Diversity of soil microbial communities: In the perspective of targeting functional genes

Sammanfattning: Popular Abstract in English Soil as an ecosystem is a reservoir for several living organisms including microorganisms, earthworms, collembolans, nematodes and protozoans. They are involved in cycling the nutrients through degrading the organic compounds (source of carbon essential for all living organisms) like plant residues and respire part of it as carbon dioxide. Organic compounds get stored in the biomass of the organisms and contribute to the soil organic pool. Agricultural practices like tillage destroy the biological structure of soils and disrupt connections of fungal hyphae. Mainly microorganisms such as bacteria and fungi degrade the organic material and make nutrients including nitrogen and phosphorus available for plants. Agricultural intensification due to the growing need for food together with global population, these practices including application of pesticides, have caused several environmental issues like soil erosion, increased atmospheric carbon dioxide and loss of biodiversity in soils. It is important to understand these processes and how they affect the organisms in order to find a way towards sustainable agriculture. As part of this thesis, the effects of different agricultural practices on a particular group of microorganism known as arbuscular mycorrhizal fungi were analysed. These fungi are known to colonize the roots of plants such as barley and wheat and they are specialized in helping them get nutrients from places the plant roots wont be able to reach by forming a tissue structure called hyphae that acts like a pipeline. These fungal communities were mainly affected by the conventional agricultural practices with inorganic fertilizers and pesticides and the fungal diversity was highest in grassland soils. It was also found from a greenhouse experiment that the organic farming produced same amount of barley grains as the conventional farming while maintaining a higher fungal diversity. In order to understand the microbial processes in environments such as nutrient cycling in soil, it is important to understand the genetic potentials of these microbes through which they would be able to carryout these processes. Most research that was being done on environmental communities was based on the different kinds of organisms that survive in those environments. This is mainly because it is technically easier to measure the different kinds of organisms than to measure their possible potential. It is much harder to look into the genetic potential of various kinds of organisms that live in those conditions that would also have various genetic potentials. This issue was addressed in this thesis by developing a method based on a genetic method that is well established in medical research to select and look particularly in certain region of a human genome for disease related modifications in the genome. Here in this thesis, we took that method and developed a similar method for researchers that are interested in understanding biological processes carried out by multiple organisms together, as we call it communities. Here they could select and look particularly into the genetic potential of these communities to carry out the biological processes of interest. This is of course based on the genetic information that is available about the different organisms to carry out the specific tasks in those processes. We have also developed a webpage that will assist the researchers in using this method for the processes that they are interested in studying mainly related to environmental and ecological studies. In this thesis, this method was also applied on soils from grasslands and conventional agriculture to understand and find the differences in microbial potential in degrading organic compounds from these soils. It was found that the different management of these soils affected the ability of the organisms in degrading the organic compounds and not the kinds of organisms in the soils. The amount of nitrogen in the organic compounds present in these soils changes the genetic potential of the microbial community and amount of carbon changes the kinds of organisms populated in those soils. The potential and the diversity of the organisms in these soils were not related. This shows that it is important to look at the potential rather than kinds of the organism in these kinds of environments. With this knowledge of their potential, the microbial responses to environmental changes, such as application of fertilizers where only the active microbes will respond, is currently being measured using the same approach. It will also improve our understanding of these organisms, once we use similar approaches in different soils like rainforest and peatland that are currently under the threat and prevent from loosing organic materials in these soils due to global changes.