含好氧不产氧光合基因簇和Xanthorhodopsin-like基因的Sphingomonas sp.MIM37:基因组及光促生长分析

Sphingomonas sp.MIM37 possessing aerobic anoxygenic photosynthetic gene cluster and xanthorhodopsin-like gene: its genome draft and growth stimulation by illumination

【目的】菌株MIM37为具有两种光能利用途径的光合异养细菌,分析其基因组和光照对生长的影响,为理解光能利用途径、光营养生物多样性以及光合作用的进化和功能等提供线索。【方法】采用平板涂布划线法分离菌株,结合形态观察及16S r RNA基因和光合基因序列同源性与系统发育分析进行初步分类鉴定;以分光光度法和荧光显微观察法测定光照和黑暗培养下培养液细胞浓度和单细胞体积;构建片段长度为300-500 bp的Illumina PE文库,以Illumina Hiseq2000进行基因组测序,以SOAPdenovo和Gap Closer组装序列,以RAST在线软件注释基因组。【结果】从内蒙古腾格里沙漠天鹅湖表层水中分离获得一株细菌MIM37,经16S r RNA基因、puf M和视紫质基因同源性和系统发育分析均显示其与Sphingomonas属亲缘关系最为密切;相对黑暗培养,光照刺激下的最大细胞浓度和单细胞体积大小分别提高了1.2和5.6倍;基因组注释显示MIM37代谢途径多样,含典型好氧菌的呼吸电子传递链,具有完整的好氧不产氧细菌的光合基因簇及Xanthorhodopsin-like视紫质蛋白基因,合成铁载体,还原重金属,降解微囊藻毒素和多环芳烃类等。【结论】MIM37属于Sphingomonas属,具有两种光能利用途径,光照可明显促进其生长,多样的代谢模式可能使其在自然环境中极具竞争力、分布广泛并具有应用于修复环境污染的潜力。

[Objective] The genome of the photoheterotrophic bacterium MIM37, possessing anoxygenic photosynthetic gene cluster（PGC） and xanthorhodopsin-like gene, was sequenced and the stimulated growth by illumination was determined, which is helpful in shedding light upon the diversity of photosynthetic pathway and phototrophic bacteria, and the evolution and role of photosynthesis. [Methods] The isolation was performed by the traditional plate spread and streak. To classify and identify the isolate preliminarily, the morphological feature and, the homology and phylogeny of 16 S r RNA gene, puf M and rhodopsin genes were analyzed. Spectrophotometry and fluorescence microscopy were employed separately to reveal the concentration and size shifts of the cell cultured under illumination or dark. Illumina PE library of 300-500 bp fragments was constructed for Illumina Hiseq2000 genome sequencing. Sequences were assembled through the software of SOAPdenovo and Gap Closer and the online software of RAST was used to annotate. [Results] We obtained a bacterial strain MIM 37 from Lake Swan in Desert Tenggeli in Inner Mongolia. The homology and phylogeny analysis based on 16 S r RNA gene, puf M and rhodopsin genes respectively, showed that the strain most closely related to the members of Sphingomonas genus. Compared with the dark condition, light condition increased the maximum of the cell concentration and volume by 1.2 and 5.6 folds respectively. The genome draft sequence demonstrated that MIM37 has diverse metabolic pathways with electron transport chain of the typical aerobic respiration, intact aerobic phototrophic photosynthetic gene cluster and xanthorhodopsin-like genes, siderophore biosynthesis, heavy metal reduction, the degradation of microcystin and polyaromatic hydrocarbon and etc. [Conclusion] The strain MIM37 is a member of the genus Sphingomonas and possesses two different phototrophic pathways. Light may stimulate its growth markedly. The diverse metabolic pathways may be helpful for the strain in the survival and wide distribution in natural ecosystems, and make strain MIM37 useful in environmental pollutes bioremediation.