Steering biodiversity to optimize microbial community function
(2019)
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- Abstract
- Microorganisms are ubiquitous on Earth, with beneficial activities that lie at the heart of the water-energy-food-health nexus and some of the most exciting opportunities in science and technology to tackle the societal and environmental challenges in the twenty-first century. However, there is still a lack of consensus view about the relevance and the role of microbial community diversity in ensuring ecosystem functioning and robustness. Because microbial functional versatility and diversity represent unique resources for upholding ecosystem services and novel biotechnological applications, this PhD thesis presents the methodology and applications of natural and synthetic microbial communities to study the links between microbial diversity, functioning and robustness. The applied research framework focuses on steering microbial communities for improved applications in environmental biotechnology: (i) bioremediation of soils contaminated by polycyclic aromatic hydrocarbons (PAHs) and (ii) biological treatment of wastewater under psychrophilic conditions. The ultimate aim of this work is to better understand the link between microbial diversity and ecosystem processes, in order to provide guidance to strategies for optimizing bioaugmentation under different environmental scenarios. First, using a dilution-to-extinction approach, natural soil microbial communities were manipulated to investigate the importance of microbial diversity for the biodegradation of phenanthrene by natural attenuation. A decrease in soil microbial diversity resulted in a reduced capability of native microbial communities to degrade phenanthrene. The positive linear relationship between bacterial species richness and degradation indicated that functional redundancy of microbial communities is not as widespread as usually thought, in particular for specialized microbial functions. In a second set of experiments, I focused on the role of microbial diversity in the rational formulation of bioaugmentation inocula to achieve higher biodegradation in soils contaminated with PAHs or in wastewater treatment under psychrophilic conditions. Using in vitro assembly of microbial isolates, I showed that both functional diversity and redundancy are needed in the formulation of an efficient and robust inoculum, that increases the chance of successful bioaugmentation. Moreover, the use of phylogenetic diversity was identified as a promising community assembly rule to formulate consortia with higher degradation activity. Finally, focusing on the ecological properties of PAH-contaminated soil environments, I examined the effects of available niches and the diversity of the autochthonous microbiome on the successful establishment of bioaugmented strains. In a very selective environment, conferred by the presence of a mixture of PAH molecules, resident community composition and species identity can explain better the fate of bioaugmentation of specialized species than other dimensions of diversity, such as richness or evenness. Overall, this research work stresses the importance of preserving microbial diversity to deliver ecosystem functions essential for human health and provides practical recommendations for predicting, controlling and improving bioaugmentation in contaminated environments and wastewater treatment plants.
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Augelletti, F. (2019). Steering biodiversity to optimize microbial community function. https://hdl.handle.net/2078.5/124966