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The effect of soil habitat connectivity on microbial interactions, community structure and diversity: a microcosm-based approach

By A.B. Wolf

Abstract

Soils contain tremendous microbial phylogenetic and functional diversity. Recent advances in the application of molecular methods into microbial ecology have provided a new appreciation of the extent of soil-borne microbial diversity, but our understanding of the forces that shape and maintain this tremendous source of biodiversity still remain rudimentary. The overall aim of the work presented in this thesis was to increase our understanding of the forces that allow for the tremendous amount of diversity to be maintained in soil microbial communities. Specifically, the aim of this research was to elucidate the role of soil habitat connectivity, as determined by soil structure and hydration status on microbial resource competition and habitat utilization, the structure and diversity of complex bacterial and fungal communities and specific microbial groups with different life-history strategies, bacterial:fungal ratios and colonization potential of bacteria with different motility mechanisms. In order to allow for specific examination of habitat properties and microbial interactions and community dynamics, the work presented in this thesis relied on the development and application of a sand microcosm system, which allows for the independent manipulation of specific soil parameters. This system was applied to study resource competition between filamentous and non-filamentous bacteria, the diversity and community structure of complex bacterial and fungal communities as impacted by soil connectivity and bacterial motility in a soil-like environment. In an experiment designed to examine the effect of connectivity on the growth dynamics of filamentous versus non-filamentous bacteria, it was demonstrated that filamentous bacteria have a relative competitive advantage over non-filamentous bacteria in poorly connected soils, a result that was attributed to their ability to bridge air-gaps and thus explore new micro-habitats. Similar to filamentous bacteria, the fungal hyphal growth form provides fungi with a relative advantage over most bacteria in poorly connected soils, as demonstrated by tracking bacterial and fungal PLFAs in a community-level experiment. High-throughput sequence analysis of ribosomal RNA genes of bacterial and fungal communities revealed a contrasting effect of habitat connectivity on bacteria and fungi. While decreased habitat connectivity facilitated the maintenance of higher bacterial diversity and richness, fungal communities exhibited the opposite trend with greater diversity and richness in well-connected soils. Pore size generally had a greater impact than matric potential in structuring the microbial. Lastly, in an examination of bacterial motility, it was demonstrated that habitat pore size, matric potential and nutrient availability differentially impact the mobility of different bacterial species. Also, only a small fraction of the total bacterial species present in a natural soil community was able to expand rapidly through a soil-like sand microcosm system. In total, this thesis demonstrates that habitat connectivity, as determined by pore geometry and hydration status, has a great impact on microbial interactions and plays an important role in structuring bacterial and fungal communities in soil

Publisher: Utrecht University
Year: 2014
OAI identifier: oai:dspace.library.uu.nl:1874/293156
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