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Microbial ecology: the relationships between community diversity, structure and function

Final Activity Report Summary - MICROCOMXT (Microbial ecology: the relationships between community diversity, structure and function)

The aim of this project was to find out whether microorganisms, which perform a large number of absolutely essential processes that allow our global ecosystem to continue functioning, are distributed in the environment in patterns similar to large organisms such as plants and animals. If they are then ideas that have been developed over many years by ecologists could be used to determine how these microbial communities might change as the climate changes and how they might function in the global ecosystem in the future.

To achieve this aim the project was divided into 2 main parts. The first was to investigate the distribution of two different microbial groups, called Desulfobulbus and Methanosaeta, along an estuary in Essex, UK. Here we found that different members of the Desulfobulbus group were found at different sites along the estuary, with distinctly different members of the group found at high, medium and low salinity sites. Conversely, Methanosaeta members were found all along the estuary with no sign of them being limited to specific parts of the estuary. We used multiple methods to show that these patterns were real, including an experiment where we put freshwater sediment into marine conditions and vice versa and showed that Desulfobulbus strains were generally limited to growth in the specific conditions they had originally been found in. Desulfobulbus are capable of using a number of different of different energy and food sources making them a "generalist" microbe while Methanosaeta use only acetate for all their needs and so are very strict specialists.

To see whether the difference in distribution we saw was due to the organisms being generalist or specialist we analysed 2 other groups, Desulfobacter, a specialist and Methanosarcina, a generalist. Our data showed that the specialist Desulfobacter also showed no indication of being differentially distributed along the estuary while the generalist Methanosarcina was differentially distributed like Desulfobulbus. These results indicate that organisms that can utilise more substrates as energy and food sources are more likely to adapt to specific conditions than organisms that have a simple metabolism. This will help us understand how and why microbes are distributed around the planet.

The second aspect of the project investigated whether the ability of microbes to change how they respire (breathe) is dependent on whether the conditions they are in are constant or always changing. Using a very well-known microbe, Paracoccus denitrificans, which is capable of growing in the presence or absence of oxygen, we investigated what happened if this organism was keep growing under oxygen-rich conditions. We suggested that if it always had oxygen to use it would eventually lose the ability to grow without oxygen (anaerobic growth) and in the meantime the genes that are used to grow anaerobically would slowly mutate. We grew P. denitrificans either constantly or by sub-culturing every day or two for between 150 and 1000 generations.

Data suggests that the longer P. denitrificans is grown in aerobic conditions the less good it is at growing anaerobically and that it expresses anaerobic genes much less than it did originally. This would indicate that our idea that in the absence of a substrate the ability to use that substrate decreases and that in the environment changing conditions help organisms maintain their ability to be flexible and ready to meet change.