by: ERA-CAPS (BENZEX) Swiss State Secretariat for Education, Research and Innovation (Project C15.0111) Swiss Sino Science and Technology Exchange Programme (EG 03-032016) Interfaculty Research Cooperation “One Health” of the University of Bern
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