In wild tobacco, Nicotiana attenuata , variation among bacterial communities of isogenic plants is mainly shaped by the local soil microbiota independently of the plants' capacity to produce jasmonic acidCommunicative & Integrative Biology

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Authors
Rakesh Santhanam, Ian T Baldwin, Karin Groten
Year
2015
DOI
10.1080/19420889.2015.1017160
Subject
Agricultural and Biological Sciences (all)

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Communicative & Integrative Biology

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In wild tobacco, Nicotiana attenuata, variation among bacterial communities of isogenic plants is mainly shaped by the local soil microbiota independently of the plants' capacity to produce jasmonic acid

Rakesh Santhanam, Ian T Baldwin & Karin Groten

To cite this article: Rakesh Santhanam, Ian T Baldwin & Karin Groten (2015) In wild tobacco, Nicotiana attenuata, variation among bacterial communities of isogenic plants is mainly shaped by the local soil microbiota independently of the plants' capacity to produce jasmonic acid, Communicative & Integrative Biology, 8:2, e1017160, DOI: 10.1080/19420889.2015.1017160

To link to this article: http://dx.doi.org/10.1080/19420889.2015.1017160 © 2015 The Author(s). Published with license by Taylor & Francis Group, LLC©

Rakesh Santhanam, Ian T Baldwin, and Karin

Groten

Accepted author version posted online: 01

May 2015.

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In wild tobacco, Nicotiana attenuata, variation among bacterial communities of isogenic plants is mainly shaped by the local soil microbiota independently of the plants’ capacity to produce jasmonic acid

Rakesh Santhanam, Ian T Baldwin, and Karin Groten*

Department of Molecular Ecology; Max Planck Institute for Chemical Ecology; Jena, Germany

Keywords: Nicotiana attenuata, jasmonic acid, bacterial communities, leaf- and root-associated bacteria, plant growth promotion, opportunistic mutualism

The phytohormone jasmonic acid (JA) plays a central role in defense against necrotrophic pathogens and herbivores in Nicotiana attenuata. Recently Santhanam et al.1 showed that JA does not have a major role in shaping the root- and shoot associated bacterial communities, though a few taxa differed among control (empty vector, EV) plants and plants impaired in their capacity to produce JA (irAOC). In this addendum, we provide additional data showing that the composition of the plant bacterial communities is mainly shaped by tissue type. The qualitative data analysis revealed that at the order level, 5 bacterial OTUs formed a core community found in all tissues irrespective of genotypes, while 9

OTUs were different among roots and shoots. The heterogeneity among individual plants was high masking the potential genotype effect on bacterial communities. Using a culture-dependent approach, 3 of 18 bacterial taxa retrieved either only from one of the genotypes or from both had a growth promoting effect on EV and irAOC seedlings. The data suggest that the local soil niche in which the roots grows is a major driver of the variability in root bacterial communities recruited by different individuals, and the plant growth-promoting effects of some taxa are independent of the genotype.

Plants harbor a diverse range of bacterial communities2,3 which are influenced by many biotic and abiotic factors.2 Several studies showed that tissue types such as leaves and roots influence the bacterial community composition, and harbor distinct communities.1,4 It is often assumed that root bacterial communities are shaped by soil microbiota,5-7 and leaf bacterial communities by air, sunlight irradiation, stomata and mineral content of the leaves.8-10 However, 4 independent studies using

Arabidopsis as a model system indicated that at the phylum level, core communities such as Actinobacteria, Bacteriodetes and Proteobacteria can be found in all roots independent of soil type and genotypes,2,4,5-7 strongly indicating that bacteria do not randomly colonize roots, but certain phyla preferentially colonize plant roots.

In a previous study,1 we analyzed leaf and root bacterial community of isogenic field grown plants impaired in JA-production (irAOC) and control plants (empty vector, EV) by culture dependent and independent (pyrosequencing) approaches. Based on the quantitative data, we showed that leaf bacterial communities are different from those of roots.1 Here, we demonstrate that based on qualitative data (presence and absence of OTUs at 97% similarity) leaf bacterial communities are clearly distinct from roots (Fig. 1A), and within each tissue type (root vs leaf) plants impaired in JA production and EV plants do not show a genotype-specific pattern. These data are consistent with our previous findings, and similar results were obtained by Bodenhausen et al,4 who showed that leaf bacterial communities of Arabidopsis thaliana are different from those of roots and concluded that organ type (root vs leaf) type influences the composition of the bacterial communities.

Though root and leaf bacterial communities were clearly distinct,1 a bacterial core community was present in all © Rakesh Santhanam, Ian T Baldwin, and Karin Groten *Correspondence to: Karin Groten; Email: kgroten@ice.mpg.de

Submitted: 12/01/2014; Revised: 12/29/2014; Accepted: 01/05/2015 http://dx.doi.org/10.1080/19420889.2015.1017160

This is an Open Access article distributed under the terms of the Creative Commons Attribution-Non-Commercial License (http://creativecommons.org/licenses/ by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The moral rights of the named author(s) have been asserted. www.tandfonline.com e1017160-1Communicative & Integrative Biology

Communicative & Integrative Biology 8:2, e1017160; March/April 2015; Published with license by Taylor & Francis Group, LLC

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N ov em be r 2 01 5 samples of field-grown N. attenuata plants irrespective of the genotype (Fig. 1B). At the order level, this core community consisted of 5 OTUs retrieved from all roots and shoots from 27 OTUs found in total. These 5 OTUs belonged to the bacterial phyla Bacteriodetes, Proteobacteria and Firmicutes. Additionally, 9 OTUs were present in all root samples, representing also 2 additional bacterial phyla, Actinobacteria and Deinococcus-thermus, indicating a rootspecific enrichment. In accordance with our study, Actinobacteria were shown in a previous studies to be enriched in roots irrespective of soil types.5,6 Deinococcus-thermus taxa are described as highly resistant to environmental hazards and can survive high doses of gamma and UV radiation.11,12 Interestingly, N. attenuata’ s native habitat, the Great