Population genomics of bacteria

地球上的所有生命都依赖于细菌，它们推动着全球物质和能量的循环，提供营养，分解废物和清理污染。当然，其中一些也使我们生病或破坏我们的庄稼。现在我们知道了数百种不同细菌的完整DNA序列，我们可以看到几乎所有这些不同的功能都是由“辅助基因”执行的。细菌就像计算机：它们有一个“基本的基因组”，使系统保持运行，在所有细菌中几乎都是一样的，就像计算机的硬件和操作系统。然后是提供特殊适应的辅助基因组，随着时间的推移，每个细菌通过与其他细菌交换获得了这些基因的独特集合，就像计算机积累软件包和数据一样。我们项目的目标是描述和理解辅助基因（软件包）的发生模式如何与细菌的基本基因组（操作系统）相关。是不是有些套餐广受欢迎，而有些套餐只针对专家？某些软件包是否仅限于特定的操作系统？如果一个系统只有一个软件包，那么它是否还可能拥有一整套其他软件包？我们将从一铲土壤中采集细菌样本，利用某些经过充分研究的特性，从土壤中发现的数千种细菌中筛选出几种相关物种。首先，我们将通过确定它们的核糖体RNA基因和一些提供“管家”功能的基因的DNA序列来检查它们的硬件和操作系统。这就像阅读制造商的名称（核糖体RNA用于识别细菌种类），并检查主要硬件组件和操作系统是否仍然是最初安装的版本。然后，我们将筛选他们数百个不同的软件包（附属基因）。为了做到这一点，我们通过在载玻片上打印数千个微小的DNA斑点来制作微阵列。每个DNA斑点都有不同基因的部分序列，所以当荧光标记的细菌DNA在载玻片上冲洗时，如果匹配的DNA存在，斑点就会发出荧光。这是因为DNA的单链会与匹配的链强烈结合，形成双螺旋。每个斑点的荧光可以在一个特殊的阅读器中测量，所以通过这种方式我们可以检查数百种细菌菌株，看看它们安装了什么辅助基因。我们预计，即使是属于同一物种、基本基因组相同的细菌，它们携带的辅助基因也会有所不同。我们还希望看到相同的辅助基因出现在不同的细菌物种中。已经有很多例子表明这些事情发生了。我们这个项目的目的是更系统地评估情况，观察大量的基因和细菌，以便我们能够得出一些强有力的一般性结论，并开始了解基因的哪些特性决定了它在分布上是广泛的还是有限的。

All life on earth depends on bacteria, which drive the global cycles of matter and energy, provide nutrients, decompose waste and clean up pollution. Of course, some of them also make us ill or destroy our crops. Now that we know the complete DNA sequences of hundreds of different bacteria, we can see that nearly all these diverse functions are carried out by 'accessory genes'. Bacteria are like computers: they have a 'basic genome' that keeps the system running and is much the same in all bacteria, rather like the hardware and operating system of a computer. Then there are sets of accessory genes that provide special adaptations, and over time each bacterium acquires a unique collection of these by swapping with other bacteria, just as computers accumulate software packages and data. The goal of our project is to describe and understand how the patterns of occurrence of accessory genes (software packages) relate to the basic genome (operating system) of the bacteria. Are some packages widely popular and others only for specialists? Are some packages limited to particular operating systems? If a system has one package, is there a whole set of other packages that it is likely to have as well? We will sample bacteria from a single spadeful of soil, using certain well-studied properties tosift out just a few related species from all the thousands that are found in soil. First we will check out their hardware and operating system by determining the DNA sequence of their ribosomal RNA genes and some genes that provide 'housekeeping' functions. This is like reading the manufacturer's name (ribosomal RNA is used to identify bacterial species) and checking whether the main hardware components and the operating system are still the versions originally installed. Then we will screen them for hundreds of different software packages (accessory genes). To do this, we make a microarray by printing thousands of tiny spots of DNA on a glass slide. Each DNA spot has the sequence of part of a different gene, so when fluorescently-labelled DNA from a bacterium is washed over the slide, the spots become fluorescent if the matching DNA is present. This happens because a single strand of DNA will bind strongly to a matching strand to make a double helix. The fluorescence of each spot can be measured in a special reader, so in this way we can check hundreds of bacterial strains to see what accessory genes they have installed. We expect that even those bacteria that belong to the same species and have essentially the same basic genome will differ in the accessory genes that they carry. We also expect to see the same accessory genes turn up in different bacterial species. There are already many examples that show that these things happen. The purpose of our project is to assess the situation more systematically, looking at large numbers of genes and bacteria so that we can draw some strong general conclusions and begin to understand what properties of a gene determine whether it will be widespread or restricted in distribution.