The structure of microbial communities: Determining factors and spatial scale

我们的星球之所以继续运转，是因为生命所必需的成分，如碳和氮，在所谓的全球生物地球化学循环中，不断地在生命形式和矿物形式之间循环。所有这些周期中的某些关键步骤都依赖于微生物。因此，如果我们想要了解我们的星球如何继续维持生命，以及它将如何适应不断变化的环境，了解微生物在自然界中的工作方式是非常重要的；我们需要了解微生物的生态学。然而，微生物的生态学很难研究，因为微生物在任何给定的环境中都是如此之小和如此之多。大多数关于微生物的研究着眼于大的分组，类似于同时研究所有植物，这使得很难确定哪些因素，如温度、盐度或pH，在塑造环境中存在哪些特定微生物方面起着重要作用。此外，直到最近，甚至不可能检测到环境中存在的所有不同微生物，也不可能知道微生物群体在空间上如何变化，它们的分布规模，无论是在非常小的距离上，与它们的物理大小相似，还是在更大的距离上。我们已经采取措施，通过只分析一小部分明确定义的微生物，而不是试图研究所有微生物，来解决这些采样规模和识别环境中微生物的问题。这类似于生态学家研究动植物模型群的方法。我们的微生物模型群是Desulfobulus，这是一个细菌群(属)，经常在河流、湖泊、河口和海洋沉积物中发现。我们之前的研究表明，这一组的不同成员(物种)只在英国科尔纳河口的某些部分发现，其模式类似于对对虾Gammarus等较大生物的研究。我们对我们检测到的模式的解释是，Desulfobulus物种仅限于河口特定盐度的区域(它们的“生态位”)，随着时间的推移，它们彼此变得不同。我们还表明，通过使用一种新的技术，焦磷酸测序，我们可以检测到河口所有不同类型的硫球藻类。这意味着我们现在有了一种方法，可以正确地解决在维持我们在这个社区中看到的模式方面哪些因素很重要的问题。在这个项目中，我们将使用精心设计的实验，将河口一端的沉积物放在河口另一端的消毒水中培养，以确定在河口海洋端发现的Desulfobulus物种是否能够在淡水条件下生长得同样好。这将告诉我们，在河口检测到的物种中，是否有一些或所有物种只能在它们的本地条件下繁衍生息(因此仅限于它们自己的特定生态位)。我们还将测试淡水Desulobulus物种的存在是否会对淡水条件下海洋物种的生长产生额外的影响，这是一项测试，看看Desulfobulbus物种之间的竞争是否对群落的形成也很重要。为了确定对Desulfobulbus群落进行采样的比例，我们将每500米对整个河口进行采样，并在其中两个站点内采样，间隔50米，然后在其中两个站点内采样，间隔5米，直到相距仅5厘米的采样。将对这些样本进行分析，以确定这些嵌套样本中存在的Desulfobulus类型是否在不同的尺度上有所不同。因此，该项目将通过对存在的硫球藻物种进行完整采样，来调查形成科尔纳河口微生物群落的重要因素是什么。这将是微生物生态学向前迈出的重要一步，并将极大地提高我们对微生物在全球生态系统中如何发挥作用的理解。

Our planet continues to function because components essential for life, such as carbon and nitrogen, are constantly being recycled between living and mineral forms in what are called global biogeochemical cycles. Certain critical steps in all of these cycles are dependent on microbes. So, if we want to understand how our planet continues to sustain life, and how it will adapt to a changing environment, it is very important that we understand how microbes work in the natural world; we need to understand the ecology of microbes.However, the ecology of microbes is difficult to study because microbes are so small and so numerous in any given environment. Most studies on microbes look at large grouping, similar to studying all plants at once, which makes it difficult to determine what factors, such as temperature, salinity or pH, are important in shaping which specific microbes are present in an environment. Also, until recently, it was not possible to even detect all of the different microbes that were present in an environment, nor to know how microbial groups vary in space, the scale of their distribution, be it over very small distances that are similar to their physical size or over much larger distances.We have taken steps to resolve these problems of sampling scale and identifying microbes in the environment by taking the focused approach of analysing only a small, well defined group of microbes, rather that trying to study them all. This is similar to how ecologists study model groups of plants and animals. Our microbial model group is Desulfobulbus, a bacterial group (genus) that is always found in river, lake, estuarine and ocean sediments. Our previous studies have shown that different members (species) of this group are found only in certain parts of the Colne estuary, UK, in a pattern that is similar to that seen in studies of larger organisms such as the shrimp Gammarus. We interpreted the pattern we detected as being indicative of Desulfobulbus species being limited to only regions of the estuary that were at a specific salinity (their "niche") and that they had become different from each other over time. We have also shown that by using a new technique, pyrosequencing, we can detect all of the different Desulfobulbus types in the estuary. This means that we now have a way to properly address questions about what factors are important in maintaining the patterns we see in this community. In this project we will use carefully designed experiments in which we incubate sediment from one end of the estuary in sterilised water from the other end of the estuary in order to determine whether the Desulfobulbus species found in say the marine end of the estuary are able to grow just as well under freshwater conditions. This will tell us whether some, or all, of the species detected in the estuary are only able to thrive under their native conditions (so are limited to their own specific niche). We will also test whether the presence of, say, freshwater Desulfobulbus species has an additional effect on the growth of marine species under freshwater conditions, a test of whether competition between Desulfobulbus species is also important in how the community is shaped. To determine at what scale to sample the Desulfobulbus community we will sample all along the estuary every 500m and also sample within 2 of these sites, at 50m intervals, then within two of these sites at 5m intervals, down to samples that are only 5cm apart. These samples will be analysed to see whether the Desulfobulbus types present within these nested samples are different at different scales. Therefore this project will investigate what are the important factors that shape the microbial community in the Colne estuary by completely sampling the Desulfobulbus species that are present. This will be a major step forward in the ecology of microbes and will greatly improve our understanding of how microbes function in the global ecosystem.