Rahimlou Saleh, Hosseyni Moghadam Mahdieh S, Gazis Romina, Karlsen-Ayala Elena, Bahram Mohammad, James Timothy Y, Tedersoo Leho
Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409, Tartu, Estonia.
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
Mol Genet Genomics. 2024 Dec 28;300(1):9. doi: 10.1007/s00438-024-02218-2.
Root nodule symbiosis is traditionally recognized in the Fabales, Fagales, Cucurbitales, and Rosales orders within the Rosid I clade of angiosperms. However, ambiguous root nodule formation has been reported in Zygophyllaceae and Roystonea regia (Arecaceae), although a detailed analysis has yet to be conducted. We aimed to perform morphological analyses of root structures in these plants and utilize metagenomic techniques to identify and characterize the bacterial populations within the nodule-like structures. We collected root samples of Tribulus terrestris (Zygophyllaceae) and Roystonea regia from West Asia and the Caribbean, respectively. We conducted detailed morphological analyses of nodule-like structures, isolated and genome-sequenced the endophytes, and employed metagenomic techniques to identify the bacterial populations within these formations. We observed nodule-like structures in both plant species. Symbiosomes, which are hallmark structures of nodulating plants, were not detected. Metagenome sequence data analysis revealed potential nodulating and nitrogen-fixing bacteria in the nodule-like structures of both species. Canonical nodulation and nitrogen-fixation genes were identified in microbes associated with the nodules. However, the phylogenomic analysis showed that the bacteria isolated from T. terrestris and R. regia are within Gammaproteobacteria and Bacilli, which are not typically known as nodulating bacteria. The observed structures differ significantly from traditional nodules found in legumes and actinorhizal plants, suggesting unique characteristics with hosting nitrogen-fixing bacteria. Although bacteria identified through in silico analysis or culture are well-known nitrogen-fixers, their specific role in root nodule formation remains to be investigated.
根瘤共生传统上在被子植物蔷薇分支 I 的豆目、壳斗目、葫芦目和蔷薇目科中被认可。然而，尽管尚未进行详细分析，但在蒺藜科和王棕（棕榈科）中已报道有不明确的根瘤形成。我们旨在对这些植物的根系结构进行形态学分析，并利用宏基因组技术鉴定和表征类根瘤结构内的细菌种群。我们分别从西亚和加勒比地区采集了蒺藜（蒺藜科）和王棕的根样本。我们对类根瘤结构进行了详细的形态学分析，分离并对内生菌进行了基因组测序，并采用宏基因组技术鉴定这些结构内的细菌种群。我们在这两种植物中都观察到了类根瘤结构。未检测到作为结瘤植物标志性结构的共生体。宏基因组序列数据分析揭示了这两个物种类根瘤结构中潜在的结瘤和固氮细菌。在与根瘤相关的微生物中鉴定出了典型的结瘤和固氮基因。然而，系统发育基因组分析表明，从蒺藜和王棕中分离出的细菌属于γ-变形菌纲和芽孢杆菌属，它们通常不被认为是结瘤细菌。观察到的结构与豆科植物和放线菌根植物中的传统根瘤有显著差异，这表明在容纳固氮细菌方面具有独特特征。尽管通过计算机分析或培养鉴定出的细菌是众所周知的固氮菌，但其在根瘤形成中的具体作用仍有待研究。
