Distinct Growth Strategies of Soil Bacteria as Revealed by Large-Scale Colony Tracking
Distinct Growth Strategies of Soil Bacteria as Revealed by Large-Scale Colony Tracking
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DOI：
10.1128/aem.06585-11
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发表时间：
2012-03-01
影响因子：
4.4
通讯作者：
Kishony, Roy
中科院分区：
文献类型：
--
作者：
Ernebjerg, Morten;Kishony, Roy
近年来，随着测序技术的进步，我们对微生物生态学的理解有了显著的提高，但对环境细菌表型特征的全面调查仍然很少。这些表型数据对于理解微生物的生长策略和微生物生态系统的多样性至关重要。在这里，我们描述了使用一系列平板扫描仪加上自动图像分析对数千个细菌菌落生长的高通量测量。我们使用该系统来研究未经处理土壤中微生物群落成员的生长特性。该系统提供了CFU数量、菌落生长速率和出现时间的高质量测量，使我们能够直接研究这些特性在混合环境样品中的分布。我们发现土壤细菌表现出广泛的生长策略，这些策略可以分为几个集群，这些集群不能简化为土壤细菌的任何经典的二分类，例如，分为copotopos和oligotrophs。我们还发现，在早期，当附近有其他菌落存在但不太密集时，细胞最有可能形成菌落。这种在中等电镀密度下培养能力的最大化表明，先前观察到的高密度导致较少菌落的趋势部分被微生物之间相互作用引起的诱导菌落形成所抵消。这些结果提示了新的土壤细菌生长类型分类和物种相互作用对菌落生长的潜在影响。
Our understanding of microbial ecology has been significantly furthered in recent years by advances in sequencing techniques, but comprehensive surveys of the phenotypic characteristics of environmental bacteria remain rare. Such phenotypic data are crucial for understanding the microbial strategies for growth and the diversity of microbial ecosystems. Here, we describe a high-throughput measurement of the growth of thousands of bacterial colonies using an array of flat-bed scanners coupled with automated image analysis. We used this system to investigate the growth properties of members of a microbial community from untreated soil. The system provides high-quality measurements of the number of CFU, colony growth rates, and appearance times, allowing us to directly study the distribution of these properties in mixed environmental samples. We find that soil bacteria display a wide range of growth strategies which can be grouped into several clusters that cannot be reduced to any of the classical dichotomous divisions of soil bacteria, e.g., into copiotophs and oligotrophs. We also find that, at early times, cells are most likely to form colonies when other, nearby colonies are present but not too dense. This maximization of culturability at intermediate plating densities suggests that the previously observed tendency for high density to lead to fewer colonies is partly offset by the induction of colony formation caused by interactions between microbes. These results suggest new types of growth classification of soil bacteria and potential effects of species interactions on colony growth.