IRD, Cirad, University of Montpellier, IPME, Montpellier, France.
IRD, UMR LSTM, Campus de Baillarguet, Montpellier, France.
BMC Genomics. 2018 Jan 30;19(1):105. doi: 10.1186/s12864-018-4487-2.
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.
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.
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.
根瘤菌共生体属于α变形菌纲和β变形菌纲（分别称为“α”和“β”-根瘤菌）。大多数关于共生的遗传基础的知识都是基于属于α-根瘤菌的模式菌株。含羞草是一种豆科植物，它为研究β-根瘤菌与α-根瘤菌相比在共生固氮方面的适应性提供了极好的机会。在之前的一项研究（Melkonian 等人，Environ Microbiol 16:2099-111, 2014）中，我们描述了属于伯克霍尔德氏菌、金氏杆菌属和根瘤菌属的含羞草共生体的共生竞争力。
在本文中，我们对 B. phymatum STM815 (BP)、C. taiwanensis LMG19424 (CT) 和 R. mesoamericanum STM3625 (RM) 的转录组（通过 RNAseq）进行了比较分析，这些条件模拟了共生的早期步骤（即根分泌物的感知）。BP 表现出最强的转录组变化，无论是在数量上还是在质量上，这反映了它在共生早期步骤中的高竞争力及其作为共生体的古老进化历史，而 CT 的反应最小，这与它作为年轻共生体的地位相关（可能是通过从伯克霍尔德氏菌祖先那里获得共生基因），而 RM 则表现出α变形菌根际细菌的典型反应。有趣的是，nodulation 基因的上调是这三种菌株唯一的共同反应；例外的是一个上调的基因编码一个假定的脂肪酸羟化酶，这似乎是一个专门针对含羞草共生体的新的共生基因。
对根分泌物的转录反应与每个菌株的结瘤竞争力相关，其中伯克霍尔德氏菌 phymatum 似乎是含羞草的最佳特化共生体。
