Transcriptomic Profiling of Burkholderia Phymatum STM815
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Klonowska et al. BMC Genomics (2018) 19:105 DOI 10.1186/s12864-018-4487-2 RESEARCHARTICLE Open Access Transcriptomic profiling of Burkholderia phymatum STM815, Cupriavidus taiwanensis LMG19424 and Rhizobium mesoamericanum STM3625 in response to Mimosa pudica root exudates illuminates the molecular basis of their nodulation competitiveness and symbiotic evolutionary history Agnieszka Klonowska1†, Rémy Melkonian2†, Lucie Miché2,3, Pierre Tisseyre2 and Lionel Moulin1*† Abstract Background: Rhizobial symbionts belong to the classes Alphaproteobacteria and Betaproteobacteria (called “alpha” and “beta”-rhizobia). Most knowledge on the genetic basis of symbiosis is based on model strains belonging to alpha-rhizobia. Mimosa pudica is a legume that offers an excellent opportunity to study the adaptation toward symbiotic nitrogen fixation in beta-rhizobia compared to alpha-rhizobia. In a previous study (Melkonian et al., Environ Microbiol 16:2099–111, 2014) we described the symbiotic competitiveness of M. pudica symbionts belonging to Burkholderia, Cupriavidus and Rhizobium species. Results: In this article we present a comparative analysis of the transcriptomes (by RNAseq) of B. phymatum STM815 (BP), C. taiwanensis LMG19424 (CT) and R. mesoamericanum STM3625 (RM) in conditions mimicking the early steps of symbiosis (i.e. perception of root exudates). BP exhibited the strongest transcriptome shift both quantitatively and qualitatively, which mirrors its high competitiveness in the early steps of symbiosis and its ancient evolutionary history as a symbiont, while CT had a minimal response which correlates with its status as a younger symbiont (probably via acquisition of symbiotic genes from a Burkholderia ancestor) and RM had a typical response of Alphaproteobacterial rhizospheric bacteria. Interestingly, the upregulation of nodulation genes was the only common response among the three strains; the exception was an up-regulated gene encoding a putative fatty acid hydroxylase, which appears to be a novel symbiotic gene specific to Mimosa symbionts. Conclusion: The transcriptional response to root exudates was correlated to each strain nodulation competitiveness, with Burkholderia phymatum appearing as the best specialised symbiont of Mimosa pudica. Keywords: Symbiosis, Transcriptome, Beta-rhizobia, Alpha-rhizobia, RNA-seq * Correspondence: [email protected] †Equal contributors 1IRD, Cirad, University of Montpellier, IPME, Montpellier, France Full list of author information is available at the end of the article © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Klonowska et al. BMC Genomics (2018) 19:105 Page 2 of 22 Background scenario seems to be different as their nod gene phyloge- Rhizobia are a functional group of bacteria able to develop nies mirror that of the Burkholderia species (based on a nitrogen-fixing symbiosis with legumes. Symbiotic asso- their 16S rRNA and housekeeping genes), which has led ciations between legumes and rhizobia usually begin with several authors to hypothesise an ancient transfer of an exchange of diffusible signals among which (iso)flavo- nodulation genes to a burkholderia ancestor followed by noids present in the root exudates are responsible for the vertical transmission and coevolution with endemic host production and secretion of bacterial lipochitooligosac- species [30]. In the case of Cupriavidus, the nodulating charides (LCOs), known as Nod factors (NF). The recog- species were proposed to be recent symbionts compared nition of NF by the roots leads to the formation of the to Burkholderia based on phylogenetic and genomic root nodule, wherein bacteria are able to fix atmospheric analyses [31], but in the light of recent findings and nitrogen to sustain plant growth in exchange for carbon – analyses (nodC gene phylogeny, symbiotic specificity) its containing metabolites [1]. The biosynthesis of NF and origin and evolution may be more complex [5]. nitrogen fixation enzymes are encoded by nod and nif Mimosa pudica is a legume that has the rare ability to genes respectively [2]. be nodulated naturally by both alpha (Rhizobium spp.) Rhizobial species are mainly distributed among four and beta-rhizobia (Burkholderia, Cupriavidus). Diversity genera of Alphaproteobacteria (Rhizobium, Sinorhizobium, studies showed that proportions between beta- and alpha- Mesorhizobium, Bradyrhizobium; and a few species in rhizobia hosted in nodules of M. pudica vary significantly seven other genera) and two genera of Betaproteobacteria in different geographical locations. For example, Burkhol- (Burkholderia, Cupriavidus) leading to the proposal of the deria were found to be predominant in nodules of M. terms alpha- and beta-rhizobia to distinguish both classes pudica in Barro Colorado Island and in French Guiana of symbionts [3]. The discovery of beta-rhizobia in 2001 [ 10, 32], whereas the proportions of Burkholderia and changed dramatically our perspectives on the genetic Cupriavidus symbionts were more equal in Costa Rica, backgrounds required to host the ability to form symbi- China and India [18, 20, 24], and finally Cupriavidus was oses with legumes by extending this possibility to a new found to be predominant in nodules of M. pudica in subclass of Proteobacteria. If beta-rhizobia appeared Taiwan and in New Caledonia [23, 33]. Several parameters controversial at the time of their discovery, it is now well can help explain the proportions of symbionts in nodules established that Burkholderia species are the main symbi- of M. pudica in worldwide diversity studies, but soil char- onts of several endemic species of the Mimosoideae and acteristics, especially the presence of combined nitrogen Papilinoideae legume subfamilies in Brazil and South affect strain competitiveness [34]. In a previous study [35], Africa [4–7], which raises questions about the origin of we made a large survey of strain nodulation competitive- symbiosis and performance of these new symbionts ness between Burkholderia, Cupriavidus and Rhizobium compared to alpha-rhizobia. Many symbiotic species of species and showed that B. phymatum and B. tuberum sv. Burkholderia (recently rearranged in the Paraburkholderia mimosae are the most competitive species on Mimosa genus [8]) have been described from mimosoids: B. phy- pudica,butCupriavidus taiwanensis could compete with matum [9], B. tuberum [10], B. mimosarum [11], B. Burkholderia when tested on specific M. pudica genotypes nodosa [12, 13], B. sabiae [14], B. symbiotica [15], B. dia- (on variety unijuga from Taiwan where Cupriavidus domi- zotrophica [16], B. piptadeniae and B. ribeironis [17], nates in nodules of this variety). In the case of Rhizobium while Cupriavidus symbionts (C. taiwanensis, C. necator, species, all species were poorly competitive, despite the C. pinatubonensis) were detected mostly in invasive fact that R. mesoamericanum are frequently found in Mimosa species (M. pudica, M. pigra, M. diplotricha)in diversity studies, although in small proportions, such as in South, Central and North America [10, 18, 19], in Asia Costa Rica [18], Mexico [36], New Caledonia [23]and (China, India, Taiwan, Philippines, New Caledonia, Papua French Guiana [10], which raises questions about their New Guinea) [20–24], but also in native Mimosa and capacity to be maintained as M. pudica symbionts. The Parapiptadenia species in Uruguay [25, 26]. only case of a Rhizobium species dominating in the nod- Diversity studies of alpha-rhizobia showed incongru- ules of M. pudica is R. altiplani in central Brazil [37]. ence between rhizobial house-keeping genes and symbi- Several molecular factors linked to nodulation com- otic nod genes phylogenies. Phylogenetic analyses have petitiveness have been described in rhizobia, including i) shown that the different rhizobial lineages diverged well the nodulation gene set [38], ii) rhizobial motility [39] before the appearance of legumes [27], so that their bac- and specific adhesiveness to the plant roots [40], iii) terial nodulation capacity would have been acquired sub- adjustment of rhizobial cell-surface characteristics (EPS stantially after the diversification of rhizobia in one or and LPS) [41], iv) induction of type III or type IV secre- several lineages, and was then spread by lateral gene tion system expression [42] and v) induction of pSym transfer among the different genera and species [28, 29]. conjugal transfer genes [43]. Until now, all these studies For the Mimosoid Burkholderia legume symbionts, the have been performed on alpha rhizobia, which leaves Klonowska et al. BMC Genomics (2018) 19:105 Page 3 of 22 many questions about the specific adaptations that genes compared to the other two strains. The symbiotic might be found in beta-rhizobia which could explain plasmids in all three rhizobia shared poor syntenies their competitiveness superiority over alpha-rhizobia in (Additional file 1: Figure S2), with almost only the nod Mimosa species. Beyond the activation of nod and nif and nif gene regions