Timm Collin M, Campbell Alisha G, Utturkar Sagar M, Jun Se-Ran, Parales Rebecca E, Tan Watumesa A, Robeson Michael S, Lu Tse-Yuan S, Jawdy Sara, Brown Steven D, Ussery David W, Schadt Christopher W, Tuskan Gerald A, Doktycz Mitchel J, Weston David J, Pelletier Dale A
Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.
Department of Natural Sciences, Northwest Missouri State University Maryville, MO, USA.
Front Microbiol. 2015 Oct 14;6:1118. doi: 10.3389/fmicb.2015.01118. eCollection 2015.
The bacterial microbiota of plants is diverse, with 1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work, we used phenotypic analysis, comparative genomics, and metabolic models to investigate the differences between 19 sequenced Pseudomonas fluorescens strains. These isolates represent a single OTU and were collected from the rhizosphere and endosphere of Populus deltoides. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for plant-bacterial interactions are enriched in endosphere isolate genomes. Further, growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased toward endosphere isolates. Endosphere isolates have significantly more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways representative of plant-bacterial interactions but show metabolic bias toward chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria and are enriched among closely related isolates.
植物的细菌微生物群具有多样性，任何一株植物都与数千个可操作分类单元（OTU）相关联。在这项研究中，我们使用表型分析、比较基因组学和代谢模型来研究19株测序的荧光假单胞菌菌株之间的差异。这些分离株代表一个单一的OTU，是从三角叶杨的根际和内生菌中收集的。虽然没有任何性状是根际或内生荧光假单胞菌分离株所特有的，但与植物-细菌相互作用相关的多种途径在内生菌分离株基因组中得到了富集。此外，诸如磷溶解、蛋白酶活性、反硝化作用和促进根系生长等生长表型偏向于内生菌分离株。内生菌分离株具有更多用于植物信号化合物的代谢途径，并且代谢范围增加，包括利用富含能量的核苷酸和糖类，这与内生菌定殖一致。根际荧光假单胞菌具有较少代表植物-细菌相互作用的途径，但对根际分泌物中常见的化学底物表现出代谢偏向。这项研究揭示了可能有助于细菌定殖于内生菌的多种功能，并且在密切相关的分离株中得到了富集。
