Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States.
Environ Sci Technol. 2013 Sep 3;47(17):9841-9. doi: 10.1021/es4018656. Epub 2013 Aug 13.
Microbial community responses to environmental stresses are critical for microbial growth, survival, and adaptation. To fill major gaps in our ability to discern the influence of environmental changes on microbial communities from engineered and natural environments, a functional gene-based microarray, termed StressChip, has been developed. First, 46 functional genes involved in microbial responses to environmental stresses such as changes to temperature, osmolarity, oxidative status, nutrient limitation, or general stress response were selected and curated. A total of 22,855 probes were designed, covering 79,628 coding sequences from 985 bacterial, 76 archaeal, and 59 eukaryotic species/strains. Probe specificity was computationally verified. Second, the usefulness of functional genes as indicators of stress response was examined by surveying their distribution in metagenome data sets. The abundance of individual stress response genes is consistent with expected distributions based on respective habitats. Third, the StressChip was used to analyze marine microbial communities from the Deepwater Horizon oil spill. That functional stress response genes were detected in higher abundance (p < 0.05) in oil plume compared to nonplume samples indicated shifts in community composition and structure, consistent with previous results. In summary, StressChip provides a new tool for accessing microbial community functional structure and responses to environmental changes.
微生物群落对环境压力的反应对于微生物的生长、存活和适应至关重要。为了填补我们从工程和自然环境中辨别环境变化对微生物群落影响的能力方面的重大空白，开发了一种基于功能基因的微阵列，称为 StressChip。首先，选择了 46 个与微生物对环境压力的反应相关的功能基因，例如温度、渗透压、氧化状态、营养限制或一般应激反应的变化。总共设计了 22855 个探针，涵盖了来自 985 种细菌、76 种古细菌和 59 种真核生物/菌株的 79628 个编码序列。通过计算验证了探针的特异性。其次，通过调查其在宏基因组数据集的分布，研究了功能基因作为应激反应指标的有用性。个别应激反应基因的丰度与各自栖息地的预期分布一致。第三，使用 StressChip 分析了深水地平线溢油事件中的海洋微生物群落。与非油斑样品相比，功能应激反应基因在油斑中检测到更高的丰度（p < 0.05），表明群落组成和结构发生了变化，这与先前的结果一致。总之，StressChip 为获取微生物群落功能结构和对环境变化的响应提供了一种新工具。
