Idea paper: Predicting culturability of microbes from population dynamics under field conditions,Ecological Research

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Idea paper: Predicting culturability of microbes from population dynamics under field conditions
Ecological Research ( IF 1.7 ) Pub Date : 2020-03-11 , DOI: 10.1111/1440-1703.12104
Masayuki Ushio _{1,

2,

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Affiliation

Isolation and cultivation of microbes from environmental samples have been fundamental and important for species identification and investigating functions and ecology of target microbes. Although cultivation and isolation of microbes are not easy, the natural environment can “culture” any endemic microbes, and thus key information for culturing and isolating microbes may be encoded in the natural population dynamics of microbes. In this article, I present the idea that culturability of microbes may be inferred by quantifying the dynamic properties of microbes using nonlinear time series analysis and empirical dynamic modeling (EDM). To briefly demonstrate the idea, I analyzed high‐frequency, quantitative microbial time series obtained for experimental rice plots. I selected bacterial phyla that included sufficient numbers of microbial taxa and analyzed 398 microbial taxa using EDM. The nine phyla analyzed generally followed a similar pattern: many microbial taxa fell into the “Simple” dynamics category, and a small proportion of taxa were categorized in “Simple but nonlinear” or “Nearly random” dynamics categories. The present analysis suggested that many microbes in the study system might be cultivated by modifying a relatively small number of conditions. However, the present idea as well as the result is preliminary, and more precise taxonomic information (i.e., species‐level identification) and a culturability data set will help to validate the idea. If the present idea was found to be valid, a priori evaluation of the culturability of microbes would become possible, which would avoid unnecessary costs (labor, time and money) of attempts to cultivate microbes.

中文翻译：

想法文件：根据田间条件下的种群动态预测微生物的可培养性

从环境样品中分离和培养微生物对于物种鉴定以及研究目标微生物的功能和生态学已经至关重要。尽管培养和分离微生物并不容易，但是自然环境可以“培养”任何特有的微生物，因此，用于培养和分离微生物的关键信息可以编码在微生物的自然种群动态中。在本文中，我提出了一种想法，即可以通过使用非线性时间序列分析和经验动态建模（EDM）量化微生物的动态特性来推断微生物的可培养性。为了简要说明这一想法，我分析了从实验稻田获得的高频，定量微生物时间序列。我选择了包括足够数量的微生物分类群的细菌门，并使用EDM分析了398个微生物分类群。分析的九个门总体上遵循类似的模式：许多微生物分类单元属于“简单”动力学类别，而一小部分分类单元则归类为“简单但非线性”或“几乎随机”动力学类别。目前的分析表明，可以通过修改相对较少的条件来培养研究系统中的许多微生物。但是，目前的想法及其结果是初步的，更精确的分类信息（即物种级别识别）和可培养性数据集将有助于验证该想法。如果发现目前的想法是正确的，则可以对微生物的可培养性进行事先评估，

更新日期：2020-03-11

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