Comparative Genomics of Pseudomonas sp. Strain SI-3 Associated With Macroalga Ulva prolifera, the Causative Species for Green Tide in the Yellow Sea.
Comparative Genomics of Pseudomonas sp. Strain SI-3 Associated With Macroalga Ulva prolifera, the Causative Species for Green Tide in the Yellow Sea.
复制标题
假单胞菌属的比较基因组学。
DOI：
10.3389/fmicb.2018.01458
复制
发表时间：
2018
影响因子：
5.2
通讯作者：
Wu C
中科院分区：
文献类型：
--
作者：
Fu H;Jiang P;Zhao J;Wu C
藻类-细菌组合在海洋生境中广泛存在，然而，细菌对大型藻类水华的贡献几乎是未知的。在这项研究中，从引起世界上最大的黄海绿潮的物种--增殖石榴中分离出一株潜在的内生菌株SI-3，该菌株经过严格的漂白处理以消除附生植物。测定了SI-3的基因组序列，大小为4.8Mb，发现SI-3与斯氏假单胞菌的序列比较接近。为了评价SI-3作为一种潜在的内生菌的特性，比较了SI-3和其他20株斯氏假单胞菌的基因组。我们发现，SI-3比大多数斯图泽里螺杆菌菌株具有更多的菌株特异性基因。COG分析表明，与包括4个根际细菌在内的20个斯图泽里菌株相比，SI-3具有更高比例的转录调控和信号转导基因，这表明SI-3与其宿主之间存在复杂的相互作用网络。P.Stutzeri以其在降解芳香族化合物方面的代谢多样性而闻名。然而，在SI-3的几个芳香族化合物降解途径中观察到显著的基因丢失，这可能是一种与寄主相关的进化适应。KEGG分析表明，SI-3的基因组中存在异化硝酸盐还原为铵(DNRA)和反硝化作用这两个相互竞争的异化硝酸盐还原途径，这两个途径与大多数其他20株斯图策里菌株一样。我们推测，与微藻水华一样，SI-3的DNRA可能通过保存形态上的氮而在美国增殖杆菌的氮素获取方面贡献了竞争优势。总体而言，这些数据表明假单胞菌属(Pseudomonas sp.)SI-3菌株是研究藻类与细菌相互作用及其对藻类水华生态影响的合适候选菌株。
Algae-bacteria associations occurred widely in marine habitats, however, contributions of bacteria to macroalgal blooming were almost unknown. In this study, a potential endophytic strain SI-3 was isolated from Ulva prolifera, the causative species for the world's largest green tide in the Yellow Sea, following a strict bleaching treatment to eliminate epiphytes. The genomic sequence of SI-3 was determined in size of 4.8 Mb and SI-3 was found to be mostly closed to Pseudomonas stutzeri. To evaluate the characteristics of SI-3 as a potential endophyte, the genomes of SI-3 and other 20 P. stutzeri strains were compared. We found that SI-3 had more strain-specific genes than most of the 20 P. stutzeri strains. Clusters of Orthologous Groups (COGs) analysis revealed that SI-3 had a higher proportion of genes assigned to transcriptional regulation and signal transduction compared with the 20 P. stutzeri strains, including four rhizosphere bacteria, indicating a complicated interaction network between SI-3 and its host. P. stutzeri is renowned for its metabolic versatility in aromatic compounds degradation. However, significant gene loss was observed in several aromatic compounds degradation pathways in SI-3, which may be an evolutional adaptation that developed upon association with its host. KEGG analysis revealed that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification, two competing dissimilatory nitrate reduction pathways, co-occurred in the genome of SI-3, like most of the other 20 P. stutzeri strains. We speculated that DNRA of SI-3 may contribute a competitive advantage in nitrogen acquisition of U. prolifera by conserving nitrogen in form, as in the case of microalgae bloom. Collectively, these data suggest that Pseudomonas sp. strain SI-3 was a suitable candidate for investigation of the algae-bacteria interaction with U. prolifera and the ecological impacts on algal blooming.