基于高通量测序的4种硝化细菌富集培养物微生物群落结构分析

【目的】比较分析4种硝化细菌富集培养物(以铵盐为氮源的淡水富集物A、以亚硝酸盐为氮源的淡水富集物B、以铵盐为氮源的低温淡水富集物C和以亚硝酸盐为氮源的海水富集物D)的微生物群落结构与组成。【方法】分别提取样品的总DNA,采用高通量测序技术,分析微生物群落的组成、丰度和多样性。【结果】在不同微生物的分类水平,4个样品共检测到24门47纲129属。4个样品的优势菌门均为变形菌门;样品A、B、C的优势菌纲为β-变形菌纲和γ-变形菌纲,样品D的优势菌纲为γ-变形菌纲、δ-变形菌纲和芽孢杆菌纲;而优势菌属各不相同,其中样品A为亚硝化单胞菌属(24.56%),样品B为链霉菌属(7.15%),样品C为噬菌弧菌属(19.36%)和类诺卡氏菌属(19.35%),样品D为嗜酸菌属(13.6%)和柄杆菌属(11.5%)。共检测出7种具有硝化功能的细菌,其中样品A、B和D中主要是亚硝化单胞菌属,占比分别为24.56%、4.94%和0.63%,样品C主要为Nitrospirillum(0.69%)和硝化螺旋菌属(0.69%)。此外在样品中还检测到红灯食烷菌、羽扇豆根瘤菌等有益菌,以及弧菌属、伯克霍尔德菌等致病菌。【结论】阐述了4个样品微生物群落结构的多样性,确定了不同培养物中起主要作用的硝化细菌类群以及其它与环境物质循环相关或具有特殊生理特性的菌群,研究结果为硝化细菌富集培养物的实际应用奠定了基础。     

A genomics approach to improve the analysis and design of strain selections

Strain engineering has been traditionally centered on the use of mutation, selection, and screening to develop improved strains. Although mutational and screening methods are well-characterized, selection remains poorly understood. We hypothesized that we could use a genome-wide method for assessing laboratory selections to design selections with enhanced sensitivity (true positives) and specificity (true negatives) towards a single desired phenotype. To test this hypothesis, we first applied multi-SCale Analysis of Library Enrichments (SCALEs) to identify genes conferring increased fitness in continuous flow selections with increasing levels of 3-hydroxypropionic acid (3-HP). We found that this selection not only enriched for 3-HP tolerance phenotypes but also for wall adherence phenotypes (41% false positives). Using this genome-wide data, we designed a serial-batch selection with a decreasing 3-HP gradient. Further examination by ROC analysis confirmed that the serial-batch approach resulted in significantly increased sensitivity (46%) and specificity (10%) for our desired phenotype (3-HP tolerance).