Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat

RESEARCH ARTICLE Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat Akitomo Kawasaki1, Suzanne Donn2, Peter R. Ryan1, Ulrike Mathesius3, Rosangela Devilla1, Amanda Jones1, Michelle Watt1,4* a11111 1 CSIRO Agriculture and Food, Canberra, ACT, Australia, 2 Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia, 3 Division of Plant Science, Research School of Biology, Australian National University, ACT, Australia, 4 Institute of Bio and Geosciences (IBG 2), Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany * Abstract OPEN ACCESS Citation: Kawasaki A, Donn S, Ryan PR, Mathesius U, Devilla R, Jones A, et al. (2016) Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat. PLoS ONE 11(10): e0164533. doi:10.1371/journal. pone.0164533 Editor: Hikmet Budak, Montana State University Bozeman, UNITED STATES Received: April 17, 2016 Accepted: September 27, 2016 Published: October 11, 2016 Copyright: © 2016 Kawasaki et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The rhizosphere microbiome is regulated by plant genotype, root exudates and environment. There is substantial interest in breeding and managing crops that host root microbial communities that increase productivity. The eudicot model species Arabidopsis has been used to investigate these processes, however a model for monocotyledons is also required. We characterized the rhizosphere microbiome and root exudates of Brachypodium distachyon, to develop it as a rhizosphere model for cereal species like wheat. The Brachypodium rhizosphere microbial community was dominated by Burkholderiales. However, these communities were also dependent on how tightly they were bound to roots, the root type they were associated with (nodal or seminal roots), and their location along the roots. Moreover, the functional gene categories detected in microorganisms isolated from around root tips differed from those isolated from bases of roots. The Brachypodium rhizosphere microbiota and root exudate profiles were similar to those reported for wheat rhizospheres, and different to Arabidopsis. The differences in root system development and cell wall chemistry between monocotyledons and eudicots may also influence the microorganism composition of these major plant types. Brachypodium is a promising model for investigating the microbiome of wheat. Data Availability Statement: All data are contained within the paper and the supporting information. Funding: AK had a CSIRO OCE Postdoctoral Fellowship to carry out this work. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Please note that the Forschungszentrum Juelich is not a private entity. It is a public, not-for-profit research centre Introduction Brachypodium distachyon was proposed as a model species for the Pooideae family in 2001 because of its small stature, rapid life cycle, and small genome size of 272 Mb [1]. B. distachyon and other Brachypodium species are now important tools for investigating grasses because the growing availability of genetic resources include a fully sequenced genome, a large collection of accessions [2] and T-DNA mutants [3]. Brachypodium serves as a functional genomics model in elucidating cereal genomes [4] as well as for studying small noncoding RNAs such as microRNAs [5, 6]. This species has also been studied for flowering time variation [7], plant-pathogen PLOS ONE | DOI:10.1371/journal.pone.0164533 October 11, 2016 1 / 25 Rhizosphere Microbiome and Exudates of Brachypodium distachyon Bd21-3 focusing on societal research needs (with majority public funds, and these from German Federal Government (90%) and State Government (10%)) (http://www.fz-juelich.de/portal/EN/AboutUs/ FactsFigures/_node.html), and is a member of the Helmholtz Association of German research centres, Germany’s largest public research association dedicated to research for state and society (https:// www.helmholtz.de/en/about_us/). relations [8–10], plant microbe relations [11, 12], and for root architecture and genetics [13– 15]. Brachypodium provides a convenient model for studying cereal root systems because its mature roots are less than a third of the size of cereal crops such as wheat, maize and rice, and therefore are more amenable to laboratory and glasshouse studies [14]. This paper reports on the characterization of the root microbiome and exudates of Brachypodium to validate their role as a model for rhizosphere biology in cereal crops. Rhizosphere biology can influence the productivity of plants [16, 17]. Rhizosphere microorganisms benefit plant growth by increasing nutrient supply to plants, suppressing pathogens, and by carrying out other less studied roles [18]. Plant growth promoting (PGP) strains of Azospirillum and Herbaspirillum have been reported to colonize Brachypodium roots and enhance growth of some Brachypodium genotypes under low or no nitrogen conditions [11]. Inoculation with the PGP strain Bacillus subtilis B26 increased Brachypodium biomass and also enhanced plant drought resistance [12]. Plants release between 5 and 25% of net fixed carbon into the rhizosphere in the form of compounds ranging from simple organic anions to complex polymer mucilages [19]. Such root exudates can alter the rhizosphere microbial community structure and diversity compared to the bulk soil, and each plant species harbours a set of specific rhizosphere microbial populations due, in part, to differences in composition of the root exudates [20, 21]. Root exudation is also influenced by various biotic and abiotic factors in the surrounding environment, which can lead to a significant shift in the rhizosphere microbiota [22–25]. There is a requirement to understand the plant-soil interface sufficiently well to allow the rhizosphere to be engineered to benefit plant fitness in cereals [16, 26–28]. An important step is the development of robust plant models for this complex system. Characterizing the core microbial communities in the rhizosphere and identifying the major root exudates are critical inputs to such models. This information is now being collected in model plants such as Arabidopsis [29, 30] and in crop species such as wheat [31, 32], rice [33], and maize [34]. A recent study used Arabidopsis, Brachypodium and Medicago to investigate shifts in the microbial populations in the soil over successive plantings, and the three models modified the soil microbiomes differently [35]. We hypothesized that the root microbiome and root exudates of Brachypodium would be more similar to wheat than to (...truncated)