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The structure of microbial communities: Determining factors and spatial scale

微生物群落的结构：决定因素和空间尺度

基本信息

批准号：
NE/J024503/1
负责人：
Kevin J Purdy
金额：
$ 51.12万
依托单位：
University of Warwick
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2013
资助国家：
英国
起止时间：
2013 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=NE%2FJ024503%2F1
关键词：
structure microbial communities Determining factors

项目摘要

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.

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，在所谓的全球地球化学循环中不断地在生命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。因此，如果我们想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，我们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，因为微生物在任何特定环境中都是如此之小，数量如此之多。大多数关于微生物的研究着眼于大的群体，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值，在塑造环境中存在哪些特定微生物方面很重要。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中如何变化，它们的分布规模，无论是在非常小的距离，类似于他们的物理大小或在更大的距离。我们已经采取措施，以解决这些问题的采样规模和确定微生物在环境中，采取重点这是一种只分析一小部分定义明确的微生物的方法，而不是试图研究所有微生物。这类似于生态学家研究植物和动物模型群体的方式。我们的微生物模型组是Desulfobulbus，这是一个细菌组（属），总是在河流，湖泊，河口和海洋沉积物中发现。我们以前的研究表明，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发现，其模式与对大型生物（如虾Gammarus）的研究相似。我们解释的模式，我们检测到的指示Desulfobulbus物种仅限于在特定的盐度（他们的“生态位”）的河口地区，他们已经成为彼此不同的时间。我们还表明，通过使用一种新的技术，焦磷酸测序，我们可以检测到所有不同的Desulfobulbus类型的河口。这意味着，我们现在有一种方法来适当地解决问题，即在维持我们在这个社区中看到的模式方面，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，在实验中，我们将河口一端的沉积物孵育在河口另一端的消毒水中，以确定在河口的海洋端发现的Desulfobulbus物种是否能够在淡水条件下生长。这将告诉我们，在河口检测到的一些或全部物种是否只能在它们的原生条件下茁壮成长（因此仅限于它们自己的特定生态位）。我们还将测试，例如，淡水Desulfobulbus物种的存在是否对淡水条件下的海洋物种的生长有额外的影响，测试Desulfobulbus物种之间的竞争是否也对群落的形成很重要。为了确定在什么样的规模采样Desulfobulbus社区，我们将采样所有沿着河口每500米，也采样在这些网站的2个，在50米的间隔，然后在这些网站的两个在5米的间隔，下降到样本，只有5厘米的距离。将对这些样本进行分析，以确定这些嵌套样本中存在的脱硫菌类型在不同规模下是否不同。因此，本项目将通过对存在的Desulfobulbus物种进行全面采样，调查影响科尔恩河口微生物群落的重要因素。这将是微生物生态学的一个重大进步，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。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Nitrous oxide as a function of oxygen and archaeal gene abundance in the North Pacific.

DOI：
10.1038/ncomms13451
发表时间：
2016-12-01
期刊：
NATURE COMMUNICATIONS
影响因子：
16.6
作者：
Trimmer, Mark;Chronopoulou, Panagiota-Myrsini;Maanoja, Susanna T.;Upstill-Goddard, Robert C.;Kitidis, Vassilis;Purdy, Kevin J.
通讯作者：
Purdy, Kevin J.

Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment.

DOI：
10.1038/s41396-018-0269-8
发表时间：
2019-03
期刊：
The ISME journal
影响因子：
0
作者：
Jameson E;Stephenson J;Jones H;Millard A;Kaster AK;Purdy KJ;Airs R;Murrell JC;Chen Y
通讯作者：
Chen Y

Erratum: Riverbed methanotrophy sustained by high carbon conversion efficiency

勘误：高碳转化效率维持河床甲烷氧化