Gkarmiri Konstantia, Mahmood Shahid, Ekblad Alf, Alström Sadhna, Högberg Nils, Finlay Roger
Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Appl Environ Microbiol. 2017 Oct 31;83(22). doi: 10.1128/AEM.01938-17. Print 2017 Nov 15.
RNA stable isotope probing and high-throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing the roots and rhizosphere soil of oilseed rape to identify taxa assimilating plant-derived carbon following CO labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other, and there were highly significant differences between their DNA- and RNA-based community profiles. , , , , , , and were the most active bacterial phyla in the rhizosphere soil. were more active in roots. The most abundant bacterial genera were well represented in both the C- and C-RNA fractions, while the fungal taxa were more differentiated. , , and were dominant in roots, whereas and () were dominant in rhizosphere soil. " Nitrososphaera" was enriched in C in rhizosphere soil. and were abundant in the C-RNA fraction of roots; was abundant in both roots and rhizosphere soil and heavily C enriched. was dominant in rhizosphere soil and less abundant, but was C enriched in roots. The patterns of colonization and C acquisition revealed in this study assist in identifying microbial taxa that may be superior competitors for plant-derived carbon in the rhizosphere of This microbiome study characterizes the active bacteria and fungi colonizing the roots and rhizosphere soil of using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following CO labeling and compares these with other less active groups not incorporating a plant assimilate. is an economically and globally important oilseed crop, cultivated for edible oil, biofuel production, and phytoextraction of heavy metals; however, it is susceptible to several diseases. The identification of the fungal and bacterial species successfully competing for plant-derived carbon, enabling them to colonize the roots and rhizosphere soil of this plant, should enable the identification of microorganisms that can be evaluated in more detailed functional studies and ultimately be used to improve plant health and productivity in sustainable agriculture.
利用RNA稳定同位素探测和高通量测序技术，对定殖在油菜根和根际土壤中的细菌和真菌活性微生物群落进行表征，以鉴定在¹³CO₂标记后同化植物衍生碳的分类群。细菌和真菌的根际土壤相关群落彼此不同，并且基于DNA和RNA的群落图谱之间存在高度显著差异。变形菌门、放线菌门、酸杆菌门、绿弯菌门、芽单胞菌门、拟杆菌门和疣微菌门是根际土壤中最活跃的细菌门。厚壁菌门在根中更活跃。最丰富的细菌属在¹³C和¹²C-RNA组分中均有很好的体现，而真菌分类群的差异更大。镰刀菌属、炭疽菌属和赤霉菌属在根中占主导地位，而曲霉属和青霉属（组）在根际土壤中占主导地位。“亚硝化球菌属”在根际土壤的¹³C中富集。嗜热油杆菌属和贪铜菌属在根的¹³C-RNA组分中含量丰富；根瘤菌属在根和根际土壤中均含量丰富且¹³C高度富集。假单胞菌属在根际土壤中占主导地位且含量较少，但在根中¹³C富集。本研究中揭示的定殖和碳获取模式有助于识别在油菜根际可能是植物衍生碳的优势竞争者的微生物分类群。这项微生物群落研究利用高通量测序和RNA稳定同位素探测技术，对定殖在油菜根和根际土壤中的活性细菌和真菌进行了表征。它鉴定了在¹³CO₂标记后同化植物衍生碳的分类群，并将这些分类群与其他未纳入植物同化物的活性较低的群体进行了比较。油菜是一种在经济上具有全球重要性的油料作物，用于生产食用油、生物燃料以及重金属植物提取；然而，它易受多种病害影响。鉴定成功竞争植物衍生碳、使其能够定殖在该植物根和根际土壤中的真菌和细菌物种，应该能够识别可在更详细的功能研究中进行评估并最终用于改善可持续农业中植物健康和生产力的微生物。
