The structure of microbial communities: Determining factors and spatial scale

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.

Microbes play a vital role in the global ecosystem, are of major importance in human health, agriculture, biotechnology and in many other aspects of society. Therefore the development of a deeper understanding of the way microbes interact with the environment, with each other and other organisms is of vital scientific, social and economic importance. This project, while it has few direct interactions with potential end-users will, by substantially improving our understanding of microbial ecology, potentially influence a wide variety of scientific, industrial, regulatory and health communities. The Pathway to Impact of this proposal describes how these potential stakeholders will be engaged.

Microbes are important in a number of industries, including the water industry, agriculture and biotechnology. The water industry depends on microbial activity to clean wastewater and has traditionally treated this as a black box but has engaged in the development of a scientific basis for their industry. This project will develop microbial ecology and moving it from being descriptive into a more theoretical and potentially predictive science. Thus, the concepts and approaches it will develop will impact on the development of wastewater treatment. Similarly, biotechnology relies upon exploiting microbial function, this is especially true of the development of bio products to replace non-renewable materials and energy sources as we develop a low-carbon, renewable society. Again as microbial ecology develops, and factors that are critical to controlling microbial function become apparent, then the task of exploiting microbes will be placed on a more solid basis. The results of this project may have direct effect on the control and management of microbial processes in the production of bioproducts such as renewable fuels and bioplastics. Other industries, such as those that produce natural mineral products for use in manufacturing, can face problems with microbial contamination and understanding of the ecology of these communities is still developing. Similarly microbial activity is responsible for a large amount of damage to cultural heritage. Dr Purdy has ongoing collaborations Omiya, a Swiss company that produces white mineral dispersions for the packaging industry, in the area of control of microbial populations in bulk products and with researchers working on the control, remediation and restoration of cultural heritage, an area that has substantial economic value given the size of the tourist industry in the UK, Europe and globally.

Human, animal and plant health are closely linked to their colonising microbes. However, many studies in this area have problems that are similar to those in studying microbes in the environment. Thus, the development of approaches and ideas in microbial ecology will positively affect human, animal and plant microbiome studies. Dr Purdy has active collaborations working on mixed microbial communities in animals and wound biofilms. Therefore there will be opportunities to engage with researchers, practitioners and industry in the area of microbial interactions with humans and other organisms of societal value.

The ability to sample effectively, to rapidly analyse samples and to place this data into an ecological context, all aspects of this project, will have substantial potential value to environmental monitoring and protection.

Microbial ecology will play a vital role as we address issues raised by a changing climate and move towards a more sustainable society by affecting large areas of basic and applied research, the environment, health and welfare and industry. Thus, securing the basis of microbial ecology and making it a more predictive science will have a significant impact on national and international research, industry and society.