Microbial adaptation to dissolved organic matter in freshwater ecosystems

Abstract

Dissolved organic matter (DOM) is the primary source of nutrients for heterotrophic bacteria at the base of the aquatic food web and its decomposition by microbes is a major flux in the global carbon cycle. Climate change is altering the composition of terrestrial DOM that enters into freshwaters, with unknown consequences for the resident bacterial communities and wider ecosystem processes. This thesis aims to characterize how bacteria adapt to compositionally-distinct DOM sources and assess the implications of these adaptations for how the DOM is degraded. Chapter 1 provides an overview of the sources and fate of dissolved organic matter in freshwater ecosystems, with a particular focus on the critical role that microbes play in the degradation of DOM and the carbon cycle. I summarize current experimental approaches for studying microbial adaptation in novel environments and outline the objectives of the thesis. Chapter 2 investigates short-term responses of a six-species bacterial community to seven DOM sources that span a gradient of bioavailability. Using full length 16S amplicon sequencing and ultra-high resolution mass spectrometry, I tracked how the six-species community changed in composition over a 14-day incubation on each source and characterized how the microbes reworked the DOM. I further correlated changes in species abundances with changes in the abundances of individual formulae to estimate the putative resource use of each bacterium and relate this to patterns of bacterial succession within the community. Chapters 3 and 4 are based on a longer, 14-week evolution experiment that tests how the model species, Pseudomonas fluorescens, adapts to the same DOM sources over ca. 100 generations, both alone and within the six-species community. I used competition assays to measure the fitness of evolved P. fluorescens clones, relative to the ancestor, and sequenced the transcriptomes of these bacteria to understand how DOM composition and biotic interactions influenced metabolic shifts in P. fluorescens over the course of the experiment (Chapter 3). I then investigated how the evolved P. fluorescens monocultures and six-species communities differed from the ancestors in their capacity to modify the DOM, analyzing ultra-high resolution mass spectrometry data to compare the molecular composition of compounds that the bacteria produced and consumed on each substrate (Chapter 4). Chapter 5 connects the main observations from Chapters 2 to 4. I discuss the results within the context of global climate change and propose directions for future research.