The structure of microbial communities: Determining factors and spatial scale

我们的星球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物和矿物形式之间循环。所有这些循环中的某些关键步骤都依赖于微生物。所以，如果我们想了解我们的星球如何继续维持生命，以及它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，因为在任何给定的环境中，微生物都是如此之小，如此之多。大多数关于微生物的研究都着眼于大群体，类似于一次研究所有植物，这使得很难确定哪些因素，如温度、盐度或pH值，对形成环境中存在的特定微生物很重要。而且，直到最近，我们还不可能检测到环境中存在的所有不同的微生物，也不可能知道微生物群在空间上是如何变化的，也不知道它们的分布规模，无论是在与它们的物理尺寸相似的非常小的距离上，还是在更大的距离上。我们已经采取措施解决采样规模和识别环境中微生物的问题，方法是采取集中的方法，只分析一小群定义明确的微生物，而不是试图研究所有微生物。这与生态学家研究植物和动物模型群的方式类似。我们的微生物模型群是Desulfobulbus，这是一种常见于河流、湖泊、河口和海洋沉积物的细菌群（属）。我们之前的研究表明，这一群体的不同成员（物种）只在英国科尔恩河口的某些地区被发现，其模式类似于对大型生物（如虾Gammarus）的研究。我们将检测到的模式解释为表明Desulfobulbus物种仅局限于处于特定盐度（其“生态位”）的河口区域，并且随着时间的推移它们已经变得彼此不同。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中所有不同类型的脱硫球。这意味着我们现在有一种方法来正确地解决问题，即在维护我们在这个社区中看到的模式时，哪些因素是重要的。在这个项目中，我们将使用精心设计的实验，我们将河口一端的沉积物放在河口另一端的消毒水中孵育，以确定在河口海洋一端发现的Desulfobulbus物种是否能够在淡水条件下同样生长。这将告诉我们，在河口探测到的某些物种，还是全部物种，是否只能在它们的自然条件下茁壮成长（因此受限于它们自己特定的生态位）。我们也会测试淡水脱硫藻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，测试脱硫藻物种之间的竞争对群落的形成是否也很重要。为了确定对Desulfobulbus群落取样的尺度我们将沿着河口每500米取样一次同时在两个地点内取样，每50米取样一次，然后在两个地点内每5米取样一次，直到采样间隔只有5厘米。这些样本将被分析，以确定这些嵌套样本中存在的Desulfobulbus类型在不同的尺度上是否不同。因此，本项目将通过对存在的Desulfobulbus物种进行全面采样，研究形成Colne河口微生物群落的重要因素。这将是微生物生态学的重要一步，并将大大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.